Query 010835
Match_columns 499
No_of_seqs 256 out of 1631
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 05:06:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010835.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010835hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK07406 RNA polymerase sigma 100.0 2E-53 4.3E-58 442.9 32.8 299 191-496 63-372 (373)
2 PRK07598 RNA polymerase sigma 100.0 3.7E-53 8.1E-58 444.1 32.0 300 191-497 60-412 (415)
3 PRK05901 RNA polymerase sigma 100.0 4.1E-53 8.9E-58 453.5 31.8 297 190-497 210-509 (509)
4 PRK05949 RNA polymerase sigma 100.0 3.7E-52 8E-57 427.9 33.5 298 191-497 18-326 (327)
5 PRK07921 RNA polymerase sigma 100.0 2.9E-51 6.2E-56 420.6 32.5 296 191-496 26-323 (324)
6 COG0568 RpoD DNA-directed RNA 100.0 9.7E-52 2.1E-56 421.4 28.8 270 191-496 67-341 (342)
7 TIGR02997 Sig70-cyanoRpoD RNA 100.0 3.9E-51 8.4E-56 415.5 30.8 286 192-484 2-298 (298)
8 PRK07405 RNA polymerase sigma 100.0 7E-51 1.5E-55 417.0 32.7 298 191-497 8-316 (317)
9 PRK09210 RNA polymerase sigma 100.0 4.3E-50 9.3E-55 418.7 31.0 272 189-497 94-367 (367)
10 PRK05658 RNA polymerase sigma 100.0 1.4E-46 3E-51 415.9 31.4 272 192-497 345-618 (619)
11 PRK06596 RNA polymerase factor 100.0 7.6E-43 1.6E-47 352.7 31.2 266 183-489 9-282 (284)
12 PRK05657 RNA polymerase sigma 100.0 6.4E-43 1.4E-47 359.4 31.0 268 189-493 51-320 (325)
13 TIGR02393 RpoD_Cterm RNA polym 100.0 3E-43 6.6E-48 346.4 27.0 236 256-497 1-238 (238)
14 PRK07500 rpoH2 RNA polymerase 100.0 3.8E-42 8.1E-47 348.4 31.6 263 191-490 6-280 (289)
15 TIGR02392 rpoH_proteo alternat 100.0 1.3E-41 2.8E-46 341.1 29.7 259 192-488 2-269 (270)
16 TIGR02394 rpoS_proteo RNA poly 100.0 2.9E-40 6.3E-45 333.6 31.3 274 182-492 4-279 (285)
17 PRK07122 RNA polymerase sigma 100.0 1.2E-39 2.6E-44 326.1 28.4 220 255-487 40-263 (264)
18 PRK07408 RNA polymerase sigma 100.0 2.7E-38 5.8E-43 314.9 29.2 226 255-490 25-254 (256)
19 TIGR02850 spore_sigG RNA polym 100.0 6.6E-38 1.4E-42 311.4 29.3 243 200-486 10-253 (254)
20 PRK05911 RNA polymerase sigma 100.0 2.2E-37 4.8E-42 308.6 29.4 227 255-489 23-255 (257)
21 PRK08215 sporulation sigma fac 100.0 6.6E-37 1.4E-41 304.8 29.5 244 200-487 13-257 (258)
22 COG1191 FliA DNA-directed RNA 100.0 5E-37 1.1E-41 302.8 27.0 240 203-489 3-246 (247)
23 TIGR02941 Sigma_B RNA polymera 100.0 2.7E-35 5.9E-40 292.4 29.9 242 204-487 8-253 (255)
24 PRK06288 RNA polymerase sigma 100.0 2.1E-35 4.6E-40 295.7 29.3 251 200-490 6-263 (268)
25 TIGR02885 spore_sigF RNA polym 100.0 1E-34 2.2E-39 284.0 26.5 221 254-487 10-231 (231)
26 TIGR02980 SigBFG RNA polymeras 100.0 3.7E-34 8E-39 279.1 27.1 222 254-487 2-226 (227)
27 PRK07670 RNA polymerase sigma 100.0 9.6E-34 2.1E-38 281.0 28.7 223 255-488 22-250 (251)
28 PRK08583 RNA polymerase sigma 100.0 2.1E-33 4.5E-38 279.2 29.1 244 204-489 8-255 (257)
29 PRK05572 sporulation sigma fac 100.0 2.2E-33 4.8E-38 278.6 29.3 243 200-488 8-251 (252)
30 TIGR02479 FliA_WhiG RNA polyme 100.0 1E-32 2.2E-37 268.9 25.3 217 260-487 1-223 (224)
31 PRK12427 flagellar biosynthesi 100.0 1.8E-31 4E-36 262.2 26.1 210 255-486 15-230 (231)
32 PRK06986 fliA flagellar biosyn 100.0 3E-31 6.4E-36 260.6 26.6 223 253-489 6-234 (236)
33 PRK05803 sporulation sigma fac 100.0 1.1E-28 2.3E-33 242.3 25.0 213 192-490 17-230 (233)
34 TIGR02846 spore_sigmaK RNA pol 99.9 2.2E-25 4.7E-30 218.2 23.8 210 192-487 15-226 (227)
35 PRK08301 sporulation sigma fac 99.9 3.6E-25 7.7E-30 217.0 23.7 208 196-489 23-232 (234)
36 TIGR02835 spore_sigmaE RNA pol 99.9 6.1E-24 1.3E-28 208.8 22.6 202 202-489 30-232 (234)
37 PRK08295 RNA polymerase factor 99.9 2.1E-23 4.6E-28 199.7 20.6 182 255-491 24-206 (208)
38 PRK09648 RNA polymerase sigma 99.9 3.1E-23 6.6E-28 196.3 20.8 179 206-488 6-188 (189)
39 PRK09646 RNA polymerase sigma 99.9 3.3E-23 7.3E-28 197.4 19.6 185 202-489 8-192 (194)
40 PRK05602 RNA polymerase sigma 99.9 5.9E-23 1.3E-27 193.9 19.6 161 255-491 20-180 (186)
41 PRK12513 RNA polymerase sigma 99.9 5.2E-23 1.1E-27 195.5 18.8 167 255-492 26-192 (194)
42 PRK12524 RNA polymerase sigma 99.9 1.8E-22 3.9E-27 192.7 19.9 181 206-491 8-188 (196)
43 PRK11922 RNA polymerase sigma 99.9 1.6E-22 3.5E-27 198.2 20.0 193 201-489 7-199 (231)
44 PRK12519 RNA polymerase sigma 99.9 1.6E-22 3.6E-27 191.9 19.2 180 206-488 11-190 (194)
45 TIGR02952 Sig70_famx2 RNA poly 99.9 1.8E-22 3.8E-27 186.7 18.7 160 255-487 11-170 (170)
46 TIGR02859 spore_sigH RNA polym 99.9 2.3E-22 5E-27 190.8 19.8 178 255-487 19-197 (198)
47 TIGR02948 SigW_bacill RNA poly 99.9 2.5E-22 5.3E-27 188.8 19.7 169 255-489 18-186 (187)
48 PRK12514 RNA polymerase sigma 99.9 2.2E-22 4.9E-27 188.6 19.2 175 209-488 4-178 (179)
49 PRK11923 algU RNA polymerase s 99.9 3.7E-22 8.1E-27 189.3 20.6 188 205-489 1-188 (193)
50 PRK12534 RNA polymerase sigma 99.9 2.5E-22 5.5E-27 189.5 19.4 181 205-488 6-186 (187)
51 PRK09641 RNA polymerase sigma 99.9 5.3E-22 1.1E-26 186.5 20.1 169 255-489 18-186 (187)
52 PRK06759 RNA polymerase factor 99.9 3.1E-22 6.6E-27 182.7 17.6 151 254-486 3-153 (154)
53 PRK09652 RNA polymerase sigma 99.9 6.4E-22 1.4E-26 183.9 19.1 171 253-489 8-178 (182)
54 PRK12538 RNA polymerase sigma 99.9 6.5E-22 1.4E-26 194.8 19.8 176 210-492 49-224 (233)
55 PRK13919 putative RNA polymera 99.9 9.3E-22 2E-26 185.3 19.7 162 255-488 23-184 (186)
56 PRK12537 RNA polymerase sigma 99.9 1.1E-21 2.4E-26 184.9 19.8 159 255-487 23-181 (182)
57 TIGR02939 RpoE_Sigma70 RNA pol 99.9 2.1E-21 4.5E-26 182.9 20.5 168 255-488 20-187 (190)
58 PRK12531 RNA polymerase sigma 99.9 2E-21 4.4E-26 185.1 19.7 187 204-491 7-193 (194)
59 PRK06811 RNA polymerase factor 99.9 1.7E-21 3.8E-26 184.8 19.0 160 255-488 18-180 (189)
60 PRK12526 RNA polymerase sigma 99.9 3.6E-21 7.9E-26 185.5 21.0 182 209-490 23-204 (206)
61 PRK12542 RNA polymerase sigma 99.9 1.3E-21 2.8E-26 184.7 16.1 174 252-496 6-179 (185)
62 PRK11924 RNA polymerase sigma 99.9 5.8E-21 1.3E-25 177.0 19.8 165 254-490 12-176 (179)
63 PRK09640 RNA polymerase sigma 99.9 2.4E-21 5.2E-26 183.6 17.3 161 253-489 24-184 (188)
64 PRK12515 RNA polymerase sigma 99.9 6.9E-21 1.5E-25 180.4 20.1 163 255-492 22-184 (189)
65 PRK09643 RNA polymerase sigma 99.9 1.2E-20 2.6E-25 179.8 20.9 158 255-489 27-184 (192)
66 TIGR02984 Sig-70_plancto1 RNA 99.9 8.6E-21 1.9E-25 178.3 18.9 180 252-487 4-188 (189)
67 PRK12543 RNA polymerase sigma 99.9 1.4E-20 3E-25 177.0 19.8 166 252-491 4-169 (179)
68 PRK09638 RNA polymerase sigma 99.9 7.1E-21 1.5E-25 177.6 17.7 157 255-487 18-174 (176)
69 TIGR03001 Sig-70_gmx1 RNA poly 99.9 1.7E-20 3.6E-25 186.1 21.1 182 210-495 25-217 (244)
70 PRK12536 RNA polymerase sigma 99.9 2E-20 4.4E-25 176.2 19.7 159 255-490 21-180 (181)
71 TIGR02999 Sig-70_X6 RNA polyme 99.9 2.4E-20 5.2E-25 175.1 19.7 160 255-487 17-182 (183)
72 PRK09649 RNA polymerase sigma 99.9 1.4E-20 2.9E-25 178.4 18.1 177 204-489 4-180 (185)
73 TIGR02954 Sig70_famx3 RNA poly 99.9 2E-20 4.4E-25 173.8 18.8 153 255-488 16-168 (169)
74 PRK12539 RNA polymerase sigma 99.9 3.8E-20 8.2E-25 174.8 20.7 172 210-490 7-182 (184)
75 PRK09645 RNA polymerase sigma 99.9 2.2E-20 4.8E-25 174.0 18.9 163 253-490 7-169 (173)
76 PRK12512 RNA polymerase sigma 99.9 3.8E-20 8.2E-25 174.3 20.2 157 255-490 22-182 (184)
77 PRK09415 RNA polymerase factor 99.9 2.5E-20 5.4E-25 175.4 18.5 164 253-489 14-177 (179)
78 PRK12520 RNA polymerase sigma 99.9 1.8E-20 3.9E-25 177.9 17.6 182 255-491 2-183 (191)
79 TIGR02985 Sig70_bacteroi1 RNA 99.9 1.5E-20 3.2E-25 171.1 15.7 161 255-487 1-161 (161)
80 PRK12522 RNA polymerase sigma 99.9 3.8E-20 8.3E-25 172.8 18.7 168 255-490 3-170 (173)
81 PRK12518 RNA polymerase sigma 99.8 2.4E-20 5.3E-25 173.8 17.0 163 254-491 10-172 (175)
82 TIGR02989 Sig-70_gvs1 RNA poly 99.8 2.1E-20 4.5E-25 171.3 16.1 159 255-487 1-159 (159)
83 TIGR02937 sigma70-ECF RNA poly 99.8 3.8E-20 8.3E-25 164.9 17.0 158 255-487 1-158 (158)
84 PRK09642 RNA polymerase sigma 99.8 3.4E-20 7.3E-25 170.6 16.2 156 262-490 2-157 (160)
85 PRK12516 RNA polymerase sigma 99.8 1.4E-19 3E-24 172.2 19.0 161 253-491 8-168 (187)
86 PRK12529 RNA polymerase sigma 99.8 7.1E-20 1.5E-24 172.4 16.5 165 251-487 9-175 (178)
87 COG1595 RpoE DNA-directed RNA 99.8 2.3E-19 5.1E-24 169.3 20.0 171 247-490 7-178 (182)
88 PRK12533 RNA polymerase sigma 99.8 1.4E-19 2.9E-24 176.5 18.9 169 254-490 17-185 (216)
89 PRK12535 RNA polymerase sigma 99.8 2.2E-19 4.7E-24 172.1 19.9 183 204-493 5-187 (196)
90 PRK12547 RNA polymerase sigma 99.8 1.8E-19 3.9E-24 167.1 18.5 161 252-490 3-163 (164)
91 TIGR02983 SigE-fam_strep RNA p 99.8 1.4E-19 2.9E-24 166.8 17.4 157 252-488 3-159 (162)
92 PRK09647 RNA polymerase sigma 99.8 2.2E-19 4.9E-24 173.1 19.4 165 253-491 26-190 (203)
93 TIGR02947 SigH_actino RNA poly 99.8 1.1E-19 2.4E-24 172.8 16.4 173 254-490 10-182 (193)
94 PRK09644 RNA polymerase sigma 99.8 1.9E-19 4.1E-24 166.8 17.6 157 257-490 3-159 (165)
95 PRK12523 RNA polymerase sigma 99.8 1.2E-19 2.6E-24 169.4 16.1 162 253-489 8-169 (172)
96 PRK09639 RNA polymerase sigma 99.8 6.2E-19 1.4E-23 162.8 18.4 161 254-490 2-162 (166)
97 PRK08241 RNA polymerase factor 99.8 8E-19 1.7E-23 181.0 20.6 174 255-485 19-199 (339)
98 PRK12530 RNA polymerase sigma 99.8 7.9E-19 1.7E-23 166.9 18.2 176 259-491 11-186 (189)
99 PRK12541 RNA polymerase sigma 99.8 9.2E-19 2E-23 161.4 18.0 157 253-486 3-159 (161)
100 PRK12528 RNA polymerase sigma 99.8 6.9E-19 1.5E-23 162.3 16.8 157 255-486 4-160 (161)
101 TIGR02943 Sig70_famx1 RNA poly 99.8 8.8E-19 1.9E-23 166.6 17.9 177 259-490 6-182 (188)
102 PRK12532 RNA polymerase sigma 99.8 7.9E-19 1.7E-23 167.1 17.5 181 258-492 8-189 (195)
103 PRK12545 RNA polymerase sigma 99.8 1.1E-18 2.4E-23 167.6 18.3 181 259-492 12-192 (201)
104 PRK12544 RNA polymerase sigma 99.8 1.2E-18 2.6E-23 168.4 18.1 181 256-490 19-199 (206)
105 PRK09637 RNA polymerase sigma 99.8 2.4E-18 5.3E-23 162.7 18.7 154 257-489 3-156 (181)
106 PRK12517 RNA polymerase sigma 99.8 2.4E-18 5.1E-23 163.7 18.7 165 248-491 16-180 (188)
107 TIGR02960 SigX5 RNA polymerase 99.8 1.5E-18 3.3E-23 177.4 18.6 187 253-489 3-192 (324)
108 PRK12540 RNA polymerase sigma 99.8 2.8E-18 6E-23 162.6 18.5 160 255-492 5-164 (182)
109 TIGR02950 SigM_subfam RNA poly 99.8 5.9E-19 1.3E-23 160.8 12.6 152 262-487 2-153 (154)
110 PRK07037 extracytoplasmic-func 99.8 4.3E-18 9.3E-23 156.9 18.0 158 259-489 2-159 (163)
111 PRK09651 RNA polymerase sigma 99.8 3.9E-18 8.6E-23 159.5 17.7 164 253-491 8-171 (172)
112 PRK12527 RNA polymerase sigma 99.8 3.8E-18 8.3E-23 157.0 17.0 155 262-490 2-156 (159)
113 TIGR02895 spore_sigI RNA polym 99.8 1.5E-17 3.3E-22 162.3 20.6 176 255-476 10-197 (218)
114 PRK12546 RNA polymerase sigma 99.8 9.6E-18 2.1E-22 159.9 18.6 156 255-489 8-163 (188)
115 TIGR02959 SigZ RNA polymerase 99.8 7.7E-18 1.7E-22 157.4 17.3 149 262-489 2-150 (170)
116 PRK12511 RNA polymerase sigma 99.8 1.7E-17 3.8E-22 157.2 17.4 158 256-490 5-162 (182)
117 PRK12525 RNA polymerase sigma 99.8 3.3E-17 7.2E-22 152.5 17.7 159 255-488 9-167 (168)
118 PRK09636 RNA polymerase sigma 99.7 1.4E-16 3.1E-21 161.5 16.8 160 255-488 4-164 (293)
119 PRK09047 RNA polymerase factor 99.7 1.3E-16 2.9E-21 146.3 14.9 156 277-491 2-158 (161)
120 PRK06704 RNA polymerase factor 99.7 2.4E-16 5.1E-21 155.1 17.3 158 246-489 9-166 (228)
121 TIGR02957 SigX4 RNA polymerase 99.7 9.5E-16 2.1E-20 154.9 17.4 156 259-488 1-157 (281)
122 PRK09635 sigI RNA polymerase s 99.7 1E-15 2.3E-20 155.6 17.7 161 255-487 5-166 (290)
123 PRK09191 two-component respons 99.6 1.4E-14 3E-19 142.2 13.4 136 256-488 2-137 (261)
124 TIGR03209 P21_Cbot clostridium 99.6 3.4E-14 7.3E-19 128.5 12.8 136 257-473 1-141 (142)
125 PRK08311 putative RNA polymera 99.5 5.3E-13 1.1E-17 132.1 20.1 78 255-332 18-97 (237)
126 PF07638 Sigma70_ECF: ECF sigm 99.5 4.5E-13 9.7E-18 127.5 18.8 178 209-488 2-184 (185)
127 PF04542 Sigma70_r2: Sigma-70 99.3 1.3E-11 2.9E-16 97.8 7.2 70 260-329 1-70 (71)
128 PF04545 Sigma70_r4: Sigma-70, 99.2 5.3E-11 1.1E-15 89.6 7.3 50 432-485 1-50 (50)
129 PF08281 Sigma70_r4_2: Sigma-7 98.9 2.6E-09 5.6E-14 81.4 7.2 53 427-483 2-54 (54)
130 PRK06930 positive control sigm 98.7 7.4E-08 1.6E-12 91.0 10.0 71 416-490 95-165 (170)
131 PF04539 Sigma70_r3: Sigma-70 98.6 1.1E-07 2.4E-12 77.7 6.4 76 339-419 1-77 (78)
132 PRK00118 putative DNA-binding 98.5 4.5E-07 9.7E-12 79.0 8.9 55 435-492 16-70 (104)
133 cd06171 Sigma70_r4 Sigma70, re 98.4 1.2E-06 2.6E-11 64.6 6.8 54 427-484 2-55 (55)
134 PRK03975 tfx putative transcri 98.3 3.4E-06 7.3E-11 77.4 8.3 52 435-490 5-56 (141)
135 TIGR00721 tfx DNA-binding prot 98.3 3.3E-06 7.1E-11 77.1 8.1 57 435-495 5-61 (137)
136 PRK04217 hypothetical protein; 98.2 2.9E-06 6.2E-11 74.7 6.0 55 435-492 41-95 (110)
137 PF04297 UPF0122: Putative hel 98.1 1.6E-05 3.5E-10 68.8 9.1 62 428-492 9-70 (101)
138 TIGR01636 phage_rinA phage tra 97.9 5.6E-05 1.2E-09 68.7 8.9 60 424-487 71-132 (134)
139 smart00421 HTH_LUXR helix_turn 97.9 3.2E-05 6.9E-10 58.0 6.1 46 435-484 2-47 (58)
140 PF00140 Sigma70_r1_2: Sigma-7 97.8 7.6E-06 1.6E-10 58.2 1.1 33 191-223 2-34 (37)
141 PF00196 GerE: Bacterial regul 97.8 5.8E-05 1.3E-09 58.4 5.8 47 435-485 2-48 (58)
142 PF07374 DUF1492: Protein of u 97.8 0.00011 2.3E-09 63.6 8.1 55 425-483 44-99 (100)
143 cd06170 LuxR_C_like C-terminal 97.8 6.9E-05 1.5E-09 56.4 6.1 45 437-485 1-45 (57)
144 TIGR03879 near_KaiC_dom probab 97.7 6.5E-05 1.4E-09 61.4 6.0 47 428-478 8-55 (73)
145 PF04967 HTH_10: HTH DNA bindi 97.5 0.00027 5.9E-09 54.3 6.2 47 437-483 1-51 (53)
146 PRK15411 rcsA colanic acid cap 97.5 0.00019 4.2E-09 69.5 6.2 46 436-485 137-182 (207)
147 PRK15201 fimbriae regulatory p 97.5 0.00024 5.2E-09 67.3 6.5 47 435-485 132-178 (198)
148 PRK13719 conjugal transfer tra 97.4 0.00027 5.8E-09 69.1 6.2 51 430-485 138-188 (217)
149 TIGR01321 TrpR trp operon repr 97.4 0.00027 5.8E-09 60.4 5.3 49 427-475 23-75 (94)
150 PRK11475 DNA-binding transcrip 97.4 0.0003 6.5E-09 68.5 6.3 46 435-484 133-178 (207)
151 PRK10840 transcriptional regul 97.4 0.0003 6.5E-09 67.5 6.2 46 435-484 149-194 (216)
152 COG4566 TtrR Response regulato 97.4 0.00085 1.8E-08 64.3 8.7 69 423-496 130-198 (202)
153 TIGR03541 reg_near_HchA LuxR f 97.3 0.00036 7.8E-09 68.9 6.2 47 435-485 170-216 (232)
154 TIGR03020 EpsA transcriptional 97.3 0.00046 9.9E-09 69.1 6.5 47 435-485 189-235 (247)
155 COG2197 CitB Response regulato 97.3 0.00045 9.8E-09 67.3 6.0 46 436-485 148-193 (211)
156 PRK10100 DNA-binding transcrip 97.3 0.00055 1.2E-08 67.0 6.5 47 435-485 154-200 (216)
157 PF13936 HTH_38: Helix-turn-he 97.2 0.00042 9.1E-09 51.0 4.1 41 435-478 3-43 (44)
158 PRK10188 DNA-binding transcrip 97.2 0.00061 1.3E-08 67.8 6.4 46 436-485 179-224 (240)
159 PRK13870 transcriptional regul 97.2 0.00058 1.3E-08 67.7 6.2 45 436-484 173-217 (234)
160 PF02001 DUF134: Protein of un 97.2 0.00085 1.8E-08 58.7 6.3 52 436-490 41-92 (106)
161 COG2771 CsgD DNA-binding HTH d 97.1 0.0017 3.7E-08 50.3 6.5 49 435-487 3-51 (65)
162 PRK09483 response regulator; P 97.0 0.0014 3E-08 61.7 6.1 46 435-484 147-192 (217)
163 PRK15369 two component system 96.9 0.002 4.2E-08 59.2 6.4 46 435-484 148-193 (211)
164 COG2739 Uncharacterized protei 96.9 0.0053 1.1E-07 52.9 8.4 49 435-486 16-64 (105)
165 COG4941 Predicted RNA polymera 96.8 0.049 1.1E-06 56.6 15.4 160 257-485 7-166 (415)
166 PRK09390 fixJ response regulat 96.7 0.0051 1.1E-07 56.2 7.1 54 428-486 134-187 (202)
167 PRK10651 transcriptional regul 96.6 0.0036 7.8E-08 58.2 5.9 47 435-485 154-200 (216)
168 PRK01381 Trp operon repressor; 96.6 0.0023 4.9E-08 55.3 4.1 48 426-473 22-73 (99)
169 COG3413 Predicted DNA binding 96.6 0.0049 1.1E-07 60.2 6.6 52 436-487 155-210 (215)
170 PF12645 HTH_16: Helix-turn-he 96.6 0.0081 1.8E-07 48.1 6.5 47 255-301 13-65 (65)
171 COG1356 tfx Transcriptional re 96.5 0.0021 4.5E-08 57.5 3.3 49 435-487 7-55 (143)
172 PRK15320 transcriptional activ 96.4 0.0066 1.4E-07 58.6 5.8 46 435-484 163-208 (251)
173 TIGR01637 phage_arpU phage tra 96.3 0.028 6.2E-07 50.5 9.4 58 428-488 71-130 (132)
174 COG1342 Predicted DNA-binding 96.1 0.014 3E-07 49.9 6.0 52 436-490 33-84 (99)
175 PRK10403 transcriptional regul 96.1 0.0094 2E-07 55.2 5.6 51 435-489 152-202 (215)
176 PRK09935 transcriptional regul 95.9 0.016 3.4E-07 53.9 6.1 46 436-485 149-194 (210)
177 PRK10360 DNA-binding transcrip 95.9 0.019 4.1E-07 53.0 6.4 47 435-485 136-182 (196)
178 PRK05658 RNA polymerase sigma 95.8 0.0099 2.1E-07 67.0 4.8 58 190-268 103-160 (619)
179 PRK04841 transcriptional regul 95.7 0.017 3.7E-07 67.0 6.4 46 435-484 837-882 (903)
180 PRK09958 DNA-binding transcrip 95.6 0.025 5.5E-07 52.6 6.2 46 435-484 142-187 (204)
181 PF13384 HTH_23: Homeodomain-l 95.6 0.012 2.5E-07 43.8 3.1 33 443-479 9-41 (50)
182 PRK13558 bacterio-opsin activa 95.6 0.021 4.5E-07 64.2 6.3 49 435-486 606-661 (665)
183 PRK15418 transcriptional regul 95.5 0.017 3.7E-07 60.0 5.1 36 443-481 20-55 (318)
184 PF00325 Crp: Bacterial regula 95.3 0.023 5E-07 39.2 3.4 27 455-485 2-28 (32)
185 PF05263 DUF722: Protein of un 95.2 0.071 1.5E-06 48.5 7.4 57 425-483 71-127 (130)
186 PF13613 HTH_Tnp_4: Helix-turn 95.1 0.05 1.1E-06 41.4 5.2 50 436-487 2-51 (53)
187 TIGR02531 yecD_yerC TrpR-relat 95.1 0.053 1.1E-06 46.0 5.8 39 435-479 35-73 (88)
188 PF02796 HTH_7: Helix-turn-hel 95.1 0.035 7.6E-07 40.9 4.1 32 441-476 11-42 (45)
189 PF13412 HTH_24: Winged helix- 95.0 0.065 1.4E-06 39.6 5.4 41 437-479 1-41 (48)
190 cd00569 HTH_Hin_like Helix-tur 94.5 0.077 1.7E-06 34.8 4.4 36 437-475 6-41 (42)
191 PF13404 HTH_AsnC-type: AsnC-t 94.2 0.11 2.4E-06 37.9 4.9 40 437-478 1-40 (42)
192 PF06530 Phage_antitermQ: Phag 94.0 0.36 7.8E-06 43.4 8.9 53 435-490 61-113 (125)
193 PF13518 HTH_28: Helix-turn-he 93.7 0.14 3.1E-06 37.9 4.9 34 443-480 4-37 (52)
194 COG2390 DeoR Transcriptional r 93.6 0.09 2E-06 54.7 4.8 36 444-482 18-53 (321)
195 PF06056 Terminase_5: Putative 93.4 0.16 3.4E-06 39.8 4.8 32 444-479 6-37 (58)
196 PF09862 DUF2089: Protein of u 93.3 0.21 4.5E-06 44.4 5.9 48 435-485 32-79 (113)
197 PF10668 Phage_terminase: Phag 93.0 0.16 3.5E-06 40.1 4.2 39 439-478 7-45 (60)
198 COG2909 MalT ATP-dependent tra 92.7 0.13 2.8E-06 59.1 4.7 44 437-484 832-875 (894)
199 PRK10430 DNA-binding transcrip 92.6 0.21 4.5E-06 48.7 5.5 46 436-481 158-204 (239)
200 smart00351 PAX Paired Box doma 92.4 0.32 7E-06 43.6 6.0 42 437-481 18-59 (125)
201 PF13730 HTH_36: Helix-turn-he 92.3 0.51 1.1E-05 35.6 6.2 46 436-485 2-51 (55)
202 PF04218 CENP-B_N: CENP-B N-te 91.5 0.2 4.4E-06 38.3 3.2 40 436-478 6-45 (53)
203 PF12802 MarR_2: MarR family; 91.1 0.43 9.3E-06 36.6 4.7 43 436-478 2-44 (62)
204 PF01371 Trp_repressor: Trp re 90.7 0.41 8.8E-06 40.6 4.4 46 435-481 25-74 (87)
205 PF08279 HTH_11: HTH domain; 90.5 0.46 9.9E-06 35.9 4.2 38 440-478 1-38 (55)
206 cd00131 PAX Paired Box domain 90.3 0.69 1.5E-05 41.8 6.0 41 437-480 18-58 (128)
207 PF12840 HTH_20: Helix-turn-he 90.2 1.1 2.4E-05 34.7 6.3 43 429-477 3-46 (61)
208 PF01726 LexA_DNA_bind: LexA D 90.1 0.57 1.2E-05 37.4 4.6 43 435-477 2-48 (65)
209 PF01022 HTH_5: Bacterial regu 90.1 0.81 1.8E-05 33.7 5.2 37 439-478 2-38 (47)
210 PHA02591 hypothetical protein; 90.0 0.54 1.2E-05 38.9 4.5 25 453-477 57-81 (83)
211 PF03444 HrcA_DNA-bdg: Winged 89.9 0.7 1.5E-05 38.4 5.1 41 437-477 2-45 (78)
212 PHA00675 hypothetical protein 89.9 0.63 1.4E-05 38.4 4.8 41 435-477 21-61 (78)
213 smart00550 Zalpha Z-DNA-bindin 89.0 1 2.2E-05 36.0 5.4 37 441-477 8-44 (68)
214 PRK11179 DNA-binding transcrip 88.6 0.83 1.8E-05 42.2 5.3 41 436-478 6-46 (153)
215 PF01325 Fe_dep_repress: Iron 88.6 0.71 1.5E-05 36.2 4.1 44 437-484 2-47 (60)
216 COG3415 Transposase and inacti 88.5 0.8 1.7E-05 42.1 5.0 35 443-480 12-46 (138)
217 PF00356 LacI: Bacterial regul 87.8 0.55 1.2E-05 35.0 2.9 22 457-478 1-22 (46)
218 PF13542 HTH_Tnp_ISL3: Helix-t 87.6 1.3 2.9E-05 32.8 5.0 26 454-479 26-51 (52)
219 PF01418 HTH_6: Helix-turn-hel 87.4 1.4 3.1E-05 36.0 5.4 52 425-477 3-56 (77)
220 PRK11169 leucine-responsive tr 87.3 0.92 2E-05 42.4 4.8 41 436-478 11-51 (164)
221 smart00344 HTH_ASNC helix_turn 87.2 1.4 3E-05 37.7 5.5 41 437-479 1-41 (108)
222 COG1508 RpoN DNA-directed RNA 87.1 24 0.00053 38.4 15.9 24 454-477 329-352 (444)
223 PF13744 HTH_37: Helix-turn-he 87.0 1.6 3.5E-05 35.9 5.6 38 453-490 29-71 (80)
224 COG3355 Predicted transcriptio 87.0 2.3 4.9E-05 38.6 6.9 50 428-483 17-66 (126)
225 PF02650 HTH_WhiA: WhiA C-term 86.9 1.3 2.8E-05 37.5 4.9 43 435-479 36-80 (85)
226 PRK11083 DNA-binding response 86.7 0.86 1.9E-05 42.7 4.3 50 436-485 154-208 (228)
227 PRK10336 DNA-binding transcrip 86.6 0.89 1.9E-05 42.4 4.4 49 436-484 149-202 (219)
228 COG2973 TrpR Trp operon repres 86.5 1.8 3.9E-05 37.4 5.6 55 423-484 27-85 (103)
229 PF13022 HTH_Tnp_1_2: Helix-tu 86.4 3.8 8.3E-05 37.7 8.0 62 435-496 9-77 (142)
230 TIGR01610 phage_O_Nterm phage 86.1 3.4 7.3E-05 35.2 7.2 47 435-485 21-73 (95)
231 PRK10046 dpiA two-component re 86.0 0.75 1.6E-05 44.5 3.6 40 435-477 160-199 (225)
232 PRK09413 IS2 repressor TnpA; R 85.9 3.7 8E-05 36.5 7.7 34 443-479 20-53 (121)
233 PRK13413 mpi multiple promoter 85.8 1.3 2.9E-05 42.4 5.2 36 438-477 159-194 (200)
234 PF13551 HTH_29: Winged helix- 85.6 7.5 0.00016 32.9 9.3 23 359-381 14-36 (112)
235 PHA02547 55 RNA polymerase sig 85.6 3.1 6.8E-05 39.4 7.2 65 263-327 45-112 (179)
236 PF01710 HTH_Tnp_IS630: Transp 85.5 8.9 0.00019 34.0 9.9 27 454-484 70-96 (119)
237 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 85.5 1.8 3.9E-05 32.9 4.6 39 436-477 4-42 (50)
238 PRK10710 DNA-binding transcrip 85.3 1.2 2.7E-05 42.2 4.7 50 436-485 160-214 (240)
239 COG0856 Orotate phosphoribosyl 85.0 1.3 2.9E-05 42.2 4.5 39 442-484 9-47 (203)
240 PF01047 MarR: MarR family; I 84.6 1.7 3.7E-05 33.0 4.3 41 437-479 1-41 (59)
241 PF13551 HTH_29: Winged helix- 84.5 1.8 3.9E-05 36.8 4.9 33 443-479 3-36 (112)
242 COG0568 RpoD DNA-directed RNA 84.3 56 0.0012 34.6 16.6 42 190-231 8-49 (342)
243 PF12728 HTH_17: Helix-turn-he 84.3 1.1 2.4E-05 33.2 3.1 24 456-479 2-25 (51)
244 COG1522 Lrp Transcriptional re 84.0 2.2 4.7E-05 38.7 5.5 42 435-478 4-45 (154)
245 PF08822 DUF1804: Protein of u 83.8 2.2 4.9E-05 40.3 5.5 42 438-481 4-45 (165)
246 PRK15479 transcriptional regul 83.7 1.8 3.9E-05 40.3 4.9 49 436-484 148-201 (221)
247 PRK00423 tfb transcription ini 83.5 36 0.00078 35.2 14.8 178 259-483 120-304 (310)
248 cd04762 HTH_MerR-trunc Helix-T 83.5 1.2 2.5E-05 31.8 2.8 25 456-480 1-25 (49)
249 KOG0484 Transcription factor P 83.2 5.6 0.00012 34.9 7.2 52 435-489 27-78 (125)
250 COG2522 Predicted transcriptio 83.1 2 4.4E-05 38.5 4.7 31 444-478 15-45 (119)
251 PF08220 HTH_DeoR: DeoR-like h 83.0 1.7 3.7E-05 33.5 3.7 24 454-477 13-36 (57)
252 PF00046 Homeobox: Homeobox do 82.7 2 4.3E-05 32.5 4.0 50 436-485 6-57 (57)
253 TIGR02154 PhoB phosphate regul 82.7 0.95 2.1E-05 42.3 2.6 49 436-484 154-207 (226)
254 TIGR03787 marine_sort_RR prote 82.6 1.8 3.9E-05 40.8 4.5 47 436-485 156-207 (227)
255 TIGR01764 excise DNA binding d 82.4 1.6 3.4E-05 31.3 3.2 24 456-479 2-25 (49)
256 PF13463 HTH_27: Winged helix 82.2 2.6 5.7E-05 32.7 4.6 42 437-479 1-42 (68)
257 PF13011 LZ_Tnp_IS481: leucine 82.0 2.6 5.6E-05 35.6 4.6 44 435-480 7-50 (85)
258 smart00342 HTH_ARAC helix_turn 81.3 20 0.00044 27.9 9.6 26 454-479 49-75 (84)
259 PF02954 HTH_8: Bacterial regu 81.1 2.4 5.2E-05 30.6 3.6 39 438-478 3-41 (42)
260 PF01978 TrmB: Sugar-specific 81.0 1.3 2.7E-05 35.1 2.4 39 436-476 5-43 (68)
261 PF13545 HTH_Crp_2: Crp-like h 80.9 2.2 4.8E-05 34.0 3.8 27 455-485 28-54 (76)
262 PF01381 HTH_3: Helix-turn-hel 80.7 1.7 3.8E-05 32.4 2.9 26 453-478 7-32 (55)
263 PF01527 HTH_Tnp_1: Transposas 80.5 1.6 3.6E-05 34.8 2.9 35 443-480 14-48 (76)
264 TIGR00122 birA_repr_reg BirA b 80.3 3.8 8.3E-05 32.4 5.0 33 443-478 4-36 (69)
265 COG1654 BirA Biotin operon rep 80.1 5.1 0.00011 33.4 5.7 30 452-485 16-45 (79)
266 CHL00148 orf27 Ycf27; Reviewed 80.0 2.4 5.1E-05 40.2 4.3 50 436-485 161-217 (240)
267 PHA01976 helix-turn-helix prot 79.9 3 6.5E-05 32.5 4.2 26 453-478 13-38 (67)
268 cd04761 HTH_MerR-SF Helix-Turn 79.6 1.5 3.2E-05 31.9 2.2 25 456-480 1-25 (49)
269 TIGR02844 spore_III_D sporulat 79.4 3.7 8.1E-05 34.3 4.7 37 439-478 6-42 (80)
270 smart00420 HTH_DEOR helix_turn 79.1 4.1 8.8E-05 29.5 4.5 25 454-478 13-37 (53)
271 TIGR03697 NtcA_cyano global ni 78.3 2.7 5.8E-05 39.2 4.1 27 455-485 143-169 (193)
272 PRK14082 hypothetical protein; 78.3 5.9 0.00013 31.7 5.2 56 254-311 8-63 (65)
273 PF14493 HTH_40: Helix-turn-he 78.3 4.7 0.0001 33.9 5.1 30 453-482 11-40 (91)
274 smart00419 HTH_CRP helix_turn_ 78.1 3.2 6.9E-05 29.8 3.6 27 455-485 8-34 (48)
275 smart00345 HTH_GNTR helix_turn 78.0 3.4 7.3E-05 30.8 3.9 28 454-485 18-46 (60)
276 PRK09954 putative kinase; Prov 77.3 4 8.6E-05 42.6 5.4 43 437-481 1-43 (362)
277 PHA00542 putative Cro-like pro 77.1 3.4 7.3E-05 34.3 3.9 27 453-479 29-55 (82)
278 PF08280 HTH_Mga: M protein tr 77.0 3.7 8E-05 31.8 3.9 36 440-477 6-41 (59)
279 PRK10072 putative transcriptio 77.0 3.4 7.4E-05 35.6 4.0 32 444-478 38-69 (96)
280 PF01726 LexA_DNA_bind: LexA D 77.0 8 0.00017 30.8 5.8 33 349-381 17-50 (65)
281 PF13560 HTH_31: Helix-turn-he 77.0 3.4 7.3E-05 32.2 3.6 26 453-478 12-37 (64)
282 cd00090 HTH_ARSR Arsenical Res 76.9 6 0.00013 30.2 5.1 37 439-478 7-43 (78)
283 PRK12423 LexA repressor; Provi 76.6 4.7 0.0001 39.0 5.3 47 435-485 2-52 (202)
284 PF08765 Mor: Mor transcriptio 76.6 5.4 0.00012 34.8 5.2 42 439-485 61-102 (108)
285 TIGR03070 couple_hipB transcri 76.4 4.2 9.1E-05 30.1 3.9 26 453-478 13-38 (58)
286 COG5484 Uncharacterized conser 76.2 3.1 6.8E-05 41.8 3.9 26 453-478 17-42 (279)
287 PF08535 KorB: KorB domain; I 76.0 2.5 5.5E-05 35.7 2.9 24 454-477 2-25 (93)
288 smart00418 HTH_ARSR helix_turn 75.5 5.8 0.00013 29.4 4.6 26 453-478 8-33 (66)
289 TIGR01889 Staph_reg_Sar staphy 74.8 14 0.0003 32.0 7.3 43 436-478 22-66 (109)
290 COG1476 Predicted transcriptio 73.8 4.8 0.0001 32.7 3.7 26 453-478 12-37 (68)
291 cd00092 HTH_CRP helix_turn_hel 73.8 5.1 0.00011 30.8 3.9 24 454-477 24-47 (67)
292 PF09339 HTH_IclR: IclR helix- 73.2 3.6 7.9E-05 30.8 2.9 25 453-477 16-40 (52)
293 PRK13918 CRP/FNR family transc 73.1 4.2 9.2E-05 38.2 4.0 27 455-485 149-175 (202)
294 cd06571 Bac_DnaA_C C-terminal 72.8 11 0.00024 31.7 6.0 32 453-484 42-74 (90)
295 TIGR01884 cas_HTH CRISPR locus 72.7 7.4 0.00016 37.5 5.6 41 435-478 139-180 (203)
296 PF13556 HTH_30: PucR C-termin 72.4 9.2 0.0002 29.6 5.0 41 444-487 4-44 (59)
297 PRK11302 DNA-binding transcrip 72.4 9.8 0.00021 38.1 6.6 62 426-488 4-71 (284)
298 PRK10870 transcriptional repre 72.2 26 0.00056 33.2 9.1 43 436-478 52-94 (176)
299 PF13411 MerR_1: MerR HTH fami 72.1 1.9 4.1E-05 33.8 1.1 25 456-480 1-25 (69)
300 PF07750 GcrA: GcrA cell cycle 71.8 4.7 0.0001 38.0 3.8 26 453-478 16-42 (162)
301 COG1510 Predicted transcriptio 71.5 3.9 8.5E-05 38.9 3.2 30 452-485 38-67 (177)
302 smart00352 POU Found in Pit-Oc 71.4 10 0.00022 31.3 5.2 32 444-478 16-53 (75)
303 smart00354 HTH_LACI helix_turn 71.0 4.2 9.2E-05 32.5 2.9 23 456-478 1-23 (70)
304 PRK11337 DNA-binding transcrip 70.9 11 0.00025 38.0 6.8 64 424-488 14-83 (292)
305 PF00292 PAX: 'Paired box' dom 70.4 9.3 0.0002 34.6 5.2 38 437-478 18-56 (125)
306 cd01104 HTH_MlrA-CarA Helix-Tu 70.3 5.6 0.00012 31.0 3.5 23 456-478 1-23 (68)
307 TIGR00498 lexA SOS regulatory 70.1 8.9 0.00019 36.6 5.5 42 436-477 3-48 (199)
308 PRK12469 RNA polymerase factor 69.5 1.3E+02 0.0028 33.4 14.8 24 356-379 368-391 (481)
309 TIGR03830 CxxCG_CxxCG_HTH puta 69.3 15 0.00031 32.3 6.3 40 435-479 63-102 (127)
310 TIGR02337 HpaR homoprotocatech 68.9 11 0.00023 32.9 5.3 41 435-477 24-64 (118)
311 TIGR02607 antidote_HigA addict 68.8 10 0.00022 30.3 4.7 26 453-478 16-41 (78)
312 COG2411 Uncharacterized conser 68.7 54 0.0012 31.4 10.0 47 435-485 136-184 (188)
313 TIGR02612 mob_myst_A mobile my 68.6 13 0.00029 34.6 6.1 51 438-492 25-81 (150)
314 PRK11161 fumarate/nitrate redu 68.4 6 0.00013 38.3 3.9 27 455-485 184-210 (235)
315 PRK11512 DNA-binding transcrip 68.3 12 0.00026 33.9 5.6 41 436-478 37-77 (144)
316 smart00347 HTH_MARR helix_turn 68.3 12 0.00027 30.5 5.4 40 436-477 7-46 (101)
317 COG1318 Predicted transcriptio 68.3 5.2 0.00011 38.1 3.3 28 454-481 60-87 (182)
318 PF12116 SpoIIID: Stage III sp 67.9 9 0.00019 32.1 4.2 36 454-489 18-53 (82)
319 PRK15482 transcriptional regul 67.9 13 0.00028 37.6 6.4 62 426-488 4-71 (285)
320 PRK00215 LexA repressor; Valid 67.7 12 0.00025 36.0 5.7 42 437-478 2-47 (205)
321 PRK11753 DNA-binding transcrip 67.6 6.8 0.00015 37.1 4.1 27 455-485 168-194 (211)
322 cd00086 homeodomain Homeodomai 67.3 12 0.00027 27.9 4.7 50 436-485 6-57 (59)
323 PF01710 HTH_Tnp_IS630: Transp 66.9 7.1 0.00015 34.6 3.8 25 453-477 16-40 (119)
324 PRK11564 stationary phase indu 66.6 14 0.00031 39.5 6.7 50 436-485 10-60 (426)
325 PRK09863 putative frv operon r 66.0 12 0.00026 41.9 6.3 46 437-485 2-47 (584)
326 cd07377 WHTH_GntR Winged helix 65.7 8.1 0.00017 29.3 3.5 26 456-485 26-51 (66)
327 COG2345 Predicted transcriptio 65.7 12 0.00025 37.2 5.3 26 453-478 23-48 (218)
328 smart00346 HTH_ICLR helix_turn 65.7 15 0.00033 30.0 5.3 26 454-479 19-44 (91)
329 cd04764 HTH_MlrA-like_sg1 Heli 64.8 8.5 0.00018 30.1 3.5 23 456-478 1-23 (67)
330 PF14502 HTH_41: Helix-turn-he 64.6 10 0.00022 28.7 3.6 26 456-485 7-32 (48)
331 PF07037 DUF1323: Putative tra 64.6 7.4 0.00016 34.9 3.3 23 456-478 1-23 (122)
332 PF00376 MerR: MerR family reg 64.5 4.3 9.4E-05 28.9 1.5 23 457-479 1-23 (38)
333 PRK09391 fixK transcriptional 63.5 8.7 0.00019 37.5 4.0 27 455-485 179-205 (230)
334 PRK01905 DNA-binding protein F 63.5 29 0.00063 28.3 6.5 38 439-478 36-73 (77)
335 smart00422 HTH_MERR helix_turn 63.3 5.7 0.00012 31.0 2.2 25 456-480 1-25 (70)
336 COG1737 RpiR Transcriptional r 63.0 16 0.00034 37.2 5.9 53 424-477 4-58 (281)
337 PRK09726 antitoxin HipB; Provi 62.6 11 0.00024 31.4 4.0 37 453-489 23-63 (88)
338 COG2512 Predicted membrane-ass 62.5 10 0.00022 38.4 4.4 42 435-477 191-232 (258)
339 PRK10411 DNA-binding transcrip 62.2 14 0.0003 36.8 5.2 42 438-481 3-44 (240)
340 PF14394 DUF4423: Domain of un 62.0 27 0.00059 33.1 6.9 28 355-382 37-66 (171)
341 PRK11557 putative DNA-binding 62.0 16 0.00035 36.6 5.8 59 429-488 3-67 (278)
342 COG1846 MarR Transcriptional r 62.0 15 0.00033 31.0 4.9 39 437-478 20-59 (126)
343 PF04539 Sigma70_r3: Sigma-70 61.7 21 0.00045 28.6 5.3 26 453-478 18-43 (78)
344 PF00165 HTH_AraC: Bacterial r 61.6 13 0.00028 26.4 3.6 27 453-479 6-32 (42)
345 PRK09863 putative frv operon r 61.4 1E+02 0.0022 34.7 12.4 106 356-484 16-121 (584)
346 COG3877 Uncharacterized protei 60.8 19 0.0004 31.8 5.0 46 435-483 40-85 (122)
347 PF05043 Mga: Mga helix-turn-h 60.7 19 0.00042 29.5 5.1 32 453-484 28-59 (87)
348 PF12298 Bot1p: Eukaryotic mit 60.6 21 0.00046 34.0 5.9 43 436-485 16-58 (172)
349 smart00389 HOX Homeodomain. DN 60.5 13 0.00029 27.5 3.7 47 436-482 6-54 (56)
350 TIGR00180 parB_part ParB-like 60.4 16 0.00034 34.9 5.1 43 435-478 101-143 (187)
351 TIGR00647 MG103 conserved hypo 60.4 19 0.0004 37.0 5.8 43 435-479 226-274 (279)
352 PF00392 GntR: Bacterial regul 60.3 9.8 0.00021 29.6 3.1 27 454-484 22-49 (64)
353 cd04763 HTH_MlrA-like Helix-Tu 60.3 11 0.00024 29.5 3.4 23 456-478 1-23 (68)
354 PRK10955 DNA-binding transcrip 59.7 6.6 0.00014 36.9 2.4 45 436-484 156-209 (232)
355 COG2944 Predicted transcriptio 59.5 20 0.00043 31.5 5.0 39 435-478 42-80 (104)
356 PRK10161 transcriptional regul 59.2 11 0.00023 35.7 3.7 50 436-485 154-208 (229)
357 PF06971 Put_DNA-bind_N: Putat 59.2 29 0.00064 26.4 5.3 46 332-377 2-48 (50)
358 PRK03573 transcriptional regul 59.1 21 0.00044 32.1 5.4 42 436-478 28-69 (144)
359 TIGR02787 codY_Gpos GTP-sensin 59.0 36 0.00079 34.3 7.4 52 428-484 169-223 (251)
360 PF13443 HTH_26: Cro/C1-type H 58.9 9.6 0.00021 29.2 2.8 27 454-480 9-35 (63)
361 PRK09706 transcriptional repre 58.5 13 0.00029 33.3 4.1 26 453-478 16-41 (135)
362 cd01392 HTH_LacI Helix-turn-he 58.0 6.4 0.00014 28.9 1.6 20 460-479 2-21 (52)
363 PF05225 HTH_psq: helix-turn-h 57.9 33 0.00072 25.2 5.3 23 456-478 17-39 (45)
364 PRK10141 DNA-binding transcrip 57.7 22 0.00047 31.8 5.1 38 438-477 15-52 (117)
365 PF12844 HTH_19: Helix-turn-he 57.6 15 0.00032 28.2 3.7 26 453-478 10-35 (64)
366 PRK03902 manganese transport t 57.6 19 0.00042 32.5 5.0 25 453-477 20-44 (142)
367 PRK14101 bifunctional glucokin 57.0 26 0.00056 39.9 6.9 65 423-488 341-411 (638)
368 PRK10402 DNA-binding transcrip 57.0 12 0.00026 36.2 3.8 44 438-485 150-195 (226)
369 smart00530 HTH_XRE Helix-turn- 56.9 14 0.00029 25.7 3.1 26 453-478 8-33 (56)
370 PRK10434 srlR DNA-bindng trans 56.3 16 0.00034 36.8 4.5 38 439-478 5-42 (256)
371 PRK09392 ftrB transcriptional 56.3 13 0.00027 36.1 3.7 27 455-485 173-199 (236)
372 smart00342 HTH_ARAC helix_turn 56.0 31 0.00067 26.8 5.4 26 455-480 1-26 (84)
373 PF12759 HTH_Tnp_IS1: InsA C-t 56.0 16 0.00035 27.4 3.3 37 437-477 7-43 (46)
374 PF04703 FaeA: FaeA-like prote 55.6 12 0.00025 29.8 2.7 25 454-478 14-38 (62)
375 PRK07598 RNA polymerase sigma 55.4 90 0.0019 33.9 10.3 26 454-479 277-302 (415)
376 PF04552 Sigma54_DBD: Sigma-54 55.2 4 8.6E-05 38.5 0.0 46 429-477 25-71 (160)
377 COG3093 VapI Plasmid maintenan 55.0 19 0.0004 31.7 4.1 35 443-478 12-46 (104)
378 COG1405 SUA7 Transcription ini 55.0 2.4E+02 0.0051 29.2 12.8 26 453-478 249-274 (285)
379 cd00093 HTH_XRE Helix-turn-hel 54.7 22 0.00047 24.8 4.0 26 454-479 11-36 (58)
380 PF02082 Rrf2: Transcriptional 54.6 21 0.00046 29.3 4.3 23 455-477 25-47 (83)
381 PRK13509 transcriptional repre 54.4 23 0.0005 35.4 5.3 38 439-478 5-42 (251)
382 PHA00738 putative HTH transcri 54.3 27 0.0006 30.8 5.0 38 438-477 11-48 (108)
383 COG1349 GlpR Transcriptional r 54.2 16 0.00034 36.7 4.1 37 438-477 4-41 (253)
384 PF02787 CPSase_L_D3: Carbamoy 53.8 1.5E+02 0.0032 26.6 9.9 24 454-477 71-94 (123)
385 PRK10219 DNA-binding transcrip 53.3 74 0.0016 27.0 7.7 27 453-479 19-45 (107)
386 PRK06424 transcription factor; 53.1 18 0.00039 33.5 4.0 26 453-478 95-120 (144)
387 PF08006 DUF1700: Protein of u 53.0 33 0.00071 32.4 5.9 56 422-478 3-63 (181)
388 PRK00135 scpB segregation and 52.8 1.1E+02 0.0024 29.5 9.5 98 353-469 15-118 (188)
389 PRK10906 DNA-binding transcrip 52.8 20 0.00042 36.0 4.5 38 439-478 5-42 (252)
390 PRK06030 hypothetical protein; 52.1 48 0.001 30.0 6.4 39 439-480 56-94 (124)
391 TIGR02395 rpoN_sigma RNA polym 52.0 94 0.002 33.8 9.9 90 356-475 317-416 (429)
392 PF08784 RPA_C: Replication pr 51.9 23 0.0005 30.2 4.2 42 436-477 44-87 (102)
393 PF00440 TetR_N: Bacterial reg 51.7 26 0.00056 25.5 3.9 23 453-475 14-36 (47)
394 PRK13890 conjugal transfer pro 51.1 21 0.00046 31.8 4.0 26 453-478 16-41 (120)
395 TIGR02395 rpoN_sigma RNA polym 51.1 18 0.0004 39.2 4.3 25 453-477 316-340 (429)
396 PF06413 Neugrin: Neugrin; In 51.0 24 0.00052 35.1 4.7 43 435-477 9-51 (225)
397 PRK13777 transcriptional regul 50.8 33 0.00072 33.0 5.5 40 436-477 42-81 (185)
398 PRK11511 DNA-binding transcrip 50.7 76 0.0017 28.1 7.6 27 453-479 23-49 (127)
399 PF04552 Sigma54_DBD: Sigma-54 50.7 20 0.00043 33.8 3.9 89 356-475 48-146 (160)
400 COG1321 TroR Mn-dependent tran 50.7 26 0.00056 32.7 4.7 25 453-477 22-46 (154)
401 COG3398 Uncharacterized protei 50.6 1.6E+02 0.0035 29.4 10.2 39 438-478 173-211 (240)
402 PF06970 RepA_N: Replication i 50.3 20 0.00042 29.6 3.4 28 450-477 42-74 (76)
403 PF04645 DUF603: Protein of un 50.2 21 0.00046 34.0 3.9 25 453-477 16-41 (181)
404 TIGR01387 cztR_silR_copR heavy 50.0 24 0.00052 32.5 4.4 49 436-484 147-200 (218)
405 smart00862 Trans_reg_C Transcr 49.6 57 0.0012 25.5 6.0 49 436-484 5-59 (78)
406 PRK00082 hrcA heat-inducible t 48.6 28 0.0006 36.6 5.1 44 435-482 2-53 (339)
407 TIGR02698 CopY_TcrY copper tra 48.6 46 0.001 30.0 5.8 44 436-481 1-48 (130)
408 PRK06266 transcription initiat 48.1 50 0.0011 31.6 6.3 49 426-478 11-59 (178)
409 PF05732 RepL: Firmicute plasm 47.9 52 0.0011 31.1 6.3 52 429-485 46-101 (165)
410 PRK00430 fis global DNA-bindin 47.5 1.1E+02 0.0024 26.2 7.7 39 438-478 53-91 (95)
411 PRK09943 DNA-binding transcrip 47.4 25 0.00055 33.2 4.2 26 453-478 18-43 (185)
412 PRK10643 DNA-binding transcrip 47.4 20 0.00043 33.2 3.5 47 436-484 149-202 (222)
413 cd04768 HTH_BmrR-like Helix-Tu 47.2 14 0.00031 31.3 2.2 25 456-480 1-25 (96)
414 PRK08359 transcription factor; 47.1 25 0.00054 33.7 4.0 31 444-477 90-120 (176)
415 TIGR00270 conserved hypothetic 47.1 26 0.00057 32.7 4.1 26 453-478 80-105 (154)
416 PRK10681 DNA-binding transcrip 47.1 34 0.00073 34.2 5.2 38 439-478 7-44 (252)
417 PRK04984 fatty acid metabolism 47.0 26 0.00056 34.2 4.3 29 453-485 28-57 (239)
418 TIGR00373 conserved hypothetic 46.9 58 0.0013 30.4 6.4 38 438-477 13-50 (158)
419 COG2826 Tra8 Transposase and i 46.8 23 0.00051 36.7 4.0 43 435-480 6-48 (318)
420 PRK04424 fatty acid biosynthes 46.6 29 0.00064 33.1 4.5 37 439-477 7-43 (185)
421 cd04775 HTH_Cfa-like Helix-Tur 46.3 15 0.00032 31.6 2.2 26 456-481 2-27 (102)
422 PF04492 Phage_rep_O: Bacterio 46.3 83 0.0018 27.3 6.8 41 435-475 28-74 (100)
423 cd04773 HTH_TioE_rpt2 Second H 46.2 15 0.00032 32.0 2.2 25 456-480 1-25 (108)
424 PRK05932 RNA polymerase factor 46.2 1.6E+02 0.0035 32.4 10.6 59 321-382 104-163 (455)
425 PF06322 Phage_NinH: Phage Nin 46.1 31 0.00067 27.5 3.6 20 457-476 18-37 (64)
426 PRK11050 manganese transport r 46.1 64 0.0014 29.7 6.5 26 453-478 49-74 (152)
427 COG4367 Uncharacterized protei 45.9 42 0.00092 28.6 4.7 41 437-477 3-45 (97)
428 cd01105 HTH_GlnR-like Helix-Tu 45.8 16 0.00035 30.5 2.3 25 456-480 2-26 (88)
429 COG2963 Transposase and inacti 45.8 43 0.00094 29.0 5.1 43 436-481 7-51 (116)
430 TIGR02147 Fsuc_second hypothet 45.6 90 0.0019 31.9 8.0 97 356-465 136-239 (271)
431 PF11662 DUF3263: Protein of u 45.5 78 0.0017 26.4 6.1 46 436-481 2-48 (77)
432 cd00592 HTH_MerR-like Helix-Tu 45.1 16 0.00035 30.8 2.2 25 456-480 1-25 (100)
433 PF08279 HTH_11: HTH domain; 45.0 52 0.0011 24.4 4.8 28 354-381 12-39 (55)
434 TIGR02325 C_P_lyase_phnF phosp 45.0 26 0.00056 34.1 3.9 26 456-485 33-58 (238)
435 PRK11414 colanic acid/biofilm 44.6 26 0.00056 33.9 3.8 29 453-485 32-60 (221)
436 TIGR03338 phnR_burk phosphonat 44.5 26 0.00057 33.4 3.8 29 453-485 32-60 (212)
437 PRK11886 bifunctional biotin-- 44.4 38 0.00082 34.9 5.2 39 440-480 5-43 (319)
438 PRK05932 RNA polymerase factor 44.3 27 0.00058 38.3 4.3 25 453-477 341-365 (455)
439 cd04766 HTH_HspR Helix-Turn-He 44.3 17 0.00036 30.5 2.1 25 456-480 2-26 (91)
440 PRK12469 RNA polymerase factor 43.7 32 0.0007 38.0 4.8 25 453-477 367-391 (481)
441 cd01107 HTH_BmrR Helix-Turn-He 43.6 18 0.00039 31.4 2.3 26 456-481 1-26 (108)
442 PRK09744 DNA-binding transcrip 43.6 33 0.0007 28.4 3.6 20 457-476 12-31 (75)
443 TIGR02812 fadR_gamma fatty aci 43.3 32 0.0007 33.5 4.3 29 453-485 27-56 (235)
444 TIGR02944 suf_reg_Xantho FeS a 43.3 31 0.00067 30.6 3.8 25 453-477 23-47 (130)
445 PF05331 DUF742: Protein of un 43.2 39 0.00085 30.1 4.4 40 435-478 39-78 (114)
446 cd04774 HTH_YfmP Helix-Turn-He 43.1 18 0.00039 30.9 2.2 25 456-480 1-25 (96)
447 cd01106 HTH_TipAL-Mta Helix-Tu 42.7 19 0.0004 30.9 2.2 25 456-480 1-25 (103)
448 COG5606 Uncharacterized conser 42.7 18 0.00039 30.8 2.0 37 444-480 30-66 (91)
449 PRK11517 transcriptional regul 42.6 44 0.00095 31.0 5.0 49 436-484 147-200 (223)
450 cd04789 HTH_Cfa Helix-Turn-Hel 42.5 19 0.00041 31.0 2.2 25 456-480 2-26 (102)
451 PRK09464 pdhR transcriptional 42.5 34 0.00073 33.8 4.3 28 454-485 32-60 (254)
452 PRK09990 DNA-binding transcrip 42.3 34 0.00073 33.7 4.3 29 453-485 28-57 (251)
453 cd04765 HTH_MlrA-like_sg2 Heli 42.1 30 0.00066 29.7 3.5 23 456-478 1-23 (99)
454 COG4709 Predicted membrane pro 42.0 61 0.0013 31.5 5.7 58 422-480 3-65 (195)
455 cd04780 HTH_MerR-like_sg5 Heli 41.9 20 0.00042 30.6 2.2 25 456-480 1-25 (95)
456 PF05930 Phage_AlpA: Prophage 41.7 31 0.00068 25.7 3.1 24 456-479 4-27 (51)
457 PRK03837 transcriptional regul 41.6 36 0.00078 33.1 4.4 27 454-484 35-62 (241)
458 cd01109 HTH_YyaN Helix-Turn-He 41.5 20 0.00043 31.3 2.3 25 456-480 1-25 (113)
459 cd04782 HTH_BltR Helix-Turn-He 41.5 20 0.00043 30.5 2.2 25 456-480 1-25 (97)
460 cd04788 HTH_NolA-AlbR Helix-Tu 41.5 20 0.00042 30.5 2.2 25 456-480 1-25 (96)
461 PRK10225 DNA-binding transcrip 41.5 35 0.00076 33.8 4.3 28 454-485 31-59 (257)
462 TIGR00637 ModE_repress ModE mo 41.4 74 0.0016 27.3 5.7 38 438-479 3-40 (99)
463 cd04772 HTH_TioE_rpt1 First He 41.0 21 0.00046 30.6 2.3 25 456-480 1-25 (99)
464 COG5566 Uncharacterized conser 40.9 35 0.00076 31.0 3.7 33 453-485 100-132 (137)
465 TIGR00738 rrf2_super rrf2 fami 40.8 52 0.0011 29.0 4.9 23 455-477 25-47 (132)
466 PF04963 Sigma54_CBD: Sigma-54 40.7 9.5 0.00021 36.8 0.1 94 357-483 52-146 (194)
467 cd01282 HTH_MerR-like_sg3 Heli 40.5 21 0.00046 31.2 2.3 25 456-480 1-25 (112)
468 PHA02943 hypothetical protein; 40.4 46 0.00099 31.3 4.5 37 438-477 10-46 (165)
469 cd00383 trans_reg_C Effector d 40.4 66 0.0014 26.2 5.2 49 436-484 23-76 (95)
470 PRK09802 DNA-binding transcrip 40.4 45 0.00097 33.8 4.9 38 439-478 17-54 (269)
471 cd01279 HTH_HspR-like Helix-Tu 40.3 20 0.00044 30.6 2.1 24 456-479 2-25 (98)
472 PRK10421 DNA-binding transcrip 40.1 38 0.00082 33.5 4.3 28 454-485 24-52 (253)
473 PRK02866 cyanate hydratase; Va 39.4 45 0.00099 31.1 4.3 33 443-478 9-41 (147)
474 PF00325 Crp: Bacterial regula 39.2 36 0.00078 23.5 2.7 23 359-381 4-26 (32)
475 PF12324 HTH_15: Helix-turn-he 38.7 65 0.0014 26.8 4.7 30 353-382 34-63 (77)
476 PHA02591 hypothetical protein; 38.7 76 0.0016 26.6 5.0 23 357-379 59-81 (83)
477 PHA02535 P terminase ATPase su 38.6 36 0.00079 38.4 4.2 33 442-478 9-41 (581)
478 PF04545 Sigma70_r4: Sigma-70, 38.5 42 0.00091 24.6 3.3 27 355-381 18-44 (50)
479 cd00131 PAX Paired Box domain 38.4 2.9E+02 0.0064 24.7 9.9 30 358-387 34-63 (128)
480 TIGR02044 CueR Cu(I)-responsiv 38.4 23 0.0005 31.6 2.2 25 456-480 1-25 (127)
481 PF10654 DUF2481: Protein of u 38.3 1E+02 0.0022 27.7 6.0 41 442-486 71-111 (126)
482 cd04783 HTH_MerR1 Helix-Turn-H 38.3 23 0.0005 31.5 2.2 25 456-480 1-25 (126)
483 cd01108 HTH_CueR Helix-Turn-He 38.1 23 0.0005 31.6 2.2 26 456-481 1-26 (127)
484 cd04767 HTH_HspR-like_MBC Heli 38.0 24 0.00051 31.7 2.2 25 456-480 2-26 (120)
485 PF13693 HTH_35: Winged helix- 37.8 24 0.00053 29.3 2.1 33 453-485 13-45 (78)
486 PRK02277 orotate phosphoribosy 37.7 29 0.00063 33.5 3.0 35 444-482 11-45 (200)
487 cd04769 HTH_MerR2 Helix-Turn-H 37.7 24 0.00053 30.9 2.2 26 456-481 1-26 (116)
488 PRK10086 DNA-binding transcrip 37.6 82 0.0018 31.8 6.4 50 429-487 7-56 (311)
489 PF01325 Fe_dep_repress: Iron 37.6 71 0.0015 24.9 4.6 34 348-381 13-46 (60)
490 TIGR02404 trehalos_R_Bsub treh 36.9 35 0.00076 33.2 3.5 26 456-485 25-50 (233)
491 PF01498 HTH_Tnp_Tc3_2: Transp 36.9 32 0.00069 27.2 2.6 26 454-479 12-42 (72)
492 TIGR00673 cynS cyanate hydrata 36.9 54 0.0012 30.7 4.4 34 442-478 11-44 (150)
493 PF00126 HTH_1: Bacterial regu 36.8 72 0.0016 24.4 4.5 24 455-478 13-36 (60)
494 PF05584 Sulfolobus_pRN: Sulfo 36.7 96 0.0021 25.5 5.3 40 436-479 3-42 (72)
495 PF04814 HNF-1_N: Hepatocyte n 36.7 27 0.00058 33.6 2.4 54 424-480 103-156 (180)
496 PF07900 DUF1670: Protein of u 36.6 4.4E+02 0.0096 26.2 11.8 29 353-381 101-129 (220)
497 PF09012 FeoC: FeoC like trans 36.6 33 0.00071 27.2 2.6 25 454-478 13-37 (69)
498 PF14549 P22_Cro: DNA-binding 36.6 38 0.00082 26.7 2.9 19 457-475 11-29 (60)
499 cd04770 HTH_HMRTR Helix-Turn-H 36.1 27 0.00059 30.8 2.3 26 456-481 1-26 (123)
500 TIGR00331 hrcA heat shock gene 35.9 56 0.0012 34.4 4.9 40 438-478 1-46 (337)
No 1
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=2e-53 Score=442.91 Aligned_cols=299 Identities=35% Similarity=0.587 Sum_probs=280.0
Q ss_pred hhHHHHHHhhccccCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhcc---------ccccChhHHHhhhhhhHHHHHHHH
Q 010835 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGS---------SLRISRPELQSILMECSLAREKLV 261 (499)
Q Consensus 191 ~~~~~yl~~i~~~~~Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~---------~~~~~~~~l~~~l~~~~~A~e~LI 261 (499)
+.+..||++|+++|+||++||.+|+++++.|..++..+.++.+..|+ +++++..+|++++..|..|++.||
T Consensus 63 d~l~~Yl~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Li 142 (373)
T PRK07406 63 DSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMV 142 (373)
T ss_pred CHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHHHH
Confidence 67889999999999999999999999999999999999999999997 578999999999998899999999
Q ss_pred HHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHH
Q 010835 262 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 341 (499)
Q Consensus 262 e~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l 341 (499)
..|+++|+++|++|.+++.+++||+|||++|||+|+++|||.+|++|+|||+||||++|.++|++++++||+|.++.+.+
T Consensus 143 ~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~~~~ 222 (373)
T PRK07406 143 QSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETI 222 (373)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchH
Q 010835 342 GLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGV 420 (499)
Q Consensus 342 ~~irka~~~L~-~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~v 420 (499)
++++++...+. ++|++||.+|||+.+|++.++|..++.....++|||.++ +++++.++.+++.+.. .+|++.+
T Consensus 223 ~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i----~~~~~~~l~d~l~d~~--~~pee~~ 296 (373)
T PRK07406 223 SRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPI----GKEEDSRLGDFIEADG--ETPEDDV 296 (373)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCC----CCCCcccHHHhcCCCC--CCHHHHH
Confidence 99999998885 789999999999999999999999988888899999985 2334456788887653 4788888
Q ss_pred HHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhh
Q 010835 421 DDWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAML 496 (499)
Q Consensus 421 e~~el~~~L~~~L~~~L~~rER~VI~LryGLd-~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~l~~~l 496 (499)
....+...|..+| ..||++||.||.+|||++ .+++|++|||+.||||++||||++.+|++|||+......|+.|+
T Consensus 297 ~~~~~~~~L~~aL-~~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~~~~~~~l~~~~ 372 (373)
T PRK07406 297 AKNLLREDLEGVL-ATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 372 (373)
T ss_pred HHHHHHHHHHHHH-HcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHh
Confidence 8888999999999 899999999999999985 57899999999999999999999999999999999999999886
No 2
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=3.7e-53 Score=444.12 Aligned_cols=300 Identities=34% Similarity=0.601 Sum_probs=274.5
Q ss_pred hhHHHHHHhhccccCCCHHHHHHHHHHHHcCCC--------------------cchhHHHHHHhhcc---------c---
Q 010835 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS--------------------LDDHKLRLKERLGS---------S--- 238 (499)
Q Consensus 191 ~~~~~yl~~i~~~~~Lt~eEe~eL~~~ik~Gd~--------------------l~~~~~~~~~~~g~---------~--- 238 (499)
|.++.||++|++.|+||++||++|+++++.+-. |+.++.++++.+|+ +
T Consensus 60 d~v~~yl~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~~~~~ 139 (415)
T PRK07598 60 DLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTADI 139 (415)
T ss_pred ChHHHHHHhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHHHhCC
Confidence 799999999999999999999999999998877 77888888888888 2
Q ss_pred -------------------cccChhHHHhhhhhhHHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhc
Q 010835 239 -------------------LRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEK 299 (499)
Q Consensus 239 -------------------~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiek 299 (499)
++|+.++|.+++..|..|+++||..|+++|++||++|.++|.+++||+|||++|||+|+++
T Consensus 140 ~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~ravek 219 (415)
T PRK07598 140 SLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEK 219 (415)
T ss_pred cHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHH
Confidence 3466667777777888999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHH
Q 010835 300 FDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNAT 378 (499)
Q Consensus 300 FDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L~-~~gr~pt~eEIA~~Lgis~e~v~~~l 378 (499)
|||.+|++|+||++||||++|.+++.+++|++|+|.|+.+.+++++++.+.+. ++|+.|+.+|||+.+|+++++|.+++
T Consensus 220 FDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l 299 (415)
T PRK07598 220 FDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVL 299 (415)
T ss_pred cCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999998884 79999999999999999999999999
Q ss_pred HhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcC-CCCCCC
Q 010835 379 EAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGL-DKECLT 457 (499)
Q Consensus 379 ~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGL-d~eg~S 457 (499)
.....++|||.++ +++++..+.+++.++. .+|++.+....+...|..+| ..|||+||.||.|+||| |++++|
T Consensus 300 ~~~~~~~SLd~~v----g~~~d~~l~d~l~~~~--~~pee~~~~~~l~~~L~~~L-~~L~~reR~VI~LRygl~d~~~~T 372 (415)
T PRK07598 300 LRVPRSVSLETKV----GKDKDTELGDLLETDD--ISPEEMLMRESLQRDLQHLL-ADLTSRERDVIRMRFGLADGHTYS 372 (415)
T ss_pred HHccCCccccccc----CCCccccHHHhccCCC--CCHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHhcCCCCCCC
Confidence 9999999999975 3333445677776543 47888888888999999999 99999999999999998 467899
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhhh
Q 010835 458 WEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV 497 (499)
Q Consensus 458 leEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~l~~~l~ 497 (499)
++|||+.||+|++||++++++|++|||+.-....++.||.
T Consensus 373 l~EIA~~LGvS~erVRqie~rAl~KLR~~~~~~~l~~y~~ 412 (415)
T PRK07598 373 LAEIGRALDLSRERVRQIESKALQKLRQPKRRNRIRDYLE 412 (415)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHHH
Confidence 9999999999999999999999999999989999999986
No 3
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=100.00 E-value=4.1e-53 Score=453.54 Aligned_cols=297 Identities=33% Similarity=0.548 Sum_probs=268.5
Q ss_pred hhhHHHHHHhhccccCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhcc-ccccChhHHHhhhhhhHHHHHHHHHHHHHHH
Q 010835 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGS-SLRISRPELQSILMECSLAREKLVMSNVRLV 268 (499)
Q Consensus 190 ~~~~~~yl~~i~~~~~Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~-~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV 268 (499)
.+.+..||++|+++|+||++||.+|+++++.|+.+++... .|. ....+.++|++++..+..|++.||..|+|||
T Consensus 210 ~d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~~~-----~~~~~~~~~~~~l~~~~~~g~~Ar~~LI~sNLrLV 284 (509)
T PRK05901 210 ADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEELLA-----EGEKLDPELRRDLQWIGRDGKRAKNHLLEANLRLV 284 (509)
T ss_pred ccHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhhhh-----hcccchhhhhhhhhhhccchHHHHHHHHHHhHHHH
Confidence 4789999999999999999999999999999987544321 111 1123567889999999999999999999999
Q ss_pred HHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHH
Q 010835 269 MSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAK 348 (499)
Q Consensus 269 ~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~ 348 (499)
++||++|.++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++|++++|++|+|+|+.+.+++++++.
T Consensus 285 vsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~~~~e~i~kl~~~~ 364 (509)
T PRK05901 285 VSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVETINKLGRIE 364 (509)
T ss_pred HHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred HHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHH
Q 010835 349 LRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKD 427 (499)
Q Consensus 349 ~~L~-~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~ 427 (499)
+.|. .+|++|+.+|||+.||+++++|..++.....++|||.++ +++++..+.+++.|... .+|++.+....+..
T Consensus 365 ~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i----~~d~~~~l~d~l~D~~~-~~p~~~~~~~~l~~ 439 (509)
T PRK05901 365 RELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTI----GKEGDSQFGDFIEDSEA-VSPVDAVSFTLLQD 439 (509)
T ss_pred HHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccccccc----ccCCcccHHHhccCCCC-CCHHHHHHHHHHHH
Confidence 8885 789999999999999999999999998888899999975 23334567888888753 47888888899999
Q ss_pred HHHHHHHhhCCHHHHHHHHHHhcCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhhh
Q 010835 428 EVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV 497 (499)
Q Consensus 428 ~L~~~L~~~L~~rER~VI~LryGLd-~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~l~~~l~ 497 (499)
.|..+| ..|+++||.||.+||||+ ++++|++|||+.||||+++|||++.+||.|||+......|+.||+
T Consensus 440 ~L~~aL-~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~~~~~~l~~~l~ 509 (509)
T PRK05901 440 QLQEVL-ETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDFLD 509 (509)
T ss_pred HHHHHH-hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 999999 899999999999999994 689999999999999999999999999999999999999999874
No 4
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00 E-value=3.7e-52 Score=427.89 Aligned_cols=298 Identities=31% Similarity=0.573 Sum_probs=275.8
Q ss_pred hhHHHHHHhhccccCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhcc---------ccccChhHHHhhhhhhHHHHHHHH
Q 010835 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGS---------SLRISRPELQSILMECSLAREKLV 261 (499)
Q Consensus 191 ~~~~~yl~~i~~~~~Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~---------~~~~~~~~l~~~l~~~~~A~e~LI 261 (499)
|.+..|+++|+++|+||++||.+|+++++.|-.++..+..+.+.+|+ .++|+..+|...+..+..|++.||
T Consensus 18 d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~~Li 97 (327)
T PRK05949 18 DMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQKMI 97 (327)
T ss_pred CHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHHHHH
Confidence 78899999999999999999999999999999999999999999998 467999999999998889999999
Q ss_pred HHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHH
Q 010835 262 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 341 (499)
Q Consensus 262 e~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l 341 (499)
..|+++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+|||+||||++|.+++.++++++|+|.|+.+.+
T Consensus 98 ~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~~~~~ 177 (327)
T PRK05949 98 EANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEKL 177 (327)
T ss_pred HHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHH-HHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchH
Q 010835 342 GLIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGV 420 (499)
Q Consensus 342 ~~irka~~~L-~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~v 420 (499)
++++++...+ .++|++|+++|||+.+|+++++|..++.....++|||.++ +++++.++.+.+.+.. .+|++.+
T Consensus 178 ~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~----~~~~~~~l~~~l~d~~--~~pe~~~ 251 (327)
T PRK05949 178 NKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRV----GDNQDTELSELLEDEG--PSPDQYI 251 (327)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCc----CCCCCccHHhhcCCCC--CCHHHHH
Confidence 9999998888 5799999999999999999999999999888999999974 2333446777777654 4788888
Q ss_pred HHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhhh
Q 010835 421 DDWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV 497 (499)
Q Consensus 421 e~~el~~~L~~~L~~~L~~rER~VI~LryGLd-~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~l~~~l~ 497 (499)
........|..+| +.||++||.||.+||||+ ++++|++|||+.||||++||+|++.+|++|||+. ...++.|+.
T Consensus 252 ~~~~~~~~L~~~L-~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~~--~~~l~~~~~ 326 (327)
T PRK05949 252 TQELLRQDLNNLL-AELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRRR--RANVKEYLA 326 (327)
T ss_pred HHHHHHHHHHHHH-HhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence 8888999999999 899999999999999994 6899999999999999999999999999999994 467787764
No 5
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=100.00 E-value=2.9e-51 Score=420.59 Aligned_cols=296 Identities=34% Similarity=0.564 Sum_probs=263.1
Q ss_pred hhHHHHHHhhccccCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHH
Q 010835 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMS 270 (499)
Q Consensus 191 ~~~~~yl~~i~~~~~Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~s 270 (499)
+.+..||++|+++|+||++||.+|+++++.|..++.... ..+.+ +.. ...+|+..+..|..|++.||..|+++|++
T Consensus 26 ~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~~~-~~~~~--~~~-~~~~l~~~~~~~~~A~~~Lv~~~~~lV~~ 101 (324)
T PRK07921 26 DLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHLLE-TRKRL--SEA-RKRDLAAVVRDGEAARRHLLEANLRLVVS 101 (324)
T ss_pred ChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhhhc-ccccc--chh-HHHHHHHHHhcCHHHHHHHHHHHHHHHHH
Confidence 678899999999999999999999999999865433311 00000 111 34578888888999999999999999999
Q ss_pred HHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHH
Q 010835 271 IAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLR 350 (499)
Q Consensus 271 IA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~ 350 (499)
+|++|.+++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++|+++++.+|+|.++.+.+++++++...
T Consensus 102 iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~~~~~~l~~~~~~ 181 (324)
T PRK07921 102 LAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRE 181 (324)
T ss_pred HHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HH-HcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHH
Q 010835 351 LE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEV 429 (499)
Q Consensus 351 L~-~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L 429 (499)
|. ++|++||.+|||+.+|++.++|..++.....++|||.++ +++++.++.++++|.. ..+|++.+...++...|
T Consensus 182 l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~----~~~~~~~l~d~l~d~~-~~~pe~~~~~~~~~~~l 256 (324)
T PRK07921 182 LHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPV----GSDEEAPLGDFIEDSE-ATSAENAVIAGLLHTDI 256 (324)
T ss_pred HHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCC----CCCCCchHHHHhcCCC-CCCHHHHHHHHHHHHHH
Confidence 85 789999999999999999999999988888899999974 2333446788888764 35788888888899999
Q ss_pred HHHHHhhCCHHHHHHHHHHhcCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhh
Q 010835 430 NKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAML 496 (499)
Q Consensus 430 ~~~L~~~L~~rER~VI~LryGLd-~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~l~~~l 496 (499)
..+| ..||++|+.||.+||||+ .+++|++|||+.||||+++|||++.+|++|||.......|+.|+
T Consensus 257 ~~~L-~~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~~~~~~l~~~~ 323 (324)
T PRK07921 257 RSVL-ATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSYA 323 (324)
T ss_pred HHHH-HhCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHHHHHHHHhh
Confidence 9999 899999999999999994 67899999999999999999999999999999999888888886
No 6
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=100.00 E-value=9.7e-52 Score=421.36 Aligned_cols=270 Identities=40% Similarity=0.641 Sum_probs=251.0
Q ss_pred hhHHHHHHhhccccCCCHHHHHHHHHHHHcCC-CcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHH
Q 010835 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGL-SLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVM 269 (499)
Q Consensus 191 ~~~~~yl~~i~~~~~Lt~eEe~eL~~~ik~Gd-~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~ 269 (499)
+.+..|+..+...|+|+++||..|+++++.|+ . ..|..+||++|+++|+
T Consensus 67 ~~~~~~~~~~~~~~~l~~~Ee~~la~~~~~g~~~------------------------------~~Ak~klv~snLRlVv 116 (342)
T COG0568 67 GRLSFYIRAIEAAPLLTPEEEKALARRLKRGERD------------------------------LDAKKKLVESNLRLVV 116 (342)
T ss_pred hhHHHHHHHHhhhcccChHHHHHHHHHHHcCCcc------------------------------HHHHHHHHHHHHHHHH
Confidence 67889999999999999999999999999995 2 1899999999999999
Q ss_pred HHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHH
Q 010835 270 SIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKL 349 (499)
Q Consensus 270 sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~ 349 (499)
+||++|.++|+++.||||||+|||++|+++|||++|++|+|||+||||++|.++|.+++|+||+|.|+.+.++++++..+
T Consensus 117 sIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrqaI~raI~~q~rtIRipvh~~e~~nkl~r~~r 196 (342)
T COG0568 117 SIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHQVELINKLRRVKR 196 (342)
T ss_pred HHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHHHHHHHHHHhcchhhHhHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999988
Q ss_pred HHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHH
Q 010835 350 RLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDE 428 (499)
Q Consensus 350 ~L~-~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~ 428 (499)
.+. +.|++|++++||+.+|+++++|..++.....++|||.++ +++++..+.++++|+.. .+|++.+....+.+.
T Consensus 197 ~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~i----g~ded~~l~d~leD~~~-~~p~~~~~~~~~~~~ 271 (342)
T COG0568 197 ELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPI----GDDEDSELGDFLEDDKS-VSPEDAVERESLKED 271 (342)
T ss_pred HHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcC----CCCcccHHHHHhhcCCc-CCHHHHHHHHHHHHH
Confidence 885 579999999999999999999999999999999999985 44455588999999863 489999999999999
Q ss_pred HHHHHHhh-CCHHHHHHHHHHhcCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH-HHHHHhhHHHhh
Q 010835 429 VNKLIIVT-LGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLK-HAARKKKMEAML 496 (499)
Q Consensus 429 L~~~L~~~-L~~rER~VI~LryGLd-~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR-~~L~~~~l~~~l 496 (499)
+...| .. |+|+|+.||++|||++ .++.|++|||+++|||+++|||++.+|++||| +.-....++.||
T Consensus 272 ~~~~L-~~~Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~isrERvRQIE~kAl~KLr~~~~~~~~~~~~l 341 (342)
T COG0568 272 LNEVL-AEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAKALRKLRRHPERSALLRSYL 341 (342)
T ss_pred HHHHH-HhcCCHHHHHHHHHHhccCCCCcchHHHHHHHhCCcHHHHHHHHHHHHHHHHHhhhhhhHHHHhh
Confidence 99999 77 9999999999999995 78999999999999999999999999999999 444555567776
No 7
>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=3.9e-51 Score=415.45 Aligned_cols=286 Identities=37% Similarity=0.644 Sum_probs=265.3
Q ss_pred hHHHHHHhhccccCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhcc---------ccccChhHHHhhhhhhHHHHHHHHH
Q 010835 192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGS---------SLRISRPELQSILMECSLAREKLVM 262 (499)
Q Consensus 192 ~~~~yl~~i~~~~~Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~---------~~~~~~~~l~~~l~~~~~A~e~LIe 262 (499)
.+..|+++|+++|+||++||.+|+++++.|-.+++.+.++++..|+ +++++..+|..++..|..|++.||.
T Consensus 2 ~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv~ 81 (298)
T TIGR02997 2 LVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMIK 81 (298)
T ss_pred cHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHHH
Confidence 4678999999999999999999999999999999999999999998 4679999999999988999999999
Q ss_pred HHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHH
Q 010835 263 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG 342 (499)
Q Consensus 263 ~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~ 342 (499)
.|+++|++||++|.++|.+++||+||||+|||+|+++|||.+|++|+|||+||||++|.+++.++++++|+|.+....++
T Consensus 82 ~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~~~~~~~~ 161 (298)
T TIGR02997 82 ANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLN 161 (298)
T ss_pred HhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHH
Q 010835 343 LIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVD 421 (499)
Q Consensus 343 ~irka~~~L~-~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve 421 (499)
+++++...+. .+|+.|+.+|||+.+|++.++|..++.....++|||.++ +++++.++.+.+.+. ..+|++.+.
T Consensus 162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~----~~~~~~~~~~~~~~~--~~~pe~~~~ 235 (298)
T TIGR02997 162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPV----GDEEDTELGDLLEDD--GESPEEQVE 235 (298)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCc----CCCCcchHHHhccCC--CCCHHHHHH
Confidence 9999988884 789999999999999999999999999888999999874 233334566666664 357888888
Q ss_pred HHHHHHHHHHHHHhhCCHHHHHHHHHHhcCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010835 422 DWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLK 484 (499)
Q Consensus 422 ~~el~~~L~~~L~~~L~~rER~VI~LryGLd-~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR 484 (499)
..+....|..+| +.|||+||.||.+||||+ .+++|++|||+.||||++||+|++++|++|||
T Consensus 236 ~~~~~~~L~~~L-~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr 298 (298)
T TIGR02997 236 RESLRQDLESLL-AELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298 (298)
T ss_pred HHHHHHHHHHHH-HcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 889999999999 899999999999999984 68999999999999999999999999999996
No 8
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=7e-51 Score=417.04 Aligned_cols=298 Identities=35% Similarity=0.596 Sum_probs=275.3
Q ss_pred hhHHHHHHhhccccCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhcc---------ccccChhHHHhhhhhhHHHHHHHH
Q 010835 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGS---------SLRISRPELQSILMECSLAREKLV 261 (499)
Q Consensus 191 ~~~~~yl~~i~~~~~Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~---------~~~~~~~~l~~~l~~~~~A~e~LI 261 (499)
|.+..||++|+++|+||++||.+|+++++.|-.++..+..+.+.+|+ +++|+..+|..++.++..|++.||
T Consensus 8 ~~~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~L~ 87 (317)
T PRK07405 8 DLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRKMV 87 (317)
T ss_pred cHHHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHHHH
Confidence 67889999999999999999999999999999999999999999998 467999999999998889999999
Q ss_pred HHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHH
Q 010835 262 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 341 (499)
Q Consensus 262 e~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l 341 (499)
..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|+|||+||||++|.++|.++++++|+|.++...+
T Consensus 88 ~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~~~~ 167 (317)
T PRK07405 88 EANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKL 167 (317)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchH
Q 010835 342 GLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGV 420 (499)
Q Consensus 342 ~~irka~~~L~-~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~v 420 (499)
++++++...+. .+|+.|+++|||+.+|++.++|.+++.....+.|||.++ +++++.++.+.+++.. .+|++.+
T Consensus 168 ~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~----~~~~~~~l~~~~~d~~--~~pe~~~ 241 (317)
T PRK07405 168 NKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRV----GDNQDTELGELLEDTG--ASPEDFA 241 (317)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCC----CCCCCccHHHhhcCCC--CCHHHHH
Confidence 99999998885 789999999999999999999999998888899999874 2333456777777653 4788888
Q ss_pred HHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhhh
Q 010835 421 DDWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV 497 (499)
Q Consensus 421 e~~el~~~L~~~L~~~L~~rER~VI~LryGLd-~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~l~~~l~ 497 (499)
+..++...|..+| +.|||+||.||.+||||+ ++++|++|||+.||||++||+|++.+|++|||+. ...+..|+.
T Consensus 242 ~~~~~~~~l~~al-~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~--~~~l~~~~~ 316 (317)
T PRK07405 242 TQSSLQLDLERLM-EDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKR--KANIQEYLA 316 (317)
T ss_pred HHHHHHHHHHHHH-HcCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence 8899999999999 899999999999999994 6899999999999999999999999999999995 456777764
No 9
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=4.3e-50 Score=418.72 Aligned_cols=272 Identities=36% Similarity=0.600 Sum_probs=254.3
Q ss_pred HhhhHHHHHHhhccccCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHH
Q 010835 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLV 268 (499)
Q Consensus 189 ~~~~~~~yl~~i~~~~~Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV 268 (499)
..|.++.||++|++.|+||++++.+|+++++.||. .|++.||..|+++|
T Consensus 94 ~~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~Gd~-------------------------------~A~~~Li~~~~~lV 142 (367)
T PRK09210 94 INDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGDE-------------------------------EAKQRLAEANLRLV 142 (367)
T ss_pred cCcHHHHHHHHhhccCCCCHHHHHHHHHHHHhhHH-------------------------------HHHHHHHHHHHHHH
Confidence 34799999999999999999999999999999998 99999999999999
Q ss_pred HHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHH
Q 010835 269 MSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAK 348 (499)
Q Consensus 269 ~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~ 348 (499)
+++|++|.+++.+++||+|||++|||+|+++|||.+|++|+|||+||||++|.++|+++.|++|+|.|+.+.++++.++.
T Consensus 143 ~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~~~~~~~~~~~~ 222 (367)
T PRK09210 143 VSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQ 222 (367)
T ss_pred HHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred HHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHH
Q 010835 349 LRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKD 427 (499)
Q Consensus 349 ~~L~-~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~ 427 (499)
+.+. ++|++||++|||+.+|+++++|.+++.....++|||.++ +++++..+.++++|... .+|++.+....+..
T Consensus 223 ~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~----~~~~~~~l~d~i~d~~~-~~p~~~~~~~~~~~ 297 (367)
T PRK09210 223 RQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPI----GEEDDSHLGDFIEDQDA-TSPADHAAYELLKE 297 (367)
T ss_pred HHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCC----CCCCcchhhhhccCCCC-CCHHHHHHHHHHHH
Confidence 8884 799999999999999999999999999888899999874 23344567888887753 57888888999999
Q ss_pred HHHHHHHhhCCHHHHHHHHHHhcCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhhh
Q 010835 428 EVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV 497 (499)
Q Consensus 428 ~L~~~L~~~L~~rER~VI~LryGLd-~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~l~~~l~ 497 (499)
.|..+| ..||++||.||.+||||+ ++++|++|||+.||||++||||++.+||+|||+......|+.|++
T Consensus 298 ~l~~~l-~~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~~~~~~~l~~~~~ 367 (367)
T PRK09210 298 QLEDVL-DTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 367 (367)
T ss_pred HHHHHH-HhCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhChHHHhHHHHhhC
Confidence 999999 999999999999999984 688999999999999999999999999999999999999999874
No 10
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=1.4e-46 Score=415.89 Aligned_cols=272 Identities=31% Similarity=0.584 Sum_probs=252.7
Q ss_pred hHHHHHHhhccccCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHHH
Q 010835 192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSI 271 (499)
Q Consensus 192 ~~~~yl~~i~~~~~Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sI 271 (499)
.++.||+++...+.|+++++..++++++.|+. .+..|.++||..|+|+|++|
T Consensus 345 ~lq~~L~~ie~~~~Ls~eElk~l~~~i~~g~~----------------------------~~~~a~~~Li~~nlrlV~~i 396 (619)
T PRK05658 345 KLQQELEAIEEETGLTIEELKEINRQISKGEA----------------------------KARRAKKEMVEANLRLVISI 396 (619)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHHhccch----------------------------hhhHHHHHHHHHHHHHHHHH
Confidence 56789999999999999999999999999985 22378999999999999999
Q ss_pred HhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHH
Q 010835 272 AQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL 351 (499)
Q Consensus 272 A~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L 351 (499)
|++|.++|++++||||||+|||++|+++|||.+|++|+|||+||||++|.++|++++|++|+|+|+.+.+++++++.+.+
T Consensus 397 A~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~irip~~~~~~~~k~~~~~~~~ 476 (619)
T PRK05658 397 AKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 476 (619)
T ss_pred HHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCceecCHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998888
Q ss_pred -HHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHH
Q 010835 352 -EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVN 430 (499)
Q Consensus 352 -~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~ 430 (499)
+++|++||+++||+.+|++.++|..++.....++|||.++ +++++.++.++++|... .+|.+.+....+...|.
T Consensus 477 ~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i----~~~~~~~l~d~i~d~~~-~~p~~~~~~~~~~~~l~ 551 (619)
T PRK05658 477 LQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPI----GDDEDSHLGDFIEDKNA-ELPIDAAIQESLREATT 551 (619)
T ss_pred HHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCC----CCCCCCchhhhcCCCCC-CChHHHHHHHHHHHHHH
Confidence 5799999999999999999999999999888999999974 33444578889988753 57888888889999999
Q ss_pred HHHHhhCCHHHHHHHHHHhcCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhhh
Q 010835 431 KLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV 497 (499)
Q Consensus 431 ~~L~~~L~~rER~VI~LryGLd-~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~l~~~l~ 497 (499)
.+| ..||++|+.||++||||+ .+++|++|||+.||||+++|||++.+|++|||+......|+.||+
T Consensus 552 ~~l-~~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr~~~~~~~l~~~~~ 618 (619)
T PRK05658 552 DVL-ASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRSFLD 618 (619)
T ss_pred HHH-HcCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHhchHHHHHHHHHhc
Confidence 999 999999999999999996 578999999999999999999999999999999999999999986
No 11
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=7.6e-43 Score=352.66 Aligned_cols=266 Identities=29% Similarity=0.440 Sum_probs=227.8
Q ss_pred cCChHHHhhhHHHHHHhhccccCCCHHHHHHHHHHH-HcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHH
Q 010835 183 MISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKI-KTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLV 261 (499)
Q Consensus 183 ~~~~e~~~~~~~~yl~~i~~~~~Lt~eEe~eL~~~i-k~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LI 261 (499)
+.+|+ +.+..|++++.++|+++.+++.+|+.++ +.||. .|++.||
T Consensus 9 ~~~~~---~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~~Gd~-------------------------------~a~~~Lv 54 (284)
T PRK06596 9 ALSPE---GNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDL-------------------------------EAAKQLV 54 (284)
T ss_pred CCCCc---cHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCCH-------------------------------HHHHHHH
Confidence 36677 7899999999999999999999999995 68997 9999999
Q ss_pred HHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHH--
Q 010835 262 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHE-- 339 (499)
Q Consensus 262 e~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e-- 339 (499)
..|+|+|+++|++|.+++.+.+||+|||++||++|+++|||++|++|+|||+|||+++|.++++++++++++|.+...
T Consensus 55 ~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~p~~~~~~~ 134 (284)
T PRK06596 55 LSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQRK 134 (284)
T ss_pred HHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeeeccchHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999999888999998653
Q ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhh-ccccccccccCCCCCCCCCCccccccccccCCCCCcc
Q 010835 340 RLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI-GKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWH 418 (499)
Q Consensus 340 ~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~-~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee 418 (499)
....+++....+. .+++|+.+|||+.||++.++|.+++... ..+.|||.+... +++++.++.+.+.+.. .+|++
T Consensus 135 ~~~~~~~~~~~l~-~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~--~~~~~~~l~~~l~d~~--~~p~~ 209 (284)
T PRK06596 135 LFFNLRKAKKRLG-WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDD--DDEESGAPQDYLEDKS--SDPAD 209 (284)
T ss_pred HHHHHHHHHHHhc-cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCC--CCCCcchHHHHcCCCC--CCchH
Confidence 2245555555554 4689999999999999999999987643 578999997421 1112235677777763 46776
Q ss_pred hHHHH----HHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010835 419 GVDDW----ALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 489 (499)
Q Consensus 419 ~ve~~----el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~ 489 (499)
.++.. ++...|..+| +.||++||.||.+|||.+ +++|++|||+.||||++||+|++.+|++|||+.+..
T Consensus 210 ~~~~~~~~~~~~~~L~~al-~~L~~rEr~VL~lry~~~-~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~l~~ 282 (284)
T PRK06596 210 VLEEDNWEDQRRALLADAL-EGLDERSRDIIEARWLDD-DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEA 282 (284)
T ss_pred HHHHHHHHHHHHHHHHHHH-hcCCHHHHHHHHHHhcCC-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 66654 3577899999 899999999999999533 689999999999999999999999999999998764
No 12
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=100.00 E-value=6.4e-43 Score=359.37 Aligned_cols=268 Identities=34% Similarity=0.579 Sum_probs=244.7
Q ss_pred HhhhHHHHHHhhccccCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHH
Q 010835 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLV 268 (499)
Q Consensus 189 ~~~~~~~yl~~i~~~~~Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV 268 (499)
..|.++.|+++|+..|+||++++..|+.+++.||. .|++.||..|.++|
T Consensus 51 ~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~Gd~-------------------------------~A~~~Li~~y~~~V 99 (325)
T PRK05657 51 VLDATQLYLNEIGYSPLLTAEEEVYFARRALRGDF-------------------------------AARQRMIESNLRLV 99 (325)
T ss_pred cccHHHHHHHHHhcCCCCCHHHHHHHHHHHHcCCH-------------------------------HHHHHHHHHhHHHH
Confidence 44789999999999999999999999999999998 99999999999999
Q ss_pred HHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHH
Q 010835 269 MSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAK 348 (499)
Q Consensus 269 ~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~ 348 (499)
+++|++|.+++.+++||+||||+++|+++++||+.+|++|+||++||||++|.++++++.+.+++|.++.+.++.+.++.
T Consensus 100 ~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~~~~~~l~~~~R~~ 179 (325)
T PRK05657 100 VKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVKELNVYLRAA 179 (325)
T ss_pred HHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999888777777
Q ss_pred HHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHH
Q 010835 349 LRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKD 427 (499)
Q Consensus 349 ~~L~-~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~ 427 (499)
..++ ..|+.|+.++||+.+|+++++|.+++.....+.|||.+. ++++..++.+.+.+... .+|+..+...+...
T Consensus 180 ~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~----~~~~~~~l~d~l~d~~~-~~pe~~~~~~e~~~ 254 (325)
T PRK05657 180 RELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPL----GGDPEKSLLDILADEQE-NGPEDTTQDDDMKQ 254 (325)
T ss_pred HHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCC----CCCCCcchhhhccCCCC-CCHHHHHHHHHHHH
Confidence 7775 679999999999999999999999998888889999863 33344456677776542 47888888888899
Q ss_pred HHHHHHHhhCCHHHHHHHHHHhcC-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHH
Q 010835 428 EVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKME 493 (499)
Q Consensus 428 ~L~~~L~~~L~~rER~VI~LryGL-d~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~l~ 493 (499)
.|..+| ..||+++|.||.++||| +++|+|++|||+.||||++||++++++|+++||+.+...++.
T Consensus 255 ~L~~aL-~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~~~~~~ 320 (325)
T PRK05657 255 SIVKWL-FELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQGLS 320 (325)
T ss_pred HHHHHH-HcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhCccc
Confidence 999999 99999999999999999 479999999999999999999999999999999999876653
No 13
>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=3e-43 Score=346.38 Aligned_cols=236 Identities=37% Similarity=0.641 Sum_probs=216.9
Q ss_pred HHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccc
Q 010835 256 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN 335 (499)
Q Consensus 256 A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~ 335 (499)
|+++||..|+++|+++|++|.+++.+++||+|||++||++|+++|||++|++|+|||+||||++|.++++++.+.+++|.
T Consensus 1 a~~~Li~~~~~lv~~ia~~~~~~~~~~eDLiQeG~igL~~A~~~fd~~~g~~FstYA~~~Ir~~I~~~l~~~~~~vrip~ 80 (238)
T TIGR02393 1 AKKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80 (238)
T ss_pred CHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCChHHHhHHHHHHHHHHHHHHcCCcEEeCH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCC
Q 010835 336 HLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 414 (499)
Q Consensus 336 ~~~e~l~~irka~~~L~-~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~ 414 (499)
++.+.++++.++...+. +.|++||.+|||+.+|++.++|.+++.....++|||.++ +++++.++.+.+.|+.. .
T Consensus 81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~----~~~~~~~l~d~l~d~~~-~ 155 (238)
T TIGR02393 81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPI----GEEEDSFLGDFIEDTSI-E 155 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCC----CCCCcccHHHHhcCCCC-C
Confidence 99999999999988885 789999999999999999999999988887899999874 22333467777877653 5
Q ss_pred CCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHH
Q 010835 415 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKME 493 (499)
Q Consensus 415 ~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd-~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~l~ 493 (499)
+|++.+...+....|..+| ..||++||.||.++|||+ ++++|++|||+.||||+++|+|++.+|++|||+.+....++
T Consensus 156 ~p~~~~~~~~~~~~l~~~l-~~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~~~~~~ 234 (238)
T TIGR02393 156 SPDDYAAKELLREQLDEVL-ETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLK 234 (238)
T ss_pred ChHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHHHhHHH
Confidence 7888888888999999999 899999999999999994 68999999999999999999999999999999999999998
Q ss_pred Hhhh
Q 010835 494 AMLV 497 (499)
Q Consensus 494 ~~l~ 497 (499)
.|++
T Consensus 235 ~~~~ 238 (238)
T TIGR02393 235 SFLD 238 (238)
T ss_pred HhhC
Confidence 8874
No 14
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=3.8e-42 Score=348.43 Aligned_cols=263 Identities=25% Similarity=0.358 Sum_probs=224.3
Q ss_pred hhHHHHHHhhccccCCCHHHHHHHHHHHH-cCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHH
Q 010835 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIK-TGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVM 269 (499)
Q Consensus 191 ~~~~~yl~~i~~~~~Lt~eEe~eL~~~ik-~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~ 269 (499)
+..+.||++|.++|+||++++.+|+.+++ .||. .|+++||..|.|+|+
T Consensus 6 ~~~~~y~~~~~~~~~l~~~~e~~L~~~~~~~gd~-------------------------------~A~~~Lv~~~~~lV~ 54 (289)
T PRK07500 6 SADRSMIRSAMKAPYLEREEEHALAYRWKDHRDE-------------------------------DALHRIISAHMRLVI 54 (289)
T ss_pred hHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCCCH-------------------------------HHHHHHHHHhHHHHH
Confidence 45677999999999999999999999974 7887 999999999999999
Q ss_pred HHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHH--HHHHHHHH
Q 010835 270 SIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHE--RLGLIRNA 347 (499)
Q Consensus 270 sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e--~l~~irka 347 (499)
++|++|.+++.+++||+||||+|||+++++|||.+|.+|+|||+||||++|.++++++++.+|+|.+..+ ...++++.
T Consensus 55 ~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~~~~~~~~~~~~~~~ 134 (289)
T PRK07500 55 SMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRL 134 (289)
T ss_pred HHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCccHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999998765 33455555
Q ss_pred HHHHH----HcCCCCCHHHHHHHhCCCHHHHHHHHHh-hccccccccccCCCCCCCCCCccccccccccCCCCCcchHHH
Q 010835 348 KLRLE----EKGVTPSVDRIAEYLNMSQKKVRNATEA-IGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDD 422 (499)
Q Consensus 348 ~~~L~----~~gr~pt~eEIA~~Lgis~e~v~~~l~~-~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~ 422 (499)
...++ .+|+.|+.+|||+.||++.++|..+... ...+.|||.+... +++.+.++.+++.++. .+|++.++.
T Consensus 135 ~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~--~~~~~~~l~d~i~d~~--~~pe~~~~~ 210 (289)
T PRK07500 135 RARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSE--EDEGRSERMDFLVDDS--PLPDEQVES 210 (289)
T ss_pred HHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCC--CCCCcccHHHhccCCC--CCchHHHHH
Confidence 55553 4799999999999999999999887643 4578999987421 1112235677887764 357665543
Q ss_pred ----HHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010835 423 ----WALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 490 (499)
Q Consensus 423 ----~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~ 490 (499)
.+....|..+| +.||++||.||.++|+ +.+++|++|||+.||||++||+|++++|+++||..+...
T Consensus 211 ~~~~~~~~~~l~~al-~~L~~rer~vl~lr~~-~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~~~ 280 (289)
T PRK07500 211 SIDGERRRRWLTQAL-QTLNERELRIIRERRL-REDGATLEALGEELGISKERVRQIEARALEKLRRALLSQ 280 (289)
T ss_pred HHHHHHHHHHHHHHH-hcCCHHHHHHHHHHhc-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 34567788999 8999999999999983 238999999999999999999999999999999998754
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=1.3e-41 Score=341.12 Aligned_cols=259 Identities=28% Similarity=0.466 Sum_probs=216.9
Q ss_pred hHHHHHHhhccccCCCHHHHHHHHHH-HHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHH
Q 010835 192 RLKGYVKGVVSEELLTHAEVVRLSKK-IKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMS 270 (499)
Q Consensus 192 ~~~~yl~~i~~~~~Lt~eEe~eL~~~-ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~s 270 (499)
++..||++|..+|+++++++.+|+.+ .+.||. .|++.||..|+|+|++
T Consensus 2 ~~~~yl~~~~~~~~l~~~~e~~l~~~~~~~gd~-------------------------------~a~~~Lv~~~~~lV~~ 50 (270)
T TIGR02392 2 SLDAYIRAVNRIPMLTPEEEYQLAKRLREHGDL-------------------------------DAAKKLVLSHLRFVVK 50 (270)
T ss_pred hHHHHHHHHhcCCCCCHHHHHHHHHHHHHCCCH-------------------------------HHHHHHHHHhHHHHHH
Confidence 56789999999999999999999999 568987 9999999999999999
Q ss_pred HHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHH--HHHHHHHHH
Q 010835 271 IAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHE--RLGLIRNAK 348 (499)
Q Consensus 271 IA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e--~l~~irka~ 348 (499)
+|++|.+++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.+++++.++.+|+|.+... ...+++++.
T Consensus 51 ~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir~p~~~~~~~~~~~~~~~~ 130 (270)
T TIGR02392 51 IARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKLFFNLRKMK 130 (270)
T ss_pred HHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCceecCchHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999888999987542 334555555
Q ss_pred HHHHHcCCCC-CHHHHHHHhCCCHHHHHHHHHhh-ccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHH---
Q 010835 349 LRLEEKGVTP-SVDRIAEYLNMSQKKVRNATEAI-GKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDW--- 423 (499)
Q Consensus 349 ~~L~~~gr~p-t~eEIA~~Lgis~e~v~~~l~~~-~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~--- 423 (499)
..+. .++.| +.+|||+.||++.++|.++.... ..+.|||.++.. ++++..++.+.+.+.. .+|++.++..
T Consensus 131 ~~~~-~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~--~~~~~~~~~~~l~d~~--~~pe~~~~~~~~~ 205 (270)
T TIGR02392 131 KRLQ-GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDD--DEDDGGAPIAYLVDKT--SDPEDTLEEEQWE 205 (270)
T ss_pred HHHh-cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCC--CCCccccHHHHhcCCC--CChHHHHHHHHHH
Confidence 5443 22556 59999999999999999986644 347899987421 1111124566777654 3677666543
Q ss_pred -HHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010835 424 -ALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 488 (499)
Q Consensus 424 -el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~ 488 (499)
++...|..+| ..||++||.||.++||. .+++|++|||+.||||+++|+|++.+|++|||+.+.
T Consensus 206 ~~~~~~L~~al-~~L~~rer~vl~l~y~~-~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~l~ 269 (270)
T TIGR02392 206 ELQRQALANAL-GSLDARSRRIIEARWLD-DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAALA 269 (270)
T ss_pred HHHHHHHHHHH-HcCCHHHHHHHHHHhcC-CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 3567899999 89999999999999942 358999999999999999999999999999999764
No 16
>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=2.9e-40 Score=333.65 Aligned_cols=274 Identities=33% Similarity=0.532 Sum_probs=243.7
Q ss_pred ccCChHHHhhhHHHHHHhhccccCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHH
Q 010835 182 SMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLV 261 (499)
Q Consensus 182 ~~~~~e~~~~~~~~yl~~i~~~~~Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LI 261 (499)
++.+.....++++.||.+|..+|.|+.+++.+|+.++++||. .|++.||
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~gd~-------------------------------~a~~~L~ 52 (285)
T TIGR02394 4 KAETETRVADVTQLYLREIGFKPLLTAEEEIAYARRALAGDF-------------------------------EARKVMI 52 (285)
T ss_pred hhhcccCcchHHHHHHHHHhccCCCCHHHHHHHHHHHHcCCH-------------------------------HHHHHHH
Confidence 333333456899999999999999999999999999999998 9999999
Q ss_pred HHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHH
Q 010835 262 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 341 (499)
Q Consensus 262 e~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l 341 (499)
..|.++|+++|++|.+++.+++||+|||++|||+++++|||.+|++|+||+.|||+.++.+++.++.+.+++|.++.+..
T Consensus 53 ~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain~~i~~~~~~~~~p~~~~~~~ 132 (285)
T TIGR02394 53 ESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVIKEL 132 (285)
T ss_pred HHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHHHHHHHcCCceeCcHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchH
Q 010835 342 GLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGV 420 (499)
Q Consensus 342 ~~irka~~~L~-~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~v 420 (499)
+.+.+..+.+. ..|++|+..++|+.+|++..++..++....+..|+|.+. ++++...+.+.+.++. ..+|++.+
T Consensus 133 ~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~----~~~~~~~~~~~~~~~~-~~~pe~~~ 207 (285)
T TIGR02394 133 NVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPL----DDDSSKSLLDTIADEQ-SIDPESLV 207 (285)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCC----CCCCCcchhhhhcCCC-CCCHHHHH
Confidence 88777766654 579999999999999999999999999888889998753 2222233445555443 24788888
Q ss_pred HHHHHHHHHHHHHHhhCCHHHHHHHHHHhcC-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010835 421 DDWALKDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM 492 (499)
Q Consensus 421 e~~el~~~L~~~L~~~L~~rER~VI~LryGL-d~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~l 492 (499)
...+....|..+| ..||+++|.||.|+||| +++++|++|||+.||+|.+||++++++|+++||+.+...+.
T Consensus 208 ~~~e~~~~L~~al-~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~~~~~ 279 (285)
T TIGR02394 208 QNDDLKQLIEAWL-AELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERDGV 279 (285)
T ss_pred HHHHHHHHHHHHH-HcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 8899999999999 99999999999999998 58999999999999999999999999999999999976544
No 17
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=1.2e-39 Score=326.14 Aligned_cols=220 Identities=25% Similarity=0.373 Sum_probs=196.7
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 334 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip 334 (499)
.++++||..|+|+|++||++|.++|++.+||+|||+|||++|+++|||++|++|+|||+||||++|.++++++.+++|+|
T Consensus 40 ~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I~~~lr~~~~~ir~P 119 (264)
T PRK07122 40 RQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVP 119 (264)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHcCCccccC
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHh--hccccccccccCCCCCCCCC-Cccccccccc
Q 010835 335 NHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEA--IGKVFSLDREAFPSLNGLPG-ETHHSYIADN 410 (499)
Q Consensus 335 ~~~~e~l~~irka~~~L~-~~gr~pt~eEIA~~Lgis~e~v~~~l~~--~~~~~SLD~~~~~~~~~~e~-~~l~e~i~d~ 410 (499)
.++.+.+++++++...+. ++|++||++|||+.||+++++|.+++.. ...+.|||.+... ++++ ..+.+.+
T Consensus 120 r~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~---~~~~~~~~~d~~--- 193 (264)
T PRK07122 120 RRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGS---GDDDARAIADTL--- 193 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccC---CCCCcccchhcc---
Confidence 999999999999988885 7999999999999999999999998865 3568999997421 1111 1233322
Q ss_pred cCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010835 411 RVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 487 (499)
Q Consensus 411 ~~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L 487 (499)
.+|+..++..+....|..+| ..||+++|.||.++| ++++|++|||+.||+|+++|++++++|+++||..+
T Consensus 194 ---~~~~~~~e~~~~~~~l~~~l-~~L~~rer~vl~l~y---~~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l 263 (264)
T PRK07122 194 ---GDVDAGLDQIENREALRPLL-AALPERERTVLVLRF---FESMTQTQIAERVGISQMHVSRLLAKTLARLRDQL 263 (264)
T ss_pred ---CCcHHHHHHHHHHHHHHHHH-HcCCHHHHHHHHHHh---cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHc
Confidence 24555667777888899999 999999999999999 79999999999999999999999999999999876
No 18
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=2.7e-38 Score=314.91 Aligned_cols=226 Identities=27% Similarity=0.373 Sum_probs=195.9
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCC-CCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNM-GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 333 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~-g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRi 333 (499)
.|+++||..|+|+|+++|++|.+. +.+++||+|||+||||+|+++|||++|++|+|||+|||+++|.++++++.+++|+
T Consensus 25 ~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~~vr~ 104 (256)
T PRK07408 25 ALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRI 104 (256)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcCCeeee
Confidence 899999999999999999999875 6779999999999999999999999999999999999999999999999999999
Q ss_pred cccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHh--hccccccccccCCCCCCCCCCccccccccc
Q 010835 334 PNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEA--IGKVFSLDREAFPSLNGLPGETHHSYIADN 410 (499)
Q Consensus 334 p~~~~e~l~~irka~~~L~-~~gr~pt~eEIA~~Lgis~e~v~~~l~~--~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~ 410 (499)
|.++.+.+++++++...+. ++|++|+++|||+.+|+++++|..++.. .....|||.+... +++....+.+.++++
T Consensus 105 pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~--~~~~~~~l~d~~~d~ 182 (256)
T PRK07408 105 PRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQ--DEDGSTSLGDLLPDP 182 (256)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCC--CCCCccccccccCCc
Confidence 9999999999999998885 7899999999999999999999998653 3568899987421 111122455565554
Q ss_pred cCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010835 411 RVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 490 (499)
Q Consensus 411 ~~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~ 490 (499)
.. .+. ....+....|..+| ..||+++|.||.++| ++++|++|||+.||+|+++|++++.+|+++||+.+..+
T Consensus 183 ~~--~~~--~~~~~~~~~l~~~l-~~L~~~~r~vl~l~y---~~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~~~ 254 (256)
T PRK07408 183 RY--RSF--QLAQEDRIRLQQAL-AQLEERTREVLEFVF---LHDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQPE 254 (256)
T ss_pred cc--chh--hhhHHHHHHHHHHH-HcCCHHHHHHHHHHH---HCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhcc
Confidence 31 121 12345567799999 899999999999999 79999999999999999999999999999999988654
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=6.6e-38 Score=311.43 Aligned_cols=243 Identities=29% Similarity=0.409 Sum_probs=213.8
Q ss_pred hccccCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHHHHhHhhCCC
Q 010835 200 VVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMG 279 (499)
Q Consensus 200 i~~~~~Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sIA~ry~~~g 279 (499)
..++|+||++++.+|+.+++.||. .|++.|+..|.++|+++|++|.+++
T Consensus 10 ~~~~~~l~~~~~~~li~~~~~gd~-------------------------------~a~~~L~~~~~~~v~~~a~~~~~~~ 58 (254)
T TIGR02850 10 TSKLPVLKNQEMRELFIRMQSGDT-------------------------------TAREKLINGNLRLVLSVIQRFNNRG 58 (254)
T ss_pred ccCCCCCCHHHHHHHHHHHHcCCH-------------------------------HHHHHHHHHhHHHHHHHHHHHhCCC
Confidence 357899999999999999999998 9999999999999999999999999
Q ss_pred CCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHH-HHcCCCC
Q 010835 280 ADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL-EEKGVTP 358 (499)
Q Consensus 280 ~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L-~~~gr~p 358 (499)
.+++||+|||++|||+++++|||.+|.+|.||+++||++.|.+++++.. .+|+|.+..+..+++.++...+ .++|++|
T Consensus 59 ~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~-~ir~p~~~~~~~~~~~~~~~~l~~~l~~~p 137 (254)
T TIGR02850 59 EYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDKLISENSKEP 137 (254)
T ss_pred CCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CccCchHHHHHHHHHHHHHHHHHHHhCCCC
Confidence 9999999999999999999999999999999999999999999999975 7899999999999988888777 4789999
Q ss_pred CHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHHHHHhhCC
Q 010835 359 SVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLG 438 (499)
Q Consensus 359 t~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~ 438 (499)
+++|||+.+|+++++|..++.....+.|||.++..+ +++..++.+.+.++. .+. ........+..++ ..||
T Consensus 138 t~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~--~~~~~~~~~~~~d~~---~~~---~~~~~~~~l~~~l-~~L~ 208 (254)
T TIGR02850 138 TVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYND--GGDPIYVMDQISDEK---NKD---SQWLEGIALKEAM-KRLN 208 (254)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCC--CCCcchhhhhcCCcc---ccH---HHHHhHHHHHHHH-HcCC
Confidence 999999999999999999999888888999875321 112234556665542 121 2333456788889 8999
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010835 439 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA 486 (499)
Q Consensus 439 ~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~ 486 (499)
+++|.||.++| ++++|++|||+.||+|+++|++++.+|+++||+.
T Consensus 209 ~rer~vi~~~~---~~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~~ 253 (254)
T TIGR02850 209 EREKMILNMRF---FEGKTQMEVAEEIGISQAQVSRLEKAALKHMRKY 253 (254)
T ss_pred HHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 99999999999 7999999999999999999999999999999975
No 20
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=100.00 E-value=2.2e-37 Score=308.60 Aligned_cols=227 Identities=27% Similarity=0.409 Sum_probs=200.1
Q ss_pred HHHHHHHHHHHHHHHHHHhHhh---CCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYD---NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 331 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~---~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~v 331 (499)
.|++.||..|+|+|+++|++|. ..+++.+||+|||++|||+|+++|||++|++|+|||+||||++|.+++++..+
T Consensus 23 ~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~-- 100 (257)
T PRK05911 23 EYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQDW-- 100 (257)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCC--
Confidence 8999999999999999999986 24578999999999999999999999999999999999999999999999865
Q ss_pred cccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHhhc--cccccccccCCCCCCCCCCccccccc
Q 010835 332 RLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDREAFPSLNGLPGETHHSYIA 408 (499)
Q Consensus 332 Rip~~~~e~l~~irka~~~L~-~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~--~~~SLD~~~~~~~~~~e~~~l~e~i~ 408 (499)
+|+++.+.++++..+...+. ++|++|+++|||+.+|++.++|..++.... .++|||.+.....+++++.++.+.++
T Consensus 101 -~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~~~~~~~~~l~~~l~ 179 (257)
T PRK05911 101 -VPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQSDDEAGLALEERIA 179 (257)
T ss_pred -CCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCCCCCccccchhhhcc
Confidence 89999999999999988885 789999999999999999999999887653 46899986432222233445777887
Q ss_pred cccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010835 409 DNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 488 (499)
Q Consensus 409 d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~ 488 (499)
|... .+|++.+...+....|..+| ..|||++|.||.++| ++++|++|||+.||+|+++|++++++|+++||+.+.
T Consensus 180 d~~~-~~~~~~~~~~~~~~~l~~al-~~L~~~er~vi~l~y---~e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l~ 254 (257)
T PRK05911 180 DERA-ETGYDVVDKKEFSSILAEAI-LALEEKERKVMALYY---YEELVLKEIGKILGVSESRVSQIHSKALLKLRATLS 254 (257)
T ss_pred CCCC-CCHHHHHHHHHHHHHHHHHH-HcCCHHHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 7653 46778888888889999999 999999999999999 899999999999999999999999999999999875
Q ss_pred H
Q 010835 489 K 489 (499)
Q Consensus 489 ~ 489 (499)
.
T Consensus 255 ~ 255 (257)
T PRK05911 255 A 255 (257)
T ss_pred h
Confidence 4
No 21
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=100.00 E-value=6.6e-37 Score=304.80 Aligned_cols=244 Identities=28% Similarity=0.419 Sum_probs=212.8
Q ss_pred hccccCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHHHHhHhhCCC
Q 010835 200 VVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMG 279 (499)
Q Consensus 200 i~~~~~Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sIA~ry~~~g 279 (499)
..++|+|+++++..|+.+++.||. .|+++||..|.|+|+++|++|.+++
T Consensus 13 ~~~~~~l~~~~~~~l~~~~~~gd~-------------------------------~a~~~l~~~~~~~v~~~a~~~~~~~ 61 (258)
T PRK08215 13 TSKLPVLKNEEMRELFERMQNGDK-------------------------------EAREKLINGNLRLVLSVIQRFNNRG 61 (258)
T ss_pred CCCCCCCCHHHHHHHHHHHHcCCH-------------------------------HHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 346789999999999999999998 9999999999999999999999999
Q ss_pred CCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHH-HcCCCC
Q 010835 280 ADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTP 358 (499)
Q Consensus 280 ~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L~-~~gr~p 358 (499)
.+++||+|||++|||+++++|||.+|.+|.||+++||+++|.+++++.. .+++|.+......++.++...+. +.|++|
T Consensus 62 ~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~~-~vrip~~~~~~~~~~~~~~~~l~~~~~r~p 140 (258)
T PRK08215 62 ENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREKLINENSKEP 140 (258)
T ss_pred CCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-ceEecHHHHHHHHHHHHHHHHHHHHhCCCC
Confidence 9999999999999999999999999999999999999999999999985 78999999998888888877774 789999
Q ss_pred CHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHHHHHhhCC
Q 010835 359 SVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLG 438 (499)
Q Consensus 359 t~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~ 438 (499)
++.|||+.+|+++++|..++.....+.|||.+..++ +++..++.+.+.++. .+ .+.......+..+| +.||
T Consensus 141 ~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~--~~~~~~~~~~~~~~~---~~---~~~~~~~~~l~~~l-~~L~ 211 (258)
T PRK08215 141 TVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHD--GGDPIYVMDQISDEK---NK---DENWLEEIALKEAM-KKLN 211 (258)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCC--CCcchhhhhhccCcc---cc---HHHHHhHHHHHHHH-HcCC
Confidence 999999999999999999988877888999875322 111223445554432 11 23334456788889 8999
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010835 439 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 487 (499)
Q Consensus 439 ~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L 487 (499)
++++.||.++| ++++|++|||+.||+|+++|++++.+|+++||+.|
T Consensus 212 ~~er~vi~~~~---~~~~t~~eIA~~lgis~~~V~~~~~~al~kLr~~l 257 (258)
T PRK08215 212 DREKLILNLRF---FQGKTQMEVAEEIGISQAQVSRLEKAALKHMRKYI 257 (258)
T ss_pred HHHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 99999999999 79999999999999999999999999999999876
No 22
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=100.00 E-value=5e-37 Score=302.78 Aligned_cols=240 Identities=34% Similarity=0.483 Sum_probs=214.9
Q ss_pred ccCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHHHHhHhhCCCC-C
Q 010835 203 EELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGA-D 281 (499)
Q Consensus 203 ~~~Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sIA~ry~~~g~-d 281 (499)
.+.++..+...+....+.|+. .+. .||+.|+|||.+||++|.+++. +
T Consensus 3 ~~~~~~~e~~~~~~~~~~g~~-------------------------------~~~-~Li~~ylpLV~~ia~k~~~r~~~~ 50 (247)
T COG1191 3 PQPLSKEEEEKLLEYYAEGDE-------------------------------EAR-RLIERYLPLVKSIARKFENRGPSE 50 (247)
T ss_pred CcccchHHHHHHHHHHHhcCH-------------------------------HHH-HHHHHHHHHHHHHHHHHHhcCCCc
Confidence 356778888889999999997 888 9999999999999999998777 9
Q ss_pred HHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHH-HcCCCCCH
Q 010835 282 MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSV 360 (499)
Q Consensus 282 ~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L~-~~gr~pt~ 360 (499)
.+||+|.|++||++|+++|||++|.+|+|||.++|+++|.+++|++. .+++|+.+.+..+++..+...++ ++||+||+
T Consensus 51 ~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~LR~~~-~v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~ 129 (247)
T COG1191 51 YDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKND-SVKVPRSLRELGRRIEEAIDELEQELGREPTD 129 (247)
T ss_pred hhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHHHHhCC-CccCcHHHHHHHHHHHHHHHHHHHHhCCCCcH
Confidence 99999999999999999999999999999999999999999999999 99999999999999999999996 79999999
Q ss_pred HHHHHHhCCCHHHHHHHHHhhc--cccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHHHHHhhCC
Q 010835 361 DRIAEYLNMSQKKVRNATEAIG--KVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLG 438 (499)
Q Consensus 361 eEIA~~Lgis~e~v~~~l~~~~--~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~ 438 (499)
.|||+.||++.++|..++.... ...|+|..... .+++. +.+ . ..+|.+.++.+++...|.+++ ..|+
T Consensus 130 ~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~---~~d~~-----~~~-~-~~~~~~~~~~~~~~~~l~~ai-~~L~ 198 (247)
T COG1191 130 EEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLK---DDDDD-----VDD-Q-IENPDDGVEKEELLEILKEAI-EPLP 198 (247)
T ss_pred HHHHHHhCCCHHHHHHHHHHhccccccchhhhhcc---ccccc-----hhh-c-cccchhHHHHHHHHHHHHHHH-HccC
Confidence 9999999999999999988874 67888875321 11111 111 1 247888889999999999999 6999
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010835 439 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 489 (499)
Q Consensus 439 ~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~ 489 (499)
++||.|+.+|| ++++|++|||+.||||+++|+|++.+|+++||+.|..
T Consensus 199 EREk~Vl~l~y---~eelt~kEI~~~LgISes~VSql~kkai~kLr~~l~~ 246 (247)
T COG1191 199 EREKLVLVLRY---KEELTQKEIAEVLGISESRVSRLHKKAIKKLRKELNK 246 (247)
T ss_pred HHHHHHHHHHH---HhccCHHHHHHHhCccHHHHHHHHHHHHHHHHHHhcc
Confidence 99999999999 8999999999999999999999999999999998753
No 23
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=100.00 E-value=2.7e-35 Score=292.41 Aligned_cols=242 Identities=27% Similarity=0.348 Sum_probs=213.0
Q ss_pred cCCCHHHHHHHHHHHHc-CCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHHHHhHhhCCCCCH
Q 010835 204 ELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADM 282 (499)
Q Consensus 204 ~~Lt~eEe~eL~~~ik~-Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~ 282 (499)
|.||++++.+|+.+++. ||. .|+++|+..|.|+|+.+|++|.+++.++
T Consensus 8 ~~l~~~~~~~li~~~~~~gd~-------------------------------~a~~~l~~~y~~~v~~~a~~~~~~~~~a 56 (255)
T TIGR02941 8 TNLTKEDVIQWIAEFQQNQNG-------------------------------EAQEKLVDHYQNLVYSIAYKYSKGGPMH 56 (255)
T ss_pred CCCCHHHHHHHHHHHHHCCCH-------------------------------HHHHHHHHHhHHHHHHHHHHHhcCCCCH
Confidence 67899999999999988 676 8999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHH-HcCCCCCHH
Q 010835 283 ADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVD 361 (499)
Q Consensus 283 EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L~-~~gr~pt~e 361 (499)
+||+||||++||+++++|+++.|.+|.||+++||++.|.+++++..+.+++|.+..+..++++++...+. .+|+.|+.+
T Consensus 57 eDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~iri~~~~~~~~~~~~~~~~~l~~~~~r~p~~~ 136 (255)
T TIGR02941 57 EDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDHLQRSPKII 136 (255)
T ss_pred HHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHHHHHHHHhCCCCCHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999988886 679999999
Q ss_pred HHHHHhCCCHHHHHHHHHhh--ccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHHHHHhhCCH
Q 010835 362 RIAEYLNMSQKKVRNATEAI--GKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGE 439 (499)
Q Consensus 362 EIA~~Lgis~e~v~~~l~~~--~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~ 439 (499)
+||+.+|++.+++..++... ....|||.++..+ ++......+ +. ..+|++.+...+....+..+| +.||+
T Consensus 137 eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~----~~~~~~~~~-~~--~~~~~~~~~~~e~~~~l~~~l-~~L~~ 208 (255)
T TIGR02941 137 EIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEAD----SDGSTVARL-DS--VGEVEDGYDQTERRMVLEKIL-PILSE 208 (255)
T ss_pred HHHHHhCCCHHHHHHHHHHHhccCCccccccccCC----CCCcccccc-cc--cCCcchHHHHHHHHHHHHHHH-HcCCH
Confidence 99999999999998877654 4678898875321 111111111 11 124666777788888899999 99999
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010835 440 REREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 487 (499)
Q Consensus 440 rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L 487 (499)
++|.||.++| ++|+|++|||+.||+|.+||++++++|+++||+.+
T Consensus 209 ~~r~ii~l~~---~~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~ 253 (255)
T TIGR02941 209 REKSIIHCTF---EENLSQKETGERLGISQMHVSRLQRQAISKLKEAA 253 (255)
T ss_pred HHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 9999999999 89999999999999999999999999999999875
No 24
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=100.00 E-value=2.1e-35 Score=295.68 Aligned_cols=251 Identities=26% Similarity=0.315 Sum_probs=218.5
Q ss_pred hccccCCCHHHHHHHHHHHHc-CCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHHHHhHhhC-
Q 010835 200 VVSEELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDN- 277 (499)
Q Consensus 200 i~~~~~Lt~eEe~eL~~~ik~-Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sIA~ry~~- 277 (499)
.+++|+||.+++.+|+.+++. ||. .|++.|+..|.|+|+.+|++|..
T Consensus 6 ~~~~~~~~~~~e~~l~~~~~~~~d~-------------------------------~a~~~l~~~y~~lv~~~a~~~~~~ 54 (268)
T PRK06288 6 SGKIPKYAQQDETELWREYKKTGDP-------------------------------KIREYLILKYSPLVKYVAGRIAVG 54 (268)
T ss_pred cCCCccccchHHHHHHHHHHHcCCH-------------------------------HHHHHHHHHHHHHHHHHHHHHHhc
Confidence 468899999999999999764 676 89999999999999999999862
Q ss_pred --CCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHH-Hc
Q 010835 278 --MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EK 354 (499)
Q Consensus 278 --~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L~-~~ 354 (499)
.+.+++||+|||++|||+++++||+.+|.+|.||+++|||+.|.+++++. .++|.+.....++++++...|+ ++
T Consensus 55 ~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~---~~~p~~~~~~~~~i~~~~~~l~~~~ 131 (268)
T PRK06288 55 MPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSI---DWIPRSVRQKARQIERAIAMLEARL 131 (268)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhc---CccCHHHHHHHHHHHHHHHHHHHHH
Confidence 56889999999999999999999999888999999999999999999865 4589999888889999988885 78
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhh--ccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHHH
Q 010835 355 GVTPSVDRIAEYLNMSQKKVRNATEAI--GKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKL 432 (499)
Q Consensus 355 gr~pt~eEIA~~Lgis~e~v~~~l~~~--~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~~ 432 (499)
|++|+.+|||+.+|++.+++.+++... ....|||.+... .++.+..++.+.+.++. .++|++.++..+....|..+
T Consensus 132 ~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~-~~~~~~~~l~~~~~~~~-~~~pe~~~~~~e~~~~l~~~ 209 (268)
T PRK06288 132 GRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFG-GDEGDEVSLMDTLESPA-ALNPDEIAEREEIKRVIVEA 209 (268)
T ss_pred CCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhcc-CCCcccchhhhhccCCC-CCCHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999988755 457888886431 11222334566666544 35788888888889999999
Q ss_pred HHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010835 433 IIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 490 (499)
Q Consensus 433 L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~ 490 (499)
| ..||+++|.||.++| ++++|++|||+.||+|.++|++++.+|+++||+.+...
T Consensus 210 l-~~L~~~~r~vl~l~~---~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~~~ 263 (268)
T PRK06288 210 I-KTLPEREKKVLILYY---YEDLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLAEI 263 (268)
T ss_pred H-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 9 899999999999999 89999999999999999999999999999999998654
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=1e-34 Score=283.99 Aligned_cols=221 Identities=33% Similarity=0.402 Sum_probs=191.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccc
Q 010835 254 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 333 (499)
Q Consensus 254 ~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRi 333 (499)
..|++.|+..|.|+|+++|++|.+++.+++||+|||++|||+++++|||.+|.+|.||+++||++.|.++++++. .+++
T Consensus 10 ~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~~~-~i~~ 88 (231)
T TIGR02885 10 KEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDG-IIKV 88 (231)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-CeEC
Confidence 399999999999999999999999999999999999999999999999999889999999999999999999986 7899
Q ss_pred cccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccC
Q 010835 334 PNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRV 412 (499)
Q Consensus 334 p~~~~e~l~~irka~~~L~-~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~ 412 (499)
|+++.....+++++...+. ++|+.|+.+|||+.+|++.+++..++.....+.|||.+...+ +++..++.+.+.++.
T Consensus 89 p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~--~~~~~~~~d~~~~~~- 165 (231)
T TIGR02885 89 SRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQD--DGDPIYLLDQIADKG- 165 (231)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCC--CCCcchhhhhcCCCC-
Confidence 9999999999999888885 689999999999999999999999988877888998874311 111223445555432
Q ss_pred CCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010835 413 ENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 487 (499)
Q Consensus 413 e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L 487 (499)
+++ ........+.+++ ..||++++.||.++| ++++|++|||+.||+|+++|++++++|+++||..|
T Consensus 166 --~~~---~~~~~~~~l~~~l-~~L~~~e~~i~~~~~---~~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~l 231 (231)
T TIGR02885 166 --SED---SDWLEKIALKEAI-SKLDERERQIIMLRY---FKDKTQTEVANMLGISQVQVSRLEKKVLKKMKEKL 231 (231)
T ss_pred --ccH---HhHHHHHHHHHHH-HcCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHhC
Confidence 122 2233456788889 999999999999999 79999999999999999999999999999999753
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=3.7e-34 Score=279.08 Aligned_cols=222 Identities=33% Similarity=0.401 Sum_probs=194.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccc
Q 010835 254 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 333 (499)
Q Consensus 254 ~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRi 333 (499)
..|++.|+..|.|+|+++|++|.+++.+.+||+|||++|||+|+++||+.+|.+|+||+++||++.|.++++++.+.+++
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 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHhhcc--ccccccccCCCCCCCCCCccccccccc
Q 010835 334 PNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGK--VFSLDREAFPSLNGLPGETHHSYIADN 410 (499)
Q Consensus 334 p~~~~e~l~~irka~~~L~-~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~--~~SLD~~~~~~~~~~e~~~l~e~i~d~ 410 (499)
|.+..+..+++.++...+. .+|++|+.+|+|+.+|++.+++..++..... ..|||.++. + +++...++.+.+
T Consensus 82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~-~-~~~~~~~~~d~~--- 156 (227)
T TIGR02980 82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIE-D-DDGDPIALLDTL--- 156 (227)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCC-C-CCCCCccccccc---
Confidence 9999999999999888885 6899999999999999999999998887644 889998742 1 111111222222
Q ss_pred cCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010835 411 RVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 487 (499)
Q Consensus 411 ~~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L 487 (499)
.+|++.++..+....|..+| ..||++++.||.++| ++|+|++|||+.||+|+++|++++++|+++||+.+
T Consensus 157 ---~~~~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~y---~~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~l 226 (227)
T TIGR02980 157 ---GDEDDALETVEDRLALKPLL-AALPERERRILLLRF---FEDKTQSEIAERLGISQMHVSRLLRRALKKLREQL 226 (227)
T ss_pred ---CCcchHHHhHHHHHHHHHHH-HcCCHHHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 24555566667788899999 999999999999999 79999999999999999999999999999999865
No 27
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=9.6e-34 Score=281.01 Aligned_cols=223 Identities=28% Similarity=0.386 Sum_probs=193.3
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhC---CCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 331 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~---~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~v 331 (499)
.|++.||..|.|+|+++|++|.+ ++.+.+||+||||+|||+++++|||++|.+|.||+++||+|.|.+++++..
T Consensus 22 ~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~d~lR~~~--- 98 (251)
T PRK07670 22 DAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKED--- 98 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC---
Confidence 99999999999999999999975 689999999999999999999999999999999999999999999999876
Q ss_pred cccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHh--hccccccccccCCCCCCCCCCccccccc
Q 010835 332 RLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEA--IGKVFSLDREAFPSLNGLPGETHHSYIA 408 (499)
Q Consensus 332 Rip~~~~e~l~~irka~~~L~-~~gr~pt~eEIA~~Lgis~e~v~~~l~~--~~~~~SLD~~~~~~~~~~e~~~l~e~i~ 408 (499)
++|.+..+.+++++.+...+. ..|+.|+..|||+.+|++.++|..++.. .....|||.++. +++++..+.+.+.
T Consensus 99 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~---~~~~~~~~~~~~~ 175 (251)
T PRK07670 99 WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTH---DQDDGENVSVTIR 175 (251)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCcccc---CCCCcchhhhhhc
Confidence 589998888888888887774 7899999999999999999999998763 467899998742 1222222333333
Q ss_pred cccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010835 409 DNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 488 (499)
Q Consensus 409 d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~ 488 (499)
+.. ..+|++.+...+....|..+| ..||+++|.||.|+| ++|+|++|||+.||+|.+||++++++|+++||..+.
T Consensus 176 ~~~-~~~~e~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~~---~~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~ 250 (251)
T PRK07670 176 DDK-TPTPEEKLLKEELIEELAEKI-KQLSEKEQLVISLFY---KEELTLTEIGQVLNLSTSRISQIHSKALFKLKKLLE 250 (251)
T ss_pred CcC-CCCHHHHHHHHHHHHHHHHHH-hcCCHHHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 332 246777777778888899999 999999999999999 899999999999999999999999999999999875
No 28
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=100.00 E-value=2.1e-33 Score=279.23 Aligned_cols=244 Identities=27% Similarity=0.327 Sum_probs=212.1
Q ss_pred cCCCHHHHHHHHHHHHc-CCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHHHHhHhhCCCCCH
Q 010835 204 ELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADM 282 (499)
Q Consensus 204 ~~Lt~eEe~eL~~~ik~-Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~ 282 (499)
|.|+++++..|+.+++. ||. .|++.||..|.++|+++|++|.+++.++
T Consensus 8 ~~l~~~e~~~li~~~~~~gd~-------------------------------~a~~~l~~~~~~~v~~~a~~~~~~~~~a 56 (257)
T PRK08583 8 TKLTKEEVNKWIAEYQENQDE-------------------------------EAQEKLVKHYKNLVESLAYKYSKGQSHH 56 (257)
T ss_pred CcCChHHHHHHHHHHHHcCCH-------------------------------HHHHHHHHHHHHHHHHHHHHHhcCCCCH
Confidence 77999999999999985 787 9999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHH-HcCCCCCHH
Q 010835 283 ADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVD 361 (499)
Q Consensus 283 EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L~-~~gr~pt~e 361 (499)
+||+||||++||+++++||+..|.+|.||+++||+|.|.+++++..+.+++|++..+..+++..+...+. ..++.|+.+
T Consensus 57 eDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~~~i~r~~~~~~~~~~~~~~~~~~~~~r~~~~~ 136 (257)
T PRK08583 57 EDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKIS 136 (257)
T ss_pred HHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHHHHHHhcCCCcCCCHHHHHHHHHHHHHHHHHHHHhCCCCCHH
Confidence 9999999999999999999998889999999999999999999999999999999998888888887775 678999999
Q ss_pred HHHHHhCCCHHHHHHHHHhh--ccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHHHHHhhCCH
Q 010835 362 RIAEYLNMSQKKVRNATEAI--GKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGE 439 (499)
Q Consensus 362 EIA~~Lgis~e~v~~~l~~~--~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~ 439 (499)
++|+.+|++.+++..+.... ....|+|.++..+.++ ....+.+. ..+|++.+...+....+..+| ..||+
T Consensus 137 e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~~~-~~~~~~~~------~~~~e~~~~~~~~~~~l~~~l-~~L~~ 208 (257)
T PRK08583 137 EIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDG-STVTLLDI------VGQQEDGYELTEQRMILEKIL-PVLSD 208 (257)
T ss_pred HHHHHhCCCHHHHHHHHHHhccCCceecCccccCCCCC-ccchHhhh------cCCcchhHHHHHHHHHHHHHH-HhCCH
Confidence 99999999999998876653 3577888764211110 11111121 135677777778888899999 89999
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010835 440 REREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 489 (499)
Q Consensus 440 rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~ 489 (499)
++|.||.++| ++|+|++|||+.||||++||++++++|+++||+.+..
T Consensus 209 ~~r~vl~l~~---~~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l~~ 255 (257)
T PRK08583 209 REKSIIQCTF---IENLSQKETGERLGISQMHVSRLQRQAIKKLREAAFL 255 (257)
T ss_pred HHHHHHHHHH---hCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 9999999999 8999999999999999999999999999999998754
No 29
>PRK05572 sporulation sigma factor SigF; Validated
Probab=100.00 E-value=2.2e-33 Score=278.55 Aligned_cols=243 Identities=33% Similarity=0.413 Sum_probs=210.6
Q ss_pred hccccCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHHHHhHhhCCC
Q 010835 200 VVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMG 279 (499)
Q Consensus 200 i~~~~~Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sIA~ry~~~g 279 (499)
-...|.||.+++.+|+.+++.||. .|++.|+..|.++|+++|++|.+++
T Consensus 8 ~~~~~~l~~~~~~~li~~~~~gd~-------------------------------~a~~~L~~~y~~~v~~~a~~~~~~~ 56 (252)
T PRK05572 8 KKKKPQLKDEENKELIKKSQDGDQ-------------------------------EARDTLVEKNLRLVWSVVQRFLNRG 56 (252)
T ss_pred CcCCCCCCHHHHHHHHHHHHcCCH-------------------------------HHHHHHHHHhHHHHHHHHHHHccCC
Confidence 346799999999999999999998 9999999999999999999999999
Q ss_pred CCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHH-HcCCCC
Q 010835 280 ADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTP 358 (499)
Q Consensus 280 ~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L~-~~gr~p 358 (499)
.+++||+|||++++|+++++|++.++.+|.||+++||++.|.+++++.. .+++|.+......+++++...+. +.|+.|
T Consensus 57 ~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~~~-~~r~~~~~~~~~~~~~~~~~~l~~~~~r~p 135 (252)
T PRK05572 57 YEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDKDELSKELGREP 135 (252)
T ss_pred CCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CCCCCHHHHHHHHHHHHHHHHHHHHHCcCC
Confidence 9999999999999999999999988889999999999999999999884 78999999999999999988875 679999
Q ss_pred CHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHHHHHhhCC
Q 010835 359 SVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLG 438 (499)
Q Consensus 359 t~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~ 438 (499)
++.|+|+.+|++.+++..+......+.||+.+...+ +....++.+.+.++. + ........|..++ +.||
T Consensus 136 ~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~--~~~~~~~~d~~~~~~-----~---~~~~~~~~l~~~l-~~L~ 204 (252)
T PRK05572 136 TIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHEN--DGDPITLLDQIADQS-----E---EDWFDKIALKEAI-RELD 204 (252)
T ss_pred CHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccC--CCCcchhhhhcCCCc-----h---hhHHHHHHHHHHH-HcCC
Confidence 999999999999999999888877888998764211 111112233333221 1 1234466788899 9999
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010835 439 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 488 (499)
Q Consensus 439 ~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~ 488 (499)
++++.||.++| ++++|++|||+.+|+|+++|++++++|+++||+.+.
T Consensus 205 ~~~~~v~~l~~---~~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l~ 251 (252)
T PRK05572 205 ERERLIVYLRY---FKDKTQSEVAKRLGISQVQVSRLEKKILKQMKEKLD 251 (252)
T ss_pred HHHHHHHHHHH---hCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence 99999999999 799999999999999999999999999999998764
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=1e-32 Score=268.86 Aligned_cols=217 Identities=32% Similarity=0.470 Sum_probs=189.8
Q ss_pred HHHHHHHHHHHHHhHhhC---CCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccccc
Q 010835 260 LVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH 336 (499)
Q Consensus 260 LIe~yl~LV~sIA~ry~~---~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~ 336 (499)
|+..|.|+|+++|++|.+ ++.+++||+|||++|||+++++|||++|.+|+||+++||++.+.+++++.. ++|.+
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 578999999999999986 789999999999999999999999999999999999999999999998864 58888
Q ss_pred HHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHhh--ccccccccccCCCCCCCCCCccccccccccCC
Q 010835 337 LHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAI--GKVFSLDREAFPSLNGLPGETHHSYIADNRVE 413 (499)
Q Consensus 337 ~~e~l~~irka~~~L~-~~gr~pt~eEIA~~Lgis~e~v~~~l~~~--~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e 413 (499)
....++++.++...+. +.|++|+.+|||+.+|++.+.|..++... ....|+|... .++.++..+.++++++. .
T Consensus 78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~---~~~~~~~~~~~~~~~~~-~ 153 (224)
T TIGR02479 78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELL---ESGDDGGSLIDRIEDDK-S 153 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcc---cCCCccchhhhhccccc-c
Confidence 8888999999988885 78999999999999999999999998754 4567787742 11223334555555433 3
Q ss_pred CCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010835 414 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 487 (499)
Q Consensus 414 ~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L 487 (499)
.+|++.+...+....|..+| ..||+++|.||.++| ++|+|++|||+.||+|.++|++++++|+++||+.+
T Consensus 154 ~~~~~~~~~~~~~~~l~~~l-~~L~~~~r~il~l~y---~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 223 (224)
T TIGR02479 154 EDPEEELEREELREALAEAI-ESLSEREQLVLSLYY---YEELNLKEIGEVLGLTESRVSQIHSQALKKLRAKL 223 (224)
T ss_pred CCHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---hCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHc
Confidence 47888888888899999999 999999999999999 89999999999999999999999999999999875
No 31
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=100.00 E-value=1.8e-31 Score=262.22 Aligned_cols=210 Identities=20% Similarity=0.313 Sum_probs=175.7
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhC---CCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 331 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~---~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~v 331 (499)
.....|+..|.|+|+++|++|.. .+.+.+||+|||++|||+|+++|||..+ +|+||++|||||+|.+++++..+
T Consensus 15 ~~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~~-- 91 (231)
T PRK12427 15 QEEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELDW-- 91 (231)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcCC--
Confidence 45568899999999999999874 5689999999999999999999998655 89999999999999999998643
Q ss_pred cccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHh--hccccccccccCCCCCCCCCCccccccc
Q 010835 332 RLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEA--IGKVFSLDREAFPSLNGLPGETHHSYIA 408 (499)
Q Consensus 332 Rip~~~~e~l~~irka~~~L~-~~gr~pt~eEIA~~Lgis~e~v~~~l~~--~~~~~SLD~~~~~~~~~~e~~~l~e~i~ 408 (499)
+|+++....++++++...+. ++|++|+.+|||+.||++.++|.+++.. ...+.|||.+...+ ++ .+.+.
T Consensus 92 -~~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~----~~---~~~~~ 163 (231)
T PRK12427 92 -RPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALE----AH---NDILQ 163 (231)
T ss_pred -CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCC----Cc---ccccC
Confidence 67788888888988888884 7899999999999999999999998764 35689999975221 11 11121
Q ss_pred cccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010835 409 DNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA 486 (499)
Q Consensus 409 d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~ 486 (499)
+ .+|+ +.......|..+| ..||+++|.||.++| ++++|++|||+.||||+++|+|++.+|+++||..
T Consensus 164 ~----~~~~---~~~~~~~~l~~~l-~~L~~~er~vi~l~~---~~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr~~ 230 (231)
T PRK12427 164 S----RDLE---ENIIIEDNLKQAL-SQLDEREQLILHLYY---QHEMSLKEIALVLDLTEARICQLNKKIAQKIKSF 230 (231)
T ss_pred C----CCHH---HHHHHHHHHHHHH-HcCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 1 1233 2233566788899 899999999999999 7999999999999999999999999999999964
No 32
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=100.00 E-value=3e-31 Score=260.64 Aligned_cols=223 Identities=27% Similarity=0.425 Sum_probs=189.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHhHhh---CCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhh
Q 010835 253 CSLAREKLVMSNVRLVMSIAQRYD---NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR 329 (499)
Q Consensus 253 ~~~A~e~LIe~yl~LV~sIA~ry~---~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R 329 (499)
+.-+.++|+..|.++|+++|++|. +++.+++||+||||++||+++++|+|..|.+|.||+++||++.|.++++++.+
T Consensus 6 ~~~~~~~L~~~~~~~v~~~a~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~~~lR~~~~ 85 (236)
T PRK06986 6 GKMDQDELVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLDW 85 (236)
T ss_pred ccccHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHcCC
Confidence 447899999999999999999997 67899999999999999999999999988899999999999999999999864
Q ss_pred cccccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHhh--ccccccccccCCCCCCCCCCccccc
Q 010835 330 TLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAI--GKVFSLDREAFPSLNGLPGETHHSY 406 (499)
Q Consensus 330 ~vRip~~~~e~l~~irka~~~L~-~~gr~pt~eEIA~~Lgis~e~v~~~l~~~--~~~~SLD~~~~~~~~~~e~~~l~e~ 406 (499)
+|.+.......+.++...+. ..|++|+.++||+.+|++.++|..++... ....|++... ++ +++.+...
T Consensus 86 ---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~----~~-~~~~~~~~ 157 (236)
T PRK06986 86 ---VPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELR----GE-HGDSILVT 157 (236)
T ss_pred ---CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccc----cC-CCcccccc
Confidence 67777666666777766664 68999999999999999999999988864 4566777753 11 22222222
Q ss_pred cccccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010835 407 IADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA 486 (499)
Q Consensus 407 i~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~ 486 (499)
..+. .++|++.+...+....|..+| ..||+++|.||.++| ++|+|++|||+.||+|.++|++++++|+++||+.
T Consensus 158 ~~~~--~~~~~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~~---~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 158 EDHQ--DEDPLQQLEDEELREALVEAI-ESLPEREQLVLSLYY---QEELNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred cCCC--CCCHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHhHh---ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 2221 346777788888889999999 999999999999999 8999999999999999999999999999999998
Q ss_pred HHH
Q 010835 487 ARK 489 (499)
Q Consensus 487 L~~ 489 (499)
+..
T Consensus 232 l~~ 234 (236)
T PRK06986 232 LGE 234 (236)
T ss_pred Hhc
Confidence 754
No 33
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=99.97 E-value=1.1e-28 Score=242.27 Aligned_cols=213 Identities=30% Similarity=0.378 Sum_probs=174.1
Q ss_pred hHHHHHHhhccccCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHHH
Q 010835 192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSI 271 (499)
Q Consensus 192 ~~~~yl~~i~~~~~Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sI 271 (499)
++..|+.+++..|+||++++..|+..++.||. .|++.|+..|.++|+++
T Consensus 17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~gd~-------------------------------~a~~~l~~~y~~~l~~~ 65 (233)
T PRK05803 17 FLVSYVKNNSFPQPLSEEEERKYLELMKEGDE-------------------------------EARNILIERNLRLVAHI 65 (233)
T ss_pred HHHHHHHHhcccCCCCHHHHHHHHHHHHcCCH-------------------------------HHHHHHHHHhHHHHHHH
Confidence 78999999999999999999999999999998 99999999999999999
Q ss_pred HhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHH
Q 010835 272 AQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL 351 (499)
Q Consensus 272 A~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L 351 (499)
|.+|.+++.+++|++|||++++|+++++|+++++.+|.+|+++|+++.+.+++++..+..+
T Consensus 66 a~~~~~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~~~~------------------- 126 (233)
T PRK05803 66 VKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTKK------------------- 126 (233)
T ss_pred HHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhcccc-------------------
Confidence 9999999999999999999999999999999888899999999999999999887643100
Q ss_pred HHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHH
Q 010835 352 EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNK 431 (499)
Q Consensus 352 ~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~ 431 (499)
..+++....++ ++.....+.+...+. .++|++.+...+....|..
T Consensus 127 --------------------------------~~~~~~~~~~~-~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~l~~ 171 (233)
T PRK05803 127 --------------------------------EVSLQDPIGVD-KEGNEISLIDILGSE--EDDVIEQVELKMEVEKLYK 171 (233)
T ss_pred --------------------------------CCCccccccCC-CCcCcccHHHHccCC--CCCHHHHHHHHHHHHHHHH
Confidence 11111110000 000111222333322 1246666677777788999
Q ss_pred HHHhhCCHHHHHHHHHHhcCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010835 432 LIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 490 (499)
Q Consensus 432 ~L~~~L~~rER~VI~LryGLd-~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~ 490 (499)
+| ..||+++|+||.++|+++ ++|+|++|||+.||+|.+||++++++|+++||+.+...
T Consensus 172 ~l-~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~~~ 230 (233)
T PRK05803 172 KI-DILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKELYRA 230 (233)
T ss_pred HH-HhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 99 999999999999999774 58999999999999999999999999999999998653
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=99.94 E-value=2.2e-25 Score=218.16 Aligned_cols=210 Identities=29% Similarity=0.361 Sum_probs=163.9
Q ss_pred hHHHHHHhhccc-cCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHH
Q 010835 192 RLKGYVKGVVSE-ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMS 270 (499)
Q Consensus 192 ~~~~yl~~i~~~-~~Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~s 270 (499)
++-+|+...++. +.|++.++..|+.++++||. .|++.|+..|.|.|++
T Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~li~~~~~gd~-------------------------------~af~~l~~~y~~~v~~ 63 (227)
T TIGR02846 15 FLVGYVTNNGSFPQPLSEEEEKKYLDRLKEGDE-------------------------------EARNVLIERNLRLVAH 63 (227)
T ss_pred HHHHHHHHHHhCCCCCCHHHHHHHHHHHHcCCH-------------------------------HHHHHHHHHhHHHHHH
Confidence 456787766654 45899999999999999998 9999999999999999
Q ss_pred HHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHH
Q 010835 271 IAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLR 350 (499)
Q Consensus 271 IA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~ 350 (499)
+|.+|.++..+++|++||+|+++|+++++|+++.+.+|.||++++++|.+.+++++..+..+
T Consensus 64 ~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~Rk~~r~~~------------------ 125 (227)
T TIGR02846 64 IVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHLRALKKTKG------------------ 125 (227)
T ss_pred HHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHHHHHhcccc------------------
Confidence 99999999999999999999999999999999888889999999999999999988653100
Q ss_pred HHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHH
Q 010835 351 LEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVN 430 (499)
Q Consensus 351 L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~ 430 (499)
..+++...... .+.....+.+...+. .++|++.+...+....|.
T Consensus 126 ---------------------------------~~~~~~~~~~~-~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~l~ 169 (227)
T TIGR02846 126 ---------------------------------EVSLQDPIGVD-KEGNEISLIDILGSD--GDSVIEQVELNLEIKKLY 169 (227)
T ss_pred ---------------------------------ceeccccccCC-cccCcccHHHHhcCC--CCChHHHHHHHHHHHHHH
Confidence 00111100000 000001111111111 235666666666778899
Q ss_pred HHHHhhCCHHHHHHHHHHhcCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010835 431 KLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 487 (499)
Q Consensus 431 ~~L~~~L~~rER~VI~LryGLd-~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L 487 (499)
++| +.||+++|+||.|+|.++ ++++|++|||++||+|++||++++++|+++||+.|
T Consensus 170 ~~i-~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~~ 226 (227)
T TIGR02846 170 KKL-SVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYKEL 226 (227)
T ss_pred HHH-HhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 999 999999999999999332 38999999999999999999999999999999875
No 35
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=99.94 E-value=3.6e-25 Score=217.01 Aligned_cols=208 Identities=24% Similarity=0.379 Sum_probs=158.7
Q ss_pred HHHhhccc-cCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHHHHhH
Q 010835 196 YVKGVVSE-ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQR 274 (499)
Q Consensus 196 yl~~i~~~-~~Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sIA~r 274 (499)
|+.++... |.+++..+.+|+.+++.||. .|++.|+..|.++|+.+|++
T Consensus 23 ~~~~~~~~~~~~~~~~~~~L~~~~~~gd~-------------------------------~af~~l~~~y~~~l~~~a~~ 71 (234)
T PRK08301 23 YIGGSEALPPPLSKEEEEYLLNKLPKGDE-------------------------------AVRSLLIERNLRLVVYIARK 71 (234)
T ss_pred HhccccccCCcCCHHHHHHHHHHHHccCH-------------------------------HHHHHHHHHhHHHHHHHHHH
Confidence 55565433 45788889999999999998 99999999999999999999
Q ss_pred hhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHc
Q 010835 275 YDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK 354 (499)
Q Consensus 275 y~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L~~~ 354 (499)
|.+++.+++|++||+|+++|+++++|++..+++|.||++++++|.+.+++++..+...
T Consensus 72 ~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~d~lRk~~~~~~---------------------- 129 (234)
T PRK08301 72 FENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNNKVKA---------------------- 129 (234)
T ss_pred hhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHHHHHHhcccc----------------------
Confidence 9999999999999999999999999999887889999999999999999987653100
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHHHHH
Q 010835 355 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLII 434 (499)
Q Consensus 355 gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~~L~ 434 (499)
..+++.+.... .+.......+...+. ...+...+........|..+|
T Consensus 130 -----------------------------~~~~~~~~~~~-~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~l~~al- 176 (234)
T PRK08301 130 -----------------------------EVSFDEPLNID-WDGNELLLSDVLGTD--NDIIYKDIEDEVDRKLLKKAL- 176 (234)
T ss_pred -----------------------------ccccccccccc-cCCCcccHHHhccCc--ccchHHHHHHHHHHHHHHHHH-
Confidence 01111110000 000000011111111 112333344455566799999
Q ss_pred hhCCHHHHHHHHHHhcCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 489 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd-~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~ 489 (499)
+.||+++|.||.|+|+|. .+|+|++|||+.||+|.+||++++++|+++||+.+..
T Consensus 177 ~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l~~ 232 (234)
T PRK08301 177 KKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEINK 232 (234)
T ss_pred HhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999663 5899999999999999999999999999999998754
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=6.1e-24 Score=208.83 Aligned_cols=202 Identities=24% Similarity=0.354 Sum_probs=155.8
Q ss_pred cccCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHHHHhHhhCCCCC
Q 010835 202 SEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGAD 281 (499)
Q Consensus 202 ~~~~Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sIA~ry~~~g~d 281 (499)
..|.|+++++..|+..++.||. .|++.|+..|.+.|+++|++|.+++.+
T Consensus 30 ~~~~~~~~~~~~l~~~~~~~d~-------------------------------~a~~~l~~~y~~~l~~~~~~~~~~~~~ 78 (234)
T TIGR02835 30 LPPPLTGEEEEALLQKLTQGDE-------------------------------SAKSTLIERNLRLVVYIARKFENTGIG 78 (234)
T ss_pred CCCcCCHHHHHHHHHHHHcCCH-------------------------------HHHHHHHHHhHHHHHHHHHHhccCCCC
Confidence 4577888999999999999998 999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHcCCCCCHH
Q 010835 282 MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVD 361 (499)
Q Consensus 282 ~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L~~~gr~pt~e 361 (499)
++|++||+++++|+++++|++..+++|.+|++.+++|.+.+++++..+...
T Consensus 79 AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~d~~Rk~~r~~~----------------------------- 129 (234)
T TIGR02835 79 IEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILMYLRRNNKTRS----------------------------- 129 (234)
T ss_pred HHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhccccC-----------------------------
Confidence 999999999999999999998877889999999999999999988654100
Q ss_pred HHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHHHHHhhCCHHH
Q 010835 362 RIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGERE 441 (499)
Q Consensus 362 EIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~rE 441 (499)
..+++.+.... ..++.....+... .. .+.+.+.+........|..+| +.||+++
T Consensus 130 ----------------------~~~~~~~~~~~-~~~~~~~~~~~~~-~~-~~~~~~~~~~~~~~~~l~~ai-~~Lp~~~ 183 (234)
T TIGR02835 130 ----------------------EVSFDEPLNVD-WDGNELLLSDVLG-TD-SDIVYKYLEEEVDRELLRKAL-AKLNDRE 183 (234)
T ss_pred ----------------------cccccccccCC-CCCCcchHHHhcC-CC-CCcHHHHHHHHHHHHHHHHHH-HhCCHHH
Confidence 01111110000 0000000011111 11 112223344455667799999 9999999
Q ss_pred HHHHHHHhcCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010835 442 REIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 489 (499)
Q Consensus 442 R~VI~LryGLd-~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~ 489 (499)
|.||.|+|.+. ++|+|++|||+.||+|.+||++++++|+++||+.+..
T Consensus 184 R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l~~ 232 (234)
T TIGR02835 184 KKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKEINR 232 (234)
T ss_pred HHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhhc
Confidence 99999998542 4899999999999999999999999999999998754
No 37
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=99.91 E-value=2.1e-23 Score=199.66 Aligned_cols=182 Identities=21% Similarity=0.313 Sum_probs=138.0
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 334 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip 334 (499)
.|++.|++.|.++|+.+|++|.++..+++|++||+|+++|+++.+|++.++.+|.||++.++++.+.+++++..+..+.+
T Consensus 24 ~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n~~~d~~r~~~r~~~~~ 103 (208)
T PRK08295 24 EALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQIITAIKTANRQKHIP 103 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhhhhcccc
Confidence 99999999999999999999999999999999999999999999999987778999999999999888887654311111
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCC
Q 010835 335 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 414 (499)
Q Consensus 335 ~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~ 414 (499)
.. ...|.+.+. ..++.+..+.+.+.++. ..
T Consensus 104 ~~----------------------------------------------~~~s~~~~~---~~~~~~~~~~~~~~~~~-~~ 133 (208)
T PRK08295 104 LN----------------------------------------------SYVSLDKPI---YDEESDRTLLDVISEAK-VT 133 (208)
T ss_pred cc----------------------------------------------ceeecCCcc---cCCccchhHHHHhcCcc-cC
Confidence 00 011111110 00111112223333222 13
Q ss_pred CCcchHHHHHHHHHHH-HHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010835 415 NPWHGVDDWALKDEVN-KLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 491 (499)
Q Consensus 415 ~Pee~ve~~el~~~L~-~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~ 491 (499)
+|++.+...+....+. .++ ..||+.+|.||.+ | ++|+|++|||+.||+|++||+.+++||+++||+.+....
T Consensus 134 ~~~~~~~~~~~~~~l~~~~~-~~L~~~~r~vl~l-~---~e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l~~~~ 206 (208)
T PRK08295 134 DPEELIISKEELEDIEEKIE-ELLSELEKEVLEL-Y---LDGKSYQEIAEELNRHVKSIDNALQRVKRKLEKYLENRE 206 (208)
T ss_pred CHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHH-H---HccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence 6666665555555554 456 8999999999999 7 699999999999999999999999999999999987653
No 38
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=99.91 E-value=3.1e-23 Score=196.31 Aligned_cols=179 Identities=20% Similarity=0.207 Sum_probs=147.9
Q ss_pred CCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHHHHhHhhCC----CCC
Q 010835 206 LTHAEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNM----GAD 281 (499)
Q Consensus 206 Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sIA~ry~~~----g~d 281 (499)
+|+++...|+..++.||. .|++.|+..|.+.|+++|.+++++ +.+
T Consensus 6 ~~~~~~~~l~~~~~~gd~-------------------------------~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~ 54 (189)
T PRK09648 6 DTGEELDALVAEAVAGDR-------------------------------RALREVLEIIRPLVVRYCRARLGGVERPGLS 54 (189)
T ss_pred CCchHHHHHHHHHHcCCH-------------------------------HHHHHHHHHHHHHHHHHHHHHhcccccCCCC
Confidence 377888889999999998 999999999999999999999865 468
Q ss_pred HHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHcCCCCCHH
Q 010835 282 MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVD 361 (499)
Q Consensus 282 ~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L~~~gr~pt~e 361 (499)
++|++||+|+++|+++.+|++. +.+|.+|++..+++.+.+++++..+....+
T Consensus 55 aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~n~~~d~~r~~~r~~~~~--------------------------- 106 (189)
T PRK09648 55 ADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAAHKVADAHRAAGRDKAVP--------------------------- 106 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHHHHHHHHHHHhCCCcccc---------------------------
Confidence 9999999999999999999864 457999999999999988887765311000
Q ss_pred HHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHHHHHhhCCHHH
Q 010835 362 RIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGERE 441 (499)
Q Consensus 362 EIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~rE 441 (499)
.+. ..+...+ ..+|++.+...+....|..+| ..||+++
T Consensus 107 -------------------------~~~-------------~~~~~~~---~~~~~~~~~~~e~~~~l~~~l-~~L~~~~ 144 (189)
T PRK09648 107 -------------------------TEE-------------VPERPSD---DAGPEERALRSESSNRMRELL-DTLPEKQ 144 (189)
T ss_pred -------------------------ccc-------------ccccccc---CCCHHHHHHHHHHHHHHHHHH-HhCCHHH
Confidence 000 0000000 135666667777788899999 9999999
Q ss_pred HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010835 442 REIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 488 (499)
Q Consensus 442 R~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~ 488 (499)
|+||.++| ++|+|++|||+.||+|.+||+++++||+++||+.+.
T Consensus 145 r~i~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 188 (189)
T PRK09648 145 REILILRV---VVGLSAEETAEAVGSTPGAVRVAQHRALARLRAEIE 188 (189)
T ss_pred HHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 99999999 899999999999999999999999999999999874
No 39
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=99.91 E-value=3.3e-23 Score=197.37 Aligned_cols=185 Identities=14% Similarity=0.158 Sum_probs=149.0
Q ss_pred cccCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHHHHhHhhCCCCC
Q 010835 202 SEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGAD 281 (499)
Q Consensus 202 ~~~~Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sIA~ry~~~g~d 281 (499)
..|+....++..|+..+++||. .|+++|+..|.++|+++|.+|.++..+
T Consensus 8 ~~~~~~~~~~~~li~~~~~g~~-------------------------------~a~~~l~~~y~~~l~~~~~~~~~~~~d 56 (194)
T PRK09646 8 TGPPAESPDLDALLRRVARGDQ-------------------------------DAFAELYDRTSSRVYGLVRRVLRDPGY 56 (194)
T ss_pred cCCCCCcccHHHHHHHHHccCH-------------------------------HHHHHHHHHHHHHHHHHHHHHhCCHHH
Confidence 3466666677789999999998 999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHcCCCCCHH
Q 010835 282 MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVD 361 (499)
Q Consensus 282 ~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L~~~gr~pt~e 361 (499)
++|++||+|+++|+++++|++.++ .|.+|++..++|.+.++++++.+..+..
T Consensus 57 AeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~r~~~~~~~~~--------------------------- 108 (194)
T PRK09646 57 SEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHRRAVDRVRSEQAASQRE--------------------------- 108 (194)
T ss_pred HHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHHHHHHHHHhhccccccc---------------------------
Confidence 999999999999999999998655 6999999999998888887764310000
Q ss_pred HHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHHHHHhhCCHHH
Q 010835 362 RIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGERE 441 (499)
Q Consensus 362 EIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~rE 441 (499)
..... . +. +.. ..++++.+...+..+.+..+| ..||+++
T Consensus 109 -----------------------~~~~~-----------~---~~--~~~-~~~~~~~~~~~~~~~~l~~~l-~~L~~~~ 147 (194)
T PRK09646 109 -----------------------VRYGA-----------R---NV--DPA-FDQVAEEVEARLERERVRDCL-DALTDTQ 147 (194)
T ss_pred -----------------------ccccc-----------c---cc--ccc-ccchHHHHHHHhHHHHHHHHH-HhCCHHH
Confidence 00000 0 00 000 113344444556667899999 8999999
Q ss_pred HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010835 442 REIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 489 (499)
Q Consensus 442 R~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~ 489 (499)
|.||.|+| ++|+|++|||+.||+|.++|+++++||+++||+.+..
T Consensus 148 r~vl~l~~---~~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l~~ 192 (194)
T PRK09646 148 RESVTLAY---YGGLTYREVAERLAVPLGTVKTRMRDGLIRLRDCLGV 192 (194)
T ss_pred HHHHHHHH---HcCCCHHHHHHHhCCChHhHHHHHHHHHHHHHHHhcc
Confidence 99999999 8999999999999999999999999999999998853
No 40
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=99.91 E-value=5.9e-23 Score=193.88 Aligned_cols=161 Identities=16% Similarity=0.193 Sum_probs=133.8
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 334 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip 334 (499)
.|++.|+..|.++|+.+|+++.+++.+++|++||+|+++|+++.+|+++ +.+|.+|++..+++.+.++++++.+.
T Consensus 20 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n~~~d~~R~~~~~---- 94 (186)
T PRK05602 20 AAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLNLCYDRLRRRREV---- 94 (186)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHHHHHHHHHhcCCC----
Confidence 9999999999999999999999999999999999999999999999986 44799999999999888887765310
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCC
Q 010835 335 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 414 (499)
Q Consensus 335 ~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~ 414 (499)
+.+. ..+ ..+. ..
T Consensus 95 ---------------------------------------------------~~~~-------------~~~-~~~~--~~ 107 (186)
T PRK05602 95 ---------------------------------------------------PVED-------------APD-VPDP--AP 107 (186)
T ss_pred ---------------------------------------------------Cccc-------------ccc-cCCC--CC
Confidence 0000 000 0011 12
Q ss_pred CCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010835 415 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 491 (499)
Q Consensus 415 ~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~ 491 (499)
.|++.+...+....+..+| ..||+++|.||.|+| ++|+|++|||+.||+|++||+++++||+++||+.+...+
T Consensus 108 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 180 (186)
T PRK05602 108 GPDAGLEARQRARRVEQAL-AALPERQREAIVLQY---YQGLSNIEAAAVMDISVDALESLLARGRRALRAQLADLP 180 (186)
T ss_pred CHHHHHHHHHHHHHHHHHH-HhCCHHHHHHhhHHH---hcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 3555556666777899999 999999999999999 899999999999999999999999999999999997654
No 41
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=99.91 E-value=5.2e-23 Score=195.52 Aligned_cols=167 Identities=19% Similarity=0.199 Sum_probs=137.6
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 334 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip 334 (499)
.|++.|+..|.+.|+++|.++.++..+++|++||+|+++|+++.+|++.. .|.+|++.++++.+.+++++..+....+
T Consensus 26 ~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~~--~f~~wl~~i~~n~~~~~~R~~~~~~~~~ 103 (194)
T PRK12513 26 AAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRA--RFRTWLYQIARNLLIDHWRRHGARQAPS 103 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCCC--chHHHHHHHHHHHHHHHHHHhccccccc
Confidence 99999999999999999999999999999999999999999999999743 6999999999999999988775421110
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCC
Q 010835 335 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 414 (499)
Q Consensus 335 ~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~ 414 (499)
. +. +... ....+. ..
T Consensus 104 ~----------------------------------------------------~~----------~~~~-~~~~~~--~~ 118 (194)
T PRK12513 104 L----------------------------------------------------DA----------DEQL-HALADD--GA 118 (194)
T ss_pred c----------------------------------------------------cc----------chhh-hhcCCC--CC
Confidence 0 00 0000 000111 23
Q ss_pred CCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010835 415 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM 492 (499)
Q Consensus 415 ~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~l 492 (499)
+|+..++..+....+..+| +.||+++|.||.|+| ++|+|++|||++||+|+++|+++++||+++||+.+...++
T Consensus 119 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~~ 192 (194)
T PRK12513 119 APEQQLSLFRDRRRLQAAL-ETLPDEQREVFLLRE---HGDLELEEIAELTGVPEETVKSRLRYALQKLRELLAEEVA 192 (194)
T ss_pred CHHHHHHHHHHHHHHHHHH-HhCCHhHhhheeeeh---ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 5666666777788899999 999999999999999 8999999999999999999999999999999999987654
No 42
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=99.90 E-value=1.8e-22 Score=192.66 Aligned_cols=181 Identities=18% Similarity=0.199 Sum_probs=146.7
Q ss_pred CCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHH
Q 010835 206 LTHAEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADL 285 (499)
Q Consensus 206 Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDL 285 (499)
++...+..|+.++..||. .|++.|+..|.+.|+.+|.++.++..+++|+
T Consensus 8 ~~~~~~~~li~~~~~gd~-------------------------------~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDl 56 (196)
T PRK12524 8 LSDVSDEALLVLYANGDP-------------------------------AAARALTLRLAPRALAVATRVLGDRAEAEDV 56 (196)
T ss_pred CCCcCHHHHHHHHHCCCH-------------------------------HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHH
Confidence 344455678888888887 9999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHH
Q 010835 286 VQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAE 365 (499)
Q Consensus 286 iQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~ 365 (499)
+||+++++|+.+.+|++.. ..|.+|++..+++.+.+.+++..+.
T Consensus 57 vQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~n~~~d~~Rk~~~~----------------------------------- 100 (196)
T PRK12524 57 TQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVCNLCTDRLRRRRRA----------------------------------- 100 (196)
T ss_pred HHHHHHHHHHhhhcccccc-chHHHHHHHHHHHHHHHHHHhhcCC-----------------------------------
Confidence 9999999999999998533 4699999999999888887765320
Q ss_pred HhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHH
Q 010835 366 YLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREII 445 (499)
Q Consensus 366 ~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI 445 (499)
...++.. + +. .+. ..+|++.+...+....|..+| +.||+++|.||
T Consensus 101 ------------------~~~~~~~--------~-----~~-~~~--~~~~~~~~~~~~~~~~l~~~l-~~L~~~~r~i~ 145 (196)
T PRK12524 101 ------------------SVDLDDA--------P-----EP-ADA--APGAEEALIEGDRMRALDAAL-AALPERQRQAV 145 (196)
T ss_pred ------------------CCCcccc--------c-----cc-ccc--CCCHHHHHHHHHHHHHHHHHH-HhCCHHHHHHH
Confidence 0000000 0 00 011 123555566677778899999 89999999999
Q ss_pred HHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010835 446 RLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 491 (499)
Q Consensus 446 ~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~ 491 (499)
.|+| ++|++++|||+.||+|..||+++++||+++||+.+...+
T Consensus 146 ~L~~---~~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~~ 188 (196)
T PRK12524 146 VLRH---IEGLSNPEIAEVMEIGVEAVESLTARGKRALAALLAGQR 188 (196)
T ss_pred HHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 9999 899999999999999999999999999999999987643
No 43
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=99.90 E-value=1.6e-22 Score=198.25 Aligned_cols=193 Identities=19% Similarity=0.217 Sum_probs=157.0
Q ss_pred ccccCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHHHHhHhhCCCC
Q 010835 201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGA 280 (499)
Q Consensus 201 ~~~~~Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sIA~ry~~~g~ 280 (499)
...|+|+...+..|+..++.||. .|++.|+..|.+.|+++|.++.+++.
T Consensus 7 ~~~~~~~~~~~~~l~~~~~~gd~-------------------------------~a~~~l~~~y~~~l~~~a~~~~~~~~ 55 (231)
T PRK11922 7 SRPPPLSAASDRELVARVLAGDE-------------------------------AAFEALMRRHNRRLYRTARAILRNDA 55 (231)
T ss_pred CCCCCcCcccHHHHHHHHHcCCH-------------------------------HHHHHHHHHHHHHHHHHHHHHhCChh
Confidence 45689999999999999999998 99999999999999999999999999
Q ss_pred CHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHcCCCCCH
Q 010835 281 DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSV 360 (499)
Q Consensus 281 d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L~~~gr~pt~ 360 (499)
+++|++||+|+++|+++++|++. ..|.+|++..+++.+.+++++..+...++..
T Consensus 56 ~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~Rk~~r~~~~~~~------------------------ 109 (231)
T PRK11922 56 EAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNEALGRLRRRRRLVNLAEM------------------------ 109 (231)
T ss_pred hHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHHHHHHHHhhcccccchhc------------------------
Confidence 99999999999999999999975 3799999999999999888776542111000
Q ss_pred HHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHHHHHhhCCHH
Q 010835 361 DRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGER 440 (499)
Q Consensus 361 eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~r 440 (499)
.. .+...++ ......+ ...+|++.+...+..+.|..+| ..||++
T Consensus 110 ---------------------------~~-----~~~~~~~-~~~~~~~--~~~~~e~~~~~~e~~~~l~~~l-~~L~~~ 153 (231)
T PRK11922 110 ---------------------------VM-----ASTIAGG-ERTPLAD--PAEDPERAAARREIRALLERAI-DALPDA 153 (231)
T ss_pred ---------------------------cc-----ccccccc-cccccCc--ccCChHHHHHHHHHHHHHHHHH-HhCCHH
Confidence 00 0000000 0000011 1236777777788888899999 999999
Q ss_pred HHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010835 441 EREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 489 (499)
Q Consensus 441 ER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~ 489 (499)
+|+||.++| .+|+|++|||+.||+|.++|+++++||+++||+.+..
T Consensus 154 ~r~i~~l~~---~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~~ 199 (231)
T PRK11922 154 FRAVFVLRV---VEELSVEETAQALGLPEETVKTRLHRARRLLRESLAR 199 (231)
T ss_pred Hhhhheeeh---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 999999998 8999999999999999999999999999999999865
No 44
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=99.90 E-value=1.6e-22 Score=191.89 Aligned_cols=180 Identities=23% Similarity=0.313 Sum_probs=144.3
Q ss_pred CCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHH
Q 010835 206 LTHAEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADL 285 (499)
Q Consensus 206 Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDL 285 (499)
++...+.+|+.+++.||. .|++.|+..|.+.|+.+|+++.++..+++|+
T Consensus 11 ~~~~~~~~l~~~~~~gd~-------------------------------~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDl 59 (194)
T PRK12519 11 LSSRSDAELFSALKAGQS-------------------------------AALGVLYDRHAGLVYGLALKILGNSQEAEDL 59 (194)
T ss_pred CCcccHHHHHHHHHcCCH-------------------------------HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence 344566778888999987 9999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHH
Q 010835 286 VQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAE 365 (499)
Q Consensus 286 iQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~ 365 (499)
+||+|+++|+. ..|++..+ +|.||++.++++.+.++++++.+.....
T Consensus 60 vQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~~d~~Rk~~~~~~~~------------------------------- 106 (194)
T PRK12519 60 TQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRAIDRLRSRRSRQRLL------------------------------- 106 (194)
T ss_pred HHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHHHHHHHhcccccchh-------------------------------
Confidence 99999999976 67887554 7999999999999999988764310000
Q ss_pred HhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHH
Q 010835 366 YLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREII 445 (499)
Q Consensus 366 ~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI 445 (499)
+. .... ...+. ..++|++.+...+....|..+| ..||++++.||
T Consensus 107 ----------------------~~---------~~~~---~~~~~-~~~~~~~~~~~~~~~~~l~~~l-~~L~~~~~~v~ 150 (194)
T PRK12519 107 ----------------------ER---------WQQE---LLGEA-SEDTPLEQASLAERSQRVQTAL-AQLPESQRQVL 150 (194)
T ss_pred ----------------------hh---------hhhh---hcccc-cCCCHHHHHHHHHHHHHHHHHH-HhCCHHHhhhh
Confidence 00 0000 00000 0124555556666677889999 99999999999
Q ss_pred HHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010835 446 RLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 488 (499)
Q Consensus 446 ~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~ 488 (499)
.|+| ++|+|++|||+.||+|.++|+++++||+++||+.+.
T Consensus 151 ~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 190 (194)
T PRK12519 151 ELAY---YEGLSQSEIAKRLGIPLGTVKARARQGLLKLRELLQ 190 (194)
T ss_pred hhhh---hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 9999 899999999999999999999999999999999875
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=99.90 E-value=1.8e-22 Score=186.72 Aligned_cols=160 Identities=17% Similarity=0.226 Sum_probs=132.7
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 334 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip 334 (499)
.|++.|+..|.+.+++++.++.++..+++|++||+++++|+++++|+...+ +|.+|++..+++.+.+++++..+....+
T Consensus 11 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R~~~~~~~~~ 89 (170)
T TIGR02952 11 DAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFRGSKRHPLFS 89 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHHhcCCCCCCc
Confidence 999999999999999999999999999999999999999999999997544 7999999999999999988764311000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCC
Q 010835 335 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 414 (499)
Q Consensus 335 ~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~ 414 (499)
.+. ..+.... ..
T Consensus 90 ----------------------------------------------------~~~-------------~~~~~~~---~~ 101 (170)
T TIGR02952 90 ----------------------------------------------------LDV-------------FKELLSN---EP 101 (170)
T ss_pred ----------------------------------------------------HHH-------------HhhcCCC---CC
Confidence 000 0000000 12
Q ss_pred CCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010835 415 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 487 (499)
Q Consensus 415 ~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L 487 (499)
+|++.+...+....+..+| ..|||++|.||.++| ++|+|++|||+.||+|.+||+++++||+++||+.|
T Consensus 102 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~~---~~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~l 170 (170)
T TIGR02952 102 NPEEAILKEEANEKLLKAL-KILTPKQQHVIALRF---GQNLPIAEVARILGKTEGAVKILQFRAIKKLARQM 170 (170)
T ss_pred CHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence 5666666677778899999 999999999999999 89999999999999999999999999999999864
No 46
>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=99.90 E-value=2.3e-22 Score=190.82 Aligned_cols=178 Identities=18% Similarity=0.255 Sum_probs=133.9
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 334 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip 334 (499)
.|++.|+..|.|.|+.+|+++.++..+++|++||+|+++|+++.+|+++.+.+|.||++.+|++.+.++++...+..+.+
T Consensus 19 ~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~~~~~~~r~~~~~~~~~ 98 (198)
T TIGR02859 19 HALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTRQIITAIKTATRQKHIP 98 (198)
T ss_pred HHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 99999999999999999999999999999999999999999999999987778999999999998888876553211110
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCC
Q 010835 335 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 414 (499)
Q Consensus 335 ~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~ 414 (499)
. ....|++.+. ..++++.++.+.+.+.. ..
T Consensus 99 ~----------------------------------------------~~~~~~~~~~---~~~~~~~~~~~~~~~~~-~~ 128 (198)
T TIGR02859 99 L----------------------------------------------NSYVSLNKPI---YDEESDRTLLDVISGAK-VT 128 (198)
T ss_pred h----------------------------------------------hhhcCccccc---ccccccchHHHHhhccc-cC
Confidence 0 0012222211 01111112222222211 23
Q ss_pred CCcchHHHHHHHHHHHHHHHhh-CCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010835 415 NPWHGVDDWALKDEVNKLIIVT-LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 487 (499)
Q Consensus 415 ~Pee~ve~~el~~~L~~~L~~~-L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L 487 (499)
+|++.+...+....|.++| +. |++.++.|+. +| ++|+|++|||+.||+|.++|++.++||+++||+.+
T Consensus 129 ~~e~~~~~~e~~~~l~~~l-~~Ll~~~~~~i~~-~~---~~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~~l 197 (198)
T TIGR02859 129 DPEELIISQEEYGDIESKM-NELLSDLEWKVLQ-SY---LDGKSYQEIACDLNRHVKSIDNALQRVKRKLEKYL 197 (198)
T ss_pred CHHHHHHHHHHHHHHHHHH-HHhcCHHHHHHHH-HH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhc
Confidence 6777777777778899999 77 5666777765 46 69999999999999999999999999999999875
No 47
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=99.90 E-value=2.5e-22 Score=188.77 Aligned_cols=169 Identities=25% Similarity=0.275 Sum_probs=133.8
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 334 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip 334 (499)
.|+.+|+..|.|.|+.+|++|.+++.+++|++||+++++|+++.+|++.. +|.+|++..+++.+.+++++..+...
T Consensus 18 ~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~~~~rk~~~~~~-- 93 (187)
T TIGR02948 18 NAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLTIDRLRKRKPDFY-- 93 (187)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHHHHHHhhccccc--
Confidence 99999999999999999999999999999999999999999999999865 69999999999988888766432000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCC
Q 010835 335 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 414 (499)
Q Consensus 335 ~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~ 414 (499)
++.. ..+.+.....+...+. .+
T Consensus 94 ----------------------------------------------------~~~~----~~~~~~~~~~~~~~~~--~~ 115 (187)
T TIGR02948 94 ----------------------------------------------------LDDE----VQGTDGLTMESQLAAD--EA 115 (187)
T ss_pred ----------------------------------------------------cccc----ccCccccccccccccC--cC
Confidence 0000 0000011111111111 13
Q ss_pred CCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010835 415 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 489 (499)
Q Consensus 415 ~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~ 489 (499)
+|++.+...+....+..+| ..|||++|.||.++| ++|+|++|||+.||+|+++|+++++||+++||..+..
T Consensus 116 ~~~~~~~~~e~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l~~ 186 (187)
T TIGR02948 116 PPEDQVISLELRDTIQQEI-QALPPKYRMVIVLKY---MEDLSLKEISEILDLPVGTVKTRIHRGREALRKQLRH 186 (187)
T ss_pred CHHHHHHHHHHHHHHHHHH-HhCCHHHhHHhhhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhhc
Confidence 5666666667777899999 899999999999998 8999999999999999999999999999999998753
No 48
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=99.90 E-value=2.2e-22 Score=188.62 Aligned_cols=175 Identities=16% Similarity=0.169 Sum_probs=141.6
Q ss_pred HHHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHH
Q 010835 209 AEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQG 288 (499)
Q Consensus 209 eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQE 288 (499)
.+...|+..++.||. .|+..|+..|.+.|+.+|.++.++..+++|++||
T Consensus 4 ~~~~~li~~~~~g~~-------------------------------~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe 52 (179)
T PRK12514 4 DDIEKLIVRVSLGDR-------------------------------DAFSSLYDATSAKLFGICLRVLKDRSEAEEALQD 52 (179)
T ss_pred hHHHHHHHHHHcCCH-------------------------------HHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHH
Confidence 456667888888887 9999999999999999999999999999999999
Q ss_pred HHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhC
Q 010835 289 GLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLN 368 (499)
Q Consensus 289 G~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lg 368 (499)
+|+++|+++++|++..+ .|.+|++..++|.+.+++++..+. ..+
T Consensus 53 ~fl~~~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~R~~~~~-~~~---------------------------------- 96 (179)
T PRK12514 53 VYVKIWTKADRFAVSGL-SPMTWLITIARNHAIDRLRARKAV-AVD---------------------------------- 96 (179)
T ss_pred HHHHHHHhHHhcCcccc-cHHHHHHHHHHHHHHHHHHhcCCc-ccc----------------------------------
Confidence 99999999999986543 699999999999888888765320 000
Q ss_pred CCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHH
Q 010835 369 MSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLY 448 (499)
Q Consensus 369 is~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~Lr 448 (499)
++. ..+. .+. ..+|++.+...+....|..+| ..||++++.||.++
T Consensus 97 ------------------~~~-------------~~~~-~~~--~~~~e~~~~~~~~~~~l~~~l-~~L~~~~r~i~~l~ 141 (179)
T PRK12514 97 ------------------IDE-------------AHDL-ADP--SPGPEAEVIAGDEGQRIDACL-EELEKDRAAAVRRA 141 (179)
T ss_pred ------------------ccc-------------chhc-ccc--CCCHHHHHHhHHHHHHHHHHH-HhCCHHHHHHHHHH
Confidence 000 0000 000 124555555555566788999 99999999999999
Q ss_pred hcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010835 449 YGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 488 (499)
Q Consensus 449 yGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~ 488 (499)
| ++|+|++|||+.||+|.++|+++++||+++||+.+.
T Consensus 142 ~---~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 178 (179)
T PRK12514 142 Y---LEGLSYKELAERHDVPLNTMRTWLRRSLLKLRECLS 178 (179)
T ss_pred H---HcCCCHHHHHHHHCCChHHHHHHHHHHHHHHHHHhc
Confidence 9 899999999999999999999999999999999874
No 49
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=99.90 E-value=3.7e-22 Score=189.32 Aligned_cols=188 Identities=21% Similarity=0.246 Sum_probs=148.7
Q ss_pred CCCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHHHHhHhhCCCCCHHH
Q 010835 205 LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMAD 284 (499)
Q Consensus 205 ~Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~ED 284 (499)
+||+..+..|+..++.||. .|++.|+..|.+.|+++++++.++..+++|
T Consensus 1 ~~~~~~~~~ll~~~~~gd~-------------------------------~a~~~l~~~y~~~l~~~~~~~~~~~~daeD 49 (193)
T PRK11923 1 MLTQEEDQQLVERVQRGDK-------------------------------RAFDLLVLKYQHKILGLIVRFVHDTAEAQD 49 (193)
T ss_pred CCccccHHHHHHHHHcCCH-------------------------------HHHHHHHHHHHHHHHHHHHHHhCCHhhHHH
Confidence 3566666788888999987 999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHH
Q 010835 285 LVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIA 364 (499)
Q Consensus 285 LiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L~~~gr~pt~eEIA 364 (499)
++||+++++|+++.+|++.. .|.+|++..+++.+.++++++.+.....
T Consensus 50 lvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~~d~~rk~~~~~~~~------------------------------ 97 (193)
T PRK11923 50 VAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTAKNHLVSRGRRPPDS------------------------------ 97 (193)
T ss_pred HHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHHHHHHHHhcCCCccc------------------------------
Confidence 99999999999999999864 5999999999998888887654310000
Q ss_pred HHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHH
Q 010835 365 EYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREI 444 (499)
Q Consensus 365 ~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~V 444 (499)
...++... ..++. ..+.+ ..+|+..+...+....+..+| ..||+++|.|
T Consensus 98 -------------------~~~~~~~~-----~~~~~---~~~~~---~~~~e~~~~~~~~~~~l~~~l-~~L~~~~r~v 146 (193)
T PRK11923 98 -------------------DVSSEDAE-----FYDGD---HALKD---IESPERALLRDEIEGTVHRTI-QQLPEDLRTA 146 (193)
T ss_pred -------------------cccccchh-----hhccc---ccccC---cCCHHHHHHHHHHHHHHHHHH-HhCCHHHhHH
Confidence 00000000 00000 00111 135666666777788899999 9999999999
Q ss_pred HHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010835 445 IRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 489 (499)
Q Consensus 445 I~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~ 489 (499)
|.++| .+|+|++|||+.||+|..+|+++++||+++||+.+..
T Consensus 147 ~~l~~---~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~ 188 (193)
T PRK11923 147 LTLRE---FDGLSYEDIASVMQCPVGTVRSRIFRAREAIDKALQP 188 (193)
T ss_pred HhhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 99999 8999999999999999999999999999999998864
No 50
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=99.90 E-value=2.5e-22 Score=189.54 Aligned_cols=181 Identities=19% Similarity=0.192 Sum_probs=144.8
Q ss_pred CCCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHHHHhHhhCCCCCHHH
Q 010835 205 LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMAD 284 (499)
Q Consensus 205 ~Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~ED 284 (499)
-....++..++..+..||. .+++.|+..|.+.|+++|+++.++..+++|
T Consensus 6 ~~~~~~~~~l~~~~~~~~~-------------------------------~~~~~l~~~y~~~l~~~~~~~~~~~~~aeD 54 (187)
T PRK12534 6 GHDDDETGRLLTATAGGDR-------------------------------HAFEALYRQTSPKLFGVCLRMIPQRAEAEE 54 (187)
T ss_pred CCCcchHHHHHHHHHcCCH-------------------------------HHHHHHHHHhhHHHHHHHHHHhcCHHHHHH
Confidence 3344566678888888887 999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHH
Q 010835 285 LVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIA 364 (499)
Q Consensus 285 LiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L~~~gr~pt~eEIA 364 (499)
++||+|+++|+++++|++.++ .|.+|++..++|.+.+++++..+...
T Consensus 55 lvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~~d~~R~~~~~~~-------------------------------- 101 (187)
T PRK12534 55 VLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKAIDHLRANAPQRR-------------------------------- 101 (187)
T ss_pred HHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHHHHHhcccccc--------------------------------
Confidence 999999999999999998654 58899999999988888876542000
Q ss_pred HHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHH
Q 010835 365 EYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREI 444 (499)
Q Consensus 365 ~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~V 444 (499)
..+++. ..+.. +. ..+|.+.....+....+..+| ..||++++.|
T Consensus 102 -------------------~~~~~~-------------~~~~~-~~--~~~~~~~~~~~e~~~~l~~~l-~~L~~~~r~i 145 (187)
T PRK12534 102 -------------------NVALDD-------------AGELR-AA--DASPLERTERASTRRRIDHCL-AELEPPRSEL 145 (187)
T ss_pred -------------------cccccc-------------hhhhc-cc--cCChhhHHHHHHHHHHHHHHH-HhCCHHHHHH
Confidence 000000 00000 00 123444555666778899999 9999999999
Q ss_pred HHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010835 445 IRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 488 (499)
Q Consensus 445 I~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~ 488 (499)
|.++| .+|+|++|||+.||+|+++|+++++||+++||+.+.
T Consensus 146 ~~l~~---~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l~ 186 (187)
T PRK12534 146 IRTAF---FEGITYEELAARTDTPIGTVKSWIRRGLAKLKACLE 186 (187)
T ss_pred HHHHH---HcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHHHc
Confidence 99999 899999999999999999999999999999999874
No 51
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=99.89 E-value=5.3e-22 Score=186.51 Aligned_cols=169 Identities=24% Similarity=0.269 Sum_probs=135.0
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 334 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip 334 (499)
.|+..|+..|.|+|+++|+++.++..+++|++||+++++|+++.+|++.. +|.+|++..+++.+.+++++..+..
T Consensus 18 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~~~d~~R~~~~~~--- 92 (187)
T PRK09641 18 NAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNLTIDRLRKRKPDY--- 92 (187)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHHHHHHHHhcCccc---
Confidence 99999999999999999999999999999999999999999999999753 6999999999998888887654210
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCC
Q 010835 335 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 414 (499)
Q Consensus 335 ~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~ 414 (499)
+++.. ..+++.....+.+.+. ..
T Consensus 93 ---------------------------------------------------~~~~~----~~~~~~~~~~~~~~~~--~~ 115 (187)
T PRK09641 93 ---------------------------------------------------YLDAE----VAGTEGLTMYSQLAAD--DA 115 (187)
T ss_pred ---------------------------------------------------ccccc----ccCCcchhhhcccccC--cC
Confidence 00000 0000111111111111 23
Q ss_pred CCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010835 415 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 489 (499)
Q Consensus 415 ~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~ 489 (499)
+|++.+...+....+..+| ..||++++.||.++| .+|++++|||+.||||.++|++.++||+++||+.+..
T Consensus 116 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~il~l~~---~~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l~~ 186 (187)
T PRK09641 116 LPEEQVVSLELQETIQEAI-LQLPEKYRTVIVLKY---IEDLSLKEISEILDLPVGTVKTRIHRGREALRKQLRH 186 (187)
T ss_pred CHHHHHHHHHHHHHHHHHH-HhCCHHHHHHhhhHH---hhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 5666667777778899999 999999999999999 8999999999999999999999999999999998753
No 52
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=99.89 E-value=3.1e-22 Score=182.67 Aligned_cols=151 Identities=20% Similarity=0.219 Sum_probs=124.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccc
Q 010835 254 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 333 (499)
Q Consensus 254 ~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRi 333 (499)
..||+.|++.|.|+|+.+++++ ++..+++|++||+++++|+++++|++..+ +|.+|++..+++.+.++++++.+..
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 3799999999999999999886 55689999999999999999999998666 7999999999999999988764200
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCC
Q 010835 334 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE 413 (499)
Q Consensus 334 p~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e 413 (499)
+.. . . .
T Consensus 79 ------------------------------------------------------~~~------~----------~----~ 84 (154)
T PRK06759 79 ------------------------------------------------------EKC------V----------C----V 84 (154)
T ss_pred ------------------------------------------------------ccc------c----------c----c
Confidence 000 0 0 0
Q ss_pred CCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010835 414 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA 486 (499)
Q Consensus 414 ~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~ 486 (499)
++|++.....+....|..+| ..||+++|.||.++| ++|+|++|||+.||+|.++|+++++||+++||+.
T Consensus 85 ~~~~~~~~~~~~~~~l~~~l-~~L~~~~r~ii~l~~---~~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 85 GEYEDHFHFEDVEMKVKDFM-SVLDEKEKYIIFERF---FVGKTMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred CCCcccccHHHHHHHHHHHH-HhCCHHHHHHHHHHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 12222233444567788999 999999999999999 8999999999999999999999999999999974
No 53
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=99.89 E-value=6.4e-22 Score=183.90 Aligned_cols=171 Identities=24% Similarity=0.219 Sum_probs=136.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccc
Q 010835 253 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 332 (499)
Q Consensus 253 ~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vR 332 (499)
+..|++.|+..|.+.|+.++++|.+++.+.+|++||++++||+++++|+ .+.+|.+|++..+++.+.+.+++..+...
T Consensus 8 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~r~~~~~~~ 85 (182)
T PRK09652 8 DRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYLRKQGRRPP 85 (182)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHHHcccCCCC
Confidence 3499999999999999999999999999999999999999999999999 34589999999999988888777643111
Q ss_pred ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccC
Q 010835 333 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRV 412 (499)
Q Consensus 333 ip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~ 412 (499)
.+ +++. .+.++....+.+.+
T Consensus 86 ~~---------------------------------------------------~~~~------~~~~~~~~~~~~~~--- 105 (182)
T PRK09652 86 AS---------------------------------------------------DVDA------EEAEDFDLADALRD--- 105 (182)
T ss_pred cc---------------------------------------------------cccc------cccccccccccccc---
Confidence 00 0000 00000001111111
Q ss_pred CCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010835 413 ENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 489 (499)
Q Consensus 413 e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~ 489 (499)
..+|++.+...+....+..+| ..|||+++.||.++| ++|+|++|||+.||+|+.+|++++++|+++||+.+..
T Consensus 106 ~~~~~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~~---~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 178 (182)
T PRK09652 106 ISTPENELLSAELEQRVRAAI-ESLPEELRTAITLRE---IEGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQP 178 (182)
T ss_pred ccChHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 235666777777888899999 899999999999998 8999999999999999999999999999999998753
No 54
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=99.89 E-value=6.5e-22 Score=194.84 Aligned_cols=176 Identities=19% Similarity=0.216 Sum_probs=143.5
Q ss_pred HHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHH
Q 010835 210 EVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGG 289 (499)
Q Consensus 210 Ee~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG 289 (499)
.+.+|+.+++.||. .||+.|+..|.+.|+.+++++.++..+++|++||+
T Consensus 49 ~d~~Li~~~~~gd~-------------------------------~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEv 97 (233)
T PRK12538 49 EDEELLDRLATDDE-------------------------------AAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDT 97 (233)
T ss_pred cHHHHHHHHHhCCH-------------------------------HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH
Confidence 34568899999998 99999999999999999999999999999999999
Q ss_pred HHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCC
Q 010835 290 LIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNM 369 (499)
Q Consensus 290 ~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgi 369 (499)
|+++|+.+++|++..+ +|.+|++..+++.+.+++++..+. .
T Consensus 98 fl~l~~~~~~~~~~~~-~f~~WL~~IarN~~id~~Rk~~~~-~------------------------------------- 138 (233)
T PRK12538 98 MLKVWTHRGRWQHGRA-KFSTWLYRVVSNRCIDLRRKPRTE-N------------------------------------- 138 (233)
T ss_pred HHHHHHHHHHcccccc-cHHHHHHHHHHHHHHHHHHhhccc-c-------------------------------------
Confidence 9999999999986444 799999999999888887653210 0
Q ss_pred CHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHh
Q 010835 370 SQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYY 449 (499)
Q Consensus 370 s~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~Lry 449 (499)
++. ..+. .+. ..++++.+...+....|..+| ..||+++|+||.|+|
T Consensus 139 -----------------~~~-------------~~~~-~~~--~~~~~~~~~~~e~~~~l~~~L-~~Lp~~~R~v~~L~~ 184 (233)
T PRK12538 139 -----------------VDA-------------VPEV-ADG--KPDAVSVIERNELSDLLEAAM-QRLPEQQRIAVILSY 184 (233)
T ss_pred -----------------ccc-------------cccc-ccC--CCCHHHHHHHHHHHHHHHHHH-HhCCHHHHHHhhhHH
Confidence 000 0000 000 123444455566677899999 999999999999999
Q ss_pred cCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010835 450 GLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM 492 (499)
Q Consensus 450 GLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~l 492 (499)
++|+|++|||+.||+|.++|+++++||+++||+.+...+.
T Consensus 185 ---~eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~~~~~ 224 (233)
T PRK12538 185 ---HENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLRRHER 224 (233)
T ss_pred ---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 8999999999999999999999999999999999876543
No 55
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=99.89 E-value=9.3e-22 Score=185.34 Aligned_cols=162 Identities=18% Similarity=0.250 Sum_probs=127.3
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 334 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip 334 (499)
.|++.|+..|.+.|+.+|+++.+++.+++|++||+++++|+++.+|++..+ .|.+|++..++|.+.+++++..+...
T Consensus 23 ~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~rk~~~~~~-- 99 (186)
T PRK13919 23 EALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRG-SARAWLLALAHHAAVDHVRRRAARPQ-- 99 (186)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCcccc-chHHHHHHHHHHHHHHHHHhhhcccc--
Confidence 999999999999999999999999999999999999999999999987543 69999999999999888877542100
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCC
Q 010835 335 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 414 (499)
Q Consensus 335 ~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~ 414 (499)
. ++. ....... . +. .
T Consensus 100 -------------------------------------------------~--~~~-------~~~~~~~---~-~~---~ 114 (186)
T PRK13919 100 -------------------------------------------------P--LEP-------DEREPEA---F-DL---P 114 (186)
T ss_pred -------------------------------------------------c--ccc-------ccccccc---c-cC---C
Confidence 0 000 0000000 0 00 0
Q ss_pred CCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010835 415 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 488 (499)
Q Consensus 415 ~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~ 488 (499)
+|....+.......|..+| +.||+++|.||.|+| .+|+|++|||+.||+|.++|+.+++||+++||+.+.
T Consensus 115 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~~---~~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l~ 184 (186)
T PRK13919 115 GPGLDEEGHLDRTRLGRAL-KALSPEERRVIEVLY---YQGYTHREAAQLLGLPLGTLKTRARRALSRLKEVLR 184 (186)
T ss_pred CccccHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence 1111122333456788999 999999999999999 899999999999999999999999999999999874
No 56
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=99.89 E-value=1.1e-21 Score=184.92 Aligned_cols=159 Identities=19% Similarity=0.279 Sum_probs=129.7
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 334 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip 334 (499)
.|++.|+..|.+.|+.++.++.++..+++|++||+|+.+|+.+++|++..+ .|.+|++..+++.+.+++++..+....
T Consensus 23 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wL~~iarn~~~d~~r~~~~~~~~- 100 (182)
T PRK12537 23 RALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARG-SARGWIYSVTRHLALNVLRDTRREVVL- 100 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHHHHHhccccCcc-
Confidence 999999999999999999999999999999999999999999999986443 699999999999999998876431000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCC
Q 010835 335 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 414 (499)
Q Consensus 335 ~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~ 414 (499)
+.. .. +...+ ..
T Consensus 101 -----------------------------------------------------~~~--------~~----~~~~~---~~ 112 (182)
T PRK12537 101 -----------------------------------------------------DDD--------AE----ETAQT---LH 112 (182)
T ss_pred -----------------------------------------------------ccc--------hh----hhccc---cc
Confidence 000 00 00000 11
Q ss_pred CCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010835 415 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 487 (499)
Q Consensus 415 ~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L 487 (499)
++++..+..+....+..+| +.||+++|+||.++| ++|+|++|||+.||+|.++|+++++||+++||+.+
T Consensus 113 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~i~~l~~---~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 181 (182)
T PRK12537 113 EIIDDFDLWANSGKIHRCL-EQLEPARRNCILHAY---VDGCSHAEIAQRLGAPLGTVKAWIKRSLKALRECM 181 (182)
T ss_pred chHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCChhhHHHHHHHHHHHHHHHh
Confidence 2333344455567888999 999999999999999 89999999999999999999999999999999876
No 57
>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=99.88 E-value=2.1e-21 Score=182.90 Aligned_cols=168 Identities=21% Similarity=0.228 Sum_probs=133.2
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 334 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip 334 (499)
.|++.|+..|.+.|+.+|+++.++..+++|++||+++++|+++.+|++. .+|.+|++..+++.+.+++++..+.....
T Consensus 20 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~~~~~~r~~~r~~~~~ 97 (190)
T TIGR02939 20 QAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNTAKNHLVAQGRRPPTS 97 (190)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHHHHHHHHHhccCCCcc
Confidence 9999999999999999999999999999999999999999999999975 36999999999998888877654311000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCC
Q 010835 335 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 414 (499)
Q Consensus 335 ~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~ 414 (499)
..+.+. .....+ ........
T Consensus 98 -------------------------------------------------~~~~~~----------~~~~~~-~~~~~~~~ 117 (190)
T TIGR02939 98 -------------------------------------------------DVEIED----------AEHFEG-ADRLREID 117 (190)
T ss_pred -------------------------------------------------cccccc----------hhhhcc-cccccccC
Confidence 000000 000000 00000013
Q ss_pred CCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010835 415 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 488 (499)
Q Consensus 415 ~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~ 488 (499)
+|++.+...+....+..+| ..||+++|.||.++| .+|+|++|||+.||+|.++|+++++||+++||+.+.
T Consensus 118 ~~e~~~~~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l~ 187 (190)
T TIGR02939 118 TPERLLLSRELEQTVMRAV-EALPEDLRTAITLRE---LEGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRLR 187 (190)
T ss_pred ChHHHHHHHHHHHHHHHHH-HcCCHHHhhhhhhhh---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 5666666777788899999 999999999999999 899999999999999999999999999999999885
No 58
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=99.88 E-value=2e-21 Score=185.09 Aligned_cols=187 Identities=19% Similarity=0.195 Sum_probs=144.2
Q ss_pred cCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHHHHhHhhCCCCCHH
Q 010835 204 ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMA 283 (499)
Q Consensus 204 ~~Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~E 283 (499)
|+.+..+...|+.+++.||. .||+.|+..|.+.|+.+|.++.++..+++
T Consensus 7 ~~~~~~~~~~li~~~~~~d~-------------------------------~af~~l~~~y~~~l~~~~~~~~~~~~~Ae 55 (194)
T PRK12531 7 HTFGRQEWLECMEKVKSRDK-------------------------------QAFALVFSYYAPKLKQFAMKHVGNEQVAM 55 (194)
T ss_pred cccccHhHHHHHHHHHcCCH-------------------------------HHHHHHHHHHHHHHHHHHHHHhCCHHHHH
Confidence 44455677778889999998 99999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHcCCCCCHHHH
Q 010835 284 DLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRI 363 (499)
Q Consensus 284 DLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L~~~gr~pt~eEI 363 (499)
|++||+|+.+|+.+.+|++..+ .|.+|++..++|.+.+++++..+.....
T Consensus 56 DlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn~~ld~~Rk~~~~~~~~----------------------------- 105 (194)
T PRK12531 56 EMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRNLCFDLLRKQKGKDLHI----------------------------- 105 (194)
T ss_pred HHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHHHHHHHHHHhccccccc-----------------------------
Confidence 9999999999999999997544 6999999999999999988764310000
Q ss_pred HHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHH
Q 010835 364 AEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGERERE 443 (499)
Q Consensus 364 A~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~ 443 (499)
..+. ..........+.+ ...|+ .......+.++| ..||+++|.
T Consensus 106 ----------------------~~~~-------~~~~~~~~~~~~~---~~~~e----~~~~~~~l~~~l-~~Lp~~~r~ 148 (194)
T PRK12531 106 ----------------------HADD-------IWPSDYYPPDLVD---HYSPE----QDMLKEQVMKFL-DRLPKAQRD 148 (194)
T ss_pred ----------------------chhh-------ccccccccccccc---ccCHH----HHHHHHHHHHHH-HhCCHHHHH
Confidence 0000 0000000000000 01222 223345688888 999999999
Q ss_pred HHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010835 444 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 491 (499)
Q Consensus 444 VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~ 491 (499)
||.|+| .+|+|++|||+.||+|.++|+.++++|+++||+.+..+.
T Consensus 149 v~~l~~---~eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~~~~ 193 (194)
T PRK12531 149 VLQAVY---LEELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSMDAES 193 (194)
T ss_pred HHHHHH---HcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHhhhcc
Confidence 999999 899999999999999999999999999999999987654
No 59
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=99.88 E-value=1.7e-21 Score=184.83 Aligned_cols=160 Identities=21% Similarity=0.192 Sum_probs=131.6
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCC---CCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNM---GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 331 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~---g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~v 331 (499)
.|++.|+..|.+.|++++.++.++ ..+++|++||+++++|+++++|+++.+ .|.+|++..++|.+.+++++..+..
T Consensus 18 ~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~iarn~~~d~~rk~~~~~ 96 (189)
T PRK06811 18 KALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAISKYKAIDYKRKLTKNN 96 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHHHHHHHHHHHHhcccc
Confidence 999999999999999999999875 357999999999999999999997544 7999999999999999988765310
Q ss_pred cccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCcccccccccc
Q 010835 332 RLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNR 411 (499)
Q Consensus 332 Rip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~ 411 (499)
... +.+.. . .+.
T Consensus 97 ~~~---------------------------------------------------~~~~~---------------~-~~~- 108 (189)
T PRK06811 97 EID---------------------------------------------------SIDEF---------------I-LIS- 108 (189)
T ss_pred ccc---------------------------------------------------cchhh---------------h-hcc-
Confidence 000 00000 0 000
Q ss_pred CCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010835 412 VENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 488 (499)
Q Consensus 412 ~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~ 488 (499)
..+|++.+...+....|..+| ..|||++|.||.|+| .+|+|++|||++||+|..+|+++++||+++||+..-
T Consensus 109 -~~~~~~~~~~~e~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~~ 180 (189)
T PRK06811 109 -EESIENEIILKENKEEILKLI-NDLEKLDREIFIRRY---LLGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNKL 180 (189)
T ss_pred -cCCHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHccc
Confidence 135666667777788899999 999999999999998 899999999999999999999999999999998643
No 60
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=99.88 E-value=3.6e-21 Score=185.45 Aligned_cols=182 Identities=16% Similarity=0.151 Sum_probs=141.2
Q ss_pred HHHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHH
Q 010835 209 AEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQG 288 (499)
Q Consensus 209 eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQE 288 (499)
+.+..|+..++.||. .|+++|+..|.+.|+.++.++.++..+++|++||
T Consensus 23 ~~~~~l~~~~~~~d~-------------------------------~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe 71 (206)
T PRK12526 23 ELSQWLILVAISRDK-------------------------------QAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQE 71 (206)
T ss_pred HHHHHHHHHHHcCCH-------------------------------HHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHH
Confidence 455567777888887 9999999999999999999999999999999999
Q ss_pred HHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhC
Q 010835 289 GLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLN 368 (499)
Q Consensus 289 G~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lg 368 (499)
+|+.+|+++..|++.++ .|.+|++.+++|.+.+++++..+.....
T Consensus 72 ~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d~~Rk~~~~~~~~---------------------------------- 116 (206)
T PRK12526 72 TMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFDMLRKIKAKKEQN---------------------------------- 116 (206)
T ss_pred HHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHHHHHHhccccccc----------------------------------
Confidence 99999999999997655 5999999999999999988765311000
Q ss_pred CCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHH
Q 010835 369 MSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLY 448 (499)
Q Consensus 369 is~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~Lr 448 (499)
++. +.....+.+.+. ...+ ...........|..+| ..||+++|.||.|+
T Consensus 117 ------------------~~~---------~~~~~~~~~~~~--~~~~-~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~ 165 (206)
T PRK12526 117 ------------------LGD---------DIWPIEQALAES--QSES-EEFSDHLMDKQILSYI-EKLPEAQQTVVKGV 165 (206)
T ss_pred ------------------ccc---------ccchhhhhcccc--cCch-HHHHHHHHHHHHHHHH-HhCCHHHHHHHHHH
Confidence 000 000000001111 0112 1223333446788999 89999999999999
Q ss_pred hcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010835 449 YGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 490 (499)
Q Consensus 449 yGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~ 490 (499)
| ++|+|++|||++||+|.++|+.++++|+++||+.+...
T Consensus 166 ~---~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~ 204 (206)
T PRK12526 166 Y---FQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQMGEQ 204 (206)
T ss_pred H---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence 9 89999999999999999999999999999999998654
No 61
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=1.3e-21 Score=184.73 Aligned_cols=174 Identities=17% Similarity=0.151 Sum_probs=137.5
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcc
Q 010835 252 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 331 (499)
Q Consensus 252 ~~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~v 331 (499)
++..|++.|+..|.+.|+.+|++++++..+++|++||+|+.+|+++.+|++..+..|.+|++..++|.+.+++++..+..
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 45599999999999999999999999999999999999999999999998654457999999999999888887764300
Q ss_pred cccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCcccccccccc
Q 010835 332 RLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNR 411 (499)
Q Consensus 332 Rip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~ 411 (499)
... +.. .. +.+...
T Consensus 86 ~~~-----------------------------------------------------~~~--------~~----~~~~~~- 99 (185)
T PRK12542 86 TFL-----------------------------------------------------EEY--------ER----ESIEAV- 99 (185)
T ss_pred hhh-----------------------------------------------------hhc--------cc----cchhhh-
Confidence 000 000 00 000000
Q ss_pred CCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010835 412 VENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 491 (499)
Q Consensus 412 ~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~ 491 (499)
.++|++.....+....|..+| ..|||++|+||.|+| ++|+|++|||+.||+|.+||+++++||+++||+.+....
T Consensus 100 -~~~~~~~~~~~~~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~ 174 (185)
T PRK12542 100 -DENIEEWEKRKMSEVQIDTLL-KELNESNRQVFKYKV---FYNLTYQEISSVMGITEANVRKQFERARKRVQNMIGGIQ 174 (185)
T ss_pred -hccHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccc
Confidence 112333233344456788999 999999999999999 899999999999999999999999999999999998887
Q ss_pred HHHhh
Q 010835 492 MEAML 496 (499)
Q Consensus 492 l~~~l 496 (499)
...|+
T Consensus 175 ~~~~~ 179 (185)
T PRK12542 175 HDEFK 179 (185)
T ss_pred hHHHH
Confidence 77774
No 62
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=5.8e-21 Score=177.00 Aligned_cols=165 Identities=17% Similarity=0.127 Sum_probs=136.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccc
Q 010835 254 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 333 (499)
Q Consensus 254 ~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRi 333 (499)
..|++.|++.|.+.|+++|+++.++..+++|++||+++++|+++++|+ .+.+|.+|++..+++.+.+++++..+....
T Consensus 12 ~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~~r~~~~~~~~ 89 (179)
T PRK11924 12 KEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDLLRRRRREKAV 89 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHHHHhccccccc
Confidence 399999999999999999999999999999999999999999999998 344799999999999888887765431100
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCC
Q 010835 334 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE 413 (499)
Q Consensus 334 p~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e 413 (499)
. .+. .. +...+. ..
T Consensus 90 ~----------------------------------------------------~~~---------~~----~~~~~~-~~ 103 (179)
T PRK11924 90 L----------------------------------------------------SDD---------AL----EPEFAE-TA 103 (179)
T ss_pred C----------------------------------------------------ccc---------cc----ccccCC-cc
Confidence 0 000 00 000000 13
Q ss_pred CCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010835 414 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 490 (499)
Q Consensus 414 ~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~ 490 (499)
.+|++.+...+....+..+| ..||++++.||.++| .+|++++|||+.||+|+.+|++++++|+++||+.+...
T Consensus 104 ~~~e~~~~~~e~~~~l~~~l-~~L~~~~r~i~~l~~---~~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~~~ 176 (179)
T PRK11924 104 ETPEAALLAKDDLARIDRCL-DALPVKQREVFLLRY---VEGLSYREIAEILGVPVGTVKSRLRRARQLLRECLEAQ 176 (179)
T ss_pred CCHHHHHhhHHHHHHHHHHH-HhCCHHHHHHhhHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 47778888888889999999 999999999999999 79999999999999999999999999999999988764
No 63
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=99.87 E-value=2.4e-21 Score=183.56 Aligned_cols=161 Identities=18% Similarity=0.244 Sum_probs=127.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccc
Q 010835 253 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 332 (499)
Q Consensus 253 ~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vR 332 (499)
+..|++.|+..|.|.|+++|.+|.++..+++|++||+|+.+|+++++|++. .+|.+|++.++++.+.+++++..+...
T Consensus 24 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~~~~~~ 101 (188)
T PRK09640 24 VTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLYSITYNECITQYRKERRKRR 101 (188)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcCC--CcchHHHHHHHHHHHHHHHHHhccccc
Confidence 349999999999999999999999999999999999999999999999863 479999999999999999886542100
Q ss_pred ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccC
Q 010835 333 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRV 412 (499)
Q Consensus 333 ip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~ 412 (499)
.. .+. .. +...++
T Consensus 102 ~~----------------------------------------------------~~~------------~~-~~~~~~-- 114 (188)
T PRK09640 102 LM----------------------------------------------------DAL------------SL-DPLEEA-- 114 (188)
T ss_pred Cc----------------------------------------------------chh------------hh-cccccc--
Confidence 00 000 00 000000
Q ss_pred CCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010835 413 ENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 489 (499)
Q Consensus 413 e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~ 489 (499)
. .+.....+....|..+| ..||+++|.||.|+| .+|+|++|||+.||||.++|+.++.||+++||+.+..
T Consensus 115 --~-~~~~~~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~ 184 (188)
T PRK09640 115 --S-EEKAPKPEERGGLDRWL-VHVNPIDREILVLRF---VAELEFQEIADIMHMGLSATKMRYKRALDKLREKFAG 184 (188)
T ss_pred --c-ccccccHHHHHHHHHHH-HhcChhheeeeeeHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 0 01111234456788999 999999999999999 8999999999999999999999999999999998753
No 64
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=6.9e-21 Score=180.40 Aligned_cols=163 Identities=19% Similarity=0.226 Sum_probs=133.3
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 334 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip 334 (499)
.|++.|+..|.+.|+.++.++.++..+++|++||+|+.+|+++.+|++. ..|.+|++..+++.+.+++++..+. .
T Consensus 22 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~r~~~~~-~-- 96 (189)
T PRK12515 22 TAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARFKALSALRRRKHE-E-- 96 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHHHHHHHHHccCCC-C--
Confidence 9999999999999999999999999999999999999999999999964 3799999999999888887654310 0
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCC
Q 010835 335 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 414 (499)
Q Consensus 335 ~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~ 414 (499)
+.. + .. ..+.+. .+
T Consensus 97 ----------------------------------------------------~~~---------~--~~-~~~~~~--~~ 110 (189)
T PRK12515 97 ----------------------------------------------------IDD---------E--AA-AAIEDG--AD 110 (189)
T ss_pred ----------------------------------------------------Ccc---------c--cc-cccCCC--CC
Confidence 000 0 00 001111 12
Q ss_pred CCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010835 415 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM 492 (499)
Q Consensus 415 ~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~l 492 (499)
+|+......+....+..+| +.||+++|.||.|+| .+|+|++|||+.||+|..+|+++++||+++||+.+...+.
T Consensus 111 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~~---~~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~ 184 (189)
T PRK12515 111 TPEVALQKSDTSAALRACL-AKLSPAHREIIDLVY---YHEKSVEEVGEIVGIPESTVKTRMFYARKKLAELLKAAGV 184 (189)
T ss_pred CHHHHHHhHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 4555555666677899999 999999999999999 8999999999999999999999999999999999877543
No 65
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=99.87 E-value=1.2e-20 Score=179.83 Aligned_cols=158 Identities=14% Similarity=0.144 Sum_probs=131.1
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 334 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip 334 (499)
.+++.|++.|.+.|++++.++.++..+++|++||+|+.+|+++++|++.. +|.+|++..+++.+.+++++..+....
T Consensus 27 ~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~~--~f~~wL~~i~rn~~~d~~Rk~~~~~~~- 103 (192)
T PRK09643 27 YAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDA--AVSSWLHRIVVNACLDRLRRAKARPTV- 103 (192)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCCC--ccHHHHHHHHHHHHHHHHHccccCCCC-
Confidence 99999999999999999999999999999999999999999999999753 699999999999999998876431000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCC
Q 010835 335 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 414 (499)
Q Consensus 335 ~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~ 414 (499)
+++. .. + . ..
T Consensus 104 ---------------------------------------------------~~~~----------~~---~-~-----~~ 113 (192)
T PRK09643 104 ---------------------------------------------------PLDD----------VY---P-V-----AQ 113 (192)
T ss_pred ---------------------------------------------------Cccc----------cc---c-c-----cC
Confidence 0000 00 0 0 01
Q ss_pred CCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010835 415 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 489 (499)
Q Consensus 415 ~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~ 489 (499)
+|.+.+...+....+..+| +.||+++|.||.|+| .+|+|++|||+.||+|..||++++.||+++||+.+..
T Consensus 114 ~~~~~~~~~e~~~~l~~~l-~~Lp~~~r~i~~l~~---~~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l~~ 184 (192)
T PRK09643 114 LERDPTARVETALAVQRAL-MRLPVEQRAALVAVD---MQGYSVADAARMLGVAEGTVKSRCARGRARLAELLGY 184 (192)
T ss_pred CcccHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 2333445556677899999 899999999999999 8999999999999999999999999999999998865
No 66
>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=99.87 E-value=8.6e-21 Score=178.34 Aligned_cols=180 Identities=18% Similarity=0.138 Sum_probs=136.9
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhHhh----CCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHh
Q 010835 252 ECSLAREKLVMSNVRLVMSIAQRYD----NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVEN 327 (499)
Q Consensus 252 ~~~~A~e~LIe~yl~LV~sIA~ry~----~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~ 327 (499)
++..|++.|+..|.+.|+.+|++|+ ++..+++|++||+++.+|+++.+|++..+.+|.+|++..+++.+.+++++.
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 4459999999999999999999985 356899999999999999999999876556899999999999998888765
Q ss_pred hh-cccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccc
Q 010835 328 SR-TLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSY 406 (499)
Q Consensus 328 ~R-~vRip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~ 406 (499)
.+ ..+.+ ....+++... ..++....+.+.
T Consensus 84 ~~~~~r~~-----------------------------------------------~~~~~~~~~~---~~~~~~~~~~~~ 113 (189)
T TIGR02984 84 LGAQKRDI-----------------------------------------------RREQSLDAGG---RLDESSVRLAAQ 113 (189)
T ss_pred HHHHhhhc-----------------------------------------------ccccCCCccc---ccCCcchhHHHH
Confidence 21 00000 0011111110 000111122223
Q ss_pred cccccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010835 407 IADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA 486 (499)
Q Consensus 407 i~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~ 486 (499)
+.+. .++|++.+...+....|..+| ..|||++|.||.++| ++|+|++|||+.||||+++|++.++||+++||+.
T Consensus 114 ~~~~--~~~~~~~~~~~e~~~~l~~~l-~~L~~~~r~vi~l~~---~~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~ 187 (189)
T TIGR02984 114 LAAD--GPSPSQVAARREAAVRLAQAL-AKLPEDYREVILLRH---LEGLSFAEVAERMDRSEGAVSMLWVRGLARLRQI 187 (189)
T ss_pred ccCC--CCCHHHHHHHHHHHHHHHHHH-HcCCHHHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3222 235666777777778899999 899999999999999 8999999999999999999999999999999987
Q ss_pred H
Q 010835 487 A 487 (499)
Q Consensus 487 L 487 (499)
+
T Consensus 188 l 188 (189)
T TIGR02984 188 L 188 (189)
T ss_pred h
Confidence 6
No 67
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=1.4e-20 Score=177.04 Aligned_cols=166 Identities=17% Similarity=0.161 Sum_probs=132.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcc
Q 010835 252 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 331 (499)
Q Consensus 252 ~~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~v 331 (499)
++..||+.|+..|.|.|+.++++|.++..+++|++||+++.+|+++.+|++.. +|.+|++..+++.+.++++...+..
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 45589999999999999999999999999999999999999999999999864 6999999999988777765543200
Q ss_pred cccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCcccccccccc
Q 010835 332 RLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNR 411 (499)
Q Consensus 332 Rip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~ 411 (499)
+. ++.. . +.. +..
T Consensus 82 ~~-----------------------------------------------------~~~~--------~-----~~~-~~~ 94 (179)
T PRK12543 82 RI-----------------------------------------------------FEKA--------E-----EQR-KPV 94 (179)
T ss_pred cc-----------------------------------------------------cccc--------c-----ccc-ccc
Confidence 00 0000 0 000 000
Q ss_pred CCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010835 412 VENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 491 (499)
Q Consensus 412 ~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~ 491 (499)
....|+. +...+....|..+| ..|||++|.||.|+| ++|+|++|||+.||+|.++|+..++||+++||+.+....
T Consensus 95 ~~~~~~~-~~~~~~~~~l~~~l-~~Lp~~~r~i~~l~~---~e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~ 169 (179)
T PRK12543 95 SIDFSED-VLSKESNQELIELI-HKLPYKLRQVIILRY---LHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIEE 169 (179)
T ss_pred cccChHH-HHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 0123444 56667778899999 899999999999999 899999999999999999999999999999999997653
No 68
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=99.86 E-value=7.1e-21 Score=177.58 Aligned_cols=157 Identities=16% Similarity=0.142 Sum_probs=126.1
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 334 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip 334 (499)
.|++.|+..|.|.|+.+|+++.++..+++|++||+|+++|++++.|++. .+|.+|++..+++.+.+++++..+.....
T Consensus 18 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~r~~~~~~~~~ 95 (176)
T PRK09638 18 AALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASRLYKDHLRKQKREKLRL 95 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHHhccccchh
Confidence 9999999999999999999999999999999999999999999999874 47999999999999999988764310000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCC
Q 010835 335 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 414 (499)
Q Consensus 335 ~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~ 414 (499)
+.+ .+. ..+ ..
T Consensus 96 --------------------------~~~-----------------------~~~-----------------~~~---~~ 106 (176)
T PRK09638 96 --------------------------QRA-----------------------KEE-----------------TLR---KE 106 (176)
T ss_pred --------------------------hhc-----------------------ccc-----------------cCC---cc
Confidence 000 000 000 00
Q ss_pred CCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010835 415 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 487 (499)
Q Consensus 415 ~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L 487 (499)
+ .+.....+....|..+| ..||+++|.||.++| ++|+|++|||+.||+|.++|++++.||+++||+.+
T Consensus 107 ~-~~~~~~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~l 174 (176)
T PRK09638 107 K-WEAAIKGAEWSEMLDAL-SKLDPEFRAPVILKH---YYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKEW 174 (176)
T ss_pred c-hHHHHHhhhHHHHHHHH-HcCCHHHhheeeehh---hcCCCHHHHHHHHCCChhHHHHHHHHHHHHHHHHh
Confidence 0 01122334456688899 899999999999998 89999999999999999999999999999999976
No 69
>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=99.86 E-value=1.7e-20 Score=186.13 Aligned_cols=182 Identities=16% Similarity=0.143 Sum_probs=143.2
Q ss_pred HHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHH
Q 010835 210 EVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGG 289 (499)
Q Consensus 210 Ee~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG 289 (499)
++..|+..++.||. .||+.|+..|.+.|+.++.++.++..+++|++||+
T Consensus 25 ~d~~Li~~~~~gd~-------------------------------~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEv 73 (244)
T TIGR03001 25 ADLYLACACAQGEP-------------------------------AALAALERHVLSKVPARLAGLRPPTAFVDEVLQRL 73 (244)
T ss_pred cHHHHHHHHHcCcH-------------------------------HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence 45568888888887 99999999999999999999999999999999999
Q ss_pred HHHHHH-------hhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHcCCCCCHHH
Q 010835 290 LIGLLR-------GIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDR 362 (499)
Q Consensus 290 ~IgL~r-------AiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L~~~gr~pt~eE 362 (499)
|+.+|. .+.+|++. ..|.+|++..++|.+.+++++..+...+
T Consensus 74 Flkl~~~~~~~~~~~~~~~~~--~~~~tWL~~Ia~N~~id~lRk~~r~~~~----------------------------- 122 (244)
T TIGR03001 74 RQRLLVPRAERPPRIAEYSGR--GPLLSWVRIVATRIALELQAQERRHSPV----------------------------- 122 (244)
T ss_pred HHHHHHhccchhhhhhccCCC--CchHhHHHHHHHHHHHHHHHHhcccCcc-----------------------------
Confidence 999994 78889864 3699999999999999988765421000
Q ss_pred HHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHH----HHHHHHHHHHHHhhCC
Q 010835 363 IAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDD----WALKDEVNKLIIVTLG 438 (499)
Q Consensus 363 IA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~----~el~~~L~~~L~~~L~ 438 (499)
+. .....+. .+. ..+|++.+.. .+....|.++| ++||
T Consensus 123 -------------------------~~----------~~~~~~~-~~~--~~~~e~~~~~~e~~~e~~~~l~~aL-~~Lp 163 (244)
T TIGR03001 123 -------------------------EE----------PTELAAL-PAP--GSDPELDLLRERYRQDFRQALREAL-AALS 163 (244)
T ss_pred -------------------------cc----------ccccccc-cCC--CCCHHHHHHHHhhHHHHHHHHHHHH-HhCC
Confidence 00 0000000 001 1134433332 23556789999 9999
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHh
Q 010835 439 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAM 495 (499)
Q Consensus 439 ~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~l~~~ 495 (499)
+++|+||.|+| .+|+|++|||++||||.+||+.+++||+++||+.+.+...+.|
T Consensus 164 ~~~R~v~~L~~---~eg~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~~~~~~ 217 (244)
T TIGR03001 164 ERERHLLRLHF---VDGLSMDRIGAMYQVHRSTVSRWVAQARERLLERTRRRLAERL 217 (244)
T ss_pred HHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 99999999999 8999999999999999999999999999999999988766543
No 70
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=2e-20 Score=176.20 Aligned_cols=159 Identities=19% Similarity=0.169 Sum_probs=125.6
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhC-CCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDN-MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 333 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~-~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRi 333 (499)
.|++.|+..|.+.|+.++.++.+ ...+++|++||+|+++|++++.|++. .+|.+|++..++|.+.+++++..+....
T Consensus 21 ~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~~~d~~Rk~~~~~~~ 98 (181)
T PRK12536 21 AAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYKLMDFLRSRARREAL 98 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHHHHHHHHHHhccccc
Confidence 99999999999999999998774 57899999999999999999999974 3699999999999999998876431000
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCC
Q 010835 334 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE 413 (499)
Q Consensus 334 p~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e 413 (499)
. .+++. ..+...+
T Consensus 99 ~--------------------------------------------------~~~~~-------------~~~~~~~---- 111 (181)
T PRK12536 99 H--------------------------------------------------DPLDD-------------ESELFAT---- 111 (181)
T ss_pred c--------------------------------------------------CCccc-------------hhhhcCC----
Confidence 0 00000 0000000
Q ss_pred CCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010835 414 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 490 (499)
Q Consensus 414 ~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~ 490 (499)
..++ ..+....+.++| ..||+++|.||.++| .+|+|++|||+.||+|++||++++++|+++||+.+..+
T Consensus 112 ~~~~----~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l~~~ 180 (181)
T PRK12536 112 SDDE----AAEARRDLGKLL-EQLPDRQRLPIVHVK---LEGLSVAETAQLTGLSESAVKVGIHRGLKALAAKIRGE 180 (181)
T ss_pred CCcc----hHHHHHHHHHHH-HHCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcCC
Confidence 0111 123445688999 999999999999999 89999999999999999999999999999999987643
No 71
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=99.86 E-value=2.4e-20 Score=175.08 Aligned_cols=160 Identities=16% Similarity=0.115 Sum_probs=119.6
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCC-----CHHHHHHHHHHHHHH-hhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhh
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGA-----DMADLVQGGLIGLLR-GIEKFDSSKGFKISTYVYWWIRQGVSRALVENS 328 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~-----d~EDLiQEG~IgL~r-AiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~ 328 (499)
.|++.|+..|.+.|+.+|+++.++.. +++|++||+|+.+|+ ...+|++. ..|.+|++.+++|.+.+++++..
T Consensus 17 ~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~~ 94 (183)
T TIGR02999 17 AARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAKAMRRILVDHARRRR 94 (183)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999998877 899999999999998 78889754 36999999999999888887754
Q ss_pred hcccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccc
Q 010835 329 RTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIA 408 (499)
Q Consensus 329 R~vRip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~ 408 (499)
+..+... ..+ ..+.+...
T Consensus 95 ~~~~~~~--------------------------------------------------~~~------------~~~~~~~~ 112 (183)
T TIGR02999 95 AQKRGGG--------------------------------------------------AVR------------VPLDEVLP 112 (183)
T ss_pred HHhccCC--------------------------------------------------ccc------------cccccccC
Confidence 2100000 000 00000000
Q ss_pred cccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010835 409 DNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 487 (499)
Q Consensus 409 d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L 487 (499)
...+. ..+.......+...| ..||+++|.||.|+| ++|+|++|||+.||+|.+||+.+++||+++||+.+
T Consensus 113 ----~~~~~-~~~~~~~l~~~~~~l-~~Lp~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 182 (183)
T TIGR02999 113 ----DAEAD-LDEELLDLDDALDKL-AQVDPRQAEVVELRF---FAGLTVEEIAELLGVSVRTVERDWRFARAWLADEL 182 (183)
T ss_pred ----CCCcc-HHHHHHHHHHHHHHh-hcCCHHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 01111 111111223344445 679999999999999 89999999999999999999999999999999875
No 72
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=99.86 E-value=1.4e-20 Score=178.43 Aligned_cols=177 Identities=17% Similarity=0.126 Sum_probs=138.5
Q ss_pred cCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHHHHhHhhCCCCCHH
Q 010835 204 ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMA 283 (499)
Q Consensus 204 ~~Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~E 283 (499)
|-.+.+++..|+.++++||. .||+.|+..|.+.|+.++. +.++..+++
T Consensus 4 ~~~~~~~~~~l~~~~~~gd~-------------------------------~af~~l~~~~~~~l~~~~~-~~~~~~~Ae 51 (185)
T PRK09649 4 TASDDEAVTALALSAAKGNG-------------------------------RALEAFIKATQQDVWRFVA-YLSDVGSAD 51 (185)
T ss_pred cccccHHHHHHHHHHHccCH-------------------------------HHHHHHHHHHHHHHHHHHH-HhCCHHHHH
Confidence 44556778889999999998 9999999999999999995 688889999
Q ss_pred HHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHcCCCCCHHHH
Q 010835 284 DLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRI 363 (499)
Q Consensus 284 DLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L~~~gr~pt~eEI 363 (499)
|++||+|+.+|+.+++|++. ..|.+|++..++|.+.+++++..+..+..
T Consensus 52 DivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~~~d~~Rk~~~~~~~~----------------------------- 100 (185)
T PRK09649 52 DLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVADHIRHVRSRPRTT----------------------------- 100 (185)
T ss_pred HHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHHHHHHHHHhccccccc-----------------------------
Confidence 99999999999999999964 36999999999999999988754210000
Q ss_pred HHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHH
Q 010835 364 AEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGERERE 443 (499)
Q Consensus 364 A~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~ 443 (499)
.+. .. +... ++.......+....+..+| ..||+++|.
T Consensus 101 -----------------------~~~---------~~----~~~~------~~~~~~~~~e~~~~l~~~l-~~Lp~~~r~ 137 (185)
T PRK09649 101 -----------------------RGA---------RP----EHLI------DGDRHARGFEDLVEVTTMI-ADLTTDQRE 137 (185)
T ss_pred -----------------------ccc---------ch----hhcc------ChhhhhhhHHHHHHHHHHH-HhCCHHHhH
Confidence 000 00 0000 0000011122234578889 999999999
Q ss_pred HHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010835 444 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 489 (499)
Q Consensus 444 VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~ 489 (499)
||.|+| ++|+|++|||+.||+|.++|+++++||+++||+.+..
T Consensus 138 v~~L~~---~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~~~~ 180 (185)
T PRK09649 138 ALLLTQ---LLGLSYADAAAVCGCPVGTIRSRVARARDALLADAEP 180 (185)
T ss_pred HhhhHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCc
Confidence 999999 8999999999999999999999999999999986543
No 73
>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=99.86 E-value=2e-20 Score=173.78 Aligned_cols=153 Identities=20% Similarity=0.207 Sum_probs=123.6
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 334 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip 334 (499)
.|++.|+..|.+.|+++|.++.++..+++|++||+++.+|+.+++|++.. +|.+|++..+++.+.+++++..+. .
T Consensus 16 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~--~- 90 (169)
T TIGR02954 16 PAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPK--YFNTWLTRILINECIDLLKKKKKV--I- 90 (169)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCcc--ccHHHHHHHHHHHHHHHHHhcCCc--C-
Confidence 99999999999999999999999999999999999999999999999753 699999999999888888765420 0
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCC
Q 010835 335 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 414 (499)
Q Consensus 335 ~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~ 414 (499)
+++.. .. ..+.
T Consensus 91 ---------------------------------------------------~~~~~----------~~----~~~~---- 101 (169)
T TIGR02954 91 ---------------------------------------------------PFDPN----------TS----IEKG---- 101 (169)
T ss_pred ---------------------------------------------------ccccc----------cc----cccc----
Confidence 00000 00 0000
Q ss_pred CCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010835 415 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 488 (499)
Q Consensus 415 ~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~ 488 (499)
++. .+. +....+..+| ..||+++|+||.++| ++|+|++|||+.||+|.++|+++++||+++||+.+.
T Consensus 102 ~~~--~~~-~~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~l~ 168 (169)
T TIGR02954 102 ECE--THA-DSRLDLYKAI-DTLNDKYQTAIILRY---YHDLTIKEIAEVMNKPEGTVKTYLHRALKKLKKRLE 168 (169)
T ss_pred hhh--hch-HHHHHHHHHH-HhCCHHHhHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 010 011 1123688888 899999999999999 899999999999999999999999999999999774
No 74
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=3.8e-20 Score=174.81 Aligned_cols=172 Identities=17% Similarity=0.184 Sum_probs=135.7
Q ss_pred HHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHHHHhH----hhCCCCCHHHH
Q 010835 210 EVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQR----YDNMGADMADL 285 (499)
Q Consensus 210 Ee~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sIA~r----y~~~g~d~EDL 285 (499)
....|+..++.||. .||+.|+..|.+.|+.+|++ +.++..+++|+
T Consensus 7 ~~~~l~~~~~~gd~-------------------------------~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDl 55 (184)
T PRK12539 7 ELKALMLASLDGDA-------------------------------AAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDL 55 (184)
T ss_pred HHHHHHHHHHcCCH-------------------------------HHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHH
Confidence 45567888888887 99999999999999999874 55788999999
Q ss_pred HHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHH
Q 010835 286 VQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAE 365 (499)
Q Consensus 286 iQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~ 365 (499)
+||+++.+|++++.|++.. .|.+|++..+++.+.+++++..+.. .
T Consensus 56 vQe~~l~l~~~~~~~~~~~--~f~~wl~~i~~n~~~d~~R~~~~~~-~-------------------------------- 100 (184)
T PRK12539 56 VQEALMAIHTRRHTYDPEQ--PLTPWVYAIARYKLIDHLRRTRASL-A-------------------------------- 100 (184)
T ss_pred HHHHHHHHHHHHhhcCCCC--ChHHHHHHHHHHHHHHHHHHHhccc-c--------------------------------
Confidence 9999999999999999753 6999999999998888887754200 0
Q ss_pred HhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHH
Q 010835 366 YLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREII 445 (499)
Q Consensus 366 ~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI 445 (499)
..+.+. .. +. .+.+.....+....+..+| ..||+++|+||
T Consensus 101 ------------------~~~~~~----------~~---~~--------~~~~~~~~~e~~~~l~~~l-~~L~~~~r~v~ 140 (184)
T PRK12539 101 ------------------DVPIDD----------AD---EL--------VAHDDHAAVESTLDLGRLL-ARLPEKMRLAI 140 (184)
T ss_pred ------------------ccChhh----------hc---cc--------cCCcHHhhHHHHHHHHHHH-HhCCHHHHHHH
Confidence 000000 00 00 0011112334456788999 89999999999
Q ss_pred HHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010835 446 RLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 490 (499)
Q Consensus 446 ~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~ 490 (499)
.|+| ++|+|++|||+.||+|.+||++++++|+++||+.+...
T Consensus 141 ~l~~---~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~ 182 (184)
T PRK12539 141 QAVK---LEGLSVAEAATRSGMSESAVKVSVHRGLKALAALIGRE 182 (184)
T ss_pred HHHH---HcCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHhhc
Confidence 9999 89999999999999999999999999999999988654
No 75
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=99.86 E-value=2.2e-20 Score=173.97 Aligned_cols=163 Identities=16% Similarity=0.077 Sum_probs=130.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccc
Q 010835 253 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 332 (499)
Q Consensus 253 ~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vR 332 (499)
+..+|+.|+..|.+.|+++|+++.++..+++|++||+|+.+|+..++|++.. ..|.+|++..++|.+.+++++..+...
T Consensus 7 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~Rk~~~~~~ 85 (173)
T PRK09645 7 EAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSARARPV 85 (173)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHHHHHHHhhccccc
Confidence 4589999999999999999999999999999999999999999999997533 369999999999998888876542100
Q ss_pred ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccC
Q 010835 333 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRV 412 (499)
Q Consensus 333 ip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~ 412 (499)
. . .++.. +. .
T Consensus 86 ~-----------------------------------------------------~---------~~~~~---~~-~---- 95 (173)
T PRK09645 86 E-----------------------------------------------------G---------GDDVL---GV-P---- 95 (173)
T ss_pred c-----------------------------------------------------c---------ccccc---cC-C----
Confidence 0 0 00000 00 0
Q ss_pred CCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010835 413 ENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 490 (499)
Q Consensus 413 e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~ 490 (499)
+..+.+.+...+....|..+| +.||+++|+||.|+| ++|+|++|||+.||+|.+||+.+++||+++||+.+...
T Consensus 96 ~~~~~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~L~~---~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~ 169 (173)
T PRK09645 96 EQSAPDEVDRALDRLLVADAL-AQLSPEHRAVLVRSY---YRGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQER 169 (173)
T ss_pred CCCCchHHHHHhHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhcc
Confidence 012222333444456788999 999999999999999 89999999999999999999999999999999998754
No 76
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=3.8e-20 Score=174.29 Aligned_cols=157 Identities=17% Similarity=0.208 Sum_probs=124.4
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhC----CCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDN----MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRT 330 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~----~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~ 330 (499)
.|++.|+..|.+.|+.+|+++++ +..+++|++||+++.+|...++|++. .+|.+|++..+++.+.+++++..+.
T Consensus 22 ~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn~~~d~~Rr~~~~ 99 (184)
T PRK12512 22 AAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARNKLIDALRRRGRR 99 (184)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHHHHHHHHHhhccc
Confidence 99999999999999999999885 34799999999999999999999864 3699999999999888888765421
Q ss_pred ccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccc
Q 010835 331 LRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADN 410 (499)
Q Consensus 331 vRip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~ 410 (499)
... +++. ..+.+.+.
T Consensus 100 ~~~----------------------------------------------------~~~~-------------~~~~~~~~ 114 (184)
T PRK12512 100 VFV----------------------------------------------------DIDD-------------FAETLPAE 114 (184)
T ss_pred ccC----------------------------------------------------Cchh-------------cccccccc
Confidence 000 0000 00001110
Q ss_pred cCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010835 411 RVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 490 (499)
Q Consensus 411 ~~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~ 490 (499)
.+ ........+.++| ..||+++|+||.++| .+|+|++|||+.||+|..+|+..+++|+++||..+..+
T Consensus 115 ----~~----~~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~~~ 182 (184)
T PRK12512 115 ----PA----TETLPAGDVGRHL-ETLPPRQRDVVQSIS---VEGASIKETAAKLSMSEGAVRVALHRGLAALAAKFRSE 182 (184)
T ss_pred ----ch----hhHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Confidence 00 1122345678889 899999999999999 89999999999999999999999999999999988754
No 77
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=99.85 E-value=2.5e-20 Score=175.42 Aligned_cols=164 Identities=15% Similarity=0.159 Sum_probs=134.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccc
Q 010835 253 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 332 (499)
Q Consensus 253 ~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vR 332 (499)
+..|+++|+..|.+.|+++|+++.++..+++|++||+|+.+|+++.+|++. ..|.+|++..+++.+.+++++..+...
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 458999999999999999999999999999999999999999999999864 369999999999988888877542100
Q ss_pred ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccC
Q 010835 333 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRV 412 (499)
Q Consensus 333 ip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~ 412 (499)
.+ .+. .......+
T Consensus 92 ~~----------------------------------------------------~~~------------~~~~~~~~--- 104 (179)
T PRK09415 92 IV----------------------------------------------------TED------------IFTYMESQ--- 104 (179)
T ss_pred cc----------------------------------------------------ccc------------cccccccc---
Confidence 00 000 00000000
Q ss_pred CCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010835 413 ENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 489 (499)
Q Consensus 413 e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~ 489 (499)
.++|++.+...+....|..+| .+||+++|+||.|+| ++|+|++|||+.||+|.++|++++.||+++||+.+..
T Consensus 105 ~~~~e~~~~~~e~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l~~ 177 (179)
T PRK09415 105 KESVEEEVIQNAEDERLASAV-MSLPIKYREVIYLFY---YEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEE 177 (179)
T ss_pred ccCcHHHHHHHHHHHHHHHHH-HhCCHHHhhHhHhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 135666666777788899999 899999999999999 8999999999999999999999999999999998754
No 78
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=1.8e-20 Score=177.85 Aligned_cols=182 Identities=15% Similarity=0.123 Sum_probs=136.6
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 334 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip 334 (499)
.+|+.|+..|.+.|+.+|++++++..+++|++||+|+.+|+.+++|++.. +|.+|++..++|.+.+++++..+....+
T Consensus 2 ~~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~~--~~~~WL~~ia~n~~~d~~Rk~~r~~~~~ 79 (191)
T PRK12520 2 TIAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQS--SLKTYLVGILKHKIIDAIRSGRREVRLS 79 (191)
T ss_pred cchHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhcccc--cHHHHHHHHHHHHHHHHHHhhcCcCccc
Confidence 47899999999999999999999999999999999999999999998643 6999999999999999988765421111
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCC
Q 010835 335 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 414 (499)
Q Consensus 335 ~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~ 414 (499)
..... .....++ ++. ... .+. .....++. ..
T Consensus 80 ~~~~~-----------------~~~~~~~-----------------------~~~-----~~~-~~~-~~~~~~~~--~~ 110 (191)
T PRK12520 80 LDDAD-----------------EQSDDDL-----------------------FDA-----LFA-ADG-HYREPPSD--WG 110 (191)
T ss_pred ccccc-----------------cchhhhh-----------------------hhh-----hcc-ccc-ccccCccc--cC
Confidence 00000 0000000 000 000 000 00001111 13
Q ss_pred CCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010835 415 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 491 (499)
Q Consensus 415 ~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~ 491 (499)
+|++.+...+....|..+| ..||+++|.||.|+| ++|+|++|||+.||+|.+||+++++||+++||+.+...+
T Consensus 111 ~~~~~~~~~~~~~~l~~~l-~~Lp~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 183 (191)
T PRK12520 111 DPDAALSRREFFEVLQACV-DRLPPRTGRVFMMRE---WLELETEEICQELQITATNAWVLLYRARMRLRECLDLHW 183 (191)
T ss_pred CHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5666666677778899999 999999999999999 899999999999999999999999999999999998776
No 79
>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=99.85 E-value=1.5e-20 Score=171.12 Aligned_cols=161 Identities=20% Similarity=0.217 Sum_probs=129.6
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 334 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip 334 (499)
.|+++|+..|.|.|+.+++++.++..+++|++||+++++|+++.+|++.. +|.+|++.++++.+.+++++..+....
T Consensus 1 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~~--~~~~wl~~i~r~~~~d~~r~~~~~~~~- 77 (161)
T TIGR02985 1 KAFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEVE--SFKAYLFTIVKNRSLNYLRHKQVEEKY- 77 (161)
T ss_pred ChHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhccccc--cHHHHHHHHHHHHHHHHHHHHHhHhHH-
Confidence 37999999999999999999999999999999999999999999998643 799999999999998888776431000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCC
Q 010835 335 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 414 (499)
Q Consensus 335 ~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~ 414 (499)
... +.. . .. .....+
T Consensus 78 -------------~~~------------------------------------~~~-------~-~~--------~~~~~~ 92 (161)
T TIGR02985 78 -------------QEE------------------------------------ILE-------I-EV--------DELSEN 92 (161)
T ss_pred -------------HHH------------------------------------HHh-------h-cc--------cccCCC
Confidence 000 000 0 00 000012
Q ss_pred CCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010835 415 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 487 (499)
Q Consensus 415 ~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L 487 (499)
+|++.+...+....+..++ ..||++++.||.++| .+|+|.+|||+.||+|+++|++++++|+++||+.|
T Consensus 93 ~~~~~~~~~e~~~~l~~~l-~~L~~~~r~il~l~~---~~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~l 161 (161)
T TIGR02985 93 DPEEELEAKELQLIIYKAI-EKLPEQCRKIFILSR---FEGKSYKEIAEELGISVKTVEYHISKALKELRKEL 161 (161)
T ss_pred CcHHHHHHHHHHHHHHHHH-HHCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 4555666677778899999 899999999999988 79999999999999999999999999999999753
No 80
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=3.8e-20 Score=172.77 Aligned_cols=168 Identities=13% Similarity=0.092 Sum_probs=131.7
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 334 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip 334 (499)
..+++|+..|.++|+.+|++|.++..+++|++||+++.+|+++++|++.. +|.+|++..++|.+.+++++..+....+
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 56999999999999999999999999999999999999999999999754 7999999999999999988765411000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCC
Q 010835 335 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 414 (499)
Q Consensus 335 ~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~ 414 (499)
.. .. +.....+...... ..
T Consensus 81 ~~--------------------------------------------------~~----------~~~~~~~~~~~~~-~~ 99 (173)
T PRK12522 81 LD--------------------------------------------------LF----------HKEDGGEIEFADD-VN 99 (173)
T ss_pred cc--------------------------------------------------cc----------chhhhhhhccccC-CC
Confidence 00 00 0000000000000 11
Q ss_pred CCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010835 415 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 490 (499)
Q Consensus 415 ~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~ 490 (499)
.|+. +...+..+.+..+| ..||++++.||.|+| .+|+|++|||+.||+|.++|+.+++||+++||+.+...
T Consensus 100 ~~~~-~~~~~~~~~l~~~l-~~L~~~~r~i~~l~~---~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~ 170 (173)
T PRK12522 100 ISEE-FIQKVEAEMIREVI-QLLNEKYKTVLVLYY---YEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEGF 170 (173)
T ss_pred ChHH-HHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 2222 45566778899999 899999999999999 89999999999999999999999999999999988653
No 81
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=2.4e-20 Score=173.84 Aligned_cols=163 Identities=15% Similarity=0.129 Sum_probs=126.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccc
Q 010835 254 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 333 (499)
Q Consensus 254 ~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRi 333 (499)
..|++.|+..|.+.|+.+++++.+ ..+++|++||+|+.+|+.++.|++. ..|.+|++..+++.+.+++++..+...
T Consensus 10 ~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~~~~~~- 85 (175)
T PRK12518 10 RQSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARRQFAQRPS- 85 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHHHhhcccc-
Confidence 399999999999999999999875 4789999999999999999999974 369999999999988888776532000
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCC
Q 010835 334 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE 413 (499)
Q Consensus 334 p~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e 413 (499)
. ... ..... ....
T Consensus 86 --~--------------------------------------------------~~~-------~~~~~----~~~~---- 98 (175)
T PRK12518 86 --R--------------------------------------------------IQD-------DSLND----QPSR---- 98 (175)
T ss_pred --c--------------------------------------------------hhc-------ccccc----cccC----
Confidence 0 000 00000 0000
Q ss_pred CCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010835 414 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 491 (499)
Q Consensus 414 ~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~ 491 (499)
..+.......+....+..+| +.||+++|.||.|+| ++|+|++|||+.||+|.++|++.++||+++||+.+.+.+
T Consensus 99 ~~~~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~~---~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~~~~ 172 (175)
T PRK12518 99 PSDTPDLMQLHYQDLVQQGL-QTLSLEHRAVLVLHD---LEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQQG 172 (175)
T ss_pred CCCcHHHHHHHHHHHHHHHH-HhCCHHHeeeeeehH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 01111223334446688889 899999999999999 899999999999999999999999999999999987643
No 82
>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=99.85 E-value=2.1e-20 Score=171.26 Aligned_cols=159 Identities=15% Similarity=0.176 Sum_probs=126.8
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 334 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip 334 (499)
+||+.++..|.|.|+.+|+++.++..++||++||+++.+|+++++|++.. .|.+|++..+++.+.+++++..+....
T Consensus 1 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~~- 77 (159)
T TIGR02989 1 EAFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRLV- 77 (159)
T ss_pred CHHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhcccccc-
Confidence 37899999999999999999999999999999999999999999999754 699999999999999998887531100
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCC
Q 010835 335 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 414 (499)
Q Consensus 335 ~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~ 414 (499)
.. ++. .+.+.+. .
T Consensus 78 ~~------------------------~~~----------------------------------------~~~~~~~---~ 90 (159)
T TIGR02989 78 FD------------------------DEL----------------------------------------LEALAAE---A 90 (159)
T ss_pred cC------------------------HHH----------------------------------------HHHHHhh---c
Confidence 00 000 0000000 0
Q ss_pred CCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010835 415 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 487 (499)
Q Consensus 415 ~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L 487 (499)
+|.+.....+....+..+| +.||++++.||.++| .+|++++|||+.||||+++|++.++||+++||+.+
T Consensus 91 ~~~~~~~~~~~~~~l~~~i-~~L~~~~r~v~~l~~---~~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~~~ 159 (159)
T TIGR02989 91 EATEADRSEDELQALEGCL-EKLPERQRELLQLRY---QRGVSLTALAEQLGRTVNAVYKALSRLRVRLRDCV 159 (159)
T ss_pred ccchHhhHHHHHHHHHHHH-HHCCHHHHHHHHHHH---hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcC
Confidence 1222223344556788999 999999999999998 89999999999999999999999999999999753
No 83
>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=99.85 E-value=3.8e-20 Score=164.92 Aligned_cols=158 Identities=25% Similarity=0.337 Sum_probs=131.7
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 334 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip 334 (499)
.|++.|+..|.++|+++++++..++.+.+|++||+++++|++++.|++. .+|.+|++.++++.+.+++++..+ .+
T Consensus 1 ~a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~---~~ 75 (158)
T TIGR02937 1 EAFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR---LR 75 (158)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhcc---CC
Confidence 3789999999999999999999999999999999999999999999997 589999999999999999888764 11
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCC
Q 010835 335 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 414 (499)
Q Consensus 335 ~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~ 414 (499)
.... . ........+
T Consensus 76 ~~~~--------------------------------------------------~----------------~~~~~~~~~ 89 (158)
T TIGR02937 76 RELD--------------------------------------------------L----------------LEELLDSDP 89 (158)
T ss_pred cchh--------------------------------------------------h----------------hhhcccccC
Confidence 0000 0 000000123
Q ss_pred CCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010835 415 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 487 (499)
Q Consensus 415 ~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L 487 (499)
+|.+..........+..+| ..||+.++.||.++| ..|+|..|||+.+|+|+.+|++++.+++++||+.+
T Consensus 90 ~~~~~~~~~~~~~~l~~~l-~~L~~~~~~ii~~~~---~~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~l 158 (158)
T TIGR02937 90 SPEEELEQEEEREALREAL-EKLPEREREVLVLRY---LEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158 (158)
T ss_pred CHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHhhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 4555666777788899999 899999999999998 78999999999999999999999999999999753
No 84
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=99.84 E-value=3.4e-20 Score=170.64 Aligned_cols=156 Identities=12% Similarity=0.076 Sum_probs=125.7
Q ss_pred HHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHH
Q 010835 262 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 341 (499)
Q Consensus 262 e~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l 341 (499)
+.|.+.|+.+|++++++..+++|++||+|+.+|+++++|++. .|.+|++..++|.+.+++++..+....
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 579999999999999999999999999999999999999863 499999999999999998776431000
Q ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHH
Q 010835 342 GLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVD 421 (499)
Q Consensus 342 ~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve 421 (499)
..+.. +. .+.+. ...+|++.+.
T Consensus 71 -------------------------------------------~~~~~---------~~---~~~~~---~~~~~~~~~~ 92 (160)
T PRK09642 71 -------------------------------------------LSLCK---------ET---EENIK---SSHNIEDLLL 92 (160)
T ss_pred -------------------------------------------cccch---------hh---hhhcc---CCCChHHHHH
Confidence 00000 00 00000 0124555666
Q ss_pred HHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010835 422 DWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 490 (499)
Q Consensus 422 ~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~ 490 (499)
..+....+..+| +.||+++|.||.|+| .+|+|++|||+.||+|.+||+++++||+++||+.+...
T Consensus 93 ~~e~~~~l~~~l-~~Lp~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 157 (160)
T PRK09642 93 TKEQKLLIAQKL-RELPENYRDVVLAHY---LEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKEE 157 (160)
T ss_pred HHHHHHHHHHHH-HhCCHHHHHHHHHHH---HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhh
Confidence 667778899999 999999999999999 89999999999999999999999999999999998654
No 85
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=1.4e-19 Score=172.20 Aligned_cols=161 Identities=12% Similarity=0.146 Sum_probs=128.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccc
Q 010835 253 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 332 (499)
Q Consensus 253 ~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vR 332 (499)
+..+|+.|+..|.+.|+.+|++++++..+++|++||+|+.+|+..++|++.. .|.+|++..++|.+.+++++..+...
T Consensus 8 ~~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~~--~~~awL~~Ia~n~~~d~~R~~~~~~~ 85 (187)
T PRK12516 8 GTPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGT--NMKAWLFTILRNEFYSQMRKRGREVQ 85 (187)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCcc--cHHHHHHHHHHHHHHHHHHhhcCCcc
Confidence 4589999999999999999999999999999999999999999999998643 69999999999988888877643100
Q ss_pred ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccC
Q 010835 333 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRV 412 (499)
Q Consensus 333 ip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~ 412 (499)
. .+. .+.+...
T Consensus 86 ~-----------------------------------------------------~~~------------~~~~~~~---- 96 (187)
T PRK12516 86 D-----------------------------------------------------TDG------------MFTEQLA---- 96 (187)
T ss_pred c-----------------------------------------------------ccc------------ccccccC----
Confidence 0 000 0000000
Q ss_pred CCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010835 413 ENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 491 (499)
Q Consensus 413 e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~ 491 (499)
..|+. ........|..+| ..||+++|+||.|+| ++|+|++|||+.||+|.++|+++++||+++||+.+...+
T Consensus 97 -~~~~~--~~~~~~~~l~~~L-~~Lp~~~r~i~~L~~---~~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~~~ 168 (187)
T PRK12516 97 -VHPSQ--YGTLDLQDFRAAL-DQLPDDQREAIILVG---ASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQIEG 168 (187)
T ss_pred -CCcch--hhHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence 01110 1122245688999 999999999999999 899999999999999999999999999999999997653
No 86
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=7.1e-20 Score=172.37 Aligned_cols=165 Identities=12% Similarity=-0.019 Sum_probs=128.7
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHhHhhC--CCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhh
Q 010835 251 MECSLAREKLVMSNVRLVMSIAQRYDN--MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS 328 (499)
Q Consensus 251 ~~~~~A~e~LIe~yl~LV~sIA~ry~~--~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~ 328 (499)
.++..||+.|+..|.+.|+.++..+.+ +..+++|++||+|+.+|+..++|++.....|.+|++..++|.+.+++++..
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 345599999999999999998766665 468899999999999999999998544457999999999998888876543
Q ss_pred hcccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccc
Q 010835 329 RTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIA 408 (499)
Q Consensus 329 R~vRip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~ 408 (499)
+.. . . .+. ..+...
T Consensus 89 ~~~----~-------------~------------------------------------~~~-------------~~~~~~ 102 (178)
T PRK12529 89 LEL----A-------------W------------------------------------LEA-------------LATLPE 102 (178)
T ss_pred HHh----h-------------h------------------------------------hhH-------------hhhccC
Confidence 100 0 0 000 000000
Q ss_pred cccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010835 409 DNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 487 (499)
Q Consensus 409 d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L 487 (499)
.. .++|++.+...+....|..+| ..||+++|.||.|+| .+|+|++|||+.||+|.+||+.++++|+.+++..+
T Consensus 103 ~~--~~~~e~~~~~~~~~~~l~~~l-~~Lp~~~R~v~~L~~---~~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~~ 175 (178)
T PRK12529 103 PL--HPSPEQQSVILETLHEIDALL-DTLRPRVKQAFLMAT---LDGMKQKDIAQALDIALPTVKKYIHQAYVTCLSLM 175 (178)
T ss_pred cC--CCCHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence 00 124555556666677899999 999999999999999 89999999999999999999999999999998764
No 87
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=99.84 E-value=2.3e-19 Score=169.27 Aligned_cols=171 Identities=22% Similarity=0.206 Sum_probs=136.3
Q ss_pred HhhhhhhHHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHH
Q 010835 247 QSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVE 326 (499)
Q Consensus 247 ~~~l~~~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~ 326 (499)
.....++..++..++..|.+.++.+|+++.++..+++||+||+|+.+|+++..| +. +..|.||++.+++|.+.+.+++
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~~R~ 84 (182)
T COG1595 7 AEALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDRLRK 84 (182)
T ss_pred HHHHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHHHHHH
Confidence 334455569999999999999999999999988899999999999999999999 33 3479999999999999999888
Q ss_pred hhhcccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccc
Q 010835 327 NSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSY 406 (499)
Q Consensus 327 ~~R~vRip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~ 406 (499)
..+.... .+. ......
T Consensus 85 ~~r~~~~-----------------------------------------------------~~~-----------~~~~~~ 100 (182)
T COG1595 85 RKRRRAR-----------------------------------------------------VEE-----------ADLLPE 100 (182)
T ss_pred hcccccc-----------------------------------------------------ccc-----------cccccc
Confidence 7642111 000 000000
Q ss_pred cccccCCCCCc-chHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 407 IADNRVENNPW-HGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 407 i~d~~~e~~Pe-e~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
..+.. .+. +.+...+....|..+| ..||+++|.||.|+| ++|+|++|||+.||||.+||+.++++|+.+||+
T Consensus 101 ~~~~~---~~~~~~~~~~~~~~~l~~al-~~Lp~~~R~~~~l~~---~~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~ 173 (182)
T COG1595 101 EADPA---PDLAELLLAEEELERLRRAL-ARLPPRQREAFLLRY---LEGLSYEEIAEILGISVGTVKSRLHRARKKLRE 173 (182)
T ss_pred ccCcc---cccchHHHHHHHHHHHHHHH-HhCCHHHhHHhhhHh---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 00000 111 2455677788899999 999999999999999 899999999999999999999999999999999
Q ss_pred HHHHh
Q 010835 486 AARKK 490 (499)
Q Consensus 486 ~L~~~ 490 (499)
.+...
T Consensus 174 ~l~~~ 178 (182)
T COG1595 174 QLEEA 178 (182)
T ss_pred HHhhc
Confidence 98754
No 88
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=1.4e-19 Score=176.51 Aligned_cols=169 Identities=15% Similarity=0.111 Sum_probs=135.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccc
Q 010835 254 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 333 (499)
Q Consensus 254 ~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRi 333 (499)
..+|..|+..|.+.++.+++++.++..+++|++||+|+.+|+.+++|++. .|.+|++..++|.+.++++++.+....
T Consensus 17 ~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~~~~~~~ 93 (216)
T PRK12533 17 GERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRRANAHEV 93 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhhcccccc
Confidence 48999999999999999999999999999999999999999999999853 499999999999999888776431000
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCC
Q 010835 334 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE 413 (499)
Q Consensus 334 p~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e 413 (499)
. ..+. .+.....+.+.+. .
T Consensus 94 ~---------------------------------------------------~~~~--------~~~~~~~~~~~~~--~ 112 (216)
T PRK12533 94 A---------------------------------------------------APDT--------LDDADSLDDWQPA--G 112 (216)
T ss_pred c---------------------------------------------------cccc--------ccccccccccccC--C
Confidence 0 0000 0000000000011 2
Q ss_pred CCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010835 414 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 490 (499)
Q Consensus 414 ~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~ 490 (499)
.+|++.+...+....|..+| ..||+++|+||.|+| ++++|++|||+.||||.++|+++++||+++||+.+...
T Consensus 113 ~~~e~~~~~~e~~~~l~~al-~~Lp~~~R~v~~L~y---~eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~ 185 (216)
T PRK12533 113 EDPLALLLRAEDVRLVNAAL-AKLPVEYREVLVLRE---LEDMSYREIAAIADVPVGTVMSRLARARRRLAALLGGA 185 (216)
T ss_pred CCHHHHHHHHHHHHHHHHHH-HcCCHHHHhHhhhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHccc
Confidence 35666777777888999999 999999999999999 89999999999999999999999999999999998654
No 89
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=99.83 E-value=2.2e-19 Score=172.13 Aligned_cols=183 Identities=16% Similarity=0.090 Sum_probs=139.9
Q ss_pred cCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHHHHhHhhCCCCCHH
Q 010835 204 ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMA 283 (499)
Q Consensus 204 ~~Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~E 283 (499)
|..+..+..+|+.+++.||. .|++.|+..|.+.++.++. +.++..+++
T Consensus 5 ~~~~~~~~~~l~~~~~~~d~-------------------------------~a~~~l~~~y~~~l~~~~~-~~~~~~~AE 52 (196)
T PRK12535 5 SERDDAHVTDLALAAGRGDR-------------------------------AALTEFIRETQDDVWRLLA-HLGGHDIAD 52 (196)
T ss_pred cccccHHHHHHHHHHHcCCH-------------------------------HHHHHHHHHHHHHHHHHHH-HhCCHHHHH
Confidence 34444555668888888887 9999999999999999975 678889999
Q ss_pred HHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHcCCCCCHHHH
Q 010835 284 DLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRI 363 (499)
Q Consensus 284 DLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L~~~gr~pt~eEI 363 (499)
|++||+|+.+|+..++|++. .+|.+|++..++|.+.+++++..+..+..
T Consensus 53 DivQevflkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~~~~~~----------------------------- 101 (196)
T PRK12535 53 DLTQETYLRVMSALPRFAAR--SSARTWLLSLARRVWVDNIRHDMARPRKS----------------------------- 101 (196)
T ss_pred HHHHHHHHHHHHHhhhcCCc--ccHHHHHHHHHHHHHHHHHHhhccCCCcc-----------------------------
Confidence 99999999999999999864 36999999999999999988764311100
Q ss_pred HHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHH
Q 010835 364 AEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGERERE 443 (499)
Q Consensus 364 A~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~ 443 (499)
.+ ..... .+.. .+|+... ..+....+..+| ..||+++|+
T Consensus 102 -----------------------~~----------~~~~~----~~~~--~~~~~~~-~~~~~~~l~~~l-~~Lp~~~r~ 140 (196)
T PRK12535 102 -----------------------AT----------EYEDA----AATT--ASNETTG-SWSEWIDVRTLI-DALPPERRE 140 (196)
T ss_pred -----------------------cc----------ccccc----cccc--CCcchhH-HHHHHHHHHHHH-HcCCHHHHH
Confidence 00 00000 0000 1122111 122235788899 999999999
Q ss_pred HHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHH
Q 010835 444 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKME 493 (499)
Q Consensus 444 VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~l~ 493 (499)
||.|+| ++|+|++|||+.||+|.+||+++++||+++||+.+......
T Consensus 141 v~~l~~---~~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~ 187 (196)
T PRK12535 141 ALILTQ---VLGYTYEEAAKIADVRVGTIRSRVARARADLIAATATGQAS 187 (196)
T ss_pred HhhhHH---HhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccccch
Confidence 999999 89999999999999999999999999999999998765443
No 90
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=99.83 E-value=1.8e-19 Score=167.12 Aligned_cols=161 Identities=16% Similarity=0.193 Sum_probs=127.6
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcc
Q 010835 252 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 331 (499)
Q Consensus 252 ~~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~v 331 (499)
.|...|.+++..|.+.|+.+|+++.++..+++|++||+|+.+|+...+|++.. .|.+|++..++|.+.+.+++..+..
T Consensus 3 ~~~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~~ 80 (164)
T PRK12547 3 KCSKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGT--NLKAWLFTILRNEFYSQMRKRGREV 80 (164)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhcccc
Confidence 45689999999999999999999999999999999999999999999998643 6999999999998888887754210
Q ss_pred cccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCcccccccccc
Q 010835 332 RLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNR 411 (499)
Q Consensus 332 Rip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~ 411 (499)
. . .+. . . ....
T Consensus 81 ~---~--------------------------------------------------~~~-----------~-~---~~~~- 91 (164)
T PRK12547 81 Q---D--------------------------------------------------SDG-----------V-F---TARV- 91 (164)
T ss_pred c---c--------------------------------------------------ccc-----------c-c---cccC-
Confidence 0 0 000 0 0 0000
Q ss_pred CCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010835 412 VENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 490 (499)
Q Consensus 412 ~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~ 490 (499)
..++.. +.......+..+| ..||+++|+||.|+| .+|+|++|||+.||+|+++|+++++||+++||..+...
T Consensus 92 -~~~~~~--~~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 163 (164)
T PRK12547 92 -AVHPAQ--YGSLDLQDFKKAL-NLLSADQREAIILIG---ASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLKVD 163 (164)
T ss_pred -CCCchh--hhHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence 001111 1122345788899 999999999999999 89999999999999999999999999999999988643
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=99.83 E-value=1.4e-19 Score=166.77 Aligned_cols=157 Identities=18% Similarity=0.170 Sum_probs=126.9
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcc
Q 010835 252 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 331 (499)
Q Consensus 252 ~~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~v 331 (499)
++..+++.|+..|.+.|+.+|+.++++..+++|++||+|+.+|+++++|+. ...|.+|++..+++.+.+++++..+.
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 455999999999999999999999999999999999999999999999964 34799999999999888887765320
Q ss_pred cccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCcccccccccc
Q 010835 332 RLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNR 411 (499)
Q Consensus 332 Rip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~ 411 (499)
.. . +. + . .+.
T Consensus 80 ~~----------------------------------------------------~-~~---------~------~-~~~- 89 (162)
T TIGR02983 80 EL----------------------------------------------------P-TR---------E------L-PDA- 89 (162)
T ss_pred cc----------------------------------------------------c-cc---------c------c-Ccc-
Confidence 00 0 00 0 0 000
Q ss_pred CCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010835 412 VENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 488 (499)
Q Consensus 412 ~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~ 488 (499)
++.+.....+..+.|..+| ..||+++|.||.|+| .+|+|++|||+.||+|.++|++++.||+++||+.+.
T Consensus 90 ---~~~~~~~~~~~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 159 (162)
T TIGR02983 90 ---AAPDPAPDVALRAALARAL-RRLPARQRAVVVLRY---YEDLSEAQVAEALGISVGTVKSRLSRALARLRELLE 159 (162)
T ss_pred ---cCCccchhHHHHHHHHHHH-HhCCHHHHHHhhhHH---HhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 0111122344567788899 899999999999999 899999999999999999999999999999999874
No 92
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=99.83 E-value=2.2e-19 Score=173.13 Aligned_cols=165 Identities=20% Similarity=0.258 Sum_probs=135.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccc
Q 010835 253 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 332 (499)
Q Consensus 253 ~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vR 332 (499)
+..+++.|+..|.+.|+.++.++.++..+++|++||+|+.+|+...+|++ + +|.+|++..+|+.+.+++++..+ .+
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 45999999999999999999999999999999999999999999999985 3 69999999999999998887642 00
Q ss_pred ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccC
Q 010835 333 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRV 412 (499)
Q Consensus 333 ip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~ 412 (499)
.. .++. + . +.....
T Consensus 102 ~~---------------------------------------------------~~~~---------~---~-~~~~~~-- 115 (203)
T PRK09647 102 ME---------------------------------------------------ALPE---------D---Y-DRVPGD-- 115 (203)
T ss_pred cc---------------------------------------------------cccc---------c---c-cccCCC--
Confidence 00 0000 0 0 000111
Q ss_pred CCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010835 413 ENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 491 (499)
Q Consensus 413 e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~ 491 (499)
..+|...++..++...|..+| ..||++++.||.|+| ++|++++|||+.||+|.++|++.+.||+++||+.+...+
T Consensus 116 ~~~~~~~~~~~~~~~~l~~~L-~~L~~~~r~v~~L~~---~~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~~~ 190 (203)
T PRK09647 116 EPNPEQIYHDARLDPDLQAAL-DSLPPEFRAAVVLCD---IEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAAHA 190 (203)
T ss_pred CCCHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 235555666777778899999 999999999999999 899999999999999999999999999999999987653
No 93
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=99.83 E-value=1.1e-19 Score=172.77 Aligned_cols=173 Identities=15% Similarity=0.172 Sum_probs=130.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccc
Q 010835 254 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 333 (499)
Q Consensus 254 ~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRi 333 (499)
..+|+.|+..|.+.|+.+|++++++..+++|++||+|+.+|+++.+|++. .+|.+|++..++|.+.+++++..+....
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 48999999999999999999999999999999999999999999999864 3699999999999999998876531100
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCC
Q 010835 334 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE 413 (499)
Q Consensus 334 p~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e 413 (499)
.. .+++.. ..+.. .... .... .
T Consensus 88 ~~------------------------~~~~~~-------------------~~~~~--------~~~~------~~~~-~ 109 (193)
T TIGR02947 88 SD------------------------DDDIED-------------------WQLAK--------AASH------TSNG-L 109 (193)
T ss_pred cc------------------------chhhhh-------------------hhhcc--------cccc------cccc-c
Confidence 00 000000 00000 0000 0000 0
Q ss_pred CCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010835 414 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 490 (499)
Q Consensus 414 ~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~ 490 (499)
..|+......+....|..+| ..||+++|.||.|+| .+|+|++|||+.||+|.+||+++++||+++||+.+...
T Consensus 110 ~~~e~~~~~~~~~~~l~~~l-~~Lp~~~r~i~~L~~---~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~ 182 (193)
T TIGR02947 110 RSAELEALDGLPDQDIKDAL-QGLPEEFRQAVYLAD---VEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVDV 182 (193)
T ss_pred cchhHHHHhhhhHHHHHHHH-HhCCHHHhhheeehh---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 12333333344556788999 999999999999999 89999999999999999999999999999999998653
No 94
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=99.83 E-value=1.9e-19 Score=166.84 Aligned_cols=157 Identities=15% Similarity=0.122 Sum_probs=130.2
Q ss_pred HHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccccc
Q 010835 257 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH 336 (499)
Q Consensus 257 ~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~ 336 (499)
|+.|+..|.|.|+.+|+++.++..+++|++||+|+.+|+++++|++. .|.+|++..+++.+.+++++..+.....
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~~-- 77 (165)
T PRK09644 3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFVG-- 77 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhccccc--
Confidence 67899999999999999999999999999999999999999999863 5999999999999999988765311000
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCC
Q 010835 337 LHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNP 416 (499)
Q Consensus 337 ~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~P 416 (499)
.+++ +.+. ..+|
T Consensus 78 -----------------------~~~~-----------------------------------------~~~~----~~~~ 89 (165)
T PRK09644 78 -----------------------TDEI-----------------------------------------EAIQ----AEST 89 (165)
T ss_pred -----------------------hhHH-----------------------------------------hhhc----ccCh
Confidence 0000 0000 1245
Q ss_pred cchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010835 417 WHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 490 (499)
Q Consensus 417 ee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~ 490 (499)
++.+...+....+..+| ..||+++|+||.|+| .+|+|++|||+.||+|.++|+++++||+++||+.+...
T Consensus 90 ~~~~~~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~ 159 (165)
T PRK09644 90 EEYVVAKNSYEKLIQII-HTLPVIEAQAILLCD---VHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEE 159 (165)
T ss_pred HHHHHHHHHHHHHHHHH-HhCCHHHHHHHHhHH---HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 55556666778899999 999999999999999 89999999999999999999999999999999998754
No 95
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=99.83 E-value=1.2e-19 Score=169.45 Aligned_cols=162 Identities=14% Similarity=0.084 Sum_probs=127.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccc
Q 010835 253 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 332 (499)
Q Consensus 253 ~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vR 332 (499)
+..||..|+..|.+.|+.+|.++.++..+++|++||+|+.+|+. ..|... ..|.+|++.+++|.+.+++++..+...
T Consensus 8 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~~~~~ 84 (172)
T PRK12523 8 HSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAALEQA 84 (172)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34999999999999999999999999999999999999999987 446543 369999999999999999887642000
Q ss_pred ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccC
Q 010835 333 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRV 412 (499)
Q Consensus 333 ip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~ 412 (499)
.. .++ .. .....
T Consensus 85 -----------------~~---------~~~------------------------~~----------------~~~~~-- 96 (172)
T PRK12523 85 -----------------YL---------AEL------------------------AL----------------VPEAE-- 96 (172)
T ss_pred -----------------HH---------HHH------------------------hh----------------ccccc--
Confidence 00 000 00 00000
Q ss_pred CCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010835 413 ENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 489 (499)
Q Consensus 413 e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~ 489 (499)
..+|+......+....+..+| ..||+++|.||.|+| ++|+|++|||+.||+|.+||++++++|+++||..+..
T Consensus 97 ~~~~~~~~~~~~~~~~l~~~l-~~Lp~~~r~v~~L~~---~~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l~~ 169 (172)
T PRK12523 97 QPSPEEQHLILEDLKAIDRLL-GKLSSKARAAFLYNR---LDGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIALYG 169 (172)
T ss_pred CCChHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 123444444445556799999 999999999999999 8999999999999999999999999999999998764
No 96
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=99.82 E-value=6.2e-19 Score=162.78 Aligned_cols=161 Identities=16% Similarity=0.117 Sum_probs=130.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccc
Q 010835 254 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 333 (499)
Q Consensus 254 ~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRi 333 (499)
+.||+.|+..|.+.|+.+|+++.++..+++|++||+|+.+|++ .|++ +..|.+|++..+++.+.+++++..+..+.
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 3789999999999999999999999999999999999999999 6764 34799999999999999988776431110
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCC
Q 010835 334 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE 413 (499)
Q Consensus 334 p~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e 413 (499)
... . ....+. +. .
T Consensus 78 ~~~----------------------------------------------------~-----------~~~~~~--~~--~ 90 (166)
T PRK09639 78 ILG----------------------------------------------------E-----------FQWQEV--DN--E 90 (166)
T ss_pred ccc----------------------------------------------------h-----------hhhhhc--cC--C
Confidence 000 0 000000 11 2
Q ss_pred CCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010835 414 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 490 (499)
Q Consensus 414 ~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~ 490 (499)
.+|++.....+....+..+| ..||+++|.||.++| +|++++|||+.||+|.++|++.+.+|+++||+.+...
T Consensus 91 ~~~e~~~~~~~~~~~l~~~l-~~L~~~~r~il~l~~----~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~~~ 162 (166)
T PRK09639 91 PSPEEIWIRKEEITKVQEVL-AKMTERDRTVLLLRF----SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQM 162 (166)
T ss_pred CChHHHHHHHHHHHHHHHHH-HcCCHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 35666666677777899999 999999999999998 7899999999999999999999999999999998654
No 97
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=99.82 E-value=8e-19 Score=180.99 Aligned_cols=174 Identities=19% Similarity=0.154 Sum_probs=129.2
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 334 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip 334 (499)
.|+++|+..|.+.|+++|++++++..+++|++||+|+.+|+.+++|++. .+|.+|++..++|.+.+++++..+... +
T Consensus 19 ~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~-~ 95 (339)
T PRK08241 19 DAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATNVCLDALEGRARRPL-P 95 (339)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHHHHHHHHHhhccccC-c
Confidence 9999999999999999999999999999999999999999999999853 369999999999999999887643100 0
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCC---CCCCccccccccc-
Q 010835 335 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNG---LPGETHHSYIADN- 410 (499)
Q Consensus 335 ~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~---~e~~~l~e~i~d~- 410 (499)
..++.+.....++ +......+.+.+.
T Consensus 96 --------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 125 (339)
T PRK08241 96 --------------------------------------------------TDLGAPAADPVDELVERPEVPWLEPYPDAL 125 (339)
T ss_pred --------------------------------------------------cccCCCcCcccccccccccccccCCCCccc
Confidence 0000000000000 0000000111110
Q ss_pred --cCCCCCcchHHHHH-HHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 411 --RVENNPWHGVDDWA-LKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 411 --~~e~~Pee~ve~~e-l~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
....+|++.+...+ ....|..+| ..||+++|.||.|+| ++|+|++|||+.||+|.++|+++++||+++||+
T Consensus 126 ~~~~~~~~e~~~~~~e~~~~~l~~~l-~~Lp~~~R~v~~L~~---~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 126 LDPAAADPAARVVARESVRLAFVAAL-QHLPPRQRAVLILRD---VLGWSAAEVAELLDTSVAAVNSALQRARATLAE 199 (339)
T ss_pred ccccCCChHHHHHHHHHHHHHHHHHH-HhCCHHHhhhhhhHH---hhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhh
Confidence 00135655555444 345688899 999999999999999 899999999999999999999999999999998
No 98
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=7.9e-19 Score=166.90 Aligned_cols=176 Identities=11% Similarity=0.028 Sum_probs=129.8
Q ss_pred HHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHH
Q 010835 259 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH 338 (499)
Q Consensus 259 ~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~ 338 (499)
.-+..|.+.|+.+|.+++++..+++|++||+|+.+|+.+.+|++.. +|.+|++..++|.+.++++++.+......- .
T Consensus 11 ~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~~--~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~~-~ 87 (189)
T PRK12530 11 LEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQS--ALKTWIFAILKNKIIDLIRYRKRFVNESEL-I 87 (189)
T ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCCc--cHHHHHHHHHHHHHHHHHHhhccCCCcccc-c
Confidence 4577899999999999999999999999999999999999998653 699999999999999998876531110000 0
Q ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcc
Q 010835 339 ERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWH 418 (499)
Q Consensus 339 e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee 418 (499)
.+ . ....... ...........++. ..+|++
T Consensus 88 ----------------------~~----------~---------~~~~~~~-------~~~~~~~~~~~~~~--~~~~~~ 117 (189)
T PRK12530 88 ----------------------EE----------D---------SPNSFFD-------EKGHWKPEYYEPSE--WQEVEN 117 (189)
T ss_pred ----------------------cc----------c---------cchhhhc-------ccccccccccCCcc--ccCHHH
Confidence 00 0 0000000 00000000000111 124555
Q ss_pred hHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010835 419 GVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 491 (499)
Q Consensus 419 ~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~ 491 (499)
.+...+....+..+| +.||+++|+||.|+| ++|+|++|||+.||+|.+||+++++||+++||+.+....
T Consensus 118 ~~~~~~~~~~l~~~l-~~Lp~~~R~v~~L~~---~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~ 186 (189)
T PRK12530 118 TVYKEEFWLIFEACL-NHLPAQQARVFMMRE---YLELSSEQICQECDISTSNLHVLLYRARLQLQACLSKNW 186 (189)
T ss_pred HHHHHHHHHHHHHHH-HhCCHHHHHHHhHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 666677778899999 999999999999999 899999999999999999999999999999999986543
No 99
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=9.2e-19 Score=161.42 Aligned_cols=157 Identities=11% Similarity=0.075 Sum_probs=123.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccc
Q 010835 253 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 332 (499)
Q Consensus 253 ~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vR 332 (499)
+..|++.++..|.+.|+.+|.++.++..+++|++||+++.+|+.+++|++. .|.||++..++|.+.+++++..+...
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 458999999999999999999999999999999999999999999999863 59999999999999998887653100
Q ss_pred ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccC
Q 010835 333 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRV 412 (499)
Q Consensus 333 ip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~ 412 (499)
. ..+. ...+..
T Consensus 80 ~----------------------------------------------------~~~~----------------~~~~~~- 90 (161)
T PRK12541 80 T----------------------------------------------------TIEE----------------FHLPNV- 90 (161)
T ss_pred c----------------------------------------------------chhh----------------hhccCC-
Confidence 0 0000 000000
Q ss_pred CCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010835 413 ENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA 486 (499)
Q Consensus 413 e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~ 486 (499)
.+|.+..........+..+| ..||+++|.||.|+| .+|+|++|||+.||+|.++|+++++||+++||+.
T Consensus 91 -~~~~~~~~~~~~~~~~~~~l-~~L~~~~r~v~~l~~---~~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 91 -PSTEHEYFIKHEIASWLDSL-SSLPLERRNVLLLRD---YYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred -CCcHHHHHHHhHHHHHHHHH-HHCCHHHHHHhhhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 11222222222334455788 899999999999999 8999999999999999999999999999999974
No 100
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=6.9e-19 Score=162.26 Aligned_cols=157 Identities=13% Similarity=0.073 Sum_probs=123.9
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 334 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip 334 (499)
.|+++|+..|.+.|+.+|.++.++..+++|++||+|+.+|+..+.|++. .|.+|++.++++.+.+++++..+...
T Consensus 4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~~-- 78 (161)
T PRK12528 4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQII---EPRAFLTTIAKRVLCNHYRRQDLERA-- 78 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhcccccccc---CHHHHHHHHHHHHHHHHHHHHHHHHh--
Confidence 7999999999999999999999999999999999999999999888642 58999999999999888876532000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCC
Q 010835 335 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 414 (499)
Q Consensus 335 ~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~ 414 (499)
. ..+ ++. . .+.. ..
T Consensus 79 ---------------~---------~~~------------------------~~~----------------~-~~~~-~~ 92 (161)
T PRK12528 79 ---------------Y---------LEA------------------------LAQ----------------L-PERV-AP 92 (161)
T ss_pred ---------------h---------HHH------------------------hhc----------------c-cccc-CC
Confidence 0 000 000 0 0000 01
Q ss_pred CCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010835 415 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA 486 (499)
Q Consensus 415 ~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~ 486 (499)
+++......+....|..+| ..||+++|.||.|+| ++|+|++|||+.||+|.+||++++++|+++||..
T Consensus 93 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~v~~L~~---~~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~ 160 (161)
T PRK12528 93 SEEERAIILETLVELDQLL-DGLPPLVKRAFLLAQ---VDGLGYGEIATELGISLATVKRYLNKAAMRCYFA 160 (161)
T ss_pred CHHHHHHHHHHHHHHHHHH-HHCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhc
Confidence 2322333334556788999 999999999999999 8999999999999999999999999999999864
No 101
>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=99.81 E-value=8.8e-19 Score=166.56 Aligned_cols=177 Identities=12% Similarity=0.104 Sum_probs=131.9
Q ss_pred HHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHH
Q 010835 259 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH 338 (499)
Q Consensus 259 ~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~ 338 (499)
+++..|.+.|+.+|+++.++..+++|++||+|+++|+...+|++. .+|.+|++..++|.+.+++++..+....+...
T Consensus 6 ~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~~~~- 82 (188)
T TIGR02943 6 QELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVSDLD- 82 (188)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCccccc-
Confidence 567889999999999999999999999999999999999999964 37999999999999999988765421111000
Q ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcc
Q 010835 339 ERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWH 418 (499)
Q Consensus 339 e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee 418 (499)
.+.. .-.++.. .+..+....+...+. .++|++
T Consensus 83 ----------------------~~~~-------------------~~~~~~~-----~~~~~~~~~~~~~~~--~~~~e~ 114 (188)
T TIGR02943 83 ----------------------DELD-------------------DEAFNAL-----FTQNGHWAQHGQPQH--WNTPEK 114 (188)
T ss_pred ----------------------cccc-------------------cchhhhh-----hccccchhccccccc--cCCHHH
Confidence 0000 0000000 000000000011111 235666
Q ss_pred hHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010835 419 GVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 490 (499)
Q Consensus 419 ~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~ 490 (499)
.+...+....+.++| ..||+++|+||.|+| ++|++++|||+.||+|.++|++++.||+++||+.+...
T Consensus 115 ~~~~~e~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~ 182 (188)
T TIGR02943 115 QLENKEFWEVFEACL-YHLPEQTARVFMMRE---VLGFESDEICQELEISTSNCHVLLYRARLSLRACLSIN 182 (188)
T ss_pred HHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 777777778899999 999999999999999 89999999999999999999999999999999998644
No 102
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=7.9e-19 Score=167.10 Aligned_cols=181 Identities=16% Similarity=0.174 Sum_probs=132.5
Q ss_pred HHHHHHHHHHHHHHHhHhhCCCCC-HHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccccc
Q 010835 258 EKLVMSNVRLVMSIAQRYDNMGAD-MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH 336 (499)
Q Consensus 258 e~LIe~yl~LV~sIA~ry~~~g~d-~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~ 336 (499)
+..+..|.+.|+.+|+++.++..+ ++|++||+|+.+|+++++|++. .+|.+|++..++|.+.+++++..+.......
T Consensus 8 ~~~~~~~~~~l~~~a~~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~~ 85 (195)
T PRK12532 8 DAELIESRKLLLHFARLQLPDHPDLAEDLVQETLLSAYSAGDSFQGR--ALVNSWLFAILKNKIIDALRQIGRQRKVFTL 85 (195)
T ss_pred hhhHHHHHHHHHHHHHHHcCChhhhHHHHHHHHHHHHHHhccccccc--chHHHHHHHHHHHHHHHHHHHhccccccccc
Confidence 456788999999999999999888 9999999999999999999864 3799999999999999998876531111000
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCC
Q 010835 337 LHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNP 416 (499)
Q Consensus 337 ~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~P 416 (499)
.. .+.+.+ . ...... .++....+...+. ..+|
T Consensus 86 ~~---------------------~~~~~~-----------~------~~~~~~--------~~~~~~~~~~~~~--~~~~ 117 (195)
T PRK12532 86 LD---------------------DELLDE-----------A------FESHFS--------QNGHWTPEGQPQH--WNTP 117 (195)
T ss_pred cc---------------------ccccch-----------h------hhhhhc--------cccccccccCccc--cCCH
Confidence 00 000000 0 000000 0000000000011 1357
Q ss_pred cchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010835 417 WHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM 492 (499)
Q Consensus 417 ee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~l 492 (499)
++.+...+....+..+| ..||+++|+||.|+| .+|+|++|||+.||+|.+||+++++||+++||+.+....+
T Consensus 118 e~~~~~~e~~~~l~~~l-~~L~~~~r~i~~L~~---~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~ 189 (195)
T PRK12532 118 EKSLNNNEFQKILQSCL-YNLPENTARVFTLKE---ILGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKWF 189 (195)
T ss_pred HHHHHHHHHHHHHHHHH-HhCCHHHHHHhhhHH---HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 77777777778899999 999999999999999 8999999999999999999999999999999999976643
No 103
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=1.1e-18 Score=167.63 Aligned_cols=181 Identities=15% Similarity=0.086 Sum_probs=129.7
Q ss_pred HHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHH
Q 010835 259 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH 338 (499)
Q Consensus 259 ~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~ 338 (499)
.++..|.+.|+.+|++++++..+++|++||+|+.+|+.+++|++.. .|.+|++..++|.+.+++++..+...++...
T Consensus 12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~~- 88 (201)
T PRK12545 12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQS--AHKTWVFGILRNKLIDTLRARQRTVNLSALD- 88 (201)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhccccc--hHHHHHHHHHHHHHHHHHHhhcccccccccc-
Confidence 4588999999999999999999999999999999999999999753 6999999999999999988765421111000
Q ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcc
Q 010835 339 ERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWH 418 (499)
Q Consensus 339 e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee 418 (499)
.++.. ...++... ....+.-..+...+. ..+|.+
T Consensus 89 ----------------------~~~~~------------------~~~~~~~~----~~~~~~~~~~~~~~~--~~~~~~ 122 (201)
T PRK12545 89 ----------------------AELDG------------------EALLDREL----FKDNGHWAAHAKPRP--WPKPET 122 (201)
T ss_pred ----------------------cccch------------------hhhhhhhh----hcccccccccccCcC--CCCHHH
Confidence 00000 00000000 000000000000011 124444
Q ss_pred hHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010835 419 GVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM 492 (499)
Q Consensus 419 ~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~l 492 (499)
.....+....+..+| ..||+++|.||.|+| ++|+|++|||+.||+|.+||+++++||+++||+.+...++
T Consensus 123 ~~~~~~~~~~l~~~L-~~Lp~~~r~v~~L~~---~eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~~ 192 (201)
T PRK12545 123 ILQQQQFWTLFETCL-DHLPEQIGRVFMMRE---FLDFEIDDICTELTLTANHCSVLLYRARTRLRTCLSEKGL 192 (201)
T ss_pred HHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 555556667788899 999999999999999 8999999999999999999999999999999999975543
No 104
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=1.2e-18 Score=168.44 Aligned_cols=181 Identities=14% Similarity=0.115 Sum_probs=133.4
Q ss_pred HHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccc
Q 010835 256 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN 335 (499)
Q Consensus 256 A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~ 335 (499)
.-..|+..|.+.|+.+|++++++..+++|++||+|+.+|+.+.+|++. .+|.+|++..++|.+.+++++..+....+.
T Consensus 19 ~~~~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfikl~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~~~~~~~~ 96 (206)
T PRK12544 19 QDPVFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGR--AAFKTWVFAILKNKIIDLLRQKKRHVSASS 96 (206)
T ss_pred hhHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhhcccccccc
Confidence 346789999999999999999999999999999999999999999864 369999999999999999987654211100
Q ss_pred cHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCC
Q 010835 336 HLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENN 415 (499)
Q Consensus 336 ~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~ 415 (499)
... .......+ .... + ........ .......+
T Consensus 97 ~~~-----------------~~~~~~~~-----------~~~~---------~----------~~~~~~~~-~~~~~~~~ 128 (206)
T PRK12544 97 LLR-----------------DEEEEEDF-----------EELF---------D----------ESGHWQKD-ERPQAWGN 128 (206)
T ss_pred ccc-----------------ccchhhHH-----------HHhh---------c----------cccccccc-ccccccCC
Confidence 000 00000000 0000 0 00000000 00011235
Q ss_pred CcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010835 416 PWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 490 (499)
Q Consensus 416 Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~ 490 (499)
|++.+...+....+..+| ..||+++|+||.|+| ++|+|++|||+.||+|.++|+++++||+++||+.+...
T Consensus 129 ~e~~~~~~e~~~~l~~~L-~~L~~~~r~v~~L~~---~~g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~ 199 (206)
T PRK12544 129 PEESLEQEQFWRIFEACL-DGLPAKYARVFMMRE---FIELETNEICHAVDLSVSNLNVLLYRARLRLRECLENK 199 (206)
T ss_pred HHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 666677777777889999 999999999999999 89999999999999999999999999999999999753
No 105
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=99.80 E-value=2.4e-18 Score=162.70 Aligned_cols=154 Identities=19% Similarity=0.191 Sum_probs=126.6
Q ss_pred HHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccccc
Q 010835 257 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH 336 (499)
Q Consensus 257 ~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~ 336 (499)
++.|++.|.+.|+.+|.++.++..+++|++||+++.+|+.+..|++. .+|.+|++..+++.+.+++++..+...++
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 37999999999999999887764310000
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCC
Q 010835 337 LHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNP 416 (499)
Q Consensus 337 ~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~P 416 (499)
+ + . .. .+.+
T Consensus 79 ------------------------------------------------------------~-~-~----~~-----~~~~ 87 (181)
T PRK09637 79 ------------------------------------------------------------D-D-L----LF-----EDEE 87 (181)
T ss_pred ------------------------------------------------------------h-h-h----hc-----cCCC
Confidence 0 0 0 00 0012
Q ss_pred cchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010835 417 WHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 489 (499)
Q Consensus 417 ee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~ 489 (499)
.+.....+....+..+| +.||+++|.||.|+| .+|++++|||+.||+|.++|++++.||+++||+.+..
T Consensus 88 ~~~~~~~e~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (181)
T PRK09637 88 REENAKKELAPCLRPFI-DALPEKYAEALRLTE---LEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156 (181)
T ss_pred hhHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 22234455667888889 899999999999999 8999999999999999999999999999999998865
No 106
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=2.4e-18 Score=163.73 Aligned_cols=165 Identities=17% Similarity=0.151 Sum_probs=126.9
Q ss_pred hhhhhhHHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHh
Q 010835 248 SILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVEN 327 (499)
Q Consensus 248 ~~l~~~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~ 327 (499)
+-+..+..+|+.++..|.+.|+.+|+++.++..+++|++||+|+.+|+.++.|++. ..|.+|++..+++.+.+..++.
T Consensus 16 ~~~~~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~~ 93 (188)
T PRK12517 16 SDMLSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFERK 93 (188)
T ss_pred HhhhccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHHh
Confidence 34555679999999999999999999999999999999999999999999999864 3699999999888654443221
Q ss_pred hhcccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCcccccc
Q 010835 328 SRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYI 407 (499)
Q Consensus 328 ~R~vRip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i 407 (499)
.+. ....+ .. ..
T Consensus 94 ~~~-----------------------------------------------------~~~~~-----------~~----~~ 105 (188)
T PRK12517 94 QFD-----------------------------------------------------LVDIE-----------DD----SI 105 (188)
T ss_pred ccC-----------------------------------------------------ccCcc-----------cc----cc
Confidence 100 00000 00 00
Q ss_pred ccccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010835 408 ADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 487 (499)
Q Consensus 408 ~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L 487 (499)
.+.. ..+|+. ....+.|..+| ..||+++|.||.++| .+|++++|||+.||||.++|+.+++||+++||+.+
T Consensus 106 ~~~~-~~~~e~----~~~~~~l~~~l-~~Lp~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (188)
T PRK12517 106 EDDA-SHSSEE----EMEQEWLRRQI-AKLDPEYREPLLLQV---IGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEAL 176 (188)
T ss_pred cCcc-ccChhH----HHHHHHHHHHH-HhCCHHHHHHHHHHH---HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 1100 112322 22345688899 999999999999999 89999999999999999999999999999999999
Q ss_pred HHhh
Q 010835 488 RKKK 491 (499)
Q Consensus 488 ~~~~ 491 (499)
....
T Consensus 177 ~~~~ 180 (188)
T PRK12517 177 EKPD 180 (188)
T ss_pred HHHH
Confidence 7543
No 107
>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=99.80 E-value=1.5e-18 Score=177.42 Aligned_cols=187 Identities=17% Similarity=0.115 Sum_probs=133.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccc
Q 010835 253 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 332 (499)
Q Consensus 253 ~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vR 332 (499)
+..||+.|+..|.+.|+++|++++++..+++|++||+|+.+|+.+++|++. ..|.+|++..++|.+.+++++..+...
T Consensus 3 d~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~~~ 80 (324)
T TIGR02960 3 DGAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQRRPR 80 (324)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhccCCcC
Confidence 458999999999999999999999999999999999999999999999864 369999999999999999887643100
Q ss_pred ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccc-cc-cc
Q 010835 333 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSY-IA-DN 410 (499)
Q Consensus 333 ip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~-i~-d~ 410 (499)
..... . . ......... ..........+.+. +. ..
T Consensus 81 ~~~~~-----------------~--~------------------------~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~ 116 (324)
T TIGR02960 81 PVGLG-----------------A--P------------------------SADGTAAAS-EAAEVTWLEPLPDLTLDLDD 116 (324)
T ss_pred ccccC-----------------C--C------------------------CCccccccc-ccccccccCCCCcccccccc
Confidence 00000 0 0 000000000 00000000000000 00 00
Q ss_pred cCCCCCcchHHHHH-HHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010835 411 RVENNPWHGVDDWA-LKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 489 (499)
Q Consensus 411 ~~e~~Pee~ve~~e-l~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~ 489 (499)
....+|++.+...+ +...+..+| .+||+++|.||.|+| ++|+|++|||+.||+|.++|+++++||+++||+.+..
T Consensus 117 ~~~~~~~~~~~~~e~~~~~l~~~l-~~Lp~~~R~v~~L~~---~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 192 (324)
T TIGR02960 117 PAAADPSVAAGSRESVRLAFVAAI-QYLPPRQRAVLLLRD---VLGWRAAETAELLGTSTASVNSALQRARATLDEVGPS 192 (324)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHH-HhCCHHHhhHhhhHH---HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccc
Confidence 01134555555444 445688899 999999999999999 8999999999999999999999999999999998864
No 108
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=2.8e-18 Score=162.59 Aligned_cols=160 Identities=16% Similarity=0.180 Sum_probs=126.9
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 334 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip 334 (499)
.++..++..|.+.|+++|.++.++..+++|++||+|+.+|+.+++|++.. .|.+|++..++|.+.++++++.+....
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 67889999999999999999999999999999999999999999998653 699999999999888887765431000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCC
Q 010835 335 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 414 (499)
Q Consensus 335 ~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~ 414 (499)
.+. ...+.. ..
T Consensus 82 ----------------------------------------------------~~~------------~~~~~~-----~~ 92 (182)
T PRK12540 82 ----------------------------------------------------ADG------------SYAKTL-----KS 92 (182)
T ss_pred ----------------------------------------------------ccc------------cccccc-----cC
Confidence 000 000000 01
Q ss_pred CCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010835 415 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM 492 (499)
Q Consensus 415 ~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~l 492 (499)
.|+.. .......|..+| ..||+++|+||.|+| .+|+|++|||+.||+|.++|+++++||+++||+.+.....
T Consensus 93 ~~~~~--~~~~~~~l~~~l-~~Lp~~~R~v~~L~~---~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~~ 164 (182)
T PRK12540 93 QPGQN--AHLEFEEFRAAL-DKLPQDQREALILVG---ASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDGA 164 (182)
T ss_pred CCchH--HHHHHHHHHHHH-HhCCHHHHHHhhHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 11111 112235688999 999999999999999 8999999999999999999999999999999999987653
No 109
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=99.79 E-value=5.9e-19 Score=160.81 Aligned_cols=152 Identities=15% Similarity=0.156 Sum_probs=122.3
Q ss_pred HHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHH
Q 010835 262 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 341 (499)
Q Consensus 262 e~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l 341 (499)
..|.|.|+.+++++.++..+++|++||+++.+|+++++|++ .+|.+|++..+++.+.+++++..+....+
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 57999999999999999999999999999999999999997 37999999999998888887664310000
Q ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHH
Q 010835 342 GLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVD 421 (499)
Q Consensus 342 ~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve 421 (499)
.+ .+.+...+. ..+|++.+.
T Consensus 72 -------------------~~---------------------------------------~~~~~~~~~--~~~~~~~~~ 91 (154)
T TIGR02950 72 -------------------DD---------------------------------------AIGDLEQHP--VESPEHHLL 91 (154)
T ss_pred -------------------Hh---------------------------------------hhhhccccc--cCChhHHHH
Confidence 00 000000011 124555556
Q ss_pred HHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010835 422 DWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 487 (499)
Q Consensus 422 ~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L 487 (499)
..+....+..+| ..||+.++.||.++| ++|+|++|||+.||+|.++|++.++||+++||+.+
T Consensus 92 ~~~~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~l 153 (154)
T TIGR02950 92 IKIEQEEITHHL-SRLPENYRTVLILRE---FKEFSYKEIAELLNLSLAKVKSNLFRARKELKKLL 153 (154)
T ss_pred HHHHHHHHHHHH-HhCCHhheeeeeehh---hccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 666677899999 899999999999998 79999999999999999999999999999999875
No 110
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=99.79 E-value=4.3e-18 Score=156.92 Aligned_cols=158 Identities=16% Similarity=0.182 Sum_probs=124.5
Q ss_pred HHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHH
Q 010835 259 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH 338 (499)
Q Consensus 259 ~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~ 338 (499)
.++..|.+.++++|.++.++..+++|++||+++++|+....|++. .|.+|++..+++.+.+++++..+.....
T Consensus 2 ~~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn~~~d~~R~~~~~~~~~---- 74 (163)
T PRK07037 2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRNLAIDHYRRQALENKYH---- 74 (163)
T ss_pred hHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHHHHHHHHHhhccccccc----
Confidence 357788999999999999999999999999999999998877753 4789999999998888887764210000
Q ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcc
Q 010835 339 ERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWH 418 (499)
Q Consensus 339 e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee 418 (499)
+.+.... .. .+. ..+|+.
T Consensus 75 ----------------------------------------------------------~~~~~~~-~~-~~~--~~~~~~ 92 (163)
T PRK07037 75 ----------------------------------------------------------GDEEDGL-DV-PSP--EASPEA 92 (163)
T ss_pred ----------------------------------------------------------ccccccc-cc-CCC--CCCHHH
Confidence 0000000 00 001 124555
Q ss_pred hHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010835 419 GVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 489 (499)
Q Consensus 419 ~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~ 489 (499)
.+...+..+.+..+| +.|||++|.||.++| ++|+|++|||+.||+|.++|++.+.+|+++||+.+..
T Consensus 93 ~~~~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l~~ 159 (163)
T PRK07037 93 ALINRDTLRHVADAL-SELPARTRYAFEMYR---LHGETQKDIARELGVSPTLVNFMIRDALVHCRKCLDA 159 (163)
T ss_pred HHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 666666778889999 999999999999999 8999999999999999999999999999999998854
No 111
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=99.79 E-value=3.9e-18 Score=159.50 Aligned_cols=164 Identities=15% Similarity=0.157 Sum_probs=126.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccc
Q 010835 253 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 332 (499)
Q Consensus 253 ~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vR 332 (499)
+..|++.++..|.+.|+.++.++.++..+++|++||.|+.+|+. ..|++.. +|.+|++..+++.+.+++++..+...
T Consensus 8 ~~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~~~~~ 84 (172)
T PRK09651 8 ASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNALEKA 84 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34899999999999999999999999999999999999999998 3554432 58899999999988888776532000
Q ss_pred ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccC
Q 010835 333 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRV 412 (499)
Q Consensus 333 ip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~ 412 (499)
. ...+ +. +.+..
T Consensus 85 -----------------~---------~~~~------------------------~~-----------------~~~~~- 96 (172)
T PRK09651 85 -----------------Y---------LEML------------------------AL-----------------MPEGG- 96 (172)
T ss_pred -----------------h---------hhHH------------------------hh-----------------ccccC-
Confidence 0 0000 00 00000
Q ss_pred CCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010835 413 ENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 491 (499)
Q Consensus 413 e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~ 491 (499)
.++|.......+....+..+| ..||+++|+||.|+| ++|+|++|||+.||+|.+||+.+++||+++|+...-..+
T Consensus 97 ~~~~~~~~~~~e~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~~~~~~ 171 (172)
T PRK09651 97 APSPEERESQLETLQLLDSML-DGLNGKTREAFLLSQ---LDGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLFRLEYG 171 (172)
T ss_pred CCChHHHHHHHHHHHHHHHHH-HhCCHHHhHHhhhhh---ccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHcC
Confidence 123444444455567788999 999999999999999 899999999999999999999999999999998765543
No 112
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=99.79 E-value=3.8e-18 Score=156.97 Aligned_cols=155 Identities=13% Similarity=0.078 Sum_probs=123.6
Q ss_pred HHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHH
Q 010835 262 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 341 (499)
Q Consensus 262 e~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l 341 (499)
..|.+.++.++.+++++..+++|++||+|+.+|+..+.|++. +|.+|++..+++.+.+++++..+...
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 568999999999999999999999999999999999998752 68999999999988888876532000
Q ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHH
Q 010835 342 GLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVD 421 (499)
Q Consensus 342 ~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve 421 (499)
.+++. +.+. .....++|++.+.
T Consensus 70 -------------------------------------------~~~~~-------------~~~~--~~~~~~~~~~~~~ 91 (159)
T PRK12527 70 -------------------------------------------EPLEV-------------LDEE--ERLHSPSPQTRLD 91 (159)
T ss_pred -------------------------------------------cchhh-------------hhcc--ccccCCCHHHHHH
Confidence 00000 0000 0000124556666
Q ss_pred HHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010835 422 DWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 490 (499)
Q Consensus 422 ~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~ 490 (499)
..+....+..+| ..||++++.||.|+| ++|+|++|||+.||+|.++|++++.||+++||+.+...
T Consensus 92 ~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~~~ 156 (159)
T PRK12527 92 LGQRLALLQRAL-AELPPACRDSFLLRK---LEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQW 156 (159)
T ss_pred HHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 667778899999 899999999999999 89999999999999999999999999999999998754
No 113
>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=1.5e-17 Score=162.33 Aligned_cols=176 Identities=20% Similarity=0.233 Sum_probs=129.0
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCC--CCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhh---h
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMG--ADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS---R 329 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g--~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~---R 329 (499)
. +++||..|.|+|.++|.+|.++. .+.+|++|+|++|||+|+++|||++|.+|.+||.+||++.|.+++++.. +
T Consensus 10 ~-~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dylRk~~k~~~ 88 (218)
T TIGR02895 10 E-REELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYIRKNQKYQN 88 (218)
T ss_pred H-HHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHhcccccC
Confidence 5 99999999999999999998764 5899999999999999999999999999999999999999999999987 4
Q ss_pred cccccccHHHHHHHHHHHHHHH-HHcCCCCCHHHHHHH------hCCCHHHHHHHHHhhccccccccccCCCCCCCCCCc
Q 010835 330 TLRLPNHLHERLGLIRNAKLRL-EEKGVTPSVDRIAEY------LNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGET 402 (499)
Q Consensus 330 ~vRip~~~~e~l~~irka~~~L-~~~gr~pt~eEIA~~------Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~ 402 (499)
.+++|....+....+..+...+ ++.++.|+.+||+.. .|++.+++.+
T Consensus 89 ~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~~~~L~~~gi~~~dLv~-------------------------- 142 (218)
T TIGR02895 89 LLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEYKKLLKQFGIEFVELVK-------------------------- 142 (218)
T ss_pred eeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCcHHHHhh--------------------------
Confidence 6688876555455566565555 367899999999875 3444444322
Q ss_pred cccccccccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 010835 403 HHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVG 476 (499)
Q Consensus 403 l~e~i~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~ 476 (499)
..|-+.- .....-.+...+ . -++. ++..-+. ...++.+||+..++||+.|+.+..
T Consensus 143 -----------~sPkh~d-~r~~~i~ia~~~-~-~~~~---l~~~l~~--kk~LP~k~l~~~~~v~rktier~r 197 (218)
T TIGR02895 143 -----------VSPKHRD-TRKKAIKIAKVI-V-ENEE---LLEYLIR--KKKLPIKEIEERVRISRKTIERYR 197 (218)
T ss_pred -----------cCCCCHH-HHHHHHHHHHHH-h-cCHH---HHHHHHH--hCCCCHHHHHHHcCCCHHHHHHhh
Confidence 2443332 222333333334 1 1222 2222120 356999999999999999986543
No 114
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=9.6e-18 Score=159.85 Aligned_cols=156 Identities=17% Similarity=0.249 Sum_probs=121.9
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 334 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip 334 (499)
++++.|+. |.+.|+++|++++++..+++|++||+|+.+|+.+..|+.. ..|.+|++..++|.+.+++++..+...
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 56677766 7799999999999999999999999999999999999864 369999999999988888777543100
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCC
Q 010835 335 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 414 (499)
Q Consensus 335 ~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~ 414 (499)
..+ . ...+.. ..
T Consensus 83 ---------------------------------------------------~~~-----------~-~~~~~~-----~~ 94 (188)
T PRK12546 83 ---------------------------------------------------DPE-----------G-VHAASL-----AV 94 (188)
T ss_pred ---------------------------------------------------Ccc-----------c-cccccc-----cc
Confidence 000 0 000000 01
Q ss_pred CCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010835 415 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 489 (499)
Q Consensus 415 ~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~ 489 (499)
+|.. ........+..+| ..||+++|.||.|+| .+|+|++|||+.||+|..+|+++++||+++||+.+..
T Consensus 95 ~~~~--~~~~~~~~l~~~L-~~Lp~~~r~v~~L~~---~~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~ 163 (188)
T PRK12546 95 KPAH--DGRLAMSDFRAAF-AQLPDEQREALILVG---ASGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQL 163 (188)
T ss_pred CCcc--hhHHHHHHHHHHH-HhCCHHHhHHhhhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 1111 1222345688899 999999999999999 8999999999999999999999999999999998865
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=99.78 E-value=7.7e-18 Score=157.38 Aligned_cols=149 Identities=21% Similarity=0.252 Sum_probs=121.8
Q ss_pred HHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHH
Q 010835 262 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 341 (499)
Q Consensus 262 e~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l 341 (499)
..|.+.|+.+++++.++..+++|++||+|+.+|+++++|++. .+|.+|++..+++.+.+++++..+...++
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 468999999999999999999999999999999999999963 47999999999999999988765311000
Q ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHH
Q 010835 342 GLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVD 421 (499)
Q Consensus 342 ~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve 421 (499)
. . .+. ...|.+...
T Consensus 73 -----------------------------------------------~-----------~----~~~----~~~~~~~~~ 86 (170)
T TIGR02959 73 -----------------------------------------------E-----------S----LLA----ADSAREETF 86 (170)
T ss_pred -----------------------------------------------h-----------h----hcc----cCCccHHHH
Confidence 0 0 000 012222334
Q ss_pred HHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010835 422 DWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 489 (499)
Q Consensus 422 ~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~ 489 (499)
..+....+..+| ..||+++|.||.|+| .+|+|++|||+.||+|..+|+++++||+++||..+..
T Consensus 87 ~~e~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 150 (170)
T TIGR02959 87 VKELSQCIPPMI-KELPDEYREAIRLTE---LEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLET 150 (170)
T ss_pred HHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 455667788999 899999999999999 8999999999999999999999999999999998864
No 116
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=99.76 E-value=1.7e-17 Score=157.21 Aligned_cols=158 Identities=16% Similarity=0.154 Sum_probs=123.2
Q ss_pred HHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccc
Q 010835 256 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN 335 (499)
Q Consensus 256 A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~ 335 (499)
..+..+..+++.|+.+|.++.++..+++|++||+|+.+|+.+..|++. .+|.+|++..+++.+.+++++..+.....
T Consensus 5 ~~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~~~~~~- 81 (182)
T PRK12511 5 SKRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRVEARRA- 81 (182)
T ss_pred chhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhccccccc-
Confidence 344557789999999999999999999999999999999999999864 36999999999999999887764310000
Q ss_pred cHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCC
Q 010835 336 HLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENN 415 (499)
Q Consensus 336 ~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~ 415 (499)
+. ..+. .+.. ...
T Consensus 82 ----------------------------------------------------~~-------------~~~~-~~~~-~~~ 94 (182)
T PRK12511 82 ----------------------------------------------------DE-------------LAVL-ADAS-LPA 94 (182)
T ss_pred ----------------------------------------------------cc-------------hhhc-cccC-CCc
Confidence 00 0000 0000 001
Q ss_pred CcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010835 416 PWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 490 (499)
Q Consensus 416 Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~ 490 (499)
+ .........|..+| ..||+++|+||.|+| ++|+|++|||+.||+|.+||+++++||+++||+.+...
T Consensus 95 ~---~~~~~~~~~l~~~l-~~Lp~~~R~v~~L~~---~eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~~~ 162 (182)
T PRK12511 95 A---QEHAVRLAQIRDAF-FDLPEEQRAALHLVA---IEGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEEGT 162 (182)
T ss_pred c---hHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhc
Confidence 1 11223446788899 899999999999999 89999999999999999999999999999999988754
No 117
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=99.76 E-value=3.3e-17 Score=152.54 Aligned_cols=159 Identities=14% Similarity=0.105 Sum_probs=125.5
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 334 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip 334 (499)
.++..++..|.+.++.+|.++.++..+++|++||+|+.+|+....++. ..|.+|++..++|.+.+++++...
T Consensus 9 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~----- 80 (168)
T PRK12525 9 TLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDL----- 80 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHH-----
Confidence 789999999999999999999999999999999999999986665542 269999999999988777765421
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCC
Q 010835 335 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 414 (499)
Q Consensus 335 ~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~ 414 (499)
.+. ... +++. . ... ...
T Consensus 81 ----------~~~--~~~---------------------------------~~~~----------------~-~~~-~~~ 97 (168)
T PRK12525 81 ----------ERA--YLQ---------------------------------SLAE----------------A-PEA-VQP 97 (168)
T ss_pred ----------HHH--HHH---------------------------------HHhc----------------c-ccc-ccC
Confidence 000 000 0000 0 000 012
Q ss_pred CCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010835 415 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 488 (499)
Q Consensus 415 ~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~ 488 (499)
+|++.....+....|..+| +.||+++|.||.|+| .+|+|++|||+.||+|.+||+..+.+|+++||..+.
T Consensus 98 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~v~~L~~---~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~~~ 167 (168)
T PRK12525 98 SPEEQWMVIETLLAIDRLL-DGLSGKARAAFLMSQ---LEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQGFQ 167 (168)
T ss_pred ChHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhc
Confidence 5555555666678899999 999999999999998 899999999999999999999999999999998763
No 118
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=99.72 E-value=1.4e-16 Score=161.50 Aligned_cols=160 Identities=14% Similarity=0.083 Sum_probs=122.4
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 334 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip 334 (499)
..+.++++.|.+.++.+|++++++..++||++||+|+. |.....|++ ..|.+|++..++|.+.+++++..+...
T Consensus 4 ~~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~~---~~~~~WL~~Ia~n~~~d~lR~~~~~~~-- 77 (293)
T PRK09636 4 ADAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQI---RDPRAWLTRVVTRLCLDRLRSARHRRE-- 77 (293)
T ss_pred cHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhcccccc---cCHHHHHHHHHHHHHHHHHHhhhcccc--
Confidence 56788999999999999999999999999999999999 666677752 469999999999999888876542000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCC
Q 010835 335 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 414 (499)
Q Consensus 335 ~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~ 414 (499)
.... ..+.+...+. ..
T Consensus 78 --------------------------------------------------~~~~------------~~~~e~~~~~--~~ 93 (293)
T PRK09636 78 --------------------------------------------------TYVG------------PWLPEPVVEE--LD 93 (293)
T ss_pred --------------------------------------------------cccC------------CcCCcCCCCC--CC
Confidence 0000 0000000010 11
Q ss_pred CCcchHH-HHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010835 415 NPWHGVD-DWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 488 (499)
Q Consensus 415 ~Pee~ve-~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~ 488 (499)
+|.+... ..+....+..+| +.|||++|.||.|+| .+++|++|||+.||+|.++|+++++||+++||+.+.
T Consensus 94 ~~~~~~~~~~~~~~~l~~~l-~~L~~~~R~v~~L~~---~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~ 164 (293)
T PRK09636 94 DPLEAVVAAEDLSLALMLAL-ERLSPLERAAFLLHD---VFGVPFDEIASTLGRSPAACRQLASRARKHVRAARP 164 (293)
T ss_pred ChHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 3443333 334456688889 999999999999999 899999999999999999999999999999999754
No 119
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=99.72 E-value=1.3e-16 Score=146.32 Aligned_cols=156 Identities=14% Similarity=0.100 Sum_probs=111.7
Q ss_pred CCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHcCC
Q 010835 277 NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGV 356 (499)
Q Consensus 277 ~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L~~~gr 356 (499)
++..+++|++||+|+.+|+.++.+ + +..|.+|++..++|.+.+++++..+..+....
T Consensus 2 ~~~~~AeDivQe~fl~~~~~~~~~-~--~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~-------------------- 58 (161)
T PRK09047 2 RDDDAALDIVQDAMIKLAEKYGDR-P--AAEWPPLFQRILQNRIHDWFRRQKVRNTWVSL-------------------- 58 (161)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhhc-c--cCchHHHHHHHHHHHHHHHHHhhccccccccc--------------------
Confidence 345679999999999999998873 3 34699999999999999998876431000000
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccC-CCCCcchHHHHHHHHHHHHHHHh
Q 010835 357 TPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRV-ENNPWHGVDDWALKDEVNKLIIV 435 (499)
Q Consensus 357 ~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~-e~~Pee~ve~~el~~~L~~~L~~ 435 (499)
..++... .+.++....+.+.+... ..+|++.+...+....|..+| .
T Consensus 59 ---------------------------~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l-~ 105 (161)
T PRK09047 59 ---------------------------FSSFSDD-----DDDDDFDPLETLDSADEGAESPADKLERAQVLQLIEEAI-Q 105 (161)
T ss_pred ---------------------------ccccccc-----cccccccHHHHhccccccCCCHHHHHHHHHHHHHHHHHH-H
Confidence 0000000 00001111111111110 135666777777888899999 9
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 491 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~ 491 (499)
.||+++|.||.|+| ++|+|++|||+.||+|.++|+++++||+++||+.+...+
T Consensus 106 ~Lp~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~ 158 (161)
T PRK09047 106 KLPARQREAFLLRY---WEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEAKG 158 (161)
T ss_pred hCCHHHHHHHHHHH---HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 99999999999999 899999999999999999999999999999999987654
No 120
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=99.71 E-value=2.4e-16 Score=155.07 Aligned_cols=158 Identities=16% Similarity=0.100 Sum_probs=120.9
Q ss_pred HHhhhhhhHHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHH
Q 010835 246 LQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALV 325 (499)
Q Consensus 246 l~~~l~~~~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~ 325 (499)
|.+.+..+..+++.+++.| +.|+++|.++.++..+++|++||+|+.+|+. |+.. ..|.+|++..++|.+.+.++
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 3334444448999888888 7899999999999999999999999999986 5433 25899999999998888877
Q ss_pred HhhhcccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCcccc
Q 010835 326 ENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHS 405 (499)
Q Consensus 326 ~~~R~vRip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e 405 (499)
+..+... +.. ..
T Consensus 83 k~k~~~~------------------------------------------------------~~~----------~~---- 94 (228)
T PRK06704 83 SKSVHEK------------------------------------------------------IRD----------QI---- 94 (228)
T ss_pred ccccccc------------------------------------------------------ccc----------cc----
Confidence 6542000 000 00
Q ss_pred ccccccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 406 YIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 406 ~i~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
. ..+|.+. ..+..+.+..+| ..||+++|.||.|+| .+|+|++|||+.||+|.++|+++++||+++||+
T Consensus 95 --~----~~~~~~~--~~~~~~~l~~~L-~~Lp~~~R~v~lL~~---~eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~ 162 (228)
T PRK06704 95 --T----FEEPHEK--IADLHEMVGKVL-SSLNVQQSAILLLKD---VFQYSIADIAKVCSVSEGAVKASLFRSRNRLKT 162 (228)
T ss_pred --c----cCChHHH--HHHHHHHHHHHH-HhCCHHHhhHhhhHH---hhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 0 0011111 122345678888 899999999999999 899999999999999999999999999999999
Q ss_pred HHHH
Q 010835 486 AARK 489 (499)
Q Consensus 486 ~L~~ 489 (499)
.+..
T Consensus 163 ~l~~ 166 (228)
T PRK06704 163 VSEE 166 (228)
T ss_pred HHHh
Confidence 8865
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=99.68 E-value=9.5e-16 Score=154.89 Aligned_cols=156 Identities=17% Similarity=0.083 Sum_probs=118.0
Q ss_pred HHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHH
Q 010835 259 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH 338 (499)
Q Consensus 259 ~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~ 338 (499)
++++.|.+.++.+|++++++..++||++||+++.+++. .|+.. ..|.+|++.+++|.+.+++++..+...
T Consensus 1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~~--~~~~awL~~Ia~n~~ld~lR~~~~~~~------ 70 (281)
T TIGR02957 1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQI--ENPKAYLTKVVTRRCIDVLRSARARRE------ 70 (281)
T ss_pred ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Ccccc--cCHHHHHHHHHHHHHHHHHHHhhhccc------
Confidence 36889999999999999999999999999999997775 55432 369999999999999998876542000
Q ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcc
Q 010835 339 ERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWH 418 (499)
Q Consensus 339 e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee 418 (499)
.. .. ..+.+...+. ..+|++
T Consensus 71 ----------------------------------------------~~-~~-----------~~~~e~~~~~--~~~~~~ 90 (281)
T TIGR02957 71 ----------------------------------------------VY-VG-----------PWLPEPLLTT--SADPAE 90 (281)
T ss_pred ----------------------------------------------cc-CC-----------CCCCcccCCC--CCChHH
Confidence 00 00 0000000000 124544
Q ss_pred hHHHH-HHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010835 419 GVDDW-ALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 488 (499)
Q Consensus 419 ~ve~~-el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~ 488 (499)
.++.. .+...+..+| ++|||+||.||.|+| .+++|++|||+.||+|..+|+++++||+++||+...
T Consensus 91 ~~~~~e~~~~~l~~~l-~~L~~~~R~v~~L~~---~~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~ 157 (281)
T TIGR02957 91 SVELAESLSMAYLLLL-ERLSPLERAVFVLRE---VFDYPYEEIASIVGKSEANCRQLVSRARRHLDARRP 157 (281)
T ss_pred HHHHHHHHHHHHHHHH-hhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 44433 3445677888 999999999999999 899999999999999999999999999999998653
No 122
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=99.68 E-value=1e-15 Score=155.55 Aligned_cols=161 Identities=16% Similarity=0.071 Sum_probs=123.1
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 334 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip 334 (499)
..+..+++.|.+.++.+|++++++..++||++||+|+.+|++...+. ..|.+|++...+|.+.+++++..+....+
T Consensus 5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~~----~~~~aWL~~Ia~n~~id~lRk~~~rr~~~ 80 (290)
T PRK09635 5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGDI----DDERGWLIVVTSRLCLDHIKSASTRRERP 80 (290)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCcccc----ccHHHHHHHHHHHHHHHHHhhhhccCcCc
Confidence 67899999999999999999999999999999999999999876531 25899999999999888887653200000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCC
Q 010835 335 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 414 (499)
Q Consensus 335 ~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~ 414 (499)
...+.. .++ +...+ ..
T Consensus 81 --------------------------------------------------~~~~~~-------~~~----~~~~~---~~ 96 (290)
T PRK09635 81 --------------------------------------------------QDIAAW-------HDG----DASVS---SV 96 (290)
T ss_pred --------------------------------------------------cccccc-------Ccc----ccCCC---CC
Confidence 000000 000 00000 12
Q ss_pred CCcch-HHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010835 415 NPWHG-VDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 487 (499)
Q Consensus 415 ~Pee~-ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L 487 (499)
+|++. ....+....+..+| ..|||++|.||.|+| ..++|++|||+.||+|..+|+++++||+++||...
T Consensus 97 ~~~~~~~~~~e~~~al~~~L-~~L~p~~R~vf~L~~---~~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~ 166 (290)
T PRK09635 97 DPADRVTLDDEVRLALLIML-ERLGPAERVVFVLHE---IFGLPYQQIATTIGSQASTCRQLAHRARRKINESR 166 (290)
T ss_pred CcHHHHHHHHHHHHHHHHHH-HhCCHHHHHHhhHHH---HhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence 34332 33455667788889 899999999999999 89999999999999999999999999999999854
No 123
>PRK09191 two-component response regulator; Provisional
Probab=99.58 E-value=1.4e-14 Score=142.18 Aligned_cols=136 Identities=12% Similarity=0.115 Sum_probs=110.6
Q ss_pred HHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccc
Q 010835 256 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN 335 (499)
Q Consensus 256 A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~ 335 (499)
++..|+..|.+.|+++|+++.++..+++|++||+|+.+|+...+|++.. .|.+|++.++++... ...
T Consensus 2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~~--~~~~wl~~~~~~~~~----~~~------- 68 (261)
T PRK09191 2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEAS--SPRVGLYRLFHRLWS----SAG------- 68 (261)
T ss_pred chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCCc--chhhHHHHHHHHHhc----ccc-------
Confidence 5889999999999999999999999999999999999999999998743 589999876654110 000
Q ss_pred cHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCC
Q 010835 336 HLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENN 415 (499)
Q Consensus 336 ~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~ 415 (499)
. .. .. ...
T Consensus 69 -------------------------------------------------------------~-~~---------~~-~~~ 76 (261)
T PRK09191 69 -------------------------------------------------------------A-ND---------PE-PGS 76 (261)
T ss_pred -------------------------------------------------------------c-cC---------CC-CCC
Confidence 0 00 00 001
Q ss_pred CcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010835 416 PWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 488 (499)
Q Consensus 416 Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~ 488 (499)
+.. ..+..+| +.||+++|.||.|+| ++|+|++|||+.||+|.++|+.++.+|+++||..+.
T Consensus 77 ~~~--------~~l~~~l-~~L~~~~r~v~~l~~---~~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~ 137 (261)
T PRK09191 77 PFE--------ARAERRL-AGLTPLPRQAFLLTA---LEGFSVEEAAEILGVDPAEAEALLDDARAEIARQVA 137 (261)
T ss_pred Cch--------HHHHHHH-HhCCHHHhHHHHHHH---HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCC
Confidence 111 1688889 999999999999999 899999999999999999999999999999997664
No 124
>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=99.56 E-value=3.4e-14 Score=128.49 Aligned_cols=136 Identities=19% Similarity=0.209 Sum_probs=99.8
Q ss_pred HHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhc-----CCCCCCCcchhHHHHHHHHHHHHHHHHhhhcc
Q 010835 257 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEK-----FDSSKGFKISTYVYWWIRQGVSRALVENSRTL 331 (499)
Q Consensus 257 ~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiek-----FDp~rG~kFsTYA~~wIR~aI~~al~~~~R~v 331 (499)
|+.|+..|.++++.+|++|... +|+ ||.++.+|..+.+ |++. ..|.||++..++|.+.+++++..+..
T Consensus 1 f~~~~~~y~~~l~~~~~~~~~~----~~~-qdvf~~~w~~~~~~~~~~~~~~--~~~~~wL~~iarN~~id~~Rk~~~~~ 73 (142)
T TIGR03209 1 FEEIYMNFKNTIDIFTRKYNLY----YDY-NDILYHLWIILKKIDLNKFNTE--NDLEKYISTSLKRYCLDICNKKNRDK 73 (142)
T ss_pred ChHHHHHHHHHHHHHHHHhcch----hhH-HHHHHHHHHHHHHhhhhhcCch--hHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 4689999999999999999762 344 9999999999865 5543 46999999999999999988764200
Q ss_pred cccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCcccccccccc
Q 010835 332 RLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNR 411 (499)
Q Consensus 332 Rip~~~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~ 411 (499)
+.. . .+. . .+..
T Consensus 74 ~~~---------------~------------------------------------~~~-------------~----~~~~ 85 (142)
T TIGR03209 74 KII---------------Y------------------------------------NSE-------------I----TDIK 85 (142)
T ss_pred hhh---------------h------------------------------------hhh-------------h----hccc
Confidence 000 0 000 0 0000
Q ss_pred CCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHH
Q 010835 412 VENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVR 473 (499)
Q Consensus 412 ~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVr 473 (499)
..+.+.+...+....+.++| +.||+.+|.||.|+| ++|+|++|||+.||+|.+||+
T Consensus 86 --~~~~~~~~~~~~~~~l~~~l-~~Lp~~~r~v~~l~~---~~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 86 --LSLINVYSSNDLEFEFNDLI-SILPNKQKKIIYMKF---FEDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred --cchhHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHhhc
Confidence 01112233444556788899 999999999999999 899999999999999999996
No 125
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=99.54 E-value=5.3e-13 Score=132.14 Aligned_cols=78 Identities=17% Similarity=0.207 Sum_probs=72.2
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhCCCC--CHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccc
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDNMGA--DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 332 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~~g~--d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vR 332 (499)
.|++.|+..|.|+|+++|.+++++.. +.+|++|||++++|+++++|++++|.+|.+|++.+|++.+.+++++..+...
T Consensus 18 ~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn~~iDylRk~~~~~~ 97 (237)
T PRK08311 18 ELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKRRLIDYFRKESKHNL 97 (237)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccc
Confidence 99999999999999999999998765 5999999999999999999999888789999999999999999999876433
No 126
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=99.54 E-value=4.5e-13 Score=127.48 Aligned_cols=178 Identities=22% Similarity=0.260 Sum_probs=123.9
Q ss_pred HHHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHHHHHHhHhhCC---CCCHHH-
Q 010835 209 AEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNM---GADMAD- 284 (499)
Q Consensus 209 eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV~sIA~ry~~~---g~d~ED- 284 (499)
.+..+|+.++++||. .|++.|+..|++.++.+|++++.. +.+.+|
T Consensus 2 ~~it~ll~~~~~GD~-------------------------------~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~ 50 (185)
T PF07638_consen 2 SEITELLDRWRQGDE-------------------------------AALDQLFERYYPELRRLARRRLRRERRGHDLQDT 50 (185)
T ss_pred chHHHHHHHHHCCCH-------------------------------HHHHHHHHHHHHHHHHHHHHHHhccccCCchhHH
Confidence 356789999999998 999999999999999999988742 344554
Q ss_pred -HHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHcCCCCCHHHH
Q 010835 285 -LVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRI 363 (499)
Q Consensus 285 -LiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~e~l~~irka~~~L~~~gr~pt~eEI 363 (499)
|++|+|+.+++.....+++.-..|..|+...+++.+.++++...+..|-...
T Consensus 51 ~lv~ea~lrl~~~~~~~~~~~~~~f~~~~~~~~rr~lid~~R~~~a~KRg~~~--------------------------- 103 (185)
T PF07638_consen 51 ALVHEAFLRLARRGRFVQFSDRRHFWALLARIMRRKLIDHARRRQAQKRGGDQ--------------------------- 103 (185)
T ss_pred HHHHHHHHHHhccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC---------------------------
Confidence 5778888887744333333334588888888888777777665432111000
Q ss_pred HHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHH
Q 010835 364 AEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGERERE 443 (499)
Q Consensus 364 A~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~~L~~~L~~rER~ 443 (499)
...+|+.. ..+ ...+.|+. ..++.+.+..+. . |+|+++.
T Consensus 104 -------------------~~~~l~~~----------------~~~-~~~~~~~~---~~~l~e~l~~L~-~-l~~~~~~ 142 (185)
T PF07638_consen 104 -------------------VRVELDER----------------ADS-GDEPSPEE---LLELEEALERLL-A-LDPRQRR 142 (185)
T ss_pred -------------------cccchhhh----------------hcc-ccCCCHHH---HHHHHHHHHHHH-c-cCHHHHH
Confidence 01111111 000 00123332 234555666655 4 9999999
Q ss_pred HHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010835 444 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 488 (499)
Q Consensus 444 VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~ 488 (499)
||.++| ++|+|.+|||+.||||+.||++.+..|..+|+..+.
T Consensus 143 ~v~l~~---~~Gls~~EIA~~lgiS~~tV~r~l~~aR~~l~~~l~ 184 (185)
T PF07638_consen 143 VVELRF---FEGLSVEEIAERLGISERTVRRRLRRARAWLRRELR 184 (185)
T ss_pred HHHHHH---HCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence 999999 899999999999999999999999999999998763
No 127
>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=99.26 E-value=1.3e-11 Score=97.76 Aligned_cols=70 Identities=27% Similarity=0.418 Sum_probs=66.7
Q ss_pred HHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhh
Q 010835 260 LVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR 329 (499)
Q Consensus 260 LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R 329 (499)
|++.|.|+|+++|++|.+++.+.+|++||++++||+++++|+++.+.+|.+|++..+++.+.+.+++..|
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 6899999999999999999999999999999999999999999999889999999999999999988764
No 128
>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=99.20 E-value=5.3e-11 Score=89.64 Aligned_cols=50 Identities=48% Similarity=0.679 Sum_probs=45.9
Q ss_pred HHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 432 LIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 432 ~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
+| +.|||+|+.||.++| ++++|+.|||+.||+|+++|++++.+|+++||+
T Consensus 1 Al-~~L~~~er~vi~~~y---~~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 1 AL-DQLPPREREVIRLRY---FEGLTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp HH-CTS-HHHHHHHHHHH---TST-SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred Ch-hhCCHHHHHHHHHHh---cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 46 899999999999999 899999999999999999999999999999995
No 129
>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=98.94 E-value=2.6e-09 Score=81.39 Aligned_cols=53 Identities=28% Similarity=0.464 Sum_probs=45.4
Q ss_pred HHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 010835 427 DEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL 483 (499)
Q Consensus 427 ~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKL 483 (499)
+.|..+| ..|||++|.||.++| .+|+|+.|||+.+|+|.++|++++.+|+++|
T Consensus 2 ~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~eIa~~l~~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 2 EALQQAL-AQLPERQREIFLLRY---FQGMSYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp HHHHHHH-HCS-HHHHHHHHHHH---TS---HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred HHHHHHH-HCCCHHHHHHHHHHH---HHCcCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 4678889 999999999999999 8999999999999999999999999999987
No 130
>PRK06930 positive control sigma-like factor; Validated
Probab=98.71 E-value=7.4e-08 Score=91.03 Aligned_cols=71 Identities=17% Similarity=0.156 Sum_probs=63.1
Q ss_pred CcchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010835 416 PWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 490 (499)
Q Consensus 416 Pee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~ 490 (499)
|.+.....+....|..+| +.|||++|.||.|+| .+|+|++|||+.||+|.+||++++.+|+++|++.+...
T Consensus 95 ~~~~~~~~e~~~~l~~al-~~L~~rer~V~~L~~---~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~ 165 (170)
T PRK06930 95 EPESVISEWDKIRIEDAL-SVLTEREKEVYLMHR---GYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQINES 165 (170)
T ss_pred ChhHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 444455566778899999 999999999999998 79999999999999999999999999999999988654
No 131
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=98.58 E-value=1.1e-07 Score=77.71 Aligned_cols=76 Identities=32% Similarity=0.364 Sum_probs=58.3
Q ss_pred HHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCc
Q 010835 339 ERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPW 417 (499)
Q Consensus 339 e~l~~irka~~~L~-~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pe 417 (499)
++++++.++++.|. ++||.||.+|||+.||++.++|..++.......||+.+.+ .+++.++.+++.|... .+|+
T Consensus 1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~----~~~~~~l~~~i~d~~~-~~P~ 75 (78)
T PF04539_consen 1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVG----DEDDSTLGDFIEDDDA-PSPE 75 (78)
T ss_dssp HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCS----SSSSEEGGGSSB-SSS---HH
T ss_pred ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeec----CCCCCchhheecCCCC-CChh
Confidence 35788999999995 7999999999999999999999999999999999999753 3345678888888753 4665
Q ss_pred ch
Q 010835 418 HG 419 (499)
Q Consensus 418 e~ 419 (499)
+.
T Consensus 76 e~ 77 (78)
T PF04539_consen 76 EE 77 (78)
T ss_dssp HH
T ss_pred hc
Confidence 43
No 132
>PRK00118 putative DNA-binding protein; Validated
Probab=98.52 E-value=4.5e-07 Score=78.96 Aligned_cols=55 Identities=22% Similarity=0.310 Sum_probs=51.9
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM 492 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~l 492 (499)
..||++++.||.++| .+|+|+.|||+.+|+|++||++++.+|+++||+.+.+-++
T Consensus 16 ~~L~ekqRevl~L~y---~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~ 70 (104)
T PRK00118 16 SLLTEKQRNYMELYY---LDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHL 70 (104)
T ss_pred ccCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence 799999999999999 8999999999999999999999999999999999887543
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=98.37 E-value=1.2e-06 Score=64.61 Aligned_cols=54 Identities=41% Similarity=0.605 Sum_probs=49.3
Q ss_pred HHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010835 427 DEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 484 (499)
Q Consensus 427 ~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR 484 (499)
..+..++ ..||+.++.++.++| .+++|..+||+.+|+|..+|.+++.+++.+||
T Consensus 2 ~~~~~~~-~~l~~~~~~~~~~~~---~~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 2 ERLEEAL-DKLPEREREVILLRF---GEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred HHHHHHH-HhCCHHHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 3566778 899999999999999 79999999999999999999999999998875
No 134
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=98.26 E-value=3.4e-06 Score=77.35 Aligned_cols=52 Identities=31% Similarity=0.367 Sum_probs=48.3
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 490 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~ 490 (499)
..|+|+|++||.+++ +|+|++|||+.||+|+++|++++++|+++||+.....
T Consensus 5 ~~Lt~rqreVL~lr~----~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~tl 56 (141)
T PRK03975 5 SFLTERQIEVLRLRE----RGLTQQEIADILGTSRANVSSIEKRARENIEKARETL 56 (141)
T ss_pred cCCCHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 569999999999965 9999999999999999999999999999999987654
No 135
>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=98.25 E-value=3.3e-06 Score=77.07 Aligned_cols=57 Identities=21% Similarity=0.316 Sum_probs=49.9
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHh
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAM 495 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~l~~~ 495 (499)
..|+++|++|+.|++ +|+|++|||+.||+|+++|++++++|+++||.......+-.+
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 469999999999975 999999999999999999999999999999986655544443
No 136
>PRK04217 hypothetical protein; Provisional
Probab=98.19 E-value=2.9e-06 Score=74.69 Aligned_cols=55 Identities=29% Similarity=0.279 Sum_probs=51.2
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM 492 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~l 492 (499)
..|++.+++||.++| .+++|++|||+.||||+.||++++.+|+++|+..+.....
T Consensus 41 ~~Lt~eereai~l~~---~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~~ 95 (110)
T PRK04217 41 IFMTYEEFEALRLVD---YEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGRE 95 (110)
T ss_pred ccCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 679999999999998 8999999999999999999999999999999999876544
No 137
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=98.12 E-value=1.6e-05 Score=68.83 Aligned_cols=62 Identities=31% Similarity=0.408 Sum_probs=46.5
Q ss_pred HHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010835 428 EVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM 492 (499)
Q Consensus 428 ~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~l 492 (499)
.|....-.-|+++|+.++.++| .+++|+.|||+.+|||+.+|.-.+.||.++|...-.+-++
T Consensus 9 ~L~d~Yg~LLT~kQ~~~l~lyy---~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~yE~kL~l 70 (101)
T PF04297_consen 9 LLFDFYGELLTEKQREILELYY---EEDLSLSEIAEELGISRQAVYDSIKRAEKKLEEYEEKLGL 70 (101)
T ss_dssp HHHHHHGGGS-HHHHHHHHHHC---TS---HHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHHH-H
T ss_pred HHHHHHHHHCCHHHHHHHHHHH---ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3333332459999999999999 8999999999999999999999999999999876554443
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=97.90 E-value=5.6e-05 Score=68.73 Aligned_cols=60 Identities=17% Similarity=0.243 Sum_probs=53.7
Q ss_pred HHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010835 424 ALKDEVNKLIIVTLGEREREIIRLYYGLDKEC--LTWEDISKRIGLSRERVRQVGLVALEKLKHAA 487 (499)
Q Consensus 424 el~~~L~~~L~~~L~~rER~VI~LryGLd~eg--~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L 487 (499)
...+.|..+| +.|++.+|.||.++| +++ +|+.+||..||+|+.+|.++..+|+.+|...+
T Consensus 71 ~~~~~I~~~l-~~Ld~~er~II~~rY---~~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~l 132 (134)
T TIGR01636 71 RNRDAIENCL-NEADEQTRVIIQELY---MKKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEEL 132 (134)
T ss_pred HHHHHHHHHH-HhCCHHHHHHHHHHH---ccCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 3556788888 899999999999999 444 59999999999999999999999999999865
No 139
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=97.90 E-value=3.2e-05 Score=58.00 Aligned_cols=46 Identities=37% Similarity=0.536 Sum_probs=41.8
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 484 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR 484 (499)
..|++.|+.|+.+. ..|++..|||+.+|+|+.+|++++.+++++|.
T Consensus 2 ~~l~~~e~~i~~~~----~~g~s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 2 ASLTPREREVLRLL----AEGLTNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCCCHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 46899999999875 48999999999999999999999999998886
No 140
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPro: IPR009042 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....
Probab=97.80 E-value=7.6e-06 Score=58.19 Aligned_cols=33 Identities=30% Similarity=0.483 Sum_probs=30.8
Q ss_pred hhHHHHHHhhccccCCCHHHHHHHHHHHHcCCC
Q 010835 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS 223 (499)
Q Consensus 191 ~~~~~yl~~i~~~~~Lt~eEe~eL~~~ik~Gd~ 223 (499)
|.++.||++|+++|+||++||++|+++|+.|+.
T Consensus 2 D~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~~ 34 (37)
T PF00140_consen 2 DSLRLYLKEIGRYPLLTAEEEIELARRIRKGDE 34 (37)
T ss_dssp HHHHHHHHHHHHS-EETTHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHH
Confidence 789999999999999999999999999999986
No 141
>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=97.77 E-value=5.8e-05 Score=58.38 Aligned_cols=47 Identities=28% Similarity=0.437 Sum_probs=41.4
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
..|+++|.+|+.+.. .|++.+|||+.||+|..||+.+..++++||.-
T Consensus 2 ~~LT~~E~~vl~~l~----~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 2 PSLTERELEVLRLLA----QGMSNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp GSS-HHHHHHHHHHH----TTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred CccCHHHHHHHHHHH----hcCCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 579999999999986 99999999999999999999999999999863
No 142
>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=97.77 E-value=0.00011 Score=63.56 Aligned_cols=55 Identities=35% Similarity=0.518 Sum_probs=49.1
Q ss_pred HHHHHHHHHHhhCC-HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 010835 425 LKDEVNKLIIVTLG-EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL 483 (499)
Q Consensus 425 l~~~L~~~L~~~L~-~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKL 483 (499)
....+..+| +.|+ +.+|.||.++| .+++++.+||+.||+|+.|+-+++.+|++.|
T Consensus 44 ~k~ei~~~I-~~l~d~~~r~iL~~~Y---i~~~~~~~I~~~l~~S~~t~yr~~~~Al~~L 99 (100)
T PF07374_consen 44 EKLEIRRAI-NKLEDPDERLILRMRY---INKLTWEQIAEELNISRRTYYRIHKKALKEL 99 (100)
T ss_pred HHHHHHHHH-HHccChhHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence 445677888 6775 78999999999 8999999999999999999999999999876
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=97.77 E-value=6.9e-05 Score=56.36 Aligned_cols=45 Identities=33% Similarity=0.405 Sum_probs=40.9
Q ss_pred CCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 437 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 437 L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
|+++++.|+.+.+ +++|.+|||+.+|+|+.+|++++.+++++|..
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 88999999999999999999999999888875
No 144
>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=97.75 E-value=6.5e-05 Score=61.37 Aligned_cols=47 Identities=13% Similarity=0.083 Sum_probs=41.2
Q ss_pred HHHHHHHhhCCHHHHHHHHHH-hcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 428 EVNKLIIVTLGEREREIIRLY-YGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 428 ~L~~~L~~~L~~rER~VI~Lr-yGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
.+.+-| +.||++.+.++.|. | .+++|++|||++||+|+.||++++.+
T Consensus 8 ~~~~~l-~~l~~~~r~af~L~R~---~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 8 KLAERL-TWVDSLAEAAAALARE---EAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred hHHHHH-hcCCHHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 345567 89999999999994 5 69999999999999999999999875
No 145
>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=0.00027 Score=54.29 Aligned_cols=47 Identities=32% Similarity=0.498 Sum_probs=40.9
Q ss_pred CCHHHHHHHHHHhcCC----CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 010835 437 LGEREREIIRLYYGLD----KECLTWEDISKRIGLSRERVRQVGLVALEKL 483 (499)
Q Consensus 437 L~~rER~VI~LryGLd----~eg~SleEIAe~LgIS~~rVrqi~~rALkKL 483 (499)
|+++|++||..-|-.+ -.+.|+.|||+.||||++||..++.+|.+||
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 7899999999866443 1368999999999999999999999999886
No 146
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=97.48 E-value=0.00019 Score=69.52 Aligned_cols=46 Identities=17% Similarity=0.226 Sum_probs=43.6
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
.|+++|++|+.+.- +|+|.+|||++||+|..||+.+..+.++||.-
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 99999999999999999999999999999973
No 147
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=97.48 E-value=0.00024 Score=67.26 Aligned_cols=47 Identities=17% Similarity=0.269 Sum_probs=44.3
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
..|+++|++|+.+.- +|+|.+|||+.|++|..||+....++++||.-
T Consensus 132 ~~LSpRErEVLrLLA----qGkTnKEIAe~L~IS~rTVkth~srImkKLgV 178 (198)
T PRK15201 132 RHFSVTERHLLKLIA----SGYHLSETAALLSLSEEQTKSLRRSIMRKLHV 178 (198)
T ss_pred CCCCHHHHHHHHHHH----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 579999999999985 99999999999999999999999999999974
No 148
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=97.41 E-value=0.00027 Score=69.13 Aligned_cols=51 Identities=10% Similarity=0.053 Sum_probs=46.5
Q ss_pred HHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 430 NKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 430 ~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
.+++ ..|+|+|++|+.+.- +|+|.+|||+.|++|..||+.+..+.++||.-
T Consensus 138 ~~~~-~~LS~RE~eVL~Lia----~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv 188 (217)
T PRK13719 138 LEAK-NKVTKYQNDVFILYS----FGFSHEYIAQLLNITVGSSKNKISEILKFFGI 188 (217)
T ss_pred hhcc-CCCCHHHHHHHHHHH----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 4455 789999999999985 99999999999999999999999999999863
No 149
>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=97.40 E-value=0.00027 Score=60.44 Aligned_cols=49 Identities=18% Similarity=0.281 Sum_probs=40.4
Q ss_pred HHHHHHHHhhCCHHHHHHHHHHhcCC----CCCCCHHHHHHHHCCCHHHHHHH
Q 010835 427 DEVNKLIIVTLGEREREIIRLYYGLD----KECLTWEDISKRIGLSRERVRQV 475 (499)
Q Consensus 427 ~~L~~~L~~~L~~rER~VI~LryGLd----~eg~SleEIAe~LgIS~~rVrqi 475 (499)
+.+...|..-|+|+|+.+|.+||||- ..++|++|||+.+|||+.+|.+.
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 34555554559999999999999994 35899999999999999999654
No 150
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=97.39 E-value=0.0003 Score=68.47 Aligned_cols=46 Identities=22% Similarity=0.322 Sum_probs=43.7
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 484 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR 484 (499)
..|++||++|+.+.- +|+|.+|||+.|++|..||+.+..+.++||-
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 569999999999986 9999999999999999999999999999994
No 151
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=97.39 E-value=0.0003 Score=67.48 Aligned_cols=46 Identities=26% Similarity=0.371 Sum_probs=43.4
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 484 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR 484 (499)
..|++||++|+.+.- +|+|.+|||+.|++|..||+.+..+.++||-
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 459999999999985 9999999999999999999999999999994
No 152
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=97.36 E-value=0.00085 Score=64.26 Aligned_cols=69 Identities=20% Similarity=0.259 Sum_probs=58.7
Q ss_pred HHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhh
Q 010835 423 WALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAML 496 (499)
Q Consensus 423 ~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~~l~~~l 496 (499)
......+...+ .+|+||||+|+...- .|...++||..||||+.||+.+..+.++||+..--.+-++-|+
T Consensus 130 ~~~~~~~~~~l-~tLT~RERqVl~~vV----~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~SlaeLvr~a~ 198 (202)
T COG4566 130 ADRQAAIRARL-ATLTPRERQVLDLVV----RGLMNKQIAFDLGISERTVELHRANVMEKMQARSLAELVRMAL 198 (202)
T ss_pred HHHHHHHHHHH-HhcCHHHHHHHHHHH----cCcccHHHHHHcCCchhhHHHHHHHHHHHHhhccHHHHHHHHH
Confidence 44556788888 899999999998875 8999999999999999999999999999999866555555443
No 153
>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=97.33 E-value=0.00036 Score=68.88 Aligned_cols=47 Identities=30% Similarity=0.239 Sum_probs=44.3
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
..|+++|++||.+.. +|+|..|||++||||..||+.++.++++||+.
T Consensus 170 ~~Lt~re~evl~~~a----~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~ 216 (232)
T TIGR03541 170 GVLSEREREVLAWTA----LGRRQADIAAILGISERTVENHLRSARRKLGV 216 (232)
T ss_pred ccCCHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence 479999999999975 99999999999999999999999999999984
No 154
>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=97.30 E-value=0.00046 Score=69.12 Aligned_cols=47 Identities=26% Similarity=0.237 Sum_probs=44.3
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
..|+++|++|+.+.. +|+|..|||++||||..||+.++.++++||.-
T Consensus 189 ~~LT~RE~evl~l~a----~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v 235 (247)
T TIGR03020 189 GLITAREAEILAWVR----DGKTNEEIAAILGISSLTVKNHLQHIFKKLDV 235 (247)
T ss_pred cCCCHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence 579999999999975 99999999999999999999999999999974
No 155
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=97.26 E-value=0.00045 Score=67.30 Aligned_cols=46 Identities=33% Similarity=0.380 Sum_probs=43.3
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
.|++||++|+++.- +|+|.+|||++|++|..||+.+..+.++||.-
T Consensus 148 ~LT~RE~eVL~lla----~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~v 193 (211)
T COG2197 148 LLTPRELEVLRLLA----EGLSNKEIAEELNLSEKTVKTHVSNILRKLGV 193 (211)
T ss_pred CCCHHHHHHHHHHH----CCCCHHHHHHHHCCCHhHHHHHHHHHHHHcCC
Confidence 59999999999975 99999999999999999999999999999963
No 156
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=97.26 E-value=0.00055 Score=67.03 Aligned_cols=47 Identities=19% Similarity=0.214 Sum_probs=44.3
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
..|+++|++|+.+.. +|+|.+|||+.|++|..||+.+..++++||.-
T Consensus 154 ~~Lt~rE~~Vl~l~~----~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v 200 (216)
T PRK10100 154 ALLTHREKEILNKLR----IGASNNEIARSLFISENTVKTHLYNLFKKIAV 200 (216)
T ss_pred CCCCHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 469999999999998 79999999999999999999999999999974
No 157
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=97.23 E-value=0.00042 Score=51.03 Aligned_cols=41 Identities=27% Similarity=0.320 Sum_probs=24.7
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
..|++.||..|...+ .+|+|..+||+.||+|++||.+.+.|
T Consensus 3 ~~Lt~~eR~~I~~l~---~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEALL---EQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHHHH---CS---HHHHHHHTT--HHHHHHHHHH
T ss_pred cchhhhHHHHHHHHH---HcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 468999999999888 79999999999999999999988776
No 158
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=97.22 E-value=0.00061 Score=67.76 Aligned_cols=46 Identities=22% Similarity=0.243 Sum_probs=43.6
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
.|+++|++||.+-. +|+|..|||++||||..||+.++.++++||--
T Consensus 179 ~LT~rE~evl~~~a----~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~~ 224 (240)
T PRK10188 179 NFSKREKEILKWTA----EGKTSAEIAMILSISENTVNFHQKNMQKKFNA 224 (240)
T ss_pred CCCHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 69999999999986 99999999999999999999999999999963
No 159
>PRK13870 transcriptional regulator TraR; Provisional
Probab=97.21 E-value=0.00058 Score=67.70 Aligned_cols=45 Identities=22% Similarity=0.202 Sum_probs=42.8
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 484 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR 484 (499)
.|++||++||.+-= +|+|..|||.+||||..||+.++..|++||-
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 59999999999985 9999999999999999999999999999995
No 160
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=97.20 E-value=0.00085 Score=58.72 Aligned_cols=52 Identities=31% Similarity=0.324 Sum_probs=48.3
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 490 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~ 490 (499)
.|+..|-+.|+|.+ .+++|++|.|+.||||+.|+.+++..|.+|+-..|-..
T Consensus 41 ~L~~dElEAiRL~D---~egl~QeeaA~~MgVSR~T~~ril~~ARkKiA~ALv~G 92 (106)
T PF02001_consen 41 VLTVDELEAIRLVD---YEGLSQEEAAERMGVSRPTFQRILESARKKIADALVEG 92 (106)
T ss_pred EeeHHHHHHHHHHH---HcCCCHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHCC
Confidence 58999999999988 89999999999999999999999999999999887654
No 161
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=97.09 E-value=0.0017 Score=50.29 Aligned_cols=49 Identities=31% Similarity=0.359 Sum_probs=44.0
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 487 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L 487 (499)
..|+++|.+|+.+.- .|++..|||..+++|..||+....++..||.-.-
T Consensus 3 ~~Lt~rE~~v~~l~~----~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~~ 51 (65)
T COG2771 3 ADLTPREREILRLVA----QGKSNKEIARILGISEETVKTHLRNIYRKLGVKN 51 (65)
T ss_pred ccCCHHHHHHHHHHH----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC
Confidence 368999999998875 7899999999999999999999999999987543
No 162
>PRK09483 response regulator; Provisional
Probab=96.98 E-value=0.0014 Score=61.71 Aligned_cols=46 Identities=26% Similarity=0.351 Sum_probs=42.8
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 484 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR 484 (499)
..|+++|++|+.+.. +|+|.+|||+.|++|..||+.+.++.++||-
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 569999999998865 8999999999999999999999999999984
No 163
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=96.92 E-value=0.002 Score=59.25 Aligned_cols=46 Identities=33% Similarity=0.435 Sum_probs=42.8
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 484 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR 484 (499)
..|+++|++|+.+. .+|++.+|||+.|++|..||+.++.++++||.
T Consensus 148 ~~lt~~e~~vl~l~----~~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 148 PLLTPRERQILKLI----TEGYTNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred cCCCHHHHHHHHHH----HCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 45999999999995 49999999999999999999999999999996
No 164
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=96.92 E-value=0.0053 Score=52.93 Aligned_cols=49 Identities=18% Similarity=0.318 Sum_probs=44.5
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA 486 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~ 486 (499)
.-|+++|+..+.++| .+++|+.|||+.++||+++|...+.|+-+.|-..
T Consensus 16 sLLT~KQ~~Y~~lyy---~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~Y 64 (105)
T COG2739 16 SLLTKKQKNYLELYY---LDDLSLSEIAEEFNVSRQAIYDNIKRTEKILEDY 64 (105)
T ss_pred HHHhHHHHHHHHHHH---HhhccHHHHHHHhCccHHHHHHHHHHHHHHHHHH
Confidence 458999999999999 8999999999999999999999999988777654
No 165
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=96.76 E-value=0.049 Score=56.58 Aligned_cols=160 Identities=12% Similarity=0.008 Sum_probs=102.9
Q ss_pred HHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhccccccc
Q 010835 257 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH 336 (499)
Q Consensus 257 ~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~ 336 (499)
.+..+..-.|-++.---+|+++=.-.||.+||+|+..++...+=-|-+ .-..|++..-|+.-++.+++..+.-..|.+
T Consensus 7 ie~~~r~~~~r~~a~L~r~~rd~dlAEEa~~dA~~~Ale~WPr~G~P~--~PaAWL~~v~R~~aiD~~Rr~~~~~~~~~e 84 (415)
T COG4941 7 IEAAARIERPRAMAALARYLRDLDLAEEALQDAFAAALERWPRAGPPR--NPAAWLIAVGRNRAIDRVRRRARRDAAPPE 84 (415)
T ss_pred HHHHHHHhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHhCcccCCCC--ChHHHHHHHHhhhHHHHHHHHHHhccCChh
Confidence 344455556666666667777767799999999997666665544433 256777777777777777766542222211
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCC
Q 010835 337 LHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNP 416 (499)
Q Consensus 337 ~~e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~P 416 (499)
.. ++. ++++....+...|.
T Consensus 85 l~----------------------------------------------~~~---------e~~e~~~a~~~~d~------ 103 (415)
T COG4941 85 LL----------------------------------------------LSD---------EDEEMEEAEALDDE------ 103 (415)
T ss_pred hc----------------------------------------------ccc---------cchhhhcccccccc------
Confidence 00 000 00011111111111
Q ss_pred cchHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 417 WHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 417 ee~ve~~el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
....+....|.-+..--||+.+|--+.|+. ..|+|..|||.-+=|+..++-|++.||.++++.
T Consensus 104 ---~i~Dd~LRLiFvccHPal~~~~riALtLR~---v~GLs~~eIArAFLv~e~am~QRivRAK~ri~~ 166 (415)
T COG4941 104 ---HIRDDRLRLIFVCCHPALPPEQRIALTLRL---VGGLSTAEIARAFLVPEAAMAQRIVRAKARIRE 166 (415)
T ss_pred ---ccchhhHHhhhhhcCCCCChhhHHHHHHHH---HcCCcHHHHHHHHcCCcHHHHHHHHHHHHHHHh
Confidence 112233344444433579999999999998 889999999999999999999999999999986
No 166
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=96.66 E-value=0.0051 Score=56.16 Aligned_cols=54 Identities=20% Similarity=0.318 Sum_probs=47.4
Q ss_pred HHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010835 428 EVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA 486 (499)
Q Consensus 428 ~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~ 486 (499)
.+...+ ..|++++++|+.+.+ .+++.++||+.+|+|..+|+.++.++++||+..
T Consensus 134 ~~~~~~-~~l~~~e~~vl~~~~----~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~ 187 (202)
T PRK09390 134 DIRARI-ASLSERERQVMDGLV----AGLSNKVIARDLDISPRTVEVYRANVMTKMQAG 187 (202)
T ss_pred HHHHHH-HhhhhhHHHHHHHHH----ccCchHHHHHHcCCCHHHHHHHHHHHHHHHccc
Confidence 345566 789999999999754 789999999999999999999999999999754
No 167
>PRK10651 transcriptional regulator NarL; Provisional
Probab=96.64 E-value=0.0036 Score=58.25 Aligned_cols=47 Identities=28% Similarity=0.370 Sum_probs=43.4
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
..|+++|++|+.+.. +|++.++||+.|++|..||+.++.+.++||.-
T Consensus 154 ~~Lt~rE~~vl~~l~----~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~ 200 (216)
T PRK10651 154 NQLTPRERDILKLIA----QGLPNKMIARRLDITESTVKVHVKHMLKKMKL 200 (216)
T ss_pred ccCCHHHHHHHHHHH----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 459999999999975 89999999999999999999999999999963
No 168
>PRK01381 Trp operon repressor; Provisional
Probab=96.64 E-value=0.0023 Score=55.26 Aligned_cols=48 Identities=19% Similarity=0.256 Sum_probs=38.7
Q ss_pred HHHHHHHHHhhCCHHHHHHHHHHhcCC----CCCCCHHHHHHHHCCCHHHHH
Q 010835 426 KDEVNKLIIVTLGEREREIIRLYYGLD----KECLTWEDISKRIGLSRERVR 473 (499)
Q Consensus 426 ~~~L~~~L~~~L~~rER~VI~LryGLd----~eg~SleEIAe~LgIS~~rVr 473 (499)
.+.+...|..-|+|.|+..|..|+++- ..++|++|||+.+|||..||.
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 344555553449999999999999993 235999999999999999884
No 169
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=96.58 E-value=0.0049 Score=60.17 Aligned_cols=52 Identities=27% Similarity=0.415 Sum_probs=44.4
Q ss_pred hCCHHHHHHHHHHhcCC----CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLD----KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 487 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd----~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L 487 (499)
.|+|+|++||+.-|-.+ -...+++|||+.||||++|+.+++.+|.+||=..+
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 59999999999977543 13589999999999999999999999999985443
No 170
>PF12645 HTH_16: Helix-turn-helix domain; InterPro: IPR024760 This domain appears to be a helix-turn-helix domain, suggesting a transcriptional regulatory protein. Some proteins with this domain are annotated as conjugative transposon proteins.
Probab=96.55 E-value=0.0081 Score=48.07 Aligned_cols=47 Identities=26% Similarity=0.208 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhC------CCCCHHHHHHHHHHHHHHhhhcCC
Q 010835 255 LAREKLVMSNVRLVMSIAQRYDN------MGADMADLVQGGLIGLLRGIEKFD 301 (499)
Q Consensus 255 ~A~e~LIe~yl~LV~sIA~ry~~------~g~d~EDLiQEG~IgL~rAiekFD 301 (499)
.|.++++..|.|++.+.+.+-.. ++.--+|+-|+-...|++++-+|+
T Consensus 13 ~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~ 65 (65)
T PF12645_consen 13 EAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE 65 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence 99999999999999999987332 345569999999999999999996
No 171
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=96.54 E-value=0.0021 Score=57.51 Aligned_cols=49 Identities=24% Similarity=0.316 Sum_probs=45.2
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 487 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L 487 (499)
.-|+++|-.|+.||- .|.|++|||++||.|+..|+-++.+|+.++.+.-
T Consensus 7 tflte~qikvl~lRe----kG~tQ~eIA~~L~TTraNvSaIEkrA~enIekar 55 (143)
T COG1356 7 TFLTEQQIKVLVLRE----KGLTQSEIARILKTTRANVSAIEKRALENIEKAR 55 (143)
T ss_pred ceeehhheeeeehhh----ccccHHHHHHHHccchhhHHHHHHHHHHHHHHHH
Confidence 358999999999996 9999999999999999999999999999998754
No 172
>PRK15320 transcriptional activator SprB; Provisional
Probab=96.36 E-value=0.0066 Score=58.63 Aligned_cols=46 Identities=13% Similarity=0.148 Sum_probs=43.2
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 484 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR 484 (499)
-.|+++|.+|+.+-- +|+|.+|||+.|++|.+||+.+..+.+.||.
T Consensus 163 ~~LSdREIEVL~LLA----kG~SNKEIAekL~LS~KTVSTYKnRLLeKLg 208 (251)
T PRK15320 163 PGVTQAKYALLILLS----SGHPAIELAKKFGLGTKTVSIYRKKVMYRLG 208 (251)
T ss_pred CCCCHHHHHHHHHHH----cCCCHHHHHHHhccchhhHHHHHHHHHHHcC
Confidence 578999999999875 9999999999999999999999999999986
No 173
>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=96.29 E-value=0.028 Score=50.53 Aligned_cols=58 Identities=21% Similarity=0.160 Sum_probs=49.3
Q ss_pred HHHHHHHhhCCHHHHHHHHHHhcCCCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010835 428 EVNKLIIVTLGEREREIIRLYYGLDKE--CLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 488 (499)
Q Consensus 428 ~L~~~L~~~L~~rER~VI~LryGLd~e--g~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~ 488 (499)
.+..++...|++.+|.||.++| .+ +++..+|+..||+|+.+...+..+|+.++-..+.
T Consensus 71 ~i~~ai~~~l~~~~r~Il~~~Y---l~~~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~l~ 130 (132)
T TIGR01637 71 AIVNAIVNQLDEISRQILYDKY---LEPDQKYDYQIMMELGYSHRQYYRIKKRALLRFATLYG 130 (132)
T ss_pred HHHHHHHHhCCHHHHHHHHHHH---cCccccchHHHHHHhCCcHHHHHHHHHHHHHHHHHHhC
Confidence 3444442589999999999999 66 8999999999999999999999999999876653
No 174
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=96.14 E-value=0.014 Score=49.95 Aligned_cols=52 Identities=31% Similarity=0.293 Sum_probs=47.2
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 490 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~ 490 (499)
.|+..|-+.|+|.. +++++++|-|.+||||+.|+-+.+..|++|+-..|-..
T Consensus 33 ~lt~eElEAlRLvD---~~~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~aLveG 84 (99)
T COG1342 33 ILTIEELEALRLVD---YEGLTQEEAALRMGISRQTFWRLLTSARKKVADALVEG 84 (99)
T ss_pred eecHHHHHHHHHHh---HhhccHHHHHHHhcccHHHHHHHHHHHHHHHHHHHhcC
Confidence 47888899999988 89999999999999999999999999999998887544
No 175
>PRK10403 transcriptional regulator NarP; Provisional
Probab=96.13 E-value=0.0094 Score=55.23 Aligned_cols=51 Identities=24% Similarity=0.258 Sum_probs=44.7
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 489 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~ 489 (499)
..|+++|.+|+.+.. +|+|.++||+.+++|+.||+.++.+.++||.-.-+.
T Consensus 152 ~~Lt~~e~~vl~~~~----~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~~~~ 202 (215)
T PRK10403 152 SVLTERELDVLHELA----QGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRV 202 (215)
T ss_pred ccCCHHHHHHHHHHH----CCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCHH
Confidence 458999999999875 889999999999999999999999999998644333
No 176
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=95.92 E-value=0.016 Score=53.86 Aligned_cols=46 Identities=26% Similarity=0.271 Sum_probs=41.4
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
.|+++|..|+.+.. +|+|.+|||+.|++|..||+.++.++++||.-
T Consensus 149 ~lt~re~~vl~~l~----~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~~ 194 (210)
T PRK09935 149 VLSNREVTILRYLV----SGLSNKEIADQLLLSNKTVSAHKSNIYGKLGL 194 (210)
T ss_pred cCCHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 48999999988754 88999999999999999999999999999863
No 177
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=95.88 E-value=0.019 Score=53.03 Aligned_cols=47 Identities=26% Similarity=0.321 Sum_probs=43.1
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
..|+++|++|+.+.. +|++.++||+.|++|..||+.++.+.++||.-
T Consensus 136 ~~Lt~~E~~il~~l~----~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~~ 182 (196)
T PRK10360 136 DPLTKRERQVAEKLA----QGMAVKEIAAELGLSPKTVHVHRANLMEKLGV 182 (196)
T ss_pred cCCCHHHHHHHHHHH----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 469999999999976 78999999999999999999999999999863
No 178
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=95.79 E-value=0.0099 Score=67.00 Aligned_cols=58 Identities=22% Similarity=0.348 Sum_probs=51.0
Q ss_pred hhhHHHHHHhhccccCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccChhHHHhhhhhhHHHHHHHHHHHHHHH
Q 010835 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGSSLRISRPELQSILMECSLAREKLVMSNVRLV 268 (499)
Q Consensus 190 ~~~~~~yl~~i~~~~~Lt~eEe~eL~~~ik~Gd~l~~~~~~~~~~~g~~~~~~~~~l~~~l~~~~~A~e~LIe~yl~LV 268 (499)
.|.+++||++++.+|+||+++|++++++|..|.. .+...+.++.-+.+.++..|-.+.
T Consensus 103 ~DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~---------------------~v~~al~~~P~~i~~il~~~e~v~ 160 (619)
T PRK05658 103 DDPVRMYLREMGTVELLTREGEIEIAKRIEAGEN---------------------IMIAALCESPLTIDAILEWYDRLE 160 (619)
T ss_pred CChHHHHHHHhccCcCCCcHHHHHHHHHHHHHHH---------------------HHHHHHHhCcHHHHHHHHHHHHHH
Confidence 4899999999999999999999999999999976 677788888888888888876653
No 179
>PRK04841 transcriptional regulator MalT; Provisional
Probab=95.71 E-value=0.017 Score=67.01 Aligned_cols=46 Identities=20% Similarity=0.288 Sum_probs=43.4
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 484 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR 484 (499)
..|+++|++|+.+.. +|+|.+|||+.|+||..||+.++.+...||.
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 359999999999976 9999999999999999999999999999996
No 180
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=95.63 E-value=0.025 Score=52.56 Aligned_cols=46 Identities=22% Similarity=0.294 Sum_probs=42.6
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 484 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR 484 (499)
..|+++|++|+.+.. .|.+.++||+.+++|..||+.++.+.++||.
T Consensus 142 ~~lt~~E~~vl~~l~----~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~ 187 (204)
T PRK09958 142 DSLSKQEISVMRYIL----DGKDNNDIAEKMFISNKTVSTYKSRLMEKLE 187 (204)
T ss_pred ccCCHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 469999999999976 8899999999999999999999999999984
No 181
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=95.62 E-value=0.012 Score=43.83 Aligned_cols=33 Identities=36% Similarity=0.416 Sum_probs=23.6
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010835 443 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 479 (499)
Q Consensus 443 ~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rA 479 (499)
.||.++. +|+|..+||+.||||+.||.+++.+-
T Consensus 9 ~ii~l~~----~G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 9 QIIRLLR----EGWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp -HHHHHH----HT--HHHHHHHHTS-HHHHHHHHT--
T ss_pred HHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 3666665 69999999999999999999987663
No 182
>PRK13558 bacterio-opsin activator; Provisional
Probab=95.56 E-value=0.021 Score=64.21 Aligned_cols=49 Identities=24% Similarity=0.262 Sum_probs=43.7
Q ss_pred hhCCHHHHHHHHHHhcCCCCCC-------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECL-------TWEDISKRIGLSRERVRQVGLVALEKLKHA 486 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~-------SleEIAe~LgIS~~rVrqi~~rALkKLR~~ 486 (499)
..|+++|+++|..-| ..|+ |.+|||+.||||++|+.+++.+|.+||=..
T Consensus 606 ~~lt~~q~e~l~~a~---~~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l~~~ 661 (665)
T PRK13558 606 NDLTDRQLTALQKAY---VSGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKLVGA 661 (665)
T ss_pred hhCCHHHHHHHHHHH---HcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 579999999999988 4555 999999999999999999999999998544
No 183
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=95.54 E-value=0.017 Score=59.96 Aligned_cols=36 Identities=31% Similarity=0.510 Sum_probs=33.5
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010835 443 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALE 481 (499)
Q Consensus 443 ~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALk 481 (499)
.|-.||| .+++|+.|||++||+||.+|++++.+|++
T Consensus 20 ~vA~lYY---~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~ 55 (318)
T PRK15418 20 RIAWFYY---HDGLTQSEIGERLGLTRLKVSRLLEKGRQ 55 (318)
T ss_pred HHHHHHH---hcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4778999 89999999999999999999999999986
No 184
>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=95.32 E-value=0.023 Score=39.20 Aligned_cols=27 Identities=41% Similarity=0.598 Sum_probs=19.5
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 455 CLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 455 g~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
++|.+|||+.+|+|++||+ |++++|++
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 4789999999999999996 55666654
No 185
>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=95.24 E-value=0.071 Score=48.47 Aligned_cols=57 Identities=23% Similarity=0.388 Sum_probs=44.8
Q ss_pred HHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 010835 425 LKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL 483 (499)
Q Consensus 425 l~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKL 483 (499)
..+.|...+ +.|.+.++.||.+||+-. .++|+.+||..|+++..|++.+...-...+
T Consensus 71 ~k~~id~~~-~~l~de~k~Ii~lry~~r-~~~TW~~IA~~l~i~erta~r~~~~fK~~i 127 (130)
T PF05263_consen 71 QKEAIDRWL-ETLIDEEKRIIKLRYDRR-SRRTWYQIAQKLHISERTARRWRDRFKNDI 127 (130)
T ss_pred HHHHHHHHH-HhhCHHHHHHHHHHHccc-ccchHHHHHHHhCccHHHHHHHHHHHHHHh
Confidence 345566666 899999999999999411 359999999999999999987766554433
No 186
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=95.11 E-value=0.05 Score=41.44 Aligned_cols=50 Identities=22% Similarity=0.326 Sum_probs=42.2
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 487 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L 487 (499)
+|+..++.++.+.|- ..+.++++||..+|||++||+++.+..+.-|-..+
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 578888888887551 47899999999999999999999999888776543
No 187
>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=95.09 E-value=0.053 Score=46.02 Aligned_cols=39 Identities=18% Similarity=0.288 Sum_probs=32.5
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 479 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rA 479 (499)
+.|++| ..|+.+.- .|+|..+||+.+|+|+.||.+ +.++
T Consensus 35 ~~Ls~R-~~I~~ll~----~G~S~~eIA~~LgISrsTIyR-i~R~ 73 (88)
T TIGR02531 35 QSLAQR-LQVAKMLK----QGKTYSDIEAETGASTATISR-VKRC 73 (88)
T ss_pred HhhhHH-HHHHHHHH----CCCCHHHHHHHHCcCHHHHHH-HHHh
Confidence 568888 77887764 789999999999999999988 4454
No 188
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=95.06 E-value=0.035 Score=40.87 Aligned_cols=32 Identities=34% Similarity=0.456 Sum_probs=24.5
Q ss_pred HHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 010835 441 EREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVG 476 (499)
Q Consensus 441 ER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~ 476 (499)
..+|+.|+- +|+|..+||+.+|||+.||.+++
T Consensus 11 ~~~i~~l~~----~G~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 11 IEEIKELYA----EGMSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp HHHHHHHHH----TT--HHHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHH
Confidence 456777775 88999999999999999998765
No 189
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=95.00 E-value=0.065 Score=39.55 Aligned_cols=41 Identities=22% Similarity=0.402 Sum_probs=29.8
Q ss_pred CCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010835 437 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 479 (499)
Q Consensus 437 L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rA 479 (499)
|++.++.||..-. +..+.|..|||+.+|+|..+|++++.+-
T Consensus 1 l~~~~~~Il~~l~--~~~~~t~~ela~~~~is~~tv~~~l~~L 41 (48)
T PF13412_consen 1 LDETQRKILNYLR--ENPRITQKELAEKLGISRSTVNRYLKKL 41 (48)
T ss_dssp --HHHHHHHHHHH--HCTTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCHHHHHHHHHHH--HcCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 5788888887765 1356999999999999999998776543
No 190
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=94.47 E-value=0.077 Score=34.82 Aligned_cols=36 Identities=22% Similarity=0.299 Sum_probs=28.4
Q ss_pred CCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHH
Q 010835 437 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQV 475 (499)
Q Consensus 437 L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi 475 (499)
+++.++..+...+ ..+.+..+||+.+|+++.+|.++
T Consensus 6 ~~~~~~~~i~~~~---~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 6 LTPEQIEEARRLL---AAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHh
Confidence 5566666555555 57889999999999999999875
No 191
>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=94.20 E-value=0.11 Score=37.94 Aligned_cols=40 Identities=28% Similarity=0.427 Sum_probs=27.3
Q ss_pred CCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 437 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 437 L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
|++..+.||..--. ....|+.+||+.+|+|..+|.+++.+
T Consensus 1 lD~~D~~Il~~Lq~--d~r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 1 LDELDRKILRLLQE--DGRRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp --HHHHHHHHHHHH---TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH--cCCccHHHHHHHHCcCHHHHHHHHHH
Confidence 45666777766431 24599999999999999999877654
No 192
>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=93.98 E-value=0.36 Score=43.40 Aligned_cols=53 Identities=15% Similarity=0.148 Sum_probs=48.1
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 490 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~~ 490 (499)
.+-.|.+-.+|.+|| ..+.|...||..+++|...|++.+.+|-..+...|.-.
T Consensus 61 ~~~~~~~~~ll~~~Y---v~g~s~r~IA~~~~~s~~~ir~~l~~ae~~i~g~l~~~ 113 (125)
T PF06530_consen 61 KKRDPEEYDLLILYY---VYGWSKRQIARKLKCSEGKIRKRLQRAEGFIDGCLSML 113 (125)
T ss_pred HccCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHhhhhHhhhhHHh
Confidence 457899999999999 78999999999999999999999999999999876543
No 193
>PF13518 HTH_28: Helix-turn-helix domain
Probab=93.71 E-value=0.14 Score=37.91 Aligned_cols=34 Identities=26% Similarity=0.343 Sum_probs=27.3
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 443 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 443 ~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
.||.++. +|.|+.+||..+|||+.+|.+++.+-.
T Consensus 4 ~iv~~~~----~g~s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 4 QIVELYL----EGESVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred HHHHHHH----cCCCHHHHHHHHCCCHhHHHHHHHHHH
Confidence 3555554 678999999999999999988876544
No 194
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=93.58 E-value=0.09 Score=54.74 Aligned_cols=36 Identities=39% Similarity=0.530 Sum_probs=32.4
Q ss_pred HHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 010835 444 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEK 482 (499)
Q Consensus 444 VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkK 482 (499)
+-.+|| .+|+|+.|||++||||+.+|++.+.+|+++
T Consensus 18 ~A~lYY---~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~ 53 (321)
T COG2390 18 AAWLYY---VEGLTQSEIAERLGISRATVSRLLAKAREE 53 (321)
T ss_pred HHHHHH---hcCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 556788 899999999999999999999999998763
No 195
>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=93.41 E-value=0.16 Score=39.76 Aligned_cols=32 Identities=19% Similarity=0.251 Sum_probs=27.2
Q ss_pred HHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010835 444 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 479 (499)
Q Consensus 444 VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rA 479 (499)
...||. +|++..|||+.||+++.||.+...+-
T Consensus 6 A~~LY~----~G~~~~eIA~~Lg~~~~TV~~W~~r~ 37 (58)
T PF06056_consen 6 ARSLYL----QGWSIKEIAEELGVPRSTVYSWKDRY 37 (58)
T ss_pred HHHHHH----cCCCHHHHHHHHCCChHHHHHHHHhh
Confidence 445554 89999999999999999999988764
No 196
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=93.31 E-value=0.21 Score=44.38 Aligned_cols=48 Identities=27% Similarity=0.342 Sum_probs=43.3
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
..|++.+..-|..+. ...=+++|+++.||||..|||.++.+.+++|..
T Consensus 32 ~~L~~E~~~Fi~~Fi---~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 32 ARLSPEQLEFIKLFI---KNRGNLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred hcCCHHHHHHHHHHH---HhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 689999999888876 566799999999999999999999999999875
No 197
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=93.01 E-value=0.16 Score=40.10 Aligned_cols=39 Identities=15% Similarity=0.317 Sum_probs=28.3
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 439 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 439 ~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
|.--..+.+|... ...+++.+||+.||||..||+.+..+
T Consensus 7 p~rdkA~e~y~~~-~g~i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 7 PNRDKAFEIYKES-NGKIKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred cCHHHHHHHHHHh-CCCccHHHHHHHHCCCHHHHHHHhhh
Confidence 3333455555411 35799999999999999999988654
No 198
>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]
Probab=92.66 E-value=0.13 Score=59.12 Aligned_cols=44 Identities=27% Similarity=0.297 Sum_probs=42.4
Q ss_pred CCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010835 437 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 484 (499)
Q Consensus 437 L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR 484 (499)
|+.||++|+.+.| .|+|.+|||.+|.||-.||+.++.....||.
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 8999999999998 9999999999999999999999999999985
No 199
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=92.56 E-value=0.21 Score=48.74 Aligned_cols=46 Identities=9% Similarity=0.147 Sum_probs=35.9
Q ss_pred hCCHHHHHHHHHHh-cCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYY-GLDKECLTWEDISKRIGLSRERVRQVGLVALE 481 (499)
Q Consensus 436 ~L~~rER~VI~Lry-GLd~eg~SleEIAe~LgIS~~rVrqi~~rALk 481 (499)
.|++++.+++.... +...+|+|.+|||+.||+|+.||+..+.++..
T Consensus 158 ~Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~ 204 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVN 204 (239)
T ss_pred CCCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHh
Confidence 47888877664432 22247899999999999999999999987744
No 200
>smart00351 PAX Paired Box domain.
Probab=92.36 E-value=0.32 Score=43.62 Aligned_cols=42 Identities=24% Similarity=0.161 Sum_probs=33.1
Q ss_pred CCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010835 437 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALE 481 (499)
Q Consensus 437 L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALk 481 (499)
++..+|.=|...| .+|.|..+||+.||||+.||.+++.+..+
T Consensus 18 ~s~~~R~riv~~~---~~G~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 18 LPDEERQRIVELA---QNGVRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred CCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 5555555444555 48899999999999999999999988643
No 201
>PF13730 HTH_36: Helix-turn-helix domain
Probab=92.28 E-value=0.51 Score=35.58 Aligned_cols=46 Identities=22% Similarity=0.350 Sum_probs=32.6
Q ss_pred hCCHHHHHHHHHHhcC-CCCC---CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGL-DKEC---LTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 436 ~L~~rER~VI~LryGL-d~eg---~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
.|++.++.|+..-.-. +.++ .|.+.||+.+|+|+.||. ++++.|.+
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 5888888877653333 2222 389999999999999995 55555553
No 202
>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=91.53 E-value=0.2 Score=38.27 Aligned_cols=40 Identities=25% Similarity=0.216 Sum_probs=26.8
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
.|+..++.=|.-+| ..|.+..+||..|||+++||+.++..
T Consensus 6 ~LTl~eK~~iI~~~---e~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 6 SLTLEEKLEIIKRL---EEGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp S--HHHHHHHHHHH---HCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred cCCHHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 45666665343444 47889999999999999999998765
No 203
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=91.13 E-value=0.43 Score=36.56 Aligned_cols=43 Identities=19% Similarity=0.240 Sum_probs=31.2
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
.|++.+..||..-+.-+.+++|..|||+.+++++.+|.+.+.+
T Consensus 2 glt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~ 44 (62)
T PF12802_consen 2 GLTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKR 44 (62)
T ss_dssp TSTHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 3678888888765532222389999999999999999766554
No 204
>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=90.65 E-value=0.41 Score=40.61 Aligned_cols=46 Identities=15% Similarity=0.187 Sum_probs=33.2
Q ss_pred hhCCHHHHHHHHHHhcCC----CCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLD----KECLTWEDISKRIGLSRERVRQVGLVALE 481 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd----~eg~SleEIAe~LgIS~~rVrqi~~rALk 481 (499)
+-++|.|+.-+..|+-+- .+|+|+.|||+.+|+|..||.+ .+|+|+
T Consensus 25 dL~T~~E~~~l~~R~~va~~lL~~g~syreIa~~tgvS~aTItR-vsr~Lk 74 (87)
T PF01371_consen 25 DLCTPDELEALAQRWQVAKELLDEGKSYREIAEETGVSIATITR-VSRCLK 74 (87)
T ss_dssp HHSSHHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHH-HHHHHH
T ss_pred HhCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHH-HHHHHH
Confidence 347888877666655442 2789999999999999999953 344444
No 205
>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=90.45 E-value=0.46 Score=35.85 Aligned_cols=38 Identities=26% Similarity=0.483 Sum_probs=26.0
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 440 REREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 440 rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
|++.|+.+-+- ..++.|.+|||+.||||+.||++.+..
T Consensus 1 R~~~il~~L~~-~~~~it~~eLa~~l~vS~rTi~~~i~~ 38 (55)
T PF08279_consen 1 RQKQILKLLLE-SKEPITAKELAEELGVSRRTIRRDIKE 38 (55)
T ss_dssp HHHHHHHHHHH-TTTSBEHHHHHHHCTS-HHHHHHHHHH
T ss_pred CHHHHHHHHHH-cCCCcCHHHHHHHhCCCHHHHHHHHHH
Confidence 35566655420 134599999999999999999766544
No 206
>cd00131 PAX Paired Box domain
Probab=90.29 E-value=0.69 Score=41.75 Aligned_cols=41 Identities=20% Similarity=0.101 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 437 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 437 L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
|+...|.=|...| .+|+|..+||+.||||+.||..++++-.
T Consensus 18 lS~d~R~rIv~~~---~~G~s~~~iA~~~~Vs~~tV~r~i~r~~ 58 (128)
T cd00131 18 LPDSIRQRIVELA---QSGIRPCDISRQLRVSHGCVSKILNRYY 58 (128)
T ss_pred CCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4554444333444 4899999999999999999999988755
No 207
>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=90.15 E-value=1.1 Score=34.69 Aligned_cols=43 Identities=19% Similarity=0.244 Sum_probs=32.7
Q ss_pred HHHHHHhhCCHHHHHHHHHH-hcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 429 VNKLIIVTLGEREREIIRLY-YGLDKECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 429 L~~~L~~~L~~rER~VI~Lr-yGLd~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
+.++| .+|.-+.|+.+- - .+++|..|||+.+|+++++|++.+.
T Consensus 3 i~~aL---~~p~R~~Il~~L~~---~~~~t~~ela~~l~~~~~t~s~hL~ 46 (61)
T PF12840_consen 3 IFKAL---SDPTRLRILRLLAS---NGPMTVSELAEELGISQSTVSYHLK 46 (61)
T ss_dssp HHHHH---TSHHHHHHHHHHHH---CSTBEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHh---CCHHHHHHHHHHhc---CCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 44555 467777788776 4 6899999999999999999976654
No 208
>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=90.09 E-value=0.57 Score=37.45 Aligned_cols=43 Identities=21% Similarity=0.297 Sum_probs=27.1
Q ss_pred hhCCHHHHHHHHHHhc-C--CCCCCCHHHHHHHHCCC-HHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYG-L--DKECLTWEDISKRIGLS-RERVRQVGL 477 (499)
Q Consensus 435 ~~L~~rER~VI~LryG-L--d~eg~SleEIAe~LgIS-~~rVrqi~~ 477 (499)
..|+++|++||...-. + ++-.-|..|||+.||++ .++|.+.+.
T Consensus 2 ~~LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~ 48 (65)
T PF01726_consen 2 KELTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLK 48 (65)
T ss_dssp ----HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHH
Confidence 5689999999877321 1 13456999999999996 999976553
No 209
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=90.06 E-value=0.81 Score=33.72 Aligned_cols=37 Identities=22% Similarity=0.275 Sum_probs=28.3
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 439 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 439 ~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
|.-..|+.+-. ..+++..|||+.+|+|+++|++.+..
T Consensus 2 ~~R~~Il~~L~---~~~~~~~el~~~l~~s~~~vs~hL~~ 38 (47)
T PF01022_consen 2 PTRLRILKLLS---EGPLTVSELAEELGLSQSTVSHHLKK 38 (47)
T ss_dssp HHHHHHHHHHT---TSSEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHH---hCCCchhhHHHhccccchHHHHHHHH
Confidence 44556666655 57899999999999999999877653
No 210
>PHA02591 hypothetical protein; Provisional
Probab=90.00 E-value=0.54 Score=38.90 Aligned_cols=25 Identities=28% Similarity=0.357 Sum_probs=22.8
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
..|+|.++||+.||+|.++|++.+.
T Consensus 57 eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 57 RKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 3689999999999999999999875
No 211
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=89.94 E-value=0.7 Score=38.40 Aligned_cols=41 Identities=29% Similarity=0.379 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHhcC---CCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 437 LGEREREIIRLYYGL---DKECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 437 L~~rER~VI~LryGL---d~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
|+++|++||..-.-+ ..++..-++||+.+++|..|||+.+.
T Consensus 2 Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~ 45 (78)
T PF03444_consen 2 LTERQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMA 45 (78)
T ss_pred CCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHH
Confidence 789999988763322 35678999999999999999987754
No 212
>PHA00675 hypothetical protein
Probab=89.94 E-value=0.63 Score=38.43 Aligned_cols=41 Identities=17% Similarity=0.238 Sum_probs=32.0
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
.+|++.+-+.|+..+- .+|.|+.+||+.||||+++|.+|.+
T Consensus 21 AKLt~~qV~~IR~l~~--r~G~s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 21 AKLTDAEVERIRELHE--VEGMSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred cccCHHHHHHHHHHHH--hcCccHHHHHHHhCCCHHHHHHHHc
Confidence 5677777665555430 2789999999999999999998865
No 213
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=88.96 E-value=1 Score=36.03 Aligned_cols=37 Identities=24% Similarity=0.346 Sum_probs=25.0
Q ss_pred HHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 441 EREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 441 ER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
+..|+.+-..-+.+++|..|||+.+|+++.+|++++.
T Consensus 8 ~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~ 44 (68)
T smart00550 8 EEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLY 44 (68)
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHH
Confidence 4445544331112259999999999999999975554
No 214
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=88.65 E-value=0.83 Score=42.16 Aligned_cols=41 Identities=12% Similarity=0.230 Sum_probs=32.7
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
.|++.++.||..--- ....|+.|||+.+|+|+.||+.++.+
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 578888888877540 24599999999999999999876654
No 215
>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=88.60 E-value=0.71 Score=36.19 Aligned_cols=44 Identities=30% Similarity=0.482 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHhcC--CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010835 437 LGEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGLVALEKLK 484 (499)
Q Consensus 437 L~~rER~VI~LryGL--d~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR 484 (499)
|++....-|...|-| +.+..+..+||+.||+|+.+|. .++++|.
T Consensus 2 Lt~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt----~ml~~L~ 47 (60)
T PF01325_consen 2 LTESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVT----EMLKRLA 47 (60)
T ss_dssp CSCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHH----HHHHHHH
T ss_pred CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHH----HHHHHHH
Confidence 344444444444444 3577999999999999999996 4555554
No 216
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=88.50 E-value=0.8 Score=42.10 Aligned_cols=35 Identities=20% Similarity=0.164 Sum_probs=28.9
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 443 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 443 ~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
.++..++ .+|+|.+|||+++|||.+||..++.+-.
T Consensus 12 ~~~~~~~---~~G~S~re~Ak~~gvs~sTvy~wv~r~~ 46 (138)
T COG3415 12 RVVDAVV---GEGLSCREAAKRFGVSISTVYRWVRRYR 46 (138)
T ss_pred HHHHHHH---HcCccHHHHHHHhCccHHHHHHHHHHhc
Confidence 3444554 4999999999999999999999988765
No 217
>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=87.78 E-value=0.55 Score=35.01 Aligned_cols=22 Identities=32% Similarity=0.376 Sum_probs=20.0
Q ss_pred CHHHHHHHHCCCHHHHHHHHHH
Q 010835 457 TWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 457 SleEIAe~LgIS~~rVrqi~~r 478 (499)
|++|||+..|+|..||++.++.
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 6899999999999999988864
No 218
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=87.63 E-value=1.3 Score=32.84 Aligned_cols=26 Identities=23% Similarity=0.397 Sum_probs=23.0
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010835 454 ECLTWEDISKRIGLSRERVRQVGLVA 479 (499)
Q Consensus 454 eg~SleEIAe~LgIS~~rVrqi~~rA 479 (499)
+..|.++||+.+|+|..||.+++.+.
T Consensus 26 ~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 26 ESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 44799999999999999999998764
No 219
>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=87.39 E-value=1.4 Score=35.98 Aligned_cols=52 Identities=12% Similarity=0.235 Sum_probs=35.0
Q ss_pred HHHHHHHHHHhhCCHHHHHHHHHHhcC--CCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 425 LKDEVNKLIIVTLGEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 425 l~~~L~~~L~~~L~~rER~VI~LryGL--d~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
+...|.... ..|++.|+.|.....-= +...+|..|||+..|||+.+|.+..+
T Consensus 3 l~~~i~~~~-~~ls~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~k 56 (77)
T PF01418_consen 3 LLEKIRSQY-NSLSPTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCK 56 (77)
T ss_dssp HHHHHHHHG-GGS-HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHH-hhCCHHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHH
Confidence 345566666 89999999988664310 13469999999999999999976543
No 220
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=87.34 E-value=0.92 Score=42.41 Aligned_cols=41 Identities=22% Similarity=0.241 Sum_probs=32.0
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
.|++.++.||..-- .....|+.|||+.+|+|+.+|++++.+
T Consensus 11 ~lD~~D~~IL~~Lq--~d~R~s~~eiA~~lglS~~tv~~Ri~r 51 (164)
T PRK11169 11 DLDRIDRNILNELQ--KDGRISNVELSKRVGLSPTPCLERVRR 51 (164)
T ss_pred hHHHHHHHHHHHhc--cCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 46778888887643 124599999999999999999877654
No 221
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=87.18 E-value=1.4 Score=37.73 Aligned_cols=41 Identities=22% Similarity=0.319 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010835 437 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 479 (499)
Q Consensus 437 L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rA 479 (499)
|++.++.|+....- ....|+.+||+.+|+|+.+|++++.+-
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 46778888877541 246999999999999999998666543
No 222
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=87.11 E-value=24 Score=38.44 Aligned_cols=24 Identities=17% Similarity=0.333 Sum_probs=21.2
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 454 ECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 454 eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
.++++++||+.+|++.+||++...
T Consensus 329 ~PL~LrdvA~~i~~HESTISRai~ 352 (444)
T COG1508 329 KPLVLRDVADEIGMHESTISRAIT 352 (444)
T ss_pred CcccHHHHHHHhCccHHHHHHHHh
Confidence 469999999999999999987654
No 223
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=87.02 E-value=1.6 Score=35.90 Aligned_cols=38 Identities=24% Similarity=0.385 Sum_probs=26.7
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH-----HHHHHHHHHHHHh
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGL-----VALEKLKHAARKK 490 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~-----rALkKLR~~L~~~ 490 (499)
..++|+.|+|+.+|+|+++|+++++ -.+.+|...+..-
T Consensus 29 ~~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aL 71 (80)
T PF13744_consen 29 ERGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEAL 71 (80)
T ss_dssp CCT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHT
T ss_pred HcCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHc
Confidence 5789999999999999999999884 2356666665543
No 224
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=87.01 E-value=2.3 Score=38.56 Aligned_cols=50 Identities=24% Similarity=0.344 Sum_probs=38.0
Q ss_pred HHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 010835 428 EVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL 483 (499)
Q Consensus 428 ~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKL 483 (499)
.+.+++ -.|++.+-+|+..-.- ...++|.+|||++||.+++|| +||+++|
T Consensus 17 dvl~c~-~GLs~~Dv~v~~~LL~-~~~~~tvdelae~lnr~rStv----~rsl~~L 66 (126)
T COG3355 17 DVLKCV-YGLSELDVEVYKALLE-ENGPLTVDELAEILNRSRSTV----YRSLQNL 66 (126)
T ss_pred HHHHHH-hCCcHHHHHHHHHHHh-hcCCcCHHHHHHHHCccHHHH----HHHHHHH
Confidence 444555 6899999998866431 146899999999999999999 4666655
No 225
>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=86.89 E-value=1.3 Score=37.46 Aligned_cols=43 Identities=16% Similarity=0.166 Sum_probs=32.5
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHH--CCCHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRI--GLSRERVRQVGLVA 479 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~L--gIS~~rVrqi~~rA 479 (499)
+.||+..+.+..+|. ...+.|+.|||+.+ .||++.|..++.+.
T Consensus 36 ~~l~~~l~~~a~lRl--~~Pd~SL~EL~~~~~~~iSKSgvnhrlrKl 80 (85)
T PF02650_consen 36 DKLPEKLREFAELRL--ENPDASLKELGELLEPPISKSGVNHRLRKL 80 (85)
T ss_dssp GGS-HHHHHHHHHHH--H-TTS-HHHHHHTT--T--HHHHHHHHHHH
T ss_pred ccCCHHHHHHHHHHH--HCccccHHHHHHHHcCcCcHHHHHHHHHHH
Confidence 789999999999986 24679999999999 99999998776543
No 226
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=86.71 E-value=0.86 Score=42.69 Aligned_cols=50 Identities=12% Similarity=0.013 Sum_probs=41.4
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCC-----HHHHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIGLS-----RERVRQVGLVALEKLKH 485 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS-----~~rVrqi~~rALkKLR~ 485 (499)
.|+++|.+|+.+..-=.+.++|.++|++.++.+ ..||+.++.+.++||+.
T Consensus 154 ~Lt~~E~~il~~l~~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~l~~Kl~~ 208 (228)
T PRK11083 154 TLTRYEFLLLKTLLLSPGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLRA 208 (228)
T ss_pred ecCHHHHHHHHHHHhCCCceECHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhcc
Confidence 599999999988661012369999999999986 78999999999999963
No 227
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=86.59 E-value=0.89 Score=42.40 Aligned_cols=49 Identities=18% Similarity=0.131 Sum_probs=40.4
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIG-----LSRERVRQVGLVALEKLK 484 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~Lg-----IS~~rVrqi~~rALkKLR 484 (499)
.|+++|.+|+.+..-=-+..+|.++|++.+. ++..||+.++.+.++||.
T Consensus 149 ~Lt~~E~~il~~l~~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl~ 202 (219)
T PRK10336 149 TLKPKEFALLELLMRNAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLG 202 (219)
T ss_pred ecCHHHHHHHHHHHhCCCccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhcC
Confidence 5999999999876510023499999999996 999999999999998885
No 228
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=86.48 E-value=1.8 Score=37.42 Aligned_cols=55 Identities=22% Similarity=0.321 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHHhhCCHHHHHHHHHHhcC-C---CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010835 423 WALKDEVNKLIIVTLGEREREIIRLYYGL-D---KECLTWEDISKRIGLSRERVRQVGLVALEKLK 484 (499)
Q Consensus 423 ~el~~~L~~~L~~~L~~rER~VI~LryGL-d---~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR 484 (499)
......+..++ |+|.||+-+..|+.| . ..++|.+||+..||+|-.|| .|+=+.||
T Consensus 27 ~d~~~~lL~ll---LTpdEReal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtI----TRGSN~LK 85 (103)
T COG2973 27 EDLHQPLLTLL---LTPDEREALGTRVRIVEELLRGELSQREIAQKLGVSIATI----TRGSNSLK 85 (103)
T ss_pred hHHHHHHHHHH---cCHhHHHHHHHHHHHHHHHHhccccHHHHHHHhCcchhhh----ccchhhhc
Confidence 33444555666 899999988887766 1 35799999999999999988 35544444
No 229
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=86.36 E-value=3.8 Score=37.73 Aligned_cols=62 Identities=18% Similarity=0.207 Sum_probs=38.3
Q ss_pred hhCCHHHHHHHHH-----HhcCCCCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHHhhHHHhh
Q 010835 435 VTLGEREREIIRL-----YYGLDKECLTWEDISKRIGLSRERVRQVGL--VALEKLKHAARKKKMEAML 496 (499)
Q Consensus 435 ~~L~~rER~VI~L-----ryGLd~eg~SleEIAe~LgIS~~rVrqi~~--rALkKLR~~L~~~~l~~~l 496 (499)
.+|++.|+.-..+ ..+.+.+..|+.|||+.+||++.|+-++.+ ++.....+.+....+.+++
T Consensus 9 ~~L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~~~~Fiey~n~la~~~~~~~~ 77 (142)
T PF13022_consen 9 AKLTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQQNKAFIEYKNELADRFLSSHR 77 (142)
T ss_dssp TTS-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHHH-HHHHHHHHHHHHHHHHTTH
T ss_pred HHcCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHhH
Confidence 7899998883332 222223569999999999999999999884 4556566666665555544
No 230
>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=86.11 E-value=3.4 Score=35.24 Aligned_cols=47 Identities=30% Similarity=0.412 Sum_probs=35.1
Q ss_pred hhCCHHHHHHHHH----HhcCC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRL----YYGLD--KECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 435 ~~L~~rER~VI~L----ryGLd--~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
..+++++..||.. .||.. ..++|..|||+.+|+++++|+ +++++|.+
T Consensus 21 ~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVs----r~L~~Le~ 73 (95)
T TIGR01610 21 ADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVS----DAIKSLAR 73 (95)
T ss_pred CCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 5789999887763 23431 467999999999999999996 55555543
No 231
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=86.01 E-value=0.75 Score=44.49 Aligned_cols=40 Identities=18% Similarity=0.118 Sum_probs=29.5
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
+.|+++ +|+.+.- -+..|+|.+|||+.||+|+.||+.++.
T Consensus 160 ~~Lt~r--~Vl~~~~-~g~~g~s~~eIa~~l~iS~~Tv~~~~~ 199 (225)
T PRK10046 160 DPLTLN--AVRKLFK-EPGVQHTAETVAQALTISRTTARRYLE 199 (225)
T ss_pred CHHHHH--HHHHHHH-cCCCCcCHHHHHHHhCccHHHHHHHHH
Confidence 345554 6776643 112379999999999999999998875
No 232
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=85.87 E-value=3.7 Score=36.46 Aligned_cols=34 Identities=9% Similarity=0.122 Sum_probs=28.7
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010835 443 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 479 (499)
Q Consensus 443 ~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rA 479 (499)
.++...+ ..|.|..+||+.+|||..++.++....
T Consensus 20 ~aV~~~~---~~g~sv~evA~e~gIs~~tl~~W~r~y 53 (121)
T PRK09413 20 AIVQQSF---EPGMTVSLVARQHGVAASQLFLWRKQY 53 (121)
T ss_pred HHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3555555 578999999999999999999998874
No 233
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=85.80 E-value=1.3 Score=42.44 Aligned_cols=36 Identities=19% Similarity=0.327 Sum_probs=29.1
Q ss_pred CHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 438 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 438 ~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
.+.++.|+.++- +|+|..+||+.||||++||.++..
T Consensus 159 ~~~~~~i~~~~~----~g~s~~~iak~lgis~~Tv~r~~k 194 (200)
T PRK13413 159 TGKEEKIKKLLD----KGTSKSEIARKLGVSRTTLARFLK 194 (200)
T ss_pred chhHHHHHHHHH----CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 344556776654 789999999999999999988775
No 234
>PF13551 HTH_29: Winged helix-turn helix
Probab=85.63 E-value=7.5 Score=32.87 Aligned_cols=23 Identities=22% Similarity=0.291 Sum_probs=21.3
Q ss_pred CHHHHHHHhCCCHHHHHHHHHhh
Q 010835 359 SVDRIAEYLNMSQKKVRNATEAI 381 (499)
Q Consensus 359 t~eEIA~~Lgis~e~v~~~l~~~ 381 (499)
+..+||..+|++..+|.+.+...
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~ 36 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRY 36 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHH
Confidence 79999999999999999998875
No 235
>PHA02547 55 RNA polymerase sigma factor; Provisional
Probab=85.56 E-value=3.1 Score=39.43 Aligned_cols=65 Identities=14% Similarity=0.282 Sum_probs=48.8
Q ss_pred HHHHHHHHHHhHhhCCCCC---HHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHh
Q 010835 263 SNVRLVMSIAQRYDNMGAD---MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVEN 327 (499)
Q Consensus 263 ~yl~LV~sIA~ry~~~g~d---~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~ 327 (499)
+.+.++..++++|.-++.. -+|.|-+|.-.+++.+..|||++...+-+|++..+-++..+.|...
T Consensus 45 ~imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~kE 112 (179)
T PHA02547 45 AIMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKKE 112 (179)
T ss_pred HHHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHHH
Confidence 4455556666666555554 7899999999999999999999987777777777766666655544
No 236
>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=85.54 E-value=8.9 Score=33.96 Aligned_cols=27 Identities=26% Similarity=0.433 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010835 454 ECLTWEDISKRIGLSRERVRQVGLVALEKLK 484 (499)
Q Consensus 454 eg~SleEIAe~LgIS~~rVrqi~~rALkKLR 484 (499)
.+.|+.|||+.||||.++|. ++|++|.
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 67999999999999999996 5555544
No 237
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=85.46 E-value=1.8 Score=32.95 Aligned_cols=39 Identities=31% Similarity=0.390 Sum_probs=26.5
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
.|++.||--|...+ .-|+++.|||..+|-|+..|+..+.
T Consensus 4 ~Lt~~Eqaqid~m~---qlG~s~~~isr~i~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 4 TLTDAEQAQIDVMH---QLGMSLREISRRIGRSRTCIRRYLK 42 (50)
T ss_dssp ---HHHHHHHHHHH---HTT--HHHHHHHHT--HHHHHHHHH
T ss_pred cCCHHHHHHHHHHH---HhchhHHHHHHHhCccHHHHHHHhc
Confidence 47788887776666 5789999999999999999988764
No 238
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional
Probab=85.29 E-value=1.2 Score=42.15 Aligned_cols=50 Identities=10% Similarity=0.074 Sum_probs=42.5
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIG-----LSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~Lg-----IS~~rVrqi~~rALkKLR~ 485 (499)
.|+++|++|+.+...=.+++.|.++|++.+. ++..||+..+.+.++||..
T Consensus 160 ~Lt~~e~~il~~l~~~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~lr~kl~~ 214 (240)
T PRK10710 160 DLTPAEFRLLKTLSHEPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLES 214 (240)
T ss_pred ecCHHHHHHHHHHHhCCCceEcHHHHHHHhcCcCcCCCccCHHHHHHHHHHHhhc
Confidence 5899999999987621234799999999998 9999999999999999963
No 239
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=85.04 E-value=1.3 Score=42.25 Aligned_cols=39 Identities=23% Similarity=0.206 Sum_probs=32.7
Q ss_pred HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010835 442 REIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 484 (499)
Q Consensus 442 R~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR 484 (499)
+..++|.- .|+|..|||++||+|++|++.++.|+.++..
T Consensus 9 ~kA~eLk~----~Glt~gEIAdELNvSreTa~WL~~r~~~~~~ 47 (203)
T COG0856 9 KKARELKS----KGLTTGEIADELNVSRETATWLLTRAFKKES 47 (203)
T ss_pred HHHHHHHH----CCCcHHHhhhhhhhhHHHHHHHHhhhhhccC
Confidence 44566664 8999999999999999999999999876543
No 240
>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=84.62 E-value=1.7 Score=32.97 Aligned_cols=41 Identities=22% Similarity=0.414 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010835 437 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 479 (499)
Q Consensus 437 L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rA 479 (499)
|+..|-.||..-+- ..+.+..+||+.+++++++|.+.+.+-
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 45566666666441 467999999999999999997666543
No 241
>PF13551 HTH_29: Winged helix-turn helix
Probab=84.54 E-value=1.8 Score=36.77 Aligned_cols=33 Identities=30% Similarity=0.370 Sum_probs=26.8
Q ss_pred HHHHHHhcCCCCCC-CHHHHHHHHCCCHHHHHHHHHHH
Q 010835 443 EIIRLYYGLDKECL-TWEDISKRIGLSRERVRQVGLVA 479 (499)
Q Consensus 443 ~VI~LryGLd~eg~-SleEIAe~LgIS~~rVrqi~~rA 479 (499)
.||.+.. +|. |..+||+.+|+|+.||.+++++-
T Consensus 3 ~~l~l~~----~g~~~~~~ia~~lg~s~~Tv~r~~~~~ 36 (112)
T PF13551_consen 3 QILLLLA----EGVSTIAEIARRLGISRRTVYRWLKRY 36 (112)
T ss_pred HHHHHHH----cCCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence 3555554 788 59999999999999999888763
No 242
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=84.34 E-value=56 Score=34.57 Aligned_cols=42 Identities=19% Similarity=0.268 Sum_probs=33.6
Q ss_pred hhhHHHHHHhhccccCCCHHHHHHHHHHHHcCCCcchhHHHH
Q 010835 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRL 231 (499)
Q Consensus 190 ~~~~~~yl~~i~~~~~Lt~eEe~eL~~~ik~Gd~l~~~~~~~ 231 (499)
.+.+..|+.+++..+.++++++..+.+.++....+......+
T Consensus 8 ~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 49 (342)
T COG0568 8 ADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDL 49 (342)
T ss_pred hhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHH
Confidence 378999999999999999999999999998776543333333
No 243
>PF12728 HTH_17: Helix-turn-helix domain
Probab=84.26 E-value=1.1 Score=33.22 Aligned_cols=24 Identities=25% Similarity=0.266 Sum_probs=21.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVA 479 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rA 479 (499)
+|.+|+|+.||||+.||.++..+.
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcC
Confidence 689999999999999999988654
No 244
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=84.00 E-value=2.2 Score=38.72 Aligned_cols=42 Identities=24% Similarity=0.362 Sum_probs=33.5
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
..|++.++.||..--. .-..|+.|||+.+|+|+.+|+.++.+
T Consensus 4 ~~lD~~D~~IL~~L~~--d~r~~~~eia~~lglS~~~v~~Ri~~ 45 (154)
T COG1522 4 MKLDDIDRRILRLLQE--DARISNAELAERVGLSPSTVLRRIKR 45 (154)
T ss_pred ccccHHHHHHHHHHHH--hCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4688899999887431 23599999999999999999877654
No 245
>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=83.81 E-value=2.2 Score=40.29 Aligned_cols=42 Identities=21% Similarity=0.242 Sum_probs=33.9
Q ss_pred CHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010835 438 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALE 481 (499)
Q Consensus 438 ~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALk 481 (499)
|+.-|.-++..|= ++++|++.+|...|||..|++++..+|..
T Consensus 4 ~~e~R~~~R~~YV--~~~~sLe~aA~~~gVs~~TarrWK~~Ak~ 45 (165)
T PF08822_consen 4 PQETRDAVRRAYV--FDRLSLEQAAAKCGVSYATARRWKREAKA 45 (165)
T ss_pred cHHHHHHHHHHHH--hCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3444566666661 38899999999999999999999999865
No 246
>PRK15479 transcriptional regulatory protein TctD; Provisional
Probab=83.68 E-value=1.8 Score=40.33 Aligned_cols=49 Identities=14% Similarity=0.145 Sum_probs=40.1
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIG-----LSRERVRQVGLVALEKLK 484 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~Lg-----IS~~rVrqi~~rALkKLR 484 (499)
.|+++|.+|+.+..-=-+...|.++|++.+. +|..||+.++.+.++||.
T Consensus 148 ~Lt~~E~~il~~l~~~~~~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl~ 201 (221)
T PRK15479 148 ALTPREQALLTVLMYRRTRPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKLQ 201 (221)
T ss_pred ecCHHHHHHHHHHHhCCCCcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhcC
Confidence 5999999999876510023479999999996 999999999999999985
No 247
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=83.52 E-value=36 Score=35.25 Aligned_cols=178 Identities=17% Similarity=0.065 Sum_probs=91.3
Q ss_pred HHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhHHHHHHHHHHHHHHHHhhhcccccccHH
Q 010835 259 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH 338 (499)
Q Consensus 259 ~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTYA~~wIR~aI~~al~~~~R~vRip~~~~ 338 (499)
+-+...+..|..++.++.-. +-+.|.-..+++.+.....-+|.+...++.-.|.- +++.
T Consensus 120 r~l~~a~~~I~~~~~~L~Lp-----~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYi----ACR~------------ 178 (310)
T PRK00423 120 RNLAFALSELDRIASQLGLP-----RSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYA----ACRR------------ 178 (310)
T ss_pred HHHHHHHHHHHHHHHHcCCC-----HHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHH----HHHH------------
Confidence 33344556666676665322 45666666667766555555676555544333322 2222
Q ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccC-CCCCc
Q 010835 339 ERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRV-ENNPW 417 (499)
Q Consensus 339 e~l~~irka~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~-e~~Pe 417 (499)
.+.+-|..||++..+++..++........+.+.++.+. ....+++..-.. -.-|.
T Consensus 179 ---------------~~~prtl~eI~~~~~v~~k~i~~~~~~l~k~L~~~~~~---------~~p~~~i~r~~~~L~L~~ 234 (310)
T PRK00423 179 ---------------CKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPP---------TDPIDYVPRFASELGLSG 234 (310)
T ss_pred ---------------cCCCcCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCC---------CCHHHHHHHHHHHcCCCH
Confidence 34556778899999999888887766665544443321 011122211000 01121
Q ss_pred chHHHHHHHHHHHHHHHhhC----CHH--HHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 010835 418 HGVDDWALKDEVNKLIIVTL----GER--EREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL 483 (499)
Q Consensus 418 e~ve~~el~~~L~~~L~~~L----~~r--ER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKL 483 (499)
+ +. ......+..+....| +|. ---+|-+-.-+.+.+.|++|||...||+..||++....-.+.|
T Consensus 235 ~-v~-~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l 304 (310)
T PRK00423 235 E-VQ-KKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKELAEKL 304 (310)
T ss_pred H-HH-HHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 1 11 111222222221111 122 1112222111224679999999999999999997776665544
No 248
>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=83.45 E-value=1.2 Score=31.83 Aligned_cols=25 Identities=20% Similarity=0.205 Sum_probs=22.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
+|..|+|+.||||+.||+++...+.
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 5789999999999999999987754
No 249
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=83.23 E-value=5.6 Score=34.88 Aligned_cols=52 Identities=27% Similarity=0.296 Sum_probs=46.5
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 489 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~ 489 (499)
.+|.+-||-...-+| -+-+|-+|||-.++++..+|..+.+.-..|.|+.-+.
T Consensus 27 ~QLkELErvF~ETHY---PDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~ 78 (125)
T KOG0484|consen 27 AQLKELERVFAETHY---PDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERA 78 (125)
T ss_pred HHHHHHHHHHHhhcC---CcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHH
Confidence 578889998888898 7889999999999999999999999999999986543
No 250
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=83.15 E-value=2 Score=38.52 Aligned_cols=31 Identities=29% Similarity=0.178 Sum_probs=26.3
Q ss_pred HHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 444 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 444 VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
...|+. +|+|+.+||+.||+|+.+|+|.++.
T Consensus 15 A~~L~e----eG~Sq~~iA~LLGltqaAVS~Yls~ 45 (119)
T COG2522 15 AKELIE----EGLSQYRIAKLLGLTQAAVSQYLSG 45 (119)
T ss_pred HHHHHH----cCCcHHHHHHHhCCCHHHHHHHHcc
Confidence 445565 6999999999999999999999863
No 251
>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=82.96 E-value=1.7 Score=33.52 Aligned_cols=24 Identities=13% Similarity=0.214 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 454 ECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 454 eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
...|.+|+|+.||||..|||+-+.
T Consensus 13 ~~~s~~ela~~~~VS~~TiRRDl~ 36 (57)
T PF08220_consen 13 GKVSVKELAEEFGVSEMTIRRDLN 36 (57)
T ss_pred CCEEHHHHHHHHCcCHHHHHHHHH
Confidence 568999999999999999986654
No 252
>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=82.73 E-value=2 Score=32.49 Aligned_cols=50 Identities=16% Similarity=0.256 Sum_probs=39.6
Q ss_pred hCCHHHHHHHHHHhcCCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDK--ECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~--eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
.+++.+..+|...|..+. .....++||..+||+...|..+...-..+.|+
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 578888889988885321 22457889999999999999999988877764
No 253
>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=82.72 E-value=0.95 Score=42.25 Aligned_cols=49 Identities=12% Similarity=0.192 Sum_probs=40.2
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHH-----HHHHCCCHHHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDI-----SKRIGLSRERVRQVGLVALEKLK 484 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEI-----Ae~LgIS~~rVrqi~~rALkKLR 484 (499)
.|+++|.+|+.+-..=-+.++|.++| |..++++..||+..+.+.++||.
T Consensus 154 ~Lt~~E~~il~~l~~~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~l~~Kl~ 207 (226)
T TIGR02154 154 SLGPTEFRLLHFFMTHPERVYSREQLLDRVWGRDVYVEERTVDVHIRRLRKALN 207 (226)
T ss_pred EcCHHHHHHHHHHHhCCCceEcHHHHHHHhcCCCCCCCCccHHHHHHHHHHhhc
Confidence 59999999998876211236788888 77899999999999999999986
No 254
>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator. This model describes a family of DNA-binding response regulator proteins, associated with an adjacent histidine kinase (TIGR03785) to form a two-component system. This system co-occurs with, and often is adjacent to, a proteobacterial variant form of the protein sorting transpeptidase called sortase (TIGR03784), and a single target protein for the sortase. We give this protein the gene symbol pdsR, for Proteobacterial Dedicated Sortase system Response regulator.
Probab=82.65 E-value=1.8 Score=40.84 Aligned_cols=47 Identities=11% Similarity=0.047 Sum_probs=40.6
Q ss_pred hCCHHHHHHHHHHhcCCC-CC--CCHHHH--HHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDK-EC--LTWEDI--SKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~-eg--~SleEI--Ae~LgIS~~rVrqi~~rALkKLR~ 485 (499)
.|+++|..||.+.. . .| +|.++| |..++++..||+.++.+.++||..
T Consensus 156 ~Lt~~E~~il~~l~---~~~g~v~s~~~i~~~~~~~~~~~tv~~~v~rlr~Kl~~ 207 (227)
T TIGR03787 156 DLTVTEFWMVHALA---KHPGHVKSRQQLMDAAKIVVDDSTITSHIKRIRKKFQA 207 (227)
T ss_pred cCCHHHHHHHHHHH---hCCCccccHHHHHHHhhhcCCccCHHHHHHHHHHHhcc
Confidence 49999999999875 2 24 599999 888999999999999999999963
No 255
>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=82.36 E-value=1.6 Score=31.33 Aligned_cols=24 Identities=25% Similarity=0.357 Sum_probs=21.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVA 479 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rA 479 (499)
+|.+|+|+.||||+.+|.++....
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcC
Confidence 689999999999999999988654
No 256
>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=82.15 E-value=2.6 Score=32.68 Aligned_cols=42 Identities=19% Similarity=0.313 Sum_probs=26.0
Q ss_pred CCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010835 437 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 479 (499)
Q Consensus 437 L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rA 479 (499)
|+..|..||..-. -...+++..+||+.++++..+|++.+++-
T Consensus 1 lt~~q~~vL~~l~-~~~~~~t~~~l~~~~~~~~~~vs~~i~~L 42 (68)
T PF13463_consen 1 LTRPQWQVLRALA-HSDGPMTQSDLAERLGISKSTVSRIIKKL 42 (68)
T ss_dssp --HHHHHHHHHHT---TS-BEHHHHHHHTT--HHHHHHHHHHH
T ss_pred CCHHHHHHHHHHH-ccCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4566666665543 12478999999999999999997555443
No 257
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=81.98 E-value=2.6 Score=35.64 Aligned_cols=44 Identities=14% Similarity=0.027 Sum_probs=36.4
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
..|++.-|..|..+. + .+|.+..+.|+.+|||+.|+.+++.|=.
T Consensus 7 A~Lt~~gR~~lv~~v-v-~~g~~~a~aA~~~gVS~~Ta~kW~~Ryr 50 (85)
T PF13011_consen 7 ARLTPRGRLRLVRRV-V-EQGWPVAHAAAEFGVSRRTAYKWLARYR 50 (85)
T ss_pred CCCCHHHHHHHHHHH-H-HcCCcHHHHHHHhCCCHHHHHHHHHHHH
Confidence 578999888777765 1 2689999999999999999999987644
No 258
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=81.33 E-value=20 Score=27.92 Aligned_cols=26 Identities=19% Similarity=0.194 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHHCC-CHHHHHHHHHHH
Q 010835 454 ECLTWEDISKRIGL-SRERVRQVGLVA 479 (499)
Q Consensus 454 eg~SleEIAe~LgI-S~~rVrqi~~rA 479 (499)
.+.++.+||..+|+ ++....+...+.
T Consensus 49 ~~~~~~~ia~~~g~~s~~~f~r~Fk~~ 75 (84)
T smart00342 49 TDLSVTEIALRVGFSSQSYFSRAFKKL 75 (84)
T ss_pred CCCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 36999999999999 988887665443
No 259
>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=81.09 E-value=2.4 Score=30.62 Aligned_cols=39 Identities=18% Similarity=0.187 Sum_probs=26.3
Q ss_pred CHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 438 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 438 ~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
.+-|+.+|.-.. ...+-+..+.|+.||||+.|+...+.+
T Consensus 3 ~~~E~~~i~~aL--~~~~gn~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 3 EEFEKQLIRQAL--ERCGGNVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp HHHHHHHHHHHH--HHTTT-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHH--HHhCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 445666666544 124568999999999999999876543
No 260
>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=80.96 E-value=1.3 Score=35.05 Aligned_cols=39 Identities=26% Similarity=0.313 Sum_probs=30.3
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVG 476 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~ 476 (499)
.|++.|..|+..-. ...++|..|||+.+|+++.+|...+
T Consensus 5 gLs~~E~~vy~~Ll--~~~~~t~~eIa~~l~i~~~~v~~~L 43 (68)
T PF01978_consen 5 GLSENEAKVYLALL--KNGPATAEEIAEELGISRSTVYRAL 43 (68)
T ss_dssp CHHHHHHHHHHHHH--HHCHEEHHHHHHHHTSSHHHHHHHH
T ss_pred CcCHHHHHHHHHHH--HcCCCCHHHHHHHHCcCHHHHHHHH
Confidence 57788888775532 2468999999999999999996444
No 261
>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=80.86 E-value=2.2 Score=33.97 Aligned_cols=27 Identities=44% Similarity=0.597 Sum_probs=22.1
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 455 CLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 455 g~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
++|.++||..+|+|+.+|. +.+++|++
T Consensus 28 ~lt~~~iA~~~g~sr~tv~----r~l~~l~~ 54 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVS----RILKRLKD 54 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHH----HHHHHHHH
T ss_pred cCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 5899999999999999985 55556654
No 262
>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=80.68 E-value=1.7 Score=32.39 Aligned_cols=26 Identities=15% Similarity=0.442 Sum_probs=21.6
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
..++|+.|+|+.+|+|+.+|+++++.
T Consensus 7 ~~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 7 EKGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HTTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred HcCCCHHHHHHHhCCCcchhHHHhcC
Confidence 46799999999999999999998875
No 263
>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=80.46 E-value=1.6 Score=34.78 Aligned_cols=35 Identities=11% Similarity=0.178 Sum_probs=28.9
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 443 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 443 ~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
.||..+. ..|.|..+||..+||+++++.+++....
T Consensus 14 ~~v~~~~---~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 14 QAVREYL---ESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp HHHHHHH---HHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHH---HCCCceEeeecccccccccccHHHHHHh
Confidence 3666664 5789999999999999999999998876
No 264
>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=80.31 E-value=3.8 Score=32.41 Aligned_cols=33 Identities=18% Similarity=0.288 Sum_probs=24.6
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 443 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 443 ~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
.|+.+.- ....+..|||+.+|+|+.+|++.+.+
T Consensus 4 ~il~~L~---~~~~~~~eLa~~l~vS~~tv~~~l~~ 36 (69)
T TIGR00122 4 RLLALLA---DNPFSGEKLGEALGMSRTAVNKHIQT 36 (69)
T ss_pred HHHHHHH---cCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4555533 34688999999999999999766544
No 265
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=80.10 E-value=5.1 Score=33.40 Aligned_cols=30 Identities=20% Similarity=0.441 Sum_probs=24.6
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 452 DKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 452 d~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
++...|-++||+.||+|+.+| .+.+++||.
T Consensus 16 ~~~~~SGe~La~~LgiSRtaV----wK~Iq~Lr~ 45 (79)
T COG1654 16 TGNFVSGEKLAEELGISRTAV----WKHIQQLRE 45 (79)
T ss_pred CCCcccHHHHHHHHCccHHHH----HHHHHHHHH
Confidence 356799999999999998888 566777774
No 266
>CHL00148 orf27 Ycf27; Reviewed
Probab=79.95 E-value=2.4 Score=40.23 Aligned_cols=50 Identities=18% Similarity=0.118 Sum_probs=41.6
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHH-------CCCHHHHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRI-------GLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~L-------gIS~~rVrqi~~rALkKLR~ 485 (499)
.|+++|.+|+.+...=.+.+.|.++|++.+ +++..||+.++.+.++||..
T Consensus 161 ~Lt~~E~~il~~l~~~~~~~~s~~~i~~~l~~~~~~~~~~~~tv~~~i~~lr~KL~~ 217 (240)
T CHL00148 161 RLTGMEFSLLELLISKSGEIFSRATILKEVWGYTPERHIDTRVVDVHISRLRAKLED 217 (240)
T ss_pred EcCHHHHHHHHHHHHCCCEEEcHHHHHHHhcCCCcccCCCcccHHHHHHHHHHHhcc
Confidence 589999999988651113579999999999 48999999999999999964
No 267
>PHA01976 helix-turn-helix protein
Probab=79.93 E-value=3 Score=32.50 Aligned_cols=26 Identities=12% Similarity=0.203 Sum_probs=23.6
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
..++|..|+|+.+|+|+.+|+++++.
T Consensus 13 ~~glt~~~lA~~~gvs~~~v~~~e~g 38 (67)
T PHA01976 13 ARAWSAPELSRRAGVRHSLIYDFEAD 38 (67)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 46799999999999999999998864
No 268
>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=79.59 E-value=1.5 Score=31.86 Aligned_cols=25 Identities=24% Similarity=0.333 Sum_probs=22.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
+|..|+|+.+|||+.||+.+..+.+
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999987765
No 269
>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=79.44 E-value=3.7 Score=34.26 Aligned_cols=37 Identities=24% Similarity=0.186 Sum_probs=28.6
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 439 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 439 ~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
+|+..|+.+-- ....|+.+||+.+|+|+.||++.+..
T Consensus 6 ~R~~~I~e~l~---~~~~ti~dvA~~~gvS~~TVsr~L~~ 42 (80)
T TIGR02844 6 ERVLEIGKYIV---ETKATVRETAKVFGVSKSTVHKDVTE 42 (80)
T ss_pred HHHHHHHHHHH---HCCCCHHHHHHHhCCCHHHHHHHhcC
Confidence 45566666543 35589999999999999999987754
No 270
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=79.13 E-value=4.1 Score=29.51 Aligned_cols=25 Identities=16% Similarity=0.205 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 454 ECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 454 eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
.+.+..+||+.+++|+.+|++.+..
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~ 37 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNK 37 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4699999999999999999766543
No 271
>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=78.29 E-value=2.7 Score=39.19 Aligned_cols=27 Identities=26% Similarity=0.407 Sum_probs=23.1
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 455 CLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 455 g~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
++|.+|||..+|+|+++|. |++++|++
T Consensus 143 ~~t~~~iA~~lG~tretvs----R~l~~l~~ 169 (193)
T TIGR03697 143 RLSHQAIAEAIGSTRVTIT----RLLGDLRK 169 (193)
T ss_pred CCCHHHHHHHhCCcHHHHH----HHHHHHHH
Confidence 5899999999999999995 67777765
No 272
>PRK14082 hypothetical protein; Provisional
Probab=78.29 E-value=5.9 Score=31.70 Aligned_cols=56 Identities=11% Similarity=0.024 Sum_probs=42.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhHhhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcchhH
Q 010835 254 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 311 (499)
Q Consensus 254 ~~A~e~LIe~yl~LV~sIA~ry~~~g~d~EDLiQEG~IgL~rAiekFDp~rG~kFsTY 311 (499)
....+.++..+.|.|.+-... -+-.+.+||.||--+++++.++.++...+-.|..|
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 466788999999988754322 13357899999999999999999987765556544
No 273
>PF14493 HTH_40: Helix-turn-helix domain
Probab=78.28 E-value=4.7 Score=33.90 Aligned_cols=30 Identities=23% Similarity=0.240 Sum_probs=27.4
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLVALEK 482 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~rALkK 482 (499)
.+|+|.+|||+.-|++.+||..++.++...
T Consensus 11 ~~G~si~eIA~~R~L~~sTI~~HL~~~~~~ 40 (91)
T PF14493_consen 11 QKGLSIEEIAKIRGLKESTIYGHLAELIES 40 (91)
T ss_pred HcCCCHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence 489999999999999999999999888765
No 274
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=78.12 E-value=3.2 Score=29.75 Aligned_cols=27 Identities=37% Similarity=0.603 Sum_probs=21.3
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 455 CLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 455 g~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
+++..+||+.+|+|+.+|+ +++++|.+
T Consensus 8 ~~s~~~la~~l~~s~~tv~----~~l~~L~~ 34 (48)
T smart00419 8 PLTRQEIAELLGLTRETVS----RTLKRLEK 34 (48)
T ss_pred ccCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 5899999999999999995 44455443
No 275
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=78.03 E-value=3.4 Score=30.79 Aligned_cols=28 Identities=32% Similarity=0.559 Sum_probs=21.9
Q ss_pred CCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 454 ECL-TWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 454 eg~-SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
+.+ |..|||+.+|+|+.+|+ +++++|.+
T Consensus 18 ~~l~s~~~la~~~~vs~~tv~----~~l~~L~~ 46 (60)
T smart00345 18 DKLPSERELAAQLGVSRTTVR----EALSRLEA 46 (60)
T ss_pred CcCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 345 89999999999999996 55555554
No 276
>PRK09954 putative kinase; Provisional
Probab=77.32 E-value=4 Score=42.61 Aligned_cols=43 Identities=21% Similarity=0.356 Sum_probs=34.1
Q ss_pred CCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010835 437 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALE 481 (499)
Q Consensus 437 L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALk 481 (499)
|+++++.||.+.. .....|..|||+.||+|+.+|+.++.+-.+
T Consensus 1 ~~~~~~~il~~l~--~~~~~s~~~la~~l~~s~~~v~~~i~~L~~ 43 (362)
T PRK09954 1 MNNREKEILAILR--RNPLIQQNEIADILQISRSRVAAHIMDLMR 43 (362)
T ss_pred CChHHHHHHHHHH--HCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4677888887755 123699999999999999999999986443
No 277
>PHA00542 putative Cro-like protein
Probab=77.08 E-value=3.4 Score=34.32 Aligned_cols=27 Identities=11% Similarity=0.102 Sum_probs=24.1
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLVA 479 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~rA 479 (499)
..++|..++|+.+|||+.+|.+++...
T Consensus 29 ~~glTq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 29 RAGWSQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHHcCC
Confidence 468999999999999999999998654
No 278
>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=77.05 E-value=3.7 Score=31.82 Aligned_cols=36 Identities=14% Similarity=0.358 Sum_probs=26.7
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 440 REREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 440 rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
|+..++.+-+. ...+++.|||+.+|+|..+|++.+.
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 45556666553 4679999999999999999976654
No 279
>PRK10072 putative transcriptional regulator; Provisional
Probab=77.04 E-value=3.4 Score=35.64 Aligned_cols=32 Identities=19% Similarity=0.202 Sum_probs=26.5
Q ss_pred HHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 444 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 444 VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
|-.+|. ..++|..|+|+.+|||..||+++++.
T Consensus 38 ik~LR~---~~glTQ~elA~~lGvS~~TVs~WE~G 69 (96)
T PRK10072 38 FEQLRK---GTGLKIDDFARVLGVSVAMVKEWESR 69 (96)
T ss_pred HHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 444455 46799999999999999999999863
No 280
>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=76.96 E-value=8 Score=30.83 Aligned_cols=33 Identities=33% Similarity=0.498 Sum_probs=24.7
Q ss_pred HHHHHcCCCCCHHHHHHHhCCC-HHHHHHHHHhh
Q 010835 349 LRLEEKGVTPSVDRIAEYLNMS-QKKVRNATEAI 381 (499)
Q Consensus 349 ~~L~~~gr~pt~eEIA~~Lgis-~e~v~~~l~~~ 381 (499)
....+.|..||..|||+.+|+. ...|...+...
T Consensus 17 ~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~L 50 (65)
T PF01726_consen 17 EYIEENGYPPTVREIAEALGLKSTSTVQRHLKAL 50 (65)
T ss_dssp HHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHH
T ss_pred HHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 3346789999999999999996 88888877765
No 281
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=76.96 E-value=3.4 Score=32.16 Aligned_cols=26 Identities=19% Similarity=0.385 Sum_probs=21.3
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
..++|..++|+.+|+|.++|+++++-
T Consensus 12 ~~gls~~~lA~~~g~s~s~v~~iE~G 37 (64)
T PF13560_consen 12 RAGLSQAQLADRLGVSQSTVSRIERG 37 (64)
T ss_dssp CHTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 45799999999999999999998863
No 282
>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=76.88 E-value=6 Score=30.21 Aligned_cols=37 Identities=27% Similarity=0.352 Sum_probs=26.9
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 439 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 439 ~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
+.+..|+...+ ..+.+..||++.+|+++.+|++.+.+
T Consensus 7 ~~~~~il~~l~---~~~~~~~ei~~~~~i~~~~i~~~l~~ 43 (78)
T cd00090 7 PTRLRILRLLL---EGPLTVSELAERLGLSQSTVSRHLKK 43 (78)
T ss_pred hHHHHHHHHHH---HCCcCHHHHHHHHCcCHhHHHHHHHH
Confidence 45556665544 33499999999999999999655444
No 283
>PRK12423 LexA repressor; Provisional
Probab=76.63 E-value=4.7 Score=39.01 Aligned_cols=47 Identities=19% Similarity=0.274 Sum_probs=33.2
Q ss_pred hhCCHHHHHHHHHHhc-CCCC--CCCHHHHHHHHC-CCHHHHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYG-LDKE--CLTWEDISKRIG-LSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 435 ~~L~~rER~VI~LryG-Ld~e--g~SleEIAe~Lg-IS~~rVrqi~~rALkKLR~ 485 (499)
..|++++++|+..--. +... .-|..|||+.|| +|+++|+ ++|+.|++
T Consensus 2 ~~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~----~~l~~L~~ 52 (202)
T PRK12423 2 DTLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVAR----KHVQALAE 52 (202)
T ss_pred CcCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHH----HHHHHHHH
Confidence 3589999999876321 1112 359999999999 5999997 45555555
No 284
>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=76.60 E-value=5.4 Score=34.77 Aligned_cols=42 Identities=19% Similarity=0.358 Sum_probs=27.4
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 439 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 439 ~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
.+.+.|... | +|++..++|.++|+|..+|.+++.+...+-++
T Consensus 61 ~R~~~I~~~-f----~G~n~~eLA~kyglS~r~I~~Ii~~~~~~~~~ 102 (108)
T PF08765_consen 61 LRNREIRRE-F----NGMNVRELARKYGLSERQIYRIIKRVRRRERR 102 (108)
T ss_dssp HHHHHHHHH-------SS-HHHHHHHHT--HHHHHHHHHHHHH----
T ss_pred HHHHHHHHH-h----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 345556654 3 58999999999999999999999888776554
No 285
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=76.37 E-value=4.2 Score=30.11 Aligned_cols=26 Identities=23% Similarity=0.175 Sum_probs=23.2
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
..++|++++|+.+|+|+++|+++++.
T Consensus 13 ~~gltq~~lA~~~gvs~~~vs~~e~g 38 (58)
T TIGR03070 13 ALGLTQADLADLAGVGLRFIRDVENG 38 (58)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 35799999999999999999999864
No 286
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=76.21 E-value=3.1 Score=41.83 Aligned_cols=26 Identities=15% Similarity=0.328 Sum_probs=24.1
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
.+||.+.+||+.||||+.||+.+..|
T Consensus 17 l~gmk~~dIAeklGvspntiksWKrr 42 (279)
T COG5484 17 LKGMKLKDIAEKLGVSPNTIKSWKRR 42 (279)
T ss_pred HhhccHHHHHHHhCCChHHHHHHHHh
Confidence 48899999999999999999998875
No 287
>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=76.01 E-value=2.5 Score=35.70 Aligned_cols=24 Identities=38% Similarity=0.302 Sum_probs=17.8
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 454 ECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 454 eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
.|+|..|||+++|.|++.|++++.
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 288
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=75.54 E-value=5.8 Score=29.45 Aligned_cols=26 Identities=19% Similarity=0.156 Sum_probs=22.2
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
.++.|..+|++.+|+|+.+|++.+++
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~ 33 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKK 33 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHH
Confidence 46789999999999999999766654
No 289
>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=74.75 E-value=14 Score=31.98 Aligned_cols=43 Identities=21% Similarity=0.157 Sum_probs=33.5
Q ss_pred hCCHHHHHHHHHHhcC--CCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 436 ~L~~rER~VI~LryGL--d~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
.|++.|-.||..-+-+ +..+.|..+||+.+++++++|.+.+.+
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 6899999888664311 235799999999999999999766554
No 290
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=73.79 E-value=4.8 Score=32.65 Aligned_cols=26 Identities=27% Similarity=0.369 Sum_probs=22.6
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
..++|++|+|+.+|||+.||-.+++-
T Consensus 12 ~~~ltQ~elA~~vgVsRQTi~~iEkg 37 (68)
T COG1476 12 ELGLTQEELAKLVGVSRQTIIAIEKG 37 (68)
T ss_pred HhCcCHHHHHHHcCcCHHHHHHHHcC
Confidence 45799999999999999999887653
No 291
>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=73.76 E-value=5.1 Score=30.81 Aligned_cols=24 Identities=33% Similarity=0.396 Sum_probs=20.2
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 454 ECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 454 eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
.++|..|||+.+|+|+.+|.+.+.
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~ 47 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLK 47 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHH
Confidence 569999999999999999964443
No 292
>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=73.23 E-value=3.6 Score=30.80 Aligned_cols=25 Identities=24% Similarity=0.384 Sum_probs=20.1
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
..++|..|||+.+|+++++|.+++.
T Consensus 16 ~~~~t~~eia~~~gl~~stv~r~L~ 40 (52)
T PF09339_consen 16 GGPLTLSEIARALGLPKSTVHRLLQ 40 (52)
T ss_dssp BSCEEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3568999999999999999976554
No 293
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=73.06 E-value=4.2 Score=38.24 Aligned_cols=27 Identities=22% Similarity=0.403 Sum_probs=22.6
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 455 CLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 455 g~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
.+|.++||..+|+|+++|+ |++++|++
T Consensus 149 ~~t~~~iA~~lG~tretvs----R~l~~l~~ 175 (202)
T PRK13918 149 YATHDELAAAVGSVRETVT----KVIGELSR 175 (202)
T ss_pred cCCHHHHHHHhCccHHHHH----HHHHHHHH
Confidence 5799999999999999995 66666664
No 294
>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=72.82 E-value=11 Score=31.65 Aligned_cols=32 Identities=19% Similarity=0.150 Sum_probs=25.3
Q ss_pred CCCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIG-LSRERVRQVGLVALEKLK 484 (499)
Q Consensus 453 ~eg~SleEIAe~Lg-IS~~rVrqi~~rALkKLR 484 (499)
.-++|+.+||+.|| .+.+||.....+.-++|+
T Consensus 42 ~~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~ 74 (90)
T cd06571 42 LTGLSLPEIGRAFGGRDHSTVLHAVRKIEELLE 74 (90)
T ss_pred HhCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHH
Confidence 34799999999999 999999766555555554
No 295
>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=72.70 E-value=7.4 Score=37.53 Aligned_cols=41 Identities=15% Similarity=0.173 Sum_probs=34.0
Q ss_pred hhCCHHHHHHHHHHhcCCC-CCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDK-ECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~-eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
..|++++..|+..-. . .+.+..|||+.+|+|++||++.+.+
T Consensus 139 ~~ls~~~~~IL~~l~---~~g~~s~~eia~~l~is~stv~r~L~~ 180 (203)
T TIGR01884 139 AGLSREELKVLEVLK---AEGEKSVKNIAKKLGKSLSTISRHLRE 180 (203)
T ss_pred cCCCHHHHHHHHHHH---HcCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 578999999887765 3 4689999999999999999866654
No 296
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=72.38 E-value=9.2 Score=29.56 Aligned_cols=41 Identities=15% Similarity=0.106 Sum_probs=30.2
Q ss_pred HHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010835 444 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 487 (499)
Q Consensus 444 VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L 487 (499)
.+..++ ..+.+..+.|+.|+|.+.||+.++.+.-+.+--.+
T Consensus 4 TL~~yl---~~~~n~~~tA~~L~iHrNTl~yRl~ki~~l~g~dl 44 (59)
T PF13556_consen 4 TLRAYL---ENNGNISKTARALHIHRNTLRYRLKKIEELLGLDL 44 (59)
T ss_dssp HHHHHH---HTTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--T
T ss_pred HHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCcCC
Confidence 455555 56799999999999999999999988877765443
No 297
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=72.36 E-value=9.8 Score=38.12 Aligned_cols=62 Identities=11% Similarity=0.144 Sum_probs=44.7
Q ss_pred HHHHHHHHHhhCCHHHHHHHHHHhcC--CCCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHH
Q 010835 426 KDEVNKLIIVTLGEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGLV----ALEKLKHAAR 488 (499)
Q Consensus 426 ~~~L~~~L~~~L~~rER~VI~LryGL--d~eg~SleEIAe~LgIS~~rVrqi~~r----ALkKLR~~L~ 488 (499)
...|...+ ..|++.|+.|......- +...+|..|||+..|+|..||-+.-++ +..-||..+.
T Consensus 4 ~~~i~~~~-~~Lt~~e~~Ia~yil~n~~~v~~~si~~lA~~~~vS~aTv~Rf~kklG~~gf~e~k~~l~ 71 (284)
T PRK11302 4 LEKIQSRL-EHLSKSERKVAEVILASPQTAIHSSIATLAKMANVSEPTVNRFCRSLDTKGFPDFKLHLA 71 (284)
T ss_pred HHHHHHHH-hhCCHHHHHHHHHHHhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence 45677777 89999999999775411 122589999999999999999765443 4555555544
No 298
>PRK10870 transcriptional repressor MprA; Provisional
Probab=72.22 E-value=26 Score=33.15 Aligned_cols=43 Identities=12% Similarity=0.093 Sum_probs=32.7
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
.|++.+-.||..-+..+..+.|..|||+.+++++.+|.+.+.+
T Consensus 52 gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~r 94 (176)
T PRK10870 52 GINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADE 94 (176)
T ss_pred CCCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 5888888887776522234689999999999999999766554
No 299
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=72.06 E-value=1.9 Score=33.78 Aligned_cols=25 Identities=24% Similarity=0.343 Sum_probs=21.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
||..|+|+.+|||+.||+.+..+.+
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 4788999999999999999987654
No 300
>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=71.81 E-value=4.7 Score=38.02 Aligned_cols=26 Identities=27% Similarity=0.345 Sum_probs=23.5
Q ss_pred CCCCCHHHHHHHHC-CCHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIG-LSRERVRQVGLV 478 (499)
Q Consensus 453 ~eg~SleEIAe~Lg-IS~~rVrqi~~r 478 (499)
.+|+|..|||+.|| +|+++|--..+|
T Consensus 16 ~~G~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 16 AEGLSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred HcCCCHHHHHHHhCCcchhhhhhhhhc
Confidence 59999999999999 999999877665
No 301
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=71.53 E-value=3.9 Score=38.92 Aligned_cols=30 Identities=30% Similarity=0.587 Sum_probs=24.6
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 452 DKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 452 d~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
..+++|+.||++.+|+|+++|++ ++++|..
T Consensus 38 s~~Pmtl~Ei~E~lg~Sks~vS~----~lkkL~~ 67 (177)
T COG1510 38 SRKPLTLDEIAEALGMSKSNVSM----GLKKLQD 67 (177)
T ss_pred cCCCccHHHHHHHHCCCcchHHH----HHHHHHh
Confidence 46899999999999999999964 5556553
No 302
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=71.41 E-value=10 Score=31.32 Aligned_cols=32 Identities=16% Similarity=0.195 Sum_probs=25.7
Q ss_pred HHHHHhcCCCCCCCHHHHHHHHC------CCHHHHHHHHHH
Q 010835 444 IIRLYYGLDKECLTWEDISKRIG------LSRERVRQVGLV 478 (499)
Q Consensus 444 VI~LryGLd~eg~SleEIAe~Lg------IS~~rVrqi~~r 478 (499)
+...|- .-|+|+.++|+.+| +|+.+|++++.-
T Consensus 16 lk~~R~---~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~ 53 (75)
T smart00352 16 FKQRRI---KLGFTQADVGLALGALYGPDFSQTTICRFEAL 53 (75)
T ss_pred HHHHHH---HcCCCHHHHHHHhcccccCcCCHHHHHHHHhc
Confidence 444555 46799999999999 599999998763
No 303
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=70.99 E-value=4.2 Score=32.47 Aligned_cols=23 Identities=26% Similarity=0.289 Sum_probs=20.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~r 478 (499)
.|+.|||+.+|||++||+..++.
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~ 23 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNG 23 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCC
Confidence 37889999999999999988764
No 304
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=70.86 E-value=11 Score=37.99 Aligned_cols=64 Identities=16% Similarity=0.174 Sum_probs=46.9
Q ss_pred HHHHHHHHHHHhhCCHHHHHHHHHHhcC--CCCCCCHHHHHHHHCCCHHHHHHHHH----HHHHHHHHHHH
Q 010835 424 ALKDEVNKLIIVTLGEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGL----VALEKLKHAAR 488 (499)
Q Consensus 424 el~~~L~~~L~~~L~~rER~VI~LryGL--d~eg~SleEIAe~LgIS~~rVrqi~~----rALkKLR~~L~ 488 (499)
.+...|...+ ..|++.|+.|.....-- ....+|..+||+..|+|..||-+.-+ .+..-||..+.
T Consensus 14 ~i~~~i~~~~-~~Lt~~e~~Ia~yil~~~~~v~~~si~~lA~~~~vS~aTi~Rf~kkLGf~gf~efk~~l~ 83 (292)
T PRK11337 14 GLGPYIRMKQ-EGLTPLESRVVEWLLKPGDLSEATALKDIAEALAVSEAMIVKVAKKLGFSGFRNLRSALE 83 (292)
T ss_pred hHHHHHHHHH-hhcCHHHHHHHHHHHhCHHHHHhcCHHHHHHHhCCChHHHHHHHHHcCCCCHHHHHHHHH
Confidence 3556788888 89999999999775411 12358999999999999999976544 34555555554
No 305
>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=70.43 E-value=9.3 Score=34.62 Aligned_cols=38 Identities=24% Similarity=0.204 Sum_probs=26.5
Q ss_pred CCHHH-HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 437 LGERE-REIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 437 L~~rE-R~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
||... +.||.|.. +|++.-+||.+|+||.+.|+.++.|
T Consensus 18 Lp~~~R~rIvela~----~G~rp~~Isr~l~Vs~gcVsKIl~R 56 (125)
T PF00292_consen 18 LPNELRQRIVELAK----EGVRPCDISRQLRVSHGCVSKILSR 56 (125)
T ss_dssp S-HHHHHHHHHHHH----TT--HHHHHHHHT--HHHHHHHHHH
T ss_pred CcHHHHHHHHHHhh----hcCCHHHHHHHHccchhHHHHHHHH
Confidence 44443 34777876 7999999999999999999988875
No 306
>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=70.34 E-value=5.6 Score=30.98 Aligned_cols=23 Identities=17% Similarity=0.213 Sum_probs=20.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~r 478 (499)
+|..|+|+.+|||..|++.+..+
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 47899999999999999998865
No 307
>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=70.06 E-value=8.9 Score=36.62 Aligned_cols=42 Identities=17% Similarity=0.208 Sum_probs=31.5
Q ss_pred hCCHHHHHHHHHHhc--C-CCCCCCHHHHHHHHCCC-HHHHHHHHH
Q 010835 436 TLGEREREIIRLYYG--L-DKECLTWEDISKRIGLS-RERVRQVGL 477 (499)
Q Consensus 436 ~L~~rER~VI~LryG--L-d~eg~SleEIAe~LgIS-~~rVrqi~~ 477 (499)
.|+++|+.||..-.- . +..+.|..|||+.+|++ ++||..++.
T Consensus 3 ~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~ 48 (199)
T TIGR00498 3 PLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLK 48 (199)
T ss_pred ccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHH
Confidence 589999999887431 1 12358899999999998 999975443
No 308
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=69.51 E-value=1.3e+02 Score=33.39 Aligned_cols=24 Identities=21% Similarity=0.264 Sum_probs=20.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 010835 356 VTPSVDRIAEYLNMSQKKVRNATE 379 (499)
Q Consensus 356 r~pt~eEIA~~Lgis~e~v~~~l~ 379 (499)
++-+..+||+.+|+.+.+|.++..
T Consensus 368 kPLtlkdVAe~lglHeSTVSRa~~ 391 (481)
T PRK12469 368 KPLVLRDVAEELGLHESTISRATG 391 (481)
T ss_pred cCCcHHHHHHHhCCCcchhhHHhc
Confidence 455799999999999999988765
No 309
>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=69.28 E-value=15 Score=32.27 Aligned_cols=40 Identities=15% Similarity=-0.008 Sum_probs=30.6
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 479 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rA 479 (499)
..+.+.+-.-++.. .++|.+++|+.+|+++.+|+++++..
T Consensus 63 ~~~~~~~i~~~r~~-----~gltq~~lA~~lg~~~~tis~~e~g~ 102 (127)
T TIGR03830 63 GLLTPPEIRRIRKK-----LGLSQREAAELLGGGVNAFSRYERGE 102 (127)
T ss_pred CCcCHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHCCC
Confidence 45666654444444 46999999999999999999988744
No 310
>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=68.91 E-value=11 Score=32.87 Aligned_cols=41 Identities=12% Similarity=0.252 Sum_probs=32.2
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
..|++.+..||..-+. ..+.|..|||+.+|+++.+|.+.+.
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 3688888888866541 4679999999999999999965444
No 311
>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=68.78 E-value=10 Score=30.30 Aligned_cols=26 Identities=19% Similarity=0.253 Sum_probs=23.4
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
..++|..++|+.+|+|+.+|+++++.
T Consensus 16 ~~~~t~~~lA~~~gis~~tis~~~~g 41 (78)
T TIGR02607 16 PLGLSIRALAKALGVSRSTLSRIVNG 41 (78)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 46799999999999999999998863
No 312
>COG2411 Uncharacterized conserved protein [Function unknown]
Probab=68.72 E-value=54 Score=31.43 Aligned_cols=47 Identities=32% Similarity=0.464 Sum_probs=39.4
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCC--CHHHHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGL--SRERVRQVGLVALEKLKH 485 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgI--S~~rVrqi~~rALkKLR~ 485 (499)
..|+++++.|+.+.. +.=|+..-|..||= .+.+|++.+.+|..-|.+
T Consensus 136 ~~Ls~~~~~iL~~~~----~~gslRkaA~klgg~~kr~~ir~vLrKay~~L~~ 184 (188)
T COG2411 136 DNLSERDKRILELFV----EEGSLRKAAKKLGGLEKRGRIRRVLRKAYHELKK 184 (188)
T ss_pred ccCCHHHHHHHHHHH----HcCcHHHHHHHhcCcchhhHHHHHHHHHHHHHHh
Confidence 469999999999875 77799999999985 667888888888877764
No 313
>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=68.61 E-value=13 Score=34.57 Aligned_cols=51 Identities=16% Similarity=0.223 Sum_probs=36.7
Q ss_pred CHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH------HHHHHHHHHHHhhH
Q 010835 438 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV------ALEKLKHAARKKKM 492 (499)
Q Consensus 438 ~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r------ALkKLR~~L~~~~l 492 (499)
|++.+ |=.+|- .-|+|..++|+.+|||+.+|+++++. .+..|.+.....+.
T Consensus 25 p~~~~-Ir~~R~---~lGmTq~eLAerlGVS~~tIs~iE~G~~~~~psl~~L~kIA~aLgv 81 (150)
T TIGR02612 25 PKEGW-VRAIRK---ALGMSGAQLAGRLGVTPQRVEALEKSELSGTVTLKTLRAAAEALDC 81 (150)
T ss_pred CcHHH-HHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCCCHHHHHHHHHHcCC
Confidence 44433 444454 46899999999999999999999985 45666666554443
No 314
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=68.42 E-value=6 Score=38.31 Aligned_cols=27 Identities=26% Similarity=0.452 Sum_probs=22.1
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 455 CLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 455 g~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
++|.++||..+|+|+++|. |.+++|++
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 5899999999999999996 45556654
No 315
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=68.34 E-value=12 Score=33.89 Aligned_cols=41 Identities=7% Similarity=0.087 Sum_probs=32.7
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
.|++.|-.||..-+. .++.|..|||+.+++++++|.+.+.+
T Consensus 37 glt~~q~~vL~~l~~--~~~~t~~eLa~~l~i~~~tvsr~l~~ 77 (144)
T PRK11512 37 DITAAQFKVLCSIRC--AACITPVELKKVLSVDLGALTRMLDR 77 (144)
T ss_pred CCCHHHHHHHHHHHH--cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 588888888876541 46799999999999999999765543
No 316
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=68.31 E-value=12 Score=30.53 Aligned_cols=40 Identities=25% Similarity=0.370 Sum_probs=31.0
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
.|+..+..||.+-+. ..+++..+||+.+++++.+|++.+.
T Consensus 7 ~l~~~~~~il~~l~~--~~~~~~~~la~~~~~s~~~i~~~l~ 46 (101)
T smart00347 7 GLTPTQFLVLRILYE--EGPLSVSELAKRLGVSPSTVTRVLD 46 (101)
T ss_pred CCCHHHHHHHHHHHH--cCCcCHHHHHHHHCCCchhHHHHHH
Confidence 577888888877652 2469999999999999999864443
No 317
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=68.29 E-value=5.2 Score=38.09 Aligned_cols=28 Identities=18% Similarity=0.223 Sum_probs=24.3
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010835 454 ECLTWEDISKRIGLSRERVRQVGLVALE 481 (499)
Q Consensus 454 eg~SleEIAe~LgIS~~rVrqi~~rALk 481 (499)
-++|..|||+.+|.|+.|||+++.-.-+
T Consensus 60 ag~Ti~EIAeelG~TeqTir~hlkgetk 87 (182)
T COG1318 60 AGMTISEIAEELGRTEQTVRNHLKGETK 87 (182)
T ss_pred ccCcHHHHHHHhCCCHHHHHHHHhcchh
Confidence 4799999999999999999998865444
No 318
>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=67.89 E-value=9 Score=32.05 Aligned_cols=36 Identities=19% Similarity=0.173 Sum_probs=25.6
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010835 454 ECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 489 (499)
Q Consensus 454 eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L~~ 489 (499)
...|..+.|..||||.+||..-+..-|.++-..|..
T Consensus 18 ~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in~~La~ 53 (82)
T PF12116_consen 18 TKATVRQAAKVFGVSKSTVHKDVTERLPKINPELAR 53 (82)
T ss_dssp H---HHHHHHHHTS-HHHHHHHHTTHHHHH-HHHHH
T ss_pred cccHHHHHHHHHCCcHHHHHHHHHHHHHhcCHHHHH
Confidence 578999999999999999998887777776665544
No 319
>PRK15482 transcriptional regulator MurR; Provisional
Probab=67.86 E-value=13 Score=37.57 Aligned_cols=62 Identities=13% Similarity=0.243 Sum_probs=44.4
Q ss_pred HHHHHHHHHhhCCHHHHHHHHHHhcC--CCCCCCHHHHHHHHCCCHHHHHHHHH----HHHHHHHHHHH
Q 010835 426 KDEVNKLIIVTLGEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGL----VALEKLKHAAR 488 (499)
Q Consensus 426 ~~~L~~~L~~~L~~rER~VI~LryGL--d~eg~SleEIAe~LgIS~~rVrqi~~----rALkKLR~~L~ 488 (499)
...|.... ..|++.|+.|.....-= ....+|..|||+..|+|..||-+.-+ .+...||..+.
T Consensus 4 l~~i~~~~-~~Lt~~e~~Ia~yIl~n~~~v~~~si~elA~~~~vS~aTv~Rf~kkLGf~Gf~efk~~l~ 71 (285)
T PRK15482 4 LTKIRNAE-SEFTENEQKIADFLRANVSELKSVSSRKMAKQLGISQSSIVKFAQKLGAQGFTELRMALI 71 (285)
T ss_pred HHHHHHHH-hhcCHHHHHHHHHHHhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHHhCCCCHHHHHHHHH
Confidence 35566777 89999999999875410 11249999999999999999966543 34555555554
No 320
>PRK00215 LexA repressor; Validated
Probab=67.67 E-value=12 Score=36.00 Aligned_cols=42 Identities=21% Similarity=0.234 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHhc--C-CCCCCCHHHHHHHHCC-CHHHHHHHHHH
Q 010835 437 LGEREREIIRLYYG--L-DKECLTWEDISKRIGL-SRERVRQVGLV 478 (499)
Q Consensus 437 L~~rER~VI~LryG--L-d~eg~SleEIAe~LgI-S~~rVrqi~~r 478 (499)
|+++|+.|+.+-.- . +..+.|+.|||+.+|+ +++||.+++.+
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~ 47 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKA 47 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 68888888865320 1 1346799999999999 99999766544
No 321
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=67.57 E-value=6.8 Score=37.06 Aligned_cols=27 Identities=33% Similarity=0.457 Sum_probs=22.2
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 455 CLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 455 g~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
..|.++||..+|+|+++|+ |++++|++
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 5899999999999999995 55666664
No 322
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=67.34 E-value=12 Score=27.88 Aligned_cols=50 Identities=18% Similarity=0.192 Sum_probs=38.1
Q ss_pred hCCHHHHHHHHHHhcCC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLD--KECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd--~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
.+++.+..+|.-.|..+ .......+||..+|++...|..+......+.+.
T Consensus 6 ~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 6 RFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 46777888888877432 123458899999999999999998887776653
No 323
>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=66.89 E-value=7.1 Score=34.58 Aligned_cols=25 Identities=24% Similarity=0.272 Sum_probs=23.2
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
..|.|..++|..++||+.||.+++.
T Consensus 16 ~~g~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 16 EKGKSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred HccchHHHHHHHhCcHHHHHHHHHH
Confidence 4789999999999999999999877
No 324
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=66.57 E-value=14 Score=39.54 Aligned_cols=50 Identities=18% Similarity=0.128 Sum_probs=36.4
Q ss_pred hCCHHHHHHHHHHhcC-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 436 ~L~~rER~VI~LryGL-d~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
.+++.||..+.+.+=| ..++.|+.++|+.|+||++|+.+-+.+..+.|.+
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 4677777665554323 4578999999999999999998766665555544
No 325
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=66.01 E-value=12 Score=41.89 Aligned_cols=46 Identities=22% Similarity=0.252 Sum_probs=37.6
Q ss_pred CCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 437 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 437 L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
|++|++.++.+-- .++.|..++|+.||||..||++-+...-..|+.
T Consensus 2 l~~R~~~iL~~L~---~~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~ 47 (584)
T PRK09863 2 LNERELKIVDLLE---QQDRSGGELAQQLGVSRRTIVRDIAYINFTLNG 47 (584)
T ss_pred hHHHHHHHHHHHH---cCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 5788899887642 367999999999999999999988776666665
No 326
>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=65.73 E-value=8.1 Score=29.30 Aligned_cols=26 Identities=31% Similarity=0.512 Sum_probs=20.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
.|..+||+.+|+|+.+|+ +++++|.+
T Consensus 26 ~~~~~la~~~~is~~~v~----~~l~~L~~ 51 (66)
T cd07377 26 PSERELAEELGVSRTTVR----EALRELEA 51 (66)
T ss_pred CCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 359999999999999996 55555554
No 327
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=65.72 E-value=12 Score=37.18 Aligned_cols=26 Identities=15% Similarity=0.181 Sum_probs=23.1
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
..++|..|||++||||..+||+.+..
T Consensus 23 ~g~~sa~elA~~Lgis~~avR~HL~~ 48 (218)
T COG2345 23 SGPVSADELAEELGISPMAVRRHLDD 48 (218)
T ss_pred cCCccHHHHHHHhCCCHHHHHHHHHH
Confidence 46899999999999999999988754
No 328
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=65.71 E-value=15 Score=30.05 Aligned_cols=26 Identities=23% Similarity=0.376 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010835 454 ECLTWEDISKRIGLSRERVRQVGLVA 479 (499)
Q Consensus 454 eg~SleEIAe~LgIS~~rVrqi~~rA 479 (499)
.++|..|||+.+|+++.+|++.+..-
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L 44 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTL 44 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 47999999999999999998776543
No 329
>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=64.84 E-value=8.5 Score=30.10 Aligned_cols=23 Identities=22% Similarity=0.283 Sum_probs=20.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~r 478 (499)
++..|+|+.+|||..|++.+..+
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 47889999999999999998765
No 330
>PF14502 HTH_41: Helix-turn-helix domain
Probab=64.61 E-value=10 Score=28.67 Aligned_cols=26 Identities=31% Similarity=0.401 Sum_probs=22.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
.|..|.++.+++|+.|| +.||+.|..
T Consensus 7 ~tI~e~~~~~~vs~Gti----Q~Alk~Le~ 32 (48)
T PF14502_consen 7 PTISEYSEKFGVSRGTI----QNALKFLEE 32 (48)
T ss_pred CCHHHHHHHhCcchhHH----HHHHHHHHH
Confidence 68999999999999999 678888875
No 331
>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=64.58 E-value=7.4 Score=34.92 Aligned_cols=23 Identities=22% Similarity=0.277 Sum_probs=20.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~r 478 (499)
||.+|+|+.+|+|+.||.+++.+
T Consensus 1 MT~eELA~~tG~srQTINrWvRk 23 (122)
T PF07037_consen 1 MTPEELAELTGYSRQTINRWVRK 23 (122)
T ss_pred CCHHHHHHHhCccHHHHHHHHHh
Confidence 78999999999999999988754
No 332
>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=64.52 E-value=4.3 Score=28.89 Aligned_cols=23 Identities=22% Similarity=0.289 Sum_probs=18.9
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHH
Q 010835 457 TWEDISKRIGLSRERVRQVGLVA 479 (499)
Q Consensus 457 SleEIAe~LgIS~~rVrqi~~rA 479 (499)
|..|+|+.+|||..|+|.+....
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~G 23 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYEREG 23 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHTT
T ss_pred CHHHHHHHHCCCHHHHHHHHHCC
Confidence 45799999999999999987764
No 333
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=63.52 E-value=8.7 Score=37.46 Aligned_cols=27 Identities=33% Similarity=0.490 Sum_probs=22.6
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 455 CLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 455 g~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
.+|.++||..+|+++++|. |++++|++
T Consensus 179 ~lt~~~IA~~lGisretls----R~L~~L~~ 205 (230)
T PRK09391 179 PMSRRDIADYLGLTIETVS----RALSQLQD 205 (230)
T ss_pred cCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 5799999999999999995 66666664
No 334
>PRK01905 DNA-binding protein Fis; Provisional
Probab=63.52 E-value=29 Score=28.34 Aligned_cols=38 Identities=11% Similarity=0.143 Sum_probs=26.5
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 439 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 439 ~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
+-|+.+|...+ ...+-+..+.|+.||||+.+++..+.+
T Consensus 36 ~~E~~~i~~aL--~~~~gn~s~aAr~LGIsrstL~rklkk 73 (77)
T PRK01905 36 CVEKPLLEVVM--EQAGGNQSLAAEYLGINRNTLRKKLQQ 73 (77)
T ss_pred HHHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 44566555443 134568999999999999998766553
No 335
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=63.28 E-value=5.7 Score=31.00 Aligned_cols=25 Identities=24% Similarity=0.323 Sum_probs=21.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
+|..|+|+.+|||+.+++.+....+
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~~gl 25 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYERIGL 25 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999998876544
No 336
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=62.96 E-value=16 Score=37.20 Aligned_cols=53 Identities=21% Similarity=0.290 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHhhCCHHHHHHHHHHhcC-C-CCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 424 ALKDEVNKLIIVTLGEREREIIRLYYGL-D-KECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 424 el~~~L~~~L~~~L~~rER~VI~LryGL-d-~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
.+...|.... +.|++.||.|-..-.-= + ...+|..|||+..|||+.||-+--+
T Consensus 4 ~l~~~I~~~~-~~Lt~~er~iA~yil~~~~~~~~~si~elA~~a~VS~aTv~Rf~~ 58 (281)
T COG1737 4 NLLERIRERY-DSLTKSERKIADYILANPDEVALLSIAELAERAGVSPATVVRFAR 58 (281)
T ss_pred hHHHHHHHHH-hcCCHHHHHHHHHHHhCHHHHHHHHHHHHHHHhCCCHHHHHHHHH
Confidence 3556777778 89999999998775410 0 1248999999999999999965543
No 337
>PRK09726 antitoxin HipB; Provisional
Probab=62.58 E-value=11 Score=31.37 Aligned_cols=37 Identities=14% Similarity=0.253 Sum_probs=28.5
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH----HHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLVA----LEKLKHAARK 489 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~rA----LkKLR~~L~~ 489 (499)
..++|.+++|+.+|||+.+|+++++.- +.+|.+.+..
T Consensus 23 ~~gltq~elA~~~gvs~~tis~~e~g~~~ps~~~l~~ia~~ 63 (88)
T PRK09726 23 QNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQS 63 (88)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHH
Confidence 357999999999999999999998743 3455555443
No 338
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=62.46 E-value=10 Score=38.41 Aligned_cols=42 Identities=26% Similarity=0.371 Sum_probs=33.1
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
..|++.|++||.+--+- +...++.||.+.+|.|+.||.++++
T Consensus 191 ~~L~~~e~~il~~i~~~-GGri~Q~eL~r~lglsktTvsR~L~ 232 (258)
T COG2512 191 YDLNEDEKEILDLIRER-GGRITQAELRRALGLSKTTVSRILR 232 (258)
T ss_pred CCCCHHHHHHHHHHHHh-CCEEeHHHHHHhhCCChHHHHHHHH
Confidence 57999999999885521 2338999999999999999965443
No 339
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=62.19 E-value=14 Score=36.83 Aligned_cols=42 Identities=21% Similarity=0.324 Sum_probs=32.2
Q ss_pred CHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010835 438 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALE 481 (499)
Q Consensus 438 ~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALk 481 (499)
.+|++.|+.+-.. ....+..|||+.||||..|||+.+..--.
T Consensus 3 ~~R~~~Il~~l~~--~~~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 3 AARQQAIVDLLLN--HTSLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred hHHHHHHHHHHHH--cCCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3566777766431 35699999999999999999998886533
No 340
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=62.02 E-value=27 Score=33.10 Aligned_cols=28 Identities=29% Similarity=0.446 Sum_probs=24.1
Q ss_pred CCCCCHHHHHHHh--CCCHHHHHHHHHhhc
Q 010835 355 GVTPSVDRIAEYL--NMSQKKVRNATEAIG 382 (499)
Q Consensus 355 gr~pt~eEIA~~L--gis~e~v~~~l~~~~ 382 (499)
+..+++.+||+.+ +++.+++++.+....
T Consensus 37 ~~~~d~~~iak~l~p~is~~ev~~sL~~L~ 66 (171)
T PF14394_consen 37 PFAPDPEWIAKRLRPKISAEEVRDSLEFLE 66 (171)
T ss_pred CCCCCHHHHHHHhcCCCCHHHHHHHHHHHH
Confidence 4456899999999 999999999988764
No 341
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=62.02 E-value=16 Score=36.58 Aligned_cols=59 Identities=15% Similarity=0.213 Sum_probs=41.9
Q ss_pred HHHHHHhhCCHHHHHHHHHHhcC--CCCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHH
Q 010835 429 VNKLIIVTLGEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGLV----ALEKLKHAAR 488 (499)
Q Consensus 429 L~~~L~~~L~~rER~VI~LryGL--d~eg~SleEIAe~LgIS~~rVrqi~~r----ALkKLR~~L~ 488 (499)
|.+.. ..|++.|+.|......= ....+|..|||+..|+|+.||.+.-++ +..-||..+.
T Consensus 3 i~~~~-~~Lt~~e~~ia~yil~n~~~v~~~si~elA~~~~vS~aTv~Rf~kklG~~Gf~efk~~l~ 67 (278)
T PRK11557 3 IRQRY-PGLAQSDRKLADYLLLQPDTARHLSSQQLANEAGVSQSSVVKFAQKLGYKGFPALKLALS 67 (278)
T ss_pred hhHhh-hhCCHHHHHHHHHHHhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence 34455 78999999999775511 122599999999999999999765543 4455555554
No 342
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=61.97 E-value=15 Score=30.96 Aligned_cols=39 Identities=18% Similarity=0.296 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHhcCCCCCCCH-HHHHHHHCCCHHHHHHHHHH
Q 010835 437 LGEREREIIRLYYGLDKECLTW-EDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 437 L~~rER~VI~LryGLd~eg~Sl-eEIAe~LgIS~~rVrqi~~r 478 (499)
|++.|..|+...+ ..+-.. .+||+.+++++++|.+.+.+
T Consensus 20 lt~~q~~~L~~l~---~~~~~~~~~la~~l~i~~~~vt~~l~~ 59 (126)
T COG1846 20 LTPPQYQVLLALY---EAGGITVKELAERLGLDRSTVTRLLKR 59 (126)
T ss_pred CCHHHHHHHHHHH---HhCCCcHHHHHHHHCCCHHHHHHHHHH
Confidence 8999999998776 333333 99999999999999766554
No 343
>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=61.75 E-value=21 Score=28.62 Aligned_cols=26 Identities=31% Similarity=0.340 Sum_probs=19.8
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
+..-|.+|||+.||||...|+.++..
T Consensus 18 gr~Pt~eEiA~~lgis~~~v~~~l~~ 43 (78)
T PF04539_consen 18 GREPTDEEIAEELGISVEEVRELLQA 43 (78)
T ss_dssp SS--BHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCCHHHHHHHHcccHHHHHHHHHh
Confidence 35689999999999999999877653
No 344
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=61.58 E-value=13 Score=26.41 Aligned_cols=27 Identities=26% Similarity=0.298 Sum_probs=19.2
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLVA 479 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~rA 479 (499)
.++.++++||+.+|+|+...++...+.
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 367999999999999998887766553
No 345
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=61.37 E-value=1e+02 Score=34.66 Aligned_cols=106 Identities=15% Similarity=0.117 Sum_probs=57.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHHHHHh
Q 010835 356 VTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIV 435 (499)
Q Consensus 356 r~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~~L~~ 435 (499)
...|..+||+.+|+|.++|++-.......+.=.... ...+.. +-.+.. .++. .+...+ .
T Consensus 16 ~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~--~i~~~~----Gy~l~~----~~~~----------~~~~~~-~ 74 (584)
T PRK09863 16 QDRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIG--SISGSA----KYHLEI----LNRR----------SLFQLL-Q 74 (584)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchh--heecCC----ceEEEe----CCHH----------HHHHHH-h
Confidence 357899999999999999987665442211000000 000000 111111 1110 111222 2
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 484 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR 484 (499)
.-++..+. +.++.-+ .++.++.++|+.|.||++||.+-+.+..+.+.
T Consensus 75 ~~~~e~~~-il~~Ll~-~~~~~~~~La~~l~vS~sTi~~dl~~v~~~l~ 121 (584)
T PRK09863 75 KSDNEDRL-LLLRLLL-NTFTPMAQLASALNLSRTWVAERLPRLNQRYE 121 (584)
T ss_pred cCCHHHHH-HHHHHHH-cCCccHHHHHHHhCCCHHHHHHHHHHHHHhhh
Confidence 22333332 3333212 46799999999999999999887777766655
No 346
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.77 E-value=19 Score=31.78 Aligned_cols=46 Identities=17% Similarity=0.247 Sum_probs=39.3
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL 483 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKL 483 (499)
+.|++.+-+-+++++ .--=+++||-+.+|+|..|||..+...|++|
T Consensus 40 ~~Lt~d~LeFv~lf~---r~RGnlKEvEr~lg~sYptvR~kld~vlram 85 (122)
T COG3877 40 EYLTSDQLEFVELFL---RCRGNLKEVERELGISYPTVRTKLDEVLRAM 85 (122)
T ss_pred cccCHhHhHHHHHHH---HHccCHHHHHHHHCCccHHHHHHHHHHHHHc
Confidence 678888888888877 4446899999999999999999988887765
No 347
>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=60.67 E-value=19 Score=29.55 Aligned_cols=32 Identities=22% Similarity=0.212 Sum_probs=22.1
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLVALEKLK 484 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR 484 (499)
.++.|++++|+.++||++|+.+.+...-+.|+
T Consensus 28 ~~~~s~~~la~~~~iS~sti~~~i~~l~~~l~ 59 (87)
T PF05043_consen 28 NEYVSIEDLAEELFISRSTIYRDIKKLNKYLK 59 (87)
T ss_dssp -SEEEHHHHHHHHT--HHHHHHHHHHHHHHHH
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 57899999999999999999755554444433
No 348
>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=60.57 E-value=21 Score=34.02 Aligned_cols=43 Identities=28% Similarity=0.356 Sum_probs=30.2
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
-|++.-|.-|.-.+- .+|+|.++||..+||+..||. |+-+|+.
T Consensus 16 ~lse~~r~~Iy~~~~--~~~~sv~~vS~~ygi~~~RV~-----AIvrLke 58 (172)
T PF12298_consen 16 VLSEELREQIYEDVM--QDGKSVREVSQKYGIKIQRVE-----AIVRLKE 58 (172)
T ss_pred cCCHHHHHHHHHHHH--hCCCCHHHHHHHhCCCHHHHH-----HHHHHHH
Confidence 356666654444331 578899999999999999994 5555553
No 349
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=60.53 E-value=13 Score=27.54 Aligned_cols=47 Identities=15% Similarity=0.158 Sum_probs=35.9
Q ss_pred hCCHHHHHHHHHHhcCC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLD--KECLTWEDISKRIGLSRERVRQVGLVALEK 482 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd--~eg~SleEIAe~LgIS~~rVrqi~~rALkK 482 (499)
.+++.+..+|.-.|..+ .......+||..+|++...|..+......+
T Consensus 6 ~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~ 54 (56)
T smart00389 6 SFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAK 54 (56)
T ss_pred cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhc
Confidence 46788888888887433 123568899999999999999988776654
No 350
>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=60.38 E-value=16 Score=34.87 Aligned_cols=43 Identities=28% Similarity=0.301 Sum_probs=32.2
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
..|++-|+.....+. ++..++|.++||+.+|+|+.+|++++.-
T Consensus 101 ~~lt~~e~a~~~~~l-~~~~g~s~~~iA~~lg~s~~~V~r~l~l 143 (187)
T TIGR00180 101 EDLSPIEEAQAYKRL-LEKFSMTQEDLAKKIGKSRAHITNLLRL 143 (187)
T ss_pred cCCCHHHHHHHHHHH-HHHhCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 478888876654442 1124799999999999999999887654
No 351
>TIGR00647 MG103 conserved hypothetical protein.
Probab=60.36 E-value=19 Score=37.04 Aligned_cols=43 Identities=19% Similarity=0.095 Sum_probs=36.4
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHC------CCHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIG------LSRERVRQVGLVA 479 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~Lg------IS~~rVrqi~~rA 479 (499)
+.||+.-+++..+|. ...+.|++|+|+.|. ||++.|..++.+.
T Consensus 226 ~~Lp~~L~~~a~lRl--~~Pd~SL~ELgell~~~~~~~isKSgvnhRlrKl 274 (279)
T TIGR00647 226 EKLPLNFQRICLLKI--DHPDWSLEQIAEFFASKYKVKISRSGIQHRLRKL 274 (279)
T ss_pred ccCCHHHHHHHHHHH--hCcccCHHHHHHHhccCCCCCcCHHHHHHHHHHH
Confidence 689999999999986 246799999999994 9999998776553
No 352
>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=60.32 E-value=9.8 Score=29.59 Aligned_cols=27 Identities=37% Similarity=0.615 Sum_probs=19.7
Q ss_pred CCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010835 454 ECL-TWEDISKRIGLSRERVRQVGLVALEKLK 484 (499)
Q Consensus 454 eg~-SleEIAe~LgIS~~rVrqi~~rALkKLR 484 (499)
+.+ |..+||+.+|+|+.+|+ +|+..|.
T Consensus 22 ~~lps~~~la~~~~vsr~tvr----~al~~L~ 49 (64)
T PF00392_consen 22 DRLPSERELAERYGVSRTTVR----EALRRLE 49 (64)
T ss_dssp SBE--HHHHHHHHTS-HHHHH----HHHHHHH
T ss_pred CEeCCHHHHHHHhccCCcHHH----HHHHHHH
Confidence 557 99999999999999996 4555544
No 353
>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=60.26 E-value=11 Score=29.54 Aligned_cols=23 Identities=13% Similarity=0.114 Sum_probs=20.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~r 478 (499)
++..|+|+.+|||+.|++.+...
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 47889999999999999988765
No 354
>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional
Probab=59.69 E-value=6.6 Score=36.89 Aligned_cols=45 Identities=20% Similarity=0.082 Sum_probs=37.7
Q ss_pred hCCHHHHHHHHHHhcCCCCCCC---------HHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLT---------WEDISKRIGLSRERVRQVGLVALEKLK 484 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~S---------leEIAe~LgIS~~rVrqi~~rALkKLR 484 (499)
.|+++|.+|+.+-. .+.+ ...||..++++..||+.++.+.++||.
T Consensus 156 ~Lt~~E~~~l~~l~----~~~~~v~sr~~l~~~~~~~~~~~~~~tv~~~i~~lr~Kl~ 209 (232)
T PRK10955 156 ELTGTEFTLLYLLA----QHLGQVVSREHLSQEVLGKRLTPFDRAIDMHISNLRRKLP 209 (232)
T ss_pred cCCHHHHHHHHHHH----hCCCceEcHHHHHHHHhCCCCCCCCcCHHHHHHHHHHhcc
Confidence 59999999998865 4443 467888889999999999999999986
No 355
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=59.49 E-value=20 Score=31.53 Aligned_cols=39 Identities=26% Similarity=0.198 Sum_probs=34.4
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
..|++.|-..|+-.+ ++|+.+-|..||+|.+||+.++..
T Consensus 42 ~~ls~~eIk~iRe~~-----~lSQ~vFA~~L~vs~~Tv~~WEqG 80 (104)
T COG2944 42 KTLSPTEIKAIREKL-----GLSQPVFARYLGVSVSTVRKWEQG 80 (104)
T ss_pred CCCCHHHHHHHHHHh-----CCCHHHHHHHHCCCHHHHHHHHcC
Confidence 578999888887766 599999999999999999999974
No 356
>PRK10161 transcriptional regulator PhoB; Provisional
Probab=59.24 E-value=11 Score=35.65 Aligned_cols=50 Identities=10% Similarity=0.141 Sum_probs=38.6
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHH-----HHCCCHHHHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISK-----RIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe-----~LgIS~~rVrqi~~rALkKLR~ 485 (499)
.|+++|.+|+.+..---+.+.|.++|.. .++++..||+..+.+.++||..
T Consensus 154 ~Lt~~E~~ll~~l~~~~~~~~s~~~l~~~~~~~~~~~~~~tv~~~i~rlr~Kl~~ 208 (229)
T PRK10161 154 EMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEP 208 (229)
T ss_pred EcCHHHHHHHHHHHhCCCceEcHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhcc
Confidence 5899999999876511135688777654 5678999999999999999963
No 357
>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=59.18 E-value=29 Score=26.35 Aligned_cols=46 Identities=30% Similarity=0.421 Sum_probs=32.4
Q ss_pred cccccHHHHHHHHHHHHHHHHHcCC-CCCHHHHHHHhCCCHHHHHHH
Q 010835 332 RLPNHLHERLGLIRNAKLRLEEKGV-TPSVDRIAEYLNMSQKKVRNA 377 (499)
Q Consensus 332 Rip~~~~e~l~~irka~~~L~~~gr-~pt~eEIA~~Lgis~e~v~~~ 377 (499)
.||..+.+++-...+.-..|.+.|. ..+..+||+.+|+++..|+.-
T Consensus 2 ~Ip~~ti~RL~~Y~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRKD 48 (50)
T PF06971_consen 2 KIPKATIRRLPLYLRYLEQLKEEGVERVSSQELAEALGITPAQVRKD 48 (50)
T ss_dssp S-SHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHcCCeeECHHHHHHHHCCCHHHhccc
Confidence 4666666777666677777777776 557899999999999999763
No 358
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=59.13 E-value=21 Score=32.15 Aligned_cols=42 Identities=10% Similarity=-0.024 Sum_probs=31.5
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
.|++.|-.||..-+. ..++.|..|||+.++++++||.+.+.+
T Consensus 28 glt~~q~~vL~~l~~-~~~~~t~~eLa~~l~~~~~tvt~~v~~ 69 (144)
T PRK03573 28 ELTQTHWVTLHNIHQ-LPPEQSQIQLAKAIGIEQPSLVRTLDQ 69 (144)
T ss_pred CCCHHHHHHHHHHHH-cCCCCCHHHHHHHhCCChhhHHHHHHH
Confidence 688888777765431 124689999999999999999755543
No 359
>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=58.98 E-value=36 Score=34.30 Aligned_cols=52 Identities=33% Similarity=0.399 Sum_probs=38.4
Q ss_pred HHHHHHHhhCCHHHHHHHHHHhcC-CC-C-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010835 428 EVNKLIIVTLGEREREIIRLYYGL-DK-E-CLTWEDISKRIGLSRERVRQVGLVALEKLK 484 (499)
Q Consensus 428 ~L~~~L~~~L~~rER~VI~LryGL-d~-e-g~SleEIAe~LgIS~~rVrqi~~rALkKLR 484 (499)
.+.-+| ..|+--|.+-+...+-. +. + -.+..+||+++|||+..|+ +|+++|.
T Consensus 169 ~Vq~Ai-~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ir----eAlrkLE 223 (251)
T TIGR02787 169 AVQMAI-NTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIV----NALRKLE 223 (251)
T ss_pred HHHHHH-HhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHH----HHHHHHH
Confidence 455567 89998888877665543 34 2 4899999999999999886 5555554
No 360
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=58.88 E-value=9.6 Score=29.19 Aligned_cols=27 Identities=19% Similarity=0.306 Sum_probs=20.0
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 454 ECLTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 454 eg~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
.++|..++|+..|+++.+|.++.+.-.
T Consensus 9 ~~it~~~La~~~gis~~tl~~~~~~~~ 35 (63)
T PF13443_consen 9 RGITQKDLARKTGISRSTLSRILNGKP 35 (63)
T ss_dssp TT--HHHHHHHHT--HHHHHHHHTTT-
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhccc
Confidence 578999999999999999999988653
No 361
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=58.54 E-value=13 Score=33.30 Aligned_cols=26 Identities=15% Similarity=0.101 Sum_probs=23.4
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
..++|..++|+.+|||+++|+++++.
T Consensus 16 ~~gltq~~lA~~~gvs~~~is~~E~g 41 (135)
T PRK09706 16 QLKLSQRSLAKAVKVSHVSISQWERD 41 (135)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 46799999999999999999998865
No 362
>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=58.04 E-value=6.4 Score=28.94 Aligned_cols=20 Identities=30% Similarity=0.277 Sum_probs=17.9
Q ss_pred HHHHHHCCCHHHHHHHHHHH
Q 010835 460 DISKRIGLSRERVRQVGLVA 479 (499)
Q Consensus 460 EIAe~LgIS~~rVrqi~~rA 479 (499)
+||+.+|||+.||+++++.-
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCC
Confidence 79999999999999988754
No 363
>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=57.86 E-value=33 Score=25.23 Aligned_cols=23 Identities=17% Similarity=0.270 Sum_probs=17.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~r 478 (499)
+|+.+.|+.+||++.|++.++..
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 99999999999999999866553
No 364
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=57.68 E-value=22 Score=31.77 Aligned_cols=38 Identities=16% Similarity=0.142 Sum_probs=28.6
Q ss_pred CHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 438 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 438 ~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
+|.-+.||.+-. +.++++..||++.+|+|+++|++++.
T Consensus 15 dptRl~IL~~L~--~~~~~~v~ela~~l~lsqstvS~HL~ 52 (117)
T PRK10141 15 DETRLGIVLLLR--ESGELCVCDLCTALDQSQPKISRHLA 52 (117)
T ss_pred CHHHHHHHHHHH--HcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 445556776543 13579999999999999999987654
No 365
>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=57.64 E-value=15 Score=28.19 Aligned_cols=26 Identities=23% Similarity=0.480 Sum_probs=20.5
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
..++|+.++|+.+|++++++.++++.
T Consensus 10 ~~~lt~~~~a~~~~i~~~~i~~~e~g 35 (64)
T PF12844_consen 10 EKGLTQKDLAEKLGISRSTISKIENG 35 (64)
T ss_dssp HCT--HHHHHHHHTS-HHHHHHHHTT
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 46799999999999999999999864
No 366
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=57.62 E-value=19 Score=32.51 Aligned_cols=25 Identities=16% Similarity=0.186 Sum_probs=21.0
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
....+..+||+.||+|+.+|+..+.
T Consensus 20 ~~~~~~~ela~~l~vs~~svs~~l~ 44 (142)
T PRK03902 20 KGYARVSDIAEALSVHPSSVTKMVQ 44 (142)
T ss_pred CCCcCHHHHHHHhCCChhHHHHHHH
Confidence 3567999999999999999976653
No 367
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=56.97 E-value=26 Score=39.87 Aligned_cols=65 Identities=17% Similarity=0.134 Sum_probs=47.5
Q ss_pred HHHHHHHHHHHHhhCCHHHHHHHHHHhcC--CCCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHH
Q 010835 423 WALKDEVNKLIIVTLGEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGLV----ALEKLKHAAR 488 (499)
Q Consensus 423 ~el~~~L~~~L~~~L~~rER~VI~LryGL--d~eg~SleEIAe~LgIS~~rVrqi~~r----ALkKLR~~L~ 488 (499)
..+.+.|.... ..|++.||.|.....-- +...+|..|||+..++|..||-+.-++ ...-||..+.
T Consensus 341 ~~l~~~I~~~~-~~Lt~~E~~IA~yIl~n~~~v~~~si~eLA~~~~vS~aTV~Rf~kkLGf~Gf~efK~~L~ 411 (638)
T PRK14101 341 SAVFERIRQMR-DALTPAERRVADLALNHPRSIINDPIVDIARKADVSQPTVIRFCRSLGCQGLSDFKLKLA 411 (638)
T ss_pred HHHHHHHHHHH-hhcCHHHHHHHHHHHhCHHHHHhccHHHHHHHhCCCHHHHHHHHHHhCCCCHHHHHHHHH
Confidence 34667788888 89999999999775410 122489999999999999999765543 4555665554
No 368
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=56.97 E-value=12 Score=36.25 Aligned_cols=44 Identities=11% Similarity=0.059 Sum_probs=28.8
Q ss_pred CHHHHHHHHHHhcC--CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 438 GEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 438 ~~rER~VI~LryGL--d~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
+.++|.+-.+..-- +.-+.|.++||+.+|+|+++|. |++++|++
T Consensus 150 ~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvs----R~L~~L~~ 195 (226)
T PRK10402 150 PLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLL----YVLAQFIQ 195 (226)
T ss_pred hHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHH----HHHHHHHH
Confidence 55555544443200 1124689999999999999995 66667765
No 369
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=56.90 E-value=14 Score=25.71 Aligned_cols=26 Identities=23% Similarity=0.456 Sum_probs=22.7
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
..++|..++|+.+|++..+|++++..
T Consensus 8 ~~~~s~~~la~~~~i~~~~i~~~~~~ 33 (56)
T smart00530 8 EKGLTQEELAEKLGVSRSTLSRIENG 33 (56)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 35789999999999999999987764
No 370
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=56.28 E-value=16 Score=36.76 Aligned_cols=38 Identities=11% Similarity=0.228 Sum_probs=29.7
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 439 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 439 ~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
+|++.|+.+-- .....+..|+|+.||||+.|||+-+..
T Consensus 5 eR~~~Il~~L~--~~~~v~v~eLa~~l~VS~~TIRRDL~~ 42 (256)
T PRK10434 5 QRQAAILEYLQ--KQGKTSVEELAQYFDTTGTTIRKDLVI 42 (256)
T ss_pred HHHHHHHHHHH--HcCCEEHHHHHHHHCCCHHHHHHHHHH
Confidence 56666776643 024589999999999999999998876
No 371
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=56.27 E-value=13 Score=36.13 Aligned_cols=27 Identities=15% Similarity=0.208 Sum_probs=21.6
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 455 CLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 455 g~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
++|.++||..+|+++++|. |++++|++
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 5788999999999999985 55555554
No 372
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=55.96 E-value=31 Score=26.85 Aligned_cols=26 Identities=23% Similarity=0.339 Sum_probs=22.7
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 455 CLTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 455 g~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
+.|+++||+.+|+|...+.++..+..
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~ 26 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKET 26 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHh
Confidence 36899999999999999998887765
No 373
>PF12759 HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR024431 This entry represents the helix-turn-helix domain found at the C-terminal of InsA.
Probab=55.96 E-value=16 Score=27.42 Aligned_cols=37 Identities=11% Similarity=0.101 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 437 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 437 L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
-|.-..+|+.|-+ +|.-.+++|+.|+|+..||-+.+.
T Consensus 7 kpgikeqIvema~----nG~GiRdtaRvL~I~~nTVlrtLK 43 (46)
T PF12759_consen 7 KPGIKEQIVEMAF----NGSGIRDTARVLKISINTVLRTLK 43 (46)
T ss_pred CccHHHHHHHHHh----cCCcchhhHhHhcchHHHHHHHHh
Confidence 4555668999987 889999999999999999965443
No 374
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=55.59 E-value=12 Score=29.80 Aligned_cols=25 Identities=24% Similarity=0.134 Sum_probs=20.3
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 454 ECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 454 eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
.+.+..|||+.+|+|..+||.++..
T Consensus 14 ~p~~T~eiA~~~gls~~~aR~yL~~ 38 (62)
T PF04703_consen 14 GPLKTREIADALGLSIYQARYYLEK 38 (62)
T ss_dssp S-EEHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 6799999999999999999877653
No 375
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=55.45 E-value=90 Score=33.94 Aligned_cols=26 Identities=31% Similarity=0.403 Sum_probs=22.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010835 454 ECLTWEDISKRIGLSRERVRQVGLVA 479 (499)
Q Consensus 454 eg~SleEIAe~LgIS~~rVrqi~~rA 479 (499)
..-|..|||+.+|+|...|+.++..+
T Consensus 277 R~pt~~EiA~~l~is~~~vr~~l~~~ 302 (415)
T PRK07598 277 RTPTIEDIAQELEMTPTQVREVLLRV 302 (415)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHc
Confidence 55789999999999999999886654
No 376
>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=55.16 E-value=4 Score=38.46 Aligned_cols=46 Identities=22% Similarity=0.308 Sum_probs=0.0
Q ss_pred HHHHHHhhCCHHHHHHHHHHhcC-CCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 429 VNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 429 L~~~L~~~L~~rER~VI~LryGL-d~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
|.... ..|=+.|+.-|.. |- ...++|+++||+.||++.+||++...
T Consensus 25 L~~v~-~~iv~~Q~~ff~~--g~~~l~PLt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 25 LLRVA-QAIVERQKDFFLG--GPGALKPLTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp --------------------------------------------------
T ss_pred HHHHH-HHHHHHHHHHHhc--CcccCcCCCHHHHHHHhCCCHhHHHHHHc
Confidence 33444 5556677765543 22 25789999999999999999987654
No 377
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=55.02 E-value=19 Score=31.66 Aligned_cols=35 Identities=23% Similarity=0.388 Sum_probs=26.5
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 443 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 443 ~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
+||.-.| ++.-|+|..++|+.|||++.+|..+++-
T Consensus 12 EiL~eef-lep~glt~~~lA~~lgV~r~~is~ling 46 (104)
T COG3093 12 EILREEF-LEPLGLTQTELAEALGVTRNTISELING 46 (104)
T ss_pred HHHHHHH-hccccCCHHHHHHHhCCCHHHHHHHHcC
Confidence 3555555 1222699999999999999999988764
No 378
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=54.98 E-value=2.4e+02 Score=29.16 Aligned_cols=26 Identities=19% Similarity=0.170 Sum_probs=23.0
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
....|++|||+..|||..||+++...
T Consensus 249 ~~~~tq~eva~v~~vtevTIrnryke 274 (285)
T COG1405 249 GERRTQKEVAKVAGVTEVTIRNRYKE 274 (285)
T ss_pred CCchHHHHHHHHhCCeeeHHHHHHHH
Confidence 36789999999999999999998843
No 379
>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=54.75 E-value=22 Score=24.80 Aligned_cols=26 Identities=23% Similarity=0.452 Sum_probs=22.7
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010835 454 ECLTWEDISKRIGLSRERVRQVGLVA 479 (499)
Q Consensus 454 eg~SleEIAe~LgIS~~rVrqi~~rA 479 (499)
.++|..++|+.+|+++.+|.+++...
T Consensus 11 ~~~s~~~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 11 KGLTQEELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHcCC
Confidence 57999999999999999999877643
No 380
>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=54.62 E-value=21 Score=29.25 Aligned_cols=23 Identities=22% Similarity=0.418 Sum_probs=18.5
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Q 010835 455 CLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 455 g~SleEIAe~LgIS~~rVrqi~~ 477 (499)
..|.+|||+.+|+|+..|++++.
T Consensus 25 ~~s~~eiA~~~~i~~~~l~kil~ 47 (83)
T PF02082_consen 25 PVSSKEIAERLGISPSYLRKILQ 47 (83)
T ss_dssp -BEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHH
Confidence 38999999999999999976654
No 381
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=54.43 E-value=23 Score=35.43 Aligned_cols=38 Identities=21% Similarity=0.274 Sum_probs=28.7
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 439 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 439 ~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
+|++.|+.+-- .....+.+|||+.||||..|||+.+..
T Consensus 5 ~R~~~Il~~l~--~~~~~~~~ela~~l~vS~~TirRdL~~ 42 (251)
T PRK13509 5 QRHQILLELLA--QLGFVTVEKVIERLGISPATARRDINK 42 (251)
T ss_pred HHHHHHHHHHH--HcCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 45555555432 134699999999999999999998876
No 382
>PHA00738 putative HTH transcription regulator
Probab=54.30 E-value=27 Score=30.83 Aligned_cols=38 Identities=24% Similarity=0.087 Sum_probs=28.6
Q ss_pred CHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 438 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 438 ~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
+|.-+.||.+-. +.++++.-||++.+++|+.+|++.+.
T Consensus 11 dptRr~IL~lL~--~~e~~~V~eLae~l~lSQptVS~HLK 48 (108)
T PHA00738 11 KILRRKILELIA--ENYILSASLISHTLLLSYTTVLRHLK 48 (108)
T ss_pred CHHHHHHHHHHH--HcCCccHHHHHHhhCCCHHHHHHHHH
Confidence 455566666533 13569999999999999999988764
No 383
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=54.17 E-value=16 Score=36.73 Aligned_cols=37 Identities=22% Similarity=0.344 Sum_probs=30.0
Q ss_pred CHHHHHHHHHHhcCCCC-CCCHHHHHHHHCCCHHHHHHHHH
Q 010835 438 GEREREIIRLYYGLDKE-CLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 438 ~~rER~VI~LryGLd~e-g~SleEIAe~LgIS~~rVrqi~~ 477 (499)
.+|++.|+.+-- .+ -.+.+|+|+.||||..|||+=+.
T Consensus 4 ~eR~~~Il~~l~---~~g~v~v~eLa~~~~VS~~TIRRDL~ 41 (253)
T COG1349 4 EERHQKILELLK---EKGKVSVEELAELFGVSEMTIRRDLN 41 (253)
T ss_pred HHHHHHHHHHHH---HcCcEEHHHHHHHhCCCHHHHHHhHH
Confidence 467888888754 33 48999999999999999998544
No 384
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=53.82 E-value=1.5e+02 Score=26.59 Aligned_cols=24 Identities=25% Similarity=0.309 Sum_probs=17.9
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 454 ECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 454 eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
-|.|-..||..+|++...|++...
T Consensus 71 ~GFsD~~IA~l~~~~e~~vr~~R~ 94 (123)
T PF02787_consen 71 LGFSDRQIARLWGVSEEEVRELRK 94 (123)
T ss_dssp TT--HHHHHHHHTS-HHHHHHHHH
T ss_pred cCCCHHHHHhccCCCHHHHHHHHH
Confidence 679999999999999999976544
No 385
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=53.32 E-value=74 Score=26.97 Aligned_cols=27 Identities=15% Similarity=0.180 Sum_probs=24.6
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLVA 479 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~rA 479 (499)
.++.+.++||+.+|+|+.++.++..+.
T Consensus 19 ~~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 19 DQPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 467999999999999999999888887
No 386
>PRK06424 transcription factor; Provisional
Probab=53.13 E-value=18 Score=33.48 Aligned_cols=26 Identities=8% Similarity=0.123 Sum_probs=23.7
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
..|+|++|+|+.+|+++++|+++++-
T Consensus 95 ~~GLSQ~eLA~~iGvs~stIskiE~G 120 (144)
T PRK06424 95 RLSMSQADLAAKIFERKNVIASIERG 120 (144)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 56899999999999999999999863
No 387
>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=53.03 E-value=33 Score=32.42 Aligned_cols=56 Identities=30% Similarity=0.365 Sum_probs=43.6
Q ss_pred HHHHHHHHHHHHHhhCCHHHHHHHHHHhcC---C--CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 422 DWALKDEVNKLIIVTLGEREREIIRLYYGL---D--KECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 422 ~~el~~~L~~~L~~~L~~rER~VI~LryGL---d--~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
+++-.+.|++.| ..||+.|++=+.-+|-= | .+|.|-+||.+.||=+++-++++...
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 KNEFLNELEKYL-KKLPEEEREEILEYYEEYFDDAGEEGKSEEEIIAELGSPKEIAREILAE 63 (181)
T ss_pred HHHHHHHHHHHH-HcCCHHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHcCCHHHHHHHHHHh
Confidence 566778899999 89999988855555422 1 34789999999999999988887754
No 388
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=52.82 E-value=1.1e+02 Score=29.54 Aligned_cols=98 Identities=21% Similarity=0.322 Sum_probs=63.2
Q ss_pred HcCCC-CCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHH
Q 010835 353 EKGVT-PSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNK 431 (499)
Q Consensus 353 ~~gr~-pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~ 431 (499)
..|.+ .+..+||+.++++...|..++........-+. .+-.+... .+-+....+.+....+.+
T Consensus 15 ~sg~pgls~~~La~~l~~~~~~v~~~l~~L~~~y~~~~---------~gi~i~~~-------~~~y~l~tk~e~~~~v~~ 78 (188)
T PRK00135 15 VSGEEGLSLEQLAEILELEPTEVQQLLEELQEKYEGDD---------RGLKLIEF-------NDVYKLVTKEENADYLQK 78 (188)
T ss_pred HcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhCC---------CCEEEEEE-------CCEEEEEEcHHHHHHHHH
Confidence 35675 79999999999999998888776533221110 01111110 122333334445556665
Q ss_pred HHH----hhCCHHHHHHHHHH-hcCCCCCCCHHHHHHHHCCCH
Q 010835 432 LII----VTLGEREREIIRLY-YGLDKECLTWEDISKRIGLSR 469 (499)
Q Consensus 432 ~L~----~~L~~rER~VI~Lr-yGLd~eg~SleEIAe~LgIS~ 469 (499)
++. ..|+.-.-+||... | .++.|..||+++.|++.
T Consensus 79 ~~~~~~~~~LS~aaLEtLaiIay---~qPiTr~eI~~irGv~~ 118 (188)
T PRK00135 79 LVKTPIKQSLSQAALEVLAIIAY---KQPITRIEIDEIRGVNS 118 (188)
T ss_pred HhcccccCCCCHHHHHHHHHHHH---cCCcCHHHHHHHHCCCH
Confidence 552 25999988888774 5 57999999999999986
No 389
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=52.82 E-value=20 Score=36.02 Aligned_cols=38 Identities=18% Similarity=0.253 Sum_probs=28.5
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 439 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 439 ~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
+|++.|+.+-- .....+..|||+.|+||..|||+-+..
T Consensus 5 ~R~~~Il~~l~--~~~~~~~~ela~~l~vS~~TiRRdL~~ 42 (252)
T PRK10906 5 QRHDAIIELVK--QQGYVSTEELVEHFSVSPQTIRRDLND 42 (252)
T ss_pred HHHHHHHHHHH--HcCCEeHHHHHHHhCCCHHHHHHHHHH
Confidence 56666666643 024589999999999999999986543
No 390
>PRK06030 hypothetical protein; Provisional
Probab=52.13 E-value=48 Score=29.97 Aligned_cols=39 Identities=10% Similarity=0.026 Sum_probs=28.2
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 439 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 439 ~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
+|+--+...+- .-++|+.+||+.||-+.+||.....+.-
T Consensus 56 aRqIAMYL~r~---~~~~sl~~IG~~FGRDHSTV~haikkIe 94 (124)
T PRK06030 56 IRQIAMYVAHV---SLGWPMNEVALAFGRDRTTVGHACHTVE 94 (124)
T ss_pred HHHHHHHHHHH---HcCCCHHHHHHHHCCChhHHHHHHHHHH
Confidence 44444444444 4679999999999999999977666333
No 391
>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=52.01 E-value=94 Score=33.85 Aligned_cols=90 Identities=18% Similarity=0.207 Sum_probs=52.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhh-----ccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHH
Q 010835 356 VTPSVDRIAEYLNMSQKKVRNATEAI-----GKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVN 430 (499)
Q Consensus 356 r~pt~eEIA~~Lgis~e~v~~~l~~~-----~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~ 430 (499)
++-+..+||+.+|+.+.+|.++.... .+++.|..-+ .......++...+....++..|.
T Consensus 317 kPLtlkdiA~~lglheSTVSRav~~Kyi~tp~Gi~~lk~FF----------------s~~~~~~~~g~~~S~~~Ik~~I~ 380 (429)
T TIGR02395 317 KPLTLREVAEELGLHESTISRAINNKYLQTPRGVFELKYFF----------------SRGVQTDSGEGEVSSTAIKALIK 380 (429)
T ss_pred cCCcHHHHHHHhCCCccchhhhhcCceEecCCceEEHHHhc----------------CCccCCCCCCCccCHHHHHHHHH
Confidence 46689999999999999998876532 2444444321 11100001111234455666666
Q ss_pred HHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHH-----CCCHHHHHHH
Q 010835 431 KLIIVTLGEREREIIRLYYGLDKECLTWEDISKRI-----GLSRERVRQV 475 (499)
Q Consensus 431 ~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~L-----gIS~~rVrqi 475 (499)
++| ..=++ ..++|-++||+.| .|+|.||-..
T Consensus 381 ~lI-~~E~~-------------~~PlSD~~I~~~L~~~Gi~IaRRTVaKY 416 (429)
T TIGR02395 381 ELI-AAEDK-------------RKPLSDQKIAELLKEKGIKIARRTVAKY 416 (429)
T ss_pred HHH-HhcCC-------------CCCCCHHHHHHHHHhcCCCeehHHHHHH
Confidence 666 21111 2568888888888 6787777554
No 392
>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=51.89 E-value=23 Score=30.17 Aligned_cols=42 Identities=17% Similarity=0.306 Sum_probs=29.3
Q ss_pred hCCHHHHHHHHHHhc-C-CCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYG-L-DKECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 436 ~L~~rER~VI~LryG-L-d~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
.|++.++.|+...-. - ..+|.+..+|++.|+++...|+..+.
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 467777777776543 2 25789999999999999999876554
No 393
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=51.72 E-value=26 Score=25.52 Aligned_cols=23 Identities=26% Similarity=0.455 Sum_probs=20.9
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQV 475 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi 475 (499)
+++.|.++||++.|+|++++-+.
T Consensus 14 ~~~~s~~~Ia~~~gvs~~~~y~~ 36 (47)
T PF00440_consen 14 YEAVSIRDIARRAGVSKGSFYRY 36 (47)
T ss_dssp TTTSSHHHHHHHHTSCHHHHHHH
T ss_pred HHhCCHHHHHHHHccchhhHHHH
Confidence 68999999999999999998754
No 394
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=51.14 E-value=21 Score=31.80 Aligned_cols=26 Identities=19% Similarity=0.244 Sum_probs=23.3
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
..|+|.+|+|+.+|||++++.++++.
T Consensus 16 ~~Glsq~eLA~~~Gis~~~is~iE~g 41 (120)
T PRK13890 16 ERHMTKKELSERSGVSISFLSDLTTG 41 (120)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 36799999999999999999998864
No 395
>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=51.10 E-value=18 Score=39.23 Aligned_cols=25 Identities=16% Similarity=0.286 Sum_probs=22.2
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
..++|+++||+.+|++.+||++..+
T Consensus 316 LkPLtlkdiA~~lglheSTVSRav~ 340 (429)
T TIGR02395 316 LKPLTLREVAEELGLHESTISRAIN 340 (429)
T ss_pred CcCCcHHHHHHHhCCCccchhhhhc
Confidence 4789999999999999999987654
No 396
>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=50.95 E-value=24 Score=35.13 Aligned_cols=43 Identities=26% Similarity=0.236 Sum_probs=34.3
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
..|+..+.+-|++-+-.+-+.+|...+|+.|+||+++||+|+.
T Consensus 9 k~Ls~~~~~~ir~L~~~~p~~~t~~~Lae~F~vspe~irrILk 51 (225)
T PF06413_consen 9 KKLSREAMEQIRYLHKEDPEEWTVERLAESFKVSPEAIRRILK 51 (225)
T ss_pred CCCCHHHHHHHHHHHHhCccccCHHHHHhhCCCCHHHHHHHHh
Confidence 4677777777776553344568999999999999999999875
No 397
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=50.79 E-value=33 Score=33.01 Aligned_cols=40 Identities=15% Similarity=0.096 Sum_probs=32.7
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
.|++.|..||..-+. .++.|..+||+.++++++||.+.+.
T Consensus 42 gLt~~q~~iL~~L~~--~~~itq~eLa~~l~l~~sTvtr~l~ 81 (185)
T PRK13777 42 DLNINEHHILWIAYH--LKGASISEIAKFGVMHVSTAFNFSK 81 (185)
T ss_pred CCCHHHHHHHHHHHh--CCCcCHHHHHHHHCCCHhhHHHHHH
Confidence 689999988877652 4689999999999999999866444
No 398
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=50.75 E-value=76 Score=28.14 Aligned_cols=27 Identities=22% Similarity=0.271 Sum_probs=24.6
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLVA 479 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~rA 479 (499)
.++.|++++|+.+|+|+.++.++..+.
T Consensus 23 ~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 23 ESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 467999999999999999999888877
No 399
>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=50.74 E-value=20 Score=33.81 Aligned_cols=89 Identities=19% Similarity=0.245 Sum_probs=19.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhh-----ccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHH
Q 010835 356 VTPSVDRIAEYLNMSQKKVRNATEAI-----GKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVN 430 (499)
Q Consensus 356 r~pt~eEIA~~Lgis~e~v~~~l~~~-----~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~ 430 (499)
.+-+..+||+.+|+++.+|..+...- .+.++|..- +..... .++...+....++..|.
T Consensus 48 ~PLt~~~iA~~lgl~~STVSRav~~Ky~~t~~Gi~plk~f----------------F~~~~~-~~~~~~~S~~~ik~~i~ 110 (160)
T PF04552_consen 48 KPLTMKDIADELGLHESTVSRAVKNKYIQTPRGIFPLKDF----------------FSRSVS-SGSGEEFSSEAIKARIK 110 (160)
T ss_dssp -------------------------------------S---------------------SS---SS-SS---TTH-HHHH
T ss_pred cCCCHHHHHHHhCCCHhHHHHHHcCceeecCCeeeeHHHh----------------cccccc-CCCCcccHHHHHHHHHH
Confidence 45578999999999999998765531 234444432 221110 11111122233444555
Q ss_pred HHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHH-----CCCHHHHHHH
Q 010835 431 KLIIVTLGEREREIIRLYYGLDKECLTWEDISKRI-----GLSRERVRQV 475 (499)
Q Consensus 431 ~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~L-----gIS~~rVrqi 475 (499)
++| ..=++ ..++|-++|++.| .||+.||...
T Consensus 111 ~lI-~~Ed~-------------~~PlSD~~i~~~L~~~gi~isRRTVaKY 146 (160)
T PF04552_consen 111 ELI-EEEDK-------------KKPLSDQEIAELLKEEGIKISRRTVAKY 146 (160)
T ss_dssp HHH-TTS-T-------------TS---HHHHHHHHTTTTS---HHHHHHH
T ss_pred HHH-HhcCC-------------CCCCCHHHHHHHHHHcCCCccHHHHHHH
Confidence 544 11100 2478889999999 7888888544
No 400
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=50.73 E-value=26 Score=32.70 Aligned_cols=25 Identities=24% Similarity=0.238 Sum_probs=21.0
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
.......+||+.|||++.+|...++
T Consensus 22 ~~~~~~~diA~~L~Vsp~sVt~ml~ 46 (154)
T COG1321 22 KGFARTKDIAERLKVSPPSVTEMLK 46 (154)
T ss_pred cCcccHHHHHHHhCCCcHHHHHHHH
Confidence 4458999999999999999976554
No 401
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=50.61 E-value=1.6e+02 Score=29.41 Aligned_cols=39 Identities=23% Similarity=0.126 Sum_probs=28.3
Q ss_pred CHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 438 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 438 ~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
+..+|.|+..-- ..+++|..+||..+|+|+.||+....+
T Consensus 173 n~~~k~I~~eiq--~~~~~t~~~ia~~l~ls~aTV~~~lk~ 211 (240)
T COG3398 173 NETSKAIIYEIQ--ENKCNTNLLIAYELNLSVATVAYHLKK 211 (240)
T ss_pred chhHHHHHHHHh--cCCcchHHHHHHHcCccHHHHHHHHHH
Confidence 444555664432 246799999999999999999866543
No 402
>PF06970 RepA_N: Replication initiator protein A (RepA) N-terminus; InterPro: IPR010724 This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids []. Most proteins in this entry are bacterial, but archaeal and eukaryotic members are also included.
Probab=50.29 E-value=20 Score=29.60 Aligned_cols=28 Identities=14% Similarity=0.216 Sum_probs=22.8
Q ss_pred cCCCCC-----CCHHHHHHHHCCCHHHHHHHHH
Q 010835 450 GLDKEC-----LTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 450 GLd~eg-----~SleEIAe~LgIS~~rVrqi~~ 477 (499)
++|.+| .|.+|+++.||+|+.||..+..
T Consensus 42 wiDe~G~vYi~~s~eel~~~L~~s~~tv~~~~k 74 (76)
T PF06970_consen 42 WIDENGNVYIIFSIEELMELLNCSKSTVIKAKK 74 (76)
T ss_pred cCCCCCCEEEEeeHHHHHHHHCCCHHHHHHHHH
Confidence 456555 7999999999999999976553
No 403
>PF04645 DUF603: Protein of unknown function, DUF603; InterPro: IPR006739 This family includes several uncharacterised proteins from Borrelia species.
Probab=50.15 E-value=21 Score=33.95 Aligned_cols=25 Identities=36% Similarity=0.472 Sum_probs=21.3
Q ss_pred CCC-CCHHHHHHHHCCCHHHHHHHHH
Q 010835 453 KEC-LTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 453 ~eg-~SleEIAe~LgIS~~rVrqi~~ 477 (499)
.+| ++..|||++||||+..|....+
T Consensus 16 ~eg~L~d~~Ia~~lgvs~~nV~kmR~ 41 (181)
T PF04645_consen 16 KEGRLSDAEIAKELGVSRVNVWKMRQ 41 (181)
T ss_pred hcCCccHHHHHHHHCchHHHHHHHHH
Confidence 577 9999999999999999876544
No 404
>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=50.04 E-value=24 Score=32.54 Aligned_cols=49 Identities=18% Similarity=0.108 Sum_probs=38.9
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRI-----GLSRERVRQVGLVALEKLK 484 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~L-----gIS~~rVrqi~~rALkKLR 484 (499)
.|+++|.+|+.+-..--+.-.|.++|++.+ ..+..+|..++.+-++||.
T Consensus 147 ~Lt~~E~~il~~l~~~~~~~~sr~~i~~~~~~~~~~~~~~~~~~~i~~lr~kl~ 200 (218)
T TIGR01387 147 TLTRKEFQLLWLLMRRTGEVLPRTVIASLVWGMNFDSDTNVVDVAIRRLRAKVD 200 (218)
T ss_pred eCCHHHHHHHHHHHhCCCeeEcHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhhc
Confidence 599999999998762112348999999999 4567888888888888885
No 405
>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=49.64 E-value=57 Score=25.51 Aligned_cols=49 Identities=12% Similarity=0.148 Sum_probs=32.5
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHH------CCCHHHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRI------GLSRERVRQVGLVALEKLK 484 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~L------gIS~~rVrqi~~rALkKLR 484 (499)
.|++++..+|.+-.--.....|.++|.+.+ ..+..+|++.+.+-+++|.
T Consensus 5 ~Lt~~e~~lL~~L~~~~~~~vs~~~l~~~lw~~~~~~~~~~~l~~~i~~LR~~l~ 59 (78)
T smart00862 5 KLTPKEFRLLELLLRNPGRVVSREELLEAVWGDDDDDVDDNTLDVHISRLRKKLE 59 (78)
T ss_pred ecCHHHHHHHHHHHhCCCCccCHHHHHHHHcCCCCCCCccchHHHHHHHHHHHHh
Confidence 578999998776541113468999999986 3455666666665555554
No 406
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=48.61 E-value=28 Score=36.61 Aligned_cols=44 Identities=36% Similarity=0.468 Sum_probs=35.0
Q ss_pred hhCCHHHHHHHH------HHhcCCCCCCCHHHHHHH--HCCCHHHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIR------LYYGLDKECLTWEDISKR--IGLSRERVRQVGLVALEK 482 (499)
Q Consensus 435 ~~L~~rER~VI~------LryGLd~eg~SleEIAe~--LgIS~~rVrqi~~rALkK 482 (499)
..|++|++.|+. +.. .++.+.++||+. +|+|..|||+-+.. |++
T Consensus 2 ~~l~~R~~~Il~~IV~~yi~~---~~pv~s~~l~~~~~l~~S~aTIR~dm~~-Le~ 53 (339)
T PRK00082 2 SMLDERQREILRAIVEDYIAT---GEPVGSKTLSKRYGLGVSSATIRNDMAD-LEE 53 (339)
T ss_pred CccCHHHHHHHHHHHHHHHhc---CCCcCHHHHHHHhCCCCChHHHHHHHHH-HHh
Confidence 368999999996 333 578999999977 99999999987763 444
No 407
>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=48.56 E-value=46 Score=29.97 Aligned_cols=44 Identities=16% Similarity=0.231 Sum_probs=33.8
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHH----CCCHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRI----GLSRERVRQVGLVALE 481 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~L----gIS~~rVrqi~~rALk 481 (499)
.|++.|..|+..-.. .++.|..||.+.| +++..||...+.|-.+
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 378999999877642 3578999977776 7899999887776544
No 408
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=48.10 E-value=50 Score=31.57 Aligned_cols=49 Identities=18% Similarity=0.250 Sum_probs=32.6
Q ss_pred HHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 426 KDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 426 ~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
+..+...+ . -++....|+..-. ....+|-+|||..|||+...||+++.+
T Consensus 11 ~~~l~~~~-~-~~~~~~~Vl~~L~--~~g~~tdeeLA~~Lgi~~~~VRk~L~~ 59 (178)
T PRK06266 11 QKVLFEIM-E-GDEEGFEVLKALI--KKGEVTDEEIAEQTGIKLNTVRKILYK 59 (178)
T ss_pred HHHHHHHh-c-CCccHhHHHHHHH--HcCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 33444444 3 2555566666432 124699999999999999999877654
No 409
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=47.94 E-value=52 Score=31.07 Aligned_cols=52 Identities=21% Similarity=0.450 Sum_probs=33.4
Q ss_pred HHHHHHhhCCHHHHHHHHHHh-cCCCCC---CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 429 VNKLIIVTLGEREREIIRLYY-GLDKEC---LTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 429 L~~~L~~~L~~rER~VI~Lry-GLd~eg---~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
+...+ +.+..+.-.|+.+-. -+|.++ +|+++||+.+|+|+.|| .|+++.|.+
T Consensus 46 i~~~l-~l~g~k~~~Vl~~il~~~d~~N~v~~t~~~ia~~l~iS~~Tv----~r~ik~L~e 101 (165)
T PF05732_consen 46 IIKVL-DLIGNKAFRVLMYILENMDKDNAVVATQKEIAEKLGISKPTV----SRAIKELEE 101 (165)
T ss_pred HHHHh-hhhchhHHHHHHHHHHhcCCCCeEEeeHHHHHHHhCCCHHHH----HHHHHHHHh
Confidence 44455 545455445554422 123332 79999999999999998 577777764
No 410
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=47.52 E-value=1.1e+02 Score=26.16 Aligned_cols=39 Identities=13% Similarity=0.107 Sum_probs=27.5
Q ss_pred CHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 438 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 438 ~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
.+-|+.+|...+ ...+-+..+.|+.||||+.|++..+.+
T Consensus 53 ~~~Er~~i~~aL--~~~~gn~s~AAr~LGIsRsTL~rKLkr 91 (95)
T PRK00430 53 AEVEAPLLDMVM--QYTRGNQTRAALMLGINRGTLRKKLKK 91 (95)
T ss_pred HHHHHHHHHHHH--HHcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 345666665544 124578999999999999998766554
No 411
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=47.43 E-value=25 Score=33.18 Aligned_cols=26 Identities=12% Similarity=0.189 Sum_probs=23.6
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
..++|++++|+.+|+|+++|+++++.
T Consensus 18 ~~glt~~elA~~~gis~~~is~~E~g 43 (185)
T PRK09943 18 QQGLSQRRAAELSGLTHSAISTIEQD 43 (185)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 46799999999999999999999874
No 412
>PRK10643 DNA-binding transcriptional regulator BasR; Provisional
Probab=47.35 E-value=20 Score=33.18 Aligned_cols=47 Identities=13% Similarity=-0.030 Sum_probs=35.0
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCH-HHHH-H-----HHCCCHHHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTW-EDIS-K-----RIGLSRERVRQVGLVALEKLK 484 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~Sl-eEIA-e-----~LgIS~~rVrqi~~rALkKLR 484 (499)
.|+++|.+|+.+..- ..|.+. +||+ + .++++..||+.++.+.++||.
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 589999999987541 245552 4544 4 268999999999999999885
No 413
>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=47.16 E-value=14 Score=31.32 Aligned_cols=25 Identities=28% Similarity=0.369 Sum_probs=21.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
+|..|+|+.+|||..|+|.+...++
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~~Gl 25 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDIGL 25 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 4788999999999999999887654
No 414
>PRK08359 transcription factor; Validated
Probab=47.07 E-value=25 Score=33.69 Aligned_cols=31 Identities=26% Similarity=0.503 Sum_probs=25.7
Q ss_pred HHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 444 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 444 VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
|=.+|- ..++|++|+|+.+|+++.+|+.++.
T Consensus 90 IkeaRe---~kglSQeeLA~~lgvs~stI~~iE~ 120 (176)
T PRK08359 90 VYEAIQ---KSGLSYEELSHEVGLSVNDLRRIAH 120 (176)
T ss_pred HHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 444555 5689999999999999999998864
No 415
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=47.07 E-value=26 Score=32.74 Aligned_cols=26 Identities=15% Similarity=0.251 Sum_probs=23.7
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
..++|++++|+.+|+++++|+++++-
T Consensus 80 ~~glSqeeLA~~lgvs~s~IsriE~G 105 (154)
T TIGR00270 80 KRGWSQEQLAKKIQEKESLIKKIENA 105 (154)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 46899999999999999999999863
No 416
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=47.06 E-value=34 Score=34.24 Aligned_cols=38 Identities=18% Similarity=0.240 Sum_probs=29.0
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 439 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 439 ~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
+|+..|+.+-- .....+..|+|+.||||..|||+-+..
T Consensus 7 eR~~~I~~~l~--~~~~v~v~eLa~~~~VS~~TIRRDL~~ 44 (252)
T PRK10681 7 ERIGQLLQALK--RSDKLHLKDAAALLGVSEMTIRRDLNA 44 (252)
T ss_pred HHHHHHHHHHH--HcCCCcHHHHHHHhCCCHHHHHHHHHH
Confidence 45666666532 124589999999999999999988775
No 417
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=46.99 E-value=26 Score=34.19 Aligned_cols=29 Identities=28% Similarity=0.472 Sum_probs=23.1
Q ss_pred CCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 453 KECL-TWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 453 ~eg~-SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
++.+ |-.|+|+.||||+.+|| .|+..|..
T Consensus 28 G~~LPsE~eLae~~gVSRt~VR----eAL~~L~~ 57 (239)
T PRK04984 28 GSILPAERELSELIGVTRTTLR----EVLQRLAR 57 (239)
T ss_pred CCcCCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 3567 68899999999999997 56666653
No 418
>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=46.86 E-value=58 Score=30.43 Aligned_cols=38 Identities=24% Similarity=0.147 Sum_probs=27.6
Q ss_pred CHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 438 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 438 ~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
.+....|+..-. ....+|-+|||+.||++...||.++.
T Consensus 13 g~~~v~Vl~aL~--~~~~~tdEeLa~~Lgi~~~~VRk~L~ 50 (158)
T TIGR00373 13 EEEVGLVLFSLG--IKGEFTDEEISLELGIKLNEVRKALY 50 (158)
T ss_pred ChhHHHHHHHHh--ccCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 555666666432 12469999999999999999975554
No 419
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=46.84 E-value=23 Score=36.68 Aligned_cols=43 Identities=16% Similarity=0.070 Sum_probs=35.3
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
..|+..||.-|..-. ..++|..|||+.||-.++||.+-+.|.-
T Consensus 6 ~hLT~~eR~~I~~l~---~~~~S~reIA~~LgRh~sTIsRElkRn~ 48 (318)
T COG2826 6 KHLTLFERYEIERLL---KAKMSIREIAKQLNRHHSTISRELKRNR 48 (318)
T ss_pred hhCCHHHHHHHHHHH---HcCCCHHHHHHHhCCCcchhhHHHhcCC
Confidence 368888888776655 5799999999999999999988776543
No 420
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=46.55 E-value=29 Score=33.13 Aligned_cols=37 Identities=22% Similarity=0.423 Sum_probs=27.5
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 439 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 439 ~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
+|++.|+.+-- ...-.+..++|+.||+|..|||+-+.
T Consensus 7 ~R~~~Il~~l~--~~~~~~~~~La~~~~vS~~TiRRDl~ 43 (185)
T PRK04424 7 ERQKALQELIE--ENPFITDEELAEKFGVSIQTIRLDRM 43 (185)
T ss_pred HHHHHHHHHHH--HCCCEEHHHHHHHHCcCHHHHHHHHH
Confidence 45556665533 12458999999999999999998665
No 421
>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=46.34 E-value=15 Score=31.64 Aligned_cols=26 Identities=23% Similarity=0.335 Sum_probs=22.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVALE 481 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rALk 481 (499)
++..|+|+.+|||+.|++.+...++-
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~~Gll 27 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESIGLI 27 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 68899999999999999998877553
No 422
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=46.33 E-value=83 Score=27.30 Aligned_cols=41 Identities=29% Similarity=0.513 Sum_probs=32.2
Q ss_pred hhCCHHHHHHH----HHHhcCC--CCCCCHHHHHHHHCCCHHHHHHH
Q 010835 435 VTLGEREREII----RLYYGLD--KECLTWEDISKRIGLSRERVRQV 475 (499)
Q Consensus 435 ~~L~~rER~VI----~LryGLd--~eg~SleEIAe~LgIS~~rVrqi 475 (499)
..|+.+|..|+ +.-||.+ .+-.|..+||+..|+++..|+..
T Consensus 28 ~dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~a 74 (100)
T PF04492_consen 28 ADLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKA 74 (100)
T ss_pred ccccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHH
Confidence 67899988754 5567775 34589999999999999888543
No 423
>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=46.23 E-value=15 Score=31.98 Aligned_cols=25 Identities=16% Similarity=0.311 Sum_probs=22.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
||..|+|+.+|||+.|++.+...++
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gl 25 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKEGL 25 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999987655
No 424
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=46.21 E-value=1.6e+02 Score=32.35 Aligned_cols=59 Identities=17% Similarity=0.210 Sum_probs=37.4
Q ss_pred HHHHHHhhhcccccccHHHHHHHHHHHHHHHHHcCCC-CCHHHHHHHhCCCHHHHHHHHHhhc
Q 010835 321 SRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVT-PSVDRIAEYLNMSQKKVRNATEAIG 382 (499)
Q Consensus 321 ~~al~~~~R~vRip~~~~e~l~~irka~~~L~~~gr~-pt~eEIA~~Lgis~e~v~~~l~~~~ 382 (499)
..++..+.....++..... -.......|.+.|.- .+.++||..+|++.+++..++...+
T Consensus 104 ~e~L~~Ql~~~~l~~~~~~---ia~~iI~~LD~~GyL~~~~~eia~~l~~~~~~v~~~l~~lQ 163 (455)
T PRK05932 104 QDHLLEQIELTPFSETDRA---IATYIIDALDDEGYLTEDLEEIAESLGVELDEVEAVLKRIQ 163 (455)
T ss_pred HHHHHHHHcccCCCHHHHH---HHHHHHHhCCCCCCCCCCHHHHHHHcCCCHHHHHHHHHHHh
Confidence 3455555554444433221 122234455567764 4799999999999999999987754
No 425
>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=46.13 E-value=31 Score=27.47 Aligned_cols=20 Identities=25% Similarity=0.571 Sum_probs=18.2
Q ss_pred CHHHHHHHHCCCHHHHHHHH
Q 010835 457 TWEDISKRIGLSRERVRQVG 476 (499)
Q Consensus 457 SleEIAe~LgIS~~rVrqi~ 476 (499)
++.|+|..|++++.||+...
T Consensus 18 nqtEvaR~l~c~R~TVrKY~ 37 (64)
T PF06322_consen 18 NQTEVARRLGCNRATVRKYS 37 (64)
T ss_pred cHHHHHHHhcccHHHHHHHh
Confidence 78899999999999998764
No 426
>PRK11050 manganese transport regulator MntR; Provisional
Probab=46.06 E-value=64 Score=29.74 Aligned_cols=26 Identities=23% Similarity=0.184 Sum_probs=21.6
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
.++.+..|||+.|++++++|++.+.+
T Consensus 49 ~~~~t~~eLA~~l~is~stVsr~l~~ 74 (152)
T PRK11050 49 VGEARQVDIAARLGVSQPTVAKMLKR 74 (152)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 36799999999999999999755543
No 427
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.90 E-value=42 Score=28.65 Aligned_cols=41 Identities=10% Similarity=0.127 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHHhcC--CCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 437 LGEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 437 L~~rER~VI~LryGL--d~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
|++.|+.+-.--+.- ..-.+|.++||..||+|..-|..+++
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil~ 45 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLEKILQ 45 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHHHHHH
Confidence 555555543332211 13469999999999999998877764
No 428
>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=45.84 E-value=16 Score=30.50 Aligned_cols=25 Identities=24% Similarity=0.275 Sum_probs=22.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
+|..|+|+.+|||..|++.+..+.+
T Consensus 2 ~ti~evA~~~gvs~~tLR~ye~~Gl 26 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEEKGL 26 (88)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 6899999999999999999977654
No 429
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=45.76 E-value=43 Score=29.01 Aligned_cols=43 Identities=14% Similarity=0.260 Sum_probs=32.7
Q ss_pred hCCHHHH-HHHHHHhcCCCCCCCHHHHHHHHCC-CHHHHHHHHHHHHH
Q 010835 436 TLGERER-EIIRLYYGLDKECLTWEDISKRIGL-SRERVRQVGLVALE 481 (499)
Q Consensus 436 ~L~~rER-~VI~LryGLd~eg~SleEIAe~LgI-S~~rVrqi~~rALk 481 (499)
+.|+..+ +|+.++. ..|.|..+||..+|| +...+.++......
T Consensus 7 ~~s~EfK~~iv~~~~---~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~ 51 (116)
T COG2963 7 KYSPEFKLEAVALYL---RGGDTVSEVAREFGIVSATQLYKWRIQLQK 51 (116)
T ss_pred cCCHHHHHHHHHHHH---hcCccHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 4555555 5788877 678999999999996 99988876665544
No 430
>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=45.55 E-value=90 Score=31.90 Aligned_cols=97 Identities=14% Similarity=0.227 Sum_probs=52.7
Q ss_pred CCCCHHHHHHHhC--CCHHHHHHHHHhhccccccccccCCCCCCCCCCccc---cccccccCCCCCcchH--HHHHHHHH
Q 010835 356 VTPSVDRIAEYLN--MSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHH---SYIADNRVENNPWHGV--DDWALKDE 428 (499)
Q Consensus 356 r~pt~eEIA~~Lg--is~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~---e~i~d~~~e~~Pee~v--e~~el~~~ 428 (499)
..+++++||+.++ ||.++|++.+....+.-=|.. ++ +| .+. ..+.... +.|...+ ...+..+.
T Consensus 136 ~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk------~~-~g-~y~~t~~~l~~~~--~~~~~avr~~h~q~l~l 205 (271)
T TIGR02147 136 FADDPEELAKRCFPKISAEQVKESLDLLERLGLIKK------NE-DG-FYKQTDKAVSTGD--EVIPLAVRQYQKQMIDL 205 (271)
T ss_pred CCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeE------CC-CC-cEEeecceeecCC--ccchHHHHHHHHHHHHH
Confidence 4556889999999 999999999886533211111 00 11 110 1111111 1222211 12334445
Q ss_pred HHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHH
Q 010835 429 VNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRI 465 (499)
Q Consensus 429 L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~L 465 (499)
-.++| ++.|+.+|.+=.+-+|+ ....+++|.+.+
T Consensus 206 A~~al-~~~p~~eR~~S~lT~~i--~~~~~~~i~~~i 239 (271)
T TIGR02147 206 AKEAL-DALPPSERDVSTVTFGI--SEEAYKEIVKKI 239 (271)
T ss_pred HHHHH-HhCCccccccceeeEec--CHHHHHHHHHHH
Confidence 55667 78999999988776653 334455555444
No 431
>PF11662 DUF3263: Protein of unknown function (DUF3263); InterPro: IPR021678 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=45.54 E-value=78 Score=26.36 Aligned_cols=46 Identities=24% Similarity=0.229 Sum_probs=36.2
Q ss_pred hCCHHHHHHHHH-HhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRL-YYGLDKECLTWEDISKRIGLSRERVRQVGLVALE 481 (499)
Q Consensus 436 ~L~~rER~VI~L-ryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALk 481 (499)
.|+++++.||.. +-+-...|-+-+.|-+.||+|+-+--|.++.-+.
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 589999999976 2222235788999999999999999888887653
No 432
>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=45.12 E-value=16 Score=30.78 Aligned_cols=25 Identities=24% Similarity=0.299 Sum_probs=22.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
++..|+|+.+||++.||+.+....+
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~~Gl 25 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEEKGL 25 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999877654
No 433
>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=45.03 E-value=52 Score=24.42 Aligned_cols=28 Identities=18% Similarity=0.322 Sum_probs=22.0
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhh
Q 010835 354 KGVTPSVDRIAEYLNMSQKKVRNATEAI 381 (499)
Q Consensus 354 ~gr~pt~eEIA~~Lgis~e~v~~~l~~~ 381 (499)
.+...+..+||+.+|+|...|.+.+...
T Consensus 12 ~~~~it~~eLa~~l~vS~rTi~~~i~~L 39 (55)
T PF08279_consen 12 SKEPITAKELAEELGVSRRTIRRDIKEL 39 (55)
T ss_dssp TTTSBEHHHHHHHCTS-HHHHHHHHHHH
T ss_pred cCCCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 3334789999999999999998877655
No 434
>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=44.96 E-value=26 Score=34.07 Aligned_cols=26 Identities=27% Similarity=0.405 Sum_probs=21.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
-|-.|+|+++|||+.||| +||..|..
T Consensus 33 PsE~eLa~~~~VSR~TvR----~Al~~L~~ 58 (238)
T TIGR02325 33 PAEMQLAERFGVNRHTVR----RAIAALVE 58 (238)
T ss_pred cCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 488899999999999997 56666553
No 435
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=44.58 E-value=26 Score=33.88 Aligned_cols=29 Identities=28% Similarity=0.371 Sum_probs=23.5
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
++.++..+||+.||||+..|| .||..|..
T Consensus 32 G~~L~e~~La~~lgVSRtpVR----EAL~~L~~ 60 (221)
T PRK11414 32 GARLITKNLAEQLGMSITPVR----EALLRLVS 60 (221)
T ss_pred CCccCHHHHHHHHCCCchhHH----HHHHHHHH
Confidence 366888999999999999996 66666653
No 436
>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=44.53 E-value=26 Score=33.45 Aligned_cols=29 Identities=38% Similarity=0.498 Sum_probs=23.4
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
++.++-.++|+.||||+.+|| .||..|..
T Consensus 32 G~~L~e~~La~~lgVSRtpVR----eAL~~L~~ 60 (212)
T TIGR03338 32 GAKLNESDIAARLGVSRGPVR----EAFRALEE 60 (212)
T ss_pred CCEecHHHHHHHhCCChHHHH----HHHHHHHH
Confidence 356889999999999999997 66666653
No 437
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=44.42 E-value=38 Score=34.95 Aligned_cols=39 Identities=15% Similarity=0.194 Sum_probs=29.9
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 440 REREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 440 rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
+.+.|+.+-. +....+..+||+.+|+|+.+|++.+..-.
T Consensus 5 r~~~il~~L~--~~~~~s~~~LA~~lgvsr~tV~~~l~~L~ 43 (319)
T PRK11886 5 VMLQLLSLLA--DGDFHSGEQLGEELGISRAAIWKHIQTLE 43 (319)
T ss_pred HHHHHHHHHH--cCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4556666544 13568999999999999999999887654
No 438
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=44.33 E-value=27 Score=38.31 Aligned_cols=25 Identities=16% Similarity=0.353 Sum_probs=22.2
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
..++|+++||+.+|+..+||++..+
T Consensus 341 LkPLtlkdvAe~lglheSTVSRav~ 365 (455)
T PRK05932 341 LKPLVLKDIAEELGMHESTISRATT 365 (455)
T ss_pred CcCccHHHHHHHhCCCccchhhhhc
Confidence 4789999999999999999987654
No 439
>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=44.26 E-value=17 Score=30.50 Aligned_cols=25 Identities=12% Similarity=0.134 Sum_probs=21.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
+|..|+|+.+|||+.|++.+...++
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~~Gl 26 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYERLGL 26 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 6889999999999999999886544
No 440
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=43.65 E-value=32 Score=37.99 Aligned_cols=25 Identities=16% Similarity=0.306 Sum_probs=22.2
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
..++++++||+.+|+..+||++...
T Consensus 367 LkPLtlkdVAe~lglHeSTVSRa~~ 391 (481)
T PRK12469 367 LKPLVLRDVAEELGLHESTISRATG 391 (481)
T ss_pred CcCCcHHHHHHHhCCCcchhhHHhc
Confidence 4789999999999999999987654
No 441
>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=43.64 E-value=18 Score=31.40 Aligned_cols=26 Identities=23% Similarity=0.222 Sum_probs=22.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVALE 481 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rALk 481 (499)
++..|+|+.+|||+.|+|-+...++-
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~~GLi 26 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKIGLL 26 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCC
Confidence 57889999999999999999887653
No 442
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=43.63 E-value=33 Score=28.37 Aligned_cols=20 Identities=15% Similarity=0.237 Sum_probs=18.7
Q ss_pred CHHHHHHHHCCCHHHHHHHH
Q 010835 457 TWEDISKRIGLSRERVRQVG 476 (499)
Q Consensus 457 SleEIAe~LgIS~~rVrqi~ 476 (499)
+...+|+.||||+++|+|+-
T Consensus 12 s~~kvA~aLGIs~~AVsQWG 31 (75)
T PRK09744 12 SKTKLANAAGVRLASVAAWG 31 (75)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 78899999999999999994
No 443
>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=43.27 E-value=32 Score=33.49 Aligned_cols=29 Identities=28% Similarity=0.472 Sum_probs=23.5
Q ss_pred CCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 453 KECL-TWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 453 ~eg~-SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
++.+ |-.+||+.||||+..|| .||.+|..
T Consensus 27 G~~LpsE~~La~~lgVSRtpVR----EAL~~Le~ 56 (235)
T TIGR02812 27 GSILPAERELSELIGVTRTTLR----EVLQRLAR 56 (235)
T ss_pred CCcCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 3557 78999999999999996 67777664
No 444
>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=43.27 E-value=31 Score=30.60 Aligned_cols=25 Identities=16% Similarity=0.242 Sum_probs=20.9
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
....|..|||+.+|+|+.+|.+++.
T Consensus 23 ~~~~s~~eia~~l~is~~~v~~~l~ 47 (130)
T TIGR02944 23 SQPYSAAEIAEQTGLNAPTVSKILK 47 (130)
T ss_pred CCCccHHHHHHHHCcCHHHHHHHHH
Confidence 3568999999999999999975543
No 445
>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=43.16 E-value=39 Score=30.12 Aligned_cols=40 Identities=30% Similarity=0.374 Sum_probs=35.4
Q ss_pred hhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 435 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 435 ~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
..|.+.++.|+.+.- ...|..|||..|+++.+-|+.+..-
T Consensus 39 ~~l~pE~~~Il~lC~----~~~SVAEiAA~L~lPlgVvrVLvsD 78 (114)
T PF05331_consen 39 AGLGPEHRAILELCR----RPLSVAEIAARLGLPLGVVRVLVSD 78 (114)
T ss_pred CCCCHHHHHHHHHHC----CCccHHHHHHhhCCCchhhhhhHHH
Confidence 579999999999986 5999999999999999999877653
No 446
>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=43.13 E-value=18 Score=30.90 Aligned_cols=25 Identities=20% Similarity=0.514 Sum_probs=21.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
++..|+|+.+|||..|++.+...++
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye~~Gl 25 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEEIGL 25 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5788999999999999999876543
No 447
>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=42.71 E-value=19 Score=30.89 Aligned_cols=25 Identities=20% Similarity=0.264 Sum_probs=21.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
+|..|+|+.+|||+.|++.+...++
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~~Gl 25 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDEIGL 25 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5788999999999999998877654
No 448
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=42.69 E-value=18 Score=30.81 Aligned_cols=37 Identities=14% Similarity=0.329 Sum_probs=27.2
Q ss_pred HHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 444 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 444 VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
++....+|...++++.+||+-|||++++|+-....-+
T Consensus 30 ~~~i~~~i~q~~l~Q~qiae~lgV~qprvS~l~~gk~ 66 (91)
T COG5606 30 MMAIKQWIEQAALSQAQIAELLGVTQPRVSDLARGKI 66 (91)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHhcch
Confidence 3333334445679999999999999999987665443
No 449
>PRK11517 transcriptional regulatory protein YedW; Provisional
Probab=42.61 E-value=44 Score=31.02 Aligned_cols=49 Identities=18% Similarity=0.123 Sum_probs=38.0
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRI-----GLSRERVRQVGLVALEKLK 484 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~L-----gIS~~rVrqi~~rALkKLR 484 (499)
.|+++|..|+.+-.-=-++-.|.++|.+.+ ..+..+|+.++.|-++||.
T Consensus 147 ~Lt~~E~~il~~l~~~~g~~~s~~~i~~~~w~~~~~~~~~tv~~~i~rlr~Kl~ 200 (223)
T PRK11517 147 TLTRKEFQLLWLLASRAGEIIPRTVIASEIWGINFDSDTNTVDVAIRRLRAKVD 200 (223)
T ss_pred eCCHHHHHHHHHHHhCCCccCCHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhhc
Confidence 599999999988651012347999999997 4467899999888888885
No 450
>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=42.49 E-value=19 Score=31.00 Aligned_cols=25 Identities=20% Similarity=0.363 Sum_probs=21.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
++..|+|+.+|||+.|+|.+...++
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~~Gl 26 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKLGL 26 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 6889999999999999998877654
No 451
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=42.46 E-value=34 Score=33.78 Aligned_cols=28 Identities=29% Similarity=0.477 Sum_probs=22.9
Q ss_pred CCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 454 ECL-TWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 454 eg~-SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
+.+ +-.+||+.||||+.+|| .||..|..
T Consensus 32 ~~LpsE~eLa~~lgVSRtpVR----EAL~~L~~ 60 (254)
T PRK09464 32 EKLPPERELAKQFDVSRPSLR----EAIQRLEA 60 (254)
T ss_pred CcCCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 556 78999999999999996 66666654
No 452
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=42.29 E-value=34 Score=33.70 Aligned_cols=29 Identities=24% Similarity=0.457 Sum_probs=23.3
Q ss_pred CCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 453 KECL-TWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 453 ~eg~-SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
++.+ +-.+||+.||||+..|| .||+.|..
T Consensus 28 G~~LPsE~eLa~~~gVSRtpVR----EAL~~L~~ 57 (251)
T PRK09990 28 GQALPSERRLCEKLGFSRSALR----EGLTVLRG 57 (251)
T ss_pred CCcCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 3567 78899999999999996 66766653
No 453
>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=42.13 E-value=30 Score=29.66 Aligned_cols=23 Identities=13% Similarity=0.235 Sum_probs=20.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~r 478 (499)
+|..|+|+.+|||..|+|.+...
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~~ 23 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 47889999999999999998765
No 454
>COG4709 Predicted membrane protein [Function unknown]
Probab=41.98 E-value=61 Score=31.49 Aligned_cols=58 Identities=19% Similarity=0.173 Sum_probs=44.9
Q ss_pred HHHHHHHHHHHHHhhCCHHHHHHHHHHhcC-----CCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 422 DWALKDEVNKLIIVTLGEREREIIRLYYGL-----DKECLTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 422 ~~el~~~L~~~L~~~L~~rER~VI~LryGL-----d~eg~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
+.+..++|+..| +.||+.+|.=+...|-= ..+|.|-+||++.||-+.+-.+.+..+..
T Consensus 3 k~efL~eL~~yL-~~Lp~~~r~e~m~dyeehF~~a~~~GksE~EI~~~LG~P~eiA~ei~s~~~ 65 (195)
T COG4709 3 KTEFLNELEQYL-EGLPREERREIMYDYEEHFREAQEAGKSEEEIAKDLGDPKEIAAEILSERG 65 (195)
T ss_pred HHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHhhhhcCCCHHHHHHHhCCHHHHHHHHHHHcc
Confidence 456778899999 99999998866555421 13478999999999999988877766543
No 455
>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=41.88 E-value=20 Score=30.62 Aligned_cols=25 Identities=24% Similarity=0.308 Sum_probs=21.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
|+..|+|+.+|||..|||-+...++
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye~~GL 25 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLREGL 25 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5788999999999999998877654
No 456
>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=41.65 E-value=31 Score=25.74 Aligned_cols=24 Identities=17% Similarity=0.318 Sum_probs=18.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVA 479 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rA 479 (499)
++.+|+++.+|+|+.|+.+.++..
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 568899999999999998887743
No 457
>PRK03837 transcriptional regulator NanR; Provisional
Probab=41.65 E-value=36 Score=33.11 Aligned_cols=27 Identities=33% Similarity=0.457 Sum_probs=22.5
Q ss_pred CCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010835 454 ECL-TWEDISKRIGLSRERVRQVGLVALEKLK 484 (499)
Q Consensus 454 eg~-SleEIAe~LgIS~~rVrqi~~rALkKLR 484 (499)
+.+ +..+||+.||||+.+|| .||..|.
T Consensus 35 ~~Lp~E~~Lae~~gVSRt~VR----EAL~~L~ 62 (241)
T PRK03837 35 DQLPSERELMAFFGVGRPAVR----EALQALK 62 (241)
T ss_pred CCCCCHHHHHHHhCCCHHHHH----HHHHHHH
Confidence 557 88999999999999997 6666665
No 458
>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=41.54 E-value=20 Score=31.26 Aligned_cols=25 Identities=24% Similarity=0.404 Sum_probs=22.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
+|..|+|+.+|||+.|+|.+...++
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye~~gl 25 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEKEGL 25 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5788999999999999998887665
No 459
>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=41.53 E-value=20 Score=30.51 Aligned_cols=25 Identities=20% Similarity=0.335 Sum_probs=22.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
+|..|+|+.+|||..|+|.+...++
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gl 25 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDKIGL 25 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 4788999999999999999887665
No 460
>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=41.49 E-value=20 Score=30.50 Aligned_cols=25 Identities=20% Similarity=0.395 Sum_probs=21.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
|+..|+|+.+|||..|+|.+...++
T Consensus 1 m~i~eva~~~gvs~~tlR~ye~~Gl 25 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDHIGL 25 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5788999999999999999887654
No 461
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=41.48 E-value=35 Score=33.76 Aligned_cols=28 Identities=32% Similarity=0.349 Sum_probs=22.8
Q ss_pred CCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 454 ECL-TWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 454 eg~-SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
+.+ |-.++|+.||||+.+|| .|+..|..
T Consensus 31 ~~LpsE~eLa~~~gVSRtpVR----EAL~~L~~ 59 (257)
T PRK10225 31 ERLPPEREIAEMLDVTRTVVR----EALIMLEI 59 (257)
T ss_pred CcCcCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 557 68899999999999996 66666654
No 462
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=41.40 E-value=74 Score=27.35 Aligned_cols=38 Identities=11% Similarity=0.064 Sum_probs=28.2
Q ss_pred CHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010835 438 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 479 (499)
Q Consensus 438 ~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rA 479 (499)
+.++-.+|.... +.-|+..-|+.||||+++|.+.+.+.
T Consensus 3 ~~~~l~~~~av~----~~gSis~AA~~L~iS~stvs~~I~~L 40 (99)
T TIGR00637 3 DPRRVALLKAIA----RMGSISQAAKDAGISYKSAWDYIRAM 40 (99)
T ss_pred CHHHHHHHHHHH----HhCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 445555665554 66899999999999999997655443
No 463
>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=40.99 E-value=21 Score=30.56 Aligned_cols=25 Identities=32% Similarity=0.449 Sum_probs=21.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
++..|+|+.+|||..|+|.+...++
T Consensus 1 y~i~e~A~~~gvs~~tlR~Ye~~Gl 25 (99)
T cd04772 1 YRTVDLARAIGLSPQTVRNYESLGL 25 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 4678999999999999998876554
No 464
>COG5566 Uncharacterized conserved protein [Function unknown]
Probab=40.90 E-value=35 Score=31.04 Aligned_cols=33 Identities=15% Similarity=0.201 Sum_probs=27.6
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
++|+++.|+|+.+.+|..+|.+++.|.+..=|+
T Consensus 100 ~dG~n~~eLaKkYrlS~~~Iy~VIrr~~t~krh 132 (137)
T COG5566 100 FDGSNYVELAKKYRLSENHIYRVIRRTHTSKRH 132 (137)
T ss_pred cCCccHHHHHHHhcccHHHHHHHHHHHHHHhhc
Confidence 479999999999999999999998866654443
No 465
>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=40.82 E-value=52 Score=28.96 Aligned_cols=23 Identities=22% Similarity=0.371 Sum_probs=20.1
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Q 010835 455 CLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 455 g~SleEIAe~LgIS~~rVrqi~~ 477 (499)
+.|.+|||+.+|+++.+|++++.
T Consensus 25 ~~s~~eia~~~~i~~~~v~~il~ 47 (132)
T TIGR00738 25 PVSVKEIAERQGISRSYLEKILR 47 (132)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHH
Confidence 79999999999999999976554
No 466
>PF04963 Sigma54_CBD: Sigma-54 factor, core binding domain; InterPro: IPR007046 This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme []. The centre of this domain contains a very weak similarity to a helix-turn-helix motif, which may represent a DNA binding domain.; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent; PDB: 2K9L_A 2K9M_A.
Probab=40.69 E-value=9.5 Score=36.77 Aligned_cols=94 Identities=24% Similarity=0.316 Sum_probs=0.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhhccccccccccCCCCCCCCCCccccccccccCCCCCcchHHHHHHHHHHHHHHHhh
Q 010835 357 TPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVT 436 (499)
Q Consensus 357 ~pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~e~~~l~e~i~d~~~e~~Pee~ve~~el~~~L~~~L~~~ 436 (499)
..+.++||+.++++.++|..++...+.. +|. .+-...+.+.|.--+ ..
T Consensus 52 ~~~~~eia~~l~~~~~~v~~~l~~lQ~l------------------------------eP~-GigAr~l~EcLllQl-~~ 99 (194)
T PF04963_consen 52 TESLEEIAEELGVSEEEVEKALELLQSL------------------------------EPA-GIGARDLQECLLLQL-ER 99 (194)
T ss_dssp SS-HHHHHHHCTS-HHHHHHHHHHHHTT------------------------------SS---TTTS-TTHHHHHHH-HH
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHcC------------------------------CCC-ccCcCCHHHHHHHHH-hc
Q ss_pred CCHHHHHHHHHHhcC-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 010835 437 LGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKL 483 (499)
Q Consensus 437 L~~rER~VI~LryGL-d~eg~SleEIAe~LgIS~~rVrqi~~rALkKL 483 (499)
+++.....-.+...| +.....+..||+.+|+|.+.|+..+.. +++|
T Consensus 100 ~~~~~~~~~il~~~l~~l~~~~~~~ia~~l~~s~~~v~~~~~~-Ir~L 146 (194)
T PF04963_consen 100 KGPPDLAYRILENHLELLANKDYKKIAKKLGISEEEVQEAIEL-IRTL 146 (194)
T ss_dssp S-S--TTHHHHHHHHHHHHH----------------------------
T ss_pred cCCcHHHHHHHHHHHHHHHHhhhcccccccccccccccccccc-cccc
No 467
>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=40.46 E-value=21 Score=31.20 Aligned_cols=25 Identities=20% Similarity=0.298 Sum_probs=22.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
|+..|+|+.+|||..|+|.+...++
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye~~GL 25 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEEQGL 25 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCC
Confidence 5788999999999999999987654
No 468
>PHA02943 hypothetical protein; Provisional
Probab=40.44 E-value=46 Score=31.33 Aligned_cols=37 Identities=24% Similarity=0.353 Sum_probs=27.3
Q ss_pred CHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010835 438 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 477 (499)
Q Consensus 438 ~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~ 477 (499)
-++-.+|+++-- ..+.|..|||+.||+|-+.|+.++.
T Consensus 10 ~~R~~eILE~Lk---~G~~TtseIAkaLGlS~~qa~~~Ly 46 (165)
T PHA02943 10 HTRMIKTLRLLA---DGCKTTSRIANKLGVSHSMARNALY 46 (165)
T ss_pred HHHHHHHHHHHh---cCCccHHHHHHHHCCCHHHHHHHHH
Confidence 344455666543 3568899999999999999987654
No 469
>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=40.39 E-value=66 Score=26.21 Aligned_cols=49 Identities=18% Similarity=0.135 Sum_probs=32.9
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIG-----LSRERVRQVGLVALEKLK 484 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~Lg-----IS~~rVrqi~~rALkKLR 484 (499)
.|+++|..+|.+-+-=-++..|.++|.+.+- .+..++.+.+.+-+++|.
T Consensus 23 ~Lt~~e~~lL~~L~~~~~~~vs~~~l~~~lw~~~~~~~~~~l~~~I~rLRkkl~ 76 (95)
T cd00383 23 ELTPKEFELLELLARNPGRVLSREQLLEAVWGDDYDVDDRTVDVHISRLRKKLE 76 (95)
T ss_pred EeCHHHHHHHHHHHhCCCCcCCHHHHHHHhcCCCCCCCcccHHHHHHHHHHHhc
Confidence 5899999998875521245799999999884 455556555554444443
No 470
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=40.38 E-value=45 Score=33.77 Aligned_cols=38 Identities=24% Similarity=0.274 Sum_probs=27.0
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 439 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 439 ~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
+|...|+.+--- ....+..|+|+.||||..|||+-+..
T Consensus 17 eR~~~Il~~L~~--~~~vtv~eLa~~l~VS~~TIRRDL~~ 54 (269)
T PRK09802 17 ERREQIIQRLRQ--QGSVQVNDLSALYGVSTVTIRNDLAF 54 (269)
T ss_pred HHHHHHHHHHHH--cCCEeHHHHHHHHCCCHHHHHHHHHH
Confidence 455555544220 23589999999999999999876543
No 471
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, 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 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=40.26 E-value=20 Score=30.58 Aligned_cols=24 Identities=8% Similarity=0.163 Sum_probs=21.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVA 479 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rA 479 (499)
+|..|+|+.+|||..|++.+....
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye~~G 25 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDRLG 25 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCC
Confidence 688999999999999999987644
No 472
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=40.14 E-value=38 Score=33.47 Aligned_cols=28 Identities=32% Similarity=0.429 Sum_probs=22.9
Q ss_pred CCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 454 ECL-TWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 454 eg~-SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
+.+ +-.|||+.||||+.+|| .||+.|..
T Consensus 24 ~~LpsE~eLae~~gVSRtpVR----EAL~~Le~ 52 (253)
T PRK10421 24 MKLPAERQLAMQLGVSRNSLR----EALAKLVS 52 (253)
T ss_pred CcCCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 557 68899999999999996 67776654
No 473
>PRK02866 cyanate hydratase; Validated
Probab=39.45 E-value=45 Score=31.06 Aligned_cols=33 Identities=36% Similarity=0.472 Sum_probs=27.6
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 443 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 443 ~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
.++..+- ..|+|+++||+.+|+|+.+|..+...
T Consensus 9 ~Ll~AK~---~kGLTw~~IA~~iG~S~v~vaaa~lG 41 (147)
T PRK02866 9 KILAAKK---EKGLTWADIAEAIGLSEVWVTAALLG 41 (147)
T ss_pred HHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHhC
Confidence 3566666 68999999999999999999887754
No 474
>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=39.21 E-value=36 Score=23.54 Aligned_cols=23 Identities=22% Similarity=0.486 Sum_probs=18.4
Q ss_pred CHHHHHHHhCCCHHHHHHHHHhh
Q 010835 359 SVDRIAEYLNMSQKKVRNATEAI 381 (499)
Q Consensus 359 t~eEIA~~Lgis~e~v~~~l~~~ 381 (499)
+-+|||+.+|++.+.|..++...
T Consensus 4 tr~diA~~lG~t~ETVSR~l~~l 26 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVSRILKKL 26 (32)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CHHHHHHHhCCcHHHHHHHHHHH
Confidence 56799999999999999887754
No 475
>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=38.74 E-value=65 Score=26.82 Aligned_cols=30 Identities=30% Similarity=0.397 Sum_probs=22.4
Q ss_pred HcCCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 010835 353 EKGVTPSVDRIAEYLNMSQKKVRNATEAIG 382 (499)
Q Consensus 353 ~~gr~pt~eEIA~~Lgis~e~v~~~l~~~~ 382 (499)
..|++.+...||..+|.+.++|..++....
T Consensus 34 A~G~PVt~~~LA~a~g~~~e~v~~~L~~~p 63 (77)
T PF12324_consen 34 AKGQPVTVEQLAAALGWPVEEVRAALAAMP 63 (77)
T ss_dssp TTTS-B-HHHHHHHHT--HHHHHHHHHH-T
T ss_pred HcCCCcCHHHHHHHHCCCHHHHHHHHHhCC
Confidence 459999999999999999999999988763
No 476
>PHA02591 hypothetical protein; Provisional
Probab=38.74 E-value=76 Score=26.57 Aligned_cols=23 Identities=39% Similarity=0.481 Sum_probs=20.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Q 010835 357 TPSVDRIAEYLNMSQKKVRNATE 379 (499)
Q Consensus 357 ~pt~eEIA~~Lgis~e~v~~~l~ 379 (499)
.-|.++||+.||++.+.|.+.+.
T Consensus 59 GlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 59 GFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHh
Confidence 46889999999999999988764
No 477
>PHA02535 P terminase ATPase subunit; Provisional
Probab=38.60 E-value=36 Score=38.43 Aligned_cols=33 Identities=21% Similarity=0.298 Sum_probs=27.3
Q ss_pred HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 442 REIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 442 R~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
++.+.|+. +|+|..|||+.|||++.||.++..+
T Consensus 9 ~~Av~Ly~----~G~sv~eIA~~LGv~~~Tl~~W~kr 41 (581)
T PHA02535 9 RAAKFLYW----QGWTVAEIAEELGLKSRTIYSWKER 41 (581)
T ss_pred HHHHHHHH----cCCCHHHHHHHhCCChhHHHHHhcc
Confidence 34456665 6999999999999999999988665
No 478
>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=38.53 E-value=42 Score=24.58 Aligned_cols=27 Identities=26% Similarity=0.261 Sum_probs=22.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHhh
Q 010835 355 GVTPSVDRIAEYLNMSQKKVRNATEAI 381 (499)
Q Consensus 355 gr~pt~eEIA~~Lgis~e~v~~~l~~~ 381 (499)
..+-|..|||+.+|++...|......+
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~~~~a 44 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRILKRA 44 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHHHHHH
Confidence 456789999999999999999876643
No 479
>cd00131 PAX Paired Box domain
Probab=38.40 E-value=2.9e+02 Score=24.71 Aligned_cols=30 Identities=17% Similarity=-0.002 Sum_probs=24.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHhhcccccc
Q 010835 358 PSVDRIAEYLNMSQKKVRNATEAIGKVFSL 387 (499)
Q Consensus 358 pt~eEIA~~Lgis~e~v~~~l~~~~~~~SL 387 (499)
.+..+||+.+|++...|..+.......=++
T Consensus 34 ~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v 63 (128)
T cd00131 34 IRPCDISRQLRVSHGCVSKILNRYYETGSI 63 (128)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHcCCc
Confidence 478899999999999999998877544333
No 480
>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=38.37 E-value=23 Score=31.62 Aligned_cols=25 Identities=24% Similarity=0.302 Sum_probs=22.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
|+..|+|+.+|||..|+|-+...++
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~~GL 25 (127)
T TIGR02044 1 MNIGQVAKLTGLSSKMIRYYEEKGL 25 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5788999999999999999887654
No 481
>PF10654 DUF2481: Protein of unknown function (DUF2481) ; InterPro: IPR018916 This entry is represented by Bacteriophage A500, Gp59. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=38.34 E-value=1e+02 Score=27.67 Aligned_cols=41 Identities=22% Similarity=0.160 Sum_probs=30.7
Q ss_pred HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010835 442 REIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA 486 (499)
Q Consensus 442 R~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~ 486 (499)
++.+.||. -|+|.-.||+.++||+++|-+.-.+-.+--.+.
T Consensus 71 ~Efi~LR~----AGlt~~aIAd~F~iS~s~~~nft~~n~~eYyr~ 111 (126)
T PF10654_consen 71 REFIELRH----AGLTCYAIADYFKISKSTVFNFTQNNKKEYYRI 111 (126)
T ss_pred HHHHHHHh----cCCChHHHHHHHhHHHHHHHHHHHHhHHHHHHH
Confidence 34556665 799999999999999999988775544444333
No 482
>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=38.29 E-value=23 Score=31.53 Aligned_cols=25 Identities=28% Similarity=0.365 Sum_probs=21.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
|+..|+|+.+|||..|+|.+...++
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~~GL 25 (126)
T cd04783 1 LTIGELAKAAGVNVETIRYYQRRGL 25 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5788999999999999998877654
No 483
>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=38.15 E-value=23 Score=31.62 Aligned_cols=26 Identities=23% Similarity=0.285 Sum_probs=22.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVALE 481 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rALk 481 (499)
||..|+|+.+|||..|+|.+....+-
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~~GLl 26 (127)
T cd01108 1 MNIGEAAKLTGLSAKMIRYYEEIGLI 26 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57889999999999999988876553
No 484
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). 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 spe
Probab=37.95 E-value=24 Score=31.74 Aligned_cols=25 Identities=12% Similarity=0.104 Sum_probs=22.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
++..|+|+.+|||+.|+|.+..+.+
T Consensus 2 ysI~eVA~~~GVs~~TLR~wE~~GL 26 (120)
T cd04767 2 YPIGVVAELLNIHPETLRIWERHGL 26 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 6889999999999999998877654
No 485
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=37.79 E-value=24 Score=29.34 Aligned_cols=33 Identities=21% Similarity=0.195 Sum_probs=23.8
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 453 KECLTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 453 ~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
..|.|+..||...|++..|+++.+.+.--+--+
T Consensus 13 krG~sL~~lsr~~Gl~~~tl~nal~r~~pk~E~ 45 (78)
T PF13693_consen 13 KRGTSLAALSREAGLSSSTLRNALRRPWPKGER 45 (78)
T ss_dssp TTS--HHHHHHHHSS-HHHHHHTTTSS-HHHHH
T ss_pred HcCCCHHHHHHHcCCCHHHHHHHHcCCChHHHH
Confidence 478999999999999999999888776555433
No 486
>PRK02277 orotate phosphoribosyltransferase-like protein; Provisional
Probab=37.69 E-value=29 Score=33.54 Aligned_cols=35 Identities=20% Similarity=0.139 Sum_probs=29.1
Q ss_pred HHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 010835 444 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEK 482 (499)
Q Consensus 444 VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkK 482 (499)
...|+- .|++..|||++||||++|+..+..++-.+
T Consensus 11 a~~l~~----~~~~~~~ia~el~vs~~t~~~l~~~~~~~ 45 (200)
T PRK02277 11 AAELKN----KGLSTGEIADELNVSRETATWLLTRAKKL 45 (200)
T ss_pred HHHHHH----cCCChhhhhhhhcchHHHHHHHHhcccCC
Confidence 445553 78999999999999999999999887643
No 487
>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=37.68 E-value=24 Score=30.91 Aligned_cols=26 Identities=12% Similarity=0.219 Sum_probs=22.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVALE 481 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rALk 481 (499)
||..|+|+.+|||+.|+|-+...++-
T Consensus 1 ~~ige~a~~~gvs~~tLryYe~~GLi 26 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEEKGLL 26 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999998876653
No 488
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=37.56 E-value=82 Score=31.78 Aligned_cols=50 Identities=10% Similarity=0.136 Sum_probs=37.8
Q ss_pred HHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010835 429 VNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 487 (499)
Q Consensus 429 L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rALkKLR~~L 487 (499)
-..+| ..++-++-.+|..-. +.-|+..-|+.||+|+.+|++. +++|.+.+
T Consensus 7 ~~~~~-~~~~l~~L~~f~~va----~~gs~s~AA~~L~iSQpavS~~----I~~LE~~l 56 (311)
T PRK10086 7 RNRLL-NGWQLSKLHTFEVAA----RHQSFALAADELSLTPSAVSHR----INQLEEEL 56 (311)
T ss_pred HHhhh-cCCcHHHHHHHHHHH----HcCCHHHHHHHHCCCHHHHHHH----HHHHHHHh
Confidence 34456 788888888877765 7789999999999999999755 44555443
No 489
>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=37.56 E-value=71 Score=24.89 Aligned_cols=34 Identities=26% Similarity=0.297 Sum_probs=26.7
Q ss_pred HHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhh
Q 010835 348 KLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI 381 (499)
Q Consensus 348 ~~~L~~~gr~pt~eEIA~~Lgis~e~v~~~l~~~ 381 (499)
.-.+.+.+..++..+||+.||+++..|.+++...
T Consensus 13 Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L 46 (60)
T PF01325_consen 13 IYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRL 46 (60)
T ss_dssp HHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHH
Confidence 3344556778889999999999999999988765
No 490
>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=36.91 E-value=35 Score=33.22 Aligned_cols=26 Identities=35% Similarity=0.418 Sum_probs=21.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVALEKLKH 485 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rALkKLR~ 485 (499)
-|-.|+|+++|||+.||| +|+..|..
T Consensus 25 PsE~eLa~~~gVSR~TVR----~Al~~L~~ 50 (233)
T TIGR02404 25 PSEHELMDQYGASRETVR----KALNLLTE 50 (233)
T ss_pred cCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 478999999999999997 55655543
No 491
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. 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, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.
Probab=36.87 E-value=32 Score=27.20 Aligned_cols=26 Identities=15% Similarity=0.248 Sum_probs=17.8
Q ss_pred CCCCHHHHHHHH-----CCCHHHHHHHHHHH
Q 010835 454 ECLTWEDISKRI-----GLSRERVRQVGLVA 479 (499)
Q Consensus 454 eg~SleEIAe~L-----gIS~~rVrqi~~rA 479 (499)
...|+.+|+..| +||..||++.+..+
T Consensus 12 p~~s~~~i~~~l~~~~~~vS~~TI~r~L~~~ 42 (72)
T PF01498_consen 12 PRISAREIAQELQEAGISVSKSTIRRRLREA 42 (72)
T ss_dssp ----HHHHHHHT---T--S-HHHHHHHHHHT
T ss_pred CCCCHHHHHHHHHHccCCcCHHHHHHHHHHc
Confidence 358999999998 89999999888764
No 492
>TIGR00673 cynS cyanate hydratase. Alternate names include cyanate lyase, cyanase and cyanate hydrolase.
Probab=36.85 E-value=54 Score=30.66 Aligned_cols=34 Identities=24% Similarity=0.257 Sum_probs=27.7
Q ss_pred HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 442 REIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 442 R~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
..++..+- ..|+|+++||+.+|+|+..|-.+...
T Consensus 11 ~~Ll~AK~---~KGLTwe~IAe~iG~sevwvaaa~lG 44 (150)
T TIGR00673 11 DALLESKK---KKGLTFADIADGLGLAEVFVAAALYG 44 (150)
T ss_pred HHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHhC
Confidence 34666666 68999999999999999999877654
No 493
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=36.77 E-value=72 Score=24.37 Aligned_cols=24 Identities=13% Similarity=0.102 Sum_probs=19.6
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 455 CLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 455 g~SleEIAe~LgIS~~rVrqi~~r 478 (499)
.-++...|+.||+|+++|++.+.+
T Consensus 13 ~gs~~~AA~~l~is~~~vs~~i~~ 36 (60)
T PF00126_consen 13 TGSISAAAEELGISQSAVSRQIKQ 36 (60)
T ss_dssp HSSHHHHHHHCTSSHHHHHHHHHH
T ss_pred hCCHHHHHHHhhccchHHHHHHHH
Confidence 359999999999999999755443
No 494
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=36.75 E-value=96 Score=25.50 Aligned_cols=40 Identities=20% Similarity=0.286 Sum_probs=32.8
Q ss_pred hCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010835 436 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 479 (499)
Q Consensus 436 ~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rA 479 (499)
.|+-.++-++.+-. .+.|++|+-+..|++++.+...+.+-
T Consensus 3 klt~~~~IL~~ls~----~c~TLeeL~ekTgi~k~~LlV~LsrL 42 (72)
T PF05584_consen 3 KLTVTQKILIILSK----RCCTLEELEEKTGISKNTLLVYLSRL 42 (72)
T ss_pred hhhHHHHHHHHHHh----ccCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 46667777787776 38999999999999999998777653
No 495
>PF04814 HNF-1_N: Hepatocyte nuclear factor 1 (HNF-1), N terminus; InterPro: IPR006899 This domain consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerisation sequence [] and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3) [].; GO: 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2GYP_B 1IC8_B 2H8R_B 1G2Y_D 1F93_H 1G39_D 1G2Z_B 1JB6_B.
Probab=36.72 E-value=27 Score=33.60 Aligned_cols=54 Identities=17% Similarity=0.204 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHhhCCHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010835 424 ALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 480 (499)
Q Consensus 424 el~~~L~~~L~~~L~~rER~VI~LryGLd~eg~SleEIAe~LgIS~~rVrqi~~rAL 480 (499)
+....++++| .+=|-+=++.|..|.+ ....+..+|++..|||.+.|+|+++++.
T Consensus 103 ~~~~~Ve~ll-r~D~~~VkeeIK~fl~--~h~IsQ~~V~q~TGisQS~lSq~L~kGt 156 (180)
T PF04814_consen 103 EQRAEVEELL-RRDPWRVKEEIKAFLQ--QHNISQREVVQVTGISQSHLSQHLNKGT 156 (180)
T ss_dssp HHHHHHHHCT-TS-HHHHHHHHHHHHH--HCT--CHHHHHHHT--HHHHHHHHCTB-
T ss_pred hhHHHHHHHH-hhCHHHHHHHHHHHHH--HcCCcHHHHHHHhhhhHHHHHHHHHcCC
Confidence 4446677766 5556667778888774 5689999999999999999999987664
No 496
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=36.62 E-value=4.4e+02 Score=26.25 Aligned_cols=29 Identities=14% Similarity=0.283 Sum_probs=24.6
Q ss_pred HcCCCCCHHHHHHHhCCCHHHHHHHHHhh
Q 010835 353 EKGVTPSVDRIAEYLNMSQKKVRNATEAI 381 (499)
Q Consensus 353 ~~gr~pt~eEIA~~Lgis~e~v~~~l~~~ 381 (499)
+.|--.|..++|-.||+++..|.+.....
T Consensus 101 ~QgglLT~~Dla~LL~~S~~TI~~~i~~y 129 (220)
T PF07900_consen 101 DQGGLLTQEDLAMLLGISPRTISKDIKEY 129 (220)
T ss_pred HcCCcccHHHHHHHHCCCHHHHHHHHHHH
Confidence 45778899999999999999998876655
No 497
>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=36.59 E-value=33 Score=27.21 Aligned_cols=25 Identities=16% Similarity=0.275 Sum_probs=19.0
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 010835 454 ECLTWEDISKRIGLSRERVRQVGLV 478 (499)
Q Consensus 454 eg~SleEIAe~LgIS~~rVrqi~~r 478 (499)
...|+.|||..||+|+.+|+..+..
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 5689999999999999999876653
No 498
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=36.59 E-value=38 Score=26.71 Aligned_cols=19 Identities=26% Similarity=0.358 Sum_probs=17.3
Q ss_pred CHHHHHHHHCCCHHHHHHH
Q 010835 457 TWEDISKRIGLSRERVRQV 475 (499)
Q Consensus 457 SleEIAe~LgIS~~rVrqi 475 (499)
+...+|+.||||+.+|.++
T Consensus 11 ~~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 11 GQSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp SHHHHHHHHTS-HHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHh
Confidence 7889999999999999999
No 499
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal 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=36.15 E-value=27 Score=30.75 Aligned_cols=26 Identities=19% Similarity=0.356 Sum_probs=22.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010835 456 LTWEDISKRIGLSRERVRQVGLVALE 481 (499)
Q Consensus 456 ~SleEIAe~LgIS~~rVrqi~~rALk 481 (499)
||..|+|+.+|||..|+|-+...++-
T Consensus 1 ~~I~eva~~~gvs~~tLRyYe~~GLl 26 (123)
T cd04770 1 MKIGELAKAAGVSPDTIRYYERIGLL 26 (123)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57889999999999999988776553
No 500
>TIGR00331 hrcA heat shock gene repressor HrcA. In Bacillus subtilis, hrcA is the first gene of the dnaK operon and so is itself a heat shock gene.
Probab=35.90 E-value=56 Score=34.36 Aligned_cols=40 Identities=23% Similarity=0.375 Sum_probs=29.7
Q ss_pred CHHHHHHHHH---HhcC-CCCCCCHHHHHHH--HCCCHHHHHHHHHH
Q 010835 438 GEREREIIRL---YYGL-DKECLTWEDISKR--IGLSRERVRQVGLV 478 (499)
Q Consensus 438 ~~rER~VI~L---ryGL-d~eg~SleEIAe~--LgIS~~rVrqi~~r 478 (499)
++|++.|+.. .| + ..++.+.++|++. +|+|..|||+-+..
T Consensus 1 ~~R~~~il~aIV~~~-l~~~~pv~s~~l~~~~~~~vS~aTiR~d~~~ 46 (337)
T TIGR00331 1 TERQRKILKAIVEEY-IKTGQPVGSKTLLEKYNLGLSSATIRNDMAD 46 (337)
T ss_pred ChHHHHHHHHHHHHH-HhcCCCcCHHHHHhhcCCCCChHHHHHHHHH
Confidence 4677777741 11 1 2578999999999 99999999977654
Done!