Query 011454
Match_columns 485
No_of_seqs 249 out of 1670
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 01:32:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011454.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011454hhsearch_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 1.4E-51 3.1E-56 430.4 32.5 290 191-483 60-412 (415)
2 PRK07406 RNA polymerase sigma 100.0 1.8E-50 3.8E-55 419.1 32.8 289 191-482 63-372 (373)
3 PRK05949 RNA polymerase sigma 100.0 1.4E-49 2.9E-54 407.3 33.0 288 191-483 18-326 (327)
4 TIGR02997 Sig70-cyanoRpoD RNA 100.0 2.3E-49 5E-54 400.9 31.1 276 192-470 2-298 (298)
5 PRK07405 RNA polymerase sigma 100.0 9.1E-49 2E-53 399.8 32.9 288 191-483 8-316 (317)
6 PRK05901 RNA polymerase sigma 100.0 3E-47 6.4E-52 406.8 29.9 278 191-483 211-509 (509)
7 PRK07921 RNA polymerase sigma 100.0 2.2E-46 4.8E-51 382.9 31.1 277 191-482 26-323 (324)
8 COG0568 RpoD DNA-directed RNA 100.0 7.4E-45 1.6E-49 369.4 28.2 291 190-482 8-341 (342)
9 PRK09210 RNA polymerase sigma 100.0 1E-44 2.2E-49 376.8 29.5 252 190-483 95-367 (367)
10 PRK05658 RNA polymerase sigma 100.0 3.7E-41 8E-46 371.3 29.2 253 192-483 345-618 (619)
11 PRK05657 RNA polymerase sigma 100.0 8E-39 1.7E-43 327.7 29.5 251 187-479 49-320 (325)
12 PRK06596 RNA polymerase factor 100.0 1.2E-38 2.6E-43 320.8 29.9 246 184-475 10-282 (284)
13 TIGR02393 RpoD_Cterm RNA polym 100.0 8.7E-39 1.9E-43 313.5 26.0 217 265-483 1-238 (238)
14 PRK07500 rpoH2 RNA polymerase 100.0 4.5E-38 9.8E-43 317.4 30.3 242 191-476 6-280 (289)
15 TIGR02392 rpoH_proteo alternat 100.0 7.5E-38 1.6E-42 312.6 28.8 240 192-474 2-269 (270)
16 TIGR02394 rpoS_proteo RNA poly 100.0 1.4E-36 3E-41 305.7 29.8 249 187-477 9-278 (285)
17 PRK07122 RNA polymerase sigma 100.0 1.6E-36 3.4E-41 302.5 25.4 206 264-473 40-263 (264)
18 COG1191 FliA DNA-directed RNA 100.0 1.9E-35 4E-40 290.4 26.4 227 203-475 3-246 (247)
19 PRK07408 RNA polymerase sigma 100.0 3.4E-35 7.4E-40 291.5 27.6 209 264-476 25-254 (256)
20 TIGR02850 spore_sigG RNA polym 100.0 2.5E-34 5.4E-39 284.7 27.7 228 201-473 11-254 (254)
21 PRK08215 sporulation sigma fac 100.0 8.7E-34 1.9E-38 281.3 27.6 227 202-473 15-257 (258)
22 TIGR02941 Sigma_B RNA polymera 100.0 2.1E-33 4.7E-38 277.7 28.2 226 204-473 8-253 (255)
23 PRK05911 RNA polymerase sigma 100.0 2.1E-33 4.6E-38 278.9 27.6 205 264-475 23-255 (257)
24 PRK06288 RNA polymerase sigma 100.0 2.1E-32 4.5E-37 273.0 28.1 230 200-477 6-264 (268)
25 PRK08583 RNA polymerase sigma 100.0 9.5E-32 2.1E-36 266.3 27.9 228 204-475 8-255 (257)
26 TIGR02980 SigBFG RNA polymeras 100.0 1.1E-31 2.4E-36 260.7 25.1 207 263-473 2-226 (227)
27 TIGR02885 spore_sigF RNA polym 100.0 1.4E-31 3E-36 260.8 25.1 206 263-473 10-231 (231)
28 PRK07670 RNA polymerase sigma 100.0 4.5E-31 9.7E-36 260.9 27.5 203 264-474 22-250 (251)
29 PRK05572 sporulation sigma fac 100.0 6.4E-31 1.4E-35 260.0 28.0 233 197-474 5-251 (252)
30 TIGR02479 FliA_WhiG RNA polyme 100.0 4.1E-30 8.9E-35 249.5 23.6 198 269-473 1-223 (224)
31 PRK06986 fliA flagellar biosyn 100.0 1.5E-29 3.1E-34 247.7 24.4 208 261-475 5-234 (236)
32 PRK12427 flagellar biosynthesi 100.0 3.4E-29 7.4E-34 245.1 24.5 201 264-472 15-230 (231)
33 PRK05803 sporulation sigma fac 100.0 8.3E-27 1.8E-31 227.9 24.5 212 192-476 17-230 (233)
34 TIGR02846 spore_sigmaK RNA pol 99.9 2.3E-24 4.9E-29 210.1 23.3 209 192-473 15-226 (227)
35 PRK08301 sporulation sigma fac 99.9 2.3E-24 4.9E-29 210.5 22.8 208 196-475 23-232 (234)
36 PRK09648 RNA polymerase sigma 99.9 3.6E-23 7.7E-28 195.1 20.4 179 206-474 6-188 (189)
37 TIGR02835 spore_sigmaE RNA pol 99.9 3.7E-23 8E-28 202.5 20.5 208 196-475 23-232 (234)
38 PRK09646 RNA polymerase sigma 99.9 6.3E-23 1.4E-27 194.7 19.2 183 204-475 10-192 (194)
39 PRK05602 RNA polymerase sigma 99.9 1.2E-22 2.6E-27 191.0 19.2 162 264-478 20-181 (186)
40 PRK12513 RNA polymerase sigma 99.9 1.1E-22 2.5E-27 192.4 19.0 167 264-478 26-192 (194)
41 TIGR02952 Sig70_famx2 RNA poly 99.9 1.9E-22 4.1E-27 185.8 18.9 160 264-473 11-170 (170)
42 PRK08295 RNA polymerase factor 99.9 2.7E-22 6E-27 191.2 19.2 182 264-477 24-206 (208)
43 PRK12519 RNA polymerase sigma 99.9 3.4E-22 7.4E-27 189.0 19.5 162 264-474 29-190 (194)
44 PRK06759 RNA polymerase factor 99.9 4.7E-22 1E-26 180.8 18.0 151 263-472 3-153 (154)
45 PRK11923 algU RNA polymerase s 99.9 7.9E-22 1.7E-26 186.4 20.2 188 205-475 1-188 (193)
46 PRK11922 RNA polymerase sigma 99.9 5E-22 1.1E-26 194.0 19.4 192 202-475 8-199 (231)
47 PRK12524 RNA polymerase sigma 99.9 6.9E-22 1.5E-26 187.9 19.5 163 264-477 26-188 (196)
48 PRK12514 RNA polymerase sigma 99.9 7.1E-22 1.5E-26 184.5 19.2 160 264-474 19-178 (179)
49 PRK12537 RNA polymerase sigma 99.9 1.3E-21 2.9E-26 183.6 19.7 159 264-473 23-181 (182)
50 PRK12534 RNA polymerase sigma 99.9 1.6E-21 3.5E-26 183.3 19.4 162 264-474 25-186 (187)
51 PRK12538 RNA polymerase sigma 99.9 1.4E-21 3E-26 191.8 19.6 161 264-477 63-223 (233)
52 PRK13919 putative RNA polymera 99.9 2.2E-21 4.7E-26 182.1 19.3 162 264-474 23-184 (186)
53 PRK12526 RNA polymerase sigma 99.9 4.6E-21 9.9E-26 184.0 20.8 167 264-476 38-204 (206)
54 TIGR02948 SigW_bacill RNA poly 99.9 2.8E-21 6.1E-26 180.9 18.9 169 264-475 18-186 (187)
55 PRK09652 RNA polymerase sigma 99.9 1.7E-21 3.6E-26 180.5 17.1 169 263-474 9-177 (182)
56 TIGR02859 spore_sigH RNA polym 99.9 4.7E-21 1E-25 181.2 20.1 174 264-473 19-197 (198)
57 PRK12531 RNA polymerase sigma 99.9 4.7E-21 1E-25 181.9 19.9 167 264-477 27-193 (194)
58 PRK06811 RNA polymerase factor 99.9 4E-21 8.6E-26 181.7 19.3 160 264-474 18-180 (189)
59 TIGR02939 RpoE_Sigma70 RNA pol 99.9 4.4E-21 9.5E-26 180.0 19.3 168 264-474 20-187 (190)
60 PRK12542 RNA polymerase sigma 99.9 1.2E-21 2.5E-26 184.4 15.3 173 262-482 7-179 (185)
61 PRK09640 RNA polymerase sigma 99.9 2.7E-21 5.8E-26 182.5 17.7 174 249-475 7-184 (188)
62 PRK09641 RNA polymerase sigma 99.9 5E-21 1.1E-25 179.2 19.1 169 264-475 18-186 (187)
63 PRK09643 RNA polymerase sigma 99.9 1.2E-20 2.6E-25 179.1 20.9 159 264-476 27-185 (192)
64 PRK11924 RNA polymerase sigma 99.9 1.4E-20 3E-25 173.9 19.5 165 263-476 12-176 (179)
65 PRK12515 RNA polymerase sigma 99.9 1.4E-20 3.1E-25 177.5 19.7 162 264-477 22-183 (189)
66 TIGR02954 Sig70_famx3 RNA poly 99.9 1.1E-20 2.4E-25 174.9 18.5 153 264-474 16-168 (169)
67 PRK12543 RNA polymerase sigma 99.9 1.1E-20 2.3E-25 177.1 18.6 165 262-477 5-169 (179)
68 PRK09638 RNA polymerase sigma 99.9 8.2E-21 1.8E-25 176.5 17.3 156 264-474 18-175 (176)
69 PRK12536 RNA polymerase sigma 99.9 2.9E-20 6.2E-25 174.5 20.2 158 264-475 21-179 (181)
70 PRK09645 RNA polymerase sigma 99.9 2E-20 4.4E-25 173.6 18.9 164 262-477 7-170 (173)
71 PRK12512 RNA polymerase sigma 99.9 2.7E-20 5.8E-25 174.6 19.8 157 264-476 22-182 (184)
72 PRK09649 RNA polymerase sigma 99.9 1.5E-20 3.2E-25 177.5 18.1 178 204-476 4-181 (185)
73 TIGR03001 Sig-70_gmx1 RNA poly 99.9 2.4E-20 5.3E-25 184.2 20.2 168 264-481 39-217 (244)
74 TIGR02999 Sig-70_X6 RNA polyme 99.9 2.5E-20 5.5E-25 174.3 19.1 160 264-473 17-182 (183)
75 PRK12539 RNA polymerase sigma 99.9 5.3E-20 1.1E-24 173.1 20.7 158 264-476 21-182 (184)
76 PRK09415 RNA polymerase factor 99.9 2.3E-20 4.9E-25 175.0 18.1 164 262-475 14-177 (179)
77 TIGR02985 Sig70_bacteroi1 RNA 99.9 2.1E-20 4.5E-25 169.5 17.2 161 264-473 1-161 (161)
78 TIGR02989 Sig-70_gvs1 RNA poly 99.9 2.1E-20 4.6E-25 170.5 17.1 159 264-473 1-159 (159)
79 TIGR02937 sigma70-ECF RNA poly 99.8 4.3E-20 9.2E-25 164.0 17.7 157 265-473 2-158 (158)
80 PRK12518 RNA polymerase sigma 99.8 3.1E-20 6.8E-25 172.4 17.1 162 264-477 11-172 (175)
81 PRK12520 RNA polymerase sigma 99.8 3.9E-20 8.4E-25 174.9 17.6 181 264-477 2-183 (191)
82 PRK12522 RNA polymerase sigma 99.8 7.4E-20 1.6E-24 170.2 18.6 167 264-475 3-169 (173)
83 PRK12516 RNA polymerase sigma 99.8 8.8E-20 1.9E-24 172.8 19.0 160 263-477 9-168 (187)
84 PRK09642 RNA polymerase sigma 99.8 3.9E-20 8.5E-25 169.5 16.1 157 271-477 2-158 (160)
85 PRK12535 RNA polymerase sigma 99.8 1.2E-19 2.6E-24 173.2 19.7 182 204-478 5-186 (196)
86 TIGR02983 SigE-fam_strep RNA p 99.8 1E-19 2.2E-24 166.9 17.5 157 262-475 4-160 (162)
87 TIGR02984 Sig-70_plancto1 RNA 99.8 2.3E-19 5E-24 168.0 20.1 179 262-473 5-188 (189)
88 PRK12547 RNA polymerase sigma 99.8 1.5E-19 3.3E-24 167.0 18.3 161 261-476 3-163 (164)
89 COG1595 RpoE DNA-directed RNA 99.8 3.2E-19 7E-24 167.6 19.9 169 257-476 8-178 (182)
90 PRK09644 RNA polymerase sigma 99.8 1.8E-19 3.9E-24 166.4 17.8 158 266-477 3-160 (165)
91 TIGR02947 SigH_actino RNA poly 99.8 1.1E-19 2.4E-24 172.0 16.6 172 263-476 10-182 (193)
92 PRK12523 RNA polymerase sigma 99.8 1.6E-19 3.5E-24 167.9 17.3 160 264-475 10-169 (172)
93 PRK12533 RNA polymerase sigma 99.8 2.1E-19 4.5E-24 174.5 18.7 171 261-476 15-185 (216)
94 PRK12529 RNA polymerase sigma 99.8 1.7E-19 3.6E-24 169.2 17.4 164 261-473 10-175 (178)
95 PRK09647 RNA polymerase sigma 99.8 6.1E-19 1.3E-23 169.4 18.5 165 262-477 26-190 (203)
96 PRK09639 RNA polymerase sigma 99.8 8.9E-19 1.9E-23 161.1 18.7 161 263-476 2-162 (166)
97 PRK12528 RNA polymerase sigma 99.8 7.9E-19 1.7E-23 161.2 17.5 157 264-472 4-160 (161)
98 PRK12541 RNA polymerase sigma 99.8 1.2E-18 2.5E-23 160.1 18.1 157 262-472 3-159 (161)
99 TIGR02943 Sig70_famx1 RNA poly 99.8 8.7E-19 1.9E-23 165.9 17.2 174 268-476 6-182 (188)
100 PRK08241 RNA polymerase factor 99.8 9.5E-19 2.1E-23 179.7 18.4 177 264-471 19-199 (339)
101 PRK12540 RNA polymerase sigma 99.8 1.4E-18 3E-23 163.9 18.1 160 264-478 5-164 (182)
102 PRK12532 RNA polymerase sigma 99.8 1.4E-18 3E-23 164.8 17.3 178 267-477 8-188 (195)
103 PRK12545 RNA polymerase sigma 99.8 1.4E-18 3.1E-23 166.1 17.4 178 268-477 12-191 (201)
104 PRK09637 RNA polymerase sigma 99.8 2.6E-18 5.6E-23 161.9 18.5 154 266-475 3-156 (181)
105 PRK12530 RNA polymerase sigma 99.8 1.7E-18 3.7E-23 163.9 17.4 176 268-477 11-186 (189)
106 PRK12544 RNA polymerase sigma 99.8 1.9E-18 4.1E-23 166.4 17.4 181 266-477 20-200 (206)
107 TIGR02950 SigM_subfam RNA poly 99.8 8.4E-19 1.8E-23 159.2 13.7 153 270-473 1-153 (154)
108 PRK12517 RNA polymerase sigma 99.8 4E-18 8.7E-23 161.5 18.9 160 261-476 20-179 (188)
109 PRK07037 extracytoplasmic-func 99.8 2.8E-18 6E-23 157.6 17.2 159 268-476 2-160 (163)
110 TIGR02960 SigX5 RNA polymerase 99.8 1.8E-18 3.9E-23 176.2 17.1 183 263-475 4-192 (324)
111 PRK09651 RNA polymerase sigma 99.8 5.7E-18 1.2E-22 157.8 18.6 161 263-475 9-169 (172)
112 PRK12527 RNA polymerase sigma 99.8 3.4E-18 7.5E-23 156.7 16.6 155 270-475 1-155 (159)
113 TIGR02959 SigZ RNA polymerase 99.8 4.2E-18 9.1E-23 158.5 16.9 149 271-475 2-150 (170)
114 PRK12546 RNA polymerase sigma 99.8 1.1E-17 2.3E-22 158.9 18.4 156 264-475 8-163 (188)
115 PRK12511 RNA polymerase sigma 99.8 1E-17 2.2E-22 158.1 17.6 159 265-477 5-163 (182)
116 TIGR02895 spore_sigI RNA polym 99.8 3.2E-17 6.9E-22 159.4 21.1 179 264-465 10-200 (218)
117 PRK12525 RNA polymerase sigma 99.8 5.3E-17 1.1E-21 150.6 19.6 159 264-474 9-167 (168)
118 PRK06704 RNA polymerase factor 99.7 2.7E-16 6E-21 154.0 18.2 151 262-475 16-166 (228)
119 PRK09047 RNA polymerase factor 99.7 2.8E-16 6E-21 143.6 14.8 156 286-477 2-158 (161)
120 PRK09636 RNA polymerase sigma 99.7 3.5E-16 7.5E-21 158.1 15.9 160 264-474 4-164 (293)
121 TIGR02957 SigX4 RNA polymerase 99.7 9.8E-16 2.1E-20 154.2 16.5 154 268-474 1-157 (281)
122 PRK09635 sigI RNA polymerase s 99.7 1.8E-15 3.9E-20 153.2 16.8 159 264-473 5-166 (290)
123 PRK09191 two-component respons 99.6 7.8E-15 1.7E-19 143.4 13.2 136 265-474 2-137 (261)
124 TIGR03209 P21_Cbot clostridium 99.6 3.7E-14 8.1E-19 127.7 13.1 136 266-459 1-141 (142)
125 PRK08311 putative RNA polymera 99.6 3.6E-13 7.9E-18 132.7 20.4 78 264-341 18-97 (237)
126 PF07638 Sigma70_ECF: ECF sigm 99.5 6.3E-13 1.4E-17 125.9 18.3 163 264-474 17-184 (185)
127 PF04542 Sigma70_r2: Sigma-70 99.3 1.6E-11 3.5E-16 96.8 7.8 70 269-338 1-70 (71)
128 PF04545 Sigma70_r4: Sigma-70, 99.2 6.5E-11 1.4E-15 88.7 7.2 50 418-471 1-50 (50)
129 PF08281 Sigma70_r4_2: Sigma-7 99.0 1.9E-09 4.2E-14 81.8 7.1 53 413-469 2-54 (54)
130 PRK06930 positive control sigm 98.7 6.9E-08 1.5E-12 90.8 9.8 72 401-476 94-165 (170)
131 PRK00118 putative DNA-binding 98.6 2.1E-07 4.6E-12 80.6 9.1 57 417-477 13-69 (104)
132 cd06171 Sigma70_r4 Sigma70, re 98.4 1E-06 2.2E-11 64.7 6.8 53 414-470 3-55 (55)
133 TIGR00721 tfx DNA-binding prot 98.3 2.4E-06 5.2E-11 77.6 7.9 58 421-482 5-62 (137)
134 PRK03975 tfx putative transcri 98.2 3.6E-06 7.7E-11 76.9 8.1 52 421-476 5-56 (141)
135 PRK04217 hypothetical protein; 98.2 2.1E-06 4.5E-11 75.2 6.2 58 421-481 41-98 (110)
136 PF04297 UPF0122: Putative hel 98.2 7.6E-06 1.6E-10 70.5 8.9 62 414-478 9-70 (101)
137 smart00421 HTH_LUXR helix_turn 97.9 2.6E-05 5.6E-10 58.3 6.1 46 421-470 2-47 (58)
138 PF00196 GerE: Bacterial regul 97.8 3.6E-05 7.8E-10 59.3 5.7 46 421-470 2-47 (58)
139 TIGR01636 phage_rinA phage tra 97.8 7.8E-05 1.7E-09 67.5 8.8 60 410-473 71-132 (134)
140 cd06170 LuxR_C_like C-terminal 97.8 5.4E-05 1.2E-09 56.7 6.0 45 423-471 1-45 (57)
141 PF07374 DUF1492: Protein of u 97.8 9.1E-05 2E-09 63.7 7.9 56 410-469 43-99 (100)
142 TIGR03879 near_KaiC_dom probab 97.7 7.1E-05 1.5E-09 60.8 5.7 47 415-464 9-55 (73)
143 PF04967 HTH_10: HTH DNA bindi 97.7 0.00012 2.6E-09 56.0 6.5 47 423-469 1-51 (53)
144 PRK15411 rcsA colanic acid cap 97.6 0.00011 2.4E-09 71.0 6.1 45 422-470 137-181 (207)
145 PRK11475 DNA-binding transcrip 97.6 0.00013 2.8E-09 70.7 6.3 46 421-470 133-178 (207)
146 PF00140 Sigma70_r1_2: Sigma-7 97.5 3.2E-05 6.9E-10 54.7 1.3 33 191-223 2-34 (37)
147 PRK15201 fimbriae regulatory p 97.5 0.00017 3.8E-09 67.9 6.4 47 421-471 132-178 (198)
148 PRK10840 transcriptional regul 97.5 0.00016 3.5E-09 69.1 6.1 46 421-470 149-194 (216)
149 TIGR01321 TrpR trp operon repr 97.5 0.0002 4.3E-09 61.0 5.6 49 414-462 24-76 (94)
150 PRK13719 conjugal transfer tra 97.5 0.00019 4.1E-09 69.8 6.1 50 416-470 138-187 (217)
151 COG2197 CitB Response regulato 97.5 0.00017 3.8E-09 69.9 5.9 45 422-470 148-192 (211)
152 PF13936 HTH_38: Helix-turn-he 97.4 0.0002 4.2E-09 52.5 4.0 41 421-464 3-43 (44)
153 COG4566 TtrR Response regulato 97.4 0.00069 1.5E-08 64.6 8.5 67 410-481 131-197 (202)
154 TIGR03541 reg_near_HchA LuxR f 97.4 0.00028 6.1E-09 69.3 6.1 47 421-471 170-216 (232)
155 TIGR03020 EpsA transcriptional 97.4 0.00034 7.4E-09 69.7 6.4 47 421-471 189-235 (247)
156 PRK10100 DNA-binding transcrip 97.4 0.00036 7.8E-09 68.0 6.4 47 421-471 154-200 (216)
157 PRK10188 DNA-binding transcrip 97.3 0.00043 9.3E-09 68.5 6.3 45 422-470 179-223 (240)
158 PF02001 DUF134: Protein of un 97.3 0.0006 1.3E-08 59.4 6.3 53 422-477 41-93 (106)
159 PRK13870 transcriptional regul 97.3 0.00046 9.9E-09 68.1 6.1 45 422-470 173-217 (234)
160 COG2771 CsgD DNA-binding HTH d 97.2 0.00094 2E-08 51.5 6.4 48 421-472 3-50 (65)
161 PRK09483 response regulator; P 97.1 0.00079 1.7E-08 63.1 6.1 46 421-470 147-192 (217)
162 COG4941 Predicted RNA polymera 97.1 0.012 2.6E-07 60.7 14.4 161 265-471 6-166 (415)
163 COG2739 Uncharacterized protei 97.1 0.003 6.5E-08 54.2 8.3 52 421-475 16-67 (105)
164 PRK15369 two component system 97.0 0.0013 2.9E-08 60.1 6.4 46 421-470 148-193 (211)
165 COG3413 Predicted DNA binding 96.9 0.002 4.4E-08 62.6 6.5 52 422-473 155-210 (215)
166 PRK10651 transcriptional regul 96.8 0.0021 4.6E-08 59.5 5.9 46 421-470 154-199 (216)
167 PF04539 Sigma70_r3: Sigma-70 96.7 0.0026 5.7E-08 51.5 4.9 42 349-390 2-44 (78)
168 PRK09390 fixJ response regulat 96.7 0.0045 9.7E-08 56.3 7.0 54 414-472 134-187 (202)
169 PRK15320 transcriptional activ 96.7 0.0032 6.9E-08 60.5 5.8 46 421-470 163-208 (251)
170 COG1342 Predicted DNA-binding 96.5 0.0058 1.3E-07 51.9 5.9 52 422-476 33-84 (99)
171 PRK01381 Trp operon repressor; 96.5 0.0027 5.9E-08 54.5 3.8 48 413-460 23-74 (99)
172 TIGR01637 phage_arpU phage tra 96.3 0.024 5.1E-07 50.8 9.1 58 414-474 71-130 (132)
173 COG1356 tfx Transcriptional re 96.3 0.0044 9.4E-08 55.2 4.1 50 422-475 8-57 (143)
174 PRK10403 transcriptional regul 96.3 0.0072 1.6E-07 55.8 5.9 47 421-471 152-198 (215)
175 PF12645 HTH_16: Helix-turn-he 96.2 0.021 4.4E-07 45.5 6.8 47 264-310 13-65 (65)
176 PRK10360 DNA-binding transcrip 96.2 0.012 2.5E-07 54.3 6.3 46 421-470 136-181 (196)
177 PRK09935 transcriptional regul 96.2 0.01 2.3E-07 54.9 6.0 45 422-470 149-193 (210)
178 PRK04841 transcriptional regul 96.1 0.0085 1.8E-07 69.2 6.4 45 422-470 838-882 (903)
179 PRK13558 bacterio-opsin activa 96.0 0.011 2.3E-07 66.3 6.3 53 421-473 606-662 (665)
180 PRK09958 DNA-binding transcrip 95.9 0.015 3.3E-07 53.8 6.1 46 421-470 142-187 (204)
181 PF13613 HTH_Tnp_4: Helix-turn 95.8 0.022 4.7E-07 43.3 5.2 50 422-473 2-51 (53)
182 PF13384 HTH_23: Homeodomain-l 95.7 0.0099 2.1E-07 44.0 3.0 33 429-465 9-41 (50)
183 PRK05658 RNA polymerase sigma 95.6 0.82 1.8E-05 51.5 19.0 34 190-223 103-136 (619)
184 PRK15418 transcriptional regul 95.6 0.016 3.6E-07 59.8 5.0 36 429-467 20-55 (318)
185 PF13412 HTH_24: Winged helix- 95.3 0.043 9.4E-07 40.3 5.3 41 423-465 1-41 (48)
186 TIGR02531 yecD_yerC TrpR-relat 95.3 0.037 8.1E-07 46.7 5.4 39 421-465 35-73 (88)
187 PF02796 HTH_7: Helix-turn-hel 95.2 0.03 6.5E-07 41.0 4.0 33 427-463 11-43 (45)
188 cd00569 HTH_Hin_like Helix-tur 94.9 0.051 1.1E-06 35.6 4.3 37 422-461 5-41 (42)
189 PF05263 DUF722: Protein of un 94.7 0.12 2.6E-06 46.7 7.3 56 412-469 72-127 (130)
190 PF06056 Terminase_5: Putative 94.3 0.085 1.8E-06 41.1 4.7 32 430-465 6-37 (58)
191 PF00325 Crp: Bacterial regula 94.2 0.055 1.2E-06 37.1 3.1 23 441-463 2-24 (32)
192 PF06530 Phage_antitermQ: Phag 94.2 0.31 6.6E-06 43.7 8.7 53 421-476 61-113 (125)
193 COG2909 MalT ATP-dependent tra 93.9 0.063 1.4E-06 61.3 4.6 44 423-470 832-875 (894)
194 PF01726 LexA_DNA_bind: LexA D 93.9 0.1 2.2E-06 41.5 4.6 43 421-463 2-48 (65)
195 PF13404 HTH_AsnC-type: AsnC-t 93.8 0.14 3.1E-06 37.1 4.8 40 423-464 1-40 (42)
196 PRK10430 DNA-binding transcrip 93.6 0.11 2.5E-06 50.4 5.4 46 422-467 158-204 (239)
197 PF04539 Sigma70_r3: Sigma-70 93.5 0.095 2.1E-06 42.3 3.9 37 224-260 6-42 (78)
198 PF13518 HTH_28: Helix-turn-he 93.5 0.12 2.5E-06 38.2 4.0 35 429-467 4-38 (52)
199 PF10668 Phage_terminase: Phag 93.4 0.12 2.7E-06 40.5 4.1 39 425-464 7-45 (60)
200 COG2390 DeoR Transcriptional r 93.4 0.099 2.1E-06 54.2 4.7 36 430-468 18-53 (321)
201 smart00351 PAX Paired Box doma 93.1 0.22 4.8E-06 44.4 5.9 42 422-466 17-58 (125)
202 PF09862 DUF2089: Protein of u 92.7 0.29 6.3E-06 43.2 5.9 48 421-471 32-79 (113)
203 PF12802 MarR_2: MarR family; 92.4 0.24 5.2E-06 37.8 4.6 44 422-465 2-45 (62)
204 PF04218 CENP-B_N: CENP-B N-te 92.2 0.15 3.3E-06 38.8 3.1 40 422-464 6-45 (53)
205 PF01022 HTH_5: Bacterial regu 92.0 0.4 8.6E-06 35.2 5.1 37 425-464 2-38 (47)
206 PF01371 Trp_repressor: Trp re 91.9 0.26 5.5E-06 41.6 4.4 46 421-467 25-74 (87)
207 PF12840 HTH_20: Helix-turn-he 91.7 0.64 1.4E-05 35.9 6.2 44 415-464 3-47 (61)
208 PF13730 HTH_36: Helix-turn-he 91.4 0.63 1.4E-05 34.9 5.8 42 422-463 2-47 (55)
209 PHA00675 hypothetical protein 91.2 0.41 8.9E-06 39.3 4.7 41 421-463 21-61 (78)
210 PHA02591 hypothetical protein; 91.2 0.26 5.6E-06 40.5 3.5 25 439-463 57-81 (83)
211 cd00131 PAX Paired Box domain 91.1 0.52 1.1E-05 42.4 5.9 42 422-466 17-58 (128)
212 PF13744 HTH_37: Helix-turn-he 90.5 0.47 1E-05 38.9 4.6 40 439-478 29-73 (80)
213 PF08279 HTH_11: HTH domain; 90.0 0.52 1.1E-05 35.4 4.1 38 426-464 1-38 (55)
214 PF13022 HTH_Tnp_1_2: Helix-tu 89.9 2 4.3E-05 39.4 8.5 62 421-482 9-77 (142)
215 smart00550 Zalpha Z-DNA-bindin 89.9 0.77 1.7E-05 36.6 5.3 38 427-464 8-45 (68)
216 PF01418 HTH_6: Helix-turn-hel 89.8 0.76 1.7E-05 37.4 5.3 52 412-464 4-57 (77)
217 PF01325 Fe_dep_repress: Iron 89.6 0.55 1.2E-05 36.6 4.2 41 423-463 2-44 (60)
218 COG3415 Transposase and inacti 89.4 0.63 1.4E-05 42.6 4.9 35 429-466 12-46 (138)
219 PF13542 HTH_Tnp_ISL3: Helix-t 89.2 0.9 1.9E-05 33.6 4.9 35 427-465 17-51 (52)
220 TIGR02395 rpoN_sigma RNA polym 89.0 10 0.00022 41.1 14.6 25 439-463 316-340 (429)
221 PRK11083 DNA-binding response 88.8 0.53 1.2E-05 43.9 4.3 50 422-471 154-208 (228)
222 PF00356 LacI: Bacterial regul 88.7 0.44 9.6E-06 35.3 2.9 35 443-477 1-42 (46)
223 PF01710 HTH_Tnp_IS630: Transp 88.6 4.4 9.4E-05 35.8 9.7 75 368-464 20-94 (119)
224 PRK11179 DNA-binding transcrip 88.5 0.84 1.8E-05 41.9 5.3 41 422-464 6-46 (153)
225 PF03444 HrcA_DNA-bdg: Winged 88.1 1 2.2E-05 37.2 4.9 41 423-463 2-45 (78)
226 PRK10046 dpiA two-component re 88.1 0.53 1.2E-05 45.3 3.9 40 421-463 160-199 (225)
227 PRK10336 DNA-binding transcrip 88.0 0.65 1.4E-05 43.2 4.3 49 422-470 149-202 (219)
228 PF02650 HTH_WhiA: WhiA C-term 87.9 1.6 3.4E-05 36.7 6.0 43 421-465 36-80 (85)
229 PRK09413 IS2 repressor TnpA; R 87.9 2.3 5E-05 37.6 7.4 35 428-465 19-53 (121)
230 TIGR01610 phage_O_Nterm phage 87.8 2.3 5E-05 36.1 7.1 43 421-463 21-69 (95)
231 PF01047 MarR: MarR family; I 87.6 0.94 2E-05 34.3 4.2 41 423-465 1-41 (59)
232 PRK05932 RNA polymerase factor 87.5 48 0.001 36.2 18.8 25 439-463 341-365 (455)
233 smart00344 HTH_ASNC helix_turn 87.4 1.3 2.8E-05 37.8 5.4 41 423-465 1-41 (108)
234 PRK11169 leucine-responsive tr 87.2 0.93 2E-05 42.2 4.7 41 422-464 11-51 (164)
235 PRK10710 DNA-binding transcrip 87.0 0.87 1.9E-05 43.0 4.6 50 422-471 160-214 (240)
236 COG2973 TrpR Trp operon repres 87.0 1.6 3.4E-05 37.6 5.5 48 409-459 27-78 (103)
237 PRK13413 mpi multiple promoter 86.9 1.1 2.4E-05 42.8 5.3 38 423-464 158-195 (200)
238 PHA02547 55 RNA polymerase sig 86.8 6.9 0.00015 37.0 10.1 63 274-336 47-112 (179)
239 PF13551 HTH_29: Winged helix- 86.2 5.8 0.00013 33.4 8.9 81 368-465 14-111 (112)
240 PF12728 HTH_17: Helix-turn-he 85.8 0.87 1.9E-05 33.7 3.1 24 442-465 2-25 (51)
241 PF13551 HTH_29: Winged helix- 85.4 1.5 3.3E-05 37.1 4.8 33 429-465 3-36 (112)
242 TIGR02154 PhoB phosphate regul 85.4 0.61 1.3E-05 43.4 2.5 49 422-470 154-207 (226)
243 cd04762 HTH_MerR-trunc Helix-T 85.3 0.87 1.9E-05 32.3 2.8 25 442-466 1-25 (49)
244 PRK15479 transcriptional regul 85.2 1.3 2.9E-05 41.0 4.8 49 422-470 148-201 (221)
245 TIGR03787 marine_sort_RR prote 85.2 1.2 2.6E-05 41.9 4.5 47 422-470 156-206 (227)
246 PF13463 HTH_27: Winged helix 85.1 1.6 3.5E-05 33.7 4.5 42 423-465 1-42 (68)
247 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 85.0 1.9 4.1E-05 32.7 4.5 39 422-463 4-42 (50)
248 COG2522 Predicted transcriptio 84.9 1.5 3.2E-05 39.1 4.6 24 440-463 21-44 (119)
249 COG1191 FliA DNA-directed RNA 84.9 29 0.00063 34.9 14.2 64 189-260 85-148 (247)
250 PF00046 Homeobox: Homeobox do 84.6 1.5 3.2E-05 33.0 3.9 50 422-471 6-57 (57)
251 PF08822 DUF1804: Protein of u 84.4 2 4.4E-05 40.4 5.4 42 424-467 4-45 (165)
252 TIGR01764 excise DNA binding d 83.7 1.3 2.8E-05 31.6 3.2 24 442-465 2-25 (49)
253 PF13011 LZ_Tnp_IS481: leucine 83.7 2.3 5E-05 35.8 4.9 44 421-466 7-50 (85)
254 COG1522 Lrp Transcriptional re 83.6 2.2 4.7E-05 38.6 5.3 43 421-465 4-46 (154)
255 PF01527 HTH_Tnp_1: Transposas 83.5 1.1 2.3E-05 35.7 2.8 35 429-466 14-48 (76)
256 CHL00148 orf27 Ycf27; Reviewed 83.3 1.4 3.1E-05 41.5 4.1 50 422-471 161-217 (240)
257 PRK07408 RNA polymerase sigma 83.2 2.7 5.7E-05 41.9 6.2 64 188-258 86-149 (256)
258 PRK12423 LexA repressor; Provi 83.1 2.1 4.6E-05 41.2 5.2 47 421-471 2-52 (202)
259 PF01978 TrmB: Sugar-specific 82.8 0.94 2E-05 35.6 2.2 40 422-463 5-44 (68)
260 PF01381 HTH_3: Helix-turn-hel 82.7 1.3 2.9E-05 32.9 2.9 26 439-464 7-32 (55)
261 PF08220 HTH_DeoR: DeoR-like h 82.4 1.8 3.9E-05 33.2 3.6 35 427-463 2-36 (57)
262 PRK09210 RNA polymerase sigma 82.4 11 0.00023 39.9 10.5 35 225-259 219-253 (367)
263 cd04761 HTH_MerR-SF Helix-Turn 82.3 1.1 2.3E-05 32.5 2.2 25 442-466 1-25 (49)
264 KOG0484 Transcription factor P 82.0 4.7 0.0001 35.2 6.2 53 420-475 26-78 (125)
265 PHA01976 helix-turn-helix prot 81.9 2.3 4.9E-05 33.0 4.1 26 439-464 13-38 (67)
266 PF02954 HTH_8: Bacterial regu 81.6 2.1 4.6E-05 30.7 3.5 39 424-464 3-41 (42)
267 TIGR02393 RpoD_Cterm RNA polym 81.2 15 0.00032 36.0 10.6 33 226-258 91-123 (238)
268 PRK14082 hypothetical protein; 80.9 5.4 0.00012 31.7 5.7 56 263-320 8-63 (65)
269 PRK05911 RNA polymerase sigma 80.8 21 0.00046 35.5 11.6 61 188-258 86-146 (257)
270 PHA00542 putative Cro-like pro 80.6 2.2 4.8E-05 35.2 3.8 26 439-464 29-54 (82)
271 COG0856 Orotate phosphoribosyl 80.4 2.1 4.6E-05 40.7 3.9 38 428-469 9-46 (203)
272 smart00420 HTH_DEOR helix_turn 80.2 3.6 7.9E-05 29.6 4.5 25 440-464 13-37 (53)
273 TIGR00122 birA_repr_reg BirA b 80.1 3.8 8.3E-05 32.2 4.9 33 429-464 4-36 (69)
274 TIGR03070 couple_hipB transcri 79.2 2.1 4.6E-05 31.6 3.0 25 440-464 14-38 (58)
275 PRK10072 putative transcriptio 79.2 2.6 5.7E-05 36.1 3.9 25 439-463 44-68 (96)
276 PRK05901 RNA polymerase sigma 79.1 30 0.00065 38.3 13.0 33 226-258 362-394 (509)
277 PF14493 HTH_40: Helix-turn-he 79.0 4.4 9.5E-05 33.9 5.2 30 439-468 11-40 (91)
278 smart00419 HTH_CRP helix_turn_ 78.9 2.9 6.4E-05 29.8 3.6 23 441-463 8-30 (48)
279 PF08535 KorB: KorB domain; I 78.8 1.9 4.1E-05 36.3 2.9 24 440-463 2-25 (93)
280 TIGR02844 spore_III_D sporulat 78.8 3.9 8.5E-05 33.9 4.7 37 425-464 6-42 (80)
281 cd00090 HTH_ARSR Arsenical Res 78.4 5 0.00011 30.5 5.0 37 425-464 7-43 (78)
282 COG5484 Uncharacterized conser 78.3 2.4 5.3E-05 42.4 3.9 26 439-464 17-42 (279)
283 PRK11302 DNA-binding transcrip 78.1 4.5 9.7E-05 40.4 5.9 62 412-474 4-71 (284)
284 PF09339 HTH_IclR: IclR helix- 78.0 2.3 5E-05 31.7 2.9 25 439-463 16-40 (52)
285 smart00345 HTH_GNTR helix_turn 77.9 3.5 7.5E-05 30.6 3.9 28 440-471 18-46 (60)
286 PF13560 HTH_31: Helix-turn-he 77.8 3 6.5E-05 32.3 3.6 25 439-463 12-36 (64)
287 smart00418 HTH_ARSR helix_turn 77.2 4.1 8.8E-05 30.2 4.1 26 439-464 8-33 (66)
288 PF08280 HTH_Mga: M protein tr 77.0 3.6 7.8E-05 31.7 3.7 37 426-464 6-42 (59)
289 PRK05949 RNA polymerase sigma 76.8 12 0.00026 38.9 8.7 35 224-258 180-214 (327)
290 TIGR01889 Staph_reg_Sar staphy 75.9 13 0.00028 32.1 7.3 43 422-464 22-66 (109)
291 PRK11337 DNA-binding transcrip 75.9 5.9 0.00013 39.9 6.1 65 410-475 14-84 (292)
292 PF13545 HTH_Crp_2: Crp-like h 75.8 3.1 6.8E-05 32.9 3.3 27 441-471 28-54 (76)
293 TIGR01884 cas_HTH CRISPR locus 75.7 5.5 0.00012 38.2 5.5 42 421-464 139-180 (203)
294 TIGR00498 lexA SOS regulatory 75.4 5.5 0.00012 37.9 5.4 44 421-464 2-49 (199)
295 PRK10870 transcriptional repre 75.3 14 0.00031 34.7 8.1 43 422-464 52-94 (176)
296 PF13411 MerR_1: MerR HTH fami 75.2 1.4 3.1E-05 34.3 1.1 25 442-466 1-25 (69)
297 cd00092 HTH_CRP helix_turn_hel 75.0 4.5 9.9E-05 30.9 3.9 25 440-464 24-48 (67)
298 PRK00215 LexA repressor; Valid 75.0 6.2 0.00014 37.7 5.7 42 423-464 2-47 (205)
299 PF08765 Mor: Mor transcriptio 74.9 6.3 0.00014 34.2 5.1 43 425-472 61-103 (108)
300 smart00342 HTH_ARAC helix_turn 74.9 22 0.00047 27.6 8.0 73 367-465 2-75 (84)
301 TIGR02337 HpaR homoprotocatech 74.7 6.4 0.00014 34.1 5.2 41 422-464 25-65 (118)
302 PRK07921 RNA polymerase sigma 74.6 25 0.00055 36.5 10.4 34 225-258 176-209 (324)
303 smart00354 HTH_LACI helix_turn 74.6 3.1 6.7E-05 33.1 2.9 36 442-477 1-43 (70)
304 COG2345 Predicted transcriptio 74.6 5.5 0.00012 39.2 5.2 26 439-464 23-48 (218)
305 cd06571 Bac_DnaA_C C-terminal 74.6 9.2 0.0002 32.0 5.9 31 440-470 43-74 (90)
306 COG1476 Predicted transcriptio 74.5 4.4 9.5E-05 32.7 3.7 25 439-463 12-36 (68)
307 COG3355 Predicted transcriptio 74.5 12 0.00026 33.8 6.9 51 413-469 16-66 (126)
308 TIGR03697 NtcA_cyano global ni 73.9 4.2 9E-05 37.7 4.1 27 441-471 143-169 (193)
309 cd01104 HTH_MlrA-CarA Helix-Tu 73.8 4.2 9E-05 31.6 3.5 23 442-464 1-23 (68)
310 PRK11512 DNA-binding transcrip 73.8 7.4 0.00016 35.1 5.5 41 422-464 37-77 (144)
311 PRK09954 putative kinase; Prov 73.5 6.2 0.00013 41.0 5.7 41 423-465 1-41 (362)
312 COG0568 RpoD DNA-directed RNA 73.4 12 0.00027 39.2 7.7 32 191-222 67-98 (342)
313 TIGR02612 mob_myst_A mobile my 73.4 9 0.00019 35.5 6.0 51 424-477 24-80 (150)
314 cd00086 homeodomain Homeodomai 73.2 7.4 0.00016 29.0 4.6 50 422-471 6-57 (59)
315 PRK09863 putative frv operon r 73.2 29 0.00064 38.7 11.2 104 365-471 16-122 (584)
316 smart00347 HTH_MARR helix_turn 72.9 8.3 0.00018 31.4 5.3 41 422-464 7-47 (101)
317 PF07750 GcrA: GcrA cell cycle 72.3 4.4 9.5E-05 38.0 3.8 35 427-464 7-42 (162)
318 PF13556 HTH_30: PucR C-termin 72.3 9 0.0002 29.4 4.9 42 430-474 4-45 (59)
319 PF00292 PAX: 'Paired box' dom 72.2 7.8 0.00017 34.9 5.1 38 423-464 18-56 (125)
320 PRK07598 RNA polymerase sigma 72.2 54 0.0012 35.4 12.4 26 440-465 277-302 (415)
321 TIGR02607 antidote_HigA addict 71.7 7.8 0.00017 30.8 4.7 25 439-463 16-40 (78)
322 PF01710 HTH_Tnp_IS630: Transp 71.1 5 0.00011 35.4 3.7 25 439-463 16-40 (119)
323 PRK15482 transcriptional regul 71.1 8.7 0.00019 38.6 5.9 61 413-474 5-71 (285)
324 cd07377 WHTH_GntR Winged helix 70.8 16 0.00035 27.5 6.1 26 442-471 26-51 (66)
325 PF07037 DUF1323: Putative tra 70.8 4.6 0.0001 36.0 3.3 23 442-464 1-23 (122)
326 PF12759 HTH_Tnp_IS1: InsA C-t 69.1 6.4 0.00014 29.3 3.2 38 423-464 7-44 (46)
327 PRK07500 rpoH2 RNA polymerase 69.1 86 0.0019 31.9 12.7 66 188-256 100-166 (289)
328 TIGR03830 CxxCG_CxxCG_HTH puta 69.1 13 0.00029 32.4 6.0 39 421-464 63-101 (127)
329 PRK11557 putative DNA-binding 69.0 7.6 0.00016 38.8 4.9 59 415-474 3-67 (278)
330 PF00376 MerR: MerR family reg 69.0 3.1 6.8E-05 29.5 1.5 24 443-466 1-24 (38)
331 PRK03573 transcriptional regul 68.9 11 0.00024 33.8 5.5 42 422-464 28-69 (144)
332 COG2944 Predicted transcriptio 68.9 15 0.00032 32.1 6.0 39 421-464 42-80 (104)
333 cd04764 HTH_MlrA-like_sg1 Heli 68.8 6.4 0.00014 30.7 3.5 23 442-464 1-23 (67)
334 COG1846 MarR Transcriptional r 68.7 9.3 0.0002 32.2 4.8 39 423-464 20-59 (126)
335 PRK06288 RNA polymerase sigma 68.4 88 0.0019 31.2 12.4 35 224-258 120-154 (268)
336 smart00346 HTH_ICLR helix_turn 68.3 13 0.00027 30.3 5.3 26 440-465 19-44 (91)
337 COG1510 Predicted transcriptio 68.2 5.2 0.00011 38.0 3.2 25 438-462 38-62 (177)
338 TIGR02147 Fsuc_second hypothet 68.2 56 0.0012 33.2 10.9 85 364-451 135-239 (271)
339 COG1737 RpiR Transcriptional r 67.9 11 0.00025 38.0 5.9 63 411-474 5-73 (281)
340 smart00422 HTH_MERR helix_turn 67.9 4.1 9E-05 31.7 2.2 25 442-466 1-25 (70)
341 cd01392 HTH_LacI Helix-turn-he 67.7 4.2 9.1E-05 29.8 2.1 32 446-477 2-40 (52)
342 PRK11564 stationary phase indu 66.4 14 0.0003 39.4 6.6 50 422-471 10-60 (426)
343 PRK09863 putative frv operon r 66.4 12 0.00025 41.9 6.2 46 423-471 2-47 (584)
344 smart00389 HOX Homeodomain. DN 66.3 8.7 0.00019 28.4 3.6 47 422-468 6-54 (56)
345 PRK10141 DNA-binding transcrip 66.1 12 0.00026 33.2 5.0 41 421-463 11-52 (117)
346 COG1318 Predicted transcriptio 66.0 6.2 0.00013 37.4 3.3 27 439-465 59-85 (182)
347 smart00352 POU Found in Pit-Oc 65.7 10 0.00022 31.2 4.1 33 429-464 15-53 (75)
348 PRK09726 antitoxin HipB; Provi 65.4 9 0.0002 31.8 3.9 38 440-477 24-65 (88)
349 PF00165 HTH_AraC: Bacterial r 65.2 10 0.00023 26.7 3.7 27 439-465 6-32 (42)
350 PRK10161 transcriptional regul 64.8 6.9 0.00015 36.8 3.5 50 422-471 154-208 (229)
351 COG1508 RpoN DNA-directed RNA 64.7 1.9E+02 0.004 31.7 14.5 24 440-463 329-352 (444)
352 PRK10955 DNA-binding transcrip 64.5 4.7 0.0001 37.7 2.3 45 422-470 156-209 (232)
353 PF12116 SpoIIID: Stage III sp 64.5 14 0.00031 30.7 4.7 35 440-474 18-52 (82)
354 PF00440 TetR_N: Bacterial reg 64.4 8.4 0.00018 28.0 3.1 24 439-462 14-37 (47)
355 PF13443 HTH_26: Cro/C1-type H 64.2 6.8 0.00015 29.9 2.8 26 440-465 9-34 (63)
356 TIGR00180 parB_part ParB-like 64.1 12 0.00026 35.4 5.0 43 421-464 101-143 (187)
357 PHA00738 putative HTH transcri 63.9 13 0.00029 32.6 4.7 38 424-463 11-48 (108)
358 TIGR02997 Sig70-cyanoRpoD RNA 63.6 97 0.0021 31.5 11.8 33 226-258 165-197 (298)
359 cd04763 HTH_MlrA-like Helix-Tu 63.4 9.2 0.0002 29.9 3.4 23 442-464 1-23 (68)
360 PRK10411 DNA-binding transcrip 63.2 13 0.00027 36.9 5.1 42 424-467 3-44 (240)
361 PRK12427 flagellar biosynthesi 62.8 29 0.00063 34.0 7.6 61 189-259 78-138 (231)
362 PF00392 GntR: Bacterial regul 62.8 20 0.00043 27.7 5.2 27 440-470 22-49 (64)
363 PRK11753 DNA-binding transcrip 62.7 9.6 0.00021 35.8 4.1 27 441-471 168-194 (211)
364 PF05043 Mga: Mga helix-turn-h 62.6 17 0.00036 29.8 5.0 32 439-470 28-59 (87)
365 PRK11161 fumarate/nitrate redu 62.4 9.2 0.0002 36.8 3.9 27 441-471 184-210 (235)
366 PRK13918 CRP/FNR family transc 62.1 8.3 0.00018 36.1 3.5 27 441-471 149-175 (202)
367 smart00530 HTH_XRE Helix-turn- 62.1 9.8 0.00021 26.3 3.1 25 440-464 9-33 (56)
368 PRK14101 bifunctional glucokin 61.6 16 0.00034 41.3 6.2 66 409-475 341-412 (638)
369 TIGR02787 codY_Gpos GTP-sensin 61.5 28 0.00061 34.9 7.1 54 413-471 168-224 (251)
370 PRK03902 manganese transport t 61.4 15 0.00033 33.1 4.9 25 440-464 21-45 (142)
371 PRK09706 transcriptional repre 61.4 11 0.00024 33.7 4.0 26 439-464 16-41 (135)
372 PRK07405 RNA polymerase sigma 61.1 71 0.0015 33.0 10.4 35 224-258 170-204 (317)
373 PRK07122 RNA polymerase sigma 61.1 32 0.0007 34.4 7.7 64 188-258 100-163 (264)
374 PF07900 DUF1670: Protein of u 61.1 93 0.002 30.7 10.5 93 362-472 101-193 (220)
375 PRK00423 tfb transcription ini 61.1 2E+02 0.0044 29.5 18.2 31 439-469 274-304 (310)
376 TIGR00647 MG103 conserved hypo 60.9 18 0.00038 37.1 5.7 43 421-465 226-274 (279)
377 COG2826 Tra8 Transposase and i 60.6 10 0.00022 39.1 3.9 43 421-466 6-48 (318)
378 PRK01905 DNA-binding protein F 60.6 33 0.00071 27.9 6.3 36 427-464 38-73 (77)
379 COG2512 Predicted membrane-ass 59.7 12 0.00026 37.7 4.3 43 421-464 191-233 (258)
380 COG1654 BirA Biotin operon rep 59.2 28 0.0006 28.9 5.6 29 439-471 17-45 (79)
381 PF04703 FaeA: FaeA-like prote 59.2 9.8 0.00021 30.1 2.8 25 440-464 14-38 (62)
382 PF12844 HTH_19: Helix-turn-he 59.1 13 0.00029 28.3 3.6 26 439-464 10-35 (64)
383 COG3093 VapI Plasmid maintenan 58.9 14 0.00031 32.2 4.0 35 429-464 12-46 (104)
384 PRK09391 fixK transcriptional 58.9 12 0.00026 36.4 4.0 27 441-471 179-205 (230)
385 PRK13777 transcriptional regul 58.8 20 0.00043 34.3 5.5 40 422-463 42-81 (185)
386 cd00093 HTH_XRE Helix-turn-hel 58.5 17 0.00037 25.3 3.9 25 440-464 11-35 (58)
387 PF02082 Rrf2: Transcriptional 58.2 17 0.00037 29.7 4.3 24 441-464 25-48 (83)
388 PF04492 Phage_rep_O: Bacterio 58.0 39 0.00084 29.2 6.6 43 421-463 28-76 (100)
389 PF10654 DUF2481: Protein of u 57.8 31 0.00066 30.7 5.8 41 429-473 72-112 (126)
390 PF05225 HTH_psq: helix-turn-h 57.8 25 0.00055 25.7 4.6 23 442-464 17-39 (45)
391 PRK09744 DNA-binding transcrip 57.6 14 0.0003 30.3 3.5 20 443-462 12-31 (75)
392 PRK03837 transcriptional regul 57.1 24 0.00052 34.2 5.9 39 427-470 23-62 (241)
393 PF08784 RPA_C: Replication pr 56.8 17 0.00036 30.9 4.2 42 422-463 44-87 (102)
394 TIGR01387 cztR_silR_copR heavy 56.6 16 0.00034 33.6 4.3 49 422-470 147-200 (218)
395 PRK07406 RNA polymerase sigma 55.6 2.1E+02 0.0045 30.5 12.9 59 402-463 188-261 (373)
396 PRK10643 DNA-binding transcrip 55.2 12 0.00026 34.5 3.3 47 422-470 149-202 (222)
397 PF14549 P22_Cro: DNA-binding 55.1 17 0.00037 28.5 3.5 19 443-461 11-29 (60)
398 PRK13509 transcriptional repre 54.9 22 0.00047 35.4 5.2 38 425-464 5-42 (251)
399 PF14502 HTH_41: Helix-turn-he 54.8 19 0.00042 27.1 3.6 27 441-471 6-32 (48)
400 PRK07670 RNA polymerase sigma 54.5 1.2E+02 0.0026 29.9 10.4 35 226-260 113-147 (251)
401 PRK10434 srlR DNA-bindng trans 54.4 17 0.00037 36.3 4.4 38 425-464 5-42 (256)
402 TIGR03338 phnR_burk phosphonat 54.4 30 0.00065 32.9 6.0 40 427-471 21-60 (212)
403 PRK06424 transcription factor; 54.4 16 0.00036 33.6 3.9 25 439-463 95-119 (144)
404 smart00342 HTH_ARAC helix_turn 54.2 32 0.00069 26.6 5.2 25 442-466 2-26 (84)
405 COG4367 Uncharacterized protei 54.1 26 0.00055 29.8 4.6 42 422-463 2-45 (97)
406 PF04552 Sigma54_DBD: Sigma-54 53.9 4.3 9.3E-05 38.0 0.0 42 421-463 30-71 (160)
407 COG3877 Uncharacterized protei 53.6 28 0.00061 30.5 4.9 46 421-469 40-85 (122)
408 PRK13890 conjugal transfer pro 53.5 18 0.00039 32.1 3.9 26 439-464 16-41 (120)
409 PRK09464 pdhR transcriptional 53.4 35 0.00077 33.5 6.4 40 427-471 20-60 (254)
410 cd04768 HTH_BmrR-like Helix-Tu 53.1 10 0.00022 32.1 2.2 25 442-466 1-25 (96)
411 smart00862 Trans_reg_C Transcr 52.6 46 0.001 25.9 5.9 50 422-471 5-60 (78)
412 PRK10219 DNA-binding transcrip 52.6 47 0.001 28.1 6.3 27 439-465 19-45 (107)
413 cd04775 HTH_Cfa-like Helix-Tur 52.5 10 0.00022 32.4 2.2 26 442-467 2-27 (102)
414 PF14394 DUF4423: Domain of un 52.5 28 0.00061 32.8 5.3 98 364-475 37-154 (171)
415 COG2963 Transposase and inacti 52.1 29 0.00064 29.9 5.0 44 421-467 6-51 (116)
416 PF04967 HTH_10: HTH DNA bindi 52.1 57 0.0012 24.9 5.9 48 206-263 1-48 (53)
417 PF13309 HTH_22: HTH domain 51.8 13 0.00029 29.2 2.5 21 442-462 43-63 (64)
418 PRK10421 DNA-binding transcrip 51.8 39 0.00084 33.3 6.4 40 427-471 12-52 (253)
419 cd04773 HTH_TioE_rpt2 Second H 51.8 11 0.00023 32.7 2.2 25 442-466 1-25 (108)
420 PRK11050 manganese transport r 51.8 45 0.00098 30.6 6.4 25 440-464 50-74 (152)
421 cd01105 HTH_GlnR-like Helix-Tu 51.8 12 0.00025 31.2 2.3 25 442-466 2-26 (88)
422 PF04814 HNF-1_N: Hepatocyte n 51.5 10 0.00022 36.2 2.2 56 409-467 102-157 (180)
423 COG1349 GlpR Transcriptional r 51.3 18 0.00039 36.1 4.0 37 424-463 4-41 (253)
424 PF12298 Bot1p: Eukaryotic mit 51.2 37 0.00079 32.3 5.8 40 422-463 16-55 (172)
425 PRK06266 transcription initiat 51.2 41 0.00088 32.0 6.2 49 412-464 11-59 (178)
426 PF08006 DUF1700: Protein of u 51.2 38 0.00082 31.8 6.0 56 408-464 3-63 (181)
427 PRK09392 ftrB transcriptional 51.1 17 0.00037 35.0 3.7 23 441-463 173-195 (236)
428 COG1321 TroR Mn-dependent tran 51.1 25 0.00055 32.6 4.7 25 439-463 22-46 (154)
429 PRK10225 DNA-binding transcrip 51.0 41 0.00089 33.1 6.5 40 427-471 19-59 (257)
430 PRK10906 DNA-binding transcrip 50.2 22 0.00049 35.4 4.5 38 425-464 5-42 (252)
431 COG2411 Uncharacterized conser 50.0 69 0.0015 30.6 7.2 65 402-471 118-184 (188)
432 PRK04984 fatty acid metabolism 50.0 43 0.00093 32.5 6.4 39 428-471 18-57 (239)
433 cd00592 HTH_MerR-like Helix-Tu 49.8 13 0.00027 31.3 2.2 25 442-466 1-25 (100)
434 PRK11517 transcriptional regul 49.7 28 0.00062 32.2 4.9 49 422-470 147-200 (223)
435 PRK09943 DNA-binding transcrip 49.7 22 0.00047 33.5 4.1 36 439-474 18-57 (185)
436 PRK06030 hypothetical protein; 49.6 53 0.0011 29.5 6.3 39 425-466 56-94 (124)
437 TIGR00637 ModE_repress ModE mo 49.4 45 0.00099 28.5 5.7 40 424-467 3-42 (99)
438 cd04766 HTH_HspR Helix-Turn-He 49.3 12 0.00027 31.1 2.1 25 442-466 2-26 (91)
439 PRK09480 slmA division inhibit 49.2 1.7E+02 0.0037 26.7 10.0 71 236-306 28-98 (194)
440 PF06322 Phage_NinH: Phage Nin 49.1 26 0.00056 27.8 3.6 27 430-462 11-37 (64)
441 PF06413 Neugrin: Neugrin; In 49.1 26 0.00057 34.7 4.6 43 421-463 9-51 (225)
442 PRK00135 scpB segregation and 49.0 2.2E+02 0.0047 27.4 10.8 92 363-456 16-119 (188)
443 PRK09990 DNA-binding transcrip 49.0 46 0.00099 32.6 6.4 40 427-471 17-57 (251)
444 PF05732 RepL: Firmicute plasm 48.9 46 0.00099 31.3 6.0 50 417-471 48-101 (165)
445 PHA02535 P terminase ATPase su 48.8 20 0.00043 40.3 4.2 33 428-464 9-41 (581)
446 TIGR02698 CopY_TcrY copper tra 48.7 45 0.00098 29.9 5.8 44 422-467 1-48 (130)
447 TIGR00373 conserved hypothetic 48.6 54 0.0012 30.5 6.5 40 423-464 12-51 (158)
448 cd01106 HTH_TipAL-Mta Helix-Tu 48.6 13 0.00029 31.6 2.2 25 442-466 1-25 (103)
449 PRK11414 colanic acid/biofilm 48.6 42 0.00092 32.2 6.0 39 428-471 22-60 (221)
450 cd01107 HTH_BmrR Helix-Turn-He 48.6 14 0.00029 32.0 2.3 26 442-467 1-26 (108)
451 PF04645 DUF603: Protein of un 48.5 23 0.0005 33.6 3.9 25 439-463 16-41 (181)
452 cd04789 HTH_Cfa Helix-Turn-Hel 48.2 14 0.00029 31.7 2.2 25 442-466 2-26 (102)
453 COG4709 Predicted membrane pro 47.9 45 0.00097 32.2 5.8 57 408-465 3-64 (195)
454 cd04782 HTH_BltR Helix-Turn-He 47.7 14 0.0003 31.3 2.2 25 442-466 1-25 (97)
455 cd04772 HTH_TioE_rpt1 First He 47.6 14 0.00031 31.4 2.3 25 442-466 1-25 (99)
456 cd04774 HTH_YfmP Helix-Turn-He 47.6 14 0.0003 31.4 2.2 25 442-466 1-25 (96)
457 PRK11511 DNA-binding transcrip 47.4 39 0.00085 29.9 5.2 27 439-465 23-49 (127)
458 PF02042 RWP-RK: RWP-RK domain 47.2 43 0.00094 25.6 4.5 22 441-462 15-36 (52)
459 COG2524 Predicted transcriptio 47.1 28 0.0006 35.3 4.4 42 422-463 3-47 (294)
460 TIGR00738 rrf2_super rrf2 fami 47.0 36 0.00078 29.8 4.9 24 441-464 25-48 (132)
461 cd00383 trans_reg_C Effector d 47.0 41 0.00088 27.4 4.9 49 422-470 23-76 (95)
462 cd04780 HTH_MerR-like_sg5 Heli 46.9 15 0.00032 31.2 2.2 25 442-466 1-25 (95)
463 TIGR00270 conserved hypothetic 46.9 26 0.00056 32.6 4.0 26 439-464 80-105 (154)
464 cd01109 HTH_YyaN Helix-Turn-He 46.9 15 0.00032 31.9 2.3 26 442-467 1-26 (113)
465 cd04788 HTH_NolA-AlbR Helix-Tu 46.8 14 0.00031 31.1 2.2 25 442-466 1-25 (96)
466 PF05331 DUF742: Protein of un 46.8 29 0.00064 30.8 4.1 39 421-463 39-77 (114)
467 TIGR02325 C_P_lyase_phnF phosp 46.8 56 0.0012 31.6 6.6 26 442-471 33-58 (238)
468 PF11662 DUF3263: Protein of u 46.7 71 0.0015 26.4 6.0 46 422-467 2-48 (77)
469 PF04963 Sigma54_CBD: Sigma-54 46.5 7.1 0.00015 37.5 0.2 88 366-463 52-141 (194)
470 COG1497 Predicted transcriptio 46.4 42 0.00092 33.7 5.5 38 424-464 11-48 (260)
471 TIGR02850 spore_sigG RNA polym 46.3 25 0.00053 34.9 4.0 63 189-259 95-157 (254)
472 cd04765 HTH_MlrA-like_sg2 Heli 46.2 24 0.00053 30.1 3.5 23 442-464 1-23 (99)
473 cd01282 HTH_MerR-like_sg3 Heli 46.1 15 0.00033 31.9 2.3 26 442-467 1-26 (112)
474 PRK11534 DNA-binding transcrip 46.0 61 0.0013 31.1 6.7 40 427-471 17-56 (224)
475 PF05930 Phage_AlpA: Prophage 45.9 25 0.00054 26.2 3.1 24 442-465 4-27 (51)
476 PRK11886 bifunctional biotin-- 45.4 35 0.00076 35.0 5.1 39 426-466 5-43 (319)
477 TIGR02944 suf_reg_Xantho FeS a 45.3 41 0.00088 29.7 4.9 26 439-464 23-48 (130)
478 PF05584 Sulfolobus_pRN: Sulfo 45.2 58 0.0013 26.6 5.2 41 421-465 2-42 (72)
479 PF07022 Phage_CI_repr: Bacter 45.1 10 0.00022 29.9 0.9 23 442-464 13-36 (66)
480 PF00126 HTH_1: Bacterial regu 45.0 44 0.00095 25.5 4.4 24 442-465 14-37 (60)
481 cd01279 HTH_HspR-like Helix-Tu 44.8 16 0.00034 31.1 2.1 24 442-465 2-25 (98)
482 PRK00430 fis global DNA-bindin 44.4 33 0.00071 29.3 4.0 36 427-464 56-91 (95)
483 PRK08359 transcription factor; 44.1 29 0.00063 33.1 3.9 25 439-463 96-120 (176)
484 PRK11523 DNA-binding transcrip 44.1 61 0.0013 31.8 6.5 40 427-471 18-58 (253)
485 cd04769 HTH_MerR2 Helix-Turn-H 43.9 17 0.00037 31.7 2.2 26 442-467 1-26 (116)
486 PF02787 CPSase_L_D3: Carbamoy 43.8 1.5E+02 0.0033 26.4 8.3 25 440-464 71-95 (123)
487 TIGR02684 dnstrm_HI1420 probab 43.7 62 0.0013 27.3 5.5 33 440-474 44-80 (89)
488 PF01726 LexA_DNA_bind: LexA D 43.4 82 0.0018 24.9 5.8 31 359-389 18-49 (65)
489 PRK13705 plasmid-partitioning 43.2 32 0.00069 36.6 4.6 54 412-466 4-64 (388)
490 TIGR00635 ruvB Holliday juncti 43.2 1E+02 0.0022 31.0 8.0 43 421-463 234-277 (305)
491 PRK10681 DNA-binding transcrip 43.2 43 0.00093 33.3 5.2 38 425-464 7-44 (252)
492 TIGR02395 rpoN_sigma RNA polym 43.1 2.2E+02 0.0049 30.8 11.0 83 365-461 317-416 (429)
493 cd01108 HTH_CueR Helix-Turn-He 43.1 17 0.00038 32.3 2.2 26 442-467 1-26 (127)
494 cd01111 HTH_MerD Helix-Turn-He 43.1 18 0.00039 31.4 2.2 26 442-467 1-26 (107)
495 cd04783 HTH_MerR1 Helix-Turn-H 42.9 18 0.00038 32.1 2.2 26 442-467 1-26 (126)
496 PRK10402 DNA-binding transcrip 42.9 24 0.00052 34.0 3.3 27 441-471 169-195 (226)
497 TIGR02404 trehalos_R_Bsub treh 42.8 63 0.0014 31.3 6.3 40 428-471 11-50 (233)
498 TIGR02044 CueR Cu(I)-responsiv 42.8 18 0.00038 32.2 2.2 26 442-467 1-26 (127)
499 PRK04424 fatty acid biosynthes 42.8 36 0.00078 32.4 4.4 37 425-463 7-43 (185)
500 PRK10086 DNA-binding transcrip 42.4 78 0.0017 31.8 7.1 47 413-464 5-51 (311)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=1.4e-51 Score=430.43 Aligned_cols=290 Identities=36% Similarity=0.637 Sum_probs=264.2
Q ss_pred hhHHHHHHhhccccCCCHHHHHHHHHHHHcCCc--------------------chhHHHHHHhhhCCCCchHHHHHHhh-
Q 011454 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS--------------------LDDHKLRLKERLGCEPSMEQLAASLR- 249 (485)
Q Consensus 191 ~~~~~yl~~i~~~~~Lt~eee~~L~~~ik~Gd~--------------------l~~~~~~l~~~~g~~p~~~~~a~~~~- 249 (485)
|.++.||++|++.|+||++||++|+++++.+-. |+..+.+|++.+|++|+..+||.++|
T Consensus 60 d~v~~yl~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~~~~~ 139 (415)
T PRK07598 60 DLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTADI 139 (415)
T ss_pred ChHHHHHHhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHHHhCC
Confidence 688999999999999999999999999999988 88899999999999999999995555
Q ss_pred ---------------------cChhHHHHhhhhhHHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhc
Q 011454 250 ---------------------ISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEK 308 (485)
Q Consensus 250 ---------------------~s~~~L~~~l~~~~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiek 308 (485)
++.++|++.+..|..|+++||..|+++|+++|++|.+++.+++||+|||++|||+|+++
T Consensus 140 ~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~ravek 219 (415)
T PRK07598 140 SLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEK 219 (415)
T ss_pred cHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHH
Confidence 55566666667888999999999999999999999999999999999999999999999
Q ss_pred CCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHH
Q 011454 309 FDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNAT 387 (485)
Q Consensus 309 FDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~~~kirka~~~L~-~~gr~ps~eEIae~L~is~eev~~~l 387 (485)
|||.+|++|+||++||||++|.+++.++.+++++|.++.+.+++++++...+. .+|+.|+.++||+.+|++++++++++
T Consensus 220 FDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l 299 (415)
T PRK07598 220 FDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVL 299 (415)
T ss_pred cCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999998884 78999999999999999999999987
Q ss_pred HHH-------------------HhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcc-CCCCCCHHHH
Q 011454 388 EVL-------------------AYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDI 447 (485)
Q Consensus 388 ~~~-------------------~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp~rER~VI~LryGL-~~eg~S~eEI 447 (485)
... +++++. ...|++.+....+...|..+| +.|||+||.||.|+||| +++++|++||
T Consensus 300 ~~~~~~~SLd~~vg~~~d~~l~d~l~~~--~~~pee~~~~~~l~~~L~~~L-~~L~~reR~VI~LRygl~d~~~~Tl~EI 376 (415)
T PRK07598 300 LRVPRSVSLETKVGKDKDTELGDLLETD--DISPEEMLMRESLQRDLQHLL-ADLTSRERDVIRMRFGLADGHTYSLAEI 376 (415)
T ss_pred HHccCCcccccccCCCccccHHHhccCC--CCCHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHhcCCCCCCCHHHH
Confidence 653 122211 235667777778888999999 89999999999999998 4578999999
Q ss_pred HHHHCCCHHHHHHHHHHHHHHHHHHHHhhhHHHhhh
Q 011454 448 SKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV 483 (485)
Q Consensus 448 Ae~LgIS~~tVrqi~~rALkKLRk~L~~~~l~~~l~ 483 (485)
|+.||||+++|++++++|+++||+.-....++.|+.
T Consensus 377 A~~LGvS~erVRqie~rAl~KLR~~~~~~~l~~y~~ 412 (415)
T PRK07598 377 GRALDLSRERVRQIESKALQKLRQPKRRNRIRDYLE 412 (415)
T ss_pred HHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHHH
Confidence 999999999999999999999999988889999985
No 2
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=1.8e-50 Score=419.13 Aligned_cols=289 Identities=37% Similarity=0.622 Sum_probs=268.9
Q ss_pred hhHHHHHHhhccccCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHHH
Q 011454 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (485)
Q Consensus 191 ~~~~~yl~~i~~~~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~Li 270 (485)
+.+..||++|+++|+||++||.+|+++++.|..++..+.+|.+..|++|+..+||..+|++..+|++++..+..|++.||
T Consensus 63 d~l~~Yl~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Li 142 (373)
T PRK07406 63 DSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMV 142 (373)
T ss_pred CHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHHHH
Confidence 57889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHHH
Q 011454 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 350 (485)
Q Consensus 271 e~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~~ 350 (485)
..|+++|+++|++|.+++.+++||+|||++|||+++++|||.+|++|+|||+||||++|.++|+++++.+++|.++...+
T Consensus 143 ~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~~~~ 222 (373)
T PRK07406 143 QSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETI 222 (373)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHH-------------------HhhhcccCCCCCcchHHHHH
Q 011454 351 GLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEVL-------------------AYIADNRVENNPWHGVDDWA 410 (485)
Q Consensus 351 ~kirka~~~L~-~~gr~ps~eEIae~L~is~eev~~~l~~~-------------------~~l~D~~~e~~pee~~e~~e 410 (485)
++++++...+. .+|+.|+.++||+.+|++.++|..++... +++++. ..+|++.+....
T Consensus 223 ~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d~l~d~--~~~pee~~~~~~ 300 (373)
T PRK07406 223 SRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEAD--GETPEDDVAKNL 300 (373)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHHhcCCC--CCCHHHHHHHHH
Confidence 99999998885 68999999999999999999999875542 112221 235677777788
Q ss_pred HHHHHHHHHHhhCCHHHHHHHhhHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhhHHHhh
Q 011454 411 LKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAML 482 (485)
Q Consensus 411 l~e~L~~~L~~~Lp~rER~VI~LryGL~-~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~l~~~l 482 (485)
+...|..+| +.||++||.||.++||++ .+++|++|||+.||||+++|+|++.+|++|||+......+..|+
T Consensus 301 ~~~~L~~aL-~~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~~~~~~~l~~~~ 372 (373)
T PRK07406 301 LREDLEGVL-ATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 372 (373)
T ss_pred HHHHHHHHH-HcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHh
Confidence 888999999 899999999999999984 57899999999999999999999999999999999998998886
No 3
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00 E-value=1.4e-49 Score=407.28 Aligned_cols=288 Identities=33% Similarity=0.612 Sum_probs=265.9
Q ss_pred hhHHHHHHhhccccCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHHH
Q 011454 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (485)
Q Consensus 191 ~~~~~yl~~i~~~~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~Li 270 (485)
+.+..||++|+++|+||++||++|+++++.|-.+++.+..|...+|++|+..+||..++++..+|+..+..+..|++.||
T Consensus 18 d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~~Li 97 (327)
T PRK05949 18 DMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQKMI 97 (327)
T ss_pred CHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHHHHH
Confidence 67889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHHH
Q 011454 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 350 (485)
Q Consensus 271 e~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~~ 350 (485)
+.|+++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+|||+||||++|.++|.++++++|+|.++...+
T Consensus 98 ~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~~~~~ 177 (327)
T PRK05949 98 EANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEKL 177 (327)
T ss_pred HHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHH-HHcCCCCCHHHHHHHhCCCHHHHHHHHHHH-------------------HhhhcccCCCCCcchHHHHH
Q 011454 351 GLIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEVL-------------------AYIADNRVENNPWHGVDDWA 410 (485)
Q Consensus 351 ~kirka~~~L-~~~gr~ps~eEIae~L~is~eev~~~l~~~-------------------~~l~D~~~e~~pee~~e~~e 410 (485)
++++++...+ .++|++|+.++||+.+|+++++|..++... +.++|. ..+|++.++...
T Consensus 178 ~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~--~~~pe~~~~~~~ 255 (327)
T PRK05949 178 NKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDE--GPSPDQYITQEL 255 (327)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCC--CCCHHHHHHHHH
Confidence 9999998888 578999999999999999999999885432 122222 245777777888
Q ss_pred HHHHHHHHHHhhCCHHHHHHHhhHhcc-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhhHHHhhh
Q 011454 411 LKDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV 483 (485)
Q Consensus 411 l~e~L~~~L~~~Lp~rER~VI~LryGL-~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~l~~~l~ 483 (485)
....|.++| +.|||+||.||.++||| +++++|++|||+.||||+++|++++.+|+++||+. ...+..|+.
T Consensus 256 ~~~~L~~~L-~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~~--~~~l~~~~~ 326 (327)
T PRK05949 256 LRQDLNNLL-AELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRRR--RANVKEYLA 326 (327)
T ss_pred HHHHHHHHH-HhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence 888999999 89999999999999998 46899999999999999999999999999999994 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=2.3e-49 Score=400.88 Aligned_cols=276 Identities=39% Similarity=0.675 Sum_probs=256.5
Q ss_pred hHHHHHHhhccccCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHHHH
Q 011454 192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM 271 (485)
Q Consensus 192 ~~~~yl~~i~~~~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~Lie 271 (485)
.+..||++|+.+|+||++||.+|+++++.|-.+++.+.+|.+..|++|+..+||.++|++..+|...+..|..|++.||.
T Consensus 2 ~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv~ 81 (298)
T TIGR02997 2 LVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMIK 81 (298)
T ss_pred cHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHHH
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHHHH
Q 011454 272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG 351 (485)
Q Consensus 272 ~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~~~ 351 (485)
.|+++|+++|++|.+++.+++||+||||+|||+|+++|||.+|++|+||++||||+.|.+++.++++.+++|.+....++
T Consensus 82 ~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~~~~~~~~ 161 (298)
T TIGR02997 82 ANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLN 161 (298)
T ss_pred HhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHH-HHcCCCCCHHHHHHHhCCCHHHHHHHHHHH-------------------HhhhcccCCCCCcchHHHHHH
Q 011454 352 LIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEVL-------------------AYIADNRVENNPWHGVDDWAL 411 (485)
Q Consensus 352 kirka~~~L-~~~gr~ps~eEIae~L~is~eev~~~l~~~-------------------~~l~D~~~e~~pee~~e~~el 411 (485)
++++....+ ...|+.|+.+++++.+|++.++|..++... +.+++ ...+|++.++..+.
T Consensus 162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~--~~~~pe~~~~~~~~ 239 (298)
T TIGR02997 162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLED--DGESPEEQVERESL 239 (298)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccC--CCCCHHHHHHHHHH
Confidence 999988877 468999999999999999999999886543 11122 12456777788888
Q ss_pred HHHHHHHHHhhCCHHHHHHHhhHhcc-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011454 412 KDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 412 ~e~L~~~L~~~Lp~rER~VI~LryGL-~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLR 470 (485)
...|..+| +.|||++|.||.++||| +.+++|++|||+.||||++||+|++++|++|||
T Consensus 240 ~~~L~~~L-~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr 298 (298)
T TIGR02997 240 RQDLESLL-AELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298 (298)
T ss_pred HHHHHHHH-HcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 88899999 89999999999999998 468999999999999999999999999999996
No 5
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=9.1e-49 Score=399.81 Aligned_cols=288 Identities=36% Similarity=0.625 Sum_probs=265.9
Q ss_pred hhHHHHHHhhccccCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHHH
Q 011454 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (485)
Q Consensus 191 ~~~~~yl~~i~~~~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~Li 270 (485)
+.+..||++|+++|+||++||.+|+++++.|-.++..+..|.+.+|++|+..+||.+++++..+|+..+..+..|++.||
T Consensus 8 ~~~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~L~ 87 (317)
T PRK07405 8 DLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRKMV 87 (317)
T ss_pred cHHHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHHHH
Confidence 56788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHHH
Q 011454 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 350 (485)
Q Consensus 271 e~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~~ 350 (485)
..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|+|||+||||++|.++|.++++.+|+|.+....+
T Consensus 88 ~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~~~~ 167 (317)
T PRK07405 88 EANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKL 167 (317)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHH-------------------HhhhcccCCCCCcchHHHHH
Q 011454 351 GLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEVL-------------------AYIADNRVENNPWHGVDDWA 410 (485)
Q Consensus 351 ~kirka~~~L~-~~gr~ps~eEIae~L~is~eev~~~l~~~-------------------~~l~D~~~e~~pee~~e~~e 410 (485)
++++++...+. ..|+.|+.++||+.+|++.+++.+++... +.++|. ..+|++.++..+
T Consensus 168 ~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~--~~~pe~~~~~~~ 245 (317)
T PRK07405 168 NKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDT--GASPEDFATQSS 245 (317)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCC--CCCHHHHHHHHH
Confidence 99999988884 68999999999999999999999886432 122222 245777788888
Q ss_pred HHHHHHHHHHhhCCHHHHHHHhhHhcc-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhhHHHhhh
Q 011454 411 LKDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV 483 (485)
Q Consensus 411 l~e~L~~~L~~~Lp~rER~VI~LryGL-~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~l~~~l~ 483 (485)
....|..+| +.|||++|.||.++||| |++++|++|||+.||||++||+|++.+|++|||+. ...+..|+.
T Consensus 246 ~~~~l~~al-~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~--~~~l~~~~~ 316 (317)
T PRK07405 246 LQLDLERLM-EDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKR--KANIQEYLA 316 (317)
T ss_pred HHHHHHHHH-HcCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence 889999999 89999999999999998 46899999999999999999999999999999996 356677764
No 6
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=100.00 E-value=3e-47 Score=406.76 Aligned_cols=278 Identities=35% Similarity=0.596 Sum_probs=245.6
Q ss_pred hhHHHHHHhhccccCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHHH
Q 011454 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (485)
Q Consensus 191 ~~~~~yl~~i~~~~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~Li 270 (485)
+.++.||++|+++|+||++||++|+++++.|+.++.. +. ...+|+ .....+|+.++..+..|++.||
T Consensus 211 d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~---~~-------~~~~~~---~~~~~~l~~~~~~g~~Ar~~LI 277 (509)
T PRK05901 211 DPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEEL---LA-------EGEKLD---PELRRDLQWIGRDGKRAKNHLL 277 (509)
T ss_pred cHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhh---hh-------hcccch---hhhhhhhhhhccchHHHHHHHH
Confidence 6788999999999999999999999999999863331 11 112233 2256778888899999999999
Q ss_pred HHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHHH
Q 011454 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 350 (485)
Q Consensus 271 e~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~~ 350 (485)
..|+|||+++|++|.++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++|++++|.+|+|.++...+
T Consensus 278 ~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~~~~e~i 357 (509)
T PRK05901 278 EANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVETI 357 (509)
T ss_pred HHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHH-------------------HhhhcccCCCCCcchHHHHH
Q 011454 351 GLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEVL-------------------AYIADNRVENNPWHGVDDWA 410 (485)
Q Consensus 351 ~kirka~~~L~-~~gr~ps~eEIae~L~is~eev~~~l~~~-------------------~~l~D~~~e~~pee~~e~~e 410 (485)
++++++.+.+. .+|+.|+.++||+.+|+++++|..++... +++.|.. ...|++.++...
T Consensus 358 ~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~-~~~p~~~~~~~~ 436 (509)
T PRK05901 358 NKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSE-AVSPVDAVSFTL 436 (509)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCC-CCCHHHHHHHHH
Confidence 99999988885 78999999999999999999999886543 2222222 235667777888
Q ss_pred HHHHHHHHHHhhCCHHHHHHHhhHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhhHHHhhh
Q 011454 411 LKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV 483 (485)
Q Consensus 411 l~e~L~~~L~~~Lp~rER~VI~LryGL~-~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~l~~~l~ 483 (485)
+...|..+| ..|+++||.||.+||||+ ++++|++|||+.||||+++|||++.+||+|||+......|+.||.
T Consensus 437 l~~~L~~aL-~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~~~~~~l~~~l~ 509 (509)
T PRK05901 437 LQDQLQEVL-ETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDFLD 509 (509)
T ss_pred HHHHHHHHH-hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 888999999 899999999999999994 689999999999999999999999999999999999999999874
No 7
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=100.00 E-value=2.2e-46 Score=382.94 Aligned_cols=277 Identities=34% Similarity=0.588 Sum_probs=242.0
Q ss_pred hhHHHHHHhhccccCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHHH
Q 011454 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (485)
Q Consensus 191 ~~~~~yl~~i~~~~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~Li 270 (485)
+.+..||++|+++|+||++||.+|+++++.|..++.+ +| ..+|.... ...+|...+..|..|++.||
T Consensus 26 ~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~----------~~-~~~~~~~~--~~~~l~~~~~~~~~A~~~Lv 92 (324)
T PRK07921 26 DLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL----------LE-TRKRLSEA--RKRDLAAVVRDGEAARRHLL 92 (324)
T ss_pred ChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh----------hc-cccccchh--HHHHHHHHHhcCHHHHHHHH
Confidence 5678899999999999999999999999998753332 11 12221111 35688899999999999999
Q ss_pred HHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHHH
Q 011454 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 350 (485)
Q Consensus 271 e~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~~ 350 (485)
..|+++|+++|++|.+++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++|+++.+.+++|.+..+.+
T Consensus 93 ~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~~~~ 172 (324)
T PRK07921 93 EANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQV 172 (324)
T ss_pred HHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHH-------------------HhhhcccCCCCCcchHHHHH
Q 011454 351 GLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEVL-------------------AYIADNRVENNPWHGVDDWA 410 (485)
Q Consensus 351 ~kirka~~~L~-~~gr~ps~eEIae~L~is~eev~~~l~~~-------------------~~l~D~~~e~~pee~~e~~e 410 (485)
++++++...+. .+|+.|+.++||+.+|++.++|..++... ++++|.. ..+|++.+...+
T Consensus 173 ~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~-~~~pe~~~~~~~ 251 (324)
T PRK07921 173 NKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSE-ATSAENAVIAGL 251 (324)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCC-CCCHHHHHHHHH
Confidence 99999998885 68999999999999999999999876443 1222221 234666677778
Q ss_pred HHHHHHHHHHhhCCHHHHHHHhhHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhhHHHhh
Q 011454 411 LKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAML 482 (485)
Q Consensus 411 l~e~L~~~L~~~Lp~rER~VI~LryGL~-~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~l~~~l 482 (485)
+...|..+| +.||++|+.||.+||||+ .+++|++|||+.||||+++|+|++.+|++|||+......+..|+
T Consensus 252 ~~~~l~~~L-~~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~~~~~~l~~~~ 323 (324)
T PRK07921 252 LHTDIRSVL-ATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSYA 323 (324)
T ss_pred HHHHHHHHH-HhCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHHHHHHHHhh
Confidence 888899999 899999999999999994 67899999999999999999999999999999999888888886
No 8
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=100.00 E-value=7.4e-45 Score=369.40 Aligned_cols=291 Identities=38% Similarity=0.599 Sum_probs=257.8
Q ss_pred hhhHHHHHHhhccccCCCHHHHHHHHHHHHcCCcchhHHHHHHh-hhCCCCchH---------------HHHHHhhcCh-
Q 011454 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKE-RLGCEPSME---------------QLAASLRISR- 252 (485)
Q Consensus 190 ~~~~~~yl~~i~~~~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~-~~g~~p~~~---------------~~a~~~~~s~- 252 (485)
.+.+..|+.+++..+.++.+++..+.+.++....+......+.. ..+..|+.. .|+..+..+.
T Consensus 8 ~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Ee 87 (342)
T COG0568 8 ADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEEE 87 (342)
T ss_pred hhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHHH
Confidence 45888999999999999999999999999888877666777776 677888887 5555555544
Q ss_pred hHHHHhhhhh---HHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHH
Q 011454 253 PELQSILMEC---SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGV 329 (485)
Q Consensus 253 ~~L~~~l~~~---~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I 329 (485)
.+|..++..+ ..|..+||+.|+++|++||++|.++|..+.||||||+|||++|+++|||++|++|+|||+||||++|
T Consensus 88 ~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrqaI 167 (342)
T COG0568 88 KALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAI 167 (342)
T ss_pred HHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHHHH
Confidence 5666777655 4499999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhhccccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHH------------------
Q 011454 330 SRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEVL------------------ 390 (485)
Q Consensus 330 ~~~I~~~~r~irip~~~~~~~~kirka~~~L~-~~gr~ps~eEIae~L~is~eev~~~l~~~------------------ 390 (485)
.++|.+++|+||+|.|+.+.++++++..+.+. ..|++|+.++||+.+|++.++|..++...
T Consensus 168 ~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~ded~~l 247 (342)
T COG0568 168 TRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSEL 247 (342)
T ss_pred HHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCCCcccHH
Confidence 99999999999999999999999999988885 57999999999999999999999887654
Q ss_pred -HhhhcccCCCCCcchHHHHHHHHHHHHHHHhh-CCHHHHHHHhhHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011454 391 -AYIADNRVENNPWHGVDDWALKDEVNKLIIVT-LGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALE 467 (485)
Q Consensus 391 -~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~-Lp~rER~VI~LryGL~-~eg~S~eEIAe~LgIS~~tVrqi~~rALk 467 (485)
++++|.. ..+|++.+....+.+.+...| .. |+|+|+.||++|||++ .++.|++|||+.+|||+++|||++.+|++
T Consensus 248 ~d~leD~~-~~~p~~~~~~~~~~~~~~~~L-~~~Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~isrERvRQIE~kAl~ 325 (342)
T COG0568 248 GDFLEDDK-SVSPEDAVERESLKEDLNEVL-AEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAKALR 325 (342)
T ss_pred HHHhhcCC-cCCHHHHHHHHHHHHHHHHHH-HhcCCHHHHHHHHHHhccCCCCcchHHHHHHHhCCcHHHHHHHHHHHHH
Confidence 6666665 347999999999999999999 77 9999999999999994 68999999999999999999999999999
Q ss_pred HHHHHH-HhhhHHHhh
Q 011454 468 KLKHAA-RKKKMEAML 482 (485)
Q Consensus 468 KLRk~L-~~~~l~~~l 482 (485)
|||... +...++.|+
T Consensus 326 KLr~~~~~~~~~~~~l 341 (342)
T COG0568 326 KLRRHPERSALLRSYL 341 (342)
T ss_pred HHHHhhhhhhHHHHhh
Confidence 999444 444567776
No 9
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=1e-44 Score=376.79 Aligned_cols=252 Identities=37% Similarity=0.647 Sum_probs=232.0
Q ss_pred hhhHHHHHHhhccccCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHH
Q 011454 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL 269 (485)
Q Consensus 190 ~~~~~~yl~~i~~~~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~L 269 (485)
.+.++.||++|+..|+|+++++.+|+++++.||. .|++.|
T Consensus 95 ~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~Gd~----------------------------------------~A~~~L 134 (367)
T PRK09210 95 NDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGDE----------------------------------------EAKQRL 134 (367)
T ss_pred CcHHHHHHHHhhccCCCCHHHHHHHHHHHHhhHH----------------------------------------HHHHHH
Confidence 4789999999999999999999999999999997 999999
Q ss_pred HHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHH
Q 011454 270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHER 349 (485)
Q Consensus 270 ie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~ 349 (485)
|..|+++|+++|++|.+++.+++||+|||++|||+|+++|||.+|++|+|||+||||++|.++|+++.|.+++|.++.+.
T Consensus 135 i~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~~~~ 214 (367)
T PRK09210 135 AEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 214 (367)
T ss_pred HHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHH-------------------HhhhcccCCCCCcchHHHH
Q 011454 350 LGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEVL-------------------AYIADNRVENNPWHGVDDW 409 (485)
Q Consensus 350 ~~kirka~~~L~-~~gr~ps~eEIae~L~is~eev~~~l~~~-------------------~~l~D~~~e~~pee~~e~~ 409 (485)
++++.++.+.+. .+|+.|+.++||+.+|+++++|++++... ++++|.. ..+|++.+...
T Consensus 215 ~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~-~~~p~~~~~~~ 293 (367)
T PRK09210 215 INKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQD-ATSPADHAAYE 293 (367)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCC-CCCHHHHHHHH
Confidence 999999988884 78999999999999999999999876554 1122221 24577777888
Q ss_pred HHHHHHHHHHHhhCCHHHHHHHhhHhcc-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhhHHHhhh
Q 011454 410 ALKDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV 483 (485)
Q Consensus 410 el~e~L~~~L~~~Lp~rER~VI~LryGL-~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~l~~~l~ 483 (485)
.+...|..+| ..||++||.||.+|||| |++++|++|||+.||||+++|+|++.+||+|||+.....+|+.|+.
T Consensus 294 ~~~~~l~~~l-~~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~~~~~~~l~~~~~ 367 (367)
T PRK09210 294 LLKEQLEDVL-DTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 367 (367)
T ss_pred HHHHHHHHHH-HhCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhChHHHhHHHHhhC
Confidence 8889999999 89999999999999998 4688999999999999999999999999999999999999999873
No 10
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=3.7e-41 Score=371.29 Aligned_cols=253 Identities=32% Similarity=0.632 Sum_probs=229.3
Q ss_pred hHHHHHHhhccccCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHHHH
Q 011454 192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM 271 (485)
Q Consensus 192 ~~~~yl~~i~~~~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~Lie 271 (485)
.++.||.++...+.|+++++..++++++.|+. ....|+++||.
T Consensus 345 ~lq~~L~~ie~~~~Ls~eElk~l~~~i~~g~~-------------------------------------~~~~a~~~Li~ 387 (619)
T PRK05658 345 KLQQELEAIEEETGLTIEELKEINRQISKGEA-------------------------------------KARRAKKEMVE 387 (619)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHHhccch-------------------------------------hhhHHHHHHHH
Confidence 56788999999999999999999999999985 12278999999
Q ss_pred HhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHHHH
Q 011454 272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG 351 (485)
Q Consensus 272 ~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~~~ 351 (485)
.|+|+|+++|++|.++|.+++||+|||+|||++|+++|||.+|++|+|||+||||++|.++|++++|++++|.++.+.++
T Consensus 388 ~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~irip~~~~~~~~ 467 (619)
T PRK05658 388 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 467 (619)
T ss_pred HHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCceecCHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHH-HHcCCCCCHHHHHHHhCCCHHHHHHHHHHH-------------------HhhhcccCCCCCcchHHHHHH
Q 011454 352 LIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEVL-------------------AYIADNRVENNPWHGVDDWAL 411 (485)
Q Consensus 352 kirka~~~L-~~~gr~ps~eEIae~L~is~eev~~~l~~~-------------------~~l~D~~~e~~pee~~e~~el 411 (485)
+++++...+ +++|++|+.++||+.+|++.++|..++... ++++|.. ..+|.+.+....+
T Consensus 468 k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~~~~~l~d~i~d~~-~~~p~~~~~~~~~ 546 (619)
T PRK05658 468 KLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKN-AELPIDAAIQESL 546 (619)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCCCCCchhhhcCCCC-CCChHHHHHHHHH
Confidence 999998888 479999999999999999999999886543 1222221 2356667777888
Q ss_pred HHHHHHHHHhhCCHHHHHHHhhHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhhHHHhhh
Q 011454 412 KDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV 483 (485)
Q Consensus 412 ~e~L~~~L~~~Lp~rER~VI~LryGL~-~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~l~~~l~ 483 (485)
...|..+| ..||++|+.||.+|||++ .+++|++|||+.||||+++|+|++.+|++|||+..+...|+.||.
T Consensus 547 ~~~l~~~l-~~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr~~~~~~~l~~~~~ 618 (619)
T PRK05658 547 REATTDVL-ASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRSFLD 618 (619)
T ss_pred HHHHHHHH-HcCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHhchHHHHHHHHHhc
Confidence 88999999 899999999999999995 578999999999999999999999999999999999999999985
No 11
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=100.00 E-value=8e-39 Score=327.72 Aligned_cols=251 Identities=35% Similarity=0.600 Sum_probs=224.3
Q ss_pred hHhhhhHHHHHHhhccccCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHH
Q 011454 187 ELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAR 266 (485)
Q Consensus 187 e~~~~~~~~yl~~i~~~~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~ 266 (485)
+.+-+.++.|+++|+..|+||++++..|+.+++.||. .|+
T Consensus 49 ~~~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~Gd~----------------------------------------~A~ 88 (325)
T PRK05657 49 QRVLDATQLYLNEIGYSPLLTAEEEVYFARRALRGDF----------------------------------------AAR 88 (325)
T ss_pred cccccHHHHHHHHHhcCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHH
Confidence 3455788999999999999999999999999999998 999
Q ss_pred HHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccH
Q 011454 267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHL 346 (485)
Q Consensus 267 e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~ 346 (485)
+.||..|.++|+++|++|.+++.+++||+||||+++|+++++||+.+|++|+||++||||+.|.+++.++.+.+++|.++
T Consensus 89 ~~Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~~~ 168 (325)
T PRK05657 89 QRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHV 168 (325)
T ss_pred HHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHH-------------------HhhhcccCCCCCcchH
Q 011454 347 HERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEVL-------------------AYIADNRVENNPWHGV 406 (485)
Q Consensus 347 ~~~~~kirka~~~L~-~~gr~ps~eEIae~L~is~eev~~~l~~~-------------------~~l~D~~~e~~pee~~ 406 (485)
...++.+.++...+. ..|+.|+.++||+.+|+++++|..++... +.+.+.. ..+|+..+
T Consensus 169 ~~~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~~~l~d~l~d~~-~~~pe~~~ 247 (325)
T PRK05657 169 VKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQ-ENGPEDTT 247 (325)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCCcchhhhccCCC-CCCHHHHH
Confidence 888877777777674 57899999999999999999999887543 1111111 13466667
Q ss_pred HHHHHHHHHHHHHHhhCCHHHHHHHhhHhcc-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhhHH
Q 011454 407 DDWALKDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKME 479 (485)
Q Consensus 407 e~~el~e~L~~~L~~~Lp~rER~VI~LryGL-~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~l~ 479 (485)
...+....|..+| ..||+++|.||.++||| +++++|++|||+.||||++||++++++|+++||+.+...++.
T Consensus 248 ~~~e~~~~L~~aL-~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~~~~~~ 320 (325)
T PRK05657 248 QDDDMKQSIVKWL-FELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQGLS 320 (325)
T ss_pred HHHHHHHHHHHHH-HcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhCccc
Confidence 7777888999999 89999999999999998 479999999999999999999999999999999999876653
No 12
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=1.2e-38 Score=320.79 Aligned_cols=246 Identities=30% Similarity=0.463 Sum_probs=206.7
Q ss_pred CchhHhhhhHHHHHHhhccccCCCHHHHHHHHHHH-HcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhh
Q 011454 184 ISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKI-KTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMEC 262 (485)
Q Consensus 184 ~~~e~~~~~~~~yl~~i~~~~~Lt~eee~~L~~~i-k~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~ 262 (485)
.+|+ +.+..|++++.+.|+++.+++.+|+.+. +.||.
T Consensus 10 ~~~~---~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~~Gd~--------------------------------------- 47 (284)
T PRK06596 10 LSPE---GNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDL--------------------------------------- 47 (284)
T ss_pred CCCc---cHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCCH---------------------------------------
Confidence 5677 6888999999999999999999999994 68887
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccc
Q 011454 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (485)
Q Consensus 263 ~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~iri 342 (485)
.|++.||..|+|+|+++|++|.+++.+.+||+|||++||++|+++|||++|++|+|||+|||+++|.++|+++++.+++
T Consensus 48 -~a~~~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~ 126 (284)
T PRK06596 48 -EAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKV 126 (284)
T ss_pred -HHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeeec
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999888899
Q ss_pred cccHHH--HHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHH--------Hhhhcc-c--------C---CC
Q 011454 343 PNHLHE--RLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVL--------AYIADN-R--------V---EN 400 (485)
Q Consensus 343 p~~~~~--~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~--------~~l~D~-~--------~---e~ 400 (485)
|.+... ...++++....+. .+++|+.++||+.+|+++++|..++... ..+.+. . . ..
T Consensus 127 p~~~~~~~~~~~~~~~~~~l~-~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~~~ 205 (284)
T PRK06596 127 ATTKAQRKLFFNLRKAKKRLG-WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDKSS 205 (284)
T ss_pred cchHHHHHHHHHHHHHHHHhc-cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcCCCCC
Confidence 987643 2234444444443 4588999999999999999999876432 011100 0 0 12
Q ss_pred CCcchHHHH----HHHHHHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 401 NPWHGVDDW----ALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 401 ~pee~~e~~----el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
+|++.++.. ++...|..+| +.||++||.||.++||.+ +++|++|||+.||||+++|+|++.+|++|||+.+..
T Consensus 206 ~p~~~~~~~~~~~~~~~~L~~al-~~L~~rEr~VL~lry~~~-~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~l~~ 282 (284)
T PRK06596 206 DPADVLEEDNWEDQRRALLADAL-EGLDERSRDIIEARWLDD-DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEA 282 (284)
T ss_pred CchHHHHHHHHHHHHHHHHHHHH-hcCCHHHHHHHHHHhcCC-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 355444443 3567788999 899999999999999533 689999999999999999999999999999998864
No 13
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=100.00 E-value=8.7e-39 Score=313.50 Aligned_cols=217 Identities=40% Similarity=0.695 Sum_probs=196.0
Q ss_pred HHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccc
Q 011454 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN 344 (485)
Q Consensus 265 A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~ 344 (485)
|+++||..|+++|+++|++|.+++.+.+||+|||++||++|+++|||++|++|+|||+||||++|.+++++..+.+++|.
T Consensus 1 a~~~Li~~~~~lv~~ia~~~~~~~~~~eDLiQeG~igL~~A~~~fd~~~g~~FstYA~~~Ir~~I~~~l~~~~~~vrip~ 80 (238)
T TIGR02393 1 AKKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80 (238)
T ss_pred CHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCChHHHhHHHHHHHHHHHHHHcCCcEEeCH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHH-------------------HhhhcccCCCCCcc
Q 011454 345 HLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEVL-------------------AYIADNRVENNPWH 404 (485)
Q Consensus 345 ~~~~~~~kirka~~~L~-~~gr~ps~eEIae~L~is~eev~~~l~~~-------------------~~l~D~~~e~~pee 404 (485)
+....++++.++...+. ..|++|+.++||+.+|++.+++..+.... +.+.|.. ..+|++
T Consensus 81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~-~~~p~~ 159 (238)
T TIGR02393 81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDTS-IESPDD 159 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcccHHHHhcCCC-CCChHH
Confidence 99999999999988885 68999999999999999999999875543 1222221 235666
Q ss_pred hHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhhHHHhhh
Q 011454 405 GVDDWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV 483 (485)
Q Consensus 405 ~~e~~el~e~L~~~L~~~Lp~rER~VI~LryGL~-~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~l~~~l~ 483 (485)
.++..+....|..+| +.||++||.||.++|||+ ++++|++|||+.||||+++|+|++.+|++|||+.+....++.|+.
T Consensus 160 ~~~~~~~~~~l~~~l-~~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~~~~~~~~~~ 238 (238)
T TIGR02393 160 YAAKELLREQLDEVL-ETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKSFLD 238 (238)
T ss_pred HHHHHHHHHHHHHHH-HhCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHHHhHHHHhhC
Confidence 677777888899999 899999999999999984 689999999999999999999999999999999999888888863
No 14
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=4.5e-38 Score=317.37 Aligned_cols=242 Identities=27% Similarity=0.392 Sum_probs=203.8
Q ss_pred hhHHHHHHhhccccCCCHHHHHHHHHHHH-cCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHH
Q 011454 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIK-TGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL 269 (485)
Q Consensus 191 ~~~~~yl~~i~~~~~Lt~eee~~L~~~ik-~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~L 269 (485)
+..+.||++|.++|+||++++.+|+++++ .||. .|+++|
T Consensus 6 ~~~~~y~~~~~~~~~l~~~~e~~L~~~~~~~gd~----------------------------------------~A~~~L 45 (289)
T PRK07500 6 SADRSMIRSAMKAPYLEREEEHALAYRWKDHRDE----------------------------------------DALHRI 45 (289)
T ss_pred hHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCCCH----------------------------------------HHHHHH
Confidence 35567999999999999999999999974 7887 999999
Q ss_pred HHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHH-
Q 011454 270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHE- 348 (485)
Q Consensus 270 ie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~- 348 (485)
|..|.|+|+++|++|.+++.+++||+||||+|||+++++|||.+|.+|+|||+||||++|.++|+++++.+|+|.+...
T Consensus 46 v~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~~~~~~ 125 (289)
T PRK07500 46 ISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQK 125 (289)
T ss_pred HHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCccHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999988654
Q ss_pred -HHHHHHHHHHHHH----HcCCCCCHHHHHHHhCCCHHHHHHHHHHH----------------------HhhhcccCCCC
Q 011454 349 -RLGLIRNAKLRLE----EKGVTPSVDRIAEYLNMSQKKVRNATEVL----------------------AYIADNRVENN 401 (485)
Q Consensus 349 -~~~kirka~~~L~----~~gr~ps~eEIae~L~is~eev~~~l~~~----------------------~~l~D~~~e~~ 401 (485)
...++++....+. ..|+.|+.++||+.+|++.+++..+.... +.+.|. ..+
T Consensus 126 ~~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~i~d~--~~~ 203 (289)
T PRK07500 126 ALFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDD--SPL 203 (289)
T ss_pred HHHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCCCcccHHHhccCC--CCC
Confidence 3334444444443 47899999999999999999998664321 111111 123
Q ss_pred CcchHHH----HHHHHHHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Q 011454 402 PWHGVDD----WALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 476 (485)
Q Consensus 402 pee~~e~----~el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~ 476 (485)
|++.++. .+....|..+| +.||++||.||.++|+. .+++|++|||+.||||++||+|++++|+++||..+...
T Consensus 204 pe~~~~~~~~~~~~~~~l~~al-~~L~~rer~vl~lr~~~-~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~~~ 280 (289)
T PRK07500 204 PDEQVESSIDGERRRRWLTQAL-QTLNERELRIIRERRLR-EDGATLEALGEELGISKERVRQIEARALEKLRRALLSQ 280 (289)
T ss_pred chHHHHHHHHHHHHHHHHHHHH-hcCCHHHHHHHHHHhcC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 4444332 33556788899 89999999999999842 38999999999999999999999999999999999754
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=7.5e-38 Score=312.64 Aligned_cols=240 Identities=29% Similarity=0.478 Sum_probs=197.6
Q ss_pred hHHHHHHhhccccCCCHHHHHHHHHH-HHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHHH
Q 011454 192 RLKGYVKGVVSEELLTHAEVVRLSKK-IKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (485)
Q Consensus 192 ~~~~yl~~i~~~~~Lt~eee~~L~~~-ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~Li 270 (485)
.+..||++|+.+|+++++++.+|+.+ .+.||. .|++.||
T Consensus 2 ~~~~yl~~~~~~~~l~~~~e~~l~~~~~~~gd~----------------------------------------~a~~~Lv 41 (270)
T TIGR02392 2 SLDAYIRAVNRIPMLTPEEEYQLAKRLREHGDL----------------------------------------DAAKKLV 41 (270)
T ss_pred hHHHHHHHHhcCCCCCHHHHHHHHHHHHHCCCH----------------------------------------HHHHHHH
Confidence 46789999999999999999999999 578887 9999999
Q ss_pred HHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHH--
Q 011454 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHE-- 348 (485)
Q Consensus 271 e~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~-- 348 (485)
+.|+|+|+++|++|.+++.+++||+|||++|||+|+++|||++|++|+|||.|||+++|.++|++.++.+++|.+...
T Consensus 42 ~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir~p~~~~~~~ 121 (270)
T TIGR02392 42 LSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRK 121 (270)
T ss_pred HHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCceecCchHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999998778899987542
Q ss_pred HHHHHHHHHHHHHHcCCCC-CHHHHHHHhCCCHHHHHHHHHHHH--------hhhccc------------CCCCCcchHH
Q 011454 349 RLGLIRNAKLRLEEKGVTP-SVDRIAEYLNMSQKKVRNATEVLA--------YIADNR------------VENNPWHGVD 407 (485)
Q Consensus 349 ~~~kirka~~~L~~~gr~p-s~eEIae~L~is~eev~~~l~~~~--------~l~D~~------------~e~~pee~~e 407 (485)
...+++.....+. .++.| +.++||+.+|++.++|..+..... .+.+.. ...+|++.++
T Consensus 122 ~~~~~~~~~~~~~-~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~l~d~~~~pe~~~~ 200 (270)
T TIGR02392 122 LFFNLRKMKKRLQ-GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKTSDPEDTLE 200 (270)
T ss_pred HHHHHHHHHHHHh-cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCCccccHHHHhcCCCCChHHHHH
Confidence 3334444444332 22445 589999999999999988754220 011100 0123444444
Q ss_pred HH----HHHHHHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 011454 408 DW----ALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 474 (485)
Q Consensus 408 ~~----el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~ 474 (485)
.. .....|..+| ..||++||.||.++||. .+++|++|||+.||||+++|+|++.+|++|||+.+.
T Consensus 201 ~~~~~~~~~~~L~~al-~~L~~rer~vl~l~y~~-~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~l~ 269 (270)
T TIGR02392 201 EEQWEELQRQALANAL-GSLDARSRRIIEARWLD-DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAALA 269 (270)
T ss_pred HHHHHHHHHHHHHHHH-HcCCHHHHHHHHHHhcC-CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 32 3557789999 89999999999999942 358999999999999999999999999999999874
No 16
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=100.00 E-value=1.4e-36 Score=305.65 Aligned_cols=249 Identities=35% Similarity=0.577 Sum_probs=223.2
Q ss_pred hHhhhhHHHHHHhhccccCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHH
Q 011454 187 ELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAR 266 (485)
Q Consensus 187 e~~~~~~~~yl~~i~~~~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~ 266 (485)
-.+.+.++.||++|..+|.++.+++.+|+..++.||. .|+
T Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~gd~----------------------------------------~a~ 48 (285)
T TIGR02394 9 TRVADVTQLYLREIGFKPLLTAEEEIAYARRALAGDF----------------------------------------EAR 48 (285)
T ss_pred cCcchHHHHHHHHHhccCCCCHHHHHHHHHHHHcCCH----------------------------------------HHH
Confidence 3566899999999999999999999999999999998 999
Q ss_pred HHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccH
Q 011454 267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHL 346 (485)
Q Consensus 267 e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~ 346 (485)
+.||..|.++|+++|++|.+++.+++||+||||+|||+++++||+.+|++|+||+.||++..+++++.+..+.+++|.++
T Consensus 49 ~~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain~~i~~~~~~~~~p~~~ 128 (285)
T TIGR02394 49 KVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHV 128 (285)
T ss_pred HHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHHHHHHHcCCceeCcHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHH-------------------HhhhcccCCCCCcchH
Q 011454 347 HERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEVL-------------------AYIADNRVENNPWHGV 406 (485)
Q Consensus 347 ~~~~~kirka~~~L~-~~gr~ps~eEIae~L~is~eev~~~l~~~-------------------~~l~D~~~e~~pee~~ 406 (485)
....+.+.+..+.+. ..|+.|+..++++.+|++++++.+++... +.+.+.. ..+|++.+
T Consensus 129 ~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~-~~~pe~~~ 207 (285)
T TIGR02394 129 IKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQ-SIDPESLV 207 (285)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchhhhhcCCC-CCCHHHHH
Confidence 988887776666554 57899999999999999999999876543 0111111 23567777
Q ss_pred HHHHHHHHHHHHHHhhCCHHHHHHHhhHhcc-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 011454 407 DDWALKDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 477 (485)
Q Consensus 407 e~~el~e~L~~~L~~~Lp~rER~VI~LryGL-~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~ 477 (485)
+..+....|..+| ..||+++|.||.|+||| +++++|++|||+.||||.+||++++++|+++||+.|...+
T Consensus 208 ~~~e~~~~L~~al-~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~~~~ 278 (285)
T TIGR02394 208 QNDDLKQLIEAWL-AELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERDG 278 (285)
T ss_pred HHHHHHHHHHHHH-HcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 7888888999999 89999999999999988 5799999999999999999999999999999999998654
No 17
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=1.6e-36 Score=302.50 Aligned_cols=206 Identities=25% Similarity=0.382 Sum_probs=183.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.++++||..|+|+|.++|++|.+++.+.+||+|||+|||++|+++|||++|++|+|||+||||++|.++|+++.+.+++|
T Consensus 40 ~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I~~~lr~~~~~ir~P 119 (264)
T PRK07122 40 RQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVP 119 (264)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHcCCccccC
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHHH-----hhhcc-----c-------CCCCCcch
Q 011454 344 NHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEVLA-----YIADN-----R-------VENNPWHG 405 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~-~~gr~ps~eEIae~L~is~eev~~~l~~~~-----~l~D~-----~-------~e~~pee~ 405 (485)
++..+..++++++...+. .+|+.|+.++||+.+|+++++|.+++.... .++.. . ...+|+..
T Consensus 120 r~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~d~~~~~~~~ 199 (264)
T PRK07122 120 RRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDARAIADTLGDVDAG 199 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCCCCcccchhccCCcHHH
Confidence 999999999999988885 789999999999999999999998775421 11110 0 01233444
Q ss_pred HHHHHHHHHHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 011454 406 VDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 473 (485)
Q Consensus 406 ~e~~el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L 473 (485)
++..+....|..+| +.||+++|.||.++| ++++|++|||+.||||+++|++++++|+++||+.+
T Consensus 200 ~e~~~~~~~l~~~l-~~L~~rer~vl~l~y---~~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l 263 (264)
T PRK07122 200 LDQIENREALRPLL-AALPERERTVLVLRF---FESMTQTQIAERVGISQMHVSRLLAKTLARLRDQL 263 (264)
T ss_pred HHHHHHHHHHHHHH-HcCCHHHHHHHHHHh---cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHc
Confidence 56666778899999 899999999999999 79999999999999999999999999999999976
No 18
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=100.00 E-value=1.9e-35 Score=290.41 Aligned_cols=227 Identities=33% Similarity=0.470 Sum_probs=204.3
Q ss_pred ccCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHHHHHhHHHHHHHHH
Q 011454 203 EELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ 282 (485)
Q Consensus 203 ~~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~Lie~yl~LV~sIA~ 282 (485)
.+.++..+...+....+.|+. .++ .||++|+|||.++|+
T Consensus 3 ~~~~~~~e~~~~~~~~~~g~~----------------------------------------~~~-~Li~~ylpLV~~ia~ 41 (247)
T COG1191 3 PQPLSKEEEEKLLEYYAEGDE----------------------------------------EAR-RLIERYLPLVKSIAR 41 (247)
T ss_pred CcccchHHHHHHHHHHHhcCH----------------------------------------HHH-HHHHHHHHHHHHHHH
Confidence 356778888889889998887 888 999999999999999
Q ss_pred HhcCCCC-cHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHH
Q 011454 283 RYDNMGA-DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE 361 (485)
Q Consensus 283 ry~~~~~-d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~~~kirka~~~L~ 361 (485)
+|.+++. +.|||+|.|+|||++|+++|||++|.+|+|||.++|+++|.+++|++. .+++|+++.+..+++..+.+.+.
T Consensus 42 k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~LR~~~-~v~vpR~~~~~~~~i~~~~~~l~ 120 (247)
T COG1191 42 KFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKND-SVKVPRSLRELGRRIEEAIDELE 120 (247)
T ss_pred HHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHHHHhCC-CccCcHHHHHHHHHHHHHHHHHH
Confidence 9998766 999999999999999999999999999999999999999999999999 99999999999999999999995
Q ss_pred -HcCCCCCHHHHHHHhCCCHHHHHHHHHHH---------Hhhh-ccc-----CCCCCcchHHHHHHHHHHHHHHHhhCCH
Q 011454 362 -EKGVTPSVDRIAEYLNMSQKKVRNATEVL---------AYIA-DNR-----VENNPWHGVDDWALKDEVNKLIIVTLGE 425 (485)
Q Consensus 362 -~~gr~ps~eEIae~L~is~eev~~~l~~~---------~~l~-D~~-----~e~~pee~~e~~el~e~L~~~L~~~Lp~ 425 (485)
++|++|+++|||+.+|++.+++..++... +.+. +.. ...+|.+.++.++....|.+++ ..|++
T Consensus 121 ~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~ai-~~L~E 199 (247)
T COG1191 121 QELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDDVDDQIENPDDGVEKEELLEILKEAI-EPLPE 199 (247)
T ss_pred HHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccccchhhccccchhHHHHHHHHHHHHHHH-HccCH
Confidence 79999999999999999999999887665 1111 111 1235667788889999999999 69999
Q ss_pred HHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 426 REREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 426 rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
+||.|+.++| ++++|++|||+.||||+++|+|++.+|+++||+.|..
T Consensus 200 REk~Vl~l~y---~eelt~kEI~~~LgISes~VSql~kkai~kLr~~l~~ 246 (247)
T COG1191 200 REKLVLVLRY---KEELTQKEIAEVLGISESRVSRLHKKAIKKLRKELNK 246 (247)
T ss_pred HHHHHHHHHH---HhccCHHHHHHHhCccHHHHHHHHHHHHHHHHHHhcc
Confidence 9999999999 8999999999999999999999999999999998853
No 19
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=3.4e-35 Score=291.47 Aligned_cols=209 Identities=27% Similarity=0.387 Sum_probs=181.0
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCC-CCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNM-GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~-~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~iri 342 (485)
.|+++||..|+|+|+++|++|.+. +.+++||+|||+||||+|+++|||++|++|+|||++||+++|.+++++..+.+++
T Consensus 25 ~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~~vr~ 104 (256)
T PRK07408 25 ALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRI 104 (256)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcCCeeee
Confidence 899999999999999999999875 6679999999999999999999999999999999999999999999999999999
Q ss_pred cccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHH--------H-hhhcc-c-------CCCCCcc
Q 011454 343 PNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEVL--------A-YIADN-R-------VENNPWH 404 (485)
Q Consensus 343 p~~~~~~~~kirka~~~L~-~~gr~ps~eEIae~L~is~eev~~~l~~~--------~-~l~D~-~-------~e~~pee 404 (485)
|+++....++++++...+. .+|++|+.++||+.+|++++++..+.... + .+.+. . ...+|..
T Consensus 105 pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~~~d~~~ 184 (256)
T PRK07408 105 PRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDEDGSTSLGDLLPDPRY 184 (256)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCCCccccccccCCccc
Confidence 9999999999999998885 68999999999999999999998875422 0 00000 0 0012222
Q ss_pred --hHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Q 011454 405 --GVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 476 (485)
Q Consensus 405 --~~e~~el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~ 476 (485)
.....+....|..+| ..||+++|.||.++| ++++|++|||+.||+|+++|++++++|+++||+.+...
T Consensus 185 ~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~y---~~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~~~ 254 (256)
T PRK07408 185 RSFQLAQEDRIRLQQAL-AQLEERTREVLEFVF---LHDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQPE 254 (256)
T ss_pred chhhhhHHHHHHHHHHH-HcCCHHHHHHHHHHH---HCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhcc
Confidence 113345567789999 899999999999999 79999999999999999999999999999999998754
No 20
>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=2.5e-34 Score=284.67 Aligned_cols=228 Identities=28% Similarity=0.415 Sum_probs=196.7
Q ss_pred ccccCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHHHHHhHHHHHHH
Q 011454 201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI 280 (485)
Q Consensus 201 ~~~~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~Lie~yl~LV~sI 280 (485)
..+|+|+++++.+|+.+++.||. .|++.||..|.++|+++
T Consensus 11 ~~~~~l~~~~~~~li~~~~~gd~----------------------------------------~a~~~L~~~~~~~v~~~ 50 (254)
T TIGR02850 11 SKLPVLKNQEMRELFIRMQSGDT----------------------------------------TAREKLINGNLRLVLSV 50 (254)
T ss_pred cCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHHHHHH
Confidence 46799999999999999999997 99999999999999999
Q ss_pred HHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHHHHHHHHHHHHH
Q 011454 281 AQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL 360 (485)
Q Consensus 281 A~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~~~kirka~~~L 360 (485)
|++|.+++.+++||+||||+|||+++++||+.+|.+|.||+++||++.|.++++++. .+++|++.....+++.++...+
T Consensus 51 a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~-~ir~p~~~~~~~~~~~~~~~~l 129 (254)
T TIGR02850 51 IQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDKL 129 (254)
T ss_pred HHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CccCchHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999975 7899999998888888887777
Q ss_pred -HHcCCCCCHHHHHHHhCCCHHHHHHHHHHHH---hhhcc----cCC--------CCCcchHHHHHHHHHHHHHHHhhCC
Q 011454 361 -EEKGVTPSVDRIAEYLNMSQKKVRNATEVLA---YIADN----RVE--------NNPWHGVDDWALKDEVNKLIIVTLG 424 (485)
Q Consensus 361 -~~~gr~ps~eEIae~L~is~eev~~~l~~~~---~l~D~----~~e--------~~pee~~e~~el~e~L~~~L~~~Lp 424 (485)
.++|++|+.+++|+.+|++++++..++.... .+.+. ... .+.....+.......|..++ +.||
T Consensus 130 ~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~l~~~l-~~L~ 208 (254)
T TIGR02850 130 ISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEKNKDSQWLEGIALKEAM-KRLN 208 (254)
T ss_pred HHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCCCCcchhhhhcCCccccHHHHHhHHHHHHHH-HcCC
Confidence 4689999999999999999999988766541 11110 000 01111112333455688888 8999
Q ss_pred HHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 011454 425 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 473 (485)
Q Consensus 425 ~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L 473 (485)
+++|.||.++| ++++|++|||+.||+|+++|++++++|+++||+.+
T Consensus 209 ~rer~vi~~~~---~~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~~~ 254 (254)
T TIGR02850 209 EREKMILNMRF---FEGKTQMEVAEEIGISQAQVSRLEKAALKHMRKYV 254 (254)
T ss_pred HHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence 99999999999 78999999999999999999999999999999853
No 21
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=100.00 E-value=8.7e-34 Score=281.30 Aligned_cols=227 Identities=27% Similarity=0.428 Sum_probs=196.8
Q ss_pred cccCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHHHHHhHHHHHHHH
Q 011454 202 SEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIA 281 (485)
Q Consensus 202 ~~~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~Lie~yl~LV~sIA 281 (485)
.+|+|+++++..|+.+++.||. .|++.||..|.++|+++|
T Consensus 15 ~~~~l~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~~~~~v~~~a 54 (258)
T PRK08215 15 KLPVLKNEEMRELFERMQNGDK----------------------------------------EAREKLINGNLRLVLSVI 54 (258)
T ss_pred CCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHHH
Confidence 5689999999999999999997 999999999999999999
Q ss_pred HHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHHHHHHHHHHHHH-
Q 011454 282 QRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL- 360 (485)
Q Consensus 282 ~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~~~kirka~~~L- 360 (485)
++|.+++.+++||+|||++|||+++++||+.+|.+|.||+++||++.|.+++++.. .+++|++......++.++...+
T Consensus 55 ~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~~-~vrip~~~~~~~~~~~~~~~~l~ 133 (258)
T PRK08215 55 QRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREKLI 133 (258)
T ss_pred HHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-ceEecHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999985 7899999998888888777777
Q ss_pred HHcCCCCCHHHHHHHhCCCHHHHHHHHHHHH---hhhcc-----c-------CCCCCcchHHHHHHHHHHHHHHHhhCCH
Q 011454 361 EEKGVTPSVDRIAEYLNMSQKKVRNATEVLA---YIADN-----R-------VENNPWHGVDDWALKDEVNKLIIVTLGE 425 (485)
Q Consensus 361 ~~~gr~ps~eEIae~L~is~eev~~~l~~~~---~l~D~-----~-------~e~~pee~~e~~el~e~L~~~L~~~Lp~ 425 (485)
.+.|+.|+.+++|+.+|++++++..++.... .+.+. . ...++....+.......+..++ +.||+
T Consensus 134 ~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l-~~L~~ 212 (258)
T PRK08215 134 NENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDEKNKDENWLEEIALKEAM-KKLND 212 (258)
T ss_pred HHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchhhhhhccCccccHHHHHhHHHHHHHH-HcCCH
Confidence 4689999999999999999999988765431 11110 0 0011222233444556788888 89999
Q ss_pred HHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 011454 426 REREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 473 (485)
Q Consensus 426 rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L 473 (485)
+++.||.++| ++++|++|||+.||||+++|++++++|+++||+.|
T Consensus 213 ~er~vi~~~~---~~~~t~~eIA~~lgis~~~V~~~~~~al~kLr~~l 257 (258)
T PRK08215 213 REKLILNLRF---FQGKTQMEVAEEIGISQAQVSRLEKAALKHMRKYI 257 (258)
T ss_pred HHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 9999999999 78999999999999999999999999999999976
No 22
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=100.00 E-value=2.1e-33 Score=277.74 Aligned_cols=226 Identities=28% Similarity=0.364 Sum_probs=201.3
Q ss_pred cCCCHHHHHHHHHHHHc-CCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHHHHHhHHHHHHHHH
Q 011454 204 ELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ 282 (485)
Q Consensus 204 ~~Lt~eee~~L~~~ik~-Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~Lie~yl~LV~sIA~ 282 (485)
|.|+++++.+|+.+++. ||. .|+++||..|.++|+.+|+
T Consensus 8 ~~l~~~~~~~li~~~~~~gd~----------------------------------------~a~~~l~~~y~~~v~~~a~ 47 (255)
T TIGR02941 8 TNLTKEDVIQWIAEFQQNQNG----------------------------------------EAQEKLVDHYQNLVYSIAY 47 (255)
T ss_pred CCCCHHHHHHHHHHHHHCCCH----------------------------------------HHHHHHHHHhHHHHHHHHH
Confidence 67899999999999998 576 8999999999999999999
Q ss_pred HhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHH-
Q 011454 283 RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE- 361 (485)
Q Consensus 283 ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~~~kirka~~~L~- 361 (485)
+|.+++.++|||+||||++||+++++|+++.|.+|.||+++||++.|.+++++..+.+++|.+.....++++.+...+.
T Consensus 48 ~~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~iri~~~~~~~~~~~~~~~~~l~~ 127 (255)
T TIGR02941 48 KYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTD 127 (255)
T ss_pred HHhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999888885
Q ss_pred HcCCCCCHHHHHHHhCCCHHHHHHHHHHHHh-----hhcc-------------cCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 362 EKGVTPSVDRIAEYLNMSQKKVRNATEVLAY-----IADN-------------RVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 362 ~~gr~ps~eEIae~L~is~eev~~~l~~~~~-----l~D~-------------~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
..|+.|+.+++++.+|++.+++..++..... +++. ....+|++.+...+....+..+| +.|
T Consensus 128 ~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l-~~L 206 (255)
T TIGR02941 128 HLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSDGSTVARLDSVGEVEDGYDQTERRMVLEKIL-PIL 206 (255)
T ss_pred HhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCCCcccccccccCCcchHHHHHHHHHHHHHHH-HcC
Confidence 5799999999999999999998876554310 1100 00123566667777788899999 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 473 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L 473 (485)
|+++|.||.++| ++|+|++|||+.||+|.++|++++++|+++||+.+
T Consensus 207 ~~~~r~ii~l~~---~~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~ 253 (255)
T TIGR02941 207 SEREKSIIHCTF---EENLSQKETGERLGISQMHVSRLQRQAISKLKEAA 253 (255)
T ss_pred CHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 999999999999 79999999999999999999999999999999976
No 23
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=100.00 E-value=2.1e-33 Score=278.90 Aligned_cols=205 Identities=27% Similarity=0.434 Sum_probs=177.8
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcC---CCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~---~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~i 340 (485)
.|+++||..|+|+|+.+|++|.+ .+.+.+||+|||+||||+|+++|||++|++|+|||.+|||++|.+++++..|
T Consensus 23 ~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~-- 100 (257)
T PRK05911 23 EYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQDW-- 100 (257)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCC--
Confidence 89999999999999999999862 4568999999999999999999999999999999999999999999999864
Q ss_pred cccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHHH-----hhh-------ccc--------C-
Q 011454 341 RLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEVLA-----YIA-------DNR--------V- 398 (485)
Q Consensus 341 rip~~~~~~~~kirka~~~L~-~~gr~ps~eEIae~L~is~eev~~~l~~~~-----~l~-------D~~--------~- 398 (485)
+|++..+..+++..+...+. ..|+.|+.+++|+.+|++.+++..++.... .+. +.. .
T Consensus 101 -~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~~~~~~~~~l~~~l~ 179 (257)
T PRK05911 101 -VPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQSDDEAGLALEERIA 179 (257)
T ss_pred -CCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCCCCCccccchhhhcc
Confidence 89999999999988888874 689999999999999999999988764321 011 000 0
Q ss_pred ---CCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 399 ---ENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 399 ---e~~pee~~e~~el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
...|++.++..+....|.++| +.|||++|.||.++| ++++|++|||+.||+|+++|++++++|+++||+.+..
T Consensus 180 d~~~~~~~~~~~~~~~~~~l~~al-~~L~~~er~vi~l~y---~e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l~~ 255 (257)
T PRK05911 180 DERAETGYDVVDKKEFSSILAEAI-LALEEKERKVMALYY---YEELVLKEIGKILGVSESRVSQIHSKALLKLRATLSA 255 (257)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHH-HcCCHHHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 112445556667777899999 899999999999999 7999999999999999999999999999999998864
No 24
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=100.00 E-value=2.1e-32 Score=273.00 Aligned_cols=230 Identities=28% Similarity=0.352 Sum_probs=200.2
Q ss_pred hccccCCCHHHHHHHHHHHHc-CCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHHHHHhHHHHH
Q 011454 200 VVSEELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVM 278 (485)
Q Consensus 200 i~~~~~Lt~eee~~L~~~ik~-Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~Lie~yl~LV~ 278 (485)
.+++|+||.+++.+|+.+++. ||. .|++.|+..|.|+|+
T Consensus 6 ~~~~~~~~~~~e~~l~~~~~~~~d~----------------------------------------~a~~~l~~~y~~lv~ 45 (268)
T PRK06288 6 SGKIPKYAQQDETELWREYKKTGDP----------------------------------------KIREYLILKYSPLVK 45 (268)
T ss_pred cCCCccccchHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHH
Confidence 467899999999999999765 565 899999999999999
Q ss_pred HHHHHhc-C--CCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHHHHHHHH
Q 011454 279 SIAQRYD-N--MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRN 355 (485)
Q Consensus 279 sIA~ry~-~--~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~~~kirk 355 (485)
.+|++|. + .+.+++||+||||+|||+++++||+.+|.+|.||+++||++.|.+++++. .++|++.....+++++
T Consensus 46 ~~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~---~~~p~~~~~~~~~i~~ 122 (268)
T PRK06288 46 YVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSI---DWIPRSVRQKARQIER 122 (268)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhc---CccCHHHHHHHHHHHH
Confidence 9999986 2 56789999999999999999999999898999999999999999999865 3589999888888888
Q ss_pred HHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHH---------Hhh---------------hcccCCCCCcchHHHHH
Q 011454 356 AKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEVL---------AYI---------------ADNRVENNPWHGVDDWA 410 (485)
Q Consensus 356 a~~~L~-~~gr~ps~eEIae~L~is~eev~~~l~~~---------~~l---------------~D~~~e~~pee~~e~~e 410 (485)
+...+. ..|+.|+.++||+.+|++.+.+..++... +.+ ++. ...+|+..++..+
T Consensus 123 ~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~l~~~~~~~-~~~~pe~~~~~~e 201 (268)
T PRK06288 123 AIAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLESP-AALNPDEIAEREE 201 (268)
T ss_pred HHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccCCCcccchhhhhccCC-CCCCHHHHHHHHH
Confidence 888885 68999999999999999999998876432 111 111 1235666677778
Q ss_pred HHHHHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 011454 411 LKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 477 (485)
Q Consensus 411 l~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~ 477 (485)
....|..+| ..||+++|.||.++| ++++|++|||+.||+|.++|++++++|+++||+.+...+
T Consensus 202 ~~~~l~~~l-~~L~~~~r~vl~l~~---~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~~~~ 264 (268)
T PRK06288 202 IKRVIVEAI-KTLPEREKKVLILYY---YEDLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLAEIK 264 (268)
T ss_pred HHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 888999999 899999999999999 799999999999999999999999999999999997653
No 25
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=100.00 E-value=9.5e-32 Score=266.30 Aligned_cols=228 Identities=27% Similarity=0.348 Sum_probs=201.2
Q ss_pred cCCCHHHHHHHHHHHHc-CCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHHHHHhHHHHHHHHH
Q 011454 204 ELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ 282 (485)
Q Consensus 204 ~~Lt~eee~~L~~~ik~-Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~Lie~yl~LV~sIA~ 282 (485)
|.|+++++..|+.+++. ||. .|++.||..|.++|+++|+
T Consensus 8 ~~l~~~e~~~li~~~~~~gd~----------------------------------------~a~~~l~~~~~~~v~~~a~ 47 (257)
T PRK08583 8 TKLTKEEVNKWIAEYQENQDE----------------------------------------EAQEKLVKHYKNLVESLAY 47 (257)
T ss_pred CcCChHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHHHH
Confidence 77999999999999986 787 9999999999999999999
Q ss_pred HhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHH-
Q 011454 283 RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE- 361 (485)
Q Consensus 283 ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~~~kirka~~~L~- 361 (485)
+|.+++.+++||+||||++||+++++||+..|.+|.||+++||++.|.+++++..+.+++|++.....+++..+...+.
T Consensus 48 ~~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~~~i~r~~~~~~~~~~~~~~~~~~ 127 (257)
T PRK08583 48 KYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTT 127 (257)
T ss_pred HHhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHHHHHHhcCCCcCCCHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999998889999999999999999999999999999999998888888887775
Q ss_pred HcCCCCCHHHHHHHhCCCHHHHHHHHHHHHh-----hhcc-------------cCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 362 EKGVTPSVDRIAEYLNMSQKKVRNATEVLAY-----IADN-------------RVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 362 ~~gr~ps~eEIae~L~is~eev~~~l~~~~~-----l~D~-------------~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
..++.|+.+++++.+|++.+++..+...... +.+. ....+|++..+..+....+..+| ..|
T Consensus 128 ~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l-~~L 206 (257)
T PRK08583 128 ELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDGSTVTLLDIVGQQEDGYELTEQRMILEKIL-PVL 206 (257)
T ss_pred HhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCCCCccchHhhhcCCcchhHHHHHHHHHHHHHH-HhC
Confidence 5788999999999999999998776543210 0000 01124666677777788899999 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
|+++|.||.++| ++|+|++|||+.||||++||++++++|+++||+.+..
T Consensus 207 ~~~~r~vl~l~~---~~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l~~ 255 (257)
T PRK08583 207 SDREKSIIQCTF---IENLSQKETGERLGISQMHVSRLQRQAIKKLREAAFL 255 (257)
T ss_pred CHHHHHHHHHHH---hCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 999999999999 7999999999999999999999999999999998864
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=1.1e-31 Score=260.68 Aligned_cols=207 Identities=34% Similarity=0.434 Sum_probs=182.9
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccc
Q 011454 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (485)
Q Consensus 263 ~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~iri 342 (485)
..|++.|+..|.|+|+++|++|.+++.++|||+|||++|||+++++||+.+|.+|.||+++||++.|.++++++.|.+++
T Consensus 2 ~~a~~~lv~~y~~~v~~~a~~~~~~~~~~eDl~Qe~~i~l~~a~~~f~~~~~~~F~ty~~~~i~~~~~~~~r~~~~~~ri 81 (227)
T TIGR02980 2 KEAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVRV 81 (227)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCcHHHHHHHHHHHHHHHHHHcCCceec
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHHH---------hhhccc--------CCCCCcc
Q 011454 343 PNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEVLA---------YIADNR--------VENNPWH 404 (485)
Q Consensus 343 p~~~~~~~~kirka~~~L~-~~gr~ps~eEIae~L~is~eev~~~l~~~~---------~l~D~~--------~e~~pee 404 (485)
|.+.....++++++...+. +.|+.|+.+++++.+|++.+++..++.... .+.+.. ...+|+.
T Consensus 82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~~~~~~ 161 (227)
T TIGR02980 82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTLGDEDD 161 (227)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCcccccccCCcch
Confidence 9999998889988888875 689999999999999999999987765431 111000 0113445
Q ss_pred hHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 011454 405 GVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 473 (485)
Q Consensus 405 ~~e~~el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L 473 (485)
.++..+....|..+| ..||++++.||.++| ++|+|++|||+.||+|+++|++++++|+++||+.+
T Consensus 162 ~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~y---~~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~l 226 (227)
T TIGR02980 162 ALETVEDRLALKPLL-AALPERERRILLLRF---FEDKTQSEIAERLGISQMHVSRLLRRALKKLREQL 226 (227)
T ss_pred HHHhHHHHHHHHHHH-HcCCHHHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 555667778899999 899999999999999 78999999999999999999999999999999875
No 27
>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=1.4e-31 Score=260.79 Aligned_cols=206 Identities=33% Similarity=0.442 Sum_probs=176.2
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccc
Q 011454 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (485)
Q Consensus 263 ~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~iri 342 (485)
..|++.|+..|.++|+++|++|.+++.+++||+|||++|||+++++||+.+|.+|.||+++||++.|.+++++.. .+++
T Consensus 10 ~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~~~-~i~~ 88 (231)
T TIGR02885 10 KEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDG-IIKV 88 (231)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-CeEC
Confidence 389999999999999999999999999999999999999999999999999989999999999999999999986 7899
Q ss_pred cccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHHH---hhhc----ccC------C--CCCcchH
Q 011454 343 PNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEVLA---YIAD----NRV------E--NNPWHGV 406 (485)
Q Consensus 343 p~~~~~~~~kirka~~~L~-~~gr~ps~eEIae~L~is~eev~~~l~~~~---~l~D----~~~------e--~~pee~~ 406 (485)
|+++.....+++++...+. ++|+.|+.+++|+.+|++.+++..++.... .+.+ ... + .++....
T Consensus 89 p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~~~~~ 168 (231)
T TIGR02885 89 SRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLDQIADKGSED 168 (231)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCCCcchhhhhcCCCCccH
Confidence 9999999999988888774 689999999999999999999988765431 0110 000 0 0111112
Q ss_pred HHHHHHHHHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 011454 407 DDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 473 (485)
Q Consensus 407 e~~el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L 473 (485)
+.......+.+++ +.||++++.||.++| ++++|++|||+.||||+++|++++++|+++||..|
T Consensus 169 ~~~~~~~~l~~~l-~~L~~~e~~i~~~~~---~~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~l 231 (231)
T TIGR02885 169 SDWLEKIALKEAI-SKLDERERQIIMLRY---FKDKTQTEVANMLGISQVQVSRLEKKVLKKMKEKL 231 (231)
T ss_pred HhHHHHHHHHHHH-HcCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHhC
Confidence 3333456788888 899999999999999 68999999999999999999999999999999864
No 28
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=4.5e-31 Score=260.89 Aligned_cols=203 Identities=29% Similarity=0.367 Sum_probs=177.9
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcC---CCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~---~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~i 340 (485)
.|++.||..|.|+|+.+|++|.+ +..+++|++||||+|||+++++||+.+|.+|.||+++||++.|.+++++..
T Consensus 22 ~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~d~lR~~~--- 98 (251)
T PRK07670 22 DAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKED--- 98 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC---
Confidence 99999999999999999999965 688999999999999999999999999999999999999999999999876
Q ss_pred cccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHHH----------------------hhhccc
Q 011454 341 RLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEVLA----------------------YIADNR 397 (485)
Q Consensus 341 rip~~~~~~~~kirka~~~L~-~~gr~ps~eEIae~L~is~eev~~~l~~~~----------------------~l~D~~ 397 (485)
++|.+..+.+++++.+...+. ..|+.|+.+++|+.+|++.++|..++.... .+.+.
T Consensus 99 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~- 177 (251)
T PRK07670 99 WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDDGENVSVTIRDD- 177 (251)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccCCCCcchhhhhhcCc-
Confidence 589988888888888887774 689999999999999999999998865321 00111
Q ss_pred CCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 011454 398 VENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 474 (485)
Q Consensus 398 ~e~~pee~~e~~el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~ 474 (485)
...+|++.....+....|..+| ..||+++|.||.++| ++|+|++|||+.||+|.++|++++++|+++||.++.
T Consensus 178 ~~~~~e~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~~---~~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~ 250 (251)
T PRK07670 178 KTPTPEEKLLKEELIEELAEKI-KQLSEKEQLVISLFY---KEELTLTEIGQVLNLSTSRISQIHSKALFKLKKLLE 250 (251)
T ss_pred CCCCHHHHHHHHHHHHHHHHHH-hcCCHHHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 1224555566667777899999 899999999999999 899999999999999999999999999999999875
No 29
>PRK05572 sporulation sigma factor SigF; Validated
Probab=100.00 E-value=6.4e-31 Score=259.95 Aligned_cols=233 Identities=34% Similarity=0.453 Sum_probs=199.7
Q ss_pred HHhhccccCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHHHHHhHHH
Q 011454 197 VKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRL 276 (485)
Q Consensus 197 l~~i~~~~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~Lie~yl~L 276 (485)
++.-...|.||.+++.+|+.+++.|+. .|+++||..|.++
T Consensus 5 ~~~~~~~~~l~~~~~~~li~~~~~gd~----------------------------------------~a~~~L~~~y~~~ 44 (252)
T PRK05572 5 VKNKKKKPQLKDEENKELIKKSQDGDQ----------------------------------------EARDTLVEKNLRL 44 (252)
T ss_pred hccCcCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHH
Confidence 344556799999999999999999997 9999999999999
Q ss_pred HHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHHHHHHHHH
Q 011454 277 VMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNA 356 (485)
Q Consensus 277 V~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~~~kirka 356 (485)
|+.+|++|.+++.+++||+||||+++|+++++|++.++.+|.||+++||++.|.+++++.. .+++|++......+++++
T Consensus 45 v~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~~~-~~r~~~~~~~~~~~~~~~ 123 (252)
T PRK05572 45 VWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKD 123 (252)
T ss_pred HHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CCCCCHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999988889999999999999999999885 789999999999999998
Q ss_pred HHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHHHh---hhcccC--CCCC--------cchHHHHHHHHHHHHHHHhh
Q 011454 357 KLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEVLAY---IADNRV--ENNP--------WHGVDDWALKDEVNKLIIVT 422 (485)
Q Consensus 357 ~~~L~-~~gr~ps~eEIae~L~is~eev~~~l~~~~~---l~D~~~--e~~p--------ee~~e~~el~e~L~~~L~~~ 422 (485)
...+. +.|+.|+.+++++.+|++.+++..+...... +.+... +..| ............|..++ +.
T Consensus 124 ~~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~l~~~l-~~ 202 (252)
T PRK05572 124 KDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITLLDQIADQSEEDWFDKIALKEAI-RE 202 (252)
T ss_pred HHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCCCCcchhhhhcCCCchhhHHHHHHHHHHH-Hc
Confidence 88874 5799999999999999999999876544311 111100 0011 11222344566788899 89
Q ss_pred CCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 011454 423 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 474 (485)
Q Consensus 423 Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~ 474 (485)
||++++.||.++| ++++|++|||+.+|+|+++|++++++|+++||+.+.
T Consensus 203 L~~~~~~v~~l~~---~~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l~ 251 (252)
T PRK05572 203 LDERERLIVYLRY---FKDKTQSEVAKRLGISQVQVSRLEKKILKQMKEKLD 251 (252)
T ss_pred CCHHHHHHHHHHH---hCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999 799999999999999999999999999999999874
No 30
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=99.97 E-value=4.1e-30 Score=249.54 Aligned_cols=198 Identities=31% Similarity=0.478 Sum_probs=174.4
Q ss_pred HHHHhHHHHHHHHHHhcC---CCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccccc
Q 011454 269 LVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH 345 (485)
Q Consensus 269 Lie~yl~LV~sIA~ry~~---~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~ 345 (485)
|+..|.++|+.+|++|.+ ++.+++||+|||++|||+++++|||.+|.+|+||+++||++.+.+++++.. ++|.+
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 578999999999999985 789999999999999999999999999999999999999999999998764 58988
Q ss_pred HHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHH---------Hhhhcc------------cCCCCCc
Q 011454 346 LHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEVL---------AYIADN------------RVENNPW 403 (485)
Q Consensus 346 ~~~~~~kirka~~~L~-~~gr~ps~eEIae~L~is~eev~~~l~~~---------~~l~D~------------~~e~~pe 403 (485)
....++++..+...+. ..|+.|+.+++++.+|++.++|..++... +.+.+. ....+|+
T Consensus 78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (224)
T TIGR02479 78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDKSEDPE 157 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhccccccCCHH
Confidence 8888899998888885 68999999999999999999999987532 111110 1123566
Q ss_pred chHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 011454 404 HGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 473 (485)
Q Consensus 404 e~~e~~el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L 473 (485)
+.+...+....|.++| +.||+++|.||.++| ++++|++|||+.||+|.++|++++++|+++||+.+
T Consensus 158 ~~~~~~~~~~~l~~~l-~~L~~~~r~il~l~y---~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 223 (224)
T TIGR02479 158 EELEREELREALAEAI-ESLSEREQLVLSLYY---YEELNLKEIGEVLGLTESRVSQIHSQALKKLRAKL 223 (224)
T ss_pred HHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---hCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHc
Confidence 6677778888999999 899999999999999 89999999999999999999999999999999876
No 31
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=99.97 E-value=1.5e-29 Score=247.70 Aligned_cols=208 Identities=28% Similarity=0.430 Sum_probs=178.0
Q ss_pred hhHHHHHHHHHHhHHHHHHHHHHhc---CCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhh
Q 011454 261 ECSLAREKLVMSNVRLVMSIAQRYD---NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS 337 (485)
Q Consensus 261 ~~~~A~e~Lie~yl~LV~sIA~ry~---~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~ 337 (485)
+|.-++++|+..|.++|+.+|++|. +++.+++||+||||++||+++++||+..|.+|.||+++||++.|.+++++..
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 4567999999999999999999997 6789999999999999999999999998889999999999999999999876
Q ss_pred hhccccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHHHh-----hhcc-------------cC
Q 011454 338 RTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEVLAY-----IADN-------------RV 398 (485)
Q Consensus 338 r~irip~~~~~~~~kirka~~~L~-~~gr~ps~eEIae~L~is~eev~~~l~~~~~-----l~D~-------------~~ 398 (485)
+ +|.........+......+. ..|++|+.++|++.+|++.++|..++..... +.+. ..
T Consensus 85 ~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~ 161 (236)
T PRK06986 85 W---VPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDSILVTEDHQ 161 (236)
T ss_pred C---CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCcccccccCCC
Confidence 3 67766666666666666664 6899999999999999999999987764311 1111 11
Q ss_pred CCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 399 ENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 399 e~~pee~~e~~el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
..+|++.+...+....|.++| +.||+++|.||.++| ++|+|++|||+.||||.++|++++++|+++||+.+..
T Consensus 162 ~~~~~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~~---~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~~ 234 (236)
T PRK06986 162 DEDPLQQLEDEELREALVEAI-ESLPEREQLVLSLYY---QEELNLKEIGAVLGVSESRVSQIHSQAIKRLRARLGE 234 (236)
T ss_pred CCCHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHhHh---ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 234556667777788899999 899999999999999 8999999999999999999999999999999998864
No 32
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=99.97 E-value=3.4e-29 Score=245.14 Aligned_cols=201 Identities=19% Similarity=0.315 Sum_probs=166.0
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcC---CCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~---~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~i 340 (485)
.....|+..|.|+|..+|++|.. .+.+.+||+|||++|||+|+++||+..| +|+||+++|||++|.+++++..+
T Consensus 15 ~~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~~-- 91 (231)
T PRK12427 15 QEEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELDW-- 91 (231)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcCC--
Confidence 45567899999999999999874 4679999999999999999999998666 89999999999999999998653
Q ss_pred cccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHH-----Hhhhc----ccCCC--CCcchHHH
Q 011454 341 RLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEVL-----AYIAD----NRVEN--NPWHGVDD 408 (485)
Q Consensus 341 rip~~~~~~~~kirka~~~L~-~~gr~ps~eEIae~L~is~eev~~~l~~~-----~~l~D----~~~e~--~pee~~e~ 408 (485)
+|+++....++++.+...+. ++|++|+.++||+.+|++.+++.+++... ..+++ ..... .+....+.
T Consensus 92 -~~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~~~ 170 (231)
T PRK12427 92 -RPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAHNDILQSRDLEEN 170 (231)
T ss_pred -CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCcccccCCCCHHHH
Confidence 68888888888888888884 68999999999999999999998876532 11111 11000 01111233
Q ss_pred HHHHHHHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011454 409 WALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA 472 (485)
Q Consensus 409 ~el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~ 472 (485)
......|.+++ ..||+++|.||.++| ++++|++|||+.||||+++|+|++++|+++||..
T Consensus 171 ~~~~~~l~~~l-~~L~~~er~vi~l~~---~~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr~~ 230 (231)
T PRK12427 171 IIIEDNLKQAL-SQLDEREQLILHLYY---QHEMSLKEIALVLDLTEARICQLNKKIAQKIKSF 230 (231)
T ss_pred HHHHHHHHHHH-HcCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 34566788899 899999999999999 7999999999999999999999999999999964
No 33
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=99.95 E-value=8.3e-27 Score=227.95 Aligned_cols=212 Identities=31% Similarity=0.416 Sum_probs=170.3
Q ss_pred hHHHHHHhhccccCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHHHH
Q 011454 192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM 271 (485)
Q Consensus 192 ~~~~yl~~i~~~~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~Lie 271 (485)
++..|+.++...|+||++++..|+..++.|+. .|++.|+.
T Consensus 17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~gd~----------------------------------------~a~~~l~~ 56 (233)
T PRK05803 17 FLVSYVKNNSFPQPLSEEEERKYLELMKEGDE----------------------------------------EARNILIE 56 (233)
T ss_pred HHHHHHHHhcccCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHH
Confidence 67899999999999999999999999999997 99999999
Q ss_pred HhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHHHH
Q 011454 272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG 351 (485)
Q Consensus 272 ~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~~~ 351 (485)
.|.++|+++|.+|.+++.+++|++||+|+++|+++++|+++++.+|.+|+++|+++.+.+++++..+..+..
T Consensus 57 ~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~~~~~~-------- 128 (233)
T PRK05803 57 RNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTKKEV-------- 128 (233)
T ss_pred HhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhccccCC--------
Confidence 999999999999999999999999999999999999999988889999999999999999998764310000
Q ss_pred HHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHH
Q 011454 352 LIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREI 430 (485)
Q Consensus 352 kirka~~~L~-~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp~rER~V 430 (485)
.+. ..+.+....+. +.. +..++. ..+|++.....+..+.|.++| +.||+++|+|
T Consensus 129 -------~~~~~~~~~~~~~~~------~~~---------~~~~~~--~~~~~~~~~~~~~~~~l~~~l-~~Lp~~~R~i 183 (233)
T PRK05803 129 -------SLQDPIGVDKEGNEI------SLI---------DILGSE--EDDVIEQVELKMEVEKLYKKI-DILDEREKEV 183 (233)
T ss_pred -------CccccccCCCCcCcc------cHH---------HHccCC--CCCHHHHHHHHHHHHHHHHHH-HhCCHHHHHH
Confidence 000 00000000000 000 111111 123556666667778899999 8999999999
Q ss_pred HhhHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Q 011454 431 IRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 476 (485)
Q Consensus 431 I~LryGL~-~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~ 476 (485)
|.++|+++ ++|+|++|||+.||+|.++|++++++|+++||+.+...
T Consensus 184 ~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~~~ 230 (233)
T PRK05803 184 IEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKELYRA 230 (233)
T ss_pred HHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 99999764 58999999999999999999999999999999998754
No 34
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=99.93 E-value=2.3e-24 Score=210.13 Aligned_cols=209 Identities=29% Similarity=0.392 Sum_probs=161.2
Q ss_pred hHHHHHHhhccc-cCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHHH
Q 011454 192 RLKGYVKGVVSE-ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (485)
Q Consensus 192 ~~~~yl~~i~~~-~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~Li 270 (485)
++-+|+-.-++. +.|++.++..|+.+++.|+. .|++.|+
T Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~li~~~~~gd~----------------------------------------~af~~l~ 54 (227)
T TIGR02846 15 FLVGYVTNNGSFPQPLSEEEEKKYLDRLKEGDE----------------------------------------EARNVLI 54 (227)
T ss_pred HHHHHHHHHHhCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHH
Confidence 345677766655 46999999999999999997 9999999
Q ss_pred HHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcc-ccccHHHH
Q 011454 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-LPNHLHER 349 (485)
Q Consensus 271 e~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~ir-ip~~~~~~ 349 (485)
+.|.|.|+++|.+|.++..++||++||+|+++|+++++|+++.+.+|.||+++++++.+.+++++..+... .+..
T Consensus 55 ~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~Rk~~r~~~~~~~~---- 130 (227)
T TIGR02846 55 ERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHLRALKKTKGEVSLQ---- 130 (227)
T ss_pred HHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHHHHHhccccceecc----
Confidence 99999999999999999999999999999999999999999888789999999999999999887653110 0000
Q ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHH
Q 011454 350 LGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGERERE 429 (485)
Q Consensus 350 ~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp~rER~ 429 (485)
...+.+....+ .+.. +...+ ...+|++.....+..+.|.++| +.||+++|+
T Consensus 131 -----------~~~~~~~~~~~------~~~~---------~~~~~--~~~~~~~~~~~~~~~~~l~~~i-~~L~~~~r~ 181 (227)
T TIGR02846 131 -----------DPIGVDKEGNE------ISLI---------DILGS--DGDSVIEQVELNLEIKKLYKKL-SVLDGRERE 181 (227)
T ss_pred -----------ccccCCcccCc------ccHH---------HHhcC--CCCChHHHHHHHHHHHHHHHHH-HhCCHHHHH
Confidence 00000000000 0000 00101 1124555555666667889999 999999999
Q ss_pred HHhhHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 011454 430 IIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 473 (485)
Q Consensus 430 VI~LryGL~-~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L 473 (485)
||.++|.++ ++++|++|||+.||+|+++|++++++|+++||+.|
T Consensus 182 il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~~ 226 (227)
T TIGR02846 182 VIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYKEL 226 (227)
T ss_pred HHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 999999432 38999999999999999999999999999999875
No 35
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=99.93 E-value=2.3e-24 Score=210.50 Aligned_cols=208 Identities=23% Similarity=0.379 Sum_probs=157.2
Q ss_pred HHHhhccc-cCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHHHHHhH
Q 011454 196 YVKGVVSE-ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNV 274 (485)
Q Consensus 196 yl~~i~~~-~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~Lie~yl 274 (485)
|+.++... +.+++..+..|+.+++.||. .|++.++..|.
T Consensus 23 ~~~~~~~~~~~~~~~~~~~L~~~~~~gd~----------------------------------------~af~~l~~~y~ 62 (234)
T PRK08301 23 YIGGSEALPPPLSKEEEEYLLNKLPKGDE----------------------------------------AVRSLLIERNL 62 (234)
T ss_pred HhccccccCCcCCHHHHHHHHHHHHccCH----------------------------------------HHHHHHHHHhH
Confidence 66666544 45788889999999999997 99999999999
Q ss_pred HHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHHHHHHH
Q 011454 275 RLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIR 354 (485)
Q Consensus 275 ~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~~~kir 354 (485)
++|+.+|++|.+++.+++|++||+|+++|+++++|++..+++|.||++.+++|.+.+++++..+.... .
T Consensus 63 ~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~d~lRk~~~~~~~-~---------- 131 (234)
T PRK08301 63 RLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNNKVKAE-V---------- 131 (234)
T ss_pred HHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHHHHHHhccccc-c----------
Confidence 99999999999999999999999999999999999998888899999999999999999876531000 0
Q ss_pred HHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHhhH
Q 011454 355 NAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLY 434 (485)
Q Consensus 355 ka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp~rER~VI~Lr 434 (485)
.+ ..... .+.... ..... +...+. ...+....+.......|..+| ++||+++|.||.|+
T Consensus 132 ----~~---~~~~~-~~~~~~-~~~~~---------~~~~~~--~~~~~~~~~~~~~~~~l~~al-~~Lp~~~R~v~~L~ 190 (234)
T PRK08301 132 ----SF---DEPLN-IDWDGN-ELLLS---------DVLGTD--NDIIYKDIEDEVDRKLLKKAL-KKLSDREKQIMELR 190 (234)
T ss_pred ----cc---ccccc-cccCCC-cccHH---------HhccCc--ccchHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHH
Confidence 00 00000 000000 00000 000000 111223344445566788999 89999999999999
Q ss_pred hccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 435 YGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 435 yGL~-~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
|++. .+|+|++|||+.||||.+||++++++|+++||+.+..
T Consensus 191 y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l~~ 232 (234)
T PRK08301 191 FGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEINK 232 (234)
T ss_pred hccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 8653 5899999999999999999999999999999998864
No 36
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=99.91 E-value=3.6e-23 Score=195.10 Aligned_cols=179 Identities=20% Similarity=0.217 Sum_probs=146.4
Q ss_pred CCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHHHHHhHHHHHHHHHHhc
Q 011454 206 LTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYD 285 (485)
Q Consensus 206 Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~Lie~yl~LV~sIA~ry~ 285 (485)
+|+++...|+..++.|+. .|++.|+..|.+.|+++|.++.
T Consensus 6 ~~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~~~~~l~~~~~~~~ 45 (189)
T PRK09648 6 DTGEELDALVAEAVAGDR----------------------------------------RALREVLEIIRPLVVRYCRARL 45 (189)
T ss_pred CCchHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHHHHHHh
Confidence 477888889999999997 9999999999999999999987
Q ss_pred CC----CCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHH
Q 011454 286 NM----GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE 361 (485)
Q Consensus 286 ~~----~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~~~kirka~~~L~ 361 (485)
++ ..+++|++||+|+++|+++.+|++. +.+|.+|++..+++.+.+++++..+....+
T Consensus 46 ~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~n~~~d~~r~~~r~~~~~------------------ 106 (189)
T PRK09648 46 GGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAAHKVADAHRAAGRDKAVP------------------ 106 (189)
T ss_pred cccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHHHHHHHHHHHhCCCcccc------------------
Confidence 65 3689999999999999999999864 347999999999999988887764311000
Q ss_pred HcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhccCCCC
Q 011454 362 EKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKEC 441 (485)
Q Consensus 362 ~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg 441 (485)
.+++.+ ......+|++.....+..+.|..+| ..||+++|+||.++| ++|
T Consensus 107 -------~~~~~~--------------------~~~~~~~~~~~~~~~e~~~~l~~~l-~~L~~~~r~i~~l~~---~~g 155 (189)
T PRK09648 107 -------TEEVPE--------------------RPSDDAGPEERALRSESSNRMRELL-DTLPEKQREILILRV---VVG 155 (189)
T ss_pred -------cccccc--------------------ccccCCCHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcC
Confidence 000000 0001234555666667777899999 899999999999999 799
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 474 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~ 474 (485)
+|++|||+.||+|.+||+++++||+++||+.+.
T Consensus 156 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 188 (189)
T PRK09648 156 LSAEETAEAVGSTPGAVRVAQHRALARLRAEIE 188 (189)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 999999999999999999999999999999874
No 37
>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=99.91 E-value=3.7e-23 Score=202.46 Aligned_cols=208 Identities=25% Similarity=0.387 Sum_probs=156.1
Q ss_pred HHHhhc-cccCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHHHHHhH
Q 011454 196 YVKGVV-SEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNV 274 (485)
Q Consensus 196 yl~~i~-~~~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~Lie~yl 274 (485)
|+.+.. ..+++++.++..|+..++.||. .|++.|+..|.
T Consensus 23 ~~~~~~~~~~~~~~~~~~~l~~~~~~~d~----------------------------------------~a~~~l~~~y~ 62 (234)
T TIGR02835 23 YIGGSEALPPPLTGEEEEALLQKLTQGDE----------------------------------------SAKSTLIERNL 62 (234)
T ss_pred HhcccccCCCcCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhH
Confidence 444433 3468899999999999999997 99999999999
Q ss_pred HHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHHHHHHH
Q 011454 275 RLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIR 354 (485)
Q Consensus 275 ~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~~~kir 354 (485)
+.|+++|++|.+++.+++|++||+|+++|+++++|++..+++|.+|++.++++.+.+++++..+.... ..
T Consensus 63 ~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~d~~Rk~~r~~~~-~~--------- 132 (234)
T TIGR02835 63 RLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILMYLRRNNKTRSE-VS--------- 132 (234)
T ss_pred HHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhccccCc-cc---------
Confidence 99999999999999999999999999999999999988877899999999999999999876531000 00
Q ss_pred HHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHhhH
Q 011454 355 NAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLY 434 (485)
Q Consensus 355 ka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp~rER~VI~Lr 434 (485)
+.. ......++.. .... ... +.. ...+.+..........|..+| +.||+++|.||.++
T Consensus 133 -----~~~-~~~~~~~~~~----~~~~---------~~~-~~~-~~~~~~~~~~~~~~~~l~~ai-~~Lp~~~R~ii~L~ 190 (234)
T TIGR02835 133 -----FDE-PLNVDWDGNE----LLLS---------DVL-GTD-SDIVYKYLEEEVDRELLRKAL-AKLNDREKKIMELR 190 (234)
T ss_pred -----ccc-cccCCCCCCc----chHH---------Hhc-CCC-CCcHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHH
Confidence 000 0000000000 0000 000 000 111223334445566799999 89999999999999
Q ss_pred hccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 435 YGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 435 yGL~-~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
|.+. ++|+|++|||+.||||++||++++++|+++||+.+..
T Consensus 191 ~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l~~ 232 (234)
T TIGR02835 191 FGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKEINR 232 (234)
T ss_pred HccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhhc
Confidence 8542 4899999999999999999999999999999998864
No 38
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=99.90 E-value=6.3e-23 Score=194.71 Aligned_cols=183 Identities=14% Similarity=0.155 Sum_probs=146.8
Q ss_pred cCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHHHHHhHHHHHHHHHH
Q 011454 204 ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQR 283 (485)
Q Consensus 204 ~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~Lie~yl~LV~sIA~r 283 (485)
|+..+.++..|+..++.|+. .|++.|+..|.++|+++|.+
T Consensus 10 ~~~~~~~~~~li~~~~~g~~----------------------------------------~a~~~l~~~y~~~l~~~~~~ 49 (194)
T PRK09646 10 PPAESPDLDALLRRVARGDQ----------------------------------------DAFAELYDRTSSRVYGLVRR 49 (194)
T ss_pred CCCCcccHHHHHHHHHccCH----------------------------------------HHHHHHHHHHHHHHHHHHHH
Confidence 55566677788888888887 99999999999999999999
Q ss_pred hcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHc
Q 011454 284 YDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK 363 (485)
Q Consensus 284 y~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~~~kirka~~~L~~~ 363 (485)
|.++..++||++||+|+++|+++++|++.+| .|.+|++..+++.+.++++.+.+..+...
T Consensus 50 ~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~r~~~~~~~~~~------------------- 109 (194)
T PRK09646 50 VLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHRRAVDRVRSEQAASQREV------------------- 109 (194)
T ss_pred HhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHHHHHHHHHhhcccccccc-------------------
Confidence 9999999999999999999999999998766 69999999999999888877642100000
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhccCCCCCC
Q 011454 364 GVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLT 443 (485)
Q Consensus 364 gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S 443 (485)
...... . +.. ...+++..+..+..+.|..+| ..||+++|.||.|+| ++|+|
T Consensus 110 --~~~~~~---------------------~-~~~-~~~~~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~~---~~~~s 160 (194)
T PRK09646 110 --RYGARN---------------------V-DPA-FDQVAEEVEARLERERVRDCL-DALTDTQRESVTLAY---YGGLT 160 (194)
T ss_pred --cccccc---------------------c-ccc-ccchHHHHHHHhHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCC
Confidence 000000 0 000 112333444455667888999 899999999999999 89999
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 444 WEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 444 ~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
++|||+.||+|.++|+++++||+++||+.+..
T Consensus 161 ~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l~~ 192 (194)
T PRK09646 161 YREVAERLAVPLGTVKTRMRDGLIRLRDCLGV 192 (194)
T ss_pred HHHHHHHhCCChHhHHHHHHHHHHHHHHHhcc
Confidence 99999999999999999999999999999853
No 39
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=99.90 E-value=1.2e-22 Score=191.00 Aligned_cols=162 Identities=16% Similarity=0.197 Sum_probs=133.5
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.|++.|+..|.++|+.+|+++.++..+++|++||+|+++|+++.+|++. +.+|.+|++..+++.+.++++++... +
T Consensus 20 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n~~~d~~R~~~~~---~ 95 (186)
T PRK05602 20 AAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLNLCYDRLRRRREV---P 95 (186)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHHHHHHHHHhcCCC---C
Confidence 9999999999999999999999999999999999999999999999976 34799999999999888887755310 0
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
. .++.. ..+ ....|+..+...+....+..+| ..|
T Consensus 96 ~-------------------------~~~~~------------------~~~--~~~~~~~~~~~~~~~~~l~~~l-~~L 129 (186)
T PRK05602 96 V-------------------------EDAPD------------------VPD--PAPGPDAGLEARQRARRVEQAL-AAL 129 (186)
T ss_pred c-------------------------ccccc------------------cCC--CCCCHHHHHHHHHHHHHHHHHH-HhC
Confidence 0 00000 000 0123444455556667789999 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhhH
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM 478 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~l 478 (485)
|+++|.||.|+| ++|+|++|||+.||+|++||++++++|+++||+.+...+.
T Consensus 130 ~~~~r~i~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~ 181 (186)
T PRK05602 130 PERQREAIVLQY---YQGLSNIEAAAVMDISVDALESLLARGRRALRAQLADLPG 181 (186)
T ss_pred CHHHHHHhhHHH---hcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 999999999999 8999999999999999999999999999999999987653
No 40
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=99.90 E-value=1.1e-22 Score=192.43 Aligned_cols=167 Identities=17% Similarity=0.165 Sum_probs=136.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.|++.|+..|.+.|+++|.++.++..+++|++||+|+++|+++++|++.. .|.+|++..+++.+.+++++..+....+
T Consensus 26 ~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~~--~f~~wl~~i~~n~~~~~~R~~~~~~~~~ 103 (194)
T PRK12513 26 AAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRA--RFRTWLYQIARNLLIDHWRRHGARQAPS 103 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCCC--chHHHHHHHHHHHHHHHHHHhccccccc
Confidence 99999999999999999999999999999999999999999999999753 6999999999999999987765321111
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
.. ....+ ........+|+...+..+....+..+| +.|
T Consensus 104 ~~----------------------~~~~~--------------------~~~~~~~~~~~~~~~~~~~~~~l~~~l-~~L 140 (194)
T PRK12513 104 LD----------------------ADEQL--------------------HALADDGAAPEQQLSLFRDRRRLQAAL-ETL 140 (194)
T ss_pred cc----------------------cchhh--------------------hhcCCCCCCHHHHHHHHHHHHHHHHHH-HhC
Confidence 00 00000 000111234555666667778899999 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhhH
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM 478 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~l 478 (485)
|+++|.||.|+| ++|+|++|||+.||+|+++|+++++||+++||+.+...+.
T Consensus 141 ~~~~r~i~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~~ 192 (194)
T PRK12513 141 PDEQREVFLLRE---HGDLELEEIAELTGVPEETVKSRLRYALQKLRELLAEEVA 192 (194)
T ss_pred CHhHhhheeeeh---ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 999999999999 8999999999999999999999999999999999987654
No 41
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=99.90 E-value=1.9e-22 Score=185.77 Aligned_cols=160 Identities=17% Similarity=0.193 Sum_probs=132.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.|++.|+..|.+.+++++.++.++..++||++||+|+.+|+++++|+...+ .|.+|++..+++.+.++++...+....
T Consensus 11 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R~~~~~~~~- 88 (170)
T TIGR02952 11 DAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFRGSKRHPLF- 88 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHHhcCCCCCC-
Confidence 999999999999999999999998899999999999999999999987555 799999999999999998876431100
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
..++.. .......+|++.+...+..+.+..+| ..|
T Consensus 89 ------------------------~~~~~~--------------------~~~~~~~~~~~~~~~~~~~~~l~~~l-~~L 123 (170)
T TIGR02952 89 ------------------------SLDVFK--------------------ELLSNEPNPEEAILKEEANEKLLKAL-KIL 123 (170)
T ss_pred ------------------------cHHHHh--------------------hcCCCCCCHHHHHHHHHHHHHHHHHH-HhC
Confidence 000000 00001234565666667778899999 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 473 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L 473 (485)
||++|.||.++| ++|+|++|||+.||||.++|+++++||+++||+.|
T Consensus 124 ~~~~r~vl~l~~---~~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~l 170 (170)
T TIGR02952 124 TPKQQHVIALRF---GQNLPIAEVARILGKTEGAVKILQFRAIKKLARQM 170 (170)
T ss_pred CHHHHHHHHHHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence 999999999998 79999999999999999999999999999999864
No 42
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=99.89 E-value=2.7e-22 Score=191.23 Aligned_cols=182 Identities=20% Similarity=0.290 Sum_probs=133.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.|++.|++.|.++|+.+|.+|.++..++||++||+|+++|+++.+|++.++.+|.||++.++++.+.++++...+..+.+
T Consensus 24 ~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n~~~d~~r~~~r~~~~~ 103 (208)
T PRK08295 24 EALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQIITAIKTANRQKHIP 103 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhhhhcccc
Confidence 99999999999999999999999999999999999999999999999987678999999999999888887654321111
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHH-HHHHhh
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVN-KLIIVT 422 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~-~~L~~~ 422 (485)
... . ...+... ..+..+.+.. +.+.+.. ..+|+..+...+....+. .++ ..
T Consensus 104 ~~~-------------~--~s~~~~~--~~~~~~~~~~---------~~~~~~~-~~~~~~~~~~~~~~~~l~~~~~-~~ 155 (208)
T PRK08295 104 LNS-------------Y--VSLDKPI--YDEESDRTLL---------DVISEAK-VTDPEELIISKEELEDIEEKIE-EL 155 (208)
T ss_pred ccc-------------e--eecCCcc--cCCccchhHH---------HHhcCcc-cCCHHHHHHHHHHHHHHHHHHH-Hh
Confidence 100 0 0000000 0000000000 1111111 134555555555555554 455 89
Q ss_pred CCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 011454 423 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 477 (485)
Q Consensus 423 Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~ 477 (485)
||+.+|.||.+ | ++|+|++|||+.||+|+++|++.++||+++||+++....
T Consensus 156 L~~~~r~vl~l-~---~e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l~~~~ 206 (208)
T PRK08295 156 LSELEKEVLEL-Y---LDGKSYQEIAEELNRHVKSIDNALQRVKRKLEKYLENRE 206 (208)
T ss_pred CCHHHHHHHHH-H---HccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence 99999999999 7 699999999999999999999999999999999987643
No 43
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=99.89 E-value=3.4e-22 Score=188.99 Aligned_cols=162 Identities=23% Similarity=0.315 Sum_probs=129.8
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.|++.|+..|.+.|+.+++++.++..+++|++||+|+++|+. ..|++..+ .|.||++..+++.+.++++++.+.....
T Consensus 29 ~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~~d~~Rk~~~~~~~~ 106 (194)
T PRK12519 29 AALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRAIDRLRSRRSRQRLL 106 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHHHHHHHhcccccchh
Confidence 999999999999999999999999999999999999999976 67887655 7999999999999999987764210000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
+..... ...+ .....|++.+...+....|..+| ..|
T Consensus 107 --------------------------~~~~~~----------------~~~~-~~~~~~~~~~~~~~~~~~l~~~l-~~L 142 (194)
T PRK12519 107 --------------------------ERWQQE----------------LLGE-ASEDTPLEQASLAERSQRVQTAL-AQL 142 (194)
T ss_pred --------------------------hhhhhh----------------hccc-ccCCCHHHHHHHHHHHHHHHHHH-HhC
Confidence 000000 0000 00123444555556667788999 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 474 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~ 474 (485)
|+++++||.|+| ++|+|++|||+.||+|.++|+++++||+++||+.+.
T Consensus 143 ~~~~~~v~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 190 (194)
T PRK12519 143 PESQRQVLELAY---YEGLSQSEIAKRLGIPLGTVKARARQGLLKLRELLQ 190 (194)
T ss_pred CHHHhhhhhhhh---hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999 899999999999999999999999999999999885
No 44
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=99.89 E-value=4.7e-22 Score=180.78 Aligned_cols=151 Identities=21% Similarity=0.217 Sum_probs=125.6
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccc
Q 011454 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (485)
Q Consensus 263 ~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~iri 342 (485)
..||+.|++.|.++|+.+++++ ++..++||++||+|+++|+++++|++..+ +|.+|++..+++.+.+++++..+..
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 3789999999999999999986 56679999999999999999999998666 6999999999999999987763200
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhh
Q 011454 343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVT 422 (485)
Q Consensus 343 p~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~ 422 (485)
.... ..++|++.....+....|..+| ..
T Consensus 79 ------------------~~~~---------------------------------~~~~~~~~~~~~~~~~~l~~~l-~~ 106 (154)
T PRK06759 79 ------------------EKCV---------------------------------CVGEYEDHFHFEDVEMKVKDFM-SV 106 (154)
T ss_pred ------------------cccc---------------------------------ccCCCcccccHHHHHHHHHHHH-Hh
Confidence 0000 0112333344445567788999 89
Q ss_pred CCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011454 423 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA 472 (485)
Q Consensus 423 Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~ 472 (485)
||+++|.||.++| ++|+|++|||+.||+|.++|++++.+|+++||+.
T Consensus 107 L~~~~r~ii~l~~---~~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 107 LDEKEKYIIFERF---FVGKTMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred CCHHHHHHHHHHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 9999999999999 8999999999999999999999999999999974
No 45
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=99.89 E-value=7.9e-22 Score=186.36 Aligned_cols=188 Identities=20% Similarity=0.243 Sum_probs=148.1
Q ss_pred CCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHHHHHhHHHHHHHHHHh
Q 011454 205 LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRY 284 (485)
Q Consensus 205 ~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~Lie~yl~LV~sIA~ry 284 (485)
+|++..+..|+..++.||. .|++.|+..|.+.|+.+++++
T Consensus 1 ~~~~~~~~~ll~~~~~gd~----------------------------------------~a~~~l~~~y~~~l~~~~~~~ 40 (193)
T PRK11923 1 MLTQEEDQQLVERVQRGDK----------------------------------------RAFDLLVLKYQHKILGLIVRF 40 (193)
T ss_pred CCccccHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHHHHHH
Confidence 4667777788888999987 999999999999999999999
Q ss_pred cCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHcC
Q 011454 285 DNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKG 364 (485)
Q Consensus 285 ~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~~~kirka~~~L~~~g 364 (485)
.++..+++|++||+|+++|+++.+|++.. .|.+|++..+++.+.+++++..+.....
T Consensus 41 ~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~~d~~rk~~~~~~~~--------------------- 97 (193)
T PRK11923 41 VHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTAKNHLVSRGRRPPDS--------------------- 97 (193)
T ss_pred hCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHHHHHHHHhcCCCccc---------------------
Confidence 99999999999999999999999999864 4999999999998888887654210000
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhccCCCCCCH
Q 011454 365 VTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTW 444 (485)
Q Consensus 365 r~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~ 444 (485)
....++. ... +.. ..+. ...+|+..+...+..+.+..+| ..||+++|.||.++| .+|+|+
T Consensus 98 -~~~~~~~-~~~--~~~---------~~~~---~~~~~e~~~~~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~ 157 (193)
T PRK11923 98 -DVSSEDA-EFY--DGD---------HALK---DIESPERALLRDEIEGTVHRTI-QQLPEDLRTALTLRE---FDGLSY 157 (193)
T ss_pred -cccccch-hhh--ccc---------cccc---CcCCHHHHHHHHHHHHHHHHHH-HhCCHHHhHHHhhHH---hcCCCH
Confidence 0000000 000 000 0000 0134555566677778899999 899999999999998 899999
Q ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 445 EDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 445 eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
+|||+.||+|.++|+++++||+++||+++..
T Consensus 158 ~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~ 188 (193)
T PRK11923 158 EDIASVMQCPVGTVRSRIFRAREAIDKALQP 188 (193)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999874
No 46
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=99.89 E-value=5e-22 Score=193.99 Aligned_cols=192 Identities=19% Similarity=0.185 Sum_probs=155.1
Q ss_pred cccCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHHHHHhHHHHHHHH
Q 011454 202 SEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIA 281 (485)
Q Consensus 202 ~~~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~Lie~yl~LV~sIA 281 (485)
..|+|++..+..|+..++.|+. .|++.|+..|.+.|++++
T Consensus 8 ~~~~~~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~y~~~l~~~a 47 (231)
T PRK11922 8 RPPPLSAASDRELVARVLAGDE----------------------------------------AAFEALMRRHNRRLYRTA 47 (231)
T ss_pred CCCCcCcccHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHHH
Confidence 3588999999999999999998 999999999999999999
Q ss_pred HHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHH
Q 011454 282 QRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE 361 (485)
Q Consensus 282 ~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~~~kirka~~~L~ 361 (485)
.++.++..+++|++||+|+++|+++++|++. ..|.+|++..+++.+.+++++..+...++..
T Consensus 48 ~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~Rk~~r~~~~~~~---------------- 109 (231)
T PRK11922 48 RAILRNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNEALGRLRRRRRLVNLAEM---------------- 109 (231)
T ss_pred HHHhCChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHHHHHHHHhhcccccchhc----------------
Confidence 9999999999999999999999999999986 3699999999999998888776532111000
Q ss_pred HcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhccCCCC
Q 011454 362 EKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKEC 441 (485)
Q Consensus 362 ~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg 441 (485)
......++. ..........+|++.+...+..+.|.++| ..||+++|+||.++| .+|
T Consensus 110 -----~~~~~~~~~---------------~~~~~~~~~~~~e~~~~~~e~~~~l~~~l-~~L~~~~r~i~~l~~---~~g 165 (231)
T PRK11922 110 -----VMASTIAGG---------------ERTPLADPAEDPERAAARREIRALLERAI-DALPDAFRAVFVLRV---VEE 165 (231)
T ss_pred -----ccccccccc---------------cccccCcccCChHHHHHHHHHHHHHHHHH-HhCCHHHhhhheeeh---hcC
Confidence 000000000 00000111235666677777888899999 899999999999998 799
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
+|++|||+.||+|.++|++++++|+++||+.+..
T Consensus 166 ~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~~ 199 (231)
T PRK11922 166 LSVEETAQALGLPEETVKTRLHRARRLLRESLAR 199 (231)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999975
No 47
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=99.89 E-value=6.9e-22 Score=187.89 Aligned_cols=163 Identities=17% Similarity=0.198 Sum_probs=132.9
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.|++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|+.+.+|++..+ .|.+|++..+++.+.+++++..+..
T Consensus 26 ~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~Rk~~~~~--- 101 (196)
T PRK12524 26 AAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGEA-RVSTWLYRVVCNLCTDRLRRRRRAS--- 101 (196)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhccccccc-hHHHHHHHHHHHHHHHHHHhhcCCC---
Confidence 999999999999999999999999999999999999999999999985333 6999999999998888877653200
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
...++. + . ..+ ...+|++.+...+....|..+| +.|
T Consensus 102 -----------------------~~~~~~------~-----------~-~~~--~~~~~~~~~~~~~~~~~l~~~l-~~L 137 (196)
T PRK12524 102 -----------------------VDLDDA------P-----------E-PAD--AAPGAEEALIEGDRMRALDAAL-AAL 137 (196)
T ss_pred -----------------------CCcccc------c-----------c-ccc--cCCCHHHHHHHHHHHHHHHHHH-HhC
Confidence 000000 0 0 000 0123444556666777899999 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 477 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~ 477 (485)
|+++|.||.|+| ++|++++|||+.||||.+||+++++||+++||+.+...+
T Consensus 138 ~~~~r~i~~L~~---~~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~~ 188 (196)
T PRK12524 138 PERQRQAVVLRH---IEGLSNPEIAEVMEIGVEAVESLTARGKRALAALLAGQR 188 (196)
T ss_pred CHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 999999999999 899999999999999999999999999999999998644
No 48
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=99.89 E-value=7.1e-22 Score=184.51 Aligned_cols=160 Identities=16% Similarity=0.146 Sum_probs=129.8
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.|+..|+..|.+.|+.+|.++.++..+++|++||+|+++|+++++|++..+ .|.+|++..+++.+.+++++..+. ..+
T Consensus 19 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~R~~~~~-~~~ 96 (179)
T PRK12514 19 DAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGL-SPMTWLITIARNHAIDRLRARKAV-AVD 96 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCcccc-cHHHHHHHHHHHHHHHHHHhcCCc-ccc
Confidence 999999999999999999999999999999999999999999999986544 599999999999998888765321 000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
.++.. + ..+. ...|++.+...+....|..+| ..|
T Consensus 97 -------------------------~~~~~-----------------~-~~~~--~~~~e~~~~~~~~~~~l~~~l-~~L 130 (179)
T PRK12514 97 -------------------------IDEAH-----------------D-LADP--SPGPEAEVIAGDEGQRIDACL-EEL 130 (179)
T ss_pred -------------------------cccch-----------------h-cccc--CCCHHHHHHhHHHHHHHHHHH-HhC
Confidence 00000 0 0000 123454454455556788899 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 474 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~ 474 (485)
|++++.||.++| ++|+|++|||+.||+|.++|+++++||+++||+++.
T Consensus 131 ~~~~r~i~~l~~---~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 178 (179)
T PRK12514 131 EKDRAAAVRRAY---LEGLSYKELAERHDVPLNTMRTWLRRSLLKLRECLS 178 (179)
T ss_pred CHHHHHHHHHHH---HcCCCHHHHHHHHCCChHHHHHHHHHHHHHHHHHhc
Confidence 999999999999 899999999999999999999999999999999874
No 49
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=99.88 E-value=1.3e-21 Score=183.64 Aligned_cols=159 Identities=19% Similarity=0.269 Sum_probs=129.2
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.|++.|+..|.+.++.++.++.++..+++|++||+|+.+|+.+++|++..+ .|.+|++..+++.+.+++++..+...+.
T Consensus 23 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wL~~iarn~~~d~~r~~~~~~~~~ 101 (182)
T PRK12537 23 RALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARG-SARGWIYSVTRHLALNVLRDTRREVVLD 101 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHHHHHhccccCccc
Confidence 999999999999999999999999999999999999999999999986544 6999999999999999987764211000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
.... .+.....+++...+..+....+..+| +.|
T Consensus 102 -------------------------~~~~---------------------~~~~~~~~~~~~~~~~~~~~~l~~~l-~~L 134 (182)
T PRK12537 102 -------------------------DDAE---------------------ETAQTLHEIIDDFDLWANSGKIHRCL-EQL 134 (182)
T ss_pred -------------------------cchh---------------------hhcccccchHHHHHHHHHHHHHHHHH-HhC
Confidence 0000 00000112333344445566788999 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 473 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L 473 (485)
|+++|.||.++| ++|+|++|||+.||||.++|+++++||+++||+++
T Consensus 135 ~~~~r~i~~l~~---~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 181 (182)
T PRK12537 135 EPARRNCILHAY---VDGCSHAEIAQRLGAPLGTVKAWIKRSLKALRECM 181 (182)
T ss_pred CHHHHHHHHHHH---HcCCCHHHHHHHHCCChhhHHHHHHHHHHHHHHHh
Confidence 999999999999 89999999999999999999999999999999986
No 50
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=99.88 E-value=1.6e-21 Score=183.30 Aligned_cols=162 Identities=19% Similarity=0.221 Sum_probs=131.6
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.+++.|+..|.+.|+++|+++.++..++||++||+|+++|+++++|++.++ .|.+|++..+++.+.+++++..+...
T Consensus 25 ~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~~d~~R~~~~~~~-- 101 (187)
T PRK12534 25 HAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKAIDHLRANAPQRR-- 101 (187)
T ss_pred HHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHHHHHhcccccc--
Confidence 999999999999999999999999999999999999999999999998655 58899999999988888776532100
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
....+++.. .. +. ..+|++.....+....|..+| ..|
T Consensus 102 ----------------------~~~~~~~~~-----------------~~-~~--~~~~~~~~~~~e~~~~l~~~l-~~L 138 (187)
T PRK12534 102 ----------------------NVALDDAGE-----------------LR-AA--DASPLERTERASTRRRIDHCL-AEL 138 (187)
T ss_pred ----------------------cccccchhh-----------------hc-cc--cCChhhHHHHHHHHHHHHHHH-HhC
Confidence 000000000 00 00 123444455566778899999 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 474 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~ 474 (485)
|++++.||.++| .+|+|++|||+.||+|+++|+++++||+++||+.+.
T Consensus 139 ~~~~r~i~~l~~---~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l~ 186 (187)
T PRK12534 139 EPPRSELIRTAF---FEGITYEELAARTDTPIGTVKSWIRRGLAKLKACLE 186 (187)
T ss_pred CHHHHHHHHHHH---HcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHHHc
Confidence 999999999999 899999999999999999999999999999999875
No 51
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=99.88 E-value=1.4e-21 Score=191.77 Aligned_cols=161 Identities=18% Similarity=0.224 Sum_probs=131.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.|++.|+..|.+.|+.+++++.++..++||++||+|+.+|+.+++|++..+ .|.+|++..+++.+.+++++..+.
T Consensus 63 ~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~~id~~Rk~~~~---- 137 (233)
T PRK12538 63 AAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNRCIDLRRKPRTE---- 137 (233)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHHHHHHHHhhccc----
Confidence 999999999999999999999999999999999999999999999987544 699999999999888887653210
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
. . ..+.+ ......+++..++..+....|..+| ..|
T Consensus 138 -~--------------~---------~~~~~--------------------~~~~~~~~~~~~~~~e~~~~l~~~L-~~L 172 (233)
T PRK12538 138 -N--------------V---------DAVPE--------------------VADGKPDAVSVIERNELSDLLEAAM-QRL 172 (233)
T ss_pred -c--------------c---------ccccc--------------------cccCCCCHHHHHHHHHHHHHHHHHH-HhC
Confidence 0 0 00000 0000122334455556667788999 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 477 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~ 477 (485)
|+++|+||.|+| ++|+|++|||+.||+|.++|+++++||+++||+.+...+
T Consensus 173 p~~~R~v~~L~~---~eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~~~~ 223 (233)
T PRK12538 173 PEQQRIAVILSY---HENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLRRHE 223 (233)
T ss_pred CHHHHHHhhhHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 999999999999 899999999999999999999999999999999998654
No 52
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=99.88 E-value=2.2e-21 Score=182.12 Aligned_cols=162 Identities=18% Similarity=0.248 Sum_probs=127.6
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.|++.|+..|.+.|+.+++++.+++.+++|++||+|+++|+++++|++..+ .|.+|++..+++.+.+++++..+...
T Consensus 23 ~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~rk~~~~~~-- 99 (186)
T PRK13919 23 EALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRG-SARAWLLALAHHAAVDHVRRRAARPQ-- 99 (186)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCcccc-chHHHHHHHHHHHHHHHHHhhhcccc--
Confidence 999999999999999999999999899999999999999999999987644 69999999999999988876542100
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
. + .....+. .... ...+....+.......|.++| ..|
T Consensus 100 -~--------------~-----~~~~~~~---------------------~~~~-~~~~~~~~~~~~~~~~l~~~l-~~L 136 (186)
T PRK13919 100 -P--------------L-----EPDEREP---------------------EAFD-LPGPGLDEEGHLDRTRLGRAL-KAL 136 (186)
T ss_pred -c--------------c-----ccccccc---------------------cccc-CCCccccHHHHHHHHHHHHHH-HhC
Confidence 0 0 0000000 0000 011222223333456688999 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 474 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~ 474 (485)
|+++|.||.++| .+|+|++|||+.||+|.++|+++++||+++||+.+.
T Consensus 137 ~~~~r~vl~l~~---~~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l~ 184 (186)
T PRK13919 137 SPEERRVIEVLY---YQGYTHREAAQLLGLPLGTLKTRARRALSRLKEVLR 184 (186)
T ss_pred CHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence 999999999998 899999999999999999999999999999999875
No 53
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=99.88 E-value=4.6e-21 Score=184.02 Aligned_cols=167 Identities=18% Similarity=0.193 Sum_probs=129.9
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.|+++|+..|.+.|+.++.++.++..+++|++||+|+.+|++++.|++.++ .|.+|++.++++.+.+++++..+.....
T Consensus 38 ~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d~~Rk~~~~~~~~ 116 (206)
T PRK12526 38 QAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFDMLRKIKAKKEQN 116 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHHHHHHhccccccc
Confidence 999999999999999999999999899999999999999999999997665 5999999999999999987764311000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
..++.. +.. +.+.+. ..+............|.++| ..|
T Consensus 117 ------------------------~~~~~~-----~~~---------~~~~~~---~~~~~~~~~~~~~~~l~~~l-~~L 154 (206)
T PRK12526 117 ------------------------LGDDIW-----PIE---------QALAES---QSESEEFSDHLMDKQILSYI-EKL 154 (206)
T ss_pred ------------------------cccccc-----hhh---------hhcccc---cCchHHHHHHHHHHHHHHHH-HhC
Confidence 000000 000 000000 01111222333445788999 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 476 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~ 476 (485)
|+++|.||.++| ++|+|++|||+.||+|.++|+.++++|+++||+.+...
T Consensus 155 ~~~~r~vl~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~ 204 (206)
T PRK12526 155 PEAQQTVVKGVY---FQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQMGEQ 204 (206)
T ss_pred CHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence 999999999999 89999999999999999999999999999999999754
No 54
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=99.88 E-value=2.8e-21 Score=180.87 Aligned_cols=169 Identities=22% Similarity=0.223 Sum_probs=131.6
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.|+++|+..|.+.|+.+|.+|.++..+++|++||+|+++|+++.+|++.. .|.+|++..+++.+.+++++..+.....
T Consensus 18 ~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~~~~rk~~~~~~~~ 95 (187)
T TIGR02948 18 NAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLTIDRLRKRKPDFYLD 95 (187)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHHHHHHhhccccccc
Confidence 99999999999999999999999999999999999999999999999865 5999999999998888876543110000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
......+. ..+. ....+ ...+|++.+...+....+.++| ..|
T Consensus 96 -----------------~~~~~~~~-~~~~-----------------~~~~~--~~~~~~~~~~~~e~~~~l~~~l-~~L 137 (187)
T TIGR02948 96 -----------------DEVQGTDG-LTME-----------------SQLAA--DEAPPEDQVISLELRDTIQQEI-QAL 137 (187)
T ss_pred -----------------ccccCccc-cccc-----------------ccccc--CcCCHHHHHHHHHHHHHHHHHH-HhC
Confidence 00000000 0000 00000 1124555556666677788999 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
||++|.||.++| ++|+|++|||+.||+|+++|+++++||+++||..+..
T Consensus 138 ~~~~r~v~~l~~---~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l~~ 186 (187)
T TIGR02948 138 PPKYRMVIVLKY---MEDLSLKEISEILDLPVGTVKTRIHRGREALRKQLRH 186 (187)
T ss_pred CHHHhHHhhhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhhc
Confidence 999999999998 7999999999999999999999999999999998863
No 55
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=99.88 E-value=1.7e-21 Score=180.47 Aligned_cols=169 Identities=25% Similarity=0.239 Sum_probs=133.3
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccc
Q 011454 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (485)
Q Consensus 263 ~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~iri 342 (485)
..|++.|+..|.+.|+.++++|.+++.+++|++||+++++|++++.|+ .+.+|.+|++..+++.+.+.++...+....
T Consensus 9 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~r~~~~~~~~ 86 (182)
T PRK09652 9 RAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYLRKQGRRPPA 86 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHHHcccCCCCc
Confidence 399999999999999999999999999999999999999999999999 345799999999999998888766432111
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhh
Q 011454 343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVT 422 (485)
Q Consensus 343 p~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~ 422 (485)
+. . ..++. +.. ..........+|+..+...+....+..+| ..
T Consensus 87 ~~--------------------~--~~~~~-~~~--------------~~~~~~~~~~~~~~~~~~~~~~~~l~~~l-~~ 128 (182)
T PRK09652 87 SD--------------------V--DAEEA-EDF--------------DLADALRDISTPENELLSAELEQRVRAAI-ES 128 (182)
T ss_pred cc--------------------c--ccccc-ccc--------------ccccccccccChHHHHHHHHHHHHHHHHH-Hh
Confidence 10 0 00000 000 00000011134666666667778899999 89
Q ss_pred CCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 011454 423 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 474 (485)
Q Consensus 423 Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~ 474 (485)
|||+++.||.++| ++|+|++|||+.||+|+.+|++++++|+++||+.+.
T Consensus 129 L~~~~r~vl~l~~---~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 177 (182)
T PRK09652 129 LPEELRTAITLRE---IEGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQ 177 (182)
T ss_pred CCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999998 799999999999999999999999999999999886
No 56
>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=99.87 E-value=4.7e-21 Score=181.21 Aligned_cols=174 Identities=17% Similarity=0.229 Sum_probs=129.2
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.|++.||+.|.|.|+.+|+++.++..+++|++||+|+++|+++.+|++..+..|.||++.+|++.+.++++...+..+.+
T Consensus 19 ~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~~~~~~~r~~~~~~~~~ 98 (198)
T TIGR02859 19 HALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTRQIITAIKTATRQKHIP 98 (198)
T ss_pred HHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 99999999999999999999999999999999999999999999999987678999999999998888876543211110
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCC---C-CHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHH
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVT---P-SVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLI 419 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~---p-s~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L 419 (485)
. ......... + ..+++. +.+.+.. ..+|+..+...+....|.++|
T Consensus 99 ~-------------~~~~~~~~~~~~~~~~~~~~-----------------~~~~~~~-~~~~e~~~~~~e~~~~l~~~l 147 (198)
T TIGR02859 99 L-------------NSYVSLNKPIYDEESDRTLL-----------------DVISGAK-VTDPEELIISQEEYGDIESKM 147 (198)
T ss_pred h-------------hhhcCcccccccccccchHH-----------------HHhhccc-cCCHHHHHHHHHHHHHHHHHH
Confidence 0 000000000 0 000000 1111111 235666666777778888999
Q ss_pred HhhC-CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 011454 420 IVTL-GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 473 (485)
Q Consensus 420 ~~~L-p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L 473 (485)
+.| ++.++.|+. +| ++|+|++|||+.||+|.++|++.+++|+++||+.+
T Consensus 148 -~~Ll~~~~~~i~~-~~---~~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~~l 197 (198)
T TIGR02859 148 -NELLSDLEWKVLQ-SY---LDGKSYQEIACDLNRHVKSIDNALQRVKRKLEKYL 197 (198)
T ss_pred -HHhcCHHHHHHHH-HH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhc
Confidence 774 566666665 56 69999999999999999999999999999999876
No 57
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=4.7e-21 Score=181.90 Aligned_cols=167 Identities=19% Similarity=0.201 Sum_probs=128.8
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.|++.|++.|.+.|+.+|.++.++..+++|++||+|+.+|+.+++|++..+ .|.+|++..+++.+.+++++..+....
T Consensus 27 ~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn~~ld~~Rk~~~~~~~- 104 (194)
T PRK12531 27 QAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRNLCFDLLRKQKGKDLH- 104 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHHHHHHHHHHhcccccc-
Confidence 999999999999999999999999899999999999999999999997554 699999999999999998876421000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
...++.. . . +...... ... ...+.......+.++| ..|
T Consensus 105 -----------------------~~~~~~~---~---~---------~~~~~~~-~~~--~~~e~~~~~~~l~~~l-~~L 142 (194)
T PRK12531 105 -----------------------IHADDIW---P---S---------DYYPPDL-VDH--YSPEQDMLKEQVMKFL-DRL 142 (194)
T ss_pred -----------------------cchhhcc---c---c---------ccccccc-ccc--cCHHHHHHHHHHHHHH-HhC
Confidence 0000000 0 0 0000000 000 0112223445688888 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 477 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~ 477 (485)
|+++|.||.|+| .+|+|++|||+.||||.++|+.++++|+++||+.+....
T Consensus 143 p~~~r~v~~l~~---~eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~~~~ 193 (194)
T PRK12531 143 PKAQRDVLQAVY---LEELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSMDAES 193 (194)
T ss_pred CHHHHHHHHHHH---HcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHhhhcc
Confidence 999999999999 899999999999999999999999999999999987654
No 58
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=99.87 E-value=4e-21 Score=181.66 Aligned_cols=160 Identities=22% Similarity=0.210 Sum_probs=130.8
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCC---CCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNM---GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~---~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~i 340 (485)
.|++.|+..|.+.|+.++.++.++ ..++||++||+++++|+++++|+++.+ .|.+|++..+++.+.+++++..+..
T Consensus 18 ~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~iarn~~~d~~rk~~~~~ 96 (189)
T PRK06811 18 KALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAISKYKAIDYKRKLTKNN 96 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHHHHHHHHHHHHhcccc
Confidence 999999999999999999999875 357999999999999999999997655 7999999999999999987765311
Q ss_pred cccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHH
Q 011454 341 RLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLII 420 (485)
Q Consensus 341 rip~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~ 420 (485)
... ++... ..+ ...+|++.+...+....|.++|
T Consensus 97 ~~~---------------------------~~~~~-----------------~~~--~~~~~~~~~~~~e~~~~l~~~l- 129 (189)
T PRK06811 97 EID---------------------------SIDEF-----------------ILI--SEESIENEIILKENKEEILKLI- 129 (189)
T ss_pred ccc---------------------------cchhh-----------------hhc--ccCCHHHHHHHHHHHHHHHHHH-
Confidence 000 00000 000 0134555666677778899999
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 474 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~ 474 (485)
..|||++|.||.|+| .+|+|++|||+.||+|.++|+++++||+++||+..-
T Consensus 130 ~~L~~~~r~i~~l~~---~~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~~ 180 (189)
T PRK06811 130 NDLEKLDREIFIRRY---LLGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNKL 180 (189)
T ss_pred HhCCHHHHHHHHHHH---HccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHccc
Confidence 899999999999998 799999999999999999999999999999998654
No 59
>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=4.4e-21 Score=180.03 Aligned_cols=168 Identities=21% Similarity=0.225 Sum_probs=132.2
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.|++.|+..|.+.|+.+|+++.++..+++|++||+|+++|+++++|++.. +|.+|++..+++.+.+++++..+.....
T Consensus 20 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~~--~~~~wl~~iarn~~~~~~r~~~r~~~~~ 97 (190)
T TIGR02939 20 QAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGDS--AFYTWLYRIAVNTAKNHLVAQGRRPPTS 97 (190)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCCC--ccHhHHHHHHHHHHHHHHHHhccCCCcc
Confidence 89999999999999999999999999999999999999999999998753 6999999999998888876543211000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
....++. +.. . .........+|++.+...+....+..+| ..|
T Consensus 98 ----------------------~~~~~~~-~~~--~------------~~~~~~~~~~~e~~~~~~~~~~~l~~~l-~~L 139 (190)
T TIGR02939 98 ----------------------DVEIEDA-EHF--E------------GADRLREIDTPERLLLSRELEQTVMRAV-EAL 139 (190)
T ss_pred ----------------------cccccch-hhh--c------------ccccccccCChHHHHHHHHHHHHHHHHH-HcC
Confidence 0000000 000 0 0000001134555566667778899999 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 474 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~ 474 (485)
|+++|.||.++| ++|+|++|||+.||+|.++|++.++||+++||+.++
T Consensus 140 ~~~~r~v~~l~~---~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l~ 187 (190)
T TIGR02939 140 PEDLRTAITLRE---LEGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRLR 187 (190)
T ss_pred CHHHhhhhhhhh---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 999999999999 899999999999999999999999999999999986
No 60
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=1.2e-21 Score=184.38 Aligned_cols=173 Identities=20% Similarity=0.182 Sum_probs=135.3
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcc
Q 011454 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 341 (485)
Q Consensus 262 ~~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~ir 341 (485)
+..|++.|+..|.+.|+.+|.+++++..++||++||+|+.+|+++.+|++..+..|.+|++..+++.+.+++++..+...
T Consensus 7 d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~~~~~ 86 (185)
T PRK12542 7 DYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNKRHET 86 (185)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Confidence 44899999999999999999999999999999999999999999999986544479999999999999888877642100
Q ss_pred ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHh
Q 011454 342 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIV 421 (485)
Q Consensus 342 ip~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~ 421 (485)
. ..... . + ... .....++......+....|.++| .
T Consensus 87 ~-----------------~~~~~--~---~--------------------~~~--~~~~~~~~~~~~~~~~~~l~~~l-~ 121 (185)
T PRK12542 87 F-----------------LEEYE--R---E--------------------SIE--AVDENIEEWEKRKMSEVQIDTLL-K 121 (185)
T ss_pred h-----------------hhhcc--c---c--------------------chh--hhhccHHHHHHHHHHHHHHHHHH-H
Confidence 0 00000 0 0 000 00012222223334446788999 8
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhhHHHhh
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAML 482 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~l~~~l 482 (485)
.|||++|+||.|+| ++|+|++|||+.||+|.+||++++.||+++||+.+....-..|+
T Consensus 122 ~L~~~~r~i~~l~~---~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~~~~~ 179 (185)
T PRK12542 122 ELNESNRQVFKYKV---FYNLTYQEISSVMGITEANVRKQFERARKRVQNMIGGIQHDEFK 179 (185)
T ss_pred hCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccchHHHH
Confidence 99999999999998 89999999999999999999999999999999999887766663
No 61
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=99.87 E-value=2.7e-21 Score=182.53 Aligned_cols=174 Identities=18% Similarity=0.235 Sum_probs=137.4
Q ss_pred hcChhHHHHhhhh----hHHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHH
Q 011454 249 RISRPELQSILME----CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324 (485)
Q Consensus 249 ~~s~~~L~~~l~~----~~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~ 324 (485)
.++.++|+..++. +..|++.|+..|.|.|+++|.+|.++..+++|++||+|+.+|+++++|++. .+|.+|++.+
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 3566677777763 789999999999999999999999999999999999999999999999864 3699999999
Q ss_pred HHHHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcc
Q 011454 325 IRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWH 404 (485)
Q Consensus 325 Ir~~I~~~I~~~~r~irip~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee 404 (485)
+++.+.+++++..+.... ..++.. +...+ + ...
T Consensus 85 a~n~~~d~~R~~~~~~~~-------------------------~~~~~~-----------------~~~~~----~-~~~ 117 (188)
T PRK09640 85 TYNECITQYRKERRKRRL-------------------------MDALSL-----------------DPLEE----A-SEE 117 (188)
T ss_pred HHHHHHHHHHHhcccccC-------------------------cchhhh-----------------ccccc----c-ccc
Confidence 999999998765321000 000000 00000 0 111
Q ss_pred hHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 405 GVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 405 ~~e~~el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
.....+....|.++| ..||+++|.||.|+| .+|+|++|||+.||||.++|++++.||+++||+.+..
T Consensus 118 ~~~~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~ 184 (188)
T PRK09640 118 KAPKPEERGGLDRWL-VHVNPIDREILVLRF---VAELEFQEIADIMHMGLSATKMRYKRALDKLREKFAG 184 (188)
T ss_pred ccccHHHHHHHHHHH-HhcChhheeeeeeHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 122334556788999 899999999999999 8999999999999999999999999999999998864
No 62
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=99.87 E-value=5e-21 Score=179.20 Aligned_cols=169 Identities=21% Similarity=0.206 Sum_probs=133.0
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.|+..++..|.++|+.+|+++.++..+++|++||+|+++|+++++|++.. .|.+|++..+++.+.+++++..+....
T Consensus 18 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~~~d~~R~~~~~~~~- 94 (187)
T PRK09641 18 NAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNLTIDRLRKRKPDYYL- 94 (187)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHHHHHHHHhcCccccc-
Confidence 99999999999999999999999999999999999999999999999753 699999999999998888765321000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
. .....++.... . ..+.+ ...+|++.+...+....+..+| +.|
T Consensus 95 -----------------~---~~~~~~~~~~~-----~---------~~~~~--~~~~~~~~~~~~~~~~~l~~~l-~~L 137 (187)
T PRK09641 95 -----------------D---AEVAGTEGLTM-----Y---------SQLAA--DDALPEEQVVSLELQETIQEAI-LQL 137 (187)
T ss_pred -----------------c---ccccCCcchhh-----h---------ccccc--CcCCHHHHHHHHHHHHHHHHHH-HhC
Confidence 0 00000000000 0 00001 1224555666667777899999 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
|++++.||.++| .+|++++|||+.||||.++|++.++||+++||+.+..
T Consensus 138 ~~~~r~il~l~~---~~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l~~ 186 (187)
T PRK09641 138 PEKYRTVIVLKY---IEDLSLKEISEILDLPVGTVKTRIHRGREALRKQLRH 186 (187)
T ss_pred CHHHHHHhhhHH---hhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 999999999999 7999999999999999999999999999999998853
No 63
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=99.87 E-value=1.2e-20 Score=179.12 Aligned_cols=159 Identities=14% Similarity=0.150 Sum_probs=131.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.+++.|++.|.+.|++++.++.++..++||++||+|+.+|+++++|++.. .|.+|++..+++.+.+++++..+....+
T Consensus 27 ~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~~--~f~~wL~~i~rn~~~d~~Rk~~~~~~~~ 104 (192)
T PRK09643 27 YAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDA--AVSSWLHRIVVNACLDRLRRAKARPTVP 104 (192)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCCC--ccHHHHHHHHHHHHHHHHHccccCCCCC
Confidence 99999999999999999999999999999999999999999999999753 5999999999999999988654210000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
.++. .+. ..++.+.+...+....|..+| +.|
T Consensus 105 -------------------------~~~~---------------------~~~--~~~~~~~~~~~e~~~~l~~~l-~~L 135 (192)
T PRK09643 105 -------------------------LDDV---------------------YPV--AQLERDPTARVETALAVQRAL-MRL 135 (192)
T ss_pred -------------------------cccc---------------------ccc--cCCcccHHHHHHHHHHHHHHH-HhC
Confidence 0000 000 012333445556677899999 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 476 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~ 476 (485)
|+++|.||.|+| .+|+|++|||+.||+|.++|++++.+|+++||+.+...
T Consensus 136 p~~~r~i~~l~~---~~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l~~~ 185 (192)
T PRK09643 136 PVEQRAALVAVD---MQGYSVADAARMLGVAEGTVKSRCARGRARLAELLGYL 185 (192)
T ss_pred CHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999 89999999999999999999999999999999999754
No 64
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=1.4e-20 Score=173.87 Aligned_cols=165 Identities=18% Similarity=0.150 Sum_probs=135.5
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccc
Q 011454 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (485)
Q Consensus 263 ~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~iri 342 (485)
..|++.|++.|.+.|+.+|+++.++..+++|++||+|+++|+++++|+ . +..|.+|++..+++.+.++++...+....
T Consensus 12 ~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~-~-~~~~~~~l~~i~~~~~~d~~r~~~~~~~~ 89 (179)
T PRK11924 12 KEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN-G-KGSARTWLLTIARNVCYDLLRRRRREKAV 89 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC-C-cchHHHHHHHHHHHHHHHHHHhccccccc
Confidence 399999999999999999999999999999999999999999999998 3 34799999999999988888765431100
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhh
Q 011454 343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVT 422 (485)
Q Consensus 343 p~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~ 422 (485)
. . .+... ...+. ...+|+..+...+....+..+| ..
T Consensus 90 ~------------------------~-~~~~~-----------------~~~~~-~~~~~e~~~~~~e~~~~l~~~l-~~ 125 (179)
T PRK11924 90 L------------------------S-DDALE-----------------PEFAE-TAETPEAALLAKDDLARIDRCL-DA 125 (179)
T ss_pred C------------------------c-ccccc-----------------cccCC-ccCCHHHHHhhHHHHHHHHHHH-Hh
Confidence 0 0 00000 00000 1245777777788888899999 89
Q ss_pred CCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Q 011454 423 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 476 (485)
Q Consensus 423 Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~ 476 (485)
||++++.||.++| .+|++++|||+.||+|+.+|++++++|+++||+.+...
T Consensus 126 L~~~~r~i~~l~~---~~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~~~ 176 (179)
T PRK11924 126 LPVKQREVFLLRY---VEGLSYREIAEILGVPVGTVKSRLRRARQLLRECLEAQ 176 (179)
T ss_pred CCHHHHHHhhHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999 79999999999999999999999999999999998764
No 65
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=1.4e-20 Score=177.54 Aligned_cols=162 Identities=20% Similarity=0.234 Sum_probs=132.2
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.|++.|+..|.+.++.++.++.++..++||++||+|+.+|+++.+|++. ..|.+|++..+++.+.+++++..+. .+
T Consensus 22 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~r~~~~~-~~- 97 (189)
T PRK12515 22 TAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARFKALSALRRRKHE-EI- 97 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHHHHHHHHHccCCC-CC-
Confidence 8999999999999999999999999999999999999999999999974 3699999999999888887654310 00
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
. .+.. ..+.+. ..+|+......+....+.++| +.|
T Consensus 98 ------------------------~-~~~~-----------------~~~~~~--~~~~~~~~~~~~~~~~l~~~l-~~L 132 (189)
T PRK12515 98 ------------------------D-DEAA-----------------AAIEDG--ADTPEVALQKSDTSAALRACL-AKL 132 (189)
T ss_pred ------------------------c-cccc-----------------cccCCC--CCCHHHHHHhHHHHHHHHHHH-HhC
Confidence 0 0000 000110 123444455556667788999 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 477 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~ 477 (485)
|+++|.||.++| .+|+|++|||+.||+|.++|++++.||+++||+.+...+
T Consensus 133 ~~~~r~vl~l~~---~~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 183 (189)
T PRK12515 133 SPAHREIIDLVY---YHEKSVEEVGEIVGIPESTVKTRMFYARKKLAELLKAAG 183 (189)
T ss_pred CHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 999999999999 899999999999999999999999999999999998754
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=99.86 E-value=1.1e-20 Score=174.94 Aligned_cols=153 Identities=20% Similarity=0.177 Sum_probs=123.6
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.|++.|+..|.+.|++++.++.++..++||++||+|+.+|+.+++|++.. +|.+|++..+++.+.+++++..+. .+
T Consensus 16 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~--~~ 91 (169)
T TIGR02954 16 PAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPK--YFNTWLTRILINECIDLLKKKKKV--IP 91 (169)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCcc--ccHHHHHHHHHHHHHHHHHhcCCc--Cc
Confidence 99999999999999999999999999999999999999999999998753 699999999999998888765421 00
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
...+. . ..++....+. +....+..+| ..|
T Consensus 92 ------------------------~~~~~---------------------~----~~~~~~~~~~-~~~~~l~~~l-~~L 120 (169)
T TIGR02954 92 ------------------------FDPNT---------------------S----IEKGECETHA-DSRLDLYKAI-DTL 120 (169)
T ss_pred ------------------------ccccc---------------------c----cccchhhhch-HHHHHHHHHH-HhC
Confidence 00000 0 0000000111 1123688888 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 474 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~ 474 (485)
|+++|+||.++| ++|+|++|||+.||||.++|+++++||+++||+.+.
T Consensus 121 ~~~~r~i~~l~~---~~g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~l~ 168 (169)
T TIGR02954 121 NDKYQTAIILRY---YHDLTIKEIAEVMNKPEGTVKTYLHRALKKLKKRLE 168 (169)
T ss_pred CHHHhHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 999999999999 899999999999999999999999999999999874
No 67
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=1.1e-20 Score=177.06 Aligned_cols=165 Identities=17% Similarity=0.163 Sum_probs=132.2
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcc
Q 011454 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 341 (485)
Q Consensus 262 ~~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~ir 341 (485)
+..|++.|+..|.+.|+.++++|.++..+++|++||+|+.+|+++.+|++.. .|.+|++..+++.+.++++...+..+
T Consensus 5 d~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~~~~~~ 82 (179)
T PRK12543 5 DQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKRWRRFR 82 (179)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhhccccc
Confidence 4589999999999999999999999999999999999999999999999864 59999999999988777654431100
Q ss_pred ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHh
Q 011454 342 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIV 421 (485)
Q Consensus 342 ip~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~ 421 (485)
. + ... .+. .+......|+. +...+....|..+| .
T Consensus 83 ~-----------------~-----~~~-~~~---------------------~~~~~~~~~~~-~~~~~~~~~l~~~l-~ 116 (179)
T PRK12543 83 I-----------------F-----EKA-EEQ---------------------RKPVSIDFSED-VLSKESNQELIELI-H 116 (179)
T ss_pred c-----------------c-----ccc-ccc---------------------cccccccChHH-HHHHHHHHHHHHHH-H
Confidence 0 0 000 000 00000123444 55666778899999 8
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 477 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~ 477 (485)
.|||++|.||.|+| ++|+|++|||+.||||.++|+.++++|+++||+.+....
T Consensus 117 ~Lp~~~r~i~~l~~---~e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~ 169 (179)
T PRK12543 117 KLPYKLRQVIILRY---LHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIEE 169 (179)
T ss_pred hCCHHHHHHHHHHH---HccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999998 899999999999999999999999999999999998654
No 68
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=99.86 E-value=8.2e-21 Score=176.50 Aligned_cols=156 Identities=15% Similarity=0.106 Sum_probs=126.1
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.|++.|+..|.+.|+.+|.++.++..+++|++||+|+++|+++++|++. .+|.+|++..+++.+.+++++..+....
T Consensus 18 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~r~~~~~~~~- 94 (176)
T PRK09638 18 AALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASRLYKDHLRKQKREKLR- 94 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHHhccccch-
Confidence 9999999999999999999999999999999999999999999999874 3799999999999999998875421000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCc--chHHHHHHHHHHHHHHHh
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPW--HGVDDWALKDEVNKLIIV 421 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pe--e~~e~~el~e~L~~~L~~ 421 (485)
.+.+. +.. ..+. +..........|.++| .
T Consensus 95 -------------------------~~~~~---------------------~~~--~~~~~~~~~~~~~~~~~l~~~l-~ 125 (176)
T PRK09638 95 -------------------------LQRAK---------------------EET--LRKEKWEAAIKGAEWSEMLDAL-S 125 (176)
T ss_pred -------------------------hhhcc---------------------ccc--CCccchHHHHHhhhHHHHHHHH-H
Confidence 00000 000 0011 1222333445688889 8
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 474 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~ 474 (485)
.||+++|.||.++| ++|+|++|||+.||+|.++|+++++||+++||+.+.
T Consensus 126 ~L~~~~r~v~~l~~---~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~l~ 175 (176)
T PRK09638 126 KLDPEFRAPVILKH---YYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKEWG 175 (176)
T ss_pred cCCHHHhheeeehh---hcCCCHHHHHHHHCCChhHHHHHHHHHHHHHHHHhc
Confidence 99999999999998 799999999999999999999999999999999774
No 69
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=2.9e-20 Score=174.48 Aligned_cols=158 Identities=18% Similarity=0.180 Sum_probs=125.0
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcC-CCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDN-MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~-~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~iri 342 (485)
.|++.|++.|.+.|+.++.++.+ +..++||++||+|+.+|+.++.|++.. +|.+|++..++|.+.+++++..+....
T Consensus 21 ~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~~--~~~~wl~~iarN~~~d~~Rk~~~~~~~ 98 (181)
T PRK12536 21 AAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRADQ--PLTAWVHAIARYKLMDFLRSRARREAL 98 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHHHHHHHHhccccc
Confidence 99999999999999999998764 578999999999999999999999753 699999999999999998876421000
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhh
Q 011454 343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVT 422 (485)
Q Consensus 343 p~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~ 422 (485)
..+.. +.. +... ...+ +..+....+.++| ..
T Consensus 99 ----------------------~~~~~-~~~-----------------~~~~----~~~~----~~~~~~~~l~~~l-~~ 129 (181)
T PRK12536 99 ----------------------HDPLD-DES-----------------ELFA----TSDD----EAAEARRDLGKLL-EQ 129 (181)
T ss_pred ----------------------cCCcc-chh-----------------hhcC----CCCc----chHHHHHHHHHHH-HH
Confidence 00000 000 0000 0111 1123455688999 89
Q ss_pred CCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 423 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 423 Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
||++++.||.++| .+|+|++|||+.||+|++||++++++|+++||+.+..
T Consensus 130 L~~~~r~v~~l~~---~~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l~~ 179 (181)
T PRK12536 130 LPDRQRLPIVHVK---LEGLSVAETAQLTGLSESAVKVGIHRGLKALAAKIRG 179 (181)
T ss_pred CCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 9999999999999 8999999999999999999999999999999998864
No 70
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=99.86 E-value=2e-20 Score=173.57 Aligned_cols=164 Identities=16% Similarity=0.106 Sum_probs=130.3
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcc
Q 011454 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 341 (485)
Q Consensus 262 ~~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~ir 341 (485)
++.+++.|+..|.+.|+.+|.++.++..++||++||+|+.+|+..++|++..+ .|.+|++..+++.+.+++++..+...
T Consensus 7 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~~-~~~~wL~~iarn~~~d~~Rk~~~~~~ 85 (173)
T PRK09645 7 EAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTGR-SARAWLFTVARNLVIDERRSARARPV 85 (173)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-cHHHHHHHHHHHHHHHHHHhhccccc
Confidence 34899999999999999999999999899999999999999999999975333 69999999999999888876532100
Q ss_pred ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHh
Q 011454 342 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIV 421 (485)
Q Consensus 342 ip~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~ 421 (485)
. ..++. . +.. +..+.+.....+....|..+| +
T Consensus 86 ~-------------------------~~~~~--------------------~-~~~-~~~~~~~~~~~~~~~~l~~~l-~ 117 (173)
T PRK09645 86 E-------------------------GGDDV--------------------L-GVP-EQSAPDEVDRALDRLLVADAL-A 117 (173)
T ss_pred c-------------------------ccccc--------------------c-cCC-CCCCchHHHHHhHHHHHHHHH-H
Confidence 0 00000 0 000 112223334444456788999 8
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 477 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~ 477 (485)
.||+++|+||.|+| ++|+|++|||+.||+|+++|++++++|+++||+.+...+
T Consensus 118 ~L~~~~r~vl~L~~---~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~ 170 (173)
T PRK09645 118 QLSPEHRAVLVRSY---YRGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQERG 170 (173)
T ss_pred hCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhccc
Confidence 99999999999999 899999999999999999999999999999999997543
No 71
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=2.7e-20 Score=174.64 Aligned_cols=157 Identities=18% Similarity=0.219 Sum_probs=124.1
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcC----CCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhh
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDN----MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRT 339 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~----~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~ 339 (485)
.|++.|++.|.+.|+.+|.++++ +..+++|++||+|+.+|...++|+.. ..|.+|++..+++.+.+++++..+.
T Consensus 22 ~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn~~~d~~Rr~~~~ 99 (184)
T PRK12512 22 AAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARNKLIDALRRRGRR 99 (184)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHHHHHHHHHhhccc
Confidence 99999999999999999999875 35689999999999999999999874 3699999999999988888765321
Q ss_pred ccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHH
Q 011454 340 LRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLI 419 (485)
Q Consensus 340 irip~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L 419 (485)
...+ .+++ .+. .|............+.++|
T Consensus 100 ~~~~-------------------------~~~~---------------------~~~----~~~~~~~~~~~~~~l~~~l 129 (184)
T PRK12512 100 VFVD-------------------------IDDF---------------------AET----LPAEPATETLPAGDVGRHL 129 (184)
T ss_pred ccCC-------------------------chhc---------------------ccc----ccccchhhHHHHHHHHHHH
Confidence 1000 0000 000 0000111123345688888
Q ss_pred HhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Q 011454 420 IVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 476 (485)
Q Consensus 420 ~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~ 476 (485)
+.||+++|+||.++| .+|+|++|||+.||+|.++|+..+++|+++||..+++.
T Consensus 130 -~~L~~~~r~v~~l~~---~~g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~~~ 182 (184)
T PRK12512 130 -ETLPPRQRDVVQSIS---VEGASIKETAAKLSMSEGAVRVALHRGLAALAAKFRSE 182 (184)
T ss_pred -HhCCHHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Confidence 899999999999998 89999999999999999999999999999999998753
No 72
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=99.86 E-value=1.5e-20 Score=177.46 Aligned_cols=178 Identities=17% Similarity=0.138 Sum_probs=138.5
Q ss_pred cCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHHHHHhHHHHHHHHHH
Q 011454 204 ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQR 283 (485)
Q Consensus 204 ~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~Lie~yl~LV~sIA~r 283 (485)
|-.+.+.+..|+.+++.||. .|++.||..|.+.++.++.
T Consensus 4 ~~~~~~~~~~l~~~~~~gd~----------------------------------------~af~~l~~~~~~~l~~~~~- 42 (185)
T PRK09649 4 TASDDEAVTALALSAAKGNG----------------------------------------RALEAFIKATQQDVWRFVA- 42 (185)
T ss_pred cccccHHHHHHHHHHHccCH----------------------------------------HHHHHHHHHHHHHHHHHHH-
Confidence 44566778888889999987 9999999999999999995
Q ss_pred hcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHc
Q 011454 284 YDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK 363 (485)
Q Consensus 284 y~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~~~kirka~~~L~~~ 363 (485)
+.++..++||++||+|+.+|+.+++|++.. .|.+|++..+++.+.+++++..+.....
T Consensus 43 ~~~~~~~AeDivQe~flkl~~~~~~~~~~~--~~~~Wl~~Iarn~~~d~~Rk~~~~~~~~-------------------- 100 (185)
T PRK09649 43 YLSDVGSADDLTQETFLRAIGAIPRFSARS--SARTWLLAIARHVVADHIRHVRSRPRTT-------------------- 100 (185)
T ss_pred HhCCHHHHHHHHHHHHHHHHHhccccCccc--hHHHHHHHHHHHHHHHHHHHhccccccc--------------------
Confidence 678888999999999999999999998643 6999999999999999987653210000
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhccCCCCCC
Q 011454 364 GVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLT 443 (485)
Q Consensus 364 gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S 443 (485)
.....+. . ..+.......+....|..+| .+||+++|.||.|+| ++|+|
T Consensus 101 -~~~~~~~---------------------~------~~~~~~~~~~e~~~~l~~~l-~~Lp~~~r~v~~L~~---~~g~s 148 (185)
T PRK09649 101 -RGARPEH---------------------L------IDGDRHARGFEDLVEVTTMI-ADLTTDQREALLLTQ---LLGLS 148 (185)
T ss_pred -cccchhh---------------------c------cChhhhhhhHHHHHHHHHHH-HhCCHHHhHHhhhHH---HcCCC
Confidence 0000000 0 00100111122234578888 899999999999999 89999
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Q 011454 444 WEDISKRIGLSRERVRQVGLVALEKLKHAARKK 476 (485)
Q Consensus 444 ~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~ 476 (485)
++|||+.||+|.++|++++++|+++||+.+...
T Consensus 149 ~~EIA~~lgis~~tVk~~l~Rar~~Lr~~~~~~ 181 (185)
T PRK09649 149 YADAAAVCGCPVGTIRSRVARARDALLADAEPD 181 (185)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCcc
Confidence 999999999999999999999999999966543
No 73
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=99.86 E-value=2.4e-20 Score=184.23 Aligned_cols=168 Identities=17% Similarity=0.170 Sum_probs=131.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHH-------hHhcCCCCCCcchhhHHHHHHHHHHHHHHHHh
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLR-------GIEKFDSSKGFKISTYVYWWIRQGVSRALVEN 336 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~k-------AiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~ 336 (485)
.||+.|+..|.+.|+.++.++.++..++||++||+|+.+|. .+++|++.. .|.+|++..++|.+.+++++.
T Consensus 39 ~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~~--~~~tWL~~Ia~N~~id~lRk~ 116 (244)
T TIGR03001 39 AALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGRG--PLLSWVRIVATRIALELQAQE 116 (244)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCCC--chHhHHHHHHHHHHHHHHHHh
Confidence 99999999999999999999999999999999999999994 788898643 699999999999999988765
Q ss_pred hhhccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHH----HHHH
Q 011454 337 SRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDD----WALK 412 (485)
Q Consensus 337 ~r~irip~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~----~el~ 412 (485)
.+...+. ....... ..+ ...+|++.... .+..
T Consensus 117 ~r~~~~~------------------------~~~~~~~------------------~~~--~~~~~e~~~~~~e~~~e~~ 152 (244)
T TIGR03001 117 RRHSPVE------------------------EPTELAA------------------LPA--PGSDPELDLLRERYRQDFR 152 (244)
T ss_pred cccCccc------------------------ccccccc------------------ccC--CCCCHHHHHHHHhhHHHHH
Confidence 3210000 0000000 000 01123333332 2355
Q ss_pred HHHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhhHHHh
Q 011454 413 DEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAM 481 (485)
Q Consensus 413 e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~l~~~ 481 (485)
..|.++| ++||+++|+||.|+| ++|+|++|||+.||||.+||+.++++|+++||+.+.+...+.|
T Consensus 153 ~~l~~aL-~~Lp~~~R~v~~L~~---~eg~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~~~~~~ 217 (244)
T TIGR03001 153 QALREAL-AALSERERHLLRLHF---VDGLSMDRIGAMYQVHRSTVSRWVAQARERLLERTRRRLAERL 217 (244)
T ss_pred HHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 6788999 899999999999999 8999999999999999999999999999999999987664443
No 74
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=99.86 E-value=2.5e-20 Score=174.25 Aligned_cols=160 Identities=17% Similarity=0.120 Sum_probs=119.2
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCC-----cHHHHHHHHHHHHHH-hHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhh
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGA-----DMADLVQGGLIGLLR-GIEKFDSSKGFKISTYVYWWIRQGVSRALVENS 337 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~-----d~EDLiQEG~IgL~k-AiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~ 337 (485)
.|++.|+..|.+.++.+|+++.++.. +++|++||+|+.+|+ ...+|++. + .|.+|++.++++.+.+++++..
T Consensus 17 ~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~-~-~~~~wl~~i~~n~~~d~~R~~~ 94 (183)
T TIGR02999 17 AARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR-A-HFFAAAAKAMRRILVDHARRRR 94 (183)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch-H-HHHHHHHHHHHHHHHHHHHHHH
Confidence 89999999999999999999998877 899999999999998 78889754 3 6999999999999988887653
Q ss_pred hhccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHH
Q 011454 338 RTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNK 417 (485)
Q Consensus 338 r~irip~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~ 417 (485)
+..+... ..... +.+......++ ..+.....+.+..
T Consensus 95 ~~~~~~~-------------------~~~~~------------------------~~~~~~~~~~~-~~~~~~~l~~~~~ 130 (183)
T TIGR02999 95 AQKRGGG-------------------AVRVP------------------------LDEVLPDAEAD-LDEELLDLDDALD 130 (183)
T ss_pred HHhccCC-------------------ccccc------------------------cccccCCCCcc-HHHHHHHHHHHHH
Confidence 2100000 00000 00000001111 1111112223334
Q ss_pred HHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 011454 418 LIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 473 (485)
Q Consensus 418 ~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L 473 (485)
.| ++|||++|.||.|+| ++|+|++|||+.||+|.+||+.+++||+++||+.+
T Consensus 131 ~l-~~Lp~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 182 (183)
T TIGR02999 131 KL-AQVDPRQAEVVELRF---FAGLTVEEIAELLGVSVRTVERDWRFARAWLADEL 182 (183)
T ss_pred Hh-hcCCHHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 45 679999999999999 89999999999999999999999999999999976
No 75
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=5.3e-20 Score=173.14 Aligned_cols=158 Identities=18% Similarity=0.198 Sum_probs=125.2
Q ss_pred HHHHHHHHHhHHHHHHHHH----HhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhh
Q 011454 264 LAREKLVMSNVRLVMSIAQ----RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRT 339 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~----ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~ 339 (485)
.|++.|+..|.+.|+.+++ ++.++..+++|++||+|+.+|++++.|++.. .|.+|++..+++.+.+++++..+.
T Consensus 21 ~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~~n~~~d~~R~~~~~ 98 (184)
T PRK12539 21 AAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIARYKLIDHLRRTRAS 98 (184)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHHHHHHHHHHHHHhcc
Confidence 9999999999999999987 4557889999999999999999999998753 599999999999998888765321
Q ss_pred ccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHH
Q 011454 340 LRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLI 419 (485)
Q Consensus 340 irip~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L 419 (485)
. . ....++. .. ..+.......+....|..++
T Consensus 99 ~-~-----------------------~~~~~~~---------------------~~----~~~~~~~~~~e~~~~l~~~l 129 (184)
T PRK12539 99 L-A-----------------------DVPIDDA---------------------DE----LVAHDDHAAVESTLDLGRLL 129 (184)
T ss_pred c-c-----------------------ccChhhh---------------------cc----ccCCcHHhhHHHHHHHHHHH
Confidence 0 0 0000000 00 00111122334456788999
Q ss_pred HhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Q 011454 420 IVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 476 (485)
Q Consensus 420 ~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~ 476 (485)
..||+++|.||.|+| ++|+|++|||+.||+|.+||++++++|+++||+.+...
T Consensus 130 -~~L~~~~r~v~~l~~---~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~ 182 (184)
T PRK12539 130 -ARLPEKMRLAIQAVK---LEGLSVAEAATRSGMSESAVKVSVHRGLKALAALIGRE 182 (184)
T ss_pred -HhCCHHHHHHHHHHH---HcCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHhhc
Confidence 899999999999999 79999999999999999999999999999999988643
No 76
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=99.85 E-value=2.3e-20 Score=175.03 Aligned_cols=164 Identities=16% Similarity=0.193 Sum_probs=133.2
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcc
Q 011454 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 341 (485)
Q Consensus 262 ~~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~ir 341 (485)
++.|+++|+..|.+.|++++.++.++..+++|++||+|+.+|+++++|++.. .|.+|++..+++.+.+++++..+...
T Consensus 14 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~~--~~~awl~~ia~n~~~d~~Rk~~~~~~ 91 (179)
T PRK09415 14 KEDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKS--SLKTWLYRIAINHCKDYLKSWHNKKV 91 (179)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCCc--ccHHHHHHHHHHHHHHHHHhhccccc
Confidence 3489999999999999999999999999999999999999999999998743 69999999999999888877532100
Q ss_pred ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHh
Q 011454 342 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIV 421 (485)
Q Consensus 342 ip~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~ 421 (485)
.+. .+.. +... ....+|++.+...+....|..+| .
T Consensus 92 ~~~------------------------~~~~------------------~~~~--~~~~~~e~~~~~~e~~~~l~~~l-~ 126 (179)
T PRK09415 92 IVT------------------------EDIF------------------TYME--SQKESVEEEVIQNAEDERLASAV-M 126 (179)
T ss_pred ccc------------------------cccc------------------cccc--ccccCcHHHHHHHHHHHHHHHHH-H
Confidence 000 0000 0000 01134555566667778899999 8
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
+||+++|+||.|+| ++|+|++|||+.||||.++|++++.||+++||+.+..
T Consensus 127 ~L~~~~r~v~~l~~---~~g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l~~ 177 (179)
T PRK09415 127 SLPIKYREVIYLFY---YEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEE 177 (179)
T ss_pred hCCHHHhhHhHhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999 8999999999999999999999999999999998864
No 77
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=99.85 E-value=2.1e-20 Score=169.49 Aligned_cols=161 Identities=21% Similarity=0.232 Sum_probs=129.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.|+++|+..|.+.|+.+++++.++..++||++||+|+++|+++.+|++.. +|.+|++.++++.+.+++++..+...
T Consensus 1 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~~--~~~~wl~~i~r~~~~d~~r~~~~~~~-- 76 (161)
T TIGR02985 1 KAFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEVE--SFKAYLFTIVKNRSLNYLRHKQVEEK-- 76 (161)
T ss_pred ChHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhccccc--cHHHHHHHHHHHHHHHHHHHHHhHhH--
Confidence 37899999999999999999999989999999999999999999998743 69999999999999888876642100
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
....+.. . ..+....++|+..+...+....|..++ ..|
T Consensus 77 ------------~~~~~~~------------~-----------------~~~~~~~~~~~~~~~~~e~~~~l~~~l-~~L 114 (161)
T TIGR02985 77 ------------YQEEILE------------I-----------------EVDELSENDPEEELEAKELQLIIYKAI-EKL 114 (161)
T ss_pred ------------HHHHHHh------------h-----------------cccccCCCCcHHHHHHHHHHHHHHHHH-HHC
Confidence 0000000 0 000001124555566667777899999 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 473 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L 473 (485)
|++++.||.++| .+|+|..|||+.+|+|+++|++++++|+++||+.|
T Consensus 115 ~~~~r~il~l~~---~~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~l 161 (161)
T TIGR02985 115 PEQCRKIFILSR---FEGKSYKEIAEELGISVKTVEYHISKALKELRKEL 161 (161)
T ss_pred CHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 999999999988 79999999999999999999999999999999864
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=99.85 E-value=2.1e-20 Score=170.55 Aligned_cols=159 Identities=15% Similarity=0.163 Sum_probs=127.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
+|++.++..|.+.|+.+|+++.++..++||++||+++.+|+++++|++.. .|.+|++..+++.+.+++++..+... +
T Consensus 1 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~-~ 77 (159)
T TIGR02989 1 EAFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRL-V 77 (159)
T ss_pred CHHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhccccc-c
Confidence 37899999999999999999999999999999999999999999999764 59999999999999999887643110 0
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
..++.. +.+.+. .+|.+.....+....|.+++ +.|
T Consensus 78 ------------------------~~~~~~-----------------~~~~~~---~~~~~~~~~~~~~~~l~~~i-~~L 112 (159)
T TIGR02989 78 ------------------------FDDELL-----------------EALAAE---AEATEADRSEDELQALEGCL-EKL 112 (159)
T ss_pred ------------------------cCHHHH-----------------HHHHhh---cccchHhhHHHHHHHHHHHH-HHC
Confidence 000000 001100 12333333445566788999 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 473 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L 473 (485)
|++++.||.++| .+|++++|||+.||||+++|++.++||+++||+++
T Consensus 113 ~~~~r~v~~l~~---~~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~~~ 159 (159)
T TIGR02989 113 PERQRELLQLRY---QRGVSLTALAEQLGRTVNAVYKALSRLRVRLRDCV 159 (159)
T ss_pred CHHHHHHHHHHH---hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcC
Confidence 999999999998 79999999999999999999999999999999853
No 79
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=99.85 E-value=4.3e-20 Score=164.02 Aligned_cols=157 Identities=26% Similarity=0.354 Sum_probs=131.1
Q ss_pred HHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccc
Q 011454 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN 344 (485)
Q Consensus 265 A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~ 344 (485)
|++.++..|.++|+++++++..+..+.+|++||+++++|++++.|++. .+|.+|+..++++.+.+++++..+ .+.
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 789999999999999999999998999999999999999999999998 589999999999999999887753 111
Q ss_pred cHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCC
Q 011454 345 HLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTLG 424 (485)
Q Consensus 345 ~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp 424 (485)
.. .. ..........|............|..++ +.||
T Consensus 77 ~~-----------------------~~--------------------~~~~~~~~~~~~~~~~~~~~~~~l~~~l-~~L~ 112 (158)
T TIGR02937 77 EL-----------------------DL--------------------LEELLDSDPSPEEELEQEEEREALREAL-EKLP 112 (158)
T ss_pred ch-----------------------hh--------------------hhhcccccCCHHHHHHHHHHHHHHHHHH-HhCC
Confidence 00 00 0000111234555666677778899999 8999
Q ss_pred HHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 011454 425 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 473 (485)
Q Consensus 425 ~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L 473 (485)
+.++.||.++| ..|+|..|||+.+|+|+++|+++.++++++||+.+
T Consensus 113 ~~~~~ii~~~~---~~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~l 158 (158)
T TIGR02937 113 EREREVLVLRY---LEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158 (158)
T ss_pred HHHHHHHhhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 99999999998 68999999999999999999999999999999864
No 80
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=3.1e-20 Score=172.43 Aligned_cols=162 Identities=17% Similarity=0.163 Sum_probs=125.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.|++.|+..|.+.|+.+++++.+ ..+++|++||+|+.+|+.++.|++. ..|.+|++..+++.+.+++++..+. +
T Consensus 11 ~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~~~~---~ 84 (175)
T PRK12518 11 QSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARRQFAQR---P 84 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHHHhhcc---c
Confidence 99999999999999999999875 4789999999999999999999975 3699999999999888887754310 0
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
... . ..+. .+......+.......+....+.++| +.|
T Consensus 85 ~~~--------------~---~~~~-------------------------~~~~~~~~~~~~~~~~~~~~~l~~~l-~~L 121 (175)
T PRK12518 85 SRI--------------Q---DDSL-------------------------NDQPSRPSDTPDLMQLHYQDLVQQGL-QTL 121 (175)
T ss_pred cch--------------h---cccc-------------------------cccccCCCCcHHHHHHHHHHHHHHHH-HhC
Confidence 000 0 0000 00000011122223334445688888 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 477 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~ 477 (485)
|+++|.||.|+| ++|+|++|||+.||+|.++|++.++||+++||+.+.+.+
T Consensus 122 ~~~~r~vl~l~~---~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~~~~ 172 (175)
T PRK12518 122 SLEHRAVLVLHD---LEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQQG 172 (175)
T ss_pred CHHHeeeeeehH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 999999999998 899999999999999999999999999999999998654
No 81
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=3.9e-20 Score=174.87 Aligned_cols=181 Identities=14% Similarity=0.091 Sum_probs=135.2
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.+|+.|+..|.+.|+.+|.++.++..++||++||+|+.+|+.+++|++.. +|.+|++..++|.+.+++++..+.....
T Consensus 2 ~~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~~--~~~~WL~~ia~n~~~d~~Rk~~r~~~~~ 79 (191)
T PRK12520 2 TIAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQS--SLKTYLVGILKHKIIDAIRSGRREVRLS 79 (191)
T ss_pred cchHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhcccc--cHHHHHHHHHHHHHHHHHHhhcCcCccc
Confidence 47899999999999999999999999999999999999999999998653 6999999999999999988765321111
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhc-ccCCCCCcchHHHHHHHHHHHHHHHhh
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIAD-NRVENNPWHGVDDWALKDEVNKLIIVT 422 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D-~~~e~~pee~~e~~el~e~L~~~L~~~ 422 (485)
.... .....+++...+. ... ....+ .....+|++.+...+....|..+| ..
T Consensus 80 ~~~~-----------------~~~~~~~~~~~~~-~~~---------~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l-~~ 131 (191)
T PRK12520 80 LDDA-----------------DEQSDDDLFDALF-AAD---------GHYREPPSDWGDPDAALSRREFFEVLQACV-DR 131 (191)
T ss_pred cccc-----------------ccchhhhhhhhhc-ccc---------cccccCccccCCHHHHHHHHHHHHHHHHHH-Hh
Confidence 0000 0000000000000 000 00000 000124555556666677899999 89
Q ss_pred CCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 011454 423 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 477 (485)
Q Consensus 423 Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~ 477 (485)
||+++|.||.|+| ++|+|++|||+.||+|.+||+++++||+++||+++...+
T Consensus 132 Lp~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 183 (191)
T PRK12520 132 LPPRTGRVFMMRE---WLELETEEICQELQITATNAWVLLYRARMRLRECLDLHW 183 (191)
T ss_pred CCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999 899999999999999999999999999999999998765
No 82
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=7.4e-20 Score=170.17 Aligned_cols=167 Identities=13% Similarity=0.087 Sum_probs=130.2
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
..+++|+..|.++|+.+|++|.++..++||++||+|+.+|+++++|++.. +|.+|++..+++.+.+++++..+....+
T Consensus 3 ~~~~~l~~~y~~~i~~~~~~~~~~~~daeDvvQe~~i~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~Rk~~~~~~~~ 80 (173)
T PRK12522 3 EKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE--NYKKWITTICVRTFYDFYRKKKRWKDRI 80 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcCCcc--chHHHHHHHHHHHHHHHHHHhccccccc
Confidence 56999999999999999999999999999999999999999999999754 6999999999999999987765311000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
... ..++.... +........++ .....+..+.+..+| ..|
T Consensus 81 ~~~---------------------~~~~~~~~-----------------~~~~~~~~~~~-~~~~~~~~~~l~~~l-~~L 120 (173)
T PRK12522 81 LDL---------------------FHKEDGGE-----------------IEFADDVNISE-EFIQKVEAEMIREVI-QLL 120 (173)
T ss_pred ccc---------------------cchhhhhh-----------------hccccCCCChH-HHHHHHHHHHHHHHH-HhC
Confidence 000 00000000 00000011222 244455667888999 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
|++++.||.|+| .+|+|++|||+.||+|.++|+.+++||+++||+.+..
T Consensus 121 ~~~~r~i~~l~~---~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~ 169 (173)
T PRK12522 121 NEKYKTVLVLYY---YEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEG 169 (173)
T ss_pred CHHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999 8999999999999999999999999999999998864
No 83
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=8.8e-20 Score=172.84 Aligned_cols=160 Identities=12% Similarity=0.171 Sum_probs=127.4
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccc
Q 011454 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (485)
Q Consensus 263 ~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~iri 342 (485)
..+|++|+..|.+.++.+|.+++++..++||++||+|+.+|+.+++|+... .|.+|++..++|.+.+++++..+...
T Consensus 9 ~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~~--~~~awL~~Ia~n~~~d~~R~~~~~~~- 85 (187)
T PRK12516 9 TPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGT--NMKAWLFTILRNEFYSQMRKRGREVQ- 85 (187)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCcc--cHHHHHHHHHHHHHHHHHHhhcCCcc-
Confidence 389999999999999999999999999999999999999999999998643 59999999999999888876542100
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhh
Q 011454 343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVT 422 (485)
Q Consensus 343 p~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~ 422 (485)
. .++. ..+. ....++ .........|..+| ..
T Consensus 86 --~-----------------------~~~~--------------------~~~~-~~~~~~--~~~~~~~~~l~~~L-~~ 116 (187)
T PRK12516 86 --D-----------------------TDGM--------------------FTEQ-LAVHPS--QYGTLDLQDFRAAL-DQ 116 (187)
T ss_pred --c-----------------------cccc--------------------cccc-cCCCcc--hhhHHHHHHHHHHH-Hh
Confidence 0 0000 0000 000111 11122235688889 89
Q ss_pred CCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 011454 423 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 477 (485)
Q Consensus 423 Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~ 477 (485)
||+++|+||.|+| ++|+|++|||+.||+|.++|++++++|+++||+.+...+
T Consensus 117 Lp~~~r~i~~L~~---~~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~~~ 168 (187)
T PRK12516 117 LPDDQREAIILVG---ASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQIEG 168 (187)
T ss_pred CCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence 9999999999999 899999999999999999999999999999999998654
No 84
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=99.84 E-value=3.9e-20 Score=169.53 Aligned_cols=157 Identities=10% Similarity=0.050 Sum_probs=125.4
Q ss_pred HHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHHH
Q 011454 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 350 (485)
Q Consensus 271 e~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~~ 350 (485)
+.|.+.|+.+|.+++++..++||++||+|+.+|+++++|++. .|.+|++..++|.+.+++++..+.....
T Consensus 2 ~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n~~~d~~Rk~~~~~~~~------- 71 (160)
T PRK09642 2 QTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATNHAIDYKRKKARENEEL------- 71 (160)
T ss_pred chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHHHHHHHHHHhccccccc-------
Confidence 579999999999999999999999999999999999999863 4999999999999999987654210000
Q ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHH
Q 011454 351 GLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREI 430 (485)
Q Consensus 351 ~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp~rER~V 430 (485)
....+. ........+|++.....+....|..+| ++||+++|.|
T Consensus 72 ----------------~~~~~~--------------------~~~~~~~~~~~~~~~~~e~~~~l~~~l-~~Lp~~~r~v 114 (160)
T PRK09642 72 ----------------SLCKET--------------------EENIKSSHNIEDLLLTKEQKLLIAQKL-RELPENYRDV 114 (160)
T ss_pred ----------------ccchhh--------------------hhhccCCCChHHHHHHHHHHHHHHHHH-HhCCHHHHHH
Confidence 000000 000001123555566666777899999 8999999999
Q ss_pred HhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 011454 431 IRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 477 (485)
Q Consensus 431 I~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~ 477 (485)
|.|+| ++|+|++|||+.||+|.+||+++++||+++||+.+....
T Consensus 115 ~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 158 (160)
T PRK09642 115 VLAHY---LEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKEEE 158 (160)
T ss_pred HHHHH---HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhhc
Confidence 99999 899999999999999999999999999999999997543
No 85
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=1.2e-19 Score=173.19 Aligned_cols=182 Identities=16% Similarity=0.093 Sum_probs=140.5
Q ss_pred cCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHHHHHhHHHHHHHHHH
Q 011454 204 ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQR 283 (485)
Q Consensus 204 ~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~Lie~yl~LV~sIA~r 283 (485)
|.-+..+..+|+.+++.||. .|++.|+..|.+.++.++.
T Consensus 5 ~~~~~~~~~~l~~~~~~~d~----------------------------------------~a~~~l~~~y~~~l~~~~~- 43 (196)
T PRK12535 5 SERDDAHVTDLALAAGRGDR----------------------------------------AALTEFIRETQDDVWRLLA- 43 (196)
T ss_pred cccccHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHHHH-
Confidence 45555666778888888887 9999999999999999975
Q ss_pred hcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHc
Q 011454 284 YDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK 363 (485)
Q Consensus 284 y~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~~~kirka~~~L~~~ 363 (485)
+.++..++||++||+|+.+|+..++|++.. .|.+|++..+++.+.+++++..+..+...
T Consensus 44 ~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Iarn~~id~~Rk~~~~~~~~~------------------- 102 (196)
T PRK12535 44 HLGGHDIADDLTQETYLRVMSALPRFAARS--SARTWLLSLARRVWVDNIRHDMARPRKSA------------------- 102 (196)
T ss_pred HhCCHHHHHHHHHHHHHHHHHHhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhccCCCccc-------------------
Confidence 578888999999999999999999998642 69999999999999999887642111000
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhccCCCCCC
Q 011454 364 GVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLT 443 (485)
Q Consensus 364 gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S 443 (485)
+... ...+. ...|+... ..+....+..+| +.||+++|+||.|+| ++|+|
T Consensus 103 ------~~~~------------------~~~~~--~~~~~~~~-~~~~~~~l~~~l-~~Lp~~~r~v~~l~~---~~g~s 151 (196)
T PRK12535 103 ------TEYE------------------DAAAT--TASNETTG-SWSEWIDVRTLI-DALPPERREALILTQ---VLGYT 151 (196)
T ss_pred ------cccc------------------ccccc--cCCcchhH-HHHHHHHHHHHH-HcCCHHHHHHhhhHH---HhCCC
Confidence 0000 00000 01122211 222335688888 899999999999999 89999
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhhH
Q 011454 444 WEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM 478 (485)
Q Consensus 444 ~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~l 478 (485)
++|||+.||+|.++|+++++||+++||+.+.....
T Consensus 152 ~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~~~ 186 (196)
T PRK12535 152 YEEAAKIADVRVGTIRSRVARARADLIAATATGQA 186 (196)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccccc
Confidence 99999999999999999999999999999976543
No 86
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=99.84 E-value=1e-19 Score=166.90 Aligned_cols=157 Identities=18% Similarity=0.187 Sum_probs=127.3
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcc
Q 011454 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 341 (485)
Q Consensus 262 ~~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~ir 341 (485)
+..+++.|+..|.+.|+.+|.+++++..+++|++||+|+.+|+++++|+. . ..|.+|++..+++.+.+++++..+. .
T Consensus 4 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~-~-~~~~~wl~~i~~n~~~d~~rk~~~~-~ 80 (162)
T TIGR02983 4 TEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD-P-DAPDAYVRRVLVNLARSRWRRRRLL-E 80 (162)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC-c-ccHHHHHHHHHHHHHHHHHHhhccc-c
Confidence 45899999999999999999999999999999999999999999999964 2 3799999999999888887655310 0
Q ss_pred ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHh
Q 011454 342 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIV 421 (485)
Q Consensus 342 ip~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~ 421 (485)
.+ .++ .++ ..+.......+..+.|..+| .
T Consensus 81 ~~-------------------------~~~---------------------~~~----~~~~~~~~~~~~~~~l~~~l-~ 109 (162)
T TIGR02983 81 LP-------------------------TRE---------------------LPD----AAAPDPAPDVALRAALARAL-R 109 (162)
T ss_pred cc-------------------------ccc---------------------cCc----ccCCccchhHHHHHHHHHHH-H
Confidence 00 000 000 01112223445566788889 8
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
.||+++|.||.|+| ++|+|.+|||+.||+|.++|++++.+|+++||+.+..
T Consensus 110 ~L~~~~r~i~~l~~---~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 160 (162)
T TIGR02983 110 RLPARQRAVVVLRY---YEDLSEAQVAEALGISVGTVKSRLSRALARLRELLEE 160 (162)
T ss_pred hCCHHHHHHhhhHH---HhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 99999999999999 8999999999999999999999999999999998754
No 87
>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=99.84 E-value=2.3e-19 Score=167.99 Aligned_cols=179 Identities=17% Similarity=0.157 Sum_probs=132.3
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHhc----CCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhh
Q 011454 262 CSLAREKLVMSNVRLVMSIAQRYD----NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS 337 (485)
Q Consensus 262 ~~~A~e~Lie~yl~LV~sIA~ry~----~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~ 337 (485)
+..|++.|+..|.+.|+.+|++|. ++..++||++||+|+.+|+++.+|++..+.+|.+|++..+++.+.+++++..
T Consensus 5 ~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~~~ 84 (189)
T TIGR02984 5 DQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRRHL 84 (189)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHHHH
Confidence 449999999999999999999975 3567899999999999999999998765567999999999999998887652
Q ss_pred h-hccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHH
Q 011454 338 R-TLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVN 416 (485)
Q Consensus 338 r-~irip~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~ 416 (485)
+ ..+.+. .. ......+..++. ...+. +.+.+. ..+|++.+...+....|.
T Consensus 85 ~~~~r~~~-------------~~-~~~~~~~~~~~~-------~~~~~------~~~~~~--~~~~~~~~~~~e~~~~l~ 135 (189)
T TIGR02984 85 GAQKRDIR-------------RE-QSLDAGGRLDES-------SVRLA------AQLAAD--GPSPSQVAARREAAVRLA 135 (189)
T ss_pred HHHhhhcc-------------cc-cCCCcccccCCc-------chhHH------HHccCC--CCCHHHHHHHHHHHHHHH
Confidence 1 000000 00 000000000000 00000 011111 234566666666777899
Q ss_pred HHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 011454 417 KLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 473 (485)
Q Consensus 417 ~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L 473 (485)
.+| ..|||++|.||.++| ++|+|++|||+.||||+++|++.++||+++||+.+
T Consensus 136 ~~l-~~L~~~~r~vi~l~~---~~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~l 188 (189)
T TIGR02984 136 QAL-AKLPEDYREVILLRH---LEGLSFAEVAERMDRSEGAVSMLWVRGLARLRQIL 188 (189)
T ss_pred HHH-HcCCHHHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 999 899999999999999 79999999999999999999999999999999976
No 88
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=1.5e-19 Score=167.01 Aligned_cols=161 Identities=16% Similarity=0.183 Sum_probs=127.4
Q ss_pred hhHHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhc
Q 011454 261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (485)
Q Consensus 261 ~~~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~i 340 (485)
.++..|..++..|.+.|+.+|+++.++..++||++||+|+.+|+.++.|++.. .|.+|++..+++.+.+.+++..+..
T Consensus 3 ~~~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~~ 80 (164)
T PRK12547 3 KCSKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGT--NLKAWLFTILRNEFYSQMRKRGREV 80 (164)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhcccc
Confidence 35689999999999999999999999999999999999999999999998643 5999999999999988887654210
Q ss_pred cccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHH
Q 011454 341 RLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLII 420 (485)
Q Consensus 341 rip~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~ 420 (485)
.. ..... .... ..++. .+.......+..+|
T Consensus 81 ---~~----------------------~~~~~--------------------~~~~--~~~~~--~~~~~~~~~l~~~l- 110 (164)
T PRK12547 81 ---QD----------------------SDGVF--------------------TARV--AVHPA--QYGSLDLQDFKKAL- 110 (164)
T ss_pred ---cc----------------------ccccc--------------------cccC--CCCch--hhhHHHHHHHHHHH-
Confidence 00 00000 0000 00111 11222345688889
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 476 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~ 476 (485)
..||+++|+||.|+| .+|+|++|||+.||||+++|+++++||+++||..+...
T Consensus 111 ~~L~~~~r~v~~l~~---~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 163 (164)
T PRK12547 111 NLLSADQREAIILIG---ASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLKVD 163 (164)
T ss_pred HhCCHHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence 899999999999999 89999999999999999999999999999999988643
No 89
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=99.83 E-value=3.2e-19 Score=167.64 Aligned_cols=169 Identities=21% Similarity=0.235 Sum_probs=135.2
Q ss_pred HhhhhhHHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHh
Q 011454 257 SILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVEN 336 (485)
Q Consensus 257 ~~l~~~~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~ 336 (485)
.....+..++..++..|.+.++.+++++.++..++|||+||+|+.+|+++..| ...+ .|.||++..++|.+.+.+++.
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~~~-~~~~wl~~Ia~n~~iD~~R~~ 85 (182)
T COG1595 8 EALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RGRS-SFKAWLYRIARNLAIDRLRKR 85 (182)
T ss_pred HHHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CCCC-chHHHHHHHHHHHHHHHHHHh
Confidence 34455568999999999999999999999988899999999999999999999 4333 799999999999999998876
Q ss_pred hhhccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCc--chHHHHHHHHH
Q 011454 337 SRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPW--HGVDDWALKDE 414 (485)
Q Consensus 337 ~r~irip~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pe--e~~e~~el~e~ 414 (485)
.+..... ...+ ...... ...+. ..+...+....
T Consensus 86 ~r~~~~~------------------------~~~~--------------------~~~~~~-~~~~~~~~~~~~~~~~~~ 120 (182)
T COG1595 86 KRRRARV------------------------EEAD--------------------LLPEEA-DPAPDLAELLLAEEELER 120 (182)
T ss_pred ccccccc------------------------cccc--------------------cccccc-CcccccchHHHHHHHHHH
Confidence 5321110 0000 000000 01111 23556677788
Q ss_pred HHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Q 011454 415 VNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 476 (485)
Q Consensus 415 L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~ 476 (485)
|.++| ..||+++|.+|.|+| ++|+|++|||+.||||.+||+.++++|+++||+.+...
T Consensus 121 l~~al-~~Lp~~~R~~~~l~~---~~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~~~ 178 (182)
T COG1595 121 LRRAL-ARLPPRQREAFLLRY---LEGLSYEEIAEILGISVGTVKSRLHRARKKLREQLEEA 178 (182)
T ss_pred HHHHH-HhCCHHHhHHhhhHh---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence 99999 899999999999999 89999999999999999999999999999999998764
No 90
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=99.83 E-value=1.8e-19 Score=166.35 Aligned_cols=158 Identities=16% Similarity=0.136 Sum_probs=130.3
Q ss_pred HHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccccc
Q 011454 266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH 345 (485)
Q Consensus 266 ~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~ 345 (485)
++.|++.|.+.|+.+|+++.++..++||++||+|+.+|++++.|++. .|.+|++..+++.+.+++++..+....
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 599999999999999998776421000
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCCH
Q 011454 346 LHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGE 425 (485)
Q Consensus 346 ~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp~ 425 (485)
..+++.. +. ..+|++.+...+....+..+| ..||+
T Consensus 77 ----------------------~~~~~~~------------------~~----~~~~~~~~~~~~~~~~l~~~l-~~L~~ 111 (165)
T PRK09644 77 ----------------------GTDEIEA------------------IQ----AESTEEYVVAKNSYEKLIQII-HTLPV 111 (165)
T ss_pred ----------------------chhHHhh------------------hc----ccChHHHHHHHHHHHHHHHHH-HhCCH
Confidence 0011100 00 123555555666777889999 89999
Q ss_pred HHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 011454 426 REREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 477 (485)
Q Consensus 426 rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~ 477 (485)
++|+||.|+| .+|+|++|||+.||+|.++|+++++||+++||+.+....
T Consensus 112 ~~r~v~~l~~---~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~~ 160 (165)
T PRK09644 112 IEAQAILLCD---VHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEEK 160 (165)
T ss_pred HHHHHHHhHH---HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Confidence 9999999998 899999999999999999999999999999999997543
No 91
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=99.83 E-value=1.1e-19 Score=171.99 Aligned_cols=172 Identities=14% Similarity=0.155 Sum_probs=130.1
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccc
Q 011454 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (485)
Q Consensus 263 ~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~iri 342 (485)
..+|+.|+..|.+.|+.+|.+++++..+++|++||+|+.+|+++.+|++.. +|.+|++..++|.+.+++++..+....
T Consensus 10 ~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~~--~~~~wL~~iarN~~~d~~Rk~~~~~~~ 87 (193)
T TIGR02947 10 AQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPGT--NLKAWLYRILTNTYINSYRKAQRRPQQ 87 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCCC--cchHHHHHHHHHHHHHHHHHhcCCccc
Confidence 489999999999999999999999999999999999999999999998643 699999999999999998776431100
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhccc-CCCCCcchHHHHHHHHHHHHHHHh
Q 011454 343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNR-VENNPWHGVDDWALKDEVNKLIIV 421 (485)
Q Consensus 343 p~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~-~e~~pee~~e~~el~e~L~~~L~~ 421 (485)
. ..+++... ... ....+.. ....++......+....|..+| .
T Consensus 88 ~------------------------~~~~~~~~-~~~-----------~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l-~ 130 (193)
T TIGR02947 88 S------------------------DDDDIEDW-QLA-----------KAASHTSNGLRSAELEALDGLPDQDIKDAL-Q 130 (193)
T ss_pred c------------------------cchhhhhh-hhc-----------cccccccccccchhHHHHhhhhHHHHHHHH-H
Confidence 0 00000000 000 0000000 0012222233334456788899 8
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 476 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~ 476 (485)
+||+++|.||.|+| ++|+|++|||+.||||.++|+++++||+++||+.+...
T Consensus 131 ~Lp~~~r~i~~L~~---~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~ 182 (193)
T TIGR02947 131 GLPEEFRQAVYLAD---VEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVDV 182 (193)
T ss_pred hCCHHHhhheeehh---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999 89999999999999999999999999999999999753
No 92
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=99.83 E-value=1.6e-19 Score=167.92 Aligned_cols=160 Identities=14% Similarity=0.101 Sum_probs=126.0
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.|+..|+..|.+.|+.++.++.++..+++|++||+|+.+|+. ..|... ..|.+|++..++|.+.+++++..+..
T Consensus 10 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~~~~--- 83 (172)
T PRK12523 10 ELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAALEQ--- 83 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHHHHH---
Confidence 899999999999999999999999999999999999999986 456543 36999999999999999987764200
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
... .++.. ... ....+|+......+....+.++| ..|
T Consensus 84 --------------~~~---------~~~~~------------------~~~-~~~~~~~~~~~~~~~~~~l~~~l-~~L 120 (172)
T PRK12523 84 --------------AYL---------AELAL------------------VPE-AEQPSPEEQHLILEDLKAIDRLL-GKL 120 (172)
T ss_pred --------------HHH---------HHHhh------------------ccc-ccCCChHHHHHHHHHHHHHHHHH-HhC
Confidence 000 00000 000 00123443344444456788999 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
|+++|.||.|+| ++|+|++|||+.||+|.++|++++.+|+++||..|..
T Consensus 121 p~~~r~v~~L~~---~~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l~~ 169 (172)
T PRK12523 121 SSKARAAFLYNR---LDGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIALYG 169 (172)
T ss_pred CHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 999999999999 8999999999999999999999999999999998864
No 93
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=99.83 E-value=2.1e-19 Score=174.52 Aligned_cols=171 Identities=15% Similarity=0.102 Sum_probs=134.6
Q ss_pred hhHHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhc
Q 011454 261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (485)
Q Consensus 261 ~~~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~i 340 (485)
....+|+.||..|.+.++.++.++.++..++||++||+|+.+|+.+++|++. .|.+|++..++|.+.++++++.+..
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 3448999999999999999999999999999999999999999999999853 4999999999999988887654210
Q ss_pred cccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHH
Q 011454 341 RLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLII 420 (485)
Q Consensus 341 rip~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~ 420 (485)
... ..+++.... .. ....+ ...+|++.+...+....|..+|
T Consensus 92 ~~~------------------------~~~~~~~~~--~~----------~~~~~--~~~~~e~~~~~~e~~~~l~~al- 132 (216)
T PRK12533 92 EVA------------------------APDTLDDAD--SL----------DDWQP--AGEDPLALLLRAEDVRLVNAAL- 132 (216)
T ss_pred ccc------------------------ccccccccc--cc----------ccccc--CCCCHHHHHHHHHHHHHHHHHH-
Confidence 000 000000000 00 00000 1234566666777778899999
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 476 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~ 476 (485)
..||+++|+||.|+| ++++|++|||+.||||.++|+++++||+++||+.+...
T Consensus 133 ~~Lp~~~R~v~~L~y---~eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~ 185 (216)
T PRK12533 133 AKLPVEYREVLVLRE---LEDMSYREIAAIADVPVGTVMSRLARARRRLAALLGGA 185 (216)
T ss_pred HcCCHHHHhHhhhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHccc
Confidence 899999999999999 89999999999999999999999999999999999654
No 94
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=99.83 E-value=1.7e-19 Score=169.16 Aligned_cols=164 Identities=12% Similarity=0.008 Sum_probs=127.5
Q ss_pred hhHHHHHHHHHHhHHHHHHHHHHhcC--CCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhh
Q 011454 261 ECSLAREKLVMSNVRLVMSIAQRYDN--MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR 338 (485)
Q Consensus 261 ~~~~A~e~Lie~yl~LV~sIA~ry~~--~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r 338 (485)
++..+|+.|+..|.+.|+.++.++.+ +..++||++||+|+.+|+.+++|++.....|.+|++..+++.+.+++++..+
T Consensus 10 ~d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~Rk~~~ 89 (178)
T PRK12529 10 ADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRRRQSL 89 (178)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHHHHHH
Confidence 44589999999999999998766665 4678999999999999999999975433479999999999988887765421
Q ss_pred hccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHH
Q 011454 339 TLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKL 418 (485)
Q Consensus 339 ~irip~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~ 418 (485)
. . ... +.... ..+. ...+|++.....+....|..+
T Consensus 90 ~---------------~--~~~---------~~~~~------------------~~~~-~~~~~e~~~~~~~~~~~l~~~ 124 (178)
T PRK12529 90 E---------------L--AWL---------EALAT------------------LPEP-LHPSPEQQSVILETLHEIDAL 124 (178)
T ss_pred H---------------h--hhh---------hHhhh------------------ccCc-CCCCHHHHHHHHHHHHHHHHH
Confidence 0 0 000 00000 0000 012455555566666789999
Q ss_pred HHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 011454 419 IIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 473 (485)
Q Consensus 419 L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L 473 (485)
| .+|||++|.||.|+| .+|+|++|||+.||+|.+||+.++++|+.++++.+
T Consensus 125 l-~~Lp~~~R~v~~L~~---~~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~~ 175 (178)
T PRK12529 125 L-DTLRPRVKQAFLMAT---LDGMKQKDIAQALDIALPTVKKYIHQAYVTCLSLM 175 (178)
T ss_pred H-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence 9 899999999999999 89999999999999999999999999999998875
No 95
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=99.82 E-value=6.1e-19 Score=169.43 Aligned_cols=165 Identities=19% Similarity=0.242 Sum_probs=133.6
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcc
Q 011454 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 341 (485)
Q Consensus 262 ~~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~ir 341 (485)
+..++++|+..|.+.++.++.++.++..+++|++||+|+.+|+.+.+|++ + +|.+|++..+++.+.+++++..+ .+
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 44899999999999999999999999999999999999999999999985 3 59999999999999999887532 00
Q ss_pred ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHh
Q 011454 342 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIV 421 (485)
Q Consensus 342 ip~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~ 421 (485)
.. ...++. . ... ....+|...++..+....|..+| .
T Consensus 102 ~~-----------------------~~~~~~-~-----------------~~~--~~~~~~~~~~~~~~~~~~l~~~L-~ 137 (203)
T PRK09647 102 ME-----------------------ALPEDY-D-----------------RVP--GDEPNPEQIYHDARLDPDLQAAL-D 137 (203)
T ss_pred cc-----------------------cccccc-c-----------------ccC--CCCCCHHHHHHHHHHHHHHHHHH-H
Confidence 00 000000 0 000 01224444556667777888999 8
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 477 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~ 477 (485)
.||+++|.||.|+| ++|++++|||+.||||.++|++.+.||+++||+.+...+
T Consensus 138 ~L~~~~r~v~~L~~---~~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~~~ 190 (203)
T PRK09647 138 SLPPEFRAAVVLCD---IEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAAHA 190 (203)
T ss_pred hCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999 899999999999999999999999999999999997643
No 96
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=99.82 E-value=8.9e-19 Score=161.13 Aligned_cols=161 Identities=15% Similarity=0.119 Sum_probs=129.3
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccc
Q 011454 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (485)
Q Consensus 263 ~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~iri 342 (485)
+.+++.|++.|.+.|+.+|.++.++..+++|++||+|+.+|++ .|+.. ..|.+|++..+++.+.+++++..+....
T Consensus 2 ~~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~~--~~~~~wl~~i~rn~~~d~~rk~~~~~~~ 77 (166)
T PRK09639 2 DETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKGI--ENEKGWLIKSARNVAYNYLRSEKRRRAR 77 (166)
T ss_pred chHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hcccc--cchHHHHHHHHHHHHHHHHHHhcccccc
Confidence 3789999999999999999999999999999999999999999 67643 3699999999999999988766421110
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhh
Q 011454 343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVT 422 (485)
Q Consensus 343 p~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~ 422 (485)
.. .. .... + + ....+|++.....+....+..+| ..
T Consensus 78 ~~----------------------~~----~~~~--------------~-~---~~~~~~e~~~~~~~~~~~l~~~l-~~ 112 (166)
T PRK09639 78 IL----------------------GE----FQWQ--------------E-V---DNEPSPEEIWIRKEEITKVQEVL-AK 112 (166)
T ss_pred cc----------------------ch----hhhh--------------h-c---cCCCChHHHHHHHHHHHHHHHHH-Hc
Confidence 00 00 0000 0 0 01234666666666777789999 89
Q ss_pred CCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Q 011454 423 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 476 (485)
Q Consensus 423 Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~ 476 (485)
||+++|.||.++| +|+|++|||+.||+|.++|++++.+|+++||+.+...
T Consensus 113 L~~~~r~il~l~~----~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~~~ 162 (166)
T PRK09639 113 MTERDRTVLLLRF----SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQM 162 (166)
T ss_pred CCHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 9999999999998 7899999999999999999999999999999998754
No 97
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=7.9e-19 Score=161.24 Aligned_cols=157 Identities=14% Similarity=0.103 Sum_probs=123.2
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.|+++|++.|.+.|+.++.++.++..++||++||+|+.+|+..+.|++. .|.+|++.++++.+.+++++..+.
T Consensus 4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~---- 76 (161)
T PRK12528 4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQII---EPRAFLTTIAKRVLCNHYRRQDLE---- 76 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhcccccccc---CHHHHHHHHHHHHHHHHHHHHHHH----
Confidence 7999999999999999999999999999999999999999999888642 599999999999998887765310
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
. .. .+.+.+ ..+. ....++......+....|..+| .+|
T Consensus 77 -----------~---~~--------~~~~~~------------------~~~~-~~~~~~~~~~~~~~~~~l~~~l-~~L 114 (161)
T PRK12528 77 -----------R---AY--------LEALAQ------------------LPER-VAPSEEERAIILETLVELDQLL-DGL 114 (161)
T ss_pred -----------H---hh--------HHHhhc------------------cccc-cCCCHHHHHHHHHHHHHHHHHH-HHC
Confidence 0 00 000000 0000 0112222233334456788889 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA 472 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~ 472 (485)
|+++|.||.|+| ++|+|++|||+.||+|.+||++++++|+++||..
T Consensus 115 ~~~~r~v~~L~~---~~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~ 160 (161)
T PRK12528 115 PPLVKRAFLLAQ---VDGLGYGEIATELGISLATVKRYLNKAAMRCYFA 160 (161)
T ss_pred CHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhc
Confidence 999999999999 8999999999999999999999999999999875
No 98
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=1.2e-18 Score=160.14 Aligned_cols=157 Identities=11% Similarity=0.067 Sum_probs=123.3
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcc
Q 011454 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 341 (485)
Q Consensus 262 ~~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~ir 341 (485)
...|++.++..|.+.|+.++.++.++..+++|++||+|+.+|+.+++|++. .|.||++..+++.+.+++++..+...
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 348999999999999999999999999999999999999999999999863 59999999999999998877643100
Q ss_pred ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHh
Q 011454 342 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIV 421 (485)
Q Consensus 342 ip~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~ 421 (485)
. ..++. ..+. ...|.+..........+..+| .
T Consensus 80 ~-------------------------~~~~~--------------------~~~~--~~~~~~~~~~~~~~~~~~~~l-~ 111 (161)
T PRK12541 80 T-------------------------TIEEF--------------------HLPN--VPSTEHEYFIKHEIASWLDSL-S 111 (161)
T ss_pred c-------------------------chhhh--------------------hccC--CCCcHHHHHHHhHHHHHHHHH-H
Confidence 0 00000 0000 011222222222234455778 8
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA 472 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~ 472 (485)
.||+++|.||.|+| .+|+|++|||+.||+|.++|+++++||+++||+.
T Consensus 112 ~L~~~~r~v~~l~~---~~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 112 SLPLERRNVLLLRD---YYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HCCHHHHHHhhhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 99999999999999 8999999999999999999999999999999974
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=99.81 E-value=8.7e-19 Score=165.95 Aligned_cols=174 Identities=11% Similarity=0.087 Sum_probs=130.5
Q ss_pred HHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHH
Q 011454 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH 347 (485)
Q Consensus 268 ~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~ 347 (485)
+.+..|.+.|+.+|++++++..+++|++||+|+.+|+...+|++. .+|.+|++..+++.+.+++++..+....+.-
T Consensus 6 ~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~~~-- 81 (188)
T TIGR02943 6 QELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVSDL-- 81 (188)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCcccc--
Confidence 567789999999999999999999999999999999999999875 3799999999999999998876532111100
Q ss_pred HHHHHHHHHHHHHHHcCCCCC---HHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCC
Q 011454 348 ERLGLIRNAKLRLEEKGVTPS---VDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTLG 424 (485)
Q Consensus 348 ~~~~kirka~~~L~~~gr~ps---~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp 424 (485)
..... ...+....+.... ...++ ..++|+..+...+....+.++| .+||
T Consensus 82 ----------------~~~~~~~~~~~~~~~~~~~~~---------~~~~~--~~~~~e~~~~~~e~~~~l~~~l-~~L~ 133 (188)
T TIGR02943 82 ----------------DDELDDEAFNALFTQNGHWAQ---------HGQPQ--HWNTPEKQLENKEFWEVFEACL-YHLP 133 (188)
T ss_pred ----------------ccccccchhhhhhccccchhc---------ccccc--ccCCHHHHHHHHHHHHHHHHHH-HhCC
Confidence 00000 0000000000000 00000 1134556666777778899999 8999
Q ss_pred HHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Q 011454 425 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 476 (485)
Q Consensus 425 ~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~ 476 (485)
+++|+||.|+| ++|+|++|||+.||+|.++|++++.||+++||+.+...
T Consensus 134 ~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~ 182 (188)
T TIGR02943 134 EQTARVFMMRE---VLGFESDEICQELEISTSNCHVLLYRARLSLRACLSIN 182 (188)
T ss_pred HHHHHHHHHHH---HhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999 89999999999999999999999999999999999743
No 100
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=99.81 E-value=9.5e-19 Score=179.73 Aligned_cols=177 Identities=20% Similarity=0.205 Sum_probs=127.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.|+++|+..|.+.|+.+|++++++..++||++||+|+.+|+.+++|++. ..|.+|++..++|.+.+++++..+.. .+
T Consensus 19 ~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~-~~ 95 (339)
T PRK08241 19 DAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATNVCLDALEGRARRP-LP 95 (339)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHHHHHHHHHhhcccc-Cc
Confidence 9999999999999999999999999999999999999999999999853 36999999999999999988764210 00
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcc---cCCCCCcchHHHHH-HHHHHHHHH
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADN---RVENNPWHGVDDWA-LKDEVNKLI 419 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~---~~e~~pee~~e~~e-l~e~L~~~L 419 (485)
.. .+. +..+........+...+ .+.+.+. ....+|++.+...+ ....|..+|
T Consensus 96 ~~-----------------~~~-~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l 151 (339)
T PRK08241 96 TD-----------------LGA-PAADPVDELVERPEVPW------LEPYPDALLDPAAADPAARVVARESVRLAFVAAL 151 (339)
T ss_pred cc-----------------cCC-CcCcccccccccccccc------cCCCCcccccccCCChHHHHHHHHHHHHHHHHHH
Confidence 00 000 00000000000000000 0000000 00123544444443 345688888
Q ss_pred HhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 420 IVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 420 ~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
.+||+++|.||.|+| ++|+|++|||+.||+|.++|+++++||+++||+
T Consensus 152 -~~Lp~~~R~v~~L~~---~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 152 -QHLPPRQRAVLILRD---VLGWSAAEVAELLDTSVAAVNSALQRARATLAE 199 (339)
T ss_pred -HhCCHHHhhhhhhHH---hhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhh
Confidence 899999999999999 899999999999999999999999999999999
No 101
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=1.4e-18 Score=163.93 Aligned_cols=160 Identities=16% Similarity=0.175 Sum_probs=127.0
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.++..++..|.+.|+++|.+++++..++||++||+|+.+|+.+++|++.. .|.+|++..++|.+.++++++.+....
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 67889999999999999999999999999999999999999999998654 599999999999888887765421000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
..++. ... ....++. +.......|..+| .+|
T Consensus 82 ------------------------~~~~~--------------------~~~--~~~~~~~--~~~~~~~~l~~~l-~~L 112 (182)
T PRK12540 82 ------------------------ADGSY--------------------AKT--LKSQPGQ--NAHLEFEEFRAAL-DKL 112 (182)
T ss_pred ------------------------ccccc--------------------ccc--ccCCCch--HHHHHHHHHHHHH-HhC
Confidence 00000 000 0011211 1112235688899 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhhH
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM 478 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~l 478 (485)
|+++|.||.|+| .+|+|++|||+.||+|.++|+++++||+++||+.+.....
T Consensus 113 p~~~R~v~~L~~---~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~~ 164 (182)
T PRK12540 113 PQDQREALILVG---ASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDGA 164 (182)
T ss_pred CHHHHHHhhHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 999999999999 8999999999999999999999999999999999987653
No 102
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=1.4e-18 Score=164.77 Aligned_cols=178 Identities=15% Similarity=0.188 Sum_probs=130.4
Q ss_pred HHHHHHhHHHHHHHHHHhcCCCCc-HHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccccc
Q 011454 267 EKLVMSNVRLVMSIAQRYDNMGAD-MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH 345 (485)
Q Consensus 267 e~Lie~yl~LV~sIA~ry~~~~~d-~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~ 345 (485)
+..+..|.+.|+.+|+++.++..+ +||++||+|+.+|+++++|++. + +|.+|++..+++.+.+++++..+.......
T Consensus 8 ~~~~~~~~~~l~~~a~~~~~~~~~~AEDivQevfl~~~~~~~~~~~~-~-~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~~ 85 (195)
T PRK12532 8 DAELIESRKLLLHFARLQLPDHPDLAEDLVQETLLSAYSAGDSFQGR-A-LVNSWLFAILKNKIIDALRQIGRQRKVFTL 85 (195)
T ss_pred hhhHHHHHHHHHHHHHHHcCChhhhHHHHHHHHHHHHHHhccccccc-c-hHHHHHHHHHHHHHHHHHHHhccccccccc
Confidence 356778999999999999998888 9999999999999999999864 3 699999999999999998876431110000
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcc--cCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 346 LHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADN--RVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 346 ~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~--~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
. .....++........ .. ....+. ....+|+..+...+....+..+| ..|
T Consensus 86 ~------------------~~~~~~~~~~~~~~~-~~--------~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l-~~L 137 (195)
T PRK12532 86 L------------------DDELLDEAFESHFSQ-NG--------HWTPEGQPQHWNTPEKSLNNNEFQKILQSCL-YNL 137 (195)
T ss_pred c------------------cccccchhhhhhhcc-cc--------ccccccCccccCCHHHHHHHHHHHHHHHHHH-HhC
Confidence 0 000000000000000 00 000000 01134666666677777899999 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 477 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~ 477 (485)
|+++|+||.|+| ++|+|++|||+.||+|.+||+++++||+++||+.+....
T Consensus 138 ~~~~r~i~~L~~---~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~ 188 (195)
T PRK12532 138 PENTARVFTLKE---ILGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKW 188 (195)
T ss_pred CHHHHHHhhhHH---HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 999999999999 899999999999999999999999999999999997654
No 103
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=1.4e-18 Score=166.13 Aligned_cols=178 Identities=14% Similarity=0.117 Sum_probs=127.4
Q ss_pred HHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHH
Q 011454 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH 347 (485)
Q Consensus 268 ~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~ 347 (485)
.++..|.+.++.+|++++++..++||++||+|+.+|+.+++|++.. .|.+|++..++|.+.+++++..+...++..
T Consensus 12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~-- 87 (201)
T PRK12545 12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQS--AHKTWVFGILRNKLIDTLRARQRTVNLSAL-- 87 (201)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhccccc--hHHHHHHHHHHHHHHHHHHhhccccccccc--
Confidence 3488999999999999999999999999999999999999998753 599999999999999998876532111100
Q ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhc--ccCCCCCcchHHHHHHHHHHHHHHHhhCCH
Q 011454 348 ERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIAD--NRVENNPWHGVDDWALKDEVNKLIIVTLGE 425 (485)
Q Consensus 348 ~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D--~~~e~~pee~~e~~el~e~L~~~L~~~Lp~ 425 (485)
.. ....... ++. ...... ..+... .....+|.......+....+.++| ..||+
T Consensus 88 -------------~~---~~~~~~~---~~~--~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L-~~Lp~ 142 (201)
T PRK12545 88 -------------DA---ELDGEAL---LDR--ELFKDN---GHWAAHAKPRPWPKPETILQQQQFWTLFETCL-DHLPE 142 (201)
T ss_pred -------------cc---ccchhhh---hhh--hhhccc---ccccccccCcCCCCHHHHHHHHHHHHHHHHHH-HhCCH
Confidence 00 0000000 000 000000 000000 000112333444445556788899 89999
Q ss_pred HHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 011454 426 REREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 477 (485)
Q Consensus 426 rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~ 477 (485)
++|.||.|+| ++|+|++|||+.||+|.+||++++.||+++||+.+...+
T Consensus 143 ~~r~v~~L~~---~eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~ 191 (201)
T PRK12545 143 QIGRVFMMRE---FLDFEIDDICTELTLTANHCSVLLYRARTRLRTCLSEKG 191 (201)
T ss_pred HHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 9999999999 899999999999999999999999999999999997554
No 104
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=99.80 E-value=2.6e-18 Score=161.91 Aligned_cols=154 Identities=20% Similarity=0.204 Sum_probs=126.5
Q ss_pred HHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccccc
Q 011454 266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH 345 (485)
Q Consensus 266 ~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~ 345 (485)
++.|++.|.+.|+.++.++.++..++||++||+|+.+|+.+..|++. .+|.+|++..+++.+.++++...+....+
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~~--~~~~~wL~~i~~n~~~d~~Rk~~~~~~~~-- 78 (181)
T PRK09637 3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNTIIDFYRKKNRSEELP-- 78 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhccc--cchHHHHHHHHHHHHHHHHHhccccCCcc--
Confidence 67899999999999999999999999999999999999999999853 37999999999999999887664211000
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCCH
Q 011454 346 LHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGE 425 (485)
Q Consensus 346 ~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp~ 425 (485)
.++. . ...+.+.....+....+..+| +.||+
T Consensus 79 -----------------------~~~~--------------------~-----~~~~~~~~~~~e~~~~l~~~l-~~L~~ 109 (181)
T PRK09637 79 -----------------------DDLL--------------------F-----EDEEREENAKKELAPCLRPFI-DALPE 109 (181)
T ss_pred -----------------------hhhh--------------------c-----cCCChhHHHHHHHHHHHHHHH-HhCCH
Confidence 0000 0 011222334445667788888 89999
Q ss_pred HHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 426 REREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 426 rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
++|.||.|+| ++|++++|||+.||+|.++|++++.+|+++||+.+..
T Consensus 110 ~~r~i~~l~~---~~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (181)
T PRK09637 110 KYAEALRLTE---LEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156 (181)
T ss_pred HHHHHHHHHH---hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999 8999999999999999999999999999999998875
No 105
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=1.7e-18 Score=163.92 Aligned_cols=176 Identities=11% Similarity=0.045 Sum_probs=127.7
Q ss_pred HHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHH
Q 011454 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH 347 (485)
Q Consensus 268 ~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~ 347 (485)
.-+..|.+.++.+|.+++++..+++|++||+|+.+|+.+.+|++.. +|.+|++..+++.+.++++++.+...... ..
T Consensus 11 ~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~~--~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~-~~ 87 (189)
T PRK12530 11 LEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQS--ALKTWIFAILKNKIIDLIRYRKRFVNESE-LI 87 (189)
T ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCCc--cHHHHHHHHHHHHHHHHHHhhccCCCccc-cc
Confidence 3466789999999999999999999999999999999999998653 59999999999999999887643211000 00
Q ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCCHHH
Q 011454 348 ERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGERE 427 (485)
Q Consensus 348 ~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp~rE 427 (485)
............+..... ...+ ....+|+..+...+....+..+| ++||+++
T Consensus 88 -----------------~~~~~~~~~~~~~~~~~~--------~~~~--~~~~~~~~~~~~~~~~~~l~~~l-~~Lp~~~ 139 (189)
T PRK12530 88 -----------------EEDSPNSFFDEKGHWKPE--------YYEP--SEWQEVENTVYKEEFWLIFEACL-NHLPAQQ 139 (189)
T ss_pred -----------------ccccchhhhccccccccc--------ccCC--ccccCHHHHHHHHHHHHHHHHHH-HhCCHHH
Confidence 000000000000000000 0000 00123444555666777888999 9999999
Q ss_pred HHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 011454 428 REIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 477 (485)
Q Consensus 428 R~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~ 477 (485)
|+||.|+| ++|+|++|||+.||+|.+||+++++||+++||+++....
T Consensus 140 R~v~~L~~---~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~ 186 (189)
T PRK12530 140 ARVFMMRE---YLELSSEQICQECDISTSNLHVLLYRARLQLQACLSKNW 186 (189)
T ss_pred HHHHhHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999 899999999999999999999999999999999997543
No 106
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=1.9e-18 Score=166.41 Aligned_cols=181 Identities=14% Similarity=0.109 Sum_probs=132.5
Q ss_pred HHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccccc
Q 011454 266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH 345 (485)
Q Consensus 266 ~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~ 345 (485)
-..|+..|.+.|+.+|+++.++..+++|++||+|+.+|+.+.+|++. .+|.+|++..+++.+.+++++..+....+..
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 45789999999999999999999999999999999999999999864 3699999999999999999876532111100
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCCH
Q 011454 346 LHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGE 425 (485)
Q Consensus 346 ~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp~ 425 (485)
. ........+........ . ...........+|++.+...+....+..+| ..||+
T Consensus 98 ~-----------------~~~~~~~~~~~~~~~~~-------~-~~~~~~~~~~~~~e~~~~~~e~~~~l~~~L-~~L~~ 151 (206)
T PRK12544 98 L-----------------RDEEEEEDFEELFDESG-------H-WQKDERPQAWGNPEESLEQEQFWRIFEACL-DGLPA 151 (206)
T ss_pred c-----------------cccchhhHHHHhhcccc-------c-ccccccccccCCHHHHHHHHHHHHHHHHHH-HhCCH
Confidence 0 00000000000000000 0 000000011134665666666667888899 89999
Q ss_pred HHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 011454 426 REREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 477 (485)
Q Consensus 426 rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~ 477 (485)
++|+||.|+| ++|+|++|||+.||+|.++|+++++||+++||+.+....
T Consensus 152 ~~r~v~~L~~---~~g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~~ 200 (206)
T PRK12544 152 KYARVFMMRE---FIELETNEICHAVDLSVSNLNVLLYRARLRLRECLENKW 200 (206)
T ss_pred HHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 9999999999 899999999999999999999999999999999997543
No 107
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=99.79 E-value=8.4e-19 Score=159.16 Aligned_cols=153 Identities=16% Similarity=0.177 Sum_probs=122.4
Q ss_pred HHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHH
Q 011454 270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHER 349 (485)
Q Consensus 270 ie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~ 349 (485)
++.|.+.|+.++.++.++..+++|++||+|+.+|+++++|++ + +|.+|++..+++.+.+++++..+....
T Consensus 1 y~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~--~-~f~~wl~~i~~~~~~d~~r~~~~~~~~------- 70 (154)
T TIGR02950 1 YREYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD--S-SIKPWLFRIARNAFIDWYRKDKKIQTI------- 70 (154)
T ss_pred CchHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC--C-chHHHHHHHHHHHHHHHHHHhhhhccc-------
Confidence 357999999999999999999999999999999999999997 3 699999999999998888765421000
Q ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHH
Q 011454 350 LGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGERERE 429 (485)
Q Consensus 350 ~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp~rER~ 429 (485)
..+.+.. ...+. ...|++.+...+....+.++| ..||++++.
T Consensus 71 ------------------~~~~~~~-----------------~~~~~--~~~~~~~~~~~~~~~~l~~~l-~~L~~~~r~ 112 (154)
T TIGR02950 71 ------------------DDDAIGD-----------------LEQHP--VESPEHHLLIKIEQEEITHHL-SRLPENYRT 112 (154)
T ss_pred ------------------cHhhhhh-----------------ccccc--cCChhHHHHHHHHHHHHHHHH-HhCCHhhee
Confidence 0000000 00000 123555555566667899999 899999999
Q ss_pred HHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 011454 430 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 473 (485)
Q Consensus 430 VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L 473 (485)
||.++| ++|+|++|||+.||+|.++|++.+++|+++||+.+
T Consensus 113 i~~l~~---~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~l 153 (154)
T TIGR02950 113 VLILRE---FKEFSYKEIAELLNLSLAKVKSNLFRARKELKKLL 153 (154)
T ss_pred eeeehh---hccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 999998 79999999999999999999999999999999876
No 108
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=99.79 E-value=4e-18 Score=161.50 Aligned_cols=160 Identities=18% Similarity=0.155 Sum_probs=123.8
Q ss_pred hhHHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhc
Q 011454 261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (485)
Q Consensus 261 ~~~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~i 340 (485)
.+..+++.++..|.+.|+.+|.++.++..+++|++||+|+.+|+.++.|++.. .|.+|++..+++.+.+..++..+.
T Consensus 20 ~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~~--~~~~wL~~Iarn~~~~~~r~~~~~- 96 (188)
T PRK12517 20 SKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEK--AAKAWLITILRRENARRFERKQFD- 96 (188)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCcc--chHHHHHHHHHHHHHHHHHHhccC-
Confidence 35689999999999999999999999999999999999999999999998653 699999999988654443221100
Q ss_pred cccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHH
Q 011454 341 RLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLII 420 (485)
Q Consensus 341 rip~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~ 420 (485)
....++. ...+.. ..+| +.....+.|..+|
T Consensus 97 -------------------------~~~~~~~-------------------~~~~~~-~~~~----e~~~~~~~l~~~l- 126 (188)
T PRK12517 97 -------------------------LVDIEDD-------------------SIEDDA-SHSS----EEEMEQEWLRRQI- 126 (188)
T ss_pred -------------------------ccCcccc-------------------cccCcc-ccCh----hHHHHHHHHHHHH-
Confidence 0000000 000000 0112 2223345688888
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 476 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~ 476 (485)
..||+++|.||.++| .+|++++|||+.||||.++|+.+++||+++||+.+...
T Consensus 127 ~~Lp~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 179 (188)
T PRK12517 127 AKLDPEYREPLLLQV---IGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALEKP 179 (188)
T ss_pred HhCCHHHHHHHHHHH---HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 899999999999999 89999999999999999999999999999999999754
No 109
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=99.79 E-value=2.8e-18 Score=157.60 Aligned_cols=159 Identities=16% Similarity=0.167 Sum_probs=124.1
Q ss_pred HHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHH
Q 011454 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH 347 (485)
Q Consensus 268 ~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~ 347 (485)
.++..|.+.++.+|.++.++..++||++||+|+.+|+....|++. .|.+|++..+++.+.+++++..+.....
T Consensus 2 ~~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn~~~d~~R~~~~~~~~~---- 74 (163)
T PRK07037 2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRNLAIDHYRRQALENKYH---- 74 (163)
T ss_pred hHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHHHHHHHHHhhccccccc----
Confidence 367789999999999999999999999999999999998877653 4789999999999988887654210000
Q ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCCHHH
Q 011454 348 ERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGERE 427 (485)
Q Consensus 348 ~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp~rE 427 (485)
...... ........+|+......+..+.+..+| +.|||++
T Consensus 75 ------------------~~~~~~---------------------~~~~~~~~~~~~~~~~~~~~~~l~~~l-~~L~~~~ 114 (163)
T PRK07037 75 ------------------GDEEDG---------------------LDVPSPEASPEAALINRDTLRHVADAL-SELPART 114 (163)
T ss_pred ------------------cccccc---------------------cccCCCCCCHHHHHHHHHHHHHHHHHH-HhCCHHH
Confidence 000000 000000124555555666677888999 8999999
Q ss_pred HHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Q 011454 428 REIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 476 (485)
Q Consensus 428 R~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~ 476 (485)
|.||.++| ++|+|++|||+.||+|.++|++.+.+|+++||+.+...
T Consensus 115 r~v~~l~~---~~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l~~~ 160 (163)
T PRK07037 115 RYAFEMYR---LHGETQKDIARELGVSPTLVNFMIRDALVHCRKCLDAC 160 (163)
T ss_pred HHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence 99999999 89999999999999999999999999999999998653
No 110
>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=99.79 E-value=1.8e-18 Score=176.20 Aligned_cols=183 Identities=16% Similarity=0.144 Sum_probs=130.9
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccc
Q 011454 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (485)
Q Consensus 263 ~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~iri 342 (485)
..|++.||..|.+.|+++|++++++..++||++||+|+.+|+.+++|++.. .|.+|++..++|.+.+++++..+....
T Consensus 4 ~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~~~~~ 81 (324)
T TIGR02960 4 GAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGRS--SVRTWLYRIATNACLDALEARQRRPRP 81 (324)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCccc--chHHHHHHHHHHHHHHHHHhccCCcCc
Confidence 489999999999999999999999999999999999999999999998643 699999999999999998876431100
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCHHHHH----HHh-CCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHH-HHHHHH
Q 011454 343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIA----EYL-NMSQKKVRNATEVLAYIADNRVENNPWHGVDDWA-LKDEVN 416 (485)
Q Consensus 343 p~~~~~~~~kirka~~~L~~~gr~ps~eEIa----e~L-~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~e-l~e~L~ 416 (485)
.... ............ ..+ ..+.. ..........+|++.....+ +...+.
T Consensus 82 ~~~~---------------~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~~~e~~~~~l~ 137 (324)
T TIGR02960 82 VGLG---------------APSADGTAAASEAAEVTWLEPLPDL---------TLDLDDPAAADPSVAAGSRESVRLAFV 137 (324)
T ss_pred cccC---------------CCCCcccccccccccccccCCCCcc---------ccccccCCCCCHHHHHHHHHHHHHHHH
Confidence 0000 000000000000 000 00000 00000000123444444443 445688
Q ss_pred HHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 417 KLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 417 ~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
.+| .+||+++|.||.|+| ++|+|++|||+.||+|.++|+++++||+++||+.+..
T Consensus 138 ~~l-~~Lp~~~R~v~~L~~---~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 192 (324)
T TIGR02960 138 AAI-QYLPPRQRAVLLLRD---VLGWRAAETAELLGTSTASVNSALQRARATLDEVGPS 192 (324)
T ss_pred HHH-HhCCHHHhhHhhhHH---HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccc
Confidence 889 899999999999999 8999999999999999999999999999999999874
No 111
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=99.79 E-value=5.7e-18 Score=157.77 Aligned_cols=161 Identities=16% Similarity=0.176 Sum_probs=124.9
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccc
Q 011454 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (485)
Q Consensus 263 ~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~iri 342 (485)
..|++.+++.|.+.++.++.++.++..++||++||+|+.+|+. ..|++.. +|.+|++..+++.+.+++++..+.
T Consensus 9 ~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~~~--- 82 (172)
T PRK09651 9 SLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNALE--- 82 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHHHH---
Confidence 4899999999999999999999999999999999999999998 3565433 589999999999888887754310
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhh
Q 011454 343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVT 422 (485)
Q Consensus 343 p~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~ 422 (485)
. . ..+.+. .+.+. ...+|.......+....|..+| ..
T Consensus 83 ------------~---~--------~~~~~~------------------~~~~~-~~~~~~~~~~~~e~~~~l~~~l-~~ 119 (172)
T PRK09651 83 ------------K---A--------YLEMLA------------------LMPEG-GAPSPEERESQLETLQLLDSML-DG 119 (172)
T ss_pred ------------h---h--------hhhHHh------------------hcccc-CCCChHHHHHHHHHHHHHHHHH-Hh
Confidence 0 0 000000 00000 0123443444445556788999 89
Q ss_pred CCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 423 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 423 Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
|||++|+||.|+| ++|+|++|||+.||+|.++|++++.||+++|+.+.-.
T Consensus 120 L~~~~r~i~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~~~~ 169 (172)
T PRK09651 120 LNGKTREAFLLSQ---LDGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLFRLE 169 (172)
T ss_pred CCHHHhHHhhhhh---ccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999 8999999999999999999999999999999987654
No 112
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=99.79 E-value=3.4e-18 Score=156.68 Aligned_cols=155 Identities=13% Similarity=0.111 Sum_probs=122.7
Q ss_pred HHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHH
Q 011454 270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHER 349 (485)
Q Consensus 270 ie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~ 349 (485)
++.|.+.++.++.+++++..++||++||+|+.+|+..+.|++ + +|.+|++..+++.+.+++++..+...
T Consensus 1 ~~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~--~-~~~~wL~~ia~n~~~d~~R~~~~~~~-------- 69 (159)
T PRK12527 1 MENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQI--E-HPRAFLYRTALNLVVDRHRRHRVRQA-------- 69 (159)
T ss_pred ChhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhccccccc--c-chHHHHHHHHHHHHHHHHHHHhcccc--------
Confidence 357899999999999999899999999999999999999875 2 68999999999999888875531000
Q ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHH
Q 011454 350 LGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGERERE 429 (485)
Q Consensus 350 ~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp~rER~ 429 (485)
...+.... .+.....+|++.++..+....|..+| .+||++++.
T Consensus 70 -----------------~~~~~~~~-------------------~~~~~~~~~~~~~~~~~~~~~l~~~l-~~L~~~~r~ 112 (159)
T PRK12527 70 -----------------EPLEVLDE-------------------EERLHSPSPQTRLDLGQRLALLQRAL-AELPPACRD 112 (159)
T ss_pred -----------------cchhhhhc-------------------cccccCCCHHHHHHHHHHHHHHHHHH-HhCCHHHHH
Confidence 00000000 00001124555556666677889999 899999999
Q ss_pred HHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 430 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 430 VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
||.|+| ++|+|++|||+.||+|.++|++++.||+++||+.+..
T Consensus 113 v~~l~~---~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~~ 155 (159)
T PRK12527 113 SFLLRK---LEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQ 155 (159)
T ss_pred HHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 999999 8999999999999999999999999999999999874
No 113
>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=99.79 E-value=4.2e-18 Score=158.52 Aligned_cols=149 Identities=21% Similarity=0.259 Sum_probs=121.8
Q ss_pred HHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHHH
Q 011454 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 350 (485)
Q Consensus 271 e~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~~ 350 (485)
..|.+.++.+++++.++..++||++||+|+.+|+++++|++. .+|.+|++..+++.+.+++++..+...++.
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~~--~~f~~wl~~iarn~~~d~~Rk~~~~~~~~~------ 73 (170)
T TIGR02959 2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDG--QKIQSWLYQIARNTIIDFYRSKSRSVELPE------ 73 (170)
T ss_pred chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhccCccccch------
Confidence 468999999999999999999999999999999999999864 479999999999999999887643111000
Q ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHH
Q 011454 351 GLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREI 430 (485)
Q Consensus 351 ~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp~rER~V 430 (485)
.. .. ...+.+.....+....+..+| ..||+++|.|
T Consensus 74 --------------------~~--------------------~~----~~~~~~~~~~~e~~~~l~~~l-~~L~~~~r~v 108 (170)
T TIGR02959 74 --------------------SL--------------------LA----ADSAREETFVKELSQCIPPMI-KELPDEYREA 108 (170)
T ss_pred --------------------hh--------------------cc----cCCccHHHHHHHHHHHHHHHH-HhCCHHHHHH
Confidence 00 00 012222334455566788999 8999999999
Q ss_pred HhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 431 IRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 431 I~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
|.|+| .+|+|++|||+.||+|.++|+++++||+++||..+..
T Consensus 109 ~~l~~---~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 150 (170)
T TIGR02959 109 IRLTE---LEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLET 150 (170)
T ss_pred HHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 99999 8999999999999999999999999999999999874
No 114
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=1.1e-17 Score=158.90 Aligned_cols=156 Identities=17% Similarity=0.212 Sum_probs=121.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.+++.|+. |.+.|+++|+++.++..++||++||+|+.+|+++..|+.. ..|.+|++..+++.+.+++++..+..
T Consensus 8 ~~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r~~--- 81 (188)
T PRK12546 8 DPRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKREV--- 81 (188)
T ss_pred hHHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhcccc---
Confidence 56666665 7799999999999999999999999999999999999864 36999999999998888877654210
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
. ...++. .+ .....|.. +.......+..+| ..|
T Consensus 82 ~----------------------~~~~~~---------------------~~-~~~~~~~~--~~~~~~~~l~~~L-~~L 114 (188)
T PRK12546 82 P----------------------DPEGVH---------------------AA-SLAVKPAH--DGRLAMSDFRAAF-AQL 114 (188)
T ss_pred c----------------------Cccccc---------------------cc-ccccCCcc--hhHHHHHHHHHHH-HhC
Confidence 0 000000 00 00011211 1222335688899 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
||++|.||.|+| ++|+|++|||+.||||.++|+++++||+++||+.+..
T Consensus 115 p~~~r~v~~L~~---~~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~ 163 (188)
T PRK12546 115 PDEQREALILVG---ASGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQL 163 (188)
T ss_pred CHHHhHHhhhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 999999999999 8999999999999999999999999999999999875
No 115
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=99.77 E-value=1e-17 Score=158.12 Aligned_cols=159 Identities=17% Similarity=0.199 Sum_probs=123.8
Q ss_pred HHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccc
Q 011454 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN 344 (485)
Q Consensus 265 A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~ 344 (485)
..+..+..|++.|+.+|.++.++..+++|++||+|+.+|+.+..|++.. +|.+|++..+++.+.+++++..+....
T Consensus 5 ~~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~~--~~~~WL~~Iarn~~id~~Rk~~~~~~~-- 80 (182)
T PRK12511 5 SKRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSGG--NLRTWLMSILHNAFIDELRRRRVEARR-- 80 (182)
T ss_pred chhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCcc--chHHHHHHHHHHHHHHHHHhhcccccc--
Confidence 3455577899999999999999999999999999999999999998643 699999999999999988775421000
Q ss_pred cHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCC
Q 011454 345 HLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTLG 424 (485)
Q Consensus 345 ~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp 424 (485)
.+++.. ..+. ..+ ...+.......|..+| ..||
T Consensus 81 ------------------------~~~~~~------------------~~~~---~~~-~~~~~~~~~~~l~~~l-~~Lp 113 (182)
T PRK12511 81 ------------------------ADELAV------------------LADA---SLP-AAQEHAVRLAQIRDAF-FDLP 113 (182)
T ss_pred ------------------------ccchhh------------------cccc---CCC-cchHHHHHHHHHHHHH-HhCC
Confidence 000000 0000 001 1112223445688889 8999
Q ss_pred HHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 011454 425 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 477 (485)
Q Consensus 425 ~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~ 477 (485)
+++|.||.|+| ++|+|++|||+.||||.++|++++++|+++||+.+...+
T Consensus 114 ~~~R~v~~L~~---~eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~~~~ 163 (182)
T PRK12511 114 EEQRAALHLVA---IEGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEEGTG 163 (182)
T ss_pred HHHHHHHHHHH---HcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 99999999999 899999999999999999999999999999999988543
No 116
>TIGR02895 spore_sigI RNA polymerase sigma-I factor. Members of this sigma factor protein family are strictly limited to endospore-forming species in the Firmicutes lineage of bacteria, but are not universally present among such species. Sigma-I was shown to be induced by heat shock (PubMed:11157964) in Bacillus subtilis and is suggested by its phylogenetic profile to be connected to the program of sporulation (PubMed:16311624).
Probab=99.77 E-value=3.2e-17 Score=159.43 Aligned_cols=179 Identities=20% Similarity=0.229 Sum_probs=130.0
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCC--CcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhh---h
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMG--ADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS---R 338 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~--~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~---r 338 (485)
. +++||..|.|+|.++|.+|.++. .+.||++|+|++|||+|+++||+++|.+|.+||.++|++.|.+++++.. +
T Consensus 10 ~-~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dylRk~~k~~~ 88 (218)
T TIGR02895 10 E-REELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYIRKNQKYQN 88 (218)
T ss_pred H-HHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHhcccccC
Confidence 5 99999999999999999998764 5899999999999999999999999999999999999999999999887 5
Q ss_pred hccccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHH------hCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHH
Q 011454 339 TLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEY------LNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWAL 411 (485)
Q Consensus 339 ~irip~~~~~~~~kirka~~~L~-~~gr~ps~eEIae~------L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el 411 (485)
.+++|+...+....+..+...+. ..++.|..+||+.. .|++.+++. ...|-+.-.. ..
T Consensus 89 ~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~~~~L~~~gi~~~dLv--------------~~sPkh~d~r-~~ 153 (218)
T TIGR02895 89 LLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEYKKLLKQFGIEFVELV--------------KVSPKHRDTR-KK 153 (218)
T ss_pred eeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCcHHHHh--------------hcCCCCHHHH-HH
Confidence 66888765554445555555553 56788888887654 466665432 2345544333 22
Q ss_pred HHHHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011454 412 KDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 412 ~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
.-.+...+ .. + ..++...+. ...++.+||++.++||+.|+.+..+-.
T Consensus 154 ~i~ia~~~-~~-~---~~l~~~l~~--kk~LP~k~l~~~~~v~rktier~rkyI 200 (218)
T TIGR02895 154 AIKIAKVI-VE-N---EELLEYLIR--KKKLPIKEIEERVRISRKTIERYRKYI 200 (218)
T ss_pred HHHHHHHH-hc-C---HHHHHHHHH--hCCCCHHHHHHHcCCCHHHHHHhhHHH
Confidence 23333333 11 1 122222221 356999999999999999997655443
No 117
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=99.76 E-value=5.3e-17 Score=150.60 Aligned_cols=159 Identities=13% Similarity=0.092 Sum_probs=125.1
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
.++.+++..|.+.++.+|.++.++..+++|++||+|+.+|+..+.++. ..|.+|++..++|.+.+++++....
T Consensus 9 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~~---- 81 (168)
T PRK12525 9 TLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDLE---- 81 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHHH----
Confidence 789999999999999999999999999999999999999986665542 2699999999999888877654210
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL 423 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L 423 (485)
. .... .+. + .. .....+|+......+....|..+| ..|
T Consensus 82 -----------~--~~~~---------~~~-----------------~-~~-~~~~~~~~~~~~~~~~~~~l~~~l-~~L 119 (168)
T PRK12525 82 -----------R--AYLQ---------SLA-----------------E-AP-EAVQPSPEEQWMVIETLLAIDRLL-DGL 119 (168)
T ss_pred -----------H--HHHH---------HHh-----------------c-cc-ccccCChHHHHHHHHHHHHHHHHH-HhC
Confidence 0 0000 000 0 00 001234555555666678889999 899
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 474 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~ 474 (485)
|+++|.||.|+| .+|+|++|||+.||+|.+||+.++.+|++++|..+.
T Consensus 120 ~~~~r~v~~L~~---~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~~~ 167 (168)
T PRK12525 120 SGKARAAFLMSQ---LEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQGFQ 167 (168)
T ss_pred CHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhc
Confidence 999999999998 899999999999999999999999999999998764
No 118
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=99.72 E-value=2.7e-16 Score=153.97 Aligned_cols=151 Identities=18% Similarity=0.139 Sum_probs=117.7
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcc
Q 011454 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 341 (485)
Q Consensus 262 ~~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~ir 341 (485)
+..+++.+++.| +.+++++.++.++..++||++||+|+.+|+. |+.. + .|.+|++..++|.+.+++++..+...
T Consensus 16 ~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~-~-~~~~WL~~IarN~~id~~Rk~k~~~~ 89 (228)
T PRK06704 16 NHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNK-D-ICMTLVYKIARNRWLDQIKSKSVHEK 89 (228)
T ss_pred CHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCcc-c-cHHHHHHHHHHHHHHHHHhccccccc
Confidence 337888888888 7899999999999999999999999999986 5443 2 48999999999988888776542100
Q ss_pred ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHh
Q 011454 342 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIV 421 (485)
Q Consensus 342 ip~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~ 421 (485)
+ .++. . ..++.. ...+..+.+..++ .
T Consensus 90 ~--------------------------~~~~------------------------~-~~~~~~--~~~~~~~~l~~~L-~ 115 (228)
T PRK06704 90 I--------------------------RDQI------------------------T-FEEPHE--KIADLHEMVGKVL-S 115 (228)
T ss_pred c--------------------------cccc------------------------c-cCChHH--HHHHHHHHHHHHH-H
Confidence 0 0000 0 001111 1122345678888 8
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
+||+++|.||.|+| .+|+|++|||+.||+|.++|+++++||+++||+.+..
T Consensus 116 ~Lp~~~R~v~lL~~---~eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~ 166 (228)
T PRK06704 116 SLNVQQSAILLLKD---VFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEE 166 (228)
T ss_pred hCCHHHhhHhhhHH---hhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999 7999999999999999999999999999999999865
No 119
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=99.70 E-value=2.8e-16 Score=143.65 Aligned_cols=156 Identities=13% Similarity=0.084 Sum_probs=109.8
Q ss_pred CCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHcCC
Q 011454 286 NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGV 365 (485)
Q Consensus 286 ~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~~~~~kirka~~~L~~~gr 365 (485)
++..+++|++||+|+.+|+.++.+ + +..|.+|++..++|.+.+++++..+........ ..+. ...
T Consensus 2 ~~~~~AeDivQe~fl~~~~~~~~~-~--~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~~-----------~~~~-~~~ 66 (161)
T PRK09047 2 RDDDAALDIVQDAMIKLAEKYGDR-P--AAEWPPLFQRILQNRIHDWFRRQKVRNTWVSLF-----------SSFS-DDD 66 (161)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhhc-c--cCchHHHHHHHHHHHHHHHHHhhcccccccccc-----------cccc-ccc
Confidence 455689999999999999998873 3 346999999999999999987654211000000 0000 000
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccC-CCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhccCCCCCCH
Q 011454 366 TPSVDRIAEYLNMSQKKVRNATEVLAYIADNRV-ENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTW 444 (485)
Q Consensus 366 ~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~-e~~pee~~e~~el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~ 444 (485)
.....+.. +.+.+... ..+|+..+...+....|..+| .+||+++|.||.|+| ++|+|+
T Consensus 67 ~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l-~~Lp~~~r~v~~l~~---~~g~s~ 125 (161)
T PRK09047 67 DDDDFDPL-----------------ETLDSADEGAESPADKLERAQVLQLIEEAI-QKLPARQREAFLLRY---WEDMDV 125 (161)
T ss_pred ccccccHH-----------------HHhccccccCCCHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HhcCCH
Confidence 00000000 00111110 134566666677778899999 999999999999999 899999
Q ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 011454 445 EDISKRIGLSRERVRQVGLVALEKLKHAARKKK 477 (485)
Q Consensus 445 eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~ 477 (485)
+|||+.||+|.++|++++++|+++||+.+...+
T Consensus 126 ~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~ 158 (161)
T PRK09047 126 AETAAAMGCSEGSVKTHCSRATHALAKALEAKG 158 (161)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 999999999999999999999999999997654
No 120
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=99.69 E-value=3.5e-16 Score=158.09 Aligned_cols=160 Identities=15% Similarity=0.100 Sum_probs=121.6
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
..+.++++.|.+.++.+|++++++..++||++||+|+. |.....|+. ..|.+|++..++|.+.+++++..+....
T Consensus 4 ~~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~~---~~~~~WL~~Ia~n~~~d~lR~~~~~~~~- 78 (293)
T PRK09636 4 ADAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQI---RDPRAWLTRVVTRLCLDRLRSARHRRET- 78 (293)
T ss_pred cHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhcccccc---cCHHHHHHHHHHHHHHHHHHhhhccccc-
Confidence 45778999999999999999999999999999999999 666777752 3699999999999999888765321000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHH-HHHHHHHHHHHHHhh
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVD-DWALKDEVNKLIIVT 422 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e-~~el~e~L~~~L~~~ 422 (485)
. .+.. ..+. ..+. ..+|.+... ..+....+..+| ++
T Consensus 79 ----------------~--~~~~-~~e~---------------------~~~~--~~~~~~~~~~~~~~~~~l~~~l-~~ 115 (293)
T PRK09636 79 ----------------Y--VGPW-LPEP---------------------VVEE--LDDPLEAVVAAEDLSLALMLAL-ER 115 (293)
T ss_pred ----------------c--cCCc-CCcC---------------------CCCC--CCChHHHHHHHHHHHHHHHHHH-Hh
Confidence 0 0000 0000 0000 112333322 334455688888 89
Q ss_pred CCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 011454 423 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 474 (485)
Q Consensus 423 Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~ 474 (485)
|||++|.||.|+| .+++|++|||+.||+|.++|+++++||+++||+.+.
T Consensus 116 L~~~~R~v~~L~~---~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~ 164 (293)
T PRK09636 116 LSPLERAAFLLHD---VFGVPFDEIASTLGRSPAACRQLASRARKHVRAARP 164 (293)
T ss_pred CCHHHHHHHHHHH---HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 9999999999999 799999999999999999999999999999999764
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=99.67 E-value=9.8e-16 Score=154.15 Aligned_cols=154 Identities=19% Similarity=0.135 Sum_probs=116.9
Q ss_pred HHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccccHH
Q 011454 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH 347 (485)
Q Consensus 268 ~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~~~~ 347 (485)
++++.|.+.++.+|+++.++..++||++||+|+.+++. .|+.. ..|.+|++..+++.+.+++++..+...
T Consensus 1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~~--~~~~awL~~Ia~n~~ld~lR~~~~~~~------ 70 (281)
T TIGR02957 1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQI--ENPKAYLTKVVTRRCIDVLRSARARRE------ 70 (281)
T ss_pred ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Ccccc--cCHHHHHHHHHHHHHHHHHHHhhhccc------
Confidence 47899999999999999999999999999999997765 55433 269999999999999998876532100
Q ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhccc--CCCCCcchHHHH-HHHHHHHHHHHhhCC
Q 011454 348 ERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNR--VENNPWHGVDDW-ALKDEVNKLIIVTLG 424 (485)
Q Consensus 348 ~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~--~e~~pee~~e~~-el~e~L~~~L~~~Lp 424 (485)
.. .+ +. +++.. ...+|++..+.. .+...+..+| ++||
T Consensus 71 -----------~~--~~--~~------------------------~~e~~~~~~~~~~~~~~~~e~~~~~l~~~l-~~L~ 110 (281)
T TIGR02957 71 -----------VY--VG--PW------------------------LPEPLLTTSADPAESVELAESLSMAYLLLL-ERLS 110 (281)
T ss_pred -----------cc--CC--CC------------------------CCcccCCCCCChHHHHHHHHHHHHHHHHHH-hhCC
Confidence 00 00 00 00000 012344433333 3445677788 8999
Q ss_pred HHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 011454 425 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 474 (485)
Q Consensus 425 ~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~ 474 (485)
|+||.||.|+| ..++|++|||+.||+|.++|+++++||+++||+...
T Consensus 111 ~~~R~v~~L~~---~~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~ 157 (281)
T TIGR02957 111 PLERAVFVLRE---VFDYPYEEIASIVGKSEANCRQLVSRARRHLDARRP 157 (281)
T ss_pred HHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 99999999999 799999999999999999999999999999999754
No 122
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=99.66 E-value=1.8e-15 Score=153.22 Aligned_cols=159 Identities=16% Similarity=0.084 Sum_probs=122.1
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcccc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip 343 (485)
..+..+++.|.+.++++|++++++..++||++||+|+.+|++...+. ..|.+|++...+|.+.+++++..+....+
T Consensus 5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~~----~~~~aWL~~Ia~n~~id~lRk~~~rr~~~ 80 (290)
T PRK09635 5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGDI----DDERGWLIVVTSRLCLDHIKSASTRRERP 80 (290)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCcccc----ccHHHHHHHHHHHHHHHHHhhhhccCcCc
Confidence 67889999999999999999999999999999999999999876531 25899999999999999887643210000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcc--cCCCCCcch-HHHHHHHHHHHHHHH
Q 011454 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADN--RVENNPWHG-VDDWALKDEVNKLII 420 (485)
Q Consensus 344 ~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~--~~e~~pee~-~e~~el~e~L~~~L~ 420 (485)
. ..+. ..++. ....+|++. ....+....+..+|
T Consensus 81 ~-----------------~~~~--------------------------~~~~~~~~~~~~~~~~~~~~~e~~~al~~~L- 116 (290)
T PRK09635 81 Q-----------------DIAA--------------------------WHDGDASVSSVDPADRVTLDDEVRLALLIML- 116 (290)
T ss_pred c-----------------cccc--------------------------cCccccCCCCCCcHHHHHHHHHHHHHHHHHH-
Confidence 0 0000 00000 001233332 33445566788888
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 473 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L 473 (485)
..|||++|.||.|+| +.++|++|||+.||+|.++|+++++||+++||+..
T Consensus 117 ~~L~p~~R~vf~L~~---~~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~ 166 (290)
T PRK09635 117 ERLGPAERVVFVLHE---IFGLPYQQIATTIGSQASTCRQLAHRARRKINESR 166 (290)
T ss_pred HhCCHHHHHHhhHHH---HhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence 899999999999999 79999999999999999999999999999999864
No 123
>PRK09191 two-component response regulator; Provisional
Probab=99.60 E-value=7.8e-15 Score=143.38 Aligned_cols=136 Identities=13% Similarity=0.129 Sum_probs=110.5
Q ss_pred HHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccc
Q 011454 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN 344 (485)
Q Consensus 265 A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~ 344 (485)
++..+|..|.+.++++|.++.++..+++|++||+|+.+|+....|++.. .|.+|++.++++... ...
T Consensus 2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~~--~~~~wl~~~~~~~~~----~~~------- 68 (261)
T PRK09191 2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEAS--SPRVGLYRLFHRLWS----SAG------- 68 (261)
T ss_pred chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCCc--chhhHHHHHHHHHhc----ccc-------
Confidence 5889999999999999999999999999999999999999999998753 589999876654210 000
Q ss_pred cHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCC
Q 011454 345 HLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTLG 424 (485)
Q Consensus 345 ~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp 424 (485)
.. +.. ...+.. ..+.++| ++||
T Consensus 69 --------------------~~----------------------------~~~-~~~~~~--------~~l~~~l-~~L~ 90 (261)
T PRK09191 69 --------------------AN----------------------------DPE-PGSPFE--------ARAERRL-AGLT 90 (261)
T ss_pred --------------------cc----------------------------CCC-CCCCch--------HHHHHHH-HhCC
Confidence 00 000 011110 1688888 8999
Q ss_pred HHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 011454 425 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 474 (485)
Q Consensus 425 ~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~ 474 (485)
+++|.||.|+| ++|+|++|||+.||+|.++|+.++.+|+++||..+.
T Consensus 91 ~~~r~v~~l~~---~~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~ 137 (261)
T PRK09191 91 PLPRQAFLLTA---LEGFSVEEAAEILGVDPAEAEALLDDARAEIARQVA 137 (261)
T ss_pred HHHhHHHHHHH---HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCC
Confidence 99999999999 899999999999999999999999999999998764
No 124
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=99.56 E-value=3.7e-14 Score=127.71 Aligned_cols=136 Identities=20% Similarity=0.233 Sum_probs=99.5
Q ss_pred HHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhc-----CCCCCCcchhhHHHHHHHHHHHHHHHHhhhhc
Q 011454 266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEK-----FDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (485)
Q Consensus 266 ~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiek-----FDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~i 340 (485)
|+.|+..|.++++.+|++|.. .+|+ ||+|+.+|..+.+ |++. ..|.||++..++|.+.+++++..+..
T Consensus 1 f~~~~~~y~~~l~~~~~~~~~----~~~~-qdvf~~~w~~~~~~~~~~~~~~--~~~~~wL~~iarN~~id~~Rk~~~~~ 73 (142)
T TIGR03209 1 FEEIYMNFKNTIDIFTRKYNL----YYDY-NDILYHLWIILKKIDLNKFNTE--NDLEKYISTSLKRYCLDICNKKNRDK 73 (142)
T ss_pred ChHHHHHHHHHHHHHHHHhcc----hhhH-HHHHHHHHHHHHHhhhhhcCch--hHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 468999999999999999965 2344 9999999999865 5543 36999999999999999987654210
Q ss_pred cccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHH
Q 011454 341 RLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLII 420 (485)
Q Consensus 341 rip~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~ 420 (485)
.. .. ..+.. +. ...+.+.....+....+.++|
T Consensus 74 ~~-----------------~~-------~~~~~---------------------~~--~~~~~~~~~~~~~~~~l~~~l- 105 (142)
T TIGR03209 74 KI-----------------IY-------NSEIT---------------------DI--KLSLINVYSSNDLEFEFNDLI- 105 (142)
T ss_pred hh-----------------hh-------hhhhh---------------------cc--ccchhHHHHHHHHHHHHHHHH-
Confidence 00 00 00000 00 001112233344456688889
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVR 459 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVr 459 (485)
+.||+.+|.||.|+| ++|+|++|||+.||+|.+||+
T Consensus 106 ~~Lp~~~r~v~~l~~---~~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 106 SILPNKQKKIIYMKF---FEDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHhhc
Confidence 899999999999999 899999999999999999996
No 125
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=99.55 E-value=3.6e-13 Score=132.71 Aligned_cols=78 Identities=17% Similarity=0.207 Sum_probs=72.0
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCC--cHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhcc
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNMGA--DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 341 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~~~--d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~ir 341 (485)
.|++.|++.|.|+|+++|.+++++.. +.+|++|||++++|+++++|++++|.+|.+|++.+|++.+.+++++..+...
T Consensus 18 ~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn~~iDylRk~~~~~~ 97 (237)
T PRK08311 18 ELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKRRLIDYFRKESKHNL 97 (237)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccc
Confidence 89999999999999999999998765 5999999999999999999999988789999999999999999998776433
No 126
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=99.52 E-value=6.3e-13 Score=125.94 Aligned_cols=163 Identities=23% Similarity=0.269 Sum_probs=110.6
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCC---CCcHHH--HHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhh
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDNM---GADMAD--LVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR 338 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~~---~~d~ED--LiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r 338 (485)
.|+++|+..|++.+..+|+++... +.+.+| |++|+|+.+...-...+.+....|..|+...+++.+.++++....
T Consensus 17 ~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~~~~~rr~lid~~R~~~a 96 (185)
T PF07638_consen 17 AALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALLARIMRRKLIDHARRRQA 96 (185)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999987632 234444 577888887774333233332358888888888877777665542
Q ss_pred hccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHH
Q 011454 339 TLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKL 418 (485)
Q Consensus 339 ~irip~~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~ 418 (485)
.. .|......++... .+......| .+..++.+.+..+
T Consensus 97 ~K----------------------Rg~~~~~~~l~~~------------------~~~~~~~~~---~~~~~l~e~l~~L 133 (185)
T PF07638_consen 97 QK----------------------RGGDQVRVELDER------------------ADSGDEPSP---EELLELEEALERL 133 (185)
T ss_pred Hh----------------------cCCCCcccchhhh------------------hccccCCCH---HHHHHHHHHHHHH
Confidence 11 1111110111110 000001122 2334456666666
Q ss_pred HHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 011454 419 IIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 474 (485)
Q Consensus 419 L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~ 474 (485)
. . |+|+++.+|.++| ++|+|.+|||+.||||+.||++....|..+|+..|.
T Consensus 134 ~-~-l~~~~~~~v~l~~---~~Gls~~EIA~~lgiS~~tV~r~l~~aR~~l~~~l~ 184 (185)
T PF07638_consen 134 L-A-LDPRQRRVVELRF---FEGLSVEEIAERLGISERTVRRRLRRARAWLRRELR 184 (185)
T ss_pred H-c-cCHHHHHHHHHHH---HCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence 6 4 9999999999998 899999999999999999999999999999998874
No 127
>PF04542 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR007627 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [, ]. The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation [, ].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1OR7_B 1H3L_B 2Z2S_C 2Q1Z_C 2O7G_B 1SMY_F 1IW7_P 2BE5_F 2A6E_F 2CW0_F ....
Probab=99.26 E-value=1.6e-11 Score=96.84 Aligned_cols=70 Identities=27% Similarity=0.418 Sum_probs=66.3
Q ss_pred HHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhh
Q 011454 269 LVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR 338 (485)
Q Consensus 269 Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r 338 (485)
|++.|.|+|+.++.+|.+++.++||++||++++||+++++||++.+..|.+|++..+++.+.+++++..|
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 6899999999999999999999999999999999999999999999889999999999999999987653
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=99.18 E-value=6.5e-11 Score=88.73 Aligned_cols=50 Identities=48% Similarity=0.679 Sum_probs=45.8
Q ss_pred HHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 418 LIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 418 ~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
+| +.|||+|+.||.++| ++++|+.|||+.||+|+++|+++..+|+++||+
T Consensus 1 Al-~~L~~~er~vi~~~y---~~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 1 AL-DQLPPREREVIRLRY---FEGLTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp HH-CTS-HHHHHHHHHHH---TST-SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred Ch-hhCCHHHHHHHHHHh---cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 45 899999999999999 899999999999999999999999999999995
No 129
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=98.96 E-value=1.9e-09 Score=81.76 Aligned_cols=53 Identities=28% Similarity=0.464 Sum_probs=45.4
Q ss_pred HHHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 011454 413 DEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL 469 (485)
Q Consensus 413 e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKL 469 (485)
+.|.++| ..|||++|.||.++| .+|+|+.|||+.+|+|+++|++++.+|+++|
T Consensus 2 ~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~eIa~~l~~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 2 EALQQAL-AQLPERQREIFLLRY---FQGMSYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp HHHHHHH-HCS-HHHHHHHHHHH---TS---HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred HHHHHHH-HCCCHHHHHHHHHHH---HHCcCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 5678889 899999999999999 8999999999999999999999999999986
No 130
>PRK06930 positive control sigma-like factor; Validated
Probab=98.71 E-value=6.9e-08 Score=90.83 Aligned_cols=72 Identities=17% Similarity=0.158 Sum_probs=64.0
Q ss_pred CCcchHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Q 011454 401 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 476 (485)
Q Consensus 401 ~pee~~e~~el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~ 476 (485)
.|.+.....+....|..++ +.|||++|.||.|+| .+|+|++|||+.||+|.+||++++.+|+++|++.+...
T Consensus 94 ~~~~~~~~~e~~~~l~~al-~~L~~rer~V~~L~~---~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~ 165 (170)
T PRK06930 94 EEPESVISEWDKIRIEDAL-SVLTEREKEVYLMHR---GYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQINES 165 (170)
T ss_pred CChhHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 3555555666778899999 899999999999998 79999999999999999999999999999999998754
No 131
>PRK00118 putative DNA-binding protein; Validated
Probab=98.61 E-value=2.1e-07 Score=80.59 Aligned_cols=57 Identities=21% Similarity=0.237 Sum_probs=53.4
Q ss_pred HHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 011454 417 KLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 477 (485)
Q Consensus 417 ~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~ 477 (485)
-.. ..||++++.||.++| .+|+|..|||+.+|+|++||++++.+|+++||+++.+.+
T Consensus 13 ~~~-~~L~ekqRevl~L~y---~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~ 69 (104)
T PRK00118 13 FYG-SLLTEKQRNYMELYY---LDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLH 69 (104)
T ss_pred HHh-ccCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHC
Confidence 344 799999999999999 799999999999999999999999999999999998876
No 132
>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=98.39 E-value=1e-06 Score=64.74 Aligned_cols=53 Identities=42% Similarity=0.600 Sum_probs=48.7
Q ss_pred HHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011454 414 EVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 414 ~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLR 470 (485)
.+..++ ..||+.++.++.++| .+++|..+||+.+|+|..+|++++++++.+||
T Consensus 3 ~~~~~~-~~l~~~~~~~~~~~~---~~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 3 RLEEAL-DKLPEREREVILLRF---GEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred HHHHHH-HhCCHHHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 466777 899999999999999 79999999999999999999999999988874
No 133
>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=98.28 E-value=2.4e-06 Score=77.60 Aligned_cols=58 Identities=21% Similarity=0.326 Sum_probs=51.1
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhhHHHhh
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAML 482 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~l~~~l 482 (485)
..||++|++|+.|++ +|+|++|||+.||+|+++|++++++|+++|++......+-.++
T Consensus 5 ~~Lte~qr~VL~Lr~----~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l~~~~ 62 (137)
T TIGR00721 5 TFLTERQIKVLELRE----KGLSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDFVKFI 62 (137)
T ss_pred CCCCHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHHHHHh
Confidence 369999999999975 8999999999999999999999999999999877666555443
No 134
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=98.24 E-value=3.6e-06 Score=76.85 Aligned_cols=52 Identities=31% Similarity=0.367 Sum_probs=48.3
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 476 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~ 476 (485)
..|||+|++||.+++ +|+|++|||+.||+|+++|++++++|+++||+.....
T Consensus 5 ~~Lt~rqreVL~lr~----~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~tl 56 (141)
T PRK03975 5 SFLTERQIEVLRLRE----RGLTQQEIADILGTSRANVSSIEKRARENIEKARETL 56 (141)
T ss_pred cCCCHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 469999999999965 9999999999999999999999999999999988764
No 135
>PRK04217 hypothetical protein; Provisional
Probab=98.24 E-value=2.1e-06 Score=75.20 Aligned_cols=58 Identities=28% Similarity=0.259 Sum_probs=52.6
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhhHHHh
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAM 481 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~l~~~ 481 (485)
..|++.|+++|.++| .+++|++|||+.+|||++||++++++|+++|++.+.......+
T Consensus 41 ~~Lt~eereai~l~~---~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~~~~~ 98 (110)
T PRK04217 41 IFMTYEEFEALRLVD---YEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGRELII 98 (110)
T ss_pred ccCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhccceeE
Confidence 679999999999998 8999999999999999999999999999999999986554433
No 136
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=98.21 E-value=7.6e-06 Score=70.51 Aligned_cols=62 Identities=31% Similarity=0.408 Sum_probs=47.4
Q ss_pred HHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhhH
Q 011454 414 EVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM 478 (485)
Q Consensus 414 ~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~l 478 (485)
.|....-.-|+++|+.++.++| .+++|+.|||+.+|||+.+|.-.++||.++|...=.+.++
T Consensus 9 ~L~d~Yg~LLT~kQ~~~l~lyy---~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~yE~kL~l 70 (101)
T PF04297_consen 9 LLFDFYGELLTEKQREILELYY---EEDLSLSEIAEELGISRQAVYDSIKRAEKKLEEYEEKLGL 70 (101)
T ss_dssp HHHHHHGGGS-HHHHHHHHHHC---TS---HHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHHH-H
T ss_pred HHHHHHHHHCCHHHHHHHHHHH---ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3334442459999999999999 8999999999999999999999999999999887665553
No 137
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=97.93 E-value=2.6e-05 Score=58.27 Aligned_cols=46 Identities=37% Similarity=0.523 Sum_probs=41.6
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLR 470 (485)
..|++.|+.|+.+.+ .|++..|||+.+|+|+.+|++++.+++++|+
T Consensus 2 ~~l~~~e~~i~~~~~----~g~s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 2 ASLTPREREVLRLLA----EGLTNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCCCHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 468999999997754 8899999999999999999999999988886
No 138
>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=97.85 E-value=3.6e-05 Score=59.31 Aligned_cols=46 Identities=28% Similarity=0.461 Sum_probs=41.2
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLR 470 (485)
..|+++|.+|+.+.. .|++.+|||+.+|||+.||+.+..++++||.
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 479999999999986 8999999999999999999999999999985
No 139
>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=97.85 E-value=7.8e-05 Score=67.49 Aligned_cols=60 Identities=17% Similarity=0.243 Sum_probs=53.3
Q ss_pred HHHHHHHHHHHhhCCHHHHHHHhhHhccCCCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 011454 410 ALKDEVNKLIIVTLGEREREIIRLYYGLDKEC--LTWEDISKRIGLSRERVRQVGLVALEKLKHAA 473 (485)
Q Consensus 410 el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg--~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L 473 (485)
...+.|..+| +.|++.+|.||.++| +.+ +|+.+||..+|+|+.+|.++..+++.+|+..+
T Consensus 71 ~~~~~I~~~l-~~Ld~~er~II~~rY---~~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~l 132 (134)
T TIGR01636 71 RNRDAIENCL-NEADEQTRVIIQELY---MKKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEEL 132 (134)
T ss_pred HHHHHHHHHH-HhCCHHHHHHHHHHH---ccCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 3456788888 899999999999999 443 59999999999999999999999999999875
No 140
>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=97.80 E-value=5.4e-05 Score=56.73 Aligned_cols=45 Identities=33% Similarity=0.405 Sum_probs=40.6
Q ss_pred CCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 423 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 423 Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
||++|+.|+.+.+ .++|.+|||+.+|+|+.+|++++++++++|+-
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 88999999999999999999999999888765
No 141
>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=97.79 E-value=9.1e-05 Score=63.74 Aligned_cols=56 Identities=34% Similarity=0.506 Sum_probs=49.2
Q ss_pred HHHHHHHHHHHhhCC-HHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 011454 410 ALKDEVNKLIIVTLG-EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL 469 (485)
Q Consensus 410 el~e~L~~~L~~~Lp-~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKL 469 (485)
.....+..+| ++|+ +.+|.||.++| ..+++..+||+.||+|+.|+.+++.+|++.|
T Consensus 43 ~~k~ei~~~I-~~l~d~~~r~iL~~~Y---i~~~~~~~I~~~l~~S~~t~yr~~~~Al~~L 99 (100)
T PF07374_consen 43 KEKLEIRRAI-NKLEDPDERLILRMRY---INKLTWEQIAEELNISRRTYYRIHKKALKEL 99 (100)
T ss_pred HHHHHHHHHH-HHccChhHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence 3445677778 6775 78999999999 8999999999999999999999999999876
No 142
>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=97.72 E-value=7.1e-05 Score=60.82 Aligned_cols=47 Identities=13% Similarity=0.075 Sum_probs=40.4
Q ss_pred HHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 415 VNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 415 L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
+.+-+ +.||++.+.++.|... .+++|++|||+.||+|++||++++.+
T Consensus 9 ~~~~l-~~l~~~~r~af~L~R~--~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 9 LAERL-TWVDSLAEAAAALARE--EAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHH-hcCCHHHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 44456 7999999999999531 58999999999999999999999875
No 143
>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=97.71 E-value=0.00012 Score=55.97 Aligned_cols=47 Identities=32% Similarity=0.487 Sum_probs=41.5
Q ss_pred CCHHHHHHHhhHhccCC----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 011454 423 LGEREREIIRLYYGLDK----ECLTWEDISKRIGLSRERVRQVGLVALEKL 469 (485)
Q Consensus 423 Lp~rER~VI~LryGL~~----eg~S~eEIAe~LgIS~~tVrqi~~rALkKL 469 (485)
|+++|+++|...|-.|+ .+.|..|||+.||||++||..++.+|.+||
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 78999999998775542 368999999999999999999999999886
No 144
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=97.59 E-value=0.00011 Score=70.98 Aligned_cols=45 Identities=18% Similarity=0.233 Sum_probs=43.1
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLR 470 (485)
.|+|+|++|+.+.- +|+|.+|||++||+|..||+.+..+.++||.
T Consensus 137 ~LT~RE~eVL~lla----~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 137 SLSRTESSMLRMWM----AGQGTIQISDQMNIKAKTVSSHKGNIKRKIK 181 (207)
T ss_pred cCCHHHHHHHHHHH----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 49999999999986 9999999999999999999999999999997
No 145
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=97.56 E-value=0.00013 Score=70.67 Aligned_cols=46 Identities=22% Similarity=0.322 Sum_probs=43.6
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLR 470 (485)
..|+++|++|+.+.- +|+|.+|||+.|+||..||+.+..+.++||.
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 579999999999986 8999999999999999999999999999984
No 146
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPro: IPR009042 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....
Probab=97.55 E-value=3.2e-05 Score=54.73 Aligned_cols=33 Identities=30% Similarity=0.483 Sum_probs=30.6
Q ss_pred hhHHHHHHhhccccCCCHHHHHHHHHHHHcCCc
Q 011454 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS 223 (485)
Q Consensus 191 ~~~~~yl~~i~~~~~Lt~eee~~L~~~ik~Gd~ 223 (485)
|.++.||++|+++|+||++||++|+++|+.|+.
T Consensus 2 D~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~~ 34 (37)
T PF00140_consen 2 DSLRLYLKEIGRYPLLTAEEEIELARRIRKGDE 34 (37)
T ss_dssp HHHHHHHHHHHHS-EETTHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHH
Confidence 688999999999999999999999999999986
No 147
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=97.54 E-value=0.00017 Score=67.90 Aligned_cols=47 Identities=17% Similarity=0.269 Sum_probs=44.1
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
..|+++|++|+.+.- +|+|.+|||+.|++|+.||+....++++||.-
T Consensus 132 ~~LSpRErEVLrLLA----qGkTnKEIAe~L~IS~rTVkth~srImkKLgV 178 (198)
T PRK15201 132 RHFSVTERHLLKLIA----SGYHLSETAALLSLSEEQTKSLRRSIMRKLHV 178 (198)
T ss_pred CCCCHHHHHHHHHHH----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 579999999999985 99999999999999999999999999999864
No 148
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=97.52 E-value=0.00016 Score=69.10 Aligned_cols=46 Identities=26% Similarity=0.371 Sum_probs=43.3
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLR 470 (485)
..|+++|++|+.+.- +|+|.+|||+.|+||..||+.+..+.++||.
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 8999999999999999999999999999994
No 149
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=97.49 E-value=0.0002 Score=60.96 Aligned_cols=49 Identities=16% Similarity=0.286 Sum_probs=40.7
Q ss_pred HHHHHHHhhCCHHHHHHHhhHhcc-C---CCCCCHHHHHHHHCCCHHHHHHHH
Q 011454 414 EVNKLIIVTLGEREREIIRLYYGL-D---KECLTWEDISKRIGLSRERVRQVG 462 (485)
Q Consensus 414 ~L~~~L~~~Lp~rER~VI~LryGL-~---~eg~S~eEIAe~LgIS~~tVrqi~ 462 (485)
.+..++..-|+|+|+.+|.+|||| + ..++|++|||+.+|||+.+|.+.-
T Consensus 24 ~l~~~l~~lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~s 76 (94)
T TIGR01321 24 DMQLLLELILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGS 76 (94)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHH
Confidence 444555455999999999999999 3 358999999999999999997654
No 150
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=97.48 E-value=0.00019 Score=69.84 Aligned_cols=50 Identities=10% Similarity=0.068 Sum_probs=45.8
Q ss_pred HHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011454 416 NKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 416 ~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLR 470 (485)
.++. ..|+|+|++|+.+.- +|+|.+|||+.|++|..||+.+..+.++||.
T Consensus 138 ~~~~-~~LS~RE~eVL~Lia----~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLg 187 (217)
T PRK13719 138 LEAK-NKVTKYQNDVFILYS----FGFSHEYIAQLLNITVGSSKNKISEILKFFG 187 (217)
T ss_pred hhcc-CCCCHHHHHHHHHHH----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 3455 789999999999986 8999999999999999999999999999985
No 151
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=97.48 E-value=0.00017 Score=69.92 Aligned_cols=45 Identities=33% Similarity=0.403 Sum_probs=42.8
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLR 470 (485)
.|++||++|+.+.- +|+|++|||++|++|.+||+.+..+.++||.
T Consensus 148 ~LT~RE~eVL~lla----~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~ 192 (211)
T COG2197 148 LLTPRELEVLRLLA----EGLSNKEIAEELNLSEKTVKTHVSNILRKLG 192 (211)
T ss_pred CCCHHHHHHHHHHH----CCCCHHHHHHHHCCCHhHHHHHHHHHHHHcC
Confidence 59999999999985 8999999999999999999999999999985
No 152
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=97.41 E-value=0.0002 Score=52.53 Aligned_cols=41 Identities=27% Similarity=0.320 Sum_probs=24.9
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
.+|++.||..|...+ .+|+|..+||+.||+|++||.+.++|
T Consensus 3 ~~Lt~~eR~~I~~l~---~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEALL---EQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHHHH---CS---HHHHHHHTT--HHHHHHHHHH
T ss_pred cchhhhHHHHHHHHH---HcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 479999999999888 79999999999999999999998876
No 153
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=97.39 E-value=0.00069 Score=64.59 Aligned_cols=67 Identities=19% Similarity=0.264 Sum_probs=56.1
Q ss_pred HHHHHHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhhHHHh
Q 011454 410 ALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAM 481 (485)
Q Consensus 410 el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~l~~~ 481 (485)
.....+...+ ..|+|+||+|+...- .|+.+++||..||||+.||+.+..+.++||+..--..-.+-|
T Consensus 131 ~~~~~~~~~l-~tLT~RERqVl~~vV----~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~SlaeLvr~a 197 (202)
T COG4566 131 DRQAAIRARL-ATLTPRERQVLDLVV----RGLMNKQIAFDLGISERTVELHRANVMEKMQARSLAELVRMA 197 (202)
T ss_pred HHHHHHHHHH-HhcCHHHHHHHHHHH----cCcccHHHHHHcCCchhhHHHHHHHHHHHHhhccHHHHHHHH
Confidence 3455677778 899999999999885 899999999999999999999999999999875544444443
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=97.38 E-value=0.00028 Score=69.33 Aligned_cols=47 Identities=30% Similarity=0.239 Sum_probs=44.2
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
..||++|++||.+.. +|+|..|||+.||||..||+.++.++++||+-
T Consensus 170 ~~Lt~re~evl~~~a----~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~ 216 (232)
T TIGR03541 170 GVLSEREREVLAWTA----LGRRQADIAAILGISERTVENHLRSARRKLGV 216 (232)
T ss_pred ccCCHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence 579999999999975 89999999999999999999999999999974
No 155
>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=97.36 E-value=0.00034 Score=69.75 Aligned_cols=47 Identities=26% Similarity=0.237 Sum_probs=44.2
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
..||++|++|+.+.. +|+|..|||+.||||..||+.+++++++||.-
T Consensus 189 ~~LT~RE~evl~l~a----~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v 235 (247)
T TIGR03020 189 GLITAREAEILAWVR----DGKTNEEIAAILGISSLTVKNHLQHIFKKLDV 235 (247)
T ss_pred cCCCHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence 689999999999975 99999999999999999999999999999863
No 156
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=97.36 E-value=0.00036 Score=68.02 Aligned_cols=47 Identities=19% Similarity=0.214 Sum_probs=44.0
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
..|+++|++|+.+.. +|+|++|||+.|++|..||+.+..++++||.-
T Consensus 154 ~~Lt~rE~~Vl~l~~----~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v 200 (216)
T PRK10100 154 ALLTHREKEILNKLR----IGASNNEIARSLFISENTVKTHLYNLFKKIAV 200 (216)
T ss_pred CCCCHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 469999999999998 79999999999999999999999999999863
No 157
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=97.30 E-value=0.00043 Score=68.55 Aligned_cols=45 Identities=22% Similarity=0.254 Sum_probs=43.1
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLR 470 (485)
.|+++|++||.+.. +|+|..|||++||||..||+.++.++++||-
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 9999999999999999999999999999985
No 158
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=97.29 E-value=0.0006 Score=59.39 Aligned_cols=53 Identities=32% Similarity=0.338 Sum_probs=48.9
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 477 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~~ 477 (485)
.|+..|-+.|+|.+ ++++|++|.|+.||||+.||.+++..|.+|+-.+|-...
T Consensus 41 ~L~~dElEAiRL~D---~egl~QeeaA~~MgVSR~T~~ril~~ARkKiA~ALv~Gk 93 (106)
T PF02001_consen 41 VLTVDELEAIRLVD---YEGLSQEEAAERMGVSRPTFQRILESARKKIADALVEGK 93 (106)
T ss_pred EeeHHHHHHHHHHH---HcCCCHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHCCC
Confidence 58999999999998 799999999999999999999999999999999886543
No 159
>PRK13870 transcriptional regulator TraR; Provisional
Probab=97.27 E-value=0.00046 Score=68.13 Aligned_cols=45 Identities=22% Similarity=0.202 Sum_probs=42.8
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLR 470 (485)
.|++||++||.+.= +|+|..|||.+||||..||+.++++|++||-
T Consensus 173 ~LT~RE~E~L~W~A----~GKT~~EIa~ILgISe~TV~~Hl~na~~KLg 217 (234)
T PRK13870 173 WLDPKEATYLRWIA----VGKTMEEIADVEGVKYNSVRVKLREAMKRFD 217 (234)
T ss_pred CCCHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 59999999999985 9999999999999999999999999999984
No 160
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=97.24 E-value=0.00094 Score=51.51 Aligned_cols=48 Identities=31% Similarity=0.369 Sum_probs=43.4
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA 472 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~ 472 (485)
..|+++|.+|+.+.- .|.+..|||..+++|+.||+.+..++.+||.-.
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 368999999998875 789999999999999999999999999998643
No 161
>PRK09483 response regulator; Provisional
Probab=97.14 E-value=0.00079 Score=63.15 Aligned_cols=46 Identities=26% Similarity=0.351 Sum_probs=42.7
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLR 470 (485)
..|+++|++|+.+.. +|+|.+|||+.|++|..||+.+.++.++||-
T Consensus 147 ~~Lt~rE~~vl~~~~----~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~ 192 (217)
T PRK09483 147 ASLSERELQIMLMIT----KGQKVNEISEQLNLSPKTVNSYRYRMFSKLN 192 (217)
T ss_pred cccCHHHHHHHHHHH----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 569999999998865 8999999999999999999999999999984
No 162
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=97.11 E-value=0.012 Score=60.72 Aligned_cols=161 Identities=11% Similarity=0.008 Sum_probs=100.7
Q ss_pred HHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHhhhhccccc
Q 011454 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN 344 (485)
Q Consensus 265 A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~~r~irip~ 344 (485)
..+..+..-.+.++.---+|.++-.-+||.+||+|+...+.-.+=-+.++ =..|.+..-|+.-++.+++..+.-..|.
T Consensus 6 ~ie~~~r~~~~r~~a~L~r~~rd~dlAEEa~~dA~~~Ale~WPr~G~P~~--PaAWL~~v~R~~aiD~~Rr~~~~~~~~~ 83 (415)
T COG4941 6 WIEAAARIERPRAMAALARYLRDLDLAEEALQDAFAAALERWPRAGPPRN--PAAWLIAVGRNRAIDRVRRRARRDAAPP 83 (415)
T ss_pred HHHHHHHHhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHhCcccCCCCC--hHHHHHHHHhhhHHHHHHHHHHhccCCh
Confidence 34455556666777776778777777999999999877666554444443 3567776677766666665543222221
Q ss_pred cHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCC
Q 011454 345 HLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTLG 424 (485)
Q Consensus 345 ~~~~~~~kirka~~~L~~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp 424 (485)
... ....++|... ...+++.....+....|.-|-.-.||
T Consensus 84 el~-----------------~~~e~~e~~~------------------------a~~~~d~~i~Dd~LRLiFvccHPal~ 122 (415)
T COG4941 84 ELL-----------------LSDEDEEMEE------------------------AEALDDEHIRDDRLRLIFVCCHPALP 122 (415)
T ss_pred hhc-----------------ccccchhhhc------------------------cccccccccchhhHHhhhhhcCCCCC
Confidence 110 0000011000 00011111111222222222225799
Q ss_pred HHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 425 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 425 ~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
+.+|.-+.|+. .-|+|..|||..+=|+..++-|++.||+++++.
T Consensus 123 ~~~riALtLR~---v~GLs~~eIArAFLv~e~am~QRivRAK~ri~~ 166 (415)
T COG4941 123 PEQRIALTLRL---VGGLSTAEIARAFLVPEAAMAQRIVRAKARIRE 166 (415)
T ss_pred hhhHHHHHHHH---HcCCcHHHHHHHHcCCcHHHHHHHHHHHHHHHh
Confidence 99999999998 889999999999999999999999999999986
No 163
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=97.09 E-value=0.003 Score=54.16 Aligned_cols=52 Identities=19% Similarity=0.323 Sum_probs=46.2
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
.-|+++|+..+.++| .+++|+.|||+.++||+++|...++|+-+.|-..=.+
T Consensus 16 sLLT~KQ~~Y~~lyy---~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~YE~K 67 (105)
T COG2739 16 SLLTKKQKNYLELYY---LDDLSLSEIAEEFNVSRQAIYDNIKRTEKILEDYEEK 67 (105)
T ss_pred HHHhHHHHHHHHHHH---HhhccHHHHHHHhCccHHHHHHHHHHHHHHHHHHHHH
Confidence 458999999999999 8999999999999999999999999988877665443
No 164
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=97.03 E-value=0.0013 Score=60.12 Aligned_cols=46 Identities=33% Similarity=0.435 Sum_probs=42.7
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLR 470 (485)
..|+++|++|+.+. .+|++.+|||+.+++|..||+.++.++++||.
T Consensus 148 ~~lt~~e~~vl~l~----~~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 148 PLLTPRERQILKLI----TEGYTNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred cCCCHHHHHHHHHH----HCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 46999999999985 48999999999999999999999999999995
No 165
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=96.89 E-value=0.002 Score=62.58 Aligned_cols=52 Identities=27% Similarity=0.405 Sum_probs=45.2
Q ss_pred hCCHHHHHHHhhHhccCC----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDK----ECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 473 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~----eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L 473 (485)
.|+++|++||...|-.|+ ...+.+|||+.||||++|+.+++.+|.+||=..+
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 599999999999775542 4589999999999999999999999999986554
No 166
>PRK10651 transcriptional regulator NarL; Provisional
Probab=96.82 E-value=0.0021 Score=59.53 Aligned_cols=46 Identities=28% Similarity=0.392 Sum_probs=42.9
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLR 470 (485)
..|+++|++|+.+.. +|++.++||+.+++|..||+.++.+.++||.
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 469999999999975 8999999999999999999999999999985
No 167
>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=96.72 E-value=0.0026 Score=51.52 Aligned_cols=42 Identities=36% Similarity=0.461 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 011454 349 RLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEVL 390 (485)
Q Consensus 349 ~~~kirka~~~L~-~~gr~ps~eEIae~L~is~eev~~~l~~~ 390 (485)
+++++.+++..|. ++|+.|+.+|||+.+|++.++|+.++...
T Consensus 2 ~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~ 44 (78)
T PF04539_consen 2 KLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQAS 44 (78)
T ss_dssp HHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhC
Confidence 4677888888885 78999999999999999999999998776
No 168
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=96.71 E-value=0.0045 Score=56.34 Aligned_cols=54 Identities=20% Similarity=0.318 Sum_probs=47.1
Q ss_pred HHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011454 414 EVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA 472 (485)
Q Consensus 414 ~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~ 472 (485)
.+...+ ..|++++++|+.+.+ .+++.++||+.+|+|..+|+.+..++++||+..
T Consensus 134 ~~~~~~-~~l~~~e~~vl~~~~----~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~ 187 (202)
T PRK09390 134 DIRARI-ASLSERERQVMDGLV----AGLSNKVIARDLDISPRTVEVYRANVMTKMQAG 187 (202)
T ss_pred HHHHHH-HhhhhhHHHHHHHHH----ccCchHHHHHHcCCCHHHHHHHHHHHHHHHccc
Confidence 345566 789999999999754 789999999999999999999999999999753
No 169
>PRK15320 transcriptional activator SprB; Provisional
Probab=96.67 E-value=0.0032 Score=60.50 Aligned_cols=46 Identities=13% Similarity=0.148 Sum_probs=43.0
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLR 470 (485)
..|+++|.+|+.+-- +|+|++|||+.|++|.+||+.+..+.+.||.
T Consensus 163 ~~LSdREIEVL~LLA----kG~SNKEIAekL~LS~KTVSTYKnRLLeKLg 208 (251)
T PRK15320 163 PGVTQAKYALLILLS----SGHPAIELAKKFGLGTKTVSIYRKKVMYRLG 208 (251)
T ss_pred CCCCHHHHHHHHHHH----cCCCHHHHHHHhccchhhHHHHHHHHHHHcC
Confidence 579999999999885 8999999999999999999999999999885
No 170
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=96.54 E-value=0.0058 Score=51.91 Aligned_cols=52 Identities=31% Similarity=0.293 Sum_probs=47.6
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 476 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~ 476 (485)
.|+..|-+.|+|.. +++++++|-|.+||||+.|+-+.+..|++|+-.+|-..
T Consensus 33 ~lt~eElEAlRLvD---~~~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~aLveG 84 (99)
T COG1342 33 ILTIEELEALRLVD---YEGLTQEEAALRMGISRQTFWRLLTSARKKVADALVEG 84 (99)
T ss_pred eecHHHHHHHHHHh---HhhccHHHHHHHhcccHHHHHHHHHHHHHHHHHHHhcC
Confidence 47888999999998 79999999999999999999999999999999888643
No 171
>PRK01381 Trp operon repressor; Provisional
Probab=96.52 E-value=0.0027 Score=54.52 Aligned_cols=48 Identities=19% Similarity=0.258 Sum_probs=38.2
Q ss_pred HHHHHHHHhhCCHHHHHHHhhHhccC----CCCCCHHHHHHHHCCCHHHHHH
Q 011454 413 DEVNKLIIVTLGEREREIIRLYYGLD----KECLTWEDISKRIGLSRERVRQ 460 (485)
Q Consensus 413 e~L~~~L~~~Lp~rER~VI~LryGL~----~eg~S~eEIAe~LgIS~~tVrq 460 (485)
+.+..++..-|+|.|+..|..|+++- ..++|++|||+.+|||..||.+
T Consensus 23 ~~~~~~l~~llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITR 74 (99)
T PRK01381 23 DLHLPLLTLLLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATITR 74 (99)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehh
Confidence 34445553449999999999999982 2359999999999999998863
No 172
>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=96.34 E-value=0.024 Score=50.82 Aligned_cols=58 Identities=21% Similarity=0.160 Sum_probs=49.3
Q ss_pred HHHHHHHhhCCHHHHHHHhhHhccCCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 011454 414 EVNKLIIVTLGEREREIIRLYYGLDKE--CLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 474 (485)
Q Consensus 414 ~L~~~L~~~Lp~rER~VI~LryGL~~e--g~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~ 474 (485)
.+..++...|++.+|.||.++| .. +++..+|+..||+|..+..++.++|+.++-..+.
T Consensus 71 ~i~~ai~~~l~~~~r~Il~~~Y---l~~~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~l~ 130 (132)
T TIGR01637 71 AIVNAIVNQLDEISRQILYDKY---LEPDQKYDYQIMMELGYSHRQYYRIKKRALLRFATLYG 130 (132)
T ss_pred HHHHHHHHhCCHHHHHHHHHHH---cCccccchHHHHHHhCCcHHHHHHHHHHHHHHHHHHhC
Confidence 3334332589999999999999 55 8999999999999999999999999999877664
No 173
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=96.34 E-value=0.0044 Score=55.21 Aligned_cols=50 Identities=24% Similarity=0.313 Sum_probs=45.8
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
-|+++|-.|+.||- .|.|++|||++||-++..|+-++++|+.++.+.-.-
T Consensus 8 flte~qikvl~lRe----kG~tQ~eIA~~L~TTraNvSaIEkrA~enIekarnT 57 (143)
T COG1356 8 FLTEQQIKVLVLRE----KGLTQSEIARILKTTRANVSAIEKRALENIEKARNT 57 (143)
T ss_pred eeehhheeeeehhh----ccccHHHHHHHHccchhhHHHHHHHHHHHHHHHHHH
Confidence 48999999999995 899999999999999999999999999999886543
No 174
>PRK10403 transcriptional regulator NarP; Provisional
Probab=96.34 E-value=0.0072 Score=55.82 Aligned_cols=47 Identities=23% Similarity=0.255 Sum_probs=42.9
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
..|+++|.+|+.+.. +|+|.+|||+.+++|+.||+.++.+.++||.-
T Consensus 152 ~~Lt~~e~~vl~~~~----~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~ 198 (215)
T PRK10403 152 SVLTERELDVLHELA----QGLSNKQIASVLNISEQTVKVHIRNLLRKLNV 198 (215)
T ss_pred ccCCHHHHHHHHHHH----CCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 469999999998875 88999999999999999999999999999853
No 175
>PF12645 HTH_16: Helix-turn-helix domain; InterPro: IPR024760 This domain appears to be a helix-turn-helix domain, suggesting a transcriptional regulatory protein. Some proteins with this domain are annotated as conjugative transposon proteins.
Probab=96.16 E-value=0.021 Score=45.53 Aligned_cols=47 Identities=26% Similarity=0.208 Sum_probs=40.2
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcC------CCCcHHHHHHHHHHHHHHhHhcCC
Q 011454 264 LAREKLVMSNVRLVMSIAQRYDN------MGADMADLVQGGLIGLLRGIEKFD 310 (485)
Q Consensus 264 ~A~e~Lie~yl~LV~sIA~ry~~------~~~d~EDLiQEG~IgL~kAiekFD 310 (485)
.|.++++++|.|++.+.+.+-.. ++.--+|+-|+--..|++++.+|+
T Consensus 13 ~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~ 65 (65)
T PF12645_consen 13 EAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE 65 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence 99999999999999999988321 233459999999999999999995
No 176
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=96.16 E-value=0.012 Score=54.26 Aligned_cols=46 Identities=26% Similarity=0.342 Sum_probs=42.7
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLR 470 (485)
..|+++|.+|+.+.. +|++.++||+.+++|..||+.++.+.++||.
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 469999999999976 7899999999999999999999999999985
No 177
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=96.15 E-value=0.01 Score=54.86 Aligned_cols=45 Identities=27% Similarity=0.290 Sum_probs=41.0
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLR 470 (485)
.|+++|..|+.+.. +|+|.+|||+.|++|..||+.++.++++||.
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 58999999987754 7899999999999999999999999999985
No 178
>PRK04841 transcriptional regulator MalT; Provisional
Probab=96.12 E-value=0.0085 Score=69.17 Aligned_cols=45 Identities=20% Similarity=0.302 Sum_probs=42.8
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLR 470 (485)
.|+++|.+|+.+.. +|+|++|||+.|+||.+||+.++++...||.
T Consensus 838 ~lt~~e~~v~~~~~----~g~~~~~ia~~l~~s~~tv~~h~~~~~~kl~ 882 (903)
T PRK04841 838 PLTQREWQVLGLIY----SGYSNEQIAGELDVAATTIKTHIRNLYQKLG 882 (903)
T ss_pred CCCHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 49999999999986 9999999999999999999999999999995
No 179
>PRK13558 bacterio-opsin activator; Provisional
Probab=96.01 E-value=0.011 Score=66.29 Aligned_cols=53 Identities=23% Similarity=0.204 Sum_probs=44.4
Q ss_pred hhCCHHHHHHHhhHhccCC----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDK----ECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 473 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~----eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L 473 (485)
..|+++|+++|...|-.|+ .+-|.+|||+.||||++|+.+++.+|.+||=..+
T Consensus 606 ~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l~~~~ 662 (665)
T PRK13558 606 NDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKLVGAF 662 (665)
T ss_pred hhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 5799999999999883321 2339999999999999999999999999885543
No 180
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=95.95 E-value=0.015 Score=53.81 Aligned_cols=46 Identities=22% Similarity=0.294 Sum_probs=42.6
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLR 470 (485)
..|+++|.+|+.+.. .|.+.+|||+.+++|..||+.++.+.++||.
T Consensus 142 ~~lt~~E~~vl~~l~----~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~ 187 (204)
T PRK09958 142 DSLSKQEISVMRYIL----DGKDNNDIAEKMFISNKTVSTYKSRLMEKLE 187 (204)
T ss_pred ccCCHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 469999999999886 8899999999999999999999999999983
No 181
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=95.79 E-value=0.022 Score=43.26 Aligned_cols=50 Identities=22% Similarity=0.326 Sum_probs=42.8
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 473 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L 473 (485)
+|+..++-++.+.|- ..+.++++||..+|||++||+++.+..+.-|-..+
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 688899998888661 47899999999999999999999999988876654
No 182
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=95.71 E-value=0.0099 Score=43.98 Aligned_cols=33 Identities=36% Similarity=0.416 Sum_probs=23.4
Q ss_pred HHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011454 429 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 429 ~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
.||.++. +|+|..+||+.+|||+.||++++++-
T Consensus 9 ~ii~l~~----~G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 9 QIIRLLR----EGWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp -HHHHHH----HT--HHHHHHHHTS-HHHHHHHHT--
T ss_pred HHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 3566665 69999999999999999999987763
No 183
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=95.58 E-value=0.82 Score=51.49 Aligned_cols=34 Identities=24% Similarity=0.475 Sum_probs=32.2
Q ss_pred hhhHHHHHHhhccccCCCHHHHHHHHHHHHcCCc
Q 011454 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS 223 (485)
Q Consensus 190 ~~~~~~yl~~i~~~~~Lt~eee~~L~~~ik~Gd~ 223 (485)
.|-+++||+++++.|+||.++|++++++|..|..
T Consensus 103 ~DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~ 136 (619)
T PRK05658 103 DDPVRMYLREMGTVELLTREGEIEIAKRIEAGEN 136 (619)
T ss_pred CChHHHHHHHhccCcCCCcHHHHHHHHHHHHHHH
Confidence 3799999999999999999999999999999986
No 184
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=95.55 E-value=0.016 Score=59.80 Aligned_cols=36 Identities=31% Similarity=0.510 Sum_probs=33.0
Q ss_pred HHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011454 429 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALE 467 (485)
Q Consensus 429 ~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALk 467 (485)
.|-.||| .+++|+.|||++||||+.+|++++.+|++
T Consensus 20 ~vA~lYY---~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~ 55 (318)
T PRK15418 20 RIAWFYY---HDGLTQSEIGERLGLTRLKVSRLLEKGRQ 55 (318)
T ss_pred HHHHHHH---hcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4667888 89999999999999999999999999976
No 185
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=95.33 E-value=0.043 Score=40.30 Aligned_cols=41 Identities=22% Similarity=0.374 Sum_probs=30.2
Q ss_pred CCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011454 423 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 423 Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
|++.++.||....- ..+.|..|||+.+|+|.++|++++++-
T Consensus 1 l~~~~~~Il~~l~~--~~~~t~~ela~~~~is~~tv~~~l~~L 41 (48)
T PF13412_consen 1 LDETQRKILNYLRE--NPRITQKELAEKLGISRSTVNRYLKKL 41 (48)
T ss_dssp --HHHHHHHHHHHH--CTTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH--cCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 56788888877661 356999999999999999998877654
No 186
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=95.29 E-value=0.037 Score=46.72 Aligned_cols=39 Identities=18% Similarity=0.288 Sum_probs=32.1
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
..|+++ ..|+.+.- .|+|..|||+.+|||+.||.+ +.++
T Consensus 35 ~~Ls~R-~~I~~ll~----~G~S~~eIA~~LgISrsTIyR-i~R~ 73 (88)
T TIGR02531 35 QSLAQR-LQVAKMLK----QGKTYSDIEAETGASTATISR-VKRC 73 (88)
T ss_pred HhhhHH-HHHHHHHH----CCCCHHHHHHHHCcCHHHHHH-HHHh
Confidence 467888 77777754 789999999999999999998 4444
No 187
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=95.19 E-value=0.03 Score=41.05 Aligned_cols=33 Identities=33% Similarity=0.412 Sum_probs=24.6
Q ss_pred HHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 427 EREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 427 ER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
...|+.|+- +|+|..+||+.+|||+.||.+++.
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 456777764 889999999999999999988753
No 188
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=94.90 E-value=0.051 Score=35.57 Aligned_cols=37 Identities=22% Similarity=0.292 Sum_probs=29.5
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQV 461 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi 461 (485)
.+++.++..+...+ ..+.+..+||+.+|+++.+|.++
T Consensus 5 ~~~~~~~~~i~~~~---~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 5 KLTPEQIEEARRLL---AAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred cCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHh
Confidence 35666666666666 57889999999999999999875
No 189
>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=94.69 E-value=0.12 Score=46.75 Aligned_cols=56 Identities=23% Similarity=0.422 Sum_probs=44.7
Q ss_pred HHHHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 011454 412 KDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL 469 (485)
Q Consensus 412 ~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKL 469 (485)
.+.+...+ +.|.+.++.||.++|+- ..++|+.+||..|+|+..|++.+...-.+.+
T Consensus 72 k~~id~~~-~~l~de~k~Ii~lry~~-r~~~TW~~IA~~l~i~erta~r~~~~fK~~i 127 (130)
T PF05263_consen 72 KEAIDRWL-ETLIDEEKRIIKLRYDR-RSRRTWYQIAQKLHISERTARRWRDRFKNDI 127 (130)
T ss_pred HHHHHHHH-HhhCHHHHHHHHHHHcc-cccchHHHHHHHhCccHHHHHHHHHHHHHHh
Confidence 34555566 89999999999999952 2469999999999999999988776654433
No 190
>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=94.30 E-value=0.085 Score=41.07 Aligned_cols=32 Identities=19% Similarity=0.251 Sum_probs=27.2
Q ss_pred HHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011454 430 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 430 VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
...||. .|++..|||+.||+++.||.++..+-
T Consensus 6 A~~LY~----~G~~~~eIA~~Lg~~~~TV~~W~~r~ 37 (58)
T PF06056_consen 6 ARSLYL----QGWSIKEIAEELGVPRSTVYSWKDRY 37 (58)
T ss_pred HHHHHH----cCCCHHHHHHHHCCChHHHHHHHHhh
Confidence 444554 89999999999999999999998764
No 191
>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=94.23 E-value=0.055 Score=37.14 Aligned_cols=23 Identities=35% Similarity=0.510 Sum_probs=16.9
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Q 011454 441 CLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 441 g~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
++|.+|||+.+|++++||++.+.
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l~ 24 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRILK 24 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHHHHHH
Confidence 37999999999999999985443
No 192
>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 993W gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator. GpQ positively regulates expression of the phage late gene operons. Bacterial host RNA polymerase modified by antitermination proteins transcribes through termination sites that otherwise prevent expression of the regulated genes [, ].; GO: 0003677 DNA binding, 0060567 negative regulation of transcription termination, DNA-dependent
Probab=94.16 E-value=0.31 Score=43.66 Aligned_cols=53 Identities=15% Similarity=0.148 Sum_probs=48.1
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 476 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~~ 476 (485)
.+-.|.+-.+|.++| ..++|...||..+++|..+|++.+.+|-.-+..+|.-.
T Consensus 61 ~~~~~~~~~ll~~~Y---v~g~s~r~IA~~~~~s~~~ir~~l~~ae~~i~g~l~~~ 113 (125)
T PF06530_consen 61 KKRDPEEYDLLILYY---VYGWSKRQIARKLKCSEGKIRKRLQRAEGFIDGCLSML 113 (125)
T ss_pred HccCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHhhhhHhhhhHHh
Confidence 467899999999999 78999999999999999999999999999999887543
No 193
>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]
Probab=93.89 E-value=0.063 Score=61.34 Aligned_cols=44 Identities=27% Similarity=0.297 Sum_probs=42.2
Q ss_pred CCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011454 423 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 423 Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLR 470 (485)
|+.||++|+.+.| .|+|++|||.++.||-.||+.++.+...||.
T Consensus 832 Ls~RE~eVL~Lia----~G~SN~eIa~~L~isl~TVKtH~rniy~KLg 875 (894)
T COG2909 832 LSQRELEVLGLIA----QGLSNEEIAQELFISLTTVKTHIRNIYQKLG 875 (894)
T ss_pred ccHHHHHHHHHHH----ccCCHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 8999999999998 9999999999999999999999999999885
No 194
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=93.89 E-value=0.1 Score=41.48 Aligned_cols=43 Identities=21% Similarity=0.275 Sum_probs=28.2
Q ss_pred hhCCHHHHHHHhhHhcc---CCCCCCHHHHHHHHCCC-HHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGL---DKECLTWEDISKRIGLS-RERVRQVGL 463 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL---~~eg~S~eEIAe~LgIS-~~tVrqi~~ 463 (485)
..|+++|++|+...-.. ++-.-|..|||+.+|++ .++|.+++.
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 57999999998773321 23456999999999996 999987765
No 195
>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=93.79 E-value=0.14 Score=37.13 Aligned_cols=40 Identities=28% Similarity=0.427 Sum_probs=27.3
Q ss_pred CCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 423 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 423 Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
|.+..+.||...-. ....|+.+||+.+|+|..+|.+++.+
T Consensus 1 lD~~D~~Il~~Lq~--d~r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 1 LDELDRKILRLLQE--DGRRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp --HHHHHHHHHHHH---TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH--cCCccHHHHHHHHCcCHHHHHHHHHH
Confidence 34556777766541 24589999999999999999887764
No 196
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=93.63 E-value=0.11 Score=50.38 Aligned_cols=46 Identities=9% Similarity=0.147 Sum_probs=36.2
Q ss_pred hCCHHHHHHHhhHh-ccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYY-GLDKECLTWEDISKRIGLSRERVRQVGLVALE 467 (485)
Q Consensus 422 ~Lp~rER~VI~Lry-GL~~eg~S~eEIAe~LgIS~~tVrqi~~rALk 467 (485)
.|++++.+++.... +...+|+|.+|||+.||+|+.||+.++.++..
T Consensus 158 ~Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~ 204 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVN 204 (239)
T ss_pred CCCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHh
Confidence 58899977664433 11137899999999999999999999988743
No 197
>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=93.51 E-value=0.095 Score=42.29 Aligned_cols=37 Identities=32% Similarity=0.550 Sum_probs=29.0
Q ss_pred chhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhh
Q 011454 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (485)
Q Consensus 224 l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~ 260 (485)
+..++.+|...+|++|+.+++|..+|++.+++...+.
T Consensus 6 i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~ 42 (78)
T PF04539_consen 6 IERARRELEQELGREPTDEEIAEELGISVEEVRELLQ 42 (78)
T ss_dssp HHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHH
Confidence 3567888999999999999999999999999875543
No 198
>PF13518 HTH_28: Helix-turn-helix domain
Probab=93.50 E-value=0.12 Score=38.20 Aligned_cols=35 Identities=29% Similarity=0.367 Sum_probs=27.7
Q ss_pred HHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011454 429 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALE 467 (485)
Q Consensus 429 ~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALk 467 (485)
.||.++. +|.|..+||+.+|||+.||.+++.+-..
T Consensus 4 ~iv~~~~----~g~s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 4 QIVELYL----EGESVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHH----cCCCHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 3555554 6779999999999999999988876543
No 199
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=93.40 E-value=0.12 Score=40.51 Aligned_cols=39 Identities=15% Similarity=0.317 Sum_probs=28.8
Q ss_pred HHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 425 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 425 ~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
|.--..+.+|... ...+++.|||+.||||.+||+.+..+
T Consensus 7 p~rdkA~e~y~~~-~g~i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 7 PNRDKAFEIYKES-NGKIKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred cCHHHHHHHHHHh-CCCccHHHHHHHHCCCHHHHHHHhhh
Confidence 3344455555421 25799999999999999999998764
No 200
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=93.39 E-value=0.099 Score=54.20 Aligned_cols=36 Identities=39% Similarity=0.530 Sum_probs=31.8
Q ss_pred HHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 011454 430 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEK 468 (485)
Q Consensus 430 VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkK 468 (485)
+-.+|| .+|+|+.|||++||||+.+|++.+.+|++.
T Consensus 18 ~A~lYY---~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~ 53 (321)
T COG2390 18 AAWLYY---VEGLTQSEIAERLGISRATVSRLLAKAREE 53 (321)
T ss_pred HHHHHH---hcCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 445788 899999999999999999999999998763
No 201
>smart00351 PAX Paired Box domain.
Probab=93.07 E-value=0.22 Score=44.45 Aligned_cols=42 Identities=21% Similarity=0.133 Sum_probs=34.4
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 466 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rAL 466 (485)
.++..+|.=|...| .+|.|..+||+.||||+.||.+++++..
T Consensus 17 ~~s~~~R~riv~~~---~~G~s~~~iA~~~gvs~~tV~kwi~r~~ 58 (125)
T smart00351 17 PLPDEERQRIVELA---QNGVRPCDISRQLCVSHGCVSKILGRYY 58 (125)
T ss_pred CCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 36666666555666 5889999999999999999999998864
No 202
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=92.71 E-value=0.29 Score=43.24 Aligned_cols=48 Identities=27% Similarity=0.342 Sum_probs=42.8
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
..|++.|..-|..+. ...=+++|+++.||||-.|||.++.+.+.+|..
T Consensus 32 ~~L~~E~~~Fi~~Fi---~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 32 ARLSPEQLEFIKLFI---KNRGNLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred hcCCHHHHHHHHHHH---HhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 689999999888876 455699999999999999999999999999865
No 203
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=92.44 E-value=0.24 Score=37.82 Aligned_cols=44 Identities=18% Similarity=0.225 Sum_probs=32.7
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
.|++.|..||...+.-+..++|..|||+.+++++++|.+.+.+-
T Consensus 2 glt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L 45 (62)
T PF12802_consen 2 GLTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRL 45 (62)
T ss_dssp TSTHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 37788888887766422223899999999999999998776653
No 204
>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=92.21 E-value=0.15 Score=38.82 Aligned_cols=40 Identities=25% Similarity=0.216 Sum_probs=27.9
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
.|+..++.=|.-.+ ..|.+..+||+.+||+.+||+.++..
T Consensus 6 ~LTl~eK~~iI~~~---e~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 6 SLTLEEKLEIIKRL---EEGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp S--HHHHHHHHHHH---HCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred cCCHHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 46667776444555 58889999999999999999998875
No 205
>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=92.01 E-value=0.4 Score=35.23 Aligned_cols=37 Identities=22% Similarity=0.275 Sum_probs=28.8
Q ss_pred HHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 425 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 425 ~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
|....|+.+-. ..+++..|||+.+|+|+++|++++..
T Consensus 2 ~~R~~Il~~L~---~~~~~~~el~~~l~~s~~~vs~hL~~ 38 (47)
T PF01022_consen 2 PTRLRILKLLS---EGPLTVSELAEELGLSQSTVSHHLKK 38 (47)
T ss_dssp HHHHHHHHHHT---TSSEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHH---hCCCchhhHHHhccccchHHHHHHHH
Confidence 44556666665 57799999999999999999988764
No 206
>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=91.89 E-value=0.26 Score=41.62 Aligned_cols=46 Identities=17% Similarity=0.235 Sum_probs=33.9
Q ss_pred hhCCHHHHHHHhhHhccC----CCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLD----KECLTWEDISKRIGLSRERVRQVGLVALE 467 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~----~eg~S~eEIAe~LgIS~~tVrqi~~rALk 467 (485)
+-|+|.|+.-+..|+-+- .+|+|+.|||+.+|+|..||.+. .|+|+
T Consensus 25 dL~T~~E~~~l~~R~~va~~lL~~g~syreIa~~tgvS~aTItRv-sr~Lk 74 (87)
T PF01371_consen 25 DLCTPDELEALAQRWQVAKELLDEGKSYREIAEETGVSIATITRV-SRCLK 74 (87)
T ss_dssp HHSSHHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHH-HHHHH
T ss_pred HhCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHH-HHHHH
Confidence 457888887776665441 27899999999999999999643 34444
No 207
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=91.72 E-value=0.64 Score=35.92 Aligned_cols=44 Identities=18% Similarity=0.225 Sum_probs=33.3
Q ss_pred HHHHHHhhCCHHHHHHHhhH-hccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 415 VNKLIIVTLGEREREIIRLY-YGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 415 L~~~L~~~Lp~rER~VI~Lr-yGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
+.++| .+|.-+.|+.+. - ..++|..|||+.+|+++++|++++..
T Consensus 3 i~~aL---~~p~R~~Il~~L~~---~~~~t~~ela~~l~~~~~t~s~hL~~ 47 (61)
T PF12840_consen 3 IFKAL---SDPTRLRILRLLAS---NGPMTVSELAEELGISQSTVSYHLKK 47 (61)
T ss_dssp HHHHH---TSHHHHHHHHHHHH---CSTBEHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHh---CCHHHHHHHHHHhc---CCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 34455 457777777776 4 68999999999999999999877653
No 208
>PF13730 HTH_36: Helix-turn-helix domain
Probab=91.41 E-value=0.63 Score=34.91 Aligned_cols=42 Identities=19% Similarity=0.255 Sum_probs=30.4
Q ss_pred hCCHHHHHHHhhHhcc-CCCC---CCHHHHHHHHCCCHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGL-DKEC---LTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL-~~eg---~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
.|++.++.|+....-+ +..+ .|++.||+.+|+|+.||.+.++
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIK 47 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 5888888877664433 2222 3899999999999999974443
No 209
>PHA00675 hypothetical protein
Probab=91.21 E-value=0.41 Score=39.32 Aligned_cols=41 Identities=17% Similarity=0.238 Sum_probs=33.3
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
.+|++.+-+.|+..+- .+|.|+.+||+.||||+++|.++.+
T Consensus 21 AKLt~~qV~~IR~l~~--r~G~s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 21 AKLTDAEVERIRELHE--VEGMSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred cccCHHHHHHHHHHHH--hcCccHHHHHHHhCCCHHHHHHHHc
Confidence 6788888776666540 2788999999999999999998865
No 210
>PHA02591 hypothetical protein; Provisional
Probab=91.16 E-value=0.26 Score=40.55 Aligned_cols=25 Identities=28% Similarity=0.357 Sum_probs=22.7
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
..|+|.++||+.||+++++|++.+.
T Consensus 57 eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 57 RKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 3689999999999999999998875
No 211
>cd00131 PAX Paired Box domain
Probab=91.10 E-value=0.52 Score=42.37 Aligned_cols=42 Identities=19% Similarity=0.100 Sum_probs=33.1
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 466 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rAL 466 (485)
-|+...|.-|...| .+|+|..+||+.+|||+.+|.+++++-.
T Consensus 17 ~lS~d~R~rIv~~~---~~G~s~~~iA~~~~Vs~~tV~r~i~r~~ 58 (128)
T cd00131 17 PLPDSIRQRIVELA---QSGIRPCDISRQLRVSHGCVSKILNRYY 58 (128)
T ss_pred cCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 45665555444555 5899999999999999999999988754
No 212
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=90.48 E-value=0.47 Score=38.92 Aligned_cols=40 Identities=23% Similarity=0.327 Sum_probs=29.5
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH-----HHHHHHHHHHHhhhH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGL-----VALEKLKHAARKKKM 478 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~-----rALkKLRk~L~~~~l 478 (485)
..++|+.|+|+.+|+++++|+++++ -.+.+|.+.+...+.
T Consensus 29 ~~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aLG~ 73 (80)
T PF13744_consen 29 ERGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEALGG 73 (80)
T ss_dssp CCT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHTTE
T ss_pred HcCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHcCC
Confidence 5789999999999999999999984 257788887776553
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=89.95 E-value=0.52 Score=35.37 Aligned_cols=38 Identities=26% Similarity=0.483 Sum_probs=26.5
Q ss_pred HHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 426 REREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 426 rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
|++.|+.+.+- ..+..|.+|||+.||||+.||++.+..
T Consensus 1 R~~~il~~L~~-~~~~it~~eLa~~l~vS~rTi~~~i~~ 38 (55)
T PF08279_consen 1 RQKQILKLLLE-SKEPITAKELAEELGVSRRTIRRDIKE 38 (55)
T ss_dssp HHHHHHHHHHH-TTTSBEHHHHHHHCTS-HHHHHHHHHH
T ss_pred CHHHHHHHHHH-cCCCcCHHHHHHHhCCCHHHHHHHHHH
Confidence 45566666431 134589999999999999999876654
No 214
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=89.91 E-value=2 Score=39.36 Aligned_cols=62 Identities=18% Similarity=0.207 Sum_probs=38.8
Q ss_pred hhCCHHHHHHHhhH-----hccCCCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHhhhHHHhh
Q 011454 421 VTLGEREREIIRLY-----YGLDKECLTWEDISKRIGLSRERVRQVGL--VALEKLKHAARKKKMEAML 482 (485)
Q Consensus 421 ~~Lp~rER~VI~Lr-----yGL~~eg~S~eEIAe~LgIS~~tVrqi~~--rALkKLRk~L~~~~l~~~l 482 (485)
.+|++.|+....+- .+.+.+..|+.|||+.+||++.|+.+|.+ ++.....+.+....+.+++
T Consensus 9 ~~L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~~~~Fiey~n~la~~~~~~~~ 77 (142)
T PF13022_consen 9 AKLTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQQNKAFIEYKNELADRFLSSHR 77 (142)
T ss_dssp TTS-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHHH-HHHHHHHHHHHHHHHHTTH
T ss_pred HHcCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHhH
Confidence 89999999844332 22223569999999999999999999984 4455566666655555543
No 215
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=89.90 E-value=0.77 Score=36.58 Aligned_cols=38 Identities=24% Similarity=0.329 Sum_probs=26.2
Q ss_pred HHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 427 EREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 427 ER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
+..|+.+...-+.+++|..|||+.+||+..+|++++++
T Consensus 8 ~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~ 45 (68)
T smart00550 8 EEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYS 45 (68)
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 34444443321223599999999999999999876654
No 216
>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=89.76 E-value=0.76 Score=37.39 Aligned_cols=52 Identities=10% Similarity=0.199 Sum_probs=35.6
Q ss_pred HHHHHHHHHhhCCHHHHHHHhhHhcc--CCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 412 KDEVNKLIIVTLGEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 412 ~e~L~~~L~~~Lp~rER~VI~LryGL--~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
...|.... ..|++.|+.|.....-- ....+|..|||+..|||+.+|.+..++
T Consensus 4 ~~~i~~~~-~~ls~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~kk 57 (77)
T PF01418_consen 4 LEKIRSQY-NSLSPTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCKK 57 (77)
T ss_dssp HHHHHHHG-GGS-HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHHH
T ss_pred HHHHHHHH-hhCCHHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHHH
Confidence 34566666 89999999988765411 135799999999999999999776554
No 217
>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=89.62 E-value=0.55 Score=36.63 Aligned_cols=41 Identities=27% Similarity=0.419 Sum_probs=29.2
Q ss_pred CCHHHHHHHhhHhcc--CCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 423 LGEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 423 Lp~rER~VI~LryGL--~~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
|++....-|...|-| +....+..+||+.||||+.+|...++
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 555555555565555 35678999999999999999975443
No 218
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=89.39 E-value=0.63 Score=42.59 Aligned_cols=35 Identities=20% Similarity=0.164 Sum_probs=28.9
Q ss_pred HHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011454 429 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 466 (485)
Q Consensus 429 ~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rAL 466 (485)
.++..++ .+|+|.+|||+++|||.+||..++.+-.
T Consensus 12 ~~~~~~~---~~G~S~re~Ak~~gvs~sTvy~wv~r~~ 46 (138)
T COG3415 12 RVVDAVV---GEGLSCREAAKRFGVSISTVYRWVRRYR 46 (138)
T ss_pred HHHHHHH---HcCccHHHHHHHhCccHHHHHHHHHHhc
Confidence 3444554 4899999999999999999999988754
No 219
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=89.20 E-value=0.9 Score=33.63 Aligned_cols=35 Identities=26% Similarity=0.430 Sum_probs=27.0
Q ss_pred HHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011454 427 EREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 427 ER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
++.|+.+.. +..|.++||+.+|||..||.+++.+.
T Consensus 17 ~~~i~~~~~----~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 17 EQYILKLLR----ESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHHHHHHHh----hcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 334554443 44699999999999999999998764
No 220
>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=89.03 E-value=10 Score=41.08 Aligned_cols=25 Identities=16% Similarity=0.286 Sum_probs=22.5
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
..++|+++||+.+|++.+||++...
T Consensus 316 LkPLtlkdiA~~lglheSTVSRav~ 340 (429)
T TIGR02395 316 LKPLTLREVAEELGLHESTISRAIN 340 (429)
T ss_pred CcCCcHHHHHHHhCCCccchhhhhc
Confidence 4789999999999999999998764
No 221
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=88.79 E-value=0.53 Score=43.95 Aligned_cols=50 Identities=12% Similarity=0.013 Sum_probs=41.7
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCC-----HHHHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLS-----RERVRQVGLVALEKLKH 471 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS-----~~tVrqi~~rALkKLRk 471 (485)
.|+++|.+|+.+...=.+.++|.+|||+.+..+ ..||+.++.+.++||+.
T Consensus 154 ~Lt~~E~~il~~l~~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~l~~Kl~~ 208 (228)
T PRK11083 154 TLTRYEFLLLKTLLLSPGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLRA 208 (228)
T ss_pred ecCHHHHHHHHHHHhCCCceECHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhcc
Confidence 699999999988761112469999999999986 88999999999999963
No 222
>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=88.72 E-value=0.44 Score=35.32 Aligned_cols=35 Identities=29% Similarity=0.322 Sum_probs=27.0
Q ss_pred CHHHHHHHHCCCHHHHHHHHHH-------HHHHHHHHHHhhh
Q 011454 443 TWEDISKRIGLSRERVRQVGLV-------ALEKLKHAARKKK 477 (485)
Q Consensus 443 S~eEIAe~LgIS~~tVrqi~~r-------ALkKLRk~L~~~~ 477 (485)
|++|||+..|||..||++.++. ..+++.+.++..+
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~~~~vs~~tr~rI~~~a~~lg 42 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNGPPRVSEETRERILEAAEELG 42 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTTCSSSTHHHHHHHHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHC
Confidence 6899999999999999998864 4555555555544
No 223
>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=88.57 E-value=4.4 Score=35.76 Aligned_cols=75 Identities=19% Similarity=0.194 Sum_probs=44.1
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHH
Q 011454 368 SVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDI 447 (485)
Q Consensus 368 s~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEI 447 (485)
+..++|..++|+...+...+.... ..+. ...|-..- .. ..+.|...+ -- ..+.|+.||
T Consensus 20 s~~eaa~~F~VS~~Tv~~W~k~~~-~G~~--~~k~r~~~-Ki-d~~~L~~~v-------------~~----~pd~tl~El 77 (119)
T PF01710_consen 20 SIREAAKRFGVSRNTVYRWLKRKE-TGDL--EPKPRGRK-KI-DRDELKALV-------------EE----NPDATLREL 77 (119)
T ss_pred hHHHHHHHhCcHHHHHHHHHHhcc-cccc--cccccccc-cc-cHHHHHHHH-------------HH----CCCcCHHHH
Confidence 678889999999999887766221 1111 11121100 00 011122222 11 367999999
Q ss_pred HHHHCCCHHHHHHHHHH
Q 011454 448 SKRIGLSRERVRQVGLV 464 (485)
Q Consensus 448 Ae~LgIS~~tVrqi~~r 464 (485)
|+.||||.++|...+++
T Consensus 78 a~~l~Vs~~ti~~~Lkr 94 (119)
T PF01710_consen 78 AERLGVSPSTIWRALKR 94 (119)
T ss_pred HHHcCCCHHHHHHHHHH
Confidence 99999999999755543
No 224
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=88.50 E-value=0.84 Score=41.92 Aligned_cols=41 Identities=12% Similarity=0.214 Sum_probs=33.2
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
.|++.++.||..-- - ....|+.|||+.+|+|+.+|++++++
T Consensus 6 ~lD~~D~~Il~~Lq-~-d~R~s~~eiA~~lglS~~tV~~Ri~r 46 (153)
T PRK11179 6 QIDNLDRGILEALM-E-NARTPYAELAKQFGVSPGTIHVRVEK 46 (153)
T ss_pred ccCHHHHHHHHHHH-H-cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 57888999887754 1 24589999999999999999877665
No 225
>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=88.15 E-value=1 Score=37.22 Aligned_cols=41 Identities=29% Similarity=0.379 Sum_probs=33.2
Q ss_pred CCHHHHHHHhhHhcc---CCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 423 LGEREREIIRLYYGL---DKECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 423 Lp~rER~VI~LryGL---~~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
|+++|++||....-+ ..++..-++||+.+++|..|||+...
T Consensus 2 Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~ 45 (78)
T PF03444_consen 2 LTERQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMA 45 (78)
T ss_pred CCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHH
Confidence 899999988764332 24678899999999999999997764
No 226
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=88.13 E-value=0.53 Score=45.32 Aligned_cols=40 Identities=18% Similarity=0.118 Sum_probs=30.0
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
+.|+++ +|+.+.- -+..|+|.+|||+.||||+.||++++.
T Consensus 160 ~~Lt~r--~Vl~~~~-~g~~g~s~~eIa~~l~iS~~Tv~~~~~ 199 (225)
T PRK10046 160 DPLTLN--AVRKLFK-EPGVQHTAETVAQALTISRTTARRYLE 199 (225)
T ss_pred CHHHHH--HHHHHHH-cCCCCcCHHHHHHHhCccHHHHHHHHH
Confidence 446665 6666543 112369999999999999999999875
No 227
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=88.00 E-value=0.65 Score=43.16 Aligned_cols=49 Identities=18% Similarity=0.131 Sum_probs=40.7
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIG-----LSRERVRQVGLVALEKLK 470 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~Lg-----IS~~tVrqi~~rALkKLR 470 (485)
.|+++|.+|+.+..-=.+..+|.++|++.+. ++..||+.++.+.++||.
T Consensus 149 ~Lt~~E~~il~~l~~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl~ 202 (219)
T PRK10336 149 TLKPKEFALLELLMRNAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLG 202 (219)
T ss_pred ecCHHHHHHHHHHHhCCCccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhcC
Confidence 5999999999876510123489999999996 999999999999999885
No 228
>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=87.90 E-value=1.6 Score=36.71 Aligned_cols=43 Identities=16% Similarity=0.139 Sum_probs=33.1
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHH--CCCHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRI--GLSRERVRQVGLVA 465 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~L--gIS~~tVrqi~~rA 465 (485)
+.||+..+.+..+|.- ..+.|+.|+|+.+ .||+++|..++.+.
T Consensus 36 ~~l~~~l~~~a~lRl~--~Pd~SL~EL~~~~~~~iSKSgvnhrlrKl 80 (85)
T PF02650_consen 36 DKLPEKLREFAELRLE--NPDASLKELGELLEPPISKSGVNHRLRKL 80 (85)
T ss_dssp GGS-HHHHHHHHHHHH---TTS-HHHHHHTT--T--HHHHHHHHHHH
T ss_pred ccCCHHHHHHHHHHHH--CccccHHHHHHHHcCcCcHHHHHHHHHHH
Confidence 7899999999999872 4789999999999 89999998776654
No 229
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=87.86 E-value=2.3 Score=37.61 Aligned_cols=35 Identities=9% Similarity=0.096 Sum_probs=29.1
Q ss_pred HHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011454 428 REIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 428 R~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
..++...+ ..|.|..+||+.+|||..++.++..+.
T Consensus 19 ~~aV~~~~---~~g~sv~evA~e~gIs~~tl~~W~r~y 53 (121)
T PRK09413 19 IAIVQQSF---EPGMTVSLVARQHGVAASQLFLWRKQY 53 (121)
T ss_pred HHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 34555555 578999999999999999999998874
No 230
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=87.84 E-value=2.3 Score=36.06 Aligned_cols=43 Identities=28% Similarity=0.356 Sum_probs=33.1
Q ss_pred hhCCHHHHHHHhhH----hccC--CCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 421 VTLGEREREIIRLY----YGLD--KECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 421 ~~Lp~rER~VI~Lr----yGL~--~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
..+++++..+|... ||.+ ...+|..|||+.+|+++.+|++.++
T Consensus 21 ~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~ 69 (95)
T TIGR01610 21 ADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIK 69 (95)
T ss_pred CCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHH
Confidence 57899999877632 3431 4679999999999999999975443
No 231
>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=87.61 E-value=0.94 Score=34.27 Aligned_cols=41 Identities=22% Similarity=0.414 Sum_probs=30.8
Q ss_pred CCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011454 423 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 423 Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
|++.|-.||...+- ..+.+..|||+.+++++++|.+.+.+-
T Consensus 1 lt~~q~~iL~~l~~--~~~~~~~~la~~~~~~~~~~t~~i~~L 41 (59)
T PF01047_consen 1 LTPSQFRILRILYE--NGGITQSELAEKLGISRSTVTRIIKRL 41 (59)
T ss_dssp STHHHHHHHHHHHH--HSSEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH--cCCCCHHHHHHHHCCChhHHHHHHHHH
Confidence 45667777766552 467999999999999999998776654
No 232
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=87.53 E-value=48 Score=36.21 Aligned_cols=25 Identities=16% Similarity=0.353 Sum_probs=22.4
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
..++|+++||+.+|+..+||++...
T Consensus 341 LkPLtlkdvAe~lglheSTVSRav~ 365 (455)
T PRK05932 341 LKPLVLKDIAEELGMHESTISRATT 365 (455)
T ss_pred CcCccHHHHHHHhCCCccchhhhhc
Confidence 4789999999999999999998764
No 233
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=87.45 E-value=1.3 Score=37.78 Aligned_cols=41 Identities=22% Similarity=0.319 Sum_probs=32.0
Q ss_pred CCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011454 423 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 423 Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
|++.++.|+..... ....|+.+||+.+|+|+.+|++++.+-
T Consensus 1 ld~~D~~il~~L~~--~~~~~~~~la~~l~~s~~tv~~~l~~L 41 (108)
T smart00344 1 LDEIDRKILEELQK--DARISLAELAKKVGLSPSTVHNRVKRL 41 (108)
T ss_pred CCHHHHHHHHHHHH--hCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46778888877541 246899999999999999998776654
No 234
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=87.19 E-value=0.93 Score=42.18 Aligned_cols=41 Identities=22% Similarity=0.220 Sum_probs=32.7
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
.|++.++.||..-- - ....|+.|||+.+|+|+.+|++++++
T Consensus 11 ~lD~~D~~IL~~Lq-~-d~R~s~~eiA~~lglS~~tv~~Ri~r 51 (164)
T PRK11169 11 DLDRIDRNILNELQ-K-DGRISNVELSKRVGLSPTPCLERVRR 51 (164)
T ss_pred hHHHHHHHHHHHhc-c-CCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 46777888887653 1 24589999999999999999887765
No 235
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional
Probab=87.04 E-value=0.87 Score=43.04 Aligned_cols=50 Identities=10% Similarity=0.074 Sum_probs=42.7
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIG-----LSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~Lg-----IS~~tVrqi~~rALkKLRk 471 (485)
.|+++|++|+.+...=...+.|.++|++.+. ++..||+.++.+.++||..
T Consensus 160 ~Lt~~e~~il~~l~~~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~lr~kl~~ 214 (240)
T PRK10710 160 DLTPAEFRLLKTLSHEPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLES 214 (240)
T ss_pred ecCHHHHHHHHHHHhCCCceEcHHHHHHHhcCcCcCCCccCHHHHHHHHHHHhhc
Confidence 5999999999987631134799999999998 9999999999999999963
No 236
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=87.03 E-value=1.6 Score=37.57 Aligned_cols=48 Identities=21% Similarity=0.343 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHhhCCHHHHHHHhhHhcc-C---CCCCCHHHHHHHHCCCHHHHH
Q 011454 409 WALKDEVNKLIIVTLGEREREIIRLYYGL-D---KECLTWEDISKRIGLSRERVR 459 (485)
Q Consensus 409 ~el~e~L~~~L~~~Lp~rER~VI~LryGL-~---~eg~S~eEIAe~LgIS~~tVr 459 (485)
......+..++ |+|.||+-+..|+.+ . ...+|++||+..||+|..||-
T Consensus 27 ~d~~~~lL~ll---LTpdEReal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtIT 78 (103)
T COG2973 27 EDLHQPLLTLL---LTPDEREALGTRVRIVEELLRGELSQREIAQKLGVSIATIT 78 (103)
T ss_pred hHHHHHHHHHH---cCHhHHHHHHHHHHHHHHHHhccccHHHHHHHhCcchhhhc
Confidence 34445566666 899999988888765 1 256999999999999999883
No 237
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=86.89 E-value=1.1 Score=42.78 Aligned_cols=38 Identities=21% Similarity=0.345 Sum_probs=30.0
Q ss_pred CCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 423 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 423 Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
+.+.++.|..++- +|+|..+||+.||||++||.++.+.
T Consensus 158 ~~~~~~~i~~~~~----~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 158 LTGKEEKIKKLLD----KGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred cchhHHHHHHHHH----CCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 3444566666653 7899999999999999999988763
No 238
>PHA02547 55 RNA polymerase sigma factor; Provisional
Probab=86.79 E-value=6.9 Score=36.98 Aligned_cols=63 Identities=14% Similarity=0.272 Sum_probs=46.2
Q ss_pred HHHHHHHHHHhcCCCC---cHHHHHHHHHHHHHHhHhcCCCCCCcchhhHHHHHHHHHHHHHHHHh
Q 011454 274 VRLVMSIAQRYDNMGA---DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVEN 336 (485)
Q Consensus 274 l~LV~sIA~ry~~~~~---d~EDLiQEG~IgL~kAiekFDp~rG~rFsTYA~~~Ir~~I~~~I~~~ 336 (485)
+..+-.++++|.-++. --+|.|.+|.-.+++.+++||+++...+-.|++..+-++..+.|...
T Consensus 47 mkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~kE 112 (179)
T PHA02547 47 MKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKKE 112 (179)
T ss_pred HHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHHH
Confidence 3344444455432332 37899999999999999999999988888888888777666665544
No 239
>PF13551 HTH_29: Winged helix-turn helix
Probab=86.24 E-value=5.8 Score=33.41 Aligned_cols=81 Identities=17% Similarity=0.211 Sum_probs=49.8
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHH-----Hhhhc-ccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhc-c---
Q 011454 368 SVDRIAEYLNMSQKKVRNATEVL-----AYIAD-NRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYG-L--- 437 (485)
Q Consensus 368 s~eEIae~L~is~eev~~~l~~~-----~~l~D-~~~e~~pee~~e~~el~e~L~~~L~~~Lp~rER~VI~LryG-L--- 437 (485)
+..++|..+|++..+|.+.+... +.+.+ ......|.. .|++.++..|.-.+- -
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~-----------------~l~~~~~~~l~~~~~~~p~~ 76 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRK-----------------RLSEEQRAQLIELLRENPPE 76 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCC-----------------CCCHHHHHHHHHHHHHCCCC
Confidence 68999999999999999987765 23333 221122221 144443333332220 0
Q ss_pred CCCCCCHHHHHHHH-------CCCHHHHHHHHHHH
Q 011454 438 DKECLTWEDISKRI-------GLSRERVRQVGLVA 465 (485)
Q Consensus 438 ~~eg~S~eEIAe~L-------gIS~~tVrqi~~rA 465 (485)
+....|..+|++.+ .+|.+||+++++++
T Consensus 77 g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~~~ 111 (112)
T PF13551_consen 77 GRSRWTLEELAEWLIEEEFGIDVSPSTIRRILKRA 111 (112)
T ss_pred CCCcccHHHHHHHHHHhccCccCCHHHHHHHHHHC
Confidence 01236889999866 78999999988763
No 240
>PF12728 HTH_17: Helix-turn-helix domain
Probab=85.84 E-value=0.87 Score=33.68 Aligned_cols=24 Identities=25% Similarity=0.266 Sum_probs=21.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
+|.+|+|+.||||+.||.++..+.
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcC
Confidence 689999999999999999998654
No 241
>PF13551 HTH_29: Winged helix-turn helix
Probab=85.39 E-value=1.5 Score=37.05 Aligned_cols=33 Identities=30% Similarity=0.370 Sum_probs=26.8
Q ss_pred HHHhhHhccCCCCC-CHHHHHHHHCCCHHHHHHHHHHH
Q 011454 429 EIIRLYYGLDKECL-TWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 429 ~VI~LryGL~~eg~-S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
.||.+.. +|. |..+||+.+|+|+.||.+++++-
T Consensus 3 ~~l~l~~----~g~~~~~~ia~~lg~s~~Tv~r~~~~~ 36 (112)
T PF13551_consen 3 QILLLLA----EGVSTIAEIARRLGISRRTVYRWLKRY 36 (112)
T ss_pred HHHHHHH----cCCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence 3455543 788 59999999999999999988874
No 242
>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=85.35 E-value=0.61 Score=43.38 Aligned_cols=49 Identities=12% Similarity=0.192 Sum_probs=40.5
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHH-----HHHHCCCHHHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDI-----SKRIGLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEI-----Ae~LgIS~~tVrqi~~rALkKLR 470 (485)
.|+++|.+|+.+...--..++|.++| |+.++++..||+.++.+.++||.
T Consensus 154 ~Lt~~E~~il~~l~~~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~l~~Kl~ 207 (226)
T TIGR02154 154 SLGPTEFRLLHFFMTHPERVYSREQLLDRVWGRDVYVEERTVDVHIRRLRKALN 207 (226)
T ss_pred EcCHHHHHHHHHHHhCCCceEcHHHHHHHhcCCCCCCCCccHHHHHHHHHHhhc
Confidence 59999999998876211246788888 77899999999999999999986
No 243
>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=85.26 E-value=0.87 Score=32.34 Aligned_cols=25 Identities=20% Similarity=0.205 Sum_probs=22.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVAL 466 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rAL 466 (485)
+|..|+|+.+|||+.||.++...+.
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 5889999999999999999988764
No 244
>PRK15479 transcriptional regulatory protein TctD; Provisional
Probab=85.25 E-value=1.3 Score=40.98 Aligned_cols=49 Identities=14% Similarity=0.145 Sum_probs=40.3
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIG-----LSRERVRQVGLVALEKLK 470 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~Lg-----IS~~tVrqi~~rALkKLR 470 (485)
.|+++|.+|+.+...=....+|.++|++.+. +|..||+.++.+.++||.
T Consensus 148 ~Lt~~E~~il~~l~~~~~~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl~ 201 (221)
T PRK15479 148 ALTPREQALLTVLMYRRTRPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKLQ 201 (221)
T ss_pred ecCHHHHHHHHHHHhCCCCcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhcC
Confidence 5999999999876510013479999999996 999999999999999985
No 245
>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=85.18 E-value=1.2 Score=41.89 Aligned_cols=47 Identities=9% Similarity=0.027 Sum_probs=40.4
Q ss_pred hCCHHHHHHHhhHhccCCCC--CCHHHH--HHHHCCCHHHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKEC--LTWEDI--SKRIGLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg--~S~eEI--Ae~LgIS~~tVrqi~~rALkKLR 470 (485)
.|+++|.+|+.+..- ..| +|.++| |..++++..||+.++.+.++||.
T Consensus 156 ~Lt~~E~~il~~l~~--~~g~v~s~~~i~~~~~~~~~~~tv~~~v~rlr~Kl~ 206 (227)
T TIGR03787 156 DLTVTEFWMVHALAK--HPGHVKSRQQLMDAAKIVVDDSTITSHIKRIRKKFQ 206 (227)
T ss_pred cCCHHHHHHHHHHHh--CCCccccHHHHHHHhhhcCCccCHHHHHHHHHHHhc
Confidence 599999999998761 124 599999 88899999999999999999996
No 246
>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=85.11 E-value=1.6 Score=33.71 Aligned_cols=42 Identities=19% Similarity=0.313 Sum_probs=26.9
Q ss_pred CCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011454 423 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 423 Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
|++.|..||.... -...+++..+||+.+++++.+|++.+++-
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 4566777765544 11478999999999999999998665544
No 247
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=85.05 E-value=1.9 Score=32.67 Aligned_cols=39 Identities=31% Similarity=0.390 Sum_probs=25.5
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
.|++.||--|.... ..|+++.|||+.+|-|+..|++.++
T Consensus 4 ~Lt~~Eqaqid~m~---qlG~s~~~isr~i~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 4 TLTDAEQAQIDVMH---QLGMSLREISRRIGRSRTCIRRYLK 42 (50)
T ss_dssp ---HHHHHHHHHHH---HTT--HHHHHHHHT--HHHHHHHHH
T ss_pred cCCHHHHHHHHHHH---HhchhHHHHHHHhCccHHHHHHHhc
Confidence 46777777666655 4789999999999999999987754
No 248
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=84.93 E-value=1.5 Score=39.15 Aligned_cols=24 Identities=33% Similarity=0.302 Sum_probs=22.7
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 440 ECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 440 eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
+|+|+.+||+.||+|+.+|++.++
T Consensus 21 eG~Sq~~iA~LLGltqaAVS~Yls 44 (119)
T COG2522 21 EGLSQYRIAKLLGLTQAAVSQYLS 44 (119)
T ss_pred cCCcHHHHHHHhCCCHHHHHHHHc
Confidence 689999999999999999999875
No 249
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=84.86 E-value=29 Score=34.86 Aligned_cols=64 Identities=22% Similarity=0.402 Sum_probs=46.0
Q ss_pred hhhhHHHHHHhhccccCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhh
Q 011454 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (485)
Q Consensus 189 ~~~~~~~yl~~i~~~~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~ 260 (485)
+.+.+.+||++.. +.--|.-..++.++ +..++.+|...+|++|+++++|..+|++.+++...+.
T Consensus 85 I~Gei~d~LR~~~--~v~vpR~~~~~~~~------i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~ 148 (247)
T COG1191 85 IRGEILDYLRKND--SVKVPRSLRELGRR------IEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALL 148 (247)
T ss_pred HHHHHHHHHHhCC--CccCcHHHHHHHHH------HHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHH
Confidence 4567778888866 11122334444444 4567788999999999999999999999999765443
No 250
>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=84.56 E-value=1.5 Score=33.03 Aligned_cols=50 Identities=16% Similarity=0.256 Sum_probs=39.8
Q ss_pred hCCHHHHHHHhhHhccCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDK--ECLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~--eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
.+++.+..+|...|..+. .....++||..+||+...|..+..+-..+.|+
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 578889999999885421 12457899999999999999999988877664
No 251
>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=84.40 E-value=2 Score=40.42 Aligned_cols=42 Identities=21% Similarity=0.283 Sum_probs=34.3
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALE 467 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALk 467 (485)
|+.-|.-++..| + ++++|++.+|...|||..|++++..+|..
T Consensus 4 ~~e~R~~~R~~Y-V-~~~~sLe~aA~~~gVs~~TarrWK~~Ak~ 45 (165)
T PF08822_consen 4 PQETRDAVRRAY-V-FDRLSLEQAAAKCGVSYATARRWKREAKA 45 (165)
T ss_pred cHHHHHHHHHHH-H-hCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 445566667666 1 37899999999999999999999999864
No 252
>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=83.69 E-value=1.3 Score=31.61 Aligned_cols=24 Identities=25% Similarity=0.357 Sum_probs=21.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
+|.+|+|+.||||+.+|.++.+..
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcC
Confidence 689999999999999999998765
No 253
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=83.67 E-value=2.3 Score=35.78 Aligned_cols=44 Identities=14% Similarity=0.027 Sum_probs=36.6
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 466 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rAL 466 (485)
..|+|.-|..|..+. + .+|.+..+.|+.+|||..|+++++.|=.
T Consensus 7 A~Lt~~gR~~lv~~v-v-~~g~~~a~aA~~~gVS~~Ta~kW~~Ryr 50 (85)
T PF13011_consen 7 ARLTPRGRLRLVRRV-V-EQGWPVAHAAAEFGVSRRTAYKWLARYR 50 (85)
T ss_pred CCCCHHHHHHHHHHH-H-HcCCcHHHHHHHhCCCHHHHHHHHHHHH
Confidence 468999998887765 1 2689999999999999999999987643
No 254
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=83.61 E-value=2.2 Score=38.58 Aligned_cols=43 Identities=23% Similarity=0.345 Sum_probs=34.4
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
..|.+.++.||...-. ....|+.|||+.+|+|+.+|+.++.+-
T Consensus 4 ~~lD~~D~~IL~~L~~--d~r~~~~eia~~lglS~~~v~~Ri~~L 46 (154)
T COG1522 4 MKLDDIDRRILRLLQE--DARISNAELAERVGLSPSTVLRRIKRL 46 (154)
T ss_pred ccccHHHHHHHHHHHH--hCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4688889999887541 245899999999999999998777653
No 255
>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=83.48 E-value=1.1 Score=35.72 Aligned_cols=35 Identities=11% Similarity=0.178 Sum_probs=28.7
Q ss_pred HHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011454 429 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 466 (485)
Q Consensus 429 ~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rAL 466 (485)
.||.++. ..|.|..+||..+||+++++.++.....
T Consensus 14 ~~v~~~~---~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 14 QAVREYL---ESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp HHHHHHH---HHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHH---HCCCceEeeecccccccccccHHHHHHh
Confidence 3555664 4789999999999999999999998875
No 256
>CHL00148 orf27 Ycf27; Reviewed
Probab=83.26 E-value=1.4 Score=41.54 Aligned_cols=50 Identities=18% Similarity=0.118 Sum_probs=41.8
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHH-------CCCHHHHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRI-------GLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~L-------gIS~~tVrqi~~rALkKLRk 471 (485)
.|+++|.+|+.+...-.+.++|.+||++.+ +++..||+.++.+.++||..
T Consensus 161 ~Lt~~E~~il~~l~~~~~~~~s~~~i~~~l~~~~~~~~~~~~tv~~~i~~lr~KL~~ 217 (240)
T CHL00148 161 RLTGMEFSLLELLISKSGEIFSRATILKEVWGYTPERHIDTRVVDVHISRLRAKLED 217 (240)
T ss_pred EcCHHHHHHHHHHHHCCCEEEcHHHHHHHhcCCCcccCCCcccHHHHHHHHHHHhcc
Confidence 599999999988752113579999999999 48999999999999999964
No 257
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=83.19 E-value=2.7 Score=41.94 Aligned_cols=64 Identities=22% Similarity=0.379 Sum_probs=41.6
Q ss_pred HhhhhHHHHHHhhccccCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHh
Q 011454 188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (485)
Q Consensus 188 ~~~~~~~~yl~~i~~~~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~ 258 (485)
.+.+.+..|++.....=.+ |......+.++ ..++..|...+|++|+.+++|..+|++.+++...
T Consensus 86 ~Ir~~i~~~lr~~~~~vr~-pr~~~~~~~~~------~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~ 149 (256)
T PRK07408 86 YIRGEIQHYLRDKSPTVRI-PRRWQELQRQA------KKVRQELRQELGRQPTDQEIAQALDISLEEWQEI 149 (256)
T ss_pred HHHHHHHHHHHHcCCeeee-CHHHHHHHHHH------HHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHH
Confidence 4455666677653321111 12233333333 3456788889999999999999999999998654
No 258
>PRK12423 LexA repressor; Provisional
Probab=83.06 E-value=2.1 Score=41.19 Aligned_cols=47 Identities=19% Similarity=0.297 Sum_probs=33.9
Q ss_pred hhCCHHHHHHHhhHhc-cCCC--CCCHHHHHHHHC-CCHHHHHHHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYG-LDKE--CLTWEDISKRIG-LSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 421 ~~Lp~rER~VI~LryG-L~~e--g~S~eEIAe~Lg-IS~~tVrqi~~rALkKLRk 471 (485)
..|+++|++|+...-. +... ..|..|||+.+| +|+++|+. +++.|++
T Consensus 2 ~~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~----~l~~L~~ 52 (202)
T PRK12423 2 DTLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARK----HVQALAE 52 (202)
T ss_pred CcCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHH----HHHHHHH
Confidence 4589999999876432 1112 359999999999 59999984 5555555
No 259
>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=82.81 E-value=0.94 Score=35.61 Aligned_cols=40 Identities=25% Similarity=0.287 Sum_probs=31.0
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
.|++.|..|+..-. ...+.|..|||+.+|+++.+|...++
T Consensus 5 gLs~~E~~vy~~Ll--~~~~~t~~eIa~~l~i~~~~v~~~L~ 44 (68)
T PF01978_consen 5 GLSENEAKVYLALL--KNGPATAEEIAEELGISRSTVYRALK 44 (68)
T ss_dssp CHHHHHHHHHHHHH--HHCHEEHHHHHHHHTSSHHHHHHHHH
T ss_pred CcCHHHHHHHHHHH--HcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 47778888776543 13679999999999999999975544
No 260
>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=82.72 E-value=1.3 Score=32.87 Aligned_cols=26 Identities=15% Similarity=0.442 Sum_probs=21.5
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
..++|+.|+|+.+|+|+.+|+++++.
T Consensus 7 ~~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 7 EKGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HTTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred HcCCCHHHHHHHhCCCcchhHHHhcC
Confidence 36799999999999999999999875
No 261
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=82.41 E-value=1.8 Score=33.22 Aligned_cols=35 Identities=17% Similarity=0.337 Sum_probs=25.6
Q ss_pred HHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 427 EREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 427 ER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
+..|+.+-. .....|.+|+|+.||||..||++-+.
T Consensus 2 ~~~Il~~l~--~~~~~s~~ela~~~~VS~~TiRRDl~ 36 (57)
T PF08220_consen 2 QQQILELLK--EKGKVSVKELAEEFGVSEMTIRRDLN 36 (57)
T ss_pred HHHHHHHHH--HcCCEEHHHHHHHHCcCHHHHHHHHH
Confidence 344554432 13468999999999999999987665
No 262
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=82.35 E-value=11 Score=39.90 Aligned_cols=35 Identities=26% Similarity=0.428 Sum_probs=29.6
Q ss_pred hhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhh
Q 011454 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (485)
Q Consensus 225 ~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l 259 (485)
.....+|...+|++|+.+++|..+|++.+++...+
T Consensus 219 ~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~ 253 (367)
T PRK09210 219 IRVQRQLLQELGREPTPEEIAEEMDMPPEKVREIL 253 (367)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 34566788889999999999999999999987554
No 263
>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=82.26 E-value=1.1 Score=32.49 Aligned_cols=25 Identities=24% Similarity=0.333 Sum_probs=22.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVAL 466 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rAL 466 (485)
+|..|+|+.+||++.||+.+..+.+
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999988775
No 264
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=81.95 E-value=4.7 Score=35.16 Aligned_cols=53 Identities=26% Similarity=0.279 Sum_probs=46.5
Q ss_pred HhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 420 IVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 420 ~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
..+|.+-||-...-+| -+-+|-+|||-.++++..+|..+.++-..|.|++-+.
T Consensus 26 S~QLkELErvF~ETHY---PDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~ 78 (125)
T KOG0484|consen 26 SAQLKELERVFAETHY---PDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERA 78 (125)
T ss_pred HHHHHHHHHHHHhhcC---CcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHH
Confidence 3578888888888888 6789999999999999999999999999999986553
No 265
>PHA01976 helix-turn-helix protein
Probab=81.89 E-value=2.3 Score=33.02 Aligned_cols=26 Identities=12% Similarity=0.203 Sum_probs=23.5
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
..++|+.|+|+.+|||+++|+++++.
T Consensus 13 ~~glt~~~lA~~~gvs~~~v~~~e~g 38 (67)
T PHA01976 13 ARAWSAPELSRRAGVRHSLIYDFEAD 38 (67)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 46799999999999999999998864
No 266
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=81.64 E-value=2.1 Score=30.72 Aligned_cols=39 Identities=18% Similarity=0.157 Sum_probs=26.4
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
.+-|+.+|.-..- ..+-+..+.|+.||||+.|+...+++
T Consensus 3 ~~~E~~~i~~aL~--~~~gn~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 3 EEFEKQLIRQALE--RCGGNVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp HHHHHHHHHHHHH--HTTT-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHH--HhCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 3446666665541 24568999999999999999876653
No 267
>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=81.20 E-value=15 Score=36.00 Aligned_cols=33 Identities=27% Similarity=0.489 Sum_probs=28.2
Q ss_pred hHHHHHHhhhCCCCchHHHHHHhhcChhHHHHh
Q 011454 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (485)
Q Consensus 226 ~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~ 258 (485)
.++.++...+|++|+.+++|..+|++.+++...
T Consensus 91 ~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~ 123 (238)
T TIGR02393 91 KAERQLTQELGREPTDEELAERMGMPAEKVREI 123 (238)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 455678888999999999999999999998643
No 268
>PRK14082 hypothetical protein; Provisional
Probab=80.92 E-value=5.4 Score=31.73 Aligned_cols=56 Identities=11% Similarity=0.010 Sum_probs=43.1
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhHhcCCCCCCcchhhH
Q 011454 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320 (485)
Q Consensus 263 ~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAiekFDp~rG~rFsTY 320 (485)
....+.|+..+.|.+.+-...- +..+.|||.||--+.+++.++.++...+.-|.-|
T Consensus 8 ~~e~e~ii~~FepkIkKsL~~T--~yqeREDLeQElk~Ki~eK~~~~~~~e~PGF~ef 63 (65)
T PRK14082 8 TEEIEHLIENFSPMIKKKLSNT--SYQEREDLEQELKIKIIEKADMLLCQEVPGFWEF 63 (65)
T ss_pred HHHHHHHHHHccHHHHHHHhcC--ChhhHHHHHHHHHHHHHHHHHHhhcccCCcHHHh
Confidence 3667889999999887654332 3457899999999999999999987766556544
No 269
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=80.75 E-value=21 Score=35.52 Aligned_cols=61 Identities=26% Similarity=0.294 Sum_probs=41.0
Q ss_pred HhhhhHHHHHHhhccccCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHh
Q 011454 188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (485)
Q Consensus 188 ~~~~~~~~yl~~i~~~~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~ 258 (485)
++.+.+..|++.....| ......+.++. .++..+...+|++|+.+++|..+|++.+++...
T Consensus 86 ~Ir~~i~~~lr~~~~~p----r~~~~~~~~l~------~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~ 146 (257)
T PRK05911 86 LIKAAIIDDLRKQDWVP----RSVHQKANKLA------DAMDSLRQSLGKEPTDGELCEYLNISQQELSGW 146 (257)
T ss_pred HHHHHHHHHHHhcCCCC----HHHHHHHHHHH------HHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHH
Confidence 44556666666654422 33333333333 345568888999999999999999999997544
No 270
>PHA00542 putative Cro-like protein
Probab=80.63 E-value=2.2 Score=35.25 Aligned_cols=26 Identities=12% Similarity=0.114 Sum_probs=23.5
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
..++|..++|+.+|||+.+|.+++.-
T Consensus 29 ~~glTq~elA~~lgIs~~tIsr~e~g 54 (82)
T PHA00542 29 RAGWSQEQIADATDVSQPTICRIYSG 54 (82)
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 46899999999999999999999854
No 271
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=80.38 E-value=2.1 Score=40.71 Aligned_cols=38 Identities=24% Similarity=0.211 Sum_probs=32.0
Q ss_pred HHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 011454 428 REIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL 469 (485)
Q Consensus 428 R~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKL 469 (485)
+..+.|.- .|+|..|||++||+|++|++-++.|+.++.
T Consensus 9 ~kA~eLk~----~Glt~gEIAdELNvSreTa~WL~~r~~~~~ 46 (203)
T COG0856 9 KKARELKS----KGLTTGEIADELNVSRETATWLLTRAFKKE 46 (203)
T ss_pred HHHHHHHH----CCCcHHHhhhhhhhhHHHHHHHHhhhhhcc
Confidence 44556664 899999999999999999999999987654
No 272
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=80.24 E-value=3.6 Score=29.64 Aligned_cols=25 Identities=16% Similarity=0.205 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 440 ECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 440 eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
.+++..+||+.+|+|+.+|++.+..
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~ 37 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNK 37 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4699999999999999999876644
No 273
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=80.10 E-value=3.8 Score=32.25 Aligned_cols=33 Identities=18% Similarity=0.288 Sum_probs=24.8
Q ss_pred HHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 429 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 429 ~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
.|+.+.- ....+..|||+.+|+|+.+|++.+.+
T Consensus 4 ~il~~L~---~~~~~~~eLa~~l~vS~~tv~~~l~~ 36 (69)
T TIGR00122 4 RLLALLA---DNPFSGEKLGEALGMSRTAVNKHIQT 36 (69)
T ss_pred HHHHHHH---cCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4454433 34578999999999999999876654
No 274
>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=79.22 E-value=2.1 Score=31.61 Aligned_cols=25 Identities=24% Similarity=0.187 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 440 ECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 440 eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
.++|+.++|+.+|+|+++|+++++.
T Consensus 14 ~gltq~~lA~~~gvs~~~vs~~e~g 38 (58)
T TIGR03070 14 LGLTQADLADLAGVGLRFIRDVENG 38 (58)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 5799999999999999999999853
No 275
>PRK10072 putative transcriptional regulator; Provisional
Probab=79.20 E-value=2.6 Score=36.14 Aligned_cols=25 Identities=20% Similarity=0.286 Sum_probs=23.1
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
..++|+.|+|+.+|||..||++++.
T Consensus 44 ~~glTQ~elA~~lGvS~~TVs~WE~ 68 (96)
T PRK10072 44 GTGLKIDDFARVLGVSVAMVKEWES 68 (96)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 4579999999999999999999986
No 276
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=79.13 E-value=30 Score=38.32 Aligned_cols=33 Identities=27% Similarity=0.432 Sum_probs=28.4
Q ss_pred hHHHHHHhhhCCCCchHHHHHHhhcChhHHHHh
Q 011454 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (485)
Q Consensus 226 ~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~ 258 (485)
.++.+|...+|++|+.+++|..+|++.+++...
T Consensus 362 ~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~ 394 (509)
T PRK05901 362 RIERELLQELGREPTPEELAKEMGFTPEKVREI 394 (509)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 356678888999999999999999999998654
No 277
>PF14493 HTH_40: Helix-turn-helix domain
Probab=79.04 E-value=4.4 Score=33.91 Aligned_cols=30 Identities=23% Similarity=0.240 Sum_probs=27.2
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGLVALEK 468 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~rALkK 468 (485)
.+|+|.+|||+.-|++.+||..++-++...
T Consensus 11 ~~G~si~eIA~~R~L~~sTI~~HL~~~~~~ 40 (91)
T PF14493_consen 11 QKGLSIEEIAKIRGLKESTIYGHLAELIES 40 (91)
T ss_pred HcCCCHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence 489999999999999999999999887654
No 278
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=78.90 E-value=2.9 Score=29.79 Aligned_cols=23 Identities=35% Similarity=0.458 Sum_probs=19.5
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Q 011454 441 CLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 441 g~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
+++..|||+.+|+|+.+|++.+.
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~ 30 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLK 30 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHH
Confidence 58999999999999999965443
No 279
>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=78.79 E-value=1.9 Score=36.29 Aligned_cols=24 Identities=38% Similarity=0.302 Sum_probs=18.0
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 440 ECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 440 eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
.|+|+.|||+++|.|++.|++++.
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 479999999999999999998875
No 280
>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=78.76 E-value=3.9 Score=33.95 Aligned_cols=37 Identities=24% Similarity=0.186 Sum_probs=28.0
Q ss_pred HHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 425 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 425 ~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
+|+..|+.+.- ....|..+||+.+|||..||++.+..
T Consensus 6 ~R~~~I~e~l~---~~~~ti~dvA~~~gvS~~TVsr~L~~ 42 (80)
T TIGR02844 6 ERVLEIGKYIV---ETKATVRETAKVFGVSKSTVHKDVTE 42 (80)
T ss_pred HHHHHHHHHHH---HCCCCHHHHHHHhCCCHHHHHHHhcC
Confidence 45555655543 34579999999999999999987753
No 281
>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=78.42 E-value=5 Score=30.54 Aligned_cols=37 Identities=27% Similarity=0.352 Sum_probs=27.1
Q ss_pred HHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 425 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 425 ~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
+.+..|+...+ ..+.+..||++.+|+++.+|++.+.+
T Consensus 7 ~~~~~il~~l~---~~~~~~~ei~~~~~i~~~~i~~~l~~ 43 (78)
T cd00090 7 PTRLRILRLLL---EGPLTVSELAERLGLSQSTVSRHLKK 43 (78)
T ss_pred hHHHHHHHHHH---HCCcCHHHHHHHHCcCHhHHHHHHHH
Confidence 44556665544 33499999999999999999766544
No 282
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=78.33 E-value=2.4 Score=42.36 Aligned_cols=26 Identities=15% Similarity=0.328 Sum_probs=24.2
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
.+||.+.+||+.||||+.||+.+..+
T Consensus 17 l~gmk~~dIAeklGvspntiksWKrr 42 (279)
T COG5484 17 LKGMKLKDIAEKLGVSPNTIKSWKRR 42 (279)
T ss_pred HhhccHHHHHHHhCCChHHHHHHHHh
Confidence 48899999999999999999999876
No 283
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=78.14 E-value=4.5 Score=40.40 Aligned_cols=62 Identities=11% Similarity=0.144 Sum_probs=46.5
Q ss_pred HHHHHHHHHhhCCHHHHHHHhhHhcc--CCCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHH
Q 011454 412 KDEVNKLIIVTLGEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGLV----ALEKLKHAAR 474 (485)
Q Consensus 412 ~e~L~~~L~~~Lp~rER~VI~LryGL--~~eg~S~eEIAe~LgIS~~tVrqi~~r----ALkKLRk~L~ 474 (485)
.+.|.+.+ ..|+|.|+.|......- ....+|..|||+..|+|+.||.+..++ +..-||..+.
T Consensus 4 ~~~i~~~~-~~Lt~~e~~Ia~yil~n~~~v~~~si~~lA~~~~vS~aTv~Rf~kklG~~gf~e~k~~l~ 71 (284)
T PRK11302 4 LEKIQSRL-EHLSKSERKVAEVILASPQTAIHSSIATLAKMANVSEPTVNRFCRSLDTKGFPDFKLHLA 71 (284)
T ss_pred HHHHHHHH-hhCCHHHHHHHHHHHhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence 45677777 89999999999776521 123589999999999999999776654 5566665554
No 284
>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=77.95 E-value=2.3 Score=31.72 Aligned_cols=25 Identities=24% Similarity=0.384 Sum_probs=20.7
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
..++|..|||+.+|+++++|.+++.
T Consensus 16 ~~~~t~~eia~~~gl~~stv~r~L~ 40 (52)
T PF09339_consen 16 GGPLTLSEIARALGLPKSTVHRLLQ 40 (52)
T ss_dssp BSCEEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3568999999999999999987665
No 285
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=77.89 E-value=3.5 Score=30.59 Aligned_cols=28 Identities=32% Similarity=0.602 Sum_probs=21.7
Q ss_pred CCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 440 ECL-TWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 440 eg~-S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
+.+ |..|||+.+|+|+.+|++ ++++|.+
T Consensus 18 ~~l~s~~~la~~~~vs~~tv~~----~l~~L~~ 46 (60)
T smart00345 18 DKLPSERELAAQLGVSRTTVRE----ALSRLEA 46 (60)
T ss_pred CcCcCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence 345 899999999999999975 4455543
No 286
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=77.77 E-value=3 Score=32.28 Aligned_cols=25 Identities=20% Similarity=0.444 Sum_probs=20.8
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
..++|+.++|+.+|+|+++|+++++
T Consensus 12 ~~gls~~~lA~~~g~s~s~v~~iE~ 36 (64)
T PF13560_consen 12 RAGLSQAQLADRLGVSQSTVSRIER 36 (64)
T ss_dssp CHTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 4579999999999999999999876
No 287
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=77.18 E-value=4.1 Score=30.17 Aligned_cols=26 Identities=19% Similarity=0.156 Sum_probs=22.4
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
.++.|..+|++.+|+|+.+|++.+++
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~ 33 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKK 33 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHH
Confidence 36789999999999999999877655
No 288
>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=76.96 E-value=3.6 Score=31.73 Aligned_cols=37 Identities=14% Similarity=0.331 Sum_probs=27.3
Q ss_pred HHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 426 REREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 426 rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
++-.++.+-+. ...+++.|||+.+|+|..+|++.+..
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 45566666653 46799999999999999999866543
No 289
>PRK05949 RNA polymerase sigma factor; Validated
Probab=76.80 E-value=12 Score=38.93 Aligned_cols=35 Identities=14% Similarity=0.371 Sum_probs=28.5
Q ss_pred chhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHh
Q 011454 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (485)
Q Consensus 224 l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~ 258 (485)
+..++.++...+|++|+.+++|..+|++.+++...
T Consensus 180 l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~ 214 (327)
T PRK05949 180 IKKTQRELSQKLGRSATPAEIAKELELEPSQIREY 214 (327)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 34455667778999999999999999999887643
No 290
>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=75.92 E-value=13 Score=32.06 Aligned_cols=43 Identities=19% Similarity=0.105 Sum_probs=34.1
Q ss_pred hCCHHHHHHHhhHh--ccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYY--GLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 422 ~Lp~rER~VI~Lry--GL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
.|++.|-.||...+ .-+..+.|..|||+.+++++++|.+.+.+
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 68999999886644 11235799999999999999999876654
No 291
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=75.87 E-value=5.9 Score=39.88 Aligned_cols=65 Identities=17% Similarity=0.215 Sum_probs=48.7
Q ss_pred HHHHHHHHHHHhhCCHHHHHHHhhHhcc-C-CCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHHh
Q 011454 410 ALKDEVNKLIIVTLGEREREIIRLYYGL-D-KECLTWEDISKRIGLSRERVRQVGLV----ALEKLKHAARK 475 (485)
Q Consensus 410 el~e~L~~~L~~~Lp~rER~VI~LryGL-~-~eg~S~eEIAe~LgIS~~tVrqi~~r----ALkKLRk~L~~ 475 (485)
.+...|+..+ ..|++.|+.|......- + ...+|..+||+..|+|..||-+.-++ +..-||..+..
T Consensus 14 ~i~~~i~~~~-~~Lt~~e~~Ia~yil~~~~~v~~~si~~lA~~~~vS~aTi~Rf~kkLGf~gf~efk~~l~~ 84 (292)
T PRK11337 14 GLGPYIRMKQ-EGLTPLESRVVEWLLKPGDLSEATALKDIAEALAVSEAMIVKVAKKLGFSGFRNLRSALED 84 (292)
T ss_pred hHHHHHHHHH-hhcCHHHHHHHHHHHhCHHHHHhcCHHHHHHHhCCChHHHHHHHHHcCCCCHHHHHHHHHH
Confidence 3455677778 89999999999876521 1 24589999999999999999776554 56666666653
No 292
>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=75.84 E-value=3.1 Score=32.90 Aligned_cols=27 Identities=44% Similarity=0.640 Sum_probs=21.6
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 441 CLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 441 g~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
++|.++||..+|+|+.+|.+ .+++|++
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r----~l~~l~~ 54 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSR----ILKRLKD 54 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHH----HHHHHHH
T ss_pred cCCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence 58999999999999999875 4445543
No 293
>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=75.68 E-value=5.5 Score=38.23 Aligned_cols=42 Identities=14% Similarity=0.185 Sum_probs=34.4
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
..|++++..|+..... ..+.+..|||+.+|+|++||++++.+
T Consensus 139 ~~ls~~~~~IL~~l~~--~g~~s~~eia~~l~is~stv~r~L~~ 180 (203)
T TIGR01884 139 AGLSREELKVLEVLKA--EGEKSVKNIAKKLGKSLSTISRHLRE 180 (203)
T ss_pred cCCCHHHHHHHHHHHH--cCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 5789999998877651 24679999999999999999877665
No 294
>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=75.44 E-value=5.5 Score=37.91 Aligned_cols=44 Identities=16% Similarity=0.194 Sum_probs=33.4
Q ss_pred hhCCHHHHHHHhhHhcc---CCCCCCHHHHHHHHCCC-HHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGL---DKECLTWEDISKRIGLS-RERVRQVGLV 464 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL---~~eg~S~eEIAe~LgIS-~~tVrqi~~r 464 (485)
..|+++|+.|+....-. +..+.|..|||+.+|++ ++||..++.+
T Consensus 2 ~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~ 49 (199)
T TIGR00498 2 KPLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKA 49 (199)
T ss_pred CccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHH
Confidence 35899999999875411 12347899999999998 9999866553
No 295
>PRK10870 transcriptional repressor MprA; Provisional
Probab=75.29 E-value=14 Score=34.72 Aligned_cols=43 Identities=12% Similarity=0.093 Sum_probs=33.5
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
.|++.|-.|+...+..+..+.|..|||+.+++++++|.+.+.+
T Consensus 52 gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~r 94 (176)
T PRK10870 52 GINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADE 94 (176)
T ss_pred CCCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 5888888888776522234689999999999999999876654
No 296
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=75.25 E-value=1.4 Score=34.33 Aligned_cols=25 Identities=24% Similarity=0.343 Sum_probs=22.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVAL 466 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rAL 466 (485)
||..|+|+.+|||+.||+.+..+.+
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 4789999999999999999988765
No 297
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=75.03 E-value=4.5 Score=30.94 Aligned_cols=25 Identities=32% Similarity=0.355 Sum_probs=20.9
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 440 ECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 440 eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
..+|..|||+.+|+|+.+|++.+.+
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~ 48 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKE 48 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 5689999999999999999755443
No 298
>PRK00215 LexA repressor; Validated
Probab=75.00 E-value=6.2 Score=37.71 Aligned_cols=42 Identities=21% Similarity=0.234 Sum_probs=32.2
Q ss_pred CCHHHHHHHhhHhc--c-CCCCCCHHHHHHHHCC-CHHHHHHHHHH
Q 011454 423 LGEREREIIRLYYG--L-DKECLTWEDISKRIGL-SRERVRQVGLV 464 (485)
Q Consensus 423 Lp~rER~VI~LryG--L-~~eg~S~eEIAe~LgI-S~~tVrqi~~r 464 (485)
|+++|+.|+....- . +..+.|+.|||+.+|+ +++||.+++.+
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~ 47 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKA 47 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 78899998875431 1 1345799999999999 99999877654
No 299
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=74.92 E-value=6.3 Score=34.22 Aligned_cols=43 Identities=19% Similarity=0.345 Sum_probs=27.2
Q ss_pred HHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011454 425 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA 472 (485)
Q Consensus 425 ~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~ 472 (485)
.+.+.|...+ +|.+..|+|.++|+|..+|.+++++..++-++.
T Consensus 61 ~R~~~I~~~f-----~G~n~~eLA~kyglS~r~I~~Ii~~~~~~~~~~ 103 (108)
T PF08765_consen 61 LRNREIRREF-----NGMNVRELARKYGLSERQIYRIIKRVRRRERRR 103 (108)
T ss_dssp HHHHHHHHH-------SS-HHHHHHHHT--HHHHHHHHHHHHH-----
T ss_pred HHHHHHHHHh-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHh
Confidence 3455566543 589999999999999999999999887766543
No 300
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=74.86 E-value=22 Score=27.61 Aligned_cols=73 Identities=18% Similarity=0.207 Sum_probs=43.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHH
Q 011454 367 PSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWED 446 (485)
Q Consensus 367 ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eE 446 (485)
++.+++|+.+|++...+........ ...|.... ....+ +.++.+.. ..+.++.+
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~-------~~s~~~~~----~~~r~------------~~a~~~l~---~~~~~~~~ 55 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKET-------GTTPKQYL----RDRRL------------ERARRLLR---DTDLSVTE 55 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHh-------CcCHHHHH----HHHHH------------HHHHHHHH---cCCCCHHH
Confidence 5778999999999888765533210 01111100 00111 12222222 23689999
Q ss_pred HHHHHCC-CHHHHHHHHHHH
Q 011454 447 ISKRIGL-SRERVRQVGLVA 465 (485)
Q Consensus 447 IAe~LgI-S~~tVrqi~~rA 465 (485)
||..+|+ ++....+..++.
T Consensus 56 ia~~~g~~s~~~f~r~Fk~~ 75 (84)
T smart00342 56 IALRVGFSSQSYFSRAFKKL 75 (84)
T ss_pred HHHHhCCCChHHHHHHHHHH
Confidence 9999999 998887776554
No 301
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=74.67 E-value=6.4 Score=34.13 Aligned_cols=41 Identities=12% Similarity=0.252 Sum_probs=32.8
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
.|++.|..||..... ..+.|..|||+.+|+++.+|.+.+.+
T Consensus 25 ~lt~~q~~iL~~l~~--~~~~t~~ela~~~~~~~~tvs~~l~~ 65 (118)
T TIGR02337 25 GLTEQQWRILRILAE--QGSMEFTQLANQACILRPSLTGILAR 65 (118)
T ss_pred CCCHHHHHHHHHHHH--cCCcCHHHHHHHhCCCchhHHHHHHH
Confidence 688888888876542 46799999999999999999765544
No 302
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=74.64 E-value=25 Score=36.53 Aligned_cols=34 Identities=26% Similarity=0.368 Sum_probs=28.7
Q ss_pred hhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHh
Q 011454 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (485)
Q Consensus 225 ~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~ 258 (485)
..++.+|...+|++|+.+++|..+|++.+++...
T Consensus 176 ~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~ 209 (324)
T PRK07921 176 ARIKRELHQQLGREATDEELAEESGIPEEKIADL 209 (324)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 3456678888999999999999999999998643
No 303
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=74.63 E-value=3.1 Score=33.09 Aligned_cols=36 Identities=25% Similarity=0.224 Sum_probs=26.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH-------HHHHHHHHHHhhh
Q 011454 442 LTWEDISKRIGLSRERVRQVGLV-------ALEKLKHAARKKK 477 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~r-------ALkKLRk~L~~~~ 477 (485)
.|+.|||+.+|||+.||++.++. ...++.+.+...+
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~~~~v~~~t~~~i~~~~~~~g 43 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNGNGRVSEETREKVLAAMEELG 43 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhC
Confidence 37899999999999999988764 3444555555444
No 304
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=74.62 E-value=5.5 Score=39.20 Aligned_cols=26 Identities=15% Similarity=0.181 Sum_probs=23.6
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
..++|..|||++||||..+|++++..
T Consensus 23 ~g~~sa~elA~~Lgis~~avR~HL~~ 48 (218)
T COG2345 23 SGPVSADELAEELGISPMAVRRHLDD 48 (218)
T ss_pred cCCccHHHHHHHhCCCHHHHHHHHHH
Confidence 46899999999999999999998865
No 305
>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=74.59 E-value=9.2 Score=31.96 Aligned_cols=31 Identities=19% Similarity=0.177 Sum_probs=25.1
Q ss_pred CCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHH
Q 011454 440 ECLTWEDISKRIG-LSRERVRQVGLVALEKLK 470 (485)
Q Consensus 440 eg~S~eEIAe~Lg-IS~~tVrqi~~rALkKLR 470 (485)
-++|+.+||+.|| .+.+||.....+.-+++.
T Consensus 43 ~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~ 74 (90)
T cd06571 43 TGLSLPEIGRAFGGRDHSTVLHAVRKIEELLE 74 (90)
T ss_pred hCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHH
Confidence 4799999999999 999999866665555554
No 306
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=74.48 E-value=4.4 Score=32.70 Aligned_cols=25 Identities=28% Similarity=0.428 Sum_probs=22.3
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
.-++|++|.|+.+|||+.|+..+++
T Consensus 12 ~~~ltQ~elA~~vgVsRQTi~~iEk 36 (68)
T COG1476 12 ELGLTQEELAKLVGVSRQTIIAIEK 36 (68)
T ss_pred HhCcCHHHHHHHcCcCHHHHHHHHc
Confidence 3579999999999999999988875
No 307
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=74.48 E-value=12 Score=33.75 Aligned_cols=51 Identities=24% Similarity=0.343 Sum_probs=38.3
Q ss_pred HHHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 011454 413 DEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL 469 (485)
Q Consensus 413 e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKL 469 (485)
..+.+++ =.|++.+-+|+....- ...++|..|||+.+|++++||. +|+++|
T Consensus 16 ~dvl~c~-~GLs~~Dv~v~~~LL~-~~~~~tvdelae~lnr~rStv~----rsl~~L 66 (126)
T COG3355 16 EDVLKCV-YGLSELDVEVYKALLE-ENGPLTVDELAEILNRSRSTVY----RSLQNL 66 (126)
T ss_pred HHHHHHH-hCCcHHHHHHHHHHHh-hcCCcCHHHHHHHHCccHHHHH----HHHHHH
Confidence 3455666 4899999998876541 1367999999999999999996 455444
No 308
>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=73.86 E-value=4.2 Score=37.71 Aligned_cols=27 Identities=26% Similarity=0.407 Sum_probs=22.5
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 441 CLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 441 g~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
.+|.+|||..+|+|+++|+ |++++|++
T Consensus 143 ~~t~~~iA~~lG~tretvs----R~l~~l~~ 169 (193)
T TIGR03697 143 RLSHQAIAEAIGSTRVTIT----RLLGDLRK 169 (193)
T ss_pred CCCHHHHHHHhCCcHHHHH----HHHHHHHH
Confidence 5799999999999999997 55666665
No 309
>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=73.85 E-value=4.2 Score=31.55 Aligned_cols=23 Identities=17% Similarity=0.213 Sum_probs=21.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
+|..|+|+.+|||+.|++.+.++
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 58899999999999999999875
No 310
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=73.78 E-value=7.4 Score=35.07 Aligned_cols=41 Identities=7% Similarity=0.087 Sum_probs=33.5
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
.|++.|-.||...+. ..+.|..|||+.+++++++|.+.+.+
T Consensus 37 glt~~q~~vL~~l~~--~~~~t~~eLa~~l~i~~~tvsr~l~~ 77 (144)
T PRK11512 37 DITAAQFKVLCSIRC--AACITPVELKKVLSVDLGALTRMLDR 77 (144)
T ss_pred CCCHHHHHHHHHHHH--cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 588888888876541 46799999999999999999876654
No 311
>PRK09954 putative kinase; Provisional
Probab=73.52 E-value=6.2 Score=40.98 Aligned_cols=41 Identities=22% Similarity=0.347 Sum_probs=32.3
Q ss_pred CCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011454 423 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 423 Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
|+++++.||.+.. .....|..|||+.||||+.+|+.++++-
T Consensus 1 ~~~~~~~il~~l~--~~~~~s~~~la~~l~~s~~~v~~~i~~L 41 (362)
T PRK09954 1 MNNREKEILAILR--RNPLIQQNEIADILQISRSRVAAHIMDL 41 (362)
T ss_pred CChHHHHHHHHHH--HCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4667778887755 1245899999999999999999887753
No 312
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=73.39 E-value=12 Score=39.18 Aligned_cols=32 Identities=31% Similarity=0.509 Sum_probs=30.1
Q ss_pred hhHHHHHHhhccccCCCHHHHHHHHHHHHcCC
Q 011454 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGL 222 (485)
Q Consensus 191 ~~~~~yl~~i~~~~~Lt~eee~~L~~~ik~Gd 222 (485)
..+..|+..+...|+|+++|+..|+.+++.|+
T Consensus 67 ~~~~~~~~~~~~~~~l~~~Ee~~la~~~~~g~ 98 (342)
T COG0568 67 GRLSFYIRAIEAAPLLTPEEEKALARRLKRGE 98 (342)
T ss_pred hhHHHHHHHHhhhcccChHHHHHHHHHHHcCC
Confidence 57888999999999999999999999999997
No 313
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=73.36 E-value=9 Score=35.55 Aligned_cols=51 Identities=18% Similarity=0.241 Sum_probs=37.1
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH------HHHHHHHHHHhhh
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV------ALEKLKHAARKKK 477 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r------ALkKLRk~L~~~~ 477 (485)
+|..-.|=.++- .-|+|+.++|+.+|||+++|+++++. .+..|.+.....+
T Consensus 24 ~p~~~~Ir~~R~---~lGmTq~eLAerlGVS~~tIs~iE~G~~~~~psl~~L~kIA~aLg 80 (150)
T TIGR02612 24 TPKEGWVRAIRK---ALGMSGAQLAGRLGVTPQRVEALEKSELSGTVTLKTLRAAAEALD 80 (150)
T ss_pred cCcHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCCCHHHHHHHHHHcC
Confidence 333333444455 46899999999999999999999984 4566776666544
No 314
>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=73.21 E-value=7.4 Score=28.95 Aligned_cols=50 Identities=18% Similarity=0.192 Sum_probs=38.7
Q ss_pred hCCHHHHHHHhhHhccC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLD--KECLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~--~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
.+++.+..+|.-.|..+ .......+||..+|++...|..+...-..+.+.
T Consensus 6 ~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 6 RFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 46788888888888542 123457899999999999999999887776653
No 315
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=73.20 E-value=29 Score=38.68 Aligned_cols=104 Identities=12% Similarity=0.092 Sum_probs=60.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH-HhhhcccCC--CCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhccCCCC
Q 011454 365 VTPSVDRIAEYLNMSQKKVRNATEVL-AYIADNRVE--NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKEC 441 (485)
Q Consensus 365 r~ps~eEIae~L~is~eev~~~l~~~-~~l~D~~~e--~~pee~~e~~el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg 441 (485)
...+..++|+.+|+|..+|++-+... +++.+.... ...............+...+ ..-++..+. +.++.-+ .++
T Consensus 16 ~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~~i~~~~Gy~l~~~~~~~~~~~~-~~~~~e~~~-il~~Ll~-~~~ 92 (584)
T PRK09863 16 QDRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIGSISGSAKYHLEILNRRSLFQLL-QKSDNEDRL-LLLRLLL-NTF 92 (584)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchhheecCCceEEEeCCHHHHHHHH-hcCCHHHHH-HHHHHHH-cCC
Confidence 35789999999999999998766554 333332110 00000000000012233333 333443333 3333212 467
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
.+..++|+.|.||++||.+-+.+..+.+.+
T Consensus 93 ~~~~~La~~l~vS~sTi~~dl~~v~~~l~~ 122 (584)
T PRK09863 93 TPMAQLASALNLSRTWVAERLPRLNQRYER 122 (584)
T ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHHhhhc
Confidence 999999999999999999888877776653
No 316
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=72.90 E-value=8.3 Score=31.44 Aligned_cols=41 Identities=24% Similarity=0.345 Sum_probs=32.2
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
.|+..+..||...+. ..+++..+||+.+++++.+|++.+.+
T Consensus 7 ~l~~~~~~il~~l~~--~~~~~~~~la~~~~~s~~~i~~~l~~ 47 (101)
T smart00347 7 GLTPTQFLVLRILYE--EGPLSVSELAKRLGVSPSTVTRVLDR 47 (101)
T ss_pred CCCHHHHHHHHHHHH--cCCcCHHHHHHHHCCCchhHHHHHHH
Confidence 577888888877762 24689999999999999998755443
No 317
>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=72.33 E-value=4.4 Score=38.03 Aligned_cols=35 Identities=26% Similarity=0.343 Sum_probs=27.0
Q ss_pred HHHHHhhHhccCCCCCCHHHHHHHHC-CCHHHHHHHHHH
Q 011454 427 EREIIRLYYGLDKECLTWEDISKRIG-LSRERVRQVGLV 464 (485)
Q Consensus 427 ER~VI~LryGL~~eg~S~eEIAe~Lg-IS~~tVrqi~~r 464 (485)
.-+.|.-.+ .+|+|..|||+.|| ||+++|--..+|
T Consensus 7 ~~~~L~~lw---~~G~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 7 RVERLRKLW---AEGLSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred HHHHHHHHH---HcCCCHHHHHHHhCCcchhhhhhhhhc
Confidence 334444444 59999999999999 999999776665
No 318
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=72.25 E-value=9 Score=29.44 Aligned_cols=42 Identities=14% Similarity=0.101 Sum_probs=30.2
Q ss_pred HHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 011454 430 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 474 (485)
Q Consensus 430 VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~ 474 (485)
.+..++ ..+.+..+.|+.|+|.+.||+.++.++-+.+.--+.
T Consensus 4 TL~~yl---~~~~n~~~tA~~L~iHrNTl~yRl~ki~~l~g~dl~ 45 (59)
T PF13556_consen 4 TLRAYL---ENNGNISKTARALHIHRNTLRYRLKKIEELLGLDLD 45 (59)
T ss_dssp HHHHHH---HTTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--TT
T ss_pred HHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCcCCC
Confidence 344455 467999999999999999999999988776655444
No 319
>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=72.22 E-value=7.8 Score=34.91 Aligned_cols=38 Identities=26% Similarity=0.232 Sum_probs=26.4
Q ss_pred CCHHHH-HHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 423 LGERER-EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 423 Lp~rER-~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
||..-| .||.|.. +|.+..+||.+|+||.+.|++++.|
T Consensus 18 Lp~~~R~rIvela~----~G~rp~~Isr~l~Vs~gcVsKIl~R 56 (125)
T PF00292_consen 18 LPNELRQRIVELAK----EGVRPCDISRQLRVSHGCVSKILSR 56 (125)
T ss_dssp S-HHHHHHHHHHHH----TT--HHHHHHHHT--HHHHHHHHHH
T ss_pred CcHHHHHHHHHHhh----hcCCHHHHHHHHccchhHHHHHHHH
Confidence 444444 4777776 7999999999999999999988875
No 320
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=72.19 E-value=54 Score=35.41 Aligned_cols=26 Identities=31% Similarity=0.403 Sum_probs=22.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011454 440 ECLTWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 440 eg~S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
..-|..|||+.+||+...|+.+...+
T Consensus 277 R~pt~~EiA~~l~is~~~vr~~l~~~ 302 (415)
T PRK07598 277 RTPTIEDIAQELEMTPTQVREVLLRV 302 (415)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHc
Confidence 56789999999999999999886654
No 321
>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=71.72 E-value=7.8 Score=30.82 Aligned_cols=25 Identities=20% Similarity=0.307 Sum_probs=22.9
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
..++|..++|+.+|+|+.+|+++++
T Consensus 16 ~~~~t~~~lA~~~gis~~tis~~~~ 40 (78)
T TIGR02607 16 PLGLSIRALAKALGVSRSTLSRIVN 40 (78)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 4679999999999999999999886
No 322
>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=71.13 E-value=5 Score=35.38 Aligned_cols=25 Identities=24% Similarity=0.272 Sum_probs=23.3
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
..|.|..++|..++||+.||.+++.
T Consensus 16 ~~g~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 16 EKGKSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred HccchHHHHHHHhCcHHHHHHHHHH
Confidence 5789999999999999999999977
No 323
>PRK15482 transcriptional regulator MurR; Provisional
Probab=71.05 E-value=8.7 Score=38.64 Aligned_cols=61 Identities=13% Similarity=0.257 Sum_probs=45.5
Q ss_pred HHHHHHHHhhCCHHHHHHHhhHhcc--CCCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHH
Q 011454 413 DEVNKLIIVTLGEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGLV----ALEKLKHAAR 474 (485)
Q Consensus 413 e~L~~~L~~~Lp~rER~VI~LryGL--~~eg~S~eEIAe~LgIS~~tVrqi~~r----ALkKLRk~L~ 474 (485)
..|.... ..|++.|+.|.....-- ....+|..|||+..|+|..||-+.-++ +...||..+.
T Consensus 5 ~~i~~~~-~~Lt~~e~~Ia~yIl~n~~~v~~~si~elA~~~~vS~aTv~Rf~kkLGf~Gf~efk~~l~ 71 (285)
T PRK15482 5 TKIRNAE-SEFTENEQKIADFLRANVSELKSVSSRKMAKQLGISQSSIVKFAQKLGAQGFTELRMALI 71 (285)
T ss_pred HHHHHHH-hhcCHHHHHHHHHHHhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHHhCCCCHHHHHHHHH
Confidence 4566666 78999999999876521 123599999999999999999766554 5666666554
No 324
>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=70.84 E-value=16 Score=27.47 Aligned_cols=26 Identities=31% Similarity=0.558 Sum_probs=20.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
.|.++||+.+|+|+.+|++ ++++|.+
T Consensus 26 ~~~~~la~~~~is~~~v~~----~l~~L~~ 51 (66)
T cd07377 26 PSERELAEELGVSRTTVRE----ALRELEA 51 (66)
T ss_pred CCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence 4599999999999999974 5555544
No 325
>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=70.80 E-value=4.6 Score=35.99 Aligned_cols=23 Identities=22% Similarity=0.277 Sum_probs=21.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
||.+|+|+.+|+|+.||.+++.+
T Consensus 1 MT~eELA~~tG~srQTINrWvRk 23 (122)
T PF07037_consen 1 MTPEELAELTGYSRQTINRWVRK 23 (122)
T ss_pred CCHHHHHHHhCccHHHHHHHHHh
Confidence 78999999999999999998764
No 326
>PF12759 HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR024431 This entry represents the helix-turn-helix domain found at the C-terminal of InsA.
Probab=69.12 E-value=6.4 Score=29.34 Aligned_cols=38 Identities=11% Similarity=0.080 Sum_probs=31.4
Q ss_pred CCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 423 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 423 Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
-|.-.++|+.|.+ +|.-..++|+.|+|+..||-+.+++
T Consensus 7 kpgikeqIvema~----nG~GiRdtaRvL~I~~nTVlrtLK~ 44 (46)
T PF12759_consen 7 KPGIKEQIVEMAF----NGSGIRDTARVLKISINTVLRTLKN 44 (46)
T ss_pred CccHHHHHHHHHh----cCCcchhhHhHhcchHHHHHHHHhc
Confidence 4555678999987 8899999999999999999765543
No 327
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=69.11 E-value=86 Score=31.86 Aligned_cols=66 Identities=17% Similarity=0.162 Sum_probs=37.6
Q ss_pred HhhhhHHHHHHhhccccCC-CHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHH
Q 011454 188 LIQNRLKGYVKGVVSEELL-THAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQ 256 (485)
Q Consensus 188 ~~~~~~~~yl~~i~~~~~L-t~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~ 256 (485)
++...+..|+++-...+.+ .......+..+++. +..........+|++|+.+++|..+|++.+++.
T Consensus 100 ~Ir~~I~~~lr~~~~~iR~p~~~~~~~~~~~~~~---~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~ 166 (289)
T PRK07500 100 WIRASIQDYILRNWSIVRGGTSSAQKALFFNLRR---LRARLAQADEELTKQEIHREIATALGVSLSDVE 166 (289)
T ss_pred HHHHHHHHHHHHCCCceecCccHHHHHHHHHHHH---HHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHH
Confidence 5666677777663333222 12222333333332 111122222358999999999999999999864
No 328
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=69.10 E-value=13 Score=32.39 Aligned_cols=39 Identities=15% Similarity=0.015 Sum_probs=30.5
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
..+.+.+-.-++..+ ++|+.++|+.+|+++.+|+++++-
T Consensus 63 ~~~~~~~i~~~r~~~-----gltq~~lA~~lg~~~~tis~~e~g 101 (127)
T TIGR03830 63 GLLTPPEIRRIRKKL-----GLSQREAAELLGGGVNAFSRYERG 101 (127)
T ss_pred CCcCHHHHHHHHHHc-----CCCHHHHHHHhCCCHHHHHHHHCC
Confidence 456666655555554 689999999999999999998764
No 329
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=68.99 E-value=7.6 Score=38.76 Aligned_cols=59 Identities=15% Similarity=0.213 Sum_probs=44.0
Q ss_pred HHHHHHhhCCHHHHHHHhhHhcc--CCCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHH
Q 011454 415 VNKLIIVTLGEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGLV----ALEKLKHAAR 474 (485)
Q Consensus 415 L~~~L~~~Lp~rER~VI~LryGL--~~eg~S~eEIAe~LgIS~~tVrqi~~r----ALkKLRk~L~ 474 (485)
|.+.. +.|++.|+.|......- ....+|..|+|+..|+|+.||.+..++ +..-||..+.
T Consensus 3 i~~~~-~~Lt~~e~~ia~yil~n~~~v~~~si~elA~~~~vS~aTv~Rf~kklG~~Gf~efk~~l~ 67 (278)
T PRK11557 3 IRQRY-PGLAQSDRKLADYLLLQPDTARHLSSQQLANEAGVSQSSVVKFAQKLGYKGFPALKLALS 67 (278)
T ss_pred hhHhh-hhCCHHHHHHHHHHHhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence 44555 78999999998876521 123599999999999999999876654 5566666654
No 330
>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=68.98 E-value=3.1 Score=29.46 Aligned_cols=24 Identities=25% Similarity=0.332 Sum_probs=19.6
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
Q 011454 443 TWEDISKRIGLSRERVRQVGLVAL 466 (485)
Q Consensus 443 S~eEIAe~LgIS~~tVrqi~~rAL 466 (485)
|..|+|+.+|||..|++.+...++
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~Gl 24 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYEREGL 24 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHTTS
T ss_pred CHHHHHHHHCCCHHHHHHHHHCCC
Confidence 467999999999999999887653
No 331
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=68.92 E-value=11 Score=33.78 Aligned_cols=42 Identities=12% Similarity=0.040 Sum_probs=32.5
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
.|++.|-.||...+.. .++.|..|||+.+++++++|.+.+.+
T Consensus 28 glt~~q~~vL~~l~~~-~~~~t~~eLa~~l~~~~~tvt~~v~~ 69 (144)
T PRK03573 28 ELTQTHWVTLHNIHQL-PPEQSQIQLAKAIGIEQPSLVRTLDQ 69 (144)
T ss_pred CCCHHHHHHHHHHHHc-CCCCCHHHHHHHhCCChhhHHHHHHH
Confidence 5888888877665411 24689999999999999999866554
No 332
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=68.91 E-value=15 Score=32.11 Aligned_cols=39 Identities=26% Similarity=0.198 Sum_probs=35.2
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
..|++.|-..|+-.+ ++|+.+-|..||+|.+||+.|+..
T Consensus 42 ~~ls~~eIk~iRe~~-----~lSQ~vFA~~L~vs~~Tv~~WEqG 80 (104)
T COG2944 42 KTLSPTEIKAIREKL-----GLSQPVFARYLGVSVSTVRKWEQG 80 (104)
T ss_pred CCCCHHHHHHHHHHh-----CCCHHHHHHHHCCCHHHHHHHHcC
Confidence 579999999988887 489999999999999999999975
No 333
>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=68.81 E-value=6.4 Score=30.66 Aligned_cols=23 Identities=22% Similarity=0.283 Sum_probs=21.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
+|..|+|+.+|||+.|++.+..+
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 57899999999999999999876
No 334
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=68.71 E-value=9.3 Score=32.18 Aligned_cols=39 Identities=18% Similarity=0.296 Sum_probs=31.7
Q ss_pred CCHHHHHHHhhHhccCCCCCCH-HHHHHHHCCCHHHHHHHHHH
Q 011454 423 LGEREREIIRLYYGLDKECLTW-EDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 423 Lp~rER~VI~LryGL~~eg~S~-eEIAe~LgIS~~tVrqi~~r 464 (485)
|++.|..|+...+ ..+-.. .+||+.+++++++|.+.+.+
T Consensus 20 lt~~q~~~L~~l~---~~~~~~~~~la~~l~i~~~~vt~~l~~ 59 (126)
T COG1846 20 LTPPQYQVLLALY---EAGGITVKELAERLGLDRSTVTRLLKR 59 (126)
T ss_pred CCHHHHHHHHHHH---HhCCCcHHHHHHHHCCCHHHHHHHHHH
Confidence 8999999998877 333333 99999999999999877665
No 335
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=68.38 E-value=88 Score=31.17 Aligned_cols=35 Identities=37% Similarity=0.483 Sum_probs=29.4
Q ss_pred chhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHh
Q 011454 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (485)
Q Consensus 224 l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~ 258 (485)
+..++..|...+|++|+.+++|..+|++.+++...
T Consensus 120 i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~ 154 (268)
T PRK06288 120 IERAIAMLEARLGRTPSDEEIADELGISLEEYNSL 154 (268)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHH
Confidence 44556778888999999999999999999997644
No 336
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=68.31 E-value=13 Score=30.35 Aligned_cols=26 Identities=23% Similarity=0.376 Sum_probs=22.7
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011454 440 ECLTWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 440 eg~S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
.++|..|||+.+|+++.+|++.+..-
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L 44 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTL 44 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 47999999999999999998777643
No 337
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=68.17 E-value=5.2 Score=37.96 Aligned_cols=25 Identities=24% Similarity=0.405 Sum_probs=21.8
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHH
Q 011454 438 DKECLTWEDISKRIGLSRERVRQVG 462 (485)
Q Consensus 438 ~~eg~S~eEIAe~LgIS~~tVrqi~ 462 (485)
..+++|+.||++.+|+|+++|++-+
T Consensus 38 s~~Pmtl~Ei~E~lg~Sks~vS~~l 62 (177)
T COG1510 38 SRKPLTLDEIAEALGMSKSNVSMGL 62 (177)
T ss_pred cCCCccHHHHHHHHCCCcchHHHHH
Confidence 4589999999999999999998543
No 338
>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=68.16 E-value=56 Score=33.22 Aligned_cols=85 Identities=16% Similarity=0.233 Sum_probs=48.2
Q ss_pred CCCCCHHHHHHHhC--CCHHHHHHHHHHH---Hhhhccc---C------CCCCc---chHHH---HHHHHHHHHHHHhhC
Q 011454 364 GVTPSVDRIAEYLN--MSQKKVRNATEVL---AYIADNR---V------ENNPW---HGVDD---WALKDEVNKLIIVTL 423 (485)
Q Consensus 364 gr~ps~eEIae~L~--is~eev~~~l~~~---~~l~D~~---~------e~~pe---e~~e~---~el~e~L~~~L~~~L 423 (485)
+..+++++||+.++ |+.++|+++++.. .++.-.. . -..+. ..... .+..+.-.++| +..
T Consensus 135 ~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~~g~y~~t~~~l~~~~~~~~~avr~~h~q~l~lA~~al-~~~ 213 (271)
T TIGR02147 135 PFADDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNEDGFYKQTDKAVSTGDEVIPLAVRQYQKQMIDLAKEAL-DAL 213 (271)
T ss_pred CCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECCCCcEEeecceeecCCccchHHHHHHHHHHHHHHHHHH-HhC
Confidence 34556788999998 8999999988765 2221110 0 00111 11122 22333445566 789
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHH
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRI 451 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~L 451 (485)
|+.+|.+=.+-+|+ ..-.+++|.+.+
T Consensus 214 p~~eR~~S~lT~~i--~~~~~~~i~~~i 239 (271)
T TIGR02147 214 PPSERDVSTVTFGI--SEEAYKEIVKKI 239 (271)
T ss_pred CccccccceeeEec--CHHHHHHHHHHH
Confidence 99999987777653 233444544443
No 339
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=67.88 E-value=11 Score=38.04 Aligned_cols=63 Identities=21% Similarity=0.278 Sum_probs=44.8
Q ss_pred HHHHHHHHHHhhCCHHHHHHHhhHhcc-C-CCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHH
Q 011454 411 LKDEVNKLIIVTLGEREREIIRLYYGL-D-KECLTWEDISKRIGLSRERVRQVGLV----ALEKLKHAAR 474 (485)
Q Consensus 411 l~e~L~~~L~~~Lp~rER~VI~LryGL-~-~eg~S~eEIAe~LgIS~~tVrqi~~r----ALkKLRk~L~ 474 (485)
+...|.... +.|++.||.|-....-= + ...+|..|||+..|||+.||-+.-++ +..-+|..+.
T Consensus 5 l~~~I~~~~-~~Lt~~er~iA~yil~~~~~~~~~si~elA~~a~VS~aTv~Rf~~kLGf~Gf~efk~~l~ 73 (281)
T COG1737 5 LLERIRERY-DSLTKSERKIADYILANPDEVALLSIAELAERAGVSPATVVRFARKLGFEGFSEFKLALA 73 (281)
T ss_pred HHHHHHHHH-hcCCHHHHHHHHHHHhCHHHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence 456677777 89999999998775411 0 12489999999999999999766554 4444444443
No 340
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=67.87 E-value=4.1 Score=31.66 Aligned_cols=25 Identities=24% Similarity=0.323 Sum_probs=21.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVAL 466 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rAL 466 (485)
+|..|+|+.+|||+.+++.+...++
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~~gl 25 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYERIGL 25 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999977554
No 341
>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=67.66 E-value=4.2 Score=29.79 Aligned_cols=32 Identities=28% Similarity=0.238 Sum_probs=23.5
Q ss_pred HHHHHHCCCHHHHHHHHHHH-------HHHHHHHHHhhh
Q 011454 446 DISKRIGLSRERVRQVGLVA-------LEKLKHAARKKK 477 (485)
Q Consensus 446 EIAe~LgIS~~tVrqi~~rA-------LkKLRk~L~~~~ 477 (485)
+||+.+|||+.||+++++.- ..++.+.+...+
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~~vs~~~~~~i~~~~~~l~ 40 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEELG 40 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhC
Confidence 79999999999999988753 444555554433
No 342
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=66.43 E-value=14 Score=39.40 Aligned_cols=50 Identities=18% Similarity=0.128 Sum_probs=37.9
Q ss_pred hCCHHHHHHHhhHhcc-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL-~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
.+++.||..+.+.+=| ..+..|+.++|+.|+||++|+.+-+++..+.|.+
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 4677787765554323 4577999999999999999999877776666655
No 343
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=66.42 E-value=12 Score=41.86 Aligned_cols=46 Identities=22% Similarity=0.252 Sum_probs=37.7
Q ss_pred CCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 423 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 423 Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
|++|+..|+.+-- .++.|..++|+.+|||..||++-+...-..|++
T Consensus 2 l~~R~~~iL~~L~---~~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~ 47 (584)
T PRK09863 2 LNERELKIVDLLE---QQDRSGGELAQQLGVSRRTIVRDIAYINFTLNG 47 (584)
T ss_pred hHHHHHHHHHHHH---cCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 5788899887653 367999999999999999999988866566665
No 344
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=66.30 E-value=8.7 Score=28.43 Aligned_cols=47 Identities=15% Similarity=0.158 Sum_probs=36.6
Q ss_pred hCCHHHHHHHhhHhccCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDK--ECLTWEDISKRIGLSRERVRQVGLVALEK 468 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~--eg~S~eEIAe~LgIS~~tVrqi~~rALkK 468 (485)
.+++.+..+|...|..+. ......+||+.+|++...|..+......+
T Consensus 6 ~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~ 54 (56)
T smart00389 6 SFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAK 54 (56)
T ss_pred cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhc
Confidence 478888889988884431 23457899999999999999998876654
No 345
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=66.12 E-value=12 Score=33.21 Aligned_cols=41 Identities=15% Similarity=0.146 Sum_probs=29.8
Q ss_pred hhCCHH-HHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 421 VTLGER-EREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 421 ~~Lp~r-ER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
..|.+. -+.||.+-. +..+++..|||+.+|+|+.+|++++.
T Consensus 11 kaLadptRl~IL~~L~--~~~~~~v~ela~~l~lsqstvS~HL~ 52 (117)
T PRK10141 11 KILSDETRLGIVLLLR--ESGELCVCDLCTALDQSQPKISRHLA 52 (117)
T ss_pred HHhCCHHHHHHHHHHH--HcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 445444 445666543 12579999999999999999998865
No 346
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=66.01 E-value=6.2 Score=37.41 Aligned_cols=27 Identities=22% Similarity=0.272 Sum_probs=23.8
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
..++|..|||+.+|.++.||+++++-.
T Consensus 59 kag~Ti~EIAeelG~TeqTir~hlkge 85 (182)
T COG1318 59 KAGMTISEIAEELGRTEQTVRNHLKGE 85 (182)
T ss_pred HccCcHHHHHHHhCCCHHHHHHHHhcc
Confidence 357999999999999999999988653
No 347
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=65.73 E-value=10 Score=31.22 Aligned_cols=33 Identities=15% Similarity=0.188 Sum_probs=26.0
Q ss_pred HHHhhHhccCCCCCCHHHHHHHHC------CCHHHHHHHHHH
Q 011454 429 EIIRLYYGLDKECLTWEDISKRIG------LSRERVRQVGLV 464 (485)
Q Consensus 429 ~VI~LryGL~~eg~S~eEIAe~Lg------IS~~tVrqi~~r 464 (485)
.+...|- .-|+|+.++|+.+| +|+.+|++++.-
T Consensus 15 ~lk~~R~---~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~ 53 (75)
T smart00352 15 TFKQRRI---KLGFTQADVGLALGALYGPDFSQTTICRFEAL 53 (75)
T ss_pred HHHHHHH---HcCCCHHHHHHHhcccccCcCCHHHHHHHHhc
Confidence 3344554 46799999999999 599999998763
No 348
>PRK09726 antitoxin HipB; Provisional
Probab=65.38 E-value=9 Score=31.79 Aligned_cols=38 Identities=13% Similarity=0.226 Sum_probs=29.3
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH----HHHHHHHHHhhh
Q 011454 440 ECLTWEDISKRIGLSRERVRQVGLVA----LEKLKHAARKKK 477 (485)
Q Consensus 440 eg~S~eEIAe~LgIS~~tVrqi~~rA----LkKLRk~L~~~~ 477 (485)
.++|+.++|+.+|||+.+|+++++.- +.+|.+.+...+
T Consensus 24 ~gltq~elA~~~gvs~~tis~~e~g~~~ps~~~l~~ia~~lg 65 (88)
T PRK09726 24 NGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLE 65 (88)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHcC
Confidence 57999999999999999999998742 355555554433
No 349
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=65.20 E-value=10 Score=26.74 Aligned_cols=27 Identities=26% Similarity=0.298 Sum_probs=19.8
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
.++.++.+||+.+|+|+...++..++.
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 467999999999999999888777654
No 350
>PRK10161 transcriptional regulator PhoB; Provisional
Probab=64.81 E-value=6.9 Score=36.77 Aligned_cols=50 Identities=10% Similarity=0.141 Sum_probs=38.9
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHH-----HHCCCHHHHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISK-----RIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe-----~LgIS~~tVrqi~~rALkKLRk 471 (485)
.|+++|.+|+.+..--.+.+.|.++|.. .++++..||+.++.+.++||..
T Consensus 154 ~Lt~~E~~ll~~l~~~~~~~~s~~~l~~~~~~~~~~~~~~tv~~~i~rlr~Kl~~ 208 (229)
T PRK10161 154 EMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEP 208 (229)
T ss_pred EcCHHHHHHHHHHHhCCCceEcHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhcc
Confidence 5999999999876621135678777644 5678999999999999999963
No 351
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=64.69 E-value=1.9e+02 Score=31.69 Aligned_cols=24 Identities=17% Similarity=0.333 Sum_probs=21.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 440 ECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 440 eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
.++++++||+.+|+..+||++...
T Consensus 329 ~PL~LrdvA~~i~~HESTISRai~ 352 (444)
T COG1508 329 KPLVLRDVADEIGMHESTISRAIT 352 (444)
T ss_pred CcccHHHHHHHhCccHHHHHHHHh
Confidence 468999999999999999998765
No 352
>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional
Probab=64.48 E-value=4.7 Score=37.75 Aligned_cols=45 Identities=20% Similarity=0.082 Sum_probs=38.0
Q ss_pred hCCHHHHHHHhhHhccCCCCCC---------HHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLT---------WEDISKRIGLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S---------~eEIAe~LgIS~~tVrqi~~rALkKLR 470 (485)
.|+++|.+|+.+.. .+.+ ...||..++++..||+.++.+.++||.
T Consensus 156 ~Lt~~E~~~l~~l~----~~~~~v~sr~~l~~~~~~~~~~~~~~tv~~~i~~lr~Kl~ 209 (232)
T PRK10955 156 ELTGTEFTLLYLLA----QHLGQVVSREHLSQEVLGKRLTPFDRAIDMHISNLRRKLP 209 (232)
T ss_pred cCCHHHHHHHHHHH----hCCCceEcHHHHHHHHhCCCCCCCCcCHHHHHHHHHHhcc
Confidence 69999999998876 4443 477888889999999999999999986
No 353
>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=64.45 E-value=14 Score=30.69 Aligned_cols=35 Identities=20% Similarity=0.153 Sum_probs=25.0
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 011454 440 ECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 474 (485)
Q Consensus 440 eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~ 474 (485)
...|..+.|+.+|||.+||.+-+..=|.++...|.
T Consensus 18 ~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in~~La 52 (82)
T PF12116_consen 18 TKATVRQAAKVFGVSKSTVHKDVTERLPKINPELA 52 (82)
T ss_dssp H---HHHHHHHHTS-HHHHHHHHTTHHHHH-HHHH
T ss_pred cccHHHHHHHHHCCcHHHHHHHHHHHHHhcCHHHH
Confidence 56899999999999999999888777766665553
No 354
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=64.35 E-value=8.4 Score=28.02 Aligned_cols=24 Identities=25% Similarity=0.364 Sum_probs=21.6
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVG 462 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~ 462 (485)
+.+.|..+||++.|+|++++.+..
T Consensus 14 ~~~~s~~~Ia~~~gvs~~~~y~~f 37 (47)
T PF00440_consen 14 YEAVSIRDIARRAGVSKGSFYRYF 37 (47)
T ss_dssp TTTSSHHHHHHHHTSCHHHHHHHC
T ss_pred HHhCCHHHHHHHHccchhhHHHHc
Confidence 689999999999999999998654
No 355
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=64.16 E-value=6.8 Score=29.89 Aligned_cols=26 Identities=19% Similarity=0.348 Sum_probs=19.8
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011454 440 ECLTWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 440 eg~S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
.++|..++|+.+||++.+|+++.+.-
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 57899999999999999999998854
No 356
>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=64.07 E-value=12 Score=35.44 Aligned_cols=43 Identities=28% Similarity=0.301 Sum_probs=31.7
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
..|++-|+.....+. +...++|.++||+.+|+|+.+|++.+.-
T Consensus 101 ~~lt~~e~a~~~~~l-~~~~g~s~~~iA~~lg~s~~~V~r~l~l 143 (187)
T TIGR00180 101 EDLSPIEEAQAYKRL-LEKFSMTQEDLAKKIGKSRAHITNLLRL 143 (187)
T ss_pred cCCCHHHHHHHHHHH-HHHhCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 467777766544432 1124689999999999999999988764
No 357
>PHA00738 putative HTH transcription regulator
Probab=63.91 E-value=13 Score=32.63 Aligned_cols=38 Identities=24% Similarity=0.057 Sum_probs=28.8
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
.|.-+.||.+-.. .++++..||++.+++|+.+|+++++
T Consensus 11 dptRr~IL~lL~~--~e~~~V~eLae~l~lSQptVS~HLK 48 (108)
T PHA00738 11 KILRRKILELIAE--NYILSASLISHTLLLSYTTVLRHLK 48 (108)
T ss_pred CHHHHHHHHHHHH--cCCccHHHHHHhhCCCHHHHHHHHH
Confidence 4455666665431 3469999999999999999998875
No 358
>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=63.56 E-value=97 Score=31.49 Aligned_cols=33 Identities=21% Similarity=0.454 Sum_probs=27.3
Q ss_pred hHHHHHHhhhCCCCchHHHHHHhhcChhHHHHh
Q 011454 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (485)
Q Consensus 226 ~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~ 258 (485)
..+.++...+|++|+.+++|..+|++.+++...
T Consensus 165 k~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~ 197 (298)
T TIGR02997 165 KVQRELSQKLGRTPSEAEIAEALELEPEQVREL 197 (298)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 345566678999999999999999999998644
No 359
>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=63.39 E-value=9.2 Score=29.90 Aligned_cols=23 Identities=13% Similarity=0.114 Sum_probs=20.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
++..|+|+.+|||+.|++.+...
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 47899999999999999998775
No 360
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=63.19 E-value=13 Score=36.94 Aligned_cols=42 Identities=21% Similarity=0.324 Sum_probs=32.2
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALE 467 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALk 467 (485)
.+|++.|+.+... ....+..|||+.||||+.|||+-+..--.
T Consensus 3 ~~R~~~Il~~l~~--~~~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 3 AARQQAIVDLLLN--HTSLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred hHHHHHHHHHHHH--cCCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3566677666431 35689999999999999999999886433
No 361
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=62.77 E-value=29 Score=34.02 Aligned_cols=61 Identities=23% Similarity=0.378 Sum_probs=41.1
Q ss_pred hhhhHHHHHHhhccccCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhh
Q 011454 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (485)
Q Consensus 189 ~~~~~~~yl~~i~~~~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l 259 (485)
+.+.+-.|++.....| ........++ ..+...+...+|++|+.+++|..+|++.+++.+.+
T Consensus 78 Ir~~il~~lr~~~~~~----r~vr~~~~~i------~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~ 138 (231)
T PRK12427 78 IRGAILDELRELDWRP----RRLRQKTHKT------NDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYL 138 (231)
T ss_pred HHHHHHHHHHhcCCCC----HHHHHHHHHH------HHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 4455556666644322 2333344443 34556788889999999999999999999986543
No 362
>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=62.77 E-value=20 Score=27.69 Aligned_cols=27 Identities=37% Similarity=0.660 Sum_probs=19.7
Q ss_pred CCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011454 440 ECL-TWEDISKRIGLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 440 eg~-S~eEIAe~LgIS~~tVrqi~~rALkKLR 470 (485)
+.+ |..+||+.+|||+.+|+. |+..|.
T Consensus 22 ~~lps~~~la~~~~vsr~tvr~----al~~L~ 49 (64)
T PF00392_consen 22 DRLPSERELAERYGVSRTTVRE----ALRRLE 49 (64)
T ss_dssp SBE--HHHHHHHHTS-HHHHHH----HHHHHH
T ss_pred CEeCCHHHHHHHhccCCcHHHH----HHHHHH
Confidence 456 999999999999999974 555443
No 363
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=62.65 E-value=9.6 Score=35.84 Aligned_cols=27 Identities=37% Similarity=0.540 Sum_probs=21.7
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 441 CLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 441 g~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
.+|.++||..+|+++++|++. +++|++
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~----l~~l~~ 194 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRV----LKMLED 194 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHH----HHHHHH
Confidence 479999999999999999754 555554
No 364
>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=62.56 E-value=17 Score=29.79 Aligned_cols=32 Identities=22% Similarity=0.212 Sum_probs=22.9
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLR 470 (485)
.+..|..++|+.++||++|+.+.+++..+.|+
T Consensus 28 ~~~~s~~~la~~~~iS~sti~~~i~~l~~~l~ 59 (87)
T PF05043_consen 28 NEYVSIEDLAEELFISRSTIYRDIKKLNKYLK 59 (87)
T ss_dssp -SEEEHHHHHHHHT--HHHHHHHHHHHHHHHH
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 47799999999999999999866655544444
No 365
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=62.37 E-value=9.2 Score=36.82 Aligned_cols=27 Identities=26% Similarity=0.532 Sum_probs=21.9
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 441 CLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 441 g~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
.+|+++||..+|+|+.+|++. +++|++
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~----l~~l~~ 210 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRL----LGRFQK 210 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHH----HHHHHH
Confidence 579999999999999999755 445554
No 366
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=62.08 E-value=8.3 Score=36.07 Aligned_cols=27 Identities=22% Similarity=0.442 Sum_probs=21.9
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 441 CLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 441 g~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
.+|.++||..+|+++++|++ ++++|++
T Consensus 149 ~~t~~~iA~~lG~tretvsR----~l~~l~~ 175 (202)
T PRK13918 149 YATHDELAAAVGSVRETVTK----VIGELSR 175 (202)
T ss_pred cCCHHHHHHHhCccHHHHHH----HHHHHHH
Confidence 47999999999999999974 5555554
No 367
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=62.07 E-value=9.8 Score=26.34 Aligned_cols=25 Identities=24% Similarity=0.458 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 440 ECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 440 eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
.++|..++|+.+|++..+|++++..
T Consensus 9 ~~~s~~~la~~~~i~~~~i~~~~~~ 33 (56)
T smart00530 9 KGLTQEELAEKLGVSRSTLSRIENG 33 (56)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 5689999999999999999988764
No 368
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=61.58 E-value=16 Score=41.35 Aligned_cols=66 Identities=17% Similarity=0.133 Sum_probs=49.5
Q ss_pred HHHHHHHHHHHHhhCCHHHHHHHhhHhcc--CCCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHHh
Q 011454 409 WALKDEVNKLIIVTLGEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGLV----ALEKLKHAARK 475 (485)
Q Consensus 409 ~el~e~L~~~L~~~Lp~rER~VI~LryGL--~~eg~S~eEIAe~LgIS~~tVrqi~~r----ALkKLRk~L~~ 475 (485)
..+.+.|.... +.|++.||.|.....-- ....+|..|||+..++|..||.+.-++ ...-||..+..
T Consensus 341 ~~l~~~I~~~~-~~Lt~~E~~IA~yIl~n~~~v~~~si~eLA~~~~vS~aTV~Rf~kkLGf~Gf~efK~~L~~ 412 (638)
T PRK14101 341 SAVFERIRQMR-DALTPAERRVADLALNHPRSIINDPIVDIARKADVSQPTVIRFCRSLGCQGLSDFKLKLAT 412 (638)
T ss_pred HHHHHHHHHHH-hhcCHHHHHHHHHHHhCHHHHHhccHHHHHHHhCCCHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence 34566788888 89999999999776511 123589999999999999999776654 56666666653
No 369
>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=61.50 E-value=28 Score=34.89 Aligned_cols=54 Identities=30% Similarity=0.354 Sum_probs=39.8
Q ss_pred HHHHHHHHhhCCHHHHHHHhhHhcc-CC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 413 DEVNKLIIVTLGEREREIIRLYYGL-DK--ECLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 413 e~L~~~L~~~Lp~rER~VI~LryGL-~~--eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
..++-+| ..|+--|.+.+...+-. +. .-.+..+||+++|||+..|+ +|+++|..
T Consensus 168 a~Vq~Ai-~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ir----eAlrkLE~ 224 (251)
T TIGR02787 168 AAVQMAI-NTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIV----NALRKLES 224 (251)
T ss_pred HHHHHHH-HhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 3455567 89999988887776644 33 34899999999999999887 45555543
No 370
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=61.42 E-value=15 Score=33.07 Aligned_cols=25 Identities=12% Similarity=0.121 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 440 ECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 440 eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
...+..+||+.||||+.+|++.+.+
T Consensus 21 ~~~~~~ela~~l~vs~~svs~~l~~ 45 (142)
T PRK03902 21 GYARVSDIAEALSVHPSSVTKMVQK 45 (142)
T ss_pred CCcCHHHHHHHhCCChhHHHHHHHH
Confidence 4579999999999999999876643
No 371
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=61.37 E-value=11 Score=33.72 Aligned_cols=26 Identities=15% Similarity=0.101 Sum_probs=23.4
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
..++|+.++|+.+|||+++|+++++.
T Consensus 16 ~~gltq~~lA~~~gvs~~~is~~E~g 41 (135)
T PRK09706 16 QLKLSQRSLAKAVKVSHVSISQWERD 41 (135)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 35799999999999999999998864
No 372
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=61.13 E-value=71 Score=33.00 Aligned_cols=35 Identities=17% Similarity=0.411 Sum_probs=28.3
Q ss_pred chhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHh
Q 011454 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (485)
Q Consensus 224 l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~ 258 (485)
+..++..+...+|++|+.+++|..+|++..++...
T Consensus 170 l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~ 204 (317)
T PRK07405 170 IKKAQRQLSQQLGRAATIGELAEELELTPKQVREY 204 (317)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 44556667778999999999999999998887533
No 373
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=61.13 E-value=32 Score=34.44 Aligned_cols=64 Identities=20% Similarity=0.261 Sum_probs=42.9
Q ss_pred HhhhhHHHHHHhhccccCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHh
Q 011454 188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (485)
Q Consensus 188 ~~~~~~~~yl~~i~~~~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~ 258 (485)
++...+..|+++....=.+ |....++..+++ .++..+...+|++|+.+++|..+|++.+++...
T Consensus 100 ~Irg~I~~~lr~~~~~ir~-Pr~~~~~~~~i~------~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~ 163 (264)
T PRK07122 100 TIMGEVRRHFRDNSWSVKV-PRRLKELHLRLG------RATAELSQRLGRAPTASELAAELGMDREEVVEG 163 (264)
T ss_pred HHHHHHHHHHHHcCCcccc-CHHHHHHHHHHH------HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 5666677777764331111 233334444444 345677888999999999999999999998654
No 374
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=61.10 E-value=93 Score=30.74 Aligned_cols=93 Identities=15% Similarity=0.170 Sum_probs=53.0
Q ss_pred HcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhccCCCC
Q 011454 362 EKGVTPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKEC 441 (485)
Q Consensus 362 ~~gr~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg 441 (485)
+.|.-.+..+++-.|++|..+|...+....--.... -|-..... .+- ..++ .+.++.-.| .+|
T Consensus 101 ~QgglLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~v---vPtrG~i~-----DiG----p~~t--HK~~ii~~~---l~g 163 (220)
T PF07900_consen 101 DQGGLLTQEDLAMLLGISPRTISKDIKEYQKEHGVV---VPTRGTIH-----DIG----PGVT--HKKIIIRLY---LKG 163 (220)
T ss_pred HcCCcccHHHHHHHHCCCHHHHHHHHHHHHHHcCce---eccCCccc-----ccC----Ccch--HHHHHHHHH---HcC
Confidence 467778999999999999999987655431110000 01100000 010 1112 333333334 478
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVALEKLKHA 472 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~ 472 (485)
++..|||.++.-|+++|.+.++ +.++..-+
T Consensus 164 ~~~~eiar~t~HS~~av~rYi~-~F~rV~~l 193 (220)
T PF07900_consen 164 KPTPEIARRTNHSPEAVDRYIK-DFKRVLML 193 (220)
T ss_pred CCHHHHHHHhccCHHHHHHHHH-hhHHhHHH
Confidence 8888888888888888877765 34444443
No 375
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=61.06 E-value=2e+02 Score=29.55 Aligned_cols=31 Identities=26% Similarity=0.206 Sum_probs=25.4
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGLVALEKL 469 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~rALkKL 469 (485)
+.+.|++|||+..||+..||++..+.-.+.|
T Consensus 274 g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l 304 (310)
T PRK00423 274 GERRTQREVAEVAGVTEVTVRNRYKELAEKL 304 (310)
T ss_pred CCCCCHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 4678999999999999999997766655543
No 376
>TIGR00647 MG103 conserved hypothetical protein.
Probab=60.95 E-value=18 Score=37.05 Aligned_cols=43 Identities=19% Similarity=0.095 Sum_probs=37.0
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHC------CCHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIG------LSRERVRQVGLVA 465 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~Lg------IS~~tVrqi~~rA 465 (485)
+.||+.-+++..+|. ...+.|++|+|+.|. ||++.|..++.+.
T Consensus 226 ~~Lp~~L~~~a~lRl--~~Pd~SL~ELgell~~~~~~~isKSgvnhRlrKl 274 (279)
T TIGR00647 226 EKLPLNFQRICLLKI--DHPDWSLEQIAEFFASKYKVKISRSGIQHRLRKL 274 (279)
T ss_pred ccCCHHHHHHHHHHH--hCcccCHHHHHHHhccCCCCCcCHHHHHHHHHHH
Confidence 689999999999987 256899999999994 9999998776654
No 377
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=60.60 E-value=10 Score=39.10 Aligned_cols=43 Identities=16% Similarity=0.070 Sum_probs=36.4
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 466 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rAL 466 (485)
..|+..||.-|.-.. ..++|..|||+.||..++||++-++|.-
T Consensus 6 ~hLT~~eR~~I~~l~---~~~~S~reIA~~LgRh~sTIsRElkRn~ 48 (318)
T COG2826 6 KHLTLFERYEIERLL---KAKMSIREIAKQLNRHHSTISRELKRNR 48 (318)
T ss_pred hhCCHHHHHHHHHHH---HcCCCHHHHHHHhCCCcchhhHHHhcCC
Confidence 478888998887665 5799999999999999999998877643
No 378
>PRK01905 DNA-binding protein Fis; Provisional
Probab=60.57 E-value=33 Score=27.93 Aligned_cols=36 Identities=11% Similarity=0.165 Sum_probs=25.3
Q ss_pred HHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 427 EREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 427 ER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
++.+|...+- ..+-+..+.|+.||||+.+++..+++
T Consensus 38 E~~~i~~aL~--~~~gn~s~aAr~LGIsrstL~rklkk 73 (77)
T PRK01905 38 EKPLLEVVME--QAGGNQSLAAEYLGINRNTLRKKLQQ 73 (77)
T ss_pred HHHHHHHHHH--HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 5555544431 23567999999999999998766554
No 379
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=59.70 E-value=12 Score=37.72 Aligned_cols=43 Identities=26% Similarity=0.356 Sum_probs=34.8
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
..|++.+++||.+.-+-| ...++.||.+.+|+|+.||++++++
T Consensus 191 ~~L~~~e~~il~~i~~~G-Gri~Q~eL~r~lglsktTvsR~L~~ 233 (258)
T COG2512 191 YDLNEDEKEILDLIRERG-GRITQAELRRALGLSKTTVSRILRR 233 (258)
T ss_pred CCCCHHHHHHHHHHHHhC-CEEeHHHHHHhhCCChHHHHHHHHH
Confidence 479999999999876321 3389999999999999999866554
No 380
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=59.16 E-value=28 Score=28.88 Aligned_cols=29 Identities=21% Similarity=0.446 Sum_probs=23.2
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
+.-.|-++||+.||+|+.+|- +.+++||+
T Consensus 17 ~~~~SGe~La~~LgiSRtaVw----K~Iq~Lr~ 45 (79)
T COG1654 17 GNFVSGEKLAEELGISRTAVW----KHIQQLRE 45 (79)
T ss_pred CCcccHHHHHHHHCccHHHHH----HHHHHHHH
Confidence 456899999999999998886 45556664
No 381
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=59.15 E-value=9.8 Score=30.07 Aligned_cols=25 Identities=24% Similarity=0.134 Sum_probs=20.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 440 ECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 440 eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
.+++..|||+.+|+|..+|+.++..
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 6799999999999999999987653
No 382
>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=59.06 E-value=13 Score=28.34 Aligned_cols=26 Identities=23% Similarity=0.480 Sum_probs=20.3
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
..++|+.++|+.+|+++++++++++-
T Consensus 10 ~~~lt~~~~a~~~~i~~~~i~~~e~g 35 (64)
T PF12844_consen 10 EKGLTQKDLAEKLGISRSTISKIENG 35 (64)
T ss_dssp HCT--HHHHHHHHTS-HHHHHHHHTT
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 35799999999999999999999854
No 383
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=58.92 E-value=14 Score=32.19 Aligned_cols=35 Identities=23% Similarity=0.388 Sum_probs=27.2
Q ss_pred HHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 429 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 429 ~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
+||.-.| +..-|+|..+.|+.|||++.+|..+++-
T Consensus 12 EiL~eef-lep~glt~~~lA~~lgV~r~~is~ling 46 (104)
T COG3093 12 EILREEF-LEPLGLTQTELAEALGVTRNTISELING 46 (104)
T ss_pred HHHHHHH-hccccCCHHHHHHHhCCCHHHHHHHHcC
Confidence 4666666 1112699999999999999999988763
No 384
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=58.91 E-value=12 Score=36.36 Aligned_cols=27 Identities=33% Similarity=0.533 Sum_probs=22.0
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 441 CLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 441 g~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
.+|.++||..+|+++++|++ ++++|++
T Consensus 179 ~lt~~~IA~~lGisretlsR----~L~~L~~ 205 (230)
T PRK09391 179 PMSRRDIADYLGLTIETVSR----ALSQLQD 205 (230)
T ss_pred cCCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence 47999999999999999974 5555654
No 385
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=58.80 E-value=20 Score=34.34 Aligned_cols=40 Identities=15% Similarity=0.096 Sum_probs=33.4
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
.|++.|..||...+. ..+.|+.+||+.++++++||.+.+.
T Consensus 42 gLt~~q~~iL~~L~~--~~~itq~eLa~~l~l~~sTvtr~l~ 81 (185)
T PRK13777 42 DLNINEHHILWIAYH--LKGASISEIAKFGVMHVSTAFNFSK 81 (185)
T ss_pred CCCHHHHHHHHHHHh--CCCcCHHHHHHHHCCCHhhHHHHHH
Confidence 689999998877652 4689999999999999999876554
No 386
>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=58.52 E-value=17 Score=25.28 Aligned_cols=25 Identities=24% Similarity=0.476 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 440 ECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 440 eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
.++|..++|+.+|+++.+|.+++.-
T Consensus 11 ~~~s~~~~a~~~~~~~~~v~~~~~g 35 (58)
T cd00093 11 KGLTQEELAEKLGVSRSTISRIENG 35 (58)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 5789999999999999999987764
No 387
>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=58.15 E-value=17 Score=29.69 Aligned_cols=24 Identities=21% Similarity=0.378 Sum_probs=19.1
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 441 CLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 441 g~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
..|.+|||+.+|+|+..|++++.+
T Consensus 25 ~~s~~eiA~~~~i~~~~l~kil~~ 48 (83)
T PF02082_consen 25 PVSSKEIAERLGISPSYLRKILQK 48 (83)
T ss_dssp -BEHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 389999999999999999866543
No 388
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=58.00 E-value=39 Score=29.21 Aligned_cols=43 Identities=28% Similarity=0.432 Sum_probs=33.4
Q ss_pred hhCCHHHHHHH----hhHhccC--CCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 421 VTLGEREREII----RLYYGLD--KECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 421 ~~Lp~rER~VI----~LryGL~--~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
..|+.+|..|+ +.-||.+ .+-.|..+||+..|+++.+|+..++
T Consensus 28 ~dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~ 76 (100)
T PF04492_consen 28 ADLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALN 76 (100)
T ss_pred ccccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHH
Confidence 67899988765 5567775 3458999999999999998865443
No 389
>PF10654 DUF2481: Protein of unknown function (DUF2481) ; InterPro: IPR018916 This entry is represented by Bacteriophage A500, Gp59. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=57.82 E-value=31 Score=30.67 Aligned_cols=41 Identities=20% Similarity=0.103 Sum_probs=31.9
Q ss_pred HHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 011454 429 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 473 (485)
Q Consensus 429 ~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L 473 (485)
+.+.+|. .|+|..+||+.++||+++|-+...+-.+--.+.+
T Consensus 72 Efi~LR~----AGlt~~aIAd~F~iS~s~~~nft~~n~~eYyr~F 112 (126)
T PF10654_consen 72 EFIELRH----AGLTCYAIADYFKISKSTVFNFTQNNKKEYYRIF 112 (126)
T ss_pred HHHHHHh----cCCChHHHHHHHhHHHHHHHHHHHHhHHHHHHHh
Confidence 3455564 8999999999999999999998866655555444
No 390
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=57.82 E-value=25 Score=25.73 Aligned_cols=23 Identities=17% Similarity=0.270 Sum_probs=17.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
+|+.+.|+.+||++.|++.+++.
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 99999999999999999866543
No 391
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=57.64 E-value=14 Score=30.30 Aligned_cols=20 Identities=15% Similarity=0.237 Sum_probs=19.0
Q ss_pred CHHHHHHHHCCCHHHHHHHH
Q 011454 443 TWEDISKRIGLSRERVRQVG 462 (485)
Q Consensus 443 S~eEIAe~LgIS~~tVrqi~ 462 (485)
+...+|+.||||+++|+|+-
T Consensus 12 s~~kvA~aLGIs~~AVsQWG 31 (75)
T PRK09744 12 SKTKLANAAGVRLASVAAWG 31 (75)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 88999999999999999995
No 392
>PRK03837 transcriptional regulator NanR; Provisional
Probab=57.05 E-value=24 Score=34.22 Aligned_cols=39 Identities=31% Similarity=0.366 Sum_probs=27.9
Q ss_pred HHHHHhhHhccCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011454 427 EREIIRLYYGLDKECL-TWEDISKRIGLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 427 ER~VI~LryGL~~eg~-S~eEIAe~LgIS~~tVrqi~~rALkKLR 470 (485)
...|+.-.|.- ++.+ +..++|+.+|||+.+|| .|+..|.
T Consensus 23 ~~~I~~g~l~p-G~~Lp~E~~Lae~~gVSRt~VR----EAL~~L~ 62 (241)
T PRK03837 23 EQMIRSGEFGP-GDQLPSERELMAFFGVGRPAVR----EALQALK 62 (241)
T ss_pred HHHHHhCCCCC-CCCCCCHHHHHHHhCCCHHHHH----HHHHHHH
Confidence 34555555521 3557 89999999999999997 5666665
No 393
>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=56.77 E-value=17 Score=30.86 Aligned_cols=42 Identities=17% Similarity=0.306 Sum_probs=30.1
Q ss_pred hCCHHHHHHHhhHhc-c-CCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYG-L-DKECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 422 ~Lp~rER~VI~LryG-L-~~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
.|++.+++|+...-. - ..+|.+..+|++.|+++...|+..+.
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 577888888877554 2 25789999999999999998876554
No 394
>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=56.63 E-value=16 Score=33.63 Aligned_cols=49 Identities=18% Similarity=0.108 Sum_probs=39.4
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRI-----GLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~L-----gIS~~tVrqi~~rALkKLR 470 (485)
.|+++|.+|+.+...-.+.-+|.++|++.+ ..+..+|..++.+.++||.
T Consensus 147 ~Lt~~E~~il~~l~~~~~~~~sr~~i~~~~~~~~~~~~~~~~~~~i~~lr~kl~ 200 (218)
T TIGR01387 147 TLTRKEFQLLWLLMRRTGEVLPRTVIASLVWGMNFDSDTNVVDVAIRRLRAKVD 200 (218)
T ss_pred eCCHHHHHHHHHHHhCCCeeEcHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhhc
Confidence 599999999998762112448999999999 4567888888888888885
No 395
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=55.63 E-value=2.1e+02 Score=30.52 Aligned_cols=59 Identities=15% Similarity=0.259 Sum_probs=37.2
Q ss_pred CcchHHHHHHHHHHHHHHHh-----hCCHHHHHH----------HhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 402 PWHGVDDWALKDEVNKLIIV-----TLGEREREI----------IRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 402 pee~~e~~el~e~L~~~L~~-----~Lp~rER~V----------I~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
+...+-.+-++..|.++|.+ +||-.-... +...+ +..-|.+|||+.+|++...|..+..
T Consensus 188 ~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~~~~~~i~~a~~~l~~~l---gr~Pt~~EIA~~lg~~~e~v~~~~~ 261 (373)
T PRK07406 188 KFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEF---GRKPTEEEIAESMEMTIEKLRFIAK 261 (373)
T ss_pred CHHHHHHHHHHHHHHHHHHhcCCceeCCHHHHHHHHHHHHHHHHHHHHh---CCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 44455556677777777632 355443321 22223 3556899999999999999977643
No 396
>PRK10643 DNA-binding transcriptional regulator BasR; Provisional
Probab=55.23 E-value=12 Score=34.53 Aligned_cols=47 Identities=13% Similarity=-0.043 Sum_probs=35.7
Q ss_pred hCCHHHHHHHhhHhccCCCCCCH-HHHHHH------HCCCHHHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTW-EDISKR------IGLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~-eEIAe~------LgIS~~tVrqi~~rALkKLR 470 (485)
.|+++|.+|+.+..- ..|++. +||+.. ++++..||+.++++.++||.
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 599999999987541 245553 555543 68999999999999999985
No 397
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=55.09 E-value=17 Score=28.49 Aligned_cols=19 Identities=26% Similarity=0.358 Sum_probs=17.5
Q ss_pred CHHHHHHHHCCCHHHHHHH
Q 011454 443 TWEDISKRIGLSRERVRQV 461 (485)
Q Consensus 443 S~eEIAe~LgIS~~tVrqi 461 (485)
+...+|+.||||+.+|+++
T Consensus 11 ~~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 11 GQSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp SHHHHHHHHTS-HHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHh
Confidence 8899999999999999999
No 398
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=54.86 E-value=22 Score=35.42 Aligned_cols=38 Identities=21% Similarity=0.274 Sum_probs=28.7
Q ss_pred HHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 425 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 425 ~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
+|++.|+.+.- .....+..|+|+.||||+.||++.+..
T Consensus 5 ~R~~~Il~~l~--~~~~~~~~ela~~l~vS~~TirRdL~~ 42 (251)
T PRK13509 5 QRHQILLELLA--QLGFVTVEKVIERLGISPATARRDINK 42 (251)
T ss_pred HHHHHHHHHHH--HcCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 45555555433 124589999999999999999999876
No 399
>PF14502 HTH_41: Helix-turn-helix domain
Probab=54.77 E-value=19 Score=27.06 Aligned_cols=27 Identities=30% Similarity=0.373 Sum_probs=22.9
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 441 CLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 441 g~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
=.|..|.++.+++|++|| +.||+.|..
T Consensus 6 i~tI~e~~~~~~vs~Gti----Q~Alk~Le~ 32 (48)
T PF14502_consen 6 IPTISEYSEKFGVSRGTI----QNALKFLEE 32 (48)
T ss_pred cCCHHHHHHHhCcchhHH----HHHHHHHHH
Confidence 368999999999999999 578877765
No 400
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=54.55 E-value=1.2e+02 Score=29.90 Aligned_cols=35 Identities=17% Similarity=0.246 Sum_probs=28.3
Q ss_pred hHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhh
Q 011454 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (485)
Q Consensus 226 ~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~ 260 (485)
++..++...+|++|+.+++|..+|++.+++...+.
T Consensus 113 ~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~ 147 (251)
T PRK07670 113 AAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMN 147 (251)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 34455677889999999999999999999875543
No 401
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=54.43 E-value=17 Score=36.31 Aligned_cols=38 Identities=11% Similarity=0.214 Sum_probs=29.8
Q ss_pred HHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 425 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 425 ~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
+|++.|+.+--- ....+..|+|+.||||+.|||+-+..
T Consensus 5 eR~~~Il~~L~~--~~~v~v~eLa~~l~VS~~TIRRDL~~ 42 (256)
T PRK10434 5 QRQAAILEYLQK--QGKTSVEELAQYFDTTGTTIRKDLVI 42 (256)
T ss_pred HHHHHHHHHHHH--cCCEEHHHHHHHHCCCHHHHHHHHHH
Confidence 566667766430 24589999999999999999998876
No 402
>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=54.42 E-value=30 Score=32.88 Aligned_cols=40 Identities=35% Similarity=0.394 Sum_probs=28.4
Q ss_pred HHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 427 EREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 427 ER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
...|+.-.|.- ++.++..++|+.||||+.+|| .||..|..
T Consensus 21 ~~~I~~g~l~p-G~~L~e~~La~~lgVSRtpVR----eAL~~L~~ 60 (212)
T TIGR03338 21 ERAILSGELPP-GAKLNESDIAARLGVSRGPVR----EAFRALEE 60 (212)
T ss_pred HHHHHcCCCCC-CCEecHHHHHHHhCCChHHHH----HHHHHHHH
Confidence 34455544422 356899999999999999997 56666654
No 403
>PRK06424 transcription factor; Provisional
Probab=54.40 E-value=16 Score=33.59 Aligned_cols=25 Identities=8% Similarity=0.171 Sum_probs=23.2
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
..|+|++|+|+.+|+++++|+++++
T Consensus 95 ~~GLSQ~eLA~~iGvs~stIskiE~ 119 (144)
T PRK06424 95 RLSMSQADLAAKIFERKNVIASIER 119 (144)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 4689999999999999999999986
No 404
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=54.20 E-value=32 Score=26.63 Aligned_cols=25 Identities=24% Similarity=0.393 Sum_probs=22.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVAL 466 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rAL 466 (485)
.|..+||+.+|+|...+.++..+..
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~ 26 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKET 26 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHh
Confidence 6899999999999999998887765
No 405
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.14 E-value=26 Score=29.77 Aligned_cols=42 Identities=10% Similarity=0.132 Sum_probs=29.8
Q ss_pred hCCHHHHHHHhhHhccC--CCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLD--KECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~--~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
.|+|.|+.+-.--+.-+ .-.+|.++||..||+|...|..+++
T Consensus 2 SLn~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil~ 45 (97)
T COG4367 2 SLNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLEKILQ 45 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHHHHHH
Confidence 36666666544433222 2469999999999999999987764
No 406
>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=53.85 E-value=4.3 Score=38.05 Aligned_cols=42 Identities=24% Similarity=0.279 Sum_probs=0.0
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
..|=+.|+.-|..--+ ...++|+++||+.+|++.+||++.+.
T Consensus 30 ~~iv~~Q~~ff~~g~~-~l~PLt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 30 QAIVERQKDFFLGGPG-ALKPLTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp -------------------------------------------
T ss_pred HHHHHHHHHHHhcCcc-cCcCCCHHHHHHHhCCCHhHHHHHHc
Confidence 4556666665542110 15789999999999999999998665
No 407
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.56 E-value=28 Score=30.51 Aligned_cols=46 Identities=17% Similarity=0.247 Sum_probs=38.7
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL 469 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKL 469 (485)
+-|++.|-+-+.+++ .-.=+++||-+.+|+|-.|||..+...+++|
T Consensus 40 ~~Lt~d~LeFv~lf~---r~RGnlKEvEr~lg~sYptvR~kld~vlram 85 (122)
T COG3877 40 EYLTSDQLEFVELFL---RCRGNLKEVERELGISYPTVRTKLDEVLRAM 85 (122)
T ss_pred cccCHhHhHHHHHHH---HHccCHHHHHHHHCCccHHHHHHHHHHHHHc
Confidence 568888888888877 3345899999999999999999988887765
No 408
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=53.51 E-value=18 Score=32.09 Aligned_cols=26 Identities=19% Similarity=0.244 Sum_probs=23.3
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
..|+|++|+|+.+|||+++++++++.
T Consensus 16 ~~Glsq~eLA~~~Gis~~~is~iE~g 41 (120)
T PRK13890 16 ERHMTKKELSERSGVSISFLSDLTTG 41 (120)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 36799999999999999999998863
No 409
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=53.36 E-value=35 Score=33.46 Aligned_cols=40 Identities=25% Similarity=0.286 Sum_probs=28.6
Q ss_pred HHHHHhhHhccCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 427 EREIIRLYYGLDKECL-TWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 427 ER~VI~LryGL~~eg~-S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
.+.|+...|.- ++.+ +-.++|+.||||+.+|| .|+..|..
T Consensus 20 ~~~I~~g~l~p-G~~LpsE~eLa~~lgVSRtpVR----EAL~~L~~ 60 (254)
T PRK09464 20 EFLILEGTLRP-GEKLPPERELAKQFDVSRPSLR----EAIQRLEA 60 (254)
T ss_pred HHHHHcCCCCC-CCcCCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 45556555521 2556 89999999999999997 66666654
No 410
>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=53.12 E-value=10 Score=32.08 Aligned_cols=25 Identities=28% Similarity=0.369 Sum_probs=22.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVAL 466 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rAL 466 (485)
+|..|+|+.+|||+.|++.+...++
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~~Gl 25 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDIGL 25 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999988754
No 411
>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=52.57 E-value=46 Score=25.89 Aligned_cols=50 Identities=12% Similarity=0.147 Sum_probs=33.1
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHH------CCCHHHHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRI------GLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~L------gIS~~tVrqi~~rALkKLRk 471 (485)
.|++++..+|.+..--.....|.++|.+.+ +.+..+|++.+.+-+++|..
T Consensus 5 ~Lt~~e~~lL~~L~~~~~~~vs~~~l~~~lw~~~~~~~~~~~l~~~i~~LR~~l~~ 60 (78)
T smart00862 5 KLTPKEFRLLELLLRNPGRVVSREELLEAVWGDDDDDVDDNTLDVHISRLRKKLED 60 (78)
T ss_pred ecCHHHHHHHHHHHhCCCCccCHHHHHHHHcCCCCCCCccchHHHHHHHHHHHHhc
Confidence 589999998876552112458999999986 34556666666555555543
No 412
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=52.55 E-value=47 Score=28.08 Aligned_cols=27 Identities=15% Similarity=0.180 Sum_probs=24.6
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
.++.+.++||+.+|+|+.++.++.++.
T Consensus 19 ~~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 19 DQPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 467999999999999999999988886
No 413
>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=52.51 E-value=10 Score=32.44 Aligned_cols=26 Identities=23% Similarity=0.335 Sum_probs=23.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVALE 467 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rALk 467 (485)
++..|+|+.+|||+.|++.+...++-
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~~Gll 27 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESIGLI 27 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 68999999999999999999887654
No 414
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=52.46 E-value=28 Score=32.80 Aligned_cols=98 Identities=18% Similarity=0.184 Sum_probs=54.8
Q ss_pred CCCCCHHHHHHHh--CCCHHHHHHHHHHH---Hhhhccc----------CC--CCCcchHHHHHHH---HHHHHHHHhhC
Q 011454 364 GVTPSVDRIAEYL--NMSQKKVRNATEVL---AYIADNR----------VE--NNPWHGVDDWALK---DEVNKLIIVTL 423 (485)
Q Consensus 364 gr~ps~eEIae~L--~is~eev~~~l~~~---~~l~D~~----------~e--~~pee~~e~~el~---e~L~~~L~~~L 423 (485)
+..+++.+|++.+ +++.++++++++.. .++.-.. .. .+........... +.-.++| +..
T Consensus 37 ~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~g~y~~t~~~l~~~~~~~~~avr~~h~q~~~lA~~al-~~~ 115 (171)
T PF14394_consen 37 PFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGDGKYVQTDKSLTTSSEIPSEAVRSYHKQMLELAQEAL-DRV 115 (171)
T ss_pred CCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCCCcEEEecceeeCCCCCcHHHHHHHHHHHHHHHHHHH-HhC
Confidence 4456889999999 99999999988876 1221111 10 0111122233333 3333455 678
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 475 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk~L~~ 475 (485)
|+.+|.+-.+-+|++ .-++++| +..+...++++......
T Consensus 116 p~~~R~~s~~T~~vs--~~~~~ki-----------~~~i~~fRk~i~~i~~~ 154 (171)
T PF14394_consen 116 PPEERDFSGLTMSVS--REDYEKI-----------KKEIREFRKKIIAIAEE 154 (171)
T ss_pred CccccceeeeEEEeC--HHHHHHH-----------HHHHHHHHHHHHHHHhc
Confidence 888888887776532 2233333 34444555555555443
No 415
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=52.11 E-value=29 Score=29.94 Aligned_cols=44 Identities=14% Similarity=0.241 Sum_probs=33.8
Q ss_pred hhCCHHHH-HHHhhHhccCCCCCCHHHHHHHHCC-CHHHHHHHHHHHHH
Q 011454 421 VTLGERER-EIIRLYYGLDKECLTWEDISKRIGL-SRERVRQVGLVALE 467 (485)
Q Consensus 421 ~~Lp~rER-~VI~LryGL~~eg~S~eEIAe~LgI-S~~tVrqi~~rALk 467 (485)
.+.|+..+ +|+.+++ ..|.|..+||..+|| +.+.++++..+...
T Consensus 6 r~~s~EfK~~iv~~~~---~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~ 51 (116)
T COG2963 6 KKYSPEFKLEAVALYL---RGGDTVSEVAREFGIVSATQLYKWRIQLQK 51 (116)
T ss_pred ccCCHHHHHHHHHHHH---hcCccHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 34566655 5777777 578899999999996 99999887776554
No 416
>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=52.09 E-value=57 Score=24.93 Aligned_cols=48 Identities=23% Similarity=0.247 Sum_probs=37.0
Q ss_pred CCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhhhhhH
Q 011454 206 LTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECS 263 (485)
Q Consensus 206 Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~~~~ 263 (485)
||+.|...|...+..|=. -..+..+..++|..+|+|...+-..+...+
T Consensus 1 LT~~Q~e~L~~A~~~GYf----------d~PR~~tl~elA~~lgis~st~~~~LRrae 48 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYF----------DVPRRITLEELAEELGISKSTVSEHLRRAE 48 (53)
T ss_pred CCHHHHHHHHHHHHcCCC----------CCCCcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 567777777777777765 345678899999999999999887776543
No 417
>PF13309 HTH_22: HTH domain
Probab=51.83 E-value=13 Score=29.24 Aligned_cols=21 Identities=24% Similarity=0.303 Sum_probs=18.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVG 462 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~ 462 (485)
-+...+|+.||||+.||.+.+
T Consensus 43 gav~~vA~~L~iS~~TVY~YL 63 (64)
T PF13309_consen 43 GAVEYVAEKLGISRATVYRYL 63 (64)
T ss_pred cHHHHHHHHHCCCHHHHHHHc
Confidence 488999999999999998764
No 418
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=51.83 E-value=39 Score=33.26 Aligned_cols=40 Identities=25% Similarity=0.235 Sum_probs=28.3
Q ss_pred HHHHHhhHhccCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 427 EREIIRLYYGLDKECL-TWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 427 ER~VI~LryGL~~eg~-S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
...|+...|.- ++.+ +..|+|+.||||+..|| .||+.|..
T Consensus 12 ~~~I~~g~l~p-G~~LpsE~eLae~~gVSRtpVR----EAL~~Le~ 52 (253)
T PRK10421 12 RALIEEKNLEA-GMKLPAERQLAMQLGVSRNSLR----EALAKLVS 52 (253)
T ss_pred HHHHHcCCCCC-CCcCCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 34555555521 3557 68999999999999997 66666654
No 419
>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=51.82 E-value=11 Score=32.69 Aligned_cols=25 Identities=16% Similarity=0.311 Sum_probs=22.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVAL 466 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rAL 466 (485)
||..|+|+.+|||+.|++.+...++
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gl 25 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKEGL 25 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999988765
No 420
>PRK11050 manganese transport regulator MntR; Provisional
Probab=51.82 E-value=45 Score=30.61 Aligned_cols=25 Identities=24% Similarity=0.214 Sum_probs=21.8
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 440 ECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 440 eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
++.+..|||+.++|++++|++.+.+
T Consensus 50 ~~~t~~eLA~~l~is~stVsr~l~~ 74 (152)
T PRK11050 50 GEARQVDIAARLGVSQPTVAKMLKR 74 (152)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 6789999999999999999866654
No 421
>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=51.82 E-value=12 Score=31.25 Aligned_cols=25 Identities=24% Similarity=0.275 Sum_probs=22.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVAL 466 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rAL 466 (485)
+|..|+|+.+|||..|++.+..+.+
T Consensus 2 ~ti~evA~~~gvs~~tLR~ye~~Gl 26 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEEKGL 26 (88)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 7899999999999999999987654
No 422
>PF04814 HNF-1_N: Hepatocyte nuclear factor 1 (HNF-1), N terminus; InterPro: IPR006899 This domain consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerisation sequence [] and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3) [].; GO: 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2GYP_B 1IC8_B 2H8R_B 1G2Y_D 1F93_H 1G39_D 1G2Z_B 1JB6_B.
Probab=51.49 E-value=10 Score=36.17 Aligned_cols=56 Identities=16% Similarity=0.172 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011454 409 WALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALE 467 (485)
Q Consensus 409 ~el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALk 467 (485)
.+....|+++| .+=|-.=++.|..+.+ ....++.+|++..|||++.|+|+++++.-
T Consensus 102 ~~~~~~Ve~ll-r~D~~~VkeeIK~fl~--~h~IsQ~~V~q~TGisQS~lSq~L~kGt~ 157 (180)
T PF04814_consen 102 AEQRAEVEELL-RRDPWRVKEEIKAFLQ--QHNISQREVVQVTGISQSHLSQHLNKGTP 157 (180)
T ss_dssp HHHHHHHHHCT-TS-HHHHHHHHHHHHH--HCT--CHHHHHHHT--HHHHHHHHCTB--
T ss_pred hhhHHHHHHHH-hhCHHHHHHHHHHHHH--HcCCcHHHHHHHhhhhHHHHHHHHHcCCC
Confidence 34446676666 5555566777777764 56799999999999999999999887643
No 423
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=51.34 E-value=18 Score=36.10 Aligned_cols=37 Identities=22% Similarity=0.326 Sum_probs=30.2
Q ss_pred CHHHHHHHhhHhccCC-CCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 424 GEREREIIRLYYGLDK-ECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 424 p~rER~VI~LryGL~~-eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
.+|++.|+.+-- . .-.+.+|+|+.||||..|||+=+.
T Consensus 4 ~eR~~~Il~~l~---~~g~v~v~eLa~~~~VS~~TIRRDL~ 41 (253)
T COG1349 4 EERHQKILELLK---EKGKVSVEELAELFGVSEMTIRRDLN 41 (253)
T ss_pred HHHHHHHHHHHH---HcCcEEHHHHHHHhCCCHHHHHHhHH
Confidence 468888888865 3 348999999999999999998554
No 424
>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=51.23 E-value=37 Score=32.28 Aligned_cols=40 Identities=23% Similarity=0.248 Sum_probs=29.3
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
.|++.-|.-|...+- .+|+|.++||..+||+..||.-++.
T Consensus 16 ~lse~~r~~Iy~~~~--~~~~sv~~vS~~ygi~~~RV~AIvr 55 (172)
T PF12298_consen 16 VLSEELREQIYEDVM--QDGKSVREVSQKYGIKIQRVEAIVR 55 (172)
T ss_pred cCCHHHHHHHHHHHH--hCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 366666664444441 5788999999999999999975543
No 425
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=51.22 E-value=41 Score=32.03 Aligned_cols=49 Identities=18% Similarity=0.250 Sum_probs=32.9
Q ss_pred HHHHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 412 KDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 412 ~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
...+...+ . -++....|+..-. ....+|-+|||+.|||+...||+++.+
T Consensus 11 ~~~l~~~~-~-~~~~~~~Vl~~L~--~~g~~tdeeLA~~Lgi~~~~VRk~L~~ 59 (178)
T PRK06266 11 QKVLFEIM-E-GDEEGFEVLKALI--KKGEVTDEEIAEQTGIKLNTVRKILYK 59 (178)
T ss_pred HHHHHHHh-c-CCccHhHHHHHHH--HcCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 33444444 3 2555555665433 124699999999999999999987664
No 426
>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=51.17 E-value=38 Score=31.82 Aligned_cols=56 Identities=30% Similarity=0.365 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHHHhhCCHHHHHHHhhHhcc--C---CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 408 DWALKDEVNKLIIVTLGEREREIIRLYYGL--D---KECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 408 ~~el~e~L~~~L~~~Lp~rER~VI~LryGL--~---~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
+++-.+.|++.| +.||+.|++=+.-+|-- + .+|.|-+||.+.||=++.-++++...
T Consensus 3 k~efL~~L~~~L-~~lp~~e~~e~l~~Y~e~f~d~~~~G~sEeeii~~LG~P~~iA~~i~~~ 63 (181)
T PF08006_consen 3 KNEFLNELEKYL-KKLPEEEREEILEYYEEYFDDAGEEGKSEEEIIAELGSPKEIAREILAE 63 (181)
T ss_pred HHHHHHHHHHHH-HcCCHHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHcCCHHHHHHHHHHh
Confidence 456677888889 79999988866555532 1 35789999999999998888887754
No 427
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=51.11 E-value=17 Score=35.01 Aligned_cols=23 Identities=9% Similarity=0.096 Sum_probs=19.4
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Q 011454 441 CLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 441 g~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
.+|.++||..+|+++++|++.++
T Consensus 173 ~~t~~~iA~~lG~tretvsR~l~ 195 (236)
T PRK09392 173 PYEKRVLASYLGMTPENLSRAFA 195 (236)
T ss_pred eCCHHHHHHHhCCChhHHHHHHH
Confidence 47889999999999999975543
No 428
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=51.08 E-value=25 Score=32.62 Aligned_cols=25 Identities=24% Similarity=0.238 Sum_probs=20.8
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
.......+||+.|||++.+|...++
T Consensus 22 ~~~~~~~diA~~L~Vsp~sVt~ml~ 46 (154)
T COG1321 22 KGFARTKDIAERLKVSPPSVTEMLK 46 (154)
T ss_pred cCcccHHHHHHHhCCCcHHHHHHHH
Confidence 3457999999999999999976554
No 429
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=50.98 E-value=41 Score=33.12 Aligned_cols=40 Identities=30% Similarity=0.315 Sum_probs=28.4
Q ss_pred HHHHHhhHhccCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 427 EREIIRLYYGLDKECL-TWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 427 ER~VI~LryGL~~eg~-S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
...|+...|.- ++.+ |-.++|+.||||+.+|| .|+..|..
T Consensus 19 ~~~I~~g~l~p-G~~LpsE~eLa~~~gVSRtpVR----EAL~~L~~ 59 (257)
T PRK10225 19 RDLIIKTPYNP-GERLPPEREIAEMLDVTRTVVR----EALIMLEI 59 (257)
T ss_pred HHHHHhCCCCC-CCcCcCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 34555555522 3557 68899999999999997 66666654
No 430
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=50.17 E-value=22 Score=35.43 Aligned_cols=38 Identities=18% Similarity=0.236 Sum_probs=28.7
Q ss_pred HHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 425 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 425 ~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
+|++.|+.+.-- ....+..|+|+.|+||..|||+-+..
T Consensus 5 ~R~~~Il~~l~~--~~~~~~~ela~~l~vS~~TiRRdL~~ 42 (252)
T PRK10906 5 QRHDAIIELVKQ--QGYVSTEELVEHFSVSPQTIRRDLND 42 (252)
T ss_pred HHHHHHHHHHHH--cCCEeHHHHHHHhCCCHHHHHHHHHH
Confidence 566666666430 24489999999999999999996553
No 431
>COG2411 Uncharacterized conserved protein [Function unknown]
Probab=49.97 E-value=69 Score=30.58 Aligned_cols=65 Identities=28% Similarity=0.425 Sum_probs=45.7
Q ss_pred CcchHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCC--CHHHHHHHHHHHHHHHHH
Q 011454 402 PWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGL--SRERVRQVGLVALEKLKH 471 (485)
Q Consensus 402 pee~~e~~el~e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgI--S~~tVrqi~~rALkKLRk 471 (485)
|.+..+-.++...-.+-+ +.|+++++.|+.+.. +.=|+..-|..+|= .+..|++.+.+|..-|.+
T Consensus 118 ~y~g~dp~eIA~laLe~l-~~Ls~~~~~iL~~~~----~~gslRkaA~klgg~~kr~~ir~vLrKay~~L~~ 184 (188)
T COG2411 118 PYEGRDPIEIARLALEHL-DNLSERDKRILELFV----EEGSLRKAAKKLGGLEKRGRIRRVLRKAYHELKK 184 (188)
T ss_pred cCCCCCHHHHHHHHHHhc-ccCCHHHHHHHHHHH----HcCcHHHHHHHhcCcchhhHHHHHHHHHHHHHHh
Confidence 333344444444444445 569999999999876 66799999999985 567788777777776654
No 432
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=49.96 E-value=43 Score=32.48 Aligned_cols=39 Identities=23% Similarity=0.361 Sum_probs=27.0
Q ss_pred HHHHhhHhccCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 428 REIIRLYYGLDKECL-TWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 428 R~VI~LryGL~~eg~-S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
..|+.-.|. .++.+ |-.|+|+.+|||+.+|| .|+..|..
T Consensus 18 ~~I~~g~l~-pG~~LPsE~eLae~~gVSRt~VR----eAL~~L~~ 57 (239)
T PRK04984 18 ESIWNNRFP-PGSILPAERELSELIGVTRTTLR----EVLQRLAR 57 (239)
T ss_pred HHHHcCCCC-CCCcCCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 344444441 13557 78999999999999997 56666654
No 433
>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=49.76 E-value=13 Score=31.33 Aligned_cols=25 Identities=24% Similarity=0.299 Sum_probs=22.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVAL 466 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rAL 466 (485)
|+..|+|+.+||++.||+.+...++
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~~Gl 25 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEEKGL 25 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999987665
No 434
>PRK11517 transcriptional regulatory protein YedW; Provisional
Probab=49.75 E-value=28 Score=32.17 Aligned_cols=49 Identities=18% Similarity=0.123 Sum_probs=38.6
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRI-----GLSRERVRQVGLVALEKLK 470 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~L-----gIS~~tVrqi~~rALkKLR 470 (485)
.|+++|..|+.+..-=.++-+|.++|...+ ..+..+|+.++.+.++||.
T Consensus 147 ~Lt~~E~~il~~l~~~~g~~~s~~~i~~~~w~~~~~~~~~tv~~~i~rlr~Kl~ 200 (223)
T PRK11517 147 TLTRKEFQLLWLLASRAGEIIPRTVIASEIWGINFDSDTNTVDVAIRRLRAKVD 200 (223)
T ss_pred eCCHHHHHHHHHHHhCCCccCCHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhhc
Confidence 699999999988661012447999999997 4577899999888888885
No 435
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=49.69 E-value=22 Score=33.47 Aligned_cols=36 Identities=14% Similarity=0.247 Sum_probs=28.3
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGLV----ALEKLKHAAR 474 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~r----ALkKLRk~L~ 474 (485)
..++|++|+|+.+|||+++|+++++. .+..|.+...
T Consensus 18 ~~glt~~elA~~~gis~~~is~~E~g~~~p~~~~l~~ia~ 57 (185)
T PRK09943 18 QQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLK 57 (185)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 35799999999999999999999864 3444555444
No 436
>PRK06030 hypothetical protein; Provisional
Probab=49.58 E-value=53 Score=29.55 Aligned_cols=39 Identities=10% Similarity=0.026 Sum_probs=27.8
Q ss_pred HHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011454 425 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 466 (485)
Q Consensus 425 ~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rAL 466 (485)
+||--+...+- .-++|+.+||+.+|...+||..-.++.-
T Consensus 56 aRqIAMYL~r~---~~~~sl~~IG~~FGRDHSTV~haikkIe 94 (124)
T PRK06030 56 IRQIAMYVAHV---SLGWPMNEVALAFGRDRTTVGHACHTVE 94 (124)
T ss_pred HHHHHHHHHHH---HcCCCHHHHHHHHCCChhHHHHHHHHHH
Confidence 44444444444 4679999999999999999987666433
No 437
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=49.45 E-value=45 Score=28.50 Aligned_cols=40 Identities=10% Similarity=0.043 Sum_probs=28.9
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALE 467 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALk 467 (485)
+.++-.+|.... +.-|+..-|+.||||+.+|++.+++.=+
T Consensus 3 ~~~~l~~~~av~----~~gSis~AA~~L~iS~stvs~~I~~LE~ 42 (99)
T TIGR00637 3 DPRRVALLKAIA----RMGSISQAAKDAGISYKSAWDYIRAMNN 42 (99)
T ss_pred CHHHHHHHHHHH----HhCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 445555555554 5679999999999999999866554433
No 438
>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=49.34 E-value=12 Score=31.11 Aligned_cols=25 Identities=12% Similarity=0.134 Sum_probs=22.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVAL 466 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rAL 466 (485)
+|..|+|+.+|||+.||+.+...++
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~~Gl 26 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYERLGL 26 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 6899999999999999999987654
No 439
>PRK09480 slmA division inhibitor protein; Provisional
Probab=49.19 E-value=1.7e+02 Score=26.73 Aligned_cols=71 Identities=18% Similarity=0.014 Sum_probs=52.6
Q ss_pred CCCCchHHHHHHhhcChhHHHHhhhhhHHHHHHHHHHhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhH
Q 011454 236 GCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGI 306 (485)
Q Consensus 236 g~~p~~~~~a~~~~~s~~~L~~~l~~~~~A~e~Lie~yl~LV~sIA~ry~~~~~d~EDLiQEG~IgL~kAi 306 (485)
|...|.+++|..+|++...+-.-....+.-+..+++.+..-+............+..+.++..+-.++.-+
T Consensus 28 G~~~ti~~Ia~~agvs~gt~Y~~F~~K~~L~~~v~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~ 98 (194)
T PRK09480 28 GERITTAKLAARVGVSEAALYRHFPSKARMFEGLIEFIEESLFSRINQILKDEKDTLARARLILLLLLGFA 98 (194)
T ss_pred CCccCHHHHHHHhCCCHhHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHH
Confidence 56799999999999999999999999888888888877766655555444333456666666665555543
No 440
>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=49.07 E-value=26 Score=27.77 Aligned_cols=27 Identities=26% Similarity=0.582 Sum_probs=21.9
Q ss_pred HHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHH
Q 011454 430 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVG 462 (485)
Q Consensus 430 VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~ 462 (485)
+|...|| ++.|+|..|++++.||++..
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 3445665 88999999999999998764
No 441
>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=49.06 E-value=26 Score=34.68 Aligned_cols=43 Identities=26% Similarity=0.236 Sum_probs=34.6
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
.+|+..+.+-|++-+-.+-+.+|...+|+.++||+++|+++++
T Consensus 9 k~Ls~~~~~~ir~L~~~~p~~~t~~~Lae~F~vspe~irrILk 51 (225)
T PF06413_consen 9 KKLSREAMEQIRYLHKEDPEEWTVERLAESFKVSPEAIRRILK 51 (225)
T ss_pred CCCCHHHHHHHHHHHHhCccccCHHHHHhhCCCCHHHHHHHHh
Confidence 5688888887777553334568999999999999999999875
No 442
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=49.00 E-value=2.2e+02 Score=27.41 Aligned_cols=92 Identities=24% Similarity=0.336 Sum_probs=64.4
Q ss_pred cCCC-CCHHHHHHHhCCCHHHHHHHHHHH--Hhhhccc-C----CCCCcchHHHHHHHHHHHHHHHh----hCCHHHHHH
Q 011454 363 KGVT-PSVDRIAEYLNMSQKKVRNATEVL--AYIADNR-V----ENNPWHGVDDWALKDEVNKLIIV----TLGEREREI 430 (485)
Q Consensus 363 ~gr~-ps~eEIae~L~is~eev~~~l~~~--~~l~D~~-~----e~~pee~~e~~el~e~L~~~L~~----~Lp~rER~V 430 (485)
.|.+ .+..+|++.++++..++..++... +|-.+.. . ..+-+....+.+....+.+++.. +|+.-.-++
T Consensus 16 sg~pgls~~~La~~l~~~~~~v~~~l~~L~~~y~~~~~gi~i~~~~~~y~l~tk~e~~~~v~~~~~~~~~~~LS~aaLEt 95 (188)
T PRK00135 16 SGEEGLSLEQLAEILELEPTEVQQLLEELQEKYEGDDRGLKLIEFNDVYKLVTKEENADYLQKLVKTPIKQSLSQAALEV 95 (188)
T ss_pred cCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhCCCCEEEEEECCEEEEEEcHHHHHHHHHHhcccccCCCCHHHHHH
Confidence 4554 689999999999998888887765 3332211 0 12334445556666667666522 599999998
Q ss_pred HhhHhccCCCCCCHHHHHHHHCCCHH
Q 011454 431 IRLYYGLDKECLTWEDISKRIGLSRE 456 (485)
Q Consensus 431 I~LryGL~~eg~S~eEIAe~LgIS~~ 456 (485)
|...+. .++.|..||++..|++..
T Consensus 96 LaiIay--~qPiTr~eI~~irGv~~~ 119 (188)
T PRK00135 96 LAIIAY--KQPITRIEIDEIRGVNSD 119 (188)
T ss_pred HHHHHH--cCCcCHHHHHHHHCCCHH
Confidence 888542 578999999999999863
No 443
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=48.96 E-value=46 Score=32.61 Aligned_cols=40 Identities=25% Similarity=0.395 Sum_probs=28.4
Q ss_pred HHHHHhhHhccCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 427 EREIIRLYYGLDKECL-TWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 427 ER~VI~LryGL~~eg~-S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
...|+...|.- ++.+ +-.+||+.||||+..|| .||+.|..
T Consensus 17 ~~~I~~g~l~p-G~~LPsE~eLa~~~gVSRtpVR----EAL~~L~~ 57 (251)
T PRK09990 17 ERLIVDGVLKV-GQALPSERRLCEKLGFSRSALR----EGLTVLRG 57 (251)
T ss_pred HHHHHcCCCCC-CCcCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 34455555421 3567 78999999999999997 67766654
No 444
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=48.91 E-value=46 Score=31.29 Aligned_cols=50 Identities=22% Similarity=0.482 Sum_probs=31.5
Q ss_pred HHHHhhCCHHHHHHHhhHhc-cCCC---CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 417 KLIIVTLGEREREIIRLYYG-LDKE---CLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 417 ~~L~~~Lp~rER~VI~LryG-L~~e---g~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
..+ +.+..+.-.|+.+... ++.+ -+|+++||+.+|+|+.||. ++++.|.+
T Consensus 48 ~~l-~l~g~k~~~Vl~~il~~~d~~N~v~~t~~~ia~~l~iS~~Tv~----r~ik~L~e 101 (165)
T PF05732_consen 48 KVL-DLIGNKAFRVLMYILENMDKDNAVVATQKEIAEKLGISKPTVS----RAIKELEE 101 (165)
T ss_pred HHh-hhhchhHHHHHHHHHHhcCCCCeEEeeHHHHHHHhCCCHHHHH----HHHHHHHh
Confidence 344 4444544455544331 1222 2699999999999999986 66666664
No 445
>PHA02535 P terminase ATPase subunit; Provisional
Probab=48.84 E-value=20 Score=40.27 Aligned_cols=33 Identities=21% Similarity=0.298 Sum_probs=27.5
Q ss_pred HHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 428 REIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 428 R~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
++.+.|+. +|+|..|||+.|||++.||.++..+
T Consensus 9 ~~Av~Ly~----~G~sv~eIA~~LGv~~~Tl~~W~kr 41 (581)
T PHA02535 9 RAAKFLYW----QGWTVAEIAEELGLKSRTIYSWKER 41 (581)
T ss_pred HHHHHHHH----cCCCHHHHHHHhCCChhHHHHHhcc
Confidence 44456665 6999999999999999999998765
No 446
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=48.69 E-value=45 Score=29.89 Aligned_cols=44 Identities=16% Similarity=0.231 Sum_probs=34.0
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHH----CCCHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRI----GLSRERVRQVGLVALE 467 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~L----gIS~~tVrqi~~rALk 467 (485)
.|++.|..|+..... .++.|..||.+.| +++..||...+.|-.+
T Consensus 1 ~Lt~~E~~VM~vlW~--~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~ 48 (130)
T TIGR02698 1 SISDAEWEVMRVVWT--LGETTSRDIIRILAEKKDWSDSTIKTLLGRLVD 48 (130)
T ss_pred CCCHHHHHHHHHHHc--CCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHH
Confidence 378899998877652 3568999987777 7999999888776544
No 447
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=48.63 E-value=54 Score=30.49 Aligned_cols=40 Identities=23% Similarity=0.130 Sum_probs=28.7
Q ss_pred CCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 423 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 423 Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
..+....|+..-+ ....+|-+|||+.|||+...||+++.+
T Consensus 12 ~g~~~v~Vl~aL~--~~~~~tdEeLa~~Lgi~~~~VRk~L~~ 51 (158)
T TIGR00373 12 AEEEVGLVLFSLG--IKGEFTDEEISLELGIKLNEVRKALYA 51 (158)
T ss_pred cChhHHHHHHHHh--ccCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3455555665433 135699999999999999999866554
No 448
>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=48.61 E-value=13 Score=31.64 Aligned_cols=25 Identities=20% Similarity=0.264 Sum_probs=22.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVAL 466 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rAL 466 (485)
+|..|+|+.+|||+.|++.+...++
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~~Gl 25 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDEIGL 25 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999988765
No 449
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=48.61 E-value=42 Score=32.21 Aligned_cols=39 Identities=21% Similarity=0.213 Sum_probs=27.8
Q ss_pred HHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 428 REIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 428 R~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
+.|+...+. .++.++..+||+.||||+..|| .|+..|..
T Consensus 22 ~~I~~g~l~-pG~~L~e~~La~~lgVSRtpVR----EAL~~L~~ 60 (221)
T PRK11414 22 HQLSIGALK-PGARLITKNLAEQLGMSITPVR----EALLRLVS 60 (221)
T ss_pred HHHHhCCCC-CCCccCHHHHHHHHCCCchhHH----HHHHHHHH
Confidence 445554441 1366888999999999999997 56666654
No 450
>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=48.59 E-value=14 Score=32.00 Aligned_cols=26 Identities=23% Similarity=0.222 Sum_probs=23.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVALE 467 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rALk 467 (485)
++..|+|+.+|||+.|++.+...++-
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~~GLi 26 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKIGLL 26 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCC
Confidence 57899999999999999999987653
No 451
>PF04645 DUF603: Protein of unknown function, DUF603; InterPro: IPR006739 This family includes several uncharacterised proteins from Borrelia species.
Probab=48.48 E-value=23 Score=33.56 Aligned_cols=25 Identities=36% Similarity=0.472 Sum_probs=21.1
Q ss_pred CCC-CCHHHHHHHHCCCHHHHHHHHH
Q 011454 439 KEC-LTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 439 ~eg-~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
.+| ++..|||+.||||+..|.+..+
T Consensus 16 ~eg~L~d~~Ia~~lgvs~~nV~kmR~ 41 (181)
T PF04645_consen 16 KEGRLSDAEIAKELGVSRVNVWKMRQ 41 (181)
T ss_pred hcCCccHHHHHHHHCchHHHHHHHHH
Confidence 467 9999999999999999976544
No 452
>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=48.20 E-value=14 Score=31.72 Aligned_cols=25 Identities=20% Similarity=0.363 Sum_probs=22.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVAL 466 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rAL 466 (485)
++..|+|+.+|||+.|++.+...++
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~~Gl 26 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKLGL 26 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 6899999999999999998887654
No 453
>COG4709 Predicted membrane protein [Function unknown]
Probab=47.87 E-value=45 Score=32.19 Aligned_cols=57 Identities=19% Similarity=0.201 Sum_probs=44.4
Q ss_pred HHHHHHHHHHHHHhhCCHHHHHHHhhHhcc-----CCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011454 408 DWALKDEVNKLIIVTLGEREREIIRLYYGL-----DKECLTWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 408 ~~el~e~L~~~L~~~Lp~rER~VI~LryGL-----~~eg~S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
+.+...+|++.| +.||+.+|.=+...|-- +.+|.|-+||++.||=+.+-.+.+..+.
T Consensus 3 k~efL~eL~~yL-~~Lp~~~r~e~m~dyeehF~~a~~~GksE~EI~~~LG~P~eiA~ei~s~~ 64 (195)
T COG4709 3 KTEFLNELEQYL-EGLPREERREIMYDYEEHFREAQEAGKSEEEIAKDLGDPKEIAAEILSER 64 (195)
T ss_pred HHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHhhhhcCCCHHHHHHHhCCHHHHHHHHHHHc
Confidence 456667888999 89999999877665521 1358999999999999998887776654
No 454
>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=47.70 E-value=14 Score=31.29 Aligned_cols=25 Identities=20% Similarity=0.335 Sum_probs=22.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVAL 466 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rAL 466 (485)
+|..|+|+.+|||..|++.+...++
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gl 25 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDKIGL 25 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999988765
No 455
>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=47.57 E-value=14 Score=31.41 Aligned_cols=25 Identities=32% Similarity=0.449 Sum_probs=21.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVAL 466 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rAL 466 (485)
++..|+|+.+|||..|++.+...++
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 456
>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=47.56 E-value=14 Score=31.41 Aligned_cols=25 Identities=20% Similarity=0.514 Sum_probs=22.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVAL 466 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rAL 466 (485)
|+..|+|+.+|||..|++.+...++
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye~~Gl 25 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEEIGL 25 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999987654
No 457
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=47.44 E-value=39 Score=29.87 Aligned_cols=27 Identities=22% Similarity=0.271 Sum_probs=24.6
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
.+..+.+++|+.+|+|+.++.++.++.
T Consensus 23 ~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 23 ESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 467999999999999999999988876
No 458
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=47.20 E-value=43 Score=25.59 Aligned_cols=22 Identities=18% Similarity=0.333 Sum_probs=17.7
Q ss_pred CCCHHHHHHHHCCCHHHHHHHH
Q 011454 441 CLTWEDISKRIGLSRERVRQVG 462 (485)
Q Consensus 441 g~S~eEIAe~LgIS~~tVrqi~ 462 (485)
.++.+|.|+.|||+..+++++-
T Consensus 15 hlp~~eAA~~Lgv~~T~LKr~C 36 (52)
T PF02042_consen 15 HLPIKEAAKELGVSVTTLKRRC 36 (52)
T ss_pred CCCHHHHHHHhCCCHHHHHHHH
Confidence 3899999999999987776554
No 459
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=47.14 E-value=28 Score=35.35 Aligned_cols=42 Identities=21% Similarity=0.267 Sum_probs=32.6
Q ss_pred hCCHHHHHHHhhHhcc-C--CCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGL-D--KECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL-~--~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
.|++-|++||..-.-| . .....-+|||+.+|..++|||+..+
T Consensus 3 ~LT~~QkeIL~aLi~LY~~~~r~IKgeeIA~~l~rnpGTVRNqmq 47 (294)
T COG2524 3 ELTSSQKEILQALINLYRRKKRPIKGEEIAEVLNRNPGTVRNQMQ 47 (294)
T ss_pred cccHHHHHHHHHHHHHHHhcCCCcchHHHHHHHccCcchHHHHHH
Confidence 5888899988764433 1 1245679999999999999998875
No 460
>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=47.00 E-value=36 Score=29.84 Aligned_cols=24 Identities=21% Similarity=0.355 Sum_probs=20.9
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 441 CLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 441 g~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
..|.+|||+.+|+|+.+|++++..
T Consensus 25 ~~s~~eia~~~~i~~~~v~~il~~ 48 (132)
T TIGR00738 25 PVSVKEIAERQGISRSYLEKILRT 48 (132)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHH
Confidence 689999999999999999866543
No 461
>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=46.98 E-value=41 Score=27.35 Aligned_cols=49 Identities=18% Similarity=0.135 Sum_probs=33.3
Q ss_pred hCCHHHHHHHhhHhccCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLYYGLDKECLTWEDISKRIG-----LSRERVRQVGLVALEKLK 470 (485)
Q Consensus 422 ~Lp~rER~VI~LryGL~~eg~S~eEIAe~Lg-----IS~~tVrqi~~rALkKLR 470 (485)
.|+++|..+|.+..-=..+..|.++|.+.+- .+..++.+.+.+.+++|.
T Consensus 23 ~Lt~~e~~lL~~L~~~~~~~vs~~~l~~~lw~~~~~~~~~~l~~~I~rLRkkl~ 76 (95)
T cd00383 23 ELTPKEFELLELLARNPGRVLSREQLLEAVWGDDYDVDDRTVDVHISRLRKKLE 76 (95)
T ss_pred EeCHHHHHHHHHHHhCCCCcCCHHHHHHHhcCCCCCCCcccHHHHHHHHHHHhc
Confidence 5899999999876621235789999999884 455555555554444443
No 462
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=46.94 E-value=15 Score=31.23 Aligned_cols=25 Identities=24% Similarity=0.308 Sum_probs=22.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVAL 466 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rAL 466 (485)
|+..|+|+.+|||..||+-+...++
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye~~GL 25 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLREGL 25 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999998887655
No 463
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=46.91 E-value=26 Score=32.61 Aligned_cols=26 Identities=15% Similarity=0.251 Sum_probs=23.6
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
..++|++++|+.+|+++++|+++++-
T Consensus 80 ~~glSqeeLA~~lgvs~s~IsriE~G 105 (154)
T TIGR00270 80 KRGWSQEQLAKKIQEKESLIKKIENA 105 (154)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 46799999999999999999999863
No 464
>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=46.86 E-value=15 Score=31.93 Aligned_cols=26 Identities=23% Similarity=0.353 Sum_probs=22.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVALE 467 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rALk 467 (485)
||..|+|+.+|||+.|++.+...++-
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 465
>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=46.78 E-value=14 Score=31.15 Aligned_cols=25 Identities=20% Similarity=0.395 Sum_probs=22.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVAL 466 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rAL 466 (485)
|+..|+|+.+|||..|++.+...++
T Consensus 1 m~i~eva~~~gvs~~tlR~ye~~Gl 25 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDHIGL 25 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999987664
No 466
>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=46.77 E-value=29 Score=30.75 Aligned_cols=39 Identities=31% Similarity=0.408 Sum_probs=34.9
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
..|.+.++.|+.+.- ...|..|||..++++.+-|+.+..
T Consensus 39 ~~l~pE~~~Il~lC~----~~~SVAEiAA~L~lPlgVvrVLvs 77 (114)
T PF05331_consen 39 AGLGPEHRAILELCR----RPLSVAEIAARLGLPLGVVRVLVS 77 (114)
T ss_pred CCCCHHHHHHHHHHC----CCccHHHHHHhhCCCchhhhhhHH
Confidence 579999999999986 589999999999999999987764
No 467
>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=46.76 E-value=56 Score=31.56 Aligned_cols=26 Identities=27% Similarity=0.405 Sum_probs=21.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
-|-.|+|+++|||+.||| +|+..|.+
T Consensus 33 PsE~eLa~~~~VSR~TvR----~Al~~L~~ 58 (238)
T TIGR02325 33 PAEMQLAERFGVNRHTVR----RAIAALVE 58 (238)
T ss_pred cCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 489999999999999998 56666654
No 468
>PF11662 DUF3263: Protein of unknown function (DUF3263); InterPro: IPR021678 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=46.67 E-value=71 Score=26.45 Aligned_cols=46 Identities=24% Similarity=0.223 Sum_probs=36.3
Q ss_pred hCCHHHHHHHhhH-hccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011454 422 TLGEREREIIRLY-YGLDKECLTWEDISKRIGLSRERVRQVGLVALE 467 (485)
Q Consensus 422 ~Lp~rER~VI~Lr-yGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALk 467 (485)
.|+++++.||..- -+-...|-+-+.|-+.||+|+-+-.|.++..+.
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 5899999999762 111235778999999999999999999887653
No 469
>PF04963 Sigma54_CBD: Sigma-54 factor, core binding domain; InterPro: IPR007046 This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme []. The centre of this domain contains a very weak similarity to a helix-turn-helix motif, which may represent a DNA binding domain.; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent; PDB: 2K9L_A 2K9M_A.
Probab=46.50 E-value=7.1 Score=37.47 Aligned_cols=88 Identities=22% Similarity=0.249 Sum_probs=31.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHhhhcccCCCCCcchHHHHHHHHHHHHHHHhhC--CHHHHHHHhhHhccCCCCCC
Q 011454 366 TPSVDRIAEYLNMSQKKVRNATEVLAYIADNRVENNPWHGVDDWALKDEVNKLIIVTL--GEREREIIRLYYGLDKECLT 443 (485)
Q Consensus 366 ~ps~eEIae~L~is~eev~~~l~~~~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~L--p~rER~VI~LryGL~~eg~S 443 (485)
..+.+++++.++++.+++..++.....++..... ...+.+-|.--+ ..+ ++.-..||.-++- ......
T Consensus 52 ~~~~~eia~~l~~~~~~v~~~l~~lQ~leP~Gig--------Ar~l~EcLllQl-~~~~~~~~~~~il~~~l~-~l~~~~ 121 (194)
T PF04963_consen 52 TESLEEIAEELGVSEEEVEKALELLQSLEPAGIG--------ARDLQECLLLQL-ERKGPPDLAYRILENHLE-LLANKD 121 (194)
T ss_dssp SS-HHHHHHHCTS-HHHHHHHHHHHHTTSS--TT--------TS-TTHHHHHHH-HHS-S--TTHHHHHHHHH-HHHH--
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHcCCCCccC--------cCCHHHHHHHHH-hccCCcHHHHHHHHHHHH-HHHHhh
Confidence 4578999999999999999998877554433221 111112111112 222 2333445554441 123457
Q ss_pred HHHHHHHHCCCHHHHHHHHH
Q 011454 444 WEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 444 ~eEIAe~LgIS~~tVrqi~~ 463 (485)
++.||+.+|+|...|...+.
T Consensus 122 ~~~ia~~l~~s~~~v~~~~~ 141 (194)
T PF04963_consen 122 YKKIAKKLGISEEEVQEAIE 141 (194)
T ss_dssp --------------------
T ss_pred hccccccccccccccccccc
Confidence 89999999999999976554
No 470
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=46.45 E-value=42 Score=33.66 Aligned_cols=38 Identities=11% Similarity=0.016 Sum_probs=27.6
Q ss_pred CHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 424 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 424 p~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
+..|-.+....+ .....++|||+.||||.+.|+.+++.
T Consensus 11 t~fqIL~ei~~~---qp~v~q~eIA~~lgiT~QaVsehiK~ 48 (260)
T COG1497 11 TRFQILSEIAVR---QPRVKQKEIAKKLGITLQAVSEHIKE 48 (260)
T ss_pred hHHHHHHHHHHh---CCCCCHHHHHHHcCCCHHHHHHHHHH
Confidence 333444444455 45689999999999999999887654
No 471
>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=46.28 E-value=25 Score=34.87 Aligned_cols=63 Identities=16% Similarity=0.268 Sum_probs=39.6
Q ss_pred hhhhHHHHHHhhccccCCCHHHHHHHHHHHHcCCcchhHHHHHHhhhCCCCchHHHHHHhhcChhHHHHhh
Q 011454 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (485)
Q Consensus 189 ~~~~~~~yl~~i~~~~~Lt~eee~~L~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l 259 (485)
+.+.+..|++...... + |.....++.++. .++.++...+|++|+.+++|..+|++.+++...+
T Consensus 95 irn~~~~~lr~~~~ir-~-p~~~~~~~~~~~------~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~ 157 (254)
T TIGR02850 95 IIGEIRRYLRDNNPIR-V-SRSLRDIAYKAL------QVRDKLISENSKEPTVSEIAKELKVPQEEVVFAL 157 (254)
T ss_pred HHHHHHHHHHhCCCcc-C-chHHHHHHHHHH------HHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 4455556666533211 1 223333433333 2455677789999999999999999999986543
No 472
>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=46.22 E-value=24 Score=30.13 Aligned_cols=23 Identities=13% Similarity=0.235 Sum_probs=20.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
+|..|+|+.+|||..|++.+...
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~~ 23 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 57899999999999999999766
No 473
>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=46.10 E-value=15 Score=31.92 Aligned_cols=26 Identities=19% Similarity=0.250 Sum_probs=22.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVALE 467 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rALk 467 (485)
|+..|+|+.+|||..|++.+...++-
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye~~GLl 26 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEEQGLL 26 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCC
Confidence 57899999999999999999887653
No 474
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=45.95 E-value=61 Score=31.10 Aligned_cols=40 Identities=28% Similarity=0.323 Sum_probs=28.5
Q ss_pred HHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 427 EREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 427 ER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
...|+...|- .++.++..++|+.||||+..|| .|+.+|..
T Consensus 17 ~~~I~~g~l~-pG~~L~e~eLae~lgVSRtpVR----EAL~~L~~ 56 (224)
T PRK11534 17 KNDIIRGNFQ-PDEKLRMSLLTSRYALGVGPLR----EALSQLVA 56 (224)
T ss_pred HHHHHhCCCC-CCCcCCHHHHHHHHCCChHHHH----HHHHHHHH
Confidence 3455655551 1356889999999999999987 56666653
No 475
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=45.87 E-value=25 Score=26.16 Aligned_cols=24 Identities=17% Similarity=0.318 Sum_probs=19.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
++.+|+++.+|+|+.|+.+..+..
T Consensus 4 l~~~ev~~~~g~s~~ti~~~~k~g 27 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTIYRLIKDG 27 (51)
T ss_dssp E-HHHHHHHHSS-HHHHHHHHHHH
T ss_pred ccHHHHHHHHCCCHHHHHHHHhcc
Confidence 478999999999999999887744
No 476
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=45.43 E-value=35 Score=35.03 Aligned_cols=39 Identities=15% Similarity=0.194 Sum_probs=29.6
Q ss_pred HHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011454 426 REREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 466 (485)
Q Consensus 426 rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rAL 466 (485)
+.+.|+.+.. +....+..+||+.+|||+.+|++.+++-.
T Consensus 5 r~~~il~~L~--~~~~~s~~~LA~~lgvsr~tV~~~l~~L~ 43 (319)
T PRK11886 5 VMLQLLSLLA--DGDFHSGEQLGEELGISRAAIWKHIQTLE 43 (319)
T ss_pred HHHHHHHHHH--cCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4556665544 13468999999999999999999887644
No 477
>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=45.28 E-value=41 Score=29.67 Aligned_cols=26 Identities=15% Similarity=0.213 Sum_probs=21.7
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
....|..|||+.+|+|+.+|++++.+
T Consensus 23 ~~~~s~~eia~~l~is~~~v~~~l~~ 48 (130)
T TIGR02944 23 SQPYSAAEIAEQTGLNAPTVSKILKQ 48 (130)
T ss_pred CCCccHHHHHHHHCcCHHHHHHHHHH
Confidence 35689999999999999999866553
No 478
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=45.17 E-value=58 Score=26.62 Aligned_cols=41 Identities=20% Similarity=0.265 Sum_probs=34.3
Q ss_pred hhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011454 421 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 421 ~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
.+|+-.|+.++.+.. .+.|++|+-+.+|++++.+...+.+-
T Consensus 2 ~klt~~~~IL~~ls~----~c~TLeeL~ekTgi~k~~LlV~LsrL 42 (72)
T PF05584_consen 2 KKLTVTQKILIILSK----RCCTLEELEEKTGISKNTLLVYLSRL 42 (72)
T ss_pred chhhHHHHHHHHHHh----ccCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 357778888888887 38999999999999999998877653
No 479
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=45.09 E-value=10 Score=29.89 Aligned_cols=23 Identities=13% Similarity=0.284 Sum_probs=18.4
Q ss_pred CCHHHHHHHHCCCHHHHH-HHHHH
Q 011454 442 LTWEDISKRIGLSRERVR-QVGLV 464 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVr-qi~~r 464 (485)
.+..|+|+.+|||+++|+ .+..|
T Consensus 13 ~~~~~lA~~lgis~st~s~~~~~r 36 (66)
T PF07022_consen 13 KSDKELAERLGISKSTLSNNWKKR 36 (66)
T ss_dssp SSCHHHHCCTT--HHHHH-HHHHS
T ss_pred CCHHHHHHHhCcCHHHhhHHHHhC
Confidence 377899999999999999 77776
No 480
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=45.04 E-value=44 Score=25.47 Aligned_cols=24 Identities=13% Similarity=0.093 Sum_probs=20.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
-|+...|+.||||+++|++.+++.
T Consensus 14 gs~~~AA~~l~is~~~vs~~i~~L 37 (60)
T PF00126_consen 14 GSISAAAEELGISQSAVSRQIKQL 37 (60)
T ss_dssp SSHHHHHHHCTSSHHHHHHHHHHH
T ss_pred CCHHHHHHHhhccchHHHHHHHHH
Confidence 499999999999999998655443
No 481
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=44.83 E-value=16 Score=31.12 Aligned_cols=24 Identities=8% Similarity=0.163 Sum_probs=21.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVA 465 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rA 465 (485)
++..|+|+.+|||+.+++.+...+
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye~~G 25 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDRLG 25 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCC
Confidence 689999999999999999987655
No 482
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=44.44 E-value=33 Score=29.28 Aligned_cols=36 Identities=11% Similarity=0.079 Sum_probs=25.5
Q ss_pred HHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 427 EREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 427 ER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
|+.+|...+- ..+-...+.|+.||||+.|+++.+++
T Consensus 56 Er~~i~~aL~--~~~gn~s~AAr~LGIsRsTL~rKLkr 91 (95)
T PRK00430 56 EAPLLDMVMQ--YTRGNQTRAALMLGINRGTLRKKLKK 91 (95)
T ss_pred HHHHHHHHHH--HcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 5555544431 23567999999999999998776654
No 483
>PRK08359 transcription factor; Validated
Probab=44.14 E-value=29 Score=33.10 Aligned_cols=25 Identities=32% Similarity=0.634 Sum_probs=22.6
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 439 KECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 439 ~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
..++|++|+|+.+|+++.+|++++.
T Consensus 96 ~kglSQeeLA~~lgvs~stI~~iE~ 120 (176)
T PRK08359 96 KSGLSYEELSHEVGLSVNDLRRIAH 120 (176)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 4689999999999999999998864
No 484
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=44.05 E-value=61 Score=31.85 Aligned_cols=40 Identities=25% Similarity=0.176 Sum_probs=27.8
Q ss_pred HHHHHhhHhccCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 427 EREIIRLYYGLDKECL-TWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 427 ER~VI~LryGL~~eg~-S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
...|+...|.- ++.+ +-.++|+.||||+.+|| .|++.|..
T Consensus 18 ~~~I~~g~l~p-G~~LpsE~eLae~~gVSRtpVR----EAL~~L~~ 58 (253)
T PRK11523 18 KERIEQGVYLV-GDKLPAERFIADEKNVSRTVVR----EAIIMLEV 58 (253)
T ss_pred HHHHHcCCCCC-CCCCCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 34455555521 3567 47899999999999997 66666653
No 485
>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=43.87 E-value=17 Score=31.74 Aligned_cols=26 Identities=12% Similarity=0.219 Sum_probs=23.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVALE 467 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rALk 467 (485)
||..|+|+.+|||+.|++.....++-
T Consensus 1 ~~ige~a~~~gvs~~tLryYe~~GLi 26 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEEKGLL 26 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 68899999999999999999887654
No 486
>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=43.77 E-value=1.5e+02 Score=26.39 Aligned_cols=25 Identities=24% Similarity=0.271 Sum_probs=18.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 440 ECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 440 eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
-|.|-..||..+|++...|+.....
T Consensus 71 ~GFsD~~IA~l~~~~e~~vr~~R~~ 95 (123)
T PF02787_consen 71 LGFSDRQIARLWGVSEEEVRELRKE 95 (123)
T ss_dssp TT--HHHHHHHHTS-HHHHHHHHHH
T ss_pred cCCCHHHHHhccCCCHHHHHHHHHH
Confidence 6799999999999999999876543
No 487
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=43.66 E-value=62 Score=27.27 Aligned_cols=33 Identities=18% Similarity=0.366 Sum_probs=24.0
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHH
Q 011454 440 ECLTWEDISKRIGLSRERVRQVGLV----ALEKLKHAAR 474 (485)
Q Consensus 440 eg~S~eEIAe~LgIS~~tVrqi~~r----ALkKLRk~L~ 474 (485)
.++| ++|+..|||+.++++++.. .+..|.+.+.
T Consensus 44 ~glS--qLAe~~GIs~stLs~iE~g~~~Ps~~tL~kI~~ 80 (89)
T TIGR02684 44 RGMT--QLARKTGLSRESLYKALSGKGNPTFDTILKVTK 80 (89)
T ss_pred CChH--HHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 4566 6999999999999999865 2444444444
No 488
>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=43.41 E-value=82 Score=24.91 Aligned_cols=31 Identities=32% Similarity=0.505 Sum_probs=21.7
Q ss_pred HHHHcCCCCCHHHHHHHhCCC-HHHHHHHHHH
Q 011454 359 RLEEKGVTPSVDRIAEYLNMS-QKKVRNATEV 389 (485)
Q Consensus 359 ~L~~~gr~ps~eEIae~L~is-~eev~~~l~~ 389 (485)
.+.+.|..|+..||++.+|+. ...|...+..
T Consensus 18 ~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~ 49 (65)
T PF01726_consen 18 YIEENGYPPTVREIAEALGLKSTSTVQRHLKA 49 (65)
T ss_dssp HHHHHSS---HHHHHHHHTSSSHHHHHHHHHH
T ss_pred HHHHcCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 345689999999999999996 7777665544
No 489
>PRK13705 plasmid-partitioning protein SopA; Provisional
Probab=43.19 E-value=32 Score=36.60 Aligned_cols=54 Identities=13% Similarity=0.116 Sum_probs=37.3
Q ss_pred HHHHHHHHHhhCCHHHHHHHhhHhcc-------CCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011454 412 KDEVNKLIIVTLGEREREIIRLYYGL-------DKECLTWEDISKRIGLSRERVRQVGLVAL 466 (485)
Q Consensus 412 ~e~L~~~L~~~Lp~rER~VI~LryGL-------~~eg~S~eEIAe~LgIS~~tVrqi~~rAL 466 (485)
.+.++.|| +.+....+.+...-|+= ....++..|+|+.+|||..|+|..+..++
T Consensus 4 ~~~~~~~~-~~~~~~~~~~~~~~~~~~~p~~~k~~r~~~i~e~A~~~gvs~~tiR~ye~~gl 64 (388)
T PRK13705 4 METLNQCI-NAGHEMTKAIAIAQFNDDSPEARKITRRWRIGEAADLVGVSSQAIRDAEKAGR 64 (388)
T ss_pred HHHHHHHH-HHHHHHHHHHHHHHhCcCCCccccccCCCCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 44566677 66666666666554410 11346899999999999999998866543
No 490
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=43.17 E-value=1e+02 Score=30.95 Aligned_cols=43 Identities=14% Similarity=0.247 Sum_probs=33.8
Q ss_pred hhCCHHHHHHHh-hHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 421 VTLGEREREIIR-LYYGLDKECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 421 ~~Lp~rER~VI~-LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
..|++.++..+. +.--++..+.+..+||+.||++..++++...
T Consensus 234 ~~l~~~~~~~L~al~~~~~~~~~~~~~ia~~lg~~~~~~~~~~e 277 (305)
T TIGR00635 234 LGLDEIDRKLLSVLIEQFQGGPVGLKTLAAALGEDADTIEDVYE 277 (305)
T ss_pred CCCCHHHHHHHHHHHHHhCCCcccHHHHHHHhCCCcchHHHhhh
Confidence 578999999887 4332223568999999999999999988665
No 491
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=43.16 E-value=43 Score=33.32 Aligned_cols=38 Identities=18% Similarity=0.233 Sum_probs=29.1
Q ss_pred HHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 425 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 425 ~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
+|+..|+.+--- ....+..|+|+.||||..|||+=+..
T Consensus 7 eR~~~I~~~l~~--~~~v~v~eLa~~~~VS~~TIRRDL~~ 44 (252)
T PRK10681 7 ERIGQLLQALKR--SDKLHLKDAAALLGVSEMTIRRDLNA 44 (252)
T ss_pred HHHHHHHHHHHH--cCCCcHHHHHHHhCCCHHHHHHHHHH
Confidence 466666665431 24589999999999999999988875
No 492
>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=43.15 E-value=2.2e+02 Score=30.81 Aligned_cols=83 Identities=16% Similarity=0.213 Sum_probs=50.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH------------HhhhcccCCCCCcchHHHHHHHHHHHHHHHhhCCHHHHHHHh
Q 011454 365 VTPSVDRIAEYLNMSQKKVRNATEVL------------AYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIR 432 (485)
Q Consensus 365 r~ps~eEIae~L~is~eev~~~l~~~------------~~l~D~~~e~~pee~~e~~el~e~L~~~L~~~Lp~rER~VI~ 432 (485)
++-+..+||+.+|+.+.+|.++.... .++.......++.+.+....++..|.++| +.=++
T Consensus 317 kPLtlkdiA~~lglheSTVSRav~~Kyi~tp~Gi~~lk~FFs~~~~~~~~g~~~S~~~Ik~~I~~lI-~~E~~------- 388 (429)
T TIGR02395 317 KPLTLREVAEELGLHESTISRAINNKYLQTPRGVFELKYFFSRGVQTDSGEGEVSSTAIKALIKELI-AAEDK------- 388 (429)
T ss_pred cCCcHHHHHHHhCCCccchhhhhcCceEecCCceEEHHHhcCCccCCCCCCCccCHHHHHHHHHHHH-HhcCC-------
Confidence 34578999999999999999886553 33332221111112244555555665555 11110
Q ss_pred hHhccCCCCCCHHHHHHHH-----CCCHHHHHHH
Q 011454 433 LYYGLDKECLTWEDISKRI-----GLSRERVRQV 461 (485)
Q Consensus 433 LryGL~~eg~S~eEIAe~L-----gIS~~tVrqi 461 (485)
..++|-++||+.| .|++-||-+.
T Consensus 389 ------~~PlSD~~I~~~L~~~Gi~IaRRTVaKY 416 (429)
T TIGR02395 389 ------RKPLSDQKIAELLKEKGIKIARRTVAKY 416 (429)
T ss_pred ------CCCCCHHHHHHHHHhcCCCeehHHHHHH
Confidence 2568899999988 6787777544
No 493
>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=43.15 E-value=17 Score=32.26 Aligned_cols=26 Identities=23% Similarity=0.285 Sum_probs=23.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVALE 467 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rALk 467 (485)
||..|+|+.+|||+.|++.+...++-
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~~GLl 26 (127)
T cd01108 1 MNIGEAAKLTGLSAKMIRYYEEIGLI 26 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 58899999999999999998887654
No 494
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=43.11 E-value=18 Score=31.36 Aligned_cols=26 Identities=23% Similarity=0.198 Sum_probs=22.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVALE 467 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rALk 467 (485)
+|..|+|+.+|||..|++.+...++-
T Consensus 1 y~Ige~A~~~gvs~~tlR~ye~~GLl 26 (107)
T cd01111 1 YSISQLALDAGVSVHIVRDYLLRGLL 26 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999887653
No 495
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=42.89 E-value=18 Score=32.10 Aligned_cols=26 Identities=27% Similarity=0.316 Sum_probs=22.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVALE 467 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rALk 467 (485)
|+..|+|+.+|||+.|++.+...++-
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~~GLl 26 (126)
T cd04783 1 LTIGELAKAAGVNVETIRYYQRRGLL 26 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999998877654
No 496
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=42.87 E-value=24 Score=34.02 Aligned_cols=27 Identities=11% Similarity=0.161 Sum_probs=21.9
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 441 CLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 441 g~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
..|.+|||..+|+|+++|++ ++++|++
T Consensus 169 ~~t~~~lA~~lG~sretvsR----~L~~L~~ 195 (226)
T PRK10402 169 HEKHTQAAEYLGVSYRHLLY----VLAQFIQ 195 (226)
T ss_pred cchHHHHHHHHCCcHHHHHH----HHHHHHH
Confidence 36899999999999999974 5556654
No 497
>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=42.84 E-value=63 Score=31.26 Aligned_cols=40 Identities=28% Similarity=0.280 Sum_probs=26.2
Q ss_pred HHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011454 428 REIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 471 (485)
Q Consensus 428 R~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~rALkKLRk 471 (485)
..|..-.|.-|..=-|-.|+|+++|||+.||| +|+..|..
T Consensus 11 ~~I~~g~~~~G~~LPsE~eLa~~~gVSR~TVR----~Al~~L~~ 50 (233)
T TIGR02404 11 QKITHGQYKEGDYLPSEHELMDQYGASRETVR----KALNLLTE 50 (233)
T ss_pred HHHHhCCCCCCCCCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 33444444222222489999999999999998 56555543
No 498
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=42.83 E-value=18 Score=32.17 Aligned_cols=26 Identities=23% Similarity=0.256 Sum_probs=22.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011454 442 LTWEDISKRIGLSRERVRQVGLVALE 467 (485)
Q Consensus 442 ~S~eEIAe~LgIS~~tVrqi~~rALk 467 (485)
|+..|+|+.+|||..|++.+...++-
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~~GLl 26 (127)
T TIGR02044 1 MNIGQVAKLTGLSSKMIRYYEEKGLI 26 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999998877653
No 499
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=42.80 E-value=36 Score=32.39 Aligned_cols=37 Identities=22% Similarity=0.391 Sum_probs=27.4
Q ss_pred HHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011454 425 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 463 (485)
Q Consensus 425 ~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~ 463 (485)
+|++.|+.+--- ..-.+..++|+.||+|..|||+-+.
T Consensus 7 ~R~~~Il~~l~~--~~~~~~~~La~~~~vS~~TiRRDl~ 43 (185)
T PRK04424 7 ERQKALQELIEE--NPFITDEELAEKFGVSIQTIRLDRM 43 (185)
T ss_pred HHHHHHHHHHHH--CCCEEHHHHHHHHCcCHHHHHHHHH
Confidence 455556655331 2447999999999999999998765
No 500
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=42.39 E-value=78 Score=31.81 Aligned_cols=47 Identities=9% Similarity=0.018 Sum_probs=37.1
Q ss_pred HHHHHHHHhhCCHHHHHHHhhHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011454 413 DEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 464 (485)
Q Consensus 413 e~L~~~L~~~Lp~rER~VI~LryGL~~eg~S~eEIAe~LgIS~~tVrqi~~r 464 (485)
+.-+++| ..++-++-.+|.... +.-|+..-|+.||||+.+|++.+++
T Consensus 5 ~~~~~~~-~~~~l~~L~~f~~va----~~gs~s~AA~~L~iSQpavS~~I~~ 51 (311)
T PRK10086 5 EMRNRLL-NGWQLSKLHTFEVAA----RHQSFALAADELSLTPSAVSHRINQ 51 (311)
T ss_pred HHHHhhh-cCCcHHHHHHHHHHH----HcCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3445566 788888888887765 6789999999999999999865544
Done!