Query 008352
Match_columns 569
No_of_seqs 411 out of 2351
Neff 5.8
Searched_HMMs 46136
Date Thu Mar 28 22:44:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008352.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008352hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK07598 RNA polymerase sigma 100.0 1.3E-64 2.9E-69 539.8 38.6 315 253-568 58-414 (415)
2 PRK07406 RNA polymerase sigma 100.0 8.8E-62 1.9E-66 514.4 38.6 312 253-565 61-372 (373)
3 PRK05949 RNA polymerase sigma 100.0 2.8E-61 6.1E-66 504.1 39.1 311 253-566 16-326 (327)
4 TIGR02997 Sig70-cyanoRpoD RNA 100.0 1.6E-60 3.6E-65 492.4 37.0 298 255-553 1-298 (298)
5 PRK07405 RNA polymerase sigma 100.0 3.1E-60 6.7E-65 494.5 38.5 311 253-566 6-316 (317)
6 PRK05901 RNA polymerase sigma 100.0 6E-59 1.3E-63 507.2 33.6 302 252-566 208-509 (509)
7 COG0568 RpoD DNA-directed RNA 100.0 1E-58 2.3E-63 480.9 31.9 314 253-566 7-342 (342)
8 PRK07921 RNA polymerase sigma 100.0 7.2E-58 1.6E-62 477.6 36.0 300 253-565 24-323 (324)
9 PRK09210 RNA polymerase sigma 100.0 2.4E-54 5.2E-59 458.5 33.3 276 251-566 92-367 (367)
10 PRK05658 RNA polymerase sigma 100.0 2.3E-51 5E-56 461.8 31.2 239 328-566 380-618 (619)
11 TIGR02393 RpoD_Cterm RNA polym 100.0 1.3E-47 2.7E-52 384.0 28.8 238 329-566 1-238 (238)
12 PRK05657 RNA polymerase sigma 100.0 1.4E-44 3E-49 378.2 33.3 272 253-564 51-322 (325)
13 PRK07500 rpoH2 RNA polymerase 100.0 2.4E-44 5.3E-49 370.7 32.8 264 255-560 6-281 (289)
14 PRK06596 RNA polymerase factor 100.0 2.6E-44 5.7E-49 369.6 32.7 262 253-558 12-282 (284)
15 TIGR02392 rpoH_proteo alternat 100.0 1.2E-43 2.5E-48 362.1 31.8 258 256-557 2-269 (270)
16 PRK07122 RNA polymerase sigma 100.0 4.8E-43 1E-47 356.8 28.5 220 328-556 40-263 (264)
17 PRK07408 RNA polymerase sigma 100.0 2.2E-41 4.7E-46 343.0 30.4 228 325-559 22-254 (256)
18 TIGR02394 rpoS_proteo RNA poly 100.0 8.5E-41 1.8E-45 343.4 33.5 272 250-561 8-279 (285)
19 TIGR02850 spore_sigG RNA polym 100.0 8.7E-40 1.9E-44 330.5 31.0 243 264-556 10-254 (254)
20 PRK05911 RNA polymerase sigma 100.0 1.5E-39 3.2E-44 329.9 28.9 227 325-558 20-255 (257)
21 PRK08215 sporulation sigma fac 100.0 1.9E-38 4.2E-43 321.3 31.6 243 264-556 13-257 (258)
22 COG1191 FliA DNA-directed RNA 100.0 2.1E-38 4.6E-43 318.1 28.9 223 325-558 21-246 (247)
23 PRK06288 RNA polymerase sigma 100.0 4.4E-37 9.5E-42 313.1 30.6 249 264-558 6-262 (268)
24 TIGR02941 Sigma_B RNA polymera 100.0 1.9E-36 4.1E-41 305.9 31.0 244 268-556 8-253 (255)
25 TIGR02885 spore_sigF RNA polym 100.0 1.2E-36 2.7E-41 302.6 28.0 223 324-556 7-231 (231)
26 TIGR02980 SigBFG RNA polymeras 100.0 5.5E-36 1.2E-40 296.9 28.4 221 327-556 2-226 (227)
27 PRK07670 RNA polymerase sigma 100.0 2.8E-35 6.1E-40 297.0 30.9 225 326-557 20-250 (251)
28 PRK08583 RNA polymerase sigma 100.0 1.6E-34 3.4E-39 292.2 30.9 243 268-558 8-255 (257)
29 PRK05572 sporulation sigma fac 100.0 1.9E-34 4E-39 291.2 30.9 244 262-557 6-251 (252)
30 TIGR02479 FliA_WhiG RNA polyme 100.0 1.2E-34 2.5E-39 287.4 27.0 217 333-556 1-223 (224)
31 PRK12427 flagellar biosynthesi 100.0 2.5E-34 5.4E-39 287.5 28.2 208 331-555 18-230 (231)
32 PRK06986 fliA flagellar biosyn 100.0 3.4E-33 7.3E-38 279.2 28.5 225 325-558 5-234 (236)
33 PRK05803 sporulation sigma fac 100.0 3.6E-28 7.8E-33 242.6 25.8 210 256-558 17-229 (233)
34 TIGR02846 spore_sigmaK RNA pol 99.9 1.2E-24 2.6E-29 216.6 24.6 179 325-556 45-226 (227)
35 PRK08301 sporulation sigma fac 99.9 2.3E-24 5E-29 214.9 25.1 180 325-557 49-231 (234)
36 TIGR02835 spore_sigmaE RNA pol 99.9 1.3E-23 2.9E-28 210.1 25.0 181 325-558 49-232 (234)
37 PRK08295 RNA polymerase factor 99.9 8.3E-23 1.8E-27 198.9 22.3 195 314-560 9-206 (208)
38 PRK05602 RNA polymerase sigma 99.9 2.7E-22 5.9E-27 192.7 20.7 176 314-561 5-181 (186)
39 TIGR02859 spore_sigH RNA polym 99.9 6.1E-22 1.3E-26 191.2 20.9 191 314-556 4-197 (198)
40 PRK12513 RNA polymerase sigma 99.9 5.6E-22 1.2E-26 191.7 19.0 181 314-561 11-192 (194)
41 PRK09646 RNA polymerase sigma 99.9 8.9E-22 1.9E-26 190.8 20.4 175 316-558 17-192 (194)
42 TIGR02948 SigW_bacill RNA poly 99.9 1E-21 2.2E-26 187.8 20.3 179 317-557 6-185 (187)
43 PRK09641 RNA polymerase sigma 99.9 1.4E-21 3.1E-26 186.7 20.7 180 316-557 5-185 (187)
44 PRK09648 RNA polymerase sigma 99.9 2.3E-21 4.9E-26 186.7 21.1 171 318-557 13-188 (189)
45 TIGR02952 Sig70_famx2 RNA poly 99.9 4.5E-21 9.7E-26 180.3 19.6 163 325-556 8-170 (170)
46 PRK09652 RNA polymerase sigma 99.9 6.2E-21 1.3E-25 180.3 20.0 172 324-557 6-177 (182)
47 PRK13919 putative RNA polymera 99.9 5.7E-21 1.2E-25 183.1 19.9 176 315-558 9-185 (186)
48 PRK12519 RNA polymerase sigma 99.9 4.6E-21 1E-25 185.1 19.4 174 316-557 16-190 (194)
49 PRK12514 RNA polymerase sigma 99.9 7.1E-21 1.5E-25 181.5 20.1 173 315-557 5-178 (179)
50 TIGR02939 RpoE_Sigma70 RNA pol 99.9 1E-20 2.3E-25 181.2 20.5 181 315-557 6-187 (190)
51 PRK06759 RNA polymerase factor 99.9 4.9E-21 1.1E-25 177.7 17.6 151 327-555 3-153 (154)
52 PRK06811 RNA polymerase factor 99.9 1E-20 2.2E-25 182.8 20.4 174 314-557 3-180 (189)
53 PRK11922 RNA polymerase sigma 99.9 9.7E-21 2.1E-25 189.0 20.8 173 325-558 27-199 (231)
54 PRK12524 RNA polymerase sigma 99.9 1.3E-20 2.8E-25 182.9 20.8 177 314-560 11-188 (196)
55 PRK12537 RNA polymerase sigma 99.9 1.3E-20 2.8E-25 180.7 19.8 172 315-556 9-181 (182)
56 PRK12538 RNA polymerase sigma 99.9 1.2E-20 2.5E-25 189.3 20.1 174 315-560 49-223 (233)
57 PRK11923 algU RNA polymerase s 99.9 2.4E-20 5.2E-25 180.0 21.2 180 316-557 7-187 (193)
58 PRK12534 RNA polymerase sigma 99.9 2.1E-20 4.5E-25 179.5 19.4 173 317-557 13-186 (187)
59 PRK09640 RNA polymerase sigma 99.9 1E-20 2.2E-25 182.4 17.1 173 313-557 7-183 (188)
60 TIGR02984 Sig-70_plancto1 RNA 99.9 5.9E-20 1.3E-24 175.6 21.5 180 325-556 4-188 (189)
61 PRK12515 RNA polymerase sigma 99.9 5.4E-20 1.2E-24 177.3 20.9 177 314-561 7-184 (189)
62 PRK12526 RNA polymerase sigma 99.9 4.9E-20 1.1E-24 180.7 20.7 171 324-559 34-204 (206)
63 PRK12542 RNA polymerase sigma 99.9 2.3E-20 5E-25 179.3 18.0 175 324-565 5-179 (185)
64 PRK11924 RNA polymerase sigma 99.9 5.4E-20 1.2E-24 173.4 20.0 168 324-559 9-176 (179)
65 PRK09643 RNA polymerase sigma 99.8 1E-19 2.2E-24 176.5 20.5 171 315-558 13-184 (192)
66 TIGR02954 Sig70_famx3 RNA poly 99.8 9.2E-20 2E-24 172.3 19.1 167 314-557 1-168 (169)
67 PRK09638 RNA polymerase sigma 99.8 6.8E-20 1.5E-24 173.9 18.2 172 314-557 3-175 (176)
68 TIGR02937 sigma70-ECF RNA poly 99.8 1.6E-19 3.4E-24 163.5 19.0 157 329-556 2-158 (158)
69 PRK12543 RNA polymerase sigma 99.8 1.1E-19 2.4E-24 173.8 18.8 165 325-559 4-168 (179)
70 TIGR02985 Sig70_bacteroi1 RNA 99.8 8.1E-20 1.8E-24 169.0 17.1 160 329-556 2-161 (161)
71 PRK12531 RNA polymerase sigma 99.8 1.1E-19 2.4E-24 176.2 18.7 176 319-560 17-193 (194)
72 PRK09645 RNA polymerase sigma 99.8 2.1E-19 4.6E-24 170.3 19.3 165 325-560 6-170 (173)
73 PRK12536 RNA polymerase sigma 99.8 1.7E-19 3.6E-24 173.0 17.7 169 318-559 10-180 (181)
74 PRK12522 RNA polymerase sigma 99.8 3.1E-19 6.8E-24 169.5 19.3 167 328-558 3-169 (173)
75 TIGR03001 Sig-70_gmx1 RNA poly 99.8 3.4E-19 7.4E-24 180.0 20.6 180 313-561 23-214 (244)
76 PRK12520 RNA polymerase sigma 99.8 2.3E-19 5.1E-24 173.2 18.6 182 329-561 3-184 (191)
77 PRK09415 RNA polymerase factor 99.8 3.4E-19 7.3E-24 170.7 19.3 164 326-558 14-177 (179)
78 TIGR02989 Sig-70_gvs1 RNA poly 99.8 2.1E-19 4.5E-24 167.4 17.2 158 329-556 2-159 (159)
79 PRK12539 RNA polymerase sigma 99.8 4.1E-19 8.9E-24 170.7 19.4 170 316-559 8-182 (184)
80 TIGR02999 Sig-70_X6 RNA polyme 99.8 5.4E-19 1.2E-23 168.8 18.8 171 317-556 5-182 (183)
81 PRK09649 RNA polymerase sigma 99.8 7E-19 1.5E-23 169.7 17.9 170 318-561 13-183 (185)
82 PRK12533 RNA polymerase sigma 99.8 1.6E-18 3.4E-23 172.1 20.9 171 325-559 15-185 (216)
83 PRK12529 RNA polymerase sigma 99.8 9.2E-19 2E-23 167.7 18.5 166 324-557 9-176 (178)
84 PRK12512 RNA polymerase sigma 99.8 1.2E-18 2.7E-23 166.8 19.4 166 319-559 12-182 (184)
85 PRK12518 RNA polymerase sigma 99.8 8.6E-19 1.9E-23 166.2 17.9 166 324-560 7-172 (175)
86 COG1595 RpoE DNA-directed RNA 99.8 2.3E-18 5E-23 165.4 20.6 170 322-559 9-178 (182)
87 PRK09642 RNA polymerase sigma 99.8 8.5E-19 1.8E-23 164.1 16.8 157 335-560 2-158 (160)
88 TIGR02947 SigH_actino RNA poly 99.8 6.2E-19 1.3E-23 170.5 16.3 172 327-558 10-181 (193)
89 PRK12516 RNA polymerase sigma 99.8 1.1E-18 2.5E-23 168.8 18.1 162 325-560 7-168 (187)
90 PRK09644 RNA polymerase sigma 99.8 1.9E-18 4.2E-23 162.9 17.8 158 330-560 3-160 (165)
91 TIGR02983 SigE-fam_strep RNA p 99.8 2.1E-18 4.6E-23 161.6 17.5 158 325-558 3-160 (162)
92 PRK12523 RNA polymerase sigma 99.8 1.9E-18 4E-23 164.2 17.3 162 326-558 8-169 (172)
93 PRK09647 RNA polymerase sigma 99.8 4.1E-18 9E-23 167.3 20.3 165 326-560 26-190 (203)
94 PRK12528 RNA polymerase sigma 99.8 4.4E-18 9.5E-23 159.6 18.1 157 328-555 4-160 (161)
95 PRK12545 RNA polymerase sigma 99.8 5.8E-18 1.2E-22 165.5 18.9 181 332-561 12-192 (201)
96 TIGR02895 spore_sigI RNA polym 99.8 9.4E-18 2E-22 166.8 20.6 117 323-439 4-125 (218)
97 PRK12547 RNA polymerase sigma 99.8 6.7E-18 1.4E-22 159.4 18.6 159 327-559 5-163 (164)
98 PRK12532 RNA polymerase sigma 99.8 6.8E-18 1.5E-22 163.5 18.7 180 331-560 8-188 (195)
99 TIGR02943 Sig70_famx1 RNA poly 99.8 6.2E-18 1.4E-22 163.6 18.2 178 331-559 5-182 (188)
100 PRK12541 RNA polymerase sigma 99.8 8.6E-18 1.9E-22 157.6 18.6 157 326-555 3-159 (161)
101 PRK12530 RNA polymerase sigma 99.8 7.9E-18 1.7E-22 162.9 18.8 176 331-559 10-185 (189)
102 PRK12544 RNA polymerase sigma 99.8 1.1E-17 2.4E-22 164.7 19.9 180 330-559 20-199 (206)
103 PRK09639 RNA polymerase sigma 99.8 1.1E-17 2.3E-22 157.2 18.9 160 327-558 2-161 (166)
104 PRK08241 RNA polymerase factor 99.8 9.5E-18 2.1E-22 176.0 20.4 186 318-554 8-199 (339)
105 PRK12535 RNA polymerase sigma 99.8 1.1E-17 2.5E-22 163.1 19.3 169 319-559 15-184 (196)
106 TIGR02960 SigX5 RNA polymerase 99.8 1.2E-17 2.6E-22 173.8 20.3 183 325-558 2-192 (324)
107 PRK07037 extracytoplasmic-func 99.8 2.1E-17 4.6E-22 155.0 18.5 159 332-559 2-160 (163)
108 TIGR02950 SigM_subfam RNA poly 99.8 5.6E-18 1.2E-22 157.0 14.3 152 335-556 2-153 (154)
109 PRK12540 RNA polymerase sigma 99.8 2.1E-17 4.5E-22 159.4 18.6 160 328-561 5-164 (182)
110 PRK12527 RNA polymerase sigma 99.8 1.9E-17 4.1E-22 155.0 17.6 155 335-559 2-156 (159)
111 PRK09637 RNA polymerase sigma 99.8 4.5E-17 9.7E-22 156.8 18.9 154 330-558 3-156 (181)
112 PRK09651 RNA polymerase sigma 99.8 3.9E-17 8.4E-22 155.5 18.2 164 326-560 8-171 (172)
113 PRK12517 RNA polymerase sigma 99.8 3.6E-17 7.8E-22 158.4 18.1 161 324-559 19-179 (188)
114 TIGR02959 SigZ RNA polymerase 99.7 7.3E-17 1.6E-21 153.5 17.6 148 335-557 2-149 (170)
115 PRK12546 RNA polymerase sigma 99.7 8.9E-17 1.9E-21 156.0 18.4 156 328-558 8-163 (188)
116 PRK12511 RNA polymerase sigma 99.7 6.7E-17 1.5E-21 155.9 17.1 157 330-559 6-162 (182)
117 PRK12525 RNA polymerase sigma 99.7 2.1E-16 4.5E-21 149.8 18.6 160 327-557 8-167 (168)
118 PRK09047 RNA polymerase factor 99.7 3.4E-16 7.3E-21 146.1 16.4 156 350-561 2-159 (161)
119 PRK09636 RNA polymerase sigma 99.7 5.1E-16 1.1E-20 160.3 17.8 160 328-557 4-164 (293)
120 PRK06704 RNA polymerase factor 99.7 2.7E-15 5.8E-20 150.4 18.2 158 319-558 9-166 (228)
121 TIGR02957 SigX4 RNA polymerase 99.7 3E-15 6.6E-20 153.9 17.4 156 332-557 1-157 (281)
122 PRK09635 sigI RNA polymerase s 99.6 5.7E-15 1.2E-19 152.9 18.1 161 328-556 5-166 (290)
123 PRK09191 two-component respons 99.5 8.5E-14 1.8E-18 138.9 13.0 136 329-557 2-137 (261)
124 TIGR03209 P21_Cbot clostridium 99.5 2.1E-13 4.5E-18 125.5 14.0 136 330-542 1-141 (142)
125 PRK08311 putative RNA polymera 99.5 5.3E-12 1.1E-16 127.3 19.8 88 316-403 5-95 (237)
126 PF07638 Sigma70_ECF: ECF sigm 99.4 3.2E-11 6.9E-16 116.8 18.9 174 317-557 5-184 (185)
127 PF04542 Sigma70_r2: Sigma-70 99.3 1.9E-11 4.2E-16 98.5 7.9 70 333-402 1-70 (71)
128 PF04545 Sigma70_r4: Sigma-70, 99.2 2.4E-11 5.1E-16 93.3 7.1 50 501-554 1-50 (50)
129 PF04539 Sigma70_r3: Sigma-70 99.0 6E-10 1.3E-14 92.9 7.5 77 412-488 1-77 (78)
130 PF08281 Sigma70_r4_2: Sigma-7 98.9 3.1E-09 6.6E-14 82.6 7.2 54 495-552 1-54 (54)
131 PRK06930 positive control sigm 98.7 1.2E-07 2.5E-12 91.4 9.7 71 485-559 95-165 (170)
132 PRK00118 putative DNA-binding 98.4 1E-06 2.2E-11 78.3 8.9 62 496-561 9-70 (104)
133 cd06171 Sigma70_r4 Sigma70, re 98.3 2.4E-06 5.2E-11 64.2 6.8 54 496-553 2-55 (55)
134 TIGR00721 tfx DNA-binding prot 98.2 3.8E-06 8.3E-11 78.1 6.9 57 503-564 5-61 (137)
135 PRK03975 tfx putative transcri 98.1 5.8E-06 1.3E-10 77.3 7.2 51 503-558 5-55 (141)
136 PRK04217 hypothetical protein; 98.1 6.3E-06 1.4E-10 74.0 6.5 55 503-561 41-95 (110)
137 PF00140 Sigma70_r1_2: Sigma-7 98.0 1.2E-06 2.6E-11 63.6 0.6 34 254-287 1-34 (37)
138 TIGR01636 phage_rinA phage tra 98.0 3.3E-05 7.3E-10 71.5 8.8 62 493-556 71-132 (134)
139 PF04297 UPF0122: Putative hel 97.9 3.9E-05 8.4E-10 67.8 8.4 58 497-558 9-67 (101)
140 PRK05658 RNA polymerase sigma 97.9 0.0017 3.7E-08 74.4 24.1 34 253-286 102-135 (619)
141 smart00421 HTH_LUXR helix_turn 97.8 4.3E-05 9.3E-10 58.4 5.7 46 503-553 2-47 (58)
142 PF00196 GerE: Bacterial regul 97.7 0.0001 2.2E-09 58.2 5.9 46 503-553 2-47 (58)
143 cd06170 LuxR_C_like C-terminal 97.6 0.00014 3E-09 55.7 6.0 45 505-554 1-45 (57)
144 PF07374 DUF1492: Protein of u 97.6 0.00033 7.2E-09 61.8 8.6 55 494-552 44-99 (100)
145 TIGR03879 near_KaiC_dom probab 97.6 0.00017 3.7E-09 60.2 6.1 47 497-547 8-55 (73)
146 PF04967 HTH_10: HTH DNA bindi 97.5 0.00035 7.5E-09 54.9 6.7 48 505-552 1-51 (53)
147 TIGR01321 TrpR trp operon repr 97.4 0.00022 4.8E-09 62.2 5.3 50 496-545 23-76 (94)
148 PRK15201 fimbriae regulatory p 97.3 0.00044 9.5E-09 66.8 6.5 47 503-554 132-178 (198)
149 PRK15411 rcsA colanic acid cap 97.3 0.0004 8.7E-09 68.6 6.2 46 504-554 137-182 (207)
150 PRK10840 transcriptional regul 97.3 0.00048 1E-08 67.3 6.2 46 503-553 149-194 (216)
151 PRK13870 transcriptional regul 97.3 0.00047 1E-08 69.7 6.2 46 504-554 173-218 (234)
152 PRK13719 conjugal transfer tra 97.2 0.00053 1.1E-08 68.4 6.2 50 499-553 138-187 (217)
153 TIGR03020 EpsA transcriptional 97.2 0.00054 1.2E-08 70.0 6.4 48 502-554 188-235 (247)
154 TIGR03541 reg_near_HchA LuxR f 97.2 0.00052 1.1E-08 69.1 6.2 48 502-554 169-216 (232)
155 PRK11475 DNA-binding transcrip 97.2 0.00059 1.3E-08 67.7 6.3 46 503-553 133-178 (207)
156 PRK10188 DNA-binding transcrip 97.2 0.00068 1.5E-08 68.7 6.4 45 504-553 179-223 (240)
157 PRK10100 DNA-binding transcrip 97.2 0.00072 1.6E-08 67.5 6.3 48 502-554 153-200 (216)
158 PF02001 DUF134: Protein of un 97.1 0.0012 2.6E-08 59.0 6.5 53 504-560 41-93 (106)
159 COG2197 CitB Response regulato 97.1 0.00094 2E-08 66.4 5.9 46 503-553 147-192 (211)
160 COG4566 TtrR Response regulato 97.0 0.0025 5.5E-08 62.3 8.2 59 493-556 131-189 (202)
161 COG2771 CsgD DNA-binding HTH d 97.0 0.0025 5.3E-08 50.4 6.5 48 503-555 3-50 (65)
162 PF13936 HTH_38: Helix-turn-he 96.9 0.0012 2.7E-08 49.5 4.0 41 503-547 3-43 (44)
163 PRK09483 response regulator; P 96.9 0.0018 3.9E-08 62.0 6.0 46 503-553 147-192 (217)
164 TIGR01637 phage_arpU phage tra 96.8 0.0084 1.8E-07 55.1 9.4 63 493-557 67-130 (132)
165 PRK15369 two component system 96.7 0.0032 7E-08 58.8 6.2 46 503-553 148-193 (211)
166 COG3413 Predicted DNA binding 96.6 0.0041 9E-08 61.8 6.8 53 504-556 155-210 (215)
167 PRK01381 Trp operon repressor; 96.5 0.003 6.6E-08 55.6 4.0 49 495-543 22-74 (99)
168 PRK10651 transcriptional regul 96.5 0.005 1.1E-07 58.3 5.9 46 503-553 154-199 (216)
169 PRK09390 fixJ response regulat 96.4 0.0084 1.8E-07 55.7 7.1 53 497-554 134-186 (202)
170 COG1356 tfx Transcriptional re 96.4 0.0027 5.8E-08 58.0 3.3 48 504-556 8-55 (143)
171 COG2739 Uncharacterized protei 96.2 0.019 4.2E-07 50.6 7.4 48 503-554 16-63 (105)
172 COG1342 Predicted DNA-binding 96.2 0.013 2.9E-07 51.1 6.3 52 504-559 33-84 (99)
173 PRK15320 transcriptional activ 96.0 0.013 2.8E-07 57.8 5.8 48 502-554 162-209 (251)
174 COG4941 Predicted RNA polymera 96.0 0.16 3.6E-06 53.8 14.2 159 331-555 8-167 (415)
175 PRK10403 transcriptional regul 95.9 0.014 3.1E-07 55.0 5.8 46 503-553 152-197 (215)
176 PRK09958 DNA-binding transcrip 95.5 0.028 6E-07 53.2 6.1 47 502-553 141-187 (204)
177 PRK10360 DNA-binding transcrip 95.5 0.021 4.6E-07 53.7 5.2 46 503-553 136-181 (196)
178 PRK09935 transcriptional regul 95.5 0.029 6.3E-07 53.0 6.1 45 504-553 149-193 (210)
179 PRK13558 bacterio-opsin activa 95.2 0.035 7.5E-07 63.6 6.8 55 502-556 605-662 (665)
180 PRK04841 transcriptional regul 95.2 0.03 6.4E-07 66.2 6.4 46 503-553 837-882 (903)
181 PF00325 Crp: Bacterial regula 95.0 0.03 6.4E-07 39.6 3.4 27 524-554 2-28 (32)
182 PF12645 HTH_16: Helix-turn-he 94.8 0.12 2.7E-06 42.2 7.0 56 319-374 4-65 (65)
183 TIGR02531 yecD_yerC TrpR-relat 94.6 0.07 1.5E-06 46.3 5.5 38 502-545 34-71 (88)
184 PF13412 HTH_24: Winged helix- 94.6 0.1 2.2E-06 39.4 5.6 42 505-549 1-42 (48)
185 PF13613 HTH_Tnp_4: Helix-turn 94.5 0.093 2E-06 40.8 5.4 50 504-556 2-51 (53)
186 PF05263 DUF722: Protein of un 94.4 0.2 4.3E-06 46.5 8.1 56 494-551 71-126 (130)
187 PF13384 HTH_23: Homeodomain-l 94.2 0.039 8.5E-07 41.8 2.7 32 512-548 10-41 (50)
188 PF01726 LexA_DNA_bind: LexA D 94.1 0.075 1.6E-06 43.4 4.3 44 503-546 2-48 (65)
189 PRK15418 transcriptional regul 94.1 0.07 1.5E-06 56.5 5.2 36 511-550 20-55 (318)
190 PF06530 Phage_antitermQ: Phag 93.5 0.44 9.5E-06 43.7 8.7 53 502-558 60-112 (125)
191 cd00569 HTH_Hin_like Helix-tur 93.5 0.17 3.7E-06 33.8 4.6 36 505-544 6-41 (42)
192 PF02796 HTH_7: Helix-turn-hel 93.4 0.1 2.2E-06 39.3 3.6 33 509-546 11-43 (45)
193 PF04539 Sigma70_r3: Sigma-70 93.1 0.18 4E-06 41.7 5.1 36 287-322 5-40 (78)
194 PRK05901 RNA polymerase sigma 92.8 1.6 3.6E-05 49.2 13.5 130 287-453 359-489 (509)
195 TIGR02393 RpoD_Cterm RNA polym 92.7 1.5 3.3E-05 44.0 12.0 33 288-320 89-121 (238)
196 PRK09210 RNA polymerase sigma 92.5 1.7 3.8E-05 46.9 12.9 129 288-453 218-347 (367)
197 PF13404 HTH_AsnC-type: AsnC-t 92.3 0.38 8.3E-06 35.9 5.2 40 505-547 1-40 (42)
198 PRK07921 RNA polymerase sigma 92.3 2.4 5.1E-05 45.2 13.3 34 287-320 174-207 (324)
199 PHA00675 hypothetical protein 92.2 0.26 5.7E-06 41.5 4.7 40 503-546 21-61 (78)
200 PF13730 HTH_36: Helix-turn-he 92.1 0.49 1.1E-05 36.4 6.0 47 504-554 2-51 (55)
201 PRK10430 DNA-binding transcrip 91.8 0.32 7E-06 48.3 5.9 48 504-551 158-205 (239)
202 PF09862 DUF2089: Protein of u 91.6 0.48 1.1E-05 43.0 6.1 49 502-554 31-79 (113)
203 COG1191 FliA DNA-directed RNA 91.4 5.7 0.00012 40.9 14.4 147 256-453 88-234 (247)
204 COG2390 DeoR Transcriptional r 91.3 0.27 5.8E-06 52.3 4.9 37 511-551 17-53 (321)
205 PRK07598 RNA polymerase sigma 90.9 4.9 0.00011 44.3 14.3 37 416-452 112-148 (415)
206 PF13518 HTH_28: Helix-turn-he 90.8 0.43 9.3E-06 36.0 4.4 28 523-550 11-38 (52)
207 COG2909 MalT ATP-dependent tra 90.6 0.29 6.3E-06 57.4 4.7 45 504-553 831-875 (894)
208 smart00351 PAX Paired Box doma 90.3 0.7 1.5E-05 42.3 6.1 42 505-550 18-59 (125)
209 PF06056 Terminase_5: Putative 90.2 0.57 1.2E-05 37.5 4.7 26 523-548 12-37 (58)
210 PF12802 MarR_2: MarR family; 90.1 0.62 1.3E-05 36.4 4.9 44 504-548 2-45 (62)
211 COG0568 RpoD DNA-directed RNA 90.0 4.3 9.4E-05 43.6 12.5 33 253-285 65-97 (342)
212 PF04218 CENP-B_N: CENP-B N-te 90.0 0.38 8.3E-06 37.6 3.5 40 504-547 6-45 (53)
213 PF08279 HTH_11: HTH domain; 89.7 0.59 1.3E-05 36.0 4.4 39 508-548 1-39 (55)
214 PHA02591 hypothetical protein; 89.0 0.76 1.7E-05 38.9 4.7 24 523-546 58-81 (83)
215 PRK00423 tfb transcription ini 88.9 17 0.00037 38.4 16.1 178 331-552 119-304 (310)
216 PRK11083 DNA-binding response 88.9 0.59 1.3E-05 44.6 4.7 50 504-554 154-208 (228)
217 PF10668 Phage_terminase: Phag 88.9 0.75 1.6E-05 37.2 4.5 25 523-547 21-45 (60)
218 PF02650 HTH_WhiA: WhiA C-term 88.7 0.88 1.9E-05 39.2 5.1 45 502-549 35-81 (85)
219 PF01022 HTH_5: Bacterial regu 88.1 1.2 2.7E-05 33.5 5.1 37 507-547 2-38 (47)
220 PRK05911 RNA polymerase sigma 87.8 3.8 8.3E-05 41.9 10.1 33 289-321 113-145 (257)
221 PRK07408 RNA polymerase sigma 87.7 1.5 3.3E-05 44.8 7.1 33 288-320 115-147 (256)
222 PF01325 Fe_dep_repress: Iron 87.7 0.81 1.7E-05 36.7 4.0 42 505-546 2-44 (60)
223 PRK10710 DNA-binding transcrip 87.5 0.81 1.8E-05 44.3 4.8 50 504-554 160-214 (240)
224 PHA02547 55 RNA polymerase sig 87.1 2.2 4.8E-05 41.3 7.2 64 335-398 44-110 (179)
225 PF12840 HTH_20: Helix-turn-he 87.0 2.1 4.5E-05 33.9 6.0 36 507-546 10-46 (61)
226 cd00131 PAX Paired Box domain 86.7 1.7 3.6E-05 40.1 6.1 41 505-549 18-58 (128)
227 PRK07406 RNA polymerase sigma 86.5 9.7 0.00021 41.4 12.7 34 287-320 224-257 (373)
228 PF03444 HrcA_DNA-bdg: Winged 86.3 1.6 3.4E-05 37.2 5.1 42 504-545 1-44 (78)
229 PRK10336 DNA-binding transcrip 86.2 1.1 2.3E-05 42.6 4.7 49 504-553 149-202 (219)
230 PRK15479 transcriptional regul 86.2 1.2 2.6E-05 42.3 5.0 49 504-553 148-201 (221)
231 PRK12423 LexA repressor; Provi 85.8 1.4 3.1E-05 43.5 5.4 47 504-554 3-52 (202)
232 TIGR02885 spore_sigF RNA polym 85.8 2.9 6.4E-05 41.6 7.8 32 290-321 101-132 (231)
233 PRK06288 RNA polymerase sigma 85.7 15 0.00033 37.6 13.2 35 287-321 119-153 (268)
234 PF13463 HTH_27: Winged helix 85.6 1.5 3.2E-05 34.9 4.5 42 505-548 1-42 (68)
235 PRK07122 RNA polymerase sigma 85.5 11 0.00023 38.9 11.9 34 288-321 129-162 (264)
236 smart00344 HTH_ASNC helix_turn 85.4 1.9 4.2E-05 37.6 5.6 42 505-549 1-42 (108)
237 PRK05949 RNA polymerase sigma 85.3 12 0.00027 39.8 12.6 34 288-321 180-213 (327)
238 TIGR02154 PhoB phosphate regul 85.2 0.65 1.4E-05 44.2 2.7 50 504-554 154-208 (226)
239 PF13542 HTH_Tnp_ISL3: Helix-t 84.7 2.2 4.9E-05 32.3 5.0 33 511-548 19-51 (52)
240 TIGR02850 spore_sigG RNA polym 84.4 12 0.00026 38.0 11.6 34 289-322 123-156 (254)
241 smart00550 Zalpha Z-DNA-bindin 84.0 2.2 4.8E-05 34.8 5.0 23 524-546 22-44 (68)
242 PF13744 HTH_37: Helix-turn-he 83.9 2 4.4E-05 36.1 4.8 45 512-560 23-72 (80)
243 PF09339 HTH_IclR: IclR helix- 83.9 1.4 3.1E-05 33.8 3.6 33 514-546 8-40 (52)
244 PF01371 Trp_repressor: Trp re 83.9 1.4 3E-05 38.2 3.8 46 504-550 26-74 (87)
245 PRK10046 dpiA two-component re 83.8 1.1 2.4E-05 44.2 3.7 39 504-546 161-199 (225)
246 PF01710 HTH_Tnp_IS630: Transp 83.6 11 0.00024 34.0 9.9 23 523-545 70-92 (119)
247 TIGR02997 Sig70-cyanoRpoD RNA 83.5 19 0.00041 37.6 12.9 35 287-321 162-196 (298)
248 PF12728 HTH_17: Helix-turn-he 83.3 1.3 2.7E-05 33.7 3.1 24 525-548 2-25 (51)
249 TIGR02147 Fsuc_second hypothet 83.3 31 0.00067 36.0 14.1 84 431-519 137-227 (271)
250 TIGR01610 phage_O_Nterm phage 83.2 4.6 0.0001 35.1 7.0 49 502-554 20-73 (95)
251 PF01978 TrmB: Sugar-specific 83.1 1.2 2.7E-05 35.8 3.1 40 504-546 5-44 (68)
252 smart00345 HTH_GNTR helix_turn 83.0 2 4.4E-05 32.7 4.2 30 521-554 16-46 (60)
253 PF00356 LacI: Bacterial regul 82.9 1.3 2.7E-05 33.8 2.8 22 526-547 1-22 (46)
254 TIGR03787 marine_sort_RR prote 82.6 1.8 3.9E-05 41.6 4.6 50 504-554 156-207 (227)
255 COG3355 Predicted transcriptio 82.5 4.8 0.0001 37.3 7.0 53 496-554 16-68 (126)
256 PF01418 HTH_6: Helix-turn-hel 82.5 2.7 6E-05 35.0 5.0 52 495-546 4-56 (77)
257 TIGR00498 lexA SOS regulatory 82.4 2.1 4.6E-05 41.8 5.0 44 503-546 2-48 (199)
258 PRK11179 DNA-binding transcrip 82.4 2.8 6E-05 39.5 5.6 41 504-547 6-46 (153)
259 PRK07405 RNA polymerase sigma 82.3 19 0.00041 38.2 12.5 34 287-320 169-202 (317)
260 smart00342 HTH_ARAC helix_turn 82.3 21 0.00046 28.4 10.2 74 431-548 1-75 (84)
261 PF01047 MarR: MarR family; I 82.3 2.6 5.6E-05 32.7 4.5 42 505-549 1-42 (59)
262 PRK07500 rpoH2 RNA polymerase 82.3 26 0.00055 36.6 13.3 25 430-454 244-268 (289)
263 COG3415 Transposase and inacti 82.1 2.5 5.4E-05 39.7 5.1 27 523-549 20-46 (138)
264 CHL00148 orf27 Ycf27; Reviewed 82.0 1.8 3.9E-05 41.9 4.4 50 504-554 161-217 (240)
265 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 81.5 3.6 7.7E-05 32.1 4.9 39 504-546 4-42 (50)
266 PF01726 LexA_DNA_bind: LexA D 81.4 4.7 0.0001 32.9 5.9 38 416-453 10-48 (65)
267 PRK07670 RNA polymerase sigma 81.3 24 0.00051 35.8 12.3 34 288-321 111-144 (251)
268 TIGR01764 excise DNA binding d 81.2 1.8 3.9E-05 31.7 3.1 24 525-548 2-25 (49)
269 PRK00215 LexA repressor; Valid 80.5 3 6.5E-05 40.9 5.4 45 504-548 1-48 (205)
270 cd04762 HTH_MerR-trunc Helix-T 80.5 2 4.4E-05 31.2 3.2 25 525-549 1-25 (49)
271 PF13022 HTH_Tnp_1_2: Helix-tu 80.4 6.9 0.00015 36.9 7.3 61 498-558 4-70 (142)
272 PRK13413 mpi multiple promoter 80.2 2.9 6.4E-05 40.9 5.2 34 509-547 162-195 (200)
273 PRK11564 stationary phase indu 79.8 4.4 9.6E-05 44.3 6.9 51 504-554 10-60 (426)
274 PRK11169 leucine-responsive tr 79.5 3.1 6.7E-05 39.6 4.9 41 504-547 11-51 (164)
275 COG1522 Lrp Transcriptional re 79.4 4.6 9.9E-05 37.3 5.9 42 503-547 4-45 (154)
276 COG0856 Orotate phosphoribosyl 78.8 2.5 5.5E-05 41.2 4.0 39 511-554 10-48 (203)
277 TIGR02787 codY_Gpos GTP-sensin 78.6 8.8 0.00019 39.4 8.0 56 495-554 167-224 (251)
278 PF13551 HTH_29: Winged helix- 78.5 3.8 8.3E-05 35.4 4.9 26 523-548 10-36 (112)
279 PF13011 LZ_Tnp_IS481: leucine 78.4 4.9 0.00011 34.7 5.3 44 503-549 7-50 (85)
280 PRK12469 RNA polymerase factor 78.4 1.2E+02 0.0026 34.3 17.6 47 500-546 333-391 (481)
281 PF08220 HTH_DeoR: DeoR-like h 77.9 2.6 5.6E-05 33.2 3.2 24 523-546 13-36 (57)
282 PHA01976 helix-turn-helix prot 77.7 4 8.6E-05 32.5 4.4 25 523-547 14-38 (67)
283 COG2973 TrpR Trp operon repres 77.2 4.6 0.0001 35.7 4.8 39 504-542 37-78 (103)
284 PF01381 HTH_3: Helix-turn-hel 77.0 2.6 5.5E-05 32.2 2.9 25 523-547 8-32 (55)
285 cd04761 HTH_MerR-SF Helix-Turn 76.0 2.1 4.6E-05 31.7 2.2 25 525-549 1-25 (49)
286 COG5625 Predicted transcriptio 76.0 3.8 8.2E-05 36.5 4.0 70 496-565 8-79 (113)
287 PHA00542 putative Cro-like pro 76.0 4.2 9.2E-05 34.5 4.2 26 523-548 30-55 (82)
288 PF02954 HTH_8: Bacterial regu 75.9 4.9 0.00011 29.7 4.0 39 506-547 3-41 (42)
289 PF08822 DUF1804: Protein of u 75.9 5.8 0.00013 38.4 5.6 41 507-550 5-45 (165)
290 PF08765 Mor: Mor transcriptio 75.5 5.8 0.00013 35.4 5.2 42 508-555 62-103 (108)
291 PF14394 DUF4423: Domain of un 75.4 7.9 0.00017 37.5 6.5 110 430-558 38-154 (171)
292 PF07750 GcrA: GcrA cell cycle 75.4 3.5 7.6E-05 39.7 4.0 36 508-547 6-42 (162)
293 cd06571 Bac_DnaA_C C-terminal 75.3 8.8 0.00019 32.9 6.1 32 523-554 43-75 (90)
294 PF13560 HTH_31: Helix-turn-he 75.3 3.6 7.7E-05 32.7 3.4 25 523-547 13-37 (64)
295 TIGR00122 birA_repr_reg BirA b 75.1 6.4 0.00014 31.8 4.9 25 523-547 12-36 (69)
296 smart00418 HTH_ARSR helix_turn 74.7 5.1 0.00011 30.4 4.1 26 523-548 9-34 (66)
297 TIGR03070 couple_hipB transcri 74.5 5.4 0.00012 30.1 4.2 25 523-547 14-38 (58)
298 smart00420 HTH_DEOR helix_turn 74.4 7.6 0.00016 28.7 4.9 25 523-547 13-37 (53)
299 cd00092 HTH_CRP helix_turn_hel 74.4 8.1 0.00018 30.3 5.3 28 523-554 24-51 (67)
300 TIGR02479 FliA_WhiG RNA polyme 74.2 51 0.0011 32.6 12.2 35 287-321 84-118 (224)
301 COG1476 Predicted transcriptio 74.1 4.8 0.00011 33.4 3.9 25 523-547 13-37 (68)
302 smart00419 HTH_CRP helix_turn_ 73.9 4.7 0.0001 29.5 3.6 28 523-554 7-34 (48)
303 PF13551 HTH_29: Winged helix- 73.8 9 0.00019 33.1 5.9 23 433-455 14-36 (112)
304 TIGR03697 NtcA_cyano global ni 73.1 4.3 9.3E-05 38.5 4.0 29 523-555 142-170 (193)
305 cd07377 WHTH_GntR Winged helix 72.8 7 0.00015 30.3 4.6 26 525-554 26-51 (66)
306 PRK10072 putative transcriptio 72.8 5.4 0.00012 35.2 4.2 32 512-547 38-69 (96)
307 TIGR02337 HpaR homoprotocatech 72.1 18 0.00039 32.1 7.6 42 503-547 24-65 (118)
308 TIGR03830 CxxCG_CxxCG_HTH puta 72.0 12 0.00027 33.4 6.6 46 497-548 57-102 (127)
309 TIGR02844 spore_III_D sporulat 71.9 7.8 0.00017 33.1 4.8 24 523-546 18-41 (80)
310 TIGR02612 mob_myst_A mobile my 71.9 8.4 0.00018 36.7 5.6 49 505-557 23-77 (150)
311 COG2522 Predicted transcriptio 71.9 6.6 0.00014 36.0 4.7 24 523-546 21-44 (119)
312 PF13545 HTH_Crp_2: Crp-like h 71.7 4.4 9.6E-05 32.9 3.3 28 523-554 27-54 (76)
313 PF00046 Homeobox: Homeobox do 71.5 7 0.00015 30.1 4.2 51 504-554 6-57 (57)
314 COG1654 BirA Biotin operon rep 71.4 10 0.00022 32.3 5.4 33 519-555 14-46 (79)
315 PRK05572 sporulation sigma fac 71.3 44 0.00096 33.8 11.1 33 288-320 120-152 (252)
316 TIGR02941 Sigma_B RNA polymera 70.3 41 0.00089 34.0 10.6 33 288-320 118-150 (255)
317 PF13411 MerR_1: MerR HTH fami 70.3 2.2 4.8E-05 34.1 1.2 25 525-549 1-25 (69)
318 PRK09954 putative kinase; Prov 70.2 8.3 0.00018 41.0 5.8 42 505-549 1-42 (362)
319 cd00090 HTH_ARSR Arsenical Res 70.1 12 0.00025 29.1 5.4 36 508-547 8-43 (78)
320 smart00346 HTH_ICLR helix_turn 69.9 10 0.00023 31.7 5.3 26 523-548 19-44 (91)
321 PRK08215 sporulation sigma fac 69.4 63 0.0014 32.8 11.8 32 290-321 127-158 (258)
322 PF08535 KorB: KorB domain; I 69.1 4.6 9.9E-05 34.9 2.9 24 523-546 2-25 (93)
323 PF00392 GntR: Bacterial regul 68.8 5.8 0.00013 31.6 3.3 30 521-554 20-50 (64)
324 PF06971 Put_DNA-bind_N: Putat 68.2 13 0.00029 28.9 5.0 45 406-450 3-47 (50)
325 PRK03573 transcriptional regul 67.2 16 0.00034 33.6 6.3 42 504-547 28-69 (144)
326 COG5484 Uncharacterized conser 67.1 6.9 0.00015 40.3 4.1 25 523-547 18-42 (279)
327 PRK13918 CRP/FNR family transc 67.1 6.7 0.00014 37.6 3.9 28 523-554 148-175 (202)
328 cd01104 HTH_MlrA-CarA Helix-Tu 66.8 7.1 0.00015 31.0 3.4 23 525-547 1-23 (68)
329 PF11662 DUF3263: Protein of u 66.2 20 0.00044 30.5 6.1 47 504-550 2-48 (77)
330 PRK11302 DNA-binding transcrip 66.0 9.8 0.00021 38.9 5.1 51 495-547 4-57 (284)
331 PF05043 Mga: Mga helix-turn-h 65.8 4.9 0.00011 33.9 2.4 32 523-554 29-60 (87)
332 COG1508 RpoN DNA-directed RNA 65.6 1E+02 0.0022 34.6 12.9 48 499-546 293-352 (444)
333 TIGR01884 cas_HTH CRISPR locus 65.4 17 0.00036 35.8 6.4 44 501-547 137-180 (203)
334 PF00376 MerR: MerR family reg 65.4 4 8.7E-05 29.8 1.5 23 526-548 1-23 (38)
335 PRK10870 transcriptional repre 64.7 35 0.00076 32.9 8.4 50 497-547 43-94 (176)
336 PF08280 HTH_Mga: M protein tr 64.6 8.5 0.00018 30.5 3.4 37 508-547 6-42 (59)
337 PF12116 SpoIIID: Stage III sp 64.4 9.9 0.00021 32.5 3.9 45 509-555 6-50 (82)
338 KOG0484 Transcription factor P 64.2 18 0.0004 32.4 5.7 56 497-556 19-76 (125)
339 PRK11337 DNA-binding transcrip 63.9 17 0.00037 37.4 6.5 52 494-547 15-69 (292)
340 smart00347 HTH_MARR helix_turn 63.8 17 0.00037 30.3 5.4 44 504-554 7-50 (101)
341 PF14493 HTH_40: Helix-turn-he 63.6 11 0.00023 32.4 4.1 29 523-551 12-40 (91)
342 TIGR02607 antidote_HigA addict 63.6 15 0.00032 30.0 4.8 25 523-547 17-41 (78)
343 PRK11753 DNA-binding transcrip 63.5 34 0.00074 32.9 8.2 27 524-554 168-194 (211)
344 PRK11512 DNA-binding transcrip 63.5 39 0.00084 31.1 8.2 48 497-547 28-77 (144)
345 PF02082 Rrf2: Transcriptional 63.3 12 0.00027 31.4 4.4 24 523-546 24-47 (83)
346 PRK01905 DNA-binding protein F 63.3 30 0.00065 28.9 6.7 37 508-547 37-73 (77)
347 PRK15482 transcriptional regul 63.2 12 0.00027 38.5 5.3 50 496-547 5-57 (285)
348 cd04764 HTH_MlrA-like_sg1 Heli 62.9 9.5 0.0002 30.5 3.5 23 525-547 1-23 (67)
349 TIGR02980 SigBFG RNA polymeras 62.8 61 0.0013 32.0 10.0 31 290-320 94-124 (227)
350 PRK06030 hypothetical protein; 62.7 21 0.00046 32.9 6.1 40 523-566 68-107 (124)
351 TIGR00647 MG103 conserved hypo 62.7 16 0.00034 38.4 5.9 45 502-549 225-275 (279)
352 PRK09413 IS2 repressor TnpA; R 62.1 17 0.00037 32.9 5.4 34 512-549 21-54 (121)
353 PF01527 HTH_Tnp_1: Transposas 62.0 8.4 0.00018 31.3 3.1 27 523-549 22-48 (76)
354 PRK11161 fumarate/nitrate redu 61.6 9.4 0.0002 37.7 3.9 27 524-554 184-210 (235)
355 PRK09863 putative frv operon r 61.5 46 0.00099 38.1 10.0 104 430-554 16-122 (584)
356 COG2345 Predicted transcriptio 61.3 15 0.00032 37.2 5.2 25 523-547 24-48 (218)
357 PRK11557 putative DNA-binding 61.1 16 0.00036 37.3 5.7 48 498-547 3-53 (278)
358 PRK00082 hrcA heat-inducible t 61.1 12 0.00027 40.0 5.0 65 503-568 2-80 (339)
359 smart00422 HTH_MERR helix_turn 60.9 6.6 0.00014 31.3 2.2 25 525-549 1-25 (70)
360 PRK09726 antitoxin HipB; Provi 60.9 13 0.00029 31.6 4.2 25 523-547 24-48 (88)
361 PRK06986 fliA flagellar biosyn 60.8 1.3E+02 0.0028 30.0 12.0 32 289-320 98-129 (236)
362 COG2944 Predicted transcriptio 60.7 24 0.00052 31.7 5.8 40 502-547 41-80 (104)
363 PRK04984 fatty acid metabolism 60.6 12 0.00027 37.2 4.6 30 521-554 27-57 (239)
364 PF13556 HTH_30: PucR C-termin 60.6 24 0.00051 27.9 5.3 35 523-557 11-45 (59)
365 COG1510 Predicted transcriptio 60.4 8.6 0.00019 37.5 3.2 29 522-554 39-67 (177)
366 PRK10161 transcriptional regul 60.3 10 0.00022 36.5 3.8 50 504-554 154-208 (229)
367 smart00354 HTH_LACI helix_turn 60.3 8.9 0.00019 31.3 2.9 23 525-547 1-23 (70)
368 cd04763 HTH_MlrA-like Helix-Tu 59.7 11 0.00025 30.2 3.4 23 525-547 1-23 (68)
369 TIGR01889 Staph_reg_Sar staphy 59.6 56 0.0012 28.8 8.1 44 504-547 22-66 (109)
370 TIGR02395 rpoN_sigma RNA polym 58.4 89 0.0019 34.7 11.2 24 430-453 317-340 (429)
371 PF05225 HTH_psq: helix-turn-h 58.4 24 0.00053 26.6 4.7 23 525-547 17-39 (45)
372 PF08784 RPA_C: Replication pr 58.0 16 0.00034 31.9 4.3 43 504-546 44-87 (102)
373 smart00342 HTH_ARAC helix_turn 58.0 17 0.00037 29.0 4.2 26 524-549 1-26 (84)
374 PRK09863 putative frv operon r 57.9 20 0.00044 41.0 6.3 46 505-554 2-47 (584)
375 COG1318 Predicted transcriptio 57.7 10 0.00023 36.9 3.3 28 523-550 60-87 (182)
376 PRK10955 DNA-binding transcrip 57.4 7.7 0.00017 37.2 2.4 46 504-554 156-210 (232)
377 PRK11511 DNA-binding transcrip 56.9 1.4E+02 0.0031 27.0 10.5 37 417-453 11-47 (127)
378 COG2512 Predicted membrane-ass 56.9 15 0.00032 38.0 4.5 45 503-553 191-235 (258)
379 PRK14082 hypothetical protein; 56.9 34 0.00073 28.1 5.5 55 328-384 9-63 (65)
380 PRK11414 colanic acid/biofilm 56.7 14 0.0003 36.5 4.1 37 512-554 24-60 (221)
381 TIGR01387 cztR_silR_copR heavy 56.7 16 0.00036 34.3 4.5 49 504-553 147-200 (218)
382 COG1405 SUA7 Transcription ini 56.5 2.6E+02 0.0057 29.4 14.7 26 523-548 250-275 (285)
383 PF00165 HTH_AraC: Bacterial r 56.4 16 0.00035 26.5 3.5 26 523-548 7-32 (42)
384 PRK09391 fixK transcriptional 56.4 13 0.00029 36.9 4.0 27 524-554 179-205 (230)
385 PRK10402 DNA-binding transcrip 55.6 27 0.00058 34.5 6.0 46 505-554 149-195 (226)
386 PRK11050 manganese transport r 55.4 19 0.00041 34.0 4.7 27 522-548 49-75 (152)
387 cd00086 homeodomain Homeodomai 55.3 29 0.00063 26.4 5.0 51 504-554 6-57 (59)
388 PRK03902 manganese transport t 55.3 22 0.00048 32.9 5.0 26 522-547 20-45 (142)
389 PRK15340 transcriptional regul 55.2 2.4E+02 0.0052 28.5 12.8 30 424-453 118-147 (216)
390 TIGR03338 phnR_burk phosphonat 55.2 15 0.00033 35.8 4.1 30 521-554 31-60 (212)
391 TIGR02812 fadR_gamma fatty aci 55.0 18 0.00038 36.1 4.6 31 520-554 25-56 (235)
392 TIGR02702 SufR_cyano iron-sulf 54.9 24 0.00053 34.6 5.5 26 523-548 14-39 (203)
393 PF06413 Neugrin: Neugrin; In 54.5 20 0.00043 36.5 4.8 42 504-546 10-51 (225)
394 smart00862 Trans_reg_C Transcr 54.3 40 0.00087 27.0 5.9 50 504-554 5-60 (78)
395 PRK09990 DNA-binding transcrip 53.8 19 0.00041 36.2 4.6 37 512-554 20-57 (251)
396 PF12324 HTH_15: Helix-turn-he 53.7 36 0.00079 28.9 5.5 29 428-456 35-63 (77)
397 PRK09706 transcriptional repre 53.6 19 0.00042 33.0 4.3 25 523-547 17-41 (135)
398 PF04703 FaeA: FaeA-like prote 53.6 13 0.00029 30.2 2.8 25 523-547 14-38 (62)
399 KOG1597 Transcription initiati 53.5 1.8E+02 0.0038 30.9 11.5 126 426-554 159-290 (308)
400 PRK11517 transcriptional regul 53.2 24 0.00052 33.5 5.1 49 504-553 147-200 (223)
401 PRK13239 alkylmercury lyase; P 53.2 27 0.00059 35.0 5.5 29 428-456 33-61 (206)
402 COG3093 VapI Plasmid maintenan 53.2 20 0.00044 32.1 4.1 35 511-547 12-46 (104)
403 PRK06266 transcription initiat 53.1 40 0.00087 32.9 6.6 47 497-547 13-59 (178)
404 PF01710 HTH_Tnp_IS630: Transp 52.9 19 0.0004 32.6 4.0 24 523-546 17-40 (119)
405 PRK09464 pdhR transcriptional 52.8 20 0.00043 36.1 4.7 37 512-554 23-60 (254)
406 PRK03837 transcriptional regul 52.8 21 0.00045 35.5 4.7 30 521-554 33-63 (241)
407 PRK10411 DNA-binding transcrip 52.6 25 0.00054 35.7 5.3 41 507-550 4-44 (240)
408 COG1846 MarR Transcriptional r 52.4 29 0.00063 29.8 5.1 40 505-547 20-59 (126)
409 PRK10421 DNA-binding transcrip 52.4 20 0.00044 36.1 4.6 37 512-554 15-52 (253)
410 smart00530 HTH_XRE Helix-turn- 52.4 24 0.00051 25.0 3.8 25 523-547 9-33 (56)
411 PF09012 FeoC: FeoC like trans 51.8 11 0.00023 30.7 2.1 26 522-547 12-37 (69)
412 PRK10225 DNA-binding transcrip 51.7 21 0.00045 36.1 4.6 37 512-554 22-59 (257)
413 PF12844 HTH_19: Helix-turn-he 51.4 24 0.00052 27.6 4.0 25 523-547 11-35 (64)
414 PRK09392 ftrB transcriptional 51.1 17 0.00036 36.0 3.7 27 524-554 173-199 (236)
415 PRK12469 RNA polymerase factor 51.1 1.6E+02 0.0034 33.4 11.6 24 430-453 368-391 (481)
416 TIGR00180 parB_part ParB-like 51.0 27 0.00058 34.0 5.1 43 503-547 101-143 (187)
417 smart00352 POU Found in Pit-Oc 50.7 29 0.00062 29.4 4.4 32 512-547 16-53 (75)
418 PRK13509 transcriptional repre 50.7 25 0.00054 35.9 5.0 25 523-547 18-42 (251)
419 PRK10643 DNA-binding transcrip 50.6 21 0.00046 33.6 4.3 49 504-553 149-202 (222)
420 PF12085 DUF3562: Protein of u 50.1 34 0.00073 28.3 4.6 40 526-568 9-48 (66)
421 TIGR00738 rrf2_super rrf2 fami 50.0 30 0.00066 31.1 5.0 26 522-547 23-48 (132)
422 cd01392 HTH_LacI Helix-turn-he 49.9 10 0.00022 28.4 1.6 21 528-548 1-21 (52)
423 cd04768 HTH_BmrR-like Helix-Tu 49.4 12 0.00027 32.4 2.2 25 525-549 1-25 (96)
424 PF07900 DUF1670: Protein of u 49.4 1.4E+02 0.003 30.4 9.7 38 416-454 91-128 (220)
425 COG1737 RpiR Transcriptional r 49.3 35 0.00077 35.3 5.9 52 494-547 5-59 (281)
426 cd00093 HTH_XRE Helix-turn-hel 49.1 33 0.00071 24.4 4.2 25 523-547 11-35 (58)
427 PRK06424 transcription factor; 48.9 25 0.00054 33.3 4.2 25 523-547 96-120 (144)
428 PRK10141 DNA-binding transcrip 48.7 43 0.00093 30.5 5.7 45 499-546 7-52 (117)
429 cd00383 trans_reg_C Effector d 48.4 40 0.00086 28.2 5.1 50 504-554 23-77 (95)
430 cd04768 HTH_BmrR-like Helix-Tu 48.3 1.6E+02 0.0034 25.5 8.9 35 523-557 56-90 (96)
431 PRK05932 RNA polymerase factor 48.2 1.8E+02 0.0039 32.6 11.6 24 430-453 342-365 (455)
432 COG4709 Predicted membrane pro 48.2 36 0.00079 33.7 5.3 59 491-549 3-65 (195)
433 TIGR02944 suf_reg_Xantho FeS a 48.1 29 0.00063 31.4 4.5 26 521-546 22-47 (130)
434 PF08006 DUF1700: Protein of u 48.0 38 0.00081 32.7 5.5 57 491-547 3-63 (181)
435 COG3877 Uncharacterized protei 47.9 42 0.00091 30.3 5.2 48 502-553 39-86 (122)
436 PRK11014 transcriptional repre 47.8 36 0.00077 31.5 5.1 30 521-554 22-51 (141)
437 COG3711 BglG Transcriptional a 47.5 25 0.00054 39.0 4.7 47 507-554 84-130 (491)
438 smart00389 HOX Homeodomain. DN 47.4 31 0.00066 26.1 3.9 47 505-551 7-54 (56)
439 PRK13890 conjugal transfer pro 47.4 28 0.0006 31.7 4.2 25 523-547 17-41 (120)
440 COG1321 TroR Mn-dependent tran 47.4 33 0.00072 32.7 4.9 43 505-547 4-47 (154)
441 PRK11523 DNA-binding transcrip 47.2 28 0.00061 35.1 4.7 37 512-554 21-58 (253)
442 PF02787 CPSase_L_D3: Carbamoy 47.0 1.9E+02 0.0042 26.5 9.7 43 497-546 52-94 (123)
443 cd04775 HTH_Cfa-like Helix-Tur 46.9 14 0.0003 32.5 2.1 26 525-550 2-27 (102)
444 PF13443 HTH_26: Cro/C1-type H 46.8 19 0.00041 28.1 2.7 26 523-548 9-34 (63)
445 PF06322 Phage_NinH: Phage Nin 46.5 29 0.00063 28.3 3.6 27 512-545 11-37 (64)
446 TIGR02431 pcaR_pcaU beta-ketoa 46.2 34 0.00074 34.5 5.1 27 521-547 21-47 (248)
447 PF09012 FeoC: FeoC like trans 46.1 29 0.00063 28.1 3.8 24 431-454 14-37 (69)
448 PRK10572 DNA-binding transcrip 45.8 3.4E+02 0.0074 27.6 15.5 35 420-454 188-222 (290)
449 PRK14101 bifunctional glucokin 45.7 49 0.0011 38.4 6.9 52 494-547 343-397 (638)
450 PRK15044 transcriptional regul 45.6 1.1E+02 0.0024 32.4 8.9 60 257-325 172-231 (295)
451 PRK13503 transcriptional activ 45.6 2E+02 0.0044 28.8 10.7 29 425-453 181-209 (278)
452 PF07037 DUF1323: Putative tra 45.5 23 0.0005 32.6 3.3 23 525-547 1-23 (122)
453 cd01105 HTH_GlnR-like Helix-Tu 45.4 16 0.00036 31.2 2.3 25 525-549 2-26 (88)
454 TIGR02698 CopY_TcrY copper tra 45.4 53 0.0012 30.2 5.8 45 504-551 1-49 (130)
455 cd04790 HTH_Cfa-like_unk Helix 45.3 1.4E+02 0.003 28.9 8.9 89 433-557 3-91 (172)
456 PRK09834 DNA-binding transcrip 45.2 34 0.00073 35.0 5.0 37 510-546 12-48 (263)
457 PRK09943 DNA-binding transcrip 44.8 30 0.00065 33.3 4.3 25 523-547 19-43 (185)
458 PF04552 Sigma54_DBD: Sigma-54 44.6 18 0.0004 34.7 2.7 96 430-547 48-149 (160)
459 PRK14999 histidine utilization 44.5 33 0.00071 34.4 4.7 28 523-554 34-62 (241)
460 cd04773 HTH_TioE_rpt2 Second H 44.5 16 0.00035 32.5 2.2 25 525-549 1-25 (108)
461 cd01107 HTH_BmrR Helix-Turn-He 44.5 17 0.00036 32.3 2.3 26 525-550 1-26 (108)
462 PRK08359 transcription factor; 44.4 30 0.00065 33.9 4.2 35 523-557 97-138 (176)
463 PRK09764 DNA-binding transcrip 44.4 33 0.00071 34.4 4.7 29 522-554 26-55 (240)
464 cd04782 HTH_BltR Helix-Turn-He 44.1 17 0.00037 31.6 2.2 25 525-549 1-25 (97)
465 PRK10219 DNA-binding transcrip 44.1 57 0.0012 28.3 5.6 26 523-548 20-45 (107)
466 TIGR02018 his_ut_repres histid 43.9 34 0.00073 34.0 4.6 28 523-554 23-51 (230)
467 PF12298 Bot1p: Eukaryotic mit 43.7 46 0.001 32.5 5.3 47 505-556 17-63 (172)
468 TIGR03826 YvyF flagellar opero 43.4 69 0.0015 30.1 6.3 44 417-460 32-75 (137)
469 cd04765 HTH_MlrA-like_sg2 Heli 43.4 28 0.0006 30.6 3.5 23 525-547 1-23 (99)
470 PRK09744 DNA-binding transcrip 43.2 32 0.00069 29.1 3.5 19 526-544 12-30 (75)
471 PRK11534 DNA-binding transcrip 43.2 30 0.00065 34.1 4.1 38 511-554 19-56 (224)
472 cd04772 HTH_TioE_rpt1 First He 43.2 18 0.00039 31.6 2.3 25 525-549 1-25 (99)
473 TIGR02394 rpoS_proteo RNA poly 42.9 3.9E+02 0.0084 27.6 12.5 29 293-321 140-168 (285)
474 PF00292 PAX: 'Paired box' dom 42.9 51 0.0011 30.6 5.2 33 511-548 25-57 (125)
475 cd04766 HTH_HspR Helix-Turn-He 42.7 18 0.00039 31.0 2.1 26 525-550 2-27 (91)
476 PRK10906 DNA-binding transcrip 42.7 36 0.00078 34.9 4.7 37 507-546 5-41 (252)
477 cd04774 HTH_YfmP Helix-Turn-He 42.6 1.6E+02 0.0035 25.6 8.1 91 433-559 2-95 (96)
478 cd01109 HTH_YyaN Helix-Turn-He 42.3 19 0.0004 32.1 2.3 26 525-550 1-26 (113)
479 TIGR02325 C_P_lyase_phnF phosp 42.3 29 0.00064 34.4 3.9 27 524-554 32-58 (238)
480 TIGR00270 conserved hypothetic 42.3 36 0.00077 32.5 4.3 25 523-547 81-105 (154)
481 cd04789 HTH_Cfa Helix-Turn-Hel 42.2 19 0.00041 31.7 2.2 26 525-550 2-27 (102)
482 PHA00738 putative HTH transcri 42.1 48 0.001 30.0 4.7 37 507-546 12-48 (108)
483 cd04780 HTH_MerR-like_sg5 Heli 42.1 19 0.00041 31.4 2.2 25 525-549 1-25 (95)
484 PF13412 HTH_24: Winged helix- 42.1 72 0.0016 23.6 5.1 23 431-453 17-39 (48)
485 cd04788 HTH_NolA-AlbR Helix-Tu 41.9 19 0.00041 31.3 2.1 25 525-549 1-25 (96)
486 cd01106 HTH_TipAL-Mta Helix-Tu 41.9 19 0.00041 31.5 2.2 25 525-549 1-25 (103)
487 PRK08583 RNA polymerase sigma 41.9 2E+02 0.0044 29.0 10.0 30 291-320 121-150 (257)
488 cd00592 HTH_MerR-like Helix-Tu 41.8 19 0.00042 31.0 2.2 25 525-549 1-25 (100)
489 PF04703 FaeA: FaeA-like prote 41.4 33 0.00072 27.9 3.3 25 430-454 14-38 (62)
490 PRK11511 DNA-binding transcrip 41.4 2.1E+02 0.0046 25.9 9.1 37 289-325 12-48 (127)
491 PF10078 DUF2316: Uncharacteri 41.3 55 0.0012 28.6 4.9 24 523-546 22-45 (89)
492 cd01108 HTH_CueR Helix-Turn-He 41.2 19 0.00041 32.9 2.2 27 525-551 1-27 (127)
493 cd04777 HTH_MerR-like_sg1 Heli 41.2 20 0.00044 31.6 2.3 26 525-550 1-26 (107)
494 cd01282 HTH_MerR-like_sg3 Heli 41.2 20 0.00043 32.1 2.2 26 525-550 1-26 (112)
495 PF14502 HTH_41: Helix-turn-he 41.2 50 0.0011 25.7 4.0 30 521-554 3-32 (48)
496 PF05331 DUF742: Protein of un 41.1 43 0.00093 30.5 4.4 40 503-547 39-78 (114)
497 PRK11512 DNA-binding transcrip 41.1 2.8E+02 0.0062 25.3 10.6 23 431-453 54-76 (144)
498 cd04769 HTH_MerR2 Helix-Turn-H 41.1 20 0.00043 32.2 2.2 27 525-551 1-27 (116)
499 TIGR02395 rpoN_sigma RNA polym 40.9 28 0.00061 38.6 3.8 47 500-546 282-340 (429)
500 TIGR02404 trehalos_R_Bsub treh 40.9 32 0.00069 34.2 3.9 27 524-554 24-50 (233)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=1.3e-64 Score=539.81 Aligned_cols=315 Identities=38% Similarity=0.648 Sum_probs=299.0
Q ss_pred CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHH--------------------HHHHHHHHhhhhCCCCcHHHHHHHc
Q 008352 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR--------------------LEKEKSKLQSQFGREPTLIEWAKAI 312 (569)
Q Consensus 253 ~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~--------------------le~~~~~l~~~~g~~pt~~ewA~a~ 312 (569)
.+|+++.||++|++.||||++||++|+++||.++. |++++..|++++|++||..|||.++
T Consensus 58 ~~d~v~~yl~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~~~ 137 (415)
T PRK07598 58 STDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTA 137 (415)
T ss_pred CCChHHHHHHhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHHHh
Confidence 57899999999999999999999999999999999 8999999999999999999999554
Q ss_pred ----------------------CCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhh
Q 008352 313 ----------------------GLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSV 370 (569)
Q Consensus 313 ----------------------g~~~~~L~~~l~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAi 370 (569)
|+++++|+..++.|..|+++||.+|+++|++||++|.++|++++||||||++|||+|+
T Consensus 138 ~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~rav 217 (415)
T PRK07598 138 DISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAV 217 (415)
T ss_pred CCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHH
Confidence 5566677777788999999999999999999999999999999999999999999999
Q ss_pred hhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHH
Q 008352 371 EKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLER 450 (569)
Q Consensus 371 ekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ 450 (569)
++|||++|++|+|||+||||++|.+++++++|+||+|.|+...+++++++.+.+.+++||.|+.+|||+.+|+++++|+.
T Consensus 218 ekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~ 297 (415)
T PRK07598 218 EKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVRE 297 (415)
T ss_pred HHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHH
Q 008352 451 LIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEV 530 (569)
Q Consensus 451 ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EI 530 (569)
++...+.++|||.+++++++..+.+++.++ ..+|++.+...++...|..+|..||++||.||.|||||+||+++|++||
T Consensus 298 ~l~~~~~~~SLd~~vg~~~d~~l~d~l~~~-~~~pee~~~~~~l~~~L~~~L~~L~~reR~VI~LRygl~d~~~~Tl~EI 376 (415)
T PRK07598 298 VLLRVPRSVSLETKVGKDKDTELGDLLETD-DISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEI 376 (415)
T ss_pred HHHHccCCcccccccCCCccccHHHhccCC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCCCHHHH
Confidence 999999999999999988888888887654 3478888999999999999999999999999999999999999999999
Q ss_pred HHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhhhh
Q 008352 531 GNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLL 568 (569)
Q Consensus 531 Ae~LGISrerVRqie~RALkKLR~~l~~~~L~~yldll 568 (569)
|+.||||+++||+++++|++|||+.-....+++|++.|
T Consensus 377 A~~LGvS~erVRqie~rAl~KLR~~~~~~~l~~y~~~~ 414 (415)
T PRK07598 377 GRALDLSRERVRQIESKALQKLRQPKRRNRIRDYLELL 414 (415)
T ss_pred HHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHHHhc
Confidence 99999999999999999999999998999999999765
No 2
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=8.8e-62 Score=514.37 Aligned_cols=312 Identities=37% Similarity=0.728 Sum_probs=299.9
Q ss_pred CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHH
Q 008352 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332 (569)
Q Consensus 253 ~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~ 332 (569)
..|++..||++|+++|+||+|||++|+++|+.++.+++++.+|+...|++|+..+||.++|++..+|..++..|..|++.
T Consensus 61 ~~d~l~~Yl~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~ 140 (373)
T PRK07406 61 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEK 140 (373)
T ss_pred CCCHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHH
Confidence 35789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHH
Q 008352 333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 412 (569)
Q Consensus 333 LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~ 412 (569)
||.+|+++|+++|++|.++|.+++||+|||++|||+|+++|||.+|++|+|||+||||++|.++|++++++||+|.|+..
T Consensus 141 Li~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~~ 220 (373)
T PRK07406 141 MVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYE 220 (373)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHH
Q 008352 413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ 492 (569)
Q Consensus 413 ~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~ 492 (569)
.+++++++...+.+.+||.||.+|||+.+|+++++|..++.....++|||.+++++++..+.++++++. .+|++.+...
T Consensus 221 ~~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d~l~d~~-~~pee~~~~~ 299 (373)
T PRK07406 221 TISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADG-ETPEDDVAKN 299 (373)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHHhcCCCC-CCHHHHHHHH
Confidence 999999999999999999999999999999999999999888888999999998777778888888763 4788888888
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhh
Q 008352 493 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYA 565 (569)
Q Consensus 493 el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl 565 (569)
.++..|..+|+.||++||.||.+|||++|++++|++|||+.||||++||||++.+|++|||+......|+.|+
T Consensus 300 ~~~~~L~~aL~~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~~~~~~~l~~~~ 372 (373)
T PRK07406 300 LLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 372 (373)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHh
Confidence 9999999999999999999999999999889999999999999999999999999999999999888898886
No 3
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00 E-value=2.8e-61 Score=504.09 Aligned_cols=311 Identities=40% Similarity=0.676 Sum_probs=297.5
Q ss_pred CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHH
Q 008352 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332 (569)
Q Consensus 253 ~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~ 332 (569)
.+|++..||++|+++|+||++||++|+++|+.++.+++.+..|+..+|++|+..+||.++++++.+|+..++.|+.|++.
T Consensus 16 ~~d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~~ 95 (327)
T PRK05949 16 SADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQK 95 (327)
T ss_pred CCCHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHHH
Confidence 56899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHH
Q 008352 333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 412 (569)
Q Consensus 333 LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~ 412 (569)
||..|+++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+|||+||||++|.++|.+++++||+|.|+..
T Consensus 96 Li~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~~~ 175 (327)
T PRK05949 96 MIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITE 175 (327)
T ss_pred HHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHH
Q 008352 413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ 492 (569)
Q Consensus 413 ~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~ 492 (569)
.+++++++.+.+.+++||.|+.+|||+.+|+++++|..++.....++|||.+++++++..+.++++|.. .+|++.+...
T Consensus 176 ~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~~-~~pe~~~~~~ 254 (327)
T PRK05949 176 KLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEG-PSPDQYITQE 254 (327)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCCC-CCHHHHHHHH
Confidence 999999999999999999999999999999999999999998899999999998777777888888765 5789989999
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008352 493 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 566 (569)
Q Consensus 493 el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yld 566 (569)
.+...|..+|+.||++||.||.+||||+|++++|++|||+.||||+++|||++.+|++|||+. ...++.|+.
T Consensus 255 ~~~~~L~~~L~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~~--~~~l~~~~~ 326 (327)
T PRK05949 255 LLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRRR--RANVKEYLA 326 (327)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence 999999999999999999999999999999999999999999999999999999999999994 356777764
No 4
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=100.00 E-value=1.6e-60 Score=492.44 Aligned_cols=298 Identities=44% Similarity=0.755 Sum_probs=285.6
Q ss_pred cHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHHHH
Q 008352 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI 334 (569)
Q Consensus 255 d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI 334 (569)
|++..||++++++|+||+|||.+|+++++.+..++..+.+|+.+.|++|+..+||+++|+++.+|+..++.|..|++.||
T Consensus 1 ~~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv 80 (298)
T TIGR02997 1 DLVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMI 80 (298)
T ss_pred CcHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHH
Confidence 36788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHH
Q 008352 335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL 414 (569)
Q Consensus 335 ~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l 414 (569)
.+|+++|++||++|.++|.+++||+||||+|||+|+++|||++|++|+|||+||||++|.+++.+++++||+|.++...+
T Consensus 81 ~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~~~~~~~ 160 (298)
T TIGR02997 81 KANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKL 160 (298)
T ss_pred HHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHHHH
Q 008352 415 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 494 (569)
Q Consensus 415 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~el 494 (569)
++++++...+.+.+|+.|+.+|||+.+|+++++|..++.....++|||.+++++++..+.+.+++. ..+|++.+...++
T Consensus 161 ~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~-~~~pe~~~~~~~~ 239 (298)
T TIGR02997 161 NKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDD-GESPEEQVERESL 239 (298)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccCC-CCCHHHHHHHHHH
Confidence 999999999999999999999999999999999999999888999999998776666777777774 4578889999999
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352 495 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 495 ~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 553 (569)
...|..+|+.||++||.||.+||||+|++++|++|||+.||||++||||++++|++|||
T Consensus 240 ~~~L~~~L~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr 298 (298)
T TIGR02997 240 RQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298 (298)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 99999999999999999999999999989999999999999999999999999999996
No 5
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=3.1e-60 Score=494.52 Aligned_cols=311 Identities=38% Similarity=0.641 Sum_probs=296.4
Q ss_pred CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHH
Q 008352 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332 (569)
Q Consensus 253 ~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~ 332 (569)
.+|++..||++|+++|+||+|||.+|+++|+.++.+++++..|+.++|++|+..+||.++++++.+|+..++.|+.|++.
T Consensus 6 ~~~~~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~ 85 (317)
T PRK07405 6 STDLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRK 85 (317)
T ss_pred CCcHHHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHH
Confidence 35789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHH
Q 008352 333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 412 (569)
Q Consensus 333 LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~ 412 (569)
||..|+++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+|||+||||++|.++|.+++++||+|.++..
T Consensus 86 L~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~~ 165 (317)
T PRK07405 86 MVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITE 165 (317)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHH
Q 008352 413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ 492 (569)
Q Consensus 413 ~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~ 492 (569)
.+++++++...+.+.+|+.|+.+|||+.+|+++++|..++.....++|||.+++++++..+.++++++. ..|++.+...
T Consensus 166 ~~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~~-~~pe~~~~~~ 244 (317)
T PRK07405 166 KLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTG-ASPEDFATQS 244 (317)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCCC-CCHHHHHHHH
Confidence 999999999999999999999999999999999999999988888999999998777777888888764 5789989999
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008352 493 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 566 (569)
Q Consensus 493 el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yld 566 (569)
+++..|..+|+.||++||.||.+||||+|++++|++|||+.||||++||||++.+|++|||+. ...+..|+.
T Consensus 245 ~~~~~l~~al~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~--~~~l~~~~~ 316 (317)
T PRK07405 245 SLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKR--KANIQEYLA 316 (317)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence 999999999999999999999999999999999999999999999999999999999999995 456777764
No 6
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=100.00 E-value=6e-59 Score=507.21 Aligned_cols=302 Identities=34% Similarity=0.614 Sum_probs=277.6
Q ss_pred CCCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHH
Q 008352 252 DRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSRE 331 (569)
Q Consensus 252 ~~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are 331 (569)
...|++..||++|+++|+||++||++|+++|+.+..++.. +. ...+|+.. ...+|.+.++.|..|++
T Consensus 208 ~~~d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~---~~-------~~~~~~~~---~~~~l~~~~~~g~~Ar~ 274 (509)
T PRK05901 208 ATADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEEL---LA-------EGEKLDPE---LRRDLQWIGRDGKRAKN 274 (509)
T ss_pred ccccHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhh---hh-------hcccchhh---hhhhhhhhccchHHHHH
Confidence 3568999999999999999999999999999876433321 11 11234422 45778888999999999
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHH
Q 008352 332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY 411 (569)
Q Consensus 332 ~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~ 411 (569)
+||.+|+|||++||++|.++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++|++++|+||+|.|+.
T Consensus 275 ~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~~~~ 354 (509)
T PRK05901 275 HLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMV 354 (509)
T ss_pred HHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHH
Q 008352 412 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK 491 (569)
Q Consensus 412 ~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~ 491 (569)
..++++.++.+.+.+.+||.||.+|||+.+|+++++|..++.....++|||.+++++++..+.+++.|.....|++.+..
T Consensus 355 e~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~~p~~~~~~ 434 (509)
T PRK05901 355 ETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSF 434 (509)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCCCCCHHHHHHH
Confidence 99999999999999999999999999999999999999999988899999999987777788899998877789999999
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008352 492 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 566 (569)
Q Consensus 492 ~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yld 566 (569)
..++..|..+|..|++|||.||.+||||++++++|++|||+.||||++|||||+.+||+|||+......|+.|++
T Consensus 435 ~~l~~~L~~aL~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~~~~~~l~~~l~ 509 (509)
T PRK05901 435 TLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDFLD 509 (509)
T ss_pred HHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 999999999999999999999999999999999999999999999999999999999999999998899999975
No 7
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=100.00 E-value=1e-58 Score=480.86 Aligned_cols=314 Identities=36% Similarity=0.654 Sum_probs=289.0
Q ss_pred CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhh-hhCCCCcHH---------------HHHHHcCCCH
Q 008352 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS-QFGREPTLI---------------EWAKAIGLSC 316 (569)
Q Consensus 253 ~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~-~~g~~pt~~---------------ewA~a~g~~~ 316 (569)
..|.+..|+.+++..+++++++|.++.+.++....+......+.. ..+..|+.. +|+.....++
T Consensus 7 ~~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~E 86 (342)
T COG0568 7 SADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEE 86 (342)
T ss_pred chhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHH
Confidence 356888999999999999999999999999887766666677776 677888876 6666555554
Q ss_pred -HHHHHHHhccH---HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 008352 317 -RDLKSELHSGN---SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (569)
Q Consensus 317 -~~L~~~l~~G~---~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa 392 (569)
..|..++..|. .|+.+||.+|+|||++||++|.|+|+++.||||||+|||++|+++|||++||+|||||+||||++
T Consensus 87 e~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrqa 166 (342)
T COG0568 87 EKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQA 166 (342)
T ss_pred HHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHHH
Confidence 66777777763 69999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 008352 393 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 472 (569)
Q Consensus 393 I~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~ 472 (569)
|.++|.+++|+||+|.|+...+++++++.+.+.+++|++|+.+|||+.+|+++++|+.++.....++|||.+++++++..
T Consensus 167 I~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~ded~~ 246 (342)
T COG0568 167 ITRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSE 246 (342)
T ss_pred HHHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCCCcccH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998889
Q ss_pred hhhcccCCCCCChhHHHHHHHHHHHHHHHHhc-CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008352 473 FQEITADTGVEIPDISVQKQLMRQHVRNLLTL-LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR 551 (569)
Q Consensus 473 l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~-L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkK 551 (569)
+.|+++|+...+|++.+....+.+.+...|.. |+++|+.||++|||++|+++.|++|||+.+|||++|||||+.+|++|
T Consensus 247 l~d~leD~~~~~p~~~~~~~~~~~~~~~~L~~~Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~isrERvRQIE~kAl~K 326 (342)
T COG0568 247 LGDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAKALRK 326 (342)
T ss_pred HHHHhhcCCcCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCcchHHHHHHHhCCcHHHHHHHHHHHHHH
Confidence 99999999887999999999999999999999 99999999999999999999999999999999999999999999999
Q ss_pred HHH-HhhcCchhhhhh
Q 008352 552 LKQ-SLGGKASYGYAD 566 (569)
Q Consensus 552 LR~-~l~~~~L~~yld 566 (569)
||. ......+++|++
T Consensus 327 Lr~~~~~~~~~~~~l~ 342 (342)
T COG0568 327 LRRHPERSALLRSYLD 342 (342)
T ss_pred HHHhhhhhhHHHHhhC
Confidence 994 444555677764
No 8
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=100.00 E-value=7.2e-58 Score=477.58 Aligned_cols=300 Identities=36% Similarity=0.629 Sum_probs=275.6
Q ss_pred CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHH
Q 008352 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332 (569)
Q Consensus 253 ~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~ 332 (569)
.+|++..||++++++|+||+|||.+|+++|+.+..++.. |+..+|.... ...++...++.|..|+++
T Consensus 24 ~~~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~~ 90 (324)
T PRK07921 24 AADLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARRH 90 (324)
T ss_pred CCChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHHH
Confidence 357899999999999999999999999999987655543 2223332111 346788899999999999
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHH
Q 008352 333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 412 (569)
Q Consensus 333 LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~ 412 (569)
||..|+++|+++|++|.++|.+++||+|||+||||+|+++|||++|++|+|||+||||++|.++|++++++||+|.|+..
T Consensus 91 Lv~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~~ 170 (324)
T PRK07921 91 LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVE 170 (324)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHH
Q 008352 413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ 492 (569)
Q Consensus 413 ~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~ 492 (569)
.+++++++...+.+.+||.||.+|||+.+|+++++|..++.....++|||.+++++++.++.++++|+...+|++.+...
T Consensus 171 ~~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~ 250 (324)
T PRK07921 171 QVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAG 250 (324)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCCCCCHHHHHHHH
Confidence 99999999999999999999999999999999999999998888899999999877777888999887666888888889
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhh
Q 008352 493 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYA 565 (569)
Q Consensus 493 el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl 565 (569)
+++..|..+|+.|+++|+.||.+||||+||+++|++|||+.||||++|||||+.+|++|||.......|+.|+
T Consensus 251 ~~~~~l~~~L~~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~~~~~~l~~~~ 323 (324)
T PRK07921 251 LLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSYA 323 (324)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHHHHHHHHhh
Confidence 9999999999999999999999999999999999999999999999999999999999999998888888885
No 9
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=2.4e-54 Score=458.52 Aligned_cols=276 Identities=36% Similarity=0.704 Sum_probs=262.4
Q ss_pred CCCCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHH
Q 008352 251 FDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSR 330 (569)
Q Consensus 251 ~~~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Ar 330 (569)
...+|++..||++|+++|+||++||.+|+++++. ++..|+
T Consensus 92 ~~~~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~----------------------------------------Gd~~A~ 131 (367)
T PRK09210 92 VKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEE----------------------------------------GDEEAK 131 (367)
T ss_pred cccCcHHHHHHHHhhccCCCCHHHHHHHHHHHHh----------------------------------------hHHHHH
Confidence 3457899999999999999999999999988764 235899
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhH
Q 008352 331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI 410 (569)
Q Consensus 331 e~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~ 410 (569)
+.||..|+++|+++|++|.+++.+++||+||||||||+|+++|||.+|++|+|||+||||++|.++|+++.|+||+|.|+
T Consensus 132 ~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~ 211 (367)
T PRK09210 132 QRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 211 (367)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHH
Q 008352 411 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ 490 (569)
Q Consensus 411 ~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~ 490 (569)
...++++.++.+.+.+++||.||.+|||+.+|+++++|..++.....++|||.+++++++..+.++++|....+|++.+.
T Consensus 212 ~~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~~~~p~~~~~ 291 (367)
T PRK09210 212 VETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAA 291 (367)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCCCCCHHHHHH
Confidence 99999999999999999999999999999999999999999998888999999998777778899999887778999999
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008352 491 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 566 (569)
Q Consensus 491 ~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yld 566 (569)
...++..|..+|..||++||.||.+||||+||+++|++|||+.||||++||||++.+||+|||+......|+.|++
T Consensus 292 ~~~~~~~l~~~l~~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~~~~~~~l~~~~~ 367 (367)
T PRK09210 292 YELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 367 (367)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhChHHHhHHHHhhC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999874
No 10
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=2.3e-51 Score=461.79 Aligned_cols=239 Identities=34% Similarity=0.698 Sum_probs=232.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecc
Q 008352 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 407 (569)
Q Consensus 328 ~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP 407 (569)
.|+++||.+|+|||++||++|.++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++|++++|+||+|
T Consensus 380 ~a~~~Li~~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~irip 459 (619)
T PRK05658 380 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 459 (619)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCceecC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhH
Q 008352 408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI 487 (569)
Q Consensus 408 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee 487 (569)
+|+...+++++++...+.+++||.||.+|||+.+|+++++|..++.....++|||.+++++++..+.++++|....+|++
T Consensus 460 ~~~~~~~~k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~~~~~l~d~i~d~~~~~p~~ 539 (619)
T PRK05658 460 VHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPID 539 (619)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCCCCCchhhhcCCCCCCChHH
Confidence 99999999999999999999999999999999999999999999998889999999998888778999999988788999
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008352 488 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 566 (569)
Q Consensus 488 ~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yld 566 (569)
.+....++..|..+|..||+||+.||++||||++++++|++|||+.||||++||||++.+|++|||+......|+.|+|
T Consensus 540 ~~~~~~~~~~l~~~l~~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr~~~~~~~l~~~~~ 618 (619)
T PRK05658 540 AAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRSFLD 618 (619)
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHhchHHHHHHHHHhc
Confidence 9999999999999999999999999999999998899999999999999999999999999999999999999999987
No 11
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=100.00 E-value=1.3e-47 Score=384.01 Aligned_cols=238 Identities=39% Similarity=0.753 Sum_probs=227.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecch
Q 008352 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 408 (569)
Q Consensus 329 Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~ 408 (569)
|+++||..|+++|+++|++|.++|.+++||+|||++||++|+++|||++|++|+|||+||||++|.++++++.+.+++|.
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 hHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHH
Q 008352 409 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 488 (569)
Q Consensus 409 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~ 488 (569)
++...++++.++...+.+++|+.||.+|||+.+|++++++..++......+|||.+++++++.++.+.++|+...+|++.
T Consensus 81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~p~~~ 160 (238)
T TIGR02393 81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESPDDY 160 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcccHHHHhcCCCCCChHHH
Confidence 99999999999999999999999999999999999999999998888889999999877766678888888877788888
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008352 489 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 566 (569)
Q Consensus 489 l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yld 566 (569)
+...++...|..+|+.||++||.||.++|||++++++|++|||+.||||+++|+|++.+|++|||+.+....|+.|+|
T Consensus 161 ~~~~~~~~~l~~~l~~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~~~~~~~~~~ 238 (238)
T TIGR02393 161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKSFLD 238 (238)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHHHhHHHHhhC
Confidence 888889999999999999999999999999998899999999999999999999999999999999999999999976
No 12
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=100.00 E-value=1.4e-44 Score=378.19 Aligned_cols=272 Identities=35% Similarity=0.567 Sum_probs=253.5
Q ss_pred CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHH
Q 008352 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332 (569)
Q Consensus 253 ~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~ 332 (569)
..|.++.|+.+|+..|+||+++|.+|+.+++. ++..|++.
T Consensus 51 ~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~----------------------------------------Gd~~A~~~ 90 (325)
T PRK05657 51 VLDATQLYLNEIGYSPLLTAEEEVYFARRALR----------------------------------------GDFAARQR 90 (325)
T ss_pred cccHHHHHHHHHhcCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHH
Confidence 56788999999999999999999999987654 45689999
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHH
Q 008352 333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 412 (569)
Q Consensus 333 LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~ 412 (569)
||..|.++|+++|++|.+++.+++||+||||+|+|+++++||+.+|++|+||++||||++|.++++++.+.|++|.++..
T Consensus 91 Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~~~~~ 170 (325)
T PRK05657 91 MIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVK 170 (325)
T ss_pred HHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHH
Q 008352 413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ 492 (569)
Q Consensus 413 ~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~ 492 (569)
.++++.++...+.+.+|+.|+.+|||+.+|+++++|..++.......|+|.++..+...++.+.+.+....+|+..+...
T Consensus 171 ~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~ 250 (325)
T PRK05657 171 ELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDD 250 (325)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCCcchhhhccCCCCCCHHHHHHHH
Confidence 99988899999999999999999999999999999999998888889999998777666778888877666889989888
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhh
Q 008352 493 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGY 564 (569)
Q Consensus 493 el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~y 564 (569)
+....|..+|..||+++|.||.+||||.+.+++|++|||+.||||++||++++++|+++||+.+...++..+
T Consensus 251 e~~~~L~~aL~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~~~~~~~~ 322 (325)
T PRK05657 251 DMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQGLSIE 322 (325)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhCccchh
Confidence 889999999999999999999999999888999999999999999999999999999999999998887643
No 13
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=2.4e-44 Score=370.74 Aligned_cols=264 Identities=26% Similarity=0.451 Sum_probs=226.4
Q ss_pred cHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHHHH
Q 008352 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI 334 (569)
Q Consensus 255 d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI 334 (569)
+..+.||++++++|+||+++|.+|+.+++. .++..|+++||
T Consensus 6 ~~~~~y~~~~~~~~~l~~~~e~~L~~~~~~---------------------------------------~gd~~A~~~Lv 46 (289)
T PRK07500 6 SADRSMIRSAMKAPYLEREEEHALAYRWKD---------------------------------------HRDEDALHRII 46 (289)
T ss_pred hHHHHHHHHHhcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHH
Confidence 466789999999999999999999987642 14568999999
Q ss_pred HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHH--
Q 008352 335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT-- 412 (569)
Q Consensus 335 ~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~-- 412 (569)
..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|.+|+|||+||||++|.++|+++++++|+|.+...
T Consensus 47 ~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~~~~~~~ 126 (289)
T PRK07500 47 SAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKA 126 (289)
T ss_pred HHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCccHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999988654
Q ss_pred HHHHHHHHHHHHHH---hcCCCCCHHHHHHHhCCCHHHHHHHHH-hcCCCcccCCCCCCCCCc--chhhcccCCCCCChh
Q 008352 413 LLSKVLEAKRLYIQ---EGNHSPDKEDLARRVGITVEKLERLIF-ITRMPLSMQQPVWADQDT--TFQEITADTGVEIPD 486 (569)
Q Consensus 413 ~l~ki~ka~~~l~~---~~gr~Pt~eEIA~~lgis~e~v~~ll~-~~~~~~SLD~~v~~d~~~--~l~d~i~D~~~~~pe 486 (569)
...++++.+..+.+ .+|+.|+.+|||+.||+++++|..+.. ....++|||.+++++++. ++.+.+.++.. +|+
T Consensus 127 ~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~i~d~~~-~pe 205 (289)
T PRK07500 127 LFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDSP-LPD 205 (289)
T ss_pred HHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCCCcccHHHhccCCCC-Cch
Confidence 33445555555444 689999999999999999999988753 445799999998765443 57788877643 566
Q ss_pred HHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008352 487 ISVQK----QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 560 (569)
Q Consensus 487 e~l~~----~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 560 (569)
+.+.. .+....|..+|+.||++||.||.+||+. ++++|++|||+.||||++||+|++++|++|||..+....
T Consensus 206 ~~~~~~~~~~~~~~~l~~al~~L~~rer~vl~lr~~~--~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~~~~ 281 (289)
T PRK07500 206 EQVESSIDGERRRRWLTQALQTLNERELRIIRERRLR--EDGATLEALGEELGISKERVRQIEARALEKLRRALLSQS 281 (289)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 55443 3456789999999999999999999962 378999999999999999999999999999999987543
No 14
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=2.6e-44 Score=369.63 Aligned_cols=262 Identities=27% Similarity=0.477 Sum_probs=223.9
Q ss_pred CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHH
Q 008352 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332 (569)
Q Consensus 253 ~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~ 332 (569)
+.+++..|++++++.|+||.++|.+|+.+++. .++..|++.
T Consensus 12 ~~~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~---------------------------------------~Gd~~a~~~ 52 (284)
T PRK06596 12 PEGNLDAYIQAVNKIPMLTAEEEYMLAKRLRE---------------------------------------HGDLEAAKQ 52 (284)
T ss_pred CccHHHHHHHHHhccCCCCHHHHHHHHHHHHH---------------------------------------cCCHHHHHH
Confidence 55789999999999999999999999886532 144689999
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHH
Q 008352 333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 412 (569)
Q Consensus 333 LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~ 412 (569)
||..|+++|+++|++|.+++.+++||+|||++||++|+++|||++|++|+|||+|||+++|.+++++++++|++|.+...
T Consensus 53 Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~p~~~~~ 132 (284)
T PRK06596 53 LVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQ 132 (284)
T ss_pred HHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeeeccchHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999889999987642
Q ss_pred --HHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHH-hcCCCcccCCCCCCCCC--cchhhcccCCCCCChhH
Q 008352 413 --LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF-ITRMPLSMQQPVWADQD--TTFQEITADTGVEIPDI 487 (569)
Q Consensus 413 --~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~-~~~~~~SLD~~v~~d~~--~~l~d~i~D~~~~~pee 487 (569)
...++.+....+. .+++|+.+|||+.+|+++++|..++. .....+|||.+++++++ .++.+.++|+. .+|++
T Consensus 133 ~~~~~~~~~~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~~-~~p~~ 209 (284)
T PRK06596 133 RKLFFNLRKAKKRLG--WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDKS-SDPAD 209 (284)
T ss_pred HHHHHHHHHHHHHhc--cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcCCCC-CCchH
Confidence 2344444444443 35899999999999999999999875 33478999999865532 45778887764 46776
Q ss_pred HHHHH----HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352 488 SVQKQ----LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 558 (569)
Q Consensus 488 ~l~~~----el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 558 (569)
.++.. +++..|..+|+.||++||.||.+||+. + +++|++|||+.||||++||||++++|++|||+.+..
T Consensus 210 ~~~~~~~~~~~~~~L~~al~~L~~rEr~VL~lry~~-~-~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~l~~ 282 (284)
T PRK06596 210 VLEEDNWEDQRRALLADALEGLDERSRDIIEARWLD-D-DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEA 282 (284)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC-C-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 66654 357889999999999999999999973 2 689999999999999999999999999999998764
No 15
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=100.00 E-value=1.2e-43 Score=362.08 Aligned_cols=258 Identities=28% Similarity=0.501 Sum_probs=217.0
Q ss_pred HHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHHHHH
Q 008352 256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 335 (569)
Q Consensus 256 ~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~ 335 (569)
++..||++++++|+|+.++|.+|+.++.. .++..|++.||.
T Consensus 2 ~~~~yl~~~~~~~~l~~~~e~~l~~~~~~---------------------------------------~gd~~a~~~Lv~ 42 (270)
T TIGR02392 2 SLDAYIRAVNRIPMLTPEEEYQLAKRLRE---------------------------------------HGDLDAAKKLVL 42 (270)
T ss_pred hHHHHHHHHhcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHHH
Confidence 57789999999999999999999886432 145689999999
Q ss_pred HHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHH--HH
Q 008352 336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY--TL 413 (569)
Q Consensus 336 ~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~--~~ 413 (569)
.|+++|+++|++|.+++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.+++++.++++|+|.+.. ..
T Consensus 43 ~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir~p~~~~~~~~ 122 (270)
T TIGR02392 43 SHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKL 122 (270)
T ss_pred HhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCceecCchHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999988899997654 33
Q ss_pred HHHHHHHHHHHHHhcCCCC-CHHHHHHHhCCCHHHHHHHHHhc-CCCcccCCCCCCCCC--cchhhcccCCCCCChhHHH
Q 008352 414 LSKVLEAKRLYIQEGNHSP-DKEDLARRVGITVEKLERLIFIT-RMPLSMQQPVWADQD--TTFQEITADTGVEIPDISV 489 (569)
Q Consensus 414 l~ki~ka~~~l~~~~gr~P-t~eEIA~~lgis~e~v~~ll~~~-~~~~SLD~~v~~d~~--~~l~d~i~D~~~~~pee~l 489 (569)
..++.+....+. +++.| +.+|||+.+|+++++|.+++... ...+|||.+++++++ ..+.+.+.|+. .+|++.+
T Consensus 123 ~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~l~d~~-~~pe~~~ 199 (270)
T TIGR02392 123 FFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKT-SDPEDTL 199 (270)
T ss_pred HHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCCccccHHHHhcCCC-CChHHHH
Confidence 444544444442 32555 69999999999999999986533 347999999866443 25667777765 3677666
Q ss_pred HHH----HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352 490 QKQ----LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 557 (569)
Q Consensus 490 ~~~----el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 557 (569)
... .++..|..+|..||++||.||.+||+. ++++|++|||+.||||+++|+|++++|++|||+.+.
T Consensus 200 ~~~~~~~~~~~~L~~al~~L~~rer~vl~l~y~~--~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~l~ 269 (270)
T TIGR02392 200 EEEQWEELQRQALANALGSLDARSRRIIEARWLD--DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAALA 269 (270)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhcC--CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 543 356789999999999999999999962 368999999999999999999999999999998764
No 16
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=4.8e-43 Score=356.81 Aligned_cols=220 Identities=24% Similarity=0.393 Sum_probs=201.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecc
Q 008352 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 407 (569)
Q Consensus 328 ~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP 407 (569)
.++++||.+|++||++||++|.++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++++++.++||+|
T Consensus 40 ~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I~~~lr~~~~~ir~P 119 (264)
T PRK07122 40 RQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVP 119 (264)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHcCCccccC
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCCcccCCCCCCCCCc--chhhcccCCCCC
Q 008352 408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWADQDT--TFQEITADTGVE 483 (569)
Q Consensus 408 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~--~~~~~SLD~~v~~d~~~--~l~d~i~D~~~~ 483 (569)
+++...+++++++...+.+++|+.||.+|||+.+|+++++|.+++.. ...++|||.+++++++. .+.+.++
T Consensus 120 r~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~d~~~----- 194 (264)
T PRK07122 120 RRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDARAIADTLG----- 194 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCCCCcccchhccC-----
Confidence 99999999999999999999999999999999999999999998864 45689999998654322 2333332
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352 484 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556 (569)
Q Consensus 484 ~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 556 (569)
+++..++..+....|..+|+.||+++|.||.++|+ +++|++|||+.||||.++|++++++|+++||..+
T Consensus 195 ~~~~~~e~~~~~~~l~~~l~~L~~rer~vl~l~y~----~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l 263 (264)
T PRK07122 195 DVDAGLDQIENREALRPLLAALPERERTVLVLRFF----ESMTQTQIAERVGISQMHVSRLLAKTLARLRDQL 263 (264)
T ss_pred CcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHc
Confidence 34556667777888999999999999999999998 8999999999999999999999999999999876
No 17
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=2.2e-41 Score=342.96 Aligned_cols=228 Identities=25% Similarity=0.408 Sum_probs=201.9
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCC-CCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccc
Q 008352 325 SGNSSREKLINANLRLVVHVAKQYQGR-GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 403 (569)
Q Consensus 325 ~G~~Are~LI~~nlrLV~sIArry~~~-g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~ 403 (569)
++..|+++||..|+++|+++|++|.+. +.+++||+|||+||||+|+++|||++|++|+|||+|||+++|.++++++.++
T Consensus 22 gd~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~~ 101 (256)
T PRK07408 22 PSIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPT 101 (256)
T ss_pred CCHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcCCe
Confidence 345899999999999999999999876 6679999999999999999999999999999999999999999999999999
Q ss_pred eecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHH--hcCCCcccCCCCCCCCCc--chhhcccC
Q 008352 404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF--ITRMPLSMQQPVWADQDT--TFQEITAD 479 (569)
Q Consensus 404 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~--~~~~~~SLD~~v~~d~~~--~l~d~i~D 479 (569)
||+|+++...+++++++...+.+++|++|+.+|||+.+|+++++|..++. .....+|||.++.++++. .+.+.+++
T Consensus 102 vr~pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~~~d 181 (256)
T PRK07408 102 VRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDEDGSTSLGDLLPD 181 (256)
T ss_pred eeeCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCCCccccccccCC
Confidence 99999999999999999999999999999999999999999999999864 345689999987554332 45566665
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352 480 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 559 (569)
Q Consensus 480 ~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 559 (569)
+... +. ....+....|..+|..||+++|.||.++|+ +++|++|||+.||||.++|++++.+|+++||+.+...
T Consensus 182 ~~~~-~~--~~~~~~~~~l~~~l~~L~~~~r~vl~l~y~----~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~~~ 254 (256)
T PRK07408 182 PRYR-SF--QLAQEDRIRLQQALAQLEERTREVLEFVFL----HDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQPE 254 (256)
T ss_pred cccc-hh--hhhHHHHHHHHHHHHcCCHHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhcc
Confidence 4322 11 123345677999999999999999999998 8999999999999999999999999999999988654
No 18
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=100.00 E-value=8.5e-41 Score=343.37 Aligned_cols=272 Identities=35% Similarity=0.561 Sum_probs=248.3
Q ss_pred CCCCCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHH
Q 008352 250 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSS 329 (569)
Q Consensus 250 ~~~~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~A 329 (569)
.....|.+..||.+|+.+|.||.++|.+|+.+++. ++..|
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~----------------------------------------gd~~a 47 (285)
T TIGR02394 8 ETRVADVTQLYLREIGFKPLLTAEEEIAYARRALA----------------------------------------GDFEA 47 (285)
T ss_pred ccCcchHHHHHHHHHhccCCCCHHHHHHHHHHHHc----------------------------------------CCHHH
Confidence 34467899999999999999999999999887654 34689
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchh
Q 008352 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 409 (569)
Q Consensus 330 re~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~ 409 (569)
++.||..|.++|+++|++|.+++.+++||+||||+|||+++++||+.+|++|+||+.|||+.++.+++.++.+.+++|.+
T Consensus 48 ~~~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain~~i~~~~~~~~~p~~ 127 (285)
T TIGR02394 48 RKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVH 127 (285)
T ss_pred HHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHHHHHHHcCCceeCcHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHH
Q 008352 410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV 489 (569)
Q Consensus 410 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l 489 (569)
+...++.+.+..+.+.+.+|+.|+.+++|..+|++++++..++.......|+|.++..+....+.+.+.++...+|++.+
T Consensus 128 ~~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~~~~pe~~~ 207 (285)
T TIGR02394 128 VIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLV 207 (285)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchhhhhcCCCCCCHHHHH
Confidence 99999998888888888889999999999999999999999998877889999887665555566666666556788889
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008352 490 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 561 (569)
Q Consensus 490 ~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L 561 (569)
...+....|..+|..||+++|.||.++|||.+.+++|++|||+.||||.++|++++++|+++||+.+...++
T Consensus 208 ~~~e~~~~L~~al~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~~~~~ 279 (285)
T TIGR02394 208 QNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERDGV 279 (285)
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 999999999999999999999999999988777999999999999999999999999999999999986554
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=8.7e-40 Score=330.55 Aligned_cols=243 Identities=27% Similarity=0.444 Sum_probs=215.6
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHHHHHHHHHHHHH
Q 008352 264 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH 343 (569)
Q Consensus 264 ~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~~nlrLV~s 343 (569)
.+++|+||++||.+|+.+++. ++..|++.||..|+++|++
T Consensus 10 ~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~~~~~v~~ 49 (254)
T TIGR02850 10 TSKLPVLKNQEMRELFIRMQS----------------------------------------GDTTAREKLINGNLRLVLS 49 (254)
T ss_pred ccCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHHH
Confidence 468899999999998876653 3458999999999999999
Q ss_pred HHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHHHHHHHHHHH
Q 008352 344 VAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL 423 (569)
Q Consensus 344 IArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~ 423 (569)
+|++|.+++.+++||+||||+|||+++++|||.+|.+|+||++|||+|.|.++++++. .||+|+++...++++.++...
T Consensus 50 ~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~-~ir~p~~~~~~~~~~~~~~~~ 128 (254)
T TIGR02850 50 VIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDK 128 (254)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CccCchHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999975 889999999999999999999
Q ss_pred HHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCc--chhhcccCCCCCChhHHHHHHHHHHHHHHH
Q 008352 424 YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQEITADTGVEIPDISVQKQLMRQHVRNL 501 (569)
Q Consensus 424 l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~--~l~d~i~D~~~~~pee~l~~~el~e~L~~a 501 (569)
+.+++|+.|+.+|||+.+|+++++|..++.....+.|||.++.++++. .+.+.+.|+.. .++ ....+..|..+
T Consensus 129 l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~~~d~~~-~~~----~~~~~~~l~~~ 203 (254)
T TIGR02850 129 LISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEKN-KDS----QWLEGIALKEA 203 (254)
T ss_pred HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCCCCcchhhhhcCCccc-cHH----HHHhHHHHHHH
Confidence 999999999999999999999999999998888899999987544332 45666665432 122 22344578999
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352 502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556 (569)
Q Consensus 502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 556 (569)
|..|++++|.||.+||+ +++|++|||+.||+|+++|++++++|++|||+.+
T Consensus 204 l~~L~~rer~vi~~~~~----~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~~~ 254 (254)
T TIGR02850 204 MKRLNEREKMILNMRFF----EGKTQMEVAEEIGISQAQVSRLEKAALKHMRKYV 254 (254)
T ss_pred HHcCCHHHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence 99999999999999997 8999999999999999999999999999999753
No 20
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=100.00 E-value=1.5e-39 Score=329.86 Aligned_cols=227 Identities=26% Similarity=0.391 Sum_probs=204.8
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcc
Q 008352 325 SGNSSREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS 401 (569)
Q Consensus 325 ~G~~Are~LI~~nlrLV~sIArry~~---~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~ 401 (569)
++..|+++||..|+++|+++|++|.+ .+++++||+|||+||||+|+++|||++|++|+|||.||||++|.+++++..
T Consensus 20 ~~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~ 99 (257)
T PRK05911 20 QEIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQD 99 (257)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 34589999999999999999999862 356899999999999999999999999999999999999999999999987
Q ss_pred cceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcC--CCcccCCCCCC--CC--Ccchhh
Q 008352 402 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQPVWA--DQ--DTTFQE 475 (569)
Q Consensus 402 r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~--~~~SLD~~v~~--d~--~~~l~d 475 (569)
+ +|+++...++++.++...+.+.+||.|+.+|||+.+|+++++|..++.... .++|||.++.. ++ +.++.+
T Consensus 100 ~---~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~~~~~~~~~l~~ 176 (257)
T PRK05911 100 W---VPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQSDDEAGLALEE 176 (257)
T ss_pred C---CCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCCCCCccccchhh
Confidence 5 899999999999999999999999999999999999999999999886553 46899987643 21 235677
Q ss_pred cccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352 476 ITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 555 (569)
Q Consensus 476 ~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 555 (569)
.++|.....|++.+...+....|..+|+.||++||.||.++|+ +++|++|||+.||||+++|++++.+|+++||+.
T Consensus 177 ~l~d~~~~~~~~~~~~~~~~~~l~~al~~L~~~er~vi~l~y~----e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 252 (257)
T PRK05911 177 RIADERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYYY----EELVLKEIGKILGVSESRVSQIHSKALLKLRAT 252 (257)
T ss_pred hccCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 8888766678888888888999999999999999999999998 899999999999999999999999999999998
Q ss_pred hhc
Q 008352 556 LGG 558 (569)
Q Consensus 556 l~~ 558 (569)
+..
T Consensus 253 l~~ 255 (257)
T PRK05911 253 LSA 255 (257)
T ss_pred HHh
Confidence 754
No 21
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=100.00 E-value=1.9e-38 Score=321.27 Aligned_cols=243 Identities=27% Similarity=0.463 Sum_probs=214.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHHHHHHHHHHHHH
Q 008352 264 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH 343 (569)
Q Consensus 264 ~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~~nlrLV~s 343 (569)
.+++|+|+++|+..|+.+++. ++..|++.||..|+++|++
T Consensus 13 ~~~~~~l~~~~~~~l~~~~~~----------------------------------------gd~~a~~~l~~~~~~~v~~ 52 (258)
T PRK08215 13 TSKLPVLKNEEMRELFERMQN----------------------------------------GDKEAREKLINGNLRLVLS 52 (258)
T ss_pred CCCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHHHHHHHH
Confidence 457789999999988876653 3568999999999999999
Q ss_pred HHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHHHHHHHHHHH
Q 008352 344 VAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL 423 (569)
Q Consensus 344 IArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~ 423 (569)
+|++|.+++.+++||+|||++|||+++++||+.+|++|+||+++||+++|.++++++. .||+|+++.....++.++...
T Consensus 53 ~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~~-~vrip~~~~~~~~~~~~~~~~ 131 (258)
T PRK08215 53 VIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREK 131 (258)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-ceEecHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999985 889999999999999999999
Q ss_pred HHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCc--chhhcccCCCCCChhHHHHHHHHHHHHHHH
Q 008352 424 YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQEITADTGVEIPDISVQKQLMRQHVRNL 501 (569)
Q Consensus 424 l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~--~l~d~i~D~~~~~pee~l~~~el~e~L~~a 501 (569)
+.+++|+.|+.+|||+.+|+++++|..++.....+.|||.++.++++. ++.+.++++.. .++ .......|..+
T Consensus 132 l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~-~~~----~~~~~~~l~~~ 206 (258)
T PRK08215 132 LINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDEKN-KDE----NWLEEIALKEA 206 (258)
T ss_pred HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchhhhhhccCccc-cHH----HHHhHHHHHHH
Confidence 999999999999999999999999999988777888999988654432 34555554422 222 22334578899
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352 502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556 (569)
Q Consensus 502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 556 (569)
|+.||++++.||.++|+ +++|++|||+.||||.++|++++++|+++||+.+
T Consensus 207 l~~L~~~er~vi~~~~~----~~~t~~eIA~~lgis~~~V~~~~~~al~kLr~~l 257 (258)
T PRK08215 207 MKKLNDREKLILNLRFF----QGKTQMEVAEEIGISQAQVSRLEKAALKHMRKYI 257 (258)
T ss_pred HHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999997 8999999999999999999999999999999876
No 22
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=100.00 E-value=2.1e-38 Score=318.14 Aligned_cols=223 Identities=27% Similarity=0.504 Sum_probs=202.9
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCC-CHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccc
Q 008352 325 SGNSSREKLINANLRLVVHVAKQYQGRGI-SLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 403 (569)
Q Consensus 325 ~G~~Are~LI~~nlrLV~sIArry~~~g~-~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~ 403 (569)
++..++ .||+.|+|||.+||++|.+++. +.+||+|-|+|||++|+++|||++|.+|+|||...|+++|.+++|++. .
T Consensus 21 g~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~LR~~~-~ 98 (247)
T COG1191 21 GDEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKND-S 98 (247)
T ss_pred cCHHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHHHHhCC-C
Confidence 345788 9999999999999999998877 999999999999999999999999999999999999999999999999 9
Q ss_pred eecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcC--CCcccCCCCCCCCCcchhhcccCCC
Q 008352 404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQPVWADQDTTFQEITADTG 481 (569)
Q Consensus 404 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~--~~~SLD~~v~~d~~~~l~d~i~D~~ 481 (569)
|++|+.+....+++..+...+.+++||+||++|||+.+|++.+++..++.... ..+|+|..+..+++.. .++.
T Consensus 99 v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d~~-----~~~~ 173 (247)
T COG1191 99 VKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDD-----VDDQ 173 (247)
T ss_pred ccCcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccccc-----hhhc
Confidence 99999999999999999999999999999999999999999999999887654 6788887765444333 2233
Q ss_pred CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352 482 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 558 (569)
Q Consensus 482 ~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 558 (569)
..+|.+.+++.+..+.|.+++..|++|||.||.+||. +++|++|||++||||..+|+|++++|++|||+.+..
T Consensus 174 ~~~~~~~~~~~~~~~~l~~ai~~L~EREk~Vl~l~y~----eelt~kEI~~~LgISes~VSql~kkai~kLr~~l~~ 246 (247)
T COG1191 174 IENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRYK----EELTQKEIAEVLGISESRVSRLHKKAIKKLRKELNK 246 (247)
T ss_pred cccchhHHHHHHHHHHHHHHHHccCHHHHHHHHHHHH----hccCHHHHHHHhCccHHHHHHHHHHHHHHHHHHhcc
Confidence 4467788888888889999999999999999999998 999999999999999999999999999999998753
No 23
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=100.00 E-value=4.4e-37 Score=313.13 Aligned_cols=249 Identities=20% Similarity=0.363 Sum_probs=221.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHHHHHHHHHHHHH
Q 008352 264 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH 343 (569)
Q Consensus 264 ~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~~nlrLV~s 343 (569)
-+++|+||.++|.+|+.+++. .++..+++.|+..|.++|+.
T Consensus 6 ~~~~~~~~~~~e~~l~~~~~~---------------------------------------~~d~~a~~~l~~~y~~lv~~ 46 (268)
T PRK06288 6 SGKIPKYAQQDETELWREYKK---------------------------------------TGDPKIREYLILKYSPLVKY 46 (268)
T ss_pred cCCCccccchHHHHHHHHHHH---------------------------------------cCCHHHHHHHHHHHHHHHHH
Confidence 478999999999999987653 13468999999999999999
Q ss_pred HHHHhh-C--CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHHHHHHHH
Q 008352 344 VAKQYQ-G--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEA 420 (569)
Q Consensus 344 IArry~-~--~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka 420 (569)
+|++|. + .+.+++||+||||+|||+++++||+.+|++|+||++||||+.|.+++++.. ++|+++....++++++
T Consensus 47 ~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~~---~~p~~~~~~~~~i~~~ 123 (268)
T PRK06288 47 VAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSID---WIPRSVRQKARQIERA 123 (268)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC---ccCHHHHHHHHHHHHH
Confidence 999986 2 567899999999999999999999999999999999999999999999654 6899999999999999
Q ss_pred HHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCCcccCCCCCCCC---CcchhhcccCCCCCChhHHHHHHHHH
Q 008352 421 KRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQ---DTTFQEITADTGVEIPDISVQKQLMR 495 (569)
Q Consensus 421 ~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~--~~~~SLD~~v~~d~---~~~l~d~i~D~~~~~pee~l~~~el~ 495 (569)
...+.+.+|+.|+.+|||+.+|++.+++..++... ....|||..+..++ ...+.+.++++...+|++.+...+..
T Consensus 124 ~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~l~~~~~~~~~~~pe~~~~~~e~~ 203 (268)
T PRK06288 124 IAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLESPAALNPDEIAEREEIK 203 (268)
T ss_pred HHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccCCCcccchhhhhccCCCCCCHHHHHHHHHHH
Confidence 99999999999999999999999999999987643 45789988763222 23466777776667888888888889
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352 496 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 558 (569)
Q Consensus 496 e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 558 (569)
..|..+|..||+++|.||.++|+ +++|++|||+.||+|.++|++++.+|+++||.++..
T Consensus 204 ~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~~ 262 (268)
T PRK06288 204 RVIVEAIKTLPEREKKVLILYYY----EDLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLAE 262 (268)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999998 899999999999999999999999999999998864
No 24
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=100.00 E-value=1.9e-36 Score=305.87 Aligned_cols=244 Identities=23% Similarity=0.356 Sum_probs=215.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHH
Q 008352 268 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQ 347 (569)
Q Consensus 268 ~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~~nlrLV~sIArr 347 (569)
|.||+++|.+|+.+++. .++..|+++|+..|.++|+++|++
T Consensus 8 ~~l~~~~~~~li~~~~~---------------------------------------~gd~~a~~~l~~~y~~~v~~~a~~ 48 (255)
T TIGR02941 8 TNLTKEDVIQWIAEFQQ---------------------------------------NQNGEAQEKLVDHYQNLVYSIAYK 48 (255)
T ss_pred CCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHHHHhHHHHHHHHHH
Confidence 66899999888876653 134589999999999999999999
Q ss_pred hhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHh
Q 008352 348 YQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQE 427 (569)
Q Consensus 348 y~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~ 427 (569)
|.+++.+++||+||||+|||+++++||++.|.+|.||+++||++.|.++++++.+.+++|.++....++++++...+.+.
T Consensus 49 ~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~iri~~~~~~~~~~~~~~~~~l~~~ 128 (255)
T TIGR02941 49 YSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDH 128 (255)
T ss_pred HhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHHHHHHHHHHHHhcC
Q 008352 428 GNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLL 505 (569)
Q Consensus 428 ~gr~Pt~eEIA~~lgis~e~v~~ll~~~--~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L 505 (569)
+|+.|+.+|+|+.+|++.+++..++... ....|||.++..+++......+ + ....|++.+...+....|..+|+.|
T Consensus 129 ~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~-~-~~~~~~~~~~~~e~~~~l~~~l~~L 206 (255)
T TIGR02941 129 LQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSDGSTVARL-D-SVGEVEDGYDQTERRMVLEKILPIL 206 (255)
T ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCCCcccccc-c-ccCCcchHHHHHHHHHHHHHHHHcC
Confidence 9999999999999999999998887643 4578999888655443222221 1 1224666677777888899999999
Q ss_pred CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352 506 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556 (569)
Q Consensus 506 ~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 556 (569)
|+++|.||.++|+ +++|++|||+.||||.++|++++.+|+++||+.+
T Consensus 207 ~~~~r~ii~l~~~----~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~ 253 (255)
T TIGR02941 207 SEREKSIIHCTFE----ENLSQKETGERLGISQMHVSRLQRQAISKLKEAA 253 (255)
T ss_pred CHHHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 9999999999998 8999999999999999999999999999999865
No 25
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=100.00 E-value=1.2e-36 Score=302.60 Aligned_cols=223 Identities=29% Similarity=0.469 Sum_probs=199.0
Q ss_pred hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccc
Q 008352 324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 403 (569)
Q Consensus 324 ~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~ 403 (569)
.++..|++.|+..|.++|+++|++|.+++.+++||+|||++|||+++++|||.+|.+|.||++|||++.|.++++++. .
T Consensus 7 ~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~~~-~ 85 (231)
T TIGR02885 7 NGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDG-I 85 (231)
T ss_pred cCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-C
Confidence 345699999999999999999999999999999999999999999999999999999999999999999999999986 8
Q ss_pred eecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCc--chhhcccCCC
Q 008352 404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQEITADTG 481 (569)
Q Consensus 404 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~--~l~d~i~D~~ 481 (569)
|++|+++....+++.++...+..++|+.||.+|||+.+|++++++..++.....+.|||.++.++++. ++.+.+.++.
T Consensus 86 i~~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~~ 165 (231)
T TIGR02885 86 IKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLDQIADKG 165 (231)
T ss_pred eECCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCCCcchhhhhcCCCC
Confidence 99999999999999999999999999999999999999999999999988878889999888655432 3456665543
Q ss_pred CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352 482 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556 (569)
Q Consensus 482 ~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 556 (569)
. +++ .......|..+++.||+++++||.++|+ +++|++|||+.||||+++|++++++|++|||..|
T Consensus 166 ~--~~~---~~~~~~~l~~~l~~L~~~e~~i~~~~~~----~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~l 231 (231)
T TIGR02885 166 S--EDS---DWLEKIALKEAISKLDERERQIIMLRYF----KDKTQTEVANMLGISQVQVSRLEKKVLKKMKEKL 231 (231)
T ss_pred c--cHH---hHHHHHHHHHHHHcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHhC
Confidence 2 222 2223557889999999999999999998 8999999999999999999999999999999864
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=5.5e-36 Score=296.93 Aligned_cols=221 Identities=28% Similarity=0.452 Sum_probs=198.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 008352 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 406 (569)
Q Consensus 327 ~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRl 406 (569)
..|++.||..|.++|+++|++|.+++.+.+||+|||++|||+|+++||+.+|.+|+||+++||++.|.++++++.+.+++
T Consensus 2 ~~a~~~lv~~y~~~v~~~a~~~~~~~~~~eDl~Qe~~i~l~~a~~~f~~~~~~~F~ty~~~~i~~~~~~~~r~~~~~~ri 81 (227)
T TIGR02980 2 KEAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVRV 81 (227)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCcHHHHHHHHHHHHHHHHHHcCCceec
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCC--CcccCCCCCCCCC--cchhhcccCCCC
Q 008352 407 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRM--PLSMQQPVWADQD--TTFQEITADTGV 482 (569)
Q Consensus 407 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~--~~SLD~~v~~d~~--~~l~d~i~D~~~ 482 (569)
|.++...+++++++...+.+.+|+.|+.+|+|+.+|++++++..++..... ..|||.++.++++ ..+.+.+.
T Consensus 82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~~---- 157 (227)
T TIGR02980 82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTLG---- 157 (227)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCcccccccC----
Confidence 999999999999999999999999999999999999999999998876554 8999988763222 12233322
Q ss_pred CChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352 483 EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556 (569)
Q Consensus 483 ~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 556 (569)
+++..+...+....|..+|..||+++++||.++|+ +++|++|||+.||+|+++|++++++|+++||+.+
T Consensus 158 -~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~y~----~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~l 226 (227)
T TIGR02980 158 -DEDDALETVEDRLALKPLLAALPERERRILLLRFF----EDKTQSEIAERLGISQMHVSRLLRRALKKLREQL 226 (227)
T ss_pred -CcchHHHhHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 34455556677788999999999999999999998 8999999999999999999999999999999865
No 27
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=2.8e-35 Score=297.02 Aligned_cols=225 Identities=24% Similarity=0.369 Sum_probs=202.4
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhccc
Q 008352 326 GNSSREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR 402 (569)
Q Consensus 326 G~~Are~LI~~nlrLV~sIArry~~---~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r 402 (569)
+..|++.||..|.++|+++|++|.+ ++.+.+||+||||+|||+++++||+.+|.+|+||+++||+|.|.++++++.
T Consensus 20 d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~d~lR~~~- 98 (251)
T PRK07670 20 DPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKED- 98 (251)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC-
Confidence 4589999999999999999999965 678999999999999999999999999999999999999999999999876
Q ss_pred ceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHH--hcCCCcccCCCCCCCCCc-chhhcccC
Q 008352 403 TIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF--ITRMPLSMQQPVWADQDT-TFQEITAD 479 (569)
Q Consensus 403 ~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~--~~~~~~SLD~~v~~d~~~-~l~d~i~D 479 (569)
++|.++...+++++++...+.+.+|+.|+.+|||+.+|++.++|..++. ....++|||.++.++++. .+.+.+.+
T Consensus 99 --~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~ 176 (251)
T PRK07670 99 --WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDDGENVSVTIRD 176 (251)
T ss_pred --CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccCCCCcchhhhhhcC
Confidence 6999999999999999999999999999999999999999999999876 456789999988654433 23344455
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352 480 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 557 (569)
Q Consensus 480 ~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 557 (569)
....++++.+...+....|..+|..||+++|+||.++|+ +++|++|||+.||+|.++|+++++||+++||.++.
T Consensus 177 ~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~ 250 (251)
T PRK07670 177 DKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFYK----EELTLTEIGQVLNLSTSRISQIHSKALFKLKKLLE 250 (251)
T ss_pred cCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 555578888888888889999999999999999999998 99999999999999999999999999999999875
No 28
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=100.00 E-value=1.6e-34 Score=292.21 Aligned_cols=243 Identities=24% Similarity=0.355 Sum_probs=214.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHH
Q 008352 268 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQ 347 (569)
Q Consensus 268 ~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~~nlrLV~sIArr 347 (569)
|.|+++||.+|..+++. .++..|++.||..|.++|+++|++
T Consensus 8 ~~l~~~e~~~li~~~~~---------------------------------------~gd~~a~~~l~~~~~~~v~~~a~~ 48 (257)
T PRK08583 8 TKLTKEEVNKWIAEYQE---------------------------------------NQDEEAQEKLVKHYKNLVESLAYK 48 (257)
T ss_pred CcCChHHHHHHHHHHHH---------------------------------------cCCHHHHHHHHHHHHHHHHHHHHH
Confidence 77999999888776543 134689999999999999999999
Q ss_pred hhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHh
Q 008352 348 YQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQE 427 (569)
Q Consensus 348 y~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~ 427 (569)
|.+++.+++||+||||+|||+++++||+..|.+|.||+++||+|.|.++++++.+.+++|+++....++++++...+...
T Consensus 49 ~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~~~i~r~~~~~~~~~~~~~~~~~~~ 128 (257)
T PRK08583 49 YSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTE 128 (257)
T ss_pred HhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHHHHHHhcCCCcCCCHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999998999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCCcccCCCCCCCCCc---chhhcccCCCCCChhHHHHHHHHHHHHHHHH
Q 008352 428 GNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQDT---TFQEITADTGVEIPDISVQKQLMRQHVRNLL 502 (569)
Q Consensus 428 ~gr~Pt~eEIA~~lgis~e~v~~ll~~~--~~~~SLD~~v~~d~~~---~l~d~i~D~~~~~pee~l~~~el~e~L~~aL 502 (569)
.++.|+.+++|+.+|++.+++..+.... ....|+|.+++.+++. .+.+.. ..|++.+...+....|..+|
T Consensus 129 ~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~-----~~~e~~~~~~~~~~~l~~~l 203 (257)
T PRK08583 129 LQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDGSTVTLLDIV-----GQQEDGYELTEQRMILEKIL 203 (257)
T ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCCCCccchHhhhc-----CCcchhHHHHHHHHHHHHHH
Confidence 9999999999999999999998876643 3578899887654332 122222 24566667777778899999
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352 503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 558 (569)
Q Consensus 503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 558 (569)
..||+++|+||.++|+ +++|++|||+.||||.++|++++++|+++||..+..
T Consensus 204 ~~L~~~~r~vl~l~~~----~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l~~ 255 (257)
T PRK08583 204 PVLSDREKSIIQCTFI----ENLSQKETGERLGISQMHVSRLQRQAIKKLREAAFL 255 (257)
T ss_pred HhCCHHHHHHHHHHHh----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 9999999999999998 899999999999999999999999999999998754
No 29
>PRK05572 sporulation sigma factor SigF; Validated
Probab=100.00 E-value=1.9e-34 Score=291.25 Aligned_cols=244 Identities=28% Similarity=0.430 Sum_probs=212.8
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHHHHHHHHHHH
Q 008352 262 WGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLV 341 (569)
Q Consensus 262 ~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~~nlrLV 341 (569)
+.-...|.||.+++.+|..+++. ++..|++.|+..|.++|
T Consensus 6 ~~~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~y~~~v 45 (252)
T PRK05572 6 KNKKKKPQLKDEENKELIKKSQD----------------------------------------GDQEARDTLVEKNLRLV 45 (252)
T ss_pred ccCcCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHH
Confidence 44567899999999888765442 34589999999999999
Q ss_pred HHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHHHHHHHHH
Q 008352 342 VHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAK 421 (569)
Q Consensus 342 ~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~ 421 (569)
+++|++|.+++.+++||+|||++++|+++++||+.+|.+|.||+++||++.|.+++++.. .|++|+++....++++++.
T Consensus 46 ~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~~~-~~r~~~~~~~~~~~~~~~~ 124 (252)
T PRK05572 46 WSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDK 124 (252)
T ss_pred HHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CCCCCHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999998889999999999999999999884 7899999999999999999
Q ss_pred HHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCc--chhhcccCCCCCChhHHHHHHHHHHHHH
Q 008352 422 RLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQEITADTGVEIPDISVQKQLMRQHVR 499 (569)
Q Consensus 422 ~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~--~l~d~i~D~~~~~pee~l~~~el~e~L~ 499 (569)
..+..++||.|+..|+|+.+|++++++..+......+.||+.++.+++.. ++.+.+.++.. + .......|.
T Consensus 125 ~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~~~---~----~~~~~~~l~ 197 (252)
T PRK05572 125 DELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITLLDQIADQSE---E----DWFDKIALK 197 (252)
T ss_pred HHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCCCCcchhhhhcCCCch---h----hHHHHHHHH
Confidence 99999999999999999999999999999888777889999887654322 23344433221 1 123356789
Q ss_pred HHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352 500 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 557 (569)
Q Consensus 500 ~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 557 (569)
.+|+.||+++++||.++|+ +++|++|||+.+|+|.++|++++++|+++||..+.
T Consensus 198 ~~l~~L~~~~~~v~~l~~~----~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l~ 251 (252)
T PRK05572 198 EAIRELDERERLIVYLRYF----KDKTQSEVAKRLGISQVQVSRLEKKILKQMKEKLD 251 (252)
T ss_pred HHHHcCCHHHHHHHHHHHh----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999998 89999999999999999999999999999998774
No 30
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=100.00 E-value=1.2e-34 Score=287.37 Aligned_cols=217 Identities=23% Similarity=0.419 Sum_probs=195.9
Q ss_pred HHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchh
Q 008352 333 LINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 409 (569)
Q Consensus 333 LI~~nlrLV~sIArry~~---~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~ 409 (569)
|+..|.++|+++|++|.+ ++.+++||+|||++|||+++++|||++|++|+||+++||++.+.+++++.. ++|.+
T Consensus 1 L~~~~~~lv~~~a~~~~~~~~~~~~~eDl~Qe~~~~l~~a~~~fd~~~~~~f~t~~~~~i~~~~~~~lr~~~---~~p~~ 77 (224)
T TIGR02479 1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLD---WVPRS 77 (224)
T ss_pred CHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHHcC---ccCHH
Confidence 588999999999999986 789999999999999999999999999999999999999999999999875 58999
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCCcccCCCCCCC-CCcchhhcccCCCCCChh
Q 008352 410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWAD-QDTTFQEITADTGVEIPD 486 (569)
Q Consensus 410 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~--~~~~~SLD~~v~~d-~~~~l~d~i~D~~~~~pe 486 (569)
....+++++++...+.+.+|+.|+.+|+|+.+|+++++|..++.. .....|+|....++ +...+.+.++++...+|+
T Consensus 78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (224)
T TIGR02479 78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDKSEDPE 157 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhccccccCCHH
Confidence 999999999999999999999999999999999999999999853 34567888766543 234566666655556888
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352 487 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556 (569)
Q Consensus 487 e~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 556 (569)
+.+...+....|..+|+.||+++|+||.++|+ +++|++|||+.||+|.++|++++++|+++||+++
T Consensus 158 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~y~----~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 223 (224)
T TIGR02479 158 EELEREELREALAEAIESLSEREQLVLSLYYY----EELNLKEIGEVLGLTESRVSQIHSQALKKLRAKL 223 (224)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHc
Confidence 88888888899999999999999999999998 8999999999999999999999999999999875
No 31
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=100.00 E-value=2.5e-34 Score=287.50 Aligned_cols=208 Identities=21% Similarity=0.328 Sum_probs=179.3
Q ss_pred HHHHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecc
Q 008352 331 EKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 407 (569)
Q Consensus 331 e~LI~~nlrLV~sIArry~~---~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP 407 (569)
..|+..|+++|.++|++|.+ .+.+.+||+|||++|||+|+++|||.+| +|+|||+|||||+|.+++++..+ +|
T Consensus 18 ~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~~---~~ 93 (231)
T PRK12427 18 GKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELDW---RP 93 (231)
T ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcCC---CC
Confidence 45778899999999999874 4679999999999999999999998666 89999999999999999998654 68
Q ss_pred hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCCcccCCCCCCCCCcchhhcccCCCCCCh
Q 008352 408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWADQDTTFQEITADTGVEIP 485 (569)
Q Consensus 408 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~--~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~p 485 (569)
+++....++++++...+.+++|+.|+.+|||+.+|+++++|.+++.. .....|||.+++++++.. .+.+ ..+
T Consensus 94 r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~---~~~~---~~~ 167 (231)
T PRK12427 94 RRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAHND---ILQS---RDL 167 (231)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCccc---ccCC---CCH
Confidence 88899999999999999999999999999999999999999998763 456899999886654322 2221 123
Q ss_pred hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352 486 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 555 (569)
Q Consensus 486 ee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 555 (569)
++. ......|..++..||+++|.||.++|+ +++|++|||+.||||.++|+|++++|++|||.+
T Consensus 168 ~~~---~~~~~~l~~~l~~L~~~er~vi~l~~~----~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr~~ 230 (231)
T PRK12427 168 EEN---IIIEDNLKQALSQLDEREQLILHLYYQ----HEMSLKEIALVLDLTEARICQLNKKIAQKIKSF 230 (231)
T ss_pred HHH---HHHHHHHHHHHHcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 322 234567899999999999999999998 899999999999999999999999999999964
No 32
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=100.00 E-value=3.4e-33 Score=279.18 Aligned_cols=225 Identities=23% Similarity=0.406 Sum_probs=198.2
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhh---CCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcc
Q 008352 325 SGNSSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS 401 (569)
Q Consensus 325 ~G~~Are~LI~~nlrLV~sIArry~---~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~ 401 (569)
.|.-+++.|+..|.++|+++|++|. +++.+++||+||||+|||+++++|||++|.+|+||+++||+|.|.++++++.
T Consensus 5 ~~~~~~~~L~~~~~~~v~~~a~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~~~lR~~~ 84 (236)
T PRK06986 5 EGKMDQDELVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLD 84 (236)
T ss_pred cccccHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHcC
Confidence 4677999999999999999999997 6789999999999999999999999999999999999999999999999986
Q ss_pred cceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCCcccCCCCCCCCCcchhhcccC
Q 008352 402 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWADQDTTFQEITAD 479 (569)
Q Consensus 402 r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~--~~~~~SLD~~v~~d~~~~l~d~i~D 479 (569)
+ +|..+.....++.++...+.+.+|++|+.+|||+.+|++.++|..++.. ....+|++..++++++. +.. ..+
T Consensus 85 ~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~-~~~-~~~ 159 (236)
T PRK06986 85 W---VPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDS-ILV-TED 159 (236)
T ss_pred C---CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCcc-ccc-ccC
Confidence 4 6888888888888899999999999999999999999999999998874 34567888876554432 222 223
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352 480 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 558 (569)
Q Consensus 480 ~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 558 (569)
+...+|++.+...+....|..+|+.||+++|.||.++|. +++|++|||+.||||.++|++++.+|+++||+.+..
T Consensus 160 ~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~~ 234 (236)
T PRK06986 160 HQDEDPLQQLEDEELREALVEAIESLPEREQLVLSLYYQ----EELNLKEIGAVLGVSESRVSQIHSQAIKRLRARLGE 234 (236)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHhc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 334467888888888899999999999999999999998 899999999999999999999999999999998754
No 33
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=99.96 E-value=3.6e-28 Score=242.63 Aligned_cols=210 Identities=25% Similarity=0.451 Sum_probs=171.1
Q ss_pred HHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHHHHH
Q 008352 256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 335 (569)
Q Consensus 256 ~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~ 335 (569)
.+..|+.+++..|+||+++|..|...++. ++..|++.|+.
T Consensus 17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~----------------------------------------gd~~a~~~l~~ 56 (233)
T PRK05803 17 FLVSYVKNNSFPQPLSEEEERKYLELMKE----------------------------------------GDEEARNILIE 56 (233)
T ss_pred HHHHHHHHhcccCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHH
Confidence 56789999999999999999888766542 34689999999
Q ss_pred HHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHHH
Q 008352 336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS 415 (569)
Q Consensus 336 ~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ 415 (569)
.|.++|+++|.+|.+++.+.+||+|||++++|+++++||+++|.+|.||+++|+++.+.+++++..+..
T Consensus 57 ~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~~~----------- 125 (233)
T PRK05803 57 RNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTK----------- 125 (233)
T ss_pred HhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhccc-----------
Confidence 999999999999999999999999999999999999999988899999999999999999998754210
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCC---CCcchhhcccCCCCCChhHHHHHH
Q 008352 416 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWAD---QDTTFQEITADTGVEIPDISVQKQ 492 (569)
Q Consensus 416 ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d---~~~~l~d~i~D~~~~~pee~l~~~ 492 (569)
...+++.....+ ....+.+.+.+. .+.+++.+..+
T Consensus 126 -----------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 163 (233)
T PRK05803 126 -----------------------------------------KEVSLQDPIGVDKEGNEISLIDILGSE-EDDVIEQVELK 163 (233)
T ss_pred -----------------------------------------cCCCccccccCCCCcCcccHHHHccCC-CCCHHHHHHHH
Confidence 011111111111 112233333332 23567777777
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352 493 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 558 (569)
Q Consensus 493 el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 558 (569)
+..+.|..+|+.||+++|+||.++|++.+.+++|++|||+.||||.++|+++++||+++||+.+..
T Consensus 164 ~~~~~l~~~l~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~~ 229 (233)
T PRK05803 164 MEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKELYR 229 (233)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 778889999999999999999999977666899999999999999999999999999999998764
No 34
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=99.93 E-value=1.2e-24 Score=216.61 Aligned_cols=179 Identities=30% Similarity=0.543 Sum_probs=141.8
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccce
Q 008352 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 404 (569)
Q Consensus 325 ~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~I 404 (569)
++..|++.|+..|.++|+++|.+|.++..+++||+||+|+++|+++++|+++.+.+|.||+++|++|.+.+++++..+..
T Consensus 45 gd~~af~~l~~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~Rk~~r~~ 124 (227)
T TIGR02846 45 GDEEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHLRALKKTK 124 (227)
T ss_pred CCHHHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHHHHHhccc
Confidence 34689999999999999999999999999999999999999999999999988889999999999999999998754210
Q ss_pred ecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCC---CCcchhhcccCCC
Q 008352 405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWAD---QDTTFQEITADTG 481 (569)
Q Consensus 405 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d---~~~~l~d~i~D~~ 481 (569)
...+++.....+ ....+.+...+ .
T Consensus 125 ----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~-~ 151 (227)
T TIGR02846 125 ----------------------------------------------------GEVSLQDPIGVDKEGNEISLIDILGS-D 151 (227)
T ss_pred ----------------------------------------------------cceeccccccCCcccCcccHHHHhcC-C
Confidence 001111111000 01112222222 1
Q ss_pred CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352 482 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556 (569)
Q Consensus 482 ~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 556 (569)
...+++.+...+..+.|..+|+.||+++|+||.++|.++..+++|++|||++||+|.++|++++++|+++||+.+
T Consensus 152 ~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~~ 226 (227)
T TIGR02846 152 GDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYKEL 226 (227)
T ss_pred CCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 234566666666677899999999999999999999765558999999999999999999999999999999865
No 35
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=99.93 E-value=2.3e-24 Score=214.93 Aligned_cols=180 Identities=28% Similarity=0.539 Sum_probs=139.6
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccce
Q 008352 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 404 (569)
Q Consensus 325 ~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~I 404 (569)
++..|++.|+..|.++|+.+|++|.+++.+++|++||+|+++|+++++|++..+++|.||++++++|.+.++++++.+..
T Consensus 49 gd~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~d~lRk~~~~~ 128 (234)
T PRK08301 49 GDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNNKVK 128 (234)
T ss_pred cCHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 34589999999999999999999999999999999999999999999999988889999999999999999998764210
Q ss_pred ecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCC--CC-CcchhhcccCCC
Q 008352 405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWA--DQ-DTTFQEITADTG 481 (569)
Q Consensus 405 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~--d~-~~~l~d~i~D~~ 481 (569)
...+++.+... ++ .....+...+.
T Consensus 129 ----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~- 155 (234)
T PRK08301 129 ----------------------------------------------------AEVSFDEPLNIDWDGNELLLSDVLGTD- 155 (234)
T ss_pred ----------------------------------------------------cccccccccccccCCCcccHHHhccCc-
Confidence 00111111100 00 00111222211
Q ss_pred CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352 482 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 557 (569)
Q Consensus 482 ~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 557 (569)
...++..+......+.|..+|+.||+++|+||.++|+|...+++|++|||+.||||.++|+++++||+++||+.+.
T Consensus 156 ~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l~ 231 (234)
T PRK08301 156 NDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEIN 231 (234)
T ss_pred ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 1123334455555667999999999999999999996544489999999999999999999999999999999875
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=1.3e-23 Score=210.05 Aligned_cols=181 Identities=30% Similarity=0.541 Sum_probs=141.1
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccce
Q 008352 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 404 (569)
Q Consensus 325 ~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~I 404 (569)
++..|++.|+..|.+.|+++|++|.+++.+.+||+||+++++|+++++|++..+++|.||++.+++|.+.++++++.+..
T Consensus 49 ~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~d~~Rk~~r~~ 128 (234)
T TIGR02835 49 GDESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILMYLRRNNKTR 128 (234)
T ss_pred CCHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhcccc
Confidence 34689999999999999999999999999999999999999999999999988888999999999999999998765210
Q ss_pred ecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCC---CCCCcchhhcccCCC
Q 008352 405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVW---ADQDTTFQEITADTG 481 (569)
Q Consensus 405 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~---~d~~~~l~d~i~D~~ 481 (569)
...+++.... .+......+... +.
T Consensus 129 ----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~-~~ 155 (234)
T TIGR02835 129 ----------------------------------------------------SEVSFDEPLNVDWDGNELLLSDVLG-TD 155 (234)
T ss_pred ----------------------------------------------------CcccccccccCCCCCCcchHHHhcC-CC
Confidence 0011111110 000001111111 11
Q ss_pred CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352 482 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 558 (569)
Q Consensus 482 ~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 558 (569)
.+.+++.+......+.|..+|+.||+++|.||.++|++.+++++|++|||+.||||..+|+++..+|+++||+.+..
T Consensus 156 ~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l~~ 232 (234)
T TIGR02835 156 SDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKEINR 232 (234)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhhc
Confidence 12233444555566789999999999999999999976555899999999999999999999999999999998754
No 37
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=99.91 E-value=8.3e-23 Score=198.91 Aligned_cols=195 Identities=22% Similarity=0.329 Sum_probs=149.5
Q ss_pred CCHHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 008352 314 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (569)
Q Consensus 314 ~~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa 392 (569)
++++.++..+..| ..|++.|+..|.++|+.+|++|.+++.+.+||+||++++||+++.+||+.+|.+|.||++.++++.
T Consensus 9 ~~~~~l~~~~~~~d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n~ 88 (208)
T PRK08295 9 LEDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQ 88 (208)
T ss_pred CChHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHH
Confidence 4456666666555 599999999999999999999999999999999999999999999999988789999999999999
Q ss_pred HHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCC-CCCc
Q 008352 393 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWA-DQDT 471 (569)
Q Consensus 393 I~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~-d~~~ 471 (569)
+.+++++..+..+.+. ....|.+.++.+ +.+.
T Consensus 89 ~~d~~r~~~r~~~~~~-----------------------------------------------~~~~s~~~~~~~~~~~~ 121 (208)
T PRK08295 89 IITAIKTANRQKHIPL-----------------------------------------------NSYVSLDKPIYDEESDR 121 (208)
T ss_pred HHHHHHHhhhhccccc-----------------------------------------------cceeecCCcccCCccch
Confidence 9999876432111000 011223332211 1222
Q ss_pred chhhcccCCCCCChhHHHHHHHHHHHH-HHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352 472 TFQEITADTGVEIPDISVQKQLMRQHV-RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 550 (569)
Q Consensus 472 ~l~d~i~D~~~~~pee~l~~~el~e~L-~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 550 (569)
.+.+.+.++...+|++.+...+....+ ..++..||+++|.||.+ |. +++|++|||+.||+|.++|+..+.||++
T Consensus 122 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l-~~----e~~s~~EIA~~lgis~~tV~~~l~rar~ 196 (208)
T PRK08295 122 TLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLEL-YL----DGKSYQEIAEELNRHVKSIDNALQRVKR 196 (208)
T ss_pred hHHHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHH-HH----ccCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 344444444444677666655555555 45679999999999999 77 8999999999999999999999999999
Q ss_pred HHHHHhhcCc
Q 008352 551 RLKQSLGGKA 560 (569)
Q Consensus 551 KLR~~l~~~~ 560 (569)
+||+++....
T Consensus 197 ~Lr~~l~~~~ 206 (208)
T PRK08295 197 KLEKYLENRE 206 (208)
T ss_pred HHHHHHHhhc
Confidence 9999886543
No 38
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=99.90 E-value=2.7e-22 Score=192.66 Aligned_cols=176 Identities=16% Similarity=0.250 Sum_probs=143.9
Q ss_pred CCHHHHHHHHhccH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 008352 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (569)
Q Consensus 314 ~~~~~L~~~l~~G~-~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa 392 (569)
++++.|+..+..|+ .|++.|+..|.++|+.+|++|.+++.+.+|++||+|+++|+++.+|++. +.+|.+|++..+++.
T Consensus 5 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n~ 83 (186)
T PRK05602 5 DPDEELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLNL 83 (186)
T ss_pred ccHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHHH
Confidence 45566777666554 9999999999999999999999999999999999999999999999986 457999999999999
Q ss_pred HHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 008352 393 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 472 (569)
Q Consensus 393 I~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~ 472 (569)
+.++++++.+. +.+. .
T Consensus 84 ~~d~~R~~~~~--------------------------------------------------------~~~~-~------- 99 (186)
T PRK05602 84 CYDRLRRRREV--------------------------------------------------------PVED-A------- 99 (186)
T ss_pred HHHHHHhcCCC--------------------------------------------------------Cccc-c-------
Confidence 99998865310 0000 0
Q ss_pred hhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008352 473 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 552 (569)
Q Consensus 473 l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 552 (569)
.+ ..+. ...++..+...+....+..+|..||+++|+||.++|. +++|++|||+.||+|..+|+++++||+++|
T Consensus 100 -~~-~~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~L 172 (186)
T PRK05602 100 -PD-VPDP-APGPDAGLEARQRARRVEQALAALPERQREAIVLQYY----QGLSNIEAAAVMDISVDALESLLARGRRAL 172 (186)
T ss_pred -cc-cCCC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHh----cCCCHHHHHHHhCcCHHHHHHHHHHHHHHH
Confidence 00 0011 1135555666666778999999999999999999998 899999999999999999999999999999
Q ss_pred HHHhhcCch
Q 008352 553 KQSLGGKAS 561 (569)
Q Consensus 553 R~~l~~~~L 561 (569)
|+.+...+.
T Consensus 173 r~~l~~~~~ 181 (186)
T PRK05602 173 RAQLADLPG 181 (186)
T ss_pred HHHHHhccc
Confidence 999876553
No 39
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=99.89 E-value=6.1e-22 Score=191.15 Aligned_cols=191 Identities=23% Similarity=0.325 Sum_probs=144.8
Q ss_pred CCHHHHHHHHhccH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 008352 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (569)
Q Consensus 314 ~~~~~L~~~l~~G~-~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa 392 (569)
|++..|+..+..|+ .|++.|+..|.+.|+++|+++.++..+++||+||+|+++|+++.+|++..+..|.||++.+|++.
T Consensus 4 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~~ 83 (198)
T TIGR02859 4 LEDEEIVELARQGNTHALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTRQ 83 (198)
T ss_pred cchHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHHH
Confidence 45667777776665 99999999999999999999999999999999999999999999999987779999999999999
Q ss_pred HHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCC-CCCc
Q 008352 393 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWA-DQDT 471 (569)
Q Consensus 393 I~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~-d~~~ 471 (569)
+.++++...+..+.+ .....|++.+... +++.
T Consensus 84 ~~~~~r~~~~~~~~~-----------------------------------------------~~~~~~~~~~~~~~~~~~ 116 (198)
T TIGR02859 84 IITAIKTATRQKHIP-----------------------------------------------LNSYVSLNKPIYDEESDR 116 (198)
T ss_pred HHHHHHHHHHhcccc-----------------------------------------------hhhhcCcccccccccccc
Confidence 988886532110000 0011223322211 1112
Q ss_pred chhhcccCCCCCChhHHHHHHHHHHHHHHHHhcC-CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352 472 TFQEITADTGVEIPDISVQKQLMRQHVRNLLTLL-NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 550 (569)
Q Consensus 472 ~l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L-~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 550 (569)
++.+.+.+....+|++.+...+....|.++|+.| ++.++.|+. +|. +++|++|||+.||+|.++|+..++||++
T Consensus 117 ~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~-~~~----~~~s~~eIA~~l~~s~~tV~~~l~r~r~ 191 (198)
T TIGR02859 117 TLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQ-SYL----DGKSYQEIACDLNRHVKSIDNALQRVKR 191 (198)
T ss_pred hHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHH-HHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 2333333222346777777777778899999995 566666665 566 8999999999999999999999999999
Q ss_pred HHHHHh
Q 008352 551 RLKQSL 556 (569)
Q Consensus 551 KLR~~l 556 (569)
+||+.+
T Consensus 192 ~L~~~l 197 (198)
T TIGR02859 192 KLEKYL 197 (198)
T ss_pred HHHHhc
Confidence 999875
No 40
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=99.89 E-value=5.6e-22 Score=191.68 Aligned_cols=181 Identities=18% Similarity=0.251 Sum_probs=145.9
Q ss_pred CCHHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 008352 314 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (569)
Q Consensus 314 ~~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa 392 (569)
.++..++..+..| ..|++.|+..|.+.|+++|+++.++..+.+|++||+|+++|+++++|++. ..|.+|++.++++.
T Consensus 11 ~~~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~--~~f~~wl~~i~~n~ 88 (194)
T PRK12513 11 ASDEALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPR--ARFRTWLYQIARNL 88 (194)
T ss_pred CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CchHHHHHHHHHHH
Confidence 3456666666655 49999999999999999999999999999999999999999999999975 36999999999999
Q ss_pred HHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 008352 393 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 472 (569)
Q Consensus 393 I~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~ 472 (569)
+.+++++..+....+ .+. +. .
T Consensus 89 ~~~~~R~~~~~~~~~-----------------------------------------------------~~~----~~--~ 109 (194)
T PRK12513 89 LIDHWRRHGARQAPS-----------------------------------------------------LDA----DE--Q 109 (194)
T ss_pred HHHHHHHhccccccc-----------------------------------------------------ccc----ch--h
Confidence 999998765321100 000 00 0
Q ss_pred hhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008352 473 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 552 (569)
Q Consensus 473 l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 552 (569)
. ....+ ....|+..+...+....|..+|+.||+++|.||.++|+ +++|++|||+.||+|.++|++++.||+++|
T Consensus 110 ~-~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~L 183 (194)
T PRK12513 110 L-HALAD-DGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREH----GDLELEEIAELTGVPEETVKSRLRYALQKL 183 (194)
T ss_pred h-hhcCC-CCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeehc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 0 00011 12256666667777888999999999999999999998 899999999999999999999999999999
Q ss_pred HHHhhcCch
Q 008352 553 KQSLGGKAS 561 (569)
Q Consensus 553 R~~l~~~~L 561 (569)
|+.+...++
T Consensus 184 r~~l~~~~~ 192 (194)
T PRK12513 184 RELLAEEVA 192 (194)
T ss_pred HHHHHHhhc
Confidence 999876554
No 41
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=99.89 E-value=8.9e-22 Score=190.83 Aligned_cols=175 Identities=17% Similarity=0.189 Sum_probs=139.4
Q ss_pred HHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHH
Q 008352 316 CRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR 394 (569)
Q Consensus 316 ~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~ 394 (569)
...|+..+..| ..|++.|+..|.++|+++|.+|.++..+.+|++||+|+++|+++++||+.+| .|.+|++..++|.+.
T Consensus 17 ~~~li~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~ 95 (194)
T PRK09646 17 LDALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHRRAV 95 (194)
T ss_pred HHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHHHHH
Confidence 45566655555 5999999999999999999999999999999999999999999999998765 799999999999999
Q ss_pred HHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchh
Q 008352 395 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ 474 (569)
Q Consensus 395 ~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~ 474 (569)
++++++.+..+. +..... .
T Consensus 96 d~~r~~~~~~~~-------------------------------------------------------~~~~~~---~--- 114 (194)
T PRK09646 96 DRVRSEQAASQR-------------------------------------------------------EVRYGA---R--- 114 (194)
T ss_pred HHHHhhcccccc-------------------------------------------------------cccccc---c---
Confidence 999876421000 000000 0
Q ss_pred hcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 475 EITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 475 d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
+. +.....+++.+...+..+.|..+|..||+++|.||.++|. +++|++|||+.||+|..+|+++++||+++||.
T Consensus 115 ~~--~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 115 NV--DPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYY----GGLTYREVAERLAVPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred cc--cccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCChHhHHHHHHHHHHHHHH
Confidence 00 0011123344444555678999999999999999999998 89999999999999999999999999999999
Q ss_pred Hhhc
Q 008352 555 SLGG 558 (569)
Q Consensus 555 ~l~~ 558 (569)
++..
T Consensus 189 ~l~~ 192 (194)
T PRK09646 189 CLGV 192 (194)
T ss_pred Hhcc
Confidence 8854
No 42
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=99.89 E-value=1e-21 Score=187.76 Aligned_cols=179 Identities=17% Similarity=0.257 Sum_probs=140.0
Q ss_pred HHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHH
Q 008352 317 RDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK 395 (569)
Q Consensus 317 ~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~ 395 (569)
+.|+..+..| ..|+..|+..|.+.|+.+|++|.+++.+++|++||+++++|+++.+|++.. .|.+|++..+++.+.+
T Consensus 6 ~~li~~~~~gd~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~~ 83 (187)
T TIGR02948 6 KKRIKEVRKGDENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLTID 83 (187)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHHH
Confidence 3455555444 599999999999999999999999999999999999999999999999865 5999999999999999
Q ss_pred HHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhh
Q 008352 396 AIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQE 475 (569)
Q Consensus 396 ~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d 475 (569)
++++..+... ++.....++.....+
T Consensus 84 ~~rk~~~~~~-------------------------------------------------------~~~~~~~~~~~~~~~ 108 (187)
T TIGR02948 84 RLRKRKPDFY-------------------------------------------------------LDDEVQGTDGLTMES 108 (187)
T ss_pred HHHhhccccc-------------------------------------------------------ccccccCcccccccc
Confidence 9876431100 000000000001111
Q ss_pred cccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352 476 ITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 555 (569)
Q Consensus 476 ~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 555 (569)
...+. .+.|++.+...+....+..+|..||+++|.||.++|. +++|++|||+.||+|.++|++.+.||+++||..
T Consensus 109 ~~~~~-~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 109 QLAAD-EAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYM----EDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred ccccC-cCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 11111 2256666677777778999999999999999999998 899999999999999999999999999999998
Q ss_pred hh
Q 008352 556 LG 557 (569)
Q Consensus 556 l~ 557 (569)
+.
T Consensus 184 l~ 185 (187)
T TIGR02948 184 LR 185 (187)
T ss_pred hh
Confidence 75
No 43
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=99.89 E-value=1.4e-21 Score=186.73 Aligned_cols=180 Identities=15% Similarity=0.234 Sum_probs=141.8
Q ss_pred HHHHHHHHhccH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHH
Q 008352 316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR 394 (569)
Q Consensus 316 ~~~L~~~l~~G~-~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~ 394 (569)
.+.|+..+..|+ .+++.|+..|.++|+++|+++.++..+++|++||++++||+++.+|++.. .|.+|++..+++.+.
T Consensus 5 ~~~li~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~~~ 82 (187)
T PRK09641 5 IKRLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNLTI 82 (187)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHHHH
Confidence 344555555554 99999999999999999999999999999999999999999999999853 699999999999999
Q ss_pred HHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchh
Q 008352 395 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ 474 (569)
Q Consensus 395 ~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~ 474 (569)
++++++.+.. +++.....++.....
T Consensus 83 d~~R~~~~~~-------------------------------------------------------~~~~~~~~~~~~~~~ 107 (187)
T PRK09641 83 DRLRKRKPDY-------------------------------------------------------YLDAEVAGTEGLTMY 107 (187)
T ss_pred HHHHhcCccc-------------------------------------------------------cccccccCCcchhhh
Confidence 9988754210 000000011111111
Q ss_pred hcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 475 EITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 475 d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
+.+.+. ...|++.+...+....|..+|+.||+++++||.++|. ++++++|||+.||||.++|++.+.||+++||+
T Consensus 108 ~~~~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~----~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T PRK09641 108 SQLAAD-DALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYI----EDLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred cccccC-cCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHh----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 111111 2246667777777788999999999999999999998 89999999999999999999999999999999
Q ss_pred Hhh
Q 008352 555 SLG 557 (569)
Q Consensus 555 ~l~ 557 (569)
.+.
T Consensus 183 ~l~ 185 (187)
T PRK09641 183 QLR 185 (187)
T ss_pred HHh
Confidence 875
No 44
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=99.88 E-value=2.3e-21 Score=186.72 Aligned_cols=171 Identities=23% Similarity=0.307 Sum_probs=137.9
Q ss_pred HHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCC----CCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 008352 318 DLKSELHSG-NSSREKLINANLRLVVHVAKQYQGR----GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (569)
Q Consensus 318 ~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~----g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa 392 (569)
.|+..+..| ..|++.|+..|.+.|+++|.++.++ +.+++|++||+|+++|+++.+|++. +..|.+|++..+++.
T Consensus 13 ~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~n~ 91 (189)
T PRK09648 13 ALVAEAVAGDRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAAHK 91 (189)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHHHH
Confidence 355555555 5999999999999999999998765 3689999999999999999999864 457999999999999
Q ss_pred HHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 008352 393 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 472 (569)
Q Consensus 393 I~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~ 472 (569)
+.++++++.+.... ..+ .
T Consensus 92 ~~d~~r~~~r~~~~-----------------------------------------------------~~~-~-------- 109 (189)
T PRK09648 92 VADAHRAAGRDKAV-----------------------------------------------------PTE-E-------- 109 (189)
T ss_pred HHHHHHHhCCCccc-----------------------------------------------------ccc-c--------
Confidence 99999876521100 000 0
Q ss_pred hhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008352 473 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 552 (569)
Q Consensus 473 l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 552 (569)
..+... ...+|++.+...+..+.|..+|..||+++|+||.++|+ +++|++|||+.||||..+|++.++||+++|
T Consensus 110 ~~~~~~--~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~L 183 (189)
T PRK09648 110 VPERPS--DDAGPEERALRSESSNRMRELLDTLPEKQREILILRVV----VGLSAEETAEAVGSTPGAVRVAQHRALARL 183 (189)
T ss_pred cccccc--cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 000000 11256666677777788999999999999999999998 899999999999999999999999999999
Q ss_pred HHHhh
Q 008352 553 KQSLG 557 (569)
Q Consensus 553 R~~l~ 557 (569)
|+.+.
T Consensus 184 r~~l~ 188 (189)
T PRK09648 184 RAEIE 188 (189)
T ss_pred HHHhc
Confidence 99764
No 45
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=99.87 E-value=4.5e-21 Score=180.33 Aligned_cols=163 Identities=20% Similarity=0.344 Sum_probs=134.7
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccce
Q 008352 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 404 (569)
Q Consensus 325 ~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~I 404 (569)
++..|++.|+..|.+.+++++.++.++..+++|++||+++.+|+++++|+...+ .|.+|++.++++.+.++++++.+..
T Consensus 8 ~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R~~~~~~ 86 (170)
T TIGR02952 8 REEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFRGSKRHP 86 (170)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 455999999999999999999999988899999999999999999999997555 8999999999999999998765211
Q ss_pred ecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCC
Q 008352 405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 484 (569)
Q Consensus 405 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~ 484 (569)
.. +.+. ..+... ....
T Consensus 87 ~~-----------------------------------------------------~~~~---------~~~~~~--~~~~ 102 (170)
T TIGR02952 87 LF-----------------------------------------------------SLDV---------FKELLS--NEPN 102 (170)
T ss_pred CC-----------------------------------------------------cHHH---------HhhcCC--CCCC
Confidence 00 0000 000000 1124
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352 485 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556 (569)
Q Consensus 485 pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 556 (569)
|++.+...+..+.+..+|..|||++|+||.++|. +|+|++|||+.||||..+|++...||+++||+.+
T Consensus 103 ~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~l 170 (170)
T TIGR02952 103 PEEAILKEEANEKLLKALKILTPKQQHVIALRFG----QNLPIAEVARILGKTEGAVKILQFRAIKKLARQM 170 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence 6666666677788999999999999999999998 8999999999999999999999999999999864
No 46
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=99.87 E-value=6.2e-21 Score=180.26 Aligned_cols=172 Identities=19% Similarity=0.236 Sum_probs=137.2
Q ss_pred hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccc
Q 008352 324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 403 (569)
Q Consensus 324 ~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~ 403 (569)
.++..|++.|+..|.++|++++++|.+++.+.+|++||++++||+++++|+ .+.+|.+|++.++++.+.+++++..+.
T Consensus 6 ~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~r~~~~~ 83 (182)
T PRK09652 6 RGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYLRKQGRR 83 (182)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHHHcccCC
Confidence 355689999999999999999999999999999999999999999999999 446899999999999999998875421
Q ss_pred eecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCC
Q 008352 404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE 483 (569)
Q Consensus 404 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~ 483 (569)
...+ +++ ..+.++....+...+ ..
T Consensus 84 ~~~~----------------------------------------------------~~~--~~~~~~~~~~~~~~~--~~ 107 (182)
T PRK09652 84 PPAS----------------------------------------------------DVD--AEEAEDFDLADALRD--IS 107 (182)
T ss_pred CCcc----------------------------------------------------ccc--ccccccccccccccc--cc
Confidence 1000 000 000000011111111 12
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352 484 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 557 (569)
Q Consensus 484 ~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 557 (569)
+|++.+...+....+..+|..||+++|+||.++|. .++|++|||+.||+|..+|++.+.||+++||+.+.
T Consensus 108 ~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 177 (182)
T PRK09652 108 TPENELLSAELEQRVRAAIESLPEELRTAITLREI----EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQ 177 (182)
T ss_pred ChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46667777777888999999999999999999998 89999999999999999999999999999999875
No 47
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=99.87 E-value=5.7e-21 Score=183.10 Aligned_cols=176 Identities=18% Similarity=0.270 Sum_probs=135.3
Q ss_pred CHHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 008352 315 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 393 (569)
Q Consensus 315 ~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI 393 (569)
++..+...+..| ..|++.|+..|.+.|+.++++|.+++.+++|++||+++++|+++++|++.. ..|.+|++..+++.+
T Consensus 9 ~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~-~~~~~wl~~ia~n~~ 87 (186)
T PRK13919 9 SDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRR-GSARAWLLALAHHAA 87 (186)
T ss_pred CHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCccc-cchHHHHHHHHHHHH
Confidence 456666666555 499999999999999999999999999999999999999999999998754 369999999999999
Q ss_pred HHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 008352 394 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 473 (569)
Q Consensus 394 ~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l 473 (569)
.+++++..+... ....+ ......
T Consensus 88 ~d~~rk~~~~~~----------------------------------------------------~~~~~-----~~~~~~ 110 (186)
T PRK13919 88 VDHVRRRAARPQ----------------------------------------------------PLEPD-----EREPEA 110 (186)
T ss_pred HHHHHhhhcccc----------------------------------------------------ccccc-----cccccc
Confidence 999987531100 00000 000000
Q ss_pred hhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352 474 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 474 ~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 553 (569)
.+ .+ .+..........+.|..+|..||+++|+||.++|. +++|++|||+.||+|..+|+..++||+++||
T Consensus 111 ~~-~~-----~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr 180 (186)
T PRK13919 111 FD-LP-----GPGLDEEGHLDRTRLGRALKALSPEERRVIEVLYY----QGYTHREAAQLLGLPLGTLKTRARRALSRLK 180 (186)
T ss_pred cc-CC-----CccccHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 00 00 11111122233457899999999999999999998 9999999999999999999999999999999
Q ss_pred HHhhc
Q 008352 554 QSLGG 558 (569)
Q Consensus 554 ~~l~~ 558 (569)
+.+..
T Consensus 181 ~~l~~ 185 (186)
T PRK13919 181 EVLRE 185 (186)
T ss_pred HHhcC
Confidence 98753
No 48
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=4.6e-21 Score=185.09 Aligned_cols=174 Identities=23% Similarity=0.293 Sum_probs=137.4
Q ss_pred HHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHH
Q 008352 316 CRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR 394 (569)
Q Consensus 316 ~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~ 394 (569)
+..|+..+..| ..|++.|+..|.+.|+++++++.++..+.+|++||+|+++|+. ..|++..+ .|.||++.++++.+.
T Consensus 16 ~~~l~~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~~ 93 (194)
T PRK12519 16 DAELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRAI 93 (194)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHHH
Confidence 45566655544 5999999999999999999999999899999999999999976 67887654 799999999999999
Q ss_pred HHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchh
Q 008352 395 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ 474 (569)
Q Consensus 395 ~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~ 474 (569)
++++++.+..... .+. +.
T Consensus 94 d~~Rk~~~~~~~~---------------------------~~~------------------------~~----------- 111 (194)
T PRK12519 94 DRLRSRRSRQRLL---------------------------ERW------------------------QQ----------- 111 (194)
T ss_pred HHHHhcccccchh---------------------------hhh------------------------hh-----------
Confidence 9998764210000 000 00
Q ss_pred hcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 475 EITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 475 d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
+...+.....+++.+...+....|..+|..||+++++||.++|. +|+|++|||+.||+|..+|++++.||+++||+
T Consensus 112 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 112 ELLGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYY----EGLSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred hhcccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 00000011245555666666678999999999999999999998 89999999999999999999999999999999
Q ss_pred Hhh
Q 008352 555 SLG 557 (569)
Q Consensus 555 ~l~ 557 (569)
.+.
T Consensus 188 ~l~ 190 (194)
T PRK12519 188 LLQ 190 (194)
T ss_pred HHH
Confidence 874
No 49
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=7.1e-21 Score=181.53 Aligned_cols=173 Identities=14% Similarity=0.165 Sum_probs=137.9
Q ss_pred CHHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 008352 315 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 393 (569)
Q Consensus 315 ~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI 393 (569)
+...|+..+..| ..|+..|+..|.+.|+.+|.++.++..+.+|++||+|+++|+++++|++.. ..|.||++..++|.+
T Consensus 5 ~~~~li~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~-~~~~~wl~~ia~n~~ 83 (179)
T PRK12514 5 DIEKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSG-LSPMTWLITIARNHA 83 (179)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHH
Confidence 344555555444 599999999999999999999999999999999999999999999998754 369999999999999
Q ss_pred HHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 008352 394 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 473 (569)
Q Consensus 394 ~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l 473 (569)
.++++++.+.. . .++ ..
T Consensus 84 ~d~~R~~~~~~-~-----------------------------------------------------~~~------~~--- 100 (179)
T PRK12514 84 IDRLRARKAVA-V-----------------------------------------------------DID------EA--- 100 (179)
T ss_pred HHHHHhcCCcc-c-----------------------------------------------------ccc------cc---
Confidence 99998754210 0 000 00
Q ss_pred hhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352 474 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 474 ~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 553 (569)
.+. .+. ...|++.+...+....|..+|..||+++|+||.++|. +|+|++|||+.||+|..+|++.+.||+++||
T Consensus 101 ~~~-~~~-~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 174 (179)
T PRK12514 101 HDL-ADP-SPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYL----EGLSYKELAERHDVPLNTMRTWLRRSLLKLR 174 (179)
T ss_pred hhc-ccc-CCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCChHHHHHHHHHHHHHHH
Confidence 000 001 1245555555555567899999999999999999998 8999999999999999999999999999999
Q ss_pred HHhh
Q 008352 554 QSLG 557 (569)
Q Consensus 554 ~~l~ 557 (569)
+++.
T Consensus 175 ~~l~ 178 (179)
T PRK12514 175 ECLS 178 (179)
T ss_pred HHhc
Confidence 9874
No 50
>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=99.87 E-value=1e-20 Score=181.19 Aligned_cols=181 Identities=16% Similarity=0.210 Sum_probs=141.1
Q ss_pred CHHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 008352 315 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 393 (569)
Q Consensus 315 ~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI 393 (569)
++..|+..+..| ..+++.|+..|.+.|+.+|+++.++..+.+||+||+++++|+++++|++. ..|.+|++..+++.+
T Consensus 6 ~d~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~~ 83 (190)
T TIGR02939 6 LDLELVERVQRGEKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNTA 83 (190)
T ss_pred cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHHH
Confidence 345666666655 48999999999999999999999999999999999999999999999975 369999999999999
Q ss_pred HHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 008352 394 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 473 (569)
Q Consensus 394 ~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l 473 (569)
.++++++.+..... ..+.+. ....
T Consensus 84 ~~~~r~~~r~~~~~--------------------------------------------------~~~~~~------~~~~ 107 (190)
T TIGR02939 84 KNHLVAQGRRPPTS--------------------------------------------------DVEIED------AEHF 107 (190)
T ss_pred HHHHHHhccCCCcc--------------------------------------------------cccccc------hhhh
Confidence 99887544211000 000000 0000
Q ss_pred hhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352 474 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 474 ~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 553 (569)
.+........+|++.+...+....|..+|..||+++|+||.++|. ++++++|||+.||+|..+|+..+.||+++||
T Consensus 108 ~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr 183 (190)
T TIGR02939 108 EGADRLREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLREL----EGLSYEDIARIMDCPVGTVRSRIFRAREAIA 183 (190)
T ss_pred cccccccccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhhh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 000000011246666677777788999999999999999999998 8999999999999999999999999999999
Q ss_pred HHhh
Q 008352 554 QSLG 557 (569)
Q Consensus 554 ~~l~ 557 (569)
+++.
T Consensus 184 ~~l~ 187 (190)
T TIGR02939 184 IRLR 187 (190)
T ss_pred HHhh
Confidence 9885
No 51
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=99.87 E-value=4.9e-21 Score=177.73 Aligned_cols=151 Identities=21% Similarity=0.253 Sum_probs=123.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 008352 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 406 (569)
Q Consensus 327 ~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRl 406 (569)
..|++.|+..|.++|+++++++ ++..+++|++|||++++|+++++|++..| .|.+|++..+++.+.++++++.+..
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 3689999999999999999986 56679999999999999999999998766 7999999999999999998753100
Q ss_pred chhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChh
Q 008352 407 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD 486 (569)
Q Consensus 407 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pe 486 (569)
. ... .+ +.|+
T Consensus 79 ----------------------~---------------------------------~~~-~~--------------~~~~ 88 (154)
T PRK06759 79 ----------------------E---------------------------------KCV-CV--------------GEYE 88 (154)
T ss_pred ----------------------c---------------------------------ccc-cc--------------CCCc
Confidence 0 000 00 0111
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352 487 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 555 (569)
Q Consensus 487 e~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 555 (569)
+.+...+....|..+|..||+++|+||.++|+ +++|.+|||+.||+|..+|+++..||+++||+.
T Consensus 89 ~~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~~----~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 89 DHFHFEDVEMKVKDFMSVLDEKEKYIIFERFF----VGKTMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred ccccHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 22233344567999999999999999999998 999999999999999999999999999999974
No 52
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=99.87 E-value=1e-20 Score=182.77 Aligned_cols=174 Identities=14% Similarity=0.181 Sum_probs=141.1
Q ss_pred CCHHHHHHHHhccH-HHHHHHHHHHHHHHHHHHHHhhCCC---CCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHH
Q 008352 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRG---ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV 389 (569)
Q Consensus 314 ~~~~~L~~~l~~G~-~Are~LI~~nlrLV~sIArry~~~g---~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wI 389 (569)
++++.|+..+..|+ .|++.|+..|.+.|++++.++.+++ .+.+|++||+++++|+++++|++..+ .|.||++..+
T Consensus 3 ~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~ia 81 (189)
T PRK06811 3 INEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAIS 81 (189)
T ss_pred CcHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHH
Confidence 45677777777665 9999999999999999999998863 47899999999999999999997654 7999999999
Q ss_pred HHHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCC
Q 008352 390 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQ 469 (569)
Q Consensus 390 RqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~ 469 (569)
++.+.++++++.+...+ .+.+.
T Consensus 82 rn~~~d~~rk~~~~~~~----------------------------------------------------~~~~~------ 103 (189)
T PRK06811 82 KYKAIDYKRKLTKNNEI----------------------------------------------------DSIDE------ 103 (189)
T ss_pred HHHHHHHHHHhcccccc----------------------------------------------------ccchh------
Confidence 99999999876521000 00000
Q ss_pred CcchhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352 470 DTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 549 (569)
Q Consensus 470 ~~~l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RAL 549 (569)
. .. ....++++.+...+....|..+|..||+++|.||.++|. +|+|++|||+.||+|..+|++.+.||+
T Consensus 104 ~------~~-~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIAe~lgis~~~V~~~l~Ra~ 172 (189)
T PRK06811 104 F------IL-ISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYL----LGEKIEEIAKKLGLTRSAIDNRLSRGR 172 (189)
T ss_pred h------hh-cccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----ccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 0 00 011245666666777788999999999999999999998 899999999999999999999999999
Q ss_pred HHHHHHhh
Q 008352 550 YRLKQSLG 557 (569)
Q Consensus 550 kKLR~~l~ 557 (569)
++||....
T Consensus 173 ~~Lr~~~~ 180 (189)
T PRK06811 173 KKLQKNKL 180 (189)
T ss_pred HHHHHccc
Confidence 99998643
No 53
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=9.7e-21 Score=188.96 Aligned_cols=173 Identities=19% Similarity=0.245 Sum_probs=138.1
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccce
Q 008352 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 404 (569)
Q Consensus 325 ~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~I 404 (569)
++..|++.|+..|.+.|+++|+++.+++.+.+||+||+|+++|+++++|++. ..|.+|++..+++.+.+++++..+..
T Consensus 27 gd~~a~~~l~~~y~~~l~~~a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~Rk~~r~~ 104 (231)
T PRK11922 27 GDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNEALGRLRRRRRLV 104 (231)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHHHHHHHHhhcccc
Confidence 4568999999999999999999999999999999999999999999999986 47999999999999999988765321
Q ss_pred ecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCC
Q 008352 405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 484 (569)
Q Consensus 405 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~ 484 (569)
.++. . ..+ .... ++ ...... ....+
T Consensus 105 ~~~~----------------------------~----------------------~~~-~~~~-~~--~~~~~~-~~~~~ 129 (231)
T PRK11922 105 NLAE----------------------------M----------------------VMA-STIA-GG--ERTPLA-DPAED 129 (231)
T ss_pred cchh----------------------------c----------------------ccc-cccc-cc--cccccC-cccCC
Confidence 1100 0 000 0000 00 000001 11235
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352 485 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 558 (569)
Q Consensus 485 pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 558 (569)
|++.+...+..+.|..+|..||+++|+||.++|. +++|++|||+.||+|.++|++++.||+++||+.+..
T Consensus 130 ~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~~ 199 (231)
T PRK11922 130 PERAAARREIRALLERAIDALPDAFRAVFVLRVV----EELSVEETAQALGLPEETVKTRLHRARRLLRESLAR 199 (231)
T ss_pred hHHHHHHHHHHHHHHHHHHhCCHHHhhhheeehh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 6677777788888999999999999999999988 899999999999999999999999999999998864
No 54
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=1.3e-20 Score=182.95 Aligned_cols=177 Identities=19% Similarity=0.215 Sum_probs=143.3
Q ss_pred CCHHHHHHHHhccH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 008352 314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (569)
Q Consensus 314 ~~~~~L~~~l~~G~-~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa 392 (569)
+++..|+..+..|+ .|++.|+..|.+.|+.+|.++.++..+++|++||+++++|+.+.+|++.. ..|.+|++..+++.
T Consensus 11 ~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~n~ 89 (196)
T PRK12524 11 VSDEALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVCNL 89 (196)
T ss_pred cCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHHHHH
Confidence 35667777776664 99999999999999999999999999999999999999999999998533 47999999999999
Q ss_pred HHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 008352 393 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 472 (569)
Q Consensus 393 I~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~ 472 (569)
+.++++++.+. ...++. . .
T Consensus 90 ~~d~~Rk~~~~------------------------------------------------------~~~~~~-~---~--- 108 (196)
T PRK12524 90 CTDRLRRRRRA------------------------------------------------------SVDLDD-A---P--- 108 (196)
T ss_pred HHHHHHhhcCC------------------------------------------------------CCCccc-c---c---
Confidence 99998865310 000000 0 0
Q ss_pred hhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008352 473 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 552 (569)
Q Consensus 473 l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 552 (569)
+. .+. ...+++.+...+....|..+|+.||+++|+||.|+|. ++++++|||+.||||..+|++++.||+++|
T Consensus 109 --~~-~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~~----~g~s~~eIA~~lgis~~tV~~~l~Ra~~~L 180 (196)
T PRK12524 109 --EP-ADA-APGAEEALIEGDRMRALDAALAALPERQRQAVVLRHI----EGLSNPEIAEVMEIGVEAVESLTARGKRAL 180 (196)
T ss_pred --cc-ccc-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 00 011 1235556666677788999999999999999999998 899999999999999999999999999999
Q ss_pred HHHhhcCc
Q 008352 553 KQSLGGKA 560 (569)
Q Consensus 553 R~~l~~~~ 560 (569)
|.++...+
T Consensus 181 r~~l~~~~ 188 (196)
T PRK12524 181 AALLAGQR 188 (196)
T ss_pred HHHHHhcc
Confidence 99987543
No 55
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=1.3e-20 Score=180.75 Aligned_cols=172 Identities=13% Similarity=0.161 Sum_probs=137.2
Q ss_pred CHHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 008352 315 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 393 (569)
Q Consensus 315 ~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI 393 (569)
+...|+..+.+| ..|++.|+..|.+.|+.++.++.++..+.+|++||+|+.+|+.+++|++.. ..|.+|++..+++.+
T Consensus 9 ~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~-~~~~~wL~~iarn~~ 87 (182)
T PRK12537 9 DYEACLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPAR-GSARGWIYSVTRHLA 87 (182)
T ss_pred hHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCccc-ccHHHHHHHHHHHHH
Confidence 345566666655 499999999999999999999999999999999999999999999998644 379999999999999
Q ss_pred HHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 008352 394 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 473 (569)
Q Consensus 394 ~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l 473 (569)
.+++++..+...+ +. ..
T Consensus 88 ~d~~r~~~~~~~~-------------------------------------------------------~~-----~~--- 104 (182)
T PRK12537 88 LNVLRDTRREVVL-------------------------------------------------------DD-----DA--- 104 (182)
T ss_pred HHHHHhccccCcc-------------------------------------------------------cc-----ch---
Confidence 9999876421000 00 00
Q ss_pred hhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352 474 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 474 ~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 553 (569)
.+...+ ...+++.....+....|..+|+.||+++|+||.++|. +++|++|||+.||||.++|+..+.||+++||
T Consensus 105 ~~~~~~--~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr 178 (182)
T PRK12537 105 EETAQT--LHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYV----DGCSHAEIAQRLGAPLGTVKAWIKRSLKALR 178 (182)
T ss_pred hhhccc--ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCChhhHHHHHHHHHHHHH
Confidence 000000 1123333444455667999999999999999999998 8999999999999999999999999999999
Q ss_pred HHh
Q 008352 554 QSL 556 (569)
Q Consensus 554 ~~l 556 (569)
+++
T Consensus 179 ~~l 181 (182)
T PRK12537 179 ECM 181 (182)
T ss_pred HHh
Confidence 876
No 56
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=1.2e-20 Score=189.26 Aligned_cols=174 Identities=15% Similarity=0.223 Sum_probs=140.4
Q ss_pred CHHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 008352 315 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 393 (569)
Q Consensus 315 ~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI 393 (569)
++..|+..+..| ..|++.|+..|.+.|+.+++++.++..+.+|++||+|+.+|+.+++|++..+ .|.+|++..+++.+
T Consensus 49 ~d~~Li~~~~~gd~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~~ 127 (233)
T PRK12538 49 EDEELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNRC 127 (233)
T ss_pred cHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHHH
Confidence 455666666555 4999999999999999999999999999999999999999999999987544 79999999999999
Q ss_pred HHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 008352 394 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 473 (569)
Q Consensus 394 ~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l 473 (569)
.++++++.+. . ++. . .
T Consensus 128 id~~Rk~~~~-~-------------------------------------------------------~~~-~-~------ 143 (233)
T PRK12538 128 IDLRRKPRTE-N-------------------------------------------------------VDA-V-P------ 143 (233)
T ss_pred HHHHHhhccc-c-------------------------------------------------------ccc-c-c------
Confidence 9988764210 0 000 0 0
Q ss_pred hhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352 474 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 474 ~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 553 (569)
+. .+ ....+++.+...+....|..+|..||+++|+||.|+|. +|+|++|||+.||+|.++|+++++||+++||
T Consensus 144 -~~-~~-~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~~----eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr 216 (233)
T PRK12538 144 -EV-AD-GKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSYH----ENMSNGEIAEVMDTTVAAVESLLKRGRQQLR 216 (233)
T ss_pred -cc-cc-CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 00 00 01134445555666778999999999999999999998 9999999999999999999999999999999
Q ss_pred HHhhcCc
Q 008352 554 QSLGGKA 560 (569)
Q Consensus 554 ~~l~~~~ 560 (569)
+.+...+
T Consensus 217 ~~l~~~~ 223 (233)
T PRK12538 217 DLLRRHE 223 (233)
T ss_pred HHHHHhh
Confidence 9887543
No 57
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=99.86 E-value=2.4e-20 Score=179.99 Aligned_cols=180 Identities=15% Similarity=0.203 Sum_probs=140.6
Q ss_pred HHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHH
Q 008352 316 CRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR 394 (569)
Q Consensus 316 ~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~ 394 (569)
++.|+..++.| ..+++.|+..|.+.|+.+++++.++..+.+|++||+++++|+++.+|++.. .|.+|++..+++.+.
T Consensus 7 ~~~ll~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~~ 84 (193)
T PRK11923 7 DQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTAK 84 (193)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHHH
Confidence 34555555555 599999999999999999999999989999999999999999999999874 499999999999999
Q ss_pred HHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchh
Q 008352 395 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ 474 (569)
Q Consensus 395 ~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~ 474 (569)
++++++.+.... ....++.....++.
T Consensus 85 d~~rk~~~~~~~--------------------------------------------------~~~~~~~~~~~~~~---- 110 (193)
T PRK11923 85 NHLVSRGRRPPD--------------------------------------------------SDVSSEDAEFYDGD---- 110 (193)
T ss_pred HHHHHhcCCCcc--------------------------------------------------ccccccchhhhccc----
Confidence 998765421000 00000000000000
Q ss_pred hcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 475 EITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 475 d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
..+. ....|++.+...+..+.+..+|..||+++|.||.++|. +|+|++|||+.||+|..+|++...||+++||.
T Consensus 111 ~~~~--~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 184 (193)
T PRK11923 111 HALK--DIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREF----DGLSYEDIASVMQCPVGTVRSRIFRAREAIDK 184 (193)
T ss_pred cccc--CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 0011 12256666677777889999999999999999999998 89999999999999999999999999999999
Q ss_pred Hhh
Q 008352 555 SLG 557 (569)
Q Consensus 555 ~l~ 557 (569)
++.
T Consensus 185 ~l~ 187 (193)
T PRK11923 185 ALQ 187 (193)
T ss_pred HHH
Confidence 885
No 58
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=2.1e-20 Score=179.53 Aligned_cols=173 Identities=15% Similarity=0.157 Sum_probs=136.6
Q ss_pred HHHHHHH-hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHH
Q 008352 317 RDLKSEL-HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK 395 (569)
Q Consensus 317 ~~L~~~l-~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~ 395 (569)
..+...+ .++..+++.|+..|.++|+++|+++.++..+.+|++||+|+++|+++++|++.++ .|.+|++..+++.+.+
T Consensus 13 ~~l~~~~~~~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~~d 91 (187)
T PRK12534 13 GRLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKAID 91 (187)
T ss_pred HHHHHHHHcCCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHH
Confidence 3344444 4455999999999999999999999999999999999999999999999998654 6889999999999999
Q ss_pred HHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhh
Q 008352 396 AIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQE 475 (569)
Q Consensus 396 ~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d 475 (569)
+++++.+... ..+.+. ..+
T Consensus 92 ~~R~~~~~~~----------------------------------------------------~~~~~~---------~~~ 110 (187)
T PRK12534 92 HLRANAPQRR----------------------------------------------------NVALDD---------AGE 110 (187)
T ss_pred HHHhcccccc----------------------------------------------------cccccc---------hhh
Confidence 9987541100 000000 000
Q ss_pred cccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352 476 ITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 555 (569)
Q Consensus 476 ~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 555 (569)
.. +. ..++++.....+....|..+|..||++++.|+.++|. +++|++|||+.||+|..+|+++++||+++||+.
T Consensus 111 ~~-~~-~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 184 (187)
T PRK12534 111 LR-AA-DASPLERTERASTRRRIDHCLAELEPPRSELIRTAFF----EGITYEELAARTDTPIGTVKSWIRRGLAKLKAC 184 (187)
T ss_pred hc-cc-cCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Confidence 00 00 1123444455566778999999999999999999998 899999999999999999999999999999998
Q ss_pred hh
Q 008352 556 LG 557 (569)
Q Consensus 556 l~ 557 (569)
+.
T Consensus 185 l~ 186 (187)
T PRK12534 185 LE 186 (187)
T ss_pred Hc
Confidence 74
No 59
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=99.86 E-value=1e-20 Score=182.35 Aligned_cols=173 Identities=20% Similarity=0.290 Sum_probs=136.5
Q ss_pred CCCHHHHHHHHhc----cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHH
Q 008352 313 GLSCRDLKSELHS----GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 388 (569)
Q Consensus 313 g~~~~~L~~~l~~----G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~w 388 (569)
.++++.|+..++. +..|++.|+..|.+.|+++|.+|.++..+.+|++||+++.+|+++++|++. ..|.+|++.+
T Consensus 7 ~~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~~--~~~~~wl~~i 84 (188)
T PRK09640 7 ELNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLYSI 84 (188)
T ss_pred CCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcCC--CcchHHHHHH
Confidence 4567777777763 569999999999999999999999999999999999999999999999864 4799999999
Q ss_pred HHHHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCC
Q 008352 389 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWAD 468 (569)
Q Consensus 389 IRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d 468 (569)
+++.+.+++++..+.... . .+...
T Consensus 85 a~n~~~d~~R~~~~~~~~--------------------------~---------------------------~~~~~--- 108 (188)
T PRK09640 85 TYNECITQYRKERRKRRL--------------------------M---------------------------DALSL--- 108 (188)
T ss_pred HHHHHHHHHHHhcccccC--------------------------c---------------------------chhhh---
Confidence 999999999864321000 0 00000
Q ss_pred CCcchhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352 469 QDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 548 (569)
Q Consensus 469 ~~~~l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RA 548 (569)
+...++. ++.....+....|..+|+.||+++|+||.++|. +++|++|||+.||||..+|+..+.||
T Consensus 109 ------~~~~~~~----~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra 174 (188)
T PRK09640 109 ------DPLEEAS----EEKAPKPEERGGLDRWLVHVNPIDREILVLRFV----AELEFQEIADIMHMGLSATKMRYKRA 174 (188)
T ss_pred ------ccccccc----ccccccHHHHHHHHHHHHhcChhheeeeeeHHh----cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 0000000 001112234457899999999999999999998 89999999999999999999999999
Q ss_pred HHHHHHHhh
Q 008352 549 LYRLKQSLG 557 (569)
Q Consensus 549 LkKLR~~l~ 557 (569)
+++||+.+.
T Consensus 175 ~~~Lr~~l~ 183 (188)
T PRK09640 175 LDKLREKFA 183 (188)
T ss_pred HHHHHHHHH
Confidence 999999874
No 60
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=99.85 E-value=5.9e-20 Score=175.61 Aligned_cols=180 Identities=19% Similarity=0.207 Sum_probs=138.2
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhC----CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhc
Q 008352 325 SGNSSREKLINANLRLVVHVAKQYQG----RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 400 (569)
Q Consensus 325 ~G~~Are~LI~~nlrLV~sIArry~~----~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~ 400 (569)
++..|++.|+..|.+.|+.+|++|.+ +..+.+|++||+++.+|+++.+|++..+.+|.+|++..+++.+.+++++.
T Consensus 4 ~~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~~ 83 (189)
T TIGR02984 4 GDQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRRH 83 (189)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHHH
Confidence 45699999999999999999999753 56789999999999999999999986666899999999999999998764
Q ss_pred ccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCC-CCCCcchhhcccC
Q 008352 401 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVW-ADQDTTFQEITAD 479 (569)
Q Consensus 401 ~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~-~d~~~~l~d~i~D 479 (569)
.+ +.+ |.+ ....+++.... ++....+.+.+.+
T Consensus 84 ~~-----------------~~~-------r~~-----------------------~~~~~~~~~~~~~~~~~~~~~~~~~ 116 (189)
T TIGR02984 84 LG-----------------AQK-------RDI-----------------------RREQSLDAGGRLDESSVRLAAQLAA 116 (189)
T ss_pred HH-----------------HHh-------hhc-----------------------ccccCCCcccccCCcchhHHHHccC
Confidence 20 000 000 00112221110 1111123333333
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352 480 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556 (569)
Q Consensus 480 ~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 556 (569)
...+|++.+...+....|..+|..||+++|+||.++|+ +|++++|||+.||||.++|++.+.||+++||+.+
T Consensus 117 -~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~~----~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~l 188 (189)
T TIGR02984 117 -DGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRHL----EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQIL 188 (189)
T ss_pred -CCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 23356777777777788999999999999999999998 8999999999999999999999999999999876
No 61
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=5.4e-20 Score=177.32 Aligned_cols=177 Identities=19% Similarity=0.262 Sum_probs=143.6
Q ss_pred CCHHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 008352 314 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (569)
Q Consensus 314 ~~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa 392 (569)
++++.|+..+..| ..|++.|+..|.+.|+.++.++.++..+.+|++||+|+.+|+++++|++. ..|.+|++..+++.
T Consensus 7 ~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n~ 84 (189)
T PRK12515 7 TTDEMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARFK 84 (189)
T ss_pred cCHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHHH
Confidence 4566777766655 48999999999999999999999999999999999999999999999974 47999999999999
Q ss_pred HHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 008352 393 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 472 (569)
Q Consensus 393 I~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~ 472 (569)
+.+++++..+.. +.. +.
T Consensus 85 ~~d~~r~~~~~~--------------------------------------------------------~~~----~~--- 101 (189)
T PRK12515 85 ALSALRRRKHEE--------------------------------------------------------IDD----EA--- 101 (189)
T ss_pred HHHHHHccCCCC--------------------------------------------------------Ccc----cc---
Confidence 999987643100 000 00
Q ss_pred hhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008352 473 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 552 (569)
Q Consensus 473 l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 552 (569)
. ....+ ...+++......+....+..+|+.||+++|+||.++|. ++++++|||+.||+|..+|+.++.||+++|
T Consensus 102 ~-~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~tV~~~l~Rar~~L 175 (189)
T PRK12515 102 A-AAIED-GADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYY----HEKSVEEVGEIVGIPESTVKTRMFYARKKL 175 (189)
T ss_pred c-cccCC-CCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 0 00111 12245555566666778999999999999999999998 899999999999999999999999999999
Q ss_pred HHHhhcCch
Q 008352 553 KQSLGGKAS 561 (569)
Q Consensus 553 R~~l~~~~L 561 (569)
|+.+...+.
T Consensus 176 r~~l~~~~~ 184 (189)
T PRK12515 176 AELLKAAGV 184 (189)
T ss_pred HHHHHHhcc
Confidence 999876543
No 62
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=4.9e-20 Score=180.70 Aligned_cols=171 Identities=12% Similarity=0.165 Sum_probs=133.1
Q ss_pred hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccc
Q 008352 324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 403 (569)
Q Consensus 324 ~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~ 403 (569)
.++..+++.|+..|.+.|+.++.++.++..+.+|++||+|+.+|+++..|++.++ .|.+|++.++++.+.++++++.+.
T Consensus 34 ~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d~~Rk~~~~ 112 (206)
T PRK12526 34 SRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFDMLRKIKAK 112 (206)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHHHHHHhccc
Confidence 3556999999999999999999999999889999999999999999999998665 599999999999999999876421
Q ss_pred eecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCC
Q 008352 404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE 483 (569)
Q Consensus 404 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~ 483 (569)
... . .+ ++...+.+.+.+. ..
T Consensus 113 ~~~-------------------------~----------------------------~~-----~~~~~~~~~~~~~-~~ 133 (206)
T PRK12526 113 KEQ-------------------------N----------------------------LG-----DDIWPIEQALAES-QS 133 (206)
T ss_pred ccc-------------------------c----------------------------cc-----cccchhhhhcccc-cC
Confidence 100 0 00 0000000111111 11
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352 484 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 559 (569)
Q Consensus 484 ~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 559 (569)
.+. ..........|..+|..||+++|+||.++|+ +++|++|||+.||+|..+|+.+++||+++||+.+...
T Consensus 134 ~~~-~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~ 204 (206)
T PRK12526 134 ESE-EFSDHLMDKQILSYIEKLPEAQQTVVKGVYF----QELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQMGEQ 204 (206)
T ss_pred chH-HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence 122 2233334457899999999999999999998 9999999999999999999999999999999988643
No 63
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=2.3e-20 Score=179.28 Aligned_cols=175 Identities=17% Similarity=0.207 Sum_probs=138.9
Q ss_pred hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccc
Q 008352 324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 403 (569)
Q Consensus 324 ~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~ 403 (569)
.++..|++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|+++++|++..+..|.||++..++|.+.++++++.+.
T Consensus 5 ~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~~~ 84 (185)
T PRK12542 5 NNDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNKRH 84 (185)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 34569999999999999999999999999999999999999999999999875445799999999999999999876421
Q ss_pred eecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCC
Q 008352 404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE 483 (569)
Q Consensus 404 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~ 483 (569)
.. .. +. . .. +.... ..+
T Consensus 85 ~~------------------~~------------------------------------~~-~---~~----~~~~~-~~~ 101 (185)
T PRK12542 85 ET------------------FL------------------------------------EE-Y---ER----ESIEA-VDE 101 (185)
T ss_pred hh------------------hh------------------------------------hh-c---cc----cchhh-hhc
Confidence 00 00 00 0 00 00000 001
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhh
Q 008352 484 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYG 563 (569)
Q Consensus 484 ~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~ 563 (569)
.+++.....+....|..+|..||+++|+||.|+|. +++|++|||+.||+|..+|+..+.||+++||+.+.......
T Consensus 102 ~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~~~ 177 (185)
T PRK12542 102 NIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVF----YNLTYQEISSVMGITEANVRKQFERARKRVQNMIGGIQHDE 177 (185)
T ss_pred cHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccchHH
Confidence 23333334444567999999999999999999998 89999999999999999999999999999999998877766
Q ss_pred hh
Q 008352 564 YA 565 (569)
Q Consensus 564 yl 565 (569)
|+
T Consensus 178 ~~ 179 (185)
T PRK12542 178 FK 179 (185)
T ss_pred HH
Confidence 64
No 64
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=5.4e-20 Score=173.36 Aligned_cols=168 Identities=16% Similarity=0.176 Sum_probs=138.7
Q ss_pred hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccc
Q 008352 324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 403 (569)
Q Consensus 324 ~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~ 403 (569)
.++..|++.|+..|.+.|+++|+++.++..+.+|++||++++||++++.|+ .+..|.+|++..+++.+.+++++..+.
T Consensus 9 ~~~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~~r~~~~~ 86 (179)
T PRK11924 9 TGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDLLRRRRRE 86 (179)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHHHHhcccc
Confidence 345599999999999999999999999999999999999999999999998 345899999999999999998865421
Q ss_pred eecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCC
Q 008352 404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE 483 (569)
Q Consensus 404 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~ 483 (569)
... ..+ .. .+...+....
T Consensus 87 ~~~-----------------------------------------------------~~~-~~--------~~~~~~~~~~ 104 (179)
T PRK11924 87 KAV-----------------------------------------------------LSD-DA--------LEPEFAETAE 104 (179)
T ss_pred ccc-----------------------------------------------------Ccc-cc--------cccccCCccC
Confidence 100 000 00 0000000223
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352 484 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 559 (569)
Q Consensus 484 ~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 559 (569)
+|++.+...+....+..+|..||++++.||.++|. ++++.+|||+.||+|+.+|++.+.||+++||+.+..+
T Consensus 105 ~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~~~ 176 (179)
T PRK11924 105 TPEAALLAKDDLARIDRCLDALPVKQREVFLLRYV----EGLSYREIAEILGVPVGTVKSRLRRARQLLRECLEAQ 176 (179)
T ss_pred CHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 67778888888899999999999999999999998 8999999999999999999999999999999988654
No 65
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=99.84 E-value=1e-19 Score=176.54 Aligned_cols=171 Identities=16% Similarity=0.172 Sum_probs=138.4
Q ss_pred CHHHHHHHHhccH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 008352 315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 393 (569)
Q Consensus 315 ~~~~L~~~l~~G~-~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI 393 (569)
++..++..+..|+ .+++.|+..|.+.|++++.++.++..+++|++||+|+.+|+++++|++.. .|.+|++..+++.+
T Consensus 13 ~~~~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~~--~f~~wL~~i~rn~~ 90 (192)
T PRK09643 13 SDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDA--AVSSWLHRIVVNAC 90 (192)
T ss_pred CHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCCC--ccHHHHHHHHHHHH
Confidence 4566666665554 99999999999999999999999999999999999999999999999753 59999999999999
Q ss_pred HHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 008352 394 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 473 (569)
Q Consensus 394 ~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l 473 (569)
.+++++..+... .+++. ..
T Consensus 91 ~d~~Rk~~~~~~-----------------------------------------------------~~~~~----~~---- 109 (192)
T PRK09643 91 LDRLRRAKARPT-----------------------------------------------------VPLDD----VY---- 109 (192)
T ss_pred HHHHHccccCCC-----------------------------------------------------CCccc----cc----
Confidence 999987542100 00000 00
Q ss_pred hhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352 474 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 474 ~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 553 (569)
+. . ..+++.+...+....|..+|..||+++|+||.|+|. +++|++|||+.||+|..+|+..+.||+++||
T Consensus 110 -~~-~----~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~~----~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr 179 (192)
T PRK09643 110 -PV-A----QLERDPTARVETALAVQRALMRLPVEQRAALVAVDM----QGYSVADAARMLGVAEGTVKSRCARGRARLA 179 (192)
T ss_pred -cc-c----CCcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 00 0 012233444555678999999999999999999998 8999999999999999999999999999999
Q ss_pred HHhhc
Q 008352 554 QSLGG 558 (569)
Q Consensus 554 ~~l~~ 558 (569)
+.+..
T Consensus 180 ~~l~~ 184 (192)
T PRK09643 180 ELLGY 184 (192)
T ss_pred HHHHH
Confidence 98864
No 66
>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=99.84 E-value=9.2e-20 Score=172.33 Aligned_cols=167 Identities=17% Similarity=0.211 Sum_probs=132.3
Q ss_pred CCHHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 008352 314 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (569)
Q Consensus 314 ~~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa 392 (569)
|+++.++..+..| ..|++.++..|.+.|++++.++.++..+++|++||+++.+|+++++|++. ..|.+|++..+++.
T Consensus 1 ~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~--~~~~~wl~~i~~n~ 78 (169)
T TIGR02954 1 MNDEELVKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHP--KYFNTWLTRILINE 78 (169)
T ss_pred CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCc--cccHHHHHHHHHHH
Confidence 3455666666555 49999999999999999999999999999999999999999999999975 36999999999999
Q ss_pred HHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 008352 393 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 472 (569)
Q Consensus 393 I~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~ 472 (569)
+.+++++..+.. .++.....+
T Consensus 79 ~~d~~R~~~~~~-------------------------------------------------------~~~~~~~~~---- 99 (169)
T TIGR02954 79 CIDLLKKKKKVI-------------------------------------------------------PFDPNTSIE---- 99 (169)
T ss_pred HHHHHHhcCCcC-------------------------------------------------------ccccccccc----
Confidence 999988754210 000000000
Q ss_pred hhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008352 473 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 552 (569)
Q Consensus 473 l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 552 (569)
+. .++ ... +....+..+|..||+++|+||.++|. +|+|.+|||+.||||..+|+....||+++|
T Consensus 100 ------~~---~~~--~~~-~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eiA~~lgis~~tv~~~l~Ra~~~L 163 (169)
T TIGR02954 100 ------KG---ECE--THA-DSRLDLYKAIDTLNDKYQTAIILRYY----HDLTIKEIAEVMNKPEGTVKTYLHRALKKL 163 (169)
T ss_pred ------cc---hhh--hch-HHHHHHHHHHHhCCHHHhHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 00 000 001 11236889999999999999999998 899999999999999999999999999999
Q ss_pred HHHhh
Q 008352 553 KQSLG 557 (569)
Q Consensus 553 R~~l~ 557 (569)
|+.+.
T Consensus 164 r~~l~ 168 (169)
T TIGR02954 164 KKRLE 168 (169)
T ss_pred HHHhc
Confidence 99874
No 67
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=99.84 E-value=6.8e-20 Score=173.93 Aligned_cols=172 Identities=13% Similarity=0.189 Sum_probs=134.2
Q ss_pred CCHHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 008352 314 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (569)
Q Consensus 314 ~~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa 392 (569)
|++..+...+..| ..|++.|+..|.+.|+.+|+++.++..+.+|++||+|+++|++++.|++. .+|.+|++..+++.
T Consensus 3 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n~ 80 (176)
T PRK09638 3 MDEKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASRL 80 (176)
T ss_pred ccHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHH
Confidence 3455666655555 49999999999999999999999999999999999999999999999874 47999999999999
Q ss_pred HHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 008352 393 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 472 (569)
Q Consensus 393 I~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~ 472 (569)
+.+++++..+.... .+.+ .+.
T Consensus 81 ~~d~~r~~~~~~~~---------------------------~~~~-----------------------~~~--------- 101 (176)
T PRK09638 81 YKDHLRKQKREKLR---------------------------LQRA-----------------------KEE--------- 101 (176)
T ss_pred HHHHHHHhccccch---------------------------hhhc-----------------------ccc---------
Confidence 99999875421100 0000 000
Q ss_pred hhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008352 473 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 552 (569)
Q Consensus 473 l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 552 (569)
..+ .... +..........|..+|..||+++|+||.++|. +|++++|||+.||+|..+|+..+.||+++|
T Consensus 102 ----~~~--~~~~-~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~l~is~~~V~~~l~ra~~~l 170 (176)
T PRK09638 102 ----TLR--KEKW-EAAIKGAEWSEMLDALSKLDPEFRAPVILKHY----YGYTYEEIAKMLNIPEGTVKSRVHHGIKQL 170 (176)
T ss_pred ----cCC--ccch-HHHHHhhhHHHHHHHHHcCCHHHhheeeehhh----cCCCHHHHHHHHCCChhHHHHHHHHHHHHH
Confidence 000 0000 11122234456889999999999999999998 899999999999999999999999999999
Q ss_pred HHHhh
Q 008352 553 KQSLG 557 (569)
Q Consensus 553 R~~l~ 557 (569)
|+.+.
T Consensus 171 ~~~l~ 175 (176)
T PRK09638 171 RKEWG 175 (176)
T ss_pred HHHhc
Confidence 99763
No 68
>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=99.84 E-value=1.6e-19 Score=163.53 Aligned_cols=157 Identities=25% Similarity=0.386 Sum_probs=131.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecch
Q 008352 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 408 (569)
Q Consensus 329 Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~ 408 (569)
|++.++..|.++|.++++++.+++.+.+|++|||++++|++++.|++. .+|.+|+.+++++.+.++++++.+ .+.
T Consensus 2 a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~---~~~ 76 (158)
T TIGR02937 2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR---LRR 76 (158)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhcc---CCc
Confidence 789999999999999999999999999999999999999999999998 689999999999999999988763 110
Q ss_pred hHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHH
Q 008352 409 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 488 (569)
Q Consensus 409 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~ 488 (569)
.. . .. ... ......++..
T Consensus 77 ~~---------------------------------------------------~------~~----~~~-~~~~~~~~~~ 94 (158)
T TIGR02937 77 EL---------------------------------------------------D------LL----EEL-LDSDPSPEEE 94 (158)
T ss_pred ch---------------------------------------------------h------hh----hhc-ccccCCHHHH
Confidence 00 0 00 000 0111245566
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352 489 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556 (569)
Q Consensus 489 l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 556 (569)
.........|..+|+.||++++.||.++|+ .|+|..|||+.+|+|+.+|+++..+++++||+.+
T Consensus 95 ~~~~~~~~~l~~~l~~L~~~~~~ii~~~~~----~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~l 158 (158)
T TIGR02937 95 LEQEEEREALREALEKLPEREREVLVLRYL----EGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158 (158)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 666777788999999999999999999987 7999999999999999999999999999999754
No 69
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=1.1e-19 Score=173.83 Aligned_cols=165 Identities=16% Similarity=0.182 Sum_probs=133.1
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccce
Q 008352 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 404 (569)
Q Consensus 325 ~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~I 404 (569)
++..|++.|+..|.+.|+.++++|.++..+.+|++||+++.+|+++.+|++.. .|.+|++..+++.+.+++++..+..
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 44589999999999999999999999999999999999999999999999864 5999999999999988876543100
Q ss_pred ecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCC
Q 008352 405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 484 (569)
Q Consensus 405 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~ 484 (569)
+ .++... + ..+ ......
T Consensus 82 ~------------------------------------------------------~~~~~~-~-----~~~---~~~~~~ 98 (179)
T PRK12543 82 R------------------------------------------------------IFEKAE-E-----QRK---PVSIDF 98 (179)
T ss_pred c------------------------------------------------------cccccc-c-----ccc---cccccC
Confidence 0 000000 0 000 001113
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352 485 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 559 (569)
Q Consensus 485 pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 559 (569)
|+. +...+....|..+|..||+++|+||.++|. +++|++|||+.||||..+|+..+.||+++||+.+...
T Consensus 99 ~~~-~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~~----e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~ 168 (179)
T PRK12543 99 SED-VLSKESNQELIELIHKLPYKLRQVIILRYL----HDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIE 168 (179)
T ss_pred hHH-HHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 444 556667788999999999999999999998 9999999999999999999999999999999988754
No 70
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=99.84 E-value=8.1e-20 Score=169.05 Aligned_cols=160 Identities=18% Similarity=0.204 Sum_probs=129.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecch
Q 008352 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 408 (569)
Q Consensus 329 Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~ 408 (569)
|+++|+..|.+.|+++++++.++..+.+|++||+++++|+++.+|++. .+|.+|++.++++.+.+++++..+.-.
T Consensus 2 a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~--~~~~~wl~~i~r~~~~d~~r~~~~~~~--- 76 (161)
T TIGR02985 2 AFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEV--ESFKAYLFTIVKNRSLNYLRHKQVEEK--- 76 (161)
T ss_pred hHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc--ccHHHHHHHHHHHHHHHHHHHHHhHhH---
Confidence 789999999999999999999998999999999999999999999874 479999999999999999887542100
Q ss_pred hHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHH
Q 008352 409 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 488 (569)
Q Consensus 409 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~ 488 (569)
. ...+ . ++.. .......+++.
T Consensus 77 ---------------~---------~~~~------------------------~----~~~~-------~~~~~~~~~~~ 97 (161)
T TIGR02985 77 ---------------Y---------QEEI------------------------L----EIEV-------DELSENDPEEE 97 (161)
T ss_pred ---------------H---------HHHH------------------------H----hhcc-------cccCCCCcHHH
Confidence 0 0000 0 0000 00011245566
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352 489 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556 (569)
Q Consensus 489 l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 556 (569)
+...+....|..++..||+++++||.++|. +++|.+|||+.||+|+++|++++.+|+++||+.+
T Consensus 98 ~~~~e~~~~l~~~l~~L~~~~r~il~l~~~----~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~l 161 (161)
T TIGR02985 98 LEAKELQLIIYKAIEKLPEQCRKIFILSRF----EGKSYKEIAEELGISVKTVEYHISKALKELRKEL 161 (161)
T ss_pred HHHHHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 666777788999999999999999999998 8999999999999999999999999999999864
No 71
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=1.1e-19 Score=176.21 Aligned_cols=176 Identities=12% Similarity=0.148 Sum_probs=134.0
Q ss_pred HHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHH
Q 008352 319 LKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI 397 (569)
Q Consensus 319 L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~I 397 (569)
++..+..| ..+++.|+..|.+.|+.+|.++.++..+++|++||+++.+|+.+++|++..+ .|.+|++..++|.+.+++
T Consensus 17 li~~~~~~d~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn~~ld~~ 95 (194)
T PRK12531 17 CMEKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRNLCFDLL 95 (194)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHHHHHHHH
Confidence 45555544 5999999999999999999999999889999999999999999999997544 799999999999999999
Q ss_pred HhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcc
Q 008352 398 FQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEIT 477 (569)
Q Consensus 398 r~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i 477 (569)
++..+.... . ..+... .+.. ....+
T Consensus 96 Rk~~~~~~~-------------------------~---------------------------~~~~~~-~~~~--~~~~~ 120 (194)
T PRK12531 96 RKQKGKDLH-------------------------I---------------------------HADDIW-PSDY--YPPDL 120 (194)
T ss_pred HHhcccccc-------------------------c---------------------------chhhcc-cccc--ccccc
Confidence 875421000 0 000000 0000 00000
Q ss_pred cCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352 478 ADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 557 (569)
Q Consensus 478 ~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 557 (569)
.+ ...++.. ...+.+..+|..||+++|+||.++|. +++|++|||+.||||.++|+.+++||+++||..+.
T Consensus 121 ~~--~~~~e~~----~~~~~l~~~l~~Lp~~~r~v~~l~~~----eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~ 190 (194)
T PRK12531 121 VD--HYSPEQD----MLKEQVMKFLDRLPKAQRDVLQAVYL----EELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSMD 190 (194)
T ss_pred cc--ccCHHHH----HHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHhh
Confidence 00 0122222 23356888999999999999999998 99999999999999999999999999999999987
Q ss_pred cCc
Q 008352 558 GKA 560 (569)
Q Consensus 558 ~~~ 560 (569)
...
T Consensus 191 ~~~ 193 (194)
T PRK12531 191 AES 193 (194)
T ss_pred hcc
Confidence 654
No 72
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=99.83 E-value=2.1e-19 Score=170.28 Aligned_cols=165 Identities=14% Similarity=0.133 Sum_probs=131.4
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccce
Q 008352 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 404 (569)
Q Consensus 325 ~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~I 404 (569)
.+..+++.|+..|.+.|+++|.++.++..+++|++||.|+.+|+..++|++.. ..|.+|++..++|.+.++++++.+..
T Consensus 6 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~Rk~~~~~ 84 (173)
T PRK09645 6 AEAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSARARP 84 (173)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHHHHHHHhhcccc
Confidence 35689999999999999999999999988999999999999999999997532 47999999999999999998654210
Q ss_pred ecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCC
Q 008352 405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 484 (569)
Q Consensus 405 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~ 484 (569)
. ...+ +.. +. ++. .
T Consensus 85 ~-----------------------------------------------------~~~~------~~~---~~-~~~---~ 98 (173)
T PRK09645 85 V-----------------------------------------------------EGGD------DVL---GV-PEQ---S 98 (173)
T ss_pred c-----------------------------------------------------cccc------ccc---cC-CCC---C
Confidence 0 0000 000 00 000 1
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008352 485 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 560 (569)
Q Consensus 485 pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 560 (569)
+++.+...+....|..+|+.||+++|+||.|+|. +++|++|||+.||+|..+|+.+++||+++||+.+...+
T Consensus 99 ~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~ 170 (173)
T PRK09645 99 APDEVDRALDRLLVADALAQLSPEHRAVLVRSYY----RGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQERG 170 (173)
T ss_pred CchHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhccc
Confidence 2222333344557899999999999999999998 99999999999999999999999999999999987554
No 73
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=99.83 E-value=1.7e-19 Score=172.96 Aligned_cols=169 Identities=15% Similarity=0.128 Sum_probs=130.1
Q ss_pred HHHHHH-hccHHHHHHHHHHHHHHHHHHHHHhhC-CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHH
Q 008352 318 DLKSEL-HSGNSSREKLINANLRLVVHVAKQYQG-RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK 395 (569)
Q Consensus 318 ~L~~~l-~~G~~Are~LI~~nlrLV~sIArry~~-~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~ 395 (569)
.++..+ .++..|++.|+..|.+.|+.++.++.+ ...+.+|++||+++.||+.++.|++. ..|.+|++..++|.+.+
T Consensus 10 ~~~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~~~d 87 (181)
T PRK12536 10 ALLLRGLAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYKLMD 87 (181)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHHHHH
Confidence 344444 455699999999999999999988764 57899999999999999999999975 46999999999999999
Q ss_pred HHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhh
Q 008352 396 AIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQE 475 (569)
Q Consensus 396 ~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d 475 (569)
+++++.+.... ..+++ + ..+
T Consensus 88 ~~Rk~~~~~~~---------------------------------------------------~~~~~----~-----~~~ 107 (181)
T PRK12536 88 FLRSRARREAL---------------------------------------------------HDPLD----D-----ESE 107 (181)
T ss_pred HHHHHhccccc---------------------------------------------------cCCcc----c-----hhh
Confidence 99875421000 00000 0 000
Q ss_pred cccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352 476 ITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 555 (569)
Q Consensus 476 ~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 555 (569)
...+. .++. .+....+..+|..||+++|.||.++|. +++|++|||+.||||+.+|+..++||+++||+.
T Consensus 108 ~~~~~---~~~~----~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 108 LFATS---DDEA----AEARRDLGKLLEQLPDRQRLPIVHVKL----EGLSVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred hcCCC---Ccch----HHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 00011 1111 123446899999999999999999998 999999999999999999999999999999998
Q ss_pred hhcC
Q 008352 556 LGGK 559 (569)
Q Consensus 556 l~~~ 559 (569)
+...
T Consensus 177 l~~~ 180 (181)
T PRK12536 177 IRGE 180 (181)
T ss_pred hcCC
Confidence 7643
No 74
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=99.83 E-value=3.1e-19 Score=169.49 Aligned_cols=167 Identities=16% Similarity=0.193 Sum_probs=131.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecc
Q 008352 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 407 (569)
Q Consensus 328 ~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP 407 (569)
..+++|+..|.++|+.+|++|.++..+++|++||+++.+|+++++|++.. +|.+|++..++|.+.++++++.+....+
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 45899999999999999999999999999999999999999999999853 7999999999999999998765311000
Q ss_pred hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhH
Q 008352 408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI 487 (569)
Q Consensus 408 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee 487 (569)
... .+. + ...+.........++.
T Consensus 81 ~~~--------------------------------------------------~~~----~---~~~~~~~~~~~~~~~~ 103 (173)
T PRK12522 81 LDL--------------------------------------------------FHK----E---DGGEIEFADDVNISEE 103 (173)
T ss_pred ccc--------------------------------------------------cch----h---hhhhhccccCCCChHH
Confidence 000 000 0 0000000001112333
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352 488 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 558 (569)
Q Consensus 488 ~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 558 (569)
....+..+.|..+|..||+++++||.++|. ++++++|||+.||+|..+|+..+.||+++||+.+..
T Consensus 104 -~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~ 169 (173)
T PRK12522 104 -FIQKVEAEMIREVIQLLNEKYKTVLVLYYY----EQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEG 169 (173)
T ss_pred -HHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 445556778999999999999999999998 999999999999999999999999999999998753
No 75
>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=99.83 E-value=3.4e-19 Score=179.96 Aligned_cols=180 Identities=16% Similarity=0.197 Sum_probs=141.3
Q ss_pred CCCHHHHHHHHhccH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHH-------hhhhcCCCCCCchhhH
Q 008352 313 GLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMK-------SVEKFKPQAGCRFASY 384 (569)
Q Consensus 313 g~~~~~L~~~l~~G~-~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLir-------AiekFDp~kG~rFSTY 384 (569)
+.++..|+..+++|+ .|++.|+..|.+.|+.++.++.++..+++|++||.|+.+|+ .+.+|++. ..|.||
T Consensus 23 ~~~d~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~--~~~~tW 100 (244)
T TIGR03001 23 HAADLYLACACAQGEPAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGR--GPLLSW 100 (244)
T ss_pred cccHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCC--CchHhH
Confidence 346777888877766 99999999999999999999999999999999999999994 78889864 369999
Q ss_pred HHHHHHHHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCC
Q 008352 385 AYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQP 464 (569)
Q Consensus 385 A~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~ 464 (569)
++.+++|.+.++++++.+...+ +
T Consensus 101 L~~Ia~N~~id~lRk~~r~~~~-------------------------------------------------------~-- 123 (244)
T TIGR03001 101 VRIVATRIALELQAQERRHSPV-------------------------------------------------------E-- 123 (244)
T ss_pred HHHHHHHHHHHHHHHhcccCcc-------------------------------------------------------c--
Confidence 9999999999999865421000 0
Q ss_pred CCCCCCcchhhcccCCCCCChhHHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHH
Q 008352 465 VWADQDTTFQEITADTGVEIPDISVQK----QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKER 540 (569)
Q Consensus 465 v~~d~~~~l~d~i~D~~~~~pee~l~~----~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrer 540 (569)
++. ...+. .+. ...|++.+.. .+..+.|..+|+.||+++|+||.|+|. +++|++|||++||||.++
T Consensus 124 --~~~--~~~~~-~~~-~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~----eg~S~~EIA~~Lgis~~T 193 (244)
T TIGR03001 124 --EPT--ELAAL-PAP-GSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHFV----DGLSMDRIGAMYQVHRST 193 (244)
T ss_pred --ccc--ccccc-cCC-CCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHH
Confidence 000 00000 011 1134433332 235677999999999999999999998 999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhcCch
Q 008352 541 VRQLESRALYRLKQSLGGKAS 561 (569)
Q Consensus 541 VRqie~RALkKLR~~l~~~~L 561 (569)
|+..+.||+++||+.+.+...
T Consensus 194 Vk~rl~RAr~~Lr~~l~~~~~ 214 (244)
T TIGR03001 194 VSRWVAQARERLLERTRRRLA 214 (244)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999876543
No 76
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=99.83 E-value=2.3e-19 Score=173.17 Aligned_cols=182 Identities=16% Similarity=0.158 Sum_probs=137.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecch
Q 008352 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 408 (569)
Q Consensus 329 Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~ 408 (569)
+++.|+..|.+.|+.+|.++.++..+.+|++||.|+.+|+.+++|++. .+|.+|++..++|.+.++++++.+......
T Consensus 3 ~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~--~~~~~WL~~ia~n~~~d~~Rk~~r~~~~~~ 80 (191)
T PRK12520 3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQ--SSLKTYLVGILKHKIIDAIRSGRREVRLSL 80 (191)
T ss_pred chHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--ccHHHHHHHHHHHHHHHHHHhhcCcCcccc
Confidence 689999999999999999999999999999999999999999999865 369999999999999999987653211100
Q ss_pred hHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHH
Q 008352 409 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 488 (569)
Q Consensus 409 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~ 488 (569)
.... .....++ ++... . .+ ......++. ..+|++.
T Consensus 81 ~~~~------------------~~~~~~~-----------------------~~~~~-~-~~-~~~~~~~~~-~~~~~~~ 115 (191)
T PRK12520 81 DDAD------------------EQSDDDL-----------------------FDALF-A-AD-GHYREPPSD-WGDPDAA 115 (191)
T ss_pred cccc------------------cchhhhh-----------------------hhhhc-c-cc-cccccCccc-cCCHHHH
Confidence 0000 0000000 00000 0 00 000001111 2356777
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008352 489 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 561 (569)
Q Consensus 489 l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L 561 (569)
+...+....|..+|..||+++|+||.|+|. +++|++|||+.||+|.++|++.+.||+++||+++...+.
T Consensus 116 ~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~ 184 (191)
T PRK12520 116 LSRREFFEVLQACVDRLPPRTGRVFMMREW----LELETEEICQELQITATNAWVLLYRARMRLRECLDLHWF 184 (191)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 777777788999999999999999999998 899999999999999999999999999999999987653
No 77
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=99.83 E-value=3.4e-19 Score=170.68 Aligned_cols=164 Identities=16% Similarity=0.180 Sum_probs=134.3
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhccccee
Q 008352 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 405 (569)
Q Consensus 326 G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IR 405 (569)
+..|++.|+..|.+.|+++|.++.++..+.+|++||+++.+|+++++|++. ..|.+|++..+++.+.+++++..+-..
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 458999999999999999999999999999999999999999999999874 369999999999999999887431100
Q ss_pred cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCCh
Q 008352 406 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP 485 (569)
Q Consensus 406 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~p 485 (569)
. ..+. ...... ....+|
T Consensus 92 ~-----------------------------------------------------~~~~--------~~~~~~--~~~~~~ 108 (179)
T PRK09415 92 I-----------------------------------------------------VTED--------IFTYME--SQKESV 108 (179)
T ss_pred c-----------------------------------------------------cccc--------cccccc--ccccCc
Confidence 0 0000 000000 011245
Q ss_pred hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352 486 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 558 (569)
Q Consensus 486 ee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 558 (569)
++.+...+....|..+|..||+++|+||.++|+ +|+|++|||+.||||.++|++++.||+++||+.+..
T Consensus 109 e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l~~ 177 (179)
T PRK09415 109 EEEVIQNAEDERLASAVMSLPIKYREVIYLFYY----EELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEE 177 (179)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 666666777788999999999999999999998 899999999999999999999999999999998754
No 78
>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=99.83 E-value=2.1e-19 Score=167.43 Aligned_cols=158 Identities=18% Similarity=0.218 Sum_probs=125.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecch
Q 008352 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 408 (569)
Q Consensus 329 Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~ 408 (569)
|++.++..|.+.|+.+|+++.++..+.||++||+++.+|+++++|++.. .|.+|++..+++.+.++++++.+.-.. .
T Consensus 2 ~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~~-~ 78 (159)
T TIGR02989 2 AFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRLV-F 78 (159)
T ss_pred HHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhcccccc-c
Confidence 7899999999999999999999999999999999999999999999764 599999999999999999886521100 0
Q ss_pred hHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHH
Q 008352 409 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 488 (569)
Q Consensus 409 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~ 488 (569)
.++. .+.+.+.. ++.+.
T Consensus 79 -------------------------~~~~------------------------------------~~~~~~~~--~~~~~ 95 (159)
T TIGR02989 79 -------------------------DDEL------------------------------------LEALAAEA--EATEA 95 (159)
T ss_pred -------------------------CHHH------------------------------------HHHHHhhc--ccchH
Confidence 0000 00000000 11112
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352 489 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556 (569)
Q Consensus 489 l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 556 (569)
....+....|..+++.||++++.||.++|. +|++.+|||+.||||..+|+...+||+++||+++
T Consensus 96 ~~~~~~~~~l~~~i~~L~~~~r~v~~l~~~----~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~~~ 159 (159)
T TIGR02989 96 DRSEDELQALEGCLEKLPERQRELLQLRYQ----RGVSLTALAEQLGRTVNAVYKALSRLRVRLRDCV 159 (159)
T ss_pred hhHHHHHHHHHHHHHHCCHHHHHHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcC
Confidence 223334567899999999999999999998 8999999999999999999999999999999853
No 79
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=99.83 E-value=4.1e-19 Score=170.66 Aligned_cols=170 Identities=16% Similarity=0.176 Sum_probs=130.8
Q ss_pred HHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHH----hhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHH
Q 008352 316 CRDLKSELHSG-NSSREKLINANLRLVVHVAKQ----YQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR 390 (569)
Q Consensus 316 ~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArr----y~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIR 390 (569)
...|+..+..| ..|++.|+..|.+.|+.+|++ +.++..+.+|++||+++.+|++++.|++.. .|.+|++..++
T Consensus 8 ~~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~~ 85 (184)
T PRK12539 8 LKALMLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIAR 85 (184)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHHH
Confidence 34455555544 599999999999999999874 457788999999999999999999999753 59999999999
Q ss_pred HHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCC
Q 008352 391 QTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD 470 (569)
Q Consensus 391 qaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~ 470 (569)
+.+.+++++..+.. . ....+ +.
T Consensus 86 n~~~d~~R~~~~~~--------------------------~--------------------------~~~~~------~~ 107 (184)
T PRK12539 86 YKLIDHLRRTRASL--------------------------A--------------------------DVPID------DA 107 (184)
T ss_pred HHHHHHHHHHhccc--------------------------c--------------------------ccChh------hh
Confidence 99999998753100 0 00000 00
Q ss_pred cchhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352 471 TTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 550 (569)
Q Consensus 471 ~~l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 550 (569)
. ... +.+.....+....|..+|..||+++|+||.++|. +|++++|||+.||+|..+|+.++.||++
T Consensus 108 ~---~~~-------~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~ra~~ 173 (184)
T PRK12539 108 D---ELV-------AHDDHAAVESTLDLGRLLARLPEKMRLAIQAVKL----EGLSVAEAATRSGMSESAVKVSVHRGLK 173 (184)
T ss_pred c---ccc-------CCcHHhhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 0 000 0011122234457899999999999999999998 8999999999999999999999999999
Q ss_pred HHHHHhhcC
Q 008352 551 RLKQSLGGK 559 (569)
Q Consensus 551 KLR~~l~~~ 559 (569)
+||+++...
T Consensus 174 ~Lr~~l~~~ 182 (184)
T PRK12539 174 ALAALIGRE 182 (184)
T ss_pred HHHHHHhhc
Confidence 999988643
No 80
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=99.82 E-value=5.4e-19 Score=168.76 Aligned_cols=171 Identities=19% Similarity=0.265 Sum_probs=125.6
Q ss_pred HHHHHHHhccH-HHHHHHHHHHHHHHHHHHHHhhCCCC-----CHHHHHHHHHHHHHH-hhhhcCCCCCCchhhHHHHHH
Q 008352 317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGI-----SLHDLLQEGSMGLMK-SVEKFKPQAGCRFASYAYWWV 389 (569)
Q Consensus 317 ~~L~~~l~~G~-~Are~LI~~nlrLV~sIArry~~~g~-----~~EDLIQEG~IGLir-AiekFDp~kG~rFSTYA~~wI 389 (569)
..|+..+..|+ .|++.|+..|.+.|+.+|++|.++.. +.+|++||+|+.+|+ ...+|++. ..|.+|++.++
T Consensus 5 ~~li~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~i~ 82 (183)
T TIGR02999 5 TELLQQWQNGDAAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAKAM 82 (183)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHHHH
Confidence 34555555554 89999999999999999999998877 899999999999998 78889764 36999999999
Q ss_pred HHHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCC
Q 008352 390 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQ 469 (569)
Q Consensus 390 RqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~ 469 (569)
+|.+.++++++.+..+. . . ..+...
T Consensus 83 ~n~~~d~~R~~~~~~~~----------------------~---------------------------~--~~~~~~---- 107 (183)
T TIGR02999 83 RRILVDHARRRRAQKRG----------------------G---------------------------G--AVRVPL---- 107 (183)
T ss_pred HHHHHHHHHHHHHHhcc----------------------C---------------------------C--cccccc----
Confidence 99999998764310000 0 0 000000
Q ss_pred CcchhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352 470 DTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 549 (569)
Q Consensus 470 ~~~l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RAL 549 (569)
.+..++. .++.. ......+.+...|+.||+++|+||.|+|. +|+|++|||+.||||..+|+.++.||+
T Consensus 108 ----~~~~~~~---~~~~~-~~~~~l~~~~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar 175 (183)
T TIGR02999 108 ----DEVLPDA---EADLD-EELLDLDDALDKLAQVDPRQAEVVELRFF----AGLTVEEIAELLGVSVRTVERDWRFAR 175 (183)
T ss_pred ----ccccCCC---CccHH-HHHHHHHHHHHHhhcCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 0000000 11111 11111223444567799999999999998 999999999999999999999999999
Q ss_pred HHHHHHh
Q 008352 550 YRLKQSL 556 (569)
Q Consensus 550 kKLR~~l 556 (569)
++||+.+
T Consensus 176 ~~Lr~~l 182 (183)
T TIGR02999 176 AWLADEL 182 (183)
T ss_pred HHHHHHh
Confidence 9999876
No 81
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=99.81 E-value=7e-19 Score=169.65 Aligned_cols=170 Identities=16% Similarity=0.105 Sum_probs=129.1
Q ss_pred HHHHHHhc-cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHH
Q 008352 318 DLKSELHS-GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA 396 (569)
Q Consensus 318 ~L~~~l~~-G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~ 396 (569)
.|+..+.. +..|++.|+..|.+.++.+++ +.++..+.+|++||.|+.+|+.+++|++. ..|.+|++..++|.+.++
T Consensus 13 ~l~~~~~~gd~~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~~~d~ 89 (185)
T PRK09649 13 ALALSAAKGNGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVADH 89 (185)
T ss_pred HHHHHHHccCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHHHHHH
Confidence 34444444 459999999999999999995 67888899999999999999999999864 369999999999999999
Q ss_pred HHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhc
Q 008352 397 IFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEI 476 (569)
Q Consensus 397 Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~ 476 (569)
+++..+..+. +.+. . .+.
T Consensus 90 ~Rk~~~~~~~-----------------------------------------------------~~~~-----~----~~~ 107 (185)
T PRK09649 90 IRHVRSRPRT-----------------------------------------------------TRGA-----R----PEH 107 (185)
T ss_pred HHHhcccccc-----------------------------------------------------cccc-----c----hhh
Confidence 9875311000 0000 0 000
Q ss_pred ccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352 477 TADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556 (569)
Q Consensus 477 i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 556 (569)
..+ ++......+....|..+|..||+++|+||.|+|. +++|++|||+.||+|.++|+..+.||+++||+.+
T Consensus 108 ~~~-----~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~~ 178 (185)
T PRK09649 108 LID-----GDRHARGFEDLVEVTTMIADLTTDQREALLLTQL----LGLSYADAAAVCGCPVGTIRSRVARARDALLADA 178 (185)
T ss_pred ccC-----hhhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 000 0000111122345788999999999999999998 9999999999999999999999999999999966
Q ss_pred hcCch
Q 008352 557 GGKAS 561 (569)
Q Consensus 557 ~~~~L 561 (569)
....+
T Consensus 179 ~~~~~ 183 (185)
T PRK09649 179 EPDDL 183 (185)
T ss_pred Ccccc
Confidence 55443
No 82
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=1.6e-18 Score=172.07 Aligned_cols=171 Identities=18% Similarity=0.169 Sum_probs=136.5
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccce
Q 008352 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 404 (569)
Q Consensus 325 ~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~I 404 (569)
....+++.|+..|.+.++.+++++.++..+.+|++||+|+.+|+.+++|++. .|.+|++.+++|.+.++++++.+..
T Consensus 15 ~~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~~~~~ 91 (216)
T PRK12533 15 ARGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRRANAH 91 (216)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhhcccc
Confidence 4468999999999999999999999999999999999999999999999853 4999999999999999988754210
Q ss_pred ecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCC
Q 008352 405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 484 (569)
Q Consensus 405 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~ 484 (569)
.. ........+ ..... . ++...+
T Consensus 92 ~~-----------------------------------------------------~~~~~~~~~--~~~~~-~-~~~~~~ 114 (216)
T PRK12533 92 EV-----------------------------------------------------AAPDTLDDA--DSLDD-W-QPAGED 114 (216)
T ss_pred cc-----------------------------------------------------ccccccccc--ccccc-c-ccCCCC
Confidence 00 000000000 00000 0 111235
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352 485 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 559 (569)
Q Consensus 485 pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 559 (569)
|++.+...+....|..+|..||+++|+||.|+|. +++|++|||+.||||.++|+++++||+++||+.+...
T Consensus 115 ~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~----eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~ 185 (216)
T PRK12533 115 PLALLLRAEDVRLVNAALAKLPVEYREVLVLREL----EDMSYREIAAIADVPVGTVMSRLARARRRLAALLGGA 185 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHccc
Confidence 6677777777888999999999999999999998 8999999999999999999999999999999998643
No 83
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=9.2e-19 Score=167.68 Aligned_cols=166 Identities=9% Similarity=0.032 Sum_probs=130.4
Q ss_pred hccHHHHHHHHHHHHHHHHHHHHHhhC--CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcc
Q 008352 324 HSGNSSREKLINANLRLVVHVAKQYQG--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS 401 (569)
Q Consensus 324 ~~G~~Are~LI~~nlrLV~sIArry~~--~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~ 401 (569)
.++..+++.|+..|.+.|+.++..+.+ +..+++|++||.|+.+|+..++|++.....|.||++..++|.+.++++++.
T Consensus 9 ~~d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~Rk~~ 88 (178)
T PRK12529 9 SADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRRRQS 88 (178)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHHHHH
Confidence 355699999999999999998766665 457899999999999999999998544457999999999999999887542
Q ss_pred cceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCC
Q 008352 402 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTG 481 (569)
Q Consensus 402 r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~ 481 (569)
+.. .. .+. ..+. .+..
T Consensus 89 ~~~------------------~~------------------------------------~~~---------~~~~-~~~~ 104 (178)
T PRK12529 89 LEL------------------AW------------------------------------LEA---------LATL-PEPL 104 (178)
T ss_pred HHh------------------hh------------------------------------hhH---------hhhc-cCcC
Confidence 100 00 000 0000 0011
Q ss_pred CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352 482 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 557 (569)
Q Consensus 482 ~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 557 (569)
..+|++.+...+....|..+|..||+++|.||.|+|. +|+|++|||+.||||.++|+.++.||+.+|++.+.
T Consensus 105 ~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~~~ 176 (178)
T PRK12529 105 HPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATL----DGMKQKDIAQALDIALPTVKKYIHQAYVTCLSLMP 176 (178)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhCC
Confidence 1245666666666678999999999999999999998 99999999999999999999999999999998753
No 84
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=1.2e-18 Score=166.80 Aligned_cols=166 Identities=19% Similarity=0.249 Sum_probs=128.6
Q ss_pred HHHHHh-ccHHHHHHHHHHHHHHHHHHHHHhhCC----CCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 008352 319 LKSELH-SGNSSREKLINANLRLVVHVAKQYQGR----GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 393 (569)
Q Consensus 319 L~~~l~-~G~~Are~LI~~nlrLV~sIArry~~~----g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI 393 (569)
++..+. ++..|++.|+..|.+.|+.+|+++.++ ..+++|++||+++.+|+..++|+.. ..|.+|++..+++.+
T Consensus 12 l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn~~ 89 (184)
T PRK12512 12 LMRSANAGDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARNKL 89 (184)
T ss_pred HHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHHHH
Confidence 334444 456999999999999999999998753 4689999999999999999999874 469999999999999
Q ss_pred HHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 008352 394 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 473 (569)
Q Consensus 394 ~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l 473 (569)
.++++++.+...+ .++. +
T Consensus 90 ~d~~Rr~~~~~~~-----------------------------------------------------~~~~---------~ 107 (184)
T PRK12512 90 IDALRRRGRRVFV-----------------------------------------------------DIDD---------F 107 (184)
T ss_pred HHHHHhhcccccC-----------------------------------------------------Cchh---------c
Confidence 9998865421100 0000 0
Q ss_pred hhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352 474 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 474 ~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 553 (569)
.+.+++.. +. .....+.+..+|+.||+++|+||.++|. +++|++|||+.||+|..+|+..+.||+++||
T Consensus 108 ~~~~~~~~---~~----~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr 176 (184)
T PRK12512 108 AETLPAEP---AT----ETLPAGDVGRHLETLPPRQRDVVQSISV----EGASIKETAAKLSMSEGAVRVALHRGLAALA 176 (184)
T ss_pred cccccccc---hh----hHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 00011100 00 1122346788999999999999999998 8999999999999999999999999999999
Q ss_pred HHhhcC
Q 008352 554 QSLGGK 559 (569)
Q Consensus 554 ~~l~~~ 559 (569)
..+...
T Consensus 177 ~~l~~~ 182 (184)
T PRK12512 177 AKFRSE 182 (184)
T ss_pred HHhhcC
Confidence 988754
No 85
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=8.6e-19 Score=166.21 Aligned_cols=166 Identities=17% Similarity=0.154 Sum_probs=128.0
Q ss_pred hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccc
Q 008352 324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 403 (569)
Q Consensus 324 ~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~ 403 (569)
.++..+++.|+..|.+.|+.+++++.+ ..+++|++||+|+.+|+.++.|++. ..|.+|++..+++.+.+++++..+.
T Consensus 7 ~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~~~~ 83 (175)
T PRK12518 7 RGDRQSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARRQFAQR 83 (175)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHHHhhcc
Confidence 345699999999999999999999875 4689999999999999999999974 4699999999999999998864310
Q ss_pred eecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCC
Q 008352 404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE 483 (569)
Q Consensus 404 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~ 483 (569)
-. . .+... .... ....
T Consensus 84 ~~----------------------------------------------------~--~~~~~-~~~~------~~~~--- 99 (175)
T PRK12518 84 PS----------------------------------------------------R--IQDDS-LNDQ------PSRP--- 99 (175)
T ss_pred cc----------------------------------------------------c--hhccc-cccc------ccCC---
Confidence 00 0 00000 0000 0000
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008352 484 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 560 (569)
Q Consensus 484 ~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 560 (569)
.++......+....+..+|+.||+++|+||.++|+ +|+|++|||+.||+|..+|+..+.||+++||+.+...+
T Consensus 100 ~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~~~~ 172 (175)
T PRK12518 100 SDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHDL----EDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQQG 172 (175)
T ss_pred CCcHHHHHHHHHHHHHHHHHhCCHHHeeeeeehHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 11112222334456889999999999999999998 89999999999999999999999999999999987644
No 86
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=99.81 E-value=2.3e-18 Score=165.36 Aligned_cols=170 Identities=20% Similarity=0.286 Sum_probs=135.8
Q ss_pred HHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcc
Q 008352 322 ELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS 401 (569)
Q Consensus 322 ~l~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~ 401 (569)
...++..++..++..|.+.++.+++++.++..+.+||+||+|+.+|+++..| .. +..|.||++.+++|.+.+++++..
T Consensus 9 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~~R~~~ 86 (182)
T COG1595 9 ALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDRLRKRK 86 (182)
T ss_pred HHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHHHHHHhc
Confidence 3456669999999999999999999999998899999999999999999999 33 347999999999999999999765
Q ss_pred cceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCC
Q 008352 402 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTG 481 (569)
Q Consensus 402 r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~ 481 (569)
+.... .+ +.+ ..+...+..
T Consensus 87 r~~~~------------------------------------------------------~~-----~~~--~~~~~~~~~ 105 (182)
T COG1595 87 RRRAR------------------------------------------------------VE-----EAD--LLPEEADPA 105 (182)
T ss_pred ccccc------------------------------------------------------cc-----ccc--ccccccCcc
Confidence 32211 00 000 000000011
Q ss_pred CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352 482 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 559 (569)
Q Consensus 482 ~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 559 (569)
.+.. +.+...+....|..+|..||+++|++|.|+|+ +|+|++|||+.||||.++|+..++||+++||+.+...
T Consensus 106 ~~~~-~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~----~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~~~ 178 (182)
T COG1595 106 PDLA-ELLLAEEELERLRRALARLPPRQREAFLLRYL----EGLSYEEIAEILGISVGTVKSRLHRARKKLREQLEEA 178 (182)
T ss_pred cccc-hHHHHHHHHHHHHHHHHhCCHHHhHHhhhHhh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence 0011 24556677788999999999999999999999 9999999999999999999999999999999988754
No 87
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=99.81 E-value=8.5e-19 Score=164.13 Aligned_cols=157 Identities=13% Similarity=0.044 Sum_probs=126.2
Q ss_pred HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHH
Q 008352 335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL 414 (569)
Q Consensus 335 ~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l 414 (569)
+.|.+.|+.+|.++.++..+++|++||+|+.+|+++++|++. .|.+|++..++|.+.++++++.+..+.
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 578999999999999999999999999999999999999863 499999999999999999875421000
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHHHH
Q 008352 415 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 494 (569)
Q Consensus 415 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~el 494 (569)
..+. . .. .+... ....+++.+...+.
T Consensus 71 --------------------------------------------~~~~----~-~~---~~~~~--~~~~~~~~~~~~e~ 96 (160)
T PRK09642 71 --------------------------------------------LSLC----K-ET---EENIK--SSHNIEDLLLTKEQ 96 (160)
T ss_pred --------------------------------------------cccc----h-hh---hhhcc--CCCChHHHHHHHHH
Confidence 0000 0 00 00000 11245566666677
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008352 495 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 560 (569)
Q Consensus 495 ~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 560 (569)
...|..+|+.||+++|+||.|+|. +|+|++|||+.||+|..+|+.++.||+++||+.+...+
T Consensus 97 ~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 158 (160)
T PRK09642 97 KLLIAQKLRELPENYRDVVLAHYL----EEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKEEE 158 (160)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhhc
Confidence 788999999999999999999998 99999999999999999999999999999999986543
No 88
>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=99.81 E-value=6.2e-19 Score=170.52 Aligned_cols=172 Identities=18% Similarity=0.200 Sum_probs=131.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 008352 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 406 (569)
Q Consensus 327 ~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRl 406 (569)
..+++.|+..|.+.|+.+|.++.++..+.+|++||.|+.+|+.+.+|++. ..|.+|++..++|.+.++++++.+....
T Consensus 10 ~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~~~~~~~ 87 (193)
T TIGR02947 10 AQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKAQRRPQQ 87 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHhcCCccc
Confidence 48999999999999999999999998999999999999999999999864 4699999999999999999876421100
Q ss_pred chhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChh
Q 008352 407 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD 486 (569)
Q Consensus 407 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pe 486 (569)
. ..+++. .. .+. .... + .......++
T Consensus 88 ~-------------------------~~~~~~-----------~~--------~~~----~~~~----~--~~~~~~~~e 113 (193)
T TIGR02947 88 S-------------------------DDDDIE-----------DW--------QLA----KAAS----H--TSNGLRSAE 113 (193)
T ss_pred c-------------------------cchhhh-----------hh--------hhc----cccc----c--ccccccchh
Confidence 0 000000 00 000 0000 0 000111233
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352 487 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 558 (569)
Q Consensus 487 e~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 558 (569)
......+....|..+|..||+++|+||.|+|. +++|++|||+.||||..+|+.++.||+++||+.+..
T Consensus 114 ~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 181 (193)
T TIGR02947 114 LEALDGLPDQDIKDALQGLPEEFRQAVYLADV----EGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVD 181 (193)
T ss_pred HHHHhhhhHHHHHHHHHhCCHHHhhheeehhh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 33334444567899999999999999999998 999999999999999999999999999999998864
No 89
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=1.1e-18 Score=168.83 Aligned_cols=162 Identities=20% Similarity=0.191 Sum_probs=128.9
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccce
Q 008352 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 404 (569)
Q Consensus 325 ~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~I 404 (569)
++..++..|+..|.+.++.+|.++.++..+.+|++||.|+.+|+..++|+.. ..|.+|++..++|.+.++++++.+..
T Consensus 7 ~~~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~awL~~Ia~n~~~d~~R~~~~~~ 84 (187)
T PRK12516 7 EGTPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVG--TNMKAWLFTILRNEFYSQMRKRGREV 84 (187)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCc--ccHHHHHHHHHHHHHHHHHHhhcCCc
Confidence 3468999999999999999999999999999999999999999999999865 35999999999999999998754210
Q ss_pred ecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCC
Q 008352 405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 484 (569)
Q Consensus 405 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~ 484 (569)
.. .+.. +.+.... .
T Consensus 85 ~~------------------------------------------------------~~~~--------~~~~~~~----~ 98 (187)
T PRK12516 85 QD------------------------------------------------------TDGM--------FTEQLAV----H 98 (187)
T ss_pred cc------------------------------------------------------cccc--------cccccCC----C
Confidence 00 0000 0000000 0
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008352 485 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 560 (569)
Q Consensus 485 pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 560 (569)
++. ........|..+|..||+++|+||.|+|. +++|++|||+.||||.++|+.++.||+++||+.+...+
T Consensus 99 ~~~--~~~~~~~~l~~~L~~Lp~~~r~i~~L~~~----~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~~~ 168 (187)
T PRK12516 99 PSQ--YGTLDLQDFRAALDQLPDDQREAIILVGA----SGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQIEG 168 (187)
T ss_pred cch--hhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence 110 11122346889999999999999999998 99999999999999999999999999999999987654
No 90
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=99.80 E-value=1.9e-18 Score=162.88 Aligned_cols=158 Identities=15% Similarity=0.107 Sum_probs=130.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchh
Q 008352 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 409 (569)
Q Consensus 330 re~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~ 409 (569)
++.|+..|.+.|+.+|+++.++..+.+|++||+++.+|++++.|++. .|.+|++..+++.+.+++++..+...+
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~--- 76 (165)
T PRK09644 3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFV--- 76 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhcccc---
Confidence 67899999999999999999999999999999999999999999863 599999999999999999875421000
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHH
Q 008352 410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV 489 (569)
Q Consensus 410 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l 489 (569)
..+++ +.+. ...+++.+
T Consensus 77 -----------------------~~~~~-------------------------------------~~~~---~~~~~~~~ 93 (165)
T PRK09644 77 -----------------------GTDEI-------------------------------------EAIQ---AESTEEYV 93 (165)
T ss_pred -----------------------chhHH-------------------------------------hhhc---ccChHHHH
Confidence 00000 0000 01355555
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008352 490 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 560 (569)
Q Consensus 490 ~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 560 (569)
...+....|..+|..||+++|+||.++|. +|++++|||+.||+|.++|+..+.||+++||+.+....
T Consensus 94 ~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~~ 160 (165)
T PRK09644 94 VAKNSYEKLIQIIHTLPVIEAQAILLCDV----HELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEEK 160 (165)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHhHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Confidence 66666778999999999999999999998 89999999999999999999999999999999987543
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=99.80 E-value=2.1e-18 Score=161.56 Aligned_cols=158 Identities=19% Similarity=0.205 Sum_probs=128.0
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccce
Q 008352 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 404 (569)
Q Consensus 325 ~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~I 404 (569)
++..+++.|+..|.+.|+.+|.++.++..+.+|++||+|+.+|++.++|+. ...|.+|++..+++.+.+++++..+.
T Consensus 3 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~~~d~~rk~~~~- 79 (162)
T TIGR02983 3 ATEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNLARSRWRRRRLL- 79 (162)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHHHHHHHHhhccc-
Confidence 566999999999999999999999999999999999999999999999964 34799999999999999998865410
Q ss_pred ecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCC
Q 008352 405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 484 (569)
Q Consensus 405 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~ 484 (569)
.+ .+... ++..
T Consensus 80 ~~------------------------------------------------------~~~~~------------~~~~--- 90 (162)
T TIGR02983 80 EL------------------------------------------------------PTREL------------PDAA--- 90 (162)
T ss_pred cc------------------------------------------------------ccccc------------Cccc---
Confidence 00 00000 0000
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352 485 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 558 (569)
Q Consensus 485 pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 558 (569)
++......+..+.|..+|..||+++|+||.|+|. +|+|.+|||+.||+|.++|++.+.||+++||+.+..
T Consensus 91 ~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 160 (162)
T TIGR02983 91 APDPAPDVALRAALARALRRLPARQRAVVVLRYY----EDLSEAQVAEALGISVGTVKSRLSRALARLRELLEE 160 (162)
T ss_pred CCccchhHHHHHHHHHHHHhCCHHHHHHhhhHHH----hcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 0001122344567889999999999999999998 899999999999999999999999999999998754
No 92
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=99.80 E-value=1.9e-18 Score=164.23 Aligned_cols=162 Identities=14% Similarity=0.099 Sum_probs=127.5
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhccccee
Q 008352 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 405 (569)
Q Consensus 326 G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IR 405 (569)
+..++..|+..|.+.|+.+|.++.++..+.+|++||+|+.+|+. ..|+.. ..|.+|++.+++|.+.++++++.+-
T Consensus 8 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~~~-- 82 (172)
T PRK12523 8 HSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAALE-- 82 (172)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHHHH--
Confidence 34999999999999999999999999999999999999999987 446543 3699999999999999999875310
Q ss_pred cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCCh
Q 008352 406 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP 485 (569)
Q Consensus 406 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~p 485 (569)
.... .++ . . ........|
T Consensus 83 ----------------~~~~---------~~~------------------------~------------~-~~~~~~~~~ 100 (172)
T PRK12523 83 ----------------QAYL---------AEL------------------------A------------L-VPEAEQPSP 100 (172)
T ss_pred ----------------HHHH---------HHH------------------------h------------h-cccccCCCh
Confidence 0000 000 0 0 000001134
Q ss_pred hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352 486 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 558 (569)
Q Consensus 486 ee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 558 (569)
+......+....|..+|..||+++|+||.|+|. +|+|++|||+.||+|.++|++++.||+++||..+..
T Consensus 101 ~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l~~ 169 (172)
T PRK12523 101 EEQHLILEDLKAIDRLLGKLSSKARAAFLYNRL----DGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIALYG 169 (172)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 444444444567999999999999999999998 999999999999999999999999999999998754
No 93
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=99.80 E-value=4.1e-18 Score=167.28 Aligned_cols=165 Identities=20% Similarity=0.288 Sum_probs=135.7
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhccccee
Q 008352 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 405 (569)
Q Consensus 326 G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IR 405 (569)
+..+++.|+..|.+.++.++.++.++..+.+|++||+|+.+|+...+|++ + .|.+|++..+++.+.+++++..+ .+
T Consensus 26 d~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~~-~~ 101 (203)
T PRK09647 26 TMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRAR-IR 101 (203)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhccc-Cc
Confidence 35899999999999999999999999999999999999999999999985 3 69999999999999999987541 00
Q ss_pred cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCCh
Q 008352 406 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP 485 (569)
Q Consensus 406 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~p 485 (569)
. ..++ ++ + +.... ...+|
T Consensus 102 ~----------------------------------------------------~~~~-----~~---~-~~~~~-~~~~~ 119 (203)
T PRK09647 102 M----------------------------------------------------EALP-----ED---Y-DRVPG-DEPNP 119 (203)
T ss_pred c----------------------------------------------------cccc-----cc---c-cccCC-CCCCH
Confidence 0 0000 00 0 00011 12245
Q ss_pred hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008352 486 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 560 (569)
Q Consensus 486 ee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 560 (569)
+..+...+....|..+|..||+++|.||.|+|+ ++++++|||+.||||..+|++.+.||+++||+.+...+
T Consensus 120 ~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~~----~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~~~ 190 (203)
T PRK09647 120 EQIYHDARLDPDLQAALDSLPPEFRAAVVLCDI----EGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAAHA 190 (203)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 566677777788999999999999999999998 99999999999999999999999999999999987654
No 94
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=99.79 E-value=4.4e-18 Score=159.64 Aligned_cols=157 Identities=15% Similarity=0.099 Sum_probs=124.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecc
Q 008352 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 407 (569)
Q Consensus 328 ~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP 407 (569)
.|++.|+..|.+.|+.++.++.++..+.+|++||.|+.+|+..+.|++ ..|.+|++.++++.+.+++++..+.
T Consensus 4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~---~~~~~wl~~i~~n~~~d~~R~~~~~---- 76 (161)
T PRK12528 4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQI---IEPRAFLTTIAKRVLCNHYRRQDLE---- 76 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhccccccc---cCHHHHHHHHHHHHHHHHHHHHHHH----
Confidence 689999999999999999999999999999999999999999988864 2699999999999999998864310
Q ss_pred hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhH
Q 008352 408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI 487 (569)
Q Consensus 408 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee 487 (569)
... ..++ + + .++.....++.
T Consensus 77 --------------~~~---------~~~~------------------------~------------~-~~~~~~~~~~~ 96 (161)
T PRK12528 77 --------------RAY---------LEAL------------------------A------------Q-LPERVAPSEEE 96 (161)
T ss_pred --------------Hhh---------HHHh------------------------h------------c-cccccCCCHHH
Confidence 000 0000 0 0 00001112333
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352 488 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 555 (569)
Q Consensus 488 ~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 555 (569)
.....+....|..+|..||+++|+||.|+|. +|+|++|||+.||+|.++|+..+.||+++||..
T Consensus 97 ~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~----~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~ 160 (161)
T PRK12528 97 RAIILETLVELDQLLDGLPPLVKRAFLLAQV----DGLGYGEIATELGISLATVKRYLNKAAMRCYFA 160 (161)
T ss_pred HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhc
Confidence 3333344567899999999999999999998 999999999999999999999999999999864
No 95
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=99.79 E-value=5.8e-18 Score=165.48 Aligned_cols=181 Identities=14% Similarity=0.139 Sum_probs=130.8
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHH
Q 008352 332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY 411 (569)
Q Consensus 332 ~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~ 411 (569)
.++..|.+.|+.+|+++.++..+.+|++||.|+.+|+.+++|++. ..|.+|++.+++|.+.++++++.+...++..
T Consensus 12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~-- 87 (201)
T PRK12545 12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQ--SAHKTWVFGILRNKLIDTLRARQRTVNLSAL-- 87 (201)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhcccc--chHHHHHHHHHHHHHHHHHHhhccccccccc--
Confidence 458889999999999999999999999999999999999999976 3599999999999999999876532111000
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHH
Q 008352 412 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK 491 (569)
Q Consensus 412 ~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~ 491 (569)
..++. . ...++............+..++ ....+++....
T Consensus 88 ----------------------~~~~~------~------------~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 126 (201)
T PRK12545 88 ----------------------DAELD------G------------EALLDRELFKDNGHWAAHAKPR-PWPKPETILQQ 126 (201)
T ss_pred ----------------------ccccc------h------------hhhhhhhhhcccccccccccCc-CCCCHHHHHHH
Confidence 00000 0 0000000000000000000011 11245555555
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008352 492 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 561 (569)
Q Consensus 492 ~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L 561 (569)
.+....|..+|..||+++|+||.|+|+ +++|++|||+.||+|.++|+.++.||+++||+++...++
T Consensus 127 ~~~~~~l~~~L~~Lp~~~r~v~~L~~~----eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~~ 192 (201)
T PRK12545 127 QQFWTLFETCLDHLPEQIGRVFMMREF----LDFEIDDICTELTLTANHCSVLLYRARTRLRTCLSEKGL 192 (201)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 666678899999999999999999998 999999999999999999999999999999999975443
No 96
>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=99.79 E-value=9.4e-18 Score=166.80 Aligned_cols=117 Identities=18% Similarity=0.273 Sum_probs=104.3
Q ss_pred HhccHHHHHHHHHHHHHHHHHHHHHhhCCC--CCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhc
Q 008352 323 LHSGNSSREKLINANLRLVVHVAKQYQGRG--ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 400 (569)
Q Consensus 323 l~~G~~Are~LI~~nlrLV~sIArry~~~g--~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~ 400 (569)
++.|+..+++||..|.|+|.++|.+|.++. .+.+|++|+|++|||+|+++|||++|.+|.|||.+||++.|.+++|+.
T Consensus 4 ~~~gd~~~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dylRk~ 83 (218)
T TIGR02895 4 IQPGNEEREELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYIRKN 83 (218)
T ss_pred hhcCChHHHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHhc
Confidence 445665599999999999999999998764 589999999999999999999999999999999999999999999988
Q ss_pred c---cceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHH
Q 008352 401 S---RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLAR 439 (569)
Q Consensus 401 ~---r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~ 439 (569)
. +.+++|....+....+..+...+..+.++.|+.+||+.
T Consensus 84 ~k~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~ 125 (218)
T TIGR02895 84 QKYQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILE 125 (218)
T ss_pred ccccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHH
Confidence 7 67899987666667777788888899999999999974
No 97
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=99.79 E-value=6.7e-18 Score=159.38 Aligned_cols=159 Identities=17% Similarity=0.164 Sum_probs=126.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 008352 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 406 (569)
Q Consensus 327 ~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRl 406 (569)
...+..++..|.+.|+.+|+++.++..+++|++||+++.+|+..++|++.. .|.+|++..++|.+.+++++..+...
T Consensus 5 ~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~~~- 81 (164)
T PRK12547 5 SKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGT--NLKAWLFTILRNEFYSQMRKRGREVQ- 81 (164)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhccccc-
Confidence 468999999999999999999999999999999999999999999998643 59999999999999999887542100
Q ss_pred chhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChh
Q 008352 407 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD 486 (569)
Q Consensus 407 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pe 486 (569)
. .+...... .+ ..++
T Consensus 82 ------------------------~-----------------------------~~~~~~~~---------~~---~~~~ 96 (164)
T PRK12547 82 ------------------------D-----------------------------SDGVFTAR---------VA---VHPA 96 (164)
T ss_pred ------------------------c-----------------------------cccccccc---------CC---CCch
Confidence 0 00000000 00 0111
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352 487 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 559 (569)
Q Consensus 487 e~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 559 (569)
. ........+..+|..||+++|+||.|+|. +|+|++|||+.||||.++|+..+.||+++||..+.-.
T Consensus 97 ~--~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 163 (164)
T PRK12547 97 Q--YGSLDLQDFKKALNLLSADQREAIILIGA----SGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLKVD 163 (164)
T ss_pred h--hhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence 1 11222456889999999999999999998 8999999999999999999999999999999987543
No 98
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=6.8e-18 Score=163.49 Aligned_cols=180 Identities=18% Similarity=0.166 Sum_probs=132.0
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCC-HHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchh
Q 008352 331 EKLINANLRLVVHVAKQYQGRGIS-LHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 409 (569)
Q Consensus 331 e~LI~~nlrLV~sIArry~~~g~~-~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~ 409 (569)
+..+..|.+.|+.+|+++.++..+ .+|++||+|+.+|+++++|++. .+|.+|++..++|.+.++++++.+.......
T Consensus 8 ~~~~~~~~~~l~~~a~~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~~ 85 (195)
T PRK12532 8 DAELIESRKLLLHFARLQLPDHPDLAEDLVQETLLSAYSAGDSFQGR--ALVNSWLFAILKNKIIDALRQIGRQRKVFTL 85 (195)
T ss_pred hhhHHHHHHHHHHHHHHHcCChhhhHHHHHHHHHHHHHHhccccccc--chHHHHHHHHHHHHHHHHHHHhccccccccc
Confidence 456778999999999999998888 9999999999999999999864 4799999999999999999876531110000
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHH
Q 008352 410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV 489 (569)
Q Consensus 410 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l 489 (569)
. ..+.+ .... ... ...+ .....+... ....+|+..+
T Consensus 86 ~----------------------~~~~~-----------~~~~------~~~---~~~~-~~~~~~~~~-~~~~~~e~~~ 121 (195)
T PRK12532 86 L----------------------DDELL-----------DEAF------ESH---FSQN-GHWTPEGQP-QHWNTPEKSL 121 (195)
T ss_pred c----------------------ccccc-----------chhh------hhh---hccc-cccccccCc-cccCCHHHHH
Confidence 0 00000 0000 000 0000 000000000 1123577777
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008352 490 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 560 (569)
Q Consensus 490 ~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 560 (569)
...+....+..+|..||+++|+||.|+|. +|+|++|||+.||+|..+|+.++.||+++||+++....
T Consensus 122 ~~~e~~~~l~~~l~~L~~~~r~i~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~ 188 (195)
T PRK12532 122 NNNEFQKILQSCLYNLPENTARVFTLKEI----LGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKW 188 (195)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHhhhHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 77777788999999999999999999998 89999999999999999999999999999999987554
No 99
>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=99.78 E-value=6.2e-18 Score=163.58 Aligned_cols=178 Identities=12% Similarity=0.138 Sum_probs=132.8
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhH
Q 008352 331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI 410 (569)
Q Consensus 331 e~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~ 410 (569)
.+.+..|.+.|+.+|+++.++..+.+|++||+|+.+|+..++|++. .+|.+|++..++|.+.++++++.+....+. +
T Consensus 5 ~~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~~-~ 81 (188)
T TIGR02943 5 PQELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVSD-L 81 (188)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCccc-c
Confidence 3577889999999999999999999999999999999999999975 479999999999999999987653211100 0
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHH
Q 008352 411 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ 490 (569)
Q Consensus 411 ~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~ 490 (569)
. .+. . .-.++... ...+....+..++ ....|+..+.
T Consensus 82 ------------------~-----~~~------~-------------~~~~~~~~-~~~~~~~~~~~~~-~~~~~e~~~~ 117 (188)
T TIGR02943 82 ------------------D-----DEL------D-------------DEAFNALF-TQNGHWAQHGQPQ-HWNTPEKQLE 117 (188)
T ss_pred ------------------c-----ccc------c-------------cchhhhhh-ccccchhcccccc-ccCCHHHHHH
Confidence 0 000 0 00000000 0000000011111 1235667777
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352 491 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 559 (569)
Q Consensus 491 ~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 559 (569)
..+....|..+|..||+++|+||.++|. ++++++|||+.||+|.++|++++.||+++||+++...
T Consensus 118 ~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~ 182 (188)
T TIGR02943 118 NKEFWEVFEACLYHLPEQTARVFMMREV----LGFESDEICQELEISTSNCHVLLYRARLSLRACLSIN 182 (188)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 7777788999999999999999999998 8999999999999999999999999999999998654
No 100
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=8.6e-18 Score=157.65 Aligned_cols=157 Identities=15% Similarity=0.129 Sum_probs=124.3
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhccccee
Q 008352 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 405 (569)
Q Consensus 326 G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IR 405 (569)
...+++.++..|.+.|+.++.++.++..+++|++||+++.+|+..++|++. .|.||++..++|.+.+++++..+...
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 357999999999999999999999999999999999999999999999863 59999999999999999987642100
Q ss_pred cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCCh
Q 008352 406 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP 485 (569)
Q Consensus 406 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~p 485 (569)
+ . .+ . . . .+.....+
T Consensus 80 ~--------------------------~---------------------------~~-------~--~-~--~~~~~~~~ 94 (161)
T PRK12541 80 T--------------------------T---------------------------IE-------E--F-H--LPNVPSTE 94 (161)
T ss_pred c--------------------------c---------------------------hh-------h--h-h--ccCCCCcH
Confidence 0 0 00 0 0 0 00000112
Q ss_pred hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352 486 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 555 (569)
Q Consensus 486 ee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 555 (569)
++.....+. ..+..+|..||+++|.||.|+|. +++|++|||+.||+|..+|++.+.||+++||+.
T Consensus 95 ~~~~~~~~~-~~~~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 95 HEYFIKHEI-ASWLDSLSSLPLERRNVLLLRDY----YGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HHHHHHhHH-HHHHHHHHHCCHHHHHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 222223333 34567899999999999999998 899999999999999999999999999999975
No 101
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=7.9e-18 Score=162.87 Aligned_cols=176 Identities=16% Similarity=0.116 Sum_probs=130.9
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhH
Q 008352 331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI 410 (569)
Q Consensus 331 e~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~ 410 (569)
+..|..|.+.++.+|.++.++..+++|++||.|+.+|+.+++|++. .+|.+|++..++|.+.++++++.+...... .
T Consensus 10 ~~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~-~ 86 (189)
T PRK12530 10 SLEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQ--SALKTWIFAILKNKIIDLIRYRKRFVNESE-L 86 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCC--ccHHHHHHHHHHHHHHHHHHhhccCCCccc-c
Confidence 3457778999999999999998999999999999999999999875 369999999999999999987653211000 0
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHH
Q 008352 411 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ 490 (569)
Q Consensus 411 ~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~ 490 (569)
. .+. .+.... +.......+.........++..+.
T Consensus 87 ------------------~-----~~~-------------------~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~ 120 (189)
T PRK12530 87 ------------------I-----EED-------------------SPNSFF----DEKGHWKPEYYEPSEWQEVENTVY 120 (189)
T ss_pred ------------------c-----ccc-------------------cchhhh----cccccccccccCCccccCHHHHHH
Confidence 0 000 000000 000000000000111235666677
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352 491 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 559 (569)
Q Consensus 491 ~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 559 (569)
..+....|..+|+.||+++|+||.|+|. +++|++|||+.||+|.++|+.++.||+++||+++...
T Consensus 121 ~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~ 185 (189)
T PRK12530 121 KEEFWLIFEACLNHLPAQQARVFMMREY----LELSSEQICQECDISTSNLHVLLYRARLQLQACLSKN 185 (189)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHhHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 7777888999999999999999999998 8999999999999999999999999999999998644
No 102
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=1.1e-17 Score=164.65 Aligned_cols=180 Identities=18% Similarity=0.215 Sum_probs=133.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchh
Q 008352 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 409 (569)
Q Consensus 330 re~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~ 409 (569)
-..++..|.+.|+.+|+++.++....+|++||+|+.+|+.+.+|++. .+|.+|++..++|.+.+++++..+....+..
T Consensus 20 ~~~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfikl~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~~~~~~~~~ 97 (206)
T PRK12544 20 DPVFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGR--AAFKTWVFAILKNKIIDLLRQKKRHVSASSL 97 (206)
T ss_pred hHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhhccccccccc
Confidence 36789999999999999999999999999999999999999999864 4699999999999999999876532111000
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHH
Q 008352 410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV 489 (569)
Q Consensus 410 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l 489 (569)
. . .... ...+..+. + ................|+..+
T Consensus 98 ~------------------~--~~~~---------~~~~~~~~--------------~-~~~~~~~~~~~~~~~~~e~~~ 133 (206)
T PRK12544 98 L------------------R--DEEE---------EEDFEELF--------------D-ESGHWQKDERPQAWGNPEESL 133 (206)
T ss_pred c------------------c--ccch---------hhHHHHhh--------------c-ccccccccccccccCCHHHHH
Confidence 0 0 0000 00000000 0 000000000011123567777
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352 490 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 559 (569)
Q Consensus 490 ~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 559 (569)
...+....+..+|..||+++|+||.|+|. ++++++|||+.||+|..+|++.+.||+++||+.+...
T Consensus 134 ~~~e~~~~l~~~L~~L~~~~r~v~~L~~~----~g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~ 199 (206)
T PRK12544 134 EQEQFWRIFEACLDGLPAKYARVFMMREF----IELETNEICHAVDLSVSNLNVLLYRARLRLRECLENK 199 (206)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 77777778999999999999999999999 8999999999999999999999999999999998753
No 103
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=99.78 E-value=1.1e-17 Score=157.21 Aligned_cols=160 Identities=19% Similarity=0.183 Sum_probs=129.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 008352 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 406 (569)
Q Consensus 327 ~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRl 406 (569)
+.+++.|+..|.+.|+.+|+++.++..+.+|++||+|+.+|++ .|+. +..|.+|++..+++.+.+++++..+..+.
T Consensus 2 ~~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~~~~~ 77 (166)
T PRK09639 2 DETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKRRRAR 77 (166)
T ss_pred chHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhcccccc
Confidence 3689999999999999999999999999999999999999999 6764 34799999999999999999875421100
Q ss_pred chhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChh
Q 008352 407 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD 486 (569)
Q Consensus 407 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pe 486 (569)
. +. .....+. + ....|+
T Consensus 78 ~------------------------------------------------------~~------~~~~~~~--~-~~~~~e 94 (166)
T PRK09639 78 I------------------------------------------------------LG------EFQWQEV--D-NEPSPE 94 (166)
T ss_pred c------------------------------------------------------cc------hhhhhhc--c-CCCChH
Confidence 0 00 0000000 1 122566
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352 487 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 558 (569)
Q Consensus 487 e~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 558 (569)
+.....+....|..+|..||+++|.||.++| +|++++|||+.||+|..+|+..+.||+++||+.+..
T Consensus 95 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-----~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~~ 161 (166)
T PRK09639 95 EIWIRKEEITKVQEVLAKMTERDRTVLLLRF-----SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQ 161 (166)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 6666667777899999999999999999999 489999999999999999999999999999998864
No 104
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=99.78 E-value=9.5e-18 Score=176.03 Aligned_cols=186 Identities=18% Similarity=0.203 Sum_probs=135.3
Q ss_pred HHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHH
Q 008352 318 DLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA 396 (569)
Q Consensus 318 ~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~ 396 (569)
+|+..+..| ..+++.|+..|.+.|+.+|.++.++..+.+|++||.|+.+|+.+++|++. ..|.+|++..++|.+.++
T Consensus 8 ~l~~~~~~gd~~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~ 85 (339)
T PRK08241 8 ALLARAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATNVCLDA 85 (339)
T ss_pred HHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHHHHHHH
Confidence 455555555 49999999999999999999999999999999999999999999999853 469999999999999999
Q ss_pred HHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhc
Q 008352 397 IFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEI 476 (569)
Q Consensus 397 Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~ 476 (569)
++++.+... +. ..+ .+ ..........+......+.
T Consensus 86 ~Rk~~~~~~-~~------------------~~~-~~-------------------------~~~~~~~~~~~~~~~~~~~ 120 (339)
T PRK08241 86 LEGRARRPL-PT------------------DLG-AP-------------------------AADPVDELVERPEVPWLEP 120 (339)
T ss_pred HHhhccccC-cc------------------ccC-CC-------------------------cCcccccccccccccccCC
Confidence 987542100 00 000 00 0000000000000000011
Q ss_pred ccCC----CCCChhHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008352 477 TADT----GVEIPDISVQKQL-MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR 551 (569)
Q Consensus 477 i~D~----~~~~pee~l~~~e-l~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkK 551 (569)
+.+. ...+|++.+...+ ....|..+|..||+++|+||.|+|. +++|++|||++||+|..+|++++.||+++
T Consensus 121 ~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~RAr~~ 196 (339)
T PRK08241 121 YPDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLILRDV----LGWSAAEVAELLDTSVAAVNSALQRARAT 196 (339)
T ss_pred CCcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhHHh----hCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 1110 1235665555444 4556899999999999999999998 99999999999999999999999999999
Q ss_pred HHH
Q 008352 552 LKQ 554 (569)
Q Consensus 552 LR~ 554 (569)
||+
T Consensus 197 Lr~ 199 (339)
T PRK08241 197 LAE 199 (339)
T ss_pred Hhh
Confidence 998
No 105
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=1.1e-17 Score=163.10 Aligned_cols=169 Identities=17% Similarity=0.103 Sum_probs=129.1
Q ss_pred HHHHHh-ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHH
Q 008352 319 LKSELH-SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI 397 (569)
Q Consensus 319 L~~~l~-~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~I 397 (569)
|+..+. ++..+++.|+..|.+.++.+++ +.++..+.+|++||.|+.+|+..++|++. ..|.+|++..++|.+.+++
T Consensus 15 l~~~~~~~d~~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~ 91 (196)
T PRK12535 15 LALAAGRGDRAALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAAR--SSARTWLLSLARRVWVDNI 91 (196)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCc--ccHHHHHHHHHHHHHHHHH
Confidence 444444 4459999999999999999975 67888899999999999999999999864 3699999999999999999
Q ss_pred HhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcc
Q 008352 398 FQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEIT 477 (569)
Q Consensus 398 r~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i 477 (569)
+++.+..+. ..+ .. . ...+
T Consensus 92 Rk~~~~~~~-----------------------------------------------------~~~-~~-~----~~~~-- 110 (196)
T PRK12535 92 RHDMARPRK-----------------------------------------------------SAT-EY-E----DAAA-- 110 (196)
T ss_pred HhhccCCCc-----------------------------------------------------ccc-cc-c----cccc--
Confidence 875421100 000 00 0 0000
Q ss_pred cCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352 478 ADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 557 (569)
Q Consensus 478 ~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 557 (569)
. ...++.... .+....|..+|+.||+++|+||.|+|. +++|++|||+.||+|.++|+..+.||+++||+.+.
T Consensus 111 --~-~~~~~~~~~-~~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~ 182 (196)
T PRK12535 111 --T-TASNETTGS-WSEWIDVRTLIDALPPERREALILTQV----LGYTYEEAAKIADVRVGTIRSRVARARADLIAATA 182 (196)
T ss_pred --c-cCCcchhHH-HHHHHHHHHHHHcCCHHHHHHhhhHHH----hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 0 011111111 122346889999999999999999998 89999999999999999999999999999999886
Q ss_pred cC
Q 008352 558 GK 559 (569)
Q Consensus 558 ~~ 559 (569)
..
T Consensus 183 ~~ 184 (196)
T PRK12535 183 TG 184 (196)
T ss_pred cc
Confidence 54
No 106
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=99.78 E-value=1.2e-17 Score=173.82 Aligned_cols=183 Identities=17% Similarity=0.184 Sum_probs=134.4
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccce
Q 008352 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 404 (569)
Q Consensus 325 ~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~I 404 (569)
++..+++.|+..|.+.|+++|.++.++..+.+|++||.|+.+|+.+++|++. ..|.+|++..++|.+.++++++.+..
T Consensus 2 gd~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~~ 79 (324)
T TIGR02960 2 VDGAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQRRP 79 (324)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhccCCc
Confidence 3458999999999999999999999999999999999999999999999864 46999999999999999998754210
Q ss_pred ecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhccc------
Q 008352 405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITA------ 478 (569)
Q Consensus 405 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~------ 478 (569)
.... ... . ........ ..+......+.+.
T Consensus 80 ~~~~------------------~~~--~------------------------~~~~~~~~-~~~~~~~~~~~~~~~~~~~ 114 (324)
T TIGR02960 80 RPVG------------------LGA--P------------------------SADGTAAA-SEAAEVTWLEPLPDLTLDL 114 (324)
T ss_pred Cccc------------------cCC--C------------------------CCcccccc-cccccccccCCCCcccccc
Confidence 0000 000 0 00000000 0000000000000
Q ss_pred -CCCCCChhHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352 479 -DTGVEIPDISVQKQL-MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556 (569)
Q Consensus 479 -D~~~~~pee~l~~~e-l~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 556 (569)
.....+|++.+...+ +...+..+|..||+++|+||.|+|. +++|++|||+.||+|.++|++++.||+++||+++
T Consensus 115 ~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 190 (324)
T TIGR02960 115 DDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDV----LGWRAAETAELLGTSTASVNSALQRARATLDEVG 190 (324)
T ss_pred ccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhc
Confidence 011224565555444 4567889999999999999999998 8999999999999999999999999999999988
Q ss_pred hc
Q 008352 557 GG 558 (569)
Q Consensus 557 ~~ 558 (569)
..
T Consensus 191 ~~ 192 (324)
T TIGR02960 191 PS 192 (324)
T ss_pred cc
Confidence 74
No 107
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=99.77 E-value=2.1e-17 Score=154.96 Aligned_cols=159 Identities=14% Similarity=0.214 Sum_probs=125.4
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHH
Q 008352 332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY 411 (569)
Q Consensus 332 ~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~ 411 (569)
.++..|.+.++++|.++.++..+.+|++||+++.+|+....|++. .|.+|++..+++.+.++++++.+....
T Consensus 2 ~~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn~~~d~~R~~~~~~~~----- 73 (163)
T PRK07037 2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRNLAIDHYRRQALENKY----- 73 (163)
T ss_pred hHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHHHHHHHHHhhcccccc-----
Confidence 367788999999999999999999999999999999998877763 488999999999999999875421000
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHH
Q 008352 412 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK 491 (569)
Q Consensus 412 ~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~ 491 (569)
. ..+.... +. .+. ..+++..+..
T Consensus 74 ------------------------------------------------~------~~~~~~~-~~-~~~-~~~~~~~~~~ 96 (163)
T PRK07037 74 ------------------------------------------------H------GDEEDGL-DV-PSP-EASPEAALIN 96 (163)
T ss_pred ------------------------------------------------c------ccccccc-cc-CCC-CCCHHHHHHH
Confidence 0 0000000 00 011 1245555566
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352 492 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 559 (569)
Q Consensus 492 ~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 559 (569)
.+..+.+..+|+.||+++|.||.++|. +++|++|||+.||+|.++|+..+.||+++||+.+...
T Consensus 97 ~~~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l~~~ 160 (163)
T PRK07037 97 RDTLRHVADALSELPARTRYAFEMYRL----HGETQKDIARELGVSPTLVNFMIRDALVHCRKCLDAC 160 (163)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence 666778999999999999999999998 8999999999999999999999999999999988653
No 108
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=99.77 E-value=5.6e-18 Score=157.01 Aligned_cols=152 Identities=19% Similarity=0.216 Sum_probs=122.6
Q ss_pred HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHH
Q 008352 335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL 414 (569)
Q Consensus 335 ~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l 414 (569)
..|.+.|+.++.++.++..+.+|++||+++.+|+.+++|++ .+|.+|++..+++.+.++++++.+....
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~-------- 70 (154)
T TIGR02950 2 REYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTI-------- 70 (154)
T ss_pred chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhccc--------
Confidence 57899999999999999889999999999999999999997 3799999999999999998865421000
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHHHH
Q 008352 415 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 494 (569)
Q Consensus 415 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~el 494 (569)
..+. +.+... +....|++.+...+.
T Consensus 71 -------------------~~~~-----------------------------------~~~~~~-~~~~~~~~~~~~~~~ 95 (154)
T TIGR02950 71 -------------------DDDA-----------------------------------IGDLEQ-HPVESPEHHLLIKIE 95 (154)
T ss_pred -------------------cHhh-----------------------------------hhhccc-cccCChhHHHHHHHH
Confidence 0000 000000 011245555666666
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352 495 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556 (569)
Q Consensus 495 ~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 556 (569)
...|..+|..||+++++||.++|+ +|+|++|||+.||+|..+|++...||+++||+.+
T Consensus 96 ~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~l 153 (154)
T TIGR02950 96 QEEITHHLSRLPENYRTVLILREF----KEFSYKEIAELLNLSLAKVKSNLFRARKELKKLL 153 (154)
T ss_pred HHHHHHHHHhCCHhheeeeeehhh----ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 678999999999999999999998 8999999999999999999999999999999865
No 109
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=99.77 E-value=2.1e-17 Score=159.37 Aligned_cols=160 Identities=18% Similarity=0.222 Sum_probs=126.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecc
Q 008352 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 407 (569)
Q Consensus 328 ~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP 407 (569)
.++..++..|.+.|+++|.++.++..+++|++||.|+.+|+..++|++.. .|.+|++..++|.+.++++++.+....
T Consensus 5 ~~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~~~~~- 81 (182)
T PRK12540 5 DSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGS--NLPAWLFTILRNLFRSDYRKRRREVED- 81 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCc--hHHHHHHHHHHHHHHHHHHhccccccc-
Confidence 56788999999999999999999999999999999999999999998753 599999999999999998875421000
Q ss_pred hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhH
Q 008352 408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI 487 (569)
Q Consensus 408 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee 487 (569)
.+. ...+.. +. .++.
T Consensus 82 -----------------------------------------------------~~~--------~~~~~~-~~---~~~~ 96 (182)
T PRK12540 82 -----------------------------------------------------ADG--------SYAKTL-KS---QPGQ 96 (182)
T ss_pred -----------------------------------------------------ccc--------cccccc-cC---CCch
Confidence 000 000000 00 1111
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008352 488 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 561 (569)
Q Consensus 488 ~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L 561 (569)
.. ......|..+|+.||+++|+||.|+|. +++|++|||+.||+|..+|++.+.||+++||+.+.....
T Consensus 97 ~~--~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~~ 164 (182)
T PRK12540 97 NA--HLEFEEFRAALDKLPQDQREALILVGA----SGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDGA 164 (182)
T ss_pred HH--HHHHHHHHHHHHhCCHHHHHHhhHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 11 112346899999999999999999998 999999999999999999999999999999999986553
No 110
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=99.76 E-value=1.9e-17 Score=155.04 Aligned_cols=155 Identities=12% Similarity=0.098 Sum_probs=124.3
Q ss_pred HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHH
Q 008352 335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL 414 (569)
Q Consensus 335 ~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l 414 (569)
..|.+.++.++.++.++..+.+|++||+|+.+|+..+.|++ .+|.||++..+++.+.++++++.+...
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~---~~~~~wL~~ia~n~~~d~~R~~~~~~~--------- 69 (159)
T PRK12527 2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQI---EHPRAFLYRTALNLVVDRHRRHRVRQA--------- 69 (159)
T ss_pred hhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhccccccc---cchHHHHHHHHHHHHHHHHHHHhcccc---------
Confidence 56888999999999999889999999999999999999875 279999999999999999886531000
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHHHH
Q 008352 415 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 494 (569)
Q Consensus 415 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~el 494 (569)
.+++. . .+. . .....+|++.+..++.
T Consensus 70 --------------------------------------------~~~~~-~-~~~-----~---~~~~~~~~~~~~~~~~ 95 (159)
T PRK12527 70 --------------------------------------------EPLEV-L-DEE-----E---RLHSPSPQTRLDLGQR 95 (159)
T ss_pred --------------------------------------------cchhh-h-hcc-----c---cccCCCHHHHHHHHHH
Confidence 00000 0 000 0 0011246666667777
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352 495 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 559 (569)
Q Consensus 495 ~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 559 (569)
...|..+|..||+++++||.|+|+ +++|++|||+.||+|.++|+..+.||+++||+.+...
T Consensus 96 ~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~~~ 156 (159)
T PRK12527 96 LALLQRALAELPPACRDSFLLRKL----EGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQW 156 (159)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 778999999999999999999998 9999999999999999999999999999999988643
No 111
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=99.75 E-value=4.5e-17 Score=156.82 Aligned_cols=154 Identities=21% Similarity=0.194 Sum_probs=126.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchh
Q 008352 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 409 (569)
Q Consensus 330 re~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~ 409 (569)
++.|++.|.+.|+.+|.++.++..+++|++||.++.+|+.+..|++. .+|.+|++..+++.+.++++++.+...++
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 57899999999999999999999999999999999999999999853 47999999999999999998764210000
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHH
Q 008352 410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV 489 (569)
Q Consensus 410 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l 489 (569)
.+ +...+ .+++..
T Consensus 79 ---------------------------------------------------------~~------~~~~~----~~~~~~ 91 (181)
T PRK09637 79 ---------------------------------------------------------DD------LLFED----EEREEN 91 (181)
T ss_pred ---------------------------------------------------------hh------hhccC----CChhHH
Confidence 00 00000 111222
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352 490 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 558 (569)
Q Consensus 490 ~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 558 (569)
...+....+..+|+.||+++|.||.++|. +|++.+|||+.||+|..+|+.++.||+++||+.+..
T Consensus 92 ~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (181)
T PRK09637 92 AKKELAPCLRPFIDALPEKYAEALRLTEL----EGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156 (181)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 33445667899999999999999999998 899999999999999999999999999999998763
No 112
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=99.75 E-value=3.9e-17 Score=155.49 Aligned_cols=164 Identities=15% Similarity=0.070 Sum_probs=127.0
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhccccee
Q 008352 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 405 (569)
Q Consensus 326 G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IR 405 (569)
+..|++.++..|.+.++.++.++.++..+.+||+||.|+.+|+. ..|++-. .|.+|++..+++.+.++++++.+..
T Consensus 8 ~~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~~~~- 83 (172)
T PRK09651 8 ASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNALEK- 83 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHHHHh-
Confidence 35899999999999999999999999999999999999999998 3565432 5899999999999999988643100
Q ss_pred cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCCh
Q 008352 406 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP 485 (569)
Q Consensus 406 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~p 485 (569)
. . ...+ + + +.+....+|
T Consensus 84 -----------------~----~-----~~~~------------------------~------------~-~~~~~~~~~ 100 (172)
T PRK09651 84 -----------------A----Y-----LEML------------------------A------------L-MPEGGAPSP 100 (172)
T ss_pred -----------------h----h-----hhHH------------------------h------------h-ccccCCCCh
Confidence 0 0 0000 0 0 000011133
Q ss_pred hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008352 486 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 560 (569)
Q Consensus 486 ee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 560 (569)
+......+....|..+|..||+++|+||.++|+ +++|++|||+.||+|.++|+..+.||+++|+......|
T Consensus 101 ~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~~~~~~ 171 (172)
T PRK09651 101 EERESQLETLQLLDSMLDGLNGKTREAFLLSQL----DGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLFRLEYG 171 (172)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHhHHhhhhhc----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHcC
Confidence 444444455567999999999999999999998 99999999999999999999999999999998764433
No 113
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=99.75 E-value=3.6e-17 Score=158.41 Aligned_cols=161 Identities=19% Similarity=0.155 Sum_probs=125.8
Q ss_pred hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccc
Q 008352 324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 403 (569)
Q Consensus 324 ~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~ 403 (569)
..+..+++.++..|.+.|+.+|+++.++..+++|++||.|+.+|+.++.|++. ..|.+|++..+++.+.+.++++.+.
T Consensus 19 ~~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~~~~~ 96 (188)
T PRK12517 19 LSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFERKQFD 96 (188)
T ss_pred hccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHHhccC
Confidence 45679999999999999999999999999999999999999999999999865 3699999999998765554332100
Q ss_pred eecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCC
Q 008352 404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE 483 (569)
Q Consensus 404 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~ 483 (569)
....+ . +...+....
T Consensus 97 ------------------------------------------------------~~~~~-------~----~~~~~~~~~ 111 (188)
T PRK12517 97 ------------------------------------------------------LVDIE-------D----DSIEDDASH 111 (188)
T ss_pred ------------------------------------------------------ccCcc-------c----ccccCcccc
Confidence 00000 0 000111111
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352 484 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 559 (569)
Q Consensus 484 ~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 559 (569)
.++.. ...+.|..+|..||+++|.||.++|+ ++++++|||+.||||..+|+.++.||+++||+.+...
T Consensus 112 ~~e~~----~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 179 (188)
T PRK12517 112 SSEEE----MEQEWLRRQIAKLDPEYREPLLLQVI----GGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALEKP 179 (188)
T ss_pred ChhHH----HHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 23322 22356889999999999999999998 9999999999999999999999999999999998643
No 114
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=99.74 E-value=7.3e-17 Score=153.47 Aligned_cols=148 Identities=21% Similarity=0.220 Sum_probs=120.9
Q ss_pred HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHH
Q 008352 335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL 414 (569)
Q Consensus 335 ~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l 414 (569)
..|.+.++.++.++.++..+++|++||+++.+|+++++|++. .+|.+|++..+++.+.+++++..+...++
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 468899999999999999999999999999999999999864 57999999999999999998765211000
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHHHH
Q 008352 415 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 494 (569)
Q Consensus 415 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~el 494 (569)
+ + .... ..+++.....+.
T Consensus 73 -----------------------------------------------~-----~-------~~~~---~~~~~~~~~~e~ 90 (170)
T TIGR02959 73 -----------------------------------------------E-----S-------LLAA---DSAREETFVKEL 90 (170)
T ss_pred -----------------------------------------------h-----h-------hccc---CCccHHHHHHHH
Confidence 0 0 0000 011222334445
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352 495 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 557 (569)
Q Consensus 495 ~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 557 (569)
...|..+|..||+++|.||.++|. ++++++|||+.||+|..+|++.+.||+++||..+.
T Consensus 91 ~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 91 SQCIPPMIKELPDEYREAIRLTEL----EGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 567899999999999999999998 89999999999999999999999999999999885
No 115
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=99.74 E-value=8.9e-17 Score=155.96 Aligned_cols=156 Identities=19% Similarity=0.200 Sum_probs=121.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecc
Q 008352 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 407 (569)
Q Consensus 328 ~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP 407 (569)
.+++.|+. |.+.|+++|+++.++..+.+|++||.|+.+|+.+..|+.. ..|.+|++..++|.+.+++++..+...
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 56666766 7799999999999999999999999999999999999864 469999999999999999887542100
Q ss_pred hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhH
Q 008352 408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI 487 (569)
Q Consensus 408 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee 487 (569)
..+. ...+...+.. ..+
T Consensus 83 ----------------------------------------------------~~~~--------~~~~~~~~~~--~~~- 99 (188)
T PRK12546 83 ----------------------------------------------------DPEG--------VHAASLAVKP--AHD- 99 (188)
T ss_pred ----------------------------------------------------Cccc--------ccccccccCC--cch-
Confidence 0000 0000000000 011
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352 488 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 558 (569)
Q Consensus 488 ~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 558 (569)
.......+..+|..||+++|+||.|+|. +++|.+|||+.||||..+|+..+.||+++||+.+..
T Consensus 100 ---~~~~~~~l~~~L~~Lp~~~r~v~~L~~~----~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~ 163 (188)
T PRK12546 100 ---GRLAMSDFRAAFAQLPDEQREALILVGA----SGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQL 163 (188)
T ss_pred ---hHHHHHHHHHHHHhCCHHHhHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 1122346889999999999999999998 899999999999999999999999999999998864
No 116
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=99.74 E-value=6.7e-17 Score=155.94 Aligned_cols=157 Identities=13% Similarity=0.166 Sum_probs=122.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchh
Q 008352 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 409 (569)
Q Consensus 330 re~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~ 409 (569)
.+..+..+++.|+.+|.++.++..+.+|++||.|+.+|+.+..|++. .+|.+|++..+++.+.++++++.+....
T Consensus 6 ~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~~~~~--- 80 (182)
T PRK12511 6 KRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRVEARR--- 80 (182)
T ss_pred hhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhcccccc---
Confidence 45557789999999999999999999999999999999999999864 3699999999999999999876421100
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHH
Q 008352 410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV 489 (569)
Q Consensus 410 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l 489 (569)
.+++ .+. .+.....+.
T Consensus 81 ------------------------~~~~------------------------------------~~~-~~~~~~~~~--- 96 (182)
T PRK12511 81 ------------------------ADEL------------------------------------AVL-ADASLPAAQ--- 96 (182)
T ss_pred ------------------------ccch------------------------------------hhc-cccCCCcch---
Confidence 0000 000 000000111
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352 490 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 559 (569)
Q Consensus 490 ~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 559 (569)
........|..+|..||+++|+||.|+|. +++|++|||+.||||.++|+..+.||+++||..+...
T Consensus 97 ~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~~~ 162 (182)
T PRK12511 97 EHAVRLAQIRDAFFDLPEEQRAALHLVAI----EGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEEGT 162 (182)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhc
Confidence 11223456889999999999999999998 8999999999999999999999999999999988744
No 117
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=99.73 E-value=2.1e-16 Score=149.81 Aligned_cols=160 Identities=14% Similarity=0.116 Sum_probs=126.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 008352 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 406 (569)
Q Consensus 327 ~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRl 406 (569)
..++.+++..|.+.++++|.++.++..+.+|++||.|+.+|+..+.++. ..|.+|++..++|.+.+++++...
T Consensus 8 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~---- 80 (168)
T PRK12525 8 NTLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDL---- 80 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHH----
Confidence 3789999999999999999999999999999999999999986665542 369999999999999998875320
Q ss_pred chhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChh
Q 008352 407 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD 486 (569)
Q Consensus 407 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pe 486 (569)
.+ ... ..+ + + .+......|+
T Consensus 81 --------~~------~~~---------~~~------------------------~------------~-~~~~~~~~~~ 100 (168)
T PRK12525 81 --------ER------AYL---------QSL------------------------A------------E-APEAVQPSPE 100 (168)
T ss_pred --------HH------HHH---------HHH------------------------h------------c-ccccccCChH
Confidence 00 000 000 0 0 0000112455
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352 487 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 557 (569)
Q Consensus 487 e~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 557 (569)
+.....+....|..+|..||+++|+||.|+|. +++|++|||+.||+|..+|+..+.+|+++||..+.
T Consensus 101 ~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~----eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~~~ 167 (168)
T PRK12525 101 EQWMVIETLLAIDRLLDGLSGKARAAFLMSQL----EGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQGFQ 167 (168)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhc
Confidence 55556666788999999999999999999998 99999999999999999999999999999998763
No 118
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=99.70 E-value=3.4e-16 Score=146.13 Aligned_cols=156 Identities=17% Similarity=0.183 Sum_probs=113.1
Q ss_pred CCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcC
Q 008352 350 GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGN 429 (569)
Q Consensus 350 ~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~g 429 (569)
++..+++|++||+|+.+|+.... ++ +..|.+|++..++|.+.++++++.+..+...
T Consensus 2 ~~~~~AeDivQe~fl~~~~~~~~-~~--~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~--------------------- 57 (161)
T PRK09047 2 RDDDAALDIVQDAMIKLAEKYGD-RP--AAEWPPLFQRILQNRIHDWFRRQKVRNTWVS--------------------- 57 (161)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhh-cc--cCchHHHHHHHHHHHHHHHHHhhcccccccc---------------------
Confidence 34467899999999999999886 33 3579999999999999999987542100000
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCC--CCChhHHHHHHHHHHHHHHHHhcCCH
Q 008352 430 HSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTG--VEIPDISVQKQLMRQHVRNLLTLLNP 507 (569)
Q Consensus 430 r~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~--~~~pee~l~~~el~e~L~~aL~~L~~ 507 (569)
...++.... ++++....+.+.+.. ...|++.+...+....|..+|..||+
T Consensus 58 ---------------------------~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~ 109 (161)
T PRK09047 58 ---------------------------LFSSFSDDD-DDDDFDPLETLDSADEGAESPADKLERAQVLQLIEEAIQKLPA 109 (161)
T ss_pred ---------------------------ccccccccc-ccccccHHHHhccccccCCCHHHHHHHHHHHHHHHHHHHhCCH
Confidence 000000000 000111111122211 23577777777788889999999999
Q ss_pred HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008352 508 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 561 (569)
Q Consensus 508 rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L 561 (569)
++|+||.|+|+ +|+|++|||+.||||..+|+.++.||+++||+++...++
T Consensus 110 ~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~~ 159 (161)
T PRK09047 110 RQREAFLLRYW----EDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEAKGI 159 (161)
T ss_pred HHHHHHHHHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcCc
Confidence 99999999998 999999999999999999999999999999999876553
No 119
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=99.69 E-value=5.1e-16 Score=160.26 Aligned_cols=160 Identities=16% Similarity=0.110 Sum_probs=123.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecc
Q 008352 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 407 (569)
Q Consensus 328 ~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP 407 (569)
.....++..|.+.++.+|+++.++..+.||++||.|+. |.....|+. ..|.+|++..++|.+.+++++..+.-
T Consensus 4 ~~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~~---~~~~~WL~~Ia~n~~~d~lR~~~~~~--- 76 (293)
T PRK09636 4 ADAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQI---RDPRAWLTRVVTRLCLDRLRSARHRR--- 76 (293)
T ss_pred cHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhcccccc---cCHHHHHHHHHHHHHHHHHHhhhccc---
Confidence 34678999999999999999999999999999999999 666677762 47999999999999999998653100
Q ss_pred hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhH
Q 008352 408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI 487 (569)
Q Consensus 408 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee 487 (569)
. .... .. +.+...+.. ..|++
T Consensus 77 -----------------------~---------------------------~~~~-~~-------~~e~~~~~~-~~~~~ 97 (293)
T PRK09636 77 -----------------------E---------------------------TYVG-PW-------LPEPVVEEL-DDPLE 97 (293)
T ss_pred -----------------------c---------------------------cccC-Cc-------CCcCCCCCC-CChHH
Confidence 0 0000 00 000000111 12333
Q ss_pred H-HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352 488 S-VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 557 (569)
Q Consensus 488 ~-l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 557 (569)
. ....++...+..+|+.|||++|.||.|+|. ++++++|||+.||+|..+|+++++||+++||+.+.
T Consensus 98 ~~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~~----~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~ 164 (293)
T PRK09636 98 AVVAAEDLSLALMLALERLSPLERAAFLLHDV----FGVPFDEIASTLGRSPAACRQLASRARKHVRAARP 164 (293)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 3 334455667899999999999999999998 89999999999999999999999999999999765
No 120
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=99.66 E-value=2.7e-15 Score=150.36 Aligned_cols=158 Identities=18% Similarity=0.175 Sum_probs=122.6
Q ss_pred HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHH
Q 008352 319 LKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIF 398 (569)
Q Consensus 319 L~~~l~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir 398 (569)
|.+.+..+..+++.+++.| +.+++++.++.++..+.+||+||.|+.+|+. |+.. ..|.+|++..++|.+.++++
T Consensus 9 ~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~--~~~~~WL~~IarN~~id~~R 82 (228)
T PRK06704 9 LKNHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNK--DICMTLVYKIARNRWLDQIK 82 (228)
T ss_pred HhcccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCcc--ccHHHHHHHHHHHHHHHHHh
Confidence 4444555668888888877 7899999999999999999999999999986 5543 25999999999999999988
Q ss_pred hcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhccc
Q 008352 399 QHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITA 478 (569)
Q Consensus 399 ~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~ 478 (569)
++.+.-. + .+ + ..
T Consensus 83 k~k~~~~-------------------------------~-----------------------~~-----~--~~------ 95 (228)
T PRK06704 83 SKSVHEK-------------------------------I-----------------------RD-----Q--IT------ 95 (228)
T ss_pred ccccccc-------------------------------c-----------------------cc-----c--cc------
Confidence 7541000 0 00 0 00
Q ss_pred CCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352 479 DTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 558 (569)
Q Consensus 479 D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 558 (569)
...+.... .+..+.+..+|+.||+++|.||.|+|. +++|++|||+.||+|.++|+..+.||+++||+.+..
T Consensus 96 ---~~~~~~~~--~~~~~~l~~~L~~Lp~~~R~v~lL~~~----eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~ 166 (228)
T PRK06704 96 ---FEEPHEKI--ADLHEMVGKVLSSLNVQQSAILLLKDV----FQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEE 166 (228)
T ss_pred ---cCChHHHH--HHHHHHHHHHHHhCCHHHhhHhhhHHh----hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 00111111 123456889999999999999999998 899999999999999999999999999999998865
No 121
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=99.65 E-value=3e-15 Score=153.91 Aligned_cols=156 Identities=22% Similarity=0.150 Sum_probs=118.9
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHH
Q 008352 332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY 411 (569)
Q Consensus 332 ~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~ 411 (569)
+++..|.+.++.+|+++.++..+.||++||+++.+++. .|+.. ..|.+|++.+++|.+.+++++..+--
T Consensus 1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~~--~~~~awL~~Ia~n~~ld~lR~~~~~~------- 69 (281)
T TIGR02957 1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQI--ENPKAYLTKVVTRRCIDVLRSARARR------- 69 (281)
T ss_pred ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Ccccc--cCHHHHHHHHHHHHHHHHHHHhhhcc-------
Confidence 36889999999999999999999999999999997765 45432 36999999999999999998643100
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHH
Q 008352 412 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK 491 (569)
Q Consensus 412 ~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~ 491 (569)
. . ...+. +.+...+. ...|++.+..
T Consensus 70 -------------------~---------------------------~-~~~~~-------~~e~~~~~-~~~~~~~~~~ 94 (281)
T TIGR02957 70 -------------------E---------------------------V-YVGPW-------LPEPLLTT-SADPAESVEL 94 (281)
T ss_pred -------------------c---------------------------c-cCCCC-------CCcccCCC-CCChHHHHHH
Confidence 0 0 00000 00000001 1234444433
Q ss_pred -HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352 492 -QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 557 (569)
Q Consensus 492 -~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 557 (569)
+.+...+..+|+.|||+||.||.|+|. .++|++|||+.||+|..+|+++++||+++||+...
T Consensus 95 ~e~~~~~l~~~l~~L~~~~R~v~~L~~~----~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~ 157 (281)
T TIGR02957 95 AESLSMAYLLLLERLSPLERAVFVLREV----FDYPYEEIASIVGKSEANCRQLVSRARRHLDARRP 157 (281)
T ss_pred HHHHHHHHHHHHhhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 345567889999999999999999998 89999999999999999999999999999999764
No 122
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=99.64 E-value=5.7e-15 Score=152.87 Aligned_cols=161 Identities=17% Similarity=0.135 Sum_probs=123.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecc
Q 008352 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 407 (569)
Q Consensus 328 ~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP 407 (569)
..+..++..|.+.++++|+++.++..+.||++||.|+.+|++...+ . ..|.+|++...+|.+.+++++..+.-
T Consensus 5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~-~---~~~~aWL~~Ia~n~~id~lRk~~~rr--- 77 (290)
T PRK09635 5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD-I---DDERGWLIVVTSRLCLDHIKSASTRR--- 77 (290)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc-c---ccHHHHHHHHHHHHHHHHHhhhhccC---
Confidence 5678999999999999999999999999999999999999987543 1 35999999999999999998643100
Q ss_pred hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhH
Q 008352 408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI 487 (569)
Q Consensus 408 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee 487 (569)
.. ....+. +.. .+...+ ..+|++
T Consensus 78 -----------------------~~-------------------------~~~~~~--~~~-----~~~~~~--~~~~~~ 100 (290)
T PRK09635 78 -----------------------ER-------------------------PQDIAA--WHD-----GDASVS--SVDPAD 100 (290)
T ss_pred -----------------------cC-------------------------cccccc--cCc-----cccCCC--CCCcHH
Confidence 00 000000 000 000001 112333
Q ss_pred -HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352 488 -SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556 (569)
Q Consensus 488 -~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 556 (569)
....++....+..+|..|||++|.||.|+|. .+++++|||+.||+|..+|+++++||+++||+..
T Consensus 101 ~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~~----~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~ 166 (290)
T PRK09635 101 RVTLDDEVRLALLIMLERLGPAERVVFVLHEI----FGLPYQQIATTIGSQASTCRQLAHRARRKINESR 166 (290)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHH----hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence 3445556678999999999999999999998 8999999999999999999999999999999864
No 123
>PRK09191 two-component response regulator; Provisional
Probab=99.52 E-value=8.5e-14 Score=138.90 Aligned_cols=136 Identities=17% Similarity=0.132 Sum_probs=110.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecch
Q 008352 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 408 (569)
Q Consensus 329 Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~ 408 (569)
++..|+..|.+.|+++|.++.++..+.+|++||+|+.+|+....|++. ..|.+|++.++++..... .
T Consensus 2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~~----~------- 68 (261)
T PRK09191 2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSSA----G------- 68 (261)
T ss_pred chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhccc----c-------
Confidence 578999999999999999999999999999999999999999999875 358999988765321000 0
Q ss_pred hHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHH
Q 008352 409 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 488 (569)
Q Consensus 409 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~ 488 (569)
. .+. .. ..+..
T Consensus 69 --------------------------------------------------------~-~~~---------~~--~~~~~- 79 (261)
T PRK09191 69 --------------------------------------------------------A-NDP---------EP--GSPFE- 79 (261)
T ss_pred --------------------------------------------------------c-cCC---------CC--CCCch-
Confidence 0 000 00 01111
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352 489 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 557 (569)
Q Consensus 489 l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 557 (569)
..+..+|+.||+++|+||.|+|. +++|++|||+.||+|.++|+.+..+|+++||..+.
T Consensus 80 -------~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~ 137 (261)
T PRK09191 80 -------ARAERRLAGLTPLPRQAFLLTAL----EGFSVEEAAEILGVDPAEAEALLDDARAEIARQVA 137 (261)
T ss_pred -------HHHHHHHHhCCHHHhHHHHHHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCC
Confidence 16888999999999999999998 99999999999999999999999999999998765
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=99.52 E-value=2.1e-13 Score=125.52 Aligned_cols=136 Identities=12% Similarity=0.141 Sum_probs=99.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhh-----cCCCCCCchhhHHHHHHHHHHHHHHHhcccce
Q 008352 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEK-----FKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 404 (569)
Q Consensus 330 re~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiek-----FDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~I 404 (569)
++.++..|.++++.+|++|... +| +||.++.+|..+.+ |++. ..|.||++..++|.+.++++++.+..
T Consensus 1 f~~~~~~y~~~l~~~~~~~~~~----~~-~qdvf~~~w~~~~~~~~~~~~~~--~~~~~wL~~iarN~~id~~Rk~~~~~ 73 (142)
T TIGR03209 1 FEEIYMNFKNTIDIFTRKYNLY----YD-YNDILYHLWIILKKIDLNKFNTE--NDLEKYISTSLKRYCLDICNKKNRDK 73 (142)
T ss_pred ChHHHHHHHHHHHHHHHHhcch----hh-HHHHHHHHHHHHHHhhhhhcCch--hHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 4679999999999999999652 34 49999999999875 5543 46999999999999999998653100
Q ss_pred ecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCC
Q 008352 405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 484 (569)
Q Consensus 405 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~ 484 (569)
+. . . ..++ .+ ... .
T Consensus 74 ~~-----------------~-~-------~~~~-------------------------------~~---------~~~-~ 87 (142)
T TIGR03209 74 KI-----------------I-Y-------NSEI-------------------------------TD---------IKL-S 87 (142)
T ss_pred hh-----------------h-h-------hhhh-------------------------------hc---------ccc-c
Confidence 00 0 0 0000 00 000 1
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHH
Q 008352 485 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVR 542 (569)
Q Consensus 485 pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVR 542 (569)
+.+.+...+....|..+|+.||+++|+||.|+|. +++|++|||+.||+|.++|+
T Consensus 88 ~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~----~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 88 LINVYSSNDLEFEFNDLISILPNKQKKIIYMKFF----EDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred hhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHhhc
Confidence 1122333444557889999999999999999998 99999999999999999997
No 125
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=99.45 E-value=5.3e-12 Score=127.33 Aligned_cols=88 Identities=20% Similarity=0.354 Sum_probs=77.9
Q ss_pred HHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCC--CHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 008352 316 CRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGI--SLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392 (569)
Q Consensus 316 ~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~--~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa 392 (569)
.+.++..++.| ..|++.|+..|.++|+++|.++.++.. +.+|++|||++++|+++++|++++|..|.+|+..+|++.
T Consensus 5 ~~~Li~~~~~gD~~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn~ 84 (237)
T PRK08311 5 LEDILEKIKNGDEELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKRR 84 (237)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence 34555566555 489999999999999999999998765 589999999999999999999998889999999999999
Q ss_pred HHHHHHhcccc
Q 008352 393 IRKAIFQHSRT 403 (569)
Q Consensus 393 I~~~Ir~~~r~ 403 (569)
+.+++++..+.
T Consensus 85 ~iDylRk~~~~ 95 (237)
T PRK08311 85 LIDYFRKESKH 95 (237)
T ss_pred HHHHHHHhhcc
Confidence 99999987654
No 126
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=99.38 E-value=3.2e-11 Score=116.85 Aligned_cols=174 Identities=20% Similarity=0.309 Sum_probs=118.2
Q ss_pred HHHHHHHhccH-HHHHHHHHHHHHHHHHHHHHhhCC---CCCHHH--HHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHH
Q 008352 317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGR---GISLHD--LLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR 390 (569)
Q Consensus 317 ~~L~~~l~~G~-~Are~LI~~nlrLV~sIArry~~~---g~~~ED--LIQEG~IGLirAiekFDp~kG~rFSTYA~~wIR 390 (569)
.+|+..++.|+ .|.+.|+..|++-++.+|+++... +.+.+| |++|.|+.+++.-...+.+....|..|+...++
T Consensus 5 t~ll~~~~~GD~~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~~~~~r 84 (185)
T PF07638_consen 5 TELLDRWRQGDEAALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALLARIMR 84 (185)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHHHHHHH
Confidence 34555565555 999999999999999999987633 344555 477778777763333233333468889999999
Q ss_pred HHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCC
Q 008352 391 QTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD 470 (569)
Q Consensus 391 qaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~ 470 (569)
+.+.++++++.+.. .+|.. ...+|+...
T Consensus 85 r~lid~~R~~~a~K----------------------Rg~~~-------------------------~~~~l~~~~----- 112 (185)
T PF07638_consen 85 RKLIDHARRRQAQK----------------------RGGDQ-------------------------VRVELDERA----- 112 (185)
T ss_pred HHHHHHHHHHHHHh----------------------cCCCC-------------------------cccchhhhh-----
Confidence 88888887654211 11100 011122111
Q ss_pred cchhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352 471 TTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 550 (569)
Q Consensus 471 ~~l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 550 (569)
.+...+.|+..+. +.+.+..+.. |+|++++||.++|. .|+|.+|||+.||||..+|+.....|..
T Consensus 113 -------~~~~~~~~~~~~~---l~e~l~~L~~-l~~~~~~~v~l~~~----~Gls~~EIA~~lgiS~~tV~r~l~~aR~ 177 (185)
T PF07638_consen 113 -------DSGDEPSPEELLE---LEEALERLLA-LDPRQRRVVELRFF----EGLSVEEIAERLGISERTVRRRLRRARA 177 (185)
T ss_pred -------ccccCCCHHHHHH---HHHHHHHHHc-cCHHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 0111124444332 3344555555 99999999999998 8999999999999999999999999999
Q ss_pred HHHHHhh
Q 008352 551 RLKQSLG 557 (569)
Q Consensus 551 KLR~~l~ 557 (569)
+|+..+.
T Consensus 178 ~l~~~l~ 184 (185)
T PF07638_consen 178 WLRRELR 184 (185)
T ss_pred HHHHHhc
Confidence 9998764
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=99.25 E-value=1.9e-11 Score=98.54 Aligned_cols=70 Identities=23% Similarity=0.432 Sum_probs=66.9
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhccc
Q 008352 333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR 402 (569)
Q Consensus 333 LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r 402 (569)
|++.|.++|++++++|.+++.+.+|++||++++||+++++||+++|..|.+|++..+++.+.++++++.|
T Consensus 1 L~~~~~~~l~~~~~~~~~~~~~~eD~~qe~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~r~~~r 70 (71)
T PF04542_consen 1 LYERYYPLLYRYARRYTGDPEDAEDLVQEAFIKLWRAIDSYDPDRGDSFRAWLFRIARNRILDYLRKRRR 70 (71)
T ss_dssp HHHHTHHHHHHHHHTCTTCSSHHHHHHHHHHHHHHHHHHHTSTTSSSHHHHHHHHHHHHHHHHHHHCSSS
T ss_pred CHHHHHHHHHHHHHHHhCCHhhHHHHhhHHHHHHHhhhhcccccccCCHHHHHHHHHHHHHHHHHHHhcC
Confidence 6899999999999999999999999999999999999999999999899999999999999999998764
No 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=99.23 E-value=2.4e-11 Score=93.33 Aligned_cols=50 Identities=36% Similarity=0.628 Sum_probs=46.3
Q ss_pred HHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 501 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 501 aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
+|+.||++|++||.++|+ +++|++|||+.||+|+++|++++.+|++|||+
T Consensus 1 Al~~L~~~er~vi~~~y~----~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 1 ALDQLPPREREVIRLRYF----EGLTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp HHCTS-HHHHHHHHHHHT----ST-SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred ChhhCCHHHHHHHHHHhc----CCCCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 588999999999999998 99999999999999999999999999999985
No 129
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=99.04 E-value=6e-10 Score=92.86 Aligned_cols=77 Identities=30% Similarity=0.491 Sum_probs=66.1
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHH
Q 008352 412 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 488 (569)
Q Consensus 412 ~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~ 488 (569)
+.+++|.++++.|.+++||.||.+|||+.|||++++|..++...+.+.||+.+++.+++.++.+++.|+...+|++.
T Consensus 1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d~~~~~P~e~ 77 (78)
T PF04539_consen 1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIEDDDAPSPEEE 77 (78)
T ss_dssp HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-SSS--HHHH
T ss_pred ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecCCCCCChhhc
Confidence 36789999999999999999999999999999999999999999999999999998888899999999988788764
No 130
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=98.93 E-value=3.1e-09 Score=82.58 Aligned_cols=54 Identities=30% Similarity=0.440 Sum_probs=46.5
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008352 495 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 552 (569)
Q Consensus 495 ~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 552 (569)
++.|..+|..||+++|.||.++|. +|+|++|||+.+|+|.++|++.+.+|+++|
T Consensus 1 r~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIa~~l~~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 1 REALQQALAQLPERQREIFLLRYF----QGMSYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp HHHHHHHHHCS-HHHHHHHHHHHT----S---HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH----HCcCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 357899999999999999999999 999999999999999999999999999987
No 131
>PRK06930 positive control sigma-like factor; Validated
Probab=98.65 E-value=1.2e-07 Score=91.36 Aligned_cols=71 Identities=18% Similarity=0.285 Sum_probs=62.4
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352 485 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 559 (569)
Q Consensus 485 pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 559 (569)
+.+.....+....|..+|+.||+++|+||.++|+ +|+|++|||+.||+|..+|++++.||+++|+..+...
T Consensus 95 ~~~~~~~~e~~~~l~~al~~L~~rer~V~~L~~~----eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~ 165 (170)
T PRK06930 95 EPESVISEWDKIRIEDALSVLTEREKEVYLMHRG----YGLSYSEIADYLNIKKSTVQSMIERAEKKIARQINES 165 (170)
T ss_pred ChhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 3334445556678999999999999999999998 8999999999999999999999999999999988644
No 132
>PRK00118 putative DNA-binding protein; Validated
Probab=98.43 E-value=1e-06 Score=78.27 Aligned_cols=62 Identities=21% Similarity=0.135 Sum_probs=55.6
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008352 496 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 561 (569)
Q Consensus 496 e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L 561 (569)
..+.-+...||+++++|+.++|. +++|..|||+.+|+|+.+|+.++.||+++||+++..-++
T Consensus 9 ~l~d~~~~~L~ekqRevl~L~y~----eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~ 70 (104)
T PRK00118 9 LLFDFYGSLLTEKQRNYMELYYL----DDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHL 70 (104)
T ss_pred HHHHHHhccCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence 34455668999999999999998 999999999999999999999999999999999876553
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=98.29 E-value=2.4e-06 Score=64.17 Aligned_cols=54 Identities=37% Similarity=0.589 Sum_probs=49.9
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352 496 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 496 e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 553 (569)
+.+..++..|++.++.++.++|. +++|..+||+.+|+|..+|+++..++..+||
T Consensus 2 ~~~~~~~~~l~~~~~~~~~~~~~----~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 2 ERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 35778899999999999999997 8899999999999999999999999998874
No 134
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=98.18 E-value=3.8e-06 Score=78.15 Aligned_cols=57 Identities=19% Similarity=0.269 Sum_probs=49.3
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhh
Q 008352 503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGY 564 (569)
Q Consensus 503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~y 564 (569)
..|+++|++||.+++ +|+|++|||+.||+|+.+|++++++|+++|+.......+-.+
T Consensus 5 ~~Lte~qr~VL~Lr~-----~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l~~~ 61 (137)
T TIGR00721 5 TFLTERQIKVLELRE-----KGLSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDFVKF 61 (137)
T ss_pred CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHHHHH
Confidence 359999999999975 799999999999999999999999999999986555444443
No 135
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=98.13 E-value=5.8e-06 Score=77.30 Aligned_cols=51 Identities=24% Similarity=0.399 Sum_probs=46.9
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352 503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 558 (569)
Q Consensus 503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 558 (569)
..|+++|++||.+++ +++|++|||+.||+|+.+|+.++++|+++||+....
T Consensus 5 ~~Lt~rqreVL~lr~-----~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t 55 (141)
T PRK03975 5 SFLTERQIEVLRLRE-----RGLTQQEIADILGTSRANVSSIEKRARENIEKARET 55 (141)
T ss_pred cCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 469999999999965 799999999999999999999999999999987654
No 136
>PRK04217 hypothetical protein; Provisional
Probab=98.10 E-value=6.3e-06 Score=74.01 Aligned_cols=55 Identities=20% Similarity=0.136 Sum_probs=50.9
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008352 503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 561 (569)
Q Consensus 503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L 561 (569)
..|++.|++||.++|. +++|++|||+.||||+.+|++++.+|+++|++.+.....
T Consensus 41 ~~Lt~eereai~l~~~----eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~~ 95 (110)
T PRK04217 41 IFMTYEEFEALRLVDY----EGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGRE 95 (110)
T ss_pred ccCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 5799999999999998 899999999999999999999999999999999876544
No 137
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPro: IPR009042 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....
Probab=98.04 E-value=1.2e-06 Score=63.65 Aligned_cols=34 Identities=41% Similarity=0.464 Sum_probs=30.1
Q ss_pred CcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHH
Q 008352 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR 287 (569)
Q Consensus 254 ~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~ 287 (569)
+|+++.||++|+++||||++||++|+++|+.+..
T Consensus 1 ~D~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~~ 34 (37)
T PF00140_consen 1 SDSLRLYLKEIGRYPLLTAEEEIELARRIRKGDE 34 (37)
T ss_dssp HHHHHHHHHHHHHS-EETTHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHH
Confidence 3789999999999999999999999999998654
No 138
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.
Probab=97.97 E-value=3.3e-05 Score=71.55 Aligned_cols=62 Identities=18% Similarity=0.264 Sum_probs=55.1
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352 493 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556 (569)
Q Consensus 493 el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 556 (569)
...+.|..+|+.|++.+|.||.++|+ .+..+|..+||..||+|+.+|.++..+|+.+|+..+
T Consensus 71 ~~~~~I~~~l~~Ld~~er~II~~rY~--~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~l 132 (134)
T TIGR01636 71 RNRDAIENCLNEADEQTRVIIQELYM--KKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEEL 132 (134)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHc--cCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 45677899999999999999999996 223469999999999999999999999999999865
No 139
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=97.95 E-value=3.9e-05 Score=67.85 Aligned_cols=58 Identities=28% Similarity=0.350 Sum_probs=45.3
Q ss_pred HHHHHH-hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352 497 HVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 558 (569)
Q Consensus 497 ~L~~aL-~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 558 (569)
.|.+.. .-|+++|++++.++|. +++|+.|||+.+||||..|...++||.++|...=..
T Consensus 9 ~L~d~Yg~LLT~kQ~~~l~lyy~----eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~yE~k 67 (101)
T PF04297_consen 9 LLFDFYGELLTEKQREILELYYE----EDLSLSEIAEELGISRQAVYDSIKRAEKKLEEYEEK 67 (101)
T ss_dssp HHHHHHGGGS-HHHHHHHHHHCT----S---HHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHCCHHHHHHHHHHHc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 344444 4499999999999998 999999999999999999999999999999775443
No 140
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=97.94 E-value=0.0017 Score=74.40 Aligned_cols=34 Identities=32% Similarity=0.493 Sum_probs=31.7
Q ss_pred CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHH
Q 008352 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLI 286 (569)
Q Consensus 253 ~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~ 286 (569)
.+||+++||++||+.||||+|+|+++|++|..+.
T Consensus 102 t~DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~ 135 (619)
T PRK05658 102 TDDPVRMYLREMGTVELLTREGEIEIAKRIEAGE 135 (619)
T ss_pred CCChHHHHHHHhccCcCCCcHHHHHHHHHHHHHH
Confidence 6799999999999999999999999999998754
No 141
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=97.81 E-value=4.3e-05 Score=58.38 Aligned_cols=46 Identities=26% Similarity=0.400 Sum_probs=41.4
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352 503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 553 (569)
..|+++|+.|+.+.+ .+++.+|||+.+|+|+.+|+++..+++++|+
T Consensus 2 ~~l~~~e~~i~~~~~-----~g~s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 2 ASLTPREREVLRLLA-----EGLTNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 468999999997743 6899999999999999999999999998886
No 142
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=97.67 E-value=0.0001 Score=58.19 Aligned_cols=46 Identities=24% Similarity=0.335 Sum_probs=41.2
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352 503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 553 (569)
..|+++|.+|+.+.. .|++.+|||+.+|||..+|+....++++||.
T Consensus 2 ~~LT~~E~~vl~~l~-----~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 2 PSLTERELEVLRLLA-----QGMSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp GSS-HHHHHHHHHHH-----TTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred CccCHHHHHHHHHHH-----hcCCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 479999999999987 6999999999999999999999999999985
No 143
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=97.63 E-value=0.00014 Score=55.72 Aligned_cols=45 Identities=29% Similarity=0.487 Sum_probs=40.4
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
|+++|++|+.+.+ .++|.+|||+.+|+|+.+|+...++++++|+.
T Consensus 1 l~~~e~~i~~~~~-----~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~ 45 (57)
T cd06170 1 LTPREREVLRLLA-----EGKTNKEIADILGISEKTVKTHLRNIMRKLGV 45 (57)
T ss_pred CCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 6899999998854 68999999999999999999999999888864
No 144
>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This entry is represented by Streptococcus phage 7201, Orf19. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several hypothetical, highly conserved Streptococcal and related phage proteins. The function of this family is unknown.
Probab=97.59 E-value=0.00033 Score=61.76 Aligned_cols=55 Identities=22% Similarity=0.439 Sum_probs=49.7
Q ss_pred HHHHHHHHHhcCC-HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008352 494 MRQHVRNLLTLLN-PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 552 (569)
Q Consensus 494 l~e~L~~aL~~L~-~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 552 (569)
.+..+..+++.|+ +.+|.||.++|. .+++..+|++.||+|+.++-.+.++|++.|
T Consensus 44 ~k~ei~~~I~~l~d~~~r~iL~~~Yi----~~~~~~~I~~~l~~S~~t~yr~~~~Al~~L 99 (100)
T PF07374_consen 44 EKLEIRRAINKLEDPDERLILRMRYI----NKLTWEQIAEELNISRRTYYRIHKKALKEL 99 (100)
T ss_pred HHHHHHHHHHHccChhHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence 3456788888886 799999999998 789999999999999999999999999986
No 145
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=97.57 E-value=0.00017 Score=60.19 Aligned_cols=47 Identities=19% Similarity=0.213 Sum_probs=41.9
Q ss_pred HHHHHHhcCCHHHHHHHHHH-hcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 497 HVRNLLTLLNPKERCIVRLR-FGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 497 ~L~~aL~~L~~rER~VL~LR-ygL~d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.+.+-|+.||++.+.++.|. |. +++|++|||+.||||..+|+.++++
T Consensus 8 ~~~~~l~~l~~~~r~af~L~R~~----eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 8 KLAERLTWVDSLAEAAAALAREE----AGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred hHHHHHhcCCHHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 46677899999999999994 55 8999999999999999999998875
No 146
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=97.51 E-value=0.00035 Score=54.86 Aligned_cols=48 Identities=27% Similarity=0.428 Sum_probs=42.0
Q ss_pred CCHHHHHHHHHHhccc--C-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008352 505 LNPKERCIVRLRFGIE--D-GKPKSLSEVGNIFGLSKERVRQLESRALYRL 552 (569)
Q Consensus 505 L~~rER~VL~LRygL~--d-~e~~Tl~EIAe~LGISrerVRqie~RALkKL 552 (569)
|+++|++||..-|-.+ + ...-|+.|||+.||||+.++.+++.+|.+||
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 7899999998866433 3 3688999999999999999999999999987
No 147
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=97.43 E-value=0.00022 Score=62.24 Aligned_cols=50 Identities=22% Similarity=0.240 Sum_probs=43.4
Q ss_pred HHHHHHH-hcCCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHHHHH
Q 008352 496 QHVRNLL-TLLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLE 545 (569)
Q Consensus 496 e~L~~aL-~~L~~rER~VL~LRygL~d---~e~~Tl~EIAe~LGISrerVRqie 545 (569)
+.+..+| ..|+|+|+.+|.+||++.+ ..++|++|||+.+|||+.+|.+..
T Consensus 23 ~~l~~~l~~lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~s 76 (94)
T TIGR01321 23 DDMQLLLELILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGS 76 (94)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHH
Confidence 3566667 5599999999999999997 679999999999999999998654
No 148
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=97.33 E-value=0.00044 Score=66.85 Aligned_cols=47 Identities=23% Similarity=0.352 Sum_probs=43.8
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
..|+++|++|+.+.- +|+|.+|||+.||+|..||+....++++||.-
T Consensus 132 ~~LSpRErEVLrLLA-----qGkTnKEIAe~L~IS~rTVkth~srImkKLgV 178 (198)
T PRK15201 132 RHFSVTERHLLKLIA-----SGYHLSETAALLSLSEEQTKSLRRSIMRKLHV 178 (198)
T ss_pred CCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 469999999999986 79999999999999999999999999999964
No 149
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=97.31 E-value=0.0004 Score=68.62 Aligned_cols=46 Identities=11% Similarity=0.237 Sum_probs=43.4
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
.|++||++||.+.- +|+|.+|||+.||||..||+....+.++||.-
T Consensus 137 ~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v 182 (207)
T PRK15411 137 SLSRTESSMLRMWM-----AGQGTIQISDQMNIKAKTVSSHKGNIKRKIKT 182 (207)
T ss_pred cCCHHHHHHHHHHH-----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence 49999999999986 79999999999999999999999999999963
No 150
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=97.26 E-value=0.00048 Score=67.26 Aligned_cols=46 Identities=22% Similarity=0.291 Sum_probs=43.2
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352 503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 553 (569)
..|++||++|+.+.- +|+|.+|||+.||||..||+....+.++||-
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 469999999999986 6999999999999999999999999999994
No 151
>PRK13870 transcriptional regulator TraR; Provisional
Probab=97.26 E-value=0.00047 Score=69.69 Aligned_cols=46 Identities=26% Similarity=0.364 Sum_probs=43.1
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
.|++||++||.+-- +|+|..|||.+||||..||...+++|++||-.
T Consensus 173 ~LT~RE~E~L~W~A-----~GKT~~EIa~ILgISe~TV~~Hl~na~~KLga 218 (234)
T PRK13870 173 WLDPKEATYLRWIA-----VGKTMEEIADVEGVKYNSVRVKLREAMKRFDV 218 (234)
T ss_pred CCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 59999999999986 79999999999999999999999999999943
No 152
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=97.24 E-value=0.00053 Score=68.41 Aligned_cols=50 Identities=8% Similarity=-0.050 Sum_probs=46.5
Q ss_pred HHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352 499 RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 499 ~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 553 (569)
.+++..|+++|++|+.+.- +|+|.+|||+.|++|..||+....+.++||.
T Consensus 138 ~~~~~~LS~RE~eVL~Lia-----~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLg 187 (217)
T PRK13719 138 LEAKNKVTKYQNDVFILYS-----FGFSHEYIAQLLNITVGSSKNKISEILKFFG 187 (217)
T ss_pred hhccCCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 5567899999999999986 7999999999999999999999999999994
No 153
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=97.24 E-value=0.00054 Score=69.96 Aligned_cols=48 Identities=21% Similarity=0.261 Sum_probs=44.4
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
+..|+++|++|+.+.. +|+|.+|||++||||..||+....++++||.-
T Consensus 188 ~~~LT~RE~evl~l~a-----~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v 235 (247)
T TIGR03020 188 AGLITAREAEILAWVR-----DGKTNEEIAAILGISSLTVKNHLQHIFKKLDV 235 (247)
T ss_pred ccCCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence 4579999999999965 79999999999999999999999999999964
No 154
>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=97.24 E-value=0.00052 Score=69.08 Aligned_cols=48 Identities=19% Similarity=0.267 Sum_probs=44.4
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
...|+++|++||.+.. +|+|.+|||++||||..||+..+.+|++||+.
T Consensus 169 ~~~Lt~re~evl~~~a-----~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~ 216 (232)
T TIGR03541 169 AGVLSEREREVLAWTA-----LGRRQADIAAILGISERTVENHLRSARRKLGV 216 (232)
T ss_pred hccCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence 3579999999999964 79999999999999999999999999999974
No 155
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=97.22 E-value=0.00059 Score=67.68 Aligned_cols=46 Identities=20% Similarity=0.342 Sum_probs=43.4
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352 503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 553 (569)
..|++||++||.+.. +|+|.+|||+.||||..||+....+.++||.
T Consensus 133 ~~LT~RE~eVL~ll~-----~G~snkeIA~~L~iS~~TV~~h~~~I~~KLg 178 (207)
T PRK11475 133 RMLSPTEREILRFMS-----RGYSMPQIAEQLERNIKTIRAHKFNVMSKLG 178 (207)
T ss_pred CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 469999999999987 7999999999999999999999999999994
No 156
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=97.18 E-value=0.00068 Score=68.71 Aligned_cols=45 Identities=16% Similarity=0.258 Sum_probs=43.0
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 553 (569)
.|++||++||.+-. +|+|..|||++||||..||+..+.++++||-
T Consensus 179 ~LT~rE~evl~~~a-----~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~ 223 (240)
T PRK10188 179 NFSKREKEILKWTA-----EGKTSAEIAMILSISENTVNFHQKNMQKKFN 223 (240)
T ss_pred CCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 69999999999986 7999999999999999999999999999995
No 157
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=97.16 E-value=0.00072 Score=67.46 Aligned_cols=48 Identities=17% Similarity=0.127 Sum_probs=44.4
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
+..|+++|++|+.+.+ +|+|.+|||+.||+|..||+....++++||.-
T Consensus 153 ~~~Lt~rE~~Vl~l~~-----~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v 200 (216)
T PRK10100 153 SALLTHREKEILNKLR-----IGASNNEIARSLFISENTVKTHLYNLFKKIAV 200 (216)
T ss_pred cCCCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 3469999999999998 69999999999999999999999999999964
No 158
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=97.11 E-value=0.0012 Score=58.97 Aligned_cols=53 Identities=19% Similarity=0.164 Sum_probs=48.8
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 560 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 560 (569)
.|+..|-+.|+|.+. +++|++|.|+.||||+.|+..++..|.+|+-..|....
T Consensus 41 ~L~~dElEAiRL~D~----egl~QeeaA~~MgVSR~T~~ril~~ARkKiA~ALv~Gk 93 (106)
T PF02001_consen 41 VLTVDELEAIRLVDY----EGLSQEEAAERMGVSRPTFQRILESARKKIADALVEGK 93 (106)
T ss_pred EeeHHHHHHHHHHHH----cCCCHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHCCC
Confidence 588889999999998 99999999999999999999999999999999886544
No 159
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=97.06 E-value=0.00094 Score=66.35 Aligned_cols=46 Identities=30% Similarity=0.371 Sum_probs=43.2
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352 503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 553 (569)
..|++||++|+++-- +|+|.+|||+.|++|..||+....++++||.
T Consensus 147 ~~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~ 192 (211)
T COG2197 147 ELLTPRELEVLRLLA-----EGLSNKEIAEELNLSEKTVKTHVSNILRKLG 192 (211)
T ss_pred CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHhHHHHHHHHHHHHcC
Confidence 469999999999875 7999999999999999999999999999995
No 160
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=97.01 E-value=0.0025 Score=62.32 Aligned_cols=59 Identities=17% Similarity=0.260 Sum_probs=52.9
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352 493 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556 (569)
Q Consensus 493 el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 556 (569)
.....+...+.+|++|||+|+..-- .|+..++||..||||.-||...-.+.++||+..-
T Consensus 131 ~~~~~~~~~l~tLT~RERqVl~~vV-----~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~S 189 (202)
T COG4566 131 DRQAAIRARLATLTPRERQVLDLVV-----RGLMNKQIAFDLGISERTVELHRANVMEKMQARS 189 (202)
T ss_pred HHHHHHHHHHHhcCHHHHHHHHHHH-----cCcccHHHHHHcCCchhhHHHHHHHHHHHHhhcc
Confidence 3456788999999999999999877 6999999999999999999999999999998643
No 161
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=96.97 E-value=0.0025 Score=50.35 Aligned_cols=48 Identities=33% Similarity=0.432 Sum_probs=43.3
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352 503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 555 (569)
Q Consensus 503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 555 (569)
..|+++|.+|+.+.- .|++..|||..+|+|..+|+....++.+||.-.
T Consensus 3 ~~Lt~rE~~v~~l~~-----~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~ 50 (65)
T COG2771 3 ADLTPREREILRLVA-----QGKSNKEIARILGISEETVKTHLRNIYRKLGVK 50 (65)
T ss_pred ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 368999999998876 579999999999999999999999999999643
No 162
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=96.90 E-value=0.0012 Score=49.54 Aligned_cols=41 Identities=24% Similarity=0.339 Sum_probs=24.4
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
..|++.||..|...+- +|+|..+||+.||+|+.||...++|
T Consensus 3 ~~Lt~~eR~~I~~l~~----~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEALLE----QGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHHHHC----S---HHHHHHHTT--HHHHHHHHHH
T ss_pred cchhhhHHHHHHHHHH----cCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 4689999999988776 8999999999999999999988776
No 163
>PRK09483 response regulator; Provisional
Probab=96.87 E-value=0.0018 Score=62.02 Aligned_cols=46 Identities=22% Similarity=0.300 Sum_probs=42.4
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352 503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 553 (569)
..|+++|++|+.+.. +|+|.+|||+.|++|..||+....+.++||-
T Consensus 147 ~~Lt~rE~~vl~~~~-----~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~ 192 (217)
T PRK09483 147 ASLSERELQIMLMIT-----KGQKVNEISEQLNLSPKTVNSYRYRMFSKLN 192 (217)
T ss_pred cccCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 469999999998764 7899999999999999999999999999994
No 164
>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family. This model represents a family of phage proteins, including ArpU, called a putative autolysin regulatory protein. ArpU was described as a regulator of cellular muramidase-2 of Enterococcus hirae but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors. We propose that this is a phage transcriptional activator family.
Probab=96.79 E-value=0.0084 Score=55.06 Aligned_cols=63 Identities=21% Similarity=0.231 Sum_probs=53.9
Q ss_pred HHHHHHHHHH-hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352 493 LMRQHVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 557 (569)
Q Consensus 493 el~e~L~~aL-~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 557 (569)
.....+..++ +.|++.+|+||..+|. . .++++..+|+..+|+|+.+...+.++|+.++-..+.
T Consensus 67 ~~~~~i~~ai~~~l~~~~r~Il~~~Yl-~-~~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~l~ 130 (132)
T TIGR01637 67 QEARAIVNAIVNQLDEISRQILYDKYL-E-PDQKYDYQIMMELGYSHRQYYRIKKRALLRFATLYG 130 (132)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHc-C-ccccchHHHHHHhCCcHHHHHHHHHHHHHHHHHHhC
Confidence 3445677777 9999999999999997 2 137899999999999999999999999999987654
No 165
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=96.71 E-value=0.0032 Score=58.81 Aligned_cols=46 Identities=22% Similarity=0.358 Sum_probs=42.4
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352 503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 553 (569)
..|+++|++||.+. . ++++.+|||+.+++|..||+....++++||.
T Consensus 148 ~~lt~~e~~vl~l~-~----~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 148 PLLTPRERQILKLI-T----EGYTNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred cCCCHHHHHHHHHH-H----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 45999999999984 4 7899999999999999999999999999995
No 166
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=96.65 E-value=0.0041 Score=61.85 Aligned_cols=53 Identities=23% Similarity=0.350 Sum_probs=45.9
Q ss_pred cCCHHHHHHHHHHhccc--C-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352 504 LLNPKERCIVRLRFGIE--D-GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~--d-~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 556 (569)
.|+++|++||+.-|-.+ | ....+++|||+.||||+.++.+++.+|.+||=..+
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 69999999999876543 3 36789999999999999999999999999996543
No 167
>PRK01381 Trp operon repressor; Provisional
Probab=96.48 E-value=0.003 Score=55.62 Aligned_cols=49 Identities=27% Similarity=0.316 Sum_probs=41.0
Q ss_pred HHHHHHHHhc-CCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHHH
Q 008352 495 RQHVRNLLTL-LNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQ 543 (569)
Q Consensus 495 ~e~L~~aL~~-L~~rER~VL~LRygL~d---~e~~Tl~EIAe~LGISrerVRq 543 (569)
.+.+..+|.. |+|+|+..|..||++.. ..++|+.||++.+|||..+|.+
T Consensus 22 ~~~~~~~l~~llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITR 74 (99)
T PRK01381 22 EDLHLPLLTLLLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATITR 74 (99)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehh
Confidence 3456666655 99999999999999886 4579999999999999988863
No 168
>PRK10651 transcriptional regulator NarL; Provisional
Probab=96.48 E-value=0.005 Score=58.32 Aligned_cols=46 Identities=20% Similarity=0.294 Sum_probs=42.6
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352 503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 553 (569)
..|+++|++|+.+.. ++++.++||+.+++|..||+....++++||.
T Consensus 154 ~~Lt~rE~~vl~~l~-----~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~ 199 (216)
T PRK10651 154 NQLTPRERDILKLIA-----QGLPNKMIARRLDITESTVKVHVKHMLKKMK 199 (216)
T ss_pred ccCCHHHHHHHHHHH-----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 459999999999865 7899999999999999999999999999995
No 169
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=96.44 E-value=0.0084 Score=55.72 Aligned_cols=53 Identities=13% Similarity=0.190 Sum_probs=46.8
Q ss_pred HHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 497 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 497 ~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
.+...+..|+++|++|+.+.+ .+++.++||+.+|+|..+|+....++++||+.
T Consensus 134 ~~~~~~~~l~~~e~~vl~~~~-----~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~ 186 (202)
T PRK09390 134 DIRARIASLSERERQVMDGLV-----AGLSNKVIARDLDISPRTVEVYRANVMTKMQA 186 (202)
T ss_pred HHHHHHHhhhhhHHHHHHHHH-----ccCchHHHHHHcCCCHHHHHHHHHHHHHHHcc
Confidence 355667889999999999744 57999999999999999999999999999964
No 170
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=96.41 E-value=0.0027 Score=57.95 Aligned_cols=48 Identities=25% Similarity=0.359 Sum_probs=44.3
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 556 (569)
-|+++|-.||.||- +|+|.+|||++||-|+..|+-++++|+.++.+.-
T Consensus 8 flte~qikvl~lRe-----kG~tQ~eIA~~L~TTraNvSaIEkrA~enIekar 55 (143)
T COG1356 8 FLTEQQIKVLVLRE-----KGLTQSEIARILKTTRANVSAIEKRALENIEKAR 55 (143)
T ss_pred eeehhheeeeehhh-----ccccHHHHHHHHccchhhHHHHHHHHHHHHHHHH
Confidence 48899999999997 7999999999999999999999999999998753
No 171
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=96.21 E-value=0.019 Score=50.59 Aligned_cols=48 Identities=25% Similarity=0.328 Sum_probs=44.0
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
.-|+.+|+..+.++|. .++|+.|||+.++|||..|...++|.-+.|-.
T Consensus 16 sLLT~KQ~~Y~~lyy~----dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~ 63 (105)
T COG2739 16 SLLTKKQKNYLELYYL----DDLSLSEIAEEFNVSRQAIYDNIKRTEKILED 63 (105)
T ss_pred HHHhHHHHHHHHHHHH----hhccHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence 4589999999999998 89999999999999999999999998877754
No 172
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=96.20 E-value=0.013 Score=51.09 Aligned_cols=52 Identities=19% Similarity=0.148 Sum_probs=47.3
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 559 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 559 (569)
.|+..|-+.|+|... ++++++|-|.+||||+.|+-..+..|++|+-.++...
T Consensus 33 ~lt~eElEAlRLvD~----~~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~aLveG 84 (99)
T COG1342 33 ILTIEELEALRLVDY----EGLTQEEAALRMGISRQTFWRLLTSARKKVADALVEG 84 (99)
T ss_pred eecHHHHHHHHHHhH----hhccHHHHHHHhcccHHHHHHHHHHHHHHHHHHHhcC
Confidence 367778899999988 8999999999999999999999999999999988654
No 173
>PRK15320 transcriptional activator SprB; Provisional
Probab=95.98 E-value=0.013 Score=57.75 Aligned_cols=48 Identities=19% Similarity=0.267 Sum_probs=43.8
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
--.|+++|.+|+.+-- +|+|.+|||+.|++|..||+....+.+.||.-
T Consensus 162 ~~~LSdREIEVL~LLA-----kG~SNKEIAekL~LS~KTVSTYKnRLLeKLgA 209 (251)
T PRK15320 162 PPGVTQAKYALLILLS-----SGHPAIELAKKFGLGTKTVSIYRKKVMYRLGM 209 (251)
T ss_pred CCCCCHHHHHHHHHHH-----cCCCHHHHHHHhccchhhHHHHHHHHHHHcCC
Confidence 3678999999999876 79999999999999999999999999999853
No 174
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=95.97 E-value=0.16 Score=53.85 Aligned_cols=159 Identities=18% Similarity=0.143 Sum_probs=96.5
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhH
Q 008352 331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI 410 (569)
Q Consensus 331 e~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~ 410 (569)
+..+..-.+-++.---+|+++=.-.||.+||.|+..++.-.+=-|-+ .-..|.+..-|+.-++.++++.+.-..|.
T Consensus 8 e~~~r~~~~r~~a~L~r~~rd~dlAEEa~~dA~~~Ale~WPr~G~P~--~PaAWL~~v~R~~aiD~~Rr~~~~~~~~~-- 83 (415)
T COG4941 8 EAAARIERPRAMAALARYLRDLDLAEEALQDAFAAALERWPRAGPPR--NPAAWLIAVGRNRAIDRVRRRARRDAAPP-- 83 (415)
T ss_pred HHHHHHhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHhCcccCCCC--ChHHHHHHHHhhhHHHHHHHHHHhccCCh--
Confidence 33444444444444455666656679999999986555443332222 24677777788888888777653222111
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHH
Q 008352 411 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ 490 (569)
Q Consensus 411 ~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~ 490 (569)
|+. ++ . ++.+..+. +.+++...
T Consensus 84 -------------------------el~--------------------~~------~-e~~e~~~a------~~~~d~~i 105 (415)
T COG4941 84 -------------------------ELL--------------------LS------D-EDEEMEEA------EALDDEHI 105 (415)
T ss_pred -------------------------hhc--------------------cc------c-cchhhhcc------cccccccc
Confidence 110 00 0 00000000 00111111
Q ss_pred HHHHHHHHHHHH-hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352 491 KQLMRQHVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 555 (569)
Q Consensus 491 ~~el~e~L~~aL-~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 555 (569)
.++....|.-|. -.|++.+|--|.||.. .|+|..|||..|=|+..++-|.+.||.++++..
T Consensus 106 ~Dd~LRLiFvccHPal~~~~riALtLR~v----~GLs~~eIArAFLv~e~am~QRivRAK~ri~~a 167 (415)
T COG4941 106 RDDRLRLIFVCCHPALPPEQRIALTLRLV----GGLSTAEIARAFLVPEAAMAQRIVRAKARIREA 167 (415)
T ss_pred chhhHHhhhhhcCCCCChhhHHHHHHHHH----cCCcHHHHHHHHcCCcHHHHHHHHHHHHHHHhc
Confidence 112222333333 5699999999999998 799999999999999999999999999999974
No 175
>PRK10403 transcriptional regulator NarP; Provisional
Probab=95.92 E-value=0.014 Score=55.01 Aligned_cols=46 Identities=15% Similarity=0.230 Sum_probs=42.2
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352 503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 553 (569)
..|+++|.+|+.+.. +++|.+|||+.+|+|..||+....++++||.
T Consensus 152 ~~Lt~~e~~vl~~~~-----~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 152 SVLTERELDVLHELA-----QGLSNKQIASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred ccCCHHHHHHHHHHH-----CCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 459999999998765 6899999999999999999999999999984
No 176
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=95.50 E-value=0.028 Score=53.25 Aligned_cols=47 Identities=21% Similarity=0.320 Sum_probs=42.8
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352 502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 553 (569)
+..|+++|++|+.+.. .+.+.+|||+.+++|..||+....+.++||.
T Consensus 141 ~~~lt~~E~~vl~~l~-----~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~ 187 (204)
T PRK09958 141 LDSLSKQEISVMRYIL-----DGKDNNDIAEKMFISNKTVSTYKSRLMEKLE 187 (204)
T ss_pred cccCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 3569999999999877 6889999999999999999999999999994
No 177
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=95.50 E-value=0.021 Score=53.72 Aligned_cols=46 Identities=20% Similarity=0.255 Sum_probs=42.4
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352 503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 553 (569)
..|+++|++|+.+.. ++++.++||+.+|+|..+|+....+.++||.
T Consensus 136 ~~Lt~~E~~il~~l~-----~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 136 DPLTKRERQVAEKLA-----QGMAVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred cCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 469999999999866 5799999999999999999999999999985
No 178
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=95.47 E-value=0.029 Score=53.02 Aligned_cols=45 Identities=24% Similarity=0.242 Sum_probs=40.6
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 553 (569)
.|+++|..|+.+.. +++|.+|||+.+++|..||+....++++||.
T Consensus 149 ~lt~re~~vl~~l~-----~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 149 VLSNREVTILRYLV-----SGLSNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred cCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 48999999988654 6799999999999999999999999999995
No 179
>PRK13558 bacterio-opsin activator; Provisional
Probab=95.24 E-value=0.035 Score=63.63 Aligned_cols=55 Identities=13% Similarity=0.070 Sum_probs=45.6
Q ss_pred HhcCCHHHHHHHHHHhccc---CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352 502 LTLLNPKERCIVRLRFGIE---DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556 (569)
Q Consensus 502 L~~L~~rER~VL~LRygL~---d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 556 (569)
...|+++|+++|..-|..+ -..+-|.+|||+.||||+.|+.+++.+|.+||=..+
T Consensus 605 ~~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l~~~~ 662 (665)
T PRK13558 605 ENDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKLVGAF 662 (665)
T ss_pred hhhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4689999999999988721 113349999999999999999999999999996543
No 180
>PRK04841 transcriptional regulator MalT; Provisional
Probab=95.24 E-value=0.03 Score=66.21 Aligned_cols=46 Identities=11% Similarity=0.172 Sum_probs=43.2
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352 503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 553 (569)
..|+++|++|+.+.. +|+|.+|||+.|+||..||+..+++.++||.
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 349999999999976 7999999999999999999999999999995
No 181
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=95.05 E-value=0.03 Score=39.56 Aligned_cols=27 Identities=30% Similarity=0.643 Sum_probs=19.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 524 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 524 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
++|.+|||+.+|+|+|+|. |++++|++
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 4799999999999999998 55566654
No 182
>PF12645 HTH_16: Helix-turn-helix domain; InterPro: IPR024760 This domain appears to be a helix-turn-helix domain, suggesting a transcriptional regulatory protein. Some proteins with this domain are annotated as conjugative transposon proteins.
Probab=94.81 E-value=0.12 Score=42.17 Aligned_cols=56 Identities=18% Similarity=0.287 Sum_probs=44.8
Q ss_pred HHHHHhccHHHHHHHHHHHHHHHHHHHHHhh----C--CCCCHHHHHHHHHHHHHHhhhhcC
Q 008352 319 LKSELHSGNSSREKLINANLRLVVHVAKQYQ----G--RGISLHDLLQEGSMGLMKSVEKFK 374 (569)
Q Consensus 319 L~~~l~~G~~Are~LI~~nlrLV~sIArry~----~--~g~~~EDLIQEG~IGLirAiekFD 374 (569)
+..+..|+..|.++++..|.+++.+.+.+-. + ++.--+|+-|+-...|++++-+|+
T Consensus 4 I~~A~~GD~~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~ 65 (65)
T PF12645_consen 4 IKAAKQGDPEAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE 65 (65)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence 3444556669999999999999999998722 2 233349999999999999999996
No 183
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=94.64 E-value=0.07 Score=46.26 Aligned_cols=38 Identities=13% Similarity=0.239 Sum_probs=31.5
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008352 502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE 545 (569)
Q Consensus 502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie 545 (569)
+..|++| ..|+.+.- .|+|..|||+.+|||+.||..+.
T Consensus 34 ~~~Ls~R-~~I~~ll~-----~G~S~~eIA~~LgISrsTIyRi~ 71 (88)
T TIGR02531 34 IQSLAQR-LQVAKMLK-----QGKTYSDIEAETGASTATISRVK 71 (88)
T ss_pred HHhhhHH-HHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHH
Confidence 3458899 77877754 57999999999999999999843
No 184
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=94.56 E-value=0.1 Score=39.37 Aligned_cols=42 Identities=17% Similarity=0.226 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352 505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 549 (569)
Q Consensus 505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RAL 549 (569)
|++.++.||..-+- ..+.|..|||+.+|+|..+|++++++-.
T Consensus 1 l~~~~~~Il~~l~~---~~~~t~~ela~~~~is~~tv~~~l~~L~ 42 (48)
T PF13412_consen 1 LDETQRKILNYLRE---NPRITQKELAEKLGISRSTVNRYLKKLE 42 (48)
T ss_dssp --HHHHHHHHHHHH---CTTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH---cCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 57788888876553 3569999999999999999997766543
No 185
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=94.51 E-value=0.093 Score=40.82 Aligned_cols=50 Identities=18% Similarity=0.242 Sum_probs=42.3
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 556 (569)
.|+..++-++.+.|. -.+.++++||..+|||+.+|.++.+..+.-|...+
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 578888888887664 26899999999999999999999999988876643
No 186
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=94.38 E-value=0.2 Score=46.52 Aligned_cols=56 Identities=16% Similarity=0.315 Sum_probs=46.2
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008352 494 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR 551 (569)
Q Consensus 494 l~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkK 551 (569)
..+.|...++.|.+.++.||.+||+ ...++|..+||..|+|+..+++.....-...
T Consensus 71 ~k~~id~~~~~l~de~k~Ii~lry~--~r~~~TW~~IA~~l~i~erta~r~~~~fK~~ 126 (130)
T PF05263_consen 71 QKEAIDRWLETLIDEEKRIIKLRYD--RRSRRTWYQIAQKLHISERTARRWRDRFKND 126 (130)
T ss_pred HHHHHHHHHHhhCHHHHHHHHHHHc--ccccchHHHHHHHhCccHHHHHHHHHHHHHH
Confidence 3466788889999999999999998 3346999999999999999998776554443
No 187
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=94.25 E-value=0.039 Score=41.79 Aligned_cols=32 Identities=28% Similarity=0.361 Sum_probs=22.8
Q ss_pred HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352 512 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 548 (569)
Q Consensus 512 VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RA 548 (569)
||.+.. +|+|..+||+.||||+.+|+++.++-
T Consensus 10 ii~l~~-----~G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 10 IIRLLR-----EGWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp HHHHHH-----HT--HHHHHHHHTS-HHHHHHHHT--
T ss_pred HHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 555554 58999999999999999999987663
No 188
>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=94.14 E-value=0.075 Score=43.39 Aligned_cols=44 Identities=18% Similarity=0.405 Sum_probs=29.6
Q ss_pred hcCCHHHHHHHHH--HhcccCCCCCCHHHHHHHhCCC-HHHHHHHHH
Q 008352 503 TLLNPKERCIVRL--RFGIEDGKPKSLSEVGNIFGLS-KERVRQLES 546 (569)
Q Consensus 503 ~~L~~rER~VL~L--RygL~d~e~~Tl~EIAe~LGIS-rerVRqie~ 546 (569)
..|+++|++||.. .|.-..|-+-|..|||+.||++ ..+|.+.+.
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 5799999999987 3333356788999999999997 999987654
No 189
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=94.08 E-value=0.07 Score=56.52 Aligned_cols=36 Identities=22% Similarity=0.344 Sum_probs=33.0
Q ss_pred HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352 511 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 550 (569)
Q Consensus 511 ~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 550 (569)
+|-.|+|. +++|..|||++|||||.+|.+++.+|++
T Consensus 20 ~vA~lYY~----~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~ 55 (318)
T PRK15418 20 RIAWFYYH----DGLTQSEIGERLGLTRLKVSRLLEKGRQ 55 (318)
T ss_pred HHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 46778888 9999999999999999999999999976
No 190
>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=93.50 E-value=0.44 Score=43.74 Aligned_cols=53 Identities=19% Similarity=0.137 Sum_probs=48.2
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352 502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 558 (569)
Q Consensus 502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 558 (569)
|..-.+.+-.+|.++|. .++|...||..+++|...||+...+|-.-+..++.-
T Consensus 60 L~~~~~~~~~ll~~~Yv----~g~s~r~IA~~~~~s~~~ir~~l~~ae~~i~g~l~~ 112 (125)
T PF06530_consen 60 LKKRDPEEYDLLILYYV----YGWSKRQIARKLKCSEGKIRKRLQRAEGFIDGCLSM 112 (125)
T ss_pred HHccCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHhhhhHhhhhHH
Confidence 45578999999999999 899999999999999999999999999999887643
No 191
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=93.46 E-value=0.17 Score=33.77 Aligned_cols=36 Identities=19% Similarity=0.335 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHH
Q 008352 505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL 544 (569)
Q Consensus 505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqi 544 (569)
+++.++..+...|. .+.+..+||+.+|+|+.+|..+
T Consensus 6 ~~~~~~~~i~~~~~----~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 6 LTPEQIEEARRLLA----AGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHh
Confidence 45555655555554 5779999999999999999865
No 192
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=93.41 E-value=0.1 Score=39.26 Aligned_cols=33 Identities=24% Similarity=0.296 Sum_probs=23.9
Q ss_pred HHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 509 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 509 ER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
..+|+.|+- +|+|..+||+.+|||+.||..++.
T Consensus 11 ~~~i~~l~~-----~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 11 IEEIKELYA-----EGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHHH-----TT--HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHh
Confidence 345666664 679999999999999999998753
No 193
>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=93.14 E-value=0.18 Score=41.65 Aligned_cols=36 Identities=31% Similarity=0.632 Sum_probs=28.5
Q ss_pred HHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHH
Q 008352 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322 (569)
Q Consensus 287 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~ 322 (569)
++.+++.+|+..+||+||.+|.|+.+|++.+.+...
T Consensus 5 ~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~ 40 (78)
T PF04539_consen 5 KIERARRELEQELGREPTDEEIAEELGISVEEVREL 40 (78)
T ss_dssp HHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHH
Confidence 466788999999999999999999999998877543
No 194
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=92.78 E-value=1.6 Score=49.18 Aligned_cols=130 Identities=17% Similarity=0.282 Sum_probs=70.5
Q ss_pred HHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHH-HHHH
Q 008352 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQE-GSMG 365 (569)
Q Consensus 287 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQE-G~IG 365 (569)
++.+++.+|...+|++||.+|.|..+|++.+.+..... ++ ...+++++.+.+ +...
T Consensus 359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~-------------------~~----~~~~SLD~~i~~d~~~~ 415 (509)
T PRK05901 359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQK-------------------YN----REPISLDKTIGKEGDSQ 415 (509)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH-------------------hc----CCCcccccccccCCccc
Confidence 35567788888999999999999999998877643211 01 112222222211 1111
Q ss_pred HHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCH
Q 008352 366 LMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITV 445 (569)
Q Consensus 366 LirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~ 445 (569)
+...+. |+........+.....+..+..++. .||..-...+.. .+.-..+.+-|..|||..+||+.
T Consensus 416 l~d~l~--D~~~~~p~~~~~~~~l~~~L~~aL~------~L~eREr~VI~l------RyGL~~~e~~TL~EIa~~lGVSr 481 (509)
T PRK05901 416 FGDFIE--DSEAVSPVDAVSFTLLQDQLQEVLE------TLSEREAGVIRM------RFGLTDGQPKTLDEIGQVYGVTR 481 (509)
T ss_pred HHHhcc--CCCCCCHHHHHHHHHHHHHHHHHHh------hCCHHHHHHHHH------HhhccCCCCCCHHHHHHHHCCCH
Confidence 222221 1111122333344445555555553 233322222211 11111246789999999999999
Q ss_pred HHHHHHHH
Q 008352 446 EKLERLIF 453 (569)
Q Consensus 446 e~v~~ll~ 453 (569)
++|+++..
T Consensus 482 ERVRQIe~ 489 (509)
T PRK05901 482 ERIRQIES 489 (509)
T ss_pred HHHHHHHH
Confidence 99999854
No 195
>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=92.67 E-value=1.5 Score=44.03 Aligned_cols=33 Identities=33% Similarity=0.579 Sum_probs=28.1
Q ss_pred HHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHH
Q 008352 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (569)
Q Consensus 288 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~ 320 (569)
+.++...+...+|++||.+|.|...|++.+.+.
T Consensus 89 ~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~ 121 (238)
T TIGR02393 89 LIKAERQLTQELGREPTDEELAERMGMPAEKVR 121 (238)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence 445667788889999999999999999987774
No 196
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=92.53 E-value=1.7 Score=46.89 Aligned_cols=129 Identities=19% Similarity=0.278 Sum_probs=71.6
Q ss_pred HHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHH-HHHH
Q 008352 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEG-SMGL 366 (569)
Q Consensus 288 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG-~IGL 366 (569)
+.+...+|...+|++||.+|.|...|++.+.+...+.. +.. .+++++.+.++ -..|
T Consensus 218 ~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~-------------------~~~----~~SLd~~~~~~~~~~l 274 (367)
T PRK09210 218 LIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKI-------------------AQE----PVSLETPIGEEDDSHL 274 (367)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHH-------------------hcC----CCCcCCCCCCCCcchh
Confidence 45567778888999999999999999998777543211 111 11111111110 0111
Q ss_pred HHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHH
Q 008352 367 MKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVE 446 (569)
Q Consensus 367 irAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e 446 (569)
...+. |..............++..+.++|. .+|..-...+.. .+.-..|.+-|.+|||+.+|++.+
T Consensus 275 ~d~i~--d~~~~~p~~~~~~~~~~~~l~~~l~------~L~~rEr~Vl~l------rygl~~~~~~tl~EIa~~lgvs~e 340 (367)
T PRK09210 275 GDFIE--DQDATSPADHAAYELLKEQLEDVLD------TLTDREENVLRL------RFGLDDGRTRTLEEVGKVFGVTRE 340 (367)
T ss_pred hhhcc--CCCCCCHHHHHHHHHHHHHHHHHHH------hCCHHHHHHHHH------HhccCCCCCccHHHHHHHHCCCHH
Confidence 11111 2111223444455566666666664 234322222211 111123467899999999999999
Q ss_pred HHHHHHH
Q 008352 447 KLERLIF 453 (569)
Q Consensus 447 ~v~~ll~ 453 (569)
+|+++..
T Consensus 341 rVrQi~~ 347 (367)
T PRK09210 341 RIRQIEA 347 (367)
T ss_pred HHHHHHH
Confidence 9998854
No 197
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=92.27 E-value=0.38 Score=35.88 Aligned_cols=40 Identities=35% Similarity=0.460 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
|++-.+.||..--. | ...|+.+||+.+|+|..+|.+++.+
T Consensus 1 lD~~D~~Il~~Lq~--d-~r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 1 LDELDRKILRLLQE--D-GRRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp --HHHHHHHHHHHH----TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH--c-CCccHHHHHHHHCcCHHHHHHHHHH
Confidence 34556677766443 2 5789999999999999999987764
No 198
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=92.25 E-value=2.4 Score=45.20 Aligned_cols=34 Identities=32% Similarity=0.460 Sum_probs=28.9
Q ss_pred HHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHH
Q 008352 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (569)
Q Consensus 287 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~ 320 (569)
++.+++.+|...+|++||.+|.|..+|++.+.+.
T Consensus 174 ~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~ 207 (324)
T PRK07921 174 KLARIKRELHQQLGREATDEELAEESGIPEEKIA 207 (324)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHH
Confidence 4556777888899999999999999999987764
No 199
>PHA00675 hypothetical protein
Probab=92.22 E-value=0.26 Score=41.53 Aligned_cols=40 Identities=18% Similarity=0.089 Sum_probs=31.5
Q ss_pred hcCCHHHHHHHHHHh-cccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 503 TLLNPKERCIVRLRF-GIEDGKPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 503 ~~L~~rER~VL~LRy-gL~d~e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
..|++.+-+.|+.++ - .+.|+.+||+.||||+.+|.+|..
T Consensus 21 AKLt~~qV~~IR~l~~r----~G~s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 21 AKLTDAEVERIRELHEV----EGMSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred cccCHHHHHHHHHHHHh----cCccHHHHHHHhCCCHHHHHHHHc
Confidence 356666666666655 4 678999999999999999999865
No 200
>PF13730 HTH_36: Helix-turn-helix domain
Probab=92.14 E-value=0.49 Score=36.44 Aligned_cols=47 Identities=19% Similarity=0.289 Sum_probs=34.1
Q ss_pred cCCHHHHHHHHHHhcccCCCCC---CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPK---SLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~---Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
.|++.++.|+..-..+.++.+. |.+.||+.+|+|+.||+ ++++.|.+
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 5888888887765544332222 89999999999999998 45555543
No 201
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=91.83 E-value=0.32 Score=48.34 Aligned_cols=48 Identities=15% Similarity=0.070 Sum_probs=36.8
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR 551 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkK 551 (569)
.|+++|.+++.....=..++|+|.+|||+.||+|..||+....++...
T Consensus 158 ~Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~ 205 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVNC 205 (239)
T ss_pred CCCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHhC
Confidence 488999877644331112378999999999999999999999887543
No 202
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=91.58 E-value=0.48 Score=42.96 Aligned_cols=49 Identities=20% Similarity=0.310 Sum_probs=41.8
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
+..|++.+..-|....- ..=+++|+++.||||-.|||.++.+.+.+|.-
T Consensus 31 ~~~L~~E~~~Fi~~Fi~----~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 31 FARLSPEQLEFIKLFIK----NRGNLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred hhcCCHHHHHHHHHHHH----hcCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 57899988887766554 33499999999999999999999999999975
No 203
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=91.37 E-value=5.7 Score=40.86 Aligned_cols=147 Identities=18% Similarity=0.195 Sum_probs=80.2
Q ss_pred HHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHHHHH
Q 008352 256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 335 (569)
Q Consensus 256 ~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~ 335 (569)
.+..||++-. +.--+.--.+++.+ +..+..+|+..+|++||..|.|+..|++.+++...+ ..
T Consensus 88 ei~d~LR~~~--~v~vpR~~~~~~~~------i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~----------~~ 149 (247)
T COG1191 88 EILDYLRKND--SVKVPRSLRELGRR------IEEAIDELEQELGREPTDEEIAEELGIDKEEYIEAL----------LA 149 (247)
T ss_pred HHHHHHHhCC--CccCcHHHHHHHHH------HHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHH----------HH
Confidence 4566888877 11122333444444 445778899999999999999999999988775433 22
Q ss_pred HHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHHH
Q 008352 336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS 415 (569)
Q Consensus 336 ~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ 415 (569)
.|.....++--.....+... + +...+..+..+-.|-..+.+..++.. +|..-...
T Consensus 150 ~~~~~~~sld~~~~~~~d~~--------------~---~~~~~~~~~~~~~~~~~~~l~~ai~~------L~EREk~V-- 204 (247)
T COG1191 150 INGSQLLSLDEDVLKDDDDD--------------V---DDQIENPDDGVEKEELLEILKEAIEP------LPEREKLV-- 204 (247)
T ss_pred hccccccchhhhhccccccc--------------h---hhccccchhHHHHHHHHHHHHHHHHc------cCHHHHHH--
Confidence 22222222222221111110 1 11122234445555555666655541 22211100
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 416 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF 453 (569)
Q Consensus 416 ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~ 453 (569)
+.....-+-|..|||+.||++..+|.++..
T Consensus 205 --------l~l~y~eelt~kEI~~~LgISes~VSql~k 234 (247)
T COG1191 205 --------LVLRYKEELTQKEIAEVLGISESRVSRLHK 234 (247)
T ss_pred --------HHHHHHhccCHHHHHHHhCccHHHHHHHHH
Confidence 111112256789999999999999988754
No 204
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=91.27 E-value=0.27 Score=52.29 Aligned_cols=37 Identities=22% Similarity=0.258 Sum_probs=32.4
Q ss_pred HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008352 511 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR 551 (569)
Q Consensus 511 ~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkK 551 (569)
++-.++|. +++|..|||++||||+.+|+.++.+|+++
T Consensus 17 ~~A~lYY~----~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~ 53 (321)
T COG2390 17 RAAWLYYV----EGLTQSEIAERLGISRATVSRLLAKAREE 53 (321)
T ss_pred HHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 35667887 99999999999999999999999988753
No 205
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=90.90 E-value=4.9 Score=44.32 Aligned_cols=37 Identities=22% Similarity=0.399 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHH
Q 008352 416 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLI 452 (569)
Q Consensus 416 ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll 452 (569)
.+.+.+..+..++|+.||.+|.|..+|+++..++..+
T Consensus 112 ~l~~~~~~l~~~~g~~pt~~ewa~~~~~~~~~l~~~l 148 (415)
T PRK07598 112 RLIEVRERLTSELGHRPSLERWAKTADISLADLKPTL 148 (415)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCcHHHHHHhh
Confidence 3455667888999999999999988887766666554
No 206
>PF13518 HTH_28: Helix-turn-helix domain
Probab=90.79 E-value=0.43 Score=36.03 Aligned_cols=28 Identities=25% Similarity=0.336 Sum_probs=23.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESRALY 550 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~RALk 550 (569)
++.|+.+||+.+|||+.+|+++..+-..
T Consensus 11 ~g~s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 11 EGESVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred cCCCHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 4569999999999999999988766543
No 207
>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]
Probab=90.57 E-value=0.29 Score=57.45 Aligned_cols=45 Identities=18% Similarity=0.100 Sum_probs=42.7
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 553 (569)
-|+.||++|+.+.| .|+|.+|||+.+.||-.||+....+...||.
T Consensus 831 ~Ls~RE~eVL~Lia-----~G~SN~eIa~~L~isl~TVKtH~rniy~KLg 875 (894)
T COG2909 831 PLSQRELEVLGLIA-----QGLSNEEIAQELFISLTTVKTHIRNIYQKLG 875 (894)
T ss_pred CccHHHHHHHHHHH-----ccCCHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 38999999999999 6999999999999999999999999999995
No 208
>smart00351 PAX Paired Box domain.
Probab=90.32 E-value=0.7 Score=42.31 Aligned_cols=42 Identities=14% Similarity=0.051 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352 505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 550 (569)
Q Consensus 505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 550 (569)
++..+|.=|...|- ++.+..+||+.||||+.+|..+.++...
T Consensus 18 ~s~~~R~riv~~~~----~G~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 18 LPDEERQRIVELAQ----NGVRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred CCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 45545554445554 6889999999999999999999988643
No 209
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=90.21 E-value=0.57 Score=37.46 Aligned_cols=26 Identities=19% Similarity=0.331 Sum_probs=23.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESRA 548 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~RA 548 (569)
+|++..|||+.||+++.+|.....+-
T Consensus 12 ~G~~~~eIA~~Lg~~~~TV~~W~~r~ 37 (58)
T PF06056_consen 12 QGWSIKEIAEELGVPRSTVYSWKDRY 37 (58)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHHhh
Confidence 79999999999999999999987763
No 210
>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=90.08 E-value=0.62 Score=36.42 Aligned_cols=44 Identities=23% Similarity=0.270 Sum_probs=32.5
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 548 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RA 548 (569)
.|++.+..||..-+.- ++.+.|..|||+.+|+++.+|.+++++-
T Consensus 2 glt~~q~~vL~~l~~~-~~~~~t~~~la~~l~~~~~~vs~~v~~L 45 (62)
T PF12802_consen 2 GLTPSQFRVLMALARH-PGEELTQSELAERLGISKSTVSRIVKRL 45 (62)
T ss_dssp TSTHHHHHHHHHHHHS-TTSGEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHHC-CCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4778888888776652 2234899999999999999998766543
No 211
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=89.99 E-value=4.3 Score=43.58 Aligned_cols=33 Identities=24% Similarity=0.326 Sum_probs=29.5
Q ss_pred CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHH
Q 008352 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDL 285 (569)
Q Consensus 253 ~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~ 285 (569)
....+..|+..+...|+||++||.+|+.+++.+
T Consensus 65 ~~~~~~~~~~~~~~~~~l~~~Ee~~la~~~~~g 97 (342)
T COG0568 65 PAGRLSFYIRAIEAAPLLTPEEEKALARRLKRG 97 (342)
T ss_pred hhhhHHHHHHHHhhhcccChHHHHHHHHHHHcC
Confidence 345678899999999999999999999999987
No 212
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=89.99 E-value=0.38 Score=37.59 Aligned_cols=40 Identities=20% Similarity=0.305 Sum_probs=26.9
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.|+..|+.=|.-+|- .|.+..+||..|||++.||+.+...
T Consensus 6 ~LTl~eK~~iI~~~e----~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 6 SLTLEEKLEIIKRLE----EGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp S--HHHHHHHHHHHH----CTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred cCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 466666654444454 6779999999999999999999876
No 213
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=89.69 E-value=0.59 Score=35.98 Aligned_cols=39 Identities=21% Similarity=0.417 Sum_probs=27.3
Q ss_pred HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352 508 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 548 (569)
Q Consensus 508 rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RA 548 (569)
|++.||.+-+ ..+.+.|.+|||+.||||+.||+..++..
T Consensus 1 R~~~il~~L~--~~~~~it~~eLa~~l~vS~rTi~~~i~~L 39 (55)
T PF08279_consen 1 RQKQILKLLL--ESKEPITAKELAEELGVSRRTIRRDIKEL 39 (55)
T ss_dssp HHHHHHHHHH--HTTTSBEHHHHHHHCTS-HHHHHHHHHHH
T ss_pred CHHHHHHHHH--HcCCCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 4556666542 23356999999999999999998665543
No 214
>PHA02591 hypothetical protein; Provisional
Probab=88.98 E-value=0.76 Score=38.90 Aligned_cols=24 Identities=21% Similarity=0.436 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
.|+|.++||+.||+|.++||+...
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHh
Confidence 689999999999999999999865
No 215
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=88.92 E-value=17 Score=38.39 Aligned_cols=178 Identities=12% Similarity=0.132 Sum_probs=92.8
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhH
Q 008352 331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI 410 (569)
Q Consensus 331 e~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~ 410 (569)
++-+...+..+..++.+. .+.+-+.|....+++.+..-..-+|.....++.-.|.-+++ .
T Consensus 119 er~l~~a~~~I~~~~~~L-----~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR----~----------- 178 (310)
T PRK00423 119 ERNLAFALSELDRIASQL-----GLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACR----R----------- 178 (310)
T ss_pred hHHHHHHHHHHHHHHHHc-----CCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHH----H-----------
Confidence 334444556666666655 23366777777888877666667786665555544443332 1
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchh-hcccCCCCCChhHHH
Q 008352 411 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ-EITADTGVEIPDISV 489 (569)
Q Consensus 411 ~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~-d~i~D~~~~~pee~l 489 (569)
.+-+-|..||+..++++..++..........+.++.+.. +-..+. .+...-.. +....
T Consensus 179 -----------------~~~prtl~eI~~~~~v~~k~i~~~~~~l~k~L~~~~~~~--~p~~~i~r~~~~L~L--~~~v~ 237 (310)
T PRK00423 179 -----------------CKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPT--DPIDYVPRFASELGL--SGEVQ 237 (310)
T ss_pred -----------------cCCCcCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCC--CHHHHHHHHHHHcCC--CHHHH
Confidence 233567888999999998888765443322222222211 111111 11111111 11111
Q ss_pred HHHHHHHHHHHHHh-cC----CHH--HHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008352 490 QKQLMRQHVRNLLT-LL----NPK--ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 552 (569)
Q Consensus 490 ~~~el~e~L~~aL~-~L----~~r--ER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 552 (569)
. .....+..+.+ .| +|. =--+|.+-.-+. |.+.|++|||...||+..+|++..+.-.+.|
T Consensus 238 ~--~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~-g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l 304 (310)
T PRK00423 238 K--KAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLL-GERRTQREVAEVAGVTEVTVRNRYKELAEKL 304 (310)
T ss_pred H--HHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHh-CCCCCHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 1 11122222221 11 111 111222221122 3789999999999999999998777666654
No 216
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=88.87 E-value=0.59 Score=44.63 Aligned_cols=50 Identities=14% Similarity=0.050 Sum_probs=43.4
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCC-----HHHHHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLS-----KERVRQLESRALYRLKQ 554 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGIS-----rerVRqie~RALkKLR~ 554 (569)
.|+++|.+|+.+-.. +.|.++|.+||++.++.+ ..+|+....+.++||..
T Consensus 154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~l~~Kl~~ 208 (228)
T PRK11083 154 TLTRYEFLLLKTLLL-SPGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLRA 208 (228)
T ss_pred ecCHHHHHHHHHHHh-CCCceECHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhcc
Confidence 599999999988764 445689999999999986 78999999999999974
No 217
>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=88.87 E-value=0.75 Score=37.16 Aligned_cols=25 Identities=24% Similarity=0.481 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
..+++.+||+.||||..+||....+
T Consensus 21 g~i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 21 GKIKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred CCccHHHHHHHHCCCHHHHHHHhhh
Confidence 6899999999999999999987554
No 218
>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=88.74 E-value=0.88 Score=39.24 Aligned_cols=45 Identities=29% Similarity=0.339 Sum_probs=34.4
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHh--CCCHHHHHHHHHHHH
Q 008352 502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIF--GLSKERVRQLESRAL 549 (569)
Q Consensus 502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~L--GISrerVRqie~RAL 549 (569)
++.||+..+++..+|.- ....|+.|+|+.| .||++.|..+..+..
T Consensus 35 ~~~l~~~l~~~a~lRl~---~Pd~SL~EL~~~~~~~iSKSgvnhrlrKl~ 81 (85)
T PF02650_consen 35 LDKLPEKLREFAELRLE---NPDASLKELGELLEPPISKSGVNHRLRKLK 81 (85)
T ss_dssp GGGS-HHHHHHHHHHHH----TTS-HHHHHHTT--T--HHHHHHHHHHHH
T ss_pred cccCCHHHHHHHHHHHH---CccccHHHHHHHHcCcCcHHHHHHHHHHHH
Confidence 57899999999999875 3789999999999 999999987766543
No 219
>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=88.11 E-value=1.2 Score=33.47 Aligned_cols=37 Identities=27% Similarity=0.390 Sum_probs=27.2
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 507 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 507 ~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
|.-.+|+.+-.. .+++..||++.+|+|+.+|++.++.
T Consensus 2 ~~R~~Il~~L~~----~~~~~~el~~~l~~s~~~vs~hL~~ 38 (47)
T PF01022_consen 2 PTRLRILKLLSE----GPLTVSELAEELGLSQSTVSHHLKK 38 (47)
T ss_dssp HHHHHHHHHHTT----SSEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHh----CCCchhhHHHhccccchHHHHHHHH
Confidence 334455555444 6899999999999999999987654
No 220
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=87.83 E-value=3.8 Score=41.88 Aligned_cols=33 Identities=24% Similarity=0.395 Sum_probs=26.6
Q ss_pred HHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHH
Q 008352 289 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (569)
Q Consensus 289 e~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~ 321 (569)
......|...+|++|+.+|.|+..|++.+.+..
T Consensus 113 ~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~ 145 (257)
T PRK05911 113 ADAMDSLRQSLGKEPTDGELCEYLNISQQELSG 145 (257)
T ss_pred HHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHH
Confidence 345556777889999999999999998877643
No 221
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=87.72 E-value=1.5 Score=44.76 Aligned_cols=33 Identities=30% Similarity=0.510 Sum_probs=28.3
Q ss_pred HHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHH
Q 008352 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (569)
Q Consensus 288 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~ 320 (569)
+.++..+|...+|++||.+|.|+..|++.+++.
T Consensus 115 ~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~ 147 (256)
T PRK07408 115 AKKVRQELRQELGRQPTDQEIAQALDISLEEWQ 147 (256)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHH
Confidence 455677888899999999999999999987764
No 222
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=87.70 E-value=0.81 Score=36.69 Aligned_cols=42 Identities=17% Similarity=0.368 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHhccc-CCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 505 LNPKERCIVRLRFGIE-DGKPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 505 L~~rER~VL~LRygL~-d~e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
|++....-|...|.|. ++..-+..+||+.||||+.+|...++
T Consensus 2 Lt~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~ 44 (60)
T PF01325_consen 2 LTESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLK 44 (60)
T ss_dssp CSCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHH
T ss_pred CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHH
Confidence 4455555555555554 55789999999999999999986543
No 223
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional
Probab=87.52 E-value=0.81 Score=44.25 Aligned_cols=50 Identities=18% Similarity=0.120 Sum_probs=44.5
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR~ 554 (569)
.|+++|++|+.+... +.|++.|.++|++.+. ++..+|+....+.++||..
T Consensus 160 ~Lt~~e~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~lr~kl~~ 214 (240)
T PRK10710 160 DLTPAEFRLLKTLSH-EPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLES 214 (240)
T ss_pred ecCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCcCcCCCccCHHHHHHHHHHHhhc
Confidence 599999999998764 5567899999999998 9999999999999999963
No 224
>PHA02547 55 RNA polymerase sigma factor; Provisional
Probab=87.10 E-value=2.2 Score=41.27 Aligned_cols=64 Identities=13% Similarity=0.130 Sum_probs=46.9
Q ss_pred HHHHHHHHHHHHHhhCCCCC---HHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHH
Q 008352 335 NANLRLVVHVAKQYQGRGIS---LHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIF 398 (569)
Q Consensus 335 ~~nlrLV~sIArry~~~g~~---~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir 398 (569)
.+-+..+..++++|.-+|.. -+|.|.+|.-.+++.+..||+++...+-.|.+..+-++..+-|.
T Consensus 44 ~~imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~ 110 (179)
T PHA02547 44 LAIMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIK 110 (179)
T ss_pred HHHHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHH
Confidence 33455555666665444554 48999999999999999999999877777777766666555444
No 225
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=86.97 E-value=2.1 Score=33.90 Aligned_cols=36 Identities=28% Similarity=0.374 Sum_probs=27.4
Q ss_pred HHHHHHHHHH-hcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 507 PKERCIVRLR-FGIEDGKPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 507 ~rER~VL~LR-ygL~d~e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
|.-+.||.+- -. .++|..|||+.+|++..+|++.++
T Consensus 10 p~R~~Il~~L~~~----~~~t~~ela~~l~~~~~t~s~hL~ 46 (61)
T PF12840_consen 10 PTRLRILRLLASN----GPMTVSELAEELGISQSTVSYHLK 46 (61)
T ss_dssp HHHHHHHHHHHHC----STBEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHhcC----CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 5556666665 33 899999999999999999986554
No 226
>cd00131 PAX Paired Box domain
Probab=86.75 E-value=1.7 Score=40.11 Aligned_cols=41 Identities=12% Similarity=0.017 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352 505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 549 (569)
Q Consensus 505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RAL 549 (569)
|+...|.-|...|. +|++..+||+.||||+.+|..+.++-.
T Consensus 18 lS~d~R~rIv~~~~----~G~s~~~iA~~~~Vs~~tV~r~i~r~~ 58 (128)
T cd00131 18 LPDSIRQRIVELAQ----SGIRPCDISRQLRVSHGCVSKILNRYY 58 (128)
T ss_pred CCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 44444443334454 789999999999999999999888755
No 227
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=86.55 E-value=9.7 Score=41.44 Aligned_cols=34 Identities=32% Similarity=0.584 Sum_probs=28.4
Q ss_pred HHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHH
Q 008352 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (569)
Q Consensus 287 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~ 320 (569)
++.+....|...+|+.||.+|.|+.+|++.+.+.
T Consensus 224 ~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~ 257 (373)
T PRK07406 224 RIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLR 257 (373)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence 4555677788889999999999999999987664
No 228
>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=86.27 E-value=1.6 Score=37.16 Aligned_cols=42 Identities=24% Similarity=0.400 Sum_probs=34.4
Q ss_pred cCCHHHHHHHHHHhc--ccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFG--IEDGKPKSLSEVGNIFGLSKERVRQLE 545 (569)
Q Consensus 504 ~L~~rER~VL~LRyg--L~d~e~~Tl~EIAe~LGISrerVRqie 545 (569)
.|++++++||..--- ...|++-.-++||+.+|+|..|||...
T Consensus 1 ~Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M 44 (78)
T PF03444_consen 1 MLTERQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEM 44 (78)
T ss_pred CCCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHH
Confidence 388999998876322 346789999999999999999999764
No 229
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=86.20 E-value=1.1 Score=42.65 Aligned_cols=49 Identities=16% Similarity=0.180 Sum_probs=42.1
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLK 553 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR 553 (569)
.|+++|.+|+.+..- +.|..+|.++|++.+. ++..+|+....+.++||.
T Consensus 149 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl~ 202 (219)
T PRK10336 149 TLKPKEFALLELLMR-NAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLG 202 (219)
T ss_pred ecCHHHHHHHHHHHh-CCCccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhcC
Confidence 499999999987652 3446699999999996 999999999999999985
No 230
>PRK15479 transcriptional regulatory protein TctD; Provisional
Probab=86.16 E-value=1.2 Score=42.31 Aligned_cols=49 Identities=18% Similarity=0.233 Sum_probs=41.8
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLK 553 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR 553 (569)
.|+++|.+|+.+... +.|...|.++|++.+. +|..+|.....+.++||.
T Consensus 148 ~Lt~~E~~il~~l~~-~~~~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl~ 201 (221)
T PRK15479 148 ALTPREQALLTVLMY-RRTRPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKLQ 201 (221)
T ss_pred ecCHHHHHHHHHHHh-CCCCcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhcC
Confidence 599999999987643 3346679999999986 999999999999999995
No 231
>PRK12423 LexA repressor; Provisional
Probab=85.77 E-value=1.4 Score=43.47 Aligned_cols=47 Identities=30% Similarity=0.513 Sum_probs=35.3
Q ss_pred cCCHHHHHHHHHHhc--ccCCCCCCHHHHHHHhC-CCHHHHHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFG--IEDGKPKSLSEVGNIFG-LSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 504 ~L~~rER~VL~LRyg--L~d~e~~Tl~EIAe~LG-ISrerVRqie~RALkKLR~ 554 (569)
.|++++++|+..--- ..+|-+.|..|||+.|| +|+.+|+ ++|++|++
T Consensus 3 ~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~----~~l~~L~~ 52 (202)
T PRK12423 3 TLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVAR----KHVQALAE 52 (202)
T ss_pred cCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHH----HHHHHHHH
Confidence 489999999876332 22334679999999999 5999999 46666665
No 232
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=85.75 E-value=2.9 Score=41.60 Aligned_cols=32 Identities=38% Similarity=0.579 Sum_probs=26.0
Q ss_pred HHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHH
Q 008352 290 KEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (569)
Q Consensus 290 ~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~ 321 (569)
+....+...+|+.||.+|.|+..|++.+.+..
T Consensus 101 ~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~ 132 (231)
T TIGR02885 101 YMKEELSKELGREPTINELAEALGVSPEEIVM 132 (231)
T ss_pred HHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHH
Confidence 34566777889999999999999998877643
No 233
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=85.73 E-value=15 Score=37.61 Aligned_cols=35 Identities=29% Similarity=0.532 Sum_probs=28.5
Q ss_pred HHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHH
Q 008352 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (569)
Q Consensus 287 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~ 321 (569)
++.+....|+..+|++||.+|.|...|++.+.+..
T Consensus 119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~ 153 (268)
T PRK06288 119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYNS 153 (268)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHH
Confidence 34556677888899999999999999998776643
No 234
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=85.59 E-value=1.5 Score=34.89 Aligned_cols=42 Identities=19% Similarity=0.315 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352 505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 548 (569)
Q Consensus 505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RA 548 (569)
|+..|..||..-. ..+.+++..+|++.+|+++.+|...+++.
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 4566666766554 23479999999999999999998555443
No 235
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=85.54 E-value=11 Score=38.88 Aligned_cols=34 Identities=26% Similarity=0.524 Sum_probs=28.2
Q ss_pred HHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHH
Q 008352 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (569)
Q Consensus 288 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~ 321 (569)
+.+...+|...+|++||.+|.|+..|++.+++..
T Consensus 129 i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~ 162 (264)
T PRK07122 129 LGRATAELSQRLGRAPTASELAAELGMDREEVVE 162 (264)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 4456677888899999999999999999877754
No 236
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=85.39 E-value=1.9 Score=37.61 Aligned_cols=42 Identities=29% Similarity=0.260 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352 505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 549 (569)
Q Consensus 505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RAL 549 (569)
|++.++.||..... + ...|..+||+.+|+|+.+|+....+-.
T Consensus 1 ld~~D~~il~~L~~--~-~~~~~~~la~~l~~s~~tv~~~l~~L~ 42 (108)
T smart00344 1 LDEIDRKILEELQK--D-ARISLAELAKKVGLSPSTVHNRVKRLE 42 (108)
T ss_pred CCHHHHHHHHHHHH--h-CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 46777888876543 2 468999999999999999997665543
No 237
>PRK05949 RNA polymerase sigma factor; Validated
Probab=85.34 E-value=12 Score=39.81 Aligned_cols=34 Identities=26% Similarity=0.448 Sum_probs=27.7
Q ss_pred HHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHH
Q 008352 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (569)
Q Consensus 288 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~ 321 (569)
+.+....+...+|++|+.+|.|+.+|++.+.+..
T Consensus 180 l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~ 213 (327)
T PRK05949 180 IKKTQRELSQKLGRSATPAEIAKELELEPSQIRE 213 (327)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence 4455667778889999999999999999876643
No 238
>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB. PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself. It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.
Probab=85.23 E-value=0.65 Score=44.18 Aligned_cols=50 Identities=16% Similarity=0.114 Sum_probs=42.7
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHH-----HHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEV-----GNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EI-----Ae~LGISrerVRqie~RALkKLR~ 554 (569)
.|+++|.+|+.+-.. +.|+++|.++| |+.++++..+|+....+.++||..
T Consensus 154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~l~~Kl~~ 208 (226)
T TIGR02154 154 SLGPTEFRLLHFFMT-HPERVYSREQLLDRVWGRDVYVEERTVDVHIRRLRKALNP 208 (226)
T ss_pred EcCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCCCCCCCCccHHHHHHHHHHhhcc
Confidence 599999999988764 34467898888 788999999999999999999963
No 239
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=84.71 E-value=2.2 Score=32.32 Aligned_cols=33 Identities=27% Similarity=0.405 Sum_probs=26.3
Q ss_pred HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352 511 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 548 (569)
Q Consensus 511 ~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RA 548 (569)
.|+.+.. +..|.++||+.+|||-.+|+.+..+.
T Consensus 19 ~i~~~~~-----~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 19 YILKLLR-----ESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHHHHHh-----hcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 4555544 34699999999999999999998764
No 240
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=84.36 E-value=12 Score=38.01 Aligned_cols=34 Identities=26% Similarity=0.317 Sum_probs=27.7
Q ss_pred HHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHH
Q 008352 289 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322 (569)
Q Consensus 289 e~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~ 322 (569)
.+...++...+|++||.+|.|+..|++.+.+...
T Consensus 123 ~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~ 156 (254)
T TIGR02850 123 LQVRDKLISENSKEPTVSEIAKELKVPQEEVVFA 156 (254)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHH
Confidence 3455677788899999999999999998877543
No 241
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=84.03 E-value=2.2 Score=34.85 Aligned_cols=23 Identities=17% Similarity=0.299 Sum_probs=20.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Q 008352 524 PKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 524 ~~Tl~EIAe~LGISrerVRqie~ 546 (569)
+.|..|||+.+||++.+|++++.
T Consensus 22 ~~ta~eLa~~lgl~~~~v~r~L~ 44 (68)
T smart00550 22 TSTALQLAKNLGLPKKEVNRVLY 44 (68)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHH
Confidence 59999999999999998886544
No 242
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=83.89 E-value=2 Score=36.06 Aligned_cols=45 Identities=29% Similarity=0.341 Sum_probs=29.8
Q ss_pred HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH-----HHHHHHHHHhhcCc
Q 008352 512 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES-----RALYRLKQSLGGKA 560 (569)
Q Consensus 512 VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~-----RALkKLR~~l~~~~ 560 (569)
|..++-- .++|..|+|+.+|+|+.+|.++++ -.+.+|...+..-+
T Consensus 23 i~~~~~~----~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aLG 72 (80)
T PF13744_consen 23 IRELREE----RGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEALG 72 (80)
T ss_dssp HHHHHHC----CT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHTT
T ss_pred HHHHHHH----cCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHcC
Confidence 4444444 789999999999999999999985 23566666555443
No 243
>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=83.86 E-value=1.4 Score=33.76 Aligned_cols=33 Identities=36% Similarity=0.477 Sum_probs=24.3
Q ss_pred HHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 514 RLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 514 ~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
.+.+.-..+.++|+.|||+.+|+++.+|..++.
T Consensus 8 iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~ 40 (52)
T PF09339_consen 8 ILEALAESGGPLTLSEIARALGLPKSTVHRLLQ 40 (52)
T ss_dssp HHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 344444455778999999999999999987654
No 244
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=83.85 E-value=1.4 Score=38.23 Aligned_cols=46 Identities=26% Similarity=0.345 Sum_probs=32.4
Q ss_pred cCCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLESRALY 550 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d---~e~~Tl~EIAe~LGISrerVRqie~RALk 550 (569)
-++|.|+.-|..|+-+-. .+++|+.||++.+|+|..||.+ .+|+|+
T Consensus 26 L~T~~E~~~l~~R~~va~~lL~~g~syreIa~~tgvS~aTItR-vsr~Lk 74 (87)
T PF01371_consen 26 LCTPDELEALAQRWQVAKELLDEGKSYREIAEETGVSIATITR-VSRCLK 74 (87)
T ss_dssp HSSHHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHH-HHHHHH
T ss_pred hCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHH-HHHHHH
Confidence 367777766665554332 1689999999999999999874 344444
No 245
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=83.83 E-value=1.1 Score=44.16 Aligned_cols=39 Identities=18% Similarity=0.232 Sum_probs=28.9
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
.|+++ +|+.+.- .+..|+|.+|||+.||||+.||+....
T Consensus 161 ~Lt~r--~Vl~~~~--~g~~g~s~~eIa~~l~iS~~Tv~~~~~ 199 (225)
T PRK10046 161 PLTLN--AVRKLFK--EPGVQHTAETVAQALTISRTTARRYLE 199 (225)
T ss_pred HHHHH--HHHHHHH--cCCCCcCHHHHHHHhCccHHHHHHHHH
Confidence 35564 5665542 122479999999999999999998875
No 246
>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=83.59 E-value=11 Score=34.02 Aligned_cols=23 Identities=17% Similarity=0.277 Sum_probs=20.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLE 545 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie 545 (569)
.+.|+.|||+.||||..+|...+
T Consensus 70 pd~tl~Ela~~l~Vs~~ti~~~L 92 (119)
T PF01710_consen 70 PDATLRELAERLGVSPSTIWRAL 92 (119)
T ss_pred CCcCHHHHHHHcCCCHHHHHHHH
Confidence 78999999999999999987443
No 247
>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=83.53 E-value=19 Score=37.60 Aligned_cols=35 Identities=26% Similarity=0.496 Sum_probs=28.2
Q ss_pred HHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHH
Q 008352 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (569)
Q Consensus 287 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~ 321 (569)
++.+.+..+...+|++||..|.|..+|++.+.+..
T Consensus 162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~ 196 (298)
T TIGR02997 162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRE 196 (298)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 34455667778899999999999999999877753
No 248
>PF12728 HTH_17: Helix-turn-helix domain
Probab=83.34 E-value=1.3 Score=33.67 Aligned_cols=24 Identities=17% Similarity=0.376 Sum_probs=21.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESRA 548 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~RA 548 (569)
+|.+|+|+.||||+.+|+++..+.
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcC
Confidence 689999999999999999988643
No 249
>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=83.26 E-value=31 Score=36.00 Aligned_cols=84 Identities=23% Similarity=0.320 Sum_probs=46.5
Q ss_pred CCCHHHHHHHhC--CCHHHHHHHHHhcCC--CcccCCCCCCCCCcchh-hcccCCCCCChhHH--HHHHHHHHHHHHHHh
Q 008352 431 SPDKEDLARRVG--ITVEKLERLIFITRM--PLSMQQPVWADQDTTFQ-EITADTGVEIPDIS--VQKQLMRQHVRNLLT 503 (569)
Q Consensus 431 ~Pt~eEIA~~lg--is~e~v~~ll~~~~~--~~SLD~~v~~d~~~~l~-d~i~D~~~~~pee~--l~~~el~e~L~~aL~ 503 (569)
.+++++||+.++ |+.++|++.+..... -+-.+. ++.-... ..+.. ..+.+... -...++.+.-.++|+
T Consensus 137 ~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~----~g~y~~t~~~l~~-~~~~~~~avr~~h~q~l~lA~~al~ 211 (271)
T TIGR02147 137 ADDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNE----DGFYKQTDKAVST-GDEVIPLAVRQYQKQMIDLAKEALD 211 (271)
T ss_pred CCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECC----CCcEEeecceeec-CCccchHHHHHHHHHHHHHHHHHHH
Confidence 567889999999 999999988763321 111111 1101011 11111 11122221 122344455677889
Q ss_pred cCCHHHHHHHHHHhcc
Q 008352 504 LLNPKERCIVRLRFGI 519 (569)
Q Consensus 504 ~L~~rER~VL~LRygL 519 (569)
..|+.+|.+=.+-+++
T Consensus 212 ~~p~~eR~~S~lT~~i 227 (271)
T TIGR02147 212 ALPPSERDVSTVTFGI 227 (271)
T ss_pred hCCccccccceeeEec
Confidence 9999999977766664
No 250
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=83.23 E-value=4.6 Score=35.11 Aligned_cols=49 Identities=18% Similarity=0.244 Sum_probs=36.2
Q ss_pred HhcCCHHHHHHHHHH----hccc-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 502 LTLLNPKERCIVRLR----FGIE-DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 502 L~~L~~rER~VL~LR----ygL~-d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
...+++++..||... ||.. ...+.|..|||+.+|+++++|. |++++|.+
T Consensus 20 ~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVs----r~L~~Le~ 73 (95)
T TIGR01610 20 GADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVS----DAIKSLAR 73 (95)
T ss_pred hCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 467899999877643 3322 2368999999999999999987 55556554
No 251
>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=83.06 E-value=1.2 Score=35.83 Aligned_cols=40 Identities=18% Similarity=0.239 Sum_probs=30.3
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
.|++.|..|+..-. . ..+.|..|||+.+|+++.+|+..++
T Consensus 5 gLs~~E~~vy~~Ll--~-~~~~t~~eIa~~l~i~~~~v~~~L~ 44 (68)
T PF01978_consen 5 GLSENEAKVYLALL--K-NGPATAEEIAEELGISRSTVYRALK 44 (68)
T ss_dssp CHHHHHHHHHHHHH--H-HCHEEHHHHHHHHTSSHHHHHHHHH
T ss_pred CcCHHHHHHHHHHH--H-cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 46777888775532 1 1589999999999999999985443
No 252
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=82.99 E-value=2 Score=32.72 Aligned_cols=30 Identities=37% Similarity=0.508 Sum_probs=23.4
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 521 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 521 d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
.|+.. |..|||+.+|+|+.+|++ ++++|.+
T Consensus 16 ~~~~l~s~~~la~~~~vs~~tv~~----~l~~L~~ 46 (60)
T smart00345 16 PGDKLPSERELAAQLGVSRTTVRE----ALSRLEA 46 (60)
T ss_pred CCCcCcCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence 34556 899999999999999984 5555554
No 253
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=82.91 E-value=1.3 Score=33.83 Aligned_cols=22 Identities=18% Similarity=0.356 Sum_probs=20.0
Q ss_pred CHHHHHHHhCCCHHHHHHHHHH
Q 008352 526 SLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 526 Tl~EIAe~LGISrerVRqie~R 547 (569)
|++|||+..|||..||+..++.
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 7899999999999999988764
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=82.63 E-value=1.8 Score=41.64 Aligned_cols=50 Identities=14% Similarity=0.087 Sum_probs=42.1
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHH--HHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEV--GNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EI--Ae~LGISrerVRqie~RALkKLR~ 554 (569)
.|+++|.+||.+..- +.|..+|.++| +..++++..+|+....+.++||..
T Consensus 156 ~Lt~~E~~il~~l~~-~~g~v~s~~~i~~~~~~~~~~~tv~~~v~rlr~Kl~~ 207 (227)
T TIGR03787 156 DLTVTEFWMVHALAK-HPGHVKSRQQLMDAAKIVVDDSTITSHIKRIRKKFQA 207 (227)
T ss_pred cCCHHHHHHHHHHHh-CCCccccHHHHHHHhhhcCCccCHHHHHHHHHHHhcc
Confidence 499999999988662 22355699999 888999999999999999999973
No 255
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=82.52 E-value=4.8 Score=37.30 Aligned_cols=53 Identities=21% Similarity=0.290 Sum_probs=41.3
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 496 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 496 e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
+.+..++-.|++.+-+|+..-. ..+.++|..|||+.+|++++||. ||+++|=.
T Consensus 16 ~dvl~c~~GLs~~Dv~v~~~LL--~~~~~~tvdelae~lnr~rStv~----rsl~~L~~ 68 (126)
T COG3355 16 EDVLKCVYGLSELDVEVYKALL--EENGPLTVDELAEILNRSRSTVY----RSLQNLLE 68 (126)
T ss_pred HHHHHHHhCCcHHHHHHHHHHH--hhcCCcCHHHHHHHHCccHHHHH----HHHHHHHH
Confidence 3566778899999999887654 12368999999999999999986 66666643
No 256
>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=82.49 E-value=2.7 Score=35.02 Aligned_cols=52 Identities=19% Similarity=0.247 Sum_probs=35.5
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhc-ccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 495 RQHVRNLLTLLNPKERCIVRLRFG-IEDGKPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 495 ~e~L~~aL~~L~~rER~VL~LRyg-L~d~e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
.+.|......|++.|+.|..+-.- ..+-..+|..|||+..|||..+|-+..+
T Consensus 4 ~~~i~~~~~~ls~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~k 56 (77)
T PF01418_consen 4 LEKIRSQYNSLSPTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCK 56 (77)
T ss_dssp HHHHHHHGGGS-HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHhhCCHHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHH
Confidence 456777889999999998765332 0012579999999999999999986543
No 257
>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=82.39 E-value=2.1 Score=41.79 Aligned_cols=44 Identities=18% Similarity=0.279 Sum_probs=34.3
Q ss_pred hcCCHHHHHHHHHHhc--ccCCCCCCHHHHHHHhCCC-HHHHHHHHH
Q 008352 503 TLLNPKERCIVRLRFG--IEDGKPKSLSEVGNIFGLS-KERVRQLES 546 (569)
Q Consensus 503 ~~L~~rER~VL~LRyg--L~d~e~~Tl~EIAe~LGIS-rerVRqie~ 546 (569)
..|+++|++||.+-.- ..++.+.|..|||+.+|++ +.+|+.++.
T Consensus 2 ~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~ 48 (199)
T TIGR00498 2 KPLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLK 48 (199)
T ss_pred CccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHH
Confidence 3589999999987552 2245678999999999998 999985443
No 258
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=82.36 E-value=2.8 Score=39.47 Aligned_cols=41 Identities=15% Similarity=0.276 Sum_probs=32.7
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.|++.++.||..--. | ...|+.|||+.+|+|+.+|+.+.++
T Consensus 6 ~lD~~D~~Il~~Lq~--d-~R~s~~eiA~~lglS~~tV~~Ri~r 46 (153)
T PRK11179 6 QIDNLDRGILEALME--N-ARTPYAELAKQFGVSPGTIHVRVEK 46 (153)
T ss_pred ccCHHHHHHHHHHHH--c-CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 377888888876543 2 5789999999999999999976654
No 259
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=82.28 E-value=19 Score=38.15 Aligned_cols=34 Identities=26% Similarity=0.522 Sum_probs=28.0
Q ss_pred HHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHH
Q 008352 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (569)
Q Consensus 287 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~ 320 (569)
++.+....+...+|+.||.+|.|..+|++.+.+.
T Consensus 169 ~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~ 202 (317)
T PRK07405 169 KIKKAQRQLSQQLGRAATIGELAEELELTPKQVR 202 (317)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHH
Confidence 3556677788889999999999999999876664
No 260
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=82.28 E-value=21 Score=28.41 Aligned_cols=74 Identities=22% Similarity=0.255 Sum_probs=45.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHH
Q 008352 431 SPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKER 510 (569)
Q Consensus 431 ~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER 510 (569)
+++.++||+.+|++...+..++..... .++.+.+.. ..+ .
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~~-------------------------~s~~~~~~~----~r~-----------~ 40 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKETG-------------------------TTPKQYLRD----RRL-----------E 40 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHhC-------------------------cCHHHHHHH----HHH-----------H
Confidence 368899999999999999887653210 012111111 011 1
Q ss_pred HHHHHHhcccCCCCCCHHHHHHHhCC-CHHHHHHHHHHH
Q 008352 511 CIVRLRFGIEDGKPKSLSEVGNIFGL-SKERVRQLESRA 548 (569)
Q Consensus 511 ~VL~LRygL~d~e~~Tl~EIAe~LGI-SrerVRqie~RA 548 (569)
.++.+.. . .+.++.+||..+|+ +.....+..++.
T Consensus 41 ~a~~~l~---~-~~~~~~~ia~~~g~~s~~~f~r~Fk~~ 75 (84)
T smart00342 41 RARRLLR---D-TDLSVTEIALRVGFSSQSYFSRAFKKL 75 (84)
T ss_pred HHHHHHH---c-CCCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 2222222 1 36899999999999 988887766543
No 261
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=82.27 E-value=2.6 Score=32.71 Aligned_cols=42 Identities=24% Similarity=0.384 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352 505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 549 (569)
Q Consensus 505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RAL 549 (569)
|+..|-.||..-+- ..+.|..|||+.+|+++.+|.++.++-.
T Consensus 1 lt~~q~~iL~~l~~---~~~~~~~~la~~~~~~~~~~t~~i~~L~ 42 (59)
T PF01047_consen 1 LTPSQFRILRILYE---NGGITQSELAEKLGISRSTVTRIIKRLE 42 (59)
T ss_dssp STHHHHHHHHHHHH---HSSEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH---cCCCCHHHHHHHHCCChhHHHHHHHHHH
Confidence 45566666666543 2569999999999999999987665543
No 262
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=82.26 E-value=26 Score=36.61 Aligned_cols=25 Identities=20% Similarity=0.337 Sum_probs=21.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHh
Q 008352 430 HSPDKEDLARRVGITVEKLERLIFI 454 (569)
Q Consensus 430 r~Pt~eEIA~~lgis~e~v~~ll~~ 454 (569)
..-|.+|||+.+|++.++|.++...
T Consensus 244 ~~~t~~EIa~~lgvs~~~V~q~~~~ 268 (289)
T PRK07500 244 DGATLEALGEELGISKERVRQIEAR 268 (289)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4678999999999999999988653
No 263
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=82.14 E-value=2.5 Score=39.71 Aligned_cols=27 Identities=26% Similarity=0.208 Sum_probs=24.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESRAL 549 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~RAL 549 (569)
+|+|.+|||++||||..+|...+++-.
T Consensus 20 ~G~S~re~Ak~~gvs~sTvy~wv~r~~ 46 (138)
T COG3415 20 EGLSCREAAKRFGVSISTVYRWVRRYR 46 (138)
T ss_pred cCccHHHHHHHhCccHHHHHHHHHHhc
Confidence 799999999999999999999888754
No 264
>CHL00148 orf27 Ycf27; Reviewed
Probab=82.03 E-value=1.8 Score=41.85 Aligned_cols=50 Identities=18% Similarity=0.115 Sum_probs=42.8
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHh-------CCCHHHHHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-------GLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~L-------GISrerVRqie~RALkKLR~ 554 (569)
.|+++|.+|+.+... +.|+++|.+||++.+ +++..+|..+..+.++||..
T Consensus 161 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l~~~~~~~~~~~~tv~~~i~~lr~KL~~ 217 (240)
T CHL00148 161 RLTGMEFSLLELLIS-KSGEIFSRATILKEVWGYTPERHIDTRVVDVHISRLRAKLED 217 (240)
T ss_pred EcCHHHHHHHHHHHH-CCCEEEcHHHHHHHhcCCCcccCCCcccHHHHHHHHHHHhcc
Confidence 499999999987652 345789999999999 48999999999999999974
No 265
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=81.49 E-value=3.6 Score=32.10 Aligned_cols=39 Identities=21% Similarity=0.242 Sum_probs=25.5
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
.|++-||--|....- .|+++.|||..+|-|+..|+..++
T Consensus 4 ~Lt~~Eqaqid~m~q----lG~s~~~isr~i~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 4 TLTDAEQAQIDVMHQ----LGMSLREISRRIGRSRTCIRRYLK 42 (50)
T ss_dssp ---HHHHHHHHHHHH----TT--HHHHHHHHT--HHHHHHHHH
T ss_pred cCCHHHHHHHHHHHH----hchhHHHHHHHhCccHHHHHHHhc
Confidence 467777776666555 589999999999999999997653
No 266
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=81.36 E-value=4.7 Score=32.90 Aligned_cols=38 Identities=29% Similarity=0.503 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHhCCC-HHHHHHHHH
Q 008352 416 KVLEAKRLYIQEGNHSPDKEDLARRVGIT-VEKLERLIF 453 (569)
Q Consensus 416 ki~ka~~~l~~~~gr~Pt~eEIA~~lgis-~e~v~~ll~ 453 (569)
+|-.....+..+.|..||..|||+.+|+. ...|...+.
T Consensus 10 ~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~ 48 (65)
T PF01726_consen 10 EVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLK 48 (65)
T ss_dssp HHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHH
Confidence 34444556677889999999999999997 888887765
No 267
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=81.27 E-value=24 Score=35.77 Aligned_cols=34 Identities=24% Similarity=0.375 Sum_probs=27.5
Q ss_pred HHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHH
Q 008352 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (569)
Q Consensus 288 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~ 321 (569)
+++....+...+|++|+..++|+..|++.+.+..
T Consensus 111 ~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~ 144 (251)
T PRK07670 111 VEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEA 144 (251)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHH
Confidence 3445566777889999999999999999877754
No 268
>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=81.18 E-value=1.8 Score=31.70 Aligned_cols=24 Identities=25% Similarity=0.407 Sum_probs=21.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESRA 548 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~RA 548 (569)
+|.+|+|+.||||+.+|+++.+..
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcC
Confidence 589999999999999999988654
No 269
>PRK00215 LexA repressor; Validated
Probab=80.55 E-value=3 Score=40.89 Aligned_cols=45 Identities=24% Similarity=0.304 Sum_probs=34.5
Q ss_pred cCCHHHHHHHHHHh--cccCCCCCCHHHHHHHhCC-CHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRF--GIEDGKPKSLSEVGNIFGL-SKERVRQLESRA 548 (569)
Q Consensus 504 ~L~~rER~VL~LRy--gL~d~e~~Tl~EIAe~LGI-SrerVRqie~RA 548 (569)
.|+++|++||.+-. ....+.+.|+.|||+.+|+ ++.+|..++.+-
T Consensus 1 ~lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L 48 (205)
T PRK00215 1 MLTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKAL 48 (205)
T ss_pred CCCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 37889999987543 2334578899999999999 999998765543
No 270
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=80.51 E-value=2 Score=31.22 Aligned_cols=25 Identities=16% Similarity=0.300 Sum_probs=22.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESRAL 549 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~RAL 549 (569)
+|..|+|+.+|||+.+|+.......
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 5889999999999999999988754
No 271
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=80.36 E-value=6.9 Score=36.91 Aligned_cols=61 Identities=20% Similarity=0.351 Sum_probs=34.8
Q ss_pred HHHHHhcCCHHHHHHHHHH----hcccCCCCCCHHHHHHHhCCCHHHHHHHHH--HHHHHHHHHhhc
Q 008352 498 VRNLLTLLNPKERCIVRLR----FGIEDGKPKSLSEVGNIFGLSKERVRQLES--RALYRLKQSLGG 558 (569)
Q Consensus 498 L~~aL~~L~~rER~VL~LR----ygL~d~e~~Tl~EIAe~LGISrerVRqie~--RALkKLR~~l~~ 558 (569)
+..+=..|++.|+....+. |-..+|+.+|+.|||+.+||++.+.-++.. ++.....+.+..
T Consensus 4 ~~~le~~L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~~~~Fiey~n~la~ 70 (142)
T PF13022_consen 4 LKELEAKLTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQQNKAFIEYKNELAD 70 (142)
T ss_dssp HHHHHTTS-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHHH-HHHHHHHHHHHH
T ss_pred HHHHHHHcCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHhcCHHHHHHHHHHHH
Confidence 4455578999988843332 212234789999999999999999998874 334444444333
No 272
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=80.22 E-value=2.9 Score=40.89 Aligned_cols=34 Identities=26% Similarity=0.293 Sum_probs=27.4
Q ss_pred HHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 509 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 509 ER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
++.|..++- +|+|..+||+.||||+.||.++.+.
T Consensus 162 ~~~i~~~~~-----~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 162 EEKIKKLLD-----KGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred HHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 345666543 5799999999999999999988763
No 273
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=79.79 E-value=4.4 Score=44.25 Aligned_cols=51 Identities=16% Similarity=0.203 Sum_probs=43.7
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
.+++.||..+.+.+.|...++.|+.++|+.|+||+.|+.+-+++..+.|.+
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 478888888888777777789999999999999999999988877777766
No 274
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=79.49 E-value=3.1 Score=39.64 Aligned_cols=41 Identities=22% Similarity=0.111 Sum_probs=32.0
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.|++.++.||..-- .....|+.|||+.+|+|+.+|+.+.+|
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 36777788887532 235789999999999999999977654
No 275
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=79.36 E-value=4.6 Score=37.34 Aligned_cols=42 Identities=31% Similarity=0.285 Sum_probs=33.6
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
..|++.++.||...-. | ...++.|||+.+|+|..+|+.+..+
T Consensus 4 ~~lD~~D~~IL~~L~~--d-~r~~~~eia~~lglS~~~v~~Ri~~ 45 (154)
T COG1522 4 MKLDDIDRRILRLLQE--D-ARISNAELAERVGLSPSTVLRRIKR 45 (154)
T ss_pred ccccHHHHHHHHHHHH--h-CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4578888888876432 3 4599999999999999999977654
No 276
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=78.82 E-value=2.5 Score=41.23 Aligned_cols=39 Identities=21% Similarity=0.202 Sum_probs=33.2
Q ss_pred HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 511 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 511 ~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
..+.|+- .|+|-.|||+.||+|++|++-+..|+.++...
T Consensus 10 kA~eLk~-----~Glt~gEIAdELNvSreTa~WL~~r~~~~~~~ 48 (203)
T COG0856 10 KARELKS-----KGLTTGEIADELNVSRETATWLLTRAFKKESV 48 (203)
T ss_pred HHHHHHH-----CCCcHHHhhhhhhhhHHHHHHHHhhhhhccCC
Confidence 4556665 69999999999999999999999999877643
No 277
>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=78.64 E-value=8.8 Score=39.39 Aligned_cols=56 Identities=21% Similarity=0.248 Sum_probs=44.7
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhcccCC--CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 495 RQHVRNLLTLLNPKERCIVRLRFGIEDG--KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 495 ~e~L~~aL~~L~~rER~VL~LRygL~d~--e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
+..+.-+++.|+--|.+.+...+-.-++ .-.+..+||+.+|||+..|+ +|+++|..
T Consensus 167 ka~Vq~Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ir----eAlrkLE~ 224 (251)
T TIGR02787 167 KAAVQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIV----NALRKLES 224 (251)
T ss_pred HHHHHHHHHhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 3457778999999999888877665554 46899999999999999887 56667754
No 278
>PF13551 HTH_29: Winged helix-turn helix
Probab=78.50 E-value=3.8 Score=35.44 Aligned_cols=26 Identities=19% Similarity=0.349 Sum_probs=23.1
Q ss_pred CCC-CHHHHHHHhCCCHHHHHHHHHHH
Q 008352 523 KPK-SLSEVGNIFGLSKERVRQLESRA 548 (569)
Q Consensus 523 e~~-Tl~EIAe~LGISrerVRqie~RA 548 (569)
++. |..+||+.+|||+.||..++++-
T Consensus 10 ~g~~~~~~ia~~lg~s~~Tv~r~~~~~ 36 (112)
T PF13551_consen 10 EGVSTIAEIARRLGISRRTVYRWLKRY 36 (112)
T ss_pred cCCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence 567 69999999999999999988873
No 279
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=78.44 E-value=4.9 Score=34.74 Aligned_cols=44 Identities=20% Similarity=0.243 Sum_probs=36.6
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352 503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 549 (569)
Q Consensus 503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RAL 549 (569)
..|++.-|..|..+.. + ++++..++|+.||||+.|++.+..|=.
T Consensus 7 A~Lt~~gR~~lv~~vv-~--~g~~~a~aA~~~gVS~~Ta~kW~~Ryr 50 (85)
T PF13011_consen 7 ARLTPRGRLRLVRRVV-E--QGWPVAHAAAEFGVSRRTAYKWLARYR 50 (85)
T ss_pred CCCCHHHHHHHHHHHH-H--cCCcHHHHHHHhCCCHHHHHHHHHHHH
Confidence 3588998888887763 1 579999999999999999999887744
No 280
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=78.41 E-value=1.2e+02 Score=34.28 Aligned_cols=47 Identities=21% Similarity=0.253 Sum_probs=33.7
Q ss_pred HHHhcCCHHHHHHHHH---------HhcccCC---CCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 500 NLLTLLNPKERCIVRL---------RFGIEDG---KPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 500 ~aL~~L~~rER~VL~L---------RygL~d~---e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
.++..|..|.+.+++. -|+..|. .++|+++||+.+|+..+||++...
T Consensus 333 wli~si~qR~~TllkV~~~Iv~~Q~~Ff~~G~~~LkPLtlkdVAe~lglHeSTVSRa~~ 391 (481)
T PRK12469 333 WLIRNAQQRFDTIQRVAECIVARQRDFFRYGEIALKPLVLRDVAEELGLHESTISRATG 391 (481)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCcCCcHHHHHHHhCCCcchhhHHhc
Confidence 3456777777666542 2322222 799999999999999999997654
No 281
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=77.89 E-value=2.6 Score=33.23 Aligned_cols=24 Identities=25% Similarity=0.346 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
...|.+|+|+.||||..|||.-+.
T Consensus 13 ~~~s~~ela~~~~VS~~TiRRDl~ 36 (57)
T PF08220_consen 13 GKVSVKELAEEFGVSEMTIRRDLN 36 (57)
T ss_pred CCEEHHHHHHHHCcCHHHHHHHHH
Confidence 678999999999999999996554
No 282
>PHA01976 helix-turn-helix protein
Probab=77.70 E-value=4 Score=32.48 Aligned_cols=25 Identities=16% Similarity=0.238 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.++|..|+|+.+|||+.+|.++++.
T Consensus 14 ~glt~~~lA~~~gvs~~~v~~~e~g 38 (67)
T PHA01976 14 RAWSAPELSRRAGVRHSLIYDFEAD 38 (67)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 6899999999999999999999864
No 283
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=77.23 E-value=4.6 Score=35.70 Aligned_cols=39 Identities=28% Similarity=0.376 Sum_probs=31.4
Q ss_pred cCCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHH
Q 008352 504 LLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVR 542 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d---~e~~Tl~EIAe~LGISrerVR 542 (569)
-|+|.||+-+-.|+.+.. ...+|.+||+..||+|..+|-
T Consensus 37 lLTpdEReal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtIT 78 (103)
T COG2973 37 LLTPDEREALGTRVRIVEELLRGELSQREIAQKLGVSIATIT 78 (103)
T ss_pred HcCHhHHHHHHHHHHHHHHHHhccccHHHHHHHhCcchhhhc
Confidence 388888888877776542 157999999999999998885
No 284
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=77.05 E-value=2.6 Score=32.16 Aligned_cols=25 Identities=24% Similarity=0.426 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.++|.+|+|+.+|+|+.+|..+++.
T Consensus 8 ~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 8 KGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred cCCCHHHHHHHhCCCcchhHHHhcC
Confidence 6899999999999999999999875
No 285
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=76.04 E-value=2.1 Score=31.71 Aligned_cols=25 Identities=24% Similarity=0.404 Sum_probs=22.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESRAL 549 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~RAL 549 (569)
+|..|+|+.+|||..+|+..+.+.+
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999987765
No 286
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=76.03 E-value=3.8 Score=36.48 Aligned_cols=70 Identities=23% Similarity=0.275 Sum_probs=51.5
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH--HHHHHHhhcCchhhhh
Q 008352 496 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL--YRLKQSLGGKASYGYA 565 (569)
Q Consensus 496 e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RAL--kKLR~~l~~~~L~~yl 565 (569)
..+..+|..+.-+--+|..+.+.+.-+.++-..||+..||||.-+||-...--+ --|+..+...++-.|+
T Consensus 8 ~~l~~~L~~~glk~~eI~IY~lLve~~~~mri~ei~rEl~is~rtvr~~v~~l~rrGll~relvqkgWvGYi 79 (113)
T COG5625 8 RKLGKALEAIGLKKNEIRIYSLLVEKGRGMRIREIQRELGISERTVRAAVAVLLRRGLLARELVQKGWVGYI 79 (113)
T ss_pred HHHHHHHHHcCCCcchhhhhhHHHHhcCCchHHHHHHHHhHHHHHHHHHHHHHHHhhHHHHHHHhccceeeE
Confidence 356666766555544566666655566889999999999999999998887777 4577777777776664
No 287
>PHA00542 putative Cro-like protein
Probab=76.00 E-value=4.2 Score=34.46 Aligned_cols=26 Identities=12% Similarity=0.102 Sum_probs=23.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESRA 548 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~RA 548 (569)
.++|..|+|+.+|||+.+|.++++..
T Consensus 30 ~glTq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 30 AGWSQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHcCC
Confidence 68999999999999999999998654
No 288
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=75.90 E-value=4.9 Score=29.67 Aligned_cols=39 Identities=13% Similarity=0.244 Sum_probs=25.4
Q ss_pred CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 506 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 506 ~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.+-|+.+|.-..-- .+.+..+.|+.||||+.+++..+.+
T Consensus 3 ~~~E~~~i~~aL~~---~~gn~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 3 EEFEKQLIRQALER---CGGNVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp HHHHHHHHHHHHHH---TTT-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH---hCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 34456666554431 3458899999999999999876653
No 289
>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=75.87 E-value=5.8 Score=38.38 Aligned_cols=41 Identities=22% Similarity=0.214 Sum_probs=33.6
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352 507 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 550 (569)
Q Consensus 507 ~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 550 (569)
+.=|.-++..|.+ +++|++.+|..+|||..|+|.+..+|..
T Consensus 5 ~e~R~~~R~~YV~---~~~sLe~aA~~~gVs~~TarrWK~~Ak~ 45 (165)
T PF08822_consen 5 QETRDAVRRAYVF---DRLSLEQAAAKCGVSYATARRWKREAKA 45 (165)
T ss_pred HHHHHHHHHHHHh---CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4445666666653 5799999999999999999999999864
No 290
>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=75.54 E-value=5.8 Score=35.35 Aligned_cols=42 Identities=21% Similarity=0.328 Sum_probs=26.9
Q ss_pred HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352 508 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 555 (569)
Q Consensus 508 rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 555 (569)
+.++|...+ .|++..|+|..+|+|..+|++|+++..++-++.
T Consensus 62 R~~~I~~~f------~G~n~~eLA~kyglS~r~I~~Ii~~~~~~~~~~ 103 (108)
T PF08765_consen 62 RNREIRREF------NGMNVRELARKYGLSERQIYRIIKRVRRRERRR 103 (108)
T ss_dssp HHHHHHHH--------SS-HHHHHHHHT--HHHHHHHHHHHHH-----
T ss_pred HHHHHHHHh------CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHh
Confidence 445565543 478999999999999999999999988776653
No 291
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=75.40 E-value=7.9 Score=37.50 Aligned_cols=110 Identities=17% Similarity=0.220 Sum_probs=59.0
Q ss_pred CCCCHHHHHHHh--CCCHHHHHHHHHhcCC--CcccCCCCCCCCCcchh-hcccCCCCCChhHHH--HHHHHHHHHHHHH
Q 008352 430 HSPDKEDLARRV--GITVEKLERLIFITRM--PLSMQQPVWADQDTTFQ-EITADTGVEIPDISV--QKQLMRQHVRNLL 502 (569)
Q Consensus 430 r~Pt~eEIA~~l--gis~e~v~~ll~~~~~--~~SLD~~v~~d~~~~l~-d~i~D~~~~~pee~l--~~~el~e~L~~aL 502 (569)
-.+++.+||+.+ +|+.+++++.+..... -+-.+.. +..... ..+. ...+.+...+ ...++.+.-.++|
T Consensus 38 ~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~----g~y~~t~~~l~-~~~~~~~~avr~~h~q~~~lA~~al 112 (171)
T PF14394_consen 38 FAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGD----GKYVQTDKSLT-TSSEIPSEAVRSYHKQMLELAQEAL 112 (171)
T ss_pred CCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCC----CcEEEecceee-CCCCCcHHHHHHHHHHHHHHHHHHH
Confidence 366899999999 9999999998764321 1111111 000001 1111 1111121111 1233444456677
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352 503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 558 (569)
Q Consensus 503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 558 (569)
+..|+.+|.+=.+-++++. .++ +.|+..+...++++......
T Consensus 113 ~~~p~~~R~~s~~T~~vs~---~~~-----------~ki~~~i~~fRk~i~~i~~~ 154 (171)
T PF14394_consen 113 DRVPPEERDFSGLTMSVSR---EDY-----------EKIKKEIREFRKKIIAIAEE 154 (171)
T ss_pred HhCCccccceeeeEEEeCH---HHH-----------HHHHHHHHHHHHHHHHHHhc
Confidence 8888999988777666432 223 33455556666666665544
No 292
>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=75.35 E-value=3.5 Score=39.69 Aligned_cols=36 Identities=19% Similarity=0.214 Sum_probs=28.8
Q ss_pred HHHHHHHHHhcccCCCCCCHHHHHHHhC-CCHHHHHHHHHH
Q 008352 508 KERCIVRLRFGIEDGKPKSLSEVGNIFG-LSKERVRQLESR 547 (569)
Q Consensus 508 rER~VL~LRygL~d~e~~Tl~EIAe~LG-ISrerVRqie~R 547 (569)
..-+.|.-.+. +|+|..|||+.|| ||++.|--..+|
T Consensus 6 e~~~~L~~lw~----~G~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 6 ERVERLRKLWA----EGLSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred HHHHHHHHHHH----cCCCHHHHHHHhCCcchhhhhhhhhc
Confidence 33444555555 8999999999999 999999988776
No 293
>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=75.35 E-value=8.8 Score=32.94 Aligned_cols=32 Identities=25% Similarity=0.298 Sum_probs=26.0
Q ss_pred CCCCHHHHHHHhC-CCHHHHHHHHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFG-LSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 523 e~~Tl~EIAe~LG-ISrerVRqie~RALkKLR~ 554 (569)
-++|+.+||+.|| .+..+|.....+.-+++..
T Consensus 43 ~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~ 75 (90)
T cd06571 43 TGLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE 75 (90)
T ss_pred hCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh
Confidence 4799999999999 9999999766666555543
No 294
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=75.34 E-value=3.6 Score=32.74 Aligned_cols=25 Identities=20% Similarity=0.340 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.++|..++|+.+|+|..+|+++++-
T Consensus 13 ~gls~~~lA~~~g~s~s~v~~iE~G 37 (64)
T PF13560_consen 13 AGLSQAQLADRLGVSQSTVSRIERG 37 (64)
T ss_dssp HTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 5799999999999999999999864
No 295
>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=75.09 E-value=6.4 Score=31.80 Aligned_cols=25 Identities=24% Similarity=0.388 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
...+..|||+.+|+|+.+|++...+
T Consensus 12 ~~~~~~eLa~~l~vS~~tv~~~l~~ 36 (69)
T TIGR00122 12 NPFSGEKLGEALGMSRTAVNKHIQT 36 (69)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4578999999999999999866554
No 296
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=74.74 E-value=5.1 Score=30.41 Aligned_cols=26 Identities=23% Similarity=0.344 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESRA 548 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~RA 548 (569)
++.|..+|++.+|+|+.+|+..+++-
T Consensus 9 ~~~~~~~i~~~l~is~~~v~~~l~~L 34 (66)
T smart00418 9 GELCVCELAEILGLSQSTVSHHLKKL 34 (66)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHH
Confidence 67899999999999999988766553
No 297
>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=74.50 E-value=5.4 Score=30.14 Aligned_cols=25 Identities=12% Similarity=0.279 Sum_probs=22.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.++|..++|+.+|+|+.+|+.+++.
T Consensus 14 ~gltq~~lA~~~gvs~~~vs~~e~g 38 (58)
T TIGR03070 14 LGLTQADLADLAGVGLRFIRDVENG 38 (58)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 5799999999999999999999864
No 298
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=74.45 E-value=7.6 Score=28.66 Aligned_cols=25 Identities=20% Similarity=0.376 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.+.|..+|++.+|+|+.+|++.+..
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~ 37 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNK 37 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4699999999999999999876644
No 299
>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=74.41 E-value=8.1 Score=30.29 Aligned_cols=28 Identities=29% Similarity=0.552 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
.+.|..|||+.+|+|+.+|++ ++++|++
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r----~l~~L~~ 51 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSR----TLKELEE 51 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence 578999999999999999964 4555544
No 300
>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=74.16 E-value=51 Score=32.57 Aligned_cols=35 Identities=31% Similarity=0.635 Sum_probs=28.2
Q ss_pred HHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHH
Q 008352 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (569)
Q Consensus 287 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~ 321 (569)
++.++..+|...+|++|+.+|.|+.+|++.+.+..
T Consensus 84 ~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~ 118 (224)
T TIGR02479 84 KLERAIRELEARLGREPTEEEIAEELGMDLKEYRQ 118 (224)
T ss_pred HHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHH
Confidence 34556677888899999999999999998776643
No 301
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=74.09 E-value=4.8 Score=33.36 Aligned_cols=25 Identities=16% Similarity=0.331 Sum_probs=22.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.++|.+|.|+.+|||+.||-.+++-
T Consensus 13 ~~ltQ~elA~~vgVsRQTi~~iEkg 37 (68)
T COG1476 13 LGLTQEELAKLVGVSRQTIIAIEKG 37 (68)
T ss_pred hCcCHHHHHHHcCcCHHHHHHHHcC
Confidence 5799999999999999999999864
No 302
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=73.87 E-value=4.7 Score=29.49 Aligned_cols=28 Identities=36% Similarity=0.665 Sum_probs=22.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
-+.|..|||+.+|+|+.+|+ +++++|.+
T Consensus 7 ~~~s~~~la~~l~~s~~tv~----~~l~~L~~ 34 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVS----RTLKRLEK 34 (48)
T ss_pred eccCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 36899999999999999986 45555554
No 303
>PF13551 HTH_29: Winged helix-turn helix
Probab=73.80 E-value=9 Score=33.08 Aligned_cols=23 Identities=26% Similarity=0.377 Sum_probs=21.0
Q ss_pred CHHHHHHHhCCCHHHHHHHHHhc
Q 008352 433 DKEDLARRVGITVEKLERLIFIT 455 (569)
Q Consensus 433 t~eEIA~~lgis~e~v~~ll~~~ 455 (569)
+..++|+.+|++...|..++...
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~ 36 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRY 36 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHH
Confidence 79999999999999999998754
No 304
>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=73.12 E-value=4.3 Score=38.54 Aligned_cols=29 Identities=17% Similarity=0.244 Sum_probs=24.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 555 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 555 (569)
-++|.+|||..+|+|+++|. |++++|++.
T Consensus 142 ~~~t~~~iA~~lG~tretvs----R~l~~l~~~ 170 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTIT----RLLGDLRKK 170 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHH----HHHHHHHHC
Confidence 36899999999999999987 677777763
No 305
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=72.85 E-value=7 Score=30.30 Aligned_cols=26 Identities=35% Similarity=0.465 Sum_probs=21.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
.|..+||+.+|+|+++|+ +++++|.+
T Consensus 26 ~~~~~la~~~~is~~~v~----~~l~~L~~ 51 (66)
T cd07377 26 PSERELAEELGVSRTTVR----EALRELEA 51 (66)
T ss_pred CCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 459999999999999998 55666654
No 306
>PRK10072 putative transcriptional regulator; Provisional
Probab=72.78 E-value=5.4 Score=35.16 Aligned_cols=32 Identities=28% Similarity=0.479 Sum_probs=27.0
Q ss_pred HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 512 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 512 VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
|-.+|.. .++|..|+|+.+|||..+|++++..
T Consensus 38 ik~LR~~----~glTQ~elA~~lGvS~~TVs~WE~G 69 (96)
T PRK10072 38 FEQLRKG----TGLKIDDFARVLGVSVAMVKEWESR 69 (96)
T ss_pred HHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 4455665 6899999999999999999999863
No 307
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=72.10 E-value=18 Score=32.11 Aligned_cols=42 Identities=12% Similarity=0.145 Sum_probs=32.5
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
..|++.+..||..-+. ..+.|..|||+.+|+++.+|.+++.+
T Consensus 24 ~~lt~~q~~iL~~l~~---~~~~t~~ela~~~~~~~~tvs~~l~~ 65 (118)
T TIGR02337 24 HGLTEQQWRILRILAE---QGSMEFTQLANQACILRPSLTGILAR 65 (118)
T ss_pred cCCCHHHHHHHHHHHH---cCCcCHHHHHHHhCCCchhHHHHHHH
Confidence 4688999888865442 35799999999999999999754443
No 308
>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=71.97 E-value=12 Score=33.40 Aligned_cols=46 Identities=22% Similarity=0.256 Sum_probs=34.5
Q ss_pred HHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352 497 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 548 (569)
Q Consensus 497 ~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RA 548 (569)
.....-..+.+.+-.-++..+ ++|..++|+.+|+|+.+|+++++..
T Consensus 57 ~~~~~~~~~~~~~i~~~r~~~------gltq~~lA~~lg~~~~tis~~e~g~ 102 (127)
T TIGR03830 57 FYRKVDGLLTPPEIRRIRKKL------GLSQREAAELLGGGVNAFSRYERGE 102 (127)
T ss_pred HHHHccCCcCHHHHHHHHHHc------CCCHHHHHHHhCCCHHHHHHHHCCC
Confidence 334444667777655555554 5899999999999999999988743
No 309
>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=71.94 E-value=7.8 Score=33.09 Aligned_cols=24 Identities=25% Similarity=0.447 Sum_probs=21.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
...|+++||+.+|||+.||+..+.
T Consensus 18 ~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 18 TKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHhc
Confidence 467999999999999999998665
No 310
>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=71.91 E-value=8.4 Score=36.67 Aligned_cols=49 Identities=24% Similarity=0.335 Sum_probs=36.0
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH------HHHHHHHHhh
Q 008352 505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR------ALYRLKQSLG 557 (569)
Q Consensus 505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R------ALkKLR~~l~ 557 (569)
.+|..-.|=.+|-. .|+|..|+|+.+|||+.+|.++++. -+..|.+...
T Consensus 23 ~~p~~~~Ir~~R~~----lGmTq~eLAerlGVS~~tIs~iE~G~~~~~psl~~L~kIA~ 77 (150)
T TIGR02612 23 QTPKEGWVRAIRKA----LGMSGAQLAGRLGVTPQRVEALEKSELSGTVTLKTLRAAAE 77 (150)
T ss_pred ccCcHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCCCHHHHHHHHH
Confidence 34444446666666 7899999999999999999999985 3445555444
No 311
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=71.87 E-value=6.6 Score=36.03 Aligned_cols=24 Identities=25% Similarity=0.336 Sum_probs=22.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
+|+|..+||+.||+|+..|+|.++
T Consensus 21 eG~Sq~~iA~LLGltqaAVS~Yls 44 (119)
T COG2522 21 EGLSQYRIAKLLGLTQAAVSQYLS 44 (119)
T ss_pred cCCcHHHHHHHhCCCHHHHHHHHc
Confidence 589999999999999999999875
No 312
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=71.65 E-value=4.4 Score=32.87 Aligned_cols=28 Identities=39% Similarity=0.666 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
-++|.++||..+|+|+++|. +.+++|++
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~----r~l~~l~~ 54 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVS----RILKRLKD 54 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHH----HHHHHHHH
T ss_pred ecCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 46899999999999999987 55666655
No 313
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=71.46 E-value=7 Score=30.09 Aligned_cols=51 Identities=12% Similarity=0.137 Sum_probs=39.4
Q ss_pred cCCHHHHHHHHHHhcccCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDG-KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~-e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
.+++.+..+|.-.|..+.. .....++||..+||+...|......-..+.|+
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 4678888888888875321 22356899999999999999999887777663
No 314
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=71.40 E-value=10 Score=32.34 Aligned_cols=33 Identities=18% Similarity=0.326 Sum_probs=26.3
Q ss_pred ccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352 519 IEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 555 (569)
Q Consensus 519 L~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 555 (569)
+.++...|-++||+.|||||.+|- +.+++||+.
T Consensus 14 ~~~~~~~SGe~La~~LgiSRtaVw----K~Iq~Lr~~ 46 (79)
T COG1654 14 LLTGNFVSGEKLAEELGISRTAVW----KHIQQLREE 46 (79)
T ss_pred HcCCCcccHHHHHHHHCccHHHHH----HHHHHHHHh
Confidence 345578999999999999987775 677778763
No 315
>PRK05572 sporulation sigma factor SigF; Validated
Probab=71.26 E-value=44 Score=33.80 Aligned_cols=33 Identities=33% Similarity=0.649 Sum_probs=25.5
Q ss_pred HHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHH
Q 008352 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (569)
Q Consensus 288 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~ 320 (569)
+.+....+....|+.|+..+.|+..|++.+.+.
T Consensus 120 ~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~ 152 (252)
T PRK05572 120 IRKDKDELSKELGREPTIEELAEYLGVTPEEVV 152 (252)
T ss_pred HHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHH
Confidence 334556667778999999999999998877653
No 316
>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=70.29 E-value=41 Score=34.03 Aligned_cols=33 Identities=30% Similarity=0.528 Sum_probs=26.3
Q ss_pred HHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHH
Q 008352 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (569)
Q Consensus 288 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~ 320 (569)
+......+...+|+.|+..|.|...|++.+.+.
T Consensus 118 ~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~ 150 (255)
T TIGR02941 118 IKKAIDELTDHLQRSPKIIEIADHLGLSEEEVL 150 (255)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence 334566777788999999999999999877664
No 317
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=70.25 E-value=2.2 Score=34.11 Aligned_cols=25 Identities=28% Similarity=0.514 Sum_probs=22.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESRAL 549 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~RAL 549 (569)
||..|+|+.+|||..+||..+.+.+
T Consensus 1 yti~eva~~~gvs~~tlr~y~~~gl 25 (69)
T PF13411_consen 1 YTIKEVAKLLGVSPSTLRYYEREGL 25 (69)
T ss_dssp EEHHHHHHHTTTTHHHHHHHHHTTS
T ss_pred CcHHHHHHHHCcCHHHHHHHHHhcC
Confidence 4789999999999999999988766
No 318
>PRK09954 putative kinase; Provisional
Probab=70.23 E-value=8.3 Score=41.04 Aligned_cols=42 Identities=19% Similarity=0.279 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352 505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 549 (569)
Q Consensus 505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RAL 549 (569)
|+++++.||.+..- + ...|..|||+.||||+.+|+.++++-.
T Consensus 1 ~~~~~~~il~~l~~--~-~~~s~~~la~~l~~s~~~v~~~i~~L~ 42 (362)
T PRK09954 1 MNNREKEILAILRR--N-PLIQQNEIADILQISRSRVAAHIMDLM 42 (362)
T ss_pred CChHHHHHHHHHHH--C-CCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 46677777766542 2 478999999999999999998877544
No 319
>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=70.11 E-value=12 Score=29.14 Aligned_cols=36 Identities=28% Similarity=0.399 Sum_probs=25.3
Q ss_pred HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 508 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 508 rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.+..|+...+- .+.+..||++.+|+++.+|+..+.+
T Consensus 8 ~~~~il~~l~~----~~~~~~ei~~~~~i~~~~i~~~l~~ 43 (78)
T cd00090 8 TRLRILRLLLE----GPLTVSELAERLGLSQSTVSRHLKK 43 (78)
T ss_pred HHHHHHHHHHH----CCcCHHHHHHHHCcCHhHHHHHHHH
Confidence 34455544332 2399999999999999999765544
No 320
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=69.89 E-value=10 Score=31.68 Aligned_cols=26 Identities=27% Similarity=0.349 Sum_probs=22.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESRA 548 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~RA 548 (569)
.+.|..|||+.+|+++.+|+.++..-
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L 44 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTL 44 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 57999999999999999999776554
No 321
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=69.38 E-value=63 Score=32.83 Aligned_cols=32 Identities=25% Similarity=0.345 Sum_probs=26.5
Q ss_pred HHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHH
Q 008352 290 KEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (569)
Q Consensus 290 ~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~ 321 (569)
+...++...+|++|+..|.|...|++.+.+..
T Consensus 127 ~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~ 158 (258)
T PRK08215 127 QVREKLINENSKEPTVEEIAKELEVPREEVVF 158 (258)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHH
Confidence 45566777889999999999999999887753
No 322
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=69.12 E-value=4.6 Score=34.85 Aligned_cols=24 Identities=17% Similarity=0.108 Sum_probs=17.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
.|+|..|||+.+|.|+..|.+++.
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 323
>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=68.78 E-value=5.8 Score=31.61 Aligned_cols=30 Identities=37% Similarity=0.533 Sum_probs=22.0
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 521 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 521 d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
.|+.+ |..+||+.+|||+.+|| +|+..|.+
T Consensus 20 ~g~~lps~~~la~~~~vsr~tvr----~al~~L~~ 50 (64)
T PF00392_consen 20 PGDRLPSERELAERYGVSRTTVR----EALRRLEA 50 (64)
T ss_dssp TTSBE--HHHHHHHHTS-HHHHH----HHHHHHHH
T ss_pred CCCEeCCHHHHHHHhccCCcHHH----HHHHHHHH
Confidence 44777 99999999999999998 45555543
No 324
>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=68.21 E-value=13 Score=28.90 Aligned_cols=45 Identities=22% Similarity=0.330 Sum_probs=31.9
Q ss_pred cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHH
Q 008352 406 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLER 450 (569)
Q Consensus 406 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ 450 (569)
||......+-.+.+.-..+..++-...+-.+||+.+|+++.+|++
T Consensus 3 Ip~~ti~RL~~Y~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 3 IPKATIRRLPLYLRYLEQLKEEGVERVSSQELAEALGITPAQVRK 47 (50)
T ss_dssp -SHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHcCCeeECHHHHHHHHCCCHHHhcc
Confidence 555555556666666677777777788899999999999999975
No 325
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=67.21 E-value=16 Score=33.58 Aligned_cols=42 Identities=7% Similarity=0.033 Sum_probs=32.3
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.|++.+-.||..-+. .+++.|..|||+.+|+++.+|.+...+
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 688888887766542 225689999999999999999865544
No 326
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=67.14 E-value=6.9 Score=40.27 Aligned_cols=25 Identities=20% Similarity=0.444 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
++|.+.+||+.||||+.+|+....|
T Consensus 18 ~gmk~~dIAeklGvspntiksWKrr 42 (279)
T COG5484 18 KGMKLKDIAEKLGVSPNTIKSWKRR 42 (279)
T ss_pred hhccHHHHHHHhCCChHHHHHHHHh
Confidence 7899999999999999999998765
No 327
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=67.10 E-value=6.7 Score=37.65 Aligned_cols=28 Identities=18% Similarity=0.237 Sum_probs=23.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
-+.|.++||..+|+|+++|. |++++|++
T Consensus 148 ~~~t~~~iA~~lG~tretvs----R~l~~l~~ 175 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVT----KVIGELSR 175 (202)
T ss_pred ecCCHHHHHHHhCccHHHHH----HHHHHHHH
Confidence 35799999999999999997 66667765
No 328
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=66.75 E-value=7.1 Score=31.03 Aligned_cols=23 Identities=26% Similarity=0.488 Sum_probs=20.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~R 547 (569)
+|..|+|+.+|||..++|..+++
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 57899999999999999998865
No 329
>PF11662 DUF3263: Protein of unknown function (DUF3263); InterPro: IPR021678 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=66.21 E-value=20 Score=30.45 Aligned_cols=47 Identities=19% Similarity=0.135 Sum_probs=37.0
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 550 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 550 (569)
.|+++++.||.+---.....|-+-+.|-+.||+|.-+--|+++..+.
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 68999999998732222224668899999999999999999988654
No 330
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=65.97 E-value=9.8 Score=38.87 Aligned_cols=51 Identities=14% Similarity=0.230 Sum_probs=41.0
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhcccCC---CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 495 RQHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 495 ~e~L~~aL~~L~~rER~VL~LRygL~d~---e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.+.|...+..|++.|+.|..+. ++.. ..+|..|||+..|+|..+|-+..++
T Consensus 4 ~~~i~~~~~~Lt~~e~~Ia~yi--l~n~~~v~~~si~~lA~~~~vS~aTv~Rf~kk 57 (284)
T PRK11302 4 LEKIQSRLEHLSKSERKVAEVI--LASPQTAIHSSIATLAKMANVSEPTVNRFCRS 57 (284)
T ss_pred HHHHHHHHhhCCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHH
Confidence 3567888899999999998754 3332 3589999999999999999877654
No 331
>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=65.76 E-value=4.9 Score=33.90 Aligned_cols=32 Identities=13% Similarity=0.094 Sum_probs=24.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
+..|+.++|+.++||+.++.+..++.-+.|+.
T Consensus 29 ~~~s~~~la~~~~iS~sti~~~i~~l~~~l~~ 60 (87)
T PF05043_consen 29 EYVSIEDLAEELFISRSTIYRDIKKLNKYLKK 60 (87)
T ss_dssp SEEEHHHHHHHHT--HHHHHHHHHHHHHHHHC
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 78999999999999999999777666666553
No 332
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=65.55 E-value=1e+02 Score=34.56 Aligned_cols=48 Identities=19% Similarity=0.387 Sum_probs=33.8
Q ss_pred HHHHhcCCHHHHHHHH-------HHhccc-CC----CCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 499 RNLLTLLNPKERCIVR-------LRFGIE-DG----KPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 499 ~~aL~~L~~rER~VL~-------LRygL~-d~----e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
+.++..|.-|++.++. .-+++. +| .++++++||+.+|+..+||++...
T Consensus 293 ~wLiksL~qR~~TLlkV~~~Iv~~Q~~Ff~~g~~~l~PL~LrdvA~~i~~HESTISRai~ 352 (444)
T COG1508 293 KWLIKSLEQREETLLKVAEEIVEYQKAFFEGGEEALKPLVLRDVADEIGMHESTISRAIT 352 (444)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCCcccHHHHHHHhCccHHHHHHHHh
Confidence 4456777777776553 322222 22 679999999999999999997654
No 333
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=65.43 E-value=17 Score=35.82 Aligned_cols=44 Identities=18% Similarity=0.189 Sum_probs=34.7
Q ss_pred HHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 501 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 501 aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
....|++++..|+.+-.. ..+.+..|||+.+|+|+.+|++.+.+
T Consensus 137 ~~~~ls~~~~~IL~~l~~---~g~~s~~eia~~l~is~stv~r~L~~ 180 (203)
T TIGR01884 137 LLAGLSREELKVLEVLKA---EGEKSVKNIAKKLGKSLSTISRHLRE 180 (203)
T ss_pred hhcCCCHHHHHHHHHHHH---cCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 456799999888876542 13679999999999999999866655
No 334
>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=65.35 E-value=4 Score=29.76 Aligned_cols=23 Identities=26% Similarity=0.538 Sum_probs=19.2
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHH
Q 008352 526 SLSEVGNIFGLSKERVRQLESRA 548 (569)
Q Consensus 526 Tl~EIAe~LGISrerVRqie~RA 548 (569)
|..|+|+.+|||..++|..+...
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 46799999999999999988765
No 335
>PRK10870 transcriptional repressor MprA; Provisional
Probab=64.75 E-value=35 Score=32.94 Aligned_cols=50 Identities=12% Similarity=0.118 Sum_probs=36.2
Q ss_pred HHHHHHh--cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 497 HVRNLLT--LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 497 ~L~~aL~--~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.+...+. .|++-+-.||...+. .++.+.|..|||+.+|+++.+|.+++.+
T Consensus 43 ~~~~~l~~~gLt~~q~~iL~~L~~-~~~~~it~~eLa~~l~l~~~tvsr~v~r 94 (176)
T PRK10870 43 NRNKMLKAQGINETLFMALITLES-QENHSIQPSELSCALGSSRTNATRIADE 94 (176)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHhc-CCCCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4455553 488887777766653 2235789999999999999999765554
No 336
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=64.64 E-value=8.5 Score=30.46 Aligned_cols=37 Identities=14% Similarity=0.215 Sum_probs=26.4
Q ss_pred HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 508 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 508 rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
|+-.+|.+-+. ...+|+.|||+.+|+|..+|+..+..
T Consensus 6 rq~~Ll~~L~~---~~~~~~~ela~~l~~S~rti~~~i~~ 42 (59)
T PF08280_consen 6 RQLKLLELLLK---NKWITLKELAKKLNISERTIKNDINE 42 (59)
T ss_dssp HHHHHHHHHHH---HTSBBHHHHHHHCTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHc---CCCCcHHHHHHHHCCCHHHHHHHHHH
Confidence 34455555443 36899999999999999999876543
No 337
>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=64.40 E-value=9.9 Score=32.54 Aligned_cols=45 Identities=24% Similarity=0.391 Sum_probs=28.9
Q ss_pred HHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352 509 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 555 (569)
Q Consensus 509 ER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 555 (569)
||-|-.-.|.++ ...|..+.|..||||++||..-...=|.++-..
T Consensus 6 eR~i~i~~yIi~--~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in~~ 50 (82)
T PF12116_consen 6 ERVIEIANYIIE--TKATVRQAAKVFGVSKSTVHKDVTERLPKINPE 50 (82)
T ss_dssp HHHHHHHHHHHH--H---HHHHHHHHTS-HHHHHHHHTTHHHHH-HH
T ss_pred HHHHHHHHHHHH--cccHHHHHHHHHCCcHHHHHHHHHHHHHhcCHH
Confidence 444445566555 468999999999999999998776655555443
No 338
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=64.20 E-value=18 Score=32.44 Aligned_cols=56 Identities=14% Similarity=0.204 Sum_probs=47.8
Q ss_pred HHHHHH--hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352 497 HVRNLL--TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556 (569)
Q Consensus 497 ~L~~aL--~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 556 (569)
.|+... .+|.+-||-...-+|- .-+|-+|||-.+.++..||..+...-..|.|+.-
T Consensus 19 RIRTTFTS~QLkELErvF~ETHYP----DIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE 76 (125)
T KOG0484|consen 19 RIRTTFTSAQLKELERVFAETHYP----DIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE 76 (125)
T ss_pred hhhhhhhHHHHHHHHHHHHhhcCC----cchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence 455444 6788999999999997 8899999999999999999999998888888753
No 339
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=63.90 E-value=17 Score=37.43 Aligned_cols=52 Identities=15% Similarity=0.311 Sum_probs=41.9
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHhcccCC---CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 494 MRQHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 494 l~e~L~~aL~~L~~rER~VL~LRygL~d~---e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
+...|+..+..|++.|+.|.... +.+. ..+|..+||+..|||..+|-+..++
T Consensus 15 i~~~i~~~~~~Lt~~e~~Ia~yi--l~~~~~v~~~si~~lA~~~~vS~aTi~Rf~kk 69 (292)
T PRK11337 15 LGPYIRMKQEGLTPLESRVVEWL--LKPGDLSEATALKDIAEALAVSEAMIVKVAKK 69 (292)
T ss_pred HHHHHHHHHhhcCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCChHHHHHHHHH
Confidence 34578888999999999998754 3332 4589999999999999999877654
No 340
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=63.76 E-value=17 Score=30.30 Aligned_cols=44 Identities=30% Similarity=0.477 Sum_probs=32.8
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
.|+..+..||.+-+. ..++|..+|++.+++|+.+|++ ++++|.+
T Consensus 7 ~l~~~~~~il~~l~~---~~~~~~~~la~~~~~s~~~i~~----~l~~L~~ 50 (101)
T smart00347 7 GLTPTQFLVLRILYE---EGPLSVSELAKRLGVSPSTVTR----VLDRLEK 50 (101)
T ss_pred CCCHHHHHHHHHHHH---cCCcCHHHHHHHHCCCchhHHH----HHHHHHH
Confidence 467777778777664 1468999999999999999874 4555543
No 341
>PF14493 HTH_40: Helix-turn-helix domain
Probab=63.64 E-value=11 Score=32.42 Aligned_cols=29 Identities=21% Similarity=0.245 Sum_probs=26.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESRALYR 551 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~RALkK 551 (569)
+|+|++|||+.-|++.+||...+.++...
T Consensus 12 ~G~si~eIA~~R~L~~sTI~~HL~~~~~~ 40 (91)
T PF14493_consen 12 KGLSIEEIAKIRGLKESTIYGHLAELIES 40 (91)
T ss_pred cCCCHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence 78999999999999999999999887765
No 342
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=63.63 E-value=15 Score=29.99 Aligned_cols=25 Identities=12% Similarity=0.275 Sum_probs=23.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.++|..++|+.+|+|+.+|.++++.
T Consensus 17 ~~~t~~~lA~~~gis~~tis~~~~g 41 (78)
T TIGR02607 17 LGLSIRALAKALGVSRSTLSRIVNG 41 (78)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 6799999999999999999999864
No 343
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=63.55 E-value=34 Score=32.89 Aligned_cols=27 Identities=37% Similarity=0.493 Sum_probs=22.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 524 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 524 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
..|.++||..+|+|+++|. |++++|++
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 6889999999999999987 55666665
No 344
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=63.50 E-value=39 Score=31.14 Aligned_cols=48 Identities=6% Similarity=0.020 Sum_probs=36.3
Q ss_pred HHHHHH--hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 497 HVRNLL--TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 497 ~L~~aL--~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.+...+ ..|++.|-.||..-+. ..+.|..|||+.+|+++.+|..++.+
T Consensus 28 ~~~~~l~~~glt~~q~~vL~~l~~---~~~~t~~eLa~~l~i~~~tvsr~l~~ 77 (144)
T PRK11512 28 LLNEYLSPLDITAAQFKVLCSIRC---AACITPVELKKVLSVDLGALTRMLDR 77 (144)
T ss_pred HHHHHhcccCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 344444 3588999888876542 25799999999999999999866554
No 345
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=63.32 E-value=12 Score=31.37 Aligned_cols=24 Identities=29% Similarity=0.481 Sum_probs=19.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
.+.|.+|||+.+|+|+..|+++..
T Consensus 24 ~~~s~~eiA~~~~i~~~~l~kil~ 47 (83)
T PF02082_consen 24 KPVSSKEIAERLGISPSYLRKILQ 47 (83)
T ss_dssp C-BEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHH
Confidence 458999999999999999986654
No 346
>PRK01905 DNA-binding protein Fis; Provisional
Probab=63.26 E-value=30 Score=28.93 Aligned_cols=37 Identities=11% Similarity=0.201 Sum_probs=25.3
Q ss_pred HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 508 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 508 rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
-|+.+|...+-- .+-+..+.|+.+|||+.+++...++
T Consensus 37 ~E~~~i~~aL~~---~~gn~s~aAr~LGIsrstL~rklkk 73 (77)
T PRK01905 37 VEKPLLEVVMEQ---AGGNQSLAAEYLGINRNTLRKKLQQ 73 (77)
T ss_pred HHHHHHHHHHHH---cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 355555444321 2347899999999999998766554
No 347
>PRK15482 transcriptional regulator MurR; Provisional
Probab=63.16 E-value=12 Score=38.49 Aligned_cols=50 Identities=16% Similarity=0.260 Sum_probs=40.6
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhcccCC---CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 496 QHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 496 e~L~~aL~~L~~rER~VL~LRygL~d~---e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
..|+.....|++.|+.|..+- |++. ..+|..|||+..|+|..+|-+.-++
T Consensus 5 ~~i~~~~~~Lt~~e~~Ia~yI--l~n~~~v~~~si~elA~~~~vS~aTv~Rf~kk 57 (285)
T PRK15482 5 TKIRNAESEFTENEQKIADFL--RANVSELKSVSSRKMAKQLGISQSSIVKFAQK 57 (285)
T ss_pred HHHHHHHhhcCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHH
Confidence 467788899999999998754 4432 4589999999999999999876654
No 348
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=62.86 E-value=9.5 Score=30.50 Aligned_cols=23 Identities=26% Similarity=0.473 Sum_probs=21.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~R 547 (569)
+|..|+|+.+|||..++|..+.+
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 57899999999999999999876
No 349
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=62.77 E-value=61 Score=32.01 Aligned_cols=31 Identities=32% Similarity=0.592 Sum_probs=25.2
Q ss_pred HHHHHHhhhhCCCCcHHHHHHHcCCCHHHHH
Q 008352 290 KEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (569)
Q Consensus 290 ~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~ 320 (569)
+....+....|++|+..|.|+..|++.+.+.
T Consensus 94 ~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~ 124 (227)
T TIGR02980 94 KATEELTQRLGRSPTIAEIAEELGVSEEEVV 124 (227)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHhCCCHHHHH
Confidence 3455677778999999999999999887664
No 350
>PRK06030 hypothetical protein; Provisional
Probab=62.74 E-value=21 Score=32.94 Aligned_cols=40 Identities=15% Similarity=0.003 Sum_probs=28.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 566 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yld 566 (569)
-++|+.+||+.||....||-.-.++.-+ .+....++..++
T Consensus 68 ~~~sl~~IG~~FGRDHSTV~haikkIe~----~~~d~~lk~~v~ 107 (124)
T PRK06030 68 LGWPMNEVALAFGRDRTTVGHACHTVED----LRDDAAFDARVS 107 (124)
T ss_pred cCCCHHHHHHHHCCChhHHHHHHHHHHH----HhhCHHHHHHHH
Confidence 5789999999999999999876664333 333444444443
No 351
>TIGR00647 MG103 conserved hypothetical protein.
Probab=62.74 E-value=16 Score=38.36 Aligned_cols=45 Identities=16% Similarity=0.211 Sum_probs=38.0
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC------CCHHHHHHHHHHHH
Q 008352 502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG------LSKERVRQLESRAL 549 (569)
Q Consensus 502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LG------ISrerVRqie~RAL 549 (569)
++.||+.-+++..+|.- ..+.|++|+|+.|. ||++.|..+.++..
T Consensus 225 l~~Lp~~L~~~a~lRl~---~Pd~SL~ELgell~~~~~~~isKSgvnhRlrKl~ 275 (279)
T TIGR00647 225 FEKLPLNFQRICLLKID---HPDWSLEQIAEFFASKYKVKISRSGIQHRLRKLK 275 (279)
T ss_pred cccCCHHHHHHHHHHHh---CcccCHHHHHHHhccCCCCCcCHHHHHHHHHHHH
Confidence 57899999999999974 37899999999994 99999988776543
No 352
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=62.13 E-value=17 Score=32.88 Aligned_cols=34 Identities=18% Similarity=0.197 Sum_probs=27.6
Q ss_pred HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352 512 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 549 (569)
Q Consensus 512 VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RAL 549 (569)
++...+- .+.|..+||+.+|||..+|....++..
T Consensus 21 aV~~~~~----~g~sv~evA~e~gIs~~tl~~W~r~y~ 54 (121)
T PRK09413 21 IVQQSFE----PGMTVSLVARQHGVAASQLFLWRKQYQ 54 (121)
T ss_pred HHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHh
Confidence 4444444 689999999999999999999987753
No 353
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=62.03 E-value=8.4 Score=31.28 Aligned_cols=27 Identities=22% Similarity=0.306 Sum_probs=24.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESRAL 549 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~RAL 549 (569)
.+.|..+||..+||++.+++.......
T Consensus 22 ~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 22 SGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp HHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCceEeeecccccccccccHHHHHHh
Confidence 579999999999999999999998876
No 354
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=61.60 E-value=9.4 Score=37.68 Aligned_cols=27 Identities=26% Similarity=0.527 Sum_probs=22.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 524 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 524 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
+.|.++||..+|+|+++|.+ .+++|++
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR----~l~~l~~ 210 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISR----LLGRFQK 210 (235)
T ss_pred cccHHHHHHHhCCcHHHHHH----HHHHHHH
Confidence 58999999999999999975 4566665
No 355
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=61.53 E-value=46 Score=38.09 Aligned_cols=104 Identities=15% Similarity=0.195 Sum_probs=59.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhcCCCc---ccCCCCCCCCCcchhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCC
Q 008352 430 HSPDKEDLARRVGITVEKLERLIFITRMPL---SMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLN 506 (569)
Q Consensus 430 r~Pt~eEIA~~lgis~e~v~~ll~~~~~~~---SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~ 506 (569)
...|..+||+.+|+|...|++-+..-...+ .+. .+....+-. +... ++. .+...+..-+
T Consensus 16 ~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~-~i~~~~Gy~----l~~~---~~~----------~~~~~~~~~~ 77 (584)
T PRK09863 16 QDRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIG-SISGSAKYH----LEIL---NRR----------SLFQLLQKSD 77 (584)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchh-heecCCceE----EEeC---CHH----------HHHHHHhcCC
Confidence 367999999999999999976554221100 000 000001111 1000 111 1112222223
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 507 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 507 ~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
+ |+..+.++..+ .++.++.++|+.|.||+.||.+-+.+..+.|..
T Consensus 78 ~-e~~~il~~Ll~--~~~~~~~~La~~l~vS~sTi~~dl~~v~~~l~~ 122 (584)
T PRK09863 78 N-EDRLLLLRLLL--NTFTPMAQLASALNLSRTWVAERLPRLNQRYER 122 (584)
T ss_pred H-HHHHHHHHHHH--cCCccHHHHHHHhCCCHHHHHHHHHHHHHhhhc
Confidence 3 44444444433 368999999999999999999988888877763
No 356
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=61.29 E-value=15 Score=37.20 Aligned_cols=25 Identities=28% Similarity=0.347 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.+.|..|||++||||..+||+.+..
T Consensus 24 g~~sa~elA~~Lgis~~avR~HL~~ 48 (218)
T COG2345 24 GPVSADELAEELGISPMAVRRHLDD 48 (218)
T ss_pred CCccHHHHHHHhCCCHHHHHHHHHH
Confidence 5899999999999999999987654
No 357
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=61.13 E-value=16 Score=37.25 Aligned_cols=48 Identities=17% Similarity=0.221 Sum_probs=38.6
Q ss_pred HHHHHhcCCHHHHHHHHHHhcccCC---CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 498 VRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 498 L~~aL~~L~~rER~VL~LRygL~d~---e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
|+.....|++.|+.|..+.. +.. ..+|..|+|+..|+|..+|-+..++
T Consensus 3 i~~~~~~Lt~~e~~ia~yil--~n~~~v~~~si~elA~~~~vS~aTv~Rf~kk 53 (278)
T PRK11557 3 IRQRYPGLAQSDRKLADYLL--LQPDTARHLSSQQLANEAGVSQSSVVKFAQK 53 (278)
T ss_pred hhHhhhhCCHHHHHHHHHHH--hCHHHHHhcCHHHHHHHhCCCHHHHHHHHHH
Confidence 56677889999999987543 332 3599999999999999999877654
No 358
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=61.06 E-value=12 Score=40.01 Aligned_cols=65 Identities=23% Similarity=0.283 Sum_probs=44.4
Q ss_pred hcCCHHHHHHHHH--HhcccCCCCCCHHHHHHH--hCCCHHHHHHHHHHHHHHHHHHhh----------cCchhhhhhhh
Q 008352 503 TLLNPKERCIVRL--RFGIEDGKPKSLSEVGNI--FGLSKERVRQLESRALYRLKQSLG----------GKASYGYADLL 568 (569)
Q Consensus 503 ~~L~~rER~VL~L--RygL~d~e~~Tl~EIAe~--LGISrerVRqie~RALkKLR~~l~----------~~~L~~yldll 568 (569)
..|++|+++|+.. ...+..+++-+.+++++. +|+|..|||.-+.. |.++--..+ ..+++.|+|-|
T Consensus 2 ~~l~~R~~~Il~~IV~~yi~~~~pv~s~~l~~~~~l~~S~aTIR~dm~~-Le~~G~l~~~h~sagrIPT~kGYR~YVd~L 80 (339)
T PRK00082 2 SMLDERQREILRAIVEDYIATGEPVGSKTLSKRYGLGVSSATIRNDMAD-LEELGLLEKPHTSSGRIPTDKGYRYFVDHL 80 (339)
T ss_pred CccCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHhCCCCChHHHHHHHHH-HHhCCCcCCCcCCCCCCcCHHHHHHHHHHh
Confidence 3688999999962 122344599999999977 99999999987663 454422111 23567777755
No 359
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=60.86 E-value=6.6 Score=31.31 Aligned_cols=25 Identities=28% Similarity=0.412 Sum_probs=21.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESRAL 549 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~RAL 549 (569)
+|..|+|+.+|||..++|..+...+
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~~gl 25 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYERIGL 25 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999876544
No 360
>PRK09726 antitoxin HipB; Provisional
Probab=60.85 E-value=13 Score=31.59 Aligned_cols=25 Identities=16% Similarity=0.330 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.++|..|+|+.+|||+.+|+++++.
T Consensus 24 ~gltq~elA~~~gvs~~tis~~e~g 48 (88)
T PRK09726 24 NGWTQSELAKKIGIKQATISNFENN 48 (88)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 5799999999999999999999884
No 361
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=60.83 E-value=1.3e+02 Score=30.03 Aligned_cols=32 Identities=34% Similarity=0.571 Sum_probs=25.6
Q ss_pred HHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHH
Q 008352 289 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (569)
Q Consensus 289 e~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~ 320 (569)
.+....+...+|++|+.+|+|+..|++.+.+.
T Consensus 98 ~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~ 129 (236)
T PRK06986 98 AQAIRQLEQELGREPTDTEVAEKLGLSLEEYR 129 (236)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHH
Confidence 34455666778999999999999999877664
No 362
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=60.66 E-value=24 Score=31.68 Aligned_cols=40 Identities=28% Similarity=0.392 Sum_probs=35.8
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
...|++.|-..|+-.++ +|..+-|..||+|.++|+.++..
T Consensus 41 ~~~ls~~eIk~iRe~~~------lSQ~vFA~~L~vs~~Tv~~WEqG 80 (104)
T COG2944 41 VKTLSPTEIKAIREKLG------LSQPVFARYLGVSVSTVRKWEQG 80 (104)
T ss_pred CCCCCHHHHHHHHHHhC------CCHHHHHHHHCCCHHHHHHHHcC
Confidence 46799999888888875 89999999999999999999975
No 363
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=60.63 E-value=12 Score=37.20 Aligned_cols=30 Identities=23% Similarity=0.460 Sum_probs=25.2
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 521 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 521 d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
.|+.+ |-.|+|+.||||+.+|| .||+.|..
T Consensus 27 pG~~LPsE~eLae~~gVSRt~VR----eAL~~L~~ 57 (239)
T PRK04984 27 PGSILPAERELSELIGVTRTTLR----EVLQRLAR 57 (239)
T ss_pred CCCcCCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 45788 79999999999999999 57777765
No 364
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=60.59 E-value=24 Score=27.88 Aligned_cols=35 Identities=11% Similarity=0.121 Sum_probs=27.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 557 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 557 (569)
.+.+..+.|+.|+|.++||+.++.|+-..+.-.+.
T Consensus 11 ~~~n~~~tA~~L~iHrNTl~yRl~ki~~l~g~dl~ 45 (59)
T PF13556_consen 11 NNGNISKTARALHIHRNTLRYRLKKIEELLGLDLD 45 (59)
T ss_dssp TTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--TT
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCcCCC
Confidence 56899999999999999999999988877755443
No 365
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=60.41 E-value=8.6 Score=37.48 Aligned_cols=29 Identities=34% Similarity=0.598 Sum_probs=24.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 522 GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 522 ~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
.+++|+.||++.+|+|+.+|++ ++++|..
T Consensus 39 ~~Pmtl~Ei~E~lg~Sks~vS~----~lkkL~~ 67 (177)
T COG1510 39 RKPLTLDEIAEALGMSKSNVSM----GLKKLQD 67 (177)
T ss_pred CCCccHHHHHHHHCCCcchHHH----HHHHHHh
Confidence 4899999999999999999985 5666654
No 366
>PRK10161 transcriptional regulator PhoB; Provisional
Probab=60.33 E-value=10 Score=36.53 Aligned_cols=50 Identities=14% Similarity=0.055 Sum_probs=40.3
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHH-----HhCCCHHHHHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGN-----IFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe-----~LGISrerVRqie~RALkKLR~ 554 (569)
.|+++|.+|+.+-. -+.|++.|.++|.. .++++..+|+....+.++||..
T Consensus 154 ~Lt~~E~~ll~~l~-~~~~~~~s~~~l~~~~~~~~~~~~~~tv~~~i~rlr~Kl~~ 208 (229)
T PRK10161 154 EMGPTEFKLLHFFM-THPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEP 208 (229)
T ss_pred EcCHHHHHHHHHHH-hCCCceEcHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhcc
Confidence 59999999997755 24457888777644 6688999999999999999963
No 367
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=60.32 E-value=8.9 Score=31.28 Aligned_cols=23 Identities=22% Similarity=0.416 Sum_probs=20.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~R 547 (569)
.|+.|||+.+|||+.+|+.+++.
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~ 23 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNG 23 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCC
Confidence 37899999999999999987654
No 368
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=59.71 E-value=11 Score=30.19 Aligned_cols=23 Identities=22% Similarity=0.355 Sum_probs=20.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~R 547 (569)
++..|+|+.+|||..++|..+..
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 47899999999999999998775
No 369
>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=59.60 E-value=56 Score=28.80 Aligned_cols=44 Identities=11% Similarity=0.064 Sum_probs=34.7
Q ss_pred cCCHHHHHHHHHHhcc-cCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGI-EDGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 504 ~L~~rER~VL~LRygL-~d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.|+..|-.||..-+.+ ..+.+.|..|||+.+++++.+|.+.+.+
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 6899999988765521 1236799999999999999999866554
No 370
>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=58.43 E-value=89 Score=34.72 Aligned_cols=24 Identities=17% Similarity=0.299 Sum_probs=21.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 430 HSPDKEDLARRVGITVEKLERLIF 453 (569)
Q Consensus 430 r~Pt~eEIA~~lgis~e~v~~ll~ 453 (569)
++-|..+||+.+|+.+.+|..+..
T Consensus 317 kPLtlkdiA~~lglheSTVSRav~ 340 (429)
T TIGR02395 317 KPLTLREVAEELGLHESTISRAIN 340 (429)
T ss_pred cCCcHHHHHHHhCCCccchhhhhc
Confidence 577899999999999999988865
No 371
>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=58.36 E-value=24 Score=26.58 Aligned_cols=23 Identities=13% Similarity=0.325 Sum_probs=17.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~R 547 (569)
+|+.+.|+.+||++.|++.+.+.
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 99999999999999999966543
No 372
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=58.02 E-value=16 Score=31.86 Aligned_cols=43 Identities=16% Similarity=0.244 Sum_probs=30.9
Q ss_pred cCCHHHHHHHHHHhc-ccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFG-IEDGKPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 504 ~L~~rER~VL~LRyg-L~d~e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
.|++..++|+.+.-. -...+|.+..+|++.||++...||+.+.
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 678888888877554 3345899999999999999999986554
No 373
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=57.96 E-value=17 Score=28.98 Aligned_cols=26 Identities=19% Similarity=0.471 Sum_probs=22.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352 524 PKSLSEVGNIFGLSKERVRQLESRAL 549 (569)
Q Consensus 524 ~~Tl~EIAe~LGISrerVRqie~RAL 549 (569)
+.|+++||+.+|+|...+.++..+..
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~ 26 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKET 26 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHh
Confidence 36899999999999999998887765
No 374
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=57.92 E-value=20 Score=40.96 Aligned_cols=46 Identities=24% Similarity=0.266 Sum_probs=37.3
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
|++|++++|.+-- + ++.|..++|+.||||..|||.-++..-.-|++
T Consensus 2 l~~R~~~iL~~L~---~-~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~ 47 (584)
T PRK09863 2 LNERELKIVDLLE---Q-QDRSGGELAQQLGVSRRTIVRDIAYINFTLNG 47 (584)
T ss_pred hHHHHHHHHHHHH---c-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 6788888887542 2 57999999999999999999888776666665
No 375
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=57.65 E-value=10 Score=36.87 Aligned_cols=28 Identities=18% Similarity=0.227 Sum_probs=23.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESRALY 550 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~RALk 550 (569)
-++|..|||+.+|.|+.|||.++.-.-+
T Consensus 60 ag~Ti~EIAeelG~TeqTir~hlkgetk 87 (182)
T COG1318 60 AGMTISEIAEELGRTEQTVRNHLKGETK 87 (182)
T ss_pred ccCcHHHHHHHhCCCHHHHHHHHhcchh
Confidence 4799999999999999999998765433
No 376
>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional
Probab=57.39 E-value=7.7 Score=37.18 Aligned_cols=46 Identities=13% Similarity=0.000 Sum_probs=38.2
Q ss_pred cCCHHHHHHHHHHhcccCCCCCC---------HHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKS---------LSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~T---------l~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
.|+++|.+|+.+-.. +.+ ..+||..++++..+|+....+.++||..
T Consensus 156 ~Lt~~E~~~l~~l~~-----~~~~v~sr~~l~~~~~~~~~~~~~~tv~~~i~~lr~Kl~~ 210 (232)
T PRK10955 156 ELTGTEFTLLYLLAQ-----HLGQVVSREHLSQEVLGKRLTPFDRAIDMHISNLRRKLPD 210 (232)
T ss_pred cCCHHHHHHHHHHHh-----CCCceEcHHHHHHHHhCCCCCCCCcCHHHHHHHHHHhccc
Confidence 599999999988763 333 4778888899999999999999999963
No 377
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=56.90 E-value=1.4e+02 Score=27.02 Aligned_cols=37 Identities=14% Similarity=0.117 Sum_probs=29.0
Q ss_pred HHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 417 VLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF 453 (569)
Q Consensus 417 i~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~ 453 (569)
+.++..-+.......++.++||+.+|+++..+..+..
T Consensus 11 i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk 47 (127)
T PRK11511 11 IHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFK 47 (127)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3444555556666789999999999999999988765
No 378
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=56.88 E-value=15 Score=38.05 Aligned_cols=45 Identities=33% Similarity=0.365 Sum_probs=35.2
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352 503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 553 (569)
..|++.|++||.+--+ .|...+++||-+.+|.|+.+|.. ++++|-
T Consensus 191 ~~L~~~e~~il~~i~~--~GGri~Q~eL~r~lglsktTvsR----~L~~LE 235 (258)
T COG2512 191 YDLNEDEKEILDLIRE--RGGRITQAELRRALGLSKTTVSR----ILRRLE 235 (258)
T ss_pred CCCCHHHHHHHHHHHH--hCCEEeHHHHHHhhCCChHHHHH----HHHHHH
Confidence 4689999999887544 33568999999999999999985 455554
No 379
>PRK14082 hypothetical protein; Provisional
Probab=56.87 E-value=34 Score=28.14 Aligned_cols=55 Identities=16% Similarity=0.099 Sum_probs=40.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhH
Q 008352 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASY 384 (569)
Q Consensus 328 ~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTY 384 (569)
...+.++...-+.+.+-..+- +--.-+||.||--+.+++.+..++...+.-|.-|
T Consensus 9 ~e~e~ii~~FepkIkKsL~~T--~yqeREDLeQElk~Ki~eK~~~~~~~e~PGF~ef 63 (65)
T PRK14082 9 EEIEHLIENFSPMIKKKLSNT--SYQEREDLEQELKIKIIEKADMLLCQEVPGFWEF 63 (65)
T ss_pred HHHHHHHHHccHHHHHHHhcC--ChhhHHHHHHHHHHHHHHHHHHhhcccCCcHHHh
Confidence 566778888888766544321 1246799999999999999999987766556544
No 380
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=56.72 E-value=14 Score=36.54 Aligned_cols=37 Identities=24% Similarity=0.289 Sum_probs=28.5
Q ss_pred HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 512 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 512 VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
|+...| ..|+.++..+||+.||||+..|| .||+.|..
T Consensus 24 I~~g~l--~pG~~L~e~~La~~lgVSRtpVR----EAL~~L~~ 60 (221)
T PRK11414 24 LSIGAL--KPGARLITKNLAEQLGMSITPVR----EALLRLVS 60 (221)
T ss_pred HHhCCC--CCCCccCHHHHHHHHCCCchhHH----HHHHHHHH
Confidence 444433 35688899999999999999998 57777754
No 381
>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=56.66 E-value=16 Score=34.33 Aligned_cols=49 Identities=14% Similarity=0.121 Sum_probs=41.1
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-----GLSKERVRQLESRALYRLK 553 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~L-----GISrerVRqie~RALkKLR 553 (569)
.|+++|.+|+.+-.. +.|+..|.++|.+.+ ..+..+|...+.+.++||.
T Consensus 147 ~Lt~~E~~il~~l~~-~~~~~~sr~~i~~~~~~~~~~~~~~~~~~~i~~lr~kl~ 200 (218)
T TIGR01387 147 TLTRKEFQLLWLLMR-RTGEVLPRTVIASLVWGMNFDSDTNVVDVAIRRLRAKVD 200 (218)
T ss_pred eCCHHHHHHHHHHHh-CCCeeEcHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhhc
Confidence 599999999988764 445679999999998 4667899999999999986
No 382
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=56.46 E-value=2.6e+02 Score=29.42 Aligned_cols=26 Identities=15% Similarity=0.309 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESRA 548 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~RA 548 (569)
...|.+|||+..|||..|||+..+.-
T Consensus 250 ~~~tq~eva~v~~vtevTIrnrykel 275 (285)
T COG1405 250 ERRTQKEVAKVAGVTEVTIRNRYKEL 275 (285)
T ss_pred CchHHHHHHHHhCCeeeHHHHHHHHH
Confidence 78999999999999999999988433
No 383
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=56.45 E-value=16 Score=26.49 Aligned_cols=26 Identities=15% Similarity=0.263 Sum_probs=19.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESRA 548 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~RA 548 (569)
+++|+.+||+.+|+|+...+++.++.
T Consensus 7 ~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 7 QKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 67999999999999998888766553
No 384
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=56.41 E-value=13 Score=36.90 Aligned_cols=27 Identities=37% Similarity=0.611 Sum_probs=23.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 524 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 524 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
+.|.++||..+|+++++|. |++++|++
T Consensus 179 ~lt~~~IA~~lGisretls----R~L~~L~~ 205 (230)
T PRK09391 179 PMSRRDIADYLGLTIETVS----RALSQLQD 205 (230)
T ss_pred cCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 5799999999999999987 56667765
No 385
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=55.62 E-value=27 Score=34.54 Aligned_cols=46 Identities=15% Similarity=0.141 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHhccc-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 505 LNPKERCIVRLRFGIE-DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 505 L~~rER~VL~LRygL~-d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
++.++|-+-.+...-+ +.-+.|.+|||+.+|+|+++|. |+|++|++
T Consensus 149 ~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvs----R~L~~L~~ 195 (226)
T PRK10402 149 FPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLL----YVLAQFIQ 195 (226)
T ss_pred ChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHH----HHHHHHHH
Confidence 3555665544432111 1234689999999999999987 57777776
No 386
>PRK11050 manganese transport regulator MntR; Provisional
Probab=55.42 E-value=19 Score=33.96 Aligned_cols=27 Identities=15% Similarity=0.209 Sum_probs=22.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352 522 GKPKSLSEVGNIFGLSKERVRQLESRA 548 (569)
Q Consensus 522 ~e~~Tl~EIAe~LGISrerVRqie~RA 548 (569)
+.+.+..|||+.+||++.+|++.+.+-
T Consensus 49 ~~~~t~~eLA~~l~is~stVsr~l~~L 75 (152)
T PRK11050 49 VGEARQVDIAARLGVSQPTVAKMLKRL 75 (152)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 367999999999999999998665543
No 387
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=55.27 E-value=29 Score=26.36 Aligned_cols=51 Identities=16% Similarity=0.198 Sum_probs=38.4
Q ss_pred cCCHHHHHHHHHHhcccCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDG-KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~-e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
.+++.+..+|.-.|..+.. ......+||..+|++...|+........+.+.
T Consensus 6 ~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 6 RFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 4567777888887765332 33457899999999999999998887776653
No 388
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=55.25 E-value=22 Score=32.85 Aligned_cols=26 Identities=8% Similarity=0.212 Sum_probs=21.9
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 522 GKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 522 ~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
+...+..+||+.||||+.+|+..+.+
T Consensus 20 ~~~~~~~ela~~l~vs~~svs~~l~~ 45 (142)
T PRK03902 20 KGYARVSDIAEALSVHPSSVTKMVQK 45 (142)
T ss_pred CCCcCHHHHHHHhCCChhHHHHHHHH
Confidence 35679999999999999999976544
No 389
>PRK15340 transcriptional regulator InvF; Provisional
Probab=55.25 E-value=2.4e+02 Score=28.55 Aligned_cols=30 Identities=13% Similarity=0.244 Sum_probs=24.6
Q ss_pred HHHhcCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 424 YIQEGNHSPDKEDLARRVGITVEKLERLIF 453 (569)
Q Consensus 424 l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~ 453 (569)
+........+.++||+.+|+++..+..+..
T Consensus 118 Ll~~~~~~~sleeLA~~~gvS~r~f~RlFk 147 (216)
T PRK15340 118 LLAQSTSGNTMRMLGEDYGVSYTHFRRLCS 147 (216)
T ss_pred HHhCccCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 344555678999999999999999998865
No 390
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=55.24 E-value=15 Score=35.81 Aligned_cols=30 Identities=27% Similarity=0.420 Sum_probs=25.5
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 521 DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 521 d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
.|+.++..++|+.||||+..|| .||+.|..
T Consensus 31 pG~~L~e~~La~~lgVSRtpVR----eAL~~L~~ 60 (212)
T TIGR03338 31 PGAKLNESDIAARLGVSRGPVR----EAFRALEE 60 (212)
T ss_pred CCCEecHHHHHHHhCCChHHHH----HHHHHHHH
Confidence 4588899999999999999998 57777754
No 391
>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=54.97 E-value=18 Score=36.07 Aligned_cols=31 Identities=23% Similarity=0.440 Sum_probs=26.1
Q ss_pred cCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 520 EDGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 520 ~d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
..|+.+ |-.++|+.||||+..|| .||.+|..
T Consensus 25 ~pG~~LpsE~~La~~lgVSRtpVR----EAL~~Le~ 56 (235)
T TIGR02812 25 PPGSILPAERELSELIGVTRTTLR----EVLQRLAR 56 (235)
T ss_pred CCCCcCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 356788 89999999999999998 67777765
No 392
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=54.85 E-value=24 Score=34.64 Aligned_cols=26 Identities=12% Similarity=0.176 Sum_probs=23.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESRA 548 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~RA 548 (569)
.+.|..|||+.+||++.+|++++.+-
T Consensus 14 ~~~t~~eLA~~lgis~~tV~~~L~~L 39 (203)
T TIGR02702 14 GQATAAALAEALAISPQAVRRHLKDL 39 (203)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46999999999999999999998875
No 393
>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family contains mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation []. Homologues of neugrin are found in fungi suggesting they have a alternative role or more than one function.
Probab=54.52 E-value=20 Score=36.47 Aligned_cols=42 Identities=14% Similarity=0.188 Sum_probs=33.3
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
.|+..+.+-|++-+-.+ -+.+|...+|+.|+||.+.||.|++
T Consensus 10 ~Ls~~~~~~ir~L~~~~-p~~~t~~~Lae~F~vspe~irrILk 51 (225)
T PF06413_consen 10 KLSREAMEQIRYLHKED-PEEWTVERLAESFKVSPEAIRRILK 51 (225)
T ss_pred CCCHHHHHHHHHHHHhC-ccccCHHHHHhhCCCCHHHHHHHHh
Confidence 57777777777655433 2568999999999999999999875
No 394
>smart00862 Trans_reg_C Transcriptional regulatory protein, C terminal. This domain is almost always found associated with the response regulator receiver domain. It may play a role in DNA binding.
Probab=54.33 E-value=40 Score=26.99 Aligned_cols=50 Identities=22% Similarity=0.231 Sum_probs=36.6
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHh------CCCHHHHHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF------GLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~L------GISrerVRqie~RALkKLR~ 554 (569)
.|+++|..+|.+-. ...|...|.++|.+.+ +.+..+|++.+.+.+++|..
T Consensus 5 ~Lt~~e~~lL~~L~-~~~~~~vs~~~l~~~lw~~~~~~~~~~~l~~~i~~LR~~l~~ 60 (78)
T smart00862 5 KLTPKEFRLLELLL-RNPGRVVSREELLEAVWGDDDDDVDDNTLDVHISRLRKKLED 60 (78)
T ss_pred ecCHHHHHHHHHHH-hCCCCccCHHHHHHHHcCCCCCCCccchHHHHHHHHHHHHhc
Confidence 47889999775543 3455789999999975 35677787777777777764
No 395
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=53.83 E-value=19 Score=36.24 Aligned_cols=37 Identities=24% Similarity=0.306 Sum_probs=28.5
Q ss_pred HHHHHhcccCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 512 IVRLRFGIEDGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 512 VL~LRygL~d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
|+...| ..|+.+ +-.+||+.||||+..|| .||+.|..
T Consensus 20 I~~g~l--~pG~~LPsE~eLa~~~gVSRtpVR----EAL~~L~~ 57 (251)
T PRK09990 20 IVDGVL--KVGQALPSERRLCEKLGFSRSALR----EGLTVLRG 57 (251)
T ss_pred HHcCCC--CCCCcCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 444443 356788 89999999999999998 57777764
No 396
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=53.75 E-value=36 Score=28.95 Aligned_cols=29 Identities=21% Similarity=0.239 Sum_probs=21.4
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhcC
Q 008352 428 GNHSPDKEDLARRVGITVEKLERLIFITR 456 (569)
Q Consensus 428 ~gr~Pt~eEIA~~lgis~e~v~~ll~~~~ 456 (569)
.|++.+.++||..+|++.++|..++....
T Consensus 35 ~G~PVt~~~LA~a~g~~~e~v~~~L~~~p 63 (77)
T PF12324_consen 35 KGQPVTVEQLAAALGWPVEEVRAALAAMP 63 (77)
T ss_dssp TTS-B-HHHHHHHHT--HHHHHHHHHH-T
T ss_pred cCCCcCHHHHHHHHCCCHHHHHHHHHhCC
Confidence 47799999999999999999999987653
No 397
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=53.62 E-value=19 Score=32.98 Aligned_cols=25 Identities=16% Similarity=0.104 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.++|..++|+.+|||+.+|+++++.
T Consensus 17 ~gltq~~lA~~~gvs~~~is~~E~g 41 (135)
T PRK09706 17 LKLSQRSLAKAVKVSHVSISQWERD 41 (135)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 6799999999999999999999865
No 398
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=53.62 E-value=13 Score=30.18 Aligned_cols=25 Identities=24% Similarity=0.352 Sum_probs=20.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.+.+-.|||+.+|+|+.+||.++..
T Consensus 14 ~p~~T~eiA~~~gls~~~aR~yL~~ 38 (62)
T PF04703_consen 14 GPLKTREIADALGLSIYQARYYLEK 38 (62)
T ss_dssp S-EEHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 6899999999999999999987643
No 399
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=53.53 E-value=1.8e+02 Score=30.95 Aligned_cols=126 Identities=9% Similarity=0.184 Sum_probs=66.9
Q ss_pred HhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch-hhcccCCCCCChhHHHHHHHHHHHHHHHHhc
Q 008352 426 QEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF-QEITADTGVEIPDISVQKQLMRQHVRNLLTL 504 (569)
Q Consensus 426 ~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l-~d~i~D~~~~~pee~l~~~el~e~L~~aL~~ 504 (569)
.+.+-+-|..||+...+++.+++-++.......+-.+.+...-....+ --+...-..+...+....+..+... -+..
T Consensus 159 Rq~~~pRT~kEI~~~anv~kKEIgr~~K~i~~~l~~s~~~~s~~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~--~~~~ 236 (308)
T KOG1597|consen 159 RQEDVPRTFKEISAVANVSKKEIGRCVKLIGEALETSVDLISISTGDFMPRFCSNLGLPKSAQEAATEIAEKAE--EMDI 236 (308)
T ss_pred HhcCCCchHHHHHHHHcCCHHHHHHHHHHHHHHHhccchhhhhhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHH--Hhcc
Confidence 345668899999999999999998876644332222222111011111 1122222221111111111111111 1122
Q ss_pred C---CHH--HHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 505 L---NPK--ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 505 L---~~r--ER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
+ +|. -.-+|.|--.|.+ +.+|++||++..||+..|||+-.+--+-.+-+
T Consensus 237 ~~gRsPiSIAAa~IYmisqls~-~kkt~keI~~vtgVaE~TIr~sYK~Lyp~~~~ 290 (308)
T KOG1597|consen 237 RAGRSPISIAAAAIYMISQLSD-EKKTQKEIGEVTGVAEVTIRNSYKDLYPHADK 290 (308)
T ss_pred ccCCCchhHHHHHHHHHHHhcc-CcccHHHHHHHhhhhHHHHHHHHHHHhhchhh
Confidence 2 222 2345555555555 89999999999999999999877665554443
No 400
>PRK11517 transcriptional regulatory protein YedW; Provisional
Probab=53.21 E-value=24 Score=33.50 Aligned_cols=49 Identities=14% Similarity=0.078 Sum_probs=40.6
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-----GLSKERVRQLESRALYRLK 553 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~L-----GISrerVRqie~RALkKLR 553 (569)
.|+++|.+|+.+-.- +.|+..|.++|.+.+ ..+..+|+.+..|.++||.
T Consensus 147 ~Lt~~E~~il~~l~~-~~g~~~s~~~i~~~~w~~~~~~~~~tv~~~i~rlr~Kl~ 200 (223)
T PRK11517 147 TLTRKEFQLLWLLAS-RAGEIIPRTVIASEIWGINFDSDTNTVDVAIRRLRAKVD 200 (223)
T ss_pred eCCHHHHHHHHHHHh-CCCccCCHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhhc
Confidence 599999999988653 445778999999986 4578899999999999985
No 401
>PRK13239 alkylmercury lyase; Provisional
Probab=53.19 E-value=27 Score=35.01 Aligned_cols=29 Identities=21% Similarity=0.237 Sum_probs=26.0
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhcC
Q 008352 428 GNHSPDKEDLARRVGITVEKLERLIFITR 456 (569)
Q Consensus 428 ~gr~Pt~eEIA~~lgis~e~v~~ll~~~~ 456 (569)
.||.|+..+||+.+|+++++++.+|....
T Consensus 33 ~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 33 KGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 57899999999999999999999987643
No 402
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=53.15 E-value=20 Score=32.13 Aligned_cols=35 Identities=17% Similarity=0.302 Sum_probs=27.7
Q ss_pred HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 511 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 511 ~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
+||.-.|. +.-++|..+.|+.|||++.+|..+++.
T Consensus 12 EiL~eefl--ep~glt~~~lA~~lgV~r~~is~ling 46 (104)
T COG3093 12 EILREEFL--EPLGLTQTELAEALGVTRNTISELING 46 (104)
T ss_pred HHHHHHHh--ccccCCHHHHHHHhCCCHHHHHHHHcC
Confidence 46666665 223699999999999999999998764
No 403
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=53.10 E-value=40 Score=32.93 Aligned_cols=47 Identities=9% Similarity=0.132 Sum_probs=30.4
Q ss_pred HHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 497 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 497 ~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.+..++.. ++....||..-. .. ...|-+|||+.|||+...||+++.+
T Consensus 13 ~l~~~~~~-~~~~~~Vl~~L~--~~-g~~tdeeLA~~Lgi~~~~VRk~L~~ 59 (178)
T PRK06266 13 VLFEIMEG-DEEGFEVLKALI--KK-GEVTDEEIAEQTGIKLNTVRKILYK 59 (178)
T ss_pred HHHHHhcC-CccHhHHHHHHH--Hc-CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 34444432 444445555322 22 3799999999999999999976543
No 404
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=52.93 E-value=19 Score=32.59 Aligned_cols=24 Identities=33% Similarity=0.458 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
.|.|..|+|..||||+.+|..+..
T Consensus 17 ~g~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 17 KGKSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred ccchHHHHHHHhCcHHHHHHHHHH
Confidence 678999999999999999998877
No 405
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=52.77 E-value=20 Score=36.11 Aligned_cols=37 Identities=24% Similarity=0.396 Sum_probs=28.1
Q ss_pred HHHHHhcccCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 512 IVRLRFGIEDGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 512 VL~LRygL~d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
|+.-.| ..|+.+ +-.++|+.||||+..|| .||+.|..
T Consensus 23 I~~g~l--~pG~~LpsE~eLa~~lgVSRtpVR----EAL~~L~~ 60 (254)
T PRK09464 23 ILEGTL--RPGEKLPPERELAKQFDVSRPSLR----EAIQRLEA 60 (254)
T ss_pred HHcCCC--CCCCcCCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 444443 345777 89999999999999998 57777755
No 406
>PRK03837 transcriptional regulator NanR; Provisional
Probab=52.76 E-value=21 Score=35.55 Aligned_cols=30 Identities=37% Similarity=0.496 Sum_probs=25.2
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 521 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 521 d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
.|+.+ +..+||+.||||+..|| .||..|..
T Consensus 33 pG~~Lp~E~~Lae~~gVSRt~VR----EAL~~L~~ 63 (241)
T PRK03837 33 PGDQLPSERELMAFFGVGRPAVR----EALQALKR 63 (241)
T ss_pred CCCCCCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 45778 89999999999999998 57777764
No 407
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=52.64 E-value=25 Score=35.72 Aligned_cols=41 Identities=17% Similarity=0.250 Sum_probs=31.5
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352 507 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 550 (569)
Q Consensus 507 ~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 550 (569)
+|++.|+.+-. .....+.+|||+.||||..|||+.+..--.
T Consensus 4 ~R~~~Il~~l~---~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 4 ARQQAIVDLLL---NHTSLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred HHHHHHHHHHH---HcCCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 56666665533 225789999999999999999999887544
No 408
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=52.44 E-value=29 Score=29.83 Aligned_cols=40 Identities=20% Similarity=0.348 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
|++.|..||...+..+ +.+..+||+.+++++.+|.+++.+
T Consensus 20 lt~~q~~~L~~l~~~~---~~~~~~la~~l~i~~~~vt~~l~~ 59 (126)
T COG1846 20 LTPPQYQVLLALYEAG---GITVKELAERLGLDRSTVTRLLKR 59 (126)
T ss_pred CCHHHHHHHHHHHHhC---CCcHHHHHHHHCCCHHHHHHHHHH
Confidence 9999999998877622 222299999999999999866554
No 409
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=52.40 E-value=20 Score=36.14 Aligned_cols=37 Identities=24% Similarity=0.351 Sum_probs=28.3
Q ss_pred HHHHHhcccCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 512 IVRLRFGIEDGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 512 VL~LRygL~d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
|+.-.| ..|+.+ +..|+|+.||||+..|| .||+.|..
T Consensus 15 I~~g~l--~pG~~LpsE~eLae~~gVSRtpVR----EAL~~Le~ 52 (253)
T PRK10421 15 IEEKNL--EAGMKLPAERQLAMQLGVSRNSLR----EALAKLVS 52 (253)
T ss_pred HHcCCC--CCCCcCCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 444443 355788 78999999999999998 67777765
No 410
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=52.36 E-value=24 Score=24.95 Aligned_cols=25 Identities=20% Similarity=0.388 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.++|..++|+.+|++..+|.+++..
T Consensus 9 ~~~s~~~la~~~~i~~~~i~~~~~~ 33 (56)
T smart00530 9 KGLTQEELAEKLGVSRSTLSRIENG 33 (56)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 5789999999999999999987764
No 411
>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=51.79 E-value=11 Score=30.68 Aligned_cols=26 Identities=31% Similarity=0.417 Sum_probs=20.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 522 GKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 522 ~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
+...|+.|||..||+|++.|+.++..
T Consensus 12 ~~~~S~~eLa~~~~~s~~~ve~mL~~ 37 (69)
T PF09012_consen 12 RGRVSLAELAREFGISPEAVEAMLEQ 37 (69)
T ss_dssp S-SEEHHHHHHHTT--HHHHHHHHHH
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 36789999999999999999987654
No 412
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=51.75 E-value=21 Score=36.08 Aligned_cols=37 Identities=22% Similarity=0.425 Sum_probs=28.3
Q ss_pred HHHHHhcccCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 512 IVRLRFGIEDGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 512 VL~LRygL~d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
|+.-.|. .|+.+ |-.++|+.||||+..|| .|++.|..
T Consensus 22 I~~g~l~--pG~~LpsE~eLa~~~gVSRtpVR----EAL~~L~~ 59 (257)
T PRK10225 22 IIKTPYN--PGERLPPEREIAEMLDVTRTVVR----EALIMLEI 59 (257)
T ss_pred HHhCCCC--CCCcCcCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 4444443 45788 69999999999999999 57777765
No 413
>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=51.39 E-value=24 Score=27.63 Aligned_cols=25 Identities=16% Similarity=0.405 Sum_probs=20.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.++|..++|+.+|+++.++.++++.
T Consensus 11 ~~lt~~~~a~~~~i~~~~i~~~e~g 35 (64)
T PF12844_consen 11 KGLTQKDLAEKLGISRSTISKIENG 35 (64)
T ss_dssp CT--HHHHHHHHTS-HHHHHHHHTT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 6799999999999999999999865
No 414
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=51.12 E-value=17 Score=35.99 Aligned_cols=27 Identities=22% Similarity=0.395 Sum_probs=21.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 524 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 524 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
++|.++||..+|+++++|. |++++|++
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 5778999999999999987 55566655
No 415
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=51.10 E-value=1.6e+02 Score=33.44 Aligned_cols=24 Identities=17% Similarity=0.194 Sum_probs=21.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 430 HSPDKEDLARRVGITVEKLERLIF 453 (569)
Q Consensus 430 r~Pt~eEIA~~lgis~e~v~~ll~ 453 (569)
++-+..+||+.+|+.+.+|..+..
T Consensus 368 kPLtlkdVAe~lglHeSTVSRa~~ 391 (481)
T PRK12469 368 KPLVLRDVAEELGLHESTISRATG 391 (481)
T ss_pred cCCcHHHHHHHhCCCcchhhHHhc
Confidence 577899999999999999998865
No 416
>TIGR00180 parB_part ParB-like partition proteins. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Probab=51.02 E-value=27 Score=33.96 Aligned_cols=43 Identities=19% Similarity=0.191 Sum_probs=32.0
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
..|++-|+-....+.. .. .++|.++||+.+|+|+.+|++++.-
T Consensus 101 ~~lt~~e~a~~~~~l~-~~-~g~s~~~iA~~lg~s~~~V~r~l~l 143 (187)
T TIGR00180 101 EDLSPIEEAQAYKRLL-EK-FSMTQEDLAKKIGKSRAHITNLLRL 143 (187)
T ss_pred cCCCHHHHHHHHHHHH-HH-hCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4688887765544431 11 4689999999999999999987654
No 417
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=50.74 E-value=29 Score=29.43 Aligned_cols=32 Identities=19% Similarity=0.283 Sum_probs=26.1
Q ss_pred HHHHHhcccCCCCCCHHHHHHHhC------CCHHHHHHHHHH
Q 008352 512 IVRLRFGIEDGKPKSLSEVGNIFG------LSKERVRQLESR 547 (569)
Q Consensus 512 VL~LRygL~d~e~~Tl~EIAe~LG------ISrerVRqie~R 547 (569)
+...|-- -++|..++|+.+| +|+.+|.++++-
T Consensus 16 lk~~R~~----lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~ 53 (75)
T smart00352 16 FKQRRIK----LGFTQADVGLALGALYGPDFSQTTICRFEAL 53 (75)
T ss_pred HHHHHHH----cCCCHHHHHHHhcccccCcCCHHHHHHHHhc
Confidence 4455555 6899999999999 599999998863
No 418
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=50.69 E-value=25 Score=35.91 Aligned_cols=25 Identities=16% Similarity=0.155 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
...+.+||++.||||+.|||+.+..
T Consensus 18 ~~~~~~ela~~l~vS~~TirRdL~~ 42 (251)
T PRK13509 18 GFVTVEKVIERLGISPATARRDINK 42 (251)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 5789999999999999999987654
No 419
>PRK10643 DNA-binding transcriptional regulator BasR; Provisional
Probab=50.58 E-value=21 Score=33.64 Aligned_cols=49 Identities=14% Similarity=0.059 Sum_probs=36.1
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHH-----HhCCCHHHHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGN-----IFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe-----~LGISrerVRqie~RALkKLR 553 (569)
.|+++|.+|+.+..- ..|...+.++|.+ .++++..+|+...++.++||.
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 599999999987642 2224444555544 368999999999999999985
No 420
>PF12085 DUF3562: Protein of unknown function (DUF3562); InterPro: IPR021945 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 62 to 84 amino acids in length. This protein has two completely conserved residues (A and Y) that may be functionally important.
Probab=50.08 E-value=34 Score=28.32 Aligned_cols=40 Identities=20% Similarity=0.341 Sum_probs=32.7
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhhhh
Q 008352 526 SLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLL 568 (569)
Q Consensus 526 Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yldll 568 (569)
.+++||+..|++.+.|++.....+..|+. .....+|+-++
T Consensus 9 ~i~~iA~~t~~P~e~V~~my~dt~~~l~~---~ARV~DYl~lf 48 (66)
T PF12085_consen 9 VIRSIAEETGTPAETVRRMYDDTMRELSS---GARVHDYLPLF 48 (66)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHHHc---CCchhhhHHHH
Confidence 57899999999999999999999988875 44556676554
No 421
>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=49.97 E-value=30 Score=31.14 Aligned_cols=26 Identities=19% Similarity=0.350 Sum_probs=21.9
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 522 GKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 522 ~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
+.+.|.+|||+.+|+++..|+++...
T Consensus 23 ~~~~s~~eia~~~~i~~~~v~~il~~ 48 (132)
T TIGR00738 23 EGPVSVKEIAERQGISRSYLEKILRT 48 (132)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHHH
Confidence 35899999999999999999866543
No 422
>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=49.90 E-value=10 Score=28.45 Aligned_cols=21 Identities=14% Similarity=0.248 Sum_probs=18.3
Q ss_pred HHHHHHhCCCHHHHHHHHHHH
Q 008352 528 SEVGNIFGLSKERVRQLESRA 548 (569)
Q Consensus 528 ~EIAe~LGISrerVRqie~RA 548 (569)
++||+.+|||+.+|+++++.-
T Consensus 1 ~~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 1 KDIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred CcHHHHHCcCHHHHHHHHcCC
Confidence 379999999999999998754
No 423
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=49.41 E-value=12 Score=32.42 Aligned_cols=25 Identities=20% Similarity=0.398 Sum_probs=22.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESRAL 549 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~RAL 549 (569)
+|..|+|+.+|||..++|..+...+
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~~Gl 25 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDIGL 25 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999998754
No 424
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=49.38 E-value=1.4e+02 Score=30.39 Aligned_cols=38 Identities=21% Similarity=0.276 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHh
Q 008352 416 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (569)
Q Consensus 416 ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~ 454 (569)
+|.+..++..+++| -.|..+||-.||+|+..|...+..
T Consensus 91 rIvRl~~EAy~Qgg-lLT~~Dla~LL~~S~~TI~~~i~~ 128 (220)
T PF07900_consen 91 RIVRLTNEAYDQGG-LLTQEDLAMLLGISPRTISKDIKE 128 (220)
T ss_pred HHHHHHHHHHHcCC-cccHHHHHHHHCCCHHHHHHHHHH
Confidence 33344444445555 899999999999999999887753
No 425
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=49.32 E-value=35 Score=35.33 Aligned_cols=52 Identities=19% Similarity=0.272 Sum_probs=41.2
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHhcccCC---CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 494 MRQHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 494 l~e~L~~aL~~L~~rER~VL~LRygL~d~---e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
+...|......|++.||.|-.+- |.+. ..+|..|||+..|||+.||-+..++
T Consensus 5 l~~~I~~~~~~Lt~~er~iA~yi--l~~~~~~~~~si~elA~~a~VS~aTv~Rf~~k 59 (281)
T COG1737 5 LLERIRERYDSLTKSERKIADYI--LANPDEVALLSIAELAERAGVSPATVVRFARK 59 (281)
T ss_pred HHHHHHHHHhcCCHHHHHHHHHH--HhCHHHHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 45678888999999999997654 3332 3579999999999999999866544
No 426
>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=49.14 E-value=33 Score=24.38 Aligned_cols=25 Identities=20% Similarity=0.405 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.++|..++|..+|+++.+|.+++..
T Consensus 11 ~~~s~~~~a~~~~~~~~~v~~~~~g 35 (58)
T cd00093 11 KGLTQEELAEKLGVSRSTISRIENG 35 (58)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 5789999999999999999987764
No 427
>PRK06424 transcription factor; Provisional
Probab=48.85 E-value=25 Score=33.31 Aligned_cols=25 Identities=12% Similarity=0.056 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.++|++|+|+.+|+++.+|+++++.
T Consensus 96 ~GLSQ~eLA~~iGvs~stIskiE~G 120 (144)
T PRK06424 96 LSMSQADLAAKIFERKNVIASIERG 120 (144)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 6899999999999999999999973
No 428
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=48.71 E-value=43 Score=30.55 Aligned_cols=45 Identities=16% Similarity=0.224 Sum_probs=31.6
Q ss_pred HHHHhcCCHHHH-HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 499 RNLLTLLNPKER-CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 499 ~~aL~~L~~rER-~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
.+.+..|.+.-| .||.+-. ++.+++..||++.+|+|+.+|.+.++
T Consensus 7 ~~~fkaLadptRl~IL~~L~---~~~~~~v~ela~~l~lsqstvS~HL~ 52 (117)
T PRK10141 7 LQLFKILSDETRLGIVLLLR---ESGELCVCDLCTALDQSQPKISRHLA 52 (117)
T ss_pred HHHHHHhCCHHHHHHHHHHH---HcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 355566665444 5665432 22579999999999999999987653
No 429
>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=48.39 E-value=40 Score=28.16 Aligned_cols=50 Identities=22% Similarity=0.157 Sum_probs=36.7
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR~ 554 (569)
.|+++|..+|.+-+ ...|+..|.++|.+.+. .+...+++.+.+.++||..
T Consensus 23 ~Lt~~e~~lL~~L~-~~~~~~vs~~~l~~~lw~~~~~~~~~~l~~~I~rLRkkl~~ 77 (95)
T cd00383 23 ELTPKEFELLELLA-RNPGRVLSREQLLEAVWGDDYDVDDRTVDVHISRLRKKLED 77 (95)
T ss_pred EeCHHHHHHHHHHH-hCCCCcCCHHHHHHHhcCCCCCCCcccHHHHHHHHHHHhcc
Confidence 48899999887755 35668999999999884 5666676666666666653
No 430
>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=48.28 E-value=1.6e+02 Score=25.51 Aligned_cols=35 Identities=14% Similarity=0.174 Sum_probs=27.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 557 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 557 (569)
-|+++++|.+.++.....+..++..-+..|++.+.
T Consensus 56 ~G~~l~~I~~~l~~~~~~~~~~l~~~~~~l~~~i~ 90 (96)
T cd04768 56 LGFSLAEIKELLDTEMEELTAMLLEKKQAIQQKID 90 (96)
T ss_pred cCCCHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHH
Confidence 48999999999998766777777777777766543
No 431
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=48.21 E-value=1.8e+02 Score=32.60 Aligned_cols=24 Identities=17% Similarity=0.256 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 430 HSPDKEDLARRVGITVEKLERLIF 453 (569)
Q Consensus 430 r~Pt~eEIA~~lgis~e~v~~ll~ 453 (569)
++-|..+||+.+|+.+.+|..+..
T Consensus 342 kPLtlkdvAe~lglheSTVSRav~ 365 (455)
T PRK05932 342 KPLVLKDIAEELGMHESTISRATT 365 (455)
T ss_pred cCccHHHHHHHhCCCccchhhhhc
Confidence 567899999999999999988865
No 432
>COG4709 Predicted membrane protein [Function unknown]
Probab=48.18 E-value=36 Score=33.68 Aligned_cols=59 Identities=20% Similarity=0.173 Sum_probs=45.3
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHhc--cc--CCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352 491 KQLMRQHVRNLLTLLNPKERCIVRLRFG--IE--DGKPKSLSEVGNIFGLSKERVRQLESRAL 549 (569)
Q Consensus 491 ~~el~e~L~~aL~~L~~rER~VL~LRyg--L~--d~e~~Tl~EIAe~LGISrerVRqie~RAL 549 (569)
+.+....|+..|+.||+.+|.=+...|- ++ +..++|-+||+..||=+.+-.+++..+..
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 KTEFLNELEQYLEGLPREERREIMYDYEEHFREAQEAGKSEEEIAKDLGDPKEIAAEILSERG 65 (195)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhhhhcCCCHHHHHHHhCCHHHHHHHHHHHcc
Confidence 3455667899999999999886655432 12 33789999999999999999988876654
No 433
>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=48.11 E-value=29 Score=31.43 Aligned_cols=26 Identities=27% Similarity=0.429 Sum_probs=21.9
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 521 DGKPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 521 d~e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
++.+.|..|||+.+|+|+.+|++++.
T Consensus 22 ~~~~~s~~eia~~l~is~~~v~~~l~ 47 (130)
T TIGR02944 22 DSQPYSAAEIAEQTGLNAPTVSKILK 47 (130)
T ss_pred CCCCccHHHHHHHHCcCHHHHHHHHH
Confidence 34679999999999999999986554
No 434
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=48.03 E-value=38 Score=32.69 Aligned_cols=57 Identities=23% Similarity=0.248 Sum_probs=43.5
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHhc--ccC--CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 491 KQLMRQHVRNLLTLLNPKERCIVRLRFG--IED--GKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 491 ~~el~e~L~~aL~~L~~rER~VL~LRyg--L~d--~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
+++..+.|+..|..||+.|++=+.-.|- ++| .+|+|-+||.+.||=+++-++++...
T Consensus 3 k~efL~~L~~~L~~lp~~e~~e~l~~Y~e~f~d~~~~G~sEeeii~~LG~P~~iA~~i~~~ 63 (181)
T PF08006_consen 3 KNEFLNELEKYLKKLPEEEREEILEYYEEYFDDAGEEGKSEEEIIAELGSPKEIAREILAE 63 (181)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHcCCHHHHHHHHHHh
Confidence 4455678899999999998885544432 222 36799999999999999999888754
No 435
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.89 E-value=42 Score=30.29 Aligned_cols=48 Identities=23% Similarity=0.229 Sum_probs=38.9
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352 502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553 (569)
Q Consensus 502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 553 (569)
.+.|++.+-+.+++.+- -.=+++||-..+|+|--+||..+...|++|-
T Consensus 39 F~~Lt~d~LeFv~lf~r----~RGnlKEvEr~lg~sYptvR~kld~vlramg 86 (122)
T COG3877 39 FEYLTSDQLEFVELFLR----CRGNLKEVERELGISYPTVRTKLDEVLRAMG 86 (122)
T ss_pred ccccCHhHhHHHHHHHH----HccCHHHHHHHHCCccHHHHHHHHHHHHHcC
Confidence 35677777777777765 3348999999999999999999988888763
No 436
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=47.84 E-value=36 Score=31.50 Aligned_cols=30 Identities=27% Similarity=0.617 Sum_probs=24.1
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 521 DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 521 d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
+|+..+..|||+.+|||+..||+ ++.+|++
T Consensus 22 ~g~~~s~~~ia~~~~is~~~vrk----~l~~L~~ 51 (141)
T PRK11014 22 EGRMTSISEVTEVYGVSRNHMVK----IINQLSR 51 (141)
T ss_pred CCCccCHHHHHHHHCcCHHHHHH----HHHHHHh
Confidence 45678999999999999988885 5666665
No 437
>COG3711 BglG Transcriptional antiterminator [Transcription]
Probab=47.50 E-value=25 Score=39.04 Aligned_cols=47 Identities=21% Similarity=0.138 Sum_probs=38.7
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 507 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 507 ~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
..||..+.+.+.+.+ +..++.++|..+++|+.+|..-.+....+|+.
T Consensus 84 ~~er~~~~ll~~~~~-~~~~l~~La~~l~vs~~ti~~dl~~v~~~l~~ 130 (491)
T COG3711 84 KDERIIIILLLLLLS-ELLSLHELADELFVSKSTIINDLKDVRLKLLL 130 (491)
T ss_pred hHHHHHHHHHHHHhc-ChhhHHHHHHHHHhHHHHHHHHHHHHHHHHHh
Confidence 677877777776555 78999999999999999999999876666654
No 438
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=47.43 E-value=31 Score=26.11 Aligned_cols=47 Identities=15% Similarity=0.171 Sum_probs=35.9
Q ss_pred CCHHHHHHHHHHhcccCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008352 505 LNPKERCIVRLRFGIEDG-KPKSLSEVGNIFGLSKERVRQLESRALYR 551 (569)
Q Consensus 505 L~~rER~VL~LRygL~d~-e~~Tl~EIAe~LGISrerVRqie~RALkK 551 (569)
+++.+..+|.-.|..+.. ......+||..+|++...|.........+
T Consensus 7 ~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~ 54 (56)
T smart00389 7 FTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAK 54 (56)
T ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhc
Confidence 677888888888864432 23457899999999999999988776554
No 439
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=47.42 E-value=28 Score=31.72 Aligned_cols=25 Identities=16% Similarity=0.183 Sum_probs=23.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.++|.+|+|+.+|||+.+|.++++.
T Consensus 17 ~Glsq~eLA~~~Gis~~~is~iE~g 41 (120)
T PRK13890 17 RHMTKKELSERSGVSISFLSDLTTG 41 (120)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 6799999999999999999999864
No 440
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=47.40 E-value=33 Score=32.68 Aligned_cols=43 Identities=12% Similarity=0.160 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHhccc-CCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 505 LNPKERCIVRLRFGIE-DGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 505 L~~rER~VL~LRygL~-d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
+++....-|...|.+. ++......+||+.|||++.+|.+++++
T Consensus 4 ~s~~~edYL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~r 47 (154)
T COG1321 4 LSETEEDYLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKR 47 (154)
T ss_pred cchHHHHHHHHHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHH
Confidence 4444444444444333 346789999999999999999876544
No 441
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=47.17 E-value=28 Score=35.12 Aligned_cols=37 Identities=19% Similarity=0.137 Sum_probs=27.8
Q ss_pred HHHHHhcccCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 512 IVRLRFGIEDGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 512 VL~LRygL~d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
|+...| ..|+.+ +-.+||+.||||+..|| .|++.|..
T Consensus 21 I~~g~l--~pG~~LpsE~eLae~~gVSRtpVR----EAL~~L~~ 58 (253)
T PRK11523 21 IEQGVY--LVGDKLPAERFIADEKNVSRTVVR----EAIIMLEV 58 (253)
T ss_pred HHcCCC--CCCCCCCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 444443 345788 58999999999999998 57777754
No 442
>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=47.03 E-value=1.9e+02 Score=26.49 Aligned_cols=43 Identities=23% Similarity=0.434 Sum_probs=24.8
Q ss_pred HHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 497 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 497 ~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
.|......|++. .+....- -|.|-.+||..+|++.+.||++..
T Consensus 52 ~L~~~~~~~~~~--~L~~aK~-----~GFsD~~IA~l~~~~e~~vr~~R~ 94 (123)
T PF02787_consen 52 ELKEYLNELDPE--LLRKAKR-----LGFSDRQIARLWGVSEEEVRELRK 94 (123)
T ss_dssp HHHHHGGG--HH--HHHHHHH-----TT--HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHhhccchHH--HHHHHHH-----cCCCHHHHHhccCCCHHHHHHHHH
Confidence 344434445554 3334433 468999999999999999987644
No 443
>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=46.86 E-value=14 Score=32.47 Aligned_cols=26 Identities=23% Similarity=0.384 Sum_probs=23.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESRALY 550 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~RALk 550 (569)
+|..|+|+.+|||..++|..+...+-
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~~Gll 27 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESIGLI 27 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 68999999999999999999987654
No 444
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=46.84 E-value=19 Score=28.11 Aligned_cols=26 Identities=8% Similarity=0.218 Sum_probs=19.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESRA 548 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~RA 548 (569)
.++|..++|+..||++.+|..+.+.-
T Consensus 9 ~~it~~~La~~~gis~~tl~~~~~~~ 34 (63)
T PF13443_consen 9 RGITQKDLARKTGISRSTLSRILNGK 34 (63)
T ss_dssp TT--HHHHHHHHT--HHHHHHHHTTT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcc
Confidence 57899999999999999999998865
No 445
>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=46.53 E-value=29 Score=28.29 Aligned_cols=27 Identities=22% Similarity=0.463 Sum_probs=22.8
Q ss_pred HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008352 512 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE 545 (569)
Q Consensus 512 VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie 545 (569)
+|.--|| ...|+|..||+++.|||...
T Consensus 11 lLi~~~G-------nqtEvaR~l~c~R~TVrKY~ 37 (64)
T PF06322_consen 11 LLIETYG-------NQTEVARRLGCNRATVRKYS 37 (64)
T ss_pred HHHHHhC-------cHHHHHHHhcccHHHHHHHh
Confidence 4566777 78999999999999999754
No 446
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=46.20 E-value=34 Score=34.49 Aligned_cols=27 Identities=19% Similarity=0.335 Sum_probs=23.1
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 521 DGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 521 d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.+.++|+.|||+.+|+++.+|..++.-
T Consensus 21 ~~~~~~l~eia~~lglpksT~~RlL~t 47 (248)
T TIGR02431 21 ERPRLTLTDVAEATGLTRAAARRFLLT 47 (248)
T ss_pred CCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 347899999999999999999877653
No 447
>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=46.05 E-value=29 Score=28.14 Aligned_cols=24 Identities=29% Similarity=0.401 Sum_probs=19.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHh
Q 008352 431 SPDKEDLARRVGITVEKLERLIFI 454 (569)
Q Consensus 431 ~Pt~eEIA~~lgis~e~v~~ll~~ 454 (569)
..+..+||..+|++++.|+.++..
T Consensus 14 ~~S~~eLa~~~~~s~~~ve~mL~~ 37 (69)
T PF09012_consen 14 RVSLAELAREFGISPEAVEAMLEQ 37 (69)
T ss_dssp SEEHHHHHHHTT--HHHHHHHHHH
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHH
Confidence 678999999999999999998863
No 448
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=45.80 E-value=3.4e+02 Score=27.56 Aligned_cols=35 Identities=20% Similarity=0.152 Sum_probs=26.9
Q ss_pred HHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHh
Q 008352 420 AKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454 (569)
Q Consensus 420 a~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~ 454 (569)
+...+.+......+++++|+.+|+++..+..+.+.
T Consensus 188 ~~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk~ 222 (290)
T PRK10572 188 ACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQ 222 (290)
T ss_pred HHHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 33344455566889999999999999999888653
No 449
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=45.68 E-value=49 Score=38.41 Aligned_cols=52 Identities=15% Similarity=0.278 Sum_probs=41.9
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHhcccCC---CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 494 MRQHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 494 l~e~L~~aL~~L~~rER~VL~LRygL~d~---e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
+.+.|+.....|++.||.|..+. |... ..+|..|||+..|+|..+|-+..++
T Consensus 343 l~~~I~~~~~~Lt~~E~~IA~yI--l~n~~~v~~~si~eLA~~~~vS~aTV~Rf~kk 397 (638)
T PRK14101 343 VFERIRQMRDALTPAERRVADLA--LNHPRSIINDPIVDIARKADVSQPTVIRFCRS 397 (638)
T ss_pred HHHHHHHHHhhcCHHHHHHHHHH--HhCHHHHHhccHHHHHHHhCCCHHHHHHHHHH
Confidence 45578888999999999998754 3332 4579999999999999999876654
No 450
>PRK15044 transcriptional regulator SirC; Provisional
Probab=45.59 E-value=1.1e+02 Score=32.38 Aligned_cols=60 Identities=22% Similarity=0.198 Sum_probs=43.7
Q ss_pred HHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhc
Q 008352 257 LRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325 (569)
Q Consensus 257 l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~ 325 (569)
+..|++..+..+.|..+..... .+++..-+.+..+++++.++||+.+|++...|.+.++.
T Consensus 172 Ls~~l~~~~~~~~L~~~~~is~---------~~kV~~~I~~nl~~~~SLeeLA~~lgmS~~tL~R~Fk~ 231 (295)
T PRK15044 172 ISAFVRKPGGFDFLERAIKITT---------KEKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAA 231 (295)
T ss_pred HHHHHhcccchhhHHHHhhhhH---------HHHHHHHHHhCcccCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 5667777776666655544332 33445556677889999999999999999999887754
No 451
>PRK13503 transcriptional activator RhaS; Provisional
Probab=45.57 E-value=2e+02 Score=28.80 Aligned_cols=29 Identities=17% Similarity=0.181 Sum_probs=23.7
Q ss_pred HHhcCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 425 IQEGNHSPDKEDLARRVGITVEKLERLIF 453 (569)
Q Consensus 425 ~~~~gr~Pt~eEIA~~lgis~e~v~~ll~ 453 (569)
.+......|.+++|+.+|+++..+..+..
T Consensus 181 ~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk 209 (278)
T PRK13503 181 EDHFAEEVNWEALADQFSLSLRTLHRQLK 209 (278)
T ss_pred HHhhcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 33344578999999999999999988865
No 452
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=45.54 E-value=23 Score=32.56 Aligned_cols=23 Identities=13% Similarity=0.338 Sum_probs=20.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~R 547 (569)
||-+|+|+.+|+|+.||.....+
T Consensus 1 MT~eELA~~tG~srQTINrWvRk 23 (122)
T PF07037_consen 1 MTPEELAELTGYSRQTINRWVRK 23 (122)
T ss_pred CCHHHHHHHhCccHHHHHHHHHh
Confidence 68999999999999999988754
No 453
>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=45.38 E-value=16 Score=31.17 Aligned_cols=25 Identities=28% Similarity=0.498 Sum_probs=22.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESRAL 549 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~RAL 549 (569)
+|..|+|+.+|||..++|..+.+.+
T Consensus 2 ~ti~evA~~~gvs~~tLR~ye~~Gl 26 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEEKGL 26 (88)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 6899999999999999999988764
No 454
>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=45.37 E-value=53 Score=30.23 Aligned_cols=45 Identities=13% Similarity=0.203 Sum_probs=34.3
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHh----CCCHHHHHHHHHHHHHH
Q 008352 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF----GLSKERVRQLESRALYR 551 (569)
Q Consensus 504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~L----GISrerVRqie~RALkK 551 (569)
.|++.|.+|+..-+. . ++.|..||.+.| |+++.||...+.|-.+|
T Consensus 1 ~Lt~~E~~VM~vlW~--~-~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~K 49 (130)
T TIGR02698 1 SISDAEWEVMRVVWT--L-GETTSRDIIRILAEKKDWSDSTIKTLLGRLVDK 49 (130)
T ss_pred CCCHHHHHHHHHHHc--C-CCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHC
Confidence 378889998876553 2 468999977776 79999999887776553
No 455
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, 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 domain
Probab=45.32 E-value=1.4e+02 Score=28.90 Aligned_cols=89 Identities=17% Similarity=0.216 Sum_probs=51.1
Q ss_pred CHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHH
Q 008352 433 DKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCI 512 (569)
Q Consensus 433 t~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~V 512 (569)
++.|+|+.+|+++..++.+....--+-+- .++.+ +- .-++ + +|.. | +.|
T Consensus 3 ~I~evA~~~gvs~~tLRyYe~~GLl~p~~----r~~~g--yR-------~Y~~-~---------dl~r----L----~~I 51 (172)
T cd04790 3 TISQLARQFGLSRSTLLYYERIGLLSPSA----RSESN--YR-------LYGE-R---------DLER----L----EQI 51 (172)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCCCCCc----cCCCC--Cc-------cCCH-H---------HHHH----H----HHH
Confidence 57899999999999999886532111000 00000 00 0011 1 1111 1 235
Q ss_pred HHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352 513 VRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 557 (569)
Q Consensus 513 L~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 557 (569)
..++- -|++++||...++.....+..++..-+..|++.+.
T Consensus 52 ~~lr~-----~G~sL~eI~~ll~~~~~~~~~~L~~~~~~l~~ei~ 91 (172)
T cd04790 52 CAYRS-----AGVSLEDIRSLLQQPGDDATDVLRRRLAELNREIQ 91 (172)
T ss_pred HHHHH-----cCCCHHHHHHHHhcCChhHHHHHHHHHHHHHHHHH
Confidence 55554 47999999999987766666666666666665543
No 456
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=45.23 E-value=34 Score=34.97 Aligned_cols=37 Identities=22% Similarity=0.238 Sum_probs=25.8
Q ss_pred HHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 510 RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 510 R~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
|-+-.|.+.-..+.++|+.||++.+|+++.+|.+++.
T Consensus 12 ral~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~ 48 (263)
T PRK09834 12 RGLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLE 48 (263)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3333344332333569999999999999999986554
No 457
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=44.84 E-value=30 Score=33.34 Aligned_cols=25 Identities=16% Similarity=0.290 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.++|++|+|+.+|||+.+|+++++.
T Consensus 19 ~glt~~elA~~~gis~~~is~~E~g 43 (185)
T PRK09943 19 QGLSQRRAAELSGLTHSAISTIEQD 43 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 6799999999999999999999974
No 458
>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=44.60 E-value=18 Score=34.72 Aligned_cols=96 Identities=13% Similarity=0.250 Sum_probs=0.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCc-chhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHH
Q 008352 430 HSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT-TFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPK 508 (569)
Q Consensus 430 r~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~-~l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~r 508 (569)
++-+..+||+.+|+++..|..++. +..+....+. .+.+++...........+.....+..|.++|+.=++.
T Consensus 48 ~PLt~~~iA~~lgl~~STVSRav~--------~Ky~~t~~Gi~plk~fF~~~~~~~~~~~~S~~~ik~~i~~lI~~Ed~~ 119 (160)
T PF04552_consen 48 KPLTMKDIADELGLHESTVSRAVK--------NKYIQTPRGIFPLKDFFSRSVSSGSGEEFSSEAIKARIKELIEEEDKK 119 (160)
T ss_dssp ---------------------------------------------S-----SS--SS-SS---TTH-HHHHHHHTTS-TT
T ss_pred cCCCHHHHHHHhCCCHhHHHHHHc--------CceeecCCeeeeHHHhccccccCCCCcccHHHHHHHHHHHHHHhcCCC
Q ss_pred HHHHHHHHhcccCCCCCCHHHHHHHh-----CCCHHHHHHHHHH
Q 008352 509 ERCIVRLRFGIEDGKPKSLSEVGNIF-----GLSKERVRQLESR 547 (569)
Q Consensus 509 ER~VL~LRygL~d~e~~Tl~EIAe~L-----GISrerVRqie~R 547 (569)
.++|-++|++.| .|||-||-..-..
T Consensus 120 --------------~PlSD~~i~~~L~~~gi~isRRTVaKYR~~ 149 (160)
T PF04552_consen 120 --------------KPLSDQEIAELLKEEGIKISRRTVAKYREE 149 (160)
T ss_dssp --------------S---HHHHHHHHTTTTS---HHHHHHHHHH
T ss_pred --------------CCCCHHHHHHHHHHcCCCccHHHHHHHHHH
No 459
>PRK14999 histidine utilization repressor; Provisional
Probab=44.51 E-value=33 Score=34.42 Aligned_cols=28 Identities=29% Similarity=0.387 Sum_probs=23.1
Q ss_pred CCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 523 KPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 523 e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
+.+ |-.|+|+.+|||+.||| +|+..|..
T Consensus 34 ~~LPsE~eLa~~~gVSR~TVR----~Al~~L~~ 62 (241)
T PRK14999 34 DRIPSEAELVAQYGFSRMTIN----RALRELTD 62 (241)
T ss_pred CcCCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 445 99999999999999999 56666654
No 460
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=44.51 E-value=16 Score=32.45 Aligned_cols=25 Identities=20% Similarity=0.521 Sum_probs=22.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESRAL 549 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~RAL 549 (569)
+|..|+|+.+|||..++|..+...+
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gl 25 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKEGL 25 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999988765
No 461
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=44.48 E-value=17 Score=32.27 Aligned_cols=26 Identities=19% Similarity=0.273 Sum_probs=23.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESRALY 550 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~RALk 550 (569)
++..|+|+.+|||..++|-.+...+=
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~~GLi 26 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKIGLL 26 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCC
Confidence 57899999999999999999988654
No 462
>PRK08359 transcription factor; Validated
Probab=44.44 E-value=30 Score=33.88 Aligned_cols=35 Identities=20% Similarity=0.284 Sum_probs=28.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH-------HHHHHHHHhh
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESR-------ALYRLKQSLG 557 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~R-------ALkKLR~~l~ 557 (569)
.++|++|+|+.+|+++.+|+.++.. .+.+|-+.+.
T Consensus 97 kglSQeeLA~~lgvs~stI~~iE~G~~~Ps~~~l~kLak~l~ 138 (176)
T PRK08359 97 SGLSYEELSHEVGLSVNDLRRIAHGEYEPTIKEAKKLERYFK 138 (176)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCCCcCCCHHHHHHHHHHhC
Confidence 6899999999999999999999763 4455555443
No 463
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=44.41 E-value=33 Score=34.44 Aligned_cols=29 Identities=34% Similarity=0.492 Sum_probs=23.6
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 522 GKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 522 ~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
|+.+ |-.|+|+.+|||+.||| +|+..|..
T Consensus 26 G~~LPsE~eL~~~~~VSR~TvR----~Al~~L~~ 55 (240)
T PRK09764 26 GDALPTESALQTEFGVSRVTVR----QALRQLVE 55 (240)
T ss_pred CCcCCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 3555 88999999999999999 57777754
No 464
>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=44.09 E-value=17 Score=31.64 Aligned_cols=25 Identities=20% Similarity=0.339 Sum_probs=22.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESRAL 549 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~RAL 549 (569)
+|..|+|+.+|||..++|..+..++
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gl 25 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDKIGL 25 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999988765
No 465
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=44.06 E-value=57 Score=28.27 Aligned_cols=26 Identities=19% Similarity=0.238 Sum_probs=23.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESRA 548 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~RA 548 (569)
++.|+++||+.+|+|+.+..++.++.
T Consensus 20 ~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 20 QPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 78999999999999999999888876
No 466
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=43.85 E-value=34 Score=34.02 Aligned_cols=28 Identities=32% Similarity=0.335 Sum_probs=23.1
Q ss_pred CCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 523 KPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 523 e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
+.+ |-.|+|+.+|||+.||| +|+..|.+
T Consensus 23 ~~LPsE~eLa~~~~VSR~TVR----~Al~~L~~ 51 (230)
T TIGR02018 23 HRIPSEHELVAQYGCSRMTVN----RALRELTD 51 (230)
T ss_pred CcCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 444 89999999999999999 57777754
No 467
>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=43.74 E-value=46 Score=32.47 Aligned_cols=47 Identities=21% Similarity=0.274 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352 505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556 (569)
Q Consensus 505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 556 (569)
|++.-|.-|.-.+. .+++|+++||..+||+..||.-|++ |+.+.+.+
T Consensus 17 lse~~r~~Iy~~~~---~~~~sv~~vS~~ygi~~~RV~AIvr--LkeiE~~~ 63 (172)
T PF12298_consen 17 LSEELREQIYEDVM---QDGKSVREVSQKYGIKIQRVEAIVR--LKEIEKRW 63 (172)
T ss_pred CCHHHHHHHHHHHH---hCCCCHHHHHHHhCCCHHHHHHHHH--HHHHHHHH
Confidence 55555555555543 1577999999999999999987654 34444444
No 468
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=43.44 E-value=69 Score=30.14 Aligned_cols=44 Identities=11% Similarity=0.238 Sum_probs=32.9
Q ss_pred HHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcc
Q 008352 417 VLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLS 460 (569)
Q Consensus 417 i~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~S 460 (569)
..+++.-|...-++..|+.+|++.+|++++.|..++...+-.++
T Consensus 32 f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGRL~~~ 75 (137)
T TIGR03826 32 FEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGRLQLK 75 (137)
T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCCeecc
Confidence 33444445555566789999999999999999999887765443
No 469
>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=43.42 E-value=28 Score=30.61 Aligned_cols=23 Identities=35% Similarity=0.507 Sum_probs=21.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~R 547 (569)
+|..|+|+.+|||..++|..+..
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~~ 23 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 57899999999999999999776
No 470
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=43.19 E-value=32 Score=29.08 Aligned_cols=19 Identities=21% Similarity=0.240 Sum_probs=18.4
Q ss_pred CHHHHHHHhCCCHHHHHHH
Q 008352 526 SLSEVGNIFGLSKERVRQL 544 (569)
Q Consensus 526 Tl~EIAe~LGISrerVRqi 544 (569)
+...+|+.||||.+.|+|+
T Consensus 12 s~~kvA~aLGIs~~AVsQW 30 (75)
T PRK09744 12 SKTKLANAAGVRLASVAAW 30 (75)
T ss_pred cHHHHHHHHCCCHHHHHHH
Confidence 8899999999999999998
No 471
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=43.18 E-value=30 Score=34.14 Aligned_cols=38 Identities=24% Similarity=0.299 Sum_probs=29.0
Q ss_pred HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 511 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 511 ~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
.|+.-.| ..|+.++..++|+.||||+..|| .||.+|..
T Consensus 19 ~I~~g~l--~pG~~L~e~eLae~lgVSRtpVR----EAL~~L~~ 56 (224)
T PRK11534 19 DIIRGNF--QPDEKLRMSLLTSRYALGVGPLR----EALSQLVA 56 (224)
T ss_pred HHHhCCC--CCCCcCCHHHHHHHHCCChHHHH----HHHHHHHH
Confidence 3555544 24588999999999999999998 57777754
No 472
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=43.16 E-value=18 Score=31.63 Aligned_cols=25 Identities=32% Similarity=0.421 Sum_probs=21.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESRAL 549 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~RAL 549 (569)
++..|+|+.+|||..|+|..+...+
T Consensus 1 y~i~e~A~~~gvs~~tlR~Ye~~Gl 25 (99)
T cd04772 1 YRTVDLARAIGLSPQTVRNYESLGL 25 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 4789999999999999999887654
No 473
>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=42.92 E-value=3.9e+02 Score=27.55 Aligned_cols=29 Identities=28% Similarity=0.528 Sum_probs=23.0
Q ss_pred HHHhhhhCCCCcHHHHHHHcCCCHHHHHH
Q 008352 293 SKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (569)
Q Consensus 293 ~~l~~~~g~~pt~~ewA~a~g~~~~~L~~ 321 (569)
..+....|++|+..+.|...|++...+..
T Consensus 140 ~~l~~~~~r~~~~~e~a~~l~~~~~~~~~ 168 (285)
T TIGR02394 140 RQLEKKLGREPSVEEIAELLDKPVEDVSR 168 (285)
T ss_pred HHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence 33456679999999999999998876654
No 474
>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=42.85 E-value=51 Score=30.58 Aligned_cols=33 Identities=21% Similarity=0.182 Sum_probs=24.2
Q ss_pred HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352 511 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 548 (569)
Q Consensus 511 ~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RA 548 (569)
.||.|.. ++..-.+||..|+||...|+.++.|=
T Consensus 25 rIvela~-----~G~rp~~Isr~l~Vs~gcVsKIl~Ry 57 (125)
T PF00292_consen 25 RIVELAK-----EGVRPCDISRQLRVSHGCVSKILSRY 57 (125)
T ss_dssp HHHHHHH-----TT--HHHHHHHHT--HHHHHHHHHHH
T ss_pred HHHHHhh-----hcCCHHHHHHHHccchhHHHHHHHHH
Confidence 4666765 68999999999999999999988763
No 475
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=42.69 E-value=18 Score=30.98 Aligned_cols=26 Identities=19% Similarity=0.286 Sum_probs=22.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESRALY 550 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~RALk 550 (569)
+|..|+|+.+|||..++|..+...+-
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~~Gli 27 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYERLGLL 27 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCCc
Confidence 68899999999999999999876443
No 476
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=42.68 E-value=36 Score=34.85 Aligned_cols=37 Identities=19% Similarity=0.190 Sum_probs=27.2
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 507 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 507 ~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
+|.+.|+.+-- .....+..||++.||||..|||+-+.
T Consensus 5 ~R~~~Il~~l~---~~~~~~~~ela~~l~vS~~TiRRdL~ 41 (252)
T PRK10906 5 QRHDAIIELVK---QQGYVSTEELVEHFSVSPQTIRRDLN 41 (252)
T ss_pred HHHHHHHHHHH---HcCCEeHHHHHHHhCCCHHHHHHHHH
Confidence 45555665532 22568999999999999999997543
No 477
>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=42.60 E-value=1.6e+02 Score=25.59 Aligned_cols=91 Identities=21% Similarity=0.226 Sum_probs=0.0
Q ss_pred CHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHH
Q 008352 433 DKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCI 512 (569)
Q Consensus 433 t~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~V 512 (569)
++.|+|+.+|++...++.+.. ..++.....++-.-.+...++..... |
T Consensus 2 ~I~e~a~~~gvs~~tLR~ye~--------------------~Gll~p~r~~~g~R~Y~~~dv~~l~~------------I 49 (96)
T cd04774 2 KVDEVAKRLGLTKRTLKYYEE--------------------IGLVSPERSEGRYRLYSEEDLKRLER------------I 49 (96)
T ss_pred CHHHHHHHHCcCHHHHHHHHH--------------------CCCCCCCcCCCCCEEECHHHHHHHHH------------H
Q ss_pred HHHHhcccCCCCCCHHHHHHHhCCCHHHH---HHHHHHHHHHHHHHhhcC
Q 008352 513 VRLRFGIEDGKPKSLSEVGNIFGLSKERV---RQLESRALYRLKQSLGGK 559 (569)
Q Consensus 513 L~LRygL~d~e~~Tl~EIAe~LGISrerV---Rqie~RALkKLR~~l~~~ 559 (569)
..++-. -|+++++|...++...+.+ -+.....|..+++.+..+
T Consensus 50 ~~L~~~----~G~~l~ei~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~~ 95 (96)
T cd04774 50 LRLREV----LGFSLQEVTHFLERPLEPVDGGHRYSAESLREIHDALAQQ 95 (96)
T ss_pred HHHHHH----cCCCHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHcc
No 478
>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=42.33 E-value=19 Score=32.12 Aligned_cols=26 Identities=31% Similarity=0.446 Sum_probs=23.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESRALY 550 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~RALk 550 (569)
+|..|+|+.+|||..++|..+..++-
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye~~gll 26 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEKEGLL 26 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999887653
No 479
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=42.26 E-value=29 Score=34.38 Aligned_cols=27 Identities=26% Similarity=0.432 Sum_probs=22.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 524 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 524 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
=-|-.|+|+.+|||+.||| +||..|.+
T Consensus 32 LPsE~eLa~~~~VSR~TvR----~Al~~L~~ 58 (238)
T TIGR02325 32 LPAEMQLAERFGVNRHTVR----RAIAALVE 58 (238)
T ss_pred CcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 3489999999999999999 57777765
No 480
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=42.25 E-value=36 Score=32.55 Aligned_cols=25 Identities=8% Similarity=0.157 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
.++|++++|+.+|+++.+|+++++-
T Consensus 81 ~glSqeeLA~~lgvs~s~IsriE~G 105 (154)
T TIGR00270 81 RGWSQEQLAKKIQEKESLIKKIENA 105 (154)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 6899999999999999999999963
No 481
>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=42.22 E-value=19 Score=31.70 Aligned_cols=26 Identities=23% Similarity=0.313 Sum_probs=23.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESRALY 550 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~RALk 550 (569)
++..|+|+.+|||..++|..+...+-
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~~Gll 27 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKLGLI 27 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 68999999999999999998887543
No 482
>PHA00738 putative HTH transcription regulator
Probab=42.12 E-value=48 Score=30.03 Aligned_cols=37 Identities=22% Similarity=0.033 Sum_probs=27.1
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 507 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 507 ~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
|.-+.||.+-. .+++++..||++.+++|+.+|++.++
T Consensus 12 ptRr~IL~lL~---~~e~~~V~eLae~l~lSQptVS~HLK 48 (108)
T PHA00738 12 ILRRKILELIA---ENYILSASLISHTLLLSYTTVLRHLK 48 (108)
T ss_pred HHHHHHHHHHH---HcCCccHHHHHHhhCCCHHHHHHHHH
Confidence 33455555432 23579999999999999999998753
No 483
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=42.11 E-value=19 Score=31.39 Aligned_cols=25 Identities=20% Similarity=0.262 Sum_probs=22.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESRAL 549 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~RAL 549 (569)
|+..|+|+.+|||..+||-.+...+
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye~~GL 25 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLREGL 25 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999888655
No 484
>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=42.10 E-value=72 Score=23.61 Aligned_cols=23 Identities=22% Similarity=0.453 Sum_probs=18.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Q 008352 431 SPDKEDLARRVGITVEKLERLIF 453 (569)
Q Consensus 431 ~Pt~eEIA~~lgis~e~v~~ll~ 453 (569)
..+..|||+.+|++...+...+.
T Consensus 17 ~~t~~ela~~~~is~~tv~~~l~ 39 (48)
T PF13412_consen 17 RITQKELAEKLGISRSTVNRYLK 39 (48)
T ss_dssp TS-HHHHHHHHTS-HHHHHHHHH
T ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Confidence 48899999999999999988765
No 485
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=41.93 E-value=19 Score=31.30 Aligned_cols=25 Identities=20% Similarity=0.280 Sum_probs=22.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESRAL 549 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~RAL 549 (569)
|+..|+|+.+|||..++|..+...+
T Consensus 1 m~i~eva~~~gvs~~tlR~ye~~Gl 25 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDHIGL 25 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999988654
No 486
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=41.90 E-value=19 Score=31.50 Aligned_cols=25 Identities=20% Similarity=0.339 Sum_probs=22.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESRAL 549 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~RAL 549 (569)
+|..|+|+.+|||..++|..+...+
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~~Gl 25 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDEIGL 25 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999988765
No 487
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=41.88 E-value=2e+02 Score=29.02 Aligned_cols=30 Identities=23% Similarity=0.436 Sum_probs=22.9
Q ss_pred HHHHHhhhhCCCCcHHHHHHHcCCCHHHHH
Q 008352 291 EKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (569)
Q Consensus 291 ~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~ 320 (569)
....+....|+.|+..+.+...|++.+++.
T Consensus 121 ~~~~~~~~~~r~~~~~e~a~~~~~~~~~~~ 150 (257)
T PRK08583 121 AVDELTTELQRSPKISEIADRLGVSEEEVL 150 (257)
T ss_pred HHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence 334456677999999999999998876653
No 488
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=41.85 E-value=19 Score=30.99 Aligned_cols=25 Identities=28% Similarity=0.542 Sum_probs=22.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESRAL 549 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~RAL 549 (569)
+|..|+|+.+||+..+|+..+...+
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~~Gl 25 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEEKGL 25 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999987655
No 489
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=41.43 E-value=33 Score=27.87 Aligned_cols=25 Identities=8% Similarity=0.182 Sum_probs=20.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHh
Q 008352 430 HSPDKEDLARRVGITVEKLERLIFI 454 (569)
Q Consensus 430 r~Pt~eEIA~~lgis~e~v~~ll~~ 454 (569)
.+.+..|||+.+|++.-+++.+|..
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 3788999999999999999998864
No 490
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=41.41 E-value=2.1e+02 Score=25.85 Aligned_cols=37 Identities=11% Similarity=0.081 Sum_probs=28.4
Q ss_pred HHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhc
Q 008352 289 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325 (569)
Q Consensus 289 e~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~ 325 (569)
+++..-+...+..+++..++|+.+|++...|.+.++.
T Consensus 12 ~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 12 HSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3444455667778899999999999998888776654
No 491
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=41.31 E-value=55 Score=28.63 Aligned_cols=24 Identities=25% Similarity=0.306 Sum_probs=21.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 523 KPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 523 e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
-++|.++||..||+|.+.|.+++.
T Consensus 22 ~~ls~~~ia~dL~~s~~~le~vL~ 45 (89)
T PF10078_consen 22 SGLSLEQIAADLGTSPEHLEQVLN 45 (89)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHc
Confidence 579999999999999999988764
No 492
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=41.23 E-value=19 Score=32.87 Aligned_cols=27 Identities=26% Similarity=0.379 Sum_probs=23.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESRALYR 551 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~RALkK 551 (569)
||..|+|+.+|||..++|..+...+-.
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~~GLl~ 27 (127)
T cd01108 1 MNIGEAAKLTGLSAKMIRYYEEIGLIP 27 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 578999999999999999999876643
No 493
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=41.22 E-value=20 Score=31.57 Aligned_cols=26 Identities=12% Similarity=0.179 Sum_probs=23.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESRALY 550 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~RALk 550 (569)
|+..|+|+.+|||..++|-.+...|=
T Consensus 1 m~Ige~a~~~gvs~~tlRyYe~~GLl 26 (107)
T cd04777 1 MKIGKFAKKNNITIDTVRHYIDLGLL 26 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCc
Confidence 57899999999999999999998774
No 494
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=41.18 E-value=20 Score=32.05 Aligned_cols=26 Identities=23% Similarity=0.339 Sum_probs=23.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESRALY 550 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~RALk 550 (569)
|+..|+|+.+|||..++|..+...+=
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye~~GLl 26 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEEQGLL 26 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCC
Confidence 57899999999999999999987654
No 495
>PF14502 HTH_41: Helix-turn-helix domain
Probab=41.16 E-value=50 Score=25.66 Aligned_cols=30 Identities=27% Similarity=0.447 Sum_probs=0.0
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 521 DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 521 d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
|..-.|..|.++.|++|+.+|. .||+.|.+
T Consensus 3 GdRi~tI~e~~~~~~vs~GtiQ----~Alk~Le~ 32 (48)
T PF14502_consen 3 GDRIPTISEYSEKFGVSRGTIQ----NALKFLEE 32 (48)
T ss_pred CcccCCHHHHHHHhCcchhHHH----HHHHHHHH
No 496
>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=41.11 E-value=43 Score=30.55 Aligned_cols=40 Identities=35% Similarity=0.470 Sum_probs=35.5
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352 503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547 (569)
Q Consensus 503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R 547 (569)
..|.+.++.|+.++- .+.|..|||..++++..-||.+..-
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 578999999999987 4999999999999999999987653
No 497
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=41.09 E-value=2.8e+02 Score=25.32 Aligned_cols=23 Identities=13% Similarity=0.257 Sum_probs=20.2
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Q 008352 431 SPDKEDLARRVGITVEKLERLIF 453 (569)
Q Consensus 431 ~Pt~eEIA~~lgis~e~v~~ll~ 453 (569)
..+..|||+.+|++...+..++.
T Consensus 54 ~~t~~eLa~~l~i~~~tvsr~l~ 76 (144)
T PRK11512 54 CITPVELKKVLSVDLGALTRMLD 76 (144)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Confidence 46899999999999999988765
No 498
>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=41.07 E-value=20 Score=32.20 Aligned_cols=27 Identities=19% Similarity=0.336 Sum_probs=23.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008352 525 KSLSEVGNIFGLSKERVRQLESRALYR 551 (569)
Q Consensus 525 ~Tl~EIAe~LGISrerVRqie~RALkK 551 (569)
||..|+|+.+|||..++|-.+..++=.
T Consensus 1 ~~ige~a~~~gvs~~tLryYe~~GLi~ 27 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEEKGLLP 27 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 688999999999999999999876643
No 499
>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=40.95 E-value=28 Score=38.60 Aligned_cols=47 Identities=23% Similarity=0.418 Sum_probs=32.6
Q ss_pred HHHhcCCHHHHHHHHH---------HhcccCC---CCCCHHHHHHHhCCCHHHHHHHHH
Q 008352 500 NLLTLLNPKERCIVRL---------RFGIEDG---KPKSLSEVGNIFGLSKERVRQLES 546 (569)
Q Consensus 500 ~aL~~L~~rER~VL~L---------RygL~d~---e~~Tl~EIAe~LGISrerVRqie~ 546 (569)
.++..|.-|.+.+++. -|+..|. .++|+++||+.+|+..+||++..+
T Consensus 282 ~li~~i~~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdiA~~lglheSTVSRav~ 340 (429)
T TIGR02395 282 WLIKALEQREETLLKVAEAIVEHQKDFFLGGPAALKPLTLREVAEELGLHESTISRAIN 340 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccCcCCcHHHHHHHhCCCccchhhhhc
Confidence 3445666666655432 2322232 799999999999999999997654
No 500
>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=40.92 E-value=32 Score=34.23 Aligned_cols=27 Identities=37% Similarity=0.454 Sum_probs=22.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352 524 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554 (569)
Q Consensus 524 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 554 (569)
=-|-.|+|+.+|||+.||| +|+..|.+
T Consensus 24 LPsE~eLa~~~gVSR~TVR----~Al~~L~~ 50 (233)
T TIGR02404 24 LPSEHELMDQYGASRETVR----KALNLLTE 50 (233)
T ss_pred CcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 3489999999999999999 57777754
Done!