Query 008652
Match_columns 558
No_of_seqs 414 out of 2496
Neff 5.9
Searched_HMMs 46136
Date Thu Mar 28 14:52:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008652.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008652hhsearch_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 9.5E-65 2.1E-69 539.5 38.8 315 242-557 58-414 (415)
2 PRK07406 RNA polymerase sigma 100.0 5.6E-62 1.2E-66 514.6 38.8 312 242-554 61-372 (373)
3 PRK05949 RNA polymerase sigma 100.0 2.3E-61 5E-66 503.5 39.2 311 242-555 16-326 (327)
4 TIGR02997 Sig70-cyanoRpoD RNA 100.0 1.3E-60 2.8E-65 492.0 37.1 298 244-542 1-298 (298)
5 PRK07405 RNA polymerase sigma 100.0 2.5E-60 5.4E-65 494.1 38.9 310 243-555 7-316 (317)
6 COG0568 RpoD DNA-directed RNA 100.0 4.1E-59 8.9E-64 482.6 32.4 313 243-555 8-342 (342)
7 PRK05901 RNA polymerase sigma 100.0 4E-59 8.6E-64 507.4 33.3 301 242-555 209-509 (509)
8 PRK07921 RNA polymerase sigma 100.0 5.5E-58 1.2E-62 477.3 35.2 299 243-554 25-323 (324)
9 PRK09210 RNA polymerase sigma 100.0 1.8E-54 3.8E-59 458.4 33.4 276 240-555 92-367 (367)
10 PRK05658 RNA polymerase sigma 100.0 1.4E-51 2.9E-56 462.6 31.3 274 245-555 345-618 (619)
11 TIGR02393 RpoD_Cterm RNA polym 100.0 9.6E-48 2.1E-52 383.9 28.8 238 318-555 1-238 (238)
12 PRK05657 RNA polymerase sigma 100.0 1.8E-44 3.9E-49 376.4 33.5 272 242-553 51-322 (325)
13 PRK06596 RNA polymerase factor 100.0 2.7E-44 5.9E-49 368.6 32.9 262 242-547 12-282 (284)
14 PRK07500 rpoH2 RNA polymerase 100.0 3.5E-44 7.6E-49 368.7 33.1 264 244-549 6-281 (289)
15 TIGR02392 rpoH_proteo alternat 100.0 1.2E-43 2.6E-48 361.1 32.0 258 245-546 2-269 (270)
16 PRK07122 RNA polymerase sigma 100.0 4E-43 8.6E-48 356.5 28.5 220 317-545 40-263 (264)
17 PRK07408 RNA polymerase sigma 100.0 3E-41 6.5E-46 341.1 30.7 228 314-548 22-254 (256)
18 TIGR02394 rpoS_proteo RNA poly 100.0 9.3E-41 2E-45 342.3 33.6 272 239-550 8-279 (285)
19 TIGR02850 spore_sigG RNA polym 100.0 1.2E-39 2.7E-44 328.6 31.0 243 253-545 10-254 (254)
20 PRK05911 RNA polymerase sigma 100.0 1.7E-39 3.6E-44 328.7 28.8 227 314-547 20-255 (257)
21 PRK08215 sporulation sigma fac 100.0 3.1E-38 6.7E-43 319.0 31.4 243 253-545 13-257 (258)
22 COG1191 FliA DNA-directed RNA 100.0 2.1E-38 4.6E-43 317.3 28.9 223 314-547 21-246 (247)
23 PRK06288 RNA polymerase sigma 100.0 6.7E-37 1.5E-41 311.0 30.6 249 253-547 6-262 (268)
24 TIGR02941 Sigma_B RNA polymera 100.0 3.8E-36 8.3E-41 302.9 31.0 244 257-545 8-253 (255)
25 TIGR02885 spore_sigF RNA polym 100.0 1.8E-36 4E-41 300.6 27.8 223 313-545 7-231 (231)
26 TIGR02980 SigBFG RNA polymeras 100.0 7.2E-36 1.6E-40 295.4 28.1 221 316-545 2-226 (227)
27 PRK07670 RNA polymerase sigma 100.0 4.7E-35 1E-39 294.7 31.0 225 315-546 20-250 (251)
28 PRK08583 RNA polymerase sigma 100.0 2.5E-34 5.3E-39 290.1 30.9 243 257-547 8-255 (257)
29 PRK05572 sporulation sigma fac 100.0 2.6E-34 5.6E-39 289.5 30.9 244 251-546 6-251 (252)
30 TIGR02479 FliA_WhiG RNA polyme 100.0 1.9E-34 4.1E-39 285.2 27.0 217 322-545 1-223 (224)
31 PRK12427 flagellar biosynthesi 100.0 5.3E-34 1.1E-38 284.4 28.3 209 319-544 17-230 (231)
32 PRK06986 fliA flagellar biosyn 100.0 4.6E-33 1E-37 277.5 28.4 225 314-547 5-234 (236)
33 PRK05803 sporulation sigma fac 100.0 7E-28 1.5E-32 240.0 25.9 210 245-547 17-229 (233)
34 TIGR02846 spore_sigmaK RNA pol 99.9 2.5E-24 5.4E-29 213.8 24.9 179 314-545 45-226 (227)
35 PRK08301 sporulation sigma fac 99.9 3.8E-24 8.2E-29 212.9 25.4 180 314-546 49-231 (234)
36 TIGR02835 spore_sigmaE RNA pol 99.9 2.7E-23 5.8E-28 207.3 25.3 181 314-547 49-232 (234)
37 PRK08295 RNA polymerase factor 99.9 1.4E-22 3E-27 196.9 22.5 195 303-549 9-206 (208)
38 PRK05602 RNA polymerase sigma 99.9 5.7E-22 1.2E-26 189.9 20.6 176 303-550 5-181 (186)
39 TIGR02859 spore_sigH RNA polym 99.9 1E-21 2.2E-26 189.2 21.2 191 303-545 4-197 (198)
40 PRK09646 RNA polymerase sigma 99.9 1.7E-21 3.6E-26 188.5 20.4 176 304-547 16-192 (194)
41 PRK12513 RNA polymerase sigma 99.9 1.4E-21 3.1E-26 188.4 19.1 181 303-550 11-192 (194)
42 PRK09641 RNA polymerase sigma 99.9 3.1E-21 6.6E-26 184.0 20.6 180 305-546 5-185 (187)
43 TIGR02948 SigW_bacill RNA poly 99.9 3E-21 6.5E-26 184.0 20.3 180 306-547 6-186 (187)
44 PRK09648 RNA polymerase sigma 99.9 4.4E-21 9.5E-26 184.3 21.2 171 307-546 13-188 (189)
45 TIGR02952 Sig70_famx2 RNA poly 99.9 9.5E-21 2.1E-25 177.7 19.7 163 314-545 8-170 (170)
46 PRK09652 RNA polymerase sigma 99.9 1.2E-20 2.5E-25 178.0 19.9 172 313-546 6-177 (182)
47 PRK12519 RNA polymerase sigma 99.9 8.6E-21 1.9E-25 182.8 19.4 175 304-546 15-190 (194)
48 PRK13919 putative RNA polymera 99.9 1.3E-20 2.8E-25 180.2 19.9 176 304-547 9-185 (186)
49 PRK12514 RNA polymerase sigma 99.9 1.6E-20 3.4E-25 178.7 20.1 173 304-546 5-178 (179)
50 PRK06811 RNA polymerase factor 99.9 2.5E-20 5.4E-25 179.6 20.9 174 303-546 3-180 (189)
51 PRK06759 RNA polymerase factor 99.9 1.1E-20 2.4E-25 174.9 17.7 151 316-544 3-153 (154)
52 TIGR02939 RpoE_Sigma70 RNA pol 99.9 2.6E-20 5.6E-25 178.1 20.7 181 304-546 6-187 (190)
53 PRK11922 RNA polymerase sigma 99.9 2.1E-20 4.6E-25 186.1 20.7 173 314-547 27-199 (231)
54 PRK12524 RNA polymerase sigma 99.9 3.2E-20 6.9E-25 179.8 20.7 177 303-549 11-188 (196)
55 PRK12538 RNA polymerase sigma 99.9 2.8E-20 6.2E-25 186.0 20.2 174 304-549 49-223 (233)
56 PRK12537 RNA polymerase sigma 99.9 3.5E-20 7.5E-25 177.4 19.9 172 304-545 9-181 (182)
57 PRK11923 algU RNA polymerase s 99.9 5.5E-20 1.2E-24 177.1 21.2 180 305-546 7-187 (193)
58 PRK09640 RNA polymerase sigma 99.9 1.7E-20 3.8E-25 180.3 17.0 173 302-546 7-183 (188)
59 PRK12534 RNA polymerase sigma 99.8 4.8E-20 1E-24 176.6 19.4 173 306-546 13-186 (187)
60 TIGR02984 Sig-70_plancto1 RNA 99.8 1.2E-19 2.6E-24 173.0 21.6 180 314-545 4-188 (189)
61 PRK12542 RNA polymerase sigma 99.8 4.3E-20 9.2E-25 177.0 18.2 175 314-555 6-180 (185)
62 PRK12526 RNA polymerase sigma 99.8 8.9E-20 1.9E-24 178.5 20.8 171 313-548 34-204 (206)
63 PRK11924 RNA polymerase sigma 99.8 9.4E-20 2E-24 171.4 20.1 168 313-548 9-176 (179)
64 PRK12515 RNA polymerase sigma 99.8 1.5E-19 3.3E-24 173.8 20.8 177 303-550 7-184 (189)
65 TIGR02937 sigma70-ECF RNA poly 99.8 2.3E-19 5.1E-24 162.1 19.0 157 318-545 2-158 (158)
66 PRK09643 RNA polymerase sigma 99.8 2.8E-19 6.1E-24 173.0 20.3 172 303-547 12-184 (192)
67 PRK09638 RNA polymerase sigma 99.8 1.6E-19 3.6E-24 170.9 18.1 172 303-546 3-175 (176)
68 TIGR02954 Sig70_famx3 RNA poly 99.8 2.4E-19 5.1E-24 169.1 19.0 167 303-546 1-168 (169)
69 PRK12531 RNA polymerase sigma 99.8 2.1E-19 4.5E-24 173.9 18.6 177 307-549 16-193 (194)
70 TIGR02985 Sig70_bacteroi1 RNA 99.8 2E-19 4.3E-24 166.1 17.3 160 318-545 2-161 (161)
71 PRK12543 RNA polymerase sigma 99.8 3E-19 6.5E-24 170.5 19.0 166 314-549 4-169 (179)
72 PRK09645 RNA polymerase sigma 99.8 4.5E-19 9.7E-24 167.7 19.3 165 314-549 6-170 (173)
73 PRK12522 RNA polymerase sigma 99.8 5.8E-19 1.3E-23 167.3 19.0 167 317-547 3-169 (173)
74 PRK12536 RNA polymerase sigma 99.8 3.8E-19 8.2E-24 170.1 17.8 169 307-548 10-180 (181)
75 TIGR02989 Sig-70_gvs1 RNA poly 99.8 5.2E-19 1.1E-23 164.4 17.5 158 318-545 2-159 (159)
76 PRK12520 RNA polymerase sigma 99.8 6.6E-19 1.4E-23 169.6 18.7 182 318-550 3-184 (191)
77 TIGR03001 Sig-70_gmx1 RNA poly 99.8 1.1E-18 2.4E-23 175.8 20.7 179 303-550 24-214 (244)
78 PRK09415 RNA polymerase factor 99.8 9.1E-19 2E-23 167.3 19.1 164 315-547 14-177 (179)
79 PRK12539 RNA polymerase sigma 99.8 1.2E-18 2.5E-23 167.2 19.5 169 305-547 8-181 (184)
80 TIGR02999 Sig-70_X6 RNA polyme 99.8 1.2E-18 2.5E-23 166.1 18.9 171 306-545 5-182 (183)
81 PRK12512 RNA polymerase sigma 99.8 2.2E-18 4.7E-23 164.7 20.0 166 308-548 12-182 (184)
82 PRK12518 RNA polymerase sigma 99.8 1.7E-18 3.8E-23 163.8 17.8 166 313-549 7-172 (175)
83 PRK12533 RNA polymerase sigma 99.8 3.3E-18 7.1E-23 169.4 20.5 172 313-548 14-185 (216)
84 COG1595 RpoE DNA-directed RNA 99.8 4.1E-18 8.9E-23 163.2 20.4 171 311-549 9-179 (182)
85 PRK12529 RNA polymerase sigma 99.8 2.4E-18 5.3E-23 164.4 18.6 166 313-546 9-176 (178)
86 PRK09649 RNA polymerase sigma 99.8 2E-18 4.3E-23 166.1 17.8 169 307-549 13-182 (185)
87 PRK09642 RNA polymerase sigma 99.8 1.7E-18 3.7E-23 161.7 16.7 157 324-549 2-158 (160)
88 PRK12516 RNA polymerase sigma 99.8 3.6E-18 7.8E-23 164.9 18.6 162 314-549 7-168 (187)
89 PRK09644 RNA polymerase sigma 99.8 4.4E-18 9.5E-23 160.1 18.1 158 319-549 3-160 (165)
90 TIGR02947 SigH_actino RNA poly 99.8 1.9E-18 4.2E-23 166.7 16.0 172 316-547 10-181 (193)
91 TIGR02983 SigE-fam_strep RNA p 99.8 4.2E-18 9.1E-23 159.2 17.4 158 314-547 3-160 (162)
92 PRK09647 RNA polymerase sigma 99.8 9.2E-18 2E-22 164.4 20.2 166 315-550 26-191 (203)
93 TIGR02895 spore_sigI RNA polym 99.8 6.8E-18 1.5E-22 167.3 19.4 118 312-429 4-126 (218)
94 PRK12523 RNA polymerase sigma 99.8 4.6E-18 9.9E-23 161.2 17.4 163 314-547 7-169 (172)
95 PRK12547 RNA polymerase sigma 99.8 1.4E-17 3E-22 156.9 19.2 159 316-548 5-163 (164)
96 PRK12528 RNA polymerase sigma 99.8 1.1E-17 2.3E-22 156.7 18.2 157 317-544 4-160 (161)
97 PRK12541 RNA polymerase sigma 99.8 1.7E-17 3.6E-22 155.3 18.7 157 315-544 3-159 (161)
98 TIGR02943 Sig70_famx1 RNA poly 99.8 1.3E-17 2.8E-22 161.0 18.4 178 320-548 5-182 (188)
99 PRK12532 RNA polymerase sigma 99.8 1.6E-17 3.4E-22 160.6 18.8 181 320-550 8-189 (195)
100 PRK12545 RNA polymerase sigma 99.8 1.7E-17 3.7E-22 161.7 18.9 181 321-550 12-192 (201)
101 PRK09639 RNA polymerase sigma 99.8 2.3E-17 5.1E-22 154.5 19.0 160 316-547 2-161 (166)
102 PRK12530 RNA polymerase sigma 99.8 2.2E-17 4.7E-22 159.4 18.8 177 320-549 10-186 (189)
103 PRK08241 RNA polymerase factor 99.8 2.4E-17 5.2E-22 172.6 20.5 188 306-544 7-200 (339)
104 PRK12544 RNA polymerase sigma 99.8 2.3E-17 5E-22 162.0 18.8 181 319-549 20-200 (206)
105 PRK12535 RNA polymerase sigma 99.8 3.2E-17 7E-22 159.5 19.3 170 308-549 15-185 (196)
106 TIGR02960 SigX5 RNA polymerase 99.8 3.3E-17 7.1E-22 170.1 20.3 183 314-547 2-192 (324)
107 PRK07037 extracytoplasmic-func 99.8 4.2E-17 9.1E-22 152.6 18.5 159 321-548 2-160 (163)
108 TIGR02950 SigM_subfam RNA poly 99.8 1.1E-17 2.3E-22 154.8 14.2 152 324-545 2-153 (154)
109 PRK12540 RNA polymerase sigma 99.8 4.2E-17 9E-22 156.9 18.5 160 317-550 5-164 (182)
110 PRK12527 RNA polymerase sigma 99.8 4.4E-17 9.5E-22 152.2 17.7 155 324-548 2-156 (159)
111 PRK09637 RNA polymerase sigma 99.7 9.1E-17 2E-21 154.3 18.9 154 319-547 3-156 (181)
112 PRK09651 RNA polymerase sigma 99.7 1E-16 2.2E-21 152.2 18.5 164 315-549 8-171 (172)
113 PRK12517 RNA polymerase sigma 99.7 9E-17 2E-21 155.2 18.0 161 313-548 19-179 (188)
114 PRK12546 RNA polymerase sigma 99.7 1.6E-16 3.5E-21 153.7 18.5 156 317-547 8-163 (188)
115 TIGR02959 SigZ RNA polymerase 99.7 1.5E-16 3.2E-21 150.9 17.7 149 324-547 2-150 (170)
116 PRK12511 RNA polymerase sigma 99.7 2.3E-16 5E-21 151.8 17.3 158 319-549 6-163 (182)
117 PRK12525 RNA polymerase sigma 99.7 5E-16 1.1E-20 146.8 18.8 160 316-546 8-167 (168)
118 PRK09047 RNA polymerase factor 99.7 7.9E-16 1.7E-20 143.3 16.6 156 339-550 2-159 (161)
119 PRK09636 RNA polymerase sigma 99.7 1.1E-15 2.5E-20 157.3 17.7 161 317-547 4-165 (293)
120 PRK06704 RNA polymerase factor 99.6 5.9E-15 1.3E-19 147.5 17.8 158 308-547 9-166 (228)
121 TIGR02957 SigX4 RNA polymerase 99.6 7.7E-15 1.7E-19 150.5 17.5 156 321-546 1-157 (281)
122 PRK09635 sigI RNA polymerase s 99.6 1.3E-14 2.8E-19 149.9 18.0 162 317-546 5-167 (290)
123 TIGR03209 P21_Cbot clostridium 99.5 3.2E-13 7E-18 123.9 13.8 136 319-531 1-141 (142)
124 PRK09191 two-component respons 99.5 2.6E-13 5.7E-18 135.1 14.2 137 318-547 2-138 (261)
125 PRK08311 putative RNA polymera 99.4 6.9E-12 1.5E-16 126.2 19.8 90 305-394 5-97 (237)
126 PF07638 Sigma70_ECF: ECF sigm 99.4 3.3E-11 7.2E-16 116.5 19.1 174 306-546 5-184 (185)
127 PF04545 Sigma70_r4: Sigma-70, 99.2 2.3E-11 5E-16 93.1 7.2 50 490-543 1-50 (50)
128 PF04542 Sigma70_r2: Sigma-70 99.2 3.3E-11 7.2E-16 96.9 8.2 70 322-391 1-70 (71)
129 PF04539 Sigma70_r3: Sigma-70 99.0 7.4E-10 1.6E-14 92.1 7.5 77 401-477 1-77 (78)
130 PF08281 Sigma70_r4_2: Sigma-7 98.9 3.6E-09 7.8E-14 82.0 7.2 54 484-541 1-54 (54)
131 PRK06930 positive control sigm 98.6 1.3E-07 2.8E-12 90.8 10.0 70 475-548 96-165 (170)
132 PRK00118 putative DNA-binding 98.4 9.8E-07 2.1E-11 78.2 8.9 61 486-550 10-70 (104)
133 cd06171 Sigma70_r4 Sigma70, re 98.3 2.2E-06 4.7E-11 64.2 6.8 53 486-542 3-55 (55)
134 TIGR00721 tfx DNA-binding prot 98.2 3.5E-06 7.6E-11 78.2 7.0 57 492-553 5-61 (137)
135 PRK03975 tfx putative transcri 98.2 4.8E-06 1E-10 77.6 7.2 51 492-547 5-55 (141)
136 PRK04217 hypothetical protein; 98.1 6.3E-06 1.4E-10 73.7 6.4 56 492-551 41-96 (110)
137 PF00140 Sigma70_r1_2: Sigma-7 98.0 1.6E-06 3.4E-11 62.8 0.8 35 243-277 1-35 (37)
138 TIGR01636 phage_rinA phage tra 98.0 3.4E-05 7.5E-10 71.3 8.9 63 482-546 71-133 (134)
139 PF04297 UPF0122: Putative hel 98.0 3.7E-05 8E-10 67.8 8.3 58 486-547 9-67 (101)
140 PRK05658 RNA polymerase sigma 97.9 0.003 6.5E-08 72.3 25.0 34 242-275 102-135 (619)
141 smart00421 HTH_LUXR helix_turn 97.8 4.1E-05 9E-10 58.3 5.7 46 492-542 2-47 (58)
142 PF00196 GerE: Bacterial regul 97.7 9.4E-05 2E-09 58.2 5.9 46 492-542 2-47 (58)
143 cd06170 LuxR_C_like C-terminal 97.6 0.00014 3.1E-09 55.5 6.1 45 494-543 1-45 (57)
144 PF07374 DUF1492: Protein of u 97.6 0.00036 7.8E-09 61.4 8.7 55 483-541 44-99 (100)
145 TIGR03879 near_KaiC_dom probab 97.6 0.00019 4E-09 59.7 6.1 47 486-536 8-55 (73)
146 PF04967 HTH_10: HTH DNA bindi 97.5 0.00033 7.1E-09 54.8 6.8 48 494-541 1-51 (53)
147 TIGR01321 TrpR trp operon repr 97.4 0.00022 4.8E-09 62.0 5.2 49 485-533 23-75 (94)
148 PRK15201 fimbriae regulatory p 97.3 0.00042 9E-09 66.8 6.5 47 492-543 132-178 (198)
149 PRK15411 rcsA colanic acid cap 97.3 0.00041 8.9E-09 68.3 6.3 46 493-543 137-182 (207)
150 PRK10840 transcriptional regul 97.3 0.00048 1E-08 67.1 6.2 46 492-542 149-194 (216)
151 PRK13719 conjugal transfer tra 97.2 0.00054 1.2E-08 68.1 6.2 50 488-542 138-187 (217)
152 TIGR03020 EpsA transcriptional 97.2 0.00055 1.2E-08 69.7 6.4 48 491-543 188-235 (247)
153 PRK11475 DNA-binding transcrip 97.2 0.00057 1.2E-08 67.6 6.4 46 492-542 133-178 (207)
154 PRK13870 transcriptional regul 97.2 0.00053 1.2E-08 69.1 6.2 45 493-542 173-217 (234)
155 TIGR03541 reg_near_HchA LuxR f 97.2 0.00054 1.2E-08 68.8 6.2 48 491-543 169-216 (232)
156 PRK10100 DNA-binding transcrip 97.2 0.00068 1.5E-08 67.5 6.3 48 491-543 153-200 (216)
157 PRK10188 DNA-binding transcrip 97.2 0.00072 1.6E-08 68.4 6.4 45 493-542 179-223 (240)
158 COG2197 CitB Response regulato 97.1 0.00092 2E-08 66.2 6.0 46 492-542 147-192 (211)
159 PF02001 DUF134: Protein of un 97.0 0.0015 3.3E-08 58.1 6.5 53 493-549 41-93 (106)
160 COG4566 TtrR Response regulato 97.0 0.0023 5.1E-08 62.3 8.2 59 482-545 131-189 (202)
161 COG2771 CsgD DNA-binding HTH d 97.0 0.0024 5.3E-08 50.2 6.5 48 492-544 3-50 (65)
162 PRK09483 response regulator; P 96.9 0.0017 3.7E-08 62.0 6.1 46 492-542 147-192 (217)
163 PF13936 HTH_38: Helix-turn-he 96.9 0.0013 2.9E-08 49.2 4.0 41 492-536 3-43 (44)
164 TIGR01637 phage_arpU phage tra 96.7 0.01 2.2E-07 54.3 9.4 63 482-546 67-130 (132)
165 PRK15369 two component system 96.7 0.0034 7.3E-08 58.5 6.3 46 492-542 148-193 (211)
166 COG3413 Predicted DNA binding 96.6 0.0045 9.7E-08 61.4 6.8 53 493-545 155-210 (215)
167 COG1356 tfx Transcriptional re 96.5 0.0021 4.5E-08 58.5 3.2 48 493-545 8-55 (143)
168 PRK10651 transcriptional regul 96.5 0.0049 1.1E-07 58.2 5.9 46 492-542 154-199 (216)
169 PRK01381 Trp operon repressor; 96.5 0.003 6.5E-08 55.5 3.9 48 484-531 22-73 (99)
170 PRK09390 fixJ response regulat 96.4 0.0086 1.9E-07 55.5 7.1 54 486-544 134-187 (202)
171 COG2739 Uncharacterized protei 96.4 0.013 2.7E-07 51.6 7.4 48 492-543 16-63 (105)
172 PRK15320 transcriptional activ 96.1 0.011 2.3E-07 58.2 5.9 50 489-543 160-209 (251)
173 COG1342 Predicted DNA-binding 96.0 0.02 4.3E-07 49.8 6.3 52 493-548 33-84 (99)
174 PRK10403 transcriptional regul 95.9 0.015 3.2E-07 54.7 5.9 46 492-542 152-197 (215)
175 COG4941 Predicted RNA polymera 95.6 0.29 6.3E-06 51.9 14.2 159 320-544 8-167 (415)
176 PRK10360 DNA-binding transcrip 95.6 0.02 4.4E-07 53.7 5.3 46 492-542 136-181 (196)
177 PRK09958 DNA-binding transcrip 95.5 0.027 5.8E-07 53.2 6.1 47 491-542 141-187 (204)
178 PRK09935 transcriptional regul 95.5 0.029 6.2E-07 53.0 6.1 45 493-542 149-193 (210)
179 PRK13558 bacterio-opsin activa 95.3 0.033 7.3E-07 63.6 6.8 54 491-544 605-661 (665)
180 PRK04841 transcriptional regul 95.3 0.029 6.4E-07 66.1 6.5 46 492-542 837-882 (903)
181 PF00325 Crp: Bacterial regula 95.1 0.027 5.9E-07 39.6 3.4 27 513-543 2-28 (32)
182 PF12645 HTH_16: Helix-turn-he 94.8 0.13 2.7E-06 42.0 6.9 56 308-363 4-65 (65)
183 PF13412 HTH_24: Winged helix- 94.7 0.092 2E-06 39.4 5.6 41 494-537 1-41 (48)
184 TIGR02531 yecD_yerC TrpR-relat 94.7 0.069 1.5E-06 46.1 5.5 37 492-534 35-71 (88)
185 PF13613 HTH_Tnp_4: Helix-turn 94.6 0.088 1.9E-06 40.8 5.5 50 493-545 2-51 (53)
186 PF13384 HTH_23: Homeodomain-l 94.5 0.037 7.9E-07 41.8 3.0 32 501-537 10-41 (50)
187 PF05263 DUF722: Protein of un 94.3 0.16 3.5E-06 47.0 7.4 55 483-539 71-125 (130)
188 PRK15418 transcriptional regul 94.1 0.071 1.5E-06 56.3 5.2 36 500-539 20-55 (318)
189 PF13730 HTH_36: Helix-turn-he 93.7 0.25 5.3E-06 38.0 6.4 47 493-543 2-51 (55)
190 PF02796 HTH_7: Helix-turn-hel 93.6 0.092 2E-06 39.3 3.6 33 498-535 11-43 (45)
191 PF06530 Phage_antitermQ: Phag 93.6 0.5 1.1E-05 43.2 9.1 54 491-548 60-113 (125)
192 PF01726 LexA_DNA_bind: LexA D 93.5 0.11 2.3E-06 42.4 4.2 45 491-535 1-48 (65)
193 cd00569 HTH_Hin_like Helix-tur 93.4 0.18 4E-06 33.5 4.6 36 494-533 6-41 (42)
194 PF04539 Sigma70_r3: Sigma-70 92.9 0.22 4.7E-06 41.1 5.2 37 276-312 5-41 (78)
195 PHA00675 hypothetical protein 92.5 0.24 5.2E-06 41.6 4.8 40 492-535 21-61 (78)
196 PF13404 HTH_AsnC-type: AsnC-t 92.0 0.44 9.5E-06 35.4 5.3 40 494-536 1-40 (42)
197 TIGR02393 RpoD_Cterm RNA polym 91.9 2.1 4.4E-05 43.0 11.9 35 276-310 88-122 (238)
198 PRK09210 RNA polymerase sigma 91.9 2.2 4.8E-05 45.9 12.8 129 277-442 218-347 (367)
199 PRK10430 DNA-binding transcrip 91.6 0.36 7.7E-06 47.9 6.0 48 493-540 158-205 (239)
200 PRK07921 RNA polymerase sigma 91.4 3.3 7.2E-05 44.0 13.2 35 276-310 174-208 (324)
201 COG1191 FliA DNA-directed RNA 91.3 5.9 0.00013 40.6 14.4 147 245-442 88-234 (247)
202 PF09862 DUF2089: Protein of u 91.0 0.61 1.3E-05 42.2 6.2 50 490-543 30-79 (113)
203 PRK07598 RNA polymerase sigma 91.0 5.2 0.00011 44.0 14.5 37 405-441 112-148 (415)
204 PRK05901 RNA polymerase sigma 91.0 3.3 7.2E-05 46.6 13.3 130 276-442 359-489 (509)
205 COG2390 DeoR Transcriptional r 90.9 0.31 6.8E-06 51.6 4.9 35 501-539 18-52 (321)
206 PF13518 HTH_28: Helix-turn-he 90.4 0.5 1.1E-05 35.6 4.4 27 512-538 11-37 (52)
207 smart00351 PAX Paired Box doma 90.4 0.7 1.5E-05 42.2 6.2 42 494-539 18-59 (125)
208 COG2909 MalT ATP-dependent tra 90.2 0.33 7.2E-06 56.8 4.7 44 494-542 832-875 (894)
209 PF02650 HTH_WhiA: WhiA C-term 90.2 0.61 1.3E-05 40.1 5.2 45 490-537 34-80 (85)
210 PF06056 Terminase_5: Putative 90.0 0.61 1.3E-05 37.1 4.8 26 512-537 12-37 (58)
211 PF04218 CENP-B_N: CENP-B N-te 90.0 0.39 8.5E-06 37.4 3.5 40 493-536 6-45 (53)
212 PF08279 HTH_11: HTH domain; 89.6 0.62 1.3E-05 35.8 4.4 38 497-536 1-38 (55)
213 PF12802 MarR_2: MarR family; 89.5 0.74 1.6E-05 35.9 4.9 43 493-536 2-44 (62)
214 PF10668 Phage_terminase: Phag 89.3 0.69 1.5E-05 37.2 4.5 35 500-536 11-45 (60)
215 PHA02591 hypothetical protein; 89.2 0.74 1.6E-05 38.8 4.7 24 512-535 58-81 (83)
216 PRK00423 tfb transcription ini 88.9 18 0.00039 38.1 16.2 178 320-541 119-304 (310)
217 COG0568 RpoD DNA-directed RNA 88.8 5.1 0.00011 42.9 11.9 34 242-275 65-98 (342)
218 PRK11083 DNA-binding response 88.0 0.75 1.6E-05 43.8 4.8 50 493-543 154-208 (228)
219 PF01325 Fe_dep_repress: Iron 87.6 0.82 1.8E-05 36.5 4.0 46 494-543 2-48 (60)
220 PRK07408 RNA polymerase sigma 87.5 1.6 3.4E-05 44.5 7.1 35 276-310 114-148 (256)
221 PF01022 HTH_5: Bacterial regu 87.5 1.4 3.1E-05 33.0 5.1 37 496-536 2-38 (47)
222 PF03444 HrcA_DNA-bdg: Winged 87.2 1.3 2.8E-05 37.5 5.1 42 493-534 1-44 (78)
223 PRK10710 DNA-binding transcrip 87.1 0.92 2E-05 43.8 4.9 50 493-543 160-214 (240)
224 PRK05911 RNA polymerase sigma 87.0 4.5 9.7E-05 41.3 10.0 33 278-310 113-145 (257)
225 cd00131 PAX Paired Box domain 86.7 1.7 3.7E-05 39.9 6.1 41 494-538 18-58 (128)
226 PRK05949 RNA polymerase sigma 86.5 5.9 0.00013 42.1 10.9 35 276-310 179-213 (327)
227 PF12840 HTH_20: Helix-turn-he 86.3 2.4 5.3E-05 33.4 6.0 36 496-535 10-46 (61)
228 TIGR02885 spore_sigF RNA polym 86.0 3 6.5E-05 41.4 8.0 32 279-310 101-132 (231)
229 PF13463 HTH_27: Winged helix 85.7 1.4 3.1E-05 34.8 4.5 41 494-536 1-41 (68)
230 smart00344 HTH_ASNC helix_turn 85.5 1.9 4.2E-05 37.5 5.6 41 494-537 1-41 (108)
231 PRK07122 RNA polymerase sigma 85.3 11 0.00025 38.5 12.0 34 277-310 129-162 (264)
232 PRK10336 DNA-binding transcrip 85.1 1.3 2.9E-05 41.9 4.8 49 493-542 149-202 (219)
233 PHA02547 55 RNA polymerase sig 85.1 3.3 7.2E-05 40.0 7.3 65 322-386 42-109 (179)
234 PF13022 HTH_Tnp_1_2: Helix-tu 85.1 4.4 9.6E-05 38.0 7.9 65 487-551 4-74 (142)
235 PRK15479 transcriptional regul 85.0 1.5 3.3E-05 41.5 5.1 49 493-542 148-201 (221)
236 smart00550 Zalpha Z-DNA-bindin 84.5 2.1 4.5E-05 34.9 5.0 24 512-535 21-44 (68)
237 TIGR02850 spore_sigG RNA polym 84.5 12 0.00025 38.0 11.6 35 278-312 123-157 (254)
238 PRK06288 RNA polymerase sigma 84.5 18 0.00039 36.9 13.0 35 276-310 119-153 (268)
239 PF09339 HTH_IclR: IclR helix- 84.3 1.3 2.9E-05 33.8 3.6 33 503-535 8-40 (52)
240 TIGR02154 PhoB phosphate regul 84.2 0.8 1.7E-05 43.5 2.8 49 493-542 154-207 (226)
241 PRK10046 dpiA two-component re 84.1 1.1 2.5E-05 43.9 3.9 39 493-535 161-199 (225)
242 PRK12423 LexA repressor; Provi 84.0 1.9 4.2E-05 42.4 5.5 47 493-543 3-52 (202)
243 PF13542 HTH_Tnp_ISL3: Helix-t 84.0 2.6 5.5E-05 31.9 5.0 26 512-537 26-51 (52)
244 PF01371 Trp_repressor: Trp re 84.0 1.3 2.8E-05 38.3 3.7 41 492-532 25-68 (87)
245 TIGR01610 phage_O_Nterm phage 83.6 4.5 9.7E-05 35.1 7.0 49 491-543 20-73 (95)
246 PRK07406 RNA polymerase sigma 83.5 15 0.00033 39.8 12.5 125 406-535 96-261 (373)
247 PF13744 HTH_37: Helix-turn-he 83.2 2.2 4.7E-05 35.8 4.7 44 501-548 23-71 (80)
248 COG3355 Predicted transcriptio 83.2 4.4 9.6E-05 37.4 7.0 52 486-543 17-68 (126)
249 PF12728 HTH_17: Helix-turn-he 82.9 1.3 2.9E-05 33.4 3.1 24 514-537 2-25 (51)
250 TIGR02997 Sig70-cyanoRpoD RNA 82.7 21 0.00045 37.2 12.8 35 276-310 162-196 (298)
251 PF00356 LacI: Bacterial regul 82.6 1.3 2.8E-05 33.6 2.8 22 515-536 1-22 (46)
252 smart00345 HTH_GNTR helix_turn 82.5 2.2 4.8E-05 32.4 4.2 30 510-543 16-46 (60)
253 PF01047 MarR: MarR family; I 82.2 2.7 5.7E-05 32.5 4.6 41 494-537 1-41 (59)
254 COG3415 Transposase and inacti 82.1 2.6 5.6E-05 39.5 5.1 27 512-538 20-46 (138)
255 PF01710 HTH_Tnp_IS630: Transp 82.1 14 0.00031 33.3 9.9 27 512-542 70-96 (119)
256 TIGR03787 marine_sort_RR prote 82.0 2 4.3E-05 41.2 4.6 50 493-543 156-207 (227)
257 PRK11179 DNA-binding transcrip 81.8 3.1 6.7E-05 39.1 5.7 41 493-536 6-46 (153)
258 PF01978 TrmB: Sugar-specific 81.6 1.5 3.2E-05 35.3 3.0 44 493-543 5-48 (68)
259 PRK07405 RNA polymerase sigma 81.3 21 0.00045 37.7 12.3 34 276-309 169-202 (317)
260 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 81.0 3.9 8.4E-05 31.8 4.9 39 493-535 4-42 (50)
261 PRK00215 LexA repressor; Valid 80.9 2.9 6.3E-05 40.9 5.4 44 493-536 1-47 (205)
262 PRK13413 mpi multiple promoter 80.9 2.8 6E-05 41.0 5.2 34 498-536 162-195 (200)
263 PF13011 LZ_Tnp_IS481: leucine 80.6 3.9 8.5E-05 35.2 5.3 44 492-538 7-50 (85)
264 TIGR01764 excise DNA binding d 80.6 1.9 4.2E-05 31.4 3.1 24 514-537 2-25 (49)
265 TIGR02147 Fsuc_second hypothet 80.6 54 0.0012 34.1 14.7 85 420-508 137-227 (271)
266 cd04762 HTH_MerR-trunc Helix-T 80.2 1.7 3.8E-05 31.4 2.8 25 514-538 1-25 (49)
267 CHL00148 orf27 Ycf27; Reviewed 79.9 2.5 5.5E-05 40.7 4.6 50 493-543 161-217 (240)
268 PRK07670 RNA polymerase sigma 79.8 27 0.00059 35.2 12.2 35 277-311 111-145 (251)
269 PF01418 HTH_6: Helix-turn-hel 79.7 3.4 7.3E-05 34.4 4.6 48 484-533 4-54 (77)
270 PRK11564 stationary phase indu 79.6 4.5 9.7E-05 44.1 6.9 51 493-543 10-60 (426)
271 PRK07500 rpoH2 RNA polymerase 79.2 37 0.0008 35.3 13.2 25 419-443 244-268 (289)
272 PHA00542 putative Cro-like pro 78.7 1.5 3.2E-05 37.1 2.2 26 512-537 30-55 (82)
273 PRK11169 leucine-responsive tr 78.6 3.4 7.4E-05 39.2 4.9 40 494-536 12-51 (164)
274 TIGR00498 lexA SOS regulatory 78.4 3.7 8.1E-05 39.9 5.2 43 492-534 2-47 (199)
275 PF01726 LexA_DNA_bind: LexA D 78.3 6.4 0.00014 32.0 5.7 39 405-443 10-49 (65)
276 PF13551 HTH_29: Winged helix- 78.3 4 8.6E-05 35.2 4.9 26 512-537 10-36 (112)
277 COG1522 Lrp Transcriptional re 78.1 4.5 9.8E-05 37.3 5.5 42 492-536 4-45 (154)
278 cd06571 Bac_DnaA_C C-terminal 77.9 6.8 0.00015 33.5 6.1 41 512-555 43-84 (90)
279 smart00342 HTH_ARAC helix_turn 77.5 34 0.00073 27.1 10.0 23 420-442 1-23 (84)
280 PF01381 HTH_3: Helix-turn-hel 77.2 2.5 5.4E-05 32.1 2.9 25 512-536 8-32 (55)
281 COG0856 Orotate phosphoribosyl 77.1 3.1 6.7E-05 40.5 4.1 39 500-543 10-48 (203)
282 PHA01976 helix-turn-helix prot 76.9 4.4 9.6E-05 32.1 4.4 25 512-536 14-38 (67)
283 smart00420 HTH_DEOR helix_turn 76.6 6.3 0.00014 29.0 4.9 25 512-536 13-37 (53)
284 cd04761 HTH_MerR-SF Helix-Turn 76.1 2.1 4.6E-05 31.6 2.2 26 514-539 1-26 (49)
285 PF08822 DUF1804: Protein of u 75.5 6.1 0.00013 38.1 5.6 41 496-539 5-45 (165)
286 PF08220 HTH_DeoR: DeoR-like h 75.4 4.9 0.00011 31.6 4.2 25 511-535 12-36 (57)
287 PF14394 DUF4423: Domain of un 75.1 7.4 0.00016 37.6 6.2 109 419-547 38-154 (171)
288 PF02954 HTH_8: Bacterial regu 74.6 4.8 0.0001 29.6 3.7 37 496-535 4-40 (42)
289 TIGR02787 codY_Gpos GTP-sensin 74.6 13 0.00029 38.0 8.0 55 485-543 168-224 (251)
290 PF00392 GntR: Bacterial regul 74.4 4.4 9.5E-05 32.2 3.7 30 510-543 20-50 (64)
291 smart00418 HTH_ARSR helix_turn 74.4 5.3 0.00011 30.2 4.1 25 512-536 9-33 (66)
292 PF13560 HTH_31: Helix-turn-he 74.4 4 8.6E-05 32.4 3.5 25 512-536 13-37 (64)
293 TIGR03697 NtcA_cyano global ni 74.1 3.9 8.5E-05 38.7 4.0 29 512-544 142-170 (193)
294 smart00419 HTH_CRP helix_turn_ 74.0 4.6 0.0001 29.4 3.5 28 512-543 7-34 (48)
295 COG2522 Predicted transcriptio 73.8 5.7 0.00012 36.3 4.7 24 512-535 21-44 (119)
296 TIGR03070 couple_hipB transcri 73.5 6 0.00013 29.8 4.2 25 512-536 14-38 (58)
297 cd00092 HTH_CRP helix_turn_hel 73.4 9.1 0.0002 29.9 5.4 28 512-543 24-51 (67)
298 PF07750 GcrA: GcrA cell cycle 73.4 4.3 9.2E-05 39.0 4.0 37 496-536 5-42 (162)
299 PF08765 Mor: Mor transcriptio 73.4 7.1 0.00015 34.6 5.2 42 497-544 62-103 (108)
300 TIGR03830 CxxCG_CxxCG_HTH puta 73.2 11 0.00025 33.6 6.6 48 484-537 55-102 (127)
301 TIGR02337 HpaR homoprotocatech 73.2 16 0.00034 32.4 7.5 41 492-535 24-64 (118)
302 COG1476 Predicted transcriptio 73.1 5.4 0.00012 33.0 4.0 25 512-536 13-37 (68)
303 TIGR00122 birA_repr_reg BirA b 73.0 7.8 0.00017 31.2 5.0 25 512-536 12-36 (69)
304 cd07377 WHTH_GntR Winged helix 72.4 7.3 0.00016 30.1 4.6 26 514-543 26-51 (66)
305 PRK10072 putative transcriptio 72.1 5.8 0.00013 34.8 4.2 32 501-536 38-69 (96)
306 PF13545 HTH_Crp_2: Crp-like h 71.8 4.4 9.4E-05 32.8 3.2 28 512-543 27-54 (76)
307 COG1654 BirA Biotin operon rep 71.1 11 0.00023 32.1 5.4 33 508-544 14-46 (79)
308 PF00046 Homeobox: Homeobox do 71.1 7.3 0.00016 29.9 4.2 51 493-543 6-57 (57)
309 PRK09954 putative kinase; Prov 71.0 7.9 0.00017 41.1 5.9 42 494-538 1-42 (362)
310 smart00346 HTH_ICLR helix_turn 70.6 10 0.00022 31.7 5.3 26 512-537 19-44 (91)
311 TIGR02479 FliA_WhiG RNA polyme 70.6 59 0.0013 32.0 11.6 35 276-310 84-118 (224)
312 PF13551 HTH_29: Winged helix- 70.5 12 0.00026 32.2 6.0 23 422-444 14-36 (112)
313 PRK05572 sporulation sigma fac 70.5 44 0.00095 33.7 10.9 32 278-309 121-152 (252)
314 TIGR02612 mob_myst_A mobile my 70.3 9.7 0.00021 36.1 5.6 49 495-547 24-78 (150)
315 PF13411 MerR_1: MerR HTH fami 70.1 2.2 4.9E-05 34.0 1.1 25 514-538 1-25 (69)
316 TIGR02844 spore_III_D sporulat 69.9 9.4 0.0002 32.5 4.9 24 512-535 18-41 (80)
317 COG2973 TrpR Trp operon repres 69.5 9.8 0.00021 33.6 4.9 46 493-542 37-85 (103)
318 cd00090 HTH_ARSR Arsenical Res 69.1 13 0.00028 28.8 5.4 36 497-536 8-43 (78)
319 TIGR02941 Sigma_B RNA polymera 68.7 55 0.0012 33.0 11.2 33 278-310 119-151 (255)
320 PRK13918 CRP/FNR family transc 68.4 6 0.00013 37.9 3.9 28 512-543 148-175 (202)
321 PRK00082 hrcA heat-inducible t 67.9 8.2 0.00018 41.3 5.1 65 492-557 2-80 (339)
322 PRK03573 transcriptional regul 67.8 15 0.00033 33.6 6.4 49 486-536 19-69 (144)
323 PRK08215 sporulation sigma fac 67.6 68 0.0015 32.5 11.6 33 278-310 126-158 (258)
324 TIGR00647 MG103 conserved hypo 67.5 11 0.00025 39.2 5.9 44 491-537 225-274 (279)
325 PF08535 KorB: KorB domain; I 66.8 5.4 0.00012 34.3 2.9 24 512-535 2-25 (93)
326 PRK06030 hypothetical protein; 66.7 17 0.00037 33.4 6.3 41 512-556 68-108 (124)
327 PRK11512 DNA-binding transcrip 66.4 32 0.0007 31.6 8.2 47 486-535 28-76 (144)
328 PF00376 MerR: MerR family reg 66.3 3.7 8.1E-05 29.8 1.5 24 515-538 1-24 (38)
329 smart00347 HTH_MARR helix_turn 65.6 15 0.00033 30.5 5.5 44 493-543 7-50 (101)
330 TIGR01884 cas_HTH CRISPR locus 65.4 17 0.00038 35.6 6.6 44 490-536 137-180 (203)
331 PRK10870 transcriptional repre 65.2 35 0.00075 32.9 8.5 50 486-536 43-94 (176)
332 cd01104 HTH_MlrA-CarA Helix-Tu 64.9 8.1 0.00018 30.6 3.4 23 514-536 1-23 (68)
333 PF08280 HTH_Mga: M protein tr 64.9 8.3 0.00018 30.4 3.4 36 497-535 6-41 (59)
334 COG5484 Uncharacterized conser 64.7 8.3 0.00018 39.6 4.1 25 512-536 18-42 (279)
335 PF11662 DUF3263: Protein of u 64.3 24 0.00052 29.9 6.1 47 493-539 2-48 (77)
336 PF06971 Put_DNA-bind_N: Putat 64.2 18 0.0004 28.0 5.1 45 395-439 3-47 (50)
337 PRK11302 DNA-binding transcrip 63.5 12 0.00026 38.2 5.2 49 485-535 5-56 (284)
338 PRK11161 fumarate/nitrate redu 63.5 8.2 0.00018 38.0 3.9 27 513-543 184-210 (235)
339 COG5625 Predicted transcriptio 63.5 9.7 0.00021 33.9 3.8 68 486-553 9-78 (113)
340 PF05043 Mga: Mga helix-turn-h 63.5 5.4 0.00012 33.5 2.2 31 512-542 29-59 (87)
341 TIGR01889 Staph_reg_Sar staphy 63.4 47 0.001 29.2 8.4 44 493-536 22-66 (109)
342 TIGR02607 antidote_HigA addict 63.2 15 0.00033 29.8 4.9 25 512-536 17-41 (78)
343 PF14493 HTH_40: Helix-turn-he 62.9 11 0.00024 32.2 4.1 29 512-540 12-40 (91)
344 TIGR02980 SigBFG RNA polymeras 62.5 60 0.0013 32.0 9.8 30 280-309 95-124 (227)
345 PF02082 Rrf2: Transcriptional 62.5 13 0.00029 31.0 4.4 24 512-535 24-47 (83)
346 PRK11753 DNA-binding transcrip 62.4 9.5 0.00021 36.7 4.0 27 513-543 168-194 (211)
347 PF01527 HTH_Tnp_1: Transposas 62.2 8.5 0.00018 31.2 3.1 27 512-538 22-48 (76)
348 PRK06986 fliA flagellar biosyn 62.1 1E+02 0.0022 30.6 11.6 33 278-310 98-130 (236)
349 COG2944 Predicted transcriptio 62.1 22 0.00049 31.8 5.9 40 491-536 41-80 (104)
350 PF12116 SpoIIID: Stage III sp 61.7 12 0.00026 32.0 3.8 44 498-543 6-49 (82)
351 PRK09413 IS2 repressor TnpA; R 61.3 18 0.0004 32.6 5.4 34 501-538 21-54 (121)
352 PRK04984 fatty acid metabolism 60.8 12 0.00027 37.1 4.6 30 510-543 27-57 (239)
353 smart00422 HTH_MERR helix_turn 60.5 6.7 0.00014 31.2 2.2 25 514-538 1-25 (70)
354 PRK15482 transcriptional regul 60.3 15 0.00033 37.7 5.3 49 485-535 5-56 (285)
355 cd04764 HTH_MlrA-like_sg1 Heli 60.3 11 0.00024 30.0 3.4 23 514-536 1-23 (67)
356 COG1510 Predicted transcriptio 60.3 8.6 0.00019 37.3 3.2 29 511-543 39-67 (177)
357 COG1318 Predicted transcriptio 60.2 8.9 0.00019 37.2 3.2 28 512-539 60-87 (182)
358 smart00354 HTH_LACI helix_turn 60.0 9 0.0002 31.1 2.9 23 514-536 1-23 (70)
359 PRK11337 DNA-binding transcrip 60.0 23 0.00049 36.4 6.6 51 483-535 15-68 (292)
360 KOG0484 Transcription factor P 59.8 14 0.0003 33.1 4.1 56 486-545 19-76 (125)
361 COG2345 Predicted transcriptio 59.2 17 0.00037 36.7 5.2 25 512-536 24-48 (218)
362 PF12085 DUF3562: Protein of u 58.9 25 0.00053 29.0 5.1 40 515-557 9-48 (66)
363 PRK09726 antitoxin HipB; Provi 58.7 16 0.00034 31.1 4.3 25 512-536 24-48 (88)
364 PF08784 RPA_C: Replication pr 58.6 16 0.00034 31.8 4.3 43 493-535 44-87 (102)
365 smart00342 HTH_ARAC helix_turn 58.2 17 0.00038 28.8 4.3 26 513-538 1-26 (84)
366 PRK11557 putative DNA-binding 58.1 20 0.00044 36.5 5.8 47 487-535 3-52 (278)
367 PRK09391 fixK transcriptional 58.1 12 0.00026 37.1 4.0 27 513-543 179-205 (230)
368 cd04763 HTH_MlrA-like Helix-Tu 57.7 13 0.00028 29.8 3.4 23 514-536 1-23 (68)
369 PRK10161 transcriptional regul 57.6 12 0.00026 35.9 3.8 50 493-543 154-208 (229)
370 PRK10955 DNA-binding transcrip 57.5 7.7 0.00017 37.1 2.5 46 493-543 156-210 (232)
371 PF13556 HTH_30: PucR C-termin 57.5 29 0.00063 27.2 5.3 35 512-546 11-45 (59)
372 PF05225 HTH_psq: helix-turn-h 57.0 27 0.00058 26.3 4.7 23 514-536 17-39 (45)
373 PRK14082 hypothetical protein; 56.9 35 0.00077 27.9 5.6 56 316-373 8-63 (65)
374 COG1405 SUA7 Transcription ini 56.5 2.6E+02 0.0057 29.4 14.8 25 512-536 250-274 (285)
375 PRK11414 colanic acid/biofilm 56.4 14 0.0003 36.4 4.1 31 509-543 30-60 (221)
376 PRK01905 DNA-binding protein F 55.7 46 0.001 27.7 6.5 37 497-536 37-73 (77)
377 TIGR02395 rpoN_sigma RNA polym 55.7 1.3E+02 0.0028 33.4 11.8 24 419-442 317-340 (429)
378 TIGR03338 phnR_burk phosphonat 55.3 15 0.00033 35.7 4.1 30 510-543 31-60 (212)
379 cd00086 homeodomain Homeodomai 55.2 30 0.00066 26.2 5.0 51 493-543 6-57 (59)
380 PRK09863 putative frv operon r 55.2 63 0.0014 36.9 9.7 102 420-542 17-121 (584)
381 COG2512 Predicted membrane-ass 55.1 17 0.00037 37.5 4.6 46 492-543 191-236 (258)
382 TIGR02812 fadR_gamma fatty aci 55.0 18 0.00038 36.0 4.6 31 509-543 25-56 (235)
383 PF00165 HTH_AraC: Bacterial r 54.7 18 0.00039 26.1 3.5 25 512-536 7-31 (42)
384 COG3093 VapI Plasmid maintenan 54.7 19 0.00041 32.2 4.1 35 500-536 12-46 (104)
385 TIGR02702 SufR_cyano iron-sulf 54.5 25 0.00055 34.4 5.6 26 512-537 14-39 (203)
386 PRK10411 DNA-binding transcrip 54.5 23 0.00049 35.9 5.4 41 496-539 4-44 (240)
387 PF06413 Neugrin: Neugrin; In 54.4 20 0.00044 36.3 4.9 42 493-535 10-51 (225)
388 PRK09863 putative frv operon r 54.4 25 0.00055 40.1 6.3 46 494-543 2-47 (584)
389 TIGR01387 cztR_silR_copR heavy 54.4 19 0.00042 33.8 4.6 49 493-542 147-200 (218)
390 PRK10402 DNA-binding transcrip 54.3 29 0.00063 34.2 6.0 46 494-543 149-195 (226)
391 PRK11050 manganese transport r 54.2 21 0.00044 33.6 4.7 26 511-536 49-74 (152)
392 PRK03902 manganese transport t 54.2 24 0.00051 32.5 5.0 25 511-535 20-44 (142)
393 PRK03837 transcriptional regul 53.6 20 0.00043 35.6 4.7 30 510-543 33-63 (241)
394 smart00862 Trans_reg_C Transcr 53.6 43 0.00093 26.7 6.0 50 493-543 5-60 (78)
395 PRK09990 DNA-binding transcrip 53.6 19 0.00042 36.1 4.7 31 509-543 26-57 (251)
396 PRK09464 pdhR transcriptional 52.9 20 0.00043 36.0 4.7 30 510-543 30-60 (254)
397 PRK09392 ftrB transcriptional 52.8 15 0.00033 36.2 3.7 27 513-543 173-199 (236)
398 PF06322 Phage_NinH: Phage Nin 52.6 21 0.00045 29.0 3.6 27 501-534 11-37 (64)
399 PRK10421 DNA-binding transcrip 52.3 21 0.00045 36.0 4.7 37 501-543 15-52 (253)
400 PF01710 HTH_Tnp_IS630: Transp 52.2 20 0.00043 32.3 4.0 24 512-535 17-40 (119)
401 COG1846 MarR Transcriptional r 52.1 30 0.00065 29.6 5.1 40 494-536 20-59 (126)
402 PRK09706 transcriptional repre 51.8 22 0.00047 32.5 4.3 25 512-536 17-41 (135)
403 PRK10225 DNA-binding transcrip 51.5 21 0.00046 35.9 4.6 37 501-543 22-59 (257)
404 PRK11517 transcriptional regul 51.4 27 0.00059 33.0 5.1 49 493-542 147-200 (223)
405 PRK11534 DNA-binding transcrip 51.1 22 0.00048 34.9 4.6 38 500-543 19-56 (224)
406 PRK13239 alkylmercury lyase; P 50.8 31 0.00068 34.5 5.5 29 417-445 33-61 (206)
407 PRK10141 DNA-binding transcrip 50.6 41 0.00089 30.6 5.8 49 488-543 7-56 (117)
408 smart00530 HTH_XRE Helix-turn- 50.6 27 0.00058 24.6 3.9 25 512-536 9-33 (56)
409 PRK13509 transcriptional repre 50.5 25 0.00055 35.8 5.0 26 511-536 17-42 (251)
410 PRK06266 transcription initiat 50.3 48 0.001 32.3 6.6 46 486-535 13-58 (178)
411 cd01392 HTH_LacI Helix-turn-he 50.1 11 0.00024 28.2 1.7 21 517-537 1-21 (52)
412 PF12844 HTH_19: Helix-turn-he 50.0 27 0.00057 27.3 4.0 25 512-536 11-35 (64)
413 COG1508 RpoN DNA-directed RNA 49.9 2.4E+02 0.0053 31.5 12.6 47 489-535 294-352 (444)
414 cd04768 HTH_BmrR-like Helix-Tu 49.8 12 0.00026 32.4 2.2 26 514-539 1-26 (96)
415 smart00352 POU Found in Pit-Oc 49.5 31 0.00066 29.2 4.4 31 501-535 16-52 (75)
416 TIGR00180 parB_part ParB-like 49.3 33 0.00072 33.2 5.4 43 492-536 101-143 (187)
417 PF04703 FaeA: FaeA-like prote 49.2 17 0.00037 29.4 2.8 24 512-535 14-37 (62)
418 TIGR00738 rrf2_super rrf2 fami 48.6 33 0.00072 30.8 5.0 25 511-535 23-47 (132)
419 PRK11014 transcriptional repre 48.4 24 0.00052 32.6 4.0 30 510-543 22-51 (141)
420 PHA00738 putative HTH transcri 48.0 40 0.00087 30.4 5.2 37 496-535 12-48 (108)
421 TIGR02431 pcaR_pcaU beta-ketoa 48.0 31 0.00068 34.6 5.2 26 510-535 21-46 (248)
422 TIGR02944 suf_reg_Xantho FeS a 47.9 30 0.00065 31.2 4.6 26 510-535 22-47 (130)
423 cd00383 trans_reg_C Effector d 47.8 42 0.00091 27.9 5.2 49 493-542 23-76 (95)
424 PF13443 HTH_26: Cro/C1-type H 47.8 18 0.00039 28.2 2.7 26 512-537 9-34 (63)
425 PRK10643 DNA-binding transcrip 47.6 26 0.00056 33.0 4.3 49 493-542 149-202 (222)
426 PF09012 FeoC: FeoC like trans 47.5 13 0.00028 30.1 1.9 25 512-536 13-37 (69)
427 PRK11523 DNA-binding transcrip 47.1 28 0.00061 35.0 4.7 30 510-543 28-58 (253)
428 TIGR02698 CopY_TcrY copper tra 47.0 49 0.0011 30.3 5.9 44 493-539 1-48 (130)
429 cd00093 HTH_XRE Helix-turn-hel 47.0 38 0.00082 24.0 4.2 25 512-536 11-35 (58)
430 COG1321 TroR Mn-dependent tran 46.9 35 0.00076 32.4 5.0 42 494-535 4-46 (154)
431 PRK09834 DNA-binding transcrip 46.8 31 0.00068 35.1 5.0 37 499-535 12-48 (263)
432 PF12298 Bot1p: Eukaryotic mit 46.7 40 0.00086 32.8 5.4 38 494-534 17-54 (172)
433 cd04775 HTH_Cfa-like Helix-Tur 46.7 14 0.0003 32.3 2.1 26 514-539 2-27 (102)
434 PF08006 DUF1700: Protein of u 46.5 53 0.0011 31.5 6.3 57 480-536 3-63 (181)
435 smart00389 HOX Homeodomain. DN 46.5 33 0.00072 25.8 4.0 48 493-540 6-54 (56)
436 PRK06424 transcription factor; 46.5 29 0.00062 32.8 4.3 25 512-536 96-120 (144)
437 PRK12469 RNA polymerase factor 46.3 2.2E+02 0.0047 32.2 11.8 127 374-533 331-466 (481)
438 COG3877 Uncharacterized protei 46.2 45 0.00097 30.0 5.1 47 491-541 39-85 (122)
439 COG1737 RpiR Transcriptional r 45.8 61 0.0013 33.5 7.0 50 483-534 5-57 (281)
440 cd01105 HTH_GlnR-like Helix-Tu 45.7 16 0.00035 31.1 2.3 25 514-538 2-26 (88)
441 PF12324 HTH_15: Helix-turn-he 45.6 56 0.0012 27.8 5.4 44 375-447 22-65 (77)
442 PF14502 HTH_41: Helix-turn-he 45.5 39 0.00084 26.1 4.0 29 511-543 4-32 (48)
443 PF04552 Sigma54_DBD: Sigma-54 45.4 7 0.00015 37.5 0.0 48 486-535 24-71 (160)
444 TIGR02395 rpoN_sigma RNA polym 45.4 21 0.00046 39.4 3.8 24 512-535 317-340 (429)
445 PRK05932 RNA polymerase factor 45.3 2.6E+02 0.0057 31.2 12.2 24 419-442 342-365 (455)
446 PRK13890 conjugal transfer pro 45.3 32 0.00069 31.2 4.3 25 512-536 17-41 (120)
447 PF07037 DUF1323: Putative tra 45.3 23 0.0005 32.4 3.3 23 514-536 1-23 (122)
448 PRK13777 transcriptional regul 44.9 47 0.001 32.6 5.7 40 492-534 41-80 (185)
449 cd01107 HTH_BmrR Helix-Turn-He 44.8 16 0.00035 32.2 2.3 26 514-539 1-26 (108)
450 cd04773 HTH_TioE_rpt2 Second H 44.8 16 0.00034 32.4 2.2 26 514-539 1-26 (108)
451 cd04782 HTH_BltR Helix-Turn-He 43.9 17 0.00037 31.5 2.2 26 514-539 1-26 (97)
452 cd04772 HTH_TioE_rpt1 First He 43.9 17 0.00038 31.7 2.3 26 514-539 1-26 (99)
453 COG4709 Predicted membrane pro 43.6 60 0.0013 32.1 6.0 58 481-538 4-65 (195)
454 PRK09764 DNA-binding transcrip 43.4 35 0.00076 34.1 4.7 29 511-543 26-55 (240)
455 PF00292 PAX: 'Paired box' dom 43.2 51 0.0011 30.5 5.2 33 500-537 25-57 (125)
456 PRK09943 DNA-binding transcrip 43.1 34 0.00073 32.9 4.4 25 512-536 19-43 (185)
457 PRK14999 histidine utilization 43.1 36 0.00077 34.0 4.7 28 512-543 34-62 (241)
458 TIGR02018 his_ut_repres histid 43.0 36 0.00077 33.7 4.6 28 512-543 23-51 (230)
459 COG4367 Uncharacterized protei 42.8 59 0.0013 28.3 5.2 27 420-446 23-49 (97)
460 COG1481 Uncharacterized protei 42.7 48 0.001 35.1 5.6 43 491-536 251-295 (308)
461 TIGR02325 C_P_lyase_phnF phosp 42.5 29 0.00063 34.3 3.9 27 513-543 32-58 (238)
462 cd04780 HTH_MerR-like_sg5 Heli 42.5 18 0.0004 31.4 2.2 25 514-538 1-25 (95)
463 PRK08359 transcription factor; 42.4 34 0.00074 33.4 4.2 35 512-546 97-138 (176)
464 PF05930 Phage_AlpA: Prophage 42.4 29 0.00063 26.4 3.0 24 514-537 4-27 (51)
465 cd04789 HTH_Cfa Helix-Turn-Hel 42.0 19 0.00041 31.6 2.2 27 514-540 2-28 (102)
466 cd04777 HTH_MerR-like_sg1 Heli 42.0 19 0.00042 31.6 2.3 27 514-540 1-27 (107)
467 cd04788 HTH_NolA-AlbR Helix-Tu 41.9 19 0.0004 31.2 2.1 26 514-539 1-26 (96)
468 cd04766 HTH_HspR Helix-Turn-He 41.7 19 0.00041 30.7 2.1 27 514-540 2-28 (91)
469 cd01106 HTH_TipAL-Mta Helix-Tu 41.6 19 0.00042 31.4 2.2 25 514-538 1-25 (103)
470 cd04768 HTH_BmrR-like Helix-Tu 41.6 2.3E+02 0.005 24.4 9.1 35 512-546 56-90 (96)
471 cd01108 HTH_CueR Helix-Turn-He 41.5 19 0.00041 32.8 2.2 27 514-540 1-27 (127)
472 PRK14101 bifunctional glucokin 41.3 63 0.0014 37.4 6.9 51 483-535 343-396 (638)
473 cd01109 HTH_YyaN Helix-Turn-He 41.3 20 0.00043 31.9 2.2 26 514-539 1-26 (113)
474 PRK09744 DNA-binding transcrip 41.2 36 0.00079 28.6 3.6 19 515-533 12-30 (75)
475 PRK10906 DNA-binding transcrip 41.2 41 0.00089 34.3 4.8 36 496-534 5-40 (252)
476 PF09012 FeoC: FeoC like trans 41.2 38 0.00083 27.3 3.8 24 420-443 14-37 (69)
477 cd01282 HTH_MerR-like_sg3 Heli 41.2 20 0.00043 32.0 2.2 27 514-540 1-27 (112)
478 TIGR02404 trehalos_R_Bsub treh 41.2 31 0.00067 34.2 3.9 27 513-543 24-50 (233)
479 cd00592 HTH_MerR-like Helix-Tu 41.2 20 0.00043 30.8 2.2 25 514-538 1-25 (100)
480 PRK10219 DNA-binding transcrip 41.1 71 0.0015 27.6 5.7 26 512-537 20-45 (107)
481 PRK08583 RNA polymerase sigma 41.0 2.1E+02 0.0045 28.8 9.9 25 419-443 220-244 (257)
482 TIGR02044 CueR Cu(I)-responsiv 41.0 19 0.00042 32.7 2.2 26 514-539 1-26 (127)
483 cd04765 HTH_MlrA-like_sg2 Heli 40.9 32 0.00069 30.1 3.4 23 514-536 1-23 (99)
484 cd04769 HTH_MerR2 Helix-Turn-H 40.9 20 0.00043 32.1 2.2 27 514-540 1-27 (116)
485 PRK10434 srlR DNA-bindng trans 40.8 34 0.00075 34.9 4.2 38 496-536 5-42 (256)
486 TIGR00373 conserved hypothetic 40.7 47 0.001 31.6 4.8 37 496-535 14-50 (158)
487 TIGR00270 conserved hypothetic 40.7 40 0.00086 32.1 4.3 25 512-536 81-105 (154)
488 cd04774 HTH_YfmP Helix-Turn-He 40.5 20 0.00044 31.1 2.1 26 514-539 1-26 (96)
489 PRK11886 bifunctional biotin-- 40.5 47 0.001 34.9 5.3 40 497-539 5-44 (319)
490 TIGR03826 YvyF flagellar opero 40.1 1.1E+02 0.0024 28.7 7.1 46 404-449 30-75 (137)
491 KOG1597 Transcription initiati 40.0 2.1E+02 0.0046 30.2 9.7 44 500-544 248-291 (308)
492 PF10078 DUF2316: Uncharacteri 40.0 61 0.0013 28.3 4.9 24 512-535 22-45 (89)
493 PRK10870 transcriptional repre 39.7 3.4E+02 0.0074 26.0 10.7 24 420-443 71-94 (176)
494 PRK10163 DNA-binding transcrip 39.6 52 0.0011 33.7 5.4 25 511-535 38-62 (271)
495 COG3711 BglG Transcriptional a 39.6 36 0.00078 37.6 4.5 47 496-543 84-130 (491)
496 cd01111 HTH_MerD Helix-Turn-He 39.3 22 0.00048 31.6 2.2 26 514-539 1-26 (107)
497 PF04552 Sigma54_DBD: Sigma-54 39.1 25 0.00054 33.7 2.7 24 419-442 48-71 (160)
498 PRK11569 transcriptional repre 39.1 46 0.001 34.1 4.9 25 511-535 41-65 (274)
499 cd04783 HTH_MerR1 Helix-Turn-H 39.0 22 0.00047 32.3 2.2 27 514-540 1-27 (126)
500 COG4367 Uncharacterized protei 38.9 75 0.0016 27.7 5.2 39 494-535 3-45 (97)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=9.5e-65 Score=539.53 Aligned_cols=315 Identities=38% Similarity=0.648 Sum_probs=298.7
Q ss_pred CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHH--------------------HHHHHHHHhhhhCCCCchHHHHHHc
Q 008652 242 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR--------------------LEKEKSKLQSQFGREPTLIEWAKAI 301 (558)
Q Consensus 242 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~iq~~~~--------------------le~~~~~l~~~~g~~pt~~ewA~a~ 301 (558)
..|+++.||++|++.||||++||++|+++||.++. |++++..|++.+|++||..+||.++
T Consensus 58 ~~d~v~~yl~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~~~ 137 (415)
T PRK07598 58 STDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTA 137 (415)
T ss_pred CCChHHHHHHhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHHHh
Confidence 57899999999999999999999999999999999 8999999999999999999999555
Q ss_pred ----------------------cCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhh
Q 008652 302 ----------------------GLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSV 359 (558)
Q Consensus 302 ----------------------g~~~~~L~~~l~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAi 359 (558)
||++++|+..++.|..|+++||.+|+++|+++|++|.++|++++||||||++|||+|+
T Consensus 138 ~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~rav 217 (415)
T PRK07598 138 DISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAV 217 (415)
T ss_pred CCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHH
Confidence 4566666677788899999999999999999999999999999999999999999999
Q ss_pred hhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHH
Q 008652 360 EKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLER 439 (558)
Q Consensus 360 ekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ 439 (558)
++|||++|++|+|||+||||++|.+++++++|+||+|.|+...+++++++...+.+.+||.|+.+|||+.+|+++++|+.
T Consensus 218 ekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~ 297 (415)
T PRK07598 218 EKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVRE 297 (415)
T ss_pred HHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHH
Q 008652 440 LIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEV 519 (558)
Q Consensus 440 ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EI 519 (558)
++.....++|||.+++++++..+.+.+.++ ...|++.+....+...|..+|..||++||+||.|||||+||+++|++||
T Consensus 298 ~l~~~~~~~SLd~~vg~~~d~~l~d~l~~~-~~~pee~~~~~~l~~~L~~~L~~L~~reR~VI~LRygl~d~~~~Tl~EI 376 (415)
T PRK07598 298 VLLRVPRSVSLETKVGKDKDTELGDLLETD-DISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEI 376 (415)
T ss_pred HHHHccCCcccccccCCCccccHHHhccCC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCCCHHHH
Confidence 999999999999999988888888887654 4578888888889999999999999999999999999999999999999
Q ss_pred HHHhCCCHHHHHHHHHHHHHHHHHHhhcCchHhhhhhh
Q 008652 520 GNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLL 557 (558)
Q Consensus 520 Ae~LGISrerVRqie~RALkKLR~~l~~~~L~~yldll 557 (558)
|+.||||+++||+++++|++|||+.-....+++|++.|
T Consensus 377 A~~LGvS~erVRqie~rAl~KLR~~~~~~~l~~y~~~~ 414 (415)
T PRK07598 377 GRALDLSRERVRQIESKALQKLRQPKRRNRIRDYLELL 414 (415)
T ss_pred HHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHHHhc
Confidence 99999999999999999999999999999999999865
No 2
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=5.6e-62 Score=514.61 Aligned_cols=312 Identities=37% Similarity=0.728 Sum_probs=300.0
Q ss_pred CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHHHHhhcHHHHHH
Q 008652 242 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 321 (558)
Q Consensus 242 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~ 321 (558)
..|++..||++|+++|+||++||++|+++|++++.+++.+.+|+...|++|+..+||.++|++..+|..+++.|..|++.
T Consensus 61 ~~d~l~~Yl~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~ 140 (373)
T PRK07406 61 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEK 140 (373)
T ss_pred CCCHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHH
Confidence 35789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHH
Q 008652 322 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 401 (558)
Q Consensus 322 LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~~ 401 (558)
||.+|+++|+++|++|.++|.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++|++++++||+|.|+..
T Consensus 141 Li~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~~ 220 (373)
T PRK07406 141 MVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYE 220 (373)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHH
Q 008652 402 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ 481 (558)
Q Consensus 402 ~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~le~~ 481 (558)
.+++++++...+.+.+|+.|+.+|||+.+|+++++|..++.....++|||.+++++++..+.+++++.. .+|++.+...
T Consensus 221 ~~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d~l~d~~-~~pee~~~~~ 299 (373)
T PRK07406 221 TISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADG-ETPEDDVAKN 299 (373)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHHhcCCCC-CCHHHHHHHH
Confidence 999999999999999999999999999999999999999888888999999998777778888888763 4788888888
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchHhhh
Q 008652 482 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYA 554 (558)
Q Consensus 482 ~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl 554 (558)
.+...|..+|+.||++||.||.+|||++|++++|++|||+.||||++||||++.+|++|||+......|+.|+
T Consensus 300 ~~~~~L~~aL~~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~~~~~~~l~~~~ 372 (373)
T PRK07406 300 LLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 372 (373)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHh
Confidence 8999999999999999999999999999889999999999999999999999999999999999999999886
No 3
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00 E-value=2.3e-61 Score=503.49 Aligned_cols=311 Identities=40% Similarity=0.676 Sum_probs=297.7
Q ss_pred CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHHHHhhcHHHHHH
Q 008652 242 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 321 (558)
Q Consensus 242 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~ 321 (558)
.+|++..||++|+++|+||++||++|+++|+.++.++..+..|+..+|++|+..+||.++++++.+|+..++.|+.|++.
T Consensus 16 ~~d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~~ 95 (327)
T PRK05949 16 SADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQK 95 (327)
T ss_pred CCCHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHHH
Confidence 56899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHH
Q 008652 322 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 401 (558)
Q Consensus 322 LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~~ 401 (558)
||..|+++|+++|++|.+++.+++|||||||+|||+++++|||++|++|+|||+||||++|.++|.+++++||+|.|+..
T Consensus 96 Li~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~~~ 175 (327)
T PRK05949 96 MIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITE 175 (327)
T ss_pred HHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHH
Q 008652 402 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ 481 (558)
Q Consensus 402 ~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~le~~ 481 (558)
.+++++++...+..++|++|+.+|||+.+|+++++|..++.....++|||.+++++++..+.+.++|.. ..|++.+...
T Consensus 176 ~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~~-~~pe~~~~~~ 254 (327)
T PRK05949 176 KLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEG-PSPDQYITQE 254 (327)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCCC-CCHHHHHHHH
Confidence 999999999999999999999999999999999999999998899999999998777777888887765 5788888888
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchHhhhh
Q 008652 482 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 555 (558)
Q Consensus 482 ~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yld 555 (558)
.+...|..+|+.||++||.||.+||||+|++++|++|||+.||||+++|||++.+|++|||+. ...|+.|+.
T Consensus 255 ~~~~~L~~~L~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~~--~~~l~~~~~ 326 (327)
T PRK05949 255 LLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRRR--RANVKEYLA 326 (327)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence 899999999999999999999999999999999999999999999999999999999999994 467777764
No 4
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=100.00 E-value=1.3e-60 Score=492.05 Aligned_cols=298 Identities=44% Similarity=0.755 Sum_probs=285.7
Q ss_pred hHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHHHHhhcHHHHHHHH
Q 008652 244 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI 323 (558)
Q Consensus 244 d~l~~Yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI 323 (558)
|++..||++++++|+||++||.+|+++++.++.++..+..|+.+.|++|+..+||+++|+++.+|+..++.|..|++.||
T Consensus 1 ~~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv 80 (298)
T TIGR02997 1 DLVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMI 80 (298)
T ss_pred CcHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHH
Confidence 36788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHH
Q 008652 324 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL 403 (558)
Q Consensus 324 ~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~~~l 403 (558)
.+|+++|+++|++|.++|.+++|||||||+|||+|+++|||++|++|+|||+||||++|.+++.+++++||+|.++...+
T Consensus 81 ~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~~~~~~~ 160 (298)
T TIGR02997 81 KANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKL 160 (298)
T ss_pred HHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHH
Q 008652 404 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 483 (558)
Q Consensus 404 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~le~~~~ 483 (558)
++++++...+.+.+|+.|+.+|||+.+|+++++|..++.....++|||.+++++++..+.+.+.+. ..+|++.+...++
T Consensus 161 ~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~-~~~pe~~~~~~~~ 239 (298)
T TIGR02997 161 NKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDD-GESPEEQVERESL 239 (298)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccCC-CCCHHHHHHHHHH
Confidence 999999999999999999999999999999999999999888999999999776666777777774 4578888888888
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 484 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 484 ~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
...|..+|+.||++||+||.+||||+|++++|++|||+.||||++||||++.+|++|||
T Consensus 240 ~~~L~~~L~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr 298 (298)
T TIGR02997 240 RQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298 (298)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 99999999999999999999999999999999999999999999999999999999996
No 5
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=2.5e-60 Score=494.07 Aligned_cols=310 Identities=38% Similarity=0.644 Sum_probs=296.5
Q ss_pred ChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHHHHhhcHHHHHHH
Q 008652 243 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL 322 (558)
Q Consensus 243 ~d~l~~Yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~L 322 (558)
+|++..||++|+++|+||++||++|+++|++++.+++++..|+..+|++|+..+||.++++++.+|+..++.|+.|++.|
T Consensus 7 ~~~~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~L 86 (317)
T PRK07405 7 TDLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRKM 86 (317)
T ss_pred CcHHHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHHH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHH
Q 008652 323 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTL 402 (558)
Q Consensus 323 I~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~~~ 402 (558)
|..|+++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+|||+||||++|.++|.+++++||+|.|+...
T Consensus 87 ~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~~~ 166 (317)
T PRK07405 87 VEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK 166 (317)
T ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHH
Q 008652 403 LSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQL 482 (558)
Q Consensus 403 l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~le~~~ 482 (558)
+++++++...+...+|+.|+.+|||+.+|+++++|..++.....++|||.+++++++..+.+.+++.. ..|++.+....
T Consensus 167 ~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~~-~~pe~~~~~~~ 245 (317)
T PRK07405 167 LNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTG-ASPEDFATQSS 245 (317)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCCC-CCHHHHHHHHH
Confidence 99999999999999999999999999999999999999988888999999998777777888887764 57888888888
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchHhhhh
Q 008652 483 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 555 (558)
Q Consensus 483 ~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yld 555 (558)
+...|..+|+.||++||.||.+||||+|++++|++|||+.||||++||||++.+|++|||+. ...+..|++
T Consensus 246 ~~~~l~~al~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~--~~~l~~~~~ 316 (317)
T PRK07405 246 LQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKR--KANIQEYLA 316 (317)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999995 457777764
No 6
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=100.00 E-value=4.1e-59 Score=482.64 Aligned_cols=313 Identities=36% Similarity=0.656 Sum_probs=289.1
Q ss_pred ChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhh-hhCCCCchH---------------HHHHHccCCH-
Q 008652 243 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS-QFGREPTLI---------------EWAKAIGLSC- 305 (558)
Q Consensus 243 ~d~l~~Yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~-~~g~~pt~~---------------ewA~a~g~~~- 305 (558)
.|.+..|+.+++..+++++++|.++.+.++....+......|.. ..|..|+.. +|+.....++
T Consensus 8 ~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Ee 87 (342)
T COG0568 8 ADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEEE 87 (342)
T ss_pred hhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHHH
Confidence 56888999999999999999999999999887777667777776 677888876 6666555544
Q ss_pred HHHHHHHhhcH---HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHH
Q 008652 306 RDLKSELHSGN---SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 382 (558)
Q Consensus 306 ~~L~~~l~~G~---~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI 382 (558)
..|..++..|. .|+.+||.+|+|||++||++|.++|+++.||||||+||||+|+++|||++||+|||||+||||++|
T Consensus 88 ~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrqaI 167 (342)
T COG0568 88 KALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAI 167 (342)
T ss_pred HHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHHHH
Confidence 66777777773 699999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 008652 383 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 462 (558)
Q Consensus 383 ~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l 462 (558)
.++|.+++|+||+|.|+.+.+++++++.+.+.+++|++|+.+|||+.+|+++++|..++.....++|||.|++++++..+
T Consensus 168 ~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~ded~~l 247 (342)
T COG0568 168 TRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSEL 247 (342)
T ss_pred HHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCCCcccHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999988899
Q ss_pred hhhcccCCCCChhHHHHHHHHHHHHHHHHhc-CCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008652 463 QEITADTGVEIPDISVQKQLMRQHVRNLLTL-LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 541 (558)
Q Consensus 463 ~e~i~d~~~~~pe~~le~~~~~e~L~~~L~~-L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 541 (558)
.+++.|+...+|++.+....+.+.+...|.. |+|+|+.||++|||++|+++.|++|||+.+|||++|||||+.+|++||
T Consensus 248 ~d~leD~~~~~p~~~~~~~~~~~~~~~~L~~~Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~isrERvRQIE~kAl~KL 327 (342)
T COG0568 248 GDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAKALRKL 327 (342)
T ss_pred HHHhhcCCcCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCcchHHHHHHHhCCcHHHHHHHHHHHHHHH
Confidence 9999999888999999999999999999999 999999999999999999999999999999999999999999999999
Q ss_pred HH-HhhcCchHhhhh
Q 008652 542 KQ-SLGGKASYGYAD 555 (558)
Q Consensus 542 R~-~l~~~~L~~yld 555 (558)
|. ......+++|++
T Consensus 328 r~~~~~~~~~~~~l~ 342 (342)
T COG0568 328 RRHPERSALLRSYLD 342 (342)
T ss_pred HHhhhhhhHHHHhhC
Confidence 94 444555678864
No 7
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=100.00 E-value=4e-59 Score=507.36 Aligned_cols=301 Identities=35% Similarity=0.613 Sum_probs=277.3
Q ss_pred CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHHHHhhcHHHHHH
Q 008652 242 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 321 (558)
Q Consensus 242 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~ 321 (558)
..|++..||++|+++|+||++||++|+++|+.+..++.. +. ...+|+. ....+|++.++.|..|+++
T Consensus 209 ~~d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~---~~-------~~~~~~~---~~~~~l~~~~~~g~~Ar~~ 275 (509)
T PRK05901 209 TADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEEL---LA-------EGEKLDP---ELRRDLQWIGRDGKRAKNH 275 (509)
T ss_pred cccHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhh---hh-------hcccchh---hhhhhhhhhccchHHHHHH
Confidence 468999999999999999999999999999876433321 11 1122442 2457788889999999999
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHH
Q 008652 322 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 401 (558)
Q Consensus 322 LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~~ 401 (558)
||.+|+|||++||++|.++|++++||||||+||||+|+++|||++|++|+|||+||||++|.++|++++|+||+|.|+..
T Consensus 276 LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~~~~e 355 (509)
T PRK05901 276 LLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE 355 (509)
T ss_pred HHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHH
Q 008652 402 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ 481 (558)
Q Consensus 402 ~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~le~~ 481 (558)
.++++.++...+.+.+||.|+.+|||+.+|+++++|..++.....++|||.+++++++..+.+++.|.....|++.+...
T Consensus 356 ~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~~p~~~~~~~ 435 (509)
T PRK05901 356 TINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSFT 435 (509)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCCCCCHHHHHHHH
Confidence 99999999999999999999999999999999999999999888999999999887777889999988777899989899
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchHhhhh
Q 008652 482 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 555 (558)
Q Consensus 482 ~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yld 555 (558)
.++..|..+|..|++||+.||.+||||++++++|++|||+.||||++|||||+.+||+|||.......|+.|++
T Consensus 436 ~l~~~L~~aL~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~~~~~~l~~~l~ 509 (509)
T PRK05901 436 LLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDFLD 509 (509)
T ss_pred HHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999975
No 8
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=100.00 E-value=5.5e-58 Score=477.28 Aligned_cols=299 Identities=36% Similarity=0.632 Sum_probs=275.6
Q ss_pred ChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHHHHhhcHHHHHHH
Q 008652 243 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL 322 (558)
Q Consensus 243 ~d~l~~Yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~L 322 (558)
+|++..||++++++|+||++||.+|+++|+.+..++.. |+..+|+... ...+|...++.|..|++.|
T Consensus 25 ~~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~~L 91 (324)
T PRK07921 25 ADLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARRHL 91 (324)
T ss_pred CChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHHHH
Confidence 57899999999999999999999999999987665543 2223332111 4567888999999999999
Q ss_pred HHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHH
Q 008652 323 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTL 402 (558)
Q Consensus 323 I~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~~~ 402 (558)
|..|+++|+++|++|.++|.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++|++++++||+|.|+...
T Consensus 92 v~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~~~ 171 (324)
T PRK07921 92 LEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ 171 (324)
T ss_pred HHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHH
Q 008652 403 LSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQL 482 (558)
Q Consensus 403 l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~le~~~ 482 (558)
+++++++...+.+.+|+.||.+|||+.+|+++++|..++.....++|||.+++++++.++.++++|+....|++.+....
T Consensus 172 ~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~~ 251 (324)
T PRK07921 172 VNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGL 251 (324)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCCCCCHHHHHHHHH
Confidence 99999999999999999999999999999999999999988888999999998777778889998876678888888888
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchHhhh
Q 008652 483 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYA 554 (558)
Q Consensus 483 ~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl 554 (558)
++..|..+|..|+++|+.||.+||||+|++++|++|||+.||||++|||||+.+|++|||.......|+.|+
T Consensus 252 ~~~~l~~~L~~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~~~~~~l~~~~ 323 (324)
T PRK07921 252 LHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSYA 323 (324)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHHHHHHHHhh
Confidence 999999999999999999999999999999999999999999999999999999999999998888888885
No 9
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=1.8e-54 Score=458.41 Aligned_cols=276 Identities=36% Similarity=0.704 Sum_probs=262.8
Q ss_pred CCCChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHHHHhhcHHHH
Q 008652 240 FDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSR 319 (558)
Q Consensus 240 ~~~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Ar 319 (558)
....|+++.||++|+++|+||++||.+|+++++. |+..|+
T Consensus 92 ~~~~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~----------------------------------------Gd~~A~ 131 (367)
T PRK09210 92 VKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEE----------------------------------------GDEEAK 131 (367)
T ss_pred cccCcHHHHHHHHhhccCCCCHHHHHHHHHHHHh----------------------------------------hHHHHH
Confidence 3457899999999999999999999999988764 345899
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhH
Q 008652 320 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI 399 (558)
Q Consensus 320 e~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~ 399 (558)
+.||..|+++|+++|++|.++|.+++||+|||++|||+|+++|||.+|++|+|||+||||++|.++|++++|+||+|.|+
T Consensus 132 ~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~ 211 (367)
T PRK09210 132 QRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 211 (367)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHH
Q 008652 400 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ 479 (558)
Q Consensus 400 ~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~le 479 (558)
...++++.++.+.+.+++||.||.+|||+.+|+++++|..++.....++|||.+++.+++..+.++++|.....|++.+.
T Consensus 212 ~~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~~~~p~~~~~ 291 (367)
T PRK09210 212 VETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAA 291 (367)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCCCCCHHHHHH
Confidence 99999999999999999999999999999999999999999998888999999998877778899999887778999999
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchHhhhh
Q 008652 480 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 555 (558)
Q Consensus 480 ~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yld 555 (558)
...++..|..+|..||++||.||.+||||+||+++|++|||+.||||++|||||+.+||+|||.......|+.|++
T Consensus 292 ~~~~~~~l~~~l~~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~~~~~~~l~~~~~ 367 (367)
T PRK09210 292 YELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 367 (367)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhChHHHhHHHHhhC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999974
No 10
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=1.4e-51 Score=462.57 Aligned_cols=274 Identities=34% Similarity=0.633 Sum_probs=252.4
Q ss_pred HHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHHHHhhcHHHHHHHHH
Q 008652 245 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 324 (558)
Q Consensus 245 ~l~~Yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~ 324 (558)
.+..||.++...+.||++|+.+++++|+. |. .....|+++||.
T Consensus 345 ~lq~~L~~ie~~~~Ls~eElk~l~~~i~~---------------g~----------------------~~~~~a~~~Li~ 387 (619)
T PRK05658 345 KLQQELEAIEEETGLTIEELKEINRQISK---------------GE----------------------AKARRAKKEMVE 387 (619)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHHhc---------------cc----------------------hhhhHHHHHHHH
Confidence 34456667777777777777777766654 21 012378999999
Q ss_pred HHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHH
Q 008652 325 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS 404 (558)
Q Consensus 325 ~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~~~l~ 404 (558)
+|+|||++||++|.++|++++||||||+||||+|+++|||++|++|+|||+||||++|.++|++++|+||+|+|+...++
T Consensus 388 ~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~irip~~~~~~~~ 467 (619)
T PRK05658 388 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 467 (619)
T ss_pred HHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCceecCHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHHH
Q 008652 405 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMR 484 (558)
Q Consensus 405 ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~le~~~~~ 484 (558)
+++++...+.+++||.||.+|||+.+|++.++|..++.....++|||.|++++++..+.+++.|.....|++.+....++
T Consensus 468 k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~~~~~l~d~i~d~~~~~p~~~~~~~~~~ 547 (619)
T PRK05658 468 KLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLR 547 (619)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCCCCCchhhhcCCCCCCChHHHHHHHHHH
Confidence 99999999999999999999999999999999999999888999999999888888899999998878899988888999
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchHhhhh
Q 008652 485 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 555 (558)
Q Consensus 485 e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yld 555 (558)
..|..+|..||+||+.||++||||++++++|++|||+.||||++|||||+.+|++|||+......|+.|+|
T Consensus 548 ~~l~~~l~~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr~~~~~~~l~~~~~ 618 (619)
T PRK05658 548 EATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRSFLD 618 (619)
T ss_pred HHHHHHHHcCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHhchHHHHHHHHHhc
Confidence 99999999999999999999999998899999999999999999999999999999999999999999987
No 11
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=100.00 E-value=9.6e-48 Score=383.93 Aligned_cols=238 Identities=39% Similarity=0.753 Sum_probs=227.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccch
Q 008652 318 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 397 (558)
Q Consensus 318 Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~ 397 (558)
|+++||..|+++|+++|++|.++|.+++||+|||++||++|+++|||++|++|+|||+||||++|.++++++.+.+|+|.
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 hHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHH
Q 008652 398 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 477 (558)
Q Consensus 398 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~ 477 (558)
++...++++.++...+.+.+|+.||.+|||+.+|+++++|..++......+|||.+++++++.++.+.++|+....|++.
T Consensus 81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~p~~~ 160 (238)
T TIGR02393 81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESPDDY 160 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcccHHHHhcCCCCCChHHH
Confidence 99999999999999999999999999999999999999999998888889999999977766678888888877788888
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchHhhhh
Q 008652 478 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 555 (558)
Q Consensus 478 le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yld 555 (558)
+...++...|..+|+.||++||.||.++|||++++++|++|||+.||||+++|+|++.+|++|||..+....|+.|+|
T Consensus 161 ~~~~~~~~~l~~~l~~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~~~~~~~~~~ 238 (238)
T TIGR02393 161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKSFLD 238 (238)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHHHhHHHHhhC
Confidence 888888999999999999999999999999998899999999999999999999999999999999999999999976
No 12
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=100.00 E-value=1.8e-44 Score=376.37 Aligned_cols=272 Identities=35% Similarity=0.567 Sum_probs=253.6
Q ss_pred CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHHHHhhcHHHHHH
Q 008652 242 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 321 (558)
Q Consensus 242 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~ 321 (558)
..|.++.|+.+|+..|+||+++|.+|+.+++. |+..|++.
T Consensus 51 ~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~----------------------------------------Gd~~A~~~ 90 (325)
T PRK05657 51 VLDATQLYLNEIGYSPLLTAEEEVYFARRALR----------------------------------------GDFAARQR 90 (325)
T ss_pred cccHHHHHHHHHhcCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHH
Confidence 46789999999999999999999999987654 45689999
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHH
Q 008652 322 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 401 (558)
Q Consensus 322 LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~~ 401 (558)
||..|.++|+++|++|.+++.+++||+||||+|+|+++++||+.+|++|+|||+||||++|.++++++.+.||+|.++..
T Consensus 91 Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~~~~~ 170 (325)
T PRK05657 91 MIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVK 170 (325)
T ss_pred HHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHH
Q 008652 402 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ 481 (558)
Q Consensus 402 ~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~le~~ 481 (558)
.++++.++...+...+|+.|+.+|||..+|+++++|..++.......|||.++..+...++.+.+.+.....|+..+...
T Consensus 171 ~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~ 250 (325)
T PRK05657 171 ELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDD 250 (325)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCCcchhhhccCCCCCCHHHHHHHH
Confidence 99888899999999999999999999999999999999998888889999998777666788888877666888888888
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchHhh
Q 008652 482 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGY 553 (558)
Q Consensus 482 ~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~y 553 (558)
+....|..+|..||+++|.||.+||||.+.+++|++|||+.||||+++|++++++|+++||+.+...++..+
T Consensus 251 e~~~~L~~aL~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~~~~~~~~ 322 (325)
T PRK05657 251 DMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQGLSIE 322 (325)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhCccchh
Confidence 888999999999999999999999999888999999999999999999999999999999999988887533
No 13
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=2.7e-44 Score=368.62 Aligned_cols=262 Identities=27% Similarity=0.470 Sum_probs=223.8
Q ss_pred CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHHHHhhcHHHHHH
Q 008652 242 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 321 (558)
Q Consensus 242 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~ 321 (558)
+.+++..|+.++++.|+||.++|.+|+.+++. .++..|++.
T Consensus 12 ~~~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~---------------------------------------~Gd~~a~~~ 52 (284)
T PRK06596 12 PEGNLDAYIQAVNKIPMLTAEEEYMLAKRLRE---------------------------------------HGDLEAAKQ 52 (284)
T ss_pred CccHHHHHHHHHhccCCCCHHHHHHHHHHHHH---------------------------------------cCCHHHHHH
Confidence 45789999999999999999999999887532 245689999
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHH
Q 008652 322 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 401 (558)
Q Consensus 322 LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~~ 401 (558)
||..|+++|+++|++|.+.+.+++||+|||++||++|+++|||++|++|+|||+|||+++|.+++++++++|++|.+...
T Consensus 53 Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~p~~~~~ 132 (284)
T PRK06596 53 LVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQ 132 (284)
T ss_pred HHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeeeccchHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999889999987642
Q ss_pred --HHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHh-cCCCcccCCCCCCCCC--cchhhhcccCCCCChhH
Q 008652 402 --LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI-TRMPLSMQQPVWADQD--TTFQEITADTGVEIPDI 476 (558)
Q Consensus 402 --~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~-~~~~~SLD~~i~~d~~--~~l~e~i~d~~~~~pe~ 476 (558)
...++.+....+. .+++|+.+|||+.+|+++++|..++.. ....+|||.+++++++ .++.+.++|.. ..|++
T Consensus 133 ~~~~~~~~~~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~~-~~p~~ 209 (284)
T PRK06596 133 RKLFFNLRKAKKRLG--WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDKS-SDPAD 209 (284)
T ss_pred HHHHHHHHHHHHHhc--cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcCCCC-CCchH
Confidence 3344444444443 458999999999999999999998753 3478999999865532 45778887763 45766
Q ss_pred HHHHH----HHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008652 477 SVQKQ----LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 547 (558)
Q Consensus 477 ~le~~----~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 547 (558)
.++.. .+...|..+|+.||++||.||.+|||. + +++|++|||+.||||++||||++++|++|||..+..
T Consensus 210 ~~~~~~~~~~~~~~L~~al~~L~~rEr~VL~lry~~-~-~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~l~~ 282 (284)
T PRK06596 210 VLEEDNWEDQRRALLADALEGLDERSRDIIEARWLD-D-DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEA 282 (284)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC-C-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 66554 357789999999999999999999973 2 689999999999999999999999999999998764
No 14
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=3.5e-44 Score=368.68 Aligned_cols=264 Identities=26% Similarity=0.451 Sum_probs=226.3
Q ss_pred hHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHHHHhhcHHHHHHHH
Q 008652 244 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI 323 (558)
Q Consensus 244 d~l~~Yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI 323 (558)
+..+.||+++.++|+||+++|.+|+.+++. .++..|++.||
T Consensus 6 ~~~~~y~~~~~~~~~l~~~~e~~L~~~~~~---------------------------------------~gd~~A~~~Lv 46 (289)
T PRK07500 6 SADRSMIRSAMKAPYLEREEEHALAYRWKD---------------------------------------HRDEDALHRII 46 (289)
T ss_pred hHHHHHHHHHhcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHH
Confidence 456789999999999999999999988643 14568999999
Q ss_pred HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHH--
Q 008652 324 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT-- 401 (558)
Q Consensus 324 ~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~~-- 401 (558)
..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|.+|+|||+||||++|.++|+++++++|+|.+...
T Consensus 47 ~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~~~~~~~ 126 (289)
T PRK07500 47 SAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKA 126 (289)
T ss_pred HHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCccHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999988654
Q ss_pred HHHHHHHHHHHHHH---hCCCCCCHHHHHHHhCCCHHHHHHHHH-hcCCCcccCCCCCCCCCc--chhhhcccCCCCChh
Q 008652 402 LLSKVLEAKRLYIQ---EGNHSPDKEDLARRVGITVEKLERLIF-ITRMPLSMQQPVWADQDT--TFQEITADTGVEIPD 475 (558)
Q Consensus 402 ~l~ki~ka~~~l~~---~~gr~Pt~eEIA~~lgis~e~v~~ll~-~~~~~~SLD~~i~~d~~~--~l~e~i~d~~~~~pe 475 (558)
...++++.+..+.+ .+|+.|+.+|||+.||+++++|..+.. ....++|||.+++++++. ++.+.+.++.. .|+
T Consensus 127 ~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~i~d~~~-~pe 205 (289)
T PRK07500 127 LFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDSP-LPD 205 (289)
T ss_pred HHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCCCcccHHHhccCCCC-Cch
Confidence 33445555555544 689999999999999999999988753 345799999998765443 57788877643 466
Q ss_pred HHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008652 476 ISVQK----QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 549 (558)
Q Consensus 476 ~~le~----~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 549 (558)
+.+.. .+....|..+|+.||++||.||.+||+. ++++|++|||+.||||++||+|++.+|++|||..+..+.
T Consensus 206 ~~~~~~~~~~~~~~~l~~al~~L~~rer~vl~lr~~~--~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~~~~ 281 (289)
T PRK07500 206 EQVESSIDGERRRRWLTQALQTLNERELRIIRERRLR--EDGATLEALGEELGISKERVRQIEARALEKLRRALLSQS 281 (289)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 55443 3456779999999999999999999962 378999999999999999999999999999999987554
No 15
>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=100.00 E-value=1.2e-43 Score=361.11 Aligned_cols=258 Identities=28% Similarity=0.501 Sum_probs=217.0
Q ss_pred HHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHHHHhhcHHHHHHHHH
Q 008652 245 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 324 (558)
Q Consensus 245 ~l~~Yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~ 324 (558)
++..||++++++|+|+.++|.+|+.++.. .++..|++.||.
T Consensus 2 ~~~~yl~~~~~~~~l~~~~e~~l~~~~~~---------------------------------------~gd~~a~~~Lv~ 42 (270)
T TIGR02392 2 SLDAYIRAVNRIPMLTPEEEYQLAKRLRE---------------------------------------HGDLDAAKKLVL 42 (270)
T ss_pred hHHHHHHHHhcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHHH
Confidence 57789999999999999999999886432 245689999999
Q ss_pred HHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHH--HH
Q 008652 325 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY--TL 402 (558)
Q Consensus 325 ~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~--~~ 402 (558)
.|+++|+++|++|.+++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++++++++++|+|.+.. ..
T Consensus 43 ~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir~p~~~~~~~~ 122 (270)
T TIGR02392 43 SHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKL 122 (270)
T ss_pred HhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCceecCchHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999988899997654 33
Q ss_pred HHHHHHHHHHHHHhCCCCC-CHHHHHHHhCCCHHHHHHHHHhc-CCCcccCCCCCCCCC--cchhhhcccCCCCChhHHH
Q 008652 403 LSKVLEAKRLYIQEGNHSP-DKEDLARRVGITVEKLERLIFIT-RMPLSMQQPVWADQD--TTFQEITADTGVEIPDISV 478 (558)
Q Consensus 403 l~ki~ka~~~l~~~~gr~P-t~eEIA~~lgis~e~v~~ll~~~-~~~~SLD~~i~~d~~--~~l~e~i~d~~~~~pe~~l 478 (558)
..++.++...+. +++.| +.+|||+.+|+++++|..++... ...+|||.+++++++ ..+.+.+.|.. .+|++.+
T Consensus 123 ~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~l~d~~-~~pe~~~ 199 (270)
T TIGR02392 123 FFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKT-SDPEDTL 199 (270)
T ss_pred HHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCCccccHHHHhcCCC-CChHHHH
Confidence 444444444432 32555 69999999999999999986533 347999999866543 25667777764 3566665
Q ss_pred HHH----HHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008652 479 QKQ----LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 546 (558)
Q Consensus 479 e~~----~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 546 (558)
+.. .+...|..+|..||++||.||.+||+. ++++|++|||+.||||.++|+|++.+|++|||+.+.
T Consensus 200 ~~~~~~~~~~~~L~~al~~L~~rer~vl~l~y~~--~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~l~ 269 (270)
T TIGR02392 200 EEEQWEELQRQALANALGSLDARSRRIIEARWLD--DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAALA 269 (270)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhcC--CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 543 356789999999999999999999962 368999999999999999999999999999998764
No 16
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=4e-43 Score=356.54 Aligned_cols=220 Identities=24% Similarity=0.393 Sum_probs=200.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccc
Q 008652 317 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 396 (558)
Q Consensus 317 ~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP 396 (558)
.++++||.+|++||++||++|.++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++++++.++||+|
T Consensus 40 ~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I~~~lr~~~~~ir~P 119 (264)
T PRK07122 40 RQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVP 119 (264)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHcCCccccC
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCCcccCCCCCCCCCc--chhhhcccCCCC
Q 008652 397 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWADQDT--TFQEITADTGVE 472 (558)
Q Consensus 397 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~--~~~~~SLD~~i~~d~~~--~l~e~i~d~~~~ 472 (558)
.++...+++++++...+.+++|+.||.+|||+.+|+++++|..++.. ...++|||.+++++++. .+.+.++
T Consensus 120 r~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~d~~~----- 194 (264)
T PRK07122 120 RRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDARAIADTLG----- 194 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCCCCcccchhccC-----
Confidence 99999999999999999999999999999999999999999998864 45689999998654332 2333332
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008652 473 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 545 (558)
Q Consensus 473 ~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 545 (558)
+++..++..+....|..+|+.||+++|.||.++|+ +++|++|||+.||||.++|++++++|+++||..+
T Consensus 195 ~~~~~~e~~~~~~~l~~~l~~L~~rer~vl~l~y~----~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l 263 (264)
T PRK07122 195 DVDAGLDQIENREALRPLLAALPERERTVLVLRFF----ESMTQTQIAERVGISQMHVSRLLAKTLARLRDQL 263 (264)
T ss_pred CcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHc
Confidence 34555666677888999999999999999999998 8999999999999999999999999999999876
No 17
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=3e-41 Score=341.14 Aligned_cols=228 Identities=25% Similarity=0.408 Sum_probs=201.7
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHhhCC-CCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008652 314 SGNSSREKLINANLRLVVHVAKQYQGR-GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 392 (558)
Q Consensus 314 ~G~~Are~LI~~nlrLV~sIArrY~~~-g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~ 392 (558)
++..|+++||..|+++|+++|++|.+. +.+++||+|||+||||+|+++|||++|++|+|||+|||+++|.++++++.++
T Consensus 22 gd~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~~ 101 (256)
T PRK07408 22 PSIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPT 101 (256)
T ss_pred CCHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcCCe
Confidence 345899999999999999999999875 6679999999999999999999999999999999999999999999999999
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHH--hcCCCcccCCCCCCCCCc--chhhhccc
Q 008652 393 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF--ITRMPLSMQQPVWADQDT--TFQEITAD 468 (558)
Q Consensus 393 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~--~~~~~~SLD~~i~~d~~~--~l~e~i~d 468 (558)
||+|+++...+++++++...+.+.+|++|+.+|||+.+|+++++|..++. .....+|||.+++.+++. .+.+.+++
T Consensus 102 vr~pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~~~d 181 (256)
T PRK07408 102 VRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDEDGSTSLGDLLPD 181 (256)
T ss_pred eeeCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCCCccccccccCC
Confidence 99999999999999999999999999999999999999999999999864 345689999988654332 45566665
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008652 469 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 548 (558)
Q Consensus 469 ~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 548 (558)
+... +. ....+....|..+|..||+++|.||.++|+ +++|++|||+.||+|.++|++++.+|++|||+.+...
T Consensus 182 ~~~~-~~--~~~~~~~~~l~~~l~~L~~~~r~vl~l~y~----~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~~~ 254 (256)
T PRK07408 182 PRYR-SF--QLAQEDRIRLQQALAQLEERTREVLEFVFL----HDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQPE 254 (256)
T ss_pred cccc-hh--hhhHHHHHHHHHHHHcCCHHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhcc
Confidence 4432 11 123345567999999999999999999998 8999999999999999999999999999999988654
No 18
>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=100.00 E-value=9.3e-41 Score=342.26 Aligned_cols=272 Identities=35% Similarity=0.561 Sum_probs=248.5
Q ss_pred CCCCChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHHHHhhcHHH
Q 008652 239 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSS 318 (558)
Q Consensus 239 ~~~~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~A 318 (558)
.....|.+++||.+|+.+|.||.++|.+|+..++. ++..|
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~----------------------------------------gd~~a 47 (285)
T TIGR02394 8 ETRVADVTQLYLREIGFKPLLTAEEEIAYARRALA----------------------------------------GDFEA 47 (285)
T ss_pred ccCcchHHHHHHHHHhccCCCCHHHHHHHHHHHHc----------------------------------------CCHHH
Confidence 33467899999999999999999999999887654 45689
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchh
Q 008652 319 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 398 (558)
Q Consensus 319 re~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~ 398 (558)
++.||..|.++|+++|++|.+++.+++||+|||++|||+++++||+.+|++|+||+.|||+.++++++.++.+.+++|.+
T Consensus 48 ~~~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain~~i~~~~~~~~~p~~ 127 (285)
T TIGR02394 48 RKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVH 127 (285)
T ss_pred HHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHHHHHHHcCCceeCcHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHH
Q 008652 399 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV 478 (558)
Q Consensus 399 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~l 478 (558)
+...++.+.+..+.+.+.+|+.|+.+++|..+|++++++..++......+|+|.++..++...+.+.+.++....|++.+
T Consensus 128 ~~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~~~~pe~~~ 207 (285)
T TIGR02394 128 VIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLV 207 (285)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchhhhhcCCCCCCHHHHH
Confidence 99999998888887888899999999999999999999999998888889999887665555566666666556788888
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008652 479 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 550 (558)
Q Consensus 479 e~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L 550 (558)
...+....|..+|..||+++|.||.++|||.+.+++|++|||+.||||.++|++++++|+++||+.+...++
T Consensus 208 ~~~e~~~~L~~al~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~~~~~ 279 (285)
T TIGR02394 208 QNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERDGV 279 (285)
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 888889999999999999999999999988877999999999999999999999999999999999986554
No 19
>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=100.00 E-value=1.2e-39 Score=328.63 Aligned_cols=243 Identities=27% Similarity=0.444 Sum_probs=215.8
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHH
Q 008652 253 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH 332 (558)
Q Consensus 253 i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~~nlrLV~s 332 (558)
.+++|+||++||.+|+.+++. ++..|++.||..|+++|++
T Consensus 10 ~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~~~~~v~~ 49 (254)
T TIGR02850 10 TSKLPVLKNQEMRELFIRMQS----------------------------------------GDTTAREKLINGNLRLVLS 49 (254)
T ss_pred ccCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHHH
Confidence 467899999999998877653 3468999999999999999
Q ss_pred HHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHH
Q 008652 333 VAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL 412 (558)
Q Consensus 333 IArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~ 412 (558)
+|++|.+++.+++||+|||++|||+++++|||.+|.+|+||++|||++.|.++++++. .||+|.++...++++.++...
T Consensus 50 ~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~-~ir~p~~~~~~~~~~~~~~~~ 128 (254)
T TIGR02850 50 VIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDK 128 (254)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CccCchHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999965 889999999999999999999
Q ss_pred HHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCc--chhhhcccCCCCChhHHHHHHHHHHHHHHH
Q 008652 413 YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQEITADTGVEIPDISVQKQLMRQHVRNL 490 (558)
Q Consensus 413 l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~--~l~e~i~d~~~~~pe~~le~~~~~e~L~~~ 490 (558)
+.+++|+.|+.+|||+.+|+++++|..++.....+.|||.++.++++. .+.+.+.|+.. .++ ....+..|..+
T Consensus 129 l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~~~d~~~-~~~----~~~~~~~l~~~ 203 (254)
T TIGR02850 129 LISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEKN-KDS----QWLEGIALKEA 203 (254)
T ss_pred HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCCCCcchhhhhcCCccc-cHH----HHHhHHHHHHH
Confidence 999999999999999999999999999998888899999988654432 45666665432 122 22344578999
Q ss_pred HhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008652 491 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 545 (558)
Q Consensus 491 L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 545 (558)
++.|++++|.||.+||+ +++|++|||+.||+|.++|++++.+|++|||+.+
T Consensus 204 l~~L~~rer~vi~~~~~----~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~~~ 254 (254)
T TIGR02850 204 MKRLNEREKMILNMRFF----EGKTQMEVAEEIGISQAQVSRLEKAALKHMRKYV 254 (254)
T ss_pred HHcCCHHHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence 99999999999999997 8999999999999999999999999999999753
No 20
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=100.00 E-value=1.7e-39 Score=328.67 Aligned_cols=227 Identities=26% Similarity=0.391 Sum_probs=204.7
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcc
Q 008652 314 SGNSSREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS 390 (558)
Q Consensus 314 ~G~~Are~LI~~nlrLV~sIArrY~~---~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~s 390 (558)
++..|++.||..|+++|+++|++|.+ .+++++||+|||+||||+|+++|||++|++|+|||.||||++|.++++++.
T Consensus 20 ~~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~ 99 (257)
T PRK05911 20 QEIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQD 99 (257)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 34589999999999999999999852 356899999999999999999999999999999999999999999999987
Q ss_pred cccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcC--CCcccCCCCCC--CC--Ccchhh
Q 008652 391 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQPVWA--DQ--DTTFQE 464 (558)
Q Consensus 391 r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~--~~~SLD~~i~~--d~--~~~l~e 464 (558)
+ +|+++...++++.++...+.+.+|+.|+.+|||+.+|++.++|..++.... ..+|||.++.. ++ +.++.+
T Consensus 100 ~---~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~~~~~~~~~l~~ 176 (257)
T PRK05911 100 W---VPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQSDDEAGLALEE 176 (257)
T ss_pred C---CCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCCCCCccccchhh
Confidence 5 899999999999999999999999999999999999999999999886553 46899987643 21 235677
Q ss_pred hcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008652 465 ITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 544 (558)
Q Consensus 465 ~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 544 (558)
.++|.....|++.+...+....|..+|+.||++||.||.++|+ +++|++|||+.||||.++|++++.+|+++||+.
T Consensus 177 ~l~d~~~~~~~~~~~~~~~~~~l~~al~~L~~~er~vi~l~y~----e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 252 (257)
T PRK05911 177 RIADERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYYY----EELVLKEIGKILGVSESRVSQIHSKALLKLRAT 252 (257)
T ss_pred hccCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 8887766678888888888889999999999999999999998 899999999999999999999999999999998
Q ss_pred hhc
Q 008652 545 LGG 547 (558)
Q Consensus 545 l~~ 547 (558)
+..
T Consensus 253 l~~ 255 (257)
T PRK05911 253 LSA 255 (257)
T ss_pred HHh
Confidence 854
No 21
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=100.00 E-value=3.1e-38 Score=319.04 Aligned_cols=243 Identities=27% Similarity=0.463 Sum_probs=214.8
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHH
Q 008652 253 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH 332 (558)
Q Consensus 253 i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~~nlrLV~s 332 (558)
..++|+|+++|+..|+.+++. ++..|++.||..|.++|++
T Consensus 13 ~~~~~~l~~~~~~~l~~~~~~----------------------------------------gd~~a~~~l~~~~~~~v~~ 52 (258)
T PRK08215 13 TSKLPVLKNEEMRELFERMQN----------------------------------------GDKEAREKLINGNLRLVLS 52 (258)
T ss_pred CCCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHHHHHHHH
Confidence 357789999999988877653 4568999999999999999
Q ss_pred HHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHH
Q 008652 333 VAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL 412 (558)
Q Consensus 333 IArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~ 412 (558)
+|++|.+++.+++||+|||++|||+++++||+.+|++|+||+++||++.|.++++++. .||+|.++.....++.++...
T Consensus 53 ~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~~-~vrip~~~~~~~~~~~~~~~~ 131 (258)
T PRK08215 53 VIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREK 131 (258)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-ceEecHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999985 889999999999999999999
Q ss_pred HHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCc--chhhhcccCCCCChhHHHHHHHHHHHHHHH
Q 008652 413 YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQEITADTGVEIPDISVQKQLMRQHVRNL 490 (558)
Q Consensus 413 l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~--~l~e~i~d~~~~~pe~~le~~~~~e~L~~~ 490 (558)
+.+++|+.|+.+|||+.+|+++++|..++.....+.|||.++.++++. ++.+.+.++.. .++ .......|..+
T Consensus 132 l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~-~~~----~~~~~~~l~~~ 206 (258)
T PRK08215 132 LINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDEKN-KDE----NWLEEIALKEA 206 (258)
T ss_pred HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchhhhhhccCccc-cHH----HHHhHHHHHHH
Confidence 999999999999999999999999999988777888999988655432 24455554431 122 22334578899
Q ss_pred HhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008652 491 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 545 (558)
Q Consensus 491 L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 545 (558)
|+.||+++++||.++|+ +++|++|||+.||||.++|++++++|+++||+.+
T Consensus 207 l~~L~~~er~vi~~~~~----~~~t~~eIA~~lgis~~~V~~~~~~al~kLr~~l 257 (258)
T PRK08215 207 MKKLNDREKLILNLRFF----QGKTQMEVAEEIGISQAQVSRLEKAALKHMRKYI 257 (258)
T ss_pred HHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999997 8899999999999999999999999999999876
No 22
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=100.00 E-value=2.1e-38 Score=317.30 Aligned_cols=223 Identities=27% Similarity=0.504 Sum_probs=203.2
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHhhCCCC-CHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008652 314 SGNSSREKLINANLRLVVHVAKQYQGRGI-SLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 392 (558)
Q Consensus 314 ~G~~Are~LI~~nlrLV~sIArrY~~~g~-~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~ 392 (558)
++..++ .||+.|+|||.++|++|.+++. +++||+|-|+|||++|+++|||++|.+|+|||...|+++|.+++|++. .
T Consensus 21 g~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~LR~~~-~ 98 (247)
T COG1191 21 GDEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKND-S 98 (247)
T ss_pred cCHHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHHHHhCC-C
Confidence 345888 9999999999999999998877 999999999999999999999999999999999999999999999999 9
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcC--CCcccCCCCCCCCCcchhhhcccCC
Q 008652 393 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQPVWADQDTTFQEITADTG 470 (558)
Q Consensus 393 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~--~~~SLD~~i~~d~~~~l~e~i~d~~ 470 (558)
+++|+.+....+++..+...+.+++||+||.+|||+.+|++.+++..++.... ..+|+|..+..+++.. .++.
T Consensus 99 v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d~~-----~~~~ 173 (247)
T COG1191 99 VKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDD-----VDDQ 173 (247)
T ss_pred ccCcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccccc-----hhhc
Confidence 99999999999999999999999999999999999999999999999987654 6788887765544433 2233
Q ss_pred CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008652 471 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 547 (558)
Q Consensus 471 ~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 547 (558)
..+|+..++..+..+.|.+++..|++|||.||.+||. +++|++|||+.||||..+|+|++++|++|||+.+..
T Consensus 174 ~~~~~~~~~~~~~~~~l~~ai~~L~EREk~Vl~l~y~----eelt~kEI~~~LgISes~VSql~kkai~kLr~~l~~ 246 (247)
T COG1191 174 IENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRYK----EELTQKEIAEVLGISESRVSRLHKKAIKKLRKELNK 246 (247)
T ss_pred cccchhHHHHHHHHHHHHHHHHccCHHHHHHHHHHHH----hccCHHHHHHHhCccHHHHHHHHHHHHHHHHHHhcc
Confidence 4567778888888888999999999999999999998 999999999999999999999999999999998753
No 23
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=100.00 E-value=6.7e-37 Score=311.05 Aligned_cols=249 Identities=20% Similarity=0.357 Sum_probs=221.3
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHH
Q 008652 253 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH 332 (558)
Q Consensus 253 i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~~nlrLV~s 332 (558)
.+++|+||.++|.+|+..++. .++..|++.|+..|.++|+.
T Consensus 6 ~~~~~~~~~~~e~~l~~~~~~---------------------------------------~~d~~a~~~l~~~y~~lv~~ 46 (268)
T PRK06288 6 SGKIPKYAQQDETELWREYKK---------------------------------------TGDPKIREYLILKYSPLVKY 46 (268)
T ss_pred cCCCccccchHHHHHHHHHHH---------------------------------------cCCHHHHHHHHHHHHHHHHH
Confidence 478999999999999987653 13468999999999999999
Q ss_pred HHHHhh-C--CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHH
Q 008652 333 VAKQYQ-G--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEA 409 (558)
Q Consensus 333 IArrY~-~--~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~~~l~ki~ka 409 (558)
+|++|. + .+.+++||+|||++|||+++++||+.+|++|+||++|||++.|.+++++. +++|.++....++++++
T Consensus 47 ~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~---~~~p~~~~~~~~~i~~~ 123 (268)
T PRK06288 47 VAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSI---DWIPRSVRQKARQIERA 123 (268)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhc---CccCHHHHHHHHHHHHH
Confidence 999986 3 56789999999999999999999999999999999999999999999865 46899999999999999
Q ss_pred HHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCCcccCCCCCCCC---CcchhhhcccCCCCChhHHHHHHHHH
Q 008652 410 KRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQ---DTTFQEITADTGVEIPDISVQKQLMR 484 (558)
Q Consensus 410 ~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~--~~~~SLD~~i~~d~---~~~l~e~i~d~~~~~pe~~le~~~~~ 484 (558)
...+.+.+|+.|+.+|||+.+|++.+++..++... ...+|||.++..++ ...+.+.++++...+|+..++..+..
T Consensus 124 ~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~l~~~~~~~~~~~pe~~~~~~e~~ 203 (268)
T PRK06288 124 IAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLESPAALNPDEIAEREEIK 203 (268)
T ss_pred HHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccCCCcccchhhhhccCCCCCCHHHHHHHHHHH
Confidence 99999999999999999999999999999988644 45789988764222 23466777776667888888888888
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008652 485 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 547 (558)
Q Consensus 485 e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 547 (558)
..|..+|+.||+++|+||.++|+ +++|++|||+.||+|.++|++++.+|+++||.++..
T Consensus 204 ~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~~ 262 (268)
T PRK06288 204 RVIVEAIKTLPEREKKVLILYYY----EDLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLAE 262 (268)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999998 899999999999999999999999999999998864
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=100.00 E-value=3.8e-36 Score=302.93 Aligned_cols=244 Identities=23% Similarity=0.356 Sum_probs=215.2
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHH
Q 008652 257 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQ 336 (558)
Q Consensus 257 ~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~~nlrLV~sIArr 336 (558)
|.||+++|.+|+.+++. .++..|+++||..|.++|+.+|++
T Consensus 8 ~~l~~~~~~~li~~~~~---------------------------------------~gd~~a~~~l~~~y~~~v~~~a~~ 48 (255)
T TIGR02941 8 TNLTKEDVIQWIAEFQQ---------------------------------------NQNGEAQEKLVDHYQNLVYSIAYK 48 (255)
T ss_pred CCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHHHHhHHHHHHHHHH
Confidence 66899999888877653 134689999999999999999999
Q ss_pred hhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHh
Q 008652 337 YQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQE 416 (558)
Q Consensus 337 Y~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~ 416 (558)
|.+++.+++||+|||++|||+++++||++.|.+|.||+++||++.|.++++++.+.+++|.++....++++++...+.+.
T Consensus 49 ~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~iri~~~~~~~~~~~~~~~~~l~~~ 128 (255)
T TIGR02941 49 YSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDH 128 (255)
T ss_pred HhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHHHHHHHHHHhcC
Q 008652 417 GNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLL 494 (558)
Q Consensus 417 ~gr~Pt~eEIA~~lgis~e~v~~ll~~~--~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L 494 (558)
+|+.|+.+|+|+.+|++.+++..++... ....|||.+++.+++......+ + ....|++.+...+....+..+|+.|
T Consensus 129 ~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~-~-~~~~~~~~~~~~e~~~~l~~~l~~L 206 (255)
T TIGR02941 129 LQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSDGSTVARL-D-SVGEVEDGYDQTERRMVLEKILPIL 206 (255)
T ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCCCcccccc-c-ccCCcchHHHHHHHHHHHHHHHHcC
Confidence 9999999999999999999998887643 4578999988765443222221 1 1224566667777778899999999
Q ss_pred CHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008652 495 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 545 (558)
Q Consensus 495 ~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 545 (558)
|+++|.||.++|+ +++|++|||+.||||.++|++++.+|+++||+.+
T Consensus 207 ~~~~r~ii~l~~~----~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~ 253 (255)
T TIGR02941 207 SEREKSIIHCTFE----ENLSQKETGERLGISQMHVSRLQRQAISKLKEAA 253 (255)
T ss_pred CHHHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 9999999999998 8999999999999999999999999999999865
No 25
>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=100.00 E-value=1.8e-36 Score=300.64 Aligned_cols=223 Identities=29% Similarity=0.469 Sum_probs=199.2
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008652 313 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 392 (558)
Q Consensus 313 ~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~ 392 (558)
.++..|++.||..|.++|+++|++|.+++.+++||+|||++|||+++++|||.+|.+|.||++|||++.|.++++++. .
T Consensus 7 ~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~~~-~ 85 (231)
T TIGR02885 7 NGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDG-I 85 (231)
T ss_pred cCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-C
Confidence 345699999999999999999999999999999999999999999999999999999999999999999999999986 8
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCc--chhhhcccCC
Q 008652 393 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQEITADTG 470 (558)
Q Consensus 393 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~--~l~e~i~d~~ 470 (558)
|++|.++....+++.++...+..++|+.|+.+|||+.+|++++++..++.....+.|||.+++++++. ++.+.+.++.
T Consensus 86 i~~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~~ 165 (231)
T TIGR02885 86 IKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLDQIADKG 165 (231)
T ss_pred eECCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCCCcchhhhhcCCCC
Confidence 99999999999999999999999999999999999999999999999988878889999988655432 3456665543
Q ss_pred CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008652 471 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 545 (558)
Q Consensus 471 ~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 545 (558)
. ++.. ...+..|..+++.||+++++||.++|+ +++|++|||+.||||+++|++++++|++|||..+
T Consensus 166 ~--~~~~---~~~~~~l~~~l~~L~~~e~~i~~~~~~----~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~l 231 (231)
T TIGR02885 166 S--EDSD---WLEKIALKEAISKLDERERQIIMLRYF----KDKTQTEVANMLGISQVQVSRLEKKVLKKMKEKL 231 (231)
T ss_pred c--cHHh---HHHHHHHHHHHHcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHhC
Confidence 2 2222 223557889999999999999999998 8999999999999999999999999999999764
No 26
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=100.00 E-value=7.2e-36 Score=295.43 Aligned_cols=221 Identities=28% Similarity=0.452 Sum_probs=198.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccccc
Q 008652 316 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 395 (558)
Q Consensus 316 ~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRl 395 (558)
..|++.||..|.++|+++|++|.+++.+.+||+|||++|||+|+++||+.+|.+|+||++|||++.|.++++++.+.+++
T Consensus 2 ~~a~~~lv~~y~~~v~~~a~~~~~~~~~~eDl~Qe~~i~l~~a~~~f~~~~~~~F~ty~~~~i~~~~~~~~r~~~~~~ri 81 (227)
T TIGR02980 2 KEAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVRV 81 (227)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCcHHHHHHHHHHHHHHHHHHcCCceec
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCC--CcccCCCCCCCCC--cchhhhcccCCC
Q 008652 396 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRM--PLSMQQPVWADQD--TTFQEITADTGV 471 (558)
Q Consensus 396 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~--~~SLD~~i~~d~~--~~l~e~i~d~~~ 471 (558)
|.++...+++++++...+.+.+|+.|+.+|+|+.+|++.+++..++..... ..|||.++.++++ ..+.+.+.
T Consensus 82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~~---- 157 (227)
T TIGR02980 82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTLG---- 157 (227)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCcccccccC----
Confidence 999999999999999999999999999999999999999999998876654 8999998863322 12233322
Q ss_pred CChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008652 472 EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 545 (558)
Q Consensus 472 ~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 545 (558)
+++..++..+....|..+|..||+++++||.++|+ +++|++|||+.||+|.++|++++++|+++||+.+
T Consensus 158 -~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~y~----~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~l 226 (227)
T TIGR02980 158 -DEDDALETVEDRLALKPLLAALPERERRILLLRFF----EDKTQSEIAERLGISQMHVSRLLRRALKKLREQL 226 (227)
T ss_pred -CcchHHHhHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 34455556667778999999999999999999998 8999999999999999999999999999999865
No 27
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=4.7e-35 Score=294.75 Aligned_cols=225 Identities=24% Similarity=0.369 Sum_probs=202.1
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccc
Q 008652 315 GNSSREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR 391 (558)
Q Consensus 315 G~~Are~LI~~nlrLV~sIArrY~~---~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr 391 (558)
+..|++.||..|.++|+++|++|.+ ++.+.+||+|||++|||+++++||+.+|.+|+||+++||++.|.++++++.
T Consensus 20 d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~d~lR~~~- 98 (251)
T PRK07670 20 DPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKED- 98 (251)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC-
Confidence 4589999999999999999999965 678999999999999999999999999999999999999999999999876
Q ss_pred ccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHH--hcCCCcccCCCCCCCCCc-chhhhccc
Q 008652 392 TIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF--ITRMPLSMQQPVWADQDT-TFQEITAD 468 (558)
Q Consensus 392 ~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~--~~~~~~SLD~~i~~d~~~-~l~e~i~d 468 (558)
++|.++...+++++++...+.+.+|+.|+.+|||+.+|++.++|..++. ......|||.++.++++. .+...+.+
T Consensus 99 --~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~ 176 (251)
T PRK07670 99 --WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDDGENVSVTIRD 176 (251)
T ss_pred --CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccCCCCcchhhhhhcC
Confidence 5899999999999999999999999999999999999999999999976 346789999988655433 23344455
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008652 469 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 546 (558)
Q Consensus 469 ~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 546 (558)
.....+++.+...+....|..+|..||+++|+||.++|+ +++|++|||+.||+|.++|++++.||+++||.++.
T Consensus 177 ~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~ 250 (251)
T PRK07670 177 DKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFYK----EELTLTEIGQVLNLSTSRISQIHSKALFKLKKLLE 250 (251)
T ss_pred cCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 555677777887788889999999999999999999998 99999999999999999999999999999999875
No 28
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=100.00 E-value=2.5e-34 Score=290.11 Aligned_cols=243 Identities=24% Similarity=0.355 Sum_probs=214.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHH
Q 008652 257 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQ 336 (558)
Q Consensus 257 ~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~~nlrLV~sIArr 336 (558)
|.|+++||.+|..+++. .++..|++.||..|.++|+++|++
T Consensus 8 ~~l~~~e~~~li~~~~~---------------------------------------~gd~~a~~~l~~~~~~~v~~~a~~ 48 (257)
T PRK08583 8 TKLTKEEVNKWIAEYQE---------------------------------------NQDEEAQEKLVKHYKNLVESLAYK 48 (257)
T ss_pred CcCChHHHHHHHHHHHH---------------------------------------cCCHHHHHHHHHHHHHHHHHHHHH
Confidence 77999999888876653 134689999999999999999999
Q ss_pred hhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHh
Q 008652 337 YQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQE 416 (558)
Q Consensus 337 Y~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~ 416 (558)
|.+++.+++||+||||+|||+++++||+.+|.+|.||+++||++.|.++++++.+.+++|.++....++++++...+...
T Consensus 49 ~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~~~i~r~~~~~~~~~~~~~~~~~~~ 128 (257)
T PRK08583 49 YSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTE 128 (257)
T ss_pred HhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHHHHHHhcCCCcCCCHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999998999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCCcccCCCCCCCCCc---chhhhcccCCCCChhHHHHHHHHHHHHHHHH
Q 008652 417 GNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQDT---TFQEITADTGVEIPDISVQKQLMRQHVRNLL 491 (558)
Q Consensus 417 ~gr~Pt~eEIA~~lgis~e~v~~ll~~~--~~~~SLD~~i~~d~~~---~l~e~i~d~~~~~pe~~le~~~~~e~L~~~L 491 (558)
.++.|+.+++|+.+|++.+++..+.... ....|+|.+++.+++. .+.+.. ..|+..+...+....|..+|
T Consensus 129 ~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~-----~~~e~~~~~~~~~~~l~~~l 203 (257)
T PRK08583 129 LQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDGSTVTLLDIV-----GQQEDGYELTEQRMILEKIL 203 (257)
T ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCCCCccchHhhhc-----CCcchhHHHHHHHHHHHHHH
Confidence 9999999999999999999998876643 3578899887654332 122222 24555666667777899999
Q ss_pred hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008652 492 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 547 (558)
Q Consensus 492 ~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 547 (558)
..||+++|+||.++|+ +++|++|||+.||||.++|++++++|+++||..+..
T Consensus 204 ~~L~~~~r~vl~l~~~----~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l~~ 255 (257)
T PRK08583 204 PVLSDREKSIIQCTFI----ENLSQKETGERLGISQMHVSRLQRQAIKKLREAAFL 255 (257)
T ss_pred HhCCHHHHHHHHHHHh----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 9999999999999998 899999999999999999999999999999998764
No 29
>PRK05572 sporulation sigma factor SigF; Validated
Probab=100.00 E-value=2.6e-34 Score=289.51 Aligned_cols=244 Identities=28% Similarity=0.430 Sum_probs=213.2
Q ss_pred hcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHH
Q 008652 251 WGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLV 330 (558)
Q Consensus 251 ~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~~nlrLV 330 (558)
+.-...|.||.+++.+|..+++. ++..|++.||..|.++|
T Consensus 6 ~~~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~y~~~v 45 (252)
T PRK05572 6 KNKKKKPQLKDEENKELIKKSQD----------------------------------------GDQEARDTLVEKNLRLV 45 (252)
T ss_pred ccCcCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHH
Confidence 34567899999999888766542 34689999999999999
Q ss_pred HHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHH
Q 008652 331 VHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAK 410 (558)
Q Consensus 331 ~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~~~l~ki~ka~ 410 (558)
+++|++|.+++.+++||+|||++++|+++++|++.+|.+|.||+++||++.|.+++++.. .+++|+++....++++++.
T Consensus 46 ~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~~~-~~r~~~~~~~~~~~~~~~~ 124 (252)
T PRK05572 46 WSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDK 124 (252)
T ss_pred HHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CCCCCHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999998889999999999999999999874 7899999999999999999
Q ss_pred HHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCc--chhhhcccCCCCChhHHHHHHHHHHHHH
Q 008652 411 RLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQEITADTGVEIPDISVQKQLMRQHVR 488 (558)
Q Consensus 411 ~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~--~l~e~i~d~~~~~pe~~le~~~~~e~L~ 488 (558)
..+..++|+.|+.+|+|+.+|++++++..+......+.||+.++.+++.. ++.+.+.++.. + .......|.
T Consensus 125 ~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~~~---~----~~~~~~~l~ 197 (252)
T PRK05572 125 DELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITLLDQIADQSE---E----DWFDKIALK 197 (252)
T ss_pred HHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCCCCcchhhhhcCCCch---h----hHHHHHHHH
Confidence 99999999999999999999999999999888878889999887654332 23344433221 1 123356789
Q ss_pred HHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008652 489 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 546 (558)
Q Consensus 489 ~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 546 (558)
.+++.||+++++||.++|+ +++|++|||+.+|+|.++|++++++|+++||+.+.
T Consensus 198 ~~l~~L~~~~~~v~~l~~~----~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l~ 251 (252)
T PRK05572 198 EAIRELDERERLIVYLRYF----KDKTQSEVAKRLGISQVQVSRLEKKILKQMKEKLD 251 (252)
T ss_pred HHHHcCCHHHHHHHHHHHh----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999997 89999999999999999999999999999998774
No 30
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=100.00 E-value=1.9e-34 Score=285.18 Aligned_cols=217 Identities=23% Similarity=0.419 Sum_probs=195.9
Q ss_pred HHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchh
Q 008652 322 LINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 398 (558)
Q Consensus 322 LI~~nlrLV~sIArrY~~---~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~ 398 (558)
|+..|.++|+++|++|.+ ++.+++||+|||++|||+++++|||++|++|+||+++||++.+.+++++.. ++|.+
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 789999999999999999999999999999999999999999999999865 58999
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCCcccCCCCCCC-CCcchhhhcccCCCCChh
Q 008652 399 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWAD-QDTTFQEITADTGVEIPD 475 (558)
Q Consensus 399 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~--~~~~~SLD~~i~~d-~~~~l~e~i~d~~~~~pe 475 (558)
....++++.++...+.+.+|+.|+.+|+|+.+|+++++|..++.. .....|+|....++ +...+.+.++++...+|+
T Consensus 78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (224)
T TIGR02479 78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDKSEDPE 157 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhccccccCCHH
Confidence 999999999999999999999999999999999999999999854 34567888866543 334566666655566788
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008652 476 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 545 (558)
Q Consensus 476 ~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 545 (558)
+.+...+....|..+|+.||+++|+||.++|+ +++|++|||+.||+|.++|++++++|+++||+++
T Consensus 158 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~y~----~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 223 (224)
T TIGR02479 158 EELEREELREALAEAIESLSEREQLVLSLYYY----EELNLKEIGEVLGLTESRVSQIHSQALKKLRAKL 223 (224)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHc
Confidence 88888888899999999999999999999998 8999999999999999999999999999999875
No 31
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=100.00 E-value=5.3e-34 Score=284.44 Aligned_cols=209 Identities=21% Similarity=0.327 Sum_probs=179.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccccc
Q 008652 319 REKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 395 (558)
Q Consensus 319 re~LI~~nlrLV~sIArrY~~---~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRl 395 (558)
...|+..|+++|.++|++|.+ .+.+.+||+|||++|||+|+++|||.+| +|+||++||||++|.+++++..+ +
T Consensus 17 ~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~~---~ 92 (231)
T PRK12427 17 EGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELDW---R 92 (231)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcCC---C
Confidence 346778899999999999875 4679999999999999999999998666 89999999999999999998654 6
Q ss_pred chhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCCcccCCCCCCCCCcchhhhcccCCCCC
Q 008652 396 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWADQDTTFQEITADTGVEI 473 (558)
Q Consensus 396 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~--~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~ 473 (558)
|+++....++++++...+.+++|+.|+.+|||+.+|++.++|..++.. .....|||.+++++++.. .+.+ ..
T Consensus 93 ~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~---~~~~---~~ 166 (231)
T PRK12427 93 PRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAHND---ILQS---RD 166 (231)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCccc---ccCC---CC
Confidence 888889999999999999999999999999999999999999998764 456899999886654322 2221 12
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008652 474 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 544 (558)
Q Consensus 474 pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 544 (558)
+++. ......|..++..||+++|.||.++|+ +++|++|||+.||||.++|+|++++|++|||..
T Consensus 167 ~~~~---~~~~~~l~~~l~~L~~~er~vi~l~~~----~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr~~ 230 (231)
T PRK12427 167 LEEN---IIIEDNLKQALSQLDEREQLILHLYYQ----HEMSLKEIALVLDLTEARICQLNKKIAQKIKSF 230 (231)
T ss_pred HHHH---HHHHHHHHHHHHcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 3322 224557899999999999999999998 899999999999999999999999999999964
No 32
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=100.00 E-value=4.6e-33 Score=277.51 Aligned_cols=225 Identities=23% Similarity=0.410 Sum_probs=198.4
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHhh---CCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcc
Q 008652 314 SGNSSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS 390 (558)
Q Consensus 314 ~G~~Are~LI~~nlrLV~sIArrY~---~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~s 390 (558)
.|.-+++.|+..|.++|+++|++|. +++.+++||+|||++|||+++++|||++|.+|+||+++||++.|.++++++.
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 5678999999999999999999997 6789999999999999999999999999999999999999999999999986
Q ss_pred cccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCCcccCCCCCCCCCcchhhhccc
Q 008652 391 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQDTTFQEITAD 468 (558)
Q Consensus 391 r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~--~~~~SLD~~i~~d~~~~l~e~i~d 468 (558)
+ +|.++.....++.++...+.+.+|++|+.+|||+.+|++.++|..++... ....|++..++++++. +.. ..+
T Consensus 85 ~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~-~~~-~~~ 159 (236)
T PRK06986 85 W---VPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDS-ILV-TED 159 (236)
T ss_pred C---CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCcc-ccc-ccC
Confidence 4 68888888888888999999999999999999999999999999988743 4567888877554442 222 223
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008652 469 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 547 (558)
Q Consensus 469 ~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 547 (558)
+....|+..+...+....|..+|+.||+++|.||.++|. +++|++|||+.||||.++|++++.+|+++||+.+..
T Consensus 160 ~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~~ 234 (236)
T PRK06986 160 HQDEDPLQQLEDEELREALVEAIESLPEREQLVLSLYYQ----EELNLKEIGAVLGVSESRVSQIHSQAIKRLRARLGE 234 (236)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHhc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 334567778888888889999999999999999999998 899999999999999999999999999999998754
No 33
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=99.96 E-value=7e-28 Score=239.98 Aligned_cols=210 Identities=25% Similarity=0.451 Sum_probs=171.2
Q ss_pred HHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHHHHhhcHHHHHHHHH
Q 008652 245 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 324 (558)
Q Consensus 245 ~l~~Yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~ 324 (558)
.+..|+.+++..|+||+++|..|+..++. ++..|++.|+.
T Consensus 17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~----------------------------------------gd~~a~~~l~~ 56 (233)
T PRK05803 17 FLVSYVKNNSFPQPLSEEEERKYLELMKE----------------------------------------GDEEARNILIE 56 (233)
T ss_pred HHHHHHHHhcccCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHH
Confidence 56789999999999999999888776543 34689999999
Q ss_pred HHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHH
Q 008652 325 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS 404 (558)
Q Consensus 325 ~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~~~l~ 404 (558)
.|.++|+++|.+|.+++.+.+||+|||++++|+++++||+++|.+|.+|+++|+++.+.+++++..+..
T Consensus 57 ~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~~~----------- 125 (233)
T PRK05803 57 RNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTK----------- 125 (233)
T ss_pred HhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhccc-----------
Confidence 999999999999999999999999999999999999999998999999999999999999998654210
Q ss_pred HHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCC---CCcchhhhcccCCCCChhHHHHHH
Q 008652 405 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWAD---QDTTFQEITADTGVEIPDISVQKQ 481 (558)
Q Consensus 405 ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d---~~~~l~e~i~d~~~~~pe~~le~~ 481 (558)
...+++.+.+.+ ....+.+...+. .+++++.+..+
T Consensus 126 -----------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 163 (233)
T PRK05803 126 -----------------------------------------KEVSLQDPIGVDKEGNEISLIDILGSE-EDDVIEQVELK 163 (233)
T ss_pred -----------------------------------------cCCCccccccCCCCcCcccHHHHccCC-CCCHHHHHHHH
Confidence 011111111111 112233333332 23467777777
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008652 482 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 547 (558)
Q Consensus 482 ~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 547 (558)
...+.|..+|..||+++|+||.++|++.+.+++|++|||+.||+|.++|++++.+|+++||+.+..
T Consensus 164 ~~~~~l~~~l~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~~ 229 (233)
T PRK05803 164 MEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKELYR 229 (233)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 777889999999999999999999977666999999999999999999999999999999998764
No 34
>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=99.93 E-value=2.5e-24 Score=213.84 Aligned_cols=179 Identities=30% Similarity=0.547 Sum_probs=141.7
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008652 314 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 393 (558)
Q Consensus 314 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~I 393 (558)
++..|++.|+..|.++|+++|.+|.++..+++||+||+++++|+++++|+++++.+|.||+++|+++.+.+++++..+..
T Consensus 45 gd~~af~~l~~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~Rk~~r~~ 124 (227)
T TIGR02846 45 GDEEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHLRALKKTK 124 (227)
T ss_pred CCHHHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHHHHHhccc
Confidence 44689999999999999999999999999999999999999999999999998889999999999999999998754210
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCC---CCcchhhhcccCC
Q 008652 394 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWAD---QDTTFQEITADTG 470 (558)
Q Consensus 394 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d---~~~~l~e~i~d~~ 470 (558)
+ ..+++.....+ ....+.+...+ .
T Consensus 125 ~----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~-~ 151 (227)
T TIGR02846 125 G----------------------------------------------------EVSLQDPIGVDKEGNEISLIDILGS-D 151 (227)
T ss_pred c----------------------------------------------------ceeccccccCCcccCcccHHHHhcC-C
Confidence 0 01111111000 01112222222 1
Q ss_pred CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008652 471 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 545 (558)
Q Consensus 471 ~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 545 (558)
...+++.+...+..+.|..+|+.||+++|+||.++|.++..+++|++|||+.||+|.++|++++++|+++||+.+
T Consensus 152 ~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~~ 226 (227)
T TIGR02846 152 GDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYKEL 226 (227)
T ss_pred CCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 234556666666667899999999999999999999765558999999999999999999999999999999875
No 35
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=99.93 E-value=3.8e-24 Score=212.90 Aligned_cols=180 Identities=28% Similarity=0.539 Sum_probs=139.8
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008652 314 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 393 (558)
Q Consensus 314 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~I 393 (558)
++..|++.|+..|.++|+.+|++|.+++.+++|++||+|+++|+++++|++..+++|.||+++++++.+.++++++.+..
T Consensus 49 gd~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~d~lRk~~~~~ 128 (234)
T PRK08301 49 GDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNNKVK 128 (234)
T ss_pred cCHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 34589999999999999999999999999999999999999999999999988889999999999999999998754210
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCC--CC-CcchhhhcccCC
Q 008652 394 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWA--DQ-DTTFQEITADTG 470 (558)
Q Consensus 394 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~--d~-~~~l~e~i~d~~ 470 (558)
...+++.+... +. ...+.+...+.
T Consensus 129 ----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~- 155 (234)
T PRK08301 129 ----------------------------------------------------AEVSFDEPLNIDWDGNELLLSDVLGTD- 155 (234)
T ss_pred ----------------------------------------------------cccccccccccccCCCcccHHHhccCc-
Confidence 00111111100 00 00111222211
Q ss_pred CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008652 471 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 546 (558)
Q Consensus 471 ~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 546 (558)
...++..+........|..+|+.||+++|+||.++|+|...+++|++|||+.||||.++|++++.||+++||+.+.
T Consensus 156 ~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l~ 231 (234)
T PRK08301 156 NDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEIN 231 (234)
T ss_pred ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 1223334444555667999999999999999999996544489999999999999999999999999999999875
No 36
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=99.92 E-value=2.7e-23 Score=207.35 Aligned_cols=181 Identities=30% Similarity=0.540 Sum_probs=141.1
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008652 314 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 393 (558)
Q Consensus 314 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~I 393 (558)
++..|++.|+..|.+.|+++|++|.+++.+.+|++||+++++|+++++|++..+++|.||++.++++.+.++++++.+..
T Consensus 49 ~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~d~~Rk~~r~~ 128 (234)
T TIGR02835 49 GDESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILMYLRRNNKTR 128 (234)
T ss_pred CCHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhcccc
Confidence 45689999999999999999999999999999999999999999999999988889999999999999999998765310
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCC---CCCCcchhhhcccCC
Q 008652 394 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVW---ADQDTTFQEITADTG 470 (558)
Q Consensus 394 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~---~d~~~~l~e~i~d~~ 470 (558)
...+++.++. .+......+.. ++.
T Consensus 129 ----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~-~~~ 155 (234)
T TIGR02835 129 ----------------------------------------------------SEVSFDEPLNVDWDGNELLLSDVL-GTD 155 (234)
T ss_pred ----------------------------------------------------CcccccccccCCCCCCcchHHHhc-CCC
Confidence 0011111110 00000111111 111
Q ss_pred CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008652 471 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 547 (558)
Q Consensus 471 ~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 547 (558)
.+.++..+........|..+|+.||+++|+||.++|++.+++++|++|||+.||||.++|++++.+|+++||+.+..
T Consensus 156 ~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l~~ 232 (234)
T TIGR02835 156 SDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKEINR 232 (234)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhhc
Confidence 12233444555556789999999999999999999976555899999999999999999999999999999998753
No 37
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=99.91 E-value=1.4e-22 Score=196.89 Aligned_cols=195 Identities=22% Similarity=0.329 Sum_probs=149.6
Q ss_pred CCHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008652 303 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 381 (558)
Q Consensus 303 ~~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a 381 (558)
++++.|+..++.| ..|++.|+..|.++|+.+|++|.++..+.+|++||++++||+++.+||+.+|.+|.||++.++++.
T Consensus 9 ~~~~~l~~~~~~~d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n~ 88 (208)
T PRK08295 9 LEDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQ 88 (208)
T ss_pred CChHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHH
Confidence 4556666666555 599999999999999999999999999999999999999999999999998789999999999999
Q ss_pred HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCC-CCCc
Q 008652 382 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWA-DQDT 460 (558)
Q Consensus 382 I~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~-d~~~ 460 (558)
+.+++++..+..+.+. ....|++.++.+ +.+.
T Consensus 89 ~~d~~r~~~r~~~~~~-----------------------------------------------~~~~s~~~~~~~~~~~~ 121 (208)
T PRK08295 89 IITAIKTANRQKHIPL-----------------------------------------------NSYVSLDKPIYDEESDR 121 (208)
T ss_pred HHHHHHHhhhhccccc-----------------------------------------------cceeecCCcccCCccch
Confidence 9998876432111100 011233332221 1222
Q ss_pred chhhhcccCCCCChhHHHHHHHHHHHH-HHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008652 461 TFQEITADTGVEIPDISVQKQLMRQHV-RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 539 (558)
Q Consensus 461 ~l~e~i~d~~~~~pe~~le~~~~~e~L-~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 539 (558)
.+.+.+.++....|+..+...+....+ ..++..||+++|+||.+ |. +++|.+|||+.||+|.++|+..+.||++
T Consensus 122 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l-~~----e~~s~~EIA~~lgis~~tV~~~l~rar~ 196 (208)
T PRK08295 122 TLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLEL-YL----DGKSYQEIAEELNRHVKSIDNALQRVKR 196 (208)
T ss_pred hHHHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHH-HH----ccCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 344444444444676666555555555 45679999999999999 76 8999999999999999999999999999
Q ss_pred HHHHHhhcCc
Q 008652 540 RLKQSLGGKA 549 (558)
Q Consensus 540 KLR~~l~~~~ 549 (558)
+||+++..+.
T Consensus 197 ~Lr~~l~~~~ 206 (208)
T PRK08295 197 KLEKYLENRE 206 (208)
T ss_pred HHHHHHHhhc
Confidence 9999887654
No 38
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=99.89 E-value=5.7e-22 Score=189.94 Aligned_cols=176 Identities=16% Similarity=0.250 Sum_probs=143.5
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008652 303 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 381 (558)
Q Consensus 303 ~~~~~L~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a 381 (558)
+++..|+..+..|+ .|++.|+..|.++|+.+|++|.+++.+.+|++||+|+++|+++.+|+++ +.+|.+|++..+++.
T Consensus 5 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n~ 83 (186)
T PRK05602 5 DPDEELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLNL 83 (186)
T ss_pred ccHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHHH
Confidence 45666777666555 9999999999999999999999999999999999999999999999986 457999999999999
Q ss_pred HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 008652 382 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 461 (558)
Q Consensus 382 I~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~ 461 (558)
+.++++++.+. +.+. . .
T Consensus 84 ~~d~~R~~~~~--------------------------------------------------------~~~~-~---~--- 100 (186)
T PRK05602 84 CYDRLRRRREV--------------------------------------------------------PVED-A---P--- 100 (186)
T ss_pred HHHHHHhcCCC--------------------------------------------------------Cccc-c---c---
Confidence 99988764310 0000 0 0
Q ss_pred hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008652 462 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 541 (558)
Q Consensus 462 l~e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 541 (558)
+ ..+. ...++..+...+....+..+|..||+++|+||.++|. +++|++|||+.||+|..+|+++++||+++|
T Consensus 101 --~-~~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~L 172 (186)
T PRK05602 101 --D-VPDP-APGPDAGLEARQRARRVEQALAALPERQREAIVLQYY----QGLSNIEAAAVMDISVDALESLLARGRRAL 172 (186)
T ss_pred --c-cCCC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHh----cCCCHHHHHHHhCcCHHHHHHHHHHHHHHH
Confidence 0 0001 1134555555666678999999999999999999998 899999999999999999999999999999
Q ss_pred HHHhhcCch
Q 008652 542 KQSLGGKAS 550 (558)
Q Consensus 542 R~~l~~~~L 550 (558)
|+.+...+.
T Consensus 173 r~~l~~~~~ 181 (186)
T PRK05602 173 RAQLADLPG 181 (186)
T ss_pred HHHHHhccc
Confidence 999876653
No 39
>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=99.89 E-value=1e-21 Score=189.16 Aligned_cols=191 Identities=23% Similarity=0.325 Sum_probs=145.1
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008652 303 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 381 (558)
Q Consensus 303 ~~~~~L~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a 381 (558)
|++..|+..+..|+ .|++.|+..|.+.|+.+|+++.++..+++||+||+++++|+++.+|++..+..|.||++.+|++.
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 45667777777665 99999999999999999999999999999999999999999999999988789999999999999
Q ss_pred HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCC-CCCc
Q 008652 382 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWA-DQDT 460 (558)
Q Consensus 382 I~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~-d~~~ 460 (558)
+.++++...+..+.+ .....|++.+... +++.
T Consensus 84 ~~~~~r~~~~~~~~~-----------------------------------------------~~~~~~~~~~~~~~~~~~ 116 (198)
T TIGR02859 84 IITAIKTATRQKHIP-----------------------------------------------LNSYVSLNKPIYDEESDR 116 (198)
T ss_pred HHHHHHHHHHhcccc-----------------------------------------------hhhhcCcccccccccccc
Confidence 988886532110000 0011233332211 1122
Q ss_pred chhhhcccCCCCChhHHHHHHHHHHHHHHHHhcC-CHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008652 461 TFQEITADTGVEIPDISVQKQLMRQHVRNLLTLL-NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 539 (558)
Q Consensus 461 ~l~e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L-~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 539 (558)
++.+.+.+....+|+..+...+..+.|.++|+.| ++.++.|+. +|. +++|++|||+.||+|.++|+..++||++
T Consensus 117 ~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~-~~~----~~~s~~eIA~~l~~s~~tV~~~l~r~r~ 191 (198)
T TIGR02859 117 TLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQ-SYL----DGKSYQEIACDLNRHVKSIDNALQRVKR 191 (198)
T ss_pred hHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHH-HHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 2333333222346777777777778899999985 566666665 565 8999999999999999999999999999
Q ss_pred HHHHHh
Q 008652 540 RLKQSL 545 (558)
Q Consensus 540 KLR~~l 545 (558)
+||+.+
T Consensus 192 ~L~~~l 197 (198)
T TIGR02859 192 KLEKYL 197 (198)
T ss_pred HHHHhc
Confidence 999876
No 40
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=99.88 E-value=1.7e-21 Score=188.46 Aligned_cols=176 Identities=16% Similarity=0.189 Sum_probs=139.6
Q ss_pred CHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHH
Q 008652 304 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 382 (558)
Q Consensus 304 ~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI 382 (558)
+...|+..+..| ..|++.|+..|.++|+++|.+|.++..+.+|++||+++++|+++++||+.+| .|.+|++..+++.+
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 345566666555 4999999999999999999999999999999999999999999999998765 69999999999999
Q ss_pred HHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 008652 383 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 462 (558)
Q Consensus 383 ~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l 462 (558)
.++++++.+..+. +......
T Consensus 95 ~d~~r~~~~~~~~-------------------------------------------------------~~~~~~~----- 114 (194)
T PRK09646 95 VDRVRSEQAASQR-------------------------------------------------------EVRYGAR----- 114 (194)
T ss_pred HHHHHhhcccccc-------------------------------------------------------ccccccc-----
Confidence 9999875421100 0000000
Q ss_pred hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 463 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 463 ~e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
+. +.....+++.+...+..+.|..+|..||+++|+||.++|. +++|++|||+.||+|..+|++++.||+++||
T Consensus 115 -~~--~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr 187 (194)
T PRK09646 115 -NV--DPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYY----GGLTYREVAERLAVPLGTVKTRMRDGLIRLR 187 (194)
T ss_pred -cc--cccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCChHhHHHHHHHHHHHHH
Confidence 00 0011123334444555678999999999999999999998 8999999999999999999999999999999
Q ss_pred HHhhc
Q 008652 543 QSLGG 547 (558)
Q Consensus 543 ~~l~~ 547 (558)
+.+..
T Consensus 188 ~~l~~ 192 (194)
T PRK09646 188 DCLGV 192 (194)
T ss_pred HHhcc
Confidence 98854
No 41
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=99.88 E-value=1.4e-21 Score=188.44 Aligned_cols=181 Identities=18% Similarity=0.237 Sum_probs=145.7
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008652 303 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 381 (558)
Q Consensus 303 ~~~~~L~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a 381 (558)
+++..|+..+..|+ .|++.|+..|.+.|+++|+++.++..+.+|++||+++++|+++++|++. ..|.+|++.++++.
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 34566777666564 9999999999999999999999999999999999999999999999975 36999999999999
Q ss_pred HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 008652 382 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 461 (558)
Q Consensus 382 I~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~ 461 (558)
+.+++++..+....+. ..+ . .
T Consensus 89 ~~~~~R~~~~~~~~~~---------------------------------------------------~~~------~--~ 109 (194)
T PRK12513 89 LIDHWRRHGARQAPSL---------------------------------------------------DAD------E--Q 109 (194)
T ss_pred HHHHHHHhcccccccc---------------------------------------------------ccc------h--h
Confidence 9999987653211100 000 0 0
Q ss_pred hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008652 462 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 541 (558)
Q Consensus 462 l~e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 541 (558)
+ ....+ ....|+..++..+....|..+|+.||+++|.||.++|. +++|++|||+.||+|.++|++++.||+++|
T Consensus 110 ~-~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~L 183 (194)
T PRK12513 110 L-HALAD-DGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREH----GDLELEEIAELTGVPEETVKSRLRYALQKL 183 (194)
T ss_pred h-hhcCC-CCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeehc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 0 00011 12246666666677788999999999999999999998 899999999999999999999999999999
Q ss_pred HHHhhcCch
Q 008652 542 KQSLGGKAS 550 (558)
Q Consensus 542 R~~l~~~~L 550 (558)
|+.+...++
T Consensus 184 r~~l~~~~~ 192 (194)
T PRK12513 184 RELLAEEVA 192 (194)
T ss_pred HHHHHHhhc
Confidence 999876654
No 42
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=99.88 E-value=3.1e-21 Score=184.00 Aligned_cols=180 Identities=15% Similarity=0.234 Sum_probs=141.4
Q ss_pred HHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHH
Q 008652 305 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR 383 (558)
Q Consensus 305 ~~~L~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~ 383 (558)
.+.|+..++.|+ .|++.|+..|.++|+++|+++.++..+++|++||++++||+++.+|++.. +|.+|++..+++.+.
T Consensus 5 ~~~li~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~~~ 82 (187)
T PRK09641 5 IKRLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNLTI 82 (187)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHHHH
Confidence 345555555555 99999999999999999999999999999999999999999999999853 699999999999999
Q ss_pred HHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchh
Q 008652 384 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ 463 (558)
Q Consensus 384 ~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~ 463 (558)
++++++.+.. +++.....++.....
T Consensus 83 d~~R~~~~~~-------------------------------------------------------~~~~~~~~~~~~~~~ 107 (187)
T PRK09641 83 DRLRKRKPDY-------------------------------------------------------YLDAEVAGTEGLTMY 107 (187)
T ss_pred HHHHhcCccc-------------------------------------------------------cccccccCCcchhhh
Confidence 9988654210 000000011111111
Q ss_pred hhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 464 EITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 464 e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
+.+.+. ...|++.+...+....+..+|+.||+++++||.++|. ++++++|||+.||||.++|++.+.||+++||+
T Consensus 108 ~~~~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~----~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T PRK09641 108 SQLAAD-DALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYI----EDLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred cccccC-cCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHh----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 111111 2246666667777778999999999999999999998 89999999999999999999999999999999
Q ss_pred Hhh
Q 008652 544 SLG 546 (558)
Q Consensus 544 ~l~ 546 (558)
.+.
T Consensus 183 ~l~ 185 (187)
T PRK09641 183 QLR 185 (187)
T ss_pred HHh
Confidence 875
No 43
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=99.88 E-value=3e-21 Score=184.05 Aligned_cols=180 Identities=16% Similarity=0.241 Sum_probs=139.4
Q ss_pred HHHHHHHhh-cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHH
Q 008652 306 RDLKSELHS-GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK 384 (558)
Q Consensus 306 ~~L~~~l~~-G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~ 384 (558)
+.|+..+.. +..|++.|+..|.++|+.+|++|.+++.+++|++||+++++|+++.+|++.. .|.+|++..+++.+.+
T Consensus 6 ~~li~~~~~gd~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~~ 83 (187)
T TIGR02948 6 KKRIKEVRKGDENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLTID 83 (187)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHHH
Confidence 334455544 4599999999999999999999999999999999999999999999999875 5999999999999999
Q ss_pred HHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhh
Q 008652 385 AIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQE 464 (558)
Q Consensus 385 aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e 464 (558)
++++..+... ++.....++...+.+
T Consensus 84 ~~rk~~~~~~-------------------------------------------------------~~~~~~~~~~~~~~~ 108 (187)
T TIGR02948 84 RLRKRKPDFY-------------------------------------------------------LDDEVQGTDGLTMES 108 (187)
T ss_pred HHHhhccccc-------------------------------------------------------ccccccCcccccccc
Confidence 8876432100 000000000001111
Q ss_pred hcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008652 465 ITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 544 (558)
Q Consensus 465 ~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 544 (558)
...+. .+.|++.+...+....+..+|..||+++|.||.++|. +++|++|||+.||+|.++|++.+.||+++||..
T Consensus 109 ~~~~~-~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 109 QLAAD-EAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYM----EDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred ccccC-cCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 11111 1245666666666778999999999999999999998 899999999999999999999999999999998
Q ss_pred hhc
Q 008652 545 LGG 547 (558)
Q Consensus 545 l~~ 547 (558)
+..
T Consensus 184 l~~ 186 (187)
T TIGR02948 184 LRH 186 (187)
T ss_pred hhc
Confidence 753
No 44
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=99.88 E-value=4.4e-21 Score=184.27 Aligned_cols=171 Identities=23% Similarity=0.311 Sum_probs=137.7
Q ss_pred HHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCC----CCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008652 307 DLKSELHSG-NSSREKLINANLRLVVHVAKQYQGR----GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 381 (558)
Q Consensus 307 ~L~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~----g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a 381 (558)
.|+..+..| ..|++.|+..|.+.|+.+|.++.++ +.+.+|++||+++++|+++.+|++. +..|.+|++..+++.
T Consensus 13 ~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~n~ 91 (189)
T PRK09648 13 ALVAEAVAGDRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAAHK 91 (189)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHHHH
Confidence 456666555 4999999999999999999998765 3689999999999999999999864 457999999999999
Q ss_pred HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 008652 382 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 461 (558)
Q Consensus 382 I~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~ 461 (558)
+.++++++.+.... ..+.
T Consensus 92 ~~d~~r~~~r~~~~-----------------------------------------------------~~~~--------- 109 (189)
T PRK09648 92 VADAHRAAGRDKAV-----------------------------------------------------PTEE--------- 109 (189)
T ss_pred HHHHHHHhCCCccc-----------------------------------------------------cccc---------
Confidence 99998875531100 0000
Q ss_pred hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008652 462 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 541 (558)
Q Consensus 462 l~e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 541 (558)
+.+... ...+|++.+...+..+.|..+|..||+++|+||.++|+ +++|++|||+.||+|..+|++.+.||+++|
T Consensus 110 ~~~~~~--~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~L 183 (189)
T PRK09648 110 VPERPS--DDAGPEERALRSESSNRMRELLDTLPEKQREILILRVV----VGLSAEETAEAVGSTPGAVRVAQHRALARL 183 (189)
T ss_pred cccccc--cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 000000 11246666666777778999999999999999999998 899999999999999999999999999999
Q ss_pred HHHhh
Q 008652 542 KQSLG 546 (558)
Q Consensus 542 R~~l~ 546 (558)
|+.+.
T Consensus 184 r~~l~ 188 (189)
T PRK09648 184 RAEIE 188 (189)
T ss_pred HHHhc
Confidence 99864
No 45
>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=99.87 E-value=9.5e-21 Score=177.70 Aligned_cols=163 Identities=20% Similarity=0.344 Sum_probs=134.1
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008652 314 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 393 (558)
Q Consensus 314 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~I 393 (558)
++..|++.|+..|.+.+++++.++.++..+++|++||+++++|+++++|+...+ .|.+|++.++++.+.++++++.+..
T Consensus 8 ~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R~~~~~~ 86 (170)
T TIGR02952 8 REEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFRGSKRHP 86 (170)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 456999999999999999999999998899999999999999999999997555 8999999999999999998765311
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCC
Q 008652 394 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 473 (558)
Q Consensus 394 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~ 473 (558)
.. +.+. ..+... ....
T Consensus 87 ~~-----------------------------------------------------~~~~---------~~~~~~--~~~~ 102 (170)
T TIGR02952 87 LF-----------------------------------------------------SLDV---------FKELLS--NEPN 102 (170)
T ss_pred CC-----------------------------------------------------cHHH---------HhhcCC--CCCC
Confidence 00 0000 000000 1124
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008652 474 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 545 (558)
Q Consensus 474 pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 545 (558)
|++.+...+..+.+..+|..|||++|+||.++|. +|+|++|||+.||||..+|++.+.||+++||+.+
T Consensus 103 ~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~l 170 (170)
T TIGR02952 103 PEEAILKEEANEKLLKALKILTPKQQHVIALRFG----QNLPIAEVARILGKTEGAVKILQFRAIKKLARQM 170 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence 5666666666778999999999999999999998 8999999999999999999999999999999864
No 46
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=99.87 E-value=1.2e-20 Score=178.01 Aligned_cols=172 Identities=19% Similarity=0.236 Sum_probs=136.7
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008652 313 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 392 (558)
Q Consensus 313 ~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~ 392 (558)
.++..|++.|+..|.++|+.++++|.+++.+.+|++||++++||+++++|+ .+.+|.+|++.++++.+.+.+++..+.
T Consensus 6 ~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~r~~~~~ 83 (182)
T PRK09652 6 RGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYLRKQGRR 83 (182)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHHHcccCC
Confidence 355699999999999999999999999999999999999999999999999 456899999999999999998765431
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCC
Q 008652 393 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE 472 (558)
Q Consensus 393 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~ 472 (558)
...+ +++ ..+.++....+...+ ..
T Consensus 84 ~~~~----------------------------------------------------~~~--~~~~~~~~~~~~~~~--~~ 107 (182)
T PRK09652 84 PPAS----------------------------------------------------DVD--AEEAEDFDLADALRD--IS 107 (182)
T ss_pred CCcc----------------------------------------------------ccc--ccccccccccccccc--cc
Confidence 1000 000 000000011111111 12
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008652 473 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 546 (558)
Q Consensus 473 ~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 546 (558)
+|+..+...+....+..+|..||+++++||.++|. .++|++|||+.||+|..+|++.+.+|+++||+.+.
T Consensus 108 ~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 177 (182)
T PRK09652 108 TPENELLSAELEQRVRAAIESLPEELRTAITLREI----EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQ 177 (182)
T ss_pred ChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46666666677788999999999999999999998 89999999999999999999999999999999875
No 47
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=8.6e-21 Score=182.78 Aligned_cols=175 Identities=23% Similarity=0.295 Sum_probs=137.6
Q ss_pred CHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHH
Q 008652 304 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 382 (558)
Q Consensus 304 ~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI 382 (558)
+...|+..+..| ..|++.|+..|.+.|+.+++++.++..+.+|++||+++++|+. ..|++.++ .|.||++.++++.+
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 345566655555 5999999999999999999999999899999999999999976 67887655 79999999999999
Q ss_pred HHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 008652 383 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 462 (558)
Q Consensus 383 ~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l 462 (558)
.++++++.+..... .+. +.
T Consensus 93 ~d~~Rk~~~~~~~~---------------------------~~~------------------------~~---------- 111 (194)
T PRK12519 93 IDRLRSRRSRQRLL---------------------------ERW------------------------QQ---------- 111 (194)
T ss_pred HHHHHhcccccchh---------------------------hhh------------------------hh----------
Confidence 99998755211000 000 00
Q ss_pred hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 463 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 463 ~e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
....+.....+++.+...+....|..+|..||+++++||.++|. +|+|++|||+.||+|..+|++++.||+++||
T Consensus 112 -~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 186 (194)
T PRK12519 112 -ELLGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYY----EGLSQSEIAKRLGIPLGTVKARARQGLLKLR 186 (194)
T ss_pred -hhcccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 00000011234555555666667899999999999999999998 8999999999999999999999999999999
Q ss_pred HHhh
Q 008652 543 QSLG 546 (558)
Q Consensus 543 ~~l~ 546 (558)
+.+.
T Consensus 187 ~~l~ 190 (194)
T PRK12519 187 ELLQ 190 (194)
T ss_pred HHHH
Confidence 9875
No 48
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=99.86 E-value=1.3e-20 Score=180.19 Aligned_cols=176 Identities=18% Similarity=0.270 Sum_probs=135.1
Q ss_pred CHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHH
Q 008652 304 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 382 (558)
Q Consensus 304 ~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI 382 (558)
++..+...+..| ..|++.|+..|.+.|+.++++|.+++.+.+|++||+++++|+++++|++.. ..|.+|++..+++.+
T Consensus 9 ~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~-~~~~~wl~~ia~n~~ 87 (186)
T PRK13919 9 SDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRR-GSARAWLLALAHHAA 87 (186)
T ss_pred CHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCccc-cchHHHHHHHHHHHH
Confidence 456666666555 499999999999999999999999999999999999999999999999764 369999999999999
Q ss_pred HHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 008652 383 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 462 (558)
Q Consensus 383 ~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l 462 (558)
.+++++..+..+ ....+ ......
T Consensus 88 ~d~~rk~~~~~~----------------------------------------------------~~~~~-----~~~~~~ 110 (186)
T PRK13919 88 VDHVRRRAARPQ----------------------------------------------------PLEPD-----EREPEA 110 (186)
T ss_pred HHHHHhhhcccc----------------------------------------------------ccccc-----cccccc
Confidence 999876542100 00000 000000
Q ss_pred hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 463 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 463 ~e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
.+ .. .+..........+.|..+|..||+++|+||.++|. +++|++|||+.||+|..+|+..++||+++||
T Consensus 111 ~~-~~-----~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr 180 (186)
T PRK13919 111 FD-LP-----GPGLDEEGHLDRTRLGRALKALSPEERRVIEVLYY----QGYTHREAAQLLGLPLGTLKTRARRALSRLK 180 (186)
T ss_pred cc-CC-----CccccHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 00 00 11111122233457899999999999999999998 8999999999999999999999999999999
Q ss_pred HHhhc
Q 008652 543 QSLGG 547 (558)
Q Consensus 543 ~~l~~ 547 (558)
+.+..
T Consensus 181 ~~l~~ 185 (186)
T PRK13919 181 EVLRE 185 (186)
T ss_pred HHhcC
Confidence 98753
No 49
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=1.6e-20 Score=178.74 Aligned_cols=173 Identities=14% Similarity=0.145 Sum_probs=137.6
Q ss_pred CHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHH
Q 008652 304 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 382 (558)
Q Consensus 304 ~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI 382 (558)
+...|+..+..| ..|+..|+..|.+.|+.+|.++.++..+.+|++||+++++|+++++|++..+ .|.+|.+..+++.+
T Consensus 5 ~~~~li~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~~-~~~~wl~~ia~n~~ 83 (179)
T PRK12514 5 DIEKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGL-SPMTWLITIARNHA 83 (179)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCcccc-cHHHHHHHHHHHHH
Confidence 345566655555 5999999999999999999999999999999999999999999999997543 69999999999999
Q ss_pred HHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 008652 383 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 462 (558)
Q Consensus 383 ~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l 462 (558)
.++++++.+.. . .++. .
T Consensus 84 ~d~~R~~~~~~-~-----------------------------------------------------~~~~---------~ 100 (179)
T PRK12514 84 IDRLRARKAVA-V-----------------------------------------------------DIDE---------A 100 (179)
T ss_pred HHHHHhcCCcc-c-----------------------------------------------------cccc---------c
Confidence 99987644210 0 0000 0
Q ss_pred hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 463 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 463 ~e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
.+ ..+ ....|+..+...+....|..+|..||+++++||.++|. +|+|++|||+.||+|..+|++.+.||+++||
T Consensus 101 ~~-~~~-~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 174 (179)
T PRK12514 101 HD-LAD-PSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYL----EGLSYKELAERHDVPLNTMRTWLRRSLLKLR 174 (179)
T ss_pred hh-ccc-cCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCChHHHHHHHHHHHHHHH
Confidence 00 000 01245555554445567899999999999999999998 8999999999999999999999999999999
Q ss_pred HHhh
Q 008652 543 QSLG 546 (558)
Q Consensus 543 ~~l~ 546 (558)
+++.
T Consensus 175 ~~l~ 178 (179)
T PRK12514 175 ECLS 178 (179)
T ss_pred HHhc
Confidence 9874
No 50
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=99.86 E-value=2.5e-20 Score=179.57 Aligned_cols=174 Identities=14% Similarity=0.191 Sum_probs=140.7
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCC---CCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHH
Q 008652 303 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRG---ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV 378 (558)
Q Consensus 303 ~~~~~L~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g---~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wI 378 (558)
++++.|+..+..|+ .|++.|+..|.+.|++++.++.+++ .+.+|++||+++++|+++++|+++.+ .|.+|++..+
T Consensus 3 ~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~ia 81 (189)
T PRK06811 3 INEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAIS 81 (189)
T ss_pred CcHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHH
Confidence 45667777777665 8999999999999999999998863 46999999999999999999997655 7999999999
Q ss_pred HHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCC
Q 008652 379 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQ 458 (558)
Q Consensus 379 r~aI~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~ 458 (558)
++.+.++++++.+.... .+.+..
T Consensus 82 rn~~~d~~rk~~~~~~~----------------------------------------------------~~~~~~----- 104 (189)
T PRK06811 82 KYKAIDYKRKLTKNNEI----------------------------------------------------DSIDEF----- 104 (189)
T ss_pred HHHHHHHHHHhcccccc----------------------------------------------------ccchhh-----
Confidence 99999999875531100 000000
Q ss_pred CcchhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008652 459 DTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 538 (558)
Q Consensus 459 ~~~l~e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RAL 538 (558)
. . ....++++.+...+....|..+|..|||++|.||.++|. +|+|++|||+.||+|..+|++.+.||+
T Consensus 105 ------~-~-~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIAe~lgis~~~V~~~l~Ra~ 172 (189)
T PRK06811 105 ------I-L-ISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYL----LGEKIEEIAKKLGLTRSAIDNRLSRGR 172 (189)
T ss_pred ------h-h-cccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----ccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 0 0 011245556666667778999999999999999999997 899999999999999999999999999
Q ss_pred HHHHHHhh
Q 008652 539 YRLKQSLG 546 (558)
Q Consensus 539 kKLR~~l~ 546 (558)
++||+..-
T Consensus 173 ~~Lr~~~~ 180 (189)
T PRK06811 173 KKLQKNKL 180 (189)
T ss_pred HHHHHccc
Confidence 99998643
No 51
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=99.86 E-value=1.1e-20 Score=174.90 Aligned_cols=151 Identities=21% Similarity=0.253 Sum_probs=123.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccccc
Q 008652 316 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 395 (558)
Q Consensus 316 ~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRl 395 (558)
..|++.|+..|.++|+.+++++ +...+++|++|||++++|+++++|++..| .|.+|++..+++.+.++++++.+..
T Consensus 3 ~~af~~l~~~y~~~l~~~~~~~-~~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~~~~-- 78 (154)
T PRK06759 3 PATFTEAVVLYEGLIVNQIKKL-GIYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFAVQ-- 78 (154)
T ss_pred cccHHHHHHHHHHHHHHHHHHh-CCcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHHhhc--
Confidence 4689999999999999999986 56678999999999999999999998776 7999999999999999987753100
Q ss_pred chhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChh
Q 008652 396 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD 475 (558)
Q Consensus 396 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe 475 (558)
. ... .+ +.|+
T Consensus 79 ----------------------~---------------------------------~~~-~~--------------~~~~ 88 (154)
T PRK06759 79 ----------------------E---------------------------------KCV-CV--------------GEYE 88 (154)
T ss_pred ----------------------c---------------------------------ccc-cc--------------CCCc
Confidence 0 000 00 0111
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008652 476 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 544 (558)
Q Consensus 476 ~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 544 (558)
+.+...+....|..+|..||+++|+||.++|+ +++|.+|||+.||+|..+|++++.||+++||+.
T Consensus 89 ~~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~~----~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 89 DHFHFEDVEMKVKDFMSVLDEKEKYIIFERFF----VGKTMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred ccccHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 12222334567899999999999999999998 899999999999999999999999999999974
No 52
>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=99.86 E-value=2.6e-20 Score=178.08 Aligned_cols=181 Identities=16% Similarity=0.211 Sum_probs=140.6
Q ss_pred CHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHH
Q 008652 304 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 382 (558)
Q Consensus 304 ~~~~L~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI 382 (558)
++..|+..+..|+ .+++.|+..|.+.|+.+|+++.++..+.+|++||+++++|+++++|++. ..|.+|++...++.+
T Consensus 6 ~d~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~~ 83 (190)
T TIGR02939 6 LDLELVERVQRGEKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNTA 83 (190)
T ss_pred cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHHH
Confidence 4556666666554 8999999999999999999999999999999999999999999999975 369999999999999
Q ss_pred HHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 008652 383 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 462 (558)
Q Consensus 383 ~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l 462 (558)
.++++++.+..... ..+.+.. ..+
T Consensus 84 ~~~~r~~~r~~~~~--------------------------------------------------~~~~~~~------~~~ 107 (190)
T TIGR02939 84 KNHLVAQGRRPPTS--------------------------------------------------DVEIEDA------EHF 107 (190)
T ss_pred HHHHHHhccCCCcc--------------------------------------------------cccccch------hhh
Confidence 98887544211000 0000000 000
Q ss_pred hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 463 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 463 ~e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
.+........+|++.+...+....|..+|+.||+++|+||.++|. +++|++|||+.||+|..+|++.+.||+++||
T Consensus 108 ~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr 183 (190)
T TIGR02939 108 EGADRLREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLREL----EGLSYEDIARIMDCPVGTVRSRIFRAREAIA 183 (190)
T ss_pred cccccccccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhhh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 000000011246666666677778999999999999999999998 8999999999999999999999999999999
Q ss_pred HHhh
Q 008652 543 QSLG 546 (558)
Q Consensus 543 ~~l~ 546 (558)
+++.
T Consensus 184 ~~l~ 187 (190)
T TIGR02939 184 IRLR 187 (190)
T ss_pred HHhh
Confidence 9885
No 53
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=2.1e-20 Score=186.06 Aligned_cols=173 Identities=18% Similarity=0.235 Sum_probs=137.5
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008652 314 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 393 (558)
Q Consensus 314 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~I 393 (558)
++..|++.|+..|.+.|+++|+++.+++.+.+|++||++++||+++++|++. ..|.+|++..+++.+.+++++..+..
T Consensus 27 gd~~a~~~l~~~y~~~l~~~a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~Rk~~r~~ 104 (231)
T PRK11922 27 GDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNEALGRLRRRRRLV 104 (231)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHHHHHHHHhhcccc
Confidence 4568999999999999999999999999999999999999999999999986 47999999999999999988755321
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCC
Q 008652 394 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 473 (558)
Q Consensus 394 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~ 473 (558)
.++. . . +..... ++ ...... ....+
T Consensus 105 ~~~~----------------------------~----------------------~-~~~~~~-~~--~~~~~~-~~~~~ 129 (231)
T PRK11922 105 NLAE----------------------------M----------------------V-MASTIA-GG--ERTPLA-DPAED 129 (231)
T ss_pred cchh----------------------------c----------------------c-cccccc-cc--cccccC-cccCC
Confidence 1100 0 0 000000 00 000001 11235
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008652 474 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 547 (558)
Q Consensus 474 pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 547 (558)
|++.+...+..+.|..+|+.||+++|+||.++|. +++|++|||+.||+|.++|++++.||+++||+.+..
T Consensus 130 ~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~~ 199 (231)
T PRK11922 130 PERAAARREIRALLERAIDALPDAFRAVFVLRVV----EELSVEETAQALGLPEETVKTRLHRARRLLRESLAR 199 (231)
T ss_pred hHHHHHHHHHHHHHHHHHHhCCHHHhhhheeehh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 6667777777788999999999999999999987 899999999999999999999999999999998864
No 54
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=3.2e-20 Score=179.84 Aligned_cols=177 Identities=19% Similarity=0.211 Sum_probs=142.5
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008652 303 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 381 (558)
Q Consensus 303 ~~~~~L~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a 381 (558)
+++..|+..+..|+ .|++.|+..|.+.|+.+|.++.++..+++|++||+++++|+.+.+|++.. ..|.+|++..+++.
T Consensus 11 ~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~n~ 89 (196)
T PRK12524 11 VSDEALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVCNL 89 (196)
T ss_pred cCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHHHHH
Confidence 35667777776664 99999999999999999999999999999999999999999999998533 47999999999999
Q ss_pred HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 008652 382 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 461 (558)
Q Consensus 382 I~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~ 461 (558)
+.++++++.+.. ..++. . .
T Consensus 90 ~~d~~Rk~~~~~------------------------------------------------------~~~~~-~---~--- 108 (196)
T PRK12524 90 CTDRLRRRRRAS------------------------------------------------------VDLDD-A---P--- 108 (196)
T ss_pred HHHHHHhhcCCC------------------------------------------------------CCccc-c---c---
Confidence 999887643100 00000 0 0
Q ss_pred hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008652 462 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 541 (558)
Q Consensus 462 l~e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 541 (558)
+. .+. ...+++.+...+....|..+|+.||+++|+||.|+|. ++++++|||+.||||..+|++++.||+++|
T Consensus 109 --~~-~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~~----~g~s~~eIA~~lgis~~tV~~~l~Ra~~~L 180 (196)
T PRK12524 109 --EP-ADA-APGAEEALIEGDRMRALDAALAALPERQRQAVVLRHI----EGLSNPEIAEVMEIGVEAVESLTARGKRAL 180 (196)
T ss_pred --cc-ccc-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 00 011 1234555666666778999999999999999999998 899999999999999999999999999999
Q ss_pred HHHhhcCc
Q 008652 542 KQSLGGKA 549 (558)
Q Consensus 542 R~~l~~~~ 549 (558)
|..+...+
T Consensus 181 r~~l~~~~ 188 (196)
T PRK12524 181 AALLAGQR 188 (196)
T ss_pred HHHHHhcc
Confidence 99987543
No 55
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=2.8e-20 Score=185.99 Aligned_cols=174 Identities=15% Similarity=0.223 Sum_probs=139.6
Q ss_pred CHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHH
Q 008652 304 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 382 (558)
Q Consensus 304 ~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI 382 (558)
++..|+..+..| ..|++.|+..|.+.|+.+++++.++..+.+|++||+|+++|+++++|++..+ .|.+|++..+++.+
T Consensus 49 ~d~~Li~~~~~gd~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~~ 127 (233)
T PRK12538 49 EDEELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNRC 127 (233)
T ss_pred cHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHHH
Confidence 455666666555 4999999999999999999999999999999999999999999999987554 79999999999999
Q ss_pred HHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 008652 383 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 462 (558)
Q Consensus 383 ~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l 462 (558)
.++++++.+. . ++. . .
T Consensus 128 id~~Rk~~~~-~-------------------------------------------------------~~~-~-~------ 143 (233)
T PRK12538 128 IDLRRKPRTE-N-------------------------------------------------------VDA-V-P------ 143 (233)
T ss_pred HHHHHhhccc-c-------------------------------------------------------ccc-c-c------
Confidence 9988653210 0 000 0 0
Q ss_pred hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 463 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 463 ~e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
+. .+ ....+++.+...+....|..+|..||+++|+||.|+|. +++|++|||+.||+|.++|++++.||+++||
T Consensus 144 -~~-~~-~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~~----eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr 216 (233)
T PRK12538 144 -EV-AD-GKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSYH----ENMSNGEIAEVMDTTVAAVESLLKRGRQQLR 216 (233)
T ss_pred -cc-cc-CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 00 00 01133444555566678999999999999999999998 9999999999999999999999999999999
Q ss_pred HHhhcCc
Q 008652 543 QSLGGKA 549 (558)
Q Consensus 543 ~~l~~~~ 549 (558)
+.+...+
T Consensus 217 ~~l~~~~ 223 (233)
T PRK12538 217 DLLRRHE 223 (233)
T ss_pred HHHHHhh
Confidence 9987554
No 56
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=3.5e-20 Score=177.38 Aligned_cols=172 Identities=13% Similarity=0.157 Sum_probs=136.8
Q ss_pred CHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHH
Q 008652 304 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 382 (558)
Q Consensus 304 ~~~~L~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI 382 (558)
+...|+..+.+|+ .|++.|+..|.+.|+.++.++.++..+.+|++||+|+.+|+.+++|++.. ..|.+|++..+++.+
T Consensus 9 ~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~-~~~~~wL~~iarn~~ 87 (182)
T PRK12537 9 DYEACLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPAR-GSARGWIYSVTRHLA 87 (182)
T ss_pred hHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCccc-ccHHHHHHHHHHHHH
Confidence 4455666666554 99999999999999999999999999999999999999999999998644 379999999999999
Q ss_pred HHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 008652 383 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 462 (558)
Q Consensus 383 ~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l 462 (558)
.++++++.+...+ +.. .
T Consensus 88 ~d~~r~~~~~~~~-------------------------------------------------------~~~--------~ 104 (182)
T PRK12537 88 LNVLRDTRREVVL-------------------------------------------------------DDD--------A 104 (182)
T ss_pred HHHHHhccccCcc-------------------------------------------------------ccc--------h
Confidence 9999875421100 000 0
Q ss_pred hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 463 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 463 ~e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
.+...+ ...+++..+.......|..+|+.||+++|+||.++|. +++|++|||+.||||.++|+..+.||+++||
T Consensus 105 ~~~~~~--~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr 178 (182)
T PRK12537 105 EETAQT--LHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYV----DGCSHAEIAQRLGAPLGTVKAWIKRSLKALR 178 (182)
T ss_pred hhhccc--ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCChhhHHHHHHHHHHHHH
Confidence 000000 1122333344445567899999999999999999998 8999999999999999999999999999999
Q ss_pred HHh
Q 008652 543 QSL 545 (558)
Q Consensus 543 ~~l 545 (558)
+++
T Consensus 179 ~~l 181 (182)
T PRK12537 179 ECM 181 (182)
T ss_pred HHh
Confidence 976
No 57
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=99.85 E-value=5.5e-20 Score=177.06 Aligned_cols=180 Identities=15% Similarity=0.203 Sum_probs=140.0
Q ss_pred HHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHH
Q 008652 305 CRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR 383 (558)
Q Consensus 305 ~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~ 383 (558)
++.|+..++.| ..|++.|+..|.+.|+.+++++.++..+.+|++||+++++|+++.+|++.. .|.+|++..+++.+.
T Consensus 7 ~~~ll~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~~ 84 (193)
T PRK11923 7 DQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTAK 84 (193)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHHH
Confidence 34555555555 599999999999999999999999989999999999999999999999874 499999999999999
Q ss_pred HHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchh
Q 008652 384 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ 463 (558)
Q Consensus 384 ~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~ 463 (558)
++++++.+.... ....++.....++.
T Consensus 85 d~~rk~~~~~~~--------------------------------------------------~~~~~~~~~~~~~~---- 110 (193)
T PRK11923 85 NHLVSRGRRPPD--------------------------------------------------SDVSSEDAEFYDGD---- 110 (193)
T ss_pred HHHHHhcCCCcc--------------------------------------------------ccccccchhhhccc----
Confidence 988765421100 00000000000000
Q ss_pred hhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 464 EITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 464 e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
..+. ....|+..+...+..+.+..+|..||+++|+||.++|. +|+|.+|||+.||+|..+|++.+.||+++||.
T Consensus 111 ~~~~--~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 184 (193)
T PRK11923 111 HALK--DIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREF----DGLSYEDIASVMQCPVGTVRSRIFRAREAIDK 184 (193)
T ss_pred cccc--CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 0011 12356666666777788999999999999999999998 89999999999999999999999999999999
Q ss_pred Hhh
Q 008652 544 SLG 546 (558)
Q Consensus 544 ~l~ 546 (558)
++.
T Consensus 185 ~l~ 187 (193)
T PRK11923 185 ALQ 187 (193)
T ss_pred HHH
Confidence 885
No 58
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=99.85 E-value=1.7e-20 Score=180.33 Aligned_cols=173 Identities=20% Similarity=0.290 Sum_probs=136.2
Q ss_pred cCCHHHHHHHHhh----cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHH
Q 008652 302 GLSCRDLKSELHS----GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 377 (558)
Q Consensus 302 g~~~~~L~~~l~~----G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~w 377 (558)
.++++.|+..++. +..|++.|+..|.+.|+++|.+|.++..+.+|++||+++.+|+++++|++. ..|.+|++.+
T Consensus 7 ~~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~~--~~~~~wl~~i 84 (188)
T PRK09640 7 ELNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLYSI 84 (188)
T ss_pred CCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcCC--CcchHHHHHH
Confidence 4567778777763 469999999999999999999999999999999999999999999999863 4799999999
Q ss_pred HHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCC
Q 008652 378 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWAD 457 (558)
Q Consensus 378 Ir~aI~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d 457 (558)
+++.+.+++++..+.... . .+...
T Consensus 85 a~n~~~d~~R~~~~~~~~--------------------------~---------------------------~~~~~--- 108 (188)
T PRK09640 85 TYNECITQYRKERRKRRL--------------------------M---------------------------DALSL--- 108 (188)
T ss_pred HHHHHHHHHHHhcccccC--------------------------c---------------------------chhhh---
Confidence 999999999764321000 0 00000
Q ss_pred CCcchhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008652 458 QDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 537 (558)
Q Consensus 458 ~~~~l~e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA 537 (558)
+...++. +......+....|..+|+.||+++|+||.++|. +++|++|||+.||||..+|+..+.||
T Consensus 109 ------~~~~~~~----~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra 174 (188)
T PRK09640 109 ------DPLEEAS----EEKAPKPEERGGLDRWLVHVNPIDREILVLRFV----AELEFQEIADIMHMGLSATKMRYKRA 174 (188)
T ss_pred ------ccccccc----ccccccHHHHHHHHHHHHhcChhheeeeeeHHh----cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 0000000 000111233456899999999999999999998 89999999999999999999999999
Q ss_pred HHHHHHHhh
Q 008652 538 LYRLKQSLG 546 (558)
Q Consensus 538 LkKLR~~l~ 546 (558)
+++||+.+.
T Consensus 175 ~~~Lr~~l~ 183 (188)
T PRK09640 175 LDKLREKFA 183 (188)
T ss_pred HHHHHHHHH
Confidence 999999874
No 59
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=4.8e-20 Score=176.61 Aligned_cols=173 Identities=15% Similarity=0.158 Sum_probs=136.1
Q ss_pred HHHHHHHh-hcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHH
Q 008652 306 RDLKSELH-SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK 384 (558)
Q Consensus 306 ~~L~~~l~-~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~ 384 (558)
..+..... ++..+++.|+..|.++|+.+|+++.++..+.+|++||+++++|+++++|++.++ .|.+|++..+++.+.+
T Consensus 13 ~~l~~~~~~~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~~d 91 (187)
T PRK12534 13 GRLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKAID 91 (187)
T ss_pred HHHHHHHHcCCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHH
Confidence 33444444 445999999999999999999999999999999999999999999999998654 5889999999999999
Q ss_pred HHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhh
Q 008652 385 AIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQE 464 (558)
Q Consensus 385 aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e 464 (558)
+++++.+..+ ..+++. ...
T Consensus 92 ~~R~~~~~~~----------------------------------------------------~~~~~~---------~~~ 110 (187)
T PRK12534 92 HLRANAPQRR----------------------------------------------------NVALDD---------AGE 110 (187)
T ss_pred HHHhcccccc----------------------------------------------------cccccc---------hhh
Confidence 9876542100 000000 000
Q ss_pred hcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008652 465 ITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 544 (558)
Q Consensus 465 ~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 544 (558)
.. +. ..++++.....+....|..+|..||+++++|+.++|. +++|++|||+.||+|.++|+++++||+++||+.
T Consensus 111 ~~-~~-~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 184 (187)
T PRK12534 111 LR-AA-DASPLERTERASTRRRIDHCLAELEPPRSELIRTAFF----EGITYEELAARTDTPIGTVKSWIRRGLAKLKAC 184 (187)
T ss_pred hc-cc-cCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Confidence 00 00 1123344445556678999999999999999999998 899999999999999999999999999999998
Q ss_pred hh
Q 008652 545 LG 546 (558)
Q Consensus 545 l~ 546 (558)
+.
T Consensus 185 l~ 186 (187)
T PRK12534 185 LE 186 (187)
T ss_pred Hc
Confidence 74
No 60
>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=99.85 E-value=1.2e-19 Score=173.03 Aligned_cols=180 Identities=18% Similarity=0.203 Sum_probs=137.9
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHhhC----CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhc
Q 008652 314 SGNSSREKLINANLRLVVHVAKQYQG----RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 389 (558)
Q Consensus 314 ~G~~Are~LI~~nlrLV~sIArrY~~----~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~ 389 (558)
++..|++.|+..|.+.|+.+|++|.+ +..+.+|++||+++.+|+++..|++..+..|.+|++..+++.+.++++++
T Consensus 4 ~~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~~ 83 (189)
T TIGR02984 4 GDQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRRH 83 (189)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHHH
Confidence 45699999999999999999999753 56789999999999999999999987667899999999999999988764
Q ss_pred ccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCC-CCCCcchhhhccc
Q 008652 390 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVW-ADQDTTFQEITAD 468 (558)
Q Consensus 390 sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~-~d~~~~l~e~i~d 468 (558)
.+. .. +.+ ....+++.... .+....+.+.+.+
T Consensus 84 ~~~-----------------~~-------r~~-----------------------~~~~~~~~~~~~~~~~~~~~~~~~~ 116 (189)
T TIGR02984 84 LGA-----------------QK-------RDI-----------------------RREQSLDAGGRLDESSVRLAAQLAA 116 (189)
T ss_pred HHH-----------------Hh-------hhc-----------------------ccccCCCcccccCCcchhHHHHccC
Confidence 200 00 000 00112222111 1111123333333
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008652 469 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 545 (558)
Q Consensus 469 ~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 545 (558)
...+|++.+...+....|..+|..|||++|+||.++|+ .|+|++|||+.||||.++|++.+.||+++||+.+
T Consensus 117 -~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~~----~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~l 188 (189)
T TIGR02984 117 -DGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRHL----EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQIL 188 (189)
T ss_pred -CCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 22356667777777788999999999999999999998 8999999999999999999999999999999876
No 61
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=4.3e-20 Score=177.04 Aligned_cols=175 Identities=17% Similarity=0.204 Sum_probs=139.1
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008652 314 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 393 (558)
Q Consensus 314 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~I 393 (558)
++..|++.|+..|.+.++.+|.++.++..+++|++||+++.+|+++++|++..+..|.||++..+++.+.++++++.+..
T Consensus 6 gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~~~~ 85 (185)
T PRK12542 6 NDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNKRHE 85 (185)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 45699999999999999999999999999999999999999999999998755558999999999999999988754210
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCC
Q 008652 394 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 473 (558)
Q Consensus 394 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~ 473 (558)
.. . +. . .. +.... ..+.
T Consensus 86 ~~------------------~------------------------------------~~-~---~~----~~~~~-~~~~ 102 (185)
T PRK12542 86 TF------------------L------------------------------------EE-Y---ER----ESIEA-VDEN 102 (185)
T ss_pred hh------------------h------------------------------------hh-c---cc----cchhh-hhcc
Confidence 00 0 00 0 00 00000 0012
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchHhh
Q 008652 474 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGY 553 (558)
Q Consensus 474 pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~y 553 (558)
+++..........|..+|..||+++|+||.|+|. +++|++|||+.||+|.++|+..+.||+++||+.+......+|
T Consensus 103 ~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~~~~ 178 (185)
T PRK12542 103 IEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVF----YNLTYQEISSVMGITEANVRKQFERARKRVQNMIGGIQHDEF 178 (185)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccchHHH
Confidence 3333333444567899999999999999999998 899999999999999999999999999999999988887777
Q ss_pred hh
Q 008652 554 AD 555 (558)
Q Consensus 554 ld 555 (558)
+.
T Consensus 179 ~~ 180 (185)
T PRK12542 179 KE 180 (185)
T ss_pred HH
Confidence 53
No 62
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=8.9e-20 Score=178.47 Aligned_cols=171 Identities=12% Similarity=0.158 Sum_probs=133.0
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008652 313 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 392 (558)
Q Consensus 313 ~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~ 392 (558)
.++..+++.|+..|.+.|+.++.++.++..+.+|++||+++.+|+++..|++.++ .|.+|++.++++.+.++++++.+.
T Consensus 34 ~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d~~Rk~~~~ 112 (206)
T PRK12526 34 SRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFDMLRKIKAK 112 (206)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHHHHHHhccc
Confidence 3556999999999999999999999999889999999999999999999998765 599999999999999999875431
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCC
Q 008652 393 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE 472 (558)
Q Consensus 393 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~ 472 (558)
.... ++. +...+.+.+.+. ..
T Consensus 113 ~~~~-----------------------------------------------------~~~-----~~~~~~~~~~~~-~~ 133 (206)
T PRK12526 113 KEQN-----------------------------------------------------LGD-----DIWPIEQALAES-QS 133 (206)
T ss_pred cccc-----------------------------------------------------ccc-----ccchhhhhcccc-cC
Confidence 1000 000 000000111111 11
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008652 473 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 548 (558)
Q Consensus 473 ~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 548 (558)
.+. ..........|..+|..||+++|+||.++|+ +++|++|||+.||+|..+|+..++||+++||+.+...
T Consensus 134 ~~~-~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~ 204 (206)
T PRK12526 134 ESE-EFSDHLMDKQILSYIEKLPEAQQTVVKGVYF----QELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQMGEQ 204 (206)
T ss_pred chH-HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence 122 2223334457899999999999999999998 9999999999999999999999999999999998654
No 63
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=9.4e-20 Score=171.38 Aligned_cols=168 Identities=16% Similarity=0.176 Sum_probs=138.3
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008652 313 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 392 (558)
Q Consensus 313 ~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~ 392 (558)
.++..|++.|+..|.+.|+++|+++.++..+.+|++||++++||+++++|+ .+..|.+|++..+++.+.+++++..+.
T Consensus 9 ~~~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~~r~~~~~ 86 (179)
T PRK11924 9 TGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDLLRRRRRE 86 (179)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHHHHhcccc
Confidence 345699999999999999999999999999999999999999999999998 345899999999999999998765421
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCC
Q 008652 393 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE 472 (558)
Q Consensus 393 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~ 472 (558)
... ..+ .. .+...+....
T Consensus 87 ~~~-----------------------------------------------------~~~-~~--------~~~~~~~~~~ 104 (179)
T PRK11924 87 KAV-----------------------------------------------------LSD-DA--------LEPEFAETAE 104 (179)
T ss_pred ccc-----------------------------------------------------Ccc-cc--------cccccCCccC
Confidence 100 000 00 0000000234
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008652 473 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 548 (558)
Q Consensus 473 ~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 548 (558)
.|+..+...+....+..+|..||+++++||.++|. +++|.+|||+.||+|+.+|++.+.+|+++||+.+..+
T Consensus 105 ~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~~~ 176 (179)
T PRK11924 105 TPEAALLAKDDLARIDRCLDALPVKQREVFLLRYV----EGLSYREIAEILGVPVGTVKSRLRRARQLLRECLEAQ 176 (179)
T ss_pred CHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 67777888888889999999999999999999998 8999999999999999999999999999999988654
No 64
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=1.5e-19 Score=173.80 Aligned_cols=177 Identities=19% Similarity=0.264 Sum_probs=143.1
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008652 303 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 381 (558)
Q Consensus 303 ~~~~~L~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a 381 (558)
+++..|+..+..|+ .|++.|+..|.+.++.++.++.++..+.+|++||+++.+|++.++|++. ..|.+|++..+++.
T Consensus 7 ~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n~ 84 (189)
T PRK12515 7 TTDEMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARFK 84 (189)
T ss_pred cCHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHHH
Confidence 46677777666554 8999999999999999999999999999999999999999999999974 47999999999999
Q ss_pred HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 008652 382 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 461 (558)
Q Consensus 382 I~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~ 461 (558)
+.+++++..+.. +.. +.
T Consensus 85 ~~d~~r~~~~~~--------------------------------------------------------~~~-----~~-- 101 (189)
T PRK12515 85 ALSALRRRKHEE--------------------------------------------------------IDD-----EA-- 101 (189)
T ss_pred HHHHHHccCCCC--------------------------------------------------------Ccc-----cc--
Confidence 999987543100 000 00
Q ss_pred hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008652 462 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 541 (558)
Q Consensus 462 l~e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 541 (558)
. ....+ ...+++......+....+..+|+.||+++|+||.++|. +++|++|||+.||+|..+|++++.||+++|
T Consensus 102 ~-~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~tV~~~l~Rar~~L 175 (189)
T PRK12515 102 A-AAIED-GADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYY----HEKSVEEVGEIVGIPESTVKTRMFYARKKL 175 (189)
T ss_pred c-cccCC-CCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 0 00011 12245555556666778999999999999999999998 899999999999999999999999999999
Q ss_pred HHHhhcCch
Q 008652 542 KQSLGGKAS 550 (558)
Q Consensus 542 R~~l~~~~L 550 (558)
|+.+...+.
T Consensus 176 r~~l~~~~~ 184 (189)
T PRK12515 176 AELLKAAGV 184 (189)
T ss_pred HHHHHHhcc
Confidence 999876553
No 65
>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=99.83 E-value=2.3e-19 Score=162.07 Aligned_cols=157 Identities=24% Similarity=0.383 Sum_probs=131.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccch
Q 008652 318 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 397 (558)
Q Consensus 318 Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~ 397 (558)
|++.++..|.++|.++++++.+++.+.+|++|||++++|++++.|++. .+|.+|+.+++++.+.++++++.+ . +.
T Consensus 2 a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~-~--~~ 76 (158)
T TIGR02937 2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR-L--RR 76 (158)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhcc-C--Cc
Confidence 789999999999999999999999999999999999999999999998 689999999999999999987664 1 10
Q ss_pred hHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHH
Q 008652 398 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 477 (558)
Q Consensus 398 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~ 477 (558)
.. .. . ... ......++..
T Consensus 77 ~~---------------------------------------------------~~------~----~~~-~~~~~~~~~~ 94 (158)
T TIGR02937 77 EL---------------------------------------------------DL------L----EEL-LDSDPSPEEE 94 (158)
T ss_pred ch---------------------------------------------------hh------h----hhc-ccccCCHHHH
Confidence 00 00 0 000 0111245556
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008652 478 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 545 (558)
Q Consensus 478 le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 545 (558)
.........|..+++.||++++.||.++|+ .|+|..|||+.+|+|+.+|+++..+++++||+.+
T Consensus 95 ~~~~~~~~~l~~~l~~L~~~~~~ii~~~~~----~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~l 158 (158)
T TIGR02937 95 LEQEEEREALREALEKLPEREREVLVLRYL----EGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158 (158)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 666677778999999999999999999987 7999999999999999999999999999999764
No 66
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=99.83 E-value=2.8e-19 Score=172.98 Aligned_cols=172 Identities=16% Similarity=0.167 Sum_probs=138.4
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008652 303 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 381 (558)
Q Consensus 303 ~~~~~L~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a 381 (558)
+++..++..+..|+ .+++.|+..|.+.|++++.++.++..+.+|++||+++.+|+++++|++.. .|.+|++..+++.
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 35666766666554 99999999999999999999999999999999999999999999999753 5999999999999
Q ss_pred HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 008652 382 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 461 (558)
Q Consensus 382 I~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~ 461 (558)
+.+++++..+..+. +++. ..
T Consensus 90 ~~d~~Rk~~~~~~~-----------------------------------------------------~~~~----~~--- 109 (192)
T PRK09643 90 CLDRLRRAKARPTV-----------------------------------------------------PLDD----VY--- 109 (192)
T ss_pred HHHHHHccccCCCC-----------------------------------------------------Cccc----cc---
Confidence 99999875421100 0000 00
Q ss_pred hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008652 462 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 541 (558)
Q Consensus 462 l~e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 541 (558)
+. . ..+++.+...+....|..+|+.||+++|+||.|+|. +++|++|||+.||+|..+|+..+.||+++|
T Consensus 110 --~~-~----~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~~----~g~s~~EIA~~lg~s~~tV~~rl~rar~~L 178 (192)
T PRK09643 110 --PV-A----QLERDPTARVETALAVQRALMRLPVEQRAALVAVDM----QGYSVADAARMLGVAEGTVKSRCARGRARL 178 (192)
T ss_pred --cc-c----CCcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 00 0 012223344455667999999999999999999998 899999999999999999999999999999
Q ss_pred HHHhhc
Q 008652 542 KQSLGG 547 (558)
Q Consensus 542 R~~l~~ 547 (558)
|+.+..
T Consensus 179 r~~l~~ 184 (192)
T PRK09643 179 AELLGY 184 (192)
T ss_pred HHHHHH
Confidence 998864
No 67
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=99.83 E-value=1.6e-19 Score=170.89 Aligned_cols=172 Identities=13% Similarity=0.184 Sum_probs=133.7
Q ss_pred CCHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008652 303 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 381 (558)
Q Consensus 303 ~~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a 381 (558)
|++..+......| ..|++.|+..|.+.|+.+|++|.++..+.+|++||+++++|++++.|++. .+|.+|++..+++.
T Consensus 3 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n~ 80 (176)
T PRK09638 3 MDEKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASRL 80 (176)
T ss_pred ccHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHH
Confidence 3455566655555 49999999999999999999999999999999999999999999999874 47999999999999
Q ss_pred HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 008652 382 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 461 (558)
Q Consensus 382 I~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~ 461 (558)
+.+++++..+.... .+.+ .+..
T Consensus 81 ~~d~~r~~~~~~~~---------------------------~~~~-----------------------~~~~-------- 102 (176)
T PRK09638 81 YKDHLRKQKREKLR---------------------------LQRA-----------------------KEET-------- 102 (176)
T ss_pred HHHHHHHhccccch---------------------------hhhc-----------------------cccc--------
Confidence 99999875421100 0000 0000
Q ss_pred hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008652 462 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 541 (558)
Q Consensus 462 l~e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 541 (558)
.+ .... +..........|..+|..||+++|+||.++|. +|++++|||+.||+|..+|+..+.||+++|
T Consensus 103 -----~~--~~~~-~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~l~is~~~V~~~l~ra~~~l 170 (176)
T PRK09638 103 -----LR--KEKW-EAAIKGAEWSEMLDALSKLDPEFRAPVILKHY----YGYTYEEIAKMLNIPEGTVKSRVHHGIKQL 170 (176)
T ss_pred -----CC--ccch-HHHHHhhhHHHHHHHHHcCCHHHhheeeehhh----cCCCHHHHHHHHCCChhHHHHHHHHHHHHH
Confidence 00 0000 11122233456889999999999999999987 899999999999999999999999999999
Q ss_pred HHHhh
Q 008652 542 KQSLG 546 (558)
Q Consensus 542 R~~l~ 546 (558)
|+.+.
T Consensus 171 ~~~l~ 175 (176)
T PRK09638 171 RKEWG 175 (176)
T ss_pred HHHhc
Confidence 99773
No 68
>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=99.83 E-value=2.4e-19 Score=169.13 Aligned_cols=167 Identities=17% Similarity=0.208 Sum_probs=132.2
Q ss_pred CCHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008652 303 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 381 (558)
Q Consensus 303 ~~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a 381 (558)
|+++.++..+..| ..|++.++..|.+.|++++.++.++..+.+|++||+++.+|+++++|++. ..|.+|++..+++.
T Consensus 1 ~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~--~~~~~wl~~i~~n~ 78 (169)
T TIGR02954 1 MNDEELVKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHP--KYFNTWLTRILINE 78 (169)
T ss_pred CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCc--cccHHHHHHHHHHH
Confidence 3455666666555 49999999999999999999999999999999999999999999999975 36999999999999
Q ss_pred HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 008652 382 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 461 (558)
Q Consensus 382 I~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~ 461 (558)
+.+++++..+... ++.....+
T Consensus 79 ~~d~~R~~~~~~~-------------------------------------------------------~~~~~~~~---- 99 (169)
T TIGR02954 79 CIDLLKKKKKVIP-------------------------------------------------------FDPNTSIE---- 99 (169)
T ss_pred HHHHHHhcCCcCc-------------------------------------------------------cccccccc----
Confidence 9999876542100 00000000
Q ss_pred hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008652 462 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 541 (558)
Q Consensus 462 l~e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 541 (558)
+. .++ ... .....+..+|..||+++|+||.++|. +|+|.+|||+.||||..+|+..+.||+++|
T Consensus 100 ------~~---~~~--~~~-~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eiA~~lgis~~tv~~~l~Ra~~~L 163 (169)
T TIGR02954 100 ------KG---ECE--THA-DSRLDLYKAIDTLNDKYQTAIILRYY----HDLTIKEIAEVMNKPEGTVKTYLHRALKKL 163 (169)
T ss_pred ------cc---hhh--hch-HHHHHHHHHHHhCCHHHhHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 00 000 001 11236888999999999999999998 899999999999999999999999999999
Q ss_pred HHHhh
Q 008652 542 KQSLG 546 (558)
Q Consensus 542 R~~l~ 546 (558)
|+.+.
T Consensus 164 r~~l~ 168 (169)
T TIGR02954 164 KKRLE 168 (169)
T ss_pred HHHhc
Confidence 99874
No 69
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=99.83 E-value=2.1e-19 Score=173.86 Aligned_cols=177 Identities=11% Similarity=0.143 Sum_probs=134.5
Q ss_pred HHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHH
Q 008652 307 DLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA 385 (558)
Q Consensus 307 ~L~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~a 385 (558)
.++..+..| ..|++.|+..|.+.|+.+|.++.++..+++|++||+++.+|+.+++|++.++ .|.+|++..+++.+.++
T Consensus 16 ~li~~~~~~d~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn~~ld~ 94 (194)
T PRK12531 16 ECMEKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRNLCFDL 94 (194)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHHHHHHH
Confidence 355555555 4999999999999999999999999889999999999999999999997554 69999999999999999
Q ss_pred HHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhh
Q 008652 386 IFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEI 465 (558)
Q Consensus 386 Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~ 465 (558)
+++..+.... . ..+... .+.. ....
T Consensus 95 ~Rk~~~~~~~-------------------------~---------------------------~~~~~~-~~~~--~~~~ 119 (194)
T PRK12531 95 LRKQKGKDLH-------------------------I---------------------------HADDIW-PSDY--YPPD 119 (194)
T ss_pred HHHhcccccc-------------------------c---------------------------chhhcc-cccc--cccc
Confidence 9875421000 0 000000 0000 0000
Q ss_pred cccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008652 466 TADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 545 (558)
Q Consensus 466 i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 545 (558)
+. ....++.. ...+.+..++..||+++|+||.++|. +++|.+|||+.||||.++|+..+.||+++||..+
T Consensus 120 ~~--~~~~~e~~----~~~~~l~~~l~~Lp~~~r~v~~l~~~----eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 120 LV--DHYSPEQD----MLKEQVMKFLDRLPKAQRDVLQAVYL----EELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred cc--cccCHHHH----HHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 00 00122222 22356888999999999999999998 9999999999999999999999999999999998
Q ss_pred hcCc
Q 008652 546 GGKA 549 (558)
Q Consensus 546 ~~~~ 549 (558)
....
T Consensus 190 ~~~~ 193 (194)
T PRK12531 190 DAES 193 (194)
T ss_pred hhcc
Confidence 7654
No 70
>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=99.83 E-value=2e-19 Score=166.08 Aligned_cols=160 Identities=18% Similarity=0.183 Sum_probs=129.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccch
Q 008652 318 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 397 (558)
Q Consensus 318 Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~ 397 (558)
|++.|+..|.+.|+++++++.++..+.+|++||+++++|+++.+|++. .+|.+|++.++++.+.+++++..+...
T Consensus 2 a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~--~~~~~wl~~i~r~~~~d~~r~~~~~~~--- 76 (161)
T TIGR02985 2 AFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEV--ESFKAYLFTIVKNRSLNYLRHKQVEEK--- 76 (161)
T ss_pred hHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc--ccHHHHHHHHHHHHHHHHHHHHHhHhH---
Confidence 789999999999999999999998999999999999999999999874 479999999999999999876542100
Q ss_pred hHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHH
Q 008652 398 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 477 (558)
Q Consensus 398 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~ 477 (558)
.. ..+ . ++.. .......+++.
T Consensus 77 -----------~~-------------~~~------------------------~----~~~~-------~~~~~~~~~~~ 97 (161)
T TIGR02985 77 -----------YQ-------------EEI------------------------L----EIEV-------DELSENDPEEE 97 (161)
T ss_pred -----------HH-------------HHH------------------------H----hhcc-------cccCCCCcHHH
Confidence 00 000 0 0000 00011235555
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008652 478 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 545 (558)
Q Consensus 478 le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 545 (558)
+...+....|..++..||+++++||.++|. +++|..|||+.||+|+++|++++.+|+++||+.+
T Consensus 98 ~~~~e~~~~l~~~l~~L~~~~r~il~l~~~----~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~l 161 (161)
T TIGR02985 98 LEAKELQLIIYKAIEKLPEQCRKIFILSRF----EGKSYKEIAEELGISVKTVEYHISKALKELRKEL 161 (161)
T ss_pred HHHHHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 666677778999999999999999999987 8999999999999999999999999999999764
No 71
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=99.83 E-value=3e-19 Score=170.45 Aligned_cols=166 Identities=16% Similarity=0.180 Sum_probs=132.6
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008652 314 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 393 (558)
Q Consensus 314 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~I 393 (558)
++..|++.|+..|.+.|+.++++|.++..+.+|++||+++.+|+++.+|++.. .|.+|++..+++.+.+++++..+..
T Consensus 4 ~d~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~~~~~ 81 (179)
T PRK12543 4 GDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKRWRRF 81 (179)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhhcccc
Confidence 44589999999999999999999999999999999999999999999999874 5999999999998888776533110
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCC
Q 008652 394 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 473 (558)
Q Consensus 394 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~ 473 (558)
+ .++... + ..+ ......
T Consensus 82 ~------------------------------------------------------~~~~~~-~-----~~~---~~~~~~ 98 (179)
T PRK12543 82 R------------------------------------------------------IFEKAE-E-----QRK---PVSIDF 98 (179)
T ss_pred c------------------------------------------------------cccccc-c-----ccc---cccccC
Confidence 0 000000 0 000 001113
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008652 474 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 549 (558)
Q Consensus 474 pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 549 (558)
|+. +...+....|..+|..||+++|+||.++|. +++|++|||+.||||..+|+..+.||+++||+.+....
T Consensus 99 ~~~-~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~~----e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~ 169 (179)
T PRK12543 99 SED-VLSKESNQELIELIHKLPYKLRQVIILRYL----HDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIEE 169 (179)
T ss_pred hHH-HHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444 556666778999999999999999999998 99999999999999999999999999999999886543
No 72
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=99.82 E-value=4.5e-19 Score=167.65 Aligned_cols=165 Identities=14% Similarity=0.133 Sum_probs=131.0
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008652 314 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 393 (558)
Q Consensus 314 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~I 393 (558)
++..+++.|+..|.+.|+.+|.++.++..+.+|++||.|+.+|+..++|++.. ..|.+|++..+++.+.++++++.+..
T Consensus 6 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~Rk~~~~~ 84 (173)
T PRK09645 6 AEAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSARARP 84 (173)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHHHHHHHhhcccc
Confidence 35689999999999999999999999988999999999999999999997532 46999999999999999988654210
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCC
Q 008652 394 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 473 (558)
Q Consensus 394 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~ 473 (558)
.. ..+ +.. +. .+. .
T Consensus 85 ~~-----------------------------------------------------~~~------~~~---~~-~~~---~ 98 (173)
T PRK09645 85 VE-----------------------------------------------------GGD------DVL---GV-PEQ---S 98 (173)
T ss_pred cc-----------------------------------------------------ccc------ccc---cC-CCC---C
Confidence 00 000 000 00 000 1
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008652 474 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 549 (558)
Q Consensus 474 pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 549 (558)
+++.+........|..+|+.||+++|+||.|+|. +++|++|||+.||+|.++|+..+.||+++||+.+...+
T Consensus 99 ~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~ 170 (173)
T PRK09645 99 APDEVDRALDRLLVADALAQLSPEHRAVLVRSYY----RGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQERG 170 (173)
T ss_pred CchHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhccc
Confidence 1222333334457899999999999999999998 99999999999999999999999999999999987654
No 73
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=99.82 E-value=5.8e-19 Score=167.28 Aligned_cols=167 Identities=16% Similarity=0.181 Sum_probs=130.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccc
Q 008652 317 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 396 (558)
Q Consensus 317 ~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP 396 (558)
..++.|+..|.++|+.+|++|.++..+++|++||+++.+|+++++|++.. +|.+|++..+++.+.++++++.+....+
T Consensus 3 ~~~~~l~~~y~~~i~~~~~~~~~~~~daeDvvQe~~i~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~Rk~~~~~~~~ 80 (173)
T PRK12522 3 EKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE--NYKKWITTICVRTFYDFYRKKKRWKDRI 80 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcCCcc--chHHHHHHHHHHHHHHHHHHhccccccc
Confidence 45899999999999999999999999999999999999999999999854 7999999999999999998765321000
Q ss_pred hhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhH
Q 008652 397 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI 476 (558)
Q Consensus 397 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~ 476 (558)
.. ..+. + ...+.........++.
T Consensus 81 ~~--------------------------------------------------~~~~-----~--~~~~~~~~~~~~~~~~ 103 (173)
T PRK12522 81 LD--------------------------------------------------LFHK-----E--DGGEIEFADDVNISEE 103 (173)
T ss_pred cc--------------------------------------------------ccch-----h--hhhhhccccCCCChHH
Confidence 00 0000 0 0000000001112333
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008652 477 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 547 (558)
Q Consensus 477 ~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 547 (558)
....+..+.|..+|..||+++++||.++|. ++++++|||+.||+|.++|+..+.||+++||+.+..
T Consensus 104 -~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~ 169 (173)
T PRK12522 104 -FIQKVEAEMIREVIQLLNEKYKTVLVLYYY----EQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEG 169 (173)
T ss_pred -HHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 444556778999999999999999999998 899999999999999999999999999999998754
No 74
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=99.82 E-value=3.8e-19 Score=170.09 Aligned_cols=169 Identities=15% Similarity=0.128 Sum_probs=129.8
Q ss_pred HHHHHH-hhcHHHHHHHHHHHHHHHHHHHHHhhC-CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHH
Q 008652 307 DLKSEL-HSGNSSREKLINANLRLVVHVAKQYQG-RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK 384 (558)
Q Consensus 307 ~L~~~l-~~G~~Are~LI~~nlrLV~sIArrY~~-~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~ 384 (558)
.++... .++..|++.|+..|.+.|+.++.++.+ ...+.+|++||+++.||+.++.|++. ..|.+|++..+++.+.+
T Consensus 10 ~~~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~~~d 87 (181)
T PRK12536 10 ALLLRGLAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYKLMD 87 (181)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHHHHH
Confidence 344444 455699999999999999999998764 57899999999999999999999975 46999999999999999
Q ss_pred HHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhh
Q 008652 385 AIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQE 464 (558)
Q Consensus 385 aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e 464 (558)
+++++.+.... ..+++ + ..+
T Consensus 88 ~~Rk~~~~~~~---------------------------------------------------~~~~~----~-----~~~ 107 (181)
T PRK12536 88 FLRSRARREAL---------------------------------------------------HDPLD----D-----ESE 107 (181)
T ss_pred HHHHHhccccc---------------------------------------------------cCCcc----c-----hhh
Confidence 99875421000 00000 0 000
Q ss_pred hcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008652 465 ITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 544 (558)
Q Consensus 465 ~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 544 (558)
...+. .++. .+....+.++|..||++++.||.++|. +++|.+|||+.||+|.++|+..+++|+++||+.
T Consensus 108 ~~~~~---~~~~----~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 108 LFATS---DDEA----AEARRDLGKLLEQLPDRQRLPIVHVKL----EGLSVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred hcCCC---Ccch----HHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 00011 1111 123446889999999999999999998 899999999999999999999999999999998
Q ss_pred hhcC
Q 008652 545 LGGK 548 (558)
Q Consensus 545 l~~~ 548 (558)
+...
T Consensus 177 l~~~ 180 (181)
T PRK12536 177 IRGE 180 (181)
T ss_pred hcCC
Confidence 8653
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=99.82 E-value=5.2e-19 Score=164.40 Aligned_cols=158 Identities=18% Similarity=0.217 Sum_probs=125.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccch
Q 008652 318 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 397 (558)
Q Consensus 318 Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~ 397 (558)
|++.++..|.+.|+.+|+++.++..+.+|++||+++.+|+++++|++.. .|.+|++..+++.+.++++++.+.-.. .
T Consensus 2 ~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~~-~ 78 (159)
T TIGR02989 2 AFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRLV-F 78 (159)
T ss_pred HHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhcccccc-c
Confidence 7899999999999999999999999999999999999999999999764 599999999999999999876532100 0
Q ss_pred hHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHH
Q 008652 398 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 477 (558)
Q Consensus 398 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~ 477 (558)
.++. .+.+.+. . .+...
T Consensus 79 -------------------------~~~~------------------------------------~~~~~~~-~-~~~~~ 95 (159)
T TIGR02989 79 -------------------------DDEL------------------------------------LEALAAE-A-EATEA 95 (159)
T ss_pred -------------------------CHHH------------------------------------HHHHHhh-c-ccchH
Confidence 0000 0000000 0 11111
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008652 478 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 545 (558)
Q Consensus 478 le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 545 (558)
.........|..+++.||++++.||.++|. +|++.+|||+.||||.++|+..++||+++||+++
T Consensus 96 ~~~~~~~~~l~~~i~~L~~~~r~v~~l~~~----~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~~~ 159 (159)
T TIGR02989 96 DRSEDELQALEGCLEKLPERQRELLQLRYQ----RGVSLTALAEQLGRTVNAVYKALSRLRVRLRDCV 159 (159)
T ss_pred hhHHHHHHHHHHHHHHCCHHHHHHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcC
Confidence 222334467889999999999999999998 8999999999999999999999999999999753
No 76
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=99.82 E-value=6.6e-19 Score=169.63 Aligned_cols=182 Identities=16% Similarity=0.163 Sum_probs=136.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccch
Q 008652 318 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 397 (558)
Q Consensus 318 Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~ 397 (558)
+++.|+..|.+.|+.+|.++.++..+.+|++||.++.+|+.+++|++. .+|.+|++..+++.+.++++++.+....+.
T Consensus 3 ~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~--~~~~~WL~~ia~n~~~d~~Rk~~r~~~~~~ 80 (191)
T PRK12520 3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQ--SSLKTYLVGILKHKIIDAIRSGRREVRLSL 80 (191)
T ss_pred chHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--ccHHHHHHHHHHHHHHHHHHhhcCcCcccc
Confidence 689999999999999999999999999999999999999999999865 369999999999999999987653211100
Q ss_pred hHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHH
Q 008652 398 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 477 (558)
Q Consensus 398 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~ 477 (558)
.. .......++ ++... . .+ ......++ ....|+..
T Consensus 81 ~~------------------~~~~~~~~~-----------------------~~~~~-~-~~-~~~~~~~~-~~~~~~~~ 115 (191)
T PRK12520 81 DD------------------ADEQSDDDL-----------------------FDALF-A-AD-GHYREPPS-DWGDPDAA 115 (191)
T ss_pred cc------------------cccchhhhh-----------------------hhhhc-c-cc-cccccCcc-ccCCHHHH
Confidence 00 000000000 00000 0 00 00000111 12356666
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008652 478 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 550 (558)
Q Consensus 478 le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L 550 (558)
+...+....|..+|..||+++|+||.|+|. +++|++|||+.||+|.++|++.+.||+++||+++...+.
T Consensus 116 ~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~ 184 (191)
T PRK12520 116 LSRREFFEVLQACVDRLPPRTGRVFMMREW----LELETEEICQELQITATNAWVLLYRARMRLRECLDLHWF 184 (191)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 777777788999999999999999999998 899999999999999999999999999999999987663
No 77
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=99.81 E-value=1.1e-18 Score=175.81 Aligned_cols=179 Identities=16% Similarity=0.204 Sum_probs=140.3
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHH-------hhhhcCCCCCCchhHHH
Q 008652 303 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMK-------SVEKFKPQAGCRFASYA 374 (558)
Q Consensus 303 ~~~~~L~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLir-------AiekFDp~kG~rFSTYA 374 (558)
.++..|+..++.|+ .|++.|+..|.+.|+.+++++.++..+.+|++||+|+.+|. .+.+|++. ..|.||.
T Consensus 24 ~~d~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~--~~~~tWL 101 (244)
T TIGR03001 24 AADLYLACACAQGEPAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGR--GPLLSWV 101 (244)
T ss_pred ccHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCC--CchHhHH
Confidence 46677888877766 99999999999999999999999999999999999999994 78889864 3699999
Q ss_pred HHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCC
Q 008652 375 YWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPV 454 (558)
Q Consensus 375 ~~wIr~aI~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i 454 (558)
+..++|.+.++++++.+...+ +.
T Consensus 102 ~~Ia~N~~id~lRk~~r~~~~-------------------------------------------------------~~-- 124 (244)
T TIGR03001 102 RIVATRIALELQAQERRHSPV-------------------------------------------------------EE-- 124 (244)
T ss_pred HHHHHHHHHHHHHHhcccCcc-------------------------------------------------------cc--
Confidence 999999999998764421100 00
Q ss_pred CCCCCcchhhhcccCCCCChhHHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHH
Q 008652 455 WADQDTTFQEITADTGVEIPDISVQK----QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERV 530 (558)
Q Consensus 455 ~~d~~~~l~e~i~d~~~~~pe~~le~----~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerV 530 (558)
+ + ...+. .+. ...|++.+.. .+..+.|..+|+.||+++|+||.|+|. +++|++|||++||||.++|
T Consensus 125 --~-~-~~~~~-~~~-~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~----eg~S~~EIA~~Lgis~~TV 194 (244)
T TIGR03001 125 --P-T-ELAAL-PAP-GSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHFV----DGLSMDRIGAMYQVHRSTV 194 (244)
T ss_pred --c-c-ccccc-cCC-CCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHH
Confidence 0 0 00000 011 1133333332 235567999999999999999999998 9999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhcCch
Q 008652 531 RQLESRALYRLKQSLGGKAS 550 (558)
Q Consensus 531 Rqie~RALkKLR~~l~~~~L 550 (558)
+..+.||+++||+.+.+...
T Consensus 195 k~rl~RAr~~Lr~~l~~~~~ 214 (244)
T TIGR03001 195 SRWVAQARERLLERTRRRLA 214 (244)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999876543
No 78
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=99.81 E-value=9.1e-19 Score=167.32 Aligned_cols=164 Identities=16% Similarity=0.180 Sum_probs=133.5
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccc
Q 008652 315 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 394 (558)
Q Consensus 315 G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IR 394 (558)
+..|++.|+..|.+.|++++.++.++..+.+|++||+++.+|+++++|++. ..|.+|++..+++.+.+++++..+-..
T Consensus 14 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~--~~~~awl~~ia~n~~~d~~Rk~~~~~~ 91 (179)
T PRK09415 14 KEDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGK--SSLKTWLYRIAINHCKDYLKSWHNKKV 91 (179)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--cccHHHHHHHHHHHHHHHHHhhccccc
Confidence 358999999999999999999999999999999999999999999999874 369999999999999999876432100
Q ss_pred cchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCCh
Q 008652 395 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP 474 (558)
Q Consensus 395 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~p 474 (558)
. ..+. ...... ....++
T Consensus 92 ~-----------------------------------------------------~~~~--------~~~~~~--~~~~~~ 108 (179)
T PRK09415 92 I-----------------------------------------------------VTED--------IFTYME--SQKESV 108 (179)
T ss_pred c-----------------------------------------------------cccc--------cccccc--ccccCc
Confidence 0 0000 000000 011245
Q ss_pred hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008652 475 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 547 (558)
Q Consensus 475 e~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 547 (558)
++.+...+....|..+|..||+++|+||.++|. +|+|++|||+.||||.++|++.+.||+++||+.+..
T Consensus 109 e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l~~ 177 (179)
T PRK09415 109 EEEVIQNAEDERLASAVMSLPIKYREVIYLFYY----EELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEE 177 (179)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 556666667778999999999999999999998 899999999999999999999999999999998764
No 79
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=1.2e-18 Score=167.15 Aligned_cols=169 Identities=17% Similarity=0.185 Sum_probs=130.1
Q ss_pred HHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHH----HhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHH
Q 008652 305 CRDLKSELHSG-NSSREKLINANLRLVVHVAK----QYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR 379 (558)
Q Consensus 305 ~~~L~~~l~~G-~~Are~LI~~nlrLV~sIAr----rY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr 379 (558)
...|+.....| ..|++.|+..|.+.|+.+|+ ++.++..+.+|++||+++.+|++++.|++.. .|.+|++..++
T Consensus 8 ~~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~~ 85 (184)
T PRK12539 8 LKALMLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIAR 85 (184)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHHH
Confidence 34455555545 59999999999999999987 4557788999999999999999999999753 59999999999
Q ss_pred HHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCC
Q 008652 380 QTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD 459 (558)
Q Consensus 380 ~aI~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~ 459 (558)
+.+.+++++..+.. . ....+. ..
T Consensus 86 n~~~d~~R~~~~~~-~---------------------------------------------------~~~~~~-----~~ 108 (184)
T PRK12539 86 YKLIDHLRRTRASL-A---------------------------------------------------DVPIDD-----AD 108 (184)
T ss_pred HHHHHHHHHHhccc-c---------------------------------------------------ccChhh-----hc
Confidence 99999987643210 0 000000 00
Q ss_pred cchhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008652 460 TTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 539 (558)
Q Consensus 460 ~~l~e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 539 (558)
... +.......+....|..++..||+++|+||.++|. +|+|++|||+.||+|..+|+..+.||++
T Consensus 109 ----~~~-------~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~ra~~ 173 (184)
T PRK12539 109 ----ELV-------AHDDHAAVESTLDLGRLLARLPEKMRLAIQAVKL----EGLSVAEAATRSGMSESAVKVSVHRGLK 173 (184)
T ss_pred ----ccc-------CCcHHhhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 000 0001112233457899999999999999999998 8999999999999999999999999999
Q ss_pred HHHHHhhc
Q 008652 540 RLKQSLGG 547 (558)
Q Consensus 540 KLR~~l~~ 547 (558)
+||+.+..
T Consensus 174 ~Lr~~l~~ 181 (184)
T PRK12539 174 ALAALIGR 181 (184)
T ss_pred HHHHHHhh
Confidence 99998864
No 80
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=99.81 E-value=1.2e-18 Score=166.08 Aligned_cols=171 Identities=19% Similarity=0.265 Sum_probs=125.3
Q ss_pred HHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCC-----CHHHHHHHHHHHHHH-hhhhcCCCCCCchhHHHHHHH
Q 008652 306 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGI-----SLHDLLQEGSMGLMK-SVEKFKPQAGCRFASYAYWWV 378 (558)
Q Consensus 306 ~~L~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g~-----~~eDLIQEG~IGLir-AiekFDp~kG~rFSTYA~~wI 378 (558)
+.|+..+..|+ .|++.|+..|.+.|+.+|++|.++.. +.+|++||+|+.+|+ ...+|++. ..|.+|++.++
T Consensus 5 ~~li~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~i~ 82 (183)
T TIGR02999 5 TELLQQWQNGDAAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAKAM 82 (183)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHHHH
Confidence 44555555554 89999999999999999999998877 899999999999998 78889754 36999999999
Q ss_pred HHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCC
Q 008652 379 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQ 458 (558)
Q Consensus 379 r~aI~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~ 458 (558)
++.+.++++++.+..+. . . ..+..
T Consensus 83 ~n~~~d~~R~~~~~~~~----------------------~---------------------------~--~~~~~----- 106 (183)
T TIGR02999 83 RRILVDHARRRRAQKRG----------------------G---------------------------G--AVRVP----- 106 (183)
T ss_pred HHHHHHHHHHHHHHhcc----------------------C---------------------------C--ccccc-----
Confidence 99999998764311000 0 0 00000
Q ss_pred CcchhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008652 459 DTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 538 (558)
Q Consensus 459 ~~~l~e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RAL 538 (558)
+.+..++. .++.. +.....+.+...|+.||+++|+||.|+|. +|+|++|||+.||||.++|+.++.||+
T Consensus 107 ---~~~~~~~~---~~~~~-~~~~~l~~~~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar 175 (183)
T TIGR02999 107 ---LDEVLPDA---EADLD-EELLDLDDALDKLAQVDPRQAEVVELRFF----AGLTVEEIAELLGVSVRTVERDWRFAR 175 (183)
T ss_pred ---cccccCCC---CccHH-HHHHHHHHHHHHhhcCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 00000000 11111 11111123444567799999999999998 999999999999999999999999999
Q ss_pred HHHHHHh
Q 008652 539 YRLKQSL 545 (558)
Q Consensus 539 kKLR~~l 545 (558)
++||+.+
T Consensus 176 ~~Lr~~l 182 (183)
T TIGR02999 176 AWLADEL 182 (183)
T ss_pred HHHHHHh
Confidence 9999876
No 81
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=2.2e-18 Score=164.74 Aligned_cols=166 Identities=19% Similarity=0.241 Sum_probs=128.4
Q ss_pred HHHHHh-hcHHHHHHHHHHHHHHHHHHHHHhhCC----CCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHH
Q 008652 308 LKSELH-SGNSSREKLINANLRLVVHVAKQYQGR----GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 382 (558)
Q Consensus 308 L~~~l~-~G~~Are~LI~~nlrLV~sIArrY~~~----g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI 382 (558)
++..+. ++..|++.|+..|.+.|+.+|++++++ ..+++|++||+++.+|...++|+.. ..|.+|++..+++.+
T Consensus 12 l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn~~ 89 (184)
T PRK12512 12 LMRSANAGDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARNKL 89 (184)
T ss_pred HHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHHHH
Confidence 344444 456999999999999999999998753 3689999999999999999999874 479999999999999
Q ss_pred HHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 008652 383 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 462 (558)
Q Consensus 383 ~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l 462 (558)
.++++++.+...+ .++. +
T Consensus 90 ~d~~Rr~~~~~~~-----------------------------------------------------~~~~---------~ 107 (184)
T PRK12512 90 IDALRRRGRRVFV-----------------------------------------------------DIDD---------F 107 (184)
T ss_pred HHHHHhhcccccC-----------------------------------------------------Cchh---------c
Confidence 9998765421110 0000 0
Q ss_pred hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 463 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 463 ~e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
.+.+++.. +.. ......+..+|+.||+++|+||.++|. +++|++|||+.||+|..+|+..+.||+++||
T Consensus 108 ~~~~~~~~---~~~----~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr 176 (184)
T PRK12512 108 AETLPAEP---ATE----TLPAGDVGRHLETLPPRQRDVVQSISV----EGASIKETAAKLSMSEGAVRVALHRGLAALA 176 (184)
T ss_pred cccccccc---hhh----HHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 00001100 001 112346788999999999999999998 8999999999999999999999999999999
Q ss_pred HHhhcC
Q 008652 543 QSLGGK 548 (558)
Q Consensus 543 ~~l~~~ 548 (558)
..+.+.
T Consensus 177 ~~l~~~ 182 (184)
T PRK12512 177 AKFRSE 182 (184)
T ss_pred HHhhcC
Confidence 998764
No 82
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=1.7e-18 Score=163.75 Aligned_cols=166 Identities=17% Similarity=0.146 Sum_probs=127.4
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008652 313 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 392 (558)
Q Consensus 313 ~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~ 392 (558)
.++..|++.|+..|.+.|+.+++++.+ ..+.+|++||+++.+|+.++.|++. ..|.+|++..+++.+.+++++..+.
T Consensus 7 ~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~~~~ 83 (175)
T PRK12518 7 RGDRQSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARRQFAQR 83 (175)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHHHhhcc
Confidence 345699999999999999999999875 3689999999999999999999974 4699999999999999998754311
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCC
Q 008652 393 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE 472 (558)
Q Consensus 393 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~ 472 (558)
-.. .+... .... . ...
T Consensus 84 ~~~------------------------------------------------------~~~~~-~~~~-----~-~~~--- 99 (175)
T PRK12518 84 PSR------------------------------------------------------IQDDS-LNDQ-----P-SRP--- 99 (175)
T ss_pred ccc------------------------------------------------------hhccc-cccc-----c-cCC---
Confidence 000 00000 0000 0 000
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008652 473 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 549 (558)
Q Consensus 473 ~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 549 (558)
.++......+....+..+|+.||+++|+||.++|+ +|+|++|||+.||+|..+|++.+.||+++||+.+...+
T Consensus 100 ~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~~~~ 172 (175)
T PRK12518 100 SDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHDL----EDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQQG 172 (175)
T ss_pred CCcHHHHHHHHHHHHHHHHHhCCHHHeeeeeehHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 11111222233456889999999999999999998 89999999999999999999999999999999987654
No 83
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=3.3e-18 Score=169.37 Aligned_cols=172 Identities=18% Similarity=0.162 Sum_probs=136.4
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008652 313 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 392 (558)
Q Consensus 313 ~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~ 392 (558)
.....+++.|+..|.+.++.++.++.++..+.+|++||+|+.+|+.+++|++. .|.+|++..+++.+.++++++.+.
T Consensus 14 ~~~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~~~~ 90 (216)
T PRK12533 14 AARGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRRANA 90 (216)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhhccc
Confidence 34568999999999999999999999999999999999999999999999853 499999999999999998775421
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCC
Q 008652 393 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE 472 (558)
Q Consensus 393 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~ 472 (558)
... . ....... ...... . ++...
T Consensus 91 ~~~----------------------------------------------------~-~~~~~~~--~~~~~~-~-~~~~~ 113 (216)
T PRK12533 91 HEV----------------------------------------------------A-APDTLDD--ADSLDD-W-QPAGE 113 (216)
T ss_pred ccc----------------------------------------------------c-ccccccc--cccccc-c-ccCCC
Confidence 000 0 0000000 000000 0 11123
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008652 473 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 548 (558)
Q Consensus 473 ~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 548 (558)
+|++.+...+....|..+|..||+++|+||.|+|. +++|++|||+.||||.++|+++++||+++||+.+...
T Consensus 114 ~~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~----eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~ 185 (216)
T PRK12533 114 DPLALLLRAEDVRLVNAALAKLPVEYREVLVLREL----EDMSYREIAAIADVPVGTVMSRLARARRRLAALLGGA 185 (216)
T ss_pred CHHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHccc
Confidence 56667777777788999999999999999999998 8999999999999999999999999999999998653
No 84
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=99.80 E-value=4.1e-18 Score=163.20 Aligned_cols=171 Identities=19% Similarity=0.276 Sum_probs=136.0
Q ss_pred HHhhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcc
Q 008652 311 ELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS 390 (558)
Q Consensus 311 ~l~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~s 390 (558)
...++..++..++..+.+.++.+++++.++..+.+||+||+++.+|+++..| .. +..|.||++.+++|.+.+++++..
T Consensus 9 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~~R~~~ 86 (182)
T COG1595 9 ALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDRLRKRK 86 (182)
T ss_pred HHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHHHHHHhc
Confidence 3455669999999999999999999999998899999999999999999999 33 347999999999999999998766
Q ss_pred cccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCC
Q 008652 391 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTG 470 (558)
Q Consensus 391 r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~ 470 (558)
+.... .+. .+ ......+..
T Consensus 87 r~~~~------------------------------------------------------~~~----~~---~~~~~~~~~ 105 (182)
T COG1595 87 RRRAR------------------------------------------------------VEE----AD---LLPEEADPA 105 (182)
T ss_pred ccccc------------------------------------------------------ccc----cc---ccccccCcc
Confidence 43211 000 00 000000000
Q ss_pred CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008652 471 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 549 (558)
Q Consensus 471 ~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 549 (558)
.... +.+...+....|..+|..||+++|+||.|+|+ +|+|++|||+.||||.++|+..+.+|+++||+.+...+
T Consensus 106 ~~~~-~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~----~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~~~~ 179 (182)
T COG1595 106 PDLA-ELLLAEEELERLRRALARLPPRQREAFLLRYL----EGLSYEEIAEILGISVGTVKSRLHRARKKLREQLEEAG 179 (182)
T ss_pred cccc-hHHHHHHHHHHHHHHHHhCCHHHhHHhhhHhh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhcc
Confidence 0001 24555667778999999999999999999998 99999999999999999999999999999999887543
No 85
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=2.4e-18 Score=164.38 Aligned_cols=166 Identities=9% Similarity=0.023 Sum_probs=129.7
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHHhhC--CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcc
Q 008652 313 HSGNSSREKLINANLRLVVHVAKQYQG--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS 390 (558)
Q Consensus 313 ~~G~~Are~LI~~nlrLV~sIArrY~~--~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~s 390 (558)
.++..+++.|+..|.+.|+.++.++.+ +..+++|++||.|+.+|+..++|++.....|.||++..+++.+.++++++.
T Consensus 9 ~~d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~Rk~~ 88 (178)
T PRK12529 9 SADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRRRQS 88 (178)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHHHHH
Confidence 355699999999999999998766665 357899999999999999999998544457999999999999999886532
Q ss_pred cccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCC
Q 008652 391 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTG 470 (558)
Q Consensus 391 r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~ 470 (558)
+.. .. .+. ..+. .+..
T Consensus 89 ~~~-----------------~~-------------------------------------~~~---------~~~~-~~~~ 104 (178)
T PRK12529 89 LEL-----------------AW-------------------------------------LEA---------LATL-PEPL 104 (178)
T ss_pred HHh-----------------hh-------------------------------------hhH---------hhhc-cCcC
Confidence 100 00 000 0000 0011
Q ss_pred CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008652 471 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 546 (558)
Q Consensus 471 ~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 546 (558)
..+|++.+...+....|..+|..||+++|.||.|+|. +|+|++|||+.||+|.++|+.++.||+.+|++.+.
T Consensus 105 ~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~~~ 176 (178)
T PRK12529 105 HPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATL----DGMKQKDIAQALDIALPTVKKYIHQAYVTCLSLMP 176 (178)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhCC
Confidence 1245555555566678999999999999999999998 99999999999999999999999999999998754
No 86
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=99.80 E-value=2e-18 Score=166.10 Aligned_cols=169 Identities=17% Similarity=0.123 Sum_probs=128.6
Q ss_pred HHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHH
Q 008652 307 DLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA 385 (558)
Q Consensus 307 ~L~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~a 385 (558)
.|+..+..| ..|++.|+..|.+.++.+++ +.++..+.+|++||.|+.+|+.+++|++. ..|.+|++..+++.+.++
T Consensus 13 ~l~~~~~~gd~~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~~~d~ 89 (185)
T PRK09649 13 ALALSAAKGNGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVADH 89 (185)
T ss_pred HHHHHHHccCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHHHHHH
Confidence 455555444 59999999999999999995 67888899999999999999999999964 369999999999999999
Q ss_pred HHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhh
Q 008652 386 IFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEI 465 (558)
Q Consensus 386 Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~ 465 (558)
++++.+..+. +.+. . .+.
T Consensus 90 ~Rk~~~~~~~-----------------------------------------------------~~~~-----~----~~~ 107 (185)
T PRK09649 90 IRHVRSRPRT-----------------------------------------------------TRGA-----R----PEH 107 (185)
T ss_pred HHHhcccccc-----------------------------------------------------cccc-----c----hhh
Confidence 9864421100 0000 0 000
Q ss_pred cccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008652 466 TADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 545 (558)
Q Consensus 466 i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 545 (558)
..+. +......+....|..+|..||+++|+||.|+|. +++|++|||+.||+|.++|++.+.||+++||+.+
T Consensus 108 ~~~~-----~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~~ 178 (185)
T PRK09649 108 LIDG-----DRHARGFEDLVEVTTMIADLTTDQREALLLTQL----LGLSYADAAAVCGCPVGTIRSRVARARDALLADA 178 (185)
T ss_pred ccCh-----hhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 0000 000011112235788999999999999999998 9999999999999999999999999999999976
Q ss_pred hcCc
Q 008652 546 GGKA 549 (558)
Q Consensus 546 ~~~~ 549 (558)
....
T Consensus 179 ~~~~ 182 (185)
T PRK09649 179 EPDD 182 (185)
T ss_pred Cccc
Confidence 5544
No 87
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=99.80 E-value=1.7e-18 Score=161.72 Aligned_cols=157 Identities=13% Similarity=0.039 Sum_probs=125.7
Q ss_pred HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHH
Q 008652 324 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL 403 (558)
Q Consensus 324 ~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~~~l 403 (558)
+.|.+.|+.+|.++.++..+.+|++||+|+.+|+++++|++. .|.+|++..+++.+.++++++.+..+.
T Consensus 2 ~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n~~~d~~Rk~~~~~~~-------- 70 (160)
T PRK09642 2 QTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATNHAIDYKRKKARENEE-------- 70 (160)
T ss_pred chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHHHHHHHHHHhcccccc--------
Confidence 578999999999999999999999999999999999999963 499999999999999999865421000
Q ss_pred HHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHH
Q 008652 404 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 483 (558)
Q Consensus 404 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~le~~~~ 483 (558)
..+. . . ..+... ....+++.+...+.
T Consensus 71 --------------------------------------------~~~~----~-~---~~~~~~--~~~~~~~~~~~~e~ 96 (160)
T PRK09642 71 --------------------------------------------LSLC----K-E---TEENIK--SSHNIEDLLLTKEQ 96 (160)
T ss_pred --------------------------------------------cccc----h-h---hhhhcc--CCCChHHHHHHHHH
Confidence 0000 0 0 000000 11234555666667
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008652 484 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 549 (558)
Q Consensus 484 ~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 549 (558)
...|..+|+.||+++|+||.|+|. +|+|++|||+.||+|.++|+.++.||+++||+.+...+
T Consensus 97 ~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 158 (160)
T PRK09642 97 KLLIAQKLRELPENYRDVVLAHYL----EEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKEEE 158 (160)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhhc
Confidence 778999999999999999999998 99999999999999999999999999999999986544
No 88
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=99.79 E-value=3.6e-18 Score=164.94 Aligned_cols=162 Identities=20% Similarity=0.191 Sum_probs=128.5
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008652 314 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 393 (558)
Q Consensus 314 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~I 393 (558)
++..+++.|+..|.+.++.+|.++.++..+.+|++||.++.+|+..++|+.. ..|.+|++..+++.+.++++++.+..
T Consensus 7 ~~~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~awL~~Ia~n~~~d~~R~~~~~~ 84 (187)
T PRK12516 7 EGTPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVG--TNMKAWLFTILRNEFYSQMRKRGREV 84 (187)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCc--ccHHHHHHHHHHHHHHHHHHhhcCCc
Confidence 3468999999999999999999999999999999999999999999999865 35999999999999999987754210
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCC
Q 008652 394 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 473 (558)
Q Consensus 394 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~ 473 (558)
.. .+.. +.+.... .
T Consensus 85 ~~------------------------------------------------------~~~~--------~~~~~~~----~ 98 (187)
T PRK12516 85 QD------------------------------------------------------TDGM--------FTEQLAV----H 98 (187)
T ss_pred cc------------------------------------------------------cccc--------cccccCC----C
Confidence 00 0000 0000000 0
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008652 474 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 549 (558)
Q Consensus 474 pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 549 (558)
++. ........|..+|..||+++|+||.|+|. +++|++|||+.||||.++|+.++.||+++||+.+...+
T Consensus 99 ~~~--~~~~~~~~l~~~L~~Lp~~~r~i~~L~~~----~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~~~ 168 (187)
T PRK12516 99 PSQ--YGTLDLQDFRAALDQLPDDQREAIILVGA----SGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQIEG 168 (187)
T ss_pred cch--hhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence 110 11112346889999999999999999998 99999999999999999999999999999999997654
No 89
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=99.79 E-value=4.4e-18 Score=160.07 Aligned_cols=158 Identities=15% Similarity=0.107 Sum_probs=129.8
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchh
Q 008652 319 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 398 (558)
Q Consensus 319 re~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~ 398 (558)
++.|+..|.+.|+.+|+++.++..+.+|++||+++.+|+++++|++. .|.+|++..+++.+.+++++..+....
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~--- 76 (165)
T PRK09644 3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFV--- 76 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhcccc---
Confidence 57899999999999999999999999999999999999999999863 599999999999999999875421100
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHH
Q 008652 399 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV 478 (558)
Q Consensus 399 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~l 478 (558)
..+++ +.+. ...+++.+
T Consensus 77 -----------------------~~~~~-------------------------------------~~~~---~~~~~~~~ 93 (165)
T PRK09644 77 -----------------------GTDEI-------------------------------------EAIQ---AESTEEYV 93 (165)
T ss_pred -----------------------chhHH-------------------------------------hhhc---ccChHHHH
Confidence 00000 0000 01345555
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008652 479 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 549 (558)
Q Consensus 479 e~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 549 (558)
...+....|..+|..||+++|+||.++|. +++|++|||+.||+|.++|+..+.||+++||+.+...+
T Consensus 94 ~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~~ 160 (165)
T PRK09644 94 VAKNSYEKLIQIIHTLPVIEAQAILLCDV----HELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEEK 160 (165)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHhHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Confidence 55566678999999999999999999998 89999999999999999999999999999999987543
No 90
>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=99.79 E-value=1.9e-18 Score=166.66 Aligned_cols=172 Identities=19% Similarity=0.208 Sum_probs=130.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccccc
Q 008652 316 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 395 (558)
Q Consensus 316 ~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRl 395 (558)
..+++.|+..|.+.|+.+|.++.++..+.+|++||+|+.+|+++.+|++. ..|.+|++..+++.+.++++++.+....
T Consensus 10 ~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~~~~~~~ 87 (193)
T TIGR02947 10 AQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKAQRRPQQ 87 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHhcCCccc
Confidence 48999999999999999999999998999999999999999999999864 4699999999999999999875531100
Q ss_pred chhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChh
Q 008652 396 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD 475 (558)
Q Consensus 396 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe 475 (558)
. ..+++. .. .+.. .... .......++
T Consensus 88 ~-------------------------~~~~~~-----------~~--------~~~~---~~~~-------~~~~~~~~e 113 (193)
T TIGR02947 88 S-------------------------DDDDIE-----------DW--------QLAK---AASH-------TSNGLRSAE 113 (193)
T ss_pred c-------------------------cchhhh-----------hh--------hhcc---cccc-------ccccccchh
Confidence 0 000000 00 0000 0000 000011233
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008652 476 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 547 (558)
Q Consensus 476 ~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 547 (558)
...........|..+|+.||+++|+||.|+|. +++|++|||+.||||.++|+.++.||+++||+.+..
T Consensus 114 ~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 181 (193)
T TIGR02947 114 LEALDGLPDQDIKDALQGLPEEFRQAVYLADV----EGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVD 181 (193)
T ss_pred HHHHhhhhHHHHHHHHHhCCHHHhhheeehhh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 33333344567899999999999999999998 999999999999999999999999999999998864
No 91
>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=99.79 E-value=4.2e-18 Score=159.17 Aligned_cols=158 Identities=18% Similarity=0.200 Sum_probs=127.3
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008652 314 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 393 (558)
Q Consensus 314 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~I 393 (558)
++..+++.|+..|.+.|+.+|.++.++..+.+|++||+++.+|++.++|+. ...|.+|++..+++.+.+++++..+.
T Consensus 3 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~~~d~~rk~~~~- 79 (162)
T TIGR02983 3 ATEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNLARSRWRRRRLL- 79 (162)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHHHHHHHHhhccc-
Confidence 566999999999999999999999999999999999999999999999964 34799999999999999988764420
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCC
Q 008652 394 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 473 (558)
Q Consensus 394 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~ 473 (558)
.+ .+... .+ ..
T Consensus 80 ~~------------------------------------------------------~~~~~--------~~----~~--- 90 (162)
T TIGR02983 80 EL------------------------------------------------------PTREL--------PD----AA--- 90 (162)
T ss_pred cc------------------------------------------------------ccccc--------Cc----cc---
Confidence 00 00000 00 00
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008652 474 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 547 (558)
Q Consensus 474 pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 547 (558)
+..........+.|..+|..||+++|+||.|+|. +++|.+|||+.||+|.++|++.+.||+++||+.+..
T Consensus 91 ~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 160 (162)
T TIGR02983 91 APDPAPDVALRAALARALRRLPARQRAVVVLRYY----EDLSEAQVAEALGISVGTVKSRLSRALARLRELLEE 160 (162)
T ss_pred CCccchhHHHHHHHHHHHHhCCHHHHHHhhhHHH----hcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 0001122334557889999999999999999997 899999999999999999999999999999998754
No 92
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=99.79 E-value=9.2e-18 Score=164.40 Aligned_cols=166 Identities=20% Similarity=0.290 Sum_probs=135.6
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccc
Q 008652 315 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 394 (558)
Q Consensus 315 G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IR 394 (558)
+..+++.|+..|.+.++.++.++.++..+.+|++||+++.+|++..+|++ + .|.+|++..+++.+.+++++..+ .+
T Consensus 26 d~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~~-~~ 101 (203)
T PRK09647 26 TMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRAR-IR 101 (203)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhccc-Cc
Confidence 35899999999999999999999999999999999999999999999985 3 69999999999999999987542 00
Q ss_pred cchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCCh
Q 008652 395 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP 474 (558)
Q Consensus 395 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~p 474 (558)
. ..++ ++ + +... ....+|
T Consensus 102 ~----------------------------------------------------~~~~------~~--~-~~~~-~~~~~~ 119 (203)
T PRK09647 102 M----------------------------------------------------EALP------ED--Y-DRVP-GDEPNP 119 (203)
T ss_pred c----------------------------------------------------cccc------cc--c-cccC-CCCCCH
Confidence 0 0000 00 0 0001 112245
Q ss_pred hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008652 475 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 550 (558)
Q Consensus 475 e~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L 550 (558)
+..+...+....|..+|..||+++++||.|+|+ ++++++|||+.||||..+|++.+.||+++||+.+...+-
T Consensus 120 ~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~~----~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~~~~ 191 (203)
T PRK09647 120 EQIYHDARLDPDLQAALDSLPPEFRAAVVLCDI----EGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAAHAP 191 (203)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhch
Confidence 556666777778999999999999999999998 999999999999999999999999999999999876543
No 93
>TIGR02895 spore_sigI RNA polymerase sigma-I factor. Members of this sigma factor protein family are strictly limited to endospore-forming species in the Firmicutes lineage of bacteria, but are not universally present among such species. Sigma-I was shown to be induced by heat shock (PubMed:11157964) in Bacillus subtilis and is suggested by its phylogenetic profile to be connected to the program of sporulation (PubMed:16311624).
Probab=99.78 E-value=6.8e-18 Score=167.34 Aligned_cols=118 Identities=18% Similarity=0.265 Sum_probs=104.5
Q ss_pred HhhcHHHHHHHHHHHHHHHHHHHHHhhCCC--CCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhc
Q 008652 312 LHSGNSSREKLINANLRLVVHVAKQYQGRG--ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 389 (558)
Q Consensus 312 l~~G~~Are~LI~~nlrLV~sIArrY~~~g--~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~ 389 (558)
++.|+..++.||..|.|+|.++|++|.++. .+.+|++|+|++|||+|+++|||++|.+|.+||.+||++.|.+++++.
T Consensus 4 ~~~gd~~~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dylRk~ 83 (218)
T TIGR02895 4 IQPGNEEREELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYIRKN 83 (218)
T ss_pred hhcCChHHHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHhc
Confidence 345554599999999999999999998775 589999999999999999999999999999999999999999999988
Q ss_pred c---cccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHH
Q 008652 390 S---RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARR 429 (558)
Q Consensus 390 s---r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~ 429 (558)
. +.+++|.........+..+...+..+.++.|+.+||+..
T Consensus 84 ~k~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~ 126 (218)
T TIGR02895 84 QKYQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEY 126 (218)
T ss_pred ccccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHH
Confidence 7 678899766666677777888899999999999999754
No 94
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=99.78 E-value=4.6e-18 Score=161.15 Aligned_cols=163 Identities=14% Similarity=0.094 Sum_probs=127.4
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008652 314 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 393 (558)
Q Consensus 314 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~I 393 (558)
++..++..|+..|.+.|+.++.++.++..+.+|++||+|+.+|+. ..|+.. ..|.+|++.++++.+.++++++.+..
T Consensus 7 ~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~~~~ 83 (172)
T PRK12523 7 PHSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAALEQ 83 (172)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334999999999999999999999999999999999999999987 446543 36999999999999999998753100
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCC
Q 008652 394 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 473 (558)
Q Consensus 394 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~ 473 (558)
... .++ .. ........
T Consensus 84 ------------------~~~---------~~~------------------------~~-------------~~~~~~~~ 99 (172)
T PRK12523 84 ------------------AYL---------AEL------------------------AL-------------VPEAEQPS 99 (172)
T ss_pred ------------------HHH---------HHH------------------------hh-------------cccccCCC
Confidence 000 000 00 00000113
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008652 474 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 547 (558)
Q Consensus 474 pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 547 (558)
++......+....|..+|..||+++|+||.|+|. +|+|++|||+.||+|.++|++++.||+++||..+..
T Consensus 100 ~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l~~ 169 (172)
T PRK12523 100 PEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRL----DGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIALYG 169 (172)
T ss_pred hHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 4444444444457999999999999999999998 899999999999999999999999999999998764
No 95
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=1.4e-17 Score=156.87 Aligned_cols=159 Identities=17% Similarity=0.154 Sum_probs=125.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccccc
Q 008652 316 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 395 (558)
Q Consensus 316 ~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRl 395 (558)
...+..++..|.+.|+.+|+++.++..+.+|++||+++.+|+..++|++.. .|.+|++..+++.+.+++++..+....
T Consensus 5 ~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~~~~ 82 (164)
T PRK12547 5 SKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGT--NLKAWLFTILRNEFYSQMRKRGREVQD 82 (164)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhcccccc
Confidence 467899999999999999999999999999999999999999999998643 599999999999999998765421000
Q ss_pred chhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChh
Q 008652 396 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD 475 (558)
Q Consensus 396 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe 475 (558)
.+...... .+ ..++
T Consensus 83 ------------------------------------------------------~~~~~~~~---------~~---~~~~ 96 (164)
T PRK12547 83 ------------------------------------------------------SDGVFTAR---------VA---VHPA 96 (164)
T ss_pred ------------------------------------------------------cccccccc---------CC---CCch
Confidence 00000000 00 0011
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008652 476 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 548 (558)
Q Consensus 476 ~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 548 (558)
. ........|..+|..||+++|+||.|+|. +|+|++|||+.||||.++|++.+.||+++||..+...
T Consensus 97 ~--~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 163 (164)
T PRK12547 97 Q--YGSLDLQDFKKALNLLSADQREAIILIGA----SGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLKVD 163 (164)
T ss_pred h--hhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence 1 11122356889999999999999999998 8999999999999999999999999999999988644
No 96
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=1.1e-17 Score=156.66 Aligned_cols=157 Identities=15% Similarity=0.097 Sum_probs=123.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccc
Q 008652 317 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 396 (558)
Q Consensus 317 ~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP 396 (558)
.|++.|+..|.+.|+.++.++.++..+.+|++||+++.+|+..+.|++. .|.+|.+.++++.+.+++++..+.
T Consensus 4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~---- 76 (161)
T PRK12528 4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQII---EPRAFLTTIAKRVLCNHYRRQDLE---- 76 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhcccccccc---CHHHHHHHHHHHHHHHHHHHHHHH----
Confidence 6899999999999999999999999999999999999999999888652 699999999999999998764310
Q ss_pred hhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhH
Q 008652 397 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI 476 (558)
Q Consensus 397 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~ 476 (558)
... ..++ + + ..+.....++.
T Consensus 77 --------------~~~---------~~~~------------------------~------------~-~~~~~~~~~~~ 96 (161)
T PRK12528 77 --------------RAY---------LEAL------------------------A------------Q-LPERVAPSEEE 96 (161)
T ss_pred --------------Hhh---------HHHh------------------------h------------c-cccccCCCHHH
Confidence 000 0000 0 0 00000112333
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008652 477 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 544 (558)
Q Consensus 477 ~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 544 (558)
.....+....|..+|..||+++|+||.|+|. +|+|++|||+.||+|.++|+..+.+|+++||..
T Consensus 97 ~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~----~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~ 160 (161)
T PRK12528 97 RAIILETLVELDQLLDGLPPLVKRAFLLAQV----DGLGYGEIATELGISLATVKRYLNKAAMRCYFA 160 (161)
T ss_pred HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhc
Confidence 3333344567899999999999999999998 999999999999999999999999999999864
No 97
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=99.77 E-value=1.7e-17 Score=155.32 Aligned_cols=157 Identities=15% Similarity=0.127 Sum_probs=123.8
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccc
Q 008652 315 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 394 (558)
Q Consensus 315 G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IR 394 (558)
...|++.++..|.+.|+.++.++.++..+.+|++||+++.+|+..++|++. .|.||++..+++.+.++++++.+...
T Consensus 3 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~~ 79 (161)
T PRK12541 3 RKQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEKKYKT 79 (161)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhcccccc
Confidence 357899999999999999999999999999999999999999999999863 59999999999999999987553100
Q ss_pred cchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCCh
Q 008652 395 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP 474 (558)
Q Consensus 395 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~p 474 (558)
+ . .+. + . .+.....+
T Consensus 80 ~--------------------------~---------------------------~~~---------~-~--~~~~~~~~ 94 (161)
T PRK12541 80 T--------------------------T---------------------------IEE---------F-H--LPNVPSTE 94 (161)
T ss_pred c--------------------------c---------------------------hhh---------h-h--ccCCCCcH
Confidence 0 0 000 0 0 00000112
Q ss_pred hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008652 475 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 544 (558)
Q Consensus 475 e~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 544 (558)
+......+. ..+..+|..||+++|.||.|+|. +++|.+|||+.||+|.++|++.+.||+++||+.
T Consensus 95 ~~~~~~~~~-~~~~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 95 HEYFIKHEI-ASWLDSLSSLPLERRNVLLLRDY----YGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HHHHHHhHH-HHHHHHHHHCCHHHHHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 222222222 34567899999999999999998 899999999999999999999999999999975
No 98
>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=99.77 E-value=1.3e-17 Score=160.97 Aligned_cols=178 Identities=12% Similarity=0.131 Sum_probs=132.4
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhH
Q 008652 320 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI 399 (558)
Q Consensus 320 e~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~ 399 (558)
.+++..|.+.|+.+|+++.++..+.+|++||+++.+|+..++|++. .+|.+|++..+++.+.++++++.+....+. +
T Consensus 5 ~~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~~-~ 81 (188)
T TIGR02943 5 PQELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVSD-L 81 (188)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCccc-c
Confidence 3578889999999999999999999999999999999999999975 479999999999999999987653211100 0
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHH
Q 008652 400 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ 479 (558)
Q Consensus 400 ~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~le 479 (558)
. ++. ..-.++... ...+....+... .....|+..+.
T Consensus 82 ------------------~-----~~~-------------------~~~~~~~~~-~~~~~~~~~~~~-~~~~~~e~~~~ 117 (188)
T TIGR02943 82 ------------------D-----DEL-------------------DDEAFNALF-TQNGHWAQHGQP-QHWNTPEKQLE 117 (188)
T ss_pred ------------------c-----ccc-------------------ccchhhhhh-ccccchhccccc-cccCCHHHHHH
Confidence 0 000 000000000 000000001111 11235666777
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008652 480 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 548 (558)
Q Consensus 480 ~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 548 (558)
..+....+..+|..||+++|+||.++|. ++++++|||+.||+|.++|++++.||+++||+++...
T Consensus 118 ~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~ 182 (188)
T TIGR02943 118 NKEFWEVFEACLYHLPEQTARVFMMREV----LGFESDEICQELEISTSNCHVLLYRARLSLRACLSIN 182 (188)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 7777788999999999999999999998 8999999999999999999999999999999998654
No 99
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=99.77 E-value=1.6e-17 Score=160.57 Aligned_cols=181 Identities=17% Similarity=0.134 Sum_probs=132.0
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCC-HHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchh
Q 008652 320 EKLINANLRLVVHVAKQYQGRGIS-LHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 398 (558)
Q Consensus 320 e~LI~~nlrLV~sIArrY~~~g~~-~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~ 398 (558)
+..+..|.+.|+.+|+++.++..+ .+|++||+|+.+|+++++|++. .+|.+|++..+++.+.++++++.+.......
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 456778999999999999998888 9999999999999999999864 4799999999999999999876532110000
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHH
Q 008652 399 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV 478 (558)
Q Consensus 399 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~l 478 (558)
. . .....+.. ... ...+ .....+... .....|+..+
T Consensus 86 ~------------------~-~~~~~~~~--------------------~~~---~~~~-~~~~~~~~~-~~~~~~e~~~ 121 (195)
T PRK12532 86 L------------------D-DELLDEAF--------------------ESH---FSQN-GHWTPEGQP-QHWNTPEKSL 121 (195)
T ss_pred c------------------c-ccccchhh--------------------hhh---hccc-cccccccCc-cccCCHHHHH
Confidence 0 0 00000000 000 0000 000000000 1123566777
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008652 479 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 550 (558)
Q Consensus 479 e~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L 550 (558)
...+....+..+|..||+++|+||.|+|. +|+|++|||+.||+|.++|++.+.||+++||+++....+
T Consensus 122 ~~~e~~~~l~~~l~~L~~~~r~i~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~ 189 (195)
T PRK12532 122 NNNEFQKILQSCLYNLPENTARVFTLKEI----LGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKWF 189 (195)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHhhhHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 77777778999999999999999999998 899999999999999999999999999999999976543
No 100
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=99.77 E-value=1.7e-17 Score=161.73 Aligned_cols=181 Identities=14% Similarity=0.139 Sum_probs=130.3
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHH
Q 008652 321 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY 400 (558)
Q Consensus 321 ~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~ 400 (558)
.++..|.+.++.+|+++.++..+.+|++||+|+.+|+.+++|++.. .|.+|++..+++.+.++++++.+...++.
T Consensus 12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~IarN~~~d~~Rk~~r~~~~~~--- 86 (201)
T PRK12545 12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQS--AHKTWVFGILRNKLIDTLRARQRTVNLSA--- 86 (201)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhccccc--hHHHHHHHHHHHHHHHHHHhhcccccccc---
Confidence 3488899999999999999999999999999999999999999763 59999999999999999987653211100
Q ss_pred HHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHH
Q 008652 401 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK 480 (558)
Q Consensus 401 ~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~le~ 480 (558)
...++. ....++.......+....+..++ ....++.....
T Consensus 87 ---------------------~~~~~~------------------~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 126 (201)
T PRK12545 87 ---------------------LDAELD------------------GEALLDRELFKDNGHWAAHAKPR-PWPKPETILQQ 126 (201)
T ss_pred ---------------------cccccc------------------hhhhhhhhhhcccccccccccCc-CCCCHHHHHHH
Confidence 000000 00000000000000000000011 11245555555
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008652 481 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 550 (558)
Q Consensus 481 ~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L 550 (558)
.+....|..+|..||+++|+||.|+|+ +++|++|||+.||+|.++|+..+.||+++||+++...++
T Consensus 127 ~~~~~~l~~~L~~Lp~~~r~v~~L~~~----eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~~ 192 (201)
T PRK12545 127 QQFWTLFETCLDHLPEQIGRVFMMREF----LDFEIDDICTELTLTANHCSVLLYRARTRLRTCLSEKGL 192 (201)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 556667899999999999999999998 999999999999999999999999999999999975543
No 101
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=99.77 E-value=2.3e-17 Score=154.54 Aligned_cols=160 Identities=19% Similarity=0.183 Sum_probs=128.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccccc
Q 008652 316 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 395 (558)
Q Consensus 316 ~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRl 395 (558)
+.+++.|+..|.+.|+.+|+++.++..+.+|++||+++.+|++ .|+. +..|.+|++..+++.+.+++++..+..+.
T Consensus 2 ~~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~~~~~ 77 (166)
T PRK09639 2 DETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKRRRAR 77 (166)
T ss_pred chHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhcccccc
Confidence 3689999999999999999999999999999999999999999 6764 34799999999999999999775421110
Q ss_pred chhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChh
Q 008652 396 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD 475 (558)
Q Consensus 396 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe 475 (558)
. +. .....+. + ....|+
T Consensus 78 ~------------------------------------------------------~~------~~~~~~~--~-~~~~~e 94 (166)
T PRK09639 78 I------------------------------------------------------LG------EFQWQEV--D-NEPSPE 94 (166)
T ss_pred c------------------------------------------------------cc------hhhhhhc--c-CCCChH
Confidence 0 00 0000000 1 122455
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008652 476 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 547 (558)
Q Consensus 476 ~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 547 (558)
+.....+....|..+|..||+++|.||.++| +|++++|||+.||+|..+|+..+.||+++||+.+..
T Consensus 95 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-----~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~~ 161 (166)
T PRK09639 95 EIWIRKEEITKVQEVLAKMTERDRTVLLLRF-----SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQ 161 (166)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 6666666667799999999999999999999 589999999999999999999999999999998864
No 102
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=99.77 E-value=2.2e-17 Score=159.39 Aligned_cols=177 Identities=16% Similarity=0.116 Sum_probs=130.8
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhH
Q 008652 320 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI 399 (558)
Q Consensus 320 e~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~ 399 (558)
+..|..|.+.++.+|.++.++..+++|++||+|+.+|+.+++|++. .+|.+|++..+++.+.++++++.+...... .
T Consensus 10 ~~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~-~ 86 (189)
T PRK12530 10 SLEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQ--SALKTWIFAILKNKIIDLIRYRKRFVNESE-L 86 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCC--ccHHHHHHHHHHHHHHHHHHhhccCCCccc-c
Confidence 3457778999999999999998999999999999999999999875 369999999999999999987653211000 0
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHH
Q 008652 400 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ 479 (558)
Q Consensus 400 ~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~le 479 (558)
. ++ ..+.... +.......+.........++..+.
T Consensus 87 ------------------~-----~~-------------------~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~ 120 (189)
T PRK12530 87 ------------------I-----EE-------------------DSPNSFF----DEKGHWKPEYYEPSEWQEVENTVY 120 (189)
T ss_pred ------------------c-----cc-------------------ccchhhh----cccccccccccCCccccCHHHHHH
Confidence 0 00 0000000 000000000000111234566666
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008652 480 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 549 (558)
Q Consensus 480 ~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 549 (558)
..+....|..+|+.||+++|+||.|+|. +++|++|||+.||+|.++|+.++.||+++||+++....
T Consensus 121 ~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~ 186 (189)
T PRK12530 121 KEEFWLIFEACLNHLPAQQARVFMMREY----LELSSEQICQECDISTSNLHVLLYRARLQLQACLSKNW 186 (189)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHhHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 7777788999999999999999999998 89999999999999999999999999999999986543
No 103
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=99.77 E-value=2.4e-17 Score=172.56 Aligned_cols=188 Identities=18% Similarity=0.199 Sum_probs=135.8
Q ss_pred HHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHH
Q 008652 306 RDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK 384 (558)
Q Consensus 306 ~~L~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~ 384 (558)
.+|+..+..| ..+++.|+..|.+.|+.+|+++.++..+.+|++||.|+.+|+.+++|++. ..|.+|++..+++.+.+
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 3455655555 49999999999999999999999999999999999999999999999853 46999999999999999
Q ss_pred HHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhh
Q 008652 385 AIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQE 464 (558)
Q Consensus 385 aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e 464 (558)
+++++.+... +. ..+ .+. .........+......+
T Consensus 85 ~~Rk~~~~~~-~~------------------~~~-~~~-------------------------~~~~~~~~~~~~~~~~~ 119 (339)
T PRK08241 85 ALEGRARRPL-PT------------------DLG-APA-------------------------ADPVDELVERPEVPWLE 119 (339)
T ss_pred HHHhhccccC-cc------------------ccC-CCc-------------------------CcccccccccccccccC
Confidence 9987542100 00 000 000 00000000000000001
Q ss_pred hcccC----CCCChhHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008652 465 ITADT----GVEIPDISVQKQL-MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 539 (558)
Q Consensus 465 ~i~d~----~~~~pe~~le~~~-~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 539 (558)
.+.+. ...+|++.+...+ ....|..+|..||+++|+||.|+|. +++|++|||++||+|..+|++++.||++
T Consensus 120 ~~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~RAr~ 195 (339)
T PRK08241 120 PYPDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLILRDV----LGWSAAEVAELLDTSVAAVNSALQRARA 195 (339)
T ss_pred CCCcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhHHh----hCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 11110 1234555555443 4556899999999999999999998 9999999999999999999999999999
Q ss_pred HHHHH
Q 008652 540 RLKQS 544 (558)
Q Consensus 540 KLR~~ 544 (558)
+||+.
T Consensus 196 ~Lr~~ 200 (339)
T PRK08241 196 TLAER 200 (339)
T ss_pred HHhhc
Confidence 99993
No 104
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=99.76 E-value=2.3e-17 Score=161.96 Aligned_cols=181 Identities=18% Similarity=0.203 Sum_probs=133.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchh
Q 008652 319 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 398 (558)
Q Consensus 319 re~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~ 398 (558)
-..++..|.+.|+.+|+++.++....+|++||+++.+|+.+.+|++. .+|.+|++..+++.+.+++++..+....+..
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 46788999999999999999999999999999999999999999864 4699999999999999999876542111000
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHH
Q 008652 399 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV 478 (558)
Q Consensus 399 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~l 478 (558)
.. ....+ ..+..+. + ................|+..+
T Consensus 98 ------------------~~--~~~~~---------~~~~~~~--------------~-~~~~~~~~~~~~~~~~~e~~~ 133 (206)
T PRK12544 98 ------------------LR--DEEEE---------EDFEELF--------------D-ESGHWQKDERPQAWGNPEESL 133 (206)
T ss_pred ------------------cc--ccchh---------hHHHHhh--------------c-ccccccccccccccCCHHHHH
Confidence 00 00000 0000000 0 000000000001123566667
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008652 479 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 549 (558)
Q Consensus 479 e~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 549 (558)
...+....+..+|..||+++|+||.|+|. +++|++|||+.||+|.++|++.+.||+++||+.+....
T Consensus 134 ~~~e~~~~l~~~L~~L~~~~r~v~~L~~~----~g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~~ 200 (206)
T PRK12544 134 EQEQFWRIFEACLDGLPAKYARVFMMREF----IELETNEICHAVDLSVSNLNVLLYRARLRLRECLENKW 200 (206)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 77777778899999999999999999998 89999999999999999999999999999999987543
No 105
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=99.76 E-value=3.2e-17 Score=159.55 Aligned_cols=170 Identities=16% Similarity=0.099 Sum_probs=129.4
Q ss_pred HHHHHhh-cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHH
Q 008652 308 LKSELHS-GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI 386 (558)
Q Consensus 308 L~~~l~~-G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aI 386 (558)
|+..+.. +..+++.|+..|.+.++.+++ +.++..+.+|++||.|+.+|+..++|++. ..|.+|++..+++.+.+++
T Consensus 15 l~~~~~~~d~~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~ 91 (196)
T PRK12535 15 LALAAGRGDRAALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAAR--SSARTWLLSLARRVWVDNI 91 (196)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCc--ccHHHHHHHHHHHHHHHHH
Confidence 4444444 459999999999999999975 57888899999999999999999999864 3699999999999999999
Q ss_pred HhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhc
Q 008652 387 FQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEIT 466 (558)
Q Consensus 387 r~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i 466 (558)
+++.+..+. ..+ .. . ...+
T Consensus 92 Rk~~~~~~~-----------------------------------------------------~~~-~~-~----~~~~-- 110 (196)
T PRK12535 92 RHDMARPRK-----------------------------------------------------SAT-EY-E----DAAA-- 110 (196)
T ss_pred HhhccCCCc-----------------------------------------------------ccc-cc-c----cccc--
Confidence 875421100 000 00 0 0000
Q ss_pred ccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008652 467 ADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 546 (558)
Q Consensus 467 ~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 546 (558)
. ...++..... .....|..+|+.||+++|+||.|+|. +++|++|||+.||+|.++|++.+.||+++||+.+.
T Consensus 111 --~-~~~~~~~~~~-~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~ 182 (196)
T PRK12535 111 --T-TASNETTGSW-SEWIDVRTLIDALPPERREALILTQV----LGYTYEEAAKIADVRVGTIRSRVARARADLIAATA 182 (196)
T ss_pred --c-cCCcchhHHH-HHHHHHHHHHHcCCHHHHHHhhhHHH----hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 0 0111111111 12346889999999999999999998 89999999999999999999999999999999987
Q ss_pred cCc
Q 008652 547 GKA 549 (558)
Q Consensus 547 ~~~ 549 (558)
.+.
T Consensus 183 ~~~ 185 (196)
T PRK12535 183 TGQ 185 (196)
T ss_pred ccc
Confidence 654
No 106
>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=99.76 E-value=3.3e-17 Score=170.12 Aligned_cols=183 Identities=17% Similarity=0.188 Sum_probs=134.0
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008652 314 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 393 (558)
Q Consensus 314 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~I 393 (558)
++..|++.|+..|.+.++.+|.++.++..+.+|++||.++.+|+.+++|++. ..|.+|++..+++.+.++++++.+..
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 3458999999999999999999999999999999999999999999999864 36999999999999999998754311
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcc------
Q 008652 394 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITA------ 467 (558)
Q Consensus 394 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~------ 467 (558)
.... ... . ......... .+......+.+.
T Consensus 80 ~~~~------------------~~~--~------------------------~~~~~~~~~-~~~~~~~~~~~~~~~~~~ 114 (324)
T TIGR02960 80 RPVG------------------LGA--P------------------------SADGTAAAS-EAAEVTWLEPLPDLTLDL 114 (324)
T ss_pred Cccc------------------cCC--C------------------------CCccccccc-ccccccccCCCCcccccc
Confidence 0000 000 0 000000000 000000000000
Q ss_pred -cCCCCChhHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008652 468 -DTGVEIPDISVQKQL-MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 545 (558)
Q Consensus 468 -d~~~~~pe~~le~~~-~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 545 (558)
.....+|++.+...+ ....+..+|..||+++|+||.|+|. +++|++|||+.||+|.++|++++.||+++||+++
T Consensus 115 ~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 190 (324)
T TIGR02960 115 DDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDV----LGWRAAETAELLGTSTASVNSALQRARATLDEVG 190 (324)
T ss_pred ccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhc
Confidence 011124555555444 4567889999999999999999998 8999999999999999999999999999999998
Q ss_pred hc
Q 008652 546 GG 547 (558)
Q Consensus 546 ~~ 547 (558)
..
T Consensus 191 ~~ 192 (324)
T TIGR02960 191 PS 192 (324)
T ss_pred cc
Confidence 74
No 107
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=99.76 E-value=4.2e-17 Score=152.56 Aligned_cols=159 Identities=14% Similarity=0.214 Sum_probs=124.7
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHH
Q 008652 321 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY 400 (558)
Q Consensus 321 ~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~ 400 (558)
.++..|.+.++++|.++.++..+.+|++||+++++|+....|++. .|.+|++..+++.+.++++++.+....
T Consensus 2 ~~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn~~~d~~R~~~~~~~~----- 73 (163)
T PRK07037 2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRNLAIDHYRRQALENKY----- 73 (163)
T ss_pred hHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHHHHHHHHHhhcccccc-----
Confidence 367788999999999999999999999999999999998877763 478999999999999998865421000
Q ss_pred HHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHH
Q 008652 401 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK 480 (558)
Q Consensus 401 ~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~le~ 480 (558)
. ..+.... .. .+. ...++..+..
T Consensus 74 ------------------------------------------------~------~~~~~~~-~~-~~~-~~~~~~~~~~ 96 (163)
T PRK07037 74 ------------------------------------------------H------GDEEDGL-DV-PSP-EASPEAALIN 96 (163)
T ss_pred ------------------------------------------------c------ccccccc-cc-CCC-CCCHHHHHHH
Confidence 0 0000000 00 011 1245555555
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008652 481 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 548 (558)
Q Consensus 481 ~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 548 (558)
.+..+.+..+|+.||+++|+||.++|. +++|.+|||+.||+|.++|+..+.||+++||+.+...
T Consensus 97 ~~~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l~~~ 160 (163)
T PRK07037 97 RDTLRHVADALSELPARTRYAFEMYRL----HGETQKDIARELGVSPTLVNFMIRDALVHCRKCLDAC 160 (163)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence 566678899999999999999999998 8999999999999999999999999999999988654
No 108
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=99.76 E-value=1.1e-17 Score=154.77 Aligned_cols=152 Identities=18% Similarity=0.210 Sum_probs=121.9
Q ss_pred HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHH
Q 008652 324 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL 403 (558)
Q Consensus 324 ~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~~~l 403 (558)
..|.+.|+.+++++.++..+.+|++||+++.+|+++++|++ .+|.+|++..+++.+.++++++.+....+
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~~------- 71 (154)
T TIGR02950 2 REYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTID------- 71 (154)
T ss_pred chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhcccc-------
Confidence 57899999999999999889999999999999999999997 37999999999999999987654210000
Q ss_pred HHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHH
Q 008652 404 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 483 (558)
Q Consensus 404 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~le~~~~ 483 (558)
.+.+ .+... +....|++.+...+.
T Consensus 72 -------------------~~~~------------------------------------~~~~~-~~~~~~~~~~~~~~~ 95 (154)
T TIGR02950 72 -------------------DDAI------------------------------------GDLEQ-HPVESPEHHLLIKIE 95 (154)
T ss_pred -------------------Hhhh------------------------------------hhccc-cccCChhHHHHHHHH
Confidence 0000 00000 011235555555566
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008652 484 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 545 (558)
Q Consensus 484 ~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 545 (558)
...|..+|..||+++++||.++|+ +|+|++|||+.||+|..+|++.+.||+++||+.+
T Consensus 96 ~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~l 153 (154)
T TIGR02950 96 QEEITHHLSRLPENYRTVLILREF----KEFSYKEIAELLNLSLAKVKSNLFRARKELKKLL 153 (154)
T ss_pred HHHHHHHHHhCCHhheeeeeehhh----ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 678999999999999999999998 8999999999999999999999999999999875
No 109
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=99.75 E-value=4.2e-17 Score=156.89 Aligned_cols=160 Identities=18% Similarity=0.222 Sum_probs=126.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccc
Q 008652 317 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 396 (558)
Q Consensus 317 ~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP 396 (558)
.++..++..|.+.|+.+|.++.++..+.+|++||.|+.+|+..++|++.. .|.+|++..+++.+.++++++.+....
T Consensus 5 ~~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~~~~~- 81 (182)
T PRK12540 5 DSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGS--NLPAWLFTILRNLFRSDYRKRRREVED- 81 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCc--hHHHHHHHHHHHHHHHHHHhccccccc-
Confidence 56788999999999999999999999999999999999999999998753 599999999999999988765421000
Q ss_pred hhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhH
Q 008652 397 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI 476 (558)
Q Consensus 397 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~ 476 (558)
.+. ...+.. +. .++.
T Consensus 82 -----------------------------------------------------~~~--------~~~~~~-~~---~~~~ 96 (182)
T PRK12540 82 -----------------------------------------------------ADG--------SYAKTL-KS---QPGQ 96 (182)
T ss_pred -----------------------------------------------------ccc--------cccccc-cC---CCch
Confidence 000 000000 00 1111
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008652 477 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 550 (558)
Q Consensus 477 ~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L 550 (558)
.. ......|..+|+.||+++|+||.|+|. +++|++|||+.||+|..+|++.+.||+++||+.+...+.
T Consensus 97 ~~--~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~~ 164 (182)
T PRK12540 97 NA--HLEFEEFRAALDKLPQDQREALILVGA----SGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDGA 164 (182)
T ss_pred HH--HHHHHHHHHHHHhCCHHHHHHhhHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 11 112346899999999999999999998 999999999999999999999999999999999986553
No 110
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=99.75 E-value=4.4e-17 Score=152.19 Aligned_cols=155 Identities=12% Similarity=0.100 Sum_probs=123.6
Q ss_pred HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHH
Q 008652 324 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL 403 (558)
Q Consensus 324 ~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~~~l 403 (558)
..|.+.++.++.++.++..+.+|++||+++.+|+..+.|++. +|.+|++..+++.+.++++++.+...
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~~---~~~~wL~~ia~n~~~d~~R~~~~~~~--------- 69 (159)
T PRK12527 2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIE---HPRAFLYRTALNLVVDRHRRHRVRQA--------- 69 (159)
T ss_pred hhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhcccccccc---chHHHHHHHHHHHHHHHHHHHhcccc---------
Confidence 568889999999999988899999999999999999998753 79999999999999999876431000
Q ss_pred HHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHH
Q 008652 404 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 483 (558)
Q Consensus 404 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~le~~~~ 483 (558)
.+++. . .+. .......|++.+..++.
T Consensus 70 --------------------------------------------~~~~~-~-~~~--------~~~~~~~~~~~~~~~~~ 95 (159)
T PRK12527 70 --------------------------------------------EPLEV-L-DEE--------ERLHSPSPQTRLDLGQR 95 (159)
T ss_pred --------------------------------------------cchhh-h-hcc--------ccccCCCHHHHHHHHHH
Confidence 00000 0 000 00011246666666667
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008652 484 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 548 (558)
Q Consensus 484 ~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 548 (558)
...|..+|..||+++++||.|+|+ +++|.+|||+.||+|.++|+..+.||+++||+.+...
T Consensus 96 ~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~~~ 156 (159)
T PRK12527 96 LALLQRALAELPPACRDSFLLRKL----EGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQW 156 (159)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 778999999999999999999998 9999999999999999999999999999999988643
No 111
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=99.74 E-value=9.1e-17 Score=154.30 Aligned_cols=154 Identities=21% Similarity=0.194 Sum_probs=125.8
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchh
Q 008652 319 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 398 (558)
Q Consensus 319 re~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~ 398 (558)
++.|+..|.+.|+.+|.++.++..+.+|++||.++.+|+.+..|++. ..|.+|++..+++.+.++++++.+...++
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~~--~~~~~wL~~i~~n~~~d~~Rk~~~~~~~~-- 78 (181)
T PRK09637 3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNTIIDFYRKKNRSEELP-- 78 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhccc--cchHHHHHHHHHHHHHHHHHhccccCCcc--
Confidence 67899999999999999999999999999999999999999999853 47999999999999999998654211000
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHH
Q 008652 399 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV 478 (558)
Q Consensus 399 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~l 478 (558)
.+ +...+ .+++..
T Consensus 79 ---------------------------------------------------------~~------~~~~~----~~~~~~ 91 (181)
T PRK09637 79 ---------------------------------------------------------DD------LLFED----EEREEN 91 (181)
T ss_pred ---------------------------------------------------------hh------hhccC----CChhHH
Confidence 00 00000 111122
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008652 479 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 547 (558)
Q Consensus 479 e~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 547 (558)
...+....+..+|+.||+++|+||.++|. +|++.+|||+.||+|..+|+.++.||+++||+.+..
T Consensus 92 ~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (181)
T PRK09637 92 AKKELAPCLRPFIDALPEKYAEALRLTEL----EGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156 (181)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 33345567899999999999999999998 899999999999999999999999999999998764
No 112
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=99.74 E-value=1e-16 Score=152.24 Aligned_cols=164 Identities=15% Similarity=0.070 Sum_probs=126.3
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccc
Q 008652 315 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 394 (558)
Q Consensus 315 G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IR 394 (558)
+..|++.++..|.+.++.++.++.++..+.+|++||.++.+|+. ..|++-. .|.+|++..+++.+.++++++.+..
T Consensus 8 ~~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~~~~- 83 (172)
T PRK09651 8 ASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNALEK- 83 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHHHHh-
Confidence 35899999999999999999999999999999999999999998 3565432 5889999999999999887543100
Q ss_pred cchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCCh
Q 008652 395 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP 474 (558)
Q Consensus 395 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~p 474 (558)
. . ...+ + + +.+....+|
T Consensus 84 -----------------~----~-----~~~~------------------------~------------~-~~~~~~~~~ 100 (172)
T PRK09651 84 -----------------A----Y-----LEML------------------------A------------L-MPEGGAPSP 100 (172)
T ss_pred -----------------h----h-----hhHH------------------------h------------h-ccccCCCCh
Confidence 0 0 0000 0 0 000011123
Q ss_pred hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008652 475 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 549 (558)
Q Consensus 475 e~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 549 (558)
+......+....|..+|..||+++|+||.++|+ +++|++|||+.||+|.++|+..+.||+++|+...-..|
T Consensus 101 ~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~~~~~~ 171 (172)
T PRK09651 101 EERESQLETLQLLDSMLDGLNGKTREAFLLSQL----DGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLFRLEYG 171 (172)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHhHHhhhhhc----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHcC
Confidence 333444445567899999999999999999998 99999999999999999999999999999998765444
No 113
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=99.74 E-value=9e-17 Score=155.22 Aligned_cols=161 Identities=19% Similarity=0.155 Sum_probs=124.8
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008652 313 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 392 (558)
Q Consensus 313 ~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~ 392 (558)
..+..+++.++..|.+.|+.+|+++.++..+++|++||+|+.+|+.++.|++. ..|.+|++..+++.+.+..++..+.
T Consensus 19 ~~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~~~~~ 96 (188)
T PRK12517 19 LSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFERKQFD 96 (188)
T ss_pred hccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHHhccC
Confidence 45679999999999999999999999999999999999999999999999865 3699999999888665444321100
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCC
Q 008652 393 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE 472 (558)
Q Consensus 393 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~ 472 (558)
....+ . +...+....
T Consensus 97 ------------------------------------------------------~~~~~-------~----~~~~~~~~~ 111 (188)
T PRK12517 97 ------------------------------------------------------LVDIE-------D----DSIEDDASH 111 (188)
T ss_pred ------------------------------------------------------ccCcc-------c----ccccCcccc
Confidence 00000 0 000111111
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008652 473 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 548 (558)
Q Consensus 473 ~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 548 (558)
.++.. ...+.|..+|..||+++|.||.++|. ++++++|||+.||||..+|+.++.||+++||+++...
T Consensus 112 ~~e~~----~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 179 (188)
T PRK12517 112 SSEEE----MEQEWLRRQIAKLDPEYREPLLLQVI----GGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALEKP 179 (188)
T ss_pred ChhHH----HHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 23222 22346889999999999999999998 8999999999999999999999999999999998643
No 114
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=99.73 E-value=1.6e-16 Score=153.73 Aligned_cols=156 Identities=19% Similarity=0.200 Sum_probs=121.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccc
Q 008652 317 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 396 (558)
Q Consensus 317 ~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP 396 (558)
.+++.|+. |.+.|+++|+++.++..+.+|++||.++.+|+++..|+.. ..|.+|++..+++.+.++++++.+...
T Consensus 8 ~~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r~~~-- 82 (188)
T PRK12546 8 DPRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKREVP-- 82 (188)
T ss_pred hHHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhccccc--
Confidence 56667766 7799999999999999999999999999999999999864 469999999999999998876542100
Q ss_pred hhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhH
Q 008652 397 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI 476 (558)
Q Consensus 397 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~ 476 (558)
..+. ...+...+.. ..+
T Consensus 83 ----------------------------------------------------~~~~--------~~~~~~~~~~--~~~- 99 (188)
T PRK12546 83 ----------------------------------------------------DPEG--------VHAASLAVKP--AHD- 99 (188)
T ss_pred ----------------------------------------------------Cccc--------ccccccccCC--cch-
Confidence 0000 0000000000 011
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008652 477 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 547 (558)
Q Consensus 477 ~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 547 (558)
.......+..+|..||+++|+||.|+|. +++|.+|||+.||||..+|+..+.||+++||+.+..
T Consensus 100 ---~~~~~~~l~~~L~~Lp~~~r~v~~L~~~----~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~ 163 (188)
T PRK12546 100 ---GRLAMSDFRAAFAQLPDEQREALILVGA----SGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQL 163 (188)
T ss_pred ---hHHHHHHHHHHHHhCCHHHhHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 1122346889999999999999999998 899999999999999999999999999999998865
No 115
>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=99.73 E-value=1.5e-16 Score=150.95 Aligned_cols=149 Identities=21% Similarity=0.215 Sum_probs=120.7
Q ss_pred HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHH
Q 008652 324 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL 403 (558)
Q Consensus 324 ~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~~~l 403 (558)
..|.+.++.++.++.++..+.+|++||+++.+|+++++|++. .+|.+|++..+++.+.+++++..+...++
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~~--~~f~~wl~~iarn~~~d~~Rk~~~~~~~~------- 72 (170)
T TIGR02959 2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDG--QKIQSWLYQIARNTIIDFYRSKSRSVELP------- 72 (170)
T ss_pred chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhccCccccc-------
Confidence 468899999999999999999999999999999999999964 57999999999999999998765211000
Q ss_pred HHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHH
Q 008652 404 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 483 (558)
Q Consensus 404 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~le~~~~ 483 (558)
+. .... ..+++.....+.
T Consensus 73 -----------------------------------------------~~------------~~~~---~~~~~~~~~~e~ 90 (170)
T TIGR02959 73 -----------------------------------------------ES------------LLAA---DSAREETFVKEL 90 (170)
T ss_pred -----------------------------------------------hh------------hccc---CCccHHHHHHHH
Confidence 00 0000 011222333445
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008652 484 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 547 (558)
Q Consensus 484 ~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 547 (558)
...|..+|..||+++|.||.++|. +++|++|||+.||+|..+|++.+.||+++||..+..
T Consensus 91 ~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 150 (170)
T TIGR02959 91 SQCIPPMIKELPDEYREAIRLTEL----EGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLET 150 (170)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 567899999999999999999998 899999999999999999999999999999998853
No 116
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=99.72 E-value=2.3e-16 Score=151.82 Aligned_cols=158 Identities=13% Similarity=0.166 Sum_probs=122.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchh
Q 008652 319 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 398 (558)
Q Consensus 319 re~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~ 398 (558)
.+..+..+++.|+.+|.++.++..+.+|++||.|+.+|+.+..|++. ..|.+|++..+++.+.++++++.+....
T Consensus 6 ~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~~~~~--- 80 (182)
T PRK12511 6 KRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRVEARR--- 80 (182)
T ss_pred hhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhcccccc---
Confidence 44557789999999999999998999999999999999999999864 3699999999999999999875421100
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHH
Q 008652 399 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV 478 (558)
Q Consensus 399 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~l 478 (558)
.+++ . +. .+.....+.
T Consensus 81 ------------------------~~~~------------------------~------------~~-~~~~~~~~~--- 96 (182)
T PRK12511 81 ------------------------ADEL------------------------A------------VL-ADASLPAAQ--- 96 (182)
T ss_pred ------------------------ccch------------------------h------------hc-cccCCCcch---
Confidence 0000 0 00 000000111
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008652 479 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 549 (558)
Q Consensus 479 e~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 549 (558)
........|..+|..||+++|+||.|+|. +++|++|||+.||||.++|++.+.||+++||+.+...+
T Consensus 97 ~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~~~~ 163 (182)
T PRK12511 97 EHAVRLAQIRDAFFDLPEEQRAALHLVAI----EGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEEGTG 163 (182)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 11123356889999999999999999998 89999999999999999999999999999999886543
No 117
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=99.71 E-value=5e-16 Score=146.80 Aligned_cols=160 Identities=14% Similarity=0.116 Sum_probs=126.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccccc
Q 008652 316 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 395 (558)
Q Consensus 316 ~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRl 395 (558)
+.++..++..|.+.++.+|.++.++..+.+|++||.++.+|+..+.++. ..|.+|.+..+++.+.+++++...
T Consensus 8 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~---- 80 (168)
T PRK12525 8 NTLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDL---- 80 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHH----
Confidence 4789999999999999999999999999999999999999986665542 369999999999999888765320
Q ss_pred chhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChh
Q 008652 396 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD 475 (558)
Q Consensus 396 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe 475 (558)
.+ ... +.+ + + ........|+
T Consensus 81 --------~~------~~~---------~~~------------------------~------------~-~~~~~~~~~~ 100 (168)
T PRK12525 81 --------ER------AYL---------QSL------------------------A------------E-APEAVQPSPE 100 (168)
T ss_pred --------HH------HHH---------HHH------------------------h------------c-ccccccCChH
Confidence 00 000 000 0 0 0001112455
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008652 476 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 546 (558)
Q Consensus 476 ~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 546 (558)
......+....|..+|..||+++|+||.|+|. +++|++|||+.||+|..+|+..+.+|+++||..+.
T Consensus 101 ~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~----eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~~~ 167 (168)
T PRK12525 101 EQWMVIETLLAIDRLLDGLSGKARAAFLMSQL----EGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQGFQ 167 (168)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhc
Confidence 55555556678999999999999999999998 99999999999999999999999999999998763
No 118
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=99.69 E-value=7.9e-16 Score=143.28 Aligned_cols=156 Identities=17% Similarity=0.183 Sum_probs=112.7
Q ss_pred CCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCC
Q 008652 339 GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGN 418 (558)
Q Consensus 339 ~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~g 418 (558)
++..+.+|++||+|+.+|+..+. ++ +..|.+|++..+++.+.++++++.+..+...
T Consensus 2 ~~~~~AeDivQe~fl~~~~~~~~-~~--~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~--------------------- 57 (161)
T PRK09047 2 RDDDAALDIVQDAMIKLAEKYGD-RP--AAEWPPLFQRILQNRIHDWFRRQKVRNTWVS--------------------- 57 (161)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhh-cc--cCchHHHHHHHHHHHHHHHHHhhcccccccc---------------------
Confidence 34457899999999999999886 33 3579999999999999999987542110000
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCC--CCChhHHHHHHHHHHHHHHHHhcCCH
Q 008652 419 HSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTG--VEIPDISVQKQLMRQHVRNLLTLLNP 496 (558)
Q Consensus 419 r~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~--~~~pe~~le~~~~~e~L~~~L~~L~~ 496 (558)
...++.... ++++....+.+.+.. ...|+..+...+....|..+|..||+
T Consensus 58 ---------------------------~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~ 109 (161)
T PRK09047 58 ---------------------------LFSSFSDDD-DDDDFDPLETLDSADEGAESPADKLERAQVLQLIEEAIQKLPA 109 (161)
T ss_pred ---------------------------ccccccccc-ccccccHHHHhccccccCCCHHHHHHHHHHHHHHHHHHHhCCH
Confidence 000000000 000111112222211 23567777777778889999999999
Q ss_pred HHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008652 497 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 550 (558)
Q Consensus 497 rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L 550 (558)
++|+||.|+|+ +++|++|||+.||||.++|+.++.||+++||+.+...++
T Consensus 110 ~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~~ 159 (161)
T PRK09047 110 RQREAFLLRYW----EDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEAKGI 159 (161)
T ss_pred HHHHHHHHHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcCc
Confidence 99999999998 999999999999999999999999999999999976553
No 119
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=99.68 E-value=1.1e-15 Score=157.28 Aligned_cols=161 Identities=16% Similarity=0.092 Sum_probs=123.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccc
Q 008652 317 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 396 (558)
Q Consensus 317 ~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP 396 (558)
.....++..|.+.++.+|+++.++..+.||++||.++. |.....|+ ...|.+|++..+++.+.++++++.+.-..
T Consensus 4 ~~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~---~~~~~~WL~~Ia~n~~~d~lR~~~~~~~~- 78 (293)
T PRK09636 4 ADAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQ---IRDPRAWLTRVVTRLCLDRLRSARHRRET- 78 (293)
T ss_pred cHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhccccc---ccCHHHHHHHHHHHHHHHHHHhhhccccc-
Confidence 34678999999999999999999999999999999999 66667776 24799999999999999999764320000
Q ss_pred hhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhH
Q 008652 397 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI 476 (558)
Q Consensus 397 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~ 476 (558)
..+ ..+..+ ..+.. ..|++
T Consensus 79 -------------------~~~-----------------------------~~~~e~------------~~~~~-~~~~~ 97 (293)
T PRK09636 79 -------------------YVG-----------------------------PWLPEP------------VVEEL-DDPLE 97 (293)
T ss_pred -------------------ccC-----------------------------CcCCcC------------CCCCC-CChHH
Confidence 000 000000 00111 12333
Q ss_pred H-HHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008652 477 S-VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 547 (558)
Q Consensus 477 ~-le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 547 (558)
. .........+..+|+.|||++|.||.|+|. +++|++|||+.||+|..+|++++.||+++||+.+..
T Consensus 98 ~~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~~----~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~~ 165 (293)
T PRK09636 98 AVVAAEDLSLALMLALERLSPLERAAFLLHDV----FGVPFDEIASTLGRSPAACRQLASRARKHVRAARPR 165 (293)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCC
Confidence 3 334455567899999999999999999998 899999999999999999999999999999997653
No 120
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=99.64 E-value=5.9e-15 Score=147.48 Aligned_cols=158 Identities=19% Similarity=0.178 Sum_probs=121.8
Q ss_pred HHHHHhhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHH
Q 008652 308 LKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIF 387 (558)
Q Consensus 308 L~~~l~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr 387 (558)
|.+.+.++..+++.+++.| +.++.++.++.++..+.+||+||.++.+|+. |+.. ..|.+|++..+++.+.+.++
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 4444555668888888877 7899999999999999999999999999986 5543 24899999999999999887
Q ss_pred hcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcc
Q 008652 388 QHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITA 467 (558)
Q Consensus 388 ~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~ 467 (558)
++.+.-. + .+. ..
T Consensus 83 k~k~~~~-------------------------------~-----------------------~~~-------~~------ 95 (228)
T PRK06704 83 SKSVHEK-------------------------------I-----------------------RDQ-------IT------ 95 (228)
T ss_pred ccccccc-------------------------------c-----------------------ccc-------cc------
Confidence 6542100 0 000 00
Q ss_pred cCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008652 468 DTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 547 (558)
Q Consensus 468 d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 547 (558)
...+.... ....+.+..+|+.||+++|+||.|+|. +++|++|||+.||+|.++|++.+.||+++||+.+..
T Consensus 96 ---~~~~~~~~--~~~~~~l~~~L~~Lp~~~R~v~lL~~~----eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~ 166 (228)
T PRK06704 96 ---FEEPHEKI--ADLHEMVGKVLSSLNVQQSAILLLKDV----FQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEE 166 (228)
T ss_pred ---cCChHHHH--HHHHHHHHHHHHhCCHHHhhHhhhHHh----hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 00111111 123356889999999999999999998 899999999999999999999999999999998865
No 121
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=99.63 E-value=7.7e-15 Score=150.54 Aligned_cols=156 Identities=22% Similarity=0.158 Sum_probs=118.5
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHH
Q 008652 321 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY 400 (558)
Q Consensus 321 ~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~ 400 (558)
+++..|.+.++.+|+++.++..+.||++||+++.+++. .|+. ...|.+|.+.++++.+.+++++..+.-..
T Consensus 1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~--~~~~~awL~~Ia~n~~ld~lR~~~~~~~~----- 71 (281)
T TIGR02957 1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQ--IENPKAYLTKVVTRRCIDVLRSARARREV----- 71 (281)
T ss_pred ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Cccc--ccCHHHHHHHHHHHHHHHHHHHhhhcccc-----
Confidence 36889999999999999999999999999999997775 4543 23699999999999999999764310000
Q ss_pred HHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHH
Q 008652 401 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK 480 (558)
Q Consensus 401 ~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~le~ 480 (558)
+ .+ .-+..+ ..+. ...|++.++.
T Consensus 72 ------------~---~~-----------------------------~~~~e~------------~~~~-~~~~~~~~~~ 94 (281)
T TIGR02957 72 ------------Y---VG-----------------------------PWLPEP------------LLTT-SADPAESVEL 94 (281)
T ss_pred ------------c---CC-----------------------------CCCCcc------------cCCC-CCChHHHHHH
Confidence 0 00 000000 0000 1234444433
Q ss_pred -HHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008652 481 -QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 546 (558)
Q Consensus 481 -~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 546 (558)
+.+...+..+|+.|||+||.||.|+|. .++|++|||+.||+|..+|+++++||+++||+...
T Consensus 95 ~e~~~~~l~~~l~~L~~~~R~v~~L~~~----~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~ 157 (281)
T TIGR02957 95 AESLSMAYLLLLERLSPLERAVFVLREV----FDYPYEEIASIVGKSEANCRQLVSRARRHLDARRP 157 (281)
T ss_pred HHHHHHHHHHHHhhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 345567889999999999999999998 89999999999999999999999999999999764
No 122
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=99.62 E-value=1.3e-14 Score=149.89 Aligned_cols=162 Identities=17% Similarity=0.086 Sum_probs=123.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccc
Q 008652 317 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 396 (558)
Q Consensus 317 ~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP 396 (558)
..+..++..|.+.++.+|+++.++..+.||++||.++.+|++...+ . ..|.+|++...++.+.+++++..+.-..
T Consensus 5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~-~---~~~~aWL~~Ia~n~~id~lRk~~~rr~~- 79 (290)
T PRK09635 5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD-I---DDERGWLIVVTSRLCLDHIKSASTRRER- 79 (290)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc-c---ccHHHHHHHHHHHHHHHHHhhhhccCcC-
Confidence 5678999999999999999999999999999999999999987543 1 3599999999999999998764310000
Q ss_pred hhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhH
Q 008652 397 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI 476 (558)
Q Consensus 397 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~ 476 (558)
....+.. .. + +...+ ..+|++
T Consensus 80 --------------------------------------------------~~~~~~~--~~-~----~~~~~--~~~~~~ 100 (290)
T PRK09635 80 --------------------------------------------------PQDIAAW--HD-G----DASVS--SVDPAD 100 (290)
T ss_pred --------------------------------------------------ccccccc--Cc-c----ccCCC--CCCcHH
Confidence 0000000 00 0 00001 112332
Q ss_pred -HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008652 477 -SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 546 (558)
Q Consensus 477 -~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 546 (558)
....++....+..+|..|||++|.||.|+|. .++|++|||+.||+|..+|++++.||+++||+...
T Consensus 101 ~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~~----~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~~ 167 (290)
T PRK09635 101 RVTLDDEVRLALLIMLERLGPAERVVFVLHEI----FGLPYQQIATTIGSQASTCRQLAHRARRKINESRI 167 (290)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHH----hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhCC
Confidence 3345556678999999999999999999998 89999999999999999999999999999998643
No 123
>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=99.50 E-value=3.2e-13 Score=123.94 Aligned_cols=136 Identities=12% Similarity=0.144 Sum_probs=99.7
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhh-----cCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008652 319 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEK-----FKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 393 (558)
Q Consensus 319 re~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiek-----FDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~I 393 (558)
++.++..|.++++.+|++|... +| +||.++.+|..+.+ |++. ..|.||.+..+++.+.++++++.+..
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 3679999999999999999662 34 49999999999875 5433 47999999999999999997654210
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCC
Q 008652 394 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 473 (558)
Q Consensus 394 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~ 473 (558)
+. .. ..++ + + ... .
T Consensus 74 ~~------------------~~-------~~~~------------------------~------~----------~~~-~ 87 (142)
T TIGR03209 74 KI------------------IY-------NSEI------------------------T------D----------IKL-S 87 (142)
T ss_pred hh------------------hh-------hhhh------------------------h------c----------ccc-c
Confidence 00 00 0000 0 0 000 1
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHH
Q 008652 474 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVR 531 (558)
Q Consensus 474 pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVR 531 (558)
+.+.+...+....|..+|+.||+++|+||.|+|. +++|++|||+.||+|.++|+
T Consensus 88 ~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~----~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 88 LINVYSSNDLEFEFNDLISILPNKQKKIIYMKFF----EDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred hhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHhhc
Confidence 1122233344557889999999999999999998 99999999999999999997
No 124
>PRK09191 two-component response regulator; Provisional
Probab=99.50 E-value=2.6e-13 Score=135.10 Aligned_cols=137 Identities=16% Similarity=0.119 Sum_probs=110.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccch
Q 008652 318 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 397 (558)
Q Consensus 318 Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~ 397 (558)
++..|+..|.+.|+++|.++.++..+.+|++||+++.+|+...+|++. ..|.+|++.++++.....
T Consensus 2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~~------------ 67 (261)
T PRK09191 2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSSA------------ 67 (261)
T ss_pred chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhccc------------
Confidence 578999999999999999999999999999999999999999999875 358899887655321000
Q ss_pred hHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHH
Q 008652 398 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 477 (558)
Q Consensus 398 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~ 477 (558)
.. ... .. ..+..
T Consensus 68 -------------------------------------------------------~~--~~~--------~~--~~~~~- 79 (261)
T PRK09191 68 -------------------------------------------------------GA--NDP--------EP--GSPFE- 79 (261)
T ss_pred -------------------------------------------------------cc--cCC--------CC--CCCch-
Confidence 00 000 00 01111
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008652 478 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 547 (558)
Q Consensus 478 le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 547 (558)
..+..+|+.||+++|+||.|+|. +++|++|||+.||+|.++|+.+..+|+++||..+..
T Consensus 80 -------~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~~ 138 (261)
T PRK09191 80 -------ARAERRLAGLTPLPRQAFLLTAL----EGFSVEEAAEILGVDPAEAEALLDDARAEIARQVAT 138 (261)
T ss_pred -------HHHHHHHHhCCHHHhHHHHHHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCCC
Confidence 16888999999999999999998 999999999999999999999999999999987653
No 125
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=99.44 E-value=6.9e-12 Score=126.17 Aligned_cols=90 Identities=20% Similarity=0.328 Sum_probs=78.9
Q ss_pred HHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCC--CHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008652 305 CRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGI--SLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 381 (558)
Q Consensus 305 ~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~--~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a 381 (558)
.+.++..++.| ..|++.|+..|.++|+++|.++.++.. +.+|++|||++++|+++++|++++|..|.+|+..+|++.
T Consensus 5 ~~~Li~~~~~gD~~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn~ 84 (237)
T PRK08311 5 LEDILEKIKNGDEELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKRR 84 (237)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence 34555666655 489999999999999999999998765 589999999999999999999999888999999999999
Q ss_pred HHHHHHhcccccc
Q 008652 382 IRKAIFQHSRTIR 394 (558)
Q Consensus 382 I~~aIr~~sr~IR 394 (558)
+.++++++.+...
T Consensus 85 ~iDylRk~~~~~~ 97 (237)
T PRK08311 85 LIDYFRKESKHNL 97 (237)
T ss_pred HHHHHHHhhcccc
Confidence 9999998766433
No 126
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=99.38 E-value=3.3e-11 Score=116.45 Aligned_cols=174 Identities=20% Similarity=0.300 Sum_probs=117.9
Q ss_pred HHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCC---CCCHHH--HHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHH
Q 008652 306 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGR---GISLHD--LLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR 379 (558)
Q Consensus 306 ~~L~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~---g~~~eD--LIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr 379 (558)
.+|+..++.|+ .|.+.|+..|++-++.+|+++.+. +.+.+| |++|.++.+++.-...+.+....|..|+...++
T Consensus 5 t~ll~~~~~GD~~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~~~~~r 84 (185)
T PF07638_consen 5 TELLDRWRQGDEAALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALLARIMR 84 (185)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHHHHHHH
Confidence 44566666665 999999999999999999987643 345555 467777777764333344333468888888888
Q ss_pred HHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCC
Q 008652 380 QTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD 459 (558)
Q Consensus 380 ~aI~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~ 459 (558)
+.+.+.++.+.+.. .+|.. ...+|+...
T Consensus 85 r~lid~~R~~~a~K----------------------Rg~~~-------------------------~~~~l~~~~----- 112 (185)
T PF07638_consen 85 RKLIDHARRRQAQK----------------------RGGDQ-------------------------VRVELDERA----- 112 (185)
T ss_pred HHHHHHHHHHHHHh----------------------cCCCC-------------------------cccchhhhh-----
Confidence 88888776544211 11100 011122111
Q ss_pred cchhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008652 460 TTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 539 (558)
Q Consensus 460 ~~l~e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 539 (558)
.+...+.|+..+ ++.+.+..+.. |+|++++||.++|. .|+|.+|||+.||||..+|++....|..
T Consensus 113 -------~~~~~~~~~~~~---~l~e~l~~L~~-l~~~~~~~v~l~~~----~Gls~~EIA~~lgiS~~tV~r~l~~aR~ 177 (185)
T PF07638_consen 113 -------DSGDEPSPEELL---ELEEALERLLA-LDPRQRRVVELRFF----EGLSVEEIAERLGISERTVRRRLRRARA 177 (185)
T ss_pred -------ccccCCCHHHHH---HHHHHHHHHHc-cCHHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 011112344433 23445555555 99999999999998 8999999999999999999999999999
Q ss_pred HHHHHhh
Q 008652 540 RLKQSLG 546 (558)
Q Consensus 540 KLR~~l~ 546 (558)
+|+..+.
T Consensus 178 ~l~~~l~ 184 (185)
T PF07638_consen 178 WLRRELR 184 (185)
T ss_pred HHHHHhc
Confidence 9998774
No 127
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=99.24 E-value=2.3e-11 Score=93.12 Aligned_cols=50 Identities=36% Similarity=0.628 Sum_probs=46.3
Q ss_pred HHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 490 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 490 ~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
+|+.||++|++||.++|+ +++|+.|||+.||+|+++|+++..+|++|||+
T Consensus 1 Al~~L~~~er~vi~~~y~----~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 1 ALDQLPPREREVIRLRYF----EGLTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp HHCTS-HHHHHHHHHHHT----ST-SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred ChhhCCHHHHHHHHHHhc----CCCCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 588999999999999998 99999999999999999999999999999985
No 128
>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=99.23 E-value=3.3e-11 Score=96.94 Aligned_cols=70 Identities=23% Similarity=0.432 Sum_probs=67.1
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccc
Q 008652 322 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR 391 (558)
Q Consensus 322 LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr 391 (558)
|++.|.++|++++++|.+++.+.+|++||++++||+++++||+++|..|.+|++..+++.+.++++++.|
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 6899999999999999999999999999999999999999999999899999999999999999998764
No 129
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=99.02 E-value=7.4e-10 Score=92.07 Aligned_cols=77 Identities=30% Similarity=0.491 Sum_probs=66.1
Q ss_pred HHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHH
Q 008652 401 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 477 (558)
Q Consensus 401 ~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~ 477 (558)
+.+++|.+++..|.+++||.||.+|||+.||+++++|..++...+.++||+.+++.+++..+.+++.|+...+|++.
T Consensus 1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d~~~~~P~e~ 77 (78)
T PF04539_consen 1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIEDDDAPSPEEE 77 (78)
T ss_dssp HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-SSS--HHHH
T ss_pred ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecCCCCCChhhc
Confidence 35789999999999999999999999999999999999999999999999999998888999999999988888764
No 130
>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=98.92 E-value=3.6e-09 Score=81.96 Aligned_cols=54 Identities=30% Similarity=0.440 Sum_probs=46.5
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008652 484 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 541 (558)
Q Consensus 484 ~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 541 (558)
++.|..+|..||+++|.||.++|. +++|++|||+.+|+|.++|++.+.+|+++|
T Consensus 1 r~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIa~~l~~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 1 REALQQALAQLPERQREIFLLRYF----QGMSYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp HHHHHHHHHCS-HHHHHHHHHHHT----S---HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH----HCcCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 357899999999999999999998 999999999999999999999999999987
No 131
>PRK06930 positive control sigma-like factor; Validated
Probab=98.65 E-value=1.3e-07 Score=90.77 Aligned_cols=70 Identities=19% Similarity=0.292 Sum_probs=62.0
Q ss_pred hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008652 475 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 548 (558)
Q Consensus 475 e~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 548 (558)
.+.....+....|..++..||+++|+||.++|+ +|+|++|||+.||+|.++|++++.||+++|+..+...
T Consensus 96 ~~~~~~~e~~~~l~~al~~L~~rer~V~~L~~~----eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~ 165 (170)
T PRK06930 96 PESVISEWDKIRIEDALSVLTEREKEVYLMHRG----YGLSYSEIADYLNIKKSTVQSMIERAEKKIARQINES 165 (170)
T ss_pred hhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 333444556678999999999999999999998 9999999999999999999999999999999988754
No 132
>PRK00118 putative DNA-binding protein; Validated
Probab=98.44 E-value=9.8e-07 Score=78.16 Aligned_cols=61 Identities=21% Similarity=0.146 Sum_probs=55.3
Q ss_pred HHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008652 486 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 550 (558)
Q Consensus 486 ~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L 550 (558)
.+.-....||+++++|+.++|. +++|..|||+.+|+|+.+|+.++.||+++||+++..-++
T Consensus 10 l~d~~~~~L~ekqRevl~L~y~----eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~ 70 (104)
T PRK00118 10 LFDFYGSLLTEKQRNYMELYYL----DDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHL 70 (104)
T ss_pred HHHHHhccCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence 4455668999999999999998 899999999999999999999999999999999877554
No 133
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=98.30 E-value=2.2e-06 Score=64.24 Aligned_cols=53 Identities=38% Similarity=0.589 Sum_probs=49.5
Q ss_pred HHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 486 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 486 ~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
.+..++..|++.++.++.++|. +++|..+||+.+|+|..+|+++..+++.+||
T Consensus 3 ~~~~~~~~l~~~~~~~~~~~~~----~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 3 RLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred HHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 5778899999999999999997 8899999999999999999999999998874
No 134
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=98.19 E-value=3.5e-06 Score=78.17 Aligned_cols=57 Identities=19% Similarity=0.269 Sum_probs=49.5
Q ss_pred hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchHhh
Q 008652 492 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGY 553 (558)
Q Consensus 492 ~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~y 553 (558)
..|+++|++||.+++ +|+|++|||+.||+|+.+|++++++|+++||.......+-.+
T Consensus 5 ~~Lte~qr~VL~Lr~-----~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l~~~ 61 (137)
T TIGR00721 5 TFLTERQIKVLELRE-----KGLSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDFVKF 61 (137)
T ss_pred CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHHHHH
Confidence 359999999999975 799999999999999999999999999999986555444443
No 135
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=98.16 E-value=4.8e-06 Score=77.61 Aligned_cols=51 Identities=24% Similarity=0.399 Sum_probs=47.1
Q ss_pred hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008652 492 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 547 (558)
Q Consensus 492 ~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 547 (558)
..|+++|++||.+++ +++|++|||+.||+|+.+|++++++|+++||+....
T Consensus 5 ~~Lt~rqreVL~lr~-----~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t 55 (141)
T PRK03975 5 SFLTERQIEVLRLRE-----RGLTQQEIADILGTSRANVSSIEKRARENIEKARET 55 (141)
T ss_pred cCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 469999999999965 799999999999999999999999999999987654
No 136
>PRK04217 hypothetical protein; Provisional
Probab=98.10 E-value=6.3e-06 Score=73.75 Aligned_cols=56 Identities=20% Similarity=0.134 Sum_probs=51.4
Q ss_pred hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchH
Q 008652 492 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASY 551 (558)
Q Consensus 492 ~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~ 551 (558)
..|++.|++||.++|. +++|++|||+.||||+.+|++++.+|+++|++.+......
T Consensus 41 ~~Lt~eereai~l~~~----eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~~~ 96 (110)
T PRK04217 41 IFMTYEEFEALRLVDY----EGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGREL 96 (110)
T ss_pred ccCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhccce
Confidence 5699999999999998 8999999999999999999999999999999998765543
No 137
>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=98.02 E-value=1.6e-06 Score=62.79 Aligned_cols=35 Identities=40% Similarity=0.439 Sum_probs=30.5
Q ss_pred ChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHH
Q 008652 243 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRL 277 (558)
Q Consensus 243 ~d~l~~Yl~~i~~~~lLT~eEE~eL~~~iq~~~~l 277 (558)
+|+++.||++|+++|+||++||++|+++|+.+...
T Consensus 1 ~D~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~~~ 35 (37)
T PF00140_consen 1 SDSLRLYLKEIGRYPLLTAEEEIELARRIRKGDEA 35 (37)
T ss_dssp HHHHHHHHHHHHHS-EETTHHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHHh
Confidence 37899999999999999999999999999986543
No 138
>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=97.97 E-value=3.4e-05 Score=71.26 Aligned_cols=63 Identities=19% Similarity=0.295 Sum_probs=55.5
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008652 482 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 546 (558)
Q Consensus 482 ~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 546 (558)
...+.|..+|+.|++.+|.||.++|+ .+..+|..+||..||+|+.+|+++..+|+.+|+..++
T Consensus 71 ~~~~~I~~~l~~Ld~~er~II~~rY~--~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~lG 133 (134)
T TIGR01636 71 RNRDAIENCLNEADEQTRVIIQELYM--KKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEELG 133 (134)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHc--cCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhC
Confidence 34677999999999999999999996 2234699999999999999999999999999998753
No 139
>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=97.95 E-value=3.7e-05 Score=67.76 Aligned_cols=58 Identities=28% Similarity=0.350 Sum_probs=45.2
Q ss_pred HHHHHH-hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008652 486 HVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 547 (558)
Q Consensus 486 ~L~~~L-~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 547 (558)
.|.... .-|+++|++++.++|. +++|+.|||+.+||||..|...++||.++|...-..
T Consensus 9 ~L~d~Yg~LLT~kQ~~~l~lyy~----eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~yE~k 67 (101)
T PF04297_consen 9 LLFDFYGELLTEKQREILELYYE----EDLSLSEIAEELGISRQAVYDSIKRAEKKLEEYEEK 67 (101)
T ss_dssp HHHHHHGGGS-HHHHHHHHHHCT----S---HHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHCCHHHHHHHHHHHc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 344444 4599999999999998 999999999999999999999999999999775433
No 140
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=97.90 E-value=0.003 Score=72.29 Aligned_cols=34 Identities=32% Similarity=0.493 Sum_probs=31.7
Q ss_pred CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHH
Q 008652 242 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLI 275 (558)
Q Consensus 242 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~iq~~~ 275 (558)
.+||+++||++|++.||||+|+|++++++|..+.
T Consensus 102 t~DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~ 135 (619)
T PRK05658 102 TDDPVRMYLREMGTVELLTREGEIEIAKRIEAGE 135 (619)
T ss_pred CCChHHHHHHHhccCcCCCcHHHHHHHHHHHHHH
Confidence 5799999999999999999999999999998754
No 141
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=97.82 E-value=4.1e-05 Score=58.31 Aligned_cols=46 Identities=26% Similarity=0.400 Sum_probs=41.4
Q ss_pred hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 492 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 492 ~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
..|+++|+.|+.+.+ .+++.+|||+.+|+|+.+|+++..+++++|.
T Consensus 2 ~~l~~~e~~i~~~~~-----~g~s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 2 ASLTPREREVLRLLA-----EGLTNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 468999999997754 6899999999999999999999999988885
No 142
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=97.69 E-value=9.4e-05 Score=58.19 Aligned_cols=46 Identities=24% Similarity=0.335 Sum_probs=41.2
Q ss_pred hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 492 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 492 ~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
..|+++|.+|+.+.. .|+|.+|||+.+|||..+|+....++++||.
T Consensus 2 ~~LT~~E~~vl~~l~-----~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 2 PSLTERELEVLRLLA-----QGMSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp GSS-HHHHHHHHHHH-----TTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred CccCHHHHHHHHHHH-----hcCCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 479999999999987 7999999999999999999999999999985
No 143
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=97.63 E-value=0.00014 Score=55.54 Aligned_cols=45 Identities=29% Similarity=0.487 Sum_probs=40.4
Q ss_pred CCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 494 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 494 L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
|+++|++|+.+.+ .++|.+|||+.+|+|+.+|++...+++++|+.
T Consensus 1 l~~~e~~i~~~~~-----~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~ 45 (57)
T cd06170 1 LTPREREVLRLLA-----EGKTNKEIADILGISEKTVKTHLRNIMRKLGV 45 (57)
T ss_pred CCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 6899999998854 68999999999999999999999999888864
No 144
>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This entry is represented by Streptococcus phage 7201, Orf19. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several hypothetical, highly conserved Streptococcal and related phage proteins. The function of this family is unknown.
Probab=97.58 E-value=0.00036 Score=61.35 Aligned_cols=55 Identities=22% Similarity=0.439 Sum_probs=49.8
Q ss_pred HHHHHHHHHhcCC-HHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008652 483 MRQHVRNLLTLLN-PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 541 (558)
Q Consensus 483 ~~e~L~~~L~~L~-~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 541 (558)
.+..+..+++.|+ +.+|.||.++|. .+++..+|++.||+|+.++..+..+|++.|
T Consensus 44 ~k~ei~~~I~~l~d~~~r~iL~~~Yi----~~~~~~~I~~~l~~S~~t~yr~~~~Al~~L 99 (100)
T PF07374_consen 44 EKLEIRRAINKLEDPDERLILRMRYI----NKLTWEQIAEELNISRRTYYRIHKKALKEL 99 (100)
T ss_pred HHHHHHHHHHHccChhHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence 3456888898886 799999999998 789999999999999999999999999986
No 145
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=97.56 E-value=0.00019 Score=59.74 Aligned_cols=47 Identities=19% Similarity=0.213 Sum_probs=41.6
Q ss_pred HHHHHHhcCCHHHHHHHHHH-hccCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 486 HVRNLLTLLNPKERCIVRLR-FGIEDGKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 486 ~L~~~L~~L~~rEReVL~LR-yGL~d~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
.+.+-|+.||++.+.++.|. |. +++|++|||+.||+|..+|+.++.+
T Consensus 8 ~~~~~l~~l~~~~r~af~L~R~~----eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 8 KLAERLTWVDSLAEAAAALAREE----AGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred hHHHHHhcCCHHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 45677899999999999995 45 8999999999999999999998774
No 146
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=97.53 E-value=0.00033 Score=54.81 Aligned_cols=48 Identities=27% Similarity=0.428 Sum_probs=42.3
Q ss_pred CCHHHHHHHHHHhccC--C-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008652 494 LNPKERCIVRLRFGIE--D-GKPKSLSEVGNIFGLSKERVRQLESRALYRL 541 (558)
Q Consensus 494 L~~rEReVL~LRyGL~--d-~e~~Tl~EIAe~LGISrerVRqie~RALkKL 541 (558)
|+++|++||..-|-.+ + ...-|+.|||+.||||+.++..++.+|.+||
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae~kl 51 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAERKL 51 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 7899999999876543 3 3688999999999999999999999999987
No 147
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=97.43 E-value=0.00022 Score=62.01 Aligned_cols=49 Identities=22% Similarity=0.244 Sum_probs=42.9
Q ss_pred HHHHHHH-hcCCHHHHHHHHHHhccCC---CCCCCHHHHHHHhCCCHHHHHHH
Q 008652 485 QHVRNLL-TLLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQL 533 (558)
Q Consensus 485 e~L~~~L-~~L~~rEReVL~LRyGL~d---~e~~Tl~EIAe~LGISrerVRqi 533 (558)
+.+..+| ..|+|+|+.+|.+||++.+ ..++|++|||+.+|||+.+|.+.
T Consensus 23 ~~l~~~l~~lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~ 75 (94)
T TIGR01321 23 DDMQLLLELILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRG 75 (94)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHH
Confidence 3566677 5599999999999999987 67999999999999999999754
No 148
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=97.35 E-value=0.00042 Score=66.78 Aligned_cols=47 Identities=23% Similarity=0.352 Sum_probs=43.8
Q ss_pred hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 492 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 492 ~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
..|+++|++||.+.- +|+|.+|||+.||+|..||+....++++||.-
T Consensus 132 ~~LSpRErEVLrLLA-----qGkTnKEIAe~L~IS~rTVkth~srImkKLgV 178 (198)
T PRK15201 132 RHFSVTERHLLKLIA-----SGYHLSETAALLSLSEEQTKSLRRSIMRKLHV 178 (198)
T ss_pred CCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 469999999999986 89999999999999999999999999999954
No 149
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=97.31 E-value=0.00041 Score=68.35 Aligned_cols=46 Identities=11% Similarity=0.237 Sum_probs=43.4
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
.|++||++||.+.- +|+|.+|||+.||+|..||+....+.++||.-
T Consensus 137 ~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v 182 (207)
T PRK15411 137 SLSRTESSMLRMWM-----AGQGTIQISDQMNIKAKTVSSHKGNIKRKIKT 182 (207)
T ss_pred cCCHHHHHHHHHHH-----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence 49999999999986 79999999999999999999999999999963
No 150
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=97.27 E-value=0.00048 Score=67.13 Aligned_cols=46 Identities=22% Similarity=0.291 Sum_probs=43.2
Q ss_pred hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 492 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 492 ~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
..|++||++|+.+.- +|+|.+|||+.||||..||+....+.++||-
T Consensus 149 ~~Lt~rE~evl~~~~-----~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~ 194 (216)
T PRK10840 149 KRLSPKESEVLRLFA-----EGFLVTEIAKKLNRSIKTISSQKKSAMMKLG 194 (216)
T ss_pred ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 459999999999986 7999999999999999999999999999994
No 151
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=97.24 E-value=0.00054 Score=68.12 Aligned_cols=50 Identities=8% Similarity=-0.050 Sum_probs=46.4
Q ss_pred HHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 488 RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 488 ~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
.++...|++||++||.+.- +|+|.+|||+.|++|..||+....+.++||.
T Consensus 138 ~~~~~~LS~RE~eVL~Lia-----~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLg 187 (217)
T PRK13719 138 LEAKNKVTKYQNDVFILYS-----FGFSHEYIAQLLNITVGSSKNKISEILKFFG 187 (217)
T ss_pred hhccCCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 5567899999999999986 7999999999999999999999999999994
No 152
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=97.24 E-value=0.00055 Score=69.71 Aligned_cols=48 Identities=21% Similarity=0.261 Sum_probs=44.4
Q ss_pred HhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 491 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 491 L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
+..|+++|++|+.+.. +|+|.+|||++||||..||+..+.++++||.-
T Consensus 188 ~~~LT~RE~evl~l~a-----~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v 235 (247)
T TIGR03020 188 AGLITAREAEILAWVR-----DGKTNEEIAAILGISSLTVKNHLQHIFKKLDV 235 (247)
T ss_pred ccCCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence 4579999999999965 79999999999999999999999999999964
No 153
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=97.23 E-value=0.00057 Score=67.62 Aligned_cols=46 Identities=20% Similarity=0.342 Sum_probs=43.4
Q ss_pred hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 492 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 492 ~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
..|++||++||.+.- +|+|.+|||+.|+||..||+....+.++||-
T Consensus 133 ~~LT~RE~eVL~ll~-----~G~snkeIA~~L~iS~~TV~~h~~~I~~KLg 178 (207)
T PRK11475 133 RMLSPTEREILRFMS-----RGYSMPQIAEQLERNIKTIRAHKFNVMSKLG 178 (207)
T ss_pred CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 469999999999987 7999999999999999999999999999994
No 154
>PRK13870 transcriptional regulator TraR; Provisional
Probab=97.23 E-value=0.00053 Score=69.07 Aligned_cols=45 Identities=27% Similarity=0.383 Sum_probs=42.7
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
.|++||++||.+-= +|+|..|||.+||||..||...++.|++||-
T Consensus 173 ~LT~RE~E~L~W~A-----~GKT~~EIa~ILgISe~TV~~Hl~na~~KLg 217 (234)
T PRK13870 173 WLDPKEATYLRWIA-----VGKTMEEIADVEGVKYNSVRVKLREAMKRFD 217 (234)
T ss_pred CCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 59999999999986 7999999999999999999999999999994
No 155
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=97.23 E-value=0.00054 Score=68.75 Aligned_cols=48 Identities=19% Similarity=0.267 Sum_probs=44.5
Q ss_pred HhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 491 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 491 L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
...|+++|++||.+.. +|+|..|||++||||..||+..+.++++||+.
T Consensus 169 ~~~Lt~re~evl~~~a-----~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~ 216 (232)
T TIGR03541 169 AGVLSEREREVLAWTA-----LGRRQADIAAILGISERTVENHLRSARRKLGV 216 (232)
T ss_pred hccCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence 3579999999999975 79999999999999999999999999999974
No 156
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=97.18 E-value=0.00068 Score=67.47 Aligned_cols=48 Identities=17% Similarity=0.127 Sum_probs=44.5
Q ss_pred HhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 491 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 491 L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
+..|+++|++|+.+.+ +|+|.+|||+.|++|..||+....++++||.-
T Consensus 153 ~~~Lt~rE~~Vl~l~~-----~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v 200 (216)
T PRK10100 153 SALLTHREKEILNKLR-----IGASNNEIARSLFISENTVKTHLYNLFKKIAV 200 (216)
T ss_pred cCCCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 3469999999999998 69999999999999999999999999999964
No 157
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=97.17 E-value=0.00072 Score=68.36 Aligned_cols=45 Identities=16% Similarity=0.258 Sum_probs=43.0
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
.|++||++||.+-. +|+|..|||++||||..||+..+.++++||-
T Consensus 179 ~LT~rE~evl~~~a-----~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~ 223 (240)
T PRK10188 179 NFSKREKEILKWTA-----EGKTSAEIAMILSISENTVNFHQKNMQKKFN 223 (240)
T ss_pred CCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 69999999999986 8999999999999999999999999999995
No 158
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=97.07 E-value=0.00092 Score=66.23 Aligned_cols=46 Identities=30% Similarity=0.371 Sum_probs=43.2
Q ss_pred hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 492 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 492 ~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
..|++||++|+++-- +|+|.+|||+.|++|..||+....+.++||.
T Consensus 147 ~~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~ 192 (211)
T COG2197 147 ELLTPRELEVLRLLA-----EGLSNKEIAEELNLSEKTVKTHVSNILRKLG 192 (211)
T ss_pred CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHhHHHHHHHHHHHHcC
Confidence 469999999999876 7999999999999999999999999999994
No 159
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=97.05 E-value=0.0015 Score=58.12 Aligned_cols=53 Identities=19% Similarity=0.164 Sum_probs=48.5
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 549 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 549 (558)
.|+..|-+.|+|-+. +++|++|-|+.||||+.|+-.++..|++|+-..|....
T Consensus 41 ~L~~dElEAiRL~D~----egl~QeeaA~~MgVSR~T~~ril~~ARkKiA~ALv~Gk 93 (106)
T PF02001_consen 41 VLTVDELEAIRLVDY----EGLSQEEAAERMGVSRPTFQRILESARKKIADALVEGK 93 (106)
T ss_pred EeeHHHHHHHHHHHH----cCCCHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHCCC
Confidence 478888999999998 99999999999999999999999999999999886543
No 160
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=97.04 E-value=0.0023 Score=62.33 Aligned_cols=59 Identities=17% Similarity=0.260 Sum_probs=53.0
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008652 482 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 545 (558)
Q Consensus 482 ~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 545 (558)
.....+...+.+|++|||+|+..-- .|+..++||..||||.-||...-.+.++|++..-
T Consensus 131 ~~~~~~~~~l~tLT~RERqVl~~vV-----~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~S 189 (202)
T COG4566 131 DRQAAIRARLATLTPRERQVLDLVV-----RGLMNKQIAFDLGISERTVELHRANVMEKMQARS 189 (202)
T ss_pred HHHHHHHHHHHhcCHHHHHHHHHHH-----cCcccHHHHHHcCCchhhHHHHHHHHHHHHhhcc
Confidence 3446788999999999999999887 7999999999999999999999999999998643
No 161
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=96.97 E-value=0.0024 Score=50.22 Aligned_cols=48 Identities=33% Similarity=0.432 Sum_probs=43.3
Q ss_pred hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008652 492 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 544 (558)
Q Consensus 492 ~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 544 (558)
..|+++|.+|+.+.- .|++..|||..+|+|..+|+....++.+||.-.
T Consensus 3 ~~Lt~rE~~v~~l~~-----~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~ 50 (65)
T COG2771 3 ADLTPREREILRLVA-----QGKSNKEIARILGISEETVKTHLRNIYRKLGVK 50 (65)
T ss_pred ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 368999999998876 679999999999999999999999999999653
No 162
>PRK09483 response regulator; Provisional
Probab=96.90 E-value=0.0017 Score=62.04 Aligned_cols=46 Identities=22% Similarity=0.300 Sum_probs=42.3
Q ss_pred hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 492 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 492 ~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
..|+++|++||.+.. +|+|.+|||+.|++|..||+....+.++||-
T Consensus 147 ~~Lt~rE~~vl~~~~-----~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~ 192 (217)
T PRK09483 147 ASLSERELQIMLMIT-----KGQKVNEISEQLNLSPKTVNSYRYRMFSKLN 192 (217)
T ss_pred cccCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 469999999998764 7899999999999999999999999999983
No 163
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=96.88 E-value=0.0013 Score=49.22 Aligned_cols=41 Identities=24% Similarity=0.339 Sum_probs=24.3
Q ss_pred hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 492 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 492 ~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
..|++.||..|...+- +|+|..+||+.||++++||...++|
T Consensus 3 ~~Lt~~eR~~I~~l~~----~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEALLE----QGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHHHHC----S---HHHHHHHTT--HHHHHHHHHH
T ss_pred cchhhhHHHHHHHHHH----cCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 4689999999988876 8999999999999999999988776
No 164
>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family. This model represents a family of phage proteins, including ArpU, called a putative autolysin regulatory protein. ArpU was described as a regulator of cellular muramidase-2 of Enterococcus hirae but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors. We propose that this is a phage transcriptional activator family.
Probab=96.72 E-value=0.01 Score=54.29 Aligned_cols=63 Identities=21% Similarity=0.231 Sum_probs=53.7
Q ss_pred HHHHHHHHHH-hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008652 482 LMRQHVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 546 (558)
Q Consensus 482 ~~~e~L~~~L-~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 546 (558)
.....+..++ +.|++.+|+||..+|. . .++++..+|+..+|+|+.+...+..+|+.++-..+.
T Consensus 67 ~~~~~i~~ai~~~l~~~~r~Il~~~Yl-~-~~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~l~ 130 (132)
T TIGR01637 67 QEARAIVNAIVNQLDEISRQILYDKYL-E-PDQKYDYQIMMELGYSHRQYYRIKKRALLRFATLYG 130 (132)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHc-C-ccccchHHHHHHhCCcHHHHHHHHHHHHHHHHHHhC
Confidence 3345677777 9999999999999997 2 137899999999999999999999999999977664
No 165
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=96.70 E-value=0.0034 Score=58.54 Aligned_cols=46 Identities=22% Similarity=0.358 Sum_probs=42.4
Q ss_pred hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 492 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 492 ~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
..|+++|++||.+. . ++++.+|||+.+++|..||+....++++||.
T Consensus 148 ~~lt~~e~~vl~l~-~----~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 148 PLLTPRERQILKLI-T----EGYTNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred cCCCHHHHHHHHHH-H----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 45999999999984 4 7899999999999999999999999999995
No 166
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=96.62 E-value=0.0045 Score=61.42 Aligned_cols=53 Identities=23% Similarity=0.350 Sum_probs=46.1
Q ss_pred cCCHHHHHHHHHHhccC--C-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008652 493 LLNPKERCIVRLRFGIE--D-GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 545 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~--d-~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 545 (558)
.|+++|++||+.-|-++ | ....+++|||+.||||+.++.+++.+|.+||=..+
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~~~ 210 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIEAY 210 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 69999999999877543 3 36789999999999999999999999999996543
No 167
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=96.50 E-value=0.0021 Score=58.45 Aligned_cols=48 Identities=25% Similarity=0.359 Sum_probs=44.5
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 545 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 545 (558)
-|+++|-.||.||- +|+|.+|||++||-|+..|+-|+++|+.++.+..
T Consensus 8 flte~qikvl~lRe-----kG~tQ~eIA~~L~TTraNvSaIEkrA~enIekar 55 (143)
T COG1356 8 FLTEQQIKVLVLRE-----KGLTQSEIARILKTTRANVSAIEKRALENIEKAR 55 (143)
T ss_pred eeehhheeeeehhh-----ccccHHHHHHHHccchhhHHHHHHHHHHHHHHHH
Confidence 48999999999997 7999999999999999999999999999998754
No 168
>PRK10651 transcriptional regulator NarL; Provisional
Probab=96.49 E-value=0.0049 Score=58.20 Aligned_cols=46 Identities=20% Similarity=0.294 Sum_probs=42.5
Q ss_pred hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 492 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 492 ~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
..|+++|++|+.+.. ++++.++||+.+++|..||+....++++||.
T Consensus 154 ~~Lt~rE~~vl~~l~-----~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~ 199 (216)
T PRK10651 154 NQLTPRERDILKLIA-----QGLPNKMIARRLDITESTVKVHVKHMLKKMK 199 (216)
T ss_pred ccCCHHHHHHHHHHH-----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 459999999999865 7899999999999999999999999999995
No 169
>PRK01381 Trp operon repressor; Provisional
Probab=96.48 E-value=0.003 Score=55.45 Aligned_cols=48 Identities=27% Similarity=0.312 Sum_probs=40.6
Q ss_pred HHHHHHHHhc-CCHHHHHHHHHHhccCC---CCCCCHHHHHHHhCCCHHHHH
Q 008652 484 RQHVRNLLTL-LNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVR 531 (558)
Q Consensus 484 ~e~L~~~L~~-L~~rEReVL~LRyGL~d---~e~~Tl~EIAe~LGISrerVR 531 (558)
.+.+..+|.. |+|+|+..|..||++.. ..++|+.||++.+|||..+|.
T Consensus 22 ~~~~~~~l~~llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTIT 73 (99)
T PRK01381 22 EDLHLPLLTLLLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATIT 73 (99)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeeh
Confidence 3456666755 99999999999999886 457999999999999998886
No 170
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=96.44 E-value=0.0086 Score=55.54 Aligned_cols=54 Identities=13% Similarity=0.189 Sum_probs=47.3
Q ss_pred HHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008652 486 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 544 (558)
Q Consensus 486 ~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 544 (558)
.+...+..|+++|++||.+.+ .+++.++||+.+|+|..+|+....++++||+..
T Consensus 134 ~~~~~~~~l~~~e~~vl~~~~-----~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~ 187 (202)
T PRK09390 134 DIRARIASLSERERQVMDGLV-----AGLSNKVIARDLDISPRTVEVYRANVMTKMQAG 187 (202)
T ss_pred HHHHHHHhhhhhHHHHHHHHH-----ccCchHHHHHHcCCCHHHHHHHHHHHHHHHccc
Confidence 455667889999999999744 679999999999999999999999999999653
No 171
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=96.42 E-value=0.013 Score=51.55 Aligned_cols=48 Identities=25% Similarity=0.328 Sum_probs=43.9
Q ss_pred hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 492 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 492 ~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
.-|+.+|+..+.++|. .++|+.|||+.++|||..|...++|+-+.|-.
T Consensus 16 sLLT~KQ~~Y~~lyy~----dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~ 63 (105)
T COG2739 16 SLLTKKQKNYLELYYL----DDLSLSEIAEEFNVSRQAIYDNIKRTEKILED 63 (105)
T ss_pred HHHhHHHHHHHHHHHH----hhccHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence 4589999999999998 89999999999999999999999998877744
No 172
>PRK15320 transcriptional activator SprB; Provisional
Probab=96.10 E-value=0.011 Score=58.16 Aligned_cols=50 Identities=22% Similarity=0.308 Sum_probs=44.7
Q ss_pred HHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 489 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 489 ~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
.+--.|+++|.+|+.+-- +|+|.+|||+.|++|..+|+....+.+.||.-
T Consensus 160 ~~~~~LSdREIEVL~LLA-----kG~SNKEIAekL~LS~KTVSTYKnRLLeKLgA 209 (251)
T PRK15320 160 NLPPGVTQAKYALLILLS-----SGHPAIELAKKFGLGTKTVSIYRKKVMYRLGM 209 (251)
T ss_pred cCCCCCCHHHHHHHHHHH-----cCCCHHHHHHHhccchhhHHHHHHHHHHHcCC
Confidence 334689999999999876 79999999999999999999999999999853
No 173
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=95.97 E-value=0.02 Score=49.84 Aligned_cols=52 Identities=19% Similarity=0.148 Sum_probs=46.8
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 548 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 548 (558)
.|+..|-+.|+|... ++++++|-|.+||||+.|+-..+..|++|+-..+...
T Consensus 33 ~lt~eElEAlRLvD~----~~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~aLveG 84 (99)
T COG1342 33 ILTIEELEALRLVDY----EGLTQEEAALRMGISRQTFWRLLTSARKKVADALVEG 84 (99)
T ss_pred eecHHHHHHHHHHhH----hhccHHHHHHHhcccHHHHHHHHHHHHHHHHHHHhcC
Confidence 367778889999988 8999999999999999999999999999999887654
No 174
>PRK10403 transcriptional regulator NarP; Provisional
Probab=95.90 E-value=0.015 Score=54.72 Aligned_cols=46 Identities=15% Similarity=0.230 Sum_probs=42.2
Q ss_pred hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 492 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 492 ~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
..|+++|.+|+.+.. +++|.+|||+.+|+|..||+....+.++||.
T Consensus 152 ~~Lt~~e~~vl~~~~-----~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 152 SVLTERELDVLHELA-----QGLSNKQIASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred ccCCHHHHHHHHHHH-----CCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 459999999998765 6899999999999999999999999999984
No 175
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=95.60 E-value=0.29 Score=51.89 Aligned_cols=159 Identities=18% Similarity=0.167 Sum_probs=96.5
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhH
Q 008652 320 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI 399 (558)
Q Consensus 320 e~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~ 399 (558)
+..+..-.+-++.---+|+++=.-.|+.+||.|+.-.+...+=-|-++ -..|.+..-|+.-++.++++.+.-..|.
T Consensus 8 e~~~r~~~~r~~a~L~r~~rd~dlAEEa~~dA~~~Ale~WPr~G~P~~--PaAWL~~v~R~~aiD~~Rr~~~~~~~~~-- 83 (415)
T COG4941 8 EAAARIERPRAMAALARYLRDLDLAEEALQDAFAAALERWPRAGPPRN--PAAWLIAVGRNRAIDRVRRRARRDAAPP-- 83 (415)
T ss_pred HHHHHHhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHhCcccCCCCC--hHHHHHHHHhhhHHHHHHHHHHhccCCh--
Confidence 334444444444444556666566899999999876666554433332 4566666677777777776553222211
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHH
Q 008652 400 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ 479 (558)
Q Consensus 400 ~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~le 479 (558)
|+. ++. +|......+...|. .+.
T Consensus 84 -------------------------el~--------------------~~~-----e~~e~~~a~~~~d~-------~i~ 106 (415)
T COG4941 84 -------------------------ELL--------------------LSD-----EDEEMEEAEALDDE-------HIR 106 (415)
T ss_pred -------------------------hhc--------------------ccc-----cchhhhcccccccc-------ccc
Confidence 110 000 00000000000011 111
Q ss_pred HHHHHHHHHHHH-hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008652 480 KQLMRQHVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 544 (558)
Q Consensus 480 ~~~~~e~L~~~L-~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 544 (558)
++.++ .|.-|. -.|++.+|--|.||.. -|+|..|||..|=|+..++-|.+.||.++++..
T Consensus 107 Dd~LR-LiFvccHPal~~~~riALtLR~v----~GLs~~eIArAFLv~e~am~QRivRAK~ri~~a 167 (415)
T COG4941 107 DDRLR-LIFVCCHPALPPEQRIALTLRLV----GGLSTAEIARAFLVPEAAMAQRIVRAKARIREA 167 (415)
T ss_pred hhhHH-hhhhhcCCCCChhhHHHHHHHHH----cCCcHHHHHHHHcCCcHHHHHHHHHHHHHHHhc
Confidence 12222 333333 5699999999999998 799999999999999999999999999999974
No 176
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=95.56 E-value=0.02 Score=53.69 Aligned_cols=46 Identities=20% Similarity=0.255 Sum_probs=42.3
Q ss_pred hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 492 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 492 ~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
..|+++|++|+.+.. +++|.++||+.+++|..+|+....+.++||.
T Consensus 136 ~~Lt~~E~~il~~l~-----~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 136 DPLTKRERQVAEKLA-----QGMAVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred cCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 469999999999866 6799999999999999999999999999985
No 177
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=95.55 E-value=0.027 Score=53.24 Aligned_cols=47 Identities=21% Similarity=0.320 Sum_probs=42.7
Q ss_pred HhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 491 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 491 L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
+..|+++|++|+.+.. .+.+.+|||+.+++|..||+....+.++||.
T Consensus 141 ~~~lt~~E~~vl~~l~-----~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~ 187 (204)
T PRK09958 141 LDSLSKQEISVMRYIL-----DGKDNNDIAEKMFISNKTVSTYKSRLMEKLE 187 (204)
T ss_pred cccCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 3569999999999887 6889999999999999999999999999983
No 178
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=95.50 E-value=0.029 Score=52.95 Aligned_cols=45 Identities=24% Similarity=0.242 Sum_probs=40.5
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
.|+++|.+|+.+.. +++|.+|||+.+++|..||+....++++||.
T Consensus 149 ~lt~re~~vl~~l~-----~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 149 VLSNREVTILRYLV-----SGLSNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred cCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 48999999988654 6799999999999999999999999999984
No 179
>PRK13558 bacterio-opsin activator; Provisional
Probab=95.28 E-value=0.033 Score=63.58 Aligned_cols=54 Identities=13% Similarity=0.059 Sum_probs=45.4
Q ss_pred HhcCCHHHHHHHHHHhccC---CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008652 491 LTLLNPKERCIVRLRFGIE---DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 544 (558)
Q Consensus 491 L~~L~~rEReVL~LRyGL~---d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 544 (558)
...|+++|+++|..-|..+ -..+-|++|||+.||||+.++.+++.+|.+||=..
T Consensus 605 ~~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l~~~ 661 (665)
T PRK13558 605 ENDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKLVGA 661 (665)
T ss_pred hhhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4689999999999988721 11344999999999999999999999999999554
No 180
>PRK04841 transcriptional regulator MalT; Provisional
Probab=95.26 E-value=0.029 Score=66.06 Aligned_cols=46 Identities=11% Similarity=0.172 Sum_probs=43.2
Q ss_pred hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 492 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 492 ~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
..|+++|++|+.+.. +|+|.+|||+.|+||..||+..+++.+.||.
T Consensus 837 ~~lt~~e~~v~~~~~-----~g~~~~~ia~~l~~s~~tv~~h~~~~~~kl~ 882 (903)
T PRK04841 837 SPLTQREWQVLGLIY-----SGYSNEQIAGELDVAATTIKTHIRNLYQKLG 882 (903)
T ss_pred CCCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 449999999999977 7999999999999999999999999999995
No 181
>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=95.13 E-value=0.027 Score=39.61 Aligned_cols=27 Identities=30% Similarity=0.643 Sum_probs=20.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 513 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 513 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
++|.+|||+.+|+|+|+|. |++++|++
T Consensus 2 ~mtr~diA~~lG~t~ETVS----R~l~~l~~ 28 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVS----RILKKLER 28 (32)
T ss_dssp E--HHHHHHHHTS-HHHHH----HHHHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHH----HHHHHHHH
Confidence 4789999999999999997 56666654
No 182
>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=94.76 E-value=0.13 Score=41.99 Aligned_cols=56 Identities=18% Similarity=0.287 Sum_probs=45.1
Q ss_pred HHHHHhhcHHHHHHHHHHHHHHHHHHHHHhh----C--CCCCHHHHHHHHHHHHHHhhhhcC
Q 008652 308 LKSELHSGNSSREKLINANLRLVVHVAKQYQ----G--RGISLHDLLQEGSMGLMKSVEKFK 363 (558)
Q Consensus 308 L~~~l~~G~~Are~LI~~nlrLV~sIArrY~----~--~g~~~eDLIQEG~IGLirAiekFD 363 (558)
+.++.+|+..|.++++..|.+++.+.+.+-. + ++.--+|+-|+-...|++++-+|+
T Consensus 4 I~~A~~GD~~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~ 65 (65)
T PF12645_consen 4 IKAAKQGDPEAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE 65 (65)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence 4445566679999999999999999998722 2 233349999999999999999996
No 183
>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=94.68 E-value=0.092 Score=39.43 Aligned_cols=41 Identities=17% Similarity=0.255 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008652 494 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 537 (558)
Q Consensus 494 L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA 537 (558)
|++.++.||..-+- ..+.|..|||+.+|+|..+|++++++-
T Consensus 1 l~~~~~~Il~~l~~---~~~~t~~ela~~~~is~~tv~~~l~~L 41 (48)
T PF13412_consen 1 LDETQRKILNYLRE---NPRITQKELAEKLGISRSTVNRYLKKL 41 (48)
T ss_dssp --HHHHHHHHHHHH---CTTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH---cCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 57788888876553 356999999999999999998766543
No 184
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=94.68 E-value=0.069 Score=46.14 Aligned_cols=37 Identities=14% Similarity=0.220 Sum_probs=31.0
Q ss_pred hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008652 492 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE 534 (558)
Q Consensus 492 ~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie 534 (558)
..|++| .+|+.+.- .|+|..|||+.+|||+.||..+.
T Consensus 35 ~~Ls~R-~~I~~ll~-----~G~S~~eIA~~LgISrsTIyRi~ 71 (88)
T TIGR02531 35 QSLAQR-LQVAKMLK-----QGKTYSDIEAETGASTATISRVK 71 (88)
T ss_pred HhhhHH-HHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHH
Confidence 458899 77877754 67999999999999999998833
No 185
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=94.62 E-value=0.088 Score=40.83 Aligned_cols=50 Identities=18% Similarity=0.242 Sum_probs=42.6
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 545 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 545 (558)
.|+..++-++.+.|. ..+.|++.||..+|||+.+|.++.+..+.-|-..+
T Consensus 2 kLs~~d~lll~L~~L---R~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l 51 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYL---RLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVL 51 (53)
T ss_pred CCCHHHHHHHHHHHH---HcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhc
Confidence 578888888888775 36899999999999999999999999888776554
No 186
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=94.48 E-value=0.037 Score=41.82 Aligned_cols=32 Identities=28% Similarity=0.361 Sum_probs=22.8
Q ss_pred HHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008652 501 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 537 (558)
Q Consensus 501 VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA 537 (558)
||.+.. +++|..+||+.||||+.+|+++.++-
T Consensus 10 ii~l~~-----~G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 10 IIRLLR-----EGWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp HHHHHH-----HT--HHHHHHHHTS-HHHHHHHHT--
T ss_pred HHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 555555 58999999999999999999887653
No 187
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=94.33 E-value=0.16 Score=47.01 Aligned_cols=55 Identities=16% Similarity=0.322 Sum_probs=45.8
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008652 483 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 539 (558)
Q Consensus 483 ~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 539 (558)
.++.|...++.|.+.++.||.+||+ ...++|..+||..|+|+..+++.....-..
T Consensus 71 ~k~~id~~~~~l~de~k~Ii~lry~--~r~~~TW~~IA~~l~i~erta~r~~~~fK~ 125 (130)
T PF05263_consen 71 QKEAIDRWLETLIDEEKRIIKLRYD--RRSRRTWYQIAQKLHISERTARRWRDRFKN 125 (130)
T ss_pred HHHHHHHHHHhhCHHHHHHHHHHHc--ccccchHHHHHHHhCccHHHHHHHHHHHHH
Confidence 3467788899999999999999998 334699999999999999999876655443
No 188
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=94.07 E-value=0.071 Score=56.29 Aligned_cols=36 Identities=22% Similarity=0.344 Sum_probs=32.7
Q ss_pred HHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008652 500 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 539 (558)
Q Consensus 500 eVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 539 (558)
.|-.|||. +++|++|||++|||||.+|.+++.+|++
T Consensus 20 ~vA~lYY~----~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~ 55 (318)
T PRK15418 20 RIAWFYYH----DGLTQSEIGERLGLTRLKVSRLLEKGRQ 55 (318)
T ss_pred HHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 46678887 9999999999999999999999999976
No 189
>PF13730 HTH_36: Helix-turn-helix domain
Probab=93.72 E-value=0.25 Score=38.03 Aligned_cols=47 Identities=19% Similarity=0.289 Sum_probs=34.5
Q ss_pred cCCHHHHHHHHHHhccCCCCCC---CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPK---SLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~---Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
.|++.++.|+..-..+.++.+. |.+.||+.+|+|+.+|+ ++++.|.+
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~----~~i~~L~~ 51 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQ----RAIKELEE 51 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 5888888887765554432322 89999999999999997 56666654
No 190
>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=93.60 E-value=0.092 Score=39.34 Aligned_cols=33 Identities=24% Similarity=0.296 Sum_probs=23.8
Q ss_pred HHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 498 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 498 EReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
..+|+.|+- +|+|..+||+.+|||+.||.+++.
T Consensus 11 ~~~i~~l~~-----~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 11 IEEIKELYA-----EGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHHH-----TT--HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHh
Confidence 345666664 679999999999999999998753
No 191
>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 993W gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator. GpQ positively regulates expression of the phage late gene operons. Bacterial host RNA polymerase modified by antitermination proteins transcribes through termination sites that otherwise prevent expression of the regulated genes [, ].; GO: 0003677 DNA binding, 0060567 negative regulation of transcription termination, DNA-dependent
Probab=93.56 E-value=0.5 Score=43.24 Aligned_cols=54 Identities=19% Similarity=0.121 Sum_probs=48.7
Q ss_pred HhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008652 491 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 548 (558)
Q Consensus 491 L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 548 (558)
|..-.+.+-+||.++|. .++|...||..+++|...||+.+.+|-.-+..++.-.
T Consensus 60 L~~~~~~~~~ll~~~Yv----~g~s~r~IA~~~~~s~~~ir~~l~~ae~~i~g~l~~~ 113 (125)
T PF06530_consen 60 LKKRDPEEYDLLILYYV----YGWSKRQIARKLKCSEGKIRKRLQRAEGFIDGCLSML 113 (125)
T ss_pred HHccCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHhhhhHhhhhHHh
Confidence 45578999999999999 8999999999999999999999999999998876443
No 192
>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=93.54 E-value=0.11 Score=42.36 Aligned_cols=45 Identities=18% Similarity=0.396 Sum_probs=29.1
Q ss_pred HhcCCHHHHHHHHHH--hccCCCCCCCHHHHHHHhCCC-HHHHHHHHH
Q 008652 491 LTLLNPKERCIVRLR--FGIEDGKPKSLSEVGNIFGLS-KERVRQLES 535 (558)
Q Consensus 491 L~~L~~rEReVL~LR--yGL~d~e~~Tl~EIAe~LGIS-rerVRqie~ 535 (558)
+..|+++|++||... |.-..|-+-|..|||+.||++ ..+|.+.+.
T Consensus 1 M~~LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~ 48 (65)
T PF01726_consen 1 MKELTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLK 48 (65)
T ss_dssp -----HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHH
Confidence 357999999998763 333345788999999999997 999986654
No 193
>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=93.37 E-value=0.18 Score=33.50 Aligned_cols=36 Identities=19% Similarity=0.335 Sum_probs=27.9
Q ss_pred CCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHH
Q 008652 494 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL 533 (558)
Q Consensus 494 L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqi 533 (558)
+++.++..+...|. .+.+..+||+.+|+++.+|..+
T Consensus 6 ~~~~~~~~i~~~~~----~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 6 LTPEQIEEARRLLA----AGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHh
Confidence 45555665555554 5779999999999999999875
No 194
>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=92.85 E-value=0.22 Score=41.09 Aligned_cols=37 Identities=32% Similarity=0.651 Sum_probs=29.1
Q ss_pred HHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHHHH
Q 008652 276 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL 312 (558)
Q Consensus 276 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l 312 (558)
++.+++.+|+..+||+||.+|.|...|++.+.+...+
T Consensus 5 ~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l 41 (78)
T PF04539_consen 5 KIERARRELEQELGREPTDEEIAEELGISVEEVRELL 41 (78)
T ss_dssp HHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHH
Confidence 5667889999999999999999999999988776544
No 195
>PHA00675 hypothetical protein
Probab=92.46 E-value=0.24 Score=41.60 Aligned_cols=40 Identities=18% Similarity=0.089 Sum_probs=31.8
Q ss_pred hcCCHHHHHHHHHHh-ccCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 492 TLLNPKERCIVRLRF-GIEDGKPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 492 ~~L~~rEReVL~LRy-GL~d~e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
..|++.+-+.|+.++ - .+.|+.+||..||||+++|.+|..
T Consensus 21 AKLt~~qV~~IR~l~~r----~G~s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 21 AKLTDAEVERIRELHEV----EGMSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred cccCHHHHHHHHHHHHh----cCccHHHHHHHhCCCHHHHHHHHc
Confidence 356666666666655 4 678999999999999999999865
No 196
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=92.01 E-value=0.44 Score=35.44 Aligned_cols=40 Identities=35% Similarity=0.460 Sum_probs=27.3
Q ss_pred CCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 494 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 494 L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
|++-.+.||..--. | ...|+.+||+.+|+|..+|.+++.+
T Consensus 1 lD~~D~~Il~~Lq~--d-~r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 1 LDELDRKILRLLQE--D-GRRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp --HHHHHHHHHHHH----TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH--c-CCccHHHHHHHHCcCHHHHHHHHHH
Confidence 34556667766543 2 5789999999999999999987654
No 197
>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=91.95 E-value=2.1 Score=43.00 Aligned_cols=35 Identities=31% Similarity=0.574 Sum_probs=28.7
Q ss_pred HHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHH
Q 008652 276 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 310 (558)
Q Consensus 276 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~ 310 (558)
++.++..+|...+|++||.++.|...|++.+.+..
T Consensus 88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~ 122 (238)
T TIGR02393 88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVRE 122 (238)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 34456677888899999999999999999877753
No 198
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=91.89 E-value=2.2 Score=45.94 Aligned_cols=129 Identities=19% Similarity=0.273 Sum_probs=71.3
Q ss_pred HHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHH-HHHH
Q 008652 277 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEG-SMGL 355 (558)
Q Consensus 277 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG-~IGL 355 (558)
+.+...+|...+|++||..|.|...|++.+.+...+... .. .+++++.+.++ -..|
T Consensus 218 ~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~-------------------~~----~~SLd~~~~~~~~~~l 274 (367)
T PRK09210 218 LIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIA-------------------QE----PVSLETPIGEEDDSHL 274 (367)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHh-------------------cC----CCCcCCCCCCCCcchh
Confidence 455677788889999999999999999988775433211 11 11111111110 0111
Q ss_pred HHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHH
Q 008652 356 MKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVE 435 (558)
Q Consensus 356 irAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e 435 (558)
...+. |+.............++..+.+++. .||..-...+.. .+.-..|..-|.+|||+.+|+|.+
T Consensus 275 ~d~i~--d~~~~~p~~~~~~~~~~~~l~~~l~------~L~~rEr~Vl~l------rygl~~~~~~tl~EIa~~lgvs~e 340 (367)
T PRK09210 275 GDFIE--DQDATSPADHAAYELLKEQLEDVLD------TLTDREENVLRL------RFGLDDGRTRTLEEVGKVFGVTRE 340 (367)
T ss_pred hhhcc--CCCCCCHHHHHHHHHHHHHHHHHHH------hCCHHHHHHHHH------HhccCCCCCccHHHHHHHHCCCHH
Confidence 11111 1111223334445556666666663 244332222211 111122467899999999999999
Q ss_pred HHHHHHH
Q 008652 436 KLERLIF 442 (558)
Q Consensus 436 ~v~~ll~ 442 (558)
+|+.+..
T Consensus 341 rVrQi~~ 347 (367)
T PRK09210 341 RIRQIEA 347 (367)
T ss_pred HHHHHHH
Confidence 9998854
No 199
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=91.64 E-value=0.36 Score=47.89 Aligned_cols=48 Identities=15% Similarity=0.070 Sum_probs=36.7
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR 540 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkK 540 (558)
.|+++|.+++.....=..++|+|.+|||+.||+|..||+....++...
T Consensus 158 ~Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~ 205 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVNC 205 (239)
T ss_pred CCCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHhC
Confidence 488999877654331112379999999999999999999998877543
No 200
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=91.40 E-value=3.3 Score=43.95 Aligned_cols=35 Identities=31% Similarity=0.452 Sum_probs=29.3
Q ss_pred HHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHH
Q 008652 276 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 310 (558)
Q Consensus 276 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~ 310 (558)
++.++..+|...+|++||..|.|...|++.+.+..
T Consensus 174 ~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~ 208 (324)
T PRK07921 174 KLARIKRELHQQLGREATDEELAEESGIPEEKIAD 208 (324)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence 45567778888999999999999999999877753
No 201
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=91.31 E-value=5.9 Score=40.59 Aligned_cols=147 Identities=18% Similarity=0.183 Sum_probs=81.3
Q ss_pred HHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHHHHhhcHHHHHHHHH
Q 008652 245 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 324 (558)
Q Consensus 245 ~l~~Yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~ 324 (558)
.+..||++-.. .--+.--.+++.+ +..+..+|+..+|++||..|.|+..|++.+++...+..+
T Consensus 88 ei~d~LR~~~~--v~vpR~~~~~~~~------i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~--------- 150 (247)
T COG1191 88 EILDYLRKNDS--VKVPRSLRELGRR------IEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAI--------- 150 (247)
T ss_pred HHHHHHHhCCC--ccCcHHHHHHHHH------HHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHh---------
Confidence 45668888771 1112233444444 455778889999999999999999999988775444332
Q ss_pred HHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHH
Q 008652 325 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS 404 (558)
Q Consensus 325 ~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~~~l~ 404 (558)
+.....++--.....+... + +...+..+..+-.|-..+.+..++.. +|..-..
T Consensus 151 -~~~~~~sld~~~~~~~d~~--------------~---~~~~~~~~~~~~~~~~~~~l~~ai~~------L~EREk~--- 203 (247)
T COG1191 151 -NGSQLLSLDEDVLKDDDDD--------------V---DDQIENPDDGVEKEELLEILKEAIEP------LPEREKL--- 203 (247)
T ss_pred -ccccccchhhhhccccccc--------------h---hhccccchhHHHHHHHHHHHHHHHHc------cCHHHHH---
Confidence 2222222222111111110 1 11122234445555566666666531 2221110
Q ss_pred HHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 405 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF 442 (558)
Q Consensus 405 ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~ 442 (558)
-+.....-+-|..|||+.||+|..+|..+..
T Consensus 204 -------Vl~l~y~eelt~kEI~~~LgISes~VSql~k 234 (247)
T COG1191 204 -------VLVLRYKEELTQKEIAEVLGISESRVSRLHK 234 (247)
T ss_pred -------HHHHHHHhccCHHHHHHHhCccHHHHHHHHH
Confidence 0111122356789999999999999988754
No 202
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=91.03 E-value=0.61 Score=42.18 Aligned_cols=50 Identities=20% Similarity=0.299 Sum_probs=42.4
Q ss_pred HHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 490 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 490 ~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
.+..|++.+.+-|....- ..=+++|+++.||||-.|||.++.+.+.+|.-
T Consensus 30 ~~~~L~~E~~~Fi~~Fi~----~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 30 WFARLSPEQLEFIKLFIK----NRGNLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred hhhcCCHHHHHHHHHHHH----hcCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 367899998887776554 34499999999999999999999999999965
No 203
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=91.01 E-value=5.2 Score=44.03 Aligned_cols=37 Identities=22% Similarity=0.399 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008652 405 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLI 441 (558)
Q Consensus 405 ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll 441 (558)
.+.+.+..|..++|++||.+|.|..+|+++..++..+
T Consensus 112 ~l~~~~~~l~~~~g~~pt~~ewa~~~~~~~~~l~~~l 148 (415)
T PRK07598 112 RLIEVRERLTSELGHRPSLERWAKTADISLADLKPTL 148 (415)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCcHHHHHHhh
Confidence 3445667888999999999999988887766665554
No 204
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=90.99 E-value=3.3 Score=46.65 Aligned_cols=130 Identities=17% Similarity=0.295 Sum_probs=70.1
Q ss_pred HHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHH-HHHH
Q 008652 276 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQE-GSMG 354 (558)
Q Consensus 276 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQE-G~IG 354 (558)
++.+++.+|...+|++||.+|.|...|++.+.+...... ....+++++.+.+ +...
T Consensus 359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~-----------------------~~~~~SLD~~i~~d~~~~ 415 (509)
T PRK05901 359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKY-----------------------NREPISLDKTIGKEGDSQ 415 (509)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh-----------------------cCCCcccccccccCCccc
Confidence 445577888889999999999999999998776543211 1112222222211 1111
Q ss_pred HHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCH
Q 008652 355 LMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITV 434 (558)
Q Consensus 355 LirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~ 434 (558)
+...+. |+........+..+..+..+..++. .||..-...+.. + +.-..+..-|..|||..+|+|.
T Consensus 416 l~d~l~--D~~~~~p~~~~~~~~l~~~L~~aL~------~L~eREr~VI~l----R--yGL~~~e~~TL~EIa~~lGVSr 481 (509)
T PRK05901 416 FGDFIE--DSEAVSPVDAVSFTLLQDQLQEVLE------TLSEREAGVIRM----R--FGLTDGQPKTLDEIGQVYGVTR 481 (509)
T ss_pred HHHhcc--CCCCCCHHHHHHHHHHHHHHHHHHh------hCCHHHHHHHHH----H--hhccCCCCCCHHHHHHHHCCCH
Confidence 211111 1111112233344445555555553 233322222211 1 1011246789999999999999
Q ss_pred HHHHHHHH
Q 008652 435 EKLERLIF 442 (558)
Q Consensus 435 e~v~~ll~ 442 (558)
++|+++..
T Consensus 482 ERVRQIe~ 489 (509)
T PRK05901 482 ERIRQIES 489 (509)
T ss_pred HHHHHHHH
Confidence 99998854
No 205
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=90.88 E-value=0.31 Score=51.64 Aligned_cols=35 Identities=23% Similarity=0.290 Sum_probs=31.2
Q ss_pred HHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008652 501 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 539 (558)
Q Consensus 501 VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 539 (558)
+-.+||. +++|..|||++||||+.+|+.++.+|++
T Consensus 18 ~A~lYY~----~gltQ~eIA~~LgiSR~~v~rlL~~Ar~ 52 (321)
T COG2390 18 AAWLYYV----EGLTQSEIAERLGISRATVSRLLAKARE 52 (321)
T ss_pred HHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 5567887 8999999999999999999999888875
No 206
>PF13518 HTH_28: Helix-turn-helix domain
Probab=90.39 E-value=0.5 Score=35.55 Aligned_cols=27 Identities=26% Similarity=0.382 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESRAL 538 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~RAL 538 (558)
++.|+.+||..+|||+.+|+++..+-.
T Consensus 11 ~g~s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 11 EGESVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred cCCCHHHHHHHHCCCHhHHHHHHHHHH
Confidence 456999999999999999998776543
No 207
>smart00351 PAX Paired Box domain.
Probab=90.39 E-value=0.7 Score=42.18 Aligned_cols=42 Identities=14% Similarity=0.051 Sum_probs=32.6
Q ss_pred CCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008652 494 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 539 (558)
Q Consensus 494 L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 539 (558)
++..+|.=|...|- ++.|..+||+.||||+.+|..+..+...
T Consensus 18 ~s~~~R~riv~~~~----~G~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 18 LPDEERQRIVELAQ----NGVRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred CCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 45555554555554 6889999999999999999999888643
No 208
>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]
Probab=90.21 E-value=0.33 Score=56.83 Aligned_cols=44 Identities=18% Similarity=0.119 Sum_probs=42.2
Q ss_pred CCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 494 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 494 L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
|+.||++|+.+.| .|+|.+|||+.+.||-.||+..+.+.-.||.
T Consensus 832 Ls~RE~eVL~Lia-----~G~SN~eIa~~L~isl~TVKtH~rniy~KLg 875 (894)
T COG2909 832 LSQRELEVLGLIA-----QGLSNEEIAQELFISLTTVKTHIRNIYQKLG 875 (894)
T ss_pred ccHHHHHHHHHHH-----ccCCHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 8999999999999 7999999999999999999999999999984
No 209
>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA. It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.
Probab=90.18 E-value=0.61 Score=40.09 Aligned_cols=45 Identities=29% Similarity=0.322 Sum_probs=33.9
Q ss_pred HHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHh--CCCHHHHHHHHHHH
Q 008652 490 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIF--GLSKERVRQLESRA 537 (558)
Q Consensus 490 ~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~L--GISrerVRqie~RA 537 (558)
.++.||+..+++..+|.- ....|+.|+|+.| .||++.|..+..+.
T Consensus 34 ~~~~l~~~l~~~a~lRl~---~Pd~SL~EL~~~~~~~iSKSgvnhrlrKl 80 (85)
T PF02650_consen 34 GLDKLPEKLREFAELRLE---NPDASLKELGELLEPPISKSGVNHRLRKL 80 (85)
T ss_dssp -GGGS-HHHHHHHHHHHH----TTS-HHHHHHTT--T--HHHHHHHHHHH
T ss_pred ccccCCHHHHHHHHHHHH---CccccHHHHHHHHcCcCcHHHHHHHHHHH
Confidence 358899999999999975 3789999999999 99999998776553
No 210
>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=90.05 E-value=0.61 Score=37.15 Aligned_cols=26 Identities=19% Similarity=0.331 Sum_probs=23.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESRA 537 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~RA 537 (558)
+|++..|||+.||+++.+|.....+-
T Consensus 12 ~G~~~~eIA~~Lg~~~~TV~~W~~r~ 37 (58)
T PF06056_consen 12 QGWSIKEIAEELGVPRSTVYSWKDRY 37 (58)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHHhh
Confidence 79999999999999999999887664
No 211
>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=89.96 E-value=0.39 Score=37.38 Aligned_cols=40 Identities=20% Similarity=0.305 Sum_probs=26.9
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
.|+..|+.=|.-+|- .|.+..+||..|||++.||+.|...
T Consensus 6 ~LTl~eK~~iI~~~e----~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 6 SLTLEEKLEIIKRLE----EGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp S--HHHHHHHHHHHH----CTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred cCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 466666654444454 6779999999999999999998875
No 212
>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=89.63 E-value=0.62 Score=35.77 Aligned_cols=38 Identities=21% Similarity=0.438 Sum_probs=26.8
Q ss_pred HHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 497 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 497 rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
|++.||.+-+ ..+.+.|.+|||+.||||+.+|+..+..
T Consensus 1 R~~~il~~L~--~~~~~it~~eLa~~l~vS~rTi~~~i~~ 38 (55)
T PF08279_consen 1 RQKQILKLLL--ESKEPITAKELAEELGVSRRTIRRDIKE 38 (55)
T ss_dssp HHHHHHHHHH--HTTTSBEHHHHHHHCTS-HHHHHHHHHH
T ss_pred CHHHHHHHHH--HcCCCcCHHHHHHHhCCCHHHHHHHHHH
Confidence 4556666542 2335699999999999999999865543
No 213
>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=89.50 E-value=0.74 Score=35.85 Aligned_cols=43 Identities=23% Similarity=0.287 Sum_probs=32.0
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
.|++.+..||..-+.-+ +.+.|..|||+.+|+++.+|.+++++
T Consensus 2 glt~~q~~vL~~l~~~~-~~~~t~~~la~~l~~~~~~vs~~v~~ 44 (62)
T PF12802_consen 2 GLTPSQFRVLMALARHP-GEELTQSELAERLGISKSTVSRIVKR 44 (62)
T ss_dssp TSTHHHHHHHHHHHHST-TSGEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHHCC-CCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 47888888887766522 23489999999999999999865544
No 214
>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=89.31 E-value=0.69 Score=37.24 Aligned_cols=35 Identities=17% Similarity=0.294 Sum_probs=26.3
Q ss_pred HHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 500 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 500 eVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
..+.++.. .+..+++.+||+.||||..+||....+
T Consensus 11 kA~e~y~~--~~g~i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 11 KAFEIYKE--SNGKIKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred HHHHHHHH--hCCCccHHHHHHHHCCCHHHHHHHhhh
Confidence 34444432 236899999999999999999987554
No 215
>PHA02591 hypothetical protein; Provisional
Probab=89.20 E-value=0.74 Score=38.85 Aligned_cols=24 Identities=21% Similarity=0.436 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
.|+|.++||+.||+|.++||+.+.
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHh
Confidence 689999999999999999999865
No 216
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=88.90 E-value=18 Score=38.07 Aligned_cols=178 Identities=12% Similarity=0.131 Sum_probs=92.3
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhH
Q 008652 320 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI 399 (558)
Q Consensus 320 e~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aIr~~sr~IRlP~~~ 399 (558)
++-+...+..+..++.+. .+-+-+.|....+++.+..-..-+|.....++.-.|.-+++ .
T Consensus 119 er~l~~a~~~I~~~~~~L-----~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR----~----------- 178 (310)
T PRK00423 119 ERNLAFALSELDRIASQL-----GLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACR----R----------- 178 (310)
T ss_pred hHHHHHHHHHHHHHHHHc-----CCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHH----H-----------
Confidence 344444556666666655 23356777777788877766767887666555544443332 1
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchh-hhcccCCCCChhHHH
Q 008652 400 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ-EITADTGVEIPDISV 478 (558)
Q Consensus 400 ~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~-e~i~d~~~~~pe~~l 478 (558)
.+-+-|..||+..++++..++..........+.++.+.. +-..+. .+...-.. +....
T Consensus 179 -----------------~~~prtl~eI~~~~~v~~k~i~~~~~~l~k~L~~~~~~~--~p~~~i~r~~~~L~L--~~~v~ 237 (310)
T PRK00423 179 -----------------CKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPT--DPIDYVPRFASELGL--SGEVQ 237 (310)
T ss_pred -----------------cCCCcCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCC--CHHHHHHHHHHHcCC--CHHHH
Confidence 233557788888888888887665443322222222211 111111 11111111 11111
Q ss_pred HHHHHHHHHHHHHh-cC----CHHH--HHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008652 479 QKQLMRQHVRNLLT-LL----NPKE--RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 541 (558)
Q Consensus 479 e~~~~~e~L~~~L~-~L----~~rE--ReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 541 (558)
. .....+..+.+ .| +|.- --+|.+---+. |.+.|++|||...||+..+|++..+.-.+.|
T Consensus 238 ~--~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~-g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l 304 (310)
T PRK00423 238 K--KAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLL-GERRTQREVAEVAGVTEVTVRNRYKELAEKL 304 (310)
T ss_pred H--HHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHh-CCCCCHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 1 11112222221 11 1211 11222221122 3789999999999999999997776666554
No 217
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=88.77 E-value=5.1 Score=42.93 Aligned_cols=34 Identities=24% Similarity=0.290 Sum_probs=30.0
Q ss_pred CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHH
Q 008652 242 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLI 275 (558)
Q Consensus 242 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~iq~~~ 275 (558)
....+..|+..+...|+||++||.+|+..++.+-
T Consensus 65 ~~~~~~~~~~~~~~~~~l~~~Ee~~la~~~~~g~ 98 (342)
T COG0568 65 PAGRLSFYIRAIEAAPLLTPEEEKALARRLKRGE 98 (342)
T ss_pred hhhhHHHHHHHHhhhcccChHHHHHHHHHHHcCC
Confidence 3457788999999999999999999999999873
No 218
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=88.00 E-value=0.75 Score=43.81 Aligned_cols=50 Identities=14% Similarity=0.050 Sum_probs=43.0
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCC-----HHHHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLS-----KERVRQLESRALYRLKQ 543 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGIS-----rerVRqie~RALkKLR~ 543 (558)
.|+++|.+||.+-.- +.|.++|.+||++.++.+ ..+|+....+.++||..
T Consensus 154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~l~~Kl~~ 208 (228)
T PRK11083 154 TLTRYEFLLLKTLLL-SPGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLRA 208 (228)
T ss_pred ecCHHHHHHHHHHHh-CCCceECHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhcc
Confidence 599999999988763 345679999999999986 77999999999999964
No 219
>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=87.63 E-value=0.82 Score=36.51 Aligned_cols=46 Identities=22% Similarity=0.416 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHHhccC-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 494 LNPKERCIVRLRFGIE-DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 494 L~~rEReVL~LRyGL~-d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
|++....-|..-|.|. ++...+..+||+.||||+.+|.. +++||.+
T Consensus 2 Lt~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~----ml~~L~~ 48 (60)
T PF01325_consen 2 LTESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTE----MLKRLAE 48 (60)
T ss_dssp CSCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHH----HHHHHHH
T ss_pred CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHH----HHHHHHH
Confidence 4555555555555554 55789999999999999999975 5555543
No 220
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=87.51 E-value=1.6 Score=44.48 Aligned_cols=35 Identities=29% Similarity=0.497 Sum_probs=29.1
Q ss_pred HHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHH
Q 008652 276 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 310 (558)
Q Consensus 276 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~ 310 (558)
++.+...+|...+|++||..+.|...|++.+++..
T Consensus 114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~ 148 (256)
T PRK07408 114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQE 148 (256)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHH
Confidence 34556778888999999999999999999877643
No 221
>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=87.49 E-value=1.4 Score=33.01 Aligned_cols=37 Identities=27% Similarity=0.390 Sum_probs=26.9
Q ss_pred HHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 496 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 496 ~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
|.-..||.+-.. .+++..||++.+|+|+.+|++.+..
T Consensus 2 ~~R~~Il~~L~~----~~~~~~el~~~l~~s~~~vs~hL~~ 38 (47)
T PF01022_consen 2 PTRLRILKLLSE----GPLTVSELAEELGLSQSTVSHHLKK 38 (47)
T ss_dssp HHHHHHHHHHTT----SSEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHh----CCCchhhHHHhccccchHHHHHHHH
Confidence 344455555443 6899999999999999999976543
No 222
>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=87.22 E-value=1.3 Score=37.51 Aligned_cols=42 Identities=24% Similarity=0.400 Sum_probs=34.4
Q ss_pred cCCHHHHHHHHHHhc--cCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFG--IEDGKPKSLSEVGNIFGLSKERVRQLE 534 (558)
Q Consensus 493 ~L~~rEReVL~LRyG--L~d~e~~Tl~EIAe~LGISrerVRqie 534 (558)
.|++|+++||..-.- ...+++-.-++||+.+|+|..+||..+
T Consensus 1 ~Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M 44 (78)
T PF03444_consen 1 MLTERQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEM 44 (78)
T ss_pred CCCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHH
Confidence 388999998876432 346789999999999999999999764
No 223
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional
Probab=87.07 E-value=0.92 Score=43.78 Aligned_cols=50 Identities=18% Similarity=0.120 Sum_probs=44.2
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR~ 543 (558)
.|+++|++|+.+... +.|++.|.++|++.+. ++..+|+....+.++||..
T Consensus 160 ~Lt~~e~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~lr~kl~~ 214 (240)
T PRK10710 160 DLTPAEFRLLKTLSH-EPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLES 214 (240)
T ss_pred ecCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCcCcCCCccCHHHHHHHHHHHhhc
Confidence 599999999998764 4557899999999998 9999999999999999963
No 224
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=87.03 E-value=4.5 Score=41.26 Aligned_cols=33 Identities=24% Similarity=0.395 Sum_probs=26.6
Q ss_pred HHHHHHHhhhhCCCCchHHHHHHccCCHHHHHH
Q 008652 278 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 310 (558)
Q Consensus 278 e~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~ 310 (558)
......|...+|++|+..+.|...|++.+.+..
T Consensus 113 ~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~ 145 (257)
T PRK05911 113 ADAMDSLRQSLGKEPTDGELCEYLNISQQELSG 145 (257)
T ss_pred HHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHH
Confidence 344556777889999999999999999877743
No 225
>cd00131 PAX Paired Box domain
Probab=86.67 E-value=1.7 Score=39.88 Aligned_cols=41 Identities=12% Similarity=0.017 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008652 494 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 538 (558)
Q Consensus 494 L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RAL 538 (558)
|+...|.-|...|. +|+|..+||+.||||+.+|..+.++-.
T Consensus 18 lS~d~R~rIv~~~~----~G~s~~~iA~~~~Vs~~tV~r~i~r~~ 58 (128)
T cd00131 18 LPDSIRQRIVELAQ----SGIRPCDISRQLRVSHGCVSKILNRYY 58 (128)
T ss_pred CCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 44444443444454 789999999999999999998888755
No 226
>PRK05949 RNA polymerase sigma factor; Validated
Probab=86.48 E-value=5.9 Score=42.07 Aligned_cols=35 Identities=26% Similarity=0.461 Sum_probs=28.3
Q ss_pred HHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHH
Q 008652 276 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 310 (558)
Q Consensus 276 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~ 310 (558)
++.+....+...+|++|+..+.|+..|++.+.+..
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 34455667778889999999999999999877654
No 227
>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=86.26 E-value=2.4 Score=33.38 Aligned_cols=36 Identities=28% Similarity=0.374 Sum_probs=27.4
Q ss_pred HHHHHHHHHH-hccCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 496 PKERCIVRLR-FGIEDGKPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 496 ~rEReVL~LR-yGL~d~e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
|.-+.||.+- -. .++|..|||+.+|++..+|++.+.
T Consensus 10 p~R~~Il~~L~~~----~~~t~~ela~~l~~~~~t~s~hL~ 46 (61)
T PF12840_consen 10 PTRLRILRLLASN----GPMTVSELAEELGISQSTVSYHLK 46 (61)
T ss_dssp HHHHHHHHHHHHC----STBEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHhcC----CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 5566666665 33 899999999999999999986543
No 228
>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=85.99 E-value=3 Score=41.40 Aligned_cols=32 Identities=38% Similarity=0.579 Sum_probs=26.1
Q ss_pred HHHHHHhhhhCCCCchHHHHHHccCCHHHHHH
Q 008652 279 KEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 310 (558)
Q Consensus 279 ~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~ 310 (558)
+....|...+|+.||..+.|+..|++.+.+..
T Consensus 101 ~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~ 132 (231)
T TIGR02885 101 YMKEELSKELGREPTINELAEALGVSPEEIVM 132 (231)
T ss_pred HHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHH
Confidence 34566777889999999999999999877643
No 229
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=85.69 E-value=1.4 Score=34.81 Aligned_cols=41 Identities=20% Similarity=0.332 Sum_probs=26.1
Q ss_pred CCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 494 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 494 L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
|+..|..||..-. ..+.++|..+|++.+|+++.+|...+++
T Consensus 1 lt~~q~~vL~~l~--~~~~~~t~~~l~~~~~~~~~~vs~~i~~ 41 (68)
T PF13463_consen 1 LTRPQWQVLRALA--HSDGPMTQSDLAERLGISKSTVSRIIKK 41 (68)
T ss_dssp --HHHHHHHHHHT----TS-BEHHHHHHHTT--HHHHHHHHHH
T ss_pred CCHHHHHHHHHHH--ccCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 4566777766555 2348999999999999999999854443
No 230
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=85.55 E-value=1.9 Score=37.52 Aligned_cols=41 Identities=27% Similarity=0.252 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008652 494 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 537 (558)
Q Consensus 494 L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA 537 (558)
|++.++.||..... +...|..+||+.+|+|+.+|++...+-
T Consensus 1 ld~~D~~il~~L~~---~~~~~~~~la~~l~~s~~tv~~~l~~L 41 (108)
T smart00344 1 LDEIDRKILEELQK---DARISLAELAKKVGLSPSTVHNRVKRL 41 (108)
T ss_pred CCHHHHHHHHHHHH---hCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46777888866543 246899999999999999998665543
No 231
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=85.27 E-value=11 Score=38.54 Aligned_cols=34 Identities=26% Similarity=0.524 Sum_probs=28.2
Q ss_pred HHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHH
Q 008652 277 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 310 (558)
Q Consensus 277 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~ 310 (558)
+.+...+|...+|++||..+.|...|++.+++..
T Consensus 129 i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~ 162 (264)
T PRK07122 129 LGRATAELSQRLGRAPTASELAAELGMDREEVVE 162 (264)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 4456677888899999999999999999887754
No 232
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=85.14 E-value=1.3 Score=41.89 Aligned_cols=49 Identities=16% Similarity=0.180 Sum_probs=41.6
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLK 542 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR 542 (558)
.|+++|.+|+.+..- +.|..+|.++|++.+. ++..+|+....+.++||.
T Consensus 149 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl~ 202 (219)
T PRK10336 149 TLKPKEFALLELLMR-NAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLG 202 (219)
T ss_pred ecCHHHHHHHHHHHh-CCCccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhcC
Confidence 499999999986652 3346699999999996 999999999999988885
No 233
>PHA02547 55 RNA polymerase sigma factor; Provisional
Probab=85.08 E-value=3.3 Score=39.96 Aligned_cols=65 Identities=12% Similarity=0.136 Sum_probs=45.9
Q ss_pred HHHHHHHHHHHHHHHhhCCCCC---HHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHH
Q 008652 322 LINANLRLVVHVAKQYQGRGIS---LHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI 386 (558)
Q Consensus 322 LI~~nlrLV~sIArrY~~~g~~---~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~aI 386 (558)
+=.+-+..+..++++|.-+|.. -+|.|.+|.-.+++.+..|||++...+-.|.+..+-++..+.|
T Consensus 42 ig~~imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI 109 (179)
T PHA02547 42 IGLAIMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRI 109 (179)
T ss_pred HHHHHHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHH
Confidence 3344556666666666555555 4899999999999999999999987776666655554444433
No 234
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=85.05 E-value=4.4 Score=38.02 Aligned_cols=65 Identities=18% Similarity=0.311 Sum_probs=36.9
Q ss_pred HHHHHhcCCHHHHHHHHHH----hccCCCCCCCHHHHHHHhCCCHHHHHHHHH--HHHHHHHHHhhcCchH
Q 008652 487 VRNLLTLLNPKERCIVRLR----FGIEDGKPKSLSEVGNIFGLSKERVRQLES--RALYRLKQSLGGKASY 551 (558)
Q Consensus 487 L~~~L~~L~~rEReVL~LR----yGL~d~e~~Tl~EIAe~LGISrerVRqie~--RALkKLR~~l~~~~L~ 551 (558)
+..+=..|++.|+....+- |...+|+.+|+.|||+.+||++.+..++.. +++......+....+.
T Consensus 4 ~~~le~~L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~~~~Fiey~n~la~~~~~ 74 (142)
T PF13022_consen 4 LKELEAKLTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQQNKAFIEYKNELADRFLS 74 (142)
T ss_dssp HHHHHTTS-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHHH-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHcCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHhcCHHHHHHHHHHHHHHHH
Confidence 4455578999888833221 222345789999999999999999998874 4444444444443333
No 235
>PRK15479 transcriptional regulatory protein TctD; Provisional
Probab=84.98 E-value=1.5 Score=41.50 Aligned_cols=49 Identities=18% Similarity=0.233 Sum_probs=41.4
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLK 542 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR 542 (558)
.|+++|.+|+.+..- +.|...|.++|++.+. +|..+|+....+.++||.
T Consensus 148 ~Lt~~E~~il~~l~~-~~~~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl~ 201 (221)
T PRK15479 148 ALTPREQALLTVLMY-RRTRPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKLQ 201 (221)
T ss_pred ecCHHHHHHHHHHHh-CCCCcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhcC
Confidence 599999999987652 3345679999999986 999999999999999985
No 236
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=84.52 E-value=2.1 Score=34.89 Aligned_cols=24 Identities=17% Similarity=0.303 Sum_probs=20.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
++.|..|||+.+||++.+|++++.
T Consensus 21 ~~~ta~eLa~~lgl~~~~v~r~L~ 44 (68)
T smart00550 21 ETSTALQLAKNLGLPKKEVNRVLY 44 (68)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHH
Confidence 369999999999999999875443
No 237
>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=84.52 E-value=12 Score=37.98 Aligned_cols=35 Identities=29% Similarity=0.346 Sum_probs=28.2
Q ss_pred HHHHHHHhhhhCCCCchHHHHHHccCCHHHHHHHH
Q 008652 278 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL 312 (558)
Q Consensus 278 e~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l 312 (558)
.+...++...+|++||..+.|...|++.+.+...+
T Consensus 123 ~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~ 157 (254)
T TIGR02850 123 LQVRDKLISENSKEPTVSEIAKELKVPQEEVVFAL 157 (254)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 34556777889999999999999999988775443
No 238
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=84.46 E-value=18 Score=36.91 Aligned_cols=35 Identities=29% Similarity=0.532 Sum_probs=28.6
Q ss_pred HHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHH
Q 008652 276 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 310 (558)
Q Consensus 276 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~ 310 (558)
++.+....|+..+|++||..+.|...|++.+.+..
T Consensus 119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~ 153 (268)
T PRK06288 119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYNS 153 (268)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHH
Confidence 45556677888899999999999999998876643
No 239
>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=84.31 E-value=1.3 Score=33.81 Aligned_cols=33 Identities=36% Similarity=0.477 Sum_probs=24.3
Q ss_pred HHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 503 RLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 503 ~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
.+.+.-..+.++|+.||++.+|+++.+|..++.
T Consensus 8 iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~ 40 (52)
T PF09339_consen 8 ILEALAESGGPLTLSEIARALGLPKSTVHRLLQ 40 (52)
T ss_dssp HHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 344444455778999999999999999986654
No 240
>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB. PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself. It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.
Probab=84.16 E-value=0.8 Score=43.47 Aligned_cols=49 Identities=16% Similarity=0.117 Sum_probs=41.9
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHH-----HHHhCCCHHHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEV-----GNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EI-----Ae~LGISrerVRqie~RALkKLR 542 (558)
.|+++|.+|+.+-.. +.|+++|.++| |..++++..+|+....+.++||.
T Consensus 154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~l~~Kl~ 207 (226)
T TIGR02154 154 SLGPTEFRLLHFFMT-HPERVYSREQLLDRVWGRDVYVEERTVDVHIRRLRKALN 207 (226)
T ss_pred EcCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCCCCCCCCccHHHHHHHHHHhhc
Confidence 599999999988764 33467888888 77899999999999999999996
No 241
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=84.10 E-value=1.1 Score=43.94 Aligned_cols=39 Identities=18% Similarity=0.232 Sum_probs=28.9
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
.|+++ +|+.+.- .+..++|.+|||+.||||+.||+....
T Consensus 161 ~Lt~r--~Vl~~~~--~g~~g~s~~eIa~~l~iS~~Tv~~~~~ 199 (225)
T PRK10046 161 PLTLN--AVRKLFK--EPGVQHTAETVAQALTISRTTARRYLE 199 (225)
T ss_pred HHHHH--HHHHHHH--cCCCCcCHHHHHHHhCccHHHHHHHHH
Confidence 35665 5665543 122479999999999999999998774
No 242
>PRK12423 LexA repressor; Provisional
Probab=84.01 E-value=1.9 Score=42.39 Aligned_cols=47 Identities=30% Similarity=0.513 Sum_probs=35.2
Q ss_pred cCCHHHHHHHHHHhc--cCCCCCCCHHHHHHHhC-CCHHHHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFG--IEDGKPKSLSEVGNIFG-LSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 493 ~L~~rEReVL~LRyG--L~d~e~~Tl~EIAe~LG-ISrerVRqie~RALkKLR~ 543 (558)
.|++++++|+..--- ..+|-+-|..|||+.|| +|+.+|+ ++|++|++
T Consensus 3 ~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~----~~l~~L~~ 52 (202)
T PRK12423 3 TLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVAR----KHVQALAE 52 (202)
T ss_pred cCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHH----HHHHHHHH
Confidence 489999999875332 12334569999999999 5999998 46666766
No 243
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=84.00 E-value=2.6 Score=31.89 Aligned_cols=26 Identities=27% Similarity=0.429 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESRA 537 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~RA 537 (558)
+..|.++||+.+|||-.+|+.+..+.
T Consensus 26 ~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 26 ESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 34699999999999999999988764
No 244
>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=83.97 E-value=1.3 Score=38.28 Aligned_cols=41 Identities=22% Similarity=0.327 Sum_probs=30.1
Q ss_pred hcCCHHHHHHHHHHhccCC---CCCCCHHHHHHHhCCCHHHHHH
Q 008652 492 TLLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQ 532 (558)
Q Consensus 492 ~~L~~rEReVL~LRyGL~d---~e~~Tl~EIAe~LGISrerVRq 532 (558)
+-++|.|++-|..|+-+-. .+++|+.||++.+|+|..+|.+
T Consensus 25 dL~T~~E~~~l~~R~~va~~lL~~g~syreIa~~tgvS~aTItR 68 (87)
T PF01371_consen 25 DLCTPDELEALAQRWQVAKELLDEGKSYREIAEETGVSIATITR 68 (87)
T ss_dssp HHSSHHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHH
T ss_pred HhCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHH
Confidence 3467777766665554322 1689999999999999999863
No 245
>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=83.62 E-value=4.5 Score=35.10 Aligned_cols=49 Identities=18% Similarity=0.244 Sum_probs=36.6
Q ss_pred HhcCCHHHHHHHHHH----hccC-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 491 LTLLNPKERCIVRLR----FGIE-DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 491 L~~L~~rEReVL~LR----yGL~-d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
...|++++..||..- ||.. ...+.|..|||+.+|+++++|. |++++|.+
T Consensus 20 ~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVs----r~L~~Le~ 73 (95)
T TIGR01610 20 GADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVS----DAIKSLAR 73 (95)
T ss_pred hCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 467899999877633 3422 2368999999999999999987 56666654
No 246
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=83.54 E-value=15 Score=39.80 Aligned_cols=125 Identities=16% Similarity=0.278 Sum_probs=71.0
Q ss_pred HHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcC------------CCcccCCCCCCCCCcchhhhcc------
Q 008652 406 VLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR------------MPLSMQQPVWADQDTTFQEITA------ 467 (558)
Q Consensus 406 i~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~------------~~~SLD~~i~~d~~~~l~e~i~------ 467 (558)
+.+.+..+..++|+.|+..+.|...|++...+...+.... ..+++-..... .+..+.|++.
T Consensus 96 ~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Li~~~l~lV~~iA~ry~~-~~~~~eDLiQEG~igL 174 (373)
T PRK07406 96 LEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMN-RGLSFQDLIQEGSLGL 174 (373)
T ss_pred HHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcC-CCCCHHHHHHHHHHHH
Confidence 3445667778899999999999999999877766543211 01111000000 0111111111
Q ss_pred -------cCCCCChhHHHHHHHHHHHHHHHHh------cCCHHHHH----------HHHHHhccCCCCCCCHHHHHHHhC
Q 008652 468 -------DTGVEIPDISVQKQLMRQHVRNLLT------LLNPKERC----------IVRLRFGIEDGKPKSLSEVGNIFG 524 (558)
Q Consensus 468 -------d~~~~~pe~~le~~~~~e~L~~~L~------~L~~rERe----------VL~LRyGL~d~e~~Tl~EIAe~LG 524 (558)
|+........+.....+..|..+|. +||-.-.. -+...+| ..-|..|||+.||
T Consensus 175 ~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~~~~~~i~~a~~~l~~~lg----r~Pt~~EIA~~lg 250 (373)
T PRK07406 175 IRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFG----RKPTEEEIAESME 250 (373)
T ss_pred HHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHHHHHHHHHHHHHHHHHHhC----CCCCHHHHHHHhC
Confidence 2222234455555556666666663 35544322 2223333 6668999999999
Q ss_pred CCHHHHHHHHH
Q 008652 525 LSKERVRQLES 535 (558)
Q Consensus 525 ISrerVRqie~ 535 (558)
++.+.|+.+..
T Consensus 251 ~~~e~v~~~~~ 261 (373)
T PRK07406 251 MTIEKLRFIAK 261 (373)
T ss_pred CCHHHHHHHHH
Confidence 99999987643
No 247
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=83.20 E-value=2.2 Score=35.76 Aligned_cols=44 Identities=30% Similarity=0.345 Sum_probs=28.7
Q ss_pred HHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHH-----HHHHHHHHHhhcC
Q 008652 501 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES-----RALYRLKQSLGGK 548 (558)
Q Consensus 501 VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~-----RALkKLR~~l~~~ 548 (558)
|..++-- .++|..|+|+.+|+|+.+|.++++ -.+.+|.+.+..-
T Consensus 23 i~~~~~~----~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aL 71 (80)
T PF13744_consen 23 IRELREE----RGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEAL 71 (80)
T ss_dssp HHHHHHC----CT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHT
T ss_pred HHHHHHH----cCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHc
Confidence 4444444 789999999999999999999884 2355555555443
No 248
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=83.20 E-value=4.4 Score=37.38 Aligned_cols=52 Identities=19% Similarity=0.256 Sum_probs=41.8
Q ss_pred HHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 486 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 486 ~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
.+..|+-.|++.+-+|+..-.- .+.++|..|||+.+|++++||. ||+++|=.
T Consensus 17 dvl~c~~GLs~~Dv~v~~~LL~--~~~~~tvdelae~lnr~rStv~----rsl~~L~~ 68 (126)
T COG3355 17 DVLKCVYGLSELDVEVYKALLE--ENGPLTVDELAEILNRSRSTVY----RSLQNLLE 68 (126)
T ss_pred HHHHHHhCCcHHHHHHHHHHHh--hcCCcCHHHHHHHHCccHHHHH----HHHHHHHH
Confidence 5677888999999998876541 2369999999999999999996 67777643
No 249
>PF12728 HTH_17: Helix-turn-helix domain
Probab=82.89 E-value=1.3 Score=33.41 Aligned_cols=24 Identities=17% Similarity=0.376 Sum_probs=21.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRA 537 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RA 537 (558)
+|.+|+|+.||||+.+|+++..+.
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcC
Confidence 689999999999999999987654
No 250
>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=82.68 E-value=21 Score=37.18 Aligned_cols=35 Identities=26% Similarity=0.496 Sum_probs=28.3
Q ss_pred HHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHH
Q 008652 276 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 310 (558)
Q Consensus 276 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~ 310 (558)
++.+.+..+...+|++||..+.|...|++.+.+..
T Consensus 162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~ 196 (298)
T TIGR02997 162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRE 196 (298)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 34455667778899999999999999999877753
No 251
>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=82.63 E-value=1.3 Score=33.63 Aligned_cols=22 Identities=18% Similarity=0.356 Sum_probs=19.8
Q ss_pred CHHHHHHHhCCCHHHHHHHHHH
Q 008652 515 SLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 515 Tl~EIAe~LGISrerVRqie~R 536 (558)
|++|||+..|||..+|+..++.
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~ 22 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNG 22 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTT
T ss_pred CHHHHHHHHCcCHHHHHHHHhC
Confidence 7899999999999999988763
No 252
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=82.51 E-value=2.2 Score=32.44 Aligned_cols=30 Identities=37% Similarity=0.493 Sum_probs=23.7
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 510 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 510 d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
.|... |..|||+.+|+|+.+|+ +++++|.+
T Consensus 16 ~~~~l~s~~~la~~~~vs~~tv~----~~l~~L~~ 46 (60)
T smart00345 16 PGDKLPSERELAAQLGVSRTTVR----EALSRLEA 46 (60)
T ss_pred CCCcCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 34556 89999999999999998 55666654
No 253
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=82.19 E-value=2.7 Score=32.51 Aligned_cols=41 Identities=24% Similarity=0.416 Sum_probs=29.2
Q ss_pred CCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008652 494 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 537 (558)
Q Consensus 494 L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA 537 (558)
|+..|-.||..-+- ..+.|..|||+.+|+++.+|.++..+-
T Consensus 1 lt~~q~~iL~~l~~---~~~~~~~~la~~~~~~~~~~t~~i~~L 41 (59)
T PF01047_consen 1 LTPSQFRILRILYE---NGGITQSELAEKLGISRSTVTRIIKRL 41 (59)
T ss_dssp STHHHHHHHHHHHH---HSSEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH---cCCCCHHHHHHHHCCChhHHHHHHHHH
Confidence 45566666666553 256999999999999999998665543
No 254
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=82.12 E-value=2.6 Score=39.52 Aligned_cols=27 Identities=26% Similarity=0.208 Sum_probs=24.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESRAL 538 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~RAL 538 (558)
+|+|.+|||++||||..+|.....+-.
T Consensus 20 ~G~S~re~Ak~~gvs~sTvy~wv~r~~ 46 (138)
T COG3415 20 EGLSCREAAKRFGVSISTVYRWVRRYR 46 (138)
T ss_pred cCccHHHHHHHhCccHHHHHHHHHHhc
Confidence 799999999999999999998887754
No 255
>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=82.08 E-value=14 Score=33.27 Aligned_cols=27 Identities=33% Similarity=0.471 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
.+.|+.|||+.||||..+|. ++|++|.
T Consensus 70 pd~tl~Ela~~l~Vs~~ti~----~~Lkrlg 96 (119)
T PF01710_consen 70 PDATLRELAERLGVSPSTIW----RALKRLG 96 (119)
T ss_pred CCcCHHHHHHHcCCCHHHHH----HHHHHcC
Confidence 78999999999999999887 5555553
No 256
>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator. This model describes a family of DNA-binding response regulator proteins, associated with an adjacent histidine kinase (TIGR03785) to form a two-component system. This system co-occurs with, and often is adjacent to, a proteobacterial variant form of the protein sorting transpeptidase called sortase (TIGR03784), and a single target protein for the sortase. We give this protein the gene symbol pdsR, for Proteobacterial Dedicated Sortase system Response regulator.
Probab=81.97 E-value=2 Score=41.20 Aligned_cols=50 Identities=14% Similarity=0.087 Sum_probs=41.7
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHH--HHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEV--GNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EI--Ae~LGISrerVRqie~RALkKLR~ 543 (558)
.|+++|.+||.+..- +.|..+|.++| +..++++..+|+....+.++||..
T Consensus 156 ~Lt~~E~~il~~l~~-~~g~v~s~~~i~~~~~~~~~~~tv~~~v~rlr~Kl~~ 207 (227)
T TIGR03787 156 DLTVTEFWMVHALAK-HPGHVKSRQQLMDAAKIVVDDSTITSHIKRIRKKFQA 207 (227)
T ss_pred cCCHHHHHHHHHHHh-CCCccccHHHHHHHhhhcCCccCHHHHHHHHHHHhcc
Confidence 499999999988762 22345699999 888999999999999999999963
No 257
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=81.75 E-value=3.1 Score=39.05 Aligned_cols=41 Identities=15% Similarity=0.261 Sum_probs=32.4
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
.|++.++.||..--. +...|+.|||+.+|+|+.+|+.+..+
T Consensus 6 ~lD~~D~~Il~~Lq~---d~R~s~~eiA~~lglS~~tV~~Ri~r 46 (153)
T PRK11179 6 QIDNLDRGILEALME---NARTPYAELAKQFGVSPGTIHVRVEK 46 (153)
T ss_pred ccCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 377888888876543 25789999999999999999875543
No 258
>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=81.60 E-value=1.5 Score=35.27 Aligned_cols=44 Identities=23% Similarity=0.330 Sum_probs=32.1
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
.|++.|..|+..-. . ..+.|..|||+.+|+++.+|+. ++++|.+
T Consensus 5 gLs~~E~~vy~~Ll--~-~~~~t~~eIa~~l~i~~~~v~~----~L~~L~~ 48 (68)
T PF01978_consen 5 GLSENEAKVYLALL--K-NGPATAEEIAEELGISRSTVYR----ALKSLEE 48 (68)
T ss_dssp CHHHHHHHHHHHHH--H-HCHEEHHHHHHHHTSSHHHHHH----HHHHHHH
T ss_pred CcCHHHHHHHHHHH--H-cCCCCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence 46777777775532 1 1589999999999999999974 4555543
No 259
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=81.30 E-value=21 Score=37.73 Aligned_cols=34 Identities=26% Similarity=0.522 Sum_probs=28.0
Q ss_pred HHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHH
Q 008652 276 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 309 (558)
Q Consensus 276 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~ 309 (558)
++.+...++...+|++||..+.|...|++.+.+.
T Consensus 169 ~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~ 202 (317)
T PRK07405 169 KIKKAQRQLSQQLGRAATIGELAEELELTPKQVR 202 (317)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHH
Confidence 4556677788889999999999999999876664
No 260
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=81.00 E-value=3.9 Score=31.78 Aligned_cols=39 Identities=21% Similarity=0.242 Sum_probs=25.5
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
.|++-|+--|....- .|+++.|||..+|-|+..|+..++
T Consensus 4 ~Lt~~Eqaqid~m~q----lG~s~~~isr~i~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 4 TLTDAEQAQIDVMHQ----LGMSLREISRRIGRSRTCIRRYLK 42 (50)
T ss_dssp ---HHHHHHHHHHHH----TT--HHHHHHHHT--HHHHHHHHH
T ss_pred cCCHHHHHHHHHHHH----hchhHHHHHHHhCccHHHHHHHhc
Confidence 467777776666655 689999999999999999997653
No 261
>PRK00215 LexA repressor; Validated
Probab=80.87 E-value=2.9 Score=40.86 Aligned_cols=44 Identities=25% Similarity=0.320 Sum_probs=33.8
Q ss_pred cCCHHHHHHHHHHh--ccCCCCCCCHHHHHHHhCC-CHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRF--GIEDGKPKSLSEVGNIFGL-SKERVRQLESR 536 (558)
Q Consensus 493 ~L~~rEReVL~LRy--GL~d~e~~Tl~EIAe~LGI-SrerVRqie~R 536 (558)
.|+++|++||.+-. ....+.+.|+.|||+.+|+ ++.+|..++.+
T Consensus 1 ~lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~ 47 (205)
T PRK00215 1 MLTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKA 47 (205)
T ss_pred CCCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 37889999986543 2234478899999999999 99999866544
No 262
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=80.86 E-value=2.8 Score=40.97 Aligned_cols=34 Identities=26% Similarity=0.293 Sum_probs=27.4
Q ss_pred HHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 498 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 498 EReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
++.|..++- .++|..+||+.||||+.||.++.+.
T Consensus 162 ~~~i~~~~~-----~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 162 EEKIKKLLD-----KGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred HHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 345666543 6899999999999999999988763
No 263
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=80.63 E-value=3.9 Score=35.23 Aligned_cols=44 Identities=18% Similarity=0.209 Sum_probs=36.8
Q ss_pred hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008652 492 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 538 (558)
Q Consensus 492 ~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RAL 538 (558)
..|++.-|..|..+.. ..+++..++|+.||||+.+++++..|-.
T Consensus 7 A~Lt~~gR~~lv~~vv---~~g~~~a~aA~~~gVS~~Ta~kW~~Ryr 50 (85)
T PF13011_consen 7 ARLTPRGRLRLVRRVV---EQGWPVAHAAAEFGVSRRTAYKWLARYR 50 (85)
T ss_pred CCCCHHHHHHHHHHHH---HcCCcHHHHHHHhCCCHHHHHHHHHHHH
Confidence 3689999988888774 1589999999999999999998887644
No 264
>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=80.63 E-value=1.9 Score=31.44 Aligned_cols=24 Identities=25% Similarity=0.407 Sum_probs=21.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRA 537 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RA 537 (558)
+|.+|+|+.||||+.+|+++.+..
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcC
Confidence 589999999999999999988665
No 265
>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=80.59 E-value=54 Score=34.10 Aligned_cols=85 Identities=22% Similarity=0.326 Sum_probs=45.8
Q ss_pred CCCHHHHHHHhC--CCHHHHHHHHHhcCCCcccCCCCCCCCCcchh---hhcccCCCCChh-HHHHHHHHHHHHHHHHhc
Q 008652 420 SPDKEDLARRVG--ITVEKLERLIFITRMPLSMQQPVWADQDTTFQ---EITADTGVEIPD-ISVQKQLMRQHVRNLLTL 493 (558)
Q Consensus 420 ~Pt~eEIA~~lg--is~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~---e~i~d~~~~~pe-~~le~~~~~e~L~~~L~~ 493 (558)
.++.++||+.++ ||.++|+..+......--+.. . ++..+. ..+.......+. ..-...++.+.-.++|+.
T Consensus 137 ~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk-~---~~g~y~~t~~~l~~~~~~~~~avr~~h~q~l~lA~~al~~ 212 (271)
T TIGR02147 137 ADDPEELAKRCFPKISAEQVKESLDLLERLGLIKK-N---EDGFYKQTDKAVSTGDEVIPLAVRQYQKQMIDLAKEALDA 212 (271)
T ss_pred CCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeE-C---CCCcEEeecceeecCCccchHHHHHHHHHHHHHHHHHHHh
Confidence 567889999999 999999998874322111110 0 111110 111111111111 111122334455677889
Q ss_pred CCHHHHHHHHHHhcc
Q 008652 494 LNPKERCIVRLRFGI 508 (558)
Q Consensus 494 L~~rEReVL~LRyGL 508 (558)
.|+.+|.+=.+-+|+
T Consensus 213 ~p~~eR~~S~lT~~i 227 (271)
T TIGR02147 213 LPPSERDVSTVTFGI 227 (271)
T ss_pred CCccccccceeeEec
Confidence 999999977766664
No 266
>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=80.20 E-value=1.7 Score=31.45 Aligned_cols=25 Identities=16% Similarity=0.300 Sum_probs=22.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRAL 538 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RAL 538 (558)
+|..|+|+.+|||+.+|++....+.
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 5889999999999999999988764
No 267
>CHL00148 orf27 Ycf27; Reviewed
Probab=79.88 E-value=2.5 Score=40.69 Aligned_cols=50 Identities=18% Similarity=0.115 Sum_probs=42.4
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHh-------CCCHHHHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-------GLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~L-------GISrerVRqie~RALkKLR~ 543 (558)
.|+++|.+|+.+... +.|+++|.+||++.+ +++..+|+.+..+.++||..
T Consensus 161 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l~~~~~~~~~~~~tv~~~i~~lr~KL~~ 217 (240)
T CHL00148 161 RLTGMEFSLLELLIS-KSGEIFSRATILKEVWGYTPERHIDTRVVDVHISRLRAKLED 217 (240)
T ss_pred EcCHHHHHHHHHHHH-CCCEEEcHHHHHHHhcCCCcccCCCcccHHHHHHHHHHHhcc
Confidence 499999999987652 344789999999999 48999999999999999964
No 268
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=79.78 E-value=27 Score=35.21 Aligned_cols=35 Identities=23% Similarity=0.363 Sum_probs=27.9
Q ss_pred HHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHHH
Q 008652 277 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 311 (558)
Q Consensus 277 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~ 311 (558)
+.+....+...+|++|+..++|...|++.+.+...
T Consensus 111 ~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~ 145 (251)
T PRK07670 111 VEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEAT 145 (251)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHH
Confidence 34455667778899999999999999998877543
No 269
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=79.66 E-value=3.4 Score=34.36 Aligned_cols=48 Identities=23% Similarity=0.319 Sum_probs=33.7
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhccCC---CCCCCHHHHHHHhCCCHHHHHHH
Q 008652 484 RQHVRNLLTLLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQL 533 (558)
Q Consensus 484 ~e~L~~~L~~L~~rEReVL~LRyGL~d---~e~~Tl~EIAe~LGISrerVRqi 533 (558)
...|......|++.|+.|..+- +.. -..+|..|||+..|||..+|-+.
T Consensus 4 ~~~i~~~~~~ls~~e~~Ia~yi--l~~~~~~~~~si~elA~~~~vS~sti~Rf 54 (77)
T PF01418_consen 4 LEKIRSQYNSLSPTEKKIADYI--LENPDEIAFMSISELAEKAGVSPSTIVRF 54 (77)
T ss_dssp HHHHHHHGGGS-HHHHHHHHHH--HH-HHHHCT--HHHHHHHCTS-HHHHHHH
T ss_pred HHHHHHHHhhCCHHHHHHHHHH--HhCHHHHHHccHHHHHHHcCCCHHHHHHH
Confidence 3467777899999999987643 332 25799999999999999999743
No 270
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=79.63 E-value=4.5 Score=44.08 Aligned_cols=51 Identities=16% Similarity=0.203 Sum_probs=42.8
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
.+++.||..+.+.+.|...++.|+.++|+.|+||+.||.+-+++..+.|.+
T Consensus 10 ~~s~~ER~~~il~~LL~~~~~v~l~~Lae~l~VSrsTi~~DLk~l~~~L~~ 60 (426)
T PRK11564 10 VLSAPQRRCQILLMLFQPGLTVTLETFSQLNGVDDDTARQDIAETGREIQR 60 (426)
T ss_pred CCCHHHHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 478888888877777777789999999999999999999877777666655
No 271
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=79.16 E-value=37 Score=35.33 Aligned_cols=25 Identities=20% Similarity=0.337 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHh
Q 008652 419 HSPDKEDLARRVGITVEKLERLIFI 443 (558)
Q Consensus 419 r~Pt~eEIA~~lgis~e~v~~ll~~ 443 (558)
..-|.+|||+.+|+|.++|..++..
T Consensus 244 ~~~t~~EIa~~lgvs~~~V~q~~~~ 268 (289)
T PRK07500 244 DGATLEALGEELGISKERVRQIEAR 268 (289)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4568999999999999999988653
No 272
>PHA00542 putative Cro-like protein
Probab=78.68 E-value=1.5 Score=37.12 Aligned_cols=26 Identities=12% Similarity=0.102 Sum_probs=23.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESRA 537 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~RA 537 (558)
.++|..++|+.+|||+.+|.+++...
T Consensus 30 ~glTq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 30 AGWSQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHcCC
Confidence 68999999999999999999998654
No 273
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=78.57 E-value=3.4 Score=39.23 Aligned_cols=40 Identities=23% Similarity=0.147 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 494 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 494 L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
|++.++.||..-- .....|+.|||+.+|+|+.+|+.+..+
T Consensus 12 lD~~D~~IL~~Lq---~d~R~s~~eiA~~lglS~~tv~~Ri~r 51 (164)
T PRK11169 12 LDRIDRNILNELQ---KDGRISNVELSKRVGLSPTPCLERVRR 51 (164)
T ss_pred HHHHHHHHHHHhc---cCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 6777788887533 235789999999999999999876543
No 274
>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=78.40 E-value=3.7 Score=39.93 Aligned_cols=43 Identities=19% Similarity=0.285 Sum_probs=33.6
Q ss_pred hcCCHHHHHHHHHHhc--cCCCCCCCHHHHHHHhCCC-HHHHHHHH
Q 008652 492 TLLNPKERCIVRLRFG--IEDGKPKSLSEVGNIFGLS-KERVRQLE 534 (558)
Q Consensus 492 ~~L~~rEReVL~LRyG--L~d~e~~Tl~EIAe~LGIS-rerVRqie 534 (558)
..|+++|++||.+-.- ..++.+.|..|||+.+|++ +.+|+.++
T Consensus 2 ~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l 47 (199)
T TIGR00498 2 KPLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHL 47 (199)
T ss_pred CccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHH
Confidence 3589999999887652 2245678999999999998 99998543
No 275
>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=78.33 E-value=6.4 Score=32.02 Aligned_cols=39 Identities=28% Similarity=0.483 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHhCCCCCCHHHHHHHhCCC-HHHHHHHHHh
Q 008652 405 KVLEAKRLYIQEGNHSPDKEDLARRVGIT-VEKLERLIFI 443 (558)
Q Consensus 405 ki~ka~~~l~~~~gr~Pt~eEIA~~lgis-~e~v~~ll~~ 443 (558)
+|-.....+..+.|..||..|||+.+|++ ...|...+..
T Consensus 10 ~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~ 49 (65)
T PF01726_consen 10 EVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKA 49 (65)
T ss_dssp HHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 34444556677889999999999999997 8888877653
No 276
>PF13551 HTH_29: Winged helix-turn helix
Probab=78.29 E-value=4 Score=35.22 Aligned_cols=26 Identities=19% Similarity=0.349 Sum_probs=22.9
Q ss_pred CCC-CHHHHHHHhCCCHHHHHHHHHHH
Q 008652 512 KPK-SLSEVGNIFGLSKERVRQLESRA 537 (558)
Q Consensus 512 e~~-Tl~EIAe~LGISrerVRqie~RA 537 (558)
++. |..+||+.+|+|+.||++++++-
T Consensus 10 ~g~~~~~~ia~~lg~s~~Tv~r~~~~~ 36 (112)
T PF13551_consen 10 EGVSTIAEIARRLGISRRTVYRWLKRY 36 (112)
T ss_pred cCCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence 677 69999999999999999887763
No 277
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=78.12 E-value=4.5 Score=37.27 Aligned_cols=42 Identities=31% Similarity=0.285 Sum_probs=33.2
Q ss_pred hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 492 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 492 ~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
..|++.++.||...-. | -..|+.|||+.+|+|..+|+.+..+
T Consensus 4 ~~lD~~D~~IL~~L~~--d-~r~~~~eia~~lglS~~~v~~Ri~~ 45 (154)
T COG1522 4 MKLDDIDRRILRLLQE--D-ARISNAELAERVGLSPSTVLRRIKR 45 (154)
T ss_pred ccccHHHHHHHHHHHH--h-CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4578888888876543 3 4599999999999999999876543
No 278
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=77.88 E-value=6.8 Score=33.55 Aligned_cols=41 Identities=20% Similarity=0.189 Sum_probs=28.9
Q ss_pred CCCCHHHHHHHhC-CCHHHHHHHHHHHHHHHHHHhhcCchHhhhh
Q 008652 512 KPKSLSEVGNIFG-LSKERVRQLESRALYRLKQSLGGKASYGYAD 555 (558)
Q Consensus 512 e~~Tl~EIAe~LG-ISrerVRqie~RALkKLR~~l~~~~L~~yld 555 (558)
-++|+.+||+.|| .+..+|.....+.-+++.. +..++..++
T Consensus 43 ~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~---d~~~~~~v~ 84 (90)
T cd06571 43 TGLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE---DPELKEDVE 84 (90)
T ss_pred hCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh---CHHHHHHHH
Confidence 4799999999999 9999998665555555443 134444444
No 279
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=77.46 E-value=34 Score=27.10 Aligned_cols=23 Identities=35% Similarity=0.496 Sum_probs=19.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Q 008652 420 SPDKEDLARRVGITVEKLERLIF 442 (558)
Q Consensus 420 ~Pt~eEIA~~lgis~e~v~~ll~ 442 (558)
+++.++||+.+|++...+..++.
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~ 23 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFK 23 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Confidence 36789999999999999988765
No 280
>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=77.24 E-value=2.5 Score=32.11 Aligned_cols=25 Identities=24% Similarity=0.426 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
.++|..|+|+.+|+|+.+|+.+++.
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 6899999999999999999999875
No 281
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=77.09 E-value=3.1 Score=40.50 Aligned_cols=39 Identities=21% Similarity=0.202 Sum_probs=32.9
Q ss_pred HHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 500 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 500 eVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
..+.|+- .|+|-.|||+.||+|++|++-+..|+.++...
T Consensus 10 kA~eLk~-----~Glt~gEIAdELNvSreTa~WL~~r~~~~~~~ 48 (203)
T COG0856 10 KARELKS-----KGLTTGEIADELNVSRETATWLLTRAFKKESV 48 (203)
T ss_pred HHHHHHH-----CCCcHHHhhhhhhhhHHHHHHHHhhhhhccCC
Confidence 3455654 79999999999999999999999999887643
No 282
>PHA01976 helix-turn-helix protein
Probab=76.89 E-value=4.4 Score=32.11 Aligned_cols=25 Identities=16% Similarity=0.238 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
.++|..|+|+.+|||+.+|.++++.
T Consensus 14 ~glt~~~lA~~~gvs~~~v~~~e~g 38 (67)
T PHA01976 14 RAWSAPELSRRAGVRHSLIYDFEAD 38 (67)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 6899999999999999999999864
No 283
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=76.59 E-value=6.3 Score=29.01 Aligned_cols=25 Identities=20% Similarity=0.376 Sum_probs=21.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
.+.|..+|++.+|+|+.+|++.+..
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~ 37 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNK 37 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4699999999999999999866543
No 284
>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=76.07 E-value=2.1 Score=31.62 Aligned_cols=26 Identities=23% Similarity=0.388 Sum_probs=23.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRALY 539 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RALk 539 (558)
+|..|+|+.+|||..+|+..+.+.+-
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~g~l 26 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIGLL 26 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999887763
No 285
>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=75.53 E-value=6.1 Score=38.10 Aligned_cols=41 Identities=22% Similarity=0.214 Sum_probs=33.8
Q ss_pred HHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008652 496 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 539 (558)
Q Consensus 496 ~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 539 (558)
+.=|.-++..|.+ +++|++.+|..+|||..|+|.+..+|..
T Consensus 5 ~e~R~~~R~~YV~---~~~sLe~aA~~~gVs~~TarrWK~~Ak~ 45 (165)
T PF08822_consen 5 QETRDAVRRAYVF---DRLSLEQAAAKCGVSYATARRWKREAKA 45 (165)
T ss_pred HHHHHHHHHHHHh---CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4445667777763 5799999999999999999999999864
No 286
>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=75.39 E-value=4.9 Score=31.56 Aligned_cols=25 Identities=24% Similarity=0.318 Sum_probs=21.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 511 GKPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 511 ~e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
....|.+|+|+.||||..|||.-+.
T Consensus 12 ~~~~s~~ela~~~~VS~~TiRRDl~ 36 (57)
T PF08220_consen 12 KGKVSVKELAEEFGVSEMTIRRDLN 36 (57)
T ss_pred cCCEEHHHHHHHHCcCHHHHHHHHH
Confidence 3678999999999999999996543
No 287
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=75.12 E-value=7.4 Score=37.57 Aligned_cols=109 Identities=17% Similarity=0.252 Sum_probs=58.2
Q ss_pred CCCCHHHHHHHh--CCCHHHHHHHHHhcCCCcccCCCCCCCCCcchh---hhcccCCCCChhHHHHHH---HHHHHHHHH
Q 008652 419 HSPDKEDLARRV--GITVEKLERLIFITRMPLSMQQPVWADQDTTFQ---EITADTGVEIPDISVQKQ---LMRQHVRNL 490 (558)
Q Consensus 419 r~Pt~eEIA~~l--gis~e~v~~ll~~~~~~~SLD~~i~~d~~~~l~---e~i~d~~~~~pe~~le~~---~~~e~L~~~ 490 (558)
-.++..+||+.+ +++.++++..+......--+.. +++..+. ..+. ...+.+- ...+. .+.+.-.++
T Consensus 38 ~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k----~~~g~y~~t~~~l~-~~~~~~~-~avr~~h~q~~~lA~~a 111 (171)
T PF14394_consen 38 FAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKK----DGDGKYVQTDKSLT-TSSEIPS-EAVRSYHKQMLELAQEA 111 (171)
T ss_pred CCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEE----CCCCcEEEecceee-CCCCCcH-HHHHHHHHHHHHHHHHH
Confidence 366899999999 9999999998875422111111 1111110 1111 1111111 12222 233344567
Q ss_pred HhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008652 491 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 547 (558)
Q Consensus 491 L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 547 (558)
|+.+|+.+|.+=.+-++++ ..+++ .|+..+...++++......
T Consensus 112 l~~~p~~~R~~s~~T~~vs---~~~~~-----------ki~~~i~~fRk~i~~i~~~ 154 (171)
T PF14394_consen 112 LDRVPPEERDFSGLTMSVS---REDYE-----------KIKKEIREFRKKIIAIAEE 154 (171)
T ss_pred HHhCCccccceeeeEEEeC---HHHHH-----------HHHHHHHHHHHHHHHHHhc
Confidence 7888899988877776643 22333 3445555666666655443
No 288
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=74.62 E-value=4.8 Score=29.60 Aligned_cols=37 Identities=14% Similarity=0.225 Sum_probs=24.6
Q ss_pred HHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 496 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 496 ~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
+-|+++|.-..-- .+.+..+.|+.||||+.+++..+.
T Consensus 4 ~~E~~~i~~aL~~---~~gn~~~aA~~Lgisr~tL~~klk 40 (42)
T PF02954_consen 4 EFEKQLIRQALER---CGGNVSKAARLLGISRRTLYRKLK 40 (42)
T ss_dssp HHHHHHHHHHHHH---TTT-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHHH---hCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4456666554431 345889999999999999987654
No 289
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=74.61 E-value=13 Score=37.96 Aligned_cols=55 Identities=22% Similarity=0.236 Sum_probs=43.8
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhccCCC--CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 485 QHVRNLLTLLNPKERCIVRLRFGIEDG--KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 485 e~L~~~L~~L~~rEReVL~LRyGL~d~--e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
..+.-+++.|+--|.+.+...+-.-++ .-.+..+||+.+|||+..|+ +|+++|..
T Consensus 168 a~Vq~Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ir----eAlrkLE~ 224 (251)
T TIGR02787 168 AAVQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIV----NALRKLES 224 (251)
T ss_pred HHHHHHHHhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 456777999999998888776655444 46899999999999999887 66777754
No 290
>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=74.43 E-value=4.4 Score=32.20 Aligned_cols=30 Identities=37% Similarity=0.533 Sum_probs=22.2
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 510 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 510 d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
.|+.+ |..+||+.+|||+.+|| +|+..|..
T Consensus 20 ~g~~lps~~~la~~~~vsr~tvr----~al~~L~~ 50 (64)
T PF00392_consen 20 PGDRLPSERELAERYGVSRTTVR----EALRRLEA 50 (64)
T ss_dssp TTSBE--HHHHHHHHTS-HHHHH----HHHHHHHH
T ss_pred CCCEeCCHHHHHHHhccCCcHHH----HHHHHHHH
Confidence 34677 99999999999999998 56666643
No 291
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=74.41 E-value=5.3 Score=30.21 Aligned_cols=25 Identities=24% Similarity=0.373 Sum_probs=21.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
++.|..+|++.+|+|+.+|+.++.+
T Consensus 9 ~~~~~~~i~~~l~is~~~v~~~l~~ 33 (66)
T smart00418 9 GELCVCELAEILGLSQSTVSHHLKK 33 (66)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHH
Confidence 6789999999999999998876654
No 292
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=74.39 E-value=4 Score=32.35 Aligned_cols=25 Identities=20% Similarity=0.340 Sum_probs=21.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
.++|..++|+.+|+|..+|+++++.
T Consensus 13 ~gls~~~lA~~~g~s~s~v~~iE~G 37 (64)
T PF13560_consen 13 AGLSQAQLADRLGVSQSTVSRIERG 37 (64)
T ss_dssp HTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 5799999999999999999999864
No 293
>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=74.06 E-value=3.9 Score=38.69 Aligned_cols=29 Identities=17% Similarity=0.244 Sum_probs=24.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 544 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 544 (558)
-++|.+|||..+|+|+++|. |++++|++.
T Consensus 142 ~~~t~~~iA~~lG~tretvs----R~l~~l~~~ 170 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTIT----RLLGDLRKK 170 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHH----HHHHHHHHC
Confidence 36899999999999999996 777788763
No 294
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=74.03 E-value=4.6 Score=29.44 Aligned_cols=28 Identities=36% Similarity=0.665 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
-+.|..+||+.+|+|+.+|+ +++++|.+
T Consensus 7 ~~~s~~~la~~l~~s~~tv~----~~l~~L~~ 34 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVS----RTLKRLEK 34 (48)
T ss_pred eccCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 36899999999999999986 55555554
No 295
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=73.80 E-value=5.7 Score=36.33 Aligned_cols=24 Identities=25% Similarity=0.336 Sum_probs=22.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
+|+|..+||+.||+|+..|+|.++
T Consensus 21 eG~Sq~~iA~LLGltqaAVS~Yls 44 (119)
T COG2522 21 EGLSQYRIAKLLGLTQAAVSQYLS 44 (119)
T ss_pred cCCcHHHHHHHhCCCHHHHHHHHc
Confidence 689999999999999999999875
No 296
>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=73.53 E-value=6 Score=29.78 Aligned_cols=25 Identities=12% Similarity=0.279 Sum_probs=22.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
.++|..++|+.+|+|+.+|+.+++.
T Consensus 14 ~gltq~~lA~~~gvs~~~vs~~e~g 38 (58)
T TIGR03070 14 LGLTQADLADLAGVGLRFIRDVENG 38 (58)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 5799999999999999999999864
No 297
>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=73.38 E-value=9.1 Score=29.89 Aligned_cols=28 Identities=32% Similarity=0.590 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
.+.|..|||+.+|+|+.+|+ +.+++|++
T Consensus 24 ~~~s~~ela~~~g~s~~tv~----r~l~~L~~ 51 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVS----RTLKELEE 51 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 57899999999999999996 45555554
No 298
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=73.37 E-value=4.3 Score=38.98 Aligned_cols=37 Identities=19% Similarity=0.202 Sum_probs=29.1
Q ss_pred HHHHHHHHHHhccCCCCCCCHHHHHHHhC-CCHHHHHHHHHH
Q 008652 496 PKERCIVRLRFGIEDGKPKSLSEVGNIFG-LSKERVRQLESR 536 (558)
Q Consensus 496 ~rEReVL~LRyGL~d~e~~Tl~EIAe~LG-ISrerVRqie~R 536 (558)
+..-+.|.-.+. +|+|..|||+.|| ||++.|--..+|
T Consensus 5 de~~~~L~~lw~----~G~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 5 DERVERLRKLWA----EGLSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred HHHHHHHHHHHH----cCCCHHHHHHHhCCcchhhhhhhhhc
Confidence 344445555555 8999999999999 999999877665
No 299
>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=73.35 E-value=7.1 Score=34.65 Aligned_cols=42 Identities=24% Similarity=0.408 Sum_probs=26.8
Q ss_pred HHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008652 497 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 544 (558)
Q Consensus 497 rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 544 (558)
|.++|... | .|++..|+|..+|+|..+|++|+++..++-+..
T Consensus 62 R~~~I~~~-f-----~G~n~~eLA~kyglS~r~I~~Ii~~~~~~~~~~ 103 (108)
T PF08765_consen 62 RNREIRRE-F-----NGMNVRELARKYGLSERQIYRIIKRVRRRERRR 103 (108)
T ss_dssp HHHHHHHH--------SS-HHHHHHHHT--HHHHHHHHHHHHH-----
T ss_pred HHHHHHHH-h-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHh
Confidence 44555553 3 478999999999999999999999988776543
No 300
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=73.20 E-value=11 Score=33.56 Aligned_cols=48 Identities=21% Similarity=0.248 Sum_probs=36.0
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008652 484 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 537 (558)
Q Consensus 484 ~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA 537 (558)
.+.+...-..+.+.+-.-++..+ ++|..++|+.+|+++.+|+++++..
T Consensus 55 ~~~~~~~~~~~~~~~i~~~r~~~------gltq~~lA~~lg~~~~tis~~e~g~ 102 (127)
T TIGR03830 55 ADFYRKVDGLLTPPEIRRIRKKL------GLSQREAAELLGGGVNAFSRYERGE 102 (127)
T ss_pred HHHHHHccCCcCHHHHHHHHHHc------CCCHHHHHHHhCCCHHHHHHHHCCC
Confidence 33444444677887766666665 5899999999999999999988743
No 301
>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=73.19 E-value=16 Score=32.38 Aligned_cols=41 Identities=10% Similarity=0.110 Sum_probs=32.2
Q ss_pred hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 492 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 492 ~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
..|++.+..||..-+. ..+.|..|||+.+|+++.+|.+++.
T Consensus 24 ~~lt~~q~~iL~~l~~---~~~~t~~ela~~~~~~~~tvs~~l~ 64 (118)
T TIGR02337 24 HGLTEQQWRILRILAE---QGSMEFTQLANQACILRPSLTGILA 64 (118)
T ss_pred cCCCHHHHHHHHHHHH---cCCcCHHHHHHHhCCCchhHHHHHH
Confidence 4689999888865542 3579999999999999999964433
No 302
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=73.07 E-value=5.4 Score=32.97 Aligned_cols=25 Identities=16% Similarity=0.331 Sum_probs=22.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
.++|.+|.|+.+|||+.||-.+++.
T Consensus 13 ~~ltQ~elA~~vgVsRQTi~~iEkg 37 (68)
T COG1476 13 LGLTQEELAKLVGVSRQTIIAIEKG 37 (68)
T ss_pred hCcCHHHHHHHcCcCHHHHHHHHcC
Confidence 4699999999999999999998864
No 303
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=73.01 E-value=7.8 Score=31.17 Aligned_cols=25 Identities=24% Similarity=0.388 Sum_probs=20.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
...+..|||+.+|+|+.+|++...+
T Consensus 12 ~~~~~~eLa~~l~vS~~tv~~~l~~ 36 (69)
T TIGR00122 12 NPFSGEKLGEALGMSRTAVNKHIQT 36 (69)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4578999999999999999865544
No 304
>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=72.37 E-value=7.3 Score=30.08 Aligned_cols=26 Identities=35% Similarity=0.465 Sum_probs=21.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
.|..+||+.+|+|+++|+ +++++|.+
T Consensus 26 ~~~~~la~~~~is~~~v~----~~l~~L~~ 51 (66)
T cd07377 26 PSERELAEELGVSRTTVR----EALRELEA 51 (66)
T ss_pred CCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 459999999999999998 56666655
No 305
>PRK10072 putative transcriptional regulator; Provisional
Probab=72.12 E-value=5.8 Score=34.84 Aligned_cols=32 Identities=28% Similarity=0.479 Sum_probs=26.9
Q ss_pred HHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 501 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 501 VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
|-.+|.. .++|..|+|+.+|||..+|++++..
T Consensus 38 ik~LR~~----~glTQ~elA~~lGvS~~TVs~WE~G 69 (96)
T PRK10072 38 FEQLRKG----TGLKIDDFARVLGVSVAMVKEWESR 69 (96)
T ss_pred HHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 4455665 6899999999999999999999863
No 306
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=71.85 E-value=4.4 Score=32.82 Aligned_cols=28 Identities=39% Similarity=0.666 Sum_probs=23.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
-++|.++||..+|+|+++|. +.+++|++
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~----r~l~~l~~ 54 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVS----RILKRLKD 54 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHH----HHHHHHHH
T ss_pred ecCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 36899999999999999986 56666665
No 307
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=71.11 E-value=11 Score=32.10 Aligned_cols=33 Identities=18% Similarity=0.326 Sum_probs=26.5
Q ss_pred cCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008652 508 IEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 544 (558)
Q Consensus 508 L~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 544 (558)
+.++...|-++||+.||+||.+|- +.+++||+.
T Consensus 14 ~~~~~~~SGe~La~~LgiSRtaVw----K~Iq~Lr~~ 46 (79)
T COG1654 14 LLTGNFVSGEKLAEELGISRTAVW----KHIQQLREE 46 (79)
T ss_pred HcCCCcccHHHHHHHHCccHHHHH----HHHHHHHHh
Confidence 344578999999999999988885 677788863
No 308
>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=71.10 E-value=7.3 Score=29.88 Aligned_cols=51 Identities=12% Similarity=0.137 Sum_probs=39.3
Q ss_pred cCCHHHHHHHHHHhccCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDG-KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~-e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
.+++.+..+|.-.|..+.. ......+||..+||+...|......-..+.|+
T Consensus 6 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 6 RFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 4678888899988875321 12356789999999999999998887777653
No 309
>PRK09954 putative kinase; Provisional
Probab=71.03 E-value=7.9 Score=41.07 Aligned_cols=42 Identities=19% Similarity=0.279 Sum_probs=32.6
Q ss_pred CCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008652 494 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 538 (558)
Q Consensus 494 L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RAL 538 (558)
|+++++.||.+..- + ...|..|||+.||||+.+|+.++.+-.
T Consensus 1 ~~~~~~~il~~l~~--~-~~~s~~~la~~l~~s~~~v~~~i~~L~ 42 (362)
T PRK09954 1 MNNREKEILAILRR--N-PLIQQNEIADILQISRSRVAAHIMDLM 42 (362)
T ss_pred CChHHHHHHHHHHH--C-CCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 46677778766542 2 479999999999999999998776543
No 310
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=70.61 E-value=10 Score=31.68 Aligned_cols=26 Identities=27% Similarity=0.349 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESRA 537 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~RA 537 (558)
.+.|..|||+.+|+++.+|++++..-
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L 44 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTL 44 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 57999999999999999998766543
No 311
>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=70.56 E-value=59 Score=32.01 Aligned_cols=35 Identities=31% Similarity=0.635 Sum_probs=28.2
Q ss_pred HHHHHHHHHhhhhCCCCchHHHHHHccCCHHHHHH
Q 008652 276 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 310 (558)
Q Consensus 276 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~ 310 (558)
++.+...+|...+|++|+..+.|+..|++.+.+..
T Consensus 84 ~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~ 118 (224)
T TIGR02479 84 KLERAIRELEARLGREPTEEEIAEELGMDLKEYRQ 118 (224)
T ss_pred HHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHH
Confidence 34556677888899999999999999998776643
No 312
>PF13551 HTH_29: Winged helix-turn helix
Probab=70.54 E-value=12 Score=32.16 Aligned_cols=23 Identities=26% Similarity=0.377 Sum_probs=21.0
Q ss_pred CHHHHHHHhCCCHHHHHHHHHhc
Q 008652 422 DKEDLARRVGITVEKLERLIFIT 444 (558)
Q Consensus 422 t~eEIA~~lgis~e~v~~ll~~~ 444 (558)
+..++|..+|++...|..++...
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~ 36 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRY 36 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHH
Confidence 79999999999999999998754
No 313
>PRK05572 sporulation sigma factor SigF; Validated
Probab=70.53 E-value=44 Score=33.72 Aligned_cols=32 Identities=34% Similarity=0.640 Sum_probs=25.0
Q ss_pred HHHHHHHhhhhCCCCchHHHHHHccCCHHHHH
Q 008652 278 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 309 (558)
Q Consensus 278 e~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~ 309 (558)
.+....+....|+.|+..+.|+..|++.+.+.
T Consensus 121 ~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~ 152 (252)
T PRK05572 121 RKDKDELSKELGREPTIEELAEYLGVTPEEVV 152 (252)
T ss_pred HHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHH
Confidence 34455667778999999999999998877653
No 314
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=70.33 E-value=9.7 Score=36.14 Aligned_cols=49 Identities=24% Similarity=0.349 Sum_probs=35.7
Q ss_pred CHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHH------HHHHHHHHhhc
Q 008652 495 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR------ALYRLKQSLGG 547 (558)
Q Consensus 495 ~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R------ALkKLR~~l~~ 547 (558)
+|..-.|=.+|-. .|+|..|+|+.+|||+.+|.++++. .+..|.+....
T Consensus 24 ~p~~~~Ir~~R~~----lGmTq~eLAerlGVS~~tIs~iE~G~~~~~psl~~L~kIA~a 78 (150)
T TIGR02612 24 TPKEGWVRAIRKA----LGMSGAQLAGRLGVTPQRVEALEKSELSGTVTLKTLRAAAEA 78 (150)
T ss_pred cCcHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCCCHHHHHHHHHH
Confidence 4444445556665 7899999999999999999999985 34455554433
No 315
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=70.12 E-value=2.2 Score=33.98 Aligned_cols=25 Identities=28% Similarity=0.514 Sum_probs=22.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRAL 538 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RAL 538 (558)
||..|+|+.+|||..+||..+.+.+
T Consensus 1 yti~eva~~~gvs~~tlr~y~~~gl 25 (69)
T PF13411_consen 1 YTIKEVAKLLGVSPSTLRYYEREGL 25 (69)
T ss_dssp EEHHHHHHHTTTTHHHHHHHHHTTS
T ss_pred CcHHHHHHHHCcCHHHHHHHHHhcC
Confidence 4789999999999999999988776
No 316
>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=69.94 E-value=9.4 Score=32.49 Aligned_cols=24 Identities=25% Similarity=0.447 Sum_probs=21.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
...|+++||+.+|||+.||+..+.
T Consensus 18 ~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 18 TKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHhc
Confidence 467999999999999999998665
No 317
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=69.50 E-value=9.8 Score=33.59 Aligned_cols=46 Identities=30% Similarity=0.382 Sum_probs=34.7
Q ss_pred cCCHHHHHHHHHHhccCC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d---~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
-|+|.||+-+-.|+-+-. ...+|.+||+..||+|..+|- |+-..|+
T Consensus 37 lLTpdEReal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtIT----RGSN~LK 85 (103)
T COG2973 37 LLTPDEREALGTRVRIVEELLRGELSQREIAQKLGVSIATIT----RGSNSLK 85 (103)
T ss_pred HcCHhHHHHHHHHHHHHHHHHhccccHHHHHHHhCcchhhhc----cchhhhc
Confidence 488999888877776542 158999999999999998884 4444444
No 318
>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=69.08 E-value=13 Score=28.80 Aligned_cols=36 Identities=28% Similarity=0.399 Sum_probs=25.1
Q ss_pred HHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 497 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 497 rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
.+..|+...+- .+.+..||++.+|+++.+|+..+.+
T Consensus 8 ~~~~il~~l~~----~~~~~~ei~~~~~i~~~~i~~~l~~ 43 (78)
T cd00090 8 TRLRILRLLLE----GPLTVSELAERLGLSQSTVSRHLKK 43 (78)
T ss_pred HHHHHHHHHHH----CCcCHHHHHHHHCcCHhHHHHHHHH
Confidence 34455544332 2399999999999999999755444
No 319
>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=68.68 E-value=55 Score=32.96 Aligned_cols=33 Identities=30% Similarity=0.502 Sum_probs=26.2
Q ss_pred HHHHHHHhhhhCCCCchHHHHHHccCCHHHHHH
Q 008652 278 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 310 (558)
Q Consensus 278 e~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~ 310 (558)
......+...+|+.|+..+.|...|++.+.+..
T Consensus 119 ~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~ 151 (255)
T TIGR02941 119 KKAIDELTDHLQRSPKIIEIADHLGLSEEEVLE 151 (255)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 345566777889999999999999998776643
No 320
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=68.45 E-value=6 Score=37.85 Aligned_cols=28 Identities=18% Similarity=0.237 Sum_probs=23.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
-+.|.++||..+|+|+++|. |++++|++
T Consensus 148 ~~~t~~~iA~~lG~tretvs----R~l~~l~~ 175 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVT----KVIGELSR 175 (202)
T ss_pred ecCCHHHHHHHhCccHHHHH----HHHHHHHH
Confidence 36799999999999999996 66777765
No 321
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=67.86 E-value=8.2 Score=41.27 Aligned_cols=65 Identities=23% Similarity=0.283 Sum_probs=44.7
Q ss_pred hcCCHHHHHHHHH--HhccCCCCCCCHHHHHHH--hCCCHHHHHHHHHHHHHHHHHHhh----------cCchHhhhhhh
Q 008652 492 TLLNPKERCIVRL--RFGIEDGKPKSLSEVGNI--FGLSKERVRQLESRALYRLKQSLG----------GKASYGYADLL 557 (558)
Q Consensus 492 ~~L~~rEReVL~L--RyGL~d~e~~Tl~EIAe~--LGISrerVRqie~RALkKLR~~l~----------~~~L~~yldll 557 (558)
..|++|+++|+.. ...+..+++.+.+++++. +|+|..|||.-+.. |.++--..+ ..|++.|+|.|
T Consensus 2 ~~l~~R~~~Il~~IV~~yi~~~~pv~s~~l~~~~~l~~S~aTIR~dm~~-Le~~G~l~~~h~sagrIPT~kGYR~YVd~L 80 (339)
T PRK00082 2 SMLDERQREILRAIVEDYIATGEPVGSKTLSKRYGLGVSSATIRNDMAD-LEELGLLEKPHTSSGRIPTDKGYRYFVDHL 80 (339)
T ss_pred CccCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHhCCCCChHHHHHHHHH-HHhCCCcCCCcCCCCCCcCHHHHHHHHHHh
Confidence 3588999999962 112334599999999977 99999999977653 444422111 23678888765
No 322
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=67.85 E-value=15 Score=33.57 Aligned_cols=49 Identities=8% Similarity=0.047 Sum_probs=34.9
Q ss_pred HHHHHH--hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 486 HVRNLL--TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 486 ~L~~~L--~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
.+...+ -.|++.+..||..-+. .+++.|..|||+.+|+++.+|.+...+
T Consensus 19 ~~~~~l~~~glt~~q~~vL~~l~~--~~~~~t~~eLa~~l~~~~~tvt~~v~~ 69 (144)
T PRK03573 19 LIDHRLKPLELTQTHWVTLHNIHQ--LPPEQSQIQLAKAIGIEQPSLVRTLDQ 69 (144)
T ss_pred HHHHHHHhcCCCHHHHHHHHHHHH--cCCCCCHHHHHHHhCCChhhHHHHHHH
Confidence 344444 3688888887766542 125689999999999999999854443
No 323
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=67.64 E-value=68 Score=32.45 Aligned_cols=33 Identities=24% Similarity=0.307 Sum_probs=27.0
Q ss_pred HHHHHHHhhhhCCCCchHHHHHHccCCHHHHHH
Q 008652 278 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 310 (558)
Q Consensus 278 e~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~ 310 (558)
.+...++...+|++|+..+.|...|++.+.+..
T Consensus 126 ~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~ 158 (258)
T PRK08215 126 LQVREKLINENSKEPTVEEIAKELEVPREEVVF 158 (258)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHH
Confidence 345567777889999999999999999887754
No 324
>TIGR00647 MG103 conserved hypothetical protein.
Probab=67.54 E-value=11 Score=39.25 Aligned_cols=44 Identities=16% Similarity=0.231 Sum_probs=37.6
Q ss_pred HhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhC------CCHHHHHHHHHHH
Q 008652 491 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG------LSKERVRQLESRA 537 (558)
Q Consensus 491 L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LG------ISrerVRqie~RA 537 (558)
++.||+.-+++..+|.- ..+.|++|+|+.|. ||++.|..+..+.
T Consensus 225 l~~Lp~~L~~~a~lRl~---~Pd~SL~ELgell~~~~~~~isKSgvnhRlrKl 274 (279)
T TIGR00647 225 FEKLPLNFQRICLLKID---HPDWSLEQIAEFFASKYKVKISRSGIQHRLRKL 274 (279)
T ss_pred cccCCHHHHHHHHHHHh---CcccCHHHHHHHhccCCCCCcCHHHHHHHHHHH
Confidence 57899999999999974 47899999999994 9999998776654
No 325
>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=66.81 E-value=5.4 Score=34.28 Aligned_cols=24 Identities=17% Similarity=0.108 Sum_probs=17.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
.|+|..|||+.+|.|+..|.+++.
T Consensus 2 ~G~tq~eIA~~lGks~s~Vs~~l~ 25 (93)
T PF08535_consen 2 FGWTQEEIAKRLGKSRSWVSNHLA 25 (93)
T ss_dssp TT--HHHHHHHTT--HHHHHHHHG
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 479999999999999999998764
No 326
>PRK06030 hypothetical protein; Provisional
Probab=66.74 E-value=17 Score=33.43 Aligned_cols=41 Identities=15% Similarity=0.093 Sum_probs=29.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchHhhhhh
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADL 556 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yldl 556 (558)
-++|+.+||+.||.+..||-.-.+ +.++.+.+..++..++.
T Consensus 68 ~~~sl~~IG~~FGRDHSTV~haik----kIe~~~~d~~lk~~v~~ 108 (124)
T PRK06030 68 LGWPMNEVALAFGRDRTTVGHACH----TVEDLRDDAAFDARVSV 108 (124)
T ss_pred cCCCHHHHHHHHCCChhHHHHHHH----HHHHHhhCHHHHHHHHH
Confidence 578999999999999999986665 33333345555555443
No 327
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=66.35 E-value=32 Score=31.56 Aligned_cols=47 Identities=4% Similarity=-0.013 Sum_probs=35.6
Q ss_pred HHHHHH--hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 486 HVRNLL--TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 486 ~L~~~L--~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
.+...+ ..|++-|..||..-+. ..+.|..|||+.+|+++.+|..++.
T Consensus 28 ~~~~~l~~~glt~~q~~vL~~l~~---~~~~t~~eLa~~l~i~~~tvsr~l~ 76 (144)
T PRK11512 28 LLNEYLSPLDITAAQFKVLCSIRC---AACITPVELKKVLSVDLGALTRMLD 76 (144)
T ss_pred HHHHHhcccCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 344444 3689999988876542 3579999999999999999975544
No 328
>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=66.31 E-value=3.7 Score=29.82 Aligned_cols=24 Identities=29% Similarity=0.571 Sum_probs=19.7
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHH
Q 008652 515 SLSEVGNIFGLSKERVRQLESRAL 538 (558)
Q Consensus 515 Tl~EIAe~LGISrerVRqie~RAL 538 (558)
|..|+|+.+|||..++|..+...+
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~Gl 24 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYEREGL 24 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHTTS
T ss_pred CHHHHHHHHCCCHHHHHHHHHCCC
Confidence 467999999999999999887653
No 329
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=65.63 E-value=15 Score=30.50 Aligned_cols=44 Identities=32% Similarity=0.501 Sum_probs=33.3
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
.|+..+..||.+-+. ..++|..+|++.+++++.+|+ +++++|.+
T Consensus 7 ~l~~~~~~il~~l~~---~~~~~~~~la~~~~~s~~~i~----~~l~~L~~ 50 (101)
T smart00347 7 GLTPTQFLVLRILYE---EGPLSVSELAKRLGVSPSTVT----RVLDRLEK 50 (101)
T ss_pred CCCHHHHHHHHHHHH---cCCcCHHHHHHHHCCCchhHH----HHHHHHHH
Confidence 467777778777664 246999999999999999987 45555544
No 330
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=65.43 E-value=17 Score=35.56 Aligned_cols=44 Identities=18% Similarity=0.189 Sum_probs=34.7
Q ss_pred HHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 490 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 490 ~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
....|++++..|+.+-.. ..+.+..|||+.+|+|+.+|++.+.+
T Consensus 137 ~~~~ls~~~~~IL~~l~~---~g~~s~~eia~~l~is~stv~r~L~~ 180 (203)
T TIGR01884 137 LLAGLSREELKVLEVLKA---EGEKSVKNIAKKLGKSLSTISRHLRE 180 (203)
T ss_pred hhcCCCHHHHHHHHHHHH---cCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 456799999888876542 13679999999999999999866554
No 331
>PRK10870 transcriptional repressor MprA; Provisional
Probab=65.24 E-value=35 Score=32.86 Aligned_cols=50 Identities=12% Similarity=0.118 Sum_probs=36.0
Q ss_pred HHHHHHh--cCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 486 HVRNLLT--LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 486 ~L~~~L~--~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
.+...+. .|++-+-.||..-+. .++.+.|..|||+.+|+++.+|.+++.+
T Consensus 43 ~~~~~l~~~gLt~~q~~iL~~L~~-~~~~~it~~eLa~~l~l~~~tvsr~v~r 94 (176)
T PRK10870 43 NRNKMLKAQGINETLFMALITLES-QENHSIQPSELSCALGSSRTNATRIADE 94 (176)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHhc-CCCCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4455553 488888888776653 2235789999999999999999755443
No 332
>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=64.92 E-value=8.1 Score=30.60 Aligned_cols=23 Identities=26% Similarity=0.488 Sum_probs=20.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~R 536 (558)
+|..|+|+.+|||..++|...++
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 47899999999999999998865
No 333
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=64.86 E-value=8.3 Score=30.42 Aligned_cols=36 Identities=14% Similarity=0.218 Sum_probs=26.1
Q ss_pred HHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 497 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 497 rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
|+.++|.+-+. ....|+.|||+.+|+|.-+|+..+.
T Consensus 6 rq~~Ll~~L~~---~~~~~~~ela~~l~~S~rti~~~i~ 41 (59)
T PF08280_consen 6 RQLKLLELLLK---NKWITLKELAKKLNISERTIKNDIN 41 (59)
T ss_dssp HHHHHHHHHHH---HTSBBHHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHc---CCCCcHHHHHHHHCCCHHHHHHHHH
Confidence 34455555544 4689999999999999999986554
No 334
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=64.72 E-value=8.3 Score=39.56 Aligned_cols=25 Identities=20% Similarity=0.444 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
++|.+.+||+.||||..+|+....|
T Consensus 18 ~gmk~~dIAeklGvspntiksWKrr 42 (279)
T COG5484 18 KGMKLKDIAEKLGVSPNTIKSWKRR 42 (279)
T ss_pred hhccHHHHHHHhCCChHHHHHHHHh
Confidence 7899999999999999999998765
No 335
>PF11662 DUF3263: Protein of unknown function (DUF3263); InterPro: IPR021678 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=64.30 E-value=24 Score=29.92 Aligned_cols=47 Identities=19% Similarity=0.135 Sum_probs=36.9
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 539 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 539 (558)
.|+++++.||.+---.....|-+-+.|-+.||+|.-+--|.++..+.
T Consensus 2 ~Ls~~d~~iL~fE~~ww~~~GaKe~aIre~fGls~~rYyq~Ln~LiD 48 (77)
T PF11662_consen 2 GLSDRDRAILDFERRWWRHGGAKEEAIREEFGLSPTRYYQRLNALID 48 (77)
T ss_pred CCCHHHHHHHHHHHHhCcCCCCcHHHHHHHHCCCHHHHHHHHHHHhC
Confidence 68999999997633222234668899999999999999999887653
No 336
>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=64.22 E-value=18 Score=28.00 Aligned_cols=45 Identities=22% Similarity=0.330 Sum_probs=30.6
Q ss_pred cchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHH
Q 008652 395 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLER 439 (558)
Q Consensus 395 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ 439 (558)
||......+-.+.+.-..+..++-...+-.+||+.+|+++.+|+.
T Consensus 3 Ip~~ti~RL~~Y~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 3 IPKATIRRLPLYLRYLEQLKEEGVERVSSQELAEALGITPAQVRK 47 (50)
T ss_dssp -SHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHcCCeeECHHHHHHHHCCCHHHhcc
Confidence 455555555555566666777776778899999999999999975
No 337
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=63.54 E-value=12 Score=38.16 Aligned_cols=49 Identities=14% Similarity=0.255 Sum_probs=39.3
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhccCCC---CCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 485 QHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 485 e~L~~~L~~L~~rEReVL~LRyGL~d~---e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
+.|...+..|++.|+.|..+- ++.. ..+|..|||+..|+|..+|-+..+
T Consensus 5 ~~i~~~~~~Lt~~e~~Ia~yi--l~n~~~v~~~si~~lA~~~~vS~aTv~Rf~k 56 (284)
T PRK11302 5 EKIQSRLEHLSKSERKVAEVI--LASPQTAIHSSIATLAKMANVSEPTVNRFCR 56 (284)
T ss_pred HHHHHHHhhCCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCCHHHHHHHHH
Confidence 467788899999999997654 4432 358999999999999999976544
No 338
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=63.53 E-value=8.2 Score=37.97 Aligned_cols=27 Identities=30% Similarity=0.566 Sum_probs=22.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 513 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 513 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
+.|.++||+.+|+|+++|. |.+++|++
T Consensus 184 ~lt~~~iA~~lG~sr~tvs----R~l~~l~~ 210 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETIS----RLLGRFQK 210 (235)
T ss_pred cccHHHHHHHhCCcHHHHH----HHHHHHHH
Confidence 5899999999999999997 55667765
No 339
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=63.50 E-value=9.7 Score=33.86 Aligned_cols=68 Identities=24% Similarity=0.279 Sum_probs=47.6
Q ss_pred HHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH--HHHHHHhhcCchHhh
Q 008652 486 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL--YRLKQSLGGKASYGY 553 (558)
Q Consensus 486 ~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RAL--kKLR~~l~~~~L~~y 553 (558)
.+..+|..+.=+--+|..+.+.+.-+.++-..||+..||||.-+||-...--+ --|+..+...+.-.|
T Consensus 9 ~l~~~L~~~glk~~eI~IY~lLve~~~~mri~ei~rEl~is~rtvr~~v~~l~rrGll~relvqkgWvGY 78 (113)
T COG5625 9 KLGKALEAIGLKKNEIRIYSLLVEKGRGMRIREIQRELGISERTVRAAVAVLLRRGLLARELVQKGWVGY 78 (113)
T ss_pred HHHHHHHHcCCCcchhhhhhHHHHhcCCchHHHHHHHHhHHHHHHHHHHHHHHHhhHHHHHHHhccceee
Confidence 45666666555555566666666666889999999999999999988776666 335555555555444
No 340
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=63.48 E-value=5.4 Score=33.51 Aligned_cols=31 Identities=13% Similarity=0.081 Sum_probs=23.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
+..|+.++|+.++||+.+|++..++.-+.|+
T Consensus 29 ~~~s~~~la~~~~iS~sti~~~i~~l~~~l~ 59 (87)
T PF05043_consen 29 EYVSIEDLAEELFISRSTIYRDIKKLNKYLK 59 (87)
T ss_dssp SEEEHHHHHHHHT--HHHHHHHHHHHHHHHH
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 7899999999999999999866665555544
No 341
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=63.44 E-value=47 Score=29.15 Aligned_cols=44 Identities=11% Similarity=0.064 Sum_probs=34.2
Q ss_pred cCCHHHHHHHHHHhcc-CCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGI-EDGKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL-~d~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
.|+..|-.||..-+.+ ..+.+.|..|||+.+++++.+|.+.+.+
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~ 66 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKK 66 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHH
Confidence 6899999998765521 1236799999999999999999865543
No 342
>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=63.18 E-value=15 Score=29.76 Aligned_cols=25 Identities=12% Similarity=0.275 Sum_probs=23.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
.++|..++|+.+|+|+.+|++++..
T Consensus 17 ~~~t~~~lA~~~gis~~tis~~~~g 41 (78)
T TIGR02607 17 LGLSIRALAKALGVSRSTLSRIVNG 41 (78)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 6899999999999999999999864
No 343
>PF14493 HTH_40: Helix-turn-helix domain
Probab=62.85 E-value=11 Score=32.17 Aligned_cols=29 Identities=21% Similarity=0.245 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESRALYR 540 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~RALkK 540 (558)
+|+|+.|||+.-|++.+||...+.++...
T Consensus 12 ~G~si~eIA~~R~L~~sTI~~HL~~~~~~ 40 (91)
T PF14493_consen 12 KGLSIEEIAKIRGLKESTIYGHLAELIES 40 (91)
T ss_pred cCCCHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence 78999999999999999999998887765
No 344
>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=62.46 E-value=60 Score=31.98 Aligned_cols=30 Identities=30% Similarity=0.576 Sum_probs=24.9
Q ss_pred HHHHHhhhhCCCCchHHHHHHccCCHHHHH
Q 008652 280 EKSKLQSQFGREPTLIEWAKAIGLSCRDLK 309 (558)
Q Consensus 280 ~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~ 309 (558)
....+....|++|+..+.|...|++.+.+.
T Consensus 95 ~~~~l~~~~~~~p~~~ela~~l~~~~~~v~ 124 (227)
T TIGR02980 95 ATEELTQRLGRSPTIAEIAEELGVSEEEVV 124 (227)
T ss_pred HHHHHHHHHCCCCCHHHHHHHhCCCHHHHH
Confidence 455677778999999999999999887664
No 345
>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=62.45 E-value=13 Score=31.04 Aligned_cols=24 Identities=29% Similarity=0.481 Sum_probs=19.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
.+.|.+|||+.+|+++..|+++..
T Consensus 24 ~~~s~~eiA~~~~i~~~~l~kil~ 47 (83)
T PF02082_consen 24 KPVSSKEIAERLGISPSYLRKILQ 47 (83)
T ss_dssp C-BEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHH
Confidence 458999999999999999986554
No 346
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=62.40 E-value=9.5 Score=36.68 Aligned_cols=27 Identities=37% Similarity=0.493 Sum_probs=22.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 513 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 513 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
..|.++||..+|+|+++|. |++++|++
T Consensus 168 ~~t~~~lA~~lG~tr~tvs----R~l~~l~~ 194 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVG----RVLKMLED 194 (211)
T ss_pred CCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 6899999999999999997 55667765
No 347
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=62.18 E-value=8.5 Score=31.16 Aligned_cols=27 Identities=22% Similarity=0.306 Sum_probs=24.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESRAL 538 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~RAL 538 (558)
.+.|..+||..+||+..++++......
T Consensus 22 ~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 22 SGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp HHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCceEeeecccccccccccHHHHHHh
Confidence 579999999999999999999998876
No 348
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=62.14 E-value=1e+02 Score=30.60 Aligned_cols=33 Identities=33% Similarity=0.556 Sum_probs=26.0
Q ss_pred HHHHHHHhhhhCCCCchHHHHHHccCCHHHHHH
Q 008652 278 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 310 (558)
Q Consensus 278 e~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~ 310 (558)
......+...+|++|+..++|+..|++.+.+..
T Consensus 98 ~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~ 130 (236)
T PRK06986 98 AQAIRQLEQELGREPTDTEVAEKLGLSLEEYRE 130 (236)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHH
Confidence 344556667789999999999999998876643
No 349
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=62.09 E-value=22 Score=31.77 Aligned_cols=40 Identities=28% Similarity=0.392 Sum_probs=35.7
Q ss_pred HhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 491 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 491 L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
...|++.|-..|+-.++ +|..+-|..||+|.++|+.++..
T Consensus 41 ~~~ls~~eIk~iRe~~~------lSQ~vFA~~L~vs~~Tv~~WEqG 80 (104)
T COG2944 41 VKTLSPTEIKAIREKLG------LSQPVFARYLGVSVSTVRKWEQG 80 (104)
T ss_pred CCCCCHHHHHHHHHHhC------CCHHHHHHHHCCCHHHHHHHHcC
Confidence 36799999988888875 89999999999999999999974
No 350
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=61.67 E-value=12 Score=31.97 Aligned_cols=44 Identities=25% Similarity=0.398 Sum_probs=28.5
Q ss_pred HHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 498 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 498 EReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
||-|-.-.|.++ ...|..+.|..||||++||.+-...=|.++-.
T Consensus 6 eR~i~i~~yIi~--~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in~ 49 (82)
T PF12116_consen 6 ERVIEIANYIIE--TKATVRQAAKVFGVSKSTVHKDVTERLPKINP 49 (82)
T ss_dssp HHHHHHHHHHHH--H---HHHHHHHHTS-HHHHHHHHTTHHHHH-H
T ss_pred HHHHHHHHHHHH--cccHHHHHHHHHCCcHHHHHHHHHHHHHhcCH
Confidence 444555566655 57899999999999999999877665555543
No 351
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=61.33 E-value=18 Score=32.58 Aligned_cols=34 Identities=18% Similarity=0.197 Sum_probs=27.5
Q ss_pred HHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008652 501 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 538 (558)
Q Consensus 501 VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RAL 538 (558)
++...+- .+.|..+||..+|||..+|++...+..
T Consensus 21 aV~~~~~----~g~sv~evA~e~gIs~~tl~~W~r~y~ 54 (121)
T PRK09413 21 IVQQSFE----PGMTVSLVARQHGVAASQLFLWRKQYQ 54 (121)
T ss_pred HHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHh
Confidence 4444443 689999999999999999999977653
No 352
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=60.82 E-value=12 Score=37.11 Aligned_cols=30 Identities=23% Similarity=0.460 Sum_probs=25.5
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 510 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 510 d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
.|+.+ |-.|+++.||||+.+|| .|+..|..
T Consensus 27 pG~~LPsE~eLae~~gVSRt~VR----eAL~~L~~ 57 (239)
T PRK04984 27 PGSILPAERELSELIGVTRTTLR----EVLQRLAR 57 (239)
T ss_pred CCCcCCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 45778 79999999999999998 67777765
No 353
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=60.52 E-value=6.7 Score=31.17 Aligned_cols=25 Identities=28% Similarity=0.412 Sum_probs=22.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRAL 538 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RAL 538 (558)
+|..|+|+.+|||..+||..+...+
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~~gl 25 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYERIGL 25 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999977555
No 354
>PRK15482 transcriptional regulator MurR; Provisional
Probab=60.35 E-value=15 Score=37.72 Aligned_cols=49 Identities=16% Similarity=0.247 Sum_probs=39.2
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhccCCC---CCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 485 QHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 485 e~L~~~L~~L~~rEReVL~LRyGL~d~---e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
..|......|++.|+.|..+- |++. ..+|..|||+..|+|..+|-+.-+
T Consensus 5 ~~i~~~~~~Lt~~e~~Ia~yI--l~n~~~v~~~si~elA~~~~vS~aTv~Rf~k 56 (285)
T PRK15482 5 TKIRNAESEFTENEQKIADFL--RANVSELKSVSSRKMAKQLGISQSSIVKFAQ 56 (285)
T ss_pred HHHHHHHhhcCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCCHHHHHHHHH
Confidence 467778899999999997754 4432 359999999999999999976544
No 355
>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=60.31 E-value=11 Score=29.98 Aligned_cols=23 Identities=26% Similarity=0.473 Sum_probs=21.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~R 536 (558)
+|..|+|+.+|||..++|....+
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 47899999999999999999876
No 356
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=60.29 E-value=8.6 Score=37.34 Aligned_cols=29 Identities=34% Similarity=0.590 Sum_probs=24.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 511 GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 511 ~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
.+++|+.||++.+|+|+.+|+ .++++|..
T Consensus 39 ~~Pmtl~Ei~E~lg~Sks~vS----~~lkkL~~ 67 (177)
T COG1510 39 RKPLTLDEIAEALGMSKSNVS----MGLKKLQD 67 (177)
T ss_pred CCCccHHHHHHHHCCCcchHH----HHHHHHHh
Confidence 489999999999999999997 46667754
No 357
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=60.23 E-value=8.9 Score=37.22 Aligned_cols=28 Identities=18% Similarity=0.227 Sum_probs=24.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESRALY 539 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~RALk 539 (558)
-++|..|||+.+|.|..|||.++...-+
T Consensus 60 ag~Ti~EIAeelG~TeqTir~hlkgetk 87 (182)
T COG1318 60 AGMTISEIAEELGRTEQTVRNHLKGETK 87 (182)
T ss_pred ccCcHHHHHHHhCCCHHHHHHHHhcchh
Confidence 4799999999999999999998765443
No 358
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=60.05 E-value=9 Score=31.14 Aligned_cols=23 Identities=22% Similarity=0.416 Sum_probs=20.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~R 536 (558)
.|+.|||+.+|||+.+|+.+++.
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~ 23 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNG 23 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCC
Confidence 37899999999999999987654
No 359
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=59.97 E-value=23 Score=36.43 Aligned_cols=51 Identities=16% Similarity=0.300 Sum_probs=40.5
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHhccCCC---CCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 483 MRQHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 483 ~~e~L~~~L~~L~~rEReVL~LRyGL~d~---e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
+...|+..+..|++.|+.|...- +++. ..+|..+||+..|||..+|-+..+
T Consensus 15 i~~~i~~~~~~Lt~~e~~Ia~yi--l~~~~~v~~~si~~lA~~~~vS~aTi~Rf~k 68 (292)
T PRK11337 15 LGPYIRMKQEGLTPLESRVVEWL--LKPGDLSEATALKDIAEALAVSEAMIVKVAK 68 (292)
T ss_pred HHHHHHHHHhhcCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCChHHHHHHHH
Confidence 34468888999999999998754 4332 468999999999999999976544
No 360
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=59.77 E-value=14 Score=33.14 Aligned_cols=56 Identities=14% Similarity=0.204 Sum_probs=47.1
Q ss_pred HHHHHH--hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008652 486 HVRNLL--TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 545 (558)
Q Consensus 486 ~L~~~L--~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 545 (558)
.|+..+ .+|.+-||-...-+|- .-+|-+|||-.++++..||..+...-..|.|+.-
T Consensus 19 RIRTTFTS~QLkELErvF~ETHYP----DIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE 76 (125)
T KOG0484|consen 19 RIRTTFTSAQLKELERVFAETHYP----DIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE 76 (125)
T ss_pred hhhhhhhHHHHHHHHHHHHhhcCC----cchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence 344444 6788889988888997 8899999999999999999999988888888753
No 361
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=59.23 E-value=17 Score=36.66 Aligned_cols=25 Identities=28% Similarity=0.347 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
.+.|..|||++||||..+||+.+..
T Consensus 24 g~~sa~elA~~Lgis~~avR~HL~~ 48 (218)
T COG2345 24 GPVSADELAEELGISPMAVRRHLDD 48 (218)
T ss_pred CCccHHHHHHHhCCCHHHHHHHHHH
Confidence 5899999999999999999987653
No 362
>PF12085 DUF3562: Protein of unknown function (DUF3562); InterPro: IPR021945 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 62 to 84 amino acids in length. This protein has two completely conserved residues (A and Y) that may be functionally important.
Probab=58.88 E-value=25 Score=29.00 Aligned_cols=40 Identities=20% Similarity=0.341 Sum_probs=33.4
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchHhhhhhh
Q 008652 515 SLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLL 557 (558)
Q Consensus 515 Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yldll 557 (558)
.+++||+..|++.+.|++.....+..|+. .....+|+-++
T Consensus 9 ~i~~iA~~t~~P~e~V~~my~dt~~~l~~---~ARV~DYl~lf 48 (66)
T PF12085_consen 9 VIRSIAEETGTPAETVRRMYDDTMRELSS---GARVHDYLPLF 48 (66)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHHHc---CCchhhhHHHH
Confidence 57899999999999999999999988874 45566777665
No 363
>PRK09726 antitoxin HipB; Provisional
Probab=58.72 E-value=16 Score=31.08 Aligned_cols=25 Identities=16% Similarity=0.330 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
.++|..++|+.+|||+.+|+++++.
T Consensus 24 ~gltq~elA~~~gvs~~tis~~e~g 48 (88)
T PRK09726 24 NGWTQSELAKKIGIKQATISNFENN 48 (88)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 5799999999999999999999884
No 364
>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=58.61 E-value=16 Score=31.80 Aligned_cols=43 Identities=16% Similarity=0.244 Sum_probs=30.8
Q ss_pred cCCHHHHHHHHHHhc-cCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFG-IEDGKPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 493 ~L~~rEReVL~LRyG-L~d~e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
.|++.++.|+.+.-. -...+|.+..+|++.|+++...||+.+.
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~ 87 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALD 87 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHH
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHH
Confidence 688888888877655 3445899999999999999999986543
No 365
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=58.24 E-value=17 Score=28.82 Aligned_cols=26 Identities=19% Similarity=0.471 Sum_probs=22.4
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008652 513 PKSLSEVGNIFGLSKERVRQLESRAL 538 (558)
Q Consensus 513 ~~Tl~EIAe~LGISrerVRqie~RAL 538 (558)
+.|+++||+.+|+|...+.++..+..
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~ 26 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKET 26 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHh
Confidence 36899999999999999998887665
No 366
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=58.15 E-value=20 Score=36.48 Aligned_cols=47 Identities=17% Similarity=0.212 Sum_probs=37.3
Q ss_pred HHHHHhcCCHHHHHHHHHHhccCCC---CCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 487 VRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 487 L~~~L~~L~~rEReVL~LRyGL~d~---e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
|......|++.|+.|..+- ++.. ..+|..|+|+..|+|..+|-+..+
T Consensus 3 i~~~~~~Lt~~e~~ia~yi--l~n~~~v~~~si~elA~~~~vS~aTv~Rf~k 52 (278)
T PRK11557 3 IRQRYPGLAQSDRKLADYL--LLQPDTARHLSSQQLANEAGVSQSSVVKFAQ 52 (278)
T ss_pred hhHhhhhCCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCCHHHHHHHHH
Confidence 5567788999999998754 3332 359999999999999999986654
No 367
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=58.11 E-value=12 Score=37.12 Aligned_cols=27 Identities=37% Similarity=0.611 Sum_probs=23.2
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 513 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 513 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
+.|.++||..+|+++++|. |++++|++
T Consensus 179 ~lt~~~IA~~lGisretls----R~L~~L~~ 205 (230)
T PRK09391 179 PMSRRDIADYLGLTIETVS----RALSQLQD 205 (230)
T ss_pred cCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 5799999999999999996 66777776
No 368
>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=57.74 E-value=13 Score=29.78 Aligned_cols=23 Identities=22% Similarity=0.355 Sum_probs=20.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~R 536 (558)
+|..|+|+.+|||..++|..+..
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 47899999999999999998775
No 369
>PRK10161 transcriptional regulator PhoB; Provisional
Probab=57.59 E-value=12 Score=35.91 Aligned_cols=50 Identities=14% Similarity=0.055 Sum_probs=39.9
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHH-----HhCCCHHHHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGN-----IFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe-----~LGISrerVRqie~RALkKLR~ 543 (558)
.|+++|.+||.+-. -+.|++.|.++|.. .++++..+|+....+.++||..
T Consensus 154 ~Lt~~E~~ll~~l~-~~~~~~~s~~~l~~~~~~~~~~~~~~tv~~~i~rlr~Kl~~ 208 (229)
T PRK10161 154 EMGPTEFKLLHFFM-THPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEP 208 (229)
T ss_pred EcCHHHHHHHHHHH-hCCCceEcHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhcc
Confidence 59999999987665 24457888777644 6688999999999999999963
No 370
>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional
Probab=57.51 E-value=7.7 Score=37.06 Aligned_cols=46 Identities=13% Similarity=0.018 Sum_probs=37.9
Q ss_pred cCCHHHHHHHHHHhccCCCCCCC---------HHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKS---------LSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~T---------l~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
.|+++|.+||.+-. .+.+ ..+||..++++..+|+....+.++||..
T Consensus 156 ~Lt~~E~~~l~~l~-----~~~~~v~sr~~l~~~~~~~~~~~~~~tv~~~i~~lr~Kl~~ 210 (232)
T PRK10955 156 ELTGTEFTLLYLLA-----QHLGQVVSREHLSQEVLGKRLTPFDRAIDMHISNLRRKLPD 210 (232)
T ss_pred cCCHHHHHHHHHHH-----hCCCceEcHHHHHHHHhCCCCCCCCcCHHHHHHHHHHhccc
Confidence 59999999998876 3333 4678888899999999999999999963
No 371
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=57.47 E-value=29 Score=27.24 Aligned_cols=35 Identities=11% Similarity=0.121 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 546 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 546 (558)
.+.+..+.|+.|+|.++||+.++.|+-..+--.+.
T Consensus 11 ~~~n~~~tA~~L~iHrNTl~yRl~ki~~l~g~dl~ 45 (59)
T PF13556_consen 11 NNGNISKTARALHIHRNTLRYRLKKIEELLGLDLD 45 (59)
T ss_dssp TTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--TT
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCcCCC
Confidence 57899999999999999999999888777654443
No 372
>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=57.01 E-value=27 Score=26.27 Aligned_cols=23 Identities=13% Similarity=0.325 Sum_probs=17.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~R 536 (558)
+|+.+.|+.+||++.|++.+...
T Consensus 17 ~S~r~AA~~ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 17 MSIRKAAKKYGVPRSTLRRRLRG 39 (45)
T ss_dssp S-HHHHHHHHT--HHHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHcC
Confidence 99999999999999999965543
No 373
>PRK14082 hypothetical protein; Provisional
Probab=56.94 E-value=35 Score=27.92 Aligned_cols=56 Identities=16% Similarity=0.105 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHH
Q 008652 316 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASY 373 (558)
Q Consensus 316 ~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTY 373 (558)
....+.++..+.+.+.+-... -.-.+-+||.||--+.+++.++.++...+.-|.-|
T Consensus 8 ~~e~e~ii~~FepkIkKsL~~--T~yqeREDLeQElk~Ki~eK~~~~~~~e~PGF~ef 63 (65)
T PRK14082 8 TEEIEHLIENFSPMIKKKLSN--TSYQEREDLEQELKIKIIEKADMLLCQEVPGFWEF 63 (65)
T ss_pred HHHHHHHHHHccHHHHHHHhc--CChhhHHHHHHHHHHHHHHHHHHhhcccCCcHHHh
Confidence 356778888888887765432 12246799999999999999999988776656544
No 374
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=56.53 E-value=2.6e+02 Score=29.37 Aligned_cols=25 Identities=16% Similarity=0.337 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
...|.+|||+..|||..|||+..+.
T Consensus 250 ~~~tq~eva~v~~vtevTIrnryke 274 (285)
T COG1405 250 ERRTQKEVAKVAGVTEVTIRNRYKE 274 (285)
T ss_pred CchHHHHHHHHhCCeeeHHHHHHHH
Confidence 7899999999999999999998743
No 375
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=56.44 E-value=14 Score=36.37 Aligned_cols=31 Identities=29% Similarity=0.383 Sum_probs=26.2
Q ss_pred CCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 509 EDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 509 ~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
..|+.++..+||+.||||+..|| .||+.|..
T Consensus 30 ~pG~~L~e~~La~~lgVSRtpVR----EAL~~L~~ 60 (221)
T PRK11414 30 KPGARLITKNLAEQLGMSITPVR----EALLRLVS 60 (221)
T ss_pred CCCCccCHHHHHHHHCCCchhHH----HHHHHHHH
Confidence 35688899999999999999998 67777765
No 376
>PRK01905 DNA-binding protein Fis; Provisional
Probab=55.75 E-value=46 Score=27.69 Aligned_cols=37 Identities=11% Similarity=0.201 Sum_probs=25.2
Q ss_pred HHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 497 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 497 rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
-|+.+|...+-- .+-+..+.|+.+|||+.+++..+++
T Consensus 37 ~E~~~i~~aL~~---~~gn~s~aAr~LGIsrstL~rklkk 73 (77)
T PRK01905 37 VEKPLLEVVMEQ---AGGNQSLAAEYLGINRNTLRKKLQQ 73 (77)
T ss_pred HHHHHHHHHHHH---cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 355555544431 2346899999999999998765543
No 377
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=55.70 E-value=1.3e+02 Score=33.38 Aligned_cols=24 Identities=17% Similarity=0.299 Sum_probs=21.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 419 HSPDKEDLARRVGITVEKLERLIF 442 (558)
Q Consensus 419 r~Pt~eEIA~~lgis~e~v~~ll~ 442 (558)
++-+..+||+.+|+.+.+|..+..
T Consensus 317 kPLtlkdiA~~lglheSTVSRav~ 340 (429)
T TIGR02395 317 KPLTLREVAEELGLHESTISRAIN 340 (429)
T ss_pred cCCcHHHHHHHhCCCccchhhhhc
Confidence 566899999999999999988865
No 378
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=55.33 E-value=15 Score=35.70 Aligned_cols=30 Identities=27% Similarity=0.420 Sum_probs=25.7
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 510 DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 510 d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
.|+.++..++|+.||||+..|| .||..|..
T Consensus 31 pG~~L~e~~La~~lgVSRtpVR----eAL~~L~~ 60 (212)
T TIGR03338 31 PGAKLNESDIAARLGVSRGPVR----EAFRALEE 60 (212)
T ss_pred CCCEecHHHHHHHhCCChHHHH----HHHHHHHH
Confidence 4578899999999999999998 67777765
No 379
>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=55.18 E-value=30 Score=26.18 Aligned_cols=51 Identities=16% Similarity=0.198 Sum_probs=38.6
Q ss_pred cCCHHHHHHHHHHhccCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDG-KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~-e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
.+++.+..+|.-.|..+.. ......+||..+|++...|+.....-..+.+.
T Consensus 6 ~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 6 RFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 4677788888888875432 23457889999999999999998877776553
No 380
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=55.18 E-value=63 Score=36.86 Aligned_cols=102 Identities=15% Similarity=0.176 Sum_probs=57.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhcCCC---cccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCH
Q 008652 420 SPDKEDLARRVGITVEKLERLIFITRMP---LSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNP 496 (558)
Q Consensus 420 ~Pt~eEIA~~lgis~e~v~~ll~~~~~~---~SLD~~i~~d~~~~l~e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~ 496 (558)
..|..+||+.+|+|...|++-+..-... ..+. .+....+-.+ .. .++. .+...+..-++
T Consensus 17 ~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~-~i~~~~Gy~l----~~---~~~~----------~~~~~~~~~~~ 78 (584)
T PRK09863 17 DRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIG-SISGSAKYHL----EI---LNRR----------SLFQLLQKSDN 78 (584)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchh-heecCCceEE----Ee---CCHH----------HHHHHHhcCCH
Confidence 6789999999999999997755422110 0000 0001011111 00 0111 11122222233
Q ss_pred HHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008652 497 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 497 rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 542 (558)
|+..+.++..+ .++.++.++|+.|.||+.||.+-+.+..+.|.
T Consensus 79 -e~~~il~~Ll~--~~~~~~~~La~~l~vS~sTi~~dl~~v~~~l~ 121 (584)
T PRK09863 79 -EDRLLLLRLLL--NTFTPMAQLASALNLSRTWVAERLPRLNQRYE 121 (584)
T ss_pred -HHHHHHHHHHH--cCCccHHHHHHHhCCCHHHHHHHHHHHHHhhh
Confidence 33334444433 36899999999999999999988887777665
No 381
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=55.12 E-value=17 Score=37.55 Aligned_cols=46 Identities=35% Similarity=0.391 Sum_probs=35.7
Q ss_pred hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 492 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 492 ~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
..|++.|++||.+--+ .|...++.||-+.+|+|+.+|. |++++|-+
T Consensus 191 ~~L~~~e~~il~~i~~--~GGri~Q~eL~r~lglsktTvs----R~L~~LEk 236 (258)
T COG2512 191 YDLNEDEKEILDLIRE--RGGRITQAELRRALGLSKTTVS----RILRRLEK 236 (258)
T ss_pred CCCCHHHHHHHHHHHH--hCCEEeHHHHHHhhCCChHHHH----HHHHHHHh
Confidence 4689999999887654 3346899999999999999997 45555543
No 382
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=55.03 E-value=18 Score=35.95 Aligned_cols=31 Identities=23% Similarity=0.440 Sum_probs=26.3
Q ss_pred CCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 509 EDGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 509 ~d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
..|+.+ |-.++|+.||||+..|| .||.+|..
T Consensus 25 ~pG~~LpsE~~La~~lgVSRtpVR----EAL~~Le~ 56 (235)
T TIGR02812 25 PPGSILPAERELSELIGVTRTTLR----EVLQRLAR 56 (235)
T ss_pred CCCCcCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 345788 89999999999999998 68888865
No 383
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=54.71 E-value=18 Score=26.14 Aligned_cols=25 Identities=16% Similarity=0.274 Sum_probs=18.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
.++|+.+||+.+|+|....+++.++
T Consensus 7 ~~~~l~~iA~~~g~S~~~f~r~Fk~ 31 (42)
T PF00165_consen 7 QKLTLEDIAEQAGFSPSYFSRLFKK 31 (42)
T ss_dssp SS--HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 6799999999999998888765544
No 384
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=54.68 E-value=19 Score=32.22 Aligned_cols=35 Identities=17% Similarity=0.302 Sum_probs=27.6
Q ss_pred HHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 500 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 500 eVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
+||.-.|. +.-++|..+.|+.|||++.+|..+.+.
T Consensus 12 EiL~eefl--ep~glt~~~lA~~lgV~r~~is~ling 46 (104)
T COG3093 12 EILREEFL--EPLGLTQTELAEALGVTRNTISELING 46 (104)
T ss_pred HHHHHHHh--ccccCCHHHHHHHhCCCHHHHHHHHcC
Confidence 46666665 223699999999999999999988764
No 385
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=54.53 E-value=25 Score=34.42 Aligned_cols=26 Identities=12% Similarity=0.176 Sum_probs=23.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESRA 537 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~RA 537 (558)
.+.|..|||+.+||+..+|++++.+-
T Consensus 14 ~~~t~~eLA~~lgis~~tV~~~L~~L 39 (203)
T TIGR02702 14 GQATAAALAEALAISPQAVRRHLKDL 39 (203)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46999999999999999999998765
No 386
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=54.50 E-value=23 Score=35.91 Aligned_cols=41 Identities=17% Similarity=0.236 Sum_probs=31.6
Q ss_pred HHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008652 496 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 539 (558)
Q Consensus 496 ~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 539 (558)
+|++.|+.+-.. ....+.+||++.||||..|||+.+..--.
T Consensus 4 ~R~~~Il~~l~~---~~~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 4 ARQQAIVDLLLN---HTSLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred HHHHHHHHHHHH---cCCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 566666655432 35789999999999999999998886544
No 387
>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family contains mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation []. Homologues of neugrin are found in fungi suggesting they have a alternative role or more than one function.
Probab=54.44 E-value=20 Score=36.27 Aligned_cols=42 Identities=14% Similarity=0.188 Sum_probs=33.3
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
.|+..+.+-|++-+-.+ -+.+|...+|+.|+||.+.||.|++
T Consensus 10 ~Ls~~~~~~ir~L~~~~-p~~~t~~~Lae~F~vspe~irrILk 51 (225)
T PF06413_consen 10 KLSREAMEQIRYLHKED-PEEWTVERLAESFKVSPEAIRRILK 51 (225)
T ss_pred CCCHHHHHHHHHHHHhC-ccccCHHHHHhhCCCCHHHHHHHHh
Confidence 57777777777665433 2568999999999999999999875
No 388
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=54.44 E-value=25 Score=40.07 Aligned_cols=46 Identities=24% Similarity=0.266 Sum_probs=37.0
Q ss_pred CCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 494 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 494 L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
|++|++++|.+-- + .+.|..++|+.||||.-|||+-+...=.-|++
T Consensus 2 l~~R~~~iL~~L~---~-~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~ 47 (584)
T PRK09863 2 LNERELKIVDLLE---Q-QDRSGGELAQQLGVSRRTIVRDIAYINFTLNG 47 (584)
T ss_pred hHHHHHHHHHHHH---c-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 6788888887542 2 57999999999999999999887766555655
No 389
>TIGR01387 cztR_silR_copR heavy metal response regulator. Members of this family contain a response regulator receiver domain (Pfam:PF00072) and an associated transcriptional regulatory region (Pfam:PF00486). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc. Most members encoded by genes adjacent to genes for encoding a member of the heavy metal sensor histidine kinase family (TIGRFAMs:TIGR01386), its partner in the two-component response regulator system.
Probab=54.39 E-value=19 Score=33.75 Aligned_cols=49 Identities=14% Similarity=0.121 Sum_probs=40.3
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-----GLSKERVRQLESRALYRLK 542 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~L-----GISrerVRqie~RALkKLR 542 (558)
.|+++|.+|+.+-.. +.|+..|.++|.+.+ ..+..+|..++.+.++||.
T Consensus 147 ~Lt~~E~~il~~l~~-~~~~~~sr~~i~~~~~~~~~~~~~~~~~~~i~~lr~kl~ 200 (218)
T TIGR01387 147 TLTRKEFQLLWLLMR-RTGEVLPRTVIASLVWGMNFDSDTNVVDVAIRRLRAKVD 200 (218)
T ss_pred eCCHHHHHHHHHHHh-CCCeeEcHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhhc
Confidence 599999999988764 444679999999998 4567888888888888885
No 390
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=54.29 E-value=29 Score=34.16 Aligned_cols=46 Identities=15% Similarity=0.141 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHhccC-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 494 LNPKERCIVRLRFGIE-DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 494 L~~rEReVL~LRyGL~-d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
++.++|-+-.+...-+ +.-+.|.++||+.+|+|+++|. |++++|++
T Consensus 149 ~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvs----R~L~~L~~ 195 (226)
T PRK10402 149 FPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLL----YVLAQFIQ 195 (226)
T ss_pred ChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHH----HHHHHHHH
Confidence 3556665444432111 1234689999999999999996 67777776
No 391
>PRK11050 manganese transport regulator MntR; Provisional
Probab=54.23 E-value=21 Score=33.63 Aligned_cols=26 Identities=15% Similarity=0.233 Sum_probs=21.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 511 GKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 511 ~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
+.+.+..|||+.+||++.+|++.+.+
T Consensus 49 ~~~~t~~eLA~~l~is~stVsr~l~~ 74 (152)
T PRK11050 49 VGEARQVDIAARLGVSQPTVAKMLKR 74 (152)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 36799999999999999999855543
No 392
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=54.17 E-value=24 Score=32.53 Aligned_cols=25 Identities=8% Similarity=0.185 Sum_probs=21.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 511 GKPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 511 ~e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
+...+..+||+.||||..+|+..+.
T Consensus 20 ~~~~~~~ela~~l~vs~~svs~~l~ 44 (142)
T PRK03902 20 KGYARVSDIAEALSVHPSSVTKMVQ 44 (142)
T ss_pred CCCcCHHHHHHHhCCChhHHHHHHH
Confidence 3567999999999999999986553
No 393
>PRK03837 transcriptional regulator NanR; Provisional
Probab=53.61 E-value=20 Score=35.59 Aligned_cols=30 Identities=37% Similarity=0.496 Sum_probs=25.4
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 510 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 510 d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
.|+.+ +..++|+.||||+..|| .||..|..
T Consensus 33 pG~~Lp~E~~Lae~~gVSRt~VR----EAL~~L~~ 63 (241)
T PRK03837 33 PGDQLPSERELMAFFGVGRPAVR----EALQALKR 63 (241)
T ss_pred CCCCCCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 45778 89999999999999998 67777764
No 394
>smart00862 Trans_reg_C Transcriptional regulatory protein, C terminal. This domain is almost always found associated with the response regulator receiver domain. It may play a role in DNA binding.
Probab=53.61 E-value=43 Score=26.72 Aligned_cols=50 Identities=22% Similarity=0.231 Sum_probs=35.7
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHh------CCCHHHHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF------GLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~L------GISrerVRqie~RALkKLR~ 543 (558)
.|+++|..+|.+-. ...|...|.++|.+.+ +.+..+|++...+-+++|..
T Consensus 5 ~Lt~~e~~lL~~L~-~~~~~~vs~~~l~~~lw~~~~~~~~~~~l~~~i~~LR~~l~~ 60 (78)
T smart00862 5 KLTPKEFRLLELLL-RNPGRVVSREELLEAVWGDDDDDVDDNTLDVHISRLRKKLED 60 (78)
T ss_pred ecCHHHHHHHHHHH-hCCCCccCHHHHHHHHcCCCCCCCccchHHHHHHHHHHHHhc
Confidence 47889999775544 3445789999999975 35667777777776666654
No 395
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=53.58 E-value=19 Score=36.07 Aligned_cols=31 Identities=23% Similarity=0.336 Sum_probs=26.2
Q ss_pred CCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 509 EDGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 509 ~d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
..|+.+ +-.+||+.||||+..|| .||++|..
T Consensus 26 ~pG~~LPsE~eLa~~~gVSRtpVR----EAL~~L~~ 57 (251)
T PRK09990 26 KVGQALPSERRLCEKLGFSRSALR----EGLTVLRG 57 (251)
T ss_pred CCCCcCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 355788 89999999999999998 67888865
No 396
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=52.91 E-value=20 Score=36.01 Aligned_cols=30 Identities=27% Similarity=0.443 Sum_probs=25.4
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 510 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 510 d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
.|+.+ +-.++|+.||||+..|| .||..|..
T Consensus 30 pG~~LpsE~eLa~~lgVSRtpVR----EAL~~L~~ 60 (254)
T PRK09464 30 PGEKLPPERELAKQFDVSRPSLR----EAIQRLEA 60 (254)
T ss_pred CCCcCCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 45777 89999999999999998 67777765
No 397
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=52.77 E-value=15 Score=36.19 Aligned_cols=27 Identities=22% Similarity=0.395 Sum_probs=22.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 513 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 513 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
++|.++||..+|+++++|. |++++|++
T Consensus 173 ~~t~~~iA~~lG~tretvs----R~l~~L~~ 199 (236)
T PRK09392 173 PYEKRVLASYLGMTPENLS----RAFAALAS 199 (236)
T ss_pred eCCHHHHHHHhCCChhHHH----HHHHHHHh
Confidence 5778999999999999986 55666665
No 398
>PF06322 Phage_NinH: Phage NinH protein; InterPro: IPR010454 This entry is represented by Bacteriophage 933W, NinH. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=52.59 E-value=21 Score=28.99 Aligned_cols=27 Identities=22% Similarity=0.463 Sum_probs=23.1
Q ss_pred HHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008652 501 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE 534 (558)
Q Consensus 501 VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie 534 (558)
+|.--|| ...|+|..||+++.+||+..
T Consensus 11 lLi~~~G-------nqtEvaR~l~c~R~TVrKY~ 37 (64)
T PF06322_consen 11 LLIETYG-------NQTEVARRLGCNRATVRKYS 37 (64)
T ss_pred HHHHHhC-------cHHHHHHHhcccHHHHHHHh
Confidence 4666787 78999999999999999764
No 399
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=52.27 E-value=21 Score=35.99 Aligned_cols=37 Identities=24% Similarity=0.351 Sum_probs=28.4
Q ss_pred HHHHHhccCCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 501 IVRLRFGIEDGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 501 VL~LRyGL~d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
|+.-.| ..|+.+ +..|+|+.||||+..|| .||+.|..
T Consensus 15 I~~g~l--~pG~~LpsE~eLae~~gVSRtpVR----EAL~~Le~ 52 (253)
T PRK10421 15 IEEKNL--EAGMKLPAERQLAMQLGVSRNSLR----EALAKLVS 52 (253)
T ss_pred HHcCCC--CCCCcCCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 444443 345778 78999999999999998 67888865
No 400
>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=52.21 E-value=20 Score=32.31 Aligned_cols=24 Identities=33% Similarity=0.458 Sum_probs=22.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
.|.|..|+|..||||+.+|..+..
T Consensus 17 ~g~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 17 KGKSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred ccchHHHHHHHhCcHHHHHHHHHH
Confidence 678999999999999999998876
No 401
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=52.06 E-value=30 Score=29.62 Aligned_cols=40 Identities=20% Similarity=0.345 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 494 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 494 L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
|++.|..||...+.. .+.+..+||+.+++++.+|.+++.+
T Consensus 20 lt~~q~~~L~~l~~~---~~~~~~~la~~l~i~~~~vt~~l~~ 59 (126)
T COG1846 20 LTPPQYQVLLALYEA---GGITVKELAERLGLDRSTVTRLLKR 59 (126)
T ss_pred CCHHHHHHHHHHHHh---CCCcHHHHHHHHCCCHHHHHHHHHH
Confidence 999999999887762 2222299999999999999765543
No 402
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=51.81 E-value=22 Score=32.52 Aligned_cols=25 Identities=16% Similarity=0.104 Sum_probs=23.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
.++|..++|+.+|||+.+|+++++.
T Consensus 17 ~gltq~~lA~~~gvs~~~is~~E~g 41 (135)
T PRK09706 17 LKLSQRSLAKAVKVSHVSISQWERD 41 (135)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 6799999999999999999999865
No 403
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=51.55 E-value=21 Score=35.92 Aligned_cols=37 Identities=22% Similarity=0.425 Sum_probs=28.4
Q ss_pred HHHHHhccCCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 501 IVRLRFGIEDGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 501 VL~LRyGL~d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
|+.-.|. .|+.+ |-.++|+.||||+..|| .|+..|..
T Consensus 22 I~~g~l~--pG~~LpsE~eLa~~~gVSRtpVR----EAL~~L~~ 59 (257)
T PRK10225 22 IIKTPYN--PGERLPPEREIAEMLDVTRTVVR----EALIMLEI 59 (257)
T ss_pred HHhCCCC--CCCcCcCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 4444443 45778 69999999999999998 67778865
No 404
>PRK11517 transcriptional regulatory protein YedW; Provisional
Probab=51.43 E-value=27 Score=33.02 Aligned_cols=49 Identities=14% Similarity=0.078 Sum_probs=39.8
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-----GLSKERVRQLESRALYRLK 542 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~L-----GISrerVRqie~RALkKLR 542 (558)
.|+++|.+||.+-.- +.|+..|.++|.+.+ ..+..+|+.+..|.++||.
T Consensus 147 ~Lt~~E~~il~~l~~-~~g~~~s~~~i~~~~w~~~~~~~~~tv~~~i~rlr~Kl~ 200 (223)
T PRK11517 147 TLTRKEFQLLWLLAS-RAGEIIPRTVIASEIWGINFDSDTNTVDVAIRRLRAKVD 200 (223)
T ss_pred eCCHHHHHHHHHHHh-CCCccCCHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhhc
Confidence 599999999987653 445778999999986 4467899999888888885
No 405
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=51.05 E-value=22 Score=34.94 Aligned_cols=38 Identities=24% Similarity=0.299 Sum_probs=29.1
Q ss_pred HHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 500 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 500 eVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
.|+.-.| ..|..++..++|+.||||+..|| .||.+|..
T Consensus 19 ~I~~g~l--~pG~~L~e~eLae~lgVSRtpVR----EAL~~L~~ 56 (224)
T PRK11534 19 DIIRGNF--QPDEKLRMSLLTSRYALGVGPLR----EALSQLVA 56 (224)
T ss_pred HHHhCCC--CCCCcCCHHHHHHHHCCChHHHH----HHHHHHHH
Confidence 3455444 24588899999999999999998 67777754
No 406
>PRK13239 alkylmercury lyase; Provisional
Probab=50.77 E-value=31 Score=34.48 Aligned_cols=29 Identities=21% Similarity=0.237 Sum_probs=26.1
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHhcC
Q 008652 417 GNHSPDKEDLARRVGITVEKLERLIFITR 445 (558)
Q Consensus 417 ~gr~Pt~eEIA~~lgis~e~v~~ll~~~~ 445 (558)
.|+.|+..+||+.+|+++++|+.+|....
T Consensus 33 ~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 33 KGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 57899999999999999999999987643
No 407
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=50.64 E-value=41 Score=30.57 Aligned_cols=49 Identities=16% Similarity=0.226 Sum_probs=33.6
Q ss_pred HHHHhcCCHHHH-HHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 488 RNLLTLLNPKER-CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 488 ~~~L~~L~~rER-eVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
.+.+..|.+.-| .||.+-. ++.+++..||++.+|+|+.+|++.+ +.|++
T Consensus 7 ~~~fkaLadptRl~IL~~L~---~~~~~~v~ela~~l~lsqstvS~HL----~~L~~ 56 (117)
T PRK10141 7 LQLFKILSDETRLGIVLLLR---ESGELCVCDLCTALDQSQPKISRHL----ALLRE 56 (117)
T ss_pred HHHHHHhCCHHHHHHHHHHH---HcCCcCHHHHHHHHCcCHHHHHHHH----HHHHH
Confidence 345566665444 5665433 2257999999999999999998764 45554
No 408
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=50.61 E-value=27 Score=24.59 Aligned_cols=25 Identities=20% Similarity=0.388 Sum_probs=22.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
.++|..++|+.+|++..+|.+++..
T Consensus 9 ~~~s~~~la~~~~i~~~~i~~~~~~ 33 (56)
T smart00530 9 KGLTQEELAEKLGVSRSTLSRIENG 33 (56)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 5789999999999999999987654
No 409
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=50.45 E-value=25 Score=35.75 Aligned_cols=26 Identities=15% Similarity=0.093 Sum_probs=22.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 511 GKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 511 ~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
....+.+||++.||||..|||+.+..
T Consensus 17 ~~~~~~~ela~~l~vS~~TirRdL~~ 42 (251)
T PRK13509 17 LGFVTVEKVIERLGISPATARRDINK 42 (251)
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 35789999999999999999977654
No 410
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=50.34 E-value=48 Score=32.29 Aligned_cols=46 Identities=9% Similarity=0.115 Sum_probs=30.1
Q ss_pred HHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 486 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 486 ~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
.+..++.. ++.-..||..-. .. ...|-+|||+.|||+...||+++.
T Consensus 13 ~l~~~~~~-~~~~~~Vl~~L~--~~-g~~tdeeLA~~Lgi~~~~VRk~L~ 58 (178)
T PRK06266 13 VLFEIMEG-DEEGFEVLKALI--KK-GEVTDEEIAEQTGIKLNTVRKILY 58 (178)
T ss_pred HHHHHhcC-CccHhHHHHHHH--Hc-CCcCHHHHHHHHCCCHHHHHHHHH
Confidence 44444432 444445555322 22 379999999999999999996654
No 411
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=50.08 E-value=11 Score=28.21 Aligned_cols=21 Identities=14% Similarity=0.248 Sum_probs=18.3
Q ss_pred HHHHHHhCCCHHHHHHHHHHH
Q 008652 517 SEVGNIFGLSKERVRQLESRA 537 (558)
Q Consensus 517 ~EIAe~LGISrerVRqie~RA 537 (558)
++||+.+|||+.+|+++++.-
T Consensus 1 ~~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 1 KDIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred CcHHHHHCcCHHHHHHHHcCC
Confidence 379999999999999998754
No 412
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=50.00 E-value=27 Score=27.28 Aligned_cols=25 Identities=16% Similarity=0.405 Sum_probs=20.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
.++|+.++|+.+|+++.++.++++.
T Consensus 11 ~~lt~~~~a~~~~i~~~~i~~~e~g 35 (64)
T PF12844_consen 11 KGLTQKDLAEKLGISRSTISKIENG 35 (64)
T ss_dssp CT--HHHHHHHHTS-HHHHHHHHTT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 6799999999999999999999864
No 413
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=49.90 E-value=2.4e+02 Score=31.50 Aligned_cols=47 Identities=19% Similarity=0.376 Sum_probs=32.3
Q ss_pred HHHhcCCHHHHHHHH-------HHhccC-CC----CCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 489 NLLTLLNPKERCIVR-------LRFGIE-DG----KPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 489 ~~L~~L~~rEReVL~-------LRyGL~-d~----e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
.++..|..|++.++. .-+++. +| .++++++||+.+|+..+||++...
T Consensus 294 wLiksL~qR~~TLlkV~~~Iv~~Q~~Ff~~g~~~l~PL~LrdvA~~i~~HESTISRai~ 352 (444)
T COG1508 294 WLIKSLEQREETLLKVAEEIVEYQKAFFEGGEEALKPLVLRDVADEIGMHESTISRAIT 352 (444)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCCcccHHHHHHHhCccHHHHHHHHh
Confidence 345677777765543 322222 22 579999999999999999987654
No 414
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=49.82 E-value=12 Score=32.38 Aligned_cols=26 Identities=19% Similarity=0.448 Sum_probs=23.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRALY 539 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RALk 539 (558)
+|..|+|+.+|||..++|-.+..++-
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~~Gll 26 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDIGLF 26 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999987654
No 415
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=49.51 E-value=31 Score=29.15 Aligned_cols=31 Identities=19% Similarity=0.315 Sum_probs=25.4
Q ss_pred HHHHHhccCCCCCCCHHHHHHHhC------CCHHHHHHHHH
Q 008652 501 IVRLRFGIEDGKPKSLSEVGNIFG------LSKERVRQLES 535 (558)
Q Consensus 501 VL~LRyGL~d~e~~Tl~EIAe~LG------ISrerVRqie~ 535 (558)
+...|-- -++|..++|+.+| +|..+|.++++
T Consensus 16 lk~~R~~----lGLTQ~dvA~~lg~~~g~i~SQstISR~Es 52 (75)
T smart00352 16 FKQRRIK----LGFTQADVGLALGALYGPDFSQTTICRFEA 52 (75)
T ss_pred HHHHHHH----cCCCHHHHHHHhcccccCcCCHHHHHHHHh
Confidence 3445554 6899999999999 59999999886
No 416
>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=49.32 E-value=33 Score=33.19 Aligned_cols=43 Identities=19% Similarity=0.191 Sum_probs=32.3
Q ss_pred hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 492 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 492 ~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
..|++-|+-....+.. .. .++|.++||+.+|+|+.+|++++.-
T Consensus 101 ~~lt~~e~a~~~~~l~-~~-~g~s~~~iA~~lg~s~~~V~r~l~l 143 (187)
T TIGR00180 101 EDLSPIEEAQAYKRLL-EK-FSMTQEDLAKKIGKSRAHITNLLRL 143 (187)
T ss_pred cCCCHHHHHHHHHHHH-HH-hCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4788888766554432 11 4789999999999999999987654
No 417
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=49.24 E-value=17 Score=29.44 Aligned_cols=24 Identities=25% Similarity=0.329 Sum_probs=19.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
.+.|-.|||+.+|+|+.+||.++.
T Consensus 14 ~p~~T~eiA~~~gls~~~aR~yL~ 37 (62)
T PF04703_consen 14 GPLKTREIADALGLSIYQARYYLE 37 (62)
T ss_dssp S-EEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Confidence 689999999999999999997764
No 418
>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=48.62 E-value=33 Score=30.78 Aligned_cols=25 Identities=20% Similarity=0.367 Sum_probs=21.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 511 GKPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 511 ~e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
+.+.|.+|||+.+|+++..|++++.
T Consensus 23 ~~~~s~~eia~~~~i~~~~v~~il~ 47 (132)
T TIGR00738 23 EGPVSVKEIAERQGISRSYLEKILR 47 (132)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHH
Confidence 3589999999999999999986554
No 419
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=48.38 E-value=24 Score=32.57 Aligned_cols=30 Identities=27% Similarity=0.630 Sum_probs=24.2
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 510 DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 510 d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
+|+..|..|||+.+|||+..|| +++.+|++
T Consensus 22 ~g~~~s~~~ia~~~~is~~~vr----k~l~~L~~ 51 (141)
T PRK11014 22 EGRMTSISEVTEVYGVSRNHMV----KIINQLSR 51 (141)
T ss_pred CCCccCHHHHHHHHCcCHHHHH----HHHHHHHh
Confidence 4567899999999999998887 55666765
No 420
>PHA00738 putative HTH transcription regulator
Probab=47.98 E-value=40 Score=30.37 Aligned_cols=37 Identities=22% Similarity=0.033 Sum_probs=27.2
Q ss_pred HHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 496 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 496 ~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
|.-+.||.+-. .+++++..||++.+++|+.+|++.++
T Consensus 12 ptRr~IL~lL~---~~e~~~V~eLae~l~lSQptVS~HLK 48 (108)
T PHA00738 12 ILRRKILELIA---ENYILSASLISHTLLLSYTTVLRHLK 48 (108)
T ss_pred HHHHHHHHHHH---HcCCccHHHHHHhhCCCHHHHHHHHH
Confidence 44455555432 23579999999999999999997653
No 421
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=47.98 E-value=31 Score=34.65 Aligned_cols=26 Identities=19% Similarity=0.350 Sum_probs=22.5
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 510 DGKPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 510 d~e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
...++|+.|||+.+|+++.+|..++.
T Consensus 21 ~~~~~~l~eia~~lglpksT~~RlL~ 46 (248)
T TIGR02431 21 ERPRLTLTDVAEATGLTRAAARRFLL 46 (248)
T ss_pred CCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34789999999999999999987654
No 422
>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=47.90 E-value=30 Score=31.23 Aligned_cols=26 Identities=27% Similarity=0.429 Sum_probs=21.7
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 510 DGKPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 510 d~e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
++...|..|||+.+|+|+..|++++.
T Consensus 22 ~~~~~s~~eia~~l~is~~~v~~~l~ 47 (130)
T TIGR02944 22 DSQPYSAAEIAEQTGLNAPTVSKILK 47 (130)
T ss_pred CCCCccHHHHHHHHCcCHHHHHHHHH
Confidence 34679999999999999999986543
No 423
>cd00383 trans_reg_C Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and a response regulator. The former autophosphorylates in a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. The C-terminal effector domain contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunite of RNA polymerase.
Probab=47.82 E-value=42 Score=27.92 Aligned_cols=49 Identities=22% Similarity=0.154 Sum_probs=35.2
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLK 542 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR 542 (558)
.|+++|..+|.+-+ ...|+..|.++|.+.+. .+...+++.+.+.++||.
T Consensus 23 ~Lt~~e~~lL~~L~-~~~~~~vs~~~l~~~lw~~~~~~~~~~l~~~I~rLRkkl~ 76 (95)
T cd00383 23 ELTPKEFELLELLA-RNPGRVLSREQLLEAVWGDDYDVDDRTVDVHISRLRKKLE 76 (95)
T ss_pred EeCHHHHHHHHHHH-hCCCCcCCHHHHHHHhcCCCCCCCcccHHHHHHHHHHHhc
Confidence 48899998887755 35568999999999884 566666666555555554
No 424
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=47.75 E-value=18 Score=28.15 Aligned_cols=26 Identities=8% Similarity=0.218 Sum_probs=19.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESRA 537 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~RA 537 (558)
.++|..++|+..||++.+|..+.+.-
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 57899999999999999999988765
No 425
>PRK10643 DNA-binding transcriptional regulator BasR; Provisional
Probab=47.65 E-value=26 Score=32.98 Aligned_cols=49 Identities=14% Similarity=0.059 Sum_probs=35.4
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHH-----HhCCCHHHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGN-----IFGLSKERVRQLESRALYRLK 542 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe-----~LGISrerVRqie~RALkKLR 542 (558)
.|+++|.+|+.+..- ..|...+.++|.+ .++++..+|+...++.++||.
T Consensus 149 ~Lt~~E~~il~~l~~-~~g~~~~~~~~~~~~~~~~~~~~~~tv~~~i~~lr~Kl~ 202 (222)
T PRK10643 149 ILTPKEFALLSRLML-KAGSPVHREILYQDIYNWDDEPSSNTLEVHIHNLRDKVG 202 (222)
T ss_pred ecCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhCC
Confidence 499999999987652 2223444455544 368899999999999999885
No 426
>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=47.54 E-value=13 Score=30.09 Aligned_cols=25 Identities=32% Similarity=0.446 Sum_probs=19.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
...|+.|||..||++++.|+.++..
T Consensus 13 ~~~S~~eLa~~~~~s~~~ve~mL~~ 37 (69)
T PF09012_consen 13 GRVSLAELAREFGISPEAVEAMLEQ 37 (69)
T ss_dssp -SEEHHHHHHHTT--HHHHHHHHHH
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 6789999999999999999876654
No 427
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=47.10 E-value=28 Score=34.99 Aligned_cols=30 Identities=20% Similarity=0.174 Sum_probs=25.1
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 510 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 510 d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
.|+.+ |-.+||+.||||+..|| .|++.|..
T Consensus 28 pG~~LpsE~eLae~~gVSRtpVR----EAL~~L~~ 58 (253)
T PRK11523 28 VGDKLPAERFIADEKNVSRTVVR----EAIIMLEV 58 (253)
T ss_pred CCCCCCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 45788 58999999999999998 67778765
No 428
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=47.03 E-value=49 Score=30.35 Aligned_cols=44 Identities=14% Similarity=0.185 Sum_probs=33.7
Q ss_pred cCCHHHHHHHHHHhccCCCCCCCHHHHHHHh----CCCHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF----GLSKERVRQLESRALY 539 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~L----GISrerVRqie~RALk 539 (558)
.|++.|.+|+..-.. ..+.|..||.+.| |++..||...+.|-.+
T Consensus 1 ~Lt~~E~~VM~vlW~---~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~ 48 (130)
T TIGR02698 1 SISDAEWEVMRVVWT---LGETTSRDIIRILAEKKDWSDSTIKTLLGRLVD 48 (130)
T ss_pred CCCHHHHHHHHHHHc---CCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHH
Confidence 378899998876553 2468999977776 7999999987776655
No 429
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=46.99 E-value=38 Score=23.96 Aligned_cols=25 Identities=20% Similarity=0.405 Sum_probs=22.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
.++|..++|..+|+++.+|.+++..
T Consensus 11 ~~~s~~~~a~~~~~~~~~v~~~~~g 35 (58)
T cd00093 11 KGLTQEELAEKLGVSRSTISRIENG 35 (58)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 5789999999999999999987664
No 430
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=46.90 E-value=35 Score=32.44 Aligned_cols=42 Identities=10% Similarity=0.127 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHhccC-CCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 494 LNPKERCIVRLRFGIE-DGKPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 494 L~~rEReVL~LRyGL~-d~e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
+++....-|..-|.+. ++......+||+.|||+..+|.++++
T Consensus 4 ~s~~~edYL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~ 46 (154)
T COG1321 4 LSETEEDYLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLK 46 (154)
T ss_pred cchHHHHHHHHHHHHHhccCcccHHHHHHHhCCCcHHHHHHHH
Confidence 4455555555555333 34578999999999999999986544
No 431
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=46.84 E-value=31 Score=35.11 Aligned_cols=37 Identities=22% Similarity=0.238 Sum_probs=25.7
Q ss_pred HHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 499 RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 499 ReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
|-+-.|.+.-..+.++|+.||++.+|+++.+|.+++.
T Consensus 12 ral~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~ 48 (263)
T PRK09834 12 RGLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLE 48 (263)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3333344432334569999999999999999975543
No 432
>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes. This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].
Probab=46.73 E-value=40 Score=32.81 Aligned_cols=38 Identities=24% Similarity=0.280 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008652 494 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE 534 (558)
Q Consensus 494 L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie 534 (558)
|++.-|+-|...+. .+++|+++||..+||+..||.-|+
T Consensus 17 lse~~r~~Iy~~~~---~~~~sv~~vS~~ygi~~~RV~AIv 54 (172)
T PF12298_consen 17 LSEELREQIYEDVM---QDGKSVREVSQKYGIKIQRVEAIV 54 (172)
T ss_pred CCHHHHHHHHHHHH---hCCCCHHHHHHHhCCCHHHHHHHH
Confidence 55566665555553 267799999999999999997654
No 433
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=46.68 E-value=14 Score=32.34 Aligned_cols=26 Identities=23% Similarity=0.384 Sum_probs=23.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRALY 539 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RALk 539 (558)
+|..|+|+.+|||..++|..+..++-
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~~Gll 27 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESIGLI 27 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 68899999999999999999988765
No 434
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=46.53 E-value=53 Score=31.55 Aligned_cols=57 Identities=23% Similarity=0.248 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHhc--cCC--CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 480 KQLMRQHVRNLLTLLNPKERCIVRLRFG--IED--GKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 480 ~~~~~e~L~~~L~~L~~rEReVL~LRyG--L~d--~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
+++.-+.|+..|..||+.|++=+.-+|- ++| .+|+|-+||.+.||=+++-++++...
T Consensus 3 k~efL~~L~~~L~~lp~~e~~e~l~~Y~e~f~d~~~~G~sEeeii~~LG~P~~iA~~i~~~ 63 (181)
T PF08006_consen 3 KNEFLNELEKYLKKLPEEEREEILEYYEEYFDDAGEEGKSEEEIIAELGSPKEIAREILAE 63 (181)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHcCCHHHHHHHHHHh
Confidence 3445567889999999998885544442 222 36899999999999999999888754
No 435
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=46.47 E-value=33 Score=25.81 Aligned_cols=48 Identities=15% Similarity=0.153 Sum_probs=36.2
Q ss_pred cCCHHHHHHHHHHhccCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008652 493 LLNPKERCIVRLRFGIEDG-KPKSLSEVGNIFGLSKERVRQLESRALYR 540 (558)
Q Consensus 493 ~L~~rEReVL~LRyGL~d~-e~~Tl~EIAe~LGISrerVRqie~RALkK 540 (558)
.+++.+..+|.-.|..+.. ......+||..+|++...|.........+
T Consensus 6 ~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~ 54 (56)
T smart00389 6 SFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAK 54 (56)
T ss_pred cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhc
Confidence 3678888888888874432 23457889999999999999887766554
No 436
>PRK06424 transcription factor; Provisional
Probab=46.46 E-value=29 Score=32.76 Aligned_cols=25 Identities=12% Similarity=0.056 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
.++|+.|+|+.+|+++.+|+++++.
T Consensus 96 ~GLSQ~eLA~~iGvs~stIskiE~G 120 (144)
T PRK06424 96 LSMSQADLAAKIFERKNVIASIERG 120 (144)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 6899999999999999999999863
No 437
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=46.29 E-value=2.2e+02 Score=32.21 Aligned_cols=127 Identities=13% Similarity=0.223 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCC---CCCCHHHHHHHhCCCHHHHHHHHHhcCCCccc
Q 008652 374 AYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGN---HSPDKEDLARRVGITVEKLERLIFITRMPLSM 450 (558)
Q Consensus 374 A~~wIr~aI~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~g---r~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SL 450 (558)
|.|.|+.-=.|. ..+......|.+....+-..+. ++-+..+||+.+|+.+.+|..+..
T Consensus 331 A~wli~si~qR~-----------~TllkV~~~Iv~~Q~~Ff~~G~~~LkPLtlkdVAe~lglHeSTVSRa~~-------- 391 (481)
T PRK12469 331 ARWLIRNAQQRF-----------DTIQRVAECIVARQRDFFRYGEIALKPLVLRDVAEELGLHESTISRATG-------- 391 (481)
T ss_pred HHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHhCCcccCcCCcHHHHHHHhCCCcchhhHHhc--------
Q ss_pred CCCCCCCCCc-chhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHh-----C
Q 008652 451 QQPVWADQDT-TFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-----G 524 (558)
Q Consensus 451 D~~i~~d~~~-~l~e~i~d~~~~~pe~~le~~~~~e~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~L-----G 524 (558)
+..+....+. .+-.++...-.......+.....+..|.++++.=+++ +++|-++|++.| .
T Consensus 392 ~KY~~tp~GifeLK~FFs~~v~~~~g~~~Ss~~Ik~~Ik~lI~~Ed~~--------------kPLSD~~I~~~L~~~GI~ 457 (481)
T PRK12469 392 NKYMATPRGTFEFKHFFPRKLEAAGGGECSAAAVRALIKEMIAAEQAG--------------DPLSDVALAEMLAGRGVL 457 (481)
T ss_pred CceeecCCceEeHHHhhccccCCCCCccccHHHHHHHHHHHHHhcCCC--------------CCCCHHHHHHHHHhcCCC
Q ss_pred CCHHHHHHH
Q 008652 525 LSKERVRQL 533 (558)
Q Consensus 525 ISrerVRqi 533 (558)
|+|-||-+.
T Consensus 458 IARRTVAKY 466 (481)
T PRK12469 458 IARRTVAKY 466 (481)
T ss_pred eechhHHHH
No 438
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.19 E-value=45 Score=30.02 Aligned_cols=47 Identities=23% Similarity=0.241 Sum_probs=38.7
Q ss_pred HhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008652 491 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 541 (558)
Q Consensus 491 L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 541 (558)
.+.|++.+-+.+++++- -.=+++||-..+|+|--+||..+...+++|
T Consensus 39 F~~Lt~d~LeFv~lf~r----~RGnlKEvEr~lg~sYptvR~kld~vlram 85 (122)
T COG3877 39 FEYLTSDQLEFVELFLR----CRGNLKEVERELGISYPTVRTKLDEVLRAM 85 (122)
T ss_pred ccccCHhHhHHHHHHHH----HccCHHHHHHHHCCccHHHHHHHHHHHHHc
Confidence 45688888888888775 334899999999999999999888877776
No 439
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=45.79 E-value=61 Score=33.49 Aligned_cols=50 Identities=20% Similarity=0.266 Sum_probs=39.4
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHhccCCC---CCCCHHHHHHHhCCCHHHHHHHH
Q 008652 483 MRQHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLE 534 (558)
Q Consensus 483 ~~e~L~~~L~~L~~rEReVL~LRyGL~d~---e~~Tl~EIAe~LGISrerVRqie 534 (558)
+...|......|++.||.|-.+- |.+. ..+|..|||+..|||..+|-+..
T Consensus 5 l~~~I~~~~~~Lt~~er~iA~yi--l~~~~~~~~~si~elA~~a~VS~aTv~Rf~ 57 (281)
T COG1737 5 LLERIRERYDSLTKSERKIADYI--LANPDEVALLSIAELAERAGVSPATVVRFA 57 (281)
T ss_pred HHHHHHHHHhcCCHHHHHHHHHH--HhCHHHHHHHHHHHHHHHhCCCHHHHHHHH
Confidence 44578888999999999987644 4432 35799999999999999997543
No 440
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=45.74 E-value=16 Score=31.13 Aligned_cols=25 Identities=28% Similarity=0.498 Sum_probs=22.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRAL 538 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RAL 538 (558)
+|..|+|+.+|||..++|..+.+.+
T Consensus 2 ~ti~evA~~~gvs~~tLR~ye~~Gl 26 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEEKGL 26 (88)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 6899999999999999999988765
No 441
>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=45.58 E-value=56 Score=27.75 Aligned_cols=44 Identities=16% Similarity=0.303 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCC
Q 008652 375 YWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMP 447 (558)
Q Consensus 375 ~~wIr~aI~~aIr~~sr~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~ 447 (558)
.+|+...+.+.+++ |++.+.++||..+|++.++|..++......
T Consensus 22 ~~~L~r~LLr~LA~-----------------------------G~PVt~~~LA~a~g~~~e~v~~~L~~~p~t 65 (77)
T PF12324_consen 22 FAWLLRPLLRLLAK-----------------------------GQPVTVEQLAAALGWPVEEVRAALAAMPDT 65 (77)
T ss_dssp HHHHHHHHHHHHTT-----------------------------TS-B-HHHHHHHHT--HHHHHHHHHH-TTS
T ss_pred cHHHHHHHHHHHHc-----------------------------CCCcCHHHHHHHHCCCHHHHHHHHHhCCCc
No 442
>PF14502 HTH_41: Helix-turn-helix domain
Probab=45.48 E-value=39 Score=26.14 Aligned_cols=29 Identities=28% Similarity=0.461 Sum_probs=24.9
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 511 GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 511 ~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
..-.|..|.++.|++|+.+|. .||+.|.+
T Consensus 4 dRi~tI~e~~~~~~vs~GtiQ----~Alk~Le~ 32 (48)
T PF14502_consen 4 DRIPTISEYSEKFGVSRGTIQ----NALKFLEE 32 (48)
T ss_pred cccCCHHHHHHHhCcchhHHH----HHHHHHHH
Confidence 356799999999999999995 78888876
No 443
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=45.45 E-value=7 Score=37.48 Aligned_cols=48 Identities=13% Similarity=0.212 Sum_probs=0.0
Q ss_pred HHHHHHhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 486 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 486 ~L~~~L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
.|..+...|=.+|+.-|.. |-..-.++|+++||+.+|++.+||+....
T Consensus 24 TL~~v~~~iv~~Q~~ff~~--g~~~l~PLt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 24 TLLRVAQAIVERQKDFFLG--GPGALKPLTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp --------------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHhc--CcccCcCCCHHHHHHHhCCCHhHHHHHHc
Confidence 4555566666777765542 11112799999999999999999987554
No 444
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=45.40 E-value=21 Score=39.41 Aligned_cols=24 Identities=29% Similarity=0.483 Sum_probs=21.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
.++|+++||+.+|+..+||++..+
T Consensus 317 kPLtlkdiA~~lglheSTVSRav~ 340 (429)
T TIGR02395 317 KPLTLREVAEELGLHESTISRAIN 340 (429)
T ss_pred cCCcHHHHHHHhCCCccchhhhhc
Confidence 799999999999999999997653
No 445
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=45.34 E-value=2.6e+02 Score=31.25 Aligned_cols=24 Identities=17% Similarity=0.256 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 419 HSPDKEDLARRVGITVEKLERLIF 442 (558)
Q Consensus 419 r~Pt~eEIA~~lgis~e~v~~ll~ 442 (558)
++-+..+||+.+|+.+.+|..+..
T Consensus 342 kPLtlkdvAe~lglheSTVSRav~ 365 (455)
T PRK05932 342 KPLVLKDIAEELGMHESTISRATT 365 (455)
T ss_pred cCccHHHHHHHhCCCccchhhhhc
Confidence 456899999999999999988865
No 446
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=45.32 E-value=32 Score=31.22 Aligned_cols=25 Identities=16% Similarity=0.183 Sum_probs=23.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
.++|.+|+|+.+|||+.+|.++++.
T Consensus 17 ~Glsq~eLA~~~Gis~~~is~iE~g 41 (120)
T PRK13890 17 RHMTKKELSERSGVSISFLSDLTTG 41 (120)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 6799999999999999999999864
No 447
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=45.29 E-value=23 Score=32.41 Aligned_cols=23 Identities=13% Similarity=0.338 Sum_probs=20.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~R 536 (558)
||-+|+|+.+|+|+.||.....+
T Consensus 1 MT~eELA~~tG~srQTINrWvRk 23 (122)
T PF07037_consen 1 MTPEELAELTGYSRQTINRWVRK 23 (122)
T ss_pred CCHHHHHHHhCccHHHHHHHHHh
Confidence 68999999999999999987653
No 448
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=44.87 E-value=47 Score=32.55 Aligned_cols=40 Identities=20% Similarity=0.155 Sum_probs=32.6
Q ss_pred hcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008652 492 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE 534 (558)
Q Consensus 492 ~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie 534 (558)
-.|++.|..||..-+. ..+.|..+||+.+++++.+|..++
T Consensus 41 ~gLt~~q~~iL~~L~~---~~~itq~eLa~~l~l~~sTvtr~l 80 (185)
T PRK13777 41 YDLNINEHHILWIAYH---LKGASISEIAKFGVMHVSTAFNFS 80 (185)
T ss_pred CCCCHHHHHHHHHHHh---CCCcCHHHHHHHHCCCHhhHHHHH
Confidence 3699999998876654 368999999999999999987543
No 449
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=44.81 E-value=16 Score=32.23 Aligned_cols=26 Identities=19% Similarity=0.273 Sum_probs=23.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRALY 539 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RALk 539 (558)
++..|+|+.+|||..++|-.+..++-
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~~GLi 26 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKIGLL 26 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCC
Confidence 57899999999999999999998765
No 450
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=44.76 E-value=16 Score=32.40 Aligned_cols=26 Identities=19% Similarity=0.501 Sum_probs=23.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRALY 539 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RALk 539 (558)
+|..|+|+.+|||..++|..+..++-
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gll 26 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKEGLL 26 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999887653
No 451
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=43.90 E-value=17 Score=31.51 Aligned_cols=26 Identities=19% Similarity=0.391 Sum_probs=23.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRALY 539 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RALk 539 (558)
+|..|+|+.+|||..++|..+..++-
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gll 26 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDKIGLF 26 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 47899999999999999999887763
No 452
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=43.87 E-value=17 Score=31.65 Aligned_cols=26 Identities=31% Similarity=0.396 Sum_probs=22.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRALY 539 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RALk 539 (558)
++..|+|+.+|||..++|..+..++-
T Consensus 1 y~i~e~A~~~gvs~~tlR~Ye~~Gll 26 (99)
T cd04772 1 YRTVDLARAIGLSPQTVRNYESLGLI 26 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCC
Confidence 47899999999999999999876653
No 453
>COG4709 Predicted membrane protein [Function unknown]
Probab=43.64 E-value=60 Score=32.09 Aligned_cols=58 Identities=19% Similarity=0.157 Sum_probs=44.6
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHhc--cC--CCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008652 481 QLMRQHVRNLLTLLNPKERCIVRLRFG--IE--DGKPKSLSEVGNIFGLSKERVRQLESRAL 538 (558)
Q Consensus 481 ~~~~e~L~~~L~~L~~rEReVL~LRyG--L~--d~e~~Tl~EIAe~LGISrerVRqie~RAL 538 (558)
.+.-..|+..|+.||+.+|.=+...|- ++ +..++|-+||+..||-+.+-.+++..+..
T Consensus 4 ~efL~eL~~yL~~Lp~~~r~e~m~dyeehF~~a~~~GksE~EI~~~LG~P~eiA~ei~s~~~ 65 (195)
T COG4709 4 TEFLNELEQYLEGLPREERREIMYDYEEHFREAQEAGKSEEEIAKDLGDPKEIAAEILSERG 65 (195)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhhhhcCCCHHHHHHHhCCHHHHHHHHHHHcc
Confidence 345567899999999999886655442 12 33689999999999999999888876654
No 454
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=43.36 E-value=35 Score=34.13 Aligned_cols=29 Identities=34% Similarity=0.492 Sum_probs=23.7
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 511 GKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 511 ~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
|..+ |-.|+|+.+|||+.||| +|+..|..
T Consensus 26 G~~LPsE~eL~~~~~VSR~TvR----~Al~~L~~ 55 (240)
T PRK09764 26 GDALPTESALQTEFGVSRVTVR----QALRQLVE 55 (240)
T ss_pred CCcCCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 3555 88999999999999998 67777754
No 455
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=43.21 E-value=51 Score=30.47 Aligned_cols=33 Identities=21% Similarity=0.182 Sum_probs=24.2
Q ss_pred HHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008652 500 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 537 (558)
Q Consensus 500 eVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA 537 (558)
.||.|.. .+..-.+||..|+||...|++++.|=
T Consensus 25 rIvela~-----~G~rp~~Isr~l~Vs~gcVsKIl~Ry 57 (125)
T PF00292_consen 25 RIVELAK-----EGVRPCDISRQLRVSHGCVSKILSRY 57 (125)
T ss_dssp HHHHHHH-----TT--HHHHHHHHT--HHHHHHHHHHH
T ss_pred HHHHHhh-----hcCCHHHHHHHHccchhHHHHHHHHH
Confidence 4676776 68999999999999999999888753
No 456
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=43.14 E-value=34 Score=32.89 Aligned_cols=25 Identities=16% Similarity=0.290 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
.++|+.|+|+.+|||+.+|+++++.
T Consensus 19 ~glt~~elA~~~gis~~~is~~E~g 43 (185)
T PRK09943 19 QGLSQRRAAELSGLTHSAISTIEQD 43 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 6799999999999999999999974
No 457
>PRK14999 histidine utilization repressor; Provisional
Probab=43.09 E-value=36 Score=34.05 Aligned_cols=28 Identities=29% Similarity=0.387 Sum_probs=23.2
Q ss_pred CCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 512 KPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 512 e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
..+ |-.|+|+.+|||+.||| +|+..|..
T Consensus 34 ~~LPsE~eLa~~~gVSR~TVR----~Al~~L~~ 62 (241)
T PRK14999 34 DRIPSEAELVAQYGFSRMTIN----RALRELTD 62 (241)
T ss_pred CcCCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 445 89999999999999998 57777754
No 458
>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=43.00 E-value=36 Score=33.75 Aligned_cols=28 Identities=32% Similarity=0.335 Sum_probs=23.3
Q ss_pred CCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 512 KPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 512 e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
+.+ |-.|+|+.+|||+.||| +|+..|.+
T Consensus 23 ~~LPsE~eLa~~~~VSR~TVR----~Al~~L~~ 51 (230)
T TIGR02018 23 HRIPSEHELVAQYGCSRMTVN----RALRELTD 51 (230)
T ss_pred CcCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 444 89999999999999998 67777754
No 459
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.78 E-value=59 Score=28.31 Aligned_cols=27 Identities=26% Similarity=0.382 Sum_probs=23.4
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhcCC
Q 008652 420 SPDKEDLARRVGITVEKLERLIFITRM 446 (558)
Q Consensus 420 ~Pt~eEIA~~lgis~e~v~~ll~~~~~ 446 (558)
.-++++||..||+++.+++.++.....
T Consensus 23 ~LS~~~iA~~Ln~t~~~lekil~~tqr 49 (97)
T COG4367 23 PLSDEEIATALNWTEVKLEKILQVTQR 49 (97)
T ss_pred cccHHHHHHHhCCCHHHHHHHHHHhhc
Confidence 557999999999999999999976543
No 460
>COG1481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.69 E-value=48 Score=35.13 Aligned_cols=43 Identities=30% Similarity=0.299 Sum_probs=36.1
Q ss_pred HhcCCHHHHHHHHHHhccCCCCCCCHHHHHHHhCC--CHHHHHHHHHH
Q 008652 491 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGL--SKERVRQLESR 536 (558)
Q Consensus 491 L~~L~~rEReVL~LRyGL~d~e~~Tl~EIAe~LGI--SrerVRqie~R 536 (558)
++.||++.+++-.+|.- .++.|++|||+.+.. |++.|..+..|
T Consensus 251 l~~lpe~l~e~a~LRl~---hpd~SLeeLg~~l~~~iSKSGvnHrlrk 295 (308)
T COG1481 251 LEKLPEKLREAALLRLE---HPDASLEELGELLEPPISKSGVNHRLRK 295 (308)
T ss_pred hhhCCHHHHHHHHHhhc---ChhhhHHHHHHHhcCcccHHHHHHHHHH
Confidence 47899999999999874 478999999999987 88888766544
No 461
>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=42.49 E-value=29 Score=34.32 Aligned_cols=27 Identities=26% Similarity=0.432 Sum_probs=23.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 513 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 513 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
=-|-.|+|+.+|||+.||| +|+..|..
T Consensus 32 LPsE~eLa~~~~VSR~TvR----~Al~~L~~ 58 (238)
T TIGR02325 32 LPAEMQLAERFGVNRHTVR----RAIAALVE 58 (238)
T ss_pred CcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 3489999999999999998 67777765
No 462
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=42.47 E-value=18 Score=31.35 Aligned_cols=25 Identities=20% Similarity=0.262 Sum_probs=22.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRAL 538 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RAL 538 (558)
|+..|+|+.+|||..+||-.+..++
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye~~GL 25 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLREGL 25 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999888765
No 463
>PRK08359 transcription factor; Validated
Probab=42.45 E-value=34 Score=33.38 Aligned_cols=35 Identities=20% Similarity=0.284 Sum_probs=27.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH-------HHHHHHHHhh
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESR-------ALYRLKQSLG 546 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~R-------ALkKLR~~l~ 546 (558)
.++|++|+|+.+|+++.+|+.++.. .+.+|-+.+.
T Consensus 97 kglSQeeLA~~lgvs~stI~~iE~G~~~Ps~~~l~kLak~l~ 138 (176)
T PRK08359 97 SGLSYEELSHEVGLSVNDLRRIAHGEYEPTIKEAKKLERYFK 138 (176)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCCCcCCCHHHHHHHHHHhC
Confidence 6899999999999999999999753 4455555443
No 464
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=42.44 E-value=29 Score=26.44 Aligned_cols=24 Identities=21% Similarity=0.439 Sum_probs=19.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRA 537 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RA 537 (558)
.+.+|+++.+|+|+.++....+..
T Consensus 4 l~~~ev~~~~g~s~~ti~~~~k~g 27 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTIYRLIKDG 27 (51)
T ss_dssp E-HHHHHHHHSS-HHHHHHHHHHH
T ss_pred ccHHHHHHHHCCCHHHHHHHHhcc
Confidence 478999999999999999888744
No 465
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=42.03 E-value=19 Score=31.57 Aligned_cols=27 Identities=22% Similarity=0.299 Sum_probs=23.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRALYR 540 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RALkK 540 (558)
+|..|+|+.+|||..++|..+..++-.
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~~Gll~ 28 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKLGLIT 28 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 688999999999999999998876543
No 466
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=41.99 E-value=19 Score=31.60 Aligned_cols=27 Identities=11% Similarity=0.143 Sum_probs=24.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRALYR 540 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RALkK 540 (558)
|+..|+|+.+|||..++|-.+..+|-.
T Consensus 1 m~Ige~a~~~gvs~~tlRyYe~~GLl~ 27 (107)
T cd04777 1 MKIGKFAKKNNITIDTVRHYIDLGLLI 27 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCcC
Confidence 578999999999999999999988753
No 467
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=41.93 E-value=19 Score=31.20 Aligned_cols=26 Identities=19% Similarity=0.270 Sum_probs=23.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRALY 539 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RALk 539 (558)
|+..|+|+.+|||..++|..+..++-
T Consensus 1 m~i~eva~~~gvs~~tlR~ye~~Gll 26 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDHIGLL 26 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999987654
No 468
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=41.68 E-value=19 Score=30.73 Aligned_cols=27 Identities=19% Similarity=0.273 Sum_probs=23.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRALYR 540 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RALkK 540 (558)
+|..|+|+.+|||..+||..+..++-.
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~~Gli~ 28 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYERLGLLS 28 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCCcC
Confidence 588999999999999999998765543
No 469
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=41.58 E-value=19 Score=31.35 Aligned_cols=25 Identities=20% Similarity=0.339 Sum_probs=22.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRAL 538 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RAL 538 (558)
+|..|+|+.+|||..++|..+..++
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~~Gl 25 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDEIGL 25 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999988765
No 470
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=41.55 E-value=2.3e+02 Score=24.36 Aligned_cols=35 Identities=14% Similarity=0.174 Sum_probs=27.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 546 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 546 (558)
-|+++++|.+.++.....+..++..-+..|++.+.
T Consensus 56 ~G~~l~~I~~~l~~~~~~~~~~l~~~~~~l~~~i~ 90 (96)
T cd04768 56 LGFSLAEIKELLDTEMEELTAMLLEKKQAIQQKID 90 (96)
T ss_pred cCCCHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHH
Confidence 57999999999998766777777777777766543
No 471
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=41.48 E-value=19 Score=32.81 Aligned_cols=27 Identities=26% Similarity=0.379 Sum_probs=24.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRALYR 540 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RALkK 540 (558)
||..|+|+.+|||..++|-.+..++-.
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~~GLl~ 27 (127)
T cd01108 1 MNIGEAAKLTGLSAKMIRYYEEIGLIP 27 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 578999999999999999999887754
No 472
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=41.34 E-value=63 Score=37.37 Aligned_cols=51 Identities=16% Similarity=0.285 Sum_probs=40.5
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHhccCCC---CCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 483 MRQHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 483 ~~e~L~~~L~~L~~rEReVL~LRyGL~d~---e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
+.+.|...+..|++.||.|..+- |++. ..+|..|||+..|+|..+|-+..+
T Consensus 343 l~~~I~~~~~~Lt~~E~~IA~yI--l~n~~~v~~~si~eLA~~~~vS~aTV~Rf~k 396 (638)
T PRK14101 343 VFERIRQMRDALTPAERRVADLA--LNHPRSIINDPIVDIARKADVSQPTVIRFCR 396 (638)
T ss_pred HHHHHHHHHhhcCHHHHHHHHHH--HhCHHHHHhccHHHHHHHhCCCHHHHHHHHH
Confidence 44578888999999999998754 4332 357999999999999999976544
No 473
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of 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=41.30 E-value=20 Score=31.86 Aligned_cols=26 Identities=31% Similarity=0.446 Sum_probs=23.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRALY 539 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RALk 539 (558)
+|..|+|+.+|||..++|-.+..++-
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye~~gll 26 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEKEGLL 26 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999987764
No 474
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=41.24 E-value=36 Score=28.65 Aligned_cols=19 Identities=21% Similarity=0.240 Sum_probs=18.3
Q ss_pred CHHHHHHHhCCCHHHHHHH
Q 008652 515 SLSEVGNIFGLSKERVRQL 533 (558)
Q Consensus 515 Tl~EIAe~LGISrerVRqi 533 (558)
+...+|+.||||.+.|+|.
T Consensus 12 s~~kvA~aLGIs~~AVsQW 30 (75)
T PRK09744 12 SKTKLANAAGVRLASVAAW 30 (75)
T ss_pred cHHHHHHHHCCCHHHHHHH
Confidence 8899999999999999998
No 475
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=41.23 E-value=41 Score=34.32 Aligned_cols=36 Identities=19% Similarity=0.187 Sum_probs=26.8
Q ss_pred HHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008652 496 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE 534 (558)
Q Consensus 496 ~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie 534 (558)
+|...|+.+-- .....+..||++.||||..|||+-+
T Consensus 5 ~R~~~Il~~l~---~~~~~~~~ela~~l~vS~~TiRRdL 40 (252)
T PRK10906 5 QRHDAIIELVK---QQGYVSTEELVEHFSVSPQTIRRDL 40 (252)
T ss_pred HHHHHHHHHHH---HcCCEeHHHHHHHhCCCHHHHHHHH
Confidence 45555555542 2356899999999999999999754
No 476
>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=41.22 E-value=38 Score=27.32 Aligned_cols=24 Identities=29% Similarity=0.401 Sum_probs=19.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHh
Q 008652 420 SPDKEDLARRVGITVEKLERLIFI 443 (558)
Q Consensus 420 ~Pt~eEIA~~lgis~e~v~~ll~~ 443 (558)
..+..+||..+|++++.|+.++..
T Consensus 14 ~~S~~eLa~~~~~s~~~ve~mL~~ 37 (69)
T PF09012_consen 14 RVSLAELAREFGISPEAVEAMLEQ 37 (69)
T ss_dssp SEEHHHHHHHTT--HHHHHHHHHH
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHH
Confidence 578899999999999999999874
No 477
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=41.22 E-value=20 Score=31.97 Aligned_cols=27 Identities=22% Similarity=0.301 Sum_probs=23.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRALYR 540 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RALkK 540 (558)
++..|+|+.+|||..++|-.+..++-.
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye~~GLl~ 27 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEEQGLLV 27 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCC
Confidence 578999999999999999999887653
No 478
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=41.20 E-value=31 Score=34.18 Aligned_cols=27 Identities=37% Similarity=0.454 Sum_probs=23.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 513 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 513 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
=-|-.|+|+.+|||+.||| +|+..|..
T Consensus 24 LPsE~eLa~~~gVSR~TVR----~Al~~L~~ 50 (233)
T TIGR02404 24 LPSEHELMDQYGASRETVR----KALNLLTE 50 (233)
T ss_pred CcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 3489999999999999998 67777755
No 479
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=41.17 E-value=20 Score=30.79 Aligned_cols=25 Identities=28% Similarity=0.542 Sum_probs=22.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRAL 538 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RAL 538 (558)
+|..|+|+.+||+..+|+..+..++
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~~Gl 25 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEEKGL 25 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999988765
No 480
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=41.13 E-value=71 Score=27.59 Aligned_cols=26 Identities=19% Similarity=0.238 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESRA 537 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~RA 537 (558)
++.|+++||+.+|+|+.+..++.++.
T Consensus 20 ~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 20 QPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 78999999999999999998887776
No 481
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=40.99 E-value=2.1e+02 Score=28.84 Aligned_cols=25 Identities=20% Similarity=0.320 Sum_probs=21.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHh
Q 008652 419 HSPDKEDLARRVGITVEKLERLIFI 443 (558)
Q Consensus 419 r~Pt~eEIA~~lgis~e~v~~ll~~ 443 (558)
..-+..|||+.+|++...|...+..
T Consensus 220 ~g~s~~eIA~~l~is~~tV~~~~~r 244 (257)
T PRK08583 220 ENLSQKETGERLGISQMHVSRLQRQ 244 (257)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3568999999999999999887653
No 482
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=40.96 E-value=19 Score=32.69 Aligned_cols=26 Identities=27% Similarity=0.494 Sum_probs=23.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRALY 539 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RALk 539 (558)
|+..|+|+.+|||..++|-.+..++-
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~~GLl 26 (127)
T TIGR02044 1 MNIGQVAKLTGLSSKMIRYYEEKGLI 26 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999987765
No 483
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=40.90 E-value=32 Score=30.11 Aligned_cols=23 Identities=35% Similarity=0.507 Sum_probs=21.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~R 536 (558)
+|..|+|+.+|||..++|..+..
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~~ 23 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 47899999999999999999776
No 484
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. 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 by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=40.87 E-value=20 Score=32.07 Aligned_cols=27 Identities=19% Similarity=0.336 Sum_probs=24.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRALYR 540 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RALkK 540 (558)
||..|+|+.+|||..++|-.+..++-.
T Consensus 1 ~~ige~a~~~gvs~~tLryYe~~GLi~ 27 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEEKGLLP 27 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 588999999999999999999887654
No 485
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=40.77 E-value=34 Score=34.89 Aligned_cols=38 Identities=13% Similarity=0.150 Sum_probs=28.3
Q ss_pred HHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 496 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 496 ~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
+|++.|+.+--- ....+..|+|+.||||+.|||+-+..
T Consensus 5 eR~~~Il~~L~~---~~~v~v~eLa~~l~VS~~TIRRDL~~ 42 (256)
T PRK10434 5 QRQAAILEYLQK---QGKTSVEELAQYFDTTGTTIRKDLVI 42 (256)
T ss_pred HHHHHHHHHHHH---cCCEEHHHHHHHHCCCHHHHHHHHHH
Confidence 455566655332 24689999999999999999977654
No 486
>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=40.73 E-value=47 Score=31.63 Aligned_cols=37 Identities=11% Similarity=-0.043 Sum_probs=25.8
Q ss_pred HHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 496 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 496 ~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
+....||..-+ .. ..+|-+|||+.|||+...||.++.
T Consensus 14 ~~~v~Vl~aL~--~~-~~~tdEeLa~~Lgi~~~~VRk~L~ 50 (158)
T TIGR00373 14 EEVGLVLFSLG--IK-GEFTDEEISLELGIKLNEVRKALY 50 (158)
T ss_pred hhHHHHHHHHh--cc-CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 44444554322 22 479999999999999999985443
No 487
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=40.72 E-value=40 Score=32.14 Aligned_cols=25 Identities=8% Similarity=0.157 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLESR 536 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~R 536 (558)
.++|++++|+.+|+++.+|+++++.
T Consensus 81 ~glSqeeLA~~lgvs~s~IsriE~G 105 (154)
T TIGR00270 81 RGWSQEQLAKKIQEKESLIKKIENA 105 (154)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 6899999999999999999999863
No 488
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. 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 winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=40.49 E-value=20 Score=31.13 Aligned_cols=26 Identities=27% Similarity=0.402 Sum_probs=22.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRALY 539 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RALk 539 (558)
++..|+|+.+|||..++|..+..++-
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye~~Gll 26 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEEIGLV 26 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999876544
No 489
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=40.49 E-value=47 Score=34.86 Aligned_cols=40 Identities=18% Similarity=0.151 Sum_probs=30.5
Q ss_pred HHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008652 497 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 539 (558)
Q Consensus 497 rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 539 (558)
|.++||.+.. ++...+..+||+.+|||+.+|++.+..-..
T Consensus 5 r~~~il~~L~---~~~~~s~~~LA~~lgvsr~tV~~~l~~L~~ 44 (319)
T PRK11886 5 VMLQLLSLLA---DGDFHSGEQLGEELGISRAAIWKHIQTLEE 44 (319)
T ss_pred HHHHHHHHHH---cCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4555665543 246789999999999999999998876553
No 490
>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=40.07 E-value=1.1e+02 Score=28.68 Aligned_cols=46 Identities=11% Similarity=0.235 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcc
Q 008652 404 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLS 449 (558)
Q Consensus 404 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~S 449 (558)
..+.+++.-|...-++..|..||++.+|++++.|..++...+-.++
T Consensus 30 ~~f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGRL~~~ 75 (137)
T TIGR03826 30 REFEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGRLQLK 75 (137)
T ss_pred HHHHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCCeecc
Confidence 3444455555556667789999999999999999999887765444
No 491
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=40.04 E-value=2.1e+02 Score=30.25 Aligned_cols=44 Identities=14% Similarity=0.239 Sum_probs=33.3
Q ss_pred HHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008652 500 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 544 (558)
Q Consensus 500 eVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 544 (558)
-+|.|---|.+ +.+|++||++..||+..|||+-.+--.-.+-+.
T Consensus 248 a~IYmisqls~-~kkt~keI~~vtgVaE~TIr~sYK~Lyp~~~~l 291 (308)
T KOG1597|consen 248 AAIYMISQLSD-EKKTQKEIGEVTGVAEVTIRNSYKDLYPHADKL 291 (308)
T ss_pred HHHHHHHHhcc-CcccHHHHHHHhhhhHHHHHHHHHHHhhchhhh
Confidence 35555555555 899999999999999999998776665555443
No 492
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=39.95 E-value=61 Score=28.26 Aligned_cols=24 Identities=25% Similarity=0.306 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 512 KPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 512 e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
-++|.++||..||+|.+.|.+++.
T Consensus 22 ~~ls~~~ia~dL~~s~~~le~vL~ 45 (89)
T PF10078_consen 22 SGLSLEQIAADLGTSPEHLEQVLN 45 (89)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHc
Confidence 579999999999999999988764
No 493
>PRK10870 transcriptional repressor MprA; Provisional
Probab=39.71 E-value=3.4e+02 Score=25.97 Aligned_cols=24 Identities=17% Similarity=0.142 Sum_probs=20.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHh
Q 008652 420 SPDKEDLARRVGITVEKLERLIFI 443 (558)
Q Consensus 420 ~Pt~eEIA~~lgis~e~v~~ll~~ 443 (558)
..+..+||+.+|++...+..++..
T Consensus 71 ~it~~eLa~~l~l~~~tvsr~v~r 94 (176)
T PRK10870 71 SIQPSELSCALGSSRTNATRIADE 94 (176)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHH
Confidence 457799999999999999877653
No 494
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=39.64 E-value=52 Score=33.73 Aligned_cols=25 Identities=20% Similarity=0.223 Sum_probs=21.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 511 GKPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 511 ~e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
+.++|+.|||+.+|+++.+|..++.
T Consensus 38 ~~~~tl~eIa~~lglpkStv~RlL~ 62 (271)
T PRK10163 38 GGSSSVSDISLNLDLPLSTTFRLLK 62 (271)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 3679999999999999999986554
No 495
>COG3711 BglG Transcriptional antiterminator [Transcription]
Probab=39.58 E-value=36 Score=37.65 Aligned_cols=47 Identities=21% Similarity=0.138 Sum_probs=38.4
Q ss_pred HHHHHHHHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008652 496 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 543 (558)
Q Consensus 496 ~rEReVL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 543 (558)
..||.++.+.+-+.+ +..++.++|..+++|+.+|..-.+....+|+.
T Consensus 84 ~~er~~~~ll~~~~~-~~~~l~~La~~l~vs~~ti~~dl~~v~~~l~~ 130 (491)
T COG3711 84 KDERIIIILLLLLLS-ELLSLHELADELFVSKSTIINDLKDVRLKLLL 130 (491)
T ss_pred hHHHHHHHHHHHHhc-ChhhHHHHHHHHHhHHHHHHHHHHHHHHHHHh
Confidence 677777777776555 78999999999999999999998876666654
No 496
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=39.26 E-value=22 Score=31.56 Aligned_cols=26 Identities=31% Similarity=0.261 Sum_probs=23.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRALY 539 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RALk 539 (558)
+|..|+|+.+|||..++|..+..++-
T Consensus 1 y~Ige~A~~~gvs~~tlR~ye~~GLl 26 (107)
T cd01111 1 YSISQLALDAGVSVHIVRDYLLRGLL 26 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999988764
No 497
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=39.14 E-value=25 Score=33.74 Aligned_cols=24 Identities=17% Similarity=0.322 Sum_probs=0.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 419 HSPDKEDLARRVGITVEKLERLIF 442 (558)
Q Consensus 419 r~Pt~eEIA~~lgis~e~v~~ll~ 442 (558)
++-+..+||+.+|+++..|..+..
T Consensus 48 ~PLt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 48 KPLTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp ------------------------
T ss_pred cCCCHHHHHHHhCCCHhHHHHHHc
Confidence 355789999999999999988765
No 498
>PRK11569 transcriptional repressor IclR; Provisional
Probab=39.08 E-value=46 Score=34.13 Aligned_cols=25 Identities=20% Similarity=0.316 Sum_probs=21.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 511 GKPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 511 ~e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
+.++|+.|||+.+|+++.+|..++.
T Consensus 41 ~~~~~lseia~~lglpksTv~RlL~ 65 (274)
T PRK11569 41 NGSVALTELAQQAGLPNSTTHRLLT 65 (274)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 4689999999999999999986654
No 499
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=38.98 E-value=22 Score=32.28 Aligned_cols=27 Identities=22% Similarity=0.410 Sum_probs=24.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008652 514 KSLSEVGNIFGLSKERVRQLESRALYR 540 (558)
Q Consensus 514 ~Tl~EIAe~LGISrerVRqie~RALkK 540 (558)
+|..|+|+.+|||..+||..+..++-.
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~~GLl~ 27 (126)
T cd04783 1 LTIGELAKAAGVNVETIRYYQRRGLLP 27 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 578999999999999999999887754
No 500
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.94 E-value=75 Score=27.70 Aligned_cols=39 Identities=18% Similarity=0.383 Sum_probs=27.8
Q ss_pred CCHHHHHH----HHHHhccCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008652 494 LNPKERCI----VRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 535 (558)
Q Consensus 494 L~~rEReV----L~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 535 (558)
|++.|+++ |.-.|-| -++|.++||..||+|...|..++.
T Consensus 3 Ln~eq~~~Tk~elqan~el---~~LS~~~iA~~Ln~t~~~lekil~ 45 (97)
T COG4367 3 LNPEQKQRTKQELQANFEL---CPLSDEEIATALNWTEVKLEKILQ 45 (97)
T ss_pred CCHHHHHHHHHHHHHhhhh---ccccHHHHHHHhCCCHHHHHHHHH
Confidence 55555444 3334433 579999999999999998887764
Done!