Query 010521
Match_columns 508
No_of_seqs 250 out of 1622
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 01:30:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010521.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010521hhsearch_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 1.1E-57 2.3E-62 479.7 34.3 309 191-506 60-412 (415)
2 PRK07406 RNA polymerase sigma 100.0 9.5E-57 2.1E-61 469.0 34.7 308 191-505 63-372 (373)
3 PRK05949 RNA polymerase sigma 100.0 2E-55 4.4E-60 453.1 35.1 308 190-506 17-326 (327)
4 TIGR02997 Sig70-cyanoRpoD RNA 100.0 4.2E-55 9.1E-60 445.5 32.7 295 192-493 2-298 (298)
5 PRK07405 RNA polymerase sigma 100.0 1.8E-54 3.9E-59 444.6 34.8 307 191-506 8-316 (317)
6 PRK05901 RNA polymerase sigma 100.0 5E-54 1.1E-58 461.7 31.9 298 190-506 210-509 (509)
7 COG0568 RpoD DNA-directed RNA 100.0 6.7E-53 1.4E-57 431.1 29.4 310 190-505 8-341 (342)
8 PRK07921 RNA polymerase sigma 100.0 3.6E-52 7.8E-57 428.3 32.8 296 191-505 26-323 (324)
9 PRK09210 RNA polymerase sigma 100.0 1.2E-50 2.6E-55 423.9 31.4 272 189-506 94-367 (367)
10 PRK05658 RNA polymerase sigma 100.0 3.2E-47 6.9E-52 422.0 31.6 272 192-506 345-618 (619)
11 PRK05657 RNA polymerase sigma 100.0 1.3E-43 2.9E-48 365.3 31.5 270 187-502 49-320 (325)
12 PRK06596 RNA polymerase factor 100.0 4.6E-43 9.9E-48 355.1 31.5 265 184-498 10-282 (284)
13 TIGR02393 RpoD_Cterm RNA polym 100.0 1.6E-43 3.5E-48 349.1 27.3 236 265-506 1-238 (238)
14 PRK07500 rpoH2 RNA polymerase 100.0 1.4E-42 2.9E-47 352.5 31.9 264 191-500 6-281 (289)
15 TIGR02392 rpoH_proteo alternat 100.0 2.5E-42 5.3E-47 347.1 30.3 259 192-497 2-269 (270)
16 TIGR02394 rpoS_proteo RNA poly 100.0 1.9E-40 4.2E-45 335.7 31.8 269 187-501 9-279 (285)
17 PRK07122 RNA polymerase sigma 100.0 3.8E-40 8.3E-45 330.6 27.2 220 264-496 40-263 (264)
18 PRK07408 RNA polymerase sigma 100.0 1.5E-38 3.3E-43 317.5 29.4 226 264-499 25-254 (256)
19 TIGR02850 spore_sigG RNA polym 100.0 4.7E-38 1E-42 313.3 29.5 244 200-496 10-254 (254)
20 PRK05911 RNA polymerase sigma 100.0 1.7E-37 3.6E-42 310.2 29.6 227 264-498 23-255 (257)
21 PRK08215 sporulation sigma fac 100.0 6.6E-37 1.4E-41 305.5 29.6 242 202-496 15-257 (258)
22 COG1191 FliA DNA-directed RNA 100.0 3.9E-37 8.4E-42 304.4 27.2 240 203-498 3-246 (247)
23 PRK06288 RNA polymerase sigma 100.0 1.2E-35 2.6E-40 298.1 29.5 251 200-499 6-263 (268)
24 TIGR02941 Sigma_B RNA polymera 100.0 2.1E-35 4.6E-40 293.9 30.1 242 204-496 8-253 (255)
25 TIGR02885 spore_sigF RNA polym 100.0 1.1E-34 2.5E-39 284.3 26.7 220 264-496 11-231 (231)
26 TIGR02980 SigBFG RNA polymeras 100.0 3E-34 6.6E-39 280.3 27.2 222 263-496 2-226 (227)
27 PRK07670 RNA polymerase sigma 100.0 7.5E-34 1.6E-38 282.5 28.9 223 264-497 22-250 (251)
28 PRK08583 RNA polymerase sigma 100.0 2.2E-33 4.7E-38 279.8 29.5 244 204-498 8-255 (257)
29 PRK05572 sporulation sigma fac 100.0 2.4E-33 5.2E-38 279.0 29.5 245 198-497 6-251 (252)
30 TIGR02479 FliA_WhiG RNA polyme 100.0 5.5E-33 1.2E-37 271.3 25.4 217 269-496 1-223 (224)
31 PRK06986 fliA flagellar biosyn 100.0 1.5E-31 3.2E-36 263.4 26.7 224 261-498 5-234 (236)
32 PRK12427 flagellar biosynthesi 100.0 1.2E-31 2.6E-36 264.2 25.4 210 264-495 15-230 (231)
33 PRK05803 sporulation sigma fac 100.0 2.2E-28 4.7E-33 240.6 25.2 213 192-499 17-230 (233)
34 TIGR02846 spore_sigmaK RNA pol 99.9 5.5E-25 1.2E-29 215.8 24.0 210 192-496 15-226 (227)
35 PRK08301 sporulation sigma fac 99.9 5.9E-25 1.3E-29 215.9 23.9 208 195-498 22-232 (234)
36 TIGR02835 spore_sigmaE RNA pol 99.9 1.6E-23 3.4E-28 206.4 22.8 201 203-498 31-232 (234)
37 PRK08295 RNA polymerase factor 99.9 4.6E-23 9.9E-28 197.8 20.7 182 264-500 24-206 (208)
38 PRK09648 RNA polymerase sigma 99.9 7.9E-23 1.7E-27 193.9 21.0 179 206-497 6-188 (189)
39 PRK09646 RNA polymerase sigma 99.9 9.1E-23 2E-27 194.8 19.6 184 203-498 9-192 (194)
40 PRK05602 RNA polymerase sigma 99.9 1.3E-22 2.9E-27 191.9 19.8 162 264-501 20-181 (186)
41 PRK12513 RNA polymerase sigma 99.9 1.1E-22 2.4E-27 193.7 19.0 167 264-501 26-192 (194)
42 PRK11922 RNA polymerase sigma 99.9 4.6E-22 1E-26 195.5 20.2 193 201-498 7-199 (231)
43 PRK12519 RNA polymerase sigma 99.9 4.6E-22 1E-26 189.2 19.4 180 206-497 11-190 (194)
44 PRK12524 RNA polymerase sigma 99.9 5E-22 1.1E-26 190.0 19.6 163 264-500 26-188 (196)
45 TIGR02859 spore_sigH RNA polym 99.9 6.6E-22 1.4E-26 188.1 20.0 178 264-496 19-197 (198)
46 PRK11923 algU RNA polymerase s 99.9 8.8E-22 1.9E-26 187.2 20.7 188 205-498 1-188 (193)
47 TIGR02952 Sig70_famx2 RNA poly 99.9 5.7E-22 1.2E-26 183.7 18.9 160 264-496 11-170 (170)
48 TIGR02948 SigW_bacill RNA poly 99.9 7.3E-22 1.6E-26 185.9 19.9 168 264-497 18-185 (187)
49 PRK12514 RNA polymerase sigma 99.9 7.3E-22 1.6E-26 185.6 19.3 160 264-497 19-178 (179)
50 PRK12534 RNA polymerase sigma 99.9 7.4E-22 1.6E-26 186.8 19.4 162 264-497 25-186 (187)
51 PRK09641 RNA polymerase sigma 99.9 2E-21 4.3E-26 183.0 20.1 168 264-497 18-185 (187)
52 PRK06759 RNA polymerase factor 99.9 1E-21 2.2E-26 179.6 17.5 150 264-495 4-153 (154)
53 PRK09652 RNA polymerase sigma 99.9 1.8E-21 3.9E-26 181.3 19.3 168 264-497 10-177 (182)
54 PRK12538 RNA polymerase sigma 99.9 1.5E-21 3.3E-26 192.7 19.9 162 264-501 63-224 (233)
55 PRK13919 putative RNA polymera 99.9 2.2E-21 4.8E-26 183.2 19.7 162 264-497 23-184 (186)
56 PRK12537 RNA polymerase sigma 99.9 3.9E-21 8.5E-26 181.6 19.8 159 264-496 23-181 (182)
57 TIGR02939 RpoE_Sigma70 RNA pol 99.9 6E-21 1.3E-25 180.2 20.6 168 264-497 20-187 (190)
58 PRK12526 RNA polymerase sigma 99.9 7.2E-21 1.6E-25 183.8 20.9 167 264-499 38-204 (206)
59 PRK06811 RNA polymerase factor 99.9 4.9E-21 1.1E-25 182.2 19.2 159 264-496 18-179 (189)
60 PRK12531 RNA polymerase sigma 99.9 6.7E-21 1.5E-25 182.0 19.6 187 204-500 7-193 (194)
61 PRK09640 RNA polymerase sigma 99.9 5.8E-21 1.2E-25 181.4 17.5 173 250-498 8-184 (188)
62 PRK11924 RNA polymerase sigma 99.9 1.8E-20 3.8E-25 174.2 20.0 165 263-499 12-176 (179)
63 PRK12542 RNA polymerase sigma 99.9 4.5E-21 9.8E-26 181.5 16.1 174 261-505 6-179 (185)
64 PRK12515 RNA polymerase sigma 99.9 1.8E-20 3.8E-25 178.0 20.1 163 264-501 22-184 (189)
65 PRK09643 RNA polymerase sigma 99.9 3.6E-20 7.8E-25 177.0 20.9 159 264-499 27-185 (192)
66 PRK09638 RNA polymerase sigma 99.9 2.3E-20 5E-25 174.5 18.1 158 264-497 18-175 (176)
67 TIGR02984 Sig-70_plancto1 RNA 99.9 3.2E-20 7E-25 174.8 19.1 179 262-496 5-188 (189)
68 PRK12543 RNA polymerase sigma 99.9 4.1E-20 8.9E-25 174.2 19.8 165 262-500 5-169 (179)
69 TIGR03001 Sig-70_gmx1 RNA poly 99.9 4.6E-20 1E-24 183.4 20.9 168 264-504 39-217 (244)
70 TIGR02954 Sig70_famx3 RNA poly 99.8 4.8E-20 1E-24 171.7 18.8 153 264-497 16-168 (169)
71 PRK12536 RNA polymerase sigma 99.8 6E-20 1.3E-24 173.4 19.6 158 264-498 21-179 (181)
72 PRK09649 RNA polymerase sigma 99.8 4.1E-20 8.9E-25 175.5 18.1 177 204-498 4-180 (185)
73 PRK09645 RNA polymerase sigma 99.8 6.1E-20 1.3E-24 171.4 18.9 164 262-500 7-170 (173)
74 PRK09415 RNA polymerase factor 99.8 5E-20 1.1E-24 173.8 18.4 164 262-498 14-177 (179)
75 TIGR02985 Sig70_bacteroi1 RNA 99.8 1.9E-20 4.2E-25 170.7 15.1 161 264-496 1-161 (161)
76 TIGR02999 Sig-70_X6 RNA polyme 99.8 7.5E-20 1.6E-24 172.1 19.5 160 264-496 17-182 (183)
77 TIGR02937 sigma70-ECF RNA poly 99.8 4.8E-20 1E-24 164.6 17.1 157 265-496 2-158 (158)
78 PRK12539 RNA polymerase sigma 99.8 1.4E-19 3.1E-24 171.3 20.9 158 264-499 21-182 (184)
79 PRK12520 RNA polymerase sigma 99.8 5.1E-20 1.1E-24 175.1 17.8 182 264-500 2-183 (191)
80 TIGR02989 Sig-70_gvs1 RNA poly 99.8 4E-20 8.8E-25 169.7 16.3 159 264-496 1-159 (159)
81 PRK12522 RNA polymerase sigma 99.8 8.8E-20 1.9E-24 170.7 18.6 166 264-498 3-169 (173)
82 PRK12512 RNA polymerase sigma 99.8 1.4E-19 3.1E-24 170.8 20.1 157 264-499 22-182 (184)
83 PRK12518 RNA polymerase sigma 99.8 7.6E-20 1.7E-24 170.9 17.2 162 264-500 11-172 (175)
84 PRK09642 RNA polymerase sigma 99.8 8.5E-20 1.8E-24 168.4 16.2 156 271-499 2-157 (160)
85 COG1595 RpoE DNA-directed RNA 99.8 4.2E-19 9.2E-24 167.9 20.1 169 258-499 9-178 (182)
86 PRK12533 RNA polymerase sigma 99.8 3.6E-19 7.8E-24 174.0 19.6 169 263-499 17-185 (216)
87 PRK12535 RNA polymerase sigma 99.8 4.8E-19 1E-23 170.2 20.0 164 264-503 25-188 (196)
88 PRK12516 RNA polymerase sigma 99.8 3.9E-19 8.4E-24 169.5 18.9 160 263-500 9-168 (187)
89 PRK12547 RNA polymerase sigma 99.8 4.9E-19 1.1E-23 164.6 18.5 161 261-499 3-163 (164)
90 PRK12529 RNA polymerase sigma 99.8 2.6E-19 5.5E-24 169.0 16.1 164 261-496 10-175 (178)
91 PRK09644 RNA polymerase sigma 99.8 4.7E-19 1E-23 164.6 17.6 158 266-500 3-160 (165)
92 TIGR02983 SigE-fam_strep RNA p 99.8 4.4E-19 9.5E-24 163.7 17.3 156 262-497 4-159 (162)
93 TIGR02947 SigH_actino RNA poly 99.8 2.8E-19 6E-24 170.4 16.5 172 263-498 10-181 (193)
94 PRK09647 RNA polymerase sigma 99.8 7.9E-19 1.7E-23 169.7 19.3 168 262-503 26-193 (203)
95 PRK12523 RNA polymerase sigma 99.8 3.5E-19 7.7E-24 166.7 15.7 160 264-498 10-169 (172)
96 PRK09639 RNA polymerase sigma 99.8 1.2E-18 2.5E-23 161.4 18.4 161 263-499 2-162 (166)
97 PRK08241 RNA polymerase factor 99.8 2.3E-18 4.9E-23 178.0 20.6 174 264-494 19-199 (339)
98 PRK12528 RNA polymerase sigma 99.8 1.4E-18 2.9E-23 160.7 16.4 157 264-495 4-160 (161)
99 PRK12532 RNA polymerase sigma 99.8 1.9E-18 4.1E-23 164.9 17.9 181 267-501 8-189 (195)
100 PRK12530 RNA polymerase sigma 99.8 2.4E-18 5.2E-23 164.0 18.2 176 268-500 11-186 (189)
101 PRK12545 RNA polymerase sigma 99.8 2.3E-18 5E-23 165.8 18.2 181 268-501 12-192 (201)
102 PRK12541 RNA polymerase sigma 99.8 2.8E-18 6.1E-23 158.5 18.1 156 263-495 4-159 (161)
103 TIGR02943 Sig70_famx1 RNA poly 99.8 2.3E-18 5E-23 164.1 17.9 176 268-498 6-181 (188)
104 PRK12544 RNA polymerase sigma 99.8 3.3E-18 7.2E-23 165.8 18.3 180 266-499 20-199 (206)
105 PRK12540 RNA polymerase sigma 99.8 6.1E-18 1.3E-22 160.6 18.6 160 264-501 5-164 (182)
106 PRK09637 RNA polymerase sigma 99.8 7.4E-18 1.6E-22 159.8 18.8 154 266-498 3-156 (181)
107 TIGR02950 SigM_subfam RNA poly 99.8 1.3E-18 2.8E-23 158.9 12.8 153 270-496 1-153 (154)
108 PRK07037 extracytoplasmic-func 99.8 7.6E-18 1.6E-22 155.6 17.9 158 268-498 2-159 (163)
109 PRK12517 RNA polymerase sigma 99.8 8.2E-18 1.8E-22 160.4 18.6 163 259-500 18-180 (188)
110 TIGR02960 SigX5 RNA polymerase 99.8 5.4E-18 1.2E-22 173.8 18.6 186 263-498 4-192 (324)
111 PRK09651 RNA polymerase sigma 99.8 1.2E-17 2.6E-22 156.6 17.5 162 263-499 9-170 (172)
112 TIGR02895 spore_sigI RNA polym 99.8 3E-17 6.4E-22 160.7 20.6 175 264-484 10-196 (218)
113 PRK12527 RNA polymerase sigma 99.8 1.1E-17 2.4E-22 154.2 16.6 155 271-499 2-156 (159)
114 PRK12546 RNA polymerase sigma 99.8 2.4E-17 5.3E-22 157.5 18.4 156 264-498 8-163 (188)
115 TIGR02959 SigZ RNA polymerase 99.8 2E-17 4.4E-22 154.9 17.4 149 271-498 2-150 (170)
116 PRK12511 RNA polymerase sigma 99.7 4.3E-17 9.4E-22 154.9 17.3 158 266-500 6-163 (182)
117 PRK12525 RNA polymerase sigma 99.7 6.2E-17 1.3E-21 151.1 16.7 159 264-497 9-167 (168)
118 PRK09047 RNA polymerase factor 99.7 2.5E-16 5.5E-21 144.8 15.2 156 286-500 2-158 (161)
119 PRK09636 RNA polymerase sigma 99.7 2.7E-16 5.9E-21 159.8 16.7 160 264-497 4-164 (293)
120 PRK06704 RNA polymerase factor 99.7 6.5E-16 1.4E-20 152.4 17.6 149 264-498 18-166 (228)
121 TIGR02957 SigX4 RNA polymerase 99.7 1.7E-15 3.7E-20 153.4 17.2 156 268-497 1-157 (281)
122 PRK09635 sigI RNA polymerase s 99.7 3E-15 6.5E-20 152.6 17.6 161 264-496 5-166 (290)
123 PRK09191 two-component respons 99.6 3.4E-14 7.4E-19 139.7 13.5 136 265-497 2-137 (261)
124 TIGR03209 P21_Cbot clostridium 99.5 5.6E-14 1.2E-18 127.3 12.4 136 266-482 1-141 (142)
125 PF07638 Sigma70_ECF: ECF sigm 99.5 1.1E-12 2.4E-17 125.1 18.5 163 264-497 17-184 (185)
126 PRK08311 putative RNA polymera 99.5 1.6E-12 3.5E-17 129.0 20.2 78 264-341 18-97 (237)
127 PF04542 Sigma70_r2: Sigma-70 99.3 1.4E-11 3.1E-16 97.8 7.7 70 269-338 1-70 (71)
128 PF04545 Sigma70_r4: Sigma-70, 99.2 5.7E-11 1.2E-15 89.7 7.2 50 441-494 1-50 (50)
129 PF08281 Sigma70_r4_2: Sigma-7 98.9 3.7E-09 8E-14 80.8 7.0 53 436-492 2-54 (54)
130 PRK06930 positive control sigm 98.7 1E-07 2.2E-12 90.4 9.9 71 425-499 95-165 (170)
131 PF04539 Sigma70_r3: Sigma-70 98.6 8.2E-08 1.8E-12 78.7 6.6 76 348-428 1-77 (78)
132 PRK00118 putative DNA-binding 98.5 5.4E-07 1.2E-11 78.7 8.8 55 444-501 16-70 (104)
133 cd06171 Sigma70_r4 Sigma70, re 98.3 1.7E-06 3.6E-11 64.0 6.6 54 436-493 2-55 (55)
134 TIGR00721 tfx DNA-binding prot 98.2 3.8E-06 8.2E-11 76.9 8.0 58 444-505 5-62 (137)
135 PRK03975 tfx putative transcri 98.2 4.6E-06 9.9E-11 76.7 8.2 52 444-499 5-56 (141)
136 PRK04217 hypothetical protein; 98.2 3.6E-06 7.8E-11 74.3 5.9 56 444-502 41-96 (110)
137 PF04297 UPF0122: Putative hel 98.1 1.3E-05 2.8E-10 69.6 9.0 56 444-502 16-71 (101)
138 PF00140 Sigma70_r1_2: Sigma-7 98.0 3E-06 6.5E-11 60.5 1.4 33 191-223 2-34 (37)
139 smart00421 HTH_LUXR helix_turn 97.8 4.3E-05 9.4E-10 57.4 6.1 46 444-493 2-47 (58)
140 TIGR01636 phage_rinA phage tra 97.8 7.9E-05 1.7E-09 67.9 8.7 62 433-496 71-132 (134)
141 PF00196 GerE: Bacterial regul 97.7 7E-05 1.5E-09 58.1 5.8 47 444-494 2-48 (58)
142 PF07374 DUF1492: Protein of u 97.7 0.00013 2.9E-09 63.2 7.9 56 433-492 43-99 (100)
143 cd06170 LuxR_C_like C-terminal 97.7 9.4E-05 2E-09 55.8 6.0 45 446-494 1-45 (57)
144 PF04967 HTH_10: HTH DNA bindi 97.6 0.00018 3.8E-09 55.5 6.5 47 446-492 1-51 (53)
145 TIGR03879 near_KaiC_dom probab 97.6 0.00011 2.3E-09 60.3 5.7 47 438-487 9-55 (73)
146 PRK15411 rcsA colanic acid cap 97.5 0.0002 4.4E-09 69.6 6.1 46 445-494 137-182 (207)
147 TIGR01321 TrpR trp operon repr 97.4 0.00021 4.5E-09 61.4 5.2 50 436-485 23-76 (94)
148 PRK15201 fimbriae regulatory p 97.4 0.0003 6.4E-09 66.9 6.4 47 444-494 132-178 (198)
149 PRK11475 DNA-binding transcrip 97.4 0.0003 6.5E-09 68.7 6.3 46 444-493 133-178 (207)
150 PRK13719 conjugal transfer tra 97.4 0.00032 7E-09 68.8 6.2 50 439-493 138-187 (217)
151 PRK10840 transcriptional regul 97.4 0.00032 6.9E-09 67.5 6.1 46 444-493 149-194 (216)
152 TIGR03541 reg_near_HchA LuxR f 97.3 0.00043 9.3E-09 68.5 6.1 47 444-494 170-216 (232)
153 TIGR03020 EpsA transcriptional 97.3 0.00046 1E-08 69.3 6.1 47 444-494 189-235 (247)
154 PF02001 DUF134: Protein of un 97.3 0.00066 1.4E-08 59.6 6.3 53 445-500 41-93 (106)
155 COG4566 TtrR Response regulato 97.3 0.0012 2.7E-08 63.4 8.6 68 432-504 130-197 (202)
156 COG2197 CitB Response regulato 97.3 0.00047 1E-08 67.4 5.9 45 445-493 148-192 (211)
157 PRK10100 DNA-binding transcrip 97.2 0.00058 1.2E-08 67.1 6.4 47 444-494 154-200 (216)
158 PF13936 HTH_38: Helix-turn-he 97.2 0.00048 1E-08 50.9 4.0 41 444-487 3-43 (44)
159 PRK10188 DNA-binding transcrip 97.2 0.00068 1.5E-08 67.6 6.3 46 445-494 179-224 (240)
160 PRK13870 transcriptional regul 97.2 0.00065 1.4E-08 67.5 6.1 45 445-493 173-217 (234)
161 COG2771 CsgD DNA-binding HTH d 97.0 0.0021 4.5E-08 49.9 6.4 47 444-494 3-49 (65)
162 PRK09483 response regulator; P 97.0 0.0013 2.8E-08 62.0 6.1 46 444-493 147-192 (217)
163 PRK15369 two component system 96.8 0.0025 5.4E-08 58.7 6.4 46 444-493 148-193 (211)
164 COG2739 Uncharacterized protei 96.8 0.0062 1.3E-07 52.7 8.0 50 444-496 16-65 (105)
165 COG3413 Predicted DNA binding 96.7 0.0031 6.6E-08 61.8 6.5 52 445-496 155-210 (215)
166 COG4941 Predicted RNA polymera 96.7 0.036 7.8E-07 57.7 14.2 159 267-494 8-166 (415)
167 PRK05658 RNA polymerase sigma 96.7 0.0021 4.6E-08 72.5 5.4 58 189-276 102-159 (619)
168 PRK10651 transcriptional regul 96.6 0.004 8.6E-08 58.1 5.9 46 444-493 154-199 (216)
169 PRK09390 fixJ response regulat 96.5 0.0067 1.5E-07 55.5 6.9 55 437-496 134-188 (202)
170 PF12645 HTH_16: Helix-turn-he 96.5 0.0097 2.1E-07 47.8 6.8 47 264-310 13-65 (65)
171 COG1356 tfx Transcriptional re 96.5 0.0024 5.2E-08 57.3 3.4 49 444-496 7-55 (143)
172 PRK01381 Trp operon repressor; 96.5 0.0032 7E-08 54.5 3.9 48 435-482 22-73 (99)
173 COG1342 Predicted DNA-binding 96.4 0.0079 1.7E-07 51.5 5.7 52 445-499 33-84 (99)
174 PRK15320 transcriptional activ 96.3 0.0072 1.6E-07 58.6 5.8 46 444-493 163-208 (251)
175 TIGR01637 phage_arpU phage tra 96.2 0.033 7.2E-07 50.3 9.2 61 436-497 70-130 (132)
176 PRK10403 transcriptional regul 96.0 0.012 2.6E-07 54.6 5.6 48 444-495 152-199 (215)
177 PRK10360 DNA-binding transcrip 95.8 0.02 4.4E-07 53.0 6.4 46 444-493 136-181 (196)
178 PRK09935 transcriptional regul 95.8 0.018 3.9E-07 53.6 6.0 45 445-493 149-193 (210)
179 PRK13558 bacterio-opsin activa 95.7 0.016 3.5E-07 65.3 6.2 52 444-495 606-661 (665)
180 PRK04841 transcriptional regul 95.7 0.016 3.5E-07 67.3 6.4 46 444-493 837-882 (903)
181 PRK09958 DNA-binding transcrip 95.5 0.028 6E-07 52.4 6.1 46 444-493 142-187 (204)
182 PF13384 HTH_23: Homeodomain-l 95.3 0.016 3.4E-07 43.2 3.0 32 453-488 10-41 (50)
183 PF00325 Crp: Bacterial regula 95.2 0.026 5.6E-07 39.1 3.4 27 464-494 2-28 (32)
184 PF13613 HTH_Tnp_4: Helix-turn 95.2 0.046 9.9E-07 41.8 5.1 50 445-496 2-51 (53)
185 PF13412 HTH_24: Winged helix- 95.1 0.056 1.2E-06 40.0 5.3 42 446-489 1-42 (48)
186 PRK15418 transcriptional regul 95.1 0.029 6.2E-07 58.4 5.0 36 452-490 20-55 (318)
187 PF05263 DUF722: Protein of un 94.9 0.09 2E-06 47.9 7.2 56 435-492 72-127 (130)
188 TIGR02531 yecD_yerC TrpR-relat 94.8 0.064 1.4E-06 45.7 5.6 39 444-488 35-73 (88)
189 cd00569 HTH_Hin_like Helix-tur 94.2 0.093 2E-06 34.5 4.3 37 445-484 5-41 (42)
190 PF02796 HTH_7: Helix-turn-hel 94.2 0.076 1.7E-06 39.2 4.1 32 450-485 11-42 (45)
191 PF06530 Phage_antitermQ: Phag 93.9 0.35 7.6E-06 43.6 8.7 55 444-501 61-115 (125)
192 PF04539 Sigma70_r3: Sigma-70 93.5 0.091 2E-06 42.7 3.8 36 225-260 7-42 (78)
193 PF06056 Terminase_5: Putative 92.8 0.21 4.6E-06 39.2 4.7 32 453-488 6-37 (58)
194 COG2909 MalT ATP-dependent tra 92.8 0.12 2.5E-06 59.7 4.6 45 446-494 832-876 (894)
195 PF01726 LexA_DNA_bind: LexA D 92.8 0.2 4.3E-06 40.2 4.6 43 444-486 2-48 (65)
196 PF09862 DUF2089: Protein of u 92.5 0.31 6.8E-06 43.4 5.9 48 444-494 32-79 (113)
197 PF13404 HTH_AsnC-type: AsnC-t 92.5 0.33 7.1E-06 35.5 5.0 40 446-487 1-40 (42)
198 PF13518 HTH_28: Helix-turn-he 92.4 0.2 4.4E-06 37.2 4.0 34 452-489 4-37 (52)
199 PRK10430 DNA-binding transcrip 92.4 0.22 4.7E-06 48.8 5.4 46 445-490 158-204 (239)
200 COG2390 DeoR Transcriptional r 92.4 0.17 3.6E-06 53.0 4.7 35 453-490 18-52 (321)
201 PF10668 Phage_terminase: Phag 92.2 0.23 5E-06 39.4 4.2 35 452-487 11-45 (60)
202 smart00351 PAX Paired Box doma 92.2 0.34 7.4E-06 43.6 5.9 41 446-489 18-58 (125)
203 PF04218 CENP-B_N: CENP-B N-te 92.1 0.16 3.4E-06 39.0 3.1 40 445-487 6-45 (53)
204 PF12802 MarR_2: MarR family; 91.9 0.31 6.7E-06 37.5 4.6 44 445-488 2-45 (62)
205 COG1191 FliA DNA-directed RNA 91.4 5.8 0.00013 40.1 14.2 63 189-261 85-149 (247)
206 COG0568 RpoD DNA-directed RNA 91.3 2.9 6.4E-05 44.1 12.5 32 191-222 67-98 (342)
207 PHA00675 hypothetical protein 90.7 0.49 1.1E-05 39.2 4.8 41 444-486 21-61 (78)
208 PF01371 Trp_repressor: Trp re 90.2 0.4 8.8E-06 40.8 4.1 46 444-490 25-74 (87)
209 PF13730 HTH_36: Helix-turn-he 90.0 1 2.2E-05 34.1 5.8 45 445-493 2-50 (55)
210 PRK09210 RNA polymerase sigma 90.0 2.2 4.7E-05 45.4 10.4 129 226-390 220-349 (367)
211 PF13022 HTH_Tnp_1_2: Helix-tu 89.8 1.7 3.7E-05 40.1 8.0 64 442-505 7-77 (142)
212 cd00131 PAX Paired Box domain 89.8 0.78 1.7E-05 41.5 5.9 41 446-489 18-58 (128)
213 PHA02591 hypothetical protein; 89.8 0.58 1.3E-05 38.9 4.4 25 462-486 57-81 (83)
214 PRK07408 RNA polymerase sigma 89.7 0.55 1.2E-05 47.2 5.4 60 189-258 87-149 (256)
215 TIGR02393 RpoD_Cterm RNA polym 89.5 2.9 6.2E-05 41.4 10.3 32 227-258 92-123 (238)
216 PRK05911 RNA polymerase sigma 89.3 4.7 0.0001 40.5 11.8 61 189-259 87-147 (257)
217 PF01325 Fe_dep_repress: Iron 89.1 0.69 1.5E-05 36.4 4.4 41 446-486 2-44 (60)
218 PF01022 HTH_5: Bacterial regu 89.0 1.1 2.3E-05 33.2 5.1 37 448-487 2-38 (47)
219 PF12840 HTH_20: Helix-turn-he 88.9 1.5 3.3E-05 34.1 6.2 43 438-486 3-46 (61)
220 PF08279 HTH_11: HTH domain; 88.9 0.69 1.5E-05 35.0 4.2 38 449-487 1-38 (55)
221 PF03444 HrcA_DNA-bdg: Winged 88.6 0.99 2.1E-05 37.6 5.1 41 446-486 2-45 (78)
222 PF02650 HTH_WhiA: WhiA C-term 88.0 0.97 2.1E-05 38.3 4.8 43 444-488 36-80 (85)
223 PF13744 HTH_37: Helix-turn-he 88.0 1.3 2.8E-05 36.6 5.5 39 462-500 29-72 (80)
224 PF13542 HTH_Tnp_ISL3: Helix-t 87.7 1.3 2.7E-05 33.1 4.9 35 450-488 17-51 (52)
225 TIGR01610 phage_O_Nterm phage 87.6 2.4 5.2E-05 36.2 7.2 42 444-485 21-68 (95)
226 smart00550 Zalpha Z-DNA-bindin 87.5 1.4 3E-05 35.4 5.3 24 464-487 22-45 (68)
227 PRK05901 RNA polymerase sigma 87.5 11 0.00024 41.9 14.1 32 227-258 363-394 (509)
228 PHA02547 55 RNA polymerase sig 87.3 2.1 4.6E-05 40.7 7.1 65 272-336 45-112 (179)
229 PRK11083 DNA-binding response 87.1 0.87 1.9E-05 42.8 4.6 50 445-494 154-208 (228)
230 COG3415 Transposase and inacti 87.0 1.1 2.3E-05 41.4 4.9 34 453-489 13-46 (138)
231 PRK07921 RNA polymerase sigma 86.9 5.7 0.00012 41.6 10.8 32 227-258 178-209 (324)
232 PF01047 MarR: MarR family; I 86.8 1.1 2.4E-05 34.1 4.3 42 446-489 1-42 (59)
233 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 86.7 1.4 3E-05 33.7 4.5 39 445-486 4-42 (50)
234 PRK09413 IS2 repressor TnpA; R 86.7 3.2 6.9E-05 37.0 7.7 34 452-488 20-53 (121)
235 PRK00423 tfb transcription ini 86.4 26 0.00055 36.4 15.3 179 267-492 119-304 (310)
236 smart00344 HTH_ASNC helix_turn 86.2 1.6 3.5E-05 37.4 5.5 41 446-488 1-41 (108)
237 PF00356 LacI: Bacterial regul 86.2 0.75 1.6E-05 34.4 2.9 34 466-499 1-41 (46)
238 PRK10336 DNA-binding transcrip 86.0 0.97 2.1E-05 42.3 4.3 49 445-493 149-202 (219)
239 TIGR02395 rpoN_sigma RNA polym 85.9 31 0.00067 37.6 16.2 25 462-486 316-340 (429)
240 PRK11179 DNA-binding transcrip 85.7 1.5 3.2E-05 40.6 5.3 42 445-488 6-47 (153)
241 COG3355 Predicted transcriptio 85.6 2.9 6.2E-05 38.1 6.8 51 436-492 16-66 (126)
242 PF01418 HTH_6: Helix-turn-hel 85.6 1.9 4.2E-05 35.3 5.3 52 435-487 4-57 (77)
243 COG2973 TrpR Trp operon repres 85.3 1.9 4.2E-05 37.3 5.3 46 434-482 29-78 (103)
244 PRK10710 DNA-binding transcrip 85.3 1.2 2.7E-05 42.3 4.6 49 445-493 160-213 (240)
245 PRK10046 dpiA two-component re 85.0 0.84 1.8E-05 44.2 3.4 40 444-486 160-199 (225)
246 PF01710 HTH_Tnp_IS630: Transp 84.7 10 0.00022 33.7 10.0 27 463-493 70-96 (119)
247 PRK11169 leucine-responsive tr 84.6 1.5 3.2E-05 41.2 4.7 42 445-488 11-52 (164)
248 PF13463 HTH_27: Winged helix 84.5 1.8 3.9E-05 33.8 4.5 43 446-489 1-43 (68)
249 TIGR02154 PhoB phosphate regul 84.0 0.76 1.6E-05 43.0 2.6 49 445-493 154-207 (226)
250 PRK13413 mpi multiple promoter 84.0 1.8 4E-05 41.6 5.3 37 447-487 159-195 (200)
251 PRK15479 transcriptional regul 84.0 1.7 3.7E-05 40.6 4.9 49 445-493 148-201 (221)
252 COG0856 Orotate phosphoribosyl 83.6 1.3 2.9E-05 42.3 3.9 38 451-492 9-46 (203)
253 PRK07500 rpoH2 RNA polymerase 83.4 17 0.00038 37.2 12.4 65 188-255 100-165 (289)
254 PF13551 HTH_29: Winged helix- 83.0 12 0.00026 31.7 9.4 23 368-390 14-36 (112)
255 PF12728 HTH_17: Helix-turn-he 82.8 1.4 3E-05 32.8 3.1 24 465-488 2-25 (51)
256 PF01978 TrmB: Sugar-specific 82.7 0.96 2.1E-05 35.9 2.3 41 445-487 5-45 (68)
257 PRK05949 RNA polymerase sigma 82.5 8.4 0.00018 40.4 9.8 34 225-258 181-214 (327)
258 PF13551 HTH_29: Winged helix- 82.1 2.5 5.4E-05 36.0 4.8 33 452-488 3-36 (112)
259 cd04762 HTH_MerR-trunc Helix-T 82.0 1.4 3.1E-05 31.5 2.8 25 465-489 1-25 (49)
260 TIGR03787 marine_sort_RR prote 81.9 1.9 4.2E-05 40.7 4.5 47 445-493 156-206 (227)
261 PF00046 Homeobox: Homeobox do 81.6 4.1 8.8E-05 30.9 5.3 50 445-494 6-57 (57)
262 CHL00148 orf27 Ycf27; Reviewed 81.4 1.9 4.1E-05 41.0 4.2 50 445-494 161-217 (240)
263 PRK12423 LexA repressor; Provi 81.0 2.8 6.1E-05 40.6 5.3 47 444-494 2-52 (202)
264 TIGR01764 excise DNA binding d 80.9 1.9 4.1E-05 31.0 3.2 24 465-488 2-25 (49)
265 PF08822 DUF1804: Protein of u 80.9 3.2 7E-05 39.4 5.4 42 447-490 4-45 (165)
266 PRK07598 RNA polymerase sigma 80.7 14 0.00029 40.3 10.8 38 223-260 263-300 (415)
267 TIGR02885 spore_sigF RNA polym 80.4 4.2 9.1E-05 39.8 6.4 31 228-258 103-133 (231)
268 PF01381 HTH_3: Helix-turn-hel 80.1 1.9 4E-05 32.3 2.9 26 462-487 7-32 (55)
269 PRK06288 RNA polymerase sigma 79.7 27 0.00059 35.1 12.1 34 225-258 121-154 (268)
270 COG2522 Predicted transcriptio 79.6 3.1 6.8E-05 37.4 4.6 31 453-487 15-45 (119)
271 PF08220 HTH_DeoR: DeoR-like h 79.6 2.6 5.6E-05 32.6 3.6 24 463-486 13-36 (57)
272 PF13011 LZ_Tnp_IS481: leucine 79.3 4.4 9.6E-05 34.4 5.2 44 444-489 7-50 (85)
273 COG1522 Lrp Transcriptional re 79.2 3.8 8.3E-05 37.2 5.3 43 444-488 4-46 (154)
274 PHA01976 helix-turn-helix prot 79.1 3.2 6.9E-05 32.5 4.1 26 462-487 13-38 (67)
275 smart00420 HTH_DEOR helix_turn 78.6 4.4 9.6E-05 29.4 4.5 25 463-487 13-37 (53)
276 PF02954 HTH_8: Bacterial regu 78.4 3.1 6.8E-05 30.1 3.6 38 447-486 3-40 (42)
277 cd04761 HTH_MerR-SF Helix-Turn 78.3 1.7 3.7E-05 31.6 2.2 25 465-489 1-25 (49)
278 PF01527 HTH_Tnp_1: Transposas 77.7 2.2 4.7E-05 34.2 2.8 35 452-489 14-48 (76)
279 PF01726 LexA_DNA_bind: LexA D 77.5 5.5 0.00012 31.9 5.0 31 360-390 19-50 (65)
280 PHA00542 putative Cro-like pro 77.5 3.2 6.9E-05 34.6 3.8 27 462-488 29-55 (82)
281 PRK12469 RNA polymerase factor 77.0 1.3E+02 0.0028 33.5 20.1 25 462-486 367-391 (481)
282 smart00419 HTH_CRP helix_turn_ 76.8 3.6 7.9E-05 29.5 3.6 23 464-486 8-30 (48)
283 PRK05932 RNA polymerase factor 76.7 1.3E+02 0.0027 33.3 19.4 25 462-486 341-365 (455)
284 smart00345 HTH_GNTR helix_turn 76.6 3.9 8.5E-05 30.5 3.9 27 463-493 18-45 (60)
285 TIGR03070 couple_hipB transcri 76.5 2.8 6.1E-05 31.2 3.0 25 463-487 14-38 (58)
286 COG1508 RpoN DNA-directed RNA 76.2 1.3E+02 0.0028 33.1 16.6 24 463-486 329-352 (444)
287 smart00342 HTH_ARAC helix_turn 76.0 35 0.00076 26.6 10.0 26 463-488 49-75 (84)
288 cd06571 Bac_DnaA_C C-terminal 75.9 8 0.00017 32.6 5.9 31 463-493 43-74 (90)
289 COG1476 Predicted transcriptio 75.9 3.8 8.2E-05 33.3 3.7 25 463-487 13-37 (68)
290 PRK10870 transcriptional repre 75.8 18 0.0004 34.3 9.0 44 445-488 52-95 (176)
291 PF13560 HTH_31: Helix-turn-he 75.7 3.7 8E-05 32.0 3.6 26 462-487 12-37 (64)
292 TIGR00122 birA_repr_reg BirA b 75.6 6.1 0.00013 31.3 4.9 26 462-487 11-36 (69)
293 PRK07406 RNA polymerase sigma 75.4 24 0.00053 37.7 10.7 31 227-257 228-258 (373)
294 TIGR03697 NtcA_cyano global ni 75.4 3.6 7.7E-05 38.4 4.1 27 464-494 143-169 (193)
295 PF13545 HTH_Crp_2: Crp-like h 75.3 3.3 7.2E-05 33.0 3.3 26 464-493 28-53 (76)
296 TIGR02844 spore_III_D sporulat 75.2 5.6 0.00012 33.3 4.7 37 448-487 6-42 (80)
297 TIGR01889 Staph_reg_Sar staphy 75.2 13 0.00029 32.2 7.4 44 445-488 22-67 (109)
298 PRK10072 putative transcriptio 75.1 4 8.6E-05 35.3 3.9 32 453-487 38-69 (96)
299 TIGR02479 FliA_WhiG RNA polyme 75.1 12 0.00027 36.4 7.9 34 226-259 87-120 (224)
300 cd00090 HTH_ARSR Arsenical Res 75.1 7.4 0.00016 29.8 5.2 37 448-487 7-43 (78)
301 TIGR02337 HpaR homoprotocatech 74.8 14 0.00031 32.2 7.4 42 444-487 24-65 (118)
302 smart00418 HTH_ARSR helix_turn 74.4 6.3 0.00014 29.3 4.5 27 462-488 8-34 (66)
303 PF08765 Mor: Mor transcriptio 74.3 6.6 0.00014 34.4 5.2 41 449-494 62-102 (108)
304 KOG0484 Transcription factor P 74.0 10 0.00022 33.4 6.1 51 444-497 27-77 (125)
305 PRK14082 hypothetical protein; 73.6 12 0.00025 30.2 5.8 56 263-320 8-63 (65)
306 cd00092 HTH_CRP helix_turn_hel 73.1 5.1 0.00011 30.9 3.8 24 463-486 24-47 (67)
307 PF09339 HTH_IclR: IclR helix- 73.1 3.7 8E-05 30.9 2.9 25 462-486 16-40 (52)
308 TIGR00498 lexA SOS regulatory 73.0 6.8 0.00015 37.6 5.4 43 444-486 2-48 (199)
309 PRK07405 RNA polymerase sigma 73.0 15 0.00033 38.2 8.4 35 224-258 170-204 (317)
310 PF08280 HTH_Mga: M protein tr 72.9 5.3 0.00011 31.1 3.8 37 449-487 6-42 (59)
311 PRK00215 LexA repressor; Valid 72.7 7.5 0.00016 37.4 5.7 43 446-488 2-48 (205)
312 PF08535 KorB: KorB domain; I 72.7 3.4 7.4E-05 35.0 2.9 24 463-486 2-25 (93)
313 TIGR01884 cas_HTH CRISPR locus 72.3 7.5 0.00016 37.6 5.5 42 444-487 139-180 (203)
314 PRK09954 putative kinase; Prov 72.2 6.9 0.00015 40.9 5.7 41 446-488 1-41 (362)
315 TIGR03830 CxxCG_CxxCG_HTH puta 72.1 12 0.00025 33.0 6.3 40 444-488 63-102 (127)
316 PF13411 MerR_1: MerR HTH fami 71.9 1.9 4.2E-05 33.8 1.1 25 465-489 1-25 (69)
317 COG1654 BirA Biotin operon rep 71.2 12 0.00026 31.3 5.7 30 461-494 16-45 (79)
318 PRK07670 RNA polymerase sigma 71.1 37 0.0008 33.7 10.4 34 227-260 114-147 (251)
319 TIGR02612 mob_myst_A mobile my 71.1 11 0.00023 35.4 6.0 47 453-502 30-82 (150)
320 COG5484 Uncharacterized conser 70.9 4.9 0.00011 40.6 3.9 26 462-487 17-42 (279)
321 PF14493 HTH_40: Helix-turn-he 70.1 10 0.00022 32.0 5.2 30 462-491 11-40 (91)
322 cd07377 WHTH_GntR Winged helix 70.0 17 0.00036 27.6 6.0 26 465-494 26-51 (66)
323 smart00347 HTH_MARR helix_turn 69.9 11 0.00023 31.0 5.3 41 445-487 7-47 (101)
324 PF07750 GcrA: GcrA cell cycle 69.8 5.3 0.00012 37.8 3.8 26 462-487 16-42 (162)
325 smart00354 HTH_LACI helix_turn 69.8 4.6 0.0001 32.4 2.9 23 465-487 1-23 (70)
326 PF07037 DUF1323: Putative tra 69.4 5.1 0.00011 36.0 3.3 23 465-487 1-23 (122)
327 TIGR02997 Sig70-cyanoRpoD RNA 69.4 48 0.001 34.0 11.0 32 227-258 166-197 (298)
328 PRK11512 DNA-binding transcrip 69.1 11 0.00024 34.1 5.7 41 445-487 37-77 (144)
329 PRK13918 CRP/FNR family transc 68.8 6 0.00013 37.3 4.0 27 464-494 149-175 (202)
330 cd01104 HTH_MlrA-CarA Helix-Tu 68.7 6.3 0.00014 30.8 3.5 23 465-487 1-23 (68)
331 TIGR02147 Fsuc_second hypothet 68.3 69 0.0015 32.8 11.7 97 364-474 135-239 (271)
332 TIGR02607 antidote_HigA addict 67.7 11 0.00023 30.2 4.7 26 462-487 16-41 (78)
333 PF13556 HTH_30: PucR C-termin 67.6 13 0.00028 28.8 4.9 42 453-497 4-45 (59)
334 PRK11302 DNA-binding transcrip 67.3 11 0.00024 37.8 5.8 62 435-497 4-71 (284)
335 PF12116 SpoIIID: Stage III sp 67.2 9.4 0.0002 32.1 4.2 35 463-497 18-52 (82)
336 cd00086 homeodomain Homeodomai 66.7 13 0.00027 27.9 4.7 50 445-494 6-57 (59)
337 COG1510 Predicted transcriptio 66.6 5.7 0.00012 38.0 3.2 29 461-493 38-66 (177)
338 PRK11337 DNA-binding transcrip 66.6 13 0.00027 37.8 6.0 65 433-498 14-84 (292)
339 COG2944 Predicted transcriptio 66.5 12 0.00026 33.0 5.0 39 444-487 42-80 (104)
340 PF01710 HTH_Tnp_IS630: Transp 65.8 7.5 0.00016 34.5 3.7 25 462-486 16-40 (119)
341 PF00292 PAX: 'Paired box' dom 65.4 13 0.00028 33.8 5.1 33 451-487 24-56 (125)
342 PRK03573 transcriptional regul 65.2 14 0.00031 33.3 5.5 42 445-487 28-69 (144)
343 COG1318 Predicted transcriptio 64.5 6.8 0.00015 37.5 3.3 28 463-490 60-87 (182)
344 PRK11161 fumarate/nitrate redu 64.2 8.1 0.00018 37.5 3.9 27 464-494 184-210 (235)
345 PF00376 MerR: MerR family reg 63.6 4.6 0.0001 28.9 1.5 23 466-488 1-23 (38)
346 PF00392 GntR: Bacterial regul 63.5 18 0.0004 28.1 5.2 23 463-485 22-45 (64)
347 cd04764 HTH_MlrA-like_sg1 Heli 63.4 9.4 0.0002 30.0 3.5 23 465-487 1-23 (67)
348 PF00165 HTH_AraC: Bacterial r 62.7 12 0.00026 26.7 3.7 27 462-488 6-32 (42)
349 PRK06986 fliA flagellar biosyn 62.6 49 0.0011 32.5 9.2 32 227-258 100-131 (236)
350 smart00346 HTH_ICLR helix_turn 62.6 23 0.00049 29.1 5.8 26 463-488 19-44 (91)
351 PRK11753 DNA-binding transcrip 62.5 9.6 0.00021 36.1 4.1 27 464-494 168-194 (211)
352 PRK11564 stationary phase indu 62.4 19 0.0004 38.8 6.6 50 445-494 10-60 (426)
353 TIGR00647 MG103 conserved hypo 61.9 16 0.00036 37.5 5.8 43 444-488 226-274 (279)
354 smart00422 HTH_MERR helix_turn 61.7 6.3 0.00014 30.8 2.2 25 465-489 1-25 (70)
355 COG2345 Predicted transcriptio 61.7 15 0.00032 36.6 5.2 26 462-487 23-48 (218)
356 PRK12469 RNA polymerase factor 61.7 2.7E+02 0.0058 31.1 19.1 22 368-389 371-392 (481)
357 PRK09726 antitoxin HipB; Provi 61.5 12 0.00025 31.4 3.9 38 463-500 24-65 (88)
358 PRK09863 putative frv operon r 61.4 16 0.00035 41.0 6.2 46 446-494 2-47 (584)
359 PRK10161 transcriptional regul 61.4 9 0.00019 36.2 3.6 50 445-494 154-208 (229)
360 PRK15482 transcriptional regul 61.3 20 0.00044 36.2 6.4 61 436-497 5-71 (285)
361 PRK07122 RNA polymerase sigma 60.1 23 0.00049 35.8 6.4 62 188-259 100-164 (264)
362 COG3877 Uncharacterized protei 60.1 19 0.00041 31.8 4.9 47 444-493 40-86 (122)
363 PRK12427 flagellar biosynthesi 60.0 23 0.00051 35.0 6.4 61 189-259 78-138 (231)
364 TIGR02787 codY_Gpos GTP-sensin 59.8 33 0.00071 34.7 7.3 53 436-493 168-223 (251)
365 COG1846 MarR Transcriptional r 59.6 18 0.00039 30.6 4.9 41 445-488 19-60 (126)
366 PRK09863 putative frv operon r 59.6 1E+02 0.0023 34.6 12.2 105 366-493 17-121 (584)
367 COG2512 Predicted membrane-ass 59.5 12 0.00027 38.0 4.4 43 444-487 191-233 (258)
368 TIGR00180 parB_part ParB-like 59.3 17 0.00036 34.8 5.1 43 444-487 101-143 (187)
369 cd04763 HTH_MlrA-like Helix-Tu 59.1 12 0.00026 29.5 3.4 23 465-487 1-23 (68)
370 PF05225 HTH_psq: helix-turn-h 58.9 25 0.00053 26.0 4.8 23 465-487 17-39 (45)
371 PRK10955 DNA-binding transcrip 58.7 6.9 0.00015 36.9 2.3 45 445-493 156-209 (232)
372 PF12298 Bot1p: Eukaryotic mit 58.7 23 0.0005 33.9 5.8 38 446-485 17-54 (172)
373 PF14394 DUF4423: Domain of un 58.7 37 0.0008 32.3 7.2 29 364-392 37-67 (171)
374 PRK01905 DNA-binding protein F 58.5 37 0.0008 27.9 6.3 37 449-487 37-73 (77)
375 smart00389 HOX Homeodomain. DN 58.5 15 0.00032 27.4 3.7 47 445-491 6-54 (56)
376 PF13443 HTH_26: Cro/C1-type H 58.4 9.8 0.00021 29.2 2.8 26 463-488 9-34 (63)
377 PRK09391 fixK transcriptional 58.2 12 0.00027 36.5 4.0 27 464-494 179-205 (230)
378 PF02082 Rrf2: Transcriptional 58.1 17 0.00037 29.9 4.3 24 464-487 25-48 (83)
379 PF05043 Mga: Mga helix-turn-h 57.9 7.8 0.00017 32.0 2.2 32 462-493 28-59 (87)
380 PRK10411 DNA-binding transcrip 57.9 18 0.00038 36.2 5.2 42 447-490 3-44 (240)
381 PF06971 Put_DNA-bind_N: Putat 57.6 38 0.00081 25.9 5.7 45 341-385 2-47 (50)
382 COG3093 VapI Plasmid maintenan 57.5 16 0.00034 32.3 4.0 33 452-487 12-46 (104)
383 PF04703 FaeA: FaeA-like prote 57.4 11 0.00023 30.1 2.8 25 463-487 14-38 (62)
384 PRK09706 transcriptional repre 57.0 14 0.00031 33.2 4.0 26 462-487 16-41 (135)
385 PRK06596 RNA polymerase factor 56.9 2.3E+02 0.005 28.9 14.0 26 365-390 247-272 (284)
386 COG1737 RpiR Transcriptional r 56.5 23 0.00049 36.1 5.8 63 433-496 4-72 (281)
387 PRK11557 putative DNA-binding 56.2 18 0.00039 36.3 5.0 59 438-497 3-67 (278)
388 cd01392 HTH_LacI Helix-turn-he 56.1 7.2 0.00016 28.8 1.6 21 468-488 1-21 (52)
389 smart00530 HTH_XRE Helix-turn- 56.0 14 0.00031 25.7 3.1 25 463-487 9-33 (56)
390 smart00342 HTH_ARAC helix_turn 55.5 32 0.0007 26.8 5.5 26 464-489 1-26 (84)
391 PF12844 HTH_19: Helix-turn-he 55.5 17 0.00036 28.0 3.6 25 463-487 11-35 (64)
392 PRK03902 manganese transport t 55.3 22 0.00048 32.2 5.0 25 463-487 21-45 (142)
393 PF04967 HTH_10: HTH DNA bindi 54.2 50 0.0011 25.5 5.9 48 206-263 1-48 (53)
394 TIGR02850 spore_sigG RNA polym 54.1 46 0.001 33.1 7.5 34 227-260 125-158 (254)
395 PRK09464 pdhR transcriptional 54.0 33 0.00072 33.9 6.4 40 450-494 20-60 (254)
396 PF14502 HTH_41: Helix-turn-he 53.9 21 0.00046 27.1 3.7 27 464-494 6-32 (48)
397 COG4367 Uncharacterized protei 53.7 26 0.00057 30.0 4.6 43 445-487 2-46 (97)
398 TIGR03338 phnR_burk phosphonat 53.7 30 0.00066 33.1 5.9 28 462-493 32-59 (212)
399 TIGR01387 cztR_silR_copR heavy 53.6 19 0.00042 33.3 4.4 49 445-493 147-200 (218)
400 PRK13777 transcriptional regul 53.5 27 0.00059 33.7 5.5 42 444-487 41-82 (185)
401 PRK03837 transcriptional regul 53.4 26 0.00057 34.2 5.5 38 451-493 24-62 (241)
402 COG1349 GlpR Transcriptional r 53.3 13 0.00029 37.3 3.5 37 447-486 4-41 (253)
403 COG3398 Uncharacterized protei 53.2 2.3E+02 0.005 28.5 11.7 94 367-487 116-211 (240)
404 PF08006 DUF1700: Protein of u 53.2 30 0.00065 32.8 5.7 56 431-487 3-63 (181)
405 PF04552 Sigma54_DBD: Sigma-54 53.0 18 0.00038 34.3 4.0 86 368-484 51-146 (160)
406 smart00352 POU Found in Pit-Oc 52.9 21 0.00046 29.6 3.9 26 462-487 22-53 (75)
407 PRK10219 DNA-binding transcrip 52.5 77 0.0017 26.9 7.7 27 462-488 19-45 (107)
408 PRK06030 hypothetical protein; 52.4 48 0.001 30.1 6.5 39 448-489 56-94 (124)
409 PRK10421 DNA-binding transcrip 52.4 36 0.00079 33.7 6.4 39 451-494 13-52 (253)
410 COG4709 Predicted membrane pro 52.3 30 0.00066 33.6 5.4 58 431-489 3-65 (195)
411 TIGR02395 rpoN_sigma RNA polym 52.3 93 0.002 34.0 9.9 89 366-484 318-416 (429)
412 PRK09392 ftrB transcriptional 52.2 16 0.00035 35.5 3.7 26 464-493 173-198 (236)
413 PF00440 TetR_N: Bacterial reg 52.0 25 0.00053 25.7 3.9 23 462-484 14-36 (47)
414 cd00093 HTH_XRE Helix-turn-hel 52.0 25 0.00054 24.6 3.9 26 463-488 11-36 (58)
415 PF04552 Sigma54_DBD: Sigma-54 51.6 4.9 0.00011 38.0 0.0 47 437-486 24-71 (160)
416 PRK09744 DNA-binding transcrip 51.6 20 0.00043 29.7 3.5 20 466-485 12-31 (75)
417 PRK06424 transcription factor; 51.5 19 0.00042 33.4 3.9 26 462-487 95-120 (144)
418 PRK10225 DNA-binding transcrip 51.5 39 0.00084 33.5 6.4 39 451-494 20-59 (257)
419 PF10654 DUF2481: Protein of u 51.5 46 0.001 29.9 6.0 41 452-496 72-112 (126)
420 PF08784 RPA_C: Replication pr 51.4 23 0.0005 30.3 4.2 43 445-487 44-88 (102)
421 PRK10402 DNA-binding transcrip 51.2 17 0.00037 35.3 3.8 44 447-494 150-195 (226)
422 smart00862 Trans_reg_C Transcr 50.9 53 0.0011 25.8 6.0 49 445-493 5-59 (78)
423 PRK09990 DNA-binding transcrip 50.8 40 0.00086 33.3 6.4 38 451-493 18-56 (251)
424 PF12759 HTH_Tnp_IS1: InsA C-t 50.7 22 0.00047 26.8 3.3 36 446-485 7-42 (46)
425 PRK11511 DNA-binding transcrip 50.7 78 0.0017 28.2 7.6 33 453-488 17-49 (127)
426 PF06322 Phage_NinH: Phage Nin 50.6 23 0.00051 28.3 3.6 27 453-485 11-37 (64)
427 PRK13509 transcriptional repre 50.1 29 0.00062 34.8 5.3 38 448-487 5-42 (251)
428 PRK10643 DNA-binding transcrip 49.8 17 0.00037 33.8 3.4 47 445-493 149-202 (222)
429 PRK13890 conjugal transfer pro 49.7 22 0.00048 31.7 3.9 26 462-487 16-41 (120)
430 PRK14101 bifunctional glucokin 49.6 38 0.00082 38.6 6.7 64 433-497 342-411 (638)
431 PF11662 DUF3263: Protein of u 49.0 62 0.0013 27.0 6.1 45 445-489 2-47 (77)
432 PRK11414 colanic acid/biofilm 48.8 41 0.00088 32.6 6.0 29 462-494 32-60 (221)
433 PF10078 DUF2316: Uncharacteri 48.6 23 0.0005 30.4 3.6 24 463-486 22-45 (89)
434 PRK10434 srlR DNA-bindng trans 48.5 24 0.00052 35.5 4.4 38 448-487 5-42 (256)
435 PRK10141 DNA-binding transcrip 48.2 37 0.00079 30.4 5.0 41 444-486 11-52 (117)
436 PF07900 DUF1670: Protein of u 48.2 2.1E+02 0.0046 28.5 10.7 29 362-390 101-129 (220)
437 PRK11534 DNA-binding transcrip 48.0 53 0.0012 31.8 6.7 39 450-493 17-55 (224)
438 cd04768 HTH_BmrR-like Helix-Tu 47.7 14 0.0003 31.5 2.2 25 465-489 1-25 (96)
439 PRK00135 scpB segregation and 47.7 2.4E+02 0.0052 27.4 10.9 99 362-478 15-118 (188)
440 TIGR02698 CopY_TcrY copper tra 47.3 49 0.0011 29.9 5.8 44 445-490 1-48 (130)
441 PF14549 P22_Cro: DNA-binding 47.2 27 0.00058 27.7 3.5 19 466-484 11-29 (60)
442 COG1321 TroR Mn-dependent tran 47.1 32 0.00069 32.2 4.7 26 462-487 22-47 (154)
443 TIGR02325 C_P_lyase_phnF phosp 47.1 53 0.0011 32.0 6.5 25 465-493 33-57 (238)
444 PRK04984 fatty acid metabolism 47.0 26 0.00056 34.3 4.3 29 462-494 28-57 (239)
445 cd04775 HTH_Cfa-like Helix-Tur 46.7 14 0.00031 31.8 2.2 26 465-490 2-27 (102)
446 COG2826 Tra8 Transposase and i 46.6 23 0.00049 36.9 3.9 42 444-488 6-47 (318)
447 PRK09943 DNA-binding transcrip 46.1 27 0.00058 33.1 4.1 26 462-487 18-43 (185)
448 cd04773 HTH_TioE_rpt2 Second H 46.1 15 0.00032 32.1 2.2 25 465-489 1-25 (108)
449 PF04492 Phage_rep_O: Bacterio 46.1 82 0.0018 27.4 6.8 42 444-485 28-75 (100)
450 PF05732 RepL: Firmicute plasm 45.7 62 0.0013 30.7 6.4 53 437-494 45-101 (165)
451 cd01105 HTH_GlnR-like Helix-Tu 45.6 17 0.00036 30.6 2.3 25 465-489 2-26 (88)
452 TIGR00738 rrf2_super rrf2 fami 45.6 40 0.00087 29.8 5.0 24 464-487 25-48 (132)
453 PRK08359 transcription factor; 45.4 27 0.00058 33.6 4.0 26 462-487 96-121 (176)
454 COG2963 Transposase and inacti 45.3 43 0.00094 29.1 5.0 43 445-490 7-51 (116)
455 PRK11517 transcriptional regul 44.8 39 0.00084 31.5 5.0 49 445-493 147-200 (223)
456 PRK10681 DNA-binding transcrip 44.7 32 0.00069 34.5 4.6 38 448-487 7-44 (252)
457 PRK10906 DNA-binding transcrip 44.6 31 0.00066 34.7 4.5 38 448-487 5-42 (252)
458 cd04766 HTH_HspR Helix-Turn-He 44.5 16 0.00035 30.6 2.1 25 465-489 2-26 (91)
459 PF06413 Neugrin: Neugrin; In 44.5 34 0.00074 34.1 4.7 43 444-486 9-51 (225)
460 cd01107 HTH_BmrR Helix-Turn-He 44.3 17 0.00037 31.6 2.3 26 465-490 1-26 (108)
461 TIGR00270 conserved hypothetic 44.1 30 0.00066 32.4 4.0 26 462-487 80-105 (154)
462 PF08279 HTH_11: HTH domain; 44.0 56 0.0012 24.3 4.9 26 366-391 15-40 (55)
463 PRK11523 DNA-binding transcrip 43.9 60 0.0013 32.2 6.4 38 451-493 19-57 (253)
464 PHA00738 putative HTH transcri 43.8 49 0.0011 29.4 5.0 37 448-486 12-48 (108)
465 TIGR02404 trehalos_R_Bsub treh 43.6 59 0.0013 31.7 6.2 25 465-493 25-49 (233)
466 TIGR02812 fadR_gamma fatty aci 43.5 32 0.00068 33.6 4.3 29 462-494 27-56 (235)
467 cd00592 HTH_MerR-like Helix-Tu 43.3 18 0.00039 30.6 2.2 25 465-489 1-25 (100)
468 cd04774 HTH_YfmP Helix-Turn-He 42.9 18 0.00039 31.0 2.2 25 465-489 1-25 (96)
469 cd04789 HTH_Cfa Helix-Turn-Hel 42.5 19 0.0004 31.1 2.2 25 465-489 2-26 (102)
470 cd01106 HTH_TipAL-Mta Helix-Tu 42.5 19 0.00041 31.0 2.2 25 465-489 1-25 (103)
471 PF05331 DUF742: Protein of un 42.4 40 0.00086 30.2 4.3 40 444-487 39-78 (114)
472 cd00383 trans_reg_C Effector d 42.3 59 0.0013 26.6 5.2 49 445-493 23-76 (95)
473 cd04780 HTH_MerR-like_sg5 Heli 42.2 19 0.00041 30.8 2.2 25 465-489 1-25 (95)
474 cd04782 HTH_BltR Helix-Turn-He 41.9 19 0.00042 30.7 2.2 25 465-489 1-25 (97)
475 cd04765 HTH_MlrA-like_sg2 Heli 41.9 31 0.00067 29.7 3.5 23 465-487 1-23 (99)
476 TIGR02944 suf_reg_Xantho FeS a 41.9 33 0.00072 30.5 3.8 26 462-487 23-48 (130)
477 cd04788 HTH_NolA-AlbR Helix-Tu 41.8 19 0.00042 30.7 2.2 25 465-489 1-25 (96)
478 PF04645 DUF603: Protein of un 41.7 34 0.00073 32.8 3.9 26 462-487 16-42 (181)
479 cd04772 HTH_TioE_rpt1 First He 41.6 20 0.00044 30.8 2.3 25 465-489 1-25 (99)
480 PRK00082 hrcA heat-inducible t 41.5 41 0.0009 35.5 5.0 44 444-491 2-53 (339)
481 PRK06266 transcription initiat 41.4 73 0.0016 30.5 6.3 39 447-487 21-59 (178)
482 cd01282 HTH_MerR-like_sg3 Heli 41.2 20 0.00044 31.4 2.3 25 465-489 1-25 (112)
483 PRK11886 bifunctional biotin-- 41.2 44 0.00096 34.5 5.2 39 449-489 5-43 (319)
484 cd01109 HTH_YyaN Helix-Turn-He 41.1 20 0.00044 31.3 2.3 25 465-489 1-25 (113)
485 PHA02943 hypothetical protein; 41.1 40 0.00087 31.8 4.2 35 449-486 12-46 (165)
486 PRK09480 slmA division inhibit 40.7 2.7E+02 0.0058 25.6 10.0 70 236-305 28-97 (194)
487 TIGR00637 ModE_repress ModE mo 40.4 75 0.0016 27.4 5.7 42 447-492 3-44 (99)
488 PF01325 Fe_dep_repress: Iron 40.1 63 0.0014 25.3 4.7 33 359-391 15-47 (60)
489 PRK04424 fatty acid biosynthes 40.1 41 0.0009 32.2 4.4 37 448-486 7-43 (185)
490 COG1405 SUA7 Transcription ini 40.0 4.4E+02 0.0096 27.3 13.0 28 462-489 249-276 (285)
491 PRK11050 manganese transport r 40.0 81 0.0018 29.1 6.2 26 462-487 49-74 (152)
492 PF04545 Sigma70_r4: Sigma-70, 39.9 40 0.00087 24.8 3.4 27 364-390 18-44 (50)
493 cd01279 HTH_HspR-like Helix-Tu 39.8 21 0.00045 30.6 2.1 24 465-488 2-25 (98)
494 COG4367 Uncharacterized protei 39.7 78 0.0017 27.2 5.3 40 353-392 8-49 (97)
495 PF10668 Phage_terminase: Phag 39.6 58 0.0013 25.9 4.3 32 356-387 12-43 (60)
496 COG5606 Uncharacterized conser 39.4 19 0.00041 30.8 1.6 37 462-498 39-80 (91)
497 TIGR00373 conserved hypothetic 39.4 82 0.0018 29.5 6.2 39 447-487 13-51 (158)
498 cd04769 HTH_MerR2 Helix-Turn-H 39.3 22 0.00048 31.3 2.2 26 465-490 1-26 (116)
499 PF11994 DUF3489: Protein of u 39.3 85 0.0018 25.9 5.4 41 449-491 11-51 (72)
500 PRK05932 RNA polymerase factor 39.3 2.3E+02 0.0049 31.3 10.5 35 358-392 129-164 (455)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=1.1e-57 Score=479.67 Aligned_cols=309 Identities=34% Similarity=0.596 Sum_probs=284.0
Q ss_pred hhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCc--------------------cchhHHHHHHhhCCCCchHHHHHHhcc
Q 010521 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS--------------------LDDHKLRLKERLGCEPSMEQLAASLRI 250 (508)
Q Consensus 191 ~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~--------------------l~~~~~~l~~~~g~~p~~~~~a~~~~~ 250 (508)
|.++.||++|+++|+||++||++|+++++.+-. |+..+.+|++.+|++|+..+||.++|+
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 799999999999999999999999999999988 888999999999999999999966554
Q ss_pred ----------------------ChHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhc
Q 010521 251 ----------------------SRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEK 308 (508)
Q Consensus 251 ----------------------s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiek 308 (508)
+.++|.+.+..|..|+++||.+|+++|+++|++|.++|.+++||+|||++|||+|+++
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 5555555567788999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHH
Q 010521 309 FDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNAT 387 (508)
Q Consensus 309 FDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l 387 (508)
|||.+|++|+||++||||++|.+++.+++|+|++|.|+.+.+++++++.+.+. ++|+.|+..|||+.+|+++++|+.++
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 99999999999999999999999999999999999999999999999999884 78999999999999999999999999
Q ss_pred HHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCC
Q 010521 388 EAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLT 466 (508)
Q Consensus 388 ~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~T 466 (508)
.....++|||.++ +++++..+.+++.++. .+|++.+....+...|..+| ..|||+||.||.|+|||+ ++++|
T Consensus 300 ~~~~~~~SLd~~v----g~~~d~~l~d~l~~~~--~~pee~~~~~~l~~~L~~~L-~~L~~reR~VI~LRygl~d~~~~T 372 (415)
T PRK07598 300 LRVPRSVSLETKV----GKDKDTELGDLLETDD--ISPEEMLMRESLQRDLQHLL-ADLTSRERDVIRMRFGLADGHTYS 372 (415)
T ss_pred HHccCCccccccc----CCCccccHHHhccCCC--CCHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHhcCCCCCCC
Confidence 9999999999985 2333445677776543 47888888889999999999 899999999999999984 67899
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhhh
Q 010521 467 WEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV 506 (508)
Q Consensus 467 leEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~~l~ 506 (508)
++|||+.||+|++||++++++|++|||+.-....++.|+.
T Consensus 373 l~EIA~~LGvS~erVRqie~rAl~KLR~~~~~~~l~~y~~ 412 (415)
T PRK07598 373 LAEIGRALDLSRERVRQIESKALQKLRQPKRRNRIRDYLE 412 (415)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHHH
Confidence 9999999999999999999999999999988999999985
No 2
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=9.5e-57 Score=468.97 Aligned_cols=308 Identities=35% Similarity=0.583 Sum_probs=290.5
Q ss_pred hhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHH
Q 010521 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (508)
Q Consensus 191 ~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LI 270 (508)
+++..||++|+++|+||++||++|++++++|..++..+.+|.+..|++|+..+||.++|++..+|++++..+..|++.||
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 67889999999999999999999999999999999999999999999999999999999999999999998999999999
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHH
Q 010521 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 350 (508)
Q Consensus 271 e~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l 350 (508)
.+|+++|+++|++|.+++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++|++++++||+|.|+.+.+
T Consensus 143 ~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~~~~ 222 (373)
T PRK07406 143 QSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETI 222 (373)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchH
Q 010521 351 GLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGV 429 (508)
Q Consensus 351 ~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~v 429 (508)
++++++...+. ++|+.|+.+|||+.+|+++++|..++.....++|||.++ +++++.++.+++++.. .+|++.+
T Consensus 223 ~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i----~~~~~~~l~d~l~d~~--~~pee~~ 296 (373)
T PRK07406 223 SRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPI----GKEEDSRLGDFIEADG--ETPEDDV 296 (373)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCC----CCCCcccHHHhcCCCC--CCHHHHH
Confidence 99999999885 789999999999999999999999988888999999985 2333456778887753 4788888
Q ss_pred HHHHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhh
Q 010521 430 DDWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAML 505 (508)
Q Consensus 430 e~~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~~l 505 (508)
....+...|..+| +.||++||.||.+||||+ ++++|++|||+.||||++||+|++.+|++|||+......+..|+
T Consensus 297 ~~~~~~~~L~~aL-~~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~~~~~~~l~~~~ 372 (373)
T PRK07406 297 AKNLLREDLEGVL-ATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 372 (373)
T ss_pred HHHHHHHHHHHHH-HcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHh
Confidence 8889999999999 899999999999999995 57899999999999999999999999999999999999998886
No 3
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00 E-value=2e-55 Score=453.13 Aligned_cols=308 Identities=31% Similarity=0.573 Sum_probs=286.8
Q ss_pred hhhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHH
Q 010521 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL 269 (508)
Q Consensus 190 ~~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~L 269 (508)
.|.+..||++|+++|+||++||++|+++++.|-.++..+..|++.+|++|+..+||.+++|+..+|...+..+..|++.|
T Consensus 17 ~d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~~L 96 (327)
T PRK05949 17 ADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQKM 96 (327)
T ss_pred CCHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHHHH
Confidence 36888999999999999999999999999999999999999999999999999999999999999999999998999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHH
Q 010521 270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHER 349 (508)
Q Consensus 270 Ie~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~ 349 (508)
|..|+++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+|||+||||++|.++|.+++++||+|.|+.+.
T Consensus 97 i~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~~~~ 176 (327)
T PRK05949 97 IEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK 176 (327)
T ss_pred HHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHH-HHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccch
Q 010521 350 LGLIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHG 428 (508)
Q Consensus 350 l~kir~a~~~l-~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ 428 (508)
+++++++.+.+ .++|++|+.+|||+.+|+++++|..++.....++|||.++ +++++.++.+.+++.. .+|++.
T Consensus 177 ~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~----~~~~~~~l~~~l~d~~--~~pe~~ 250 (327)
T PRK05949 177 LNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRV----GDNQDTELSELLEDEG--PSPDQY 250 (327)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCc----CCCCCccHHhhcCCCC--CCHHHH
Confidence 99999999888 5789999999999999999999999999889999999974 2333445677777653 478888
Q ss_pred HHHHHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhhh
Q 010521 429 VDDWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV 506 (508)
Q Consensus 429 ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~~l~ 506 (508)
+........|..+| +.||++||.||.+||||+ ++++|++|||+.||||+++|++++.+|++|||+. ...+..|+.
T Consensus 251 ~~~~~~~~~L~~~L-~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~~--~~~l~~~~~ 326 (327)
T PRK05949 251 ITQELLRQDLNNLL-AELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRRR--RANVKEYLA 326 (327)
T ss_pred HHHHHHHHHHHHHH-HhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence 88889999999999 899999999999999994 6899999999999999999999999999999994 456777764
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=4.2e-55 Score=445.53 Aligned_cols=295 Identities=38% Similarity=0.648 Sum_probs=276.4
Q ss_pred hHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHH
Q 010521 192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM 271 (508)
Q Consensus 192 ~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe 271 (508)
++..||++|+++|+||++||.+|+++++.|-.+++.+.+|++..|++|+..+||.++|++..+|..++..+..|++.||.
T Consensus 2 ~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv~ 81 (298)
T TIGR02997 2 LVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMIK 81 (298)
T ss_pred cHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHHH
Confidence 56789999999999999999999999999999999999999999999999999999999999999999988999999999
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHH
Q 010521 272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG 351 (508)
Q Consensus 272 ~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~ 351 (508)
.|+++|+++|++|.++|.+++||+||||+|||+|+++|||.+|++|+||++||||++|.+++.++++++|+|.+....++
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-HHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHH
Q 010521 352 LIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVD 430 (508)
Q Consensus 352 kir~a~~~l-~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve 430 (508)
+++++...+ ...|+.|+.+|||+.+|+++++|..++.....++|||.++ +++++.++.+.+++. ..+|++.+.
T Consensus 162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~----~~~~~~~~~~~~~~~--~~~pe~~~~ 235 (298)
T TIGR02997 162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPV----GDEEDTELGDLLEDD--GESPEEQVE 235 (298)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCc----CCCCcchHHHhccCC--CCCHHHHHH
Confidence 999998888 4789999999999999999999999999889999999974 222334566666664 357888899
Q ss_pred HHHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 431 DWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 431 ~~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
..+....|..+| +.||++||.||.++|||+ ++++|++|||+.||||++||+|++++|++|||
T Consensus 236 ~~~~~~~L~~~L-~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr 298 (298)
T TIGR02997 236 RESLRQDLESLL-AELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298 (298)
T ss_pred HHHHHHHHHHHH-HcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 999999999999 899999999999999994 68999999999999999999999999999996
No 5
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=1.8e-54 Score=444.57 Aligned_cols=307 Identities=35% Similarity=0.590 Sum_probs=286.0
Q ss_pred hhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHH
Q 010521 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (508)
Q Consensus 191 ~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LI 270 (508)
+++..||++|+++|+||++||.+|++++++|-.++..+..|.+.+|++|+..+||.+++++..+|...+.++..|++.||
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 57889999999999999999999999999999999999999999999999999999999999999999999899999999
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHH
Q 010521 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 350 (508)
Q Consensus 271 e~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l 350 (508)
..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|+|||+||||++|.++|.+++++||+|.++...+
T Consensus 88 ~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~~~~ 167 (317)
T PRK07405 88 EANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKL 167 (317)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchH
Q 010521 351 GLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGV 429 (508)
Q Consensus 351 ~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~v 429 (508)
++++++...+. ..|+.|+.+|||+.+|+++++|..++.....+.|||.++ +++++.++.+.+++.. .+|++.+
T Consensus 168 ~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~----~~~~~~~l~~~~~d~~--~~pe~~~ 241 (317)
T PRK07405 168 NKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRV----GDNQDTELGELLEDTG--ASPEDFA 241 (317)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCC----CCCCCccHHHhhcCCC--CCHHHHH
Confidence 99999998884 789999999999999999999999998888899999874 2333446777777653 4789889
Q ss_pred HHHHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhhh
Q 010521 430 DDWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV 506 (508)
Q Consensus 430 e~~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~~l~ 506 (508)
...++...|..+| +.||++||.||.++|||+ ++++|++|||+.||||++||+|++.+|++|||+. ...+..|+.
T Consensus 242 ~~~~~~~~l~~al-~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~--~~~l~~~~~ 316 (317)
T PRK07405 242 TQSSLQLDLERLM-EDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKR--KANIQEYLA 316 (317)
T ss_pred HHHHHHHHHHHHH-HcCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence 9999999999999 899999999999999994 6899999999999999999999999999999996 456677663
No 6
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=100.00 E-value=5e-54 Score=461.75 Aligned_cols=298 Identities=34% Similarity=0.564 Sum_probs=268.5
Q ss_pred hhhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHH
Q 010521 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL 269 (508)
Q Consensus 190 ~~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~L 269 (508)
.++++.||++|+++|+||++||++|+++++.|+.+++. +. ...+|+. ....+|++++..+..|+++|
T Consensus 210 ~d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~---~~-------~~~~~~~---~~~~~l~~~~~~g~~Ar~~L 276 (509)
T PRK05901 210 ADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEEL---LA-------EGEKLDP---ELRRDLQWIGRDGKRAKNHL 276 (509)
T ss_pred ccHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhh---hh-------hcccchh---hhhhhhhhhccchHHHHHHH
Confidence 46899999999999999999999999999999874332 11 1122332 24577899999999999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHH
Q 010521 270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHER 349 (508)
Q Consensus 270 Ie~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~ 349 (508)
|..|+|||++||++|.++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++|++++|+||+|+|+.+.
T Consensus 277 I~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~~~~e~ 356 (509)
T PRK05901 277 LEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVET 356 (509)
T ss_pred HHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccch
Q 010521 350 LGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHG 428 (508)
Q Consensus 350 l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ 428 (508)
+++++++.+.+. .+|++|+.+|||+.||+++++|..++.....++|||.++ +++++..+.+++.|.. ...|++.
T Consensus 357 i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i----~~d~~~~l~d~l~D~~-~~~p~~~ 431 (509)
T PRK05901 357 INKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTI----GKEGDSQFGDFIEDSE-AVSPVDA 431 (509)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccccccc----ccCCcccHHHhccCCC-CCCHHHH
Confidence 999999998885 789999999999999999999999998888999999975 2333346788888875 3578888
Q ss_pred HHHHHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhhh
Q 010521 429 VDDWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV 506 (508)
Q Consensus 429 ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~~l~ 506 (508)
+....+...|..+| ..|+++||.||.+||||+ ++++|++|||+.||||++||||++.+|+.|||+......++.||+
T Consensus 432 ~~~~~l~~~L~~aL-~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~~~~~~l~~~l~ 509 (509)
T PRK05901 432 VSFTLLQDQLQEVL-ETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDFLD 509 (509)
T ss_pred HHHHHHHHHHHHHH-hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 88999999999999 899999999999999995 689999999999999999999999999999999999999999874
No 7
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=100.00 E-value=6.7e-53 Score=431.06 Aligned_cols=310 Identities=36% Similarity=0.569 Sum_probs=276.8
Q ss_pred hhhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHH-hhCCCCchH---------------HHHHHhccCh-
Q 010521 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKE-RLGCEPSME---------------QLAASLRISR- 252 (508)
Q Consensus 190 ~~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~-~~g~~p~~~---------------~~a~~~~~s~- 252 (508)
.+.++.|+.+++..++++.+++..+.+.++....+......+.. ..|..|+.. +|+..+....
T Consensus 8 ~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Ee 87 (342)
T COG0568 8 ADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEEE 87 (342)
T ss_pred hhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHHH
Confidence 46889999999999999999999999999888877666667776 678888886 4444454444
Q ss_pred HHHHHhhhhh---HHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHH
Q 010521 253 PELQSILMEC---SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGV 329 (508)
Q Consensus 253 ~~L~~~l~e~---~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I 329 (508)
.+|..++..+ ..|..+||++|+++|++||++|.++|+++.||||||+|||++|+++|||++|++|+|||+||||++|
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 5566777655 4599999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcccccccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCC
Q 010521 330 SRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLP 408 (508)
Q Consensus 330 ~~~Ird~~R~irip~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~ 408 (508)
.++|.+++|+||+|+|+.+.++++++..+.+. +.|++|+.+|||+.+|+++++|..++.....++|||.|+ ++++
T Consensus 168 ~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~i----g~de 243 (342)
T COG0568 168 TRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPI----GDDE 243 (342)
T ss_pred HHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcC----CCCc
Confidence 99999999999999999999999999998885 579999999999999999999999999999999999985 3444
Q ss_pred CCccccccccccCCCCccchHHHHHHHHHHHHHHHcc-CCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521 409 GETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVT-LGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGL 486 (508)
Q Consensus 409 ~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~L~~~-Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~ 486 (508)
++.+.++++|... .+|++.+....+.+.+...| .. |+|+|+.||++|||++ +++.|++|||+.+|||++|||||+.
T Consensus 244 d~~l~d~leD~~~-~~p~~~~~~~~~~~~~~~~L-~~~Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~isrERvRQIE~ 321 (342)
T COG0568 244 DSELGDFLEDDKS-VSPEDAVERESLKEDLNEVL-AEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEA 321 (342)
T ss_pred ccHHHHHhhcCCc-CCHHHHHHHHHHHHHHHHHH-HhcCCHHHHHHHHHHhccCCCCcchHHHHHHHhCCcHHHHHHHHH
Confidence 5578999999863 48999999999999999999 77 9999999999999995 6899999999999999999999999
Q ss_pred HHHHHHHH-HHHHhhHHHhh
Q 010521 487 VALEKLKH-AARKKKMEAML 505 (508)
Q Consensus 487 rALkKLR~-~L~~~~l~~~l 505 (508)
+|++|||. .-....++.||
T Consensus 322 kAl~KLr~~~~~~~~~~~~l 341 (342)
T COG0568 322 KALRKLRRHPERSALLRSYL 341 (342)
T ss_pred HHHHHHHHhhhhhhHHHHhh
Confidence 99999994 44445567776
No 8
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=100.00 E-value=3.6e-52 Score=428.31 Aligned_cols=296 Identities=33% Similarity=0.552 Sum_probs=263.6
Q ss_pred hhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHH
Q 010521 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (508)
Q Consensus 191 ~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LI 270 (508)
+++..||++|+++|+||++||.+|+++++.|..++.. +| ..+|.... ...+|+..+..|..|++.||
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 5788999999999999999999999999998764332 11 11221111 34578888899999999999
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHH
Q 010521 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 350 (508)
Q Consensus 271 e~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l 350 (508)
..|+++|+++|++|.+++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++|+++++.|++|.++.+.+
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-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchH
Q 010521 351 GLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGV 429 (508)
Q Consensus 351 ~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~v 429 (508)
++++++...+. ++|+.|+.+|||+.+|+++++|..++.....++|||.++ +++++.++.++++|.. ..+|++.+
T Consensus 173 ~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~----~~~~~~~l~d~l~d~~-~~~pe~~~ 247 (324)
T PRK07921 173 NKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPV----GSDEEAPLGDFIEDSE-ATSAENAV 247 (324)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCC----CCCCCchHHHHhcCCC-CCCHHHHH
Confidence 99999999985 789999999999999999999999988888899999984 2333446788888764 35788888
Q ss_pred HHHHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhh
Q 010521 430 DDWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAML 505 (508)
Q Consensus 430 e~~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~~l 505 (508)
...++...|..+| ..||++|+.||.+||||+ ++++|++|||+.||||+++|+|++.+|++|||.......+..|+
T Consensus 248 ~~~~~~~~l~~~L-~~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~~~~~~l~~~~ 323 (324)
T PRK07921 248 IAGLLHTDIRSVL-ATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSYA 323 (324)
T ss_pred HHHHHHHHHHHHH-HhCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHHHHHHHHhh
Confidence 8889999999999 899999999999999994 67899999999999999999999999999999999888888876
No 9
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=1.2e-50 Score=423.95 Aligned_cols=272 Identities=36% Similarity=0.600 Sum_probs=254.1
Q ss_pred hhhhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHH
Q 010521 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREK 268 (508)
Q Consensus 189 ~~~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~ 268 (508)
..+.++.||++|++.|+||++++.+|+++++.||. .|++.
T Consensus 94 ~~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~Gd~----------------------------------------~A~~~ 133 (367)
T PRK09210 94 INDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGDE----------------------------------------EAKQR 133 (367)
T ss_pred cCcHHHHHHHHhhccCCCCHHHHHHHHHHHHhhHH----------------------------------------HHHHH
Confidence 34799999999999999999999999999999998 89999
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHH
Q 010521 269 LVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHE 348 (508)
Q Consensus 269 LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~ 348 (508)
||..|+++|+++|++|.+++.+++||+|||++|||+|+++|||.+|++|+|||+||||++|.++|++++|++++|.|+.+
T Consensus 134 Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~~~ 213 (367)
T PRK09210 134 LAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 213 (367)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccc
Q 010521 349 RLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWH 427 (508)
Q Consensus 349 ~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~ 427 (508)
.++++.++.+.+. ++|+.||.+|||+.+|+++++|++++.....++|||.++ +++++..+.++++|.. ..+|++
T Consensus 214 ~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~----~~~~~~~l~d~i~d~~-~~~p~~ 288 (367)
T PRK09210 214 TINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPI----GEEDDSHLGDFIEDQD-ATSPAD 288 (367)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCC----CCCCcchhhhhccCCC-CCCHHH
Confidence 9999999988884 789999999999999999999999999888899999974 2333456788888765 357999
Q ss_pred hHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhhh
Q 010521 428 GVDDWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV 506 (508)
Q Consensus 428 ~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~~l~ 506 (508)
.+....+...|..+| ..||++||.||.+||||+ ++++|++|||+.||||++||||++.+||+|||+.....+++.|+.
T Consensus 289 ~~~~~~~~~~l~~~l-~~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~~~~~~~l~~~~~ 367 (367)
T PRK09210 289 HAAYELLKEQLEDVL-DTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 367 (367)
T ss_pred HHHHHHHHHHHHHHH-HhCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhChHHHhHHHHhhC
Confidence 889999999999999 899999999999999994 688999999999999999999999999999999999999999873
No 10
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=3.2e-47 Score=422.01 Aligned_cols=272 Identities=31% Similarity=0.584 Sum_probs=252.7
Q ss_pred hHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHH
Q 010521 192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM 271 (508)
Q Consensus 192 ~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe 271 (508)
.++.||++|...+.|+++++..++++++.|+. .+..|+++||.
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 66789999999999999999999999999985 12278999999
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHH
Q 010521 272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG 351 (508)
Q Consensus 272 ~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~ 351 (508)
.|+|||++||++|.++|++++||+|||+|||++|+++|||.+|++|+|||+||||++|.++|++++|+||+|+|+.+.++
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-HHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHH
Q 010521 352 LIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVD 430 (508)
Q Consensus 352 kir~a~~~l-~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve 430 (508)
+++++.+.+ +++|++|+.+|||+.||+++++|..++.....++|||.|+ +++++.++.++++|... .+|.+.+.
T Consensus 468 k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i----~~~~~~~l~d~i~d~~~-~~p~~~~~ 542 (619)
T PRK05658 468 KLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPI----GDDEDSHLGDFIEDKNA-ELPIDAAI 542 (619)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCC----CCCCCCchhhhcCCCCC-CChHHHHH
Confidence 999998888 5789999999999999999999999999888999999975 23344578889888753 57988888
Q ss_pred HHHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhhh
Q 010521 431 DWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV 506 (508)
Q Consensus 431 ~~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~~l~ 506 (508)
...+...|..+| ..||++|+.||++||||+ .+++|++|||+.||||+++|||++.+|++|||+......++.||.
T Consensus 543 ~~~~~~~l~~~l-~~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr~~~~~~~l~~~~~ 618 (619)
T PRK05658 543 QESLREATTDVL-ASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRSFLD 618 (619)
T ss_pred HHHHHHHHHHHH-HcCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHhchHHHHHHHHHhc
Confidence 889999999999 899999999999999996 578999999999999999999999999999999999999999985
No 11
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=100.00 E-value=1.3e-43 Score=365.29 Aligned_cols=270 Identities=34% Similarity=0.576 Sum_probs=246.0
Q ss_pred hHhhhhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHH
Q 010521 187 ELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAR 266 (508)
Q Consensus 187 ~~~~~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~ 266 (508)
+.+.+.+++||++|+..|+||++++..|+.+++.||. .|+
T Consensus 49 ~~~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~Gd~----------------------------------------~A~ 88 (325)
T PRK05657 49 QRVLDATQLYLNEIGYSPLLTAEEEVYFARRALRGDF----------------------------------------AAR 88 (325)
T ss_pred cccccHHHHHHHHHhcCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHH
Confidence 3445789999999999999999999999999999998 999
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccH
Q 010521 267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHL 346 (508)
Q Consensus 267 e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~ 346 (508)
+.||..|.++|+++|++|.+++.+++||+||||+|+|+++++||+.+|++|+||++||||++|.++++++.+.+++|.++
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-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCc
Q 010521 347 HERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNP 425 (508)
Q Consensus 347 ~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~P 425 (508)
.+.++.+.++...+. +.|+.|+.+|||+.+|+++++|..++.....+.|||.+. ++++..++.+.+.+.. ..+|
T Consensus 169 ~~~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~----~~~~~~~l~d~l~d~~-~~~p 243 (325)
T PRK05657 169 VKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPL----GGDPEKSLLDILADEQ-ENGP 243 (325)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCC----CCCCCcchhhhccCCC-CCCH
Confidence 999888777777775 579999999999999999999999998888889999873 2333445667777654 2478
Q ss_pred cchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHH
Q 010521 426 WHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKME 502 (508)
Q Consensus 426 e~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~ 502 (508)
+..+...+....|..+| ..||+++|.||.++|||. ++++|++|||+.||||++||++++++|+++||+.|...++.
T Consensus 244 e~~~~~~e~~~~L~~aL-~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~~~~~~ 320 (325)
T PRK05657 244 EDTTQDDDMKQSIVKWL-FELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQGLS 320 (325)
T ss_pred HHHHHHHHHHHHHHHHH-HcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhCccc
Confidence 88888888889999999 899999999999999994 79999999999999999999999999999999999877654
No 12
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=4.6e-43 Score=355.12 Aligned_cols=265 Identities=29% Similarity=0.443 Sum_probs=227.0
Q ss_pred CchhHhhhhHHHHHHhhcccCCCCHHHHHHHHHHH-HcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhh
Q 010521 184 ISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKI-KTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMEC 262 (508)
Q Consensus 184 ~~~~~~~~~~~~yl~~i~~~~lLt~~EE~eL~~~i-k~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~ 262 (508)
.+|+ +.+..|++++++.|+++.++|.+|+.+. +.||.
T Consensus 10 ~~~~---~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~~Gd~--------------------------------------- 47 (284)
T PRK06596 10 LSPE---GNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDL--------------------------------------- 47 (284)
T ss_pred CCCc---cHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCCH---------------------------------------
Confidence 4555 6888999999999999999999999995 68897
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q 010521 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (508)
Q Consensus 263 ~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~iri 342 (508)
.|++.||..|+|+|+++|++|.+++.+.+||+|||++||++|+++|||++|++|+|||+|||+++|.++|+++++.+++
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 8999999999999999999999999999999999999999999999999999999999999999999999999888999
Q ss_pred cccHHH--HHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHh-CccccccccCCCCCCCCCCCccccccccc
Q 010521 343 PNHLHE--RLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI-GKVFSLDREAFPSLNGLPGETHHSYIADN 419 (508)
Q Consensus 343 p~~~~~--~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~-~~~~SLD~~~~~~~~~~~~~~l~d~i~d~ 419 (508)
|.+... ...++++....+. .+++|+.+|||+.||+++++|.+++... ..++|||.+... +++++.++.+.++|.
T Consensus 127 p~~~~~~~~~~~~~~~~~~l~-~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~--~~~~~~~l~~~l~d~ 203 (284)
T PRK06596 127 ATTKAQRKLFFNLRKAKKRLG-WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDD--DDEESGAPQDYLEDK 203 (284)
T ss_pred cchHHHHHHHHHHHHHHHHhc-cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCC--CCCCcchHHHHcCCC
Confidence 998653 2345566665554 4689999999999999999999987644 578999997421 111223466777776
Q ss_pred cCCCCccchHHHHH----HHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010521 420 RVENNPWHGVDDWA----LKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA 495 (508)
Q Consensus 420 ~~e~~Pe~~ve~~e----l~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~ 495 (508)
. .+|++.++..+ ....|..+| +.||++||.||.+|||.+ +++|++|||+.||||+++|+|++.+|++|||..
T Consensus 204 ~--~~p~~~~~~~~~~~~~~~~L~~al-~~L~~rEr~VL~lry~~~-~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~ 279 (284)
T PRK06596 204 S--SDPADVLEEDNWEDQRRALLADAL-EGLDERSRDIIEARWLDD-DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAA 279 (284)
T ss_pred C--CCchHHHHHHHHHHHHHHHHHHHH-hcCCHHHHHHHHHHhcCC-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3 46777666543 577899999 899999999999999643 689999999999999999999999999999998
Q ss_pred HHH
Q 010521 496 ARK 498 (508)
Q Consensus 496 L~~ 498 (508)
+..
T Consensus 280 l~~ 282 (284)
T PRK06596 280 IEA 282 (284)
T ss_pred HHh
Confidence 864
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=1.6e-43 Score=349.10 Aligned_cols=236 Identities=37% Similarity=0.632 Sum_probs=216.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccc
Q 010521 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN 344 (508)
Q Consensus 265 A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~ 344 (508)
|+++||..|+++|+++|++|.+++.+++||+|||++||++|+++|||++|++|+|||+||||++|.++++++.+.+++|.
T Consensus 1 a~~~Li~~~~~lv~~ia~~~~~~~~~~eDLiQeG~igL~~A~~~fd~~~g~~FstYA~~~Ir~~I~~~l~~~~~~vrip~ 80 (238)
T TIGR02393 1 AKKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80 (238)
T ss_pred CHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCChHHHhHHHHHHHHHHHHHHcCCcEEeCH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 345 HLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 345 ~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
++.+.++++.++...+. +.|++||.+|||+.+|++.++|..++.....++|||.++ +++++.++.+.++|+. ..
T Consensus 81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~----~~~~~~~l~d~l~d~~-~~ 155 (238)
T TIGR02393 81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPI----GEEEDSFLGDFIEDTS-IE 155 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCC----CCCCcccHHHHhcCCC-CC
Confidence 99999999999998885 789999999999999999999999988888899999974 2233346777787765 35
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHH
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKME 502 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~ 502 (508)
+|++.+...+....|..+| ..||++||.||.++|||+ ++++|++|||+.||||+++|+|++.+|++|||+.+....++
T Consensus 156 ~p~~~~~~~~~~~~l~~~l-~~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~~~~~~ 234 (238)
T TIGR02393 156 SPDDYAAKELLREQLDEVL-ETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLK 234 (238)
T ss_pred ChHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHHHhHHH
Confidence 7888888888999999999 899999999999999995 68999999999999999999999999999999999988888
Q ss_pred Hhhh
Q 010521 503 AMLV 506 (508)
Q Consensus 503 ~~l~ 506 (508)
.|+.
T Consensus 235 ~~~~ 238 (238)
T TIGR02393 235 SFLD 238 (238)
T ss_pred HhhC
Confidence 8863
No 14
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=1.4e-42 Score=352.50 Aligned_cols=264 Identities=25% Similarity=0.354 Sum_probs=225.0
Q ss_pred hhHHHHHHhhcccCCCCHHHHHHHHHHH-HcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHH
Q 010521 191 NRLKGYVKGVVSEELLTHAEVVRLSKKI-KTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL 269 (508)
Q Consensus 191 ~~~~~yl~~i~~~~lLt~~EE~eL~~~i-k~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~L 269 (508)
+..+.||++|.++|+||+++|.+|++++ +.||. .|+++|
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 3556799999999999999999999997 47887 999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHH-
Q 010521 270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHE- 348 (508)
Q Consensus 270 Ie~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~- 348 (508)
|..|.|+|+++|++|.+++.+++||+||||+|||+++++|||.+|.+|+|||+||||++|.++|+++++.+|+|.+..+
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 9999999999999999999999999999999999999999999999999999999999999999999999999998765
Q ss_pred -HHHHHHHHHHHHH----HcCCCCCHHHHHHHhCCCHHHHHHHHHH-hCccccccccCCCCCCCCCCCccccccccccCC
Q 010521 349 -RLGLIRNAKLRLE----EKGVTPSVDRIAEYLNMSQKKVRNATEA-IGKVFSLDREAFPSLNGLPGETHHSYIADNRVE 422 (508)
Q Consensus 349 -~l~kir~a~~~l~----~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~-~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e 422 (508)
...++++....+. .+|+.|+.+|||+.||+++++|..+... ...++|||.++.. +++.+.++.+.+++..
T Consensus 126 ~~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~--~~~~~~~l~d~i~d~~-- 201 (289)
T PRK07500 126 ALFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSE--EDEGRSERMDFLVDDS-- 201 (289)
T ss_pred HHHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCC--CCCCcccHHHhccCCC--
Confidence 3345566555553 4799999999999999999999887643 3578999987421 1122235677887764
Q ss_pred CCccchHHH----HHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521 423 NNPWHGVDD----WALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 498 (508)
Q Consensus 423 ~~Pe~~ve~----~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~ 498 (508)
.+|++.+.. .+....|..+| ..||++||.||.++|+ +.+++|++|||+.||||++||+|++++|++|||..+..
T Consensus 202 ~~pe~~~~~~~~~~~~~~~l~~al-~~L~~rer~vl~lr~~-~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~~ 279 (289)
T PRK07500 202 PLPDEQVESSIDGERRRRWLTQAL-QTLNERELRIIRERRL-REDGATLEALGEELGISKERVRQIEARALEKLRRALLS 279 (289)
T ss_pred CCchHHHHHHHHHHHHHHHHHHHH-hcCCHHHHHHHHHHhc-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 367766543 34556788999 8999999999999994 23899999999999999999999999999999999975
Q ss_pred hh
Q 010521 499 KK 500 (508)
Q Consensus 499 ~~ 500 (508)
..
T Consensus 280 ~~ 281 (289)
T PRK07500 280 QS 281 (289)
T ss_pred cC
Confidence 54
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=2.5e-42 Score=347.12 Aligned_cols=259 Identities=28% Similarity=0.459 Sum_probs=217.8
Q ss_pred hHHHHHHhhcccCCCCHHHHHHHHHH-HHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHH
Q 010521 192 RLKGYVKGVVSEELLTHAEVVRLSKK-IKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (508)
Q Consensus 192 ~~~~yl~~i~~~~lLt~~EE~eL~~~-ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LI 270 (508)
++..||++|+++|+|+++++.+|+.+ .+.||. .|++.||
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 57789999999999999999999999 578987 8999999
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHH--
Q 010521 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHE-- 348 (508)
Q Consensus 271 e~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~-- 348 (508)
..|+++|+++|++|.+++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++|+++++.+++|.+...
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 999999999999999999999999999999999999999999999999999999999999999999888999987642
Q ss_pred HHHHHHHHHHHHHHcCCCC-CHHHHHHHhCCCHHHHHHHHHHhC-ccccccccCCCCCCCCCCCccccccccccCCCCcc
Q 010521 349 RLGLIRNAKLRLEEKGVTP-SVDRIAEYLNMSQKKVRNATEAIG-KVFSLDREAFPSLNGLPGETHHSYIADNRVENNPW 426 (508)
Q Consensus 349 ~l~kir~a~~~l~~~Gr~P-t~eEIA~~Lgis~e~v~~~l~~~~-~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe 426 (508)
...+++++...+. .++.| +.+|||+.||+++++|.++..... .+.|||.++.. +++....+.+.++|.. .+|+
T Consensus 122 ~~~~~~~~~~~~~-~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~--~~~~~~~~~~~l~d~~--~~pe 196 (270)
T TIGR02392 122 LFFNLRKMKKRLQ-GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDD--DEDDGGAPIAYLVDKT--SDPE 196 (270)
T ss_pred HHHHHHHHHHHHh-cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCC--CCCccccHHHHhcCCC--CChH
Confidence 3345555555543 22566 599999999999999999876543 47899987421 1111124566777664 3677
Q ss_pred chHHHHH----HHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521 427 HGVDDWA----LKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497 (508)
Q Consensus 427 ~~ve~~e----l~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~ 497 (508)
+.+...+ +...|..+| ..||++||.||.++||. .+++|++|||+.||||+++|+|++.+|++|||+.+.
T Consensus 197 ~~~~~~~~~~~~~~~L~~al-~~L~~rer~vl~l~y~~-~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~l~ 269 (270)
T TIGR02392 197 DTLEEEQWEELQRQALANAL-GSLDARSRRIIEARWLD-DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAALA 269 (270)
T ss_pred HHHHHHHHHHHHHHHHHHHH-HcCCHHHHHHHHHHhcC-CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 7665433 557899999 89999999999999952 358999999999999999999999999999998774
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=1.9e-40 Score=335.70 Aligned_cols=269 Identities=33% Similarity=0.542 Sum_probs=241.6
Q ss_pred hHhhhhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHH
Q 010521 187 ELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAR 266 (508)
Q Consensus 187 ~~~~~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~ 266 (508)
-.+.+.+++||.+|..+|.|+.+++.+|+.+++.||. .|+
T Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~gd~----------------------------------------~a~ 48 (285)
T TIGR02394 9 TRVADVTQLYLREIGFKPLLTAEEEIAYARRALAGDF----------------------------------------EAR 48 (285)
T ss_pred cCcchHHHHHHHHHhccCCCCHHHHHHHHHHHHcCCH----------------------------------------HHH
Confidence 3466899999999999999999999999999999998 999
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccH
Q 010521 267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHL 346 (508)
Q Consensus 267 e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~ 346 (508)
+.||..|.++|+++|++|.+++.+++||+|||++|||+++++||+..|++|+||+.|||+.++.+++.++.+.+++|.++
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 HHHHHHHHHHHHHH-HHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCc
Q 010521 347 HERLGLIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNP 425 (508)
Q Consensus 347 ~~~l~kir~a~~~l-~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~P 425 (508)
.+..+.+.+..+.+ ...|+.|+..++|+.+|+++.++..++....+..|+|.+. +++...++.+.+.+.. ..+|
T Consensus 129 ~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~----~~~~~~~~~~~~~~~~-~~~p 203 (285)
T TIGR02394 129 IKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPL----DDDSSKSLLDTIADEQ-SIDP 203 (285)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCC----CCCCCcchhhhhcCCC-CCCH
Confidence 99998877766665 4579999999999999999999999999888899998753 2222233444554443 2478
Q ss_pred cchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhcc-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010521 426 WHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM 501 (508)
Q Consensus 426 e~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGL-d~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l 501 (508)
++.+...+....|..+| ..||+++|.||.++||| +++++|++|||+.||+|.+||++++++|+++||+.|...+.
T Consensus 204 e~~~~~~e~~~~L~~al-~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~~~~~ 279 (285)
T TIGR02394 204 ESLVQNDDLKQLIEAWL-AELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERDGV 279 (285)
T ss_pred HHHHHHHHHHHHHHHHH-HcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 88888999999999999 89999999999999998 47999999999999999999999999999999999986543
No 17
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=3.8e-40 Score=330.56 Aligned_cols=220 Identities=25% Similarity=0.367 Sum_probs=196.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.++++||.+|+|||+++|++|.++|.+.+||+|||+|||++|+++|||++|++|+|||+||||++|.++++++.++|++|
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-HcCCCCCHHHHHHHhCCCHHHHHHHHHHh--CccccccccCCCCCCCCCC-Cccccccccc
Q 010521 344 NHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAI--GKVFSLDREAFPSLNGLPG-ETHHSYIADN 419 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~--~~~~SLD~~~~~~~~~~~~-~~l~d~i~d~ 419 (508)
+++.+.+++++++...+. ++|+.|+.+|||+.||+++++|.+++... ..+.|||.+... ++++ ..+.+.+
T Consensus 120 r~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~---~~~~~~~~~d~~--- 193 (264)
T PRK07122 120 RRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGS---GDDDARAIADTL--- 193 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccC---CCCCcccchhcc---
Confidence 999999999999998885 78999999999999999999999988753 578999997421 1111 1233322
Q ss_pred cCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 420 RVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 420 ~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
++|+..++..+....|..+| +.||+++|.||.++| ++++|++|||+.||+|+++|++++++|+++||..+
T Consensus 194 ---~~~~~~~e~~~~~~~l~~~l-~~L~~rer~vl~l~y---~~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l 263 (264)
T PRK07122 194 ---GDVDAGLDQIENREALRPLL-AALPERERTVLVLRF---FESMTQTQIAERVGISQMHVSRLLAKTLARLRDQL 263 (264)
T ss_pred ---CCcHHHHHHHHHHHHHHHHH-HcCCHHHHHHHHHHh---cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHc
Confidence 24555667777888899999 899999999999999 79999999999999999999999999999999876
No 18
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=1.5e-38 Score=317.47 Aligned_cols=226 Identities=27% Similarity=0.373 Sum_probs=195.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCC-CCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNM-GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~-g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~iri 342 (508)
.|+++||..|+|+|+++|++|.+. +.+++||+|||+||||+|+++|||++|++|+|||++||+++|.++++++.+++++
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-HcCCCCCHHHHHHHhCCCHHHHHHHHHH--hCccccccccCCCCCCCCCCCccccccccc
Q 010521 343 PNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEA--IGKVFSLDREAFPSLNGLPGETHHSYIADN 419 (508)
Q Consensus 343 p~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~--~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~ 419 (508)
|+++.+.+++++++...+. ++|++|+.+|||+.||+++++|..++.. .....|||.+... +++....+.+.++++
T Consensus 105 pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~--~~~~~~~l~d~~~d~ 182 (256)
T PRK07408 105 PRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQ--DEDGSTSLGDLLPDP 182 (256)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCC--CCCCccccccccCCc
Confidence 9999999999999999885 7899999999999999999999998754 3568899987421 111122455555554
Q ss_pred cCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521 420 RVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 499 (508)
Q Consensus 420 ~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~ 499 (508)
.. .+. ....+....|..+| ..||+++|.||.++| ++++|++|||+.||+|+++|++++.+|+++||+.+...
T Consensus 183 ~~--~~~--~~~~~~~~~l~~~l-~~L~~~~r~vl~l~y---~~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~~~ 254 (256)
T PRK07408 183 RY--RSF--QLAQEDRIRLQQAL-AQLEERTREVLEFVF---LHDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQPE 254 (256)
T ss_pred cc--chh--hhhHHHHHHHHHHH-HcCCHHHHHHHHHHH---HCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhcc
Confidence 31 121 12345567899999 899999999999999 79999999999999999999999999999999998654
No 19
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=100.00 E-value=4.7e-38 Score=313.25 Aligned_cols=244 Identities=29% Similarity=0.407 Sum_probs=214.0
Q ss_pred hcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHH
Q 010521 200 VVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMS 279 (508)
Q Consensus 200 i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~s 279 (508)
.+++|+||++++.+|+.+++.||. .|++.||..|+++|++
T Consensus 10 ~~~~~~l~~~~~~~li~~~~~gd~----------------------------------------~a~~~L~~~~~~~v~~ 49 (254)
T TIGR02850 10 TSKLPVLKNQEMRELFIRMQSGDT----------------------------------------TAREKLINGNLRLVLS 49 (254)
T ss_pred ccCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHHHHH
Confidence 357899999999999999999997 8999999999999999
Q ss_pred HHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHH
Q 010521 280 IAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLR 359 (508)
Q Consensus 280 IAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~ 359 (508)
+|++|.+++.+++||+|||++|||+++++|||.+|.+|+||+++||++.|.++++++. .+++|++..+..+++.++...
T Consensus 50 ~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~-~ir~p~~~~~~~~~~~~~~~~ 128 (254)
T TIGR02850 50 VIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDK 128 (254)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CccCchHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999975 789999999998998888877
Q ss_pred H-HHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHH
Q 010521 360 L-EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEV 438 (508)
Q Consensus 360 l-~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L 438 (508)
+ .++|++|+.+|||+.+|+++++|..++.....+.|||.++..+ +++..++.+.+.+.. .+. ........|
T Consensus 129 l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~--~~~~~~~~~~~~d~~---~~~---~~~~~~~~l 200 (254)
T TIGR02850 129 LISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYND--GGDPIYVMDQISDEK---NKD---SQWLEGIAL 200 (254)
T ss_pred HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCC--CCCcchhhhhcCCcc---ccH---HHHHhHHHH
Confidence 7 4789999999999999999999999999888889999875311 111224556665542 121 233445678
Q ss_pred HHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 439 NKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 439 ~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
..+| ..||+++|.||.++| ++++|++|||+.||+|+++|++++.+|++|||+.+
T Consensus 201 ~~~l-~~L~~rer~vi~~~~---~~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~~~ 254 (254)
T TIGR02850 201 KEAM-KRLNEREKMILNMRF---FEGKTQMEVAEEIGISQAQVSRLEKAALKHMRKYV 254 (254)
T ss_pred HHHH-HcCCHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence 8889 899999999999999 78999999999999999999999999999999753
No 20
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=100.00 E-value=1.7e-37 Score=310.21 Aligned_cols=227 Identities=27% Similarity=0.409 Sum_probs=199.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhc---CCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYD---NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~---~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~i 340 (508)
.|+++||..|+|+|+.+|++|. ..+.+.+||+|||+||||+|+++|||++|++|+|||+||||++|.+++++..+
T Consensus 23 ~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~-- 100 (257)
T PRK05911 23 EYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQDW-- 100 (257)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCC--
Confidence 8999999999999999999986 24568999999999999999999999999999999999999999999999865
Q ss_pred cccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhC--ccccccccCCCCCCCCCCCccccccc
Q 010521 341 RLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDREAFPSLNGLPGETHHSYIA 417 (508)
Q Consensus 341 rip~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~--~~~SLD~~~~~~~~~~~~~~l~d~i~ 417 (508)
+|+++.+.++++..+...+. +.|++|+.+|||+.+|+++++|..++.... .++|||.+.....+++++.++.+.++
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 89999999999999888885 689999999999999999999999887653 46899986433222223345677787
Q ss_pred cccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521 418 DNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497 (508)
Q Consensus 418 d~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~ 497 (508)
|... ..|++.+...+....|..+| ..|||++|.||.++| ++++|++|||+.||+|+++|++++++|+++||+.+.
T Consensus 180 d~~~-~~~~~~~~~~~~~~~l~~al-~~L~~~er~vi~l~y---~e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l~ 254 (257)
T PRK05911 180 DERA-ETGYDVVDKKEFSSILAEAI-LALEEKERKVMALYY---YEELVLKEIGKILGVSESRVSQIHSKALLKLRATLS 254 (257)
T ss_pred CCCC-CCHHHHHHHHHHHHHHHHHH-HcCCHHHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 7653 46778888888889999999 899999999999999 799999999999999999999999999999999885
Q ss_pred H
Q 010521 498 K 498 (508)
Q Consensus 498 ~ 498 (508)
.
T Consensus 255 ~ 255 (257)
T PRK05911 255 A 255 (257)
T ss_pred h
Confidence 4
No 21
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=100.00 E-value=6.6e-37 Score=305.51 Aligned_cols=242 Identities=29% Similarity=0.424 Sum_probs=211.8
Q ss_pred ccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHHH
Q 010521 202 SEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIA 281 (508)
Q Consensus 202 ~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIA 281 (508)
++|+|+++++..|+.+++.||. .|+++||..|.++|+++|
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 5689999999999999999998 899999999999999999
Q ss_pred HHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHH
Q 010521 282 QRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE 361 (508)
Q Consensus 282 krY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~ 361 (508)
++|.+++.+++||+|||++|||+++++|||.+|.+|.||+++||+++|.++++++. .+++|++......++.++...+.
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 88999999998888888877774
Q ss_pred -HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHH
Q 010521 362 -EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNK 440 (508)
Q Consensus 362 -~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~ 440 (508)
+.|+.|+..|||+.+|+++++|..++.....+.|||.++..+ +....++.+.+++.. .+ .+.......+..
T Consensus 134 ~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~--~~~~~~~~~~~~~~~---~~---~~~~~~~~~l~~ 205 (258)
T PRK08215 134 NENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHD--GGDPIYVMDQISDEK---NK---DENWLEEIALKE 205 (258)
T ss_pred HHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCC--CCcchhhhhhccCcc---cc---HHHHHhHHHHHH
Confidence 789999999999999999999999988888888999875321 111223445554432 11 233345567888
Q ss_pred HHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 441 LIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 441 ~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
+| +.||++++.||.++| ++++|++|||+.||+|+++|++++.+|+++||+.|
T Consensus 206 ~l-~~L~~~er~vi~~~~---~~~~t~~eIA~~lgis~~~V~~~~~~al~kLr~~l 257 (258)
T PRK08215 206 AM-KKLNDREKLILNLRF---FQGKTQMEVAEEIGISQAQVSRLEKAALKHMRKYI 257 (258)
T ss_pred HH-HcCCHHHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 88 899999999999999 78999999999999999999999999999999876
No 22
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=100.00 E-value=3.9e-37 Score=304.36 Aligned_cols=240 Identities=34% Similarity=0.484 Sum_probs=215.0
Q ss_pred cCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHHHH
Q 010521 203 EELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ 282 (508)
Q Consensus 203 ~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAk 282 (508)
.+.++..+...+....+.|+. .+. .||++|+|||.++|+
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 356778888889999999997 888 999999999999999
Q ss_pred HhcCCCC-CHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHH
Q 010521 283 RYDNMGA-DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE 361 (508)
Q Consensus 283 rY~~~g~-d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~ 361 (508)
+|.+++. +.+||+|.|+|||++|+++|||++|.+|+|||..+|+++|.+++|++. .+++|+.+.+..+++..+...+.
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 9998877 999999999999999999999999999999999999999999999999 99999999999999999999995
Q ss_pred -HcCCCCCHHHHHHHhCCCHHHHHHHHHHhC--ccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHH
Q 010521 362 -EKGVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEV 438 (508)
Q Consensus 362 -~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~--~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L 438 (508)
++|++|+.+|||+.||++.+++..++.... ..+|+|.... ..+++. +.+. ..+|.+.++..+....|
T Consensus 121 ~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~---~~~d~~-----~~~~--~~~~~~~~~~~~~~~~l 190 (247)
T COG1191 121 QELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVL---KDDDDD-----VDDQ--IENPDDGVEKEELLEIL 190 (247)
T ss_pred HHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhc---cccccc-----hhhc--cccchhHHHHHHHHHHH
Confidence 799999999999999999999999998874 6788887532 111111 1111 24788889999999999
Q ss_pred HHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521 439 NKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 498 (508)
Q Consensus 439 ~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~ 498 (508)
.+++ ..|++|||.|+.+|| ++++|++|||+.||||+++|+|++.+|++|||+.|..
T Consensus 191 ~~ai-~~L~EREk~Vl~l~y---~eelt~kEI~~~LgISes~VSql~kkai~kLr~~l~~ 246 (247)
T COG1191 191 KEAI-EPLPEREKLVLVLRY---KEELTQKEIAEVLGISESRVSRLHKKAIKKLRKELNK 246 (247)
T ss_pred HHHH-HccCHHHHHHHHHHH---HhccCHHHHHHHhCccHHHHHHHHHHHHHHHHHHhcc
Confidence 9999 699999999999999 8999999999999999999999999999999998753
No 23
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=100.00 E-value=1.2e-35 Score=298.07 Aligned_cols=251 Identities=26% Similarity=0.325 Sum_probs=218.4
Q ss_pred hcccCCCCHHHHHHHHHHHHc-CCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHH
Q 010521 200 VVSEELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVM 278 (508)
Q Consensus 200 i~~~~lLt~~EE~eL~~~ik~-Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~ 278 (508)
.|++|+||.+++.+|+.+++. ||. .|++.|+..|.++|+
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 467999999999999999764 566 899999999999999
Q ss_pred HHHHHhc-C--CCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHH
Q 010521 279 SIAQRYD-N--MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRN 355 (508)
Q Consensus 279 sIAkrY~-~--~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~ 355 (508)
.+|++|. + .+.+++||+|||++|||+++++||+.+|.+|.||+++|||+.|.+++++. .++|.+.....+++++
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 56789999999999999999999999888999999999999999999865 4589999888889999
Q ss_pred HHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHh--CccccccccCCCCCCCCCCCccccccccccCCCCccchHHHH
Q 010521 356 AKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAI--GKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDW 432 (508)
Q Consensus 356 a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~--~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~ 432 (508)
+...+. +.|++|+.+|||+.+|++.+++.+++... ..+.|||.+...+ ++.+..++.+.++++. .++|++.++..
T Consensus 123 ~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~-~~~~~~~l~~~~~~~~-~~~pe~~~~~~ 200 (268)
T PRK06288 123 AIAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGG-DEGDEVSLMDTLESPA-ALNPDEIAERE 200 (268)
T ss_pred HHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccC-CCcccchhhhhccCCC-CCCHHHHHHHH
Confidence 888885 68999999999999999999999998765 4678998864311 1222234556666544 35788888888
Q ss_pred HHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521 433 ALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 499 (508)
Q Consensus 433 el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~ 499 (508)
+....|..+| ..||+++|.||.++| ++++|++|||+.||+|.++|++++.+|+++||..+...
T Consensus 201 e~~~~l~~~l-~~L~~~~r~vl~l~~---~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~~~ 263 (268)
T PRK06288 201 EIKRVIVEAI-KTLPEREKKVLILYY---YEDLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLAEI 263 (268)
T ss_pred HHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 8899999999 899999999999999 79999999999999999999999999999999998754
No 24
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=100.00 E-value=2.1e-35 Score=293.87 Aligned_cols=242 Identities=27% Similarity=0.342 Sum_probs=213.4
Q ss_pred CCCCHHHHHHHHHHHHc-CCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHHHH
Q 010521 204 ELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ 282 (508)
Q Consensus 204 ~lLt~~EE~eL~~~ik~-Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAk 282 (508)
|.||++++.+|+.+++. ||. .|+++||..|.++|+.+|+
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 HhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHH-
Q 010521 283 RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE- 361 (508)
Q Consensus 283 rY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~- 361 (508)
+|.+++.+++||+||||++||+++++||++.|.+|.||+++||++.|.+++++..+.+++|.+..+..++++++...+.
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 9999999999999999999999999999999999999999999999999999999999999999999999999988885
Q ss_pred HcCCCCCHHHHHHHhCCCHHHHHHHHHHh--CccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHH
Q 010521 362 EKGVTPSVDRIAEYLNMSQKKVRNATEAI--GKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVN 439 (508)
Q Consensus 362 ~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~--~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~ 439 (508)
..|+.|+.+|+|+.+|++.+++..++... ....|||.++..+ ++...... .+. ..+|++.+...+....+.
T Consensus 128 ~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~----~~~~~~~~-~~~--~~~~~~~~~~~e~~~~l~ 200 (255)
T TIGR02941 128 HLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEAD----SDGSTVAR-LDS--VGEVEDGYDQTERRMVLE 200 (255)
T ss_pred HhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCC----CCCccccc-ccc--cCCcchHHHHHHHHHHHH
Confidence 67999999999999999999999887764 4678998875321 11111111 111 124667777788888899
Q ss_pred HHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 440 KLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 440 ~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
.+| +.||+++|.||.++| ++|+|++|||+.||+|.++|++++++|+++||+.+
T Consensus 201 ~~l-~~L~~~~r~ii~l~~---~~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~ 253 (255)
T TIGR02941 201 KIL-PILSEREKSIIHCTF---EENLSQKETGERLGISQMHVSRLQRQAISKLKEAA 253 (255)
T ss_pred HHH-HcCCHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 999 899999999999999 79999999999999999999999999999999875
No 25
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=100.00 E-value=1.1e-34 Score=284.27 Aligned_cols=220 Identities=33% Similarity=0.403 Sum_probs=191.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.|++.|+..|.++|+++|++|.+++.+++||+|||++|||+++++|||..|.+|.||+++||++.|.++++++. .+++|
T Consensus 11 ~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~~~-~i~~p 89 (231)
T TIGR02885 11 EARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDG-IIKVS 89 (231)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-CeECC
Confidence 89999999999999999999999999999999999999999999999999989999999999999999999986 78999
Q ss_pred ccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCC
Q 010521 344 NHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE 422 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e 422 (508)
+++.....+++++...+. ++|+.|+.+|||+.+|++++++..++.....+.|||.+...+ +.+..++.+.+.+..
T Consensus 90 ~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~--~~~~~~~~d~~~~~~-- 165 (231)
T TIGR02885 90 RSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQD--DGDPIYLLDQIADKG-- 165 (231)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCC--CCCcchhhhhcCCCC--
Confidence 999999999999888885 689999999999999999999999988888889999874311 111223445554432
Q ss_pred CCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 423 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 423 ~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
+++ ........+.+++ +.||++++.||.++| ++++|++|||+.||+|+++|++++++|+++||..|
T Consensus 166 -~~~---~~~~~~~~l~~~l-~~L~~~e~~i~~~~~---~~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~l 231 (231)
T TIGR02885 166 -SED---SDWLEKIALKEAI-SKLDERERQIIMLRY---FKDKTQTEVANMLGISQVQVSRLEKKVLKKMKEKL 231 (231)
T ss_pred -ccH---HhHHHHHHHHHHH-HcCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHhC
Confidence 122 2233456788889 899999999999999 68999999999999999999999999999999754
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=3e-34 Score=280.34 Aligned_cols=222 Identities=33% Similarity=0.401 Sum_probs=194.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q 010521 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (508)
Q Consensus 263 ~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~iri 342 (508)
..|+++|+..|.|+|+++|++|.+++.+.+||+|||++|||+|+++||+.+|.+|+||+++||++.|.++++++.+.+++
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 37999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCc--cccccccCCCCCCCCCCCccccccccc
Q 010521 343 PNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGK--VFSLDREAFPSLNGLPGETHHSYIADN 419 (508)
Q Consensus 343 p~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~--~~SLD~~~~~~~~~~~~~~l~d~i~d~ 419 (508)
|.+..+.+++++++...+. +.|+.|+.+|+|+.+|++++++..++..... +.|||.++. + ++..+..+.+.+
T Consensus 82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~-~-~~~~~~~~~d~~--- 156 (227)
T TIGR02980 82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIE-D-DDGDPIALLDTL--- 156 (227)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCC-C-CCCCCccccccc---
Confidence 9999999899999888885 6899999999999999999999998887654 889998742 0 111111222322
Q ss_pred cCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 420 RVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 420 ~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
.+|++.++..+....|..+| ..||++|+.||.++| ++|+|++|||+.||+|+++|++++++|+++||+.+
T Consensus 157 ---~~~~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~y---~~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~l 226 (227)
T TIGR02980 157 ---GDEDDALETVEDRLALKPLL-AALPERERRILLLRF---FEDKTQSEIAERLGISQMHVSRLLRRALKKLREQL 226 (227)
T ss_pred ---CCcchHHHhHHHHHHHHHHH-HcCCHHHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 24555566667788899999 899999999999999 78999999999999999999999999999999865
No 27
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=7.5e-34 Score=282.46 Aligned_cols=223 Identities=28% Similarity=0.386 Sum_probs=193.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcC---CCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~---~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~i 340 (508)
.|++.||..|.++|+++|++|.+ ++.+.+||+||||+|||+++++|||++|.+|.||+++||+|.|.++++++.
T Consensus 22 ~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~d~lR~~~--- 98 (251)
T PRK07670 22 DAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKED--- 98 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC---
Confidence 99999999999999999999975 688999999999999999999999999999999999999999999999876
Q ss_pred cccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHH--hCccccccccCCCCCCCCCCCccccccc
Q 010521 341 RLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEA--IGKVFSLDREAFPSLNGLPGETHHSYIA 417 (508)
Q Consensus 341 rip~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~--~~~~~SLD~~~~~~~~~~~~~~l~d~i~ 417 (508)
++|.+..+.+++++.+...+. ..|+.|+..|||+.+|+++++|..++.. ...+.|||.++. +++++..+.+.+.
T Consensus 99 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~---~~~~~~~~~~~~~ 175 (251)
T PRK07670 99 WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTH---DQDDGENVSVTIR 175 (251)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCcccc---CCCCcchhhhhhc
Confidence 589998888888888887774 6899999999999999999999998764 367899998742 1222222333333
Q ss_pred cccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521 418 DNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497 (508)
Q Consensus 418 d~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~ 497 (508)
+.. ..+|++.+...+....|..+| ..||+++|.||.++| ++++|++|||+.||+|.++|++++++|+++||..+.
T Consensus 176 ~~~-~~~~e~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~~---~~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~ 250 (251)
T PRK07670 176 DDK-TPTPEEKLLKEELIEELAEKI-KQLSEKEQLVISLFY---KEELTLTEIGQVLNLSTSRISQIHSKALFKLKKLLE 250 (251)
T ss_pred CcC-CCCHHHHHHHHHHHHHHHHHH-hcCCHHHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 332 246777777788888999999 899999999999999 899999999999999999999999999999999875
No 28
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=100.00 E-value=2.2e-33 Score=279.76 Aligned_cols=244 Identities=26% Similarity=0.326 Sum_probs=212.3
Q ss_pred CCCCHHHHHHHHHHHHc-CCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHHHH
Q 010521 204 ELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ 282 (508)
Q Consensus 204 ~lLt~~EE~eL~~~ik~-Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAk 282 (508)
|.|+++++.+|+.+++. ||. .|++.||..|.++|+++|+
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 78999999999999986 787 9999999999999999999
Q ss_pred HhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHH-
Q 010521 283 RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE- 361 (508)
Q Consensus 283 rY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~- 361 (508)
+|.+++.+++||+||||++||+++++||+..|.+|.||+++||+|.|.+++++..+.+++|++.....++++.+...+.
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 HcCCCCCHHHHHHHhCCCHHHHHHHHHHh--CccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHH
Q 010521 362 EKGVTPSVDRIAEYLNMSQKKVRNATEAI--GKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVN 439 (508)
Q Consensus 362 ~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~--~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~ 439 (508)
..++.|+.+++|+.+|++.+++..+.... ..+.|+|.++..+ ++.....+.+. ..+|++.+...+....+.
T Consensus 128 ~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~-----~~~~~~~~~~~--~~~~e~~~~~~~~~~~l~ 200 (257)
T PRK08583 128 ELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEAD-----SDGSTVTLLDI--VGQQEDGYELTEQRMILE 200 (257)
T ss_pred HhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCC-----CCCccchHhhh--cCCcchhHHHHHHHHHHH
Confidence 67899999999999999999998876654 3577888764211 11111111111 135777777788888899
Q ss_pred HHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521 440 KLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 498 (508)
Q Consensus 440 ~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~ 498 (508)
.+| ..||+++|.||.++| ++|+|++|||+.||||++||++++++|+++||..+..
T Consensus 201 ~~l-~~L~~~~r~vl~l~~---~~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l~~ 255 (257)
T PRK08583 201 KIL-PVLSDREKSIIQCTF---IENLSQKETGERLGISQMHVSRLQRQAIKKLREAAFL 255 (257)
T ss_pred HHH-HhCCHHHHHHHHHHH---hCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 999 899999999999999 7999999999999999999999999999999998854
No 29
>PRK05572 sporulation sigma factor SigF; Validated
Probab=100.00 E-value=2.4e-33 Score=278.99 Aligned_cols=245 Identities=34% Similarity=0.424 Sum_probs=211.8
Q ss_pred HhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHH
Q 010521 198 KGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLV 277 (508)
Q Consensus 198 ~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV 277 (508)
+.-...|.||.+++.+|+.+++.||. .|++.||..|.++|
T Consensus 6 ~~~~~~~~l~~~~~~~li~~~~~gd~----------------------------------------~a~~~L~~~y~~~v 45 (252)
T PRK05572 6 KNKKKKPQLKDEENKELIKKSQDGDQ----------------------------------------EARDTLVEKNLRLV 45 (252)
T ss_pred ccCcCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHHH
Confidence 34456899999999999999999998 99999999999999
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHH
Q 010521 278 MSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAK 357 (508)
Q Consensus 278 ~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~ 357 (508)
+.+|++|.+++.+++||+|||++++|+++++|++.++.+|.||+++||++.|.+++++.. .+++|++......+++++.
T Consensus 46 ~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~~~-~~r~~~~~~~~~~~~~~~~ 124 (252)
T PRK05572 46 WSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDK 124 (252)
T ss_pred HHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CCCCCHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999988889999999999999999999884 7899999999999999998
Q ss_pred HHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHH
Q 010521 358 LRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKD 436 (508)
Q Consensus 358 ~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e 436 (508)
..+. +.|+.|+..|+|+.+|++++++..+......+.||+.+... ++....++.+.+.+.. . .......
T Consensus 125 ~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~--~~~~~~~~~d~~~~~~----~----~~~~~~~ 194 (252)
T PRK05572 125 DELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHE--NDGDPITLLDQIADQS----E----EDWFDKI 194 (252)
T ss_pred HHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCccc--CCCCcchhhhhcCCCc----h----hhHHHHH
Confidence 8875 67999999999999999999999998888888899876421 1111112233333221 1 1234466
Q ss_pred HHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521 437 EVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497 (508)
Q Consensus 437 ~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~ 497 (508)
.|..+| +.||++++.||.++| ++++|++|||+.+|+|+++|++++.+|+++||..|.
T Consensus 195 ~l~~~l-~~L~~~~~~v~~l~~---~~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l~ 251 (252)
T PRK05572 195 ALKEAI-RELDERERLIVYLRY---FKDKTQSEVAKRLGISQVQVSRLEKKILKQMKEKLD 251 (252)
T ss_pred HHHHHH-HcCCHHHHHHHHHHH---hCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence 788899 899999999999999 799999999999999999999999999999998874
No 30
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=100.00 E-value=5.5e-33 Score=271.33 Aligned_cols=217 Identities=32% Similarity=0.468 Sum_probs=190.2
Q ss_pred HHHHHHHHHHHHHHHhcC---CCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccccc
Q 010521 269 LVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH 345 (508)
Q Consensus 269 LIe~yl~LV~sIAkrY~~---~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~ 345 (508)
|+..|.++|+++|++|.+ ++.+++||+|||++|||+++++|||++|.+|+||+++||++.+.+++++.. ++|.+
T Consensus 1 L~~~~~~lv~~~a~~~~~~~~~~~~~eDl~Qe~~~~l~~a~~~fd~~~~~~f~t~~~~~i~~~~~~~lr~~~---~~p~~ 77 (224)
T TIGR02479 1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLD---WVPRS 77 (224)
T ss_pred CHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHHcC---ccCHH
Confidence 578999999999999986 789999999999999999999999999999999999999999999998765 58988
Q ss_pred HHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHh--CccccccccCCCCCCCCCCCccccccccccCC
Q 010521 346 LHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAI--GKVFSLDREAFPSLNGLPGETHHSYIADNRVE 422 (508)
Q Consensus 346 ~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~--~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e 422 (508)
..+.++++.++...+. +.|++|+.+|+|+.+|+++++|..++... ..+.|+|.... ++.++..+.++++++. .
T Consensus 78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~---~~~~~~~~~~~~~~~~-~ 153 (224)
T TIGR02479 78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLE---SGDDGGSLIDRIEDDK-S 153 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCccc---CCCccchhhhhccccc-c
Confidence 8888999999988885 68999999999999999999999998754 45678887521 1122334555565443 3
Q ss_pred CCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 423 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 423 ~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
++|++.+...+....|.++| ..||+++|.||.++| ++++|++|||+.||+|.++|++++++|+++||+.+
T Consensus 154 ~~~~~~~~~~~~~~~l~~~l-~~L~~~~r~il~l~y---~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 223 (224)
T TIGR02479 154 EDPEEELEREELREALAEAI-ESLSEREQLVLSLYY---YEELNLKEIGEVLGLTESRVSQIHSQALKKLRAKL 223 (224)
T ss_pred CCHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---hCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHc
Confidence 57888888888999999999 899999999999999 89999999999999999999999999999999875
No 31
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=100.00 E-value=1.5e-31 Score=263.37 Aligned_cols=224 Identities=28% Similarity=0.435 Sum_probs=190.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhc---CCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhc
Q 010521 261 ECSLAREKLVMSNVRLVMSIAQRYD---NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS 337 (508)
Q Consensus 261 e~~~A~e~LIe~yl~LV~sIAkrY~---~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~ 337 (508)
+|.-++++|+..|.++|+.+|++|. +++.+++||+||||+|||+++++|||..|.+|.||+++||++.|.++++++.
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 4557899999999999999999997 6789999999999999999999999998889999999999999999999986
Q ss_pred ccccccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHh--CccccccccCCCCCCCCCCCcccc
Q 010521 338 RTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAI--GKVFSLDREAFPSLNGLPGETHHS 414 (508)
Q Consensus 338 R~irip~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~--~~~~SLD~~~~~~~~~~~~~~l~d 414 (508)
+ +|.+......++.++...+. ..|++|+.+|||+.+|++.++|..++... ..+.|++.+. +++++.+..
T Consensus 85 ~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~-----~~~~~~~~~ 156 (236)
T PRK06986 85 W---VPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELR-----GEHGDSILV 156 (236)
T ss_pred C---CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccc-----cCCCccccc
Confidence 4 67777766666777766664 68999999999999999999999998865 4567787753 112222222
Q ss_pred ccccccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 415 YIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 415 ~i~d~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
...+. .++|++.+...+....|..+| +.||+++|.||.++| ++|+|++|||+.||+|.++|++++++|+++||+
T Consensus 157 ~~~~~--~~~~~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~~---~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 230 (236)
T PRK06986 157 TEDHQ--DEDPLQQLEDEELREALVEAI-ESLPEREQLVLSLYY---QEELNLKEIGAVLGVSESRVSQIHSQAIKRLRA 230 (236)
T ss_pred ccCCC--CCCHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHhHh---ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 22222 346778888888889999999 899999999999999 899999999999999999999999999999999
Q ss_pred HHHH
Q 010521 495 AARK 498 (508)
Q Consensus 495 ~L~~ 498 (508)
.+..
T Consensus 231 ~l~~ 234 (236)
T PRK06986 231 RLGE 234 (236)
T ss_pred HHhc
Confidence 8864
No 32
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=100.00 E-value=1.2e-31 Score=264.18 Aligned_cols=210 Identities=20% Similarity=0.305 Sum_probs=175.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcC---CCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~---~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~i 340 (508)
.-...|+..|.|+|+.+|++|.. .+.+.+||+|||++|||+|+++|||..| +|+||+++||||+|.+++++..+
T Consensus 15 ~~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~~-- 91 (231)
T PRK12427 15 QEEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELDW-- 91 (231)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcCC--
Confidence 45568899999999999999874 4679999999999999999999998666 89999999999999999998643
Q ss_pred cccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHh--CccccccccCCCCCCCCCCCccccccc
Q 010521 341 RLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAI--GKVFSLDREAFPSLNGLPGETHHSYIA 417 (508)
Q Consensus 341 rip~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~--~~~~SLD~~~~~~~~~~~~~~l~d~i~ 417 (508)
.|+++....++++++...+. ++|++|+.+|||+.||+++++|.+++... ..+.|||.++.. +++ .+.+.
T Consensus 92 -~~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~----~~~---~~~~~ 163 (231)
T PRK12427 92 -RPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLAL----EAH---NDILQ 163 (231)
T ss_pred -CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccC----CCc---ccccC
Confidence 67888888888988888884 68999999999999999999999987643 578999997421 111 11121
Q ss_pred cccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010521 418 DNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA 495 (508)
Q Consensus 418 d~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~ 495 (508)
+ .+|+ +.......|..+| ..||+++|.||.++| ++++|++|||+.||||+++|+|++.+|++|||..
T Consensus 164 ~----~~~~---~~~~~~~~l~~~l-~~L~~~er~vi~l~~---~~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr~~ 230 (231)
T PRK12427 164 S----RDLE---ENIIIEDNLKQAL-SQLDEREQLILHLYY---QHEMSLKEIALVLDLTEARICQLNKKIAQKIKSF 230 (231)
T ss_pred C----CCHH---HHHHHHHHHHHHH-HcCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 1 1233 2233566788899 899999999999999 7999999999999999999999999999999964
No 33
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=99.96 E-value=2.2e-28 Score=240.62 Aligned_cols=213 Identities=30% Similarity=0.379 Sum_probs=174.3
Q ss_pred hHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHH
Q 010521 192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM 271 (508)
Q Consensus 192 ~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe 271 (508)
++..|+.++++.|+||++++..|+..++.||. .|++.|+.
T Consensus 17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~gd~----------------------------------------~a~~~l~~ 56 (233)
T PRK05803 17 FLVSYVKNNSFPQPLSEEEERKYLELMKEGDE----------------------------------------EARNILIE 56 (233)
T ss_pred HHHHHHHHhcccCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHH
Confidence 78899999999999999999999999999997 99999999
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHH
Q 010521 272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG 351 (508)
Q Consensus 272 ~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~ 351 (508)
.|.++|+++|.+|.+++.+++|++||+++++|+++++||++++.+|.+|+++|+++.+.+++++..+..
T Consensus 57 ~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~~~----------- 125 (233)
T PRK05803 57 RNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTK----------- 125 (233)
T ss_pred HhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhccc-----------
Confidence 999999999999999999999999999999999999999988889999999999999999998764210
Q ss_pred HHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHH
Q 010521 352 LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDD 431 (508)
Q Consensus 352 kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~ 431 (508)
...+++.+.... ++....++.+.+.+. .++|++.+..
T Consensus 126 ----------------------------------------~~~~~~~~~~~~-~~~~~~~~~~~~~~~--~~~~~~~~~~ 162 (233)
T PRK05803 126 ----------------------------------------KEVSLQDPIGVD-KEGNEISLIDILGSE--EDDVIEQVEL 162 (233)
T ss_pred ----------------------------------------cCCCccccccCC-CCcCcccHHHHccCC--CCCHHHHHHH
Confidence 011111110000 000111222333322 1246677777
Q ss_pred HHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521 432 WALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 499 (508)
Q Consensus 432 ~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~ 499 (508)
....+.|..+| +.||+++|+||.++|+++ ++|+|++|||+.||+|.++|++++++|+++||+.+...
T Consensus 163 ~~~~~~l~~~l-~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~~~ 230 (233)
T PRK05803 163 KMEVEKLYKKI-DILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKELYRA 230 (233)
T ss_pred HHHHHHHHHHH-HhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 77778899999 899999999999999774 58999999999999999999999999999999998653
No 34
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=99.94 E-value=5.5e-25 Score=215.79 Aligned_cols=210 Identities=29% Similarity=0.361 Sum_probs=164.3
Q ss_pred hHHHHHHhhccc-CCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHH
Q 010521 192 RLKGYVKGVVSE-ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (508)
Q Consensus 192 ~~~~yl~~i~~~-~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LI 270 (508)
++-+|+..-|+. +.|++.++..|+.+++.||. .|++.|+
T Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~li~~~~~gd~----------------------------------------~af~~l~ 54 (227)
T TIGR02846 15 FLVGYVTNNGSFPQPLSEEEEKKYLDRLKEGDE----------------------------------------EARNVLI 54 (227)
T ss_pred HHHHHHHHHHhCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHH
Confidence 456788776644 56899999999999999998 9999999
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHH
Q 010521 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 350 (508)
Q Consensus 271 e~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l 350 (508)
..|.+.|+++|.+|.++..+++|++||+|+++|+++++|+++.+.+|.||++++++|.+.+++++..+..+
T Consensus 55 ~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~Rk~~r~~~--------- 125 (227)
T TIGR02846 55 ERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHLRALKKTKG--------- 125 (227)
T ss_pred HHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHHHHHhcccc---------
Confidence 99999999999999999999999999999999999999999888889999999999999999987643100
Q ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHH
Q 010521 351 GLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVD 430 (508)
Q Consensus 351 ~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve 430 (508)
..+++...... .+.....+.+.+.+. .++|++.+.
T Consensus 126 ------------------------------------------~~~~~~~~~~~-~~~~~~~~~~~~~~~--~~~~~~~~~ 160 (227)
T TIGR02846 126 ------------------------------------------EVSLQDPIGVD-KEGNEISLIDILGSD--GDSVIEQVE 160 (227)
T ss_pred ------------------------------------------ceeccccccCC-cccCcccHHHHhcCC--CCChHHHHH
Confidence 01111100000 000001111111111 235666666
Q ss_pred HHHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 431 DWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 431 ~~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
..+..+.|.++| +.||+++|+||.++|.++ ++++|++|||+.||+|+++|++++++|+++||+.|
T Consensus 161 ~~~~~~~l~~~i-~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~~ 226 (227)
T TIGR02846 161 LNLEIKKLYKKL-SVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYKEL 226 (227)
T ss_pred HHHHHHHHHHHH-HhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 667778899999 999999999999999442 38999999999999999999999999999999875
No 35
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=99.94 E-value=5.9e-25 Score=215.94 Aligned_cols=208 Identities=24% Similarity=0.385 Sum_probs=160.2
Q ss_pred HHHHhhccc-CCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHH
Q 010521 195 GYVKGVVSE-ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSN 273 (508)
Q Consensus 195 ~yl~~i~~~-~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~y 273 (508)
-|+.++... |.+++..+..|+.+++.||. .|++.|+..|
T Consensus 22 ~~~~~~~~~~~~~~~~~~~~L~~~~~~gd~----------------------------------------~af~~l~~~y 61 (234)
T PRK08301 22 YYIGGSEALPPPLSKEEEEYLLNKLPKGDE----------------------------------------AVRSLLIERN 61 (234)
T ss_pred HHhccccccCCcCCHHHHHHHHHHHHccCH----------------------------------------HHHHHHHHHh
Confidence 367777555 44788889999999999998 9999999999
Q ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHH
Q 010521 274 VRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLI 353 (508)
Q Consensus 274 l~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~ki 353 (508)
.++|+.+|++|.+++.+++|++||+|+++|+++++|++..+++|.||++.+++|.+.++++++.+...
T Consensus 62 ~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~d~lRk~~~~~~------------ 129 (234)
T PRK08301 62 LRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNNKVKA------------ 129 (234)
T ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHHHHHHhcccc------------
Confidence 99999999999999999999999999999999999999888889999999999999999987643100
Q ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCC-CccccccccccCCCCccchHHHH
Q 010521 354 RNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPG-ETHHSYIADNRVENNPWHGVDDW 432 (508)
Q Consensus 354 r~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~-~~l~d~i~d~~~e~~Pe~~ve~~ 432 (508)
..+++.+.. ...++. ....+...+. ...++..+...
T Consensus 130 ---------------------------------------~~~~~~~~~--~~~~~~~~~~~~~~~~~--~~~~~~~~~~~ 166 (234)
T PRK08301 130 ---------------------------------------EVSFDEPLN--IDWDGNELLLSDVLGTD--NDIIYKDIEDE 166 (234)
T ss_pred ---------------------------------------ccccccccc--cccCCCcccHHHhccCc--ccchHHHHHHH
Confidence 011111100 000000 0011111111 11233334445
Q ss_pred HHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521 433 ALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 498 (508)
Q Consensus 433 el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~ 498 (508)
.....|..+| +.||+++|.||.|+|+|. .+|+|++|||+.||+|.+||++++++|+++||+.+..
T Consensus 167 ~~~~~l~~al-~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l~~ 232 (234)
T PRK08301 167 VDRKLLKKAL-KKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEINK 232 (234)
T ss_pred HHHHHHHHHH-HhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 5566799999 899999999999999763 5899999999999999999999999999999998753
No 36
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=99.92 E-value=1.6e-23 Score=206.39 Aligned_cols=201 Identities=24% Similarity=0.359 Sum_probs=155.3
Q ss_pred cCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHHHH
Q 010521 203 EELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ 282 (508)
Q Consensus 203 ~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAk 282 (508)
.|.|+++++..|+..++.||. .|++.|+..|.+.|+++|.
T Consensus 31 ~~~~~~~~~~~l~~~~~~~d~----------------------------------------~a~~~l~~~y~~~l~~~~~ 70 (234)
T TIGR02835 31 PPPLTGEEEEALLQKLTQGDE----------------------------------------SAKSTLIERNLRLVVYIAR 70 (234)
T ss_pred CCcCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHHHHHHHH
Confidence 467888999999999999998 9999999999999999999
Q ss_pred HhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHH
Q 010521 283 RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEE 362 (508)
Q Consensus 283 rY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~~ 362 (508)
+|.+++.+++|++||+++++|+++++|++..+++|.||++.+++|.+.++++++.+...
T Consensus 71 ~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~d~~Rk~~r~~~--------------------- 129 (234)
T TIGR02835 71 KFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILMYLRRNNKTRS--------------------- 129 (234)
T ss_pred HhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhccccC---------------------
Confidence 99999999999999999999999999998887789999999999999999987653100
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHHHH
Q 010521 363 KGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLI 442 (508)
Q Consensus 363 ~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~L 442 (508)
..+++.+.... ..++.....+.. +.. .+.+++.+........|..+|
T Consensus 130 ------------------------------~~~~~~~~~~~-~~~~~~~~~~~~-~~~-~~~~~~~~~~~~~~~~l~~ai 176 (234)
T TIGR02835 130 ------------------------------EVSFDEPLNVD-WDGNELLLSDVL-GTD-SDIVYKYLEEEVDRELLRKAL 176 (234)
T ss_pred ------------------------------cccccccccCC-CCCCcchHHHhc-CCC-CCcHHHHHHHHHHHHHHHHHH
Confidence 01111110000 000000011111 111 112223344455567799999
Q ss_pred HccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521 443 IVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 498 (508)
Q Consensus 443 ~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~ 498 (508)
+.||+++|.||.++|.|. ++|+|++|||+.||+|.+||++++++|+++||+.+..
T Consensus 177 -~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l~~ 232 (234)
T TIGR02835 177 -AKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKEINR 232 (234)
T ss_pred -HhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhhc
Confidence 899999999999999543 4899999999999999999999999999999998864
No 37
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=99.91 E-value=4.6e-23 Score=197.78 Aligned_cols=182 Identities=21% Similarity=0.313 Sum_probs=137.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.|++.|+..|.++|+.+|.+|.++..+++|++||+++++|+++++|+++++.+|.||++.++++.+.+++++..+..+.+
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 99999999999999999999999999999999999999999999999987778999999999999988887654311111
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
.. ...|++.+. .+++.+..+.+.+.+.. ..
T Consensus 104 ~~----------------------------------------------~~~s~~~~~---~~~~~~~~~~~~~~~~~-~~ 133 (208)
T PRK08295 104 LN----------------------------------------------SYVSLDKPI---YDEESDRTLLDVISEAK-VT 133 (208)
T ss_pred cc----------------------------------------------ceeecCCcc---cCCccchhHHHHhcCcc-cC
Confidence 00 011222210 00111112223333222 13
Q ss_pred CccchHHHHHHHHHHH-HHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521 424 NPWHGVDDWALKDEVN-KLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 500 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~-~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~ 500 (508)
+|++.+...+....+. .++ ..||+++|.||.+ | .+|+|++|||+.||+|.++|+..++||+++||+++....
T Consensus 134 ~~~~~~~~~~~~~~l~~~~~-~~L~~~~r~vl~l-~---~e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l~~~~ 206 (208)
T PRK08295 134 DPEELIISKEELEDIEEKIE-ELLSELEKEVLEL-Y---LDGKSYQEIAEELNRHVKSIDNALQRVKRKLEKYLENRE 206 (208)
T ss_pred CHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHH-H---HccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence 6766665555555664 456 8999999999999 7 699999999999999999999999999999999987653
No 38
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=99.91 E-value=7.9e-23 Score=193.92 Aligned_cols=179 Identities=20% Similarity=0.207 Sum_probs=147.4
Q ss_pred CCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHhc
Q 010521 206 LTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYD 285 (508)
Q Consensus 206 Lt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAkrY~ 285 (508)
+|+++...|+..++.||. .|+++|+..|.+.|+.+|.++.
T Consensus 6 ~~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~~~~~l~~~~~~~~ 45 (189)
T PRK09648 6 DTGEELDALVAEAVAGDR----------------------------------------RALREVLEIIRPLVVRYCRARL 45 (189)
T ss_pred CCchHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHHHHHHh
Confidence 477888889999999997 9999999999999999999988
Q ss_pred CC----CCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHH
Q 010521 286 NM----GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE 361 (508)
Q Consensus 286 ~~----g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~ 361 (508)
++ +.+++|++||+|+++|+++.+|++. +.+|.+|++..+++.+.++++++.+....+
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 4689999999999999999999864 447999999999999999887764310000
Q ss_pred HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHHH
Q 010521 362 EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKL 441 (508)
Q Consensus 362 ~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~ 441 (508)
.+. ..+...+ ..+|++.+...+..+.|..+
T Consensus 107 ----------------------------------~~~-------------~~~~~~~---~~~~~~~~~~~e~~~~l~~~ 136 (189)
T PRK09648 107 ----------------------------------TEE-------------VPERPSD---DAGPEERALRSESSNRMREL 136 (189)
T ss_pred ----------------------------------ccc-------------ccccccc---CCCHHHHHHHHHHHHHHHHH
Confidence 000 0000001 13566666777777889999
Q ss_pred HHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521 442 IIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497 (508)
Q Consensus 442 L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~ 497 (508)
| ..||+++|+||.++| ++|+|++|||+.||+|.+||++.++||+++||+.+.
T Consensus 137 l-~~L~~~~r~i~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 188 (189)
T PRK09648 137 L-DTLPEKQREILILRV---VVGLSAEETAEAVGSTPGAVRVAQHRALARLRAEIE 188 (189)
T ss_pred H-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 9 899999999999999 799999999999999999999999999999999874
No 39
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=99.90 E-value=9.1e-23 Score=194.84 Aligned_cols=184 Identities=13% Similarity=0.148 Sum_probs=147.4
Q ss_pred cCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHHHH
Q 010521 203 EELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ 282 (508)
Q Consensus 203 ~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAk 282 (508)
.|+....++..|+..+++|+. .|+++|+..|.++|+++|.
T Consensus 9 ~~~~~~~~~~~li~~~~~g~~----------------------------------------~a~~~l~~~y~~~l~~~~~ 48 (194)
T PRK09646 9 GPPAESPDLDALLRRVARGDQ----------------------------------------DAFAELYDRTSSRVYGLVR 48 (194)
T ss_pred CCCCCcccHHHHHHHHHccCH----------------------------------------HHHHHHHHHHHHHHHHHHH
Confidence 355556667788888888887 9999999999999999999
Q ss_pred HhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHH
Q 010521 283 RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEE 362 (508)
Q Consensus 283 rY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~~ 362 (508)
+|.++..+++|++||+|+++|+++++|++..| .|.+|++..++|.+.++++++.+..+.-
T Consensus 49 ~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~r~~~~~~~~~------------------- 108 (194)
T PRK09646 49 RVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHRRAVDRVRSEQAASQRE------------------- 108 (194)
T ss_pred HHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHHHHHHHHHhhccccccc-------------------
Confidence 99999999999999999999999999998665 6999999999999998887764210000
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHHHH
Q 010521 363 KGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLI 442 (508)
Q Consensus 363 ~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~L 442 (508)
..... .+. ... ..++++.+...+..+.+..+|
T Consensus 109 -------------------------------~~~~~--------------~~~-~~~--~~~~~~~~~~~~~~~~l~~~l 140 (194)
T PRK09646 109 -------------------------------VRYGA--------------RNV-DPA--FDQVAEEVEARLERERVRDCL 140 (194)
T ss_pred -------------------------------ccccc--------------ccc-ccc--ccchHHHHHHHhHHHHHHHHH
Confidence 00000 000 000 113334444456667899999
Q ss_pred HccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521 443 IVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 498 (508)
Q Consensus 443 ~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~ 498 (508)
..||+++|.||.|+| .+|+|++|||+.||+|.++|+++++||+++||..+..
T Consensus 141 -~~L~~~~r~vl~l~~---~~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l~~ 192 (194)
T PRK09646 141 -DALTDTQRESVTLAY---YGGLTYREVAERLAVPLGTVKTRMRDGLIRLRDCLGV 192 (194)
T ss_pred -HhCCHHHHHHHHHHH---HcCCCHHHHHHHhCCChHhHHHHHHHHHHHHHHHhcc
Confidence 899999999999999 7999999999999999999999999999999998853
No 40
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=99.90 E-value=1.3e-22 Score=191.88 Aligned_cols=162 Identities=15% Similarity=0.185 Sum_probs=134.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.|++.|+..|.++|+.+|.+|.+++.+++|++||+|+++|+++.+|++. +.+|.+|++..+++.+.++++++...
T Consensus 20 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n~~~d~~R~~~~~---- 94 (186)
T PRK05602 20 AAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLNLCYDRLRRRREV---- 94 (186)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHHHHHHHHHhcCCC----
Confidence 9999999999999999999999999999999999999999999999986 44799999999999888888765310
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
+.+. ..+ ..+. ..
T Consensus 95 ---------------------------------------------------~~~~-------------~~~-~~~~--~~ 107 (186)
T PRK05602 95 ---------------------------------------------------PVED-------------APD-VPDP--AP 107 (186)
T ss_pred ---------------------------------------------------Cccc-------------ccc-cCCC--CC
Confidence 0000 000 0011 12
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM 501 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l 501 (508)
.|++.+...+....+..+| ..||+++|.||.++| ++|+|++|||+.||+|.++|+++++||+++||+.+...+.
T Consensus 108 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~ 181 (186)
T PRK05602 108 GPDAGLEARQRARRVEQAL-AALPERQREAIVLQY---YQGLSNIEAAAVMDISVDALESLLARGRRALRAQLADLPG 181 (186)
T ss_pred CHHHHHHHHHHHHHHHHHH-HhCCHHHHHHhhHHH---hcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 3555556666777899999 899999999999999 8999999999999999999999999999999999986543
No 41
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=99.90 E-value=1.1e-22 Score=193.70 Aligned_cols=167 Identities=20% Similarity=0.226 Sum_probs=137.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.|++.|+..|.+.|+++|.++.++..+++|++||+|+++|+++.+|++.. .|.+|++..+++.+.+++++..+....+
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 99999999999999999999999999999999999999999999999643 6999999999999999988765311100
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
.+. +.... ...+. ..
T Consensus 104 ----------------------------------------------------~~~----------~~~~~-~~~~~--~~ 118 (194)
T PRK12513 104 ----------------------------------------------------LDA----------DEQLH-ALADD--GA 118 (194)
T ss_pred ----------------------------------------------------ccc----------chhhh-hcCCC--CC
Confidence 000 00000 00011 23
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM 501 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l 501 (508)
+|+..++..+....+..+| +.||+++|.||.++| .+|+|++|||+.||+|+++|+++++||+++||..+...++
T Consensus 119 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~~ 192 (194)
T PRK12513 119 APEQQLSLFRDRRRLQAAL-ETLPDEQREVFLLRE---HGDLELEEIAELTGVPEETVKSRLRYALQKLRELLAEEVA 192 (194)
T ss_pred CHHHHHHHHHHHHHHHHHH-HhCCHhHhhheeeeh---ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 5666666777788899999 899999999999999 8999999999999999999999999999999999987664
No 42
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=99.89 E-value=4.6e-22 Score=195.48 Aligned_cols=193 Identities=19% Similarity=0.217 Sum_probs=156.5
Q ss_pred cccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHH
Q 010521 201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI 280 (508)
Q Consensus 201 ~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sI 280 (508)
...|+|+...+..|+..++.||. .|++.|+..|.+.|+++
T Consensus 7 ~~~~~~~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~y~~~l~~~ 46 (231)
T PRK11922 7 SRPPPLSAASDRELVARVLAGDE----------------------------------------AAFEALMRRHNRRLYRT 46 (231)
T ss_pred CCCCCcCcccHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHH
Confidence 35689999999999999999998 99999999999999999
Q ss_pred HHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHH
Q 010521 281 AQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL 360 (508)
Q Consensus 281 AkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l 360 (508)
|.++.++..+++|++||+|+++|+++++|++. ..|.+|++..+++.+.+++++..+...++..
T Consensus 47 a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~Rk~~r~~~~~~~--------------- 109 (231)
T PRK11922 47 ARAILRNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNEALGRLRRRRRLVNLAEM--------------- 109 (231)
T ss_pred HHHHhCChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHHHHHHHHhhcccccchhc---------------
Confidence 99999999999999999999999999999975 3799999999999999988776531110000
Q ss_pred HHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHH
Q 010521 361 EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNK 440 (508)
Q Consensus 361 ~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~ 440 (508)
.. .+...++ ......+ ...+|++.+...+..+.|..
T Consensus 110 ------------------------------------~~-----~~~~~~~-~~~~~~~--~~~~~e~~~~~~e~~~~l~~ 145 (231)
T PRK11922 110 ------------------------------------VM-----ASTIAGG-ERTPLAD--PAEDPERAAARREIRALLER 145 (231)
T ss_pred ------------------------------------cc-----ccccccc-cccccCc--ccCChHHHHHHHHHHHHHHH
Confidence 00 0000000 0000111 12367777777888888999
Q ss_pred HHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521 441 LIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 498 (508)
Q Consensus 441 ~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~ 498 (508)
+| ..||+++|+||.++| .+|+|++|||+.||+|.++|++++++|+++||+.+..
T Consensus 146 ~l-~~L~~~~r~i~~l~~---~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~~ 199 (231)
T PRK11922 146 AI-DALPDAFRAVFVLRV---VEELSVEETAQALGLPEETVKTRLHRARRLLRESLAR 199 (231)
T ss_pred HH-HhCCHHHhhhheeeh---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 99 899999999999998 7999999999999999999999999999999999875
No 43
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=99.89 E-value=4.6e-22 Score=189.25 Aligned_cols=180 Identities=23% Similarity=0.310 Sum_probs=143.7
Q ss_pred CCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHhc
Q 010521 206 LTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYD 285 (508)
Q Consensus 206 Lt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAkrY~ 285 (508)
++...+.+|+.+++.||. .|++.|+..|.+.|+.+|+++.
T Consensus 11 ~~~~~~~~l~~~~~~gd~----------------------------------------~a~~~L~~~y~~~l~~~~~~~~ 50 (194)
T PRK12519 11 LSSRSDAELFSALKAGQS----------------------------------------AALGVLYDRHAGLVYGLALKIL 50 (194)
T ss_pred CCcccHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHHHHHHc
Confidence 445566778888899987 9999999999999999999999
Q ss_pred CCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHcCC
Q 010521 286 NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGV 365 (508)
Q Consensus 286 ~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~~~Gr 365 (508)
++..+++|++||+|+++|+. ..|++..+ +|.||++.++++.+.++++++.+.....
T Consensus 51 ~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~~d~~Rk~~~~~~~~---------------------- 106 (194)
T PRK12519 51 GNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRAIDRLRSRRSRQRLL---------------------- 106 (194)
T ss_pred CCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHHHHHHHhcccccchh----------------------
Confidence 99999999999999999976 67887555 7999999999999999988764310000
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHHHHHcc
Q 010521 366 TPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVT 445 (508)
Q Consensus 366 ~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~L~~~ 445 (508)
+. ....+ ..+. ..+.|++.+...+....|..+| ..
T Consensus 107 -------------------------------~~---------~~~~~---~~~~-~~~~~~~~~~~~~~~~~l~~~l-~~ 141 (194)
T PRK12519 107 -------------------------------ER---------WQQEL---LGEA-SEDTPLEQASLAERSQRVQTAL-AQ 141 (194)
T ss_pred -------------------------------hh---------hhhhh---cccc-cCCCHHHHHHHHHHHHHHHHHH-Hh
Confidence 00 00000 0000 0124555555666667888999 89
Q ss_pred CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521 446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497 (508)
Q Consensus 446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~ 497 (508)
||++++.||.++| ++|+|++|||+.||+|.++|+++++||+++||+.+.
T Consensus 142 L~~~~~~v~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 190 (194)
T PRK12519 142 LPESQRQVLELAY---YEGLSQSEIAKRLGIPLGTVKARARQGLLKLRELLQ 190 (194)
T ss_pred CCHHHhhhhhhhh---hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999 899999999999999999999999999999999885
No 44
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=99.89 E-value=5e-22 Score=190.03 Aligned_cols=163 Identities=18% Similarity=0.219 Sum_probs=133.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.|++.|+..|.+.|+.+|.++.++..+++|++||+++++|+.+.+|++.. ..|.+|++..+++.+.++++++.+.
T Consensus 26 ~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~n~~~d~~Rk~~~~---- 100 (196)
T PRK12524 26 AAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVCNLCTDRLRRRRRA---- 100 (196)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHHHHHHHHHHHhhcCC----
Confidence 99999999999999999999999999999999999999999999998533 3699999999999888888765320
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
...++.. . + ..+. ..
T Consensus 101 -------------------------------------------------~~~~~~~--------~-----~-~~~~--~~ 115 (196)
T PRK12524 101 -------------------------------------------------SVDLDDA--------P-----E-PADA--AP 115 (196)
T ss_pred -------------------------------------------------CCCcccc--------c-----c-cccc--CC
Confidence 0000000 0 0 0011 12
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 500 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~ 500 (508)
+|++.+...+....|..+| +.||+++|.||.|+| ++|++++|||+.||+|..||+++++||+++||..+...+
T Consensus 116 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~i~~L~~---~~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~~ 188 (196)
T PRK12524 116 GAEEALIEGDRMRALDAAL-AALPERQRQAVVLRH---IEGLSNPEIAEVMEIGVEAVESLTARGKRALAALLAGQR 188 (196)
T ss_pred CHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 4555566667778899999 899999999999999 799999999999999999999999999999999987644
No 45
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=99.89 E-value=6.6e-22 Score=188.11 Aligned_cols=178 Identities=18% Similarity=0.264 Sum_probs=133.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.|++.||..|.+.|+.+|.++.++..+++|++||+|+++|+++.+|+++.+.+|.||++.+|++.+.++++...+..+.+
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 99999999999999999999999999999999999999999999999987778999999999998888876543210000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
. ....|++.+.. ..+.+.++.+.+.+.. .+
T Consensus 99 ~----------------------------------------------~~~~~~~~~~~---~~~~~~~~~~~~~~~~-~~ 128 (198)
T TIGR02859 99 L----------------------------------------------NSYVSLNKPIY---DEESDRTLLDVISGAK-VT 128 (198)
T ss_pred h----------------------------------------------hhhcCcccccc---cccccchHHHHhhccc-cC
Confidence 0 00122222110 0111112222222211 23
Q ss_pred CccchHHHHHHHHHHHHHHHccC-CHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTL-GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~L-p~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
+|++.....+....|.++| +.| ++.++.|+. +| .+|+|++|||+.||+|.++|+..++||+++||..+
T Consensus 129 ~~e~~~~~~e~~~~l~~~l-~~Ll~~~~~~i~~-~~---~~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~~l 197 (198)
T TIGR02859 129 DPEELIISQEEYGDIESKM-NELLSDLEWKVLQ-SY---LDGKSYQEIACDLNRHVKSIDNALQRVKRKLEKYL 197 (198)
T ss_pred CHHHHHHHHHHHHHHHHHH-HHhcCHHHHHHHH-HH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhc
Confidence 6777777777778899999 775 566666665 56 69999999999999999999999999999999875
No 46
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=99.89 E-value=8.8e-22 Score=187.16 Aligned_cols=188 Identities=21% Similarity=0.246 Sum_probs=148.9
Q ss_pred CCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHh
Q 010521 205 LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRY 284 (508)
Q Consensus 205 lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAkrY 284 (508)
+||+..+..|+..++.||. .|++.|+..|.+.|+.+++++
T Consensus 1 ~~~~~~~~~ll~~~~~gd~----------------------------------------~a~~~l~~~y~~~l~~~~~~~ 40 (193)
T PRK11923 1 MLTQEEDQQLVERVQRGDK----------------------------------------RAFDLLVLKYQHKILGLIVRF 40 (193)
T ss_pred CCccccHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHHHHHH
Confidence 3566667788888999987 899999999999999999999
Q ss_pred cCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHcC
Q 010521 285 DNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKG 364 (508)
Q Consensus 285 ~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~~~G 364 (508)
.++..+++|++||+++++|+++.+|++.. .|.+|++..+++.+.++++++.+.....
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 5999999999998888887654310000
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHHHHHc
Q 010521 365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIV 444 (508)
Q Consensus 365 r~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~L~~ 444 (508)
...++... ..++. ..+.+ ..+|+..+...+..+.+..+| .
T Consensus 98 ----------------------------~~~~~~~~-----~~~~~---~~~~~---~~~~e~~~~~~~~~~~l~~~l-~ 137 (193)
T PRK11923 98 ----------------------------DVSSEDAE-----FYDGD---HALKD---IESPERALLRDEIEGTVHRTI-Q 137 (193)
T ss_pred ----------------------------cccccchh-----hhccc---ccccC---cCCHHHHHHHHHHHHHHHHHH-H
Confidence 00000000 00000 00111 135666666777788899999 8
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 498 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~ 498 (508)
.||+++|.||.++| .+|+|++|||+.||+|..+|++.++||+++||.++..
T Consensus 138 ~L~~~~r~v~~l~~---~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~ 188 (193)
T PRK11923 138 QLPEDLRTALTLRE---FDGLSYEDIASVMQCPVGTVRSRIFRAREAIDKALQP 188 (193)
T ss_pred hCCHHHhHHHhhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999998 8999999999999999999999999999999998863
No 47
>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=99.89 E-value=5.7e-22 Score=183.70 Aligned_cols=160 Identities=18% Similarity=0.230 Sum_probs=132.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.|++.|+..|.+.+++++.++.++..+++|++||+|+++|+++++|+...+ .|.+|++..+++.+.++++.+.+....
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 ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
+.+. ..+.... ..
T Consensus 89 ---------------------------------------------------~~~~-------------~~~~~~~---~~ 101 (170)
T TIGR02952 89 ---------------------------------------------------SLDV-------------FKELLSN---EP 101 (170)
T ss_pred ---------------------------------------------------cHHH-------------HhhcCCC---CC
Confidence 0000 0000000 12
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
+|++.+...+....+..+| ..|||++|.||.++| ++|+|++|||+.||+|.++|++.++||+++||+.|
T Consensus 102 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~~---~~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~l 170 (170)
T TIGR02952 102 NPEEAILKEEANEKLLKAL-KILTPKQQHVIALRF---GQNLPIAEVARILGKTEGAVKILQFRAIKKLARQM 170 (170)
T ss_pred CHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence 5666666677778899999 899999999999999 79999999999999999999999999999999864
No 48
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=99.89 E-value=7.3e-22 Score=185.95 Aligned_cols=168 Identities=25% Similarity=0.275 Sum_probs=133.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.|+.+|+..|.+.|+.+|.+|.+++.+++|++||+++++|+++.+|++.. +|.+|++..+++.+.+++++..+..
T Consensus 18 ~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~~~~rk~~~~~--- 92 (187)
T TIGR02948 18 NAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLTIDRLRKRKPDF--- 92 (187)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHHHHHHhhcccc---
Confidence 99999999999999999999999999999999999999999999999865 6999999999998888876543100
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
.++.. ..+.++....+...+. .+
T Consensus 93 ---------------------------------------------------~~~~~----~~~~~~~~~~~~~~~~--~~ 115 (187)
T TIGR02948 93 ---------------------------------------------------YLDDE----VQGTDGLTMESQLAAD--EA 115 (187)
T ss_pred ---------------------------------------------------ccccc----ccCccccccccccccC--cC
Confidence 00000 0000010111111111 23
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~ 497 (508)
+|++.+...+....+.++| ..|||++|.||.++| .+|+|++|||+.||+|.++|++.++||+++||..+.
T Consensus 116 ~~~~~~~~~e~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l~ 185 (187)
T TIGR02948 116 PPEDQVISLELRDTIQQEI-QALPPKYRMVIVLKY---MEDLSLKEISEILDLPVGTVKTRIHRGREALRKQLR 185 (187)
T ss_pred CHHHHHHHHHHHHHHHHHH-HhCCHHHhHHhhhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhh
Confidence 5666666667777899999 899999999999998 799999999999999999999999999999999875
No 49
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=99.89 E-value=7.3e-22 Score=185.58 Aligned_cols=160 Identities=16% Similarity=0.164 Sum_probs=130.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.|+..|+..|.+.|+.+|.++.++..+++|++||+|+++|+++++|++..+ .|.+|++..++|.+.+++++..+. ..
T Consensus 19 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~R~~~~~-~~- 95 (179)
T PRK12514 19 DAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGL-SPMTWLITIARNHAIDRLRARKAV-AV- 95 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCcccc-cHHHHHHHHHHHHHHHHHHhcCCc-cc-
Confidence 999999999999999999999999999999999999999999999986544 699999999999988888765320 00
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
.++. ..+ ..+. ..
T Consensus 96 ---------------------------------------------------~~~~-------------~~~-~~~~--~~ 108 (179)
T PRK12514 96 ---------------------------------------------------DIDE-------------AHD-LADP--SP 108 (179)
T ss_pred ---------------------------------------------------cccc-------------chh-cccc--CC
Confidence 0000 000 0010 12
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~ 497 (508)
+|++.+...+....|..+| ..||++++.||.++| ++|+|++|||+.||+|.++|++.++||+++||+++.
T Consensus 109 ~~e~~~~~~~~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 178 (179)
T PRK12514 109 GPEAEVIAGDEGQRIDACL-EELEKDRAAAVRRAY---LEGLSYKELAERHDVPLNTMRTWLRRSLLKLRECLS 178 (179)
T ss_pred CHHHHHHhHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCChHHHHHHHHHHHHHHHHHhc
Confidence 4555555555556788999 899999999999999 899999999999999999999999999999999874
No 50
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=99.89 E-value=7.4e-22 Score=186.80 Aligned_cols=162 Identities=19% Similarity=0.213 Sum_probs=131.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.+++.|+..|.++|+++|.++.++..++||++||+|+++|+++++|++.++ .|.+|++..+++.+.+++++..+...
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 999999999999999999999999999999999999999999999998654 58899999999998888876532000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
..+++. ..+.. +. ..
T Consensus 102 -------------------------------------------------~~~~~~-------------~~~~~-~~--~~ 116 (187)
T PRK12534 102 -------------------------------------------------NVALDD-------------AGELR-AA--DA 116 (187)
T ss_pred -------------------------------------------------cccccc-------------hhhhc-cc--cC
Confidence 000000 00000 00 11
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~ 497 (508)
+|++.....+....+..+| ..||++++.||.++| .+|+|++|||+.||+|.++|+++++||+++||..+.
T Consensus 117 ~~~~~~~~~e~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l~ 186 (187)
T PRK12534 117 SPLERTERASTRRRIDHCL-AELEPPRSELIRTAF---FEGITYEELAARTDTPIGTVKSWIRRGLAKLKACLE 186 (187)
T ss_pred ChhhHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHHHc
Confidence 3444555566778899999 899999999999999 899999999999999999999999999999999874
No 51
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=99.88 E-value=2e-21 Score=182.99 Aligned_cols=168 Identities=24% Similarity=0.266 Sum_probs=134.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.|+..|+..|.++|+++|+++.++..+++|++||++++||+++++|++.. .|.+|++..+++.+.+++++..+..
T Consensus 18 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~~~d~~R~~~~~~--- 92 (187)
T PRK09641 18 NAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNLTIDRLRKRKPDY--- 92 (187)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHHHHHHHHhcCccc---
Confidence 99999999999999999999999999999999999999999999999753 6999999999999888887653210
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
+++... .+++.....+.+.+. ..
T Consensus 93 ---------------------------------------------------~~~~~~----~~~~~~~~~~~~~~~--~~ 115 (187)
T PRK09641 93 ---------------------------------------------------YLDAEV----AGTEGLTMYSQLAAD--DA 115 (187)
T ss_pred ---------------------------------------------------cccccc----cCCcchhhhcccccC--cC
Confidence 000000 000111111111111 23
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~ 497 (508)
+|++.+...+....+..+| ..||++++.||.++| .+|+|++|||+.||||.++|++.++||+++||+.+.
T Consensus 116 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~il~l~~---~~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l~ 185 (187)
T PRK09641 116 LPEEQVVSLELQETIQEAI-LQLPEKYRTVIVLKY---IEDLSLKEISEILDLPVGTVKTRIHRGREALRKQLR 185 (187)
T ss_pred CHHHHHHHHHHHHHHHHHH-HhCCHHHHHHhhhHH---hhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 5666667777778899999 899999999999999 799999999999999999999999999999999875
No 52
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=99.88 E-value=1e-21 Score=179.65 Aligned_cols=150 Identities=20% Similarity=0.212 Sum_probs=123.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.|++.|++.|.++|+.+++++ ++..++||++||+++++|+++++|++..+ +|.+|++..+++.+.++++++.+..
T Consensus 4 ~af~~l~~~y~~~l~~~~~~~-~~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~~~~--- 78 (154)
T PRK06759 4 ATFTEAVVLYEGLIVNQIKKL-GIYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFAVQ--- 78 (154)
T ss_pred ccHHHHHHHHHHHHHHHHHHh-CCcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHHhhc---
Confidence 799999999999999999886 55679999999999999999999998666 7999999999999999988763100
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
+.. . . .+
T Consensus 79 -----------------------------------------------------~~~------~-~-------------~~ 85 (154)
T PRK06759 79 -----------------------------------------------------EKC------V-C-------------VG 85 (154)
T ss_pred -----------------------------------------------------ccc------c-c-------------cC
Confidence 000 0 0 01
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA 495 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~ 495 (508)
+|++.....+....|..+| ..||+++|.||.++| ++|+|.+|||+.||+|.++|++++.||+++||+.
T Consensus 86 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~ii~l~~---~~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 86 EYEDHFHFEDVEMKVKDFM-SVLDEKEKYIIFERF---FVGKTMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred CCcccccHHHHHHHHHHHH-HhCCHHHHHHHHHHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 1222233344567788999 899999999999999 8999999999999999999999999999999963
No 53
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=99.88 E-value=1.8e-21 Score=181.31 Aligned_cols=168 Identities=24% Similarity=0.231 Sum_probs=134.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.|+++|+..|.++|+.++++|.+++.+.+|++||++++||+++++|+ .+.+|.+|++..+++.+.+++++..+....+
T Consensus 10 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~r~~~~~~~~~ 87 (182)
T PRK09652 10 AAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYLRKQGRRPPAS 87 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHHHcccCCCCcc
Confidence 89999999999999999999999999999999999999999999999 3458999999999999988887654311000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
+++. ...++....+.+.+ ..
T Consensus 88 ---------------------------------------------------~~~~------~~~~~~~~~~~~~~---~~ 107 (182)
T PRK09652 88 ---------------------------------------------------DVDA------EEAEDFDLADALRD---IS 107 (182)
T ss_pred ---------------------------------------------------cccc------cccccccccccccc---cc
Confidence 0000 00000001111111 23
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~ 497 (508)
+|++.+...+....+..+| ..|||+++.||.++| .+|+|++|||+.||+|+.+|++.+++|+++||+.+.
T Consensus 108 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~~---~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 177 (182)
T PRK09652 108 TPENELLSAELEQRVRAAI-ESLPEELRTAITLRE---IEGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQ 177 (182)
T ss_pred ChHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5676777777788899999 899999999999998 799999999999999999999999999999999885
No 54
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=99.88 E-value=1.5e-21 Score=192.66 Aligned_cols=162 Identities=19% Similarity=0.224 Sum_probs=132.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.|++.|+..|.+.|+.++.++.++..++||++||+|+.+|+.+++|++..+ .|.+|++..+++.+.+++++..+. .
T Consensus 63 ~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~~id~~Rk~~~~-~-- 138 (233)
T PRK12538 63 AAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNRCIDLRRKPRTE-N-- 138 (233)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHHHHHHHHhhccc-c--
Confidence 999999999999999999999999999999999999999999999986544 799999999999888887653210 0
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
++. ..+. .+. ..
T Consensus 139 ----------------------------------------------------~~~-------------~~~~-~~~--~~ 150 (233)
T PRK12538 139 ----------------------------------------------------VDA-------------VPEV-ADG--KP 150 (233)
T ss_pred ----------------------------------------------------ccc-------------cccc-ccC--CC
Confidence 000 0000 000 12
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM 501 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l 501 (508)
++++.+...+....|..+| ..||+++|+||.|+| ++|+|++|||+.||+|.++|+++++||+++||+.+...+.
T Consensus 151 ~~~~~~~~~e~~~~l~~~L-~~Lp~~~R~v~~L~~---~eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~~~~~ 224 (233)
T PRK12538 151 DAVSVIERNELSDLLEAAM-QRLPEQQRIAVILSY---HENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLRRHER 224 (233)
T ss_pred CHHHHHHHHHHHHHHHHHH-HhCCHHHHHHhhhHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 3444455566667889999 899999999999999 8999999999999999999999999999999999976553
No 55
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=99.88 E-value=2.2e-21 Score=183.21 Aligned_cols=162 Identities=18% Similarity=0.260 Sum_probs=127.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.|++.|+..|.+.|+.+|+++.+++.+++|++||+++++|+++++|++..+ .|.+|++..+++.+.+++++..+...
T Consensus 23 ~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~rk~~~~~~-- 99 (186)
T PRK13919 23 EALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRG-SARAWLLALAHHAAVDHVRRRAARPQ-- 99 (186)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCcccc-chHHHHHHHHHHHHHHHHHhhhcccc--
Confidence 999999999999999999999999999999999999999999999987543 69999999999999998876532000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
. ++.. . ..... . +. .
T Consensus 100 -------------------------------------------------~--~~~~------~-~~~~~---~-~~---~ 114 (186)
T PRK13919 100 -------------------------------------------------P--LEPD------E-REPEA---F-DL---P 114 (186)
T ss_pred -------------------------------------------------c--cccc------c-ccccc---c-cC---C
Confidence 0 0000 0 00000 0 00 0
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~ 497 (508)
+|.......+..+.|..+| +.||++++.||.++| .+|+|++|||+.||+|.++|+.+++||+++||..+.
T Consensus 115 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~~---~~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l~ 184 (186)
T PRK13919 115 GPGLDEEGHLDRTRLGRAL-KALSPEERRVIEVLY---YQGYTHREAAQLLGLPLGTLKTRARRALSRLKEVLR 184 (186)
T ss_pred CccccHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence 1111122333456788999 899999999999999 899999999999999999999999999999999875
No 56
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=99.88 E-value=3.9e-21 Score=181.62 Aligned_cols=159 Identities=19% Similarity=0.279 Sum_probs=129.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.|++.|+..|.+.++.++.++.++..+++|++||+|+.+|+.+++|++..+ .|.+|++..+++.+.+++++..+...
T Consensus 23 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wL~~iarn~~~d~~r~~~~~~~-- 99 (182)
T PRK12537 23 RALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARG-SARGWIYSVTRHLALNVLRDTRREVV-- 99 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHHHHHhccccCc--
Confidence 999999999999999999999999999999999999999999999986443 69999999999999999887642100
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
.+.. .. +...+ ..
T Consensus 100 ----------------------------------------------------~~~~--------~~----~~~~~---~~ 112 (182)
T PRK12537 100 ----------------------------------------------------LDDD--------AE----ETAQT---LH 112 (182)
T ss_pred ----------------------------------------------------cccc--------hh----hhccc---cc
Confidence 0000 00 00000 11
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
++++..+..+....+..+| +.||+++|.||.++| .+|+|++|||+.||+|.++|+..++||+++||..+
T Consensus 113 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~i~~l~~---~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 181 (182)
T PRK12537 113 EIIDDFDLWANSGKIHRCL-EQLEPARRNCILHAY---VDGCSHAEIAQRLGAPLGTVKAWIKRSLKALRECM 181 (182)
T ss_pred chHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCChhhHHHHHHHHHHHHHHHh
Confidence 2333344445567788999 899999999999999 89999999999999999999999999999999876
No 57
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=99.87 E-value=6e-21 Score=180.20 Aligned_cols=168 Identities=21% Similarity=0.228 Sum_probs=133.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.|++.|+..|.+.|+.+|+++.++..+++|++||+|+++|+.+++|++. .+|.+|++..+++.+.+++++..+.....
T Consensus 20 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~~~~~~r~~~r~~~~~ 97 (190)
T TIGR02939 20 QAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNTAKNHLVAQGRRPPTS 97 (190)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHHHHHHHHHhccCCCcc
Confidence 8999999999999999999999999999999999999999999999975 36999999999998888887554311000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
..+.+. .....+ ........
T Consensus 98 -------------------------------------------------~~~~~~----------~~~~~~-~~~~~~~~ 117 (190)
T TIGR02939 98 -------------------------------------------------DVEIED----------AEHFEG-ADRLREID 117 (190)
T ss_pred -------------------------------------------------cccccc----------hhhhcc-cccccccC
Confidence 000000 000000 00000013
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~ 497 (508)
+|++.+...+....+..+| ..||+++|.||.++| .+|+|++|||+.||+|.++|++.++||+++||+.+.
T Consensus 118 ~~e~~~~~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l~ 187 (190)
T TIGR02939 118 TPERLLLSRELEQTVMRAV-EALPEDLRTAITLRE---LEGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRLR 187 (190)
T ss_pred ChHHHHHHHHHHHHHHHHH-HcCCHHHhhhhhhhh---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 5666666777778899999 899999999999999 899999999999999999999999999999999885
No 58
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=7.2e-21 Score=183.82 Aligned_cols=167 Identities=17% Similarity=0.184 Sum_probs=130.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.|+++|+..|.+.|+.++.++.++..+++|++||+|+.+|++++.|++..+ .|.+|++.++++.+.+++++..+.....
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 5999999999999999988764311000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
++. +.....+.+.+. ..
T Consensus 117 ----------------------------------------------------~~~---------~~~~~~~~~~~~--~~ 133 (206)
T PRK12526 117 ----------------------------------------------------LGD---------DIWPIEQALAES--QS 133 (206)
T ss_pred ----------------------------------------------------ccc---------ccchhhhhcccc--cC
Confidence 000 000000001111 01
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 499 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~ 499 (508)
.+. ..........|..+| ..||+++|.||.++| ++|+|++|||+.||+|.++|+.++++|+++||..+...
T Consensus 134 ~~~-~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~ 204 (206)
T PRK12526 134 ESE-EFSDHLMDKQILSYI-EKLPEAQQTVVKGVY---FQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQMGEQ 204 (206)
T ss_pred chH-HHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence 122 222333446788999 899999999999999 89999999999999999999999999999999998754
No 59
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=99.87 E-value=4.9e-21 Score=182.16 Aligned_cols=159 Identities=22% Similarity=0.211 Sum_probs=130.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCC---CCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMG---ADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g---~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~i 340 (508)
.|++.|+..|.+.|+.++.++.+++ .+++|++||+++++|+++++|+++.+ .|.+|++..++|.+.+++++..+..
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 9999999999999999999998753 57999999999999999999997554 7999999999999999988764310
Q ss_pred cccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCcccccccccc
Q 010521 341 RLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNR 420 (508)
Q Consensus 341 rip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~ 420 (508)
.. .+.+. ...+.
T Consensus 97 ~~---------------------------------------------------~~~~~----------------~~~~~- 108 (189)
T PRK06811 97 EI---------------------------------------------------DSIDE----------------FILIS- 108 (189)
T ss_pred cc---------------------------------------------------ccchh----------------hhhcc-
Confidence 00 00000 00000
Q ss_pred CCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 421 VENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 421 ~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
.++|++.+...+....|.++| ..|||++|.||.|+| .+|+|.+|||+.||+|..+|++.++||+++||+..
T Consensus 109 -~~~~~~~~~~~e~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 109 -EESIENEIILKENKEEILKLI-NDLEKLDREIFIRRY---LLGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred -cCCHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 125666667777778899999 899999999999998 79999999999999999999999999999999753
No 60
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=6.7e-21 Score=181.96 Aligned_cols=187 Identities=19% Similarity=0.199 Sum_probs=143.7
Q ss_pred CCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHH
Q 010521 204 ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQR 283 (508)
Q Consensus 204 ~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAkr 283 (508)
|+.+..+...|+.+++.||. .|++.|+..|.+.|+.+|.+
T Consensus 7 ~~~~~~~~~~li~~~~~~d~----------------------------------------~af~~l~~~y~~~l~~~~~~ 46 (194)
T PRK12531 7 HTFGRQEWLECMEKVKSRDK----------------------------------------QAFALVFSYYAPKLKQFAMK 46 (194)
T ss_pred cccccHhHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHHHHH
Confidence 44566677778888888887 99999999999999999999
Q ss_pred hcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHc
Q 010521 284 YDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK 363 (508)
Q Consensus 284 Y~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~~~ 363 (508)
+.++..+++|++||+|+.+|+.+++|++..+ .|.+|++..++|.+.+++++..+.....
T Consensus 47 ~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn~~ld~~Rk~~~~~~~~-------------------- 105 (194)
T PRK12531 47 HVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRNLCFDLLRKQKGKDLHI-------------------- 105 (194)
T ss_pred HhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHHHHHHHHHHhccccccc--------------------
Confidence 9999899999999999999999999987544 6999999999999999988764210000
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHHHHH
Q 010521 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLII 443 (508)
Q Consensus 364 Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~L~ 443 (508)
..+.. .........+.+ ...|+ .....+.+.++|
T Consensus 106 -------------------------------~~~~~-------~~~~~~~~~~~~---~~~~e----~~~~~~~l~~~l- 139 (194)
T PRK12531 106 -------------------------------HADDI-------WPSDYYPPDLVD---HYSPE----QDMLKEQVMKFL- 139 (194)
T ss_pred -------------------------------chhhc-------cccccccccccc---ccCHH----HHHHHHHHHHHH-
Confidence 00000 000000000000 01222 223345688888
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 500 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~ 500 (508)
..||+++|.||.|+| .+|+|++|||+.||+|.++|+..+++|+++||..+....
T Consensus 140 ~~Lp~~~r~v~~l~~---~eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~~~~ 193 (194)
T PRK12531 140 DRLPKAQRDVLQAVY---LEELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSMDAES 193 (194)
T ss_pred HhCCHHHHHHHHHHH---HcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHhhhcc
Confidence 899999999999999 899999999999999999999999999999999987653
No 61
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=99.86 E-value=5.8e-21 Score=181.38 Aligned_cols=173 Identities=18% Similarity=0.247 Sum_probs=136.4
Q ss_pred cChHHHHHhhhh----hHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHH
Q 010521 250 ISRPELQSILME----CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWI 325 (508)
Q Consensus 250 ~s~~~L~~~l~e----~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wI 325 (508)
++.++|...++. ++.|++.|+..|.+.|+++|.+|.++..+++|++||+|+.+|+++++|++. .+|.+|++.++
T Consensus 8 ~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~~--~~~~~wl~~ia 85 (188)
T PRK09640 8 LNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLYSIT 85 (188)
T ss_pred CCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcCC--CcchHHHHHHH
Confidence 566677777763 789999999999999999999999999999999999999999999999863 37999999999
Q ss_pred HHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCC
Q 010521 326 RQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLN 405 (508)
Q Consensus 326 R~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~ 405 (508)
++.+.+++++..+..... .+.
T Consensus 86 ~n~~~d~~R~~~~~~~~~----------------------------------------------------~~~------- 106 (188)
T PRK09640 86 YNECITQYRKERRKRRLM----------------------------------------------------DAL------- 106 (188)
T ss_pred HHHHHHHHHHhcccccCc----------------------------------------------------chh-------
Confidence 999999988653210000 000
Q ss_pred CCCCCccccccccccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHH
Q 010521 406 GLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVG 485 (508)
Q Consensus 406 ~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~ 485 (508)
.. +...+. .+ +.....+....|..+| ..||+++|.||.++| .+|+|++|||+.||||.++|+..+
T Consensus 107 -----~~-~~~~~~----~~-~~~~~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tV~~~l 171 (188)
T PRK09640 107 -----SL-DPLEEA----SE-EKAPKPEERGGLDRWL-VHVNPIDREILVLRF---VAELEFQEIADIMHMGLSATKMRY 171 (188)
T ss_pred -----hh-cccccc----cc-cccccHHHHHHHHHHH-HhcChhheeeeeeHH---hcCCCHHHHHHHHCCCHHHHHHHH
Confidence 00 000000 00 1111234456788899 899999999999999 799999999999999999999999
Q ss_pred HHHHHHHHHHHHH
Q 010521 486 LVALEKLKHAARK 498 (508)
Q Consensus 486 ~rALkKLR~~L~~ 498 (508)
.||+++||..+..
T Consensus 172 ~Ra~~~Lr~~l~~ 184 (188)
T PRK09640 172 KRALDKLREKFAG 184 (188)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999998853
No 62
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=1.8e-20 Score=174.15 Aligned_cols=165 Identities=17% Similarity=0.136 Sum_probs=136.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q 010521 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (508)
Q Consensus 263 ~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~iri 342 (508)
..|++.|++.|.+.|+++|+++.++..+++|++||+++++|+++++|+ .+..|.+|++..+++.+.+++++..+....
T Consensus 12 ~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~~r~~~~~~~~ 89 (179)
T PRK11924 12 KEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDLLRRRRREKAV 89 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHHHHhccccccc
Confidence 399999999999999999999999999999999999999999999998 344799999999999988888765431000
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCC
Q 010521 343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE 422 (508)
Q Consensus 343 p~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e 422 (508)
. .+. .. +...+. ..
T Consensus 90 ---------------------------------------------------~-~~~---------~~----~~~~~~-~~ 103 (179)
T PRK11924 90 ---------------------------------------------------L-SDD---------AL----EPEFAE-TA 103 (179)
T ss_pred ---------------------------------------------------C-ccc---------cc----ccccCC-cc
Confidence 0 000 00 000000 13
Q ss_pred CCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521 423 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 499 (508)
Q Consensus 423 ~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~ 499 (508)
++|++.+...+....+..+| ..||++++.||.++| .+|+|++|||+.||+|+.+|++++++|+++||+.+...
T Consensus 104 ~~~e~~~~~~e~~~~l~~~l-~~L~~~~r~i~~l~~---~~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~~~ 176 (179)
T PRK11924 104 ETPEAALLAKDDLARIDRCL-DALPVKQREVFLLRY---VEGLSYREIAEILGVPVGTVKSRLRRARQLLRECLEAQ 176 (179)
T ss_pred CCHHHHHhhHHHHHHHHHHH-HhCCHHHHHHhhHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 46778888888889999999 899999999999999 79999999999999999999999999999999988754
No 63
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=4.5e-21 Score=181.50 Aligned_cols=174 Identities=18% Similarity=0.163 Sum_probs=137.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccc
Q 010521 261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (508)
Q Consensus 261 e~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~i 340 (508)
++..|++.|+..|.+.++.+|.+++++..+++|++||+|+.+|+.+.+|++..+..|.||++..++|.+.+++++..+..
T Consensus 6 gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~~~~ 85 (185)
T PRK12542 6 NDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNKRHE 85 (185)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 34599999999999999999999999999999999999999999999998654447999999999999999887764200
Q ss_pred cccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCcccccccccc
Q 010521 341 RLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNR 420 (508)
Q Consensus 341 rip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~ 420 (508)
. . .+.. .. +.....
T Consensus 86 ~------------------~-----------------------------------~~~~--------~~----~~~~~~- 99 (185)
T PRK12542 86 T------------------F-----------------------------------LEEY--------ER----ESIEAV- 99 (185)
T ss_pred h------------------h-----------------------------------hhhc--------cc----cchhhh-
Confidence 0 0 0000 00 000000
Q ss_pred CCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521 421 VENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 500 (508)
Q Consensus 421 ~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~ 500 (508)
.++|++.....+....|..+| ..|||++|+||.|+| ++|+|++|||+.||+|.+||++.++||+++||+.+....
T Consensus 100 -~~~~~~~~~~~~~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~ 174 (185)
T PRK12542 100 -DENIEEWEKRKMSEVQIDTLL-KELNESNRQVFKYKV---FYNLTYQEISSVMGITEANVRKQFERARKRVQNMIGGIQ 174 (185)
T ss_pred -hccHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccc
Confidence 112333333344456788999 899999999999998 899999999999999999999999999999999998888
Q ss_pred HHHhh
Q 010521 501 MEAML 505 (508)
Q Consensus 501 l~~~l 505 (508)
...|+
T Consensus 175 ~~~~~ 179 (185)
T PRK12542 175 HDEFK 179 (185)
T ss_pred hHHHH
Confidence 77774
No 64
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=1.8e-20 Score=178.02 Aligned_cols=163 Identities=20% Similarity=0.232 Sum_probs=133.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.|++.|+..|.+.++.++.++.++..+++|++||+|+.+|+++++|++. ..|.+|++..+++.+.+++++..+. +
T Consensus 22 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~r~~~~~---~ 96 (189)
T PRK12515 22 TAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARFKALSALRRRKHE---E 96 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHHHHHHHHHccCCC---C
Confidence 9999999999999999999999999999999999999999999999964 3799999999999888888654210 0
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
+.. +.. ..+.+. .+
T Consensus 97 ----------------------------------------------------~~~-----------~~~-~~~~~~--~~ 110 (189)
T PRK12515 97 ----------------------------------------------------IDD-----------EAA-AAIEDG--AD 110 (189)
T ss_pred ----------------------------------------------------Ccc-----------ccc-cccCCC--CC
Confidence 000 000 001111 12
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM 501 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l 501 (508)
+|+......+....+..+| +.||+++|.||.++| .+|+|++|||+.||+|..+|+++++||+++||+.+...+.
T Consensus 111 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~~---~~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~ 184 (189)
T PRK12515 111 TPEVALQKSDTSAALRACL-AKLSPAHREIIDLVY---YHEKSVEEVGEIVGIPESTVKTRMFYARKKLAELLKAAGV 184 (189)
T ss_pred CHHHHHHhHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 4555555666677889999 899999999999999 8999999999999999999999999999999999987643
No 65
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=99.86 E-value=3.6e-20 Score=176.96 Aligned_cols=159 Identities=14% Similarity=0.135 Sum_probs=131.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.+++.|+..|.+.|+++|.++.++..++||++||+|+.+|+.+++|++.. +|.+|++..+++.+.+++++..+...
T Consensus 27 ~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~~--~f~~wL~~i~rn~~~d~~Rk~~~~~~-- 102 (192)
T PRK09643 27 YAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDA--AVSSWLHRIVVNACLDRLRRAKARPT-- 102 (192)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCCC--ccHHHHHHHHHHHHHHHHHccccCCC--
Confidence 99999999999999999999999999999999999999999999999653 69999999999999999887542100
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
.+++. .. + . ..
T Consensus 103 --------------------------------------------------~~~~~----------~~---~-~-----~~ 113 (192)
T PRK09643 103 --------------------------------------------------VPLDD----------VY---P-V-----AQ 113 (192)
T ss_pred --------------------------------------------------CCccc----------cc---c-c-----cC
Confidence 00000 00 0 0 01
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 499 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~ 499 (508)
+|.+.+...+....+..+| +.||+++|.||.|+| .+|+|++|||+.||+|..+|++.+.+|+++||+.+...
T Consensus 114 ~~~~~~~~~e~~~~l~~~l-~~Lp~~~r~i~~l~~---~~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l~~~ 185 (192)
T PRK09643 114 LERDPTARVETALAVQRAL-MRLPVEQRAALVAVD---MQGYSVADAARMLGVAEGTVKSRCARGRARLAELLGYL 185 (192)
T ss_pred CcccHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 2333344556677899999 899999999999999 89999999999999999999999999999999998753
No 66
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=99.85 E-value=2.3e-20 Score=174.51 Aligned_cols=158 Identities=15% Similarity=0.123 Sum_probs=126.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.|++.|+..|.+.|+.+|.++.++..+++|++||+|+++|++++.|++. .+|.+|++..+++.+.+++++..+.....
T Consensus 18 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~r~~~~~~~~~ 95 (176)
T PRK09638 18 AALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASRLYKDHLRKQKREKLRL 95 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHHhccccchh
Confidence 9999999999999999999999999999999999999999999999864 37999999999999999988764210000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
+ ...+. ..+.
T Consensus 96 --------------------------~-----------------------~~~~~-----------------~~~~---- 105 (176)
T PRK09638 96 --------------------------Q-----------------------RAKEE-----------------TLRK---- 105 (176)
T ss_pred --------------------------h-----------------------hcccc-----------------cCCc----
Confidence 0 00000 0000
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~ 497 (508)
...+..........|..+| ..||+++|.||.++| .+|+|++|||+.||+|..+|++.++||+++||+.+.
T Consensus 106 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~l~ 175 (176)
T PRK09638 106 EKWEAAIKGAEWSEMLDAL-SKLDPEFRAPVILKH---YYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKEWG 175 (176)
T ss_pred cchHHHHHhhhHHHHHHHH-HcCCHHHhheeeehh---hcCCCHHHHHHHHCCChhHHHHHHHHHHHHHHHHhc
Confidence 0001122334456688899 899999999999998 799999999999999999999999999999999773
No 67
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=99.85 E-value=3.2e-20 Score=174.84 Aligned_cols=179 Identities=18% Similarity=0.140 Sum_probs=135.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhc----CCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhc
Q 010521 262 CSLAREKLVMSNVRLVMSIAQRYD----NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS 337 (508)
Q Consensus 262 ~~~A~e~LIe~yl~LV~sIAkrY~----~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~ 337 (508)
+..|++.|+..|.+.|+.+|++|. ++..+++|++||+++.+|+++.+|++..+.+|.+|++..+++.+.+++++..
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 349999999999999999999975 3567899999999999999999998765568999999999999998887652
Q ss_pred c-cccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCcccccc
Q 010521 338 R-TLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYI 416 (508)
Q Consensus 338 R-~irip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i 416 (508)
+ ..+.+ ....+++... ..++....+.+.+
T Consensus 85 ~~~~r~~-----------------------------------------------~~~~~~~~~~---~~~~~~~~~~~~~ 114 (189)
T TIGR02984 85 GAQKRDI-----------------------------------------------RREQSLDAGG---RLDESSVRLAAQL 114 (189)
T ss_pred HHHhhhc-----------------------------------------------ccccCCCccc---ccCCcchhHHHHc
Confidence 1 00000 0011122110 0001111222223
Q ss_pred ccccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 417 ADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 417 ~d~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
.+. .++|++.+...+....|..+| ..|||++|.||.++| .+|+|++|||+.||||+++|++.++||+++||+.+
T Consensus 115 ~~~--~~~~~~~~~~~e~~~~l~~~l-~~L~~~~r~vi~l~~---~~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~l 188 (189)
T TIGR02984 115 AAD--GPSPSQVAARREAAVRLAQAL-AKLPEDYREVILLRH---LEGLSFAEVAERMDRSEGAVSMLWVRGLARLRQIL 188 (189)
T ss_pred cCC--CCCHHHHHHHHHHHHHHHHHH-HcCCHHHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 222 235677777777778899999 899999999999999 79999999999999999999999999999999876
No 68
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=4.1e-20 Score=174.22 Aligned_cols=165 Identities=17% Similarity=0.165 Sum_probs=132.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccc
Q 010521 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 341 (508)
Q Consensus 262 ~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~ir 341 (508)
+..|++.|+..|.+.|+.++.+|.++..+++|++||+|+.+|+++.+|++.. .|.+|++..+++.+.++++...+..+
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 4489999999999999999999999999999999999999999999999764 69999999999988777655431000
Q ss_pred ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccC
Q 010521 342 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRV 421 (508)
Q Consensus 342 ip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~ 421 (508)
.++.. . ... +...
T Consensus 83 -----------------------------------------------------~~~~~--------~--~~~----~~~~ 95 (179)
T PRK12543 83 -----------------------------------------------------IFEKA--------E--EQR----KPVS 95 (179)
T ss_pred -----------------------------------------------------ccccc--------c--ccc----cccc
Confidence 00000 0 000 0000
Q ss_pred CCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521 422 ENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 500 (508)
Q Consensus 422 e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~ 500 (508)
...|++ +...+....|..+| ..|||++|.||.|+| .+|+|++|||+.||+|.++|+..+++|+++||+.+...+
T Consensus 96 ~~~~~~-~~~~~~~~~l~~~l-~~Lp~~~r~i~~l~~---~e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~ 169 (179)
T PRK12543 96 IDFSED-VLSKESNQELIELI-HKLPYKLRQVIILRY---LHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIEE 169 (179)
T ss_pred ccChHH-HHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 123444 56667778899999 899999999999998 899999999999999999999999999999999997554
No 69
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=99.85 E-value=4.6e-20 Score=183.44 Aligned_cols=168 Identities=16% Similarity=0.159 Sum_probs=132.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHH-------hhhccCCCCCCcchhHHHHHHHHHHHHHHHHh
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLR-------GIEKFDSSKGFKISTYVYWWIRQGVSRALVEN 336 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLir-------AiekFDperG~rFsTYA~~wIR~~I~~~Ird~ 336 (508)
.|++.|+..|.+.|+.++.++.++..++||++||+|+.+|. .+.+|++.. .|.||++..++|.+.+++++.
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 699999999999999998765
Q ss_pred cccccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCcccccc
Q 010521 337 SRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYI 416 (508)
Q Consensus 337 ~R~irip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i 416 (508)
.+... ++. .....+.
T Consensus 117 ~r~~~------------------------------------------------------~~~----------~~~~~~~- 131 (244)
T TIGR03001 117 RRHSP------------------------------------------------------VEE----------PTELAAL- 131 (244)
T ss_pred cccCc------------------------------------------------------ccc----------ccccccc-
Confidence 32100 000 0000000
Q ss_pred ccccCCCCccchHHH----HHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 010521 417 ADNRVENNPWHGVDD----WALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL 492 (508)
Q Consensus 417 ~d~~~e~~Pe~~ve~----~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKL 492 (508)
.+. ..+|++.+.. .+..+.|.++| ++||+++|+||.|+| .+|+|++|||+.||||.+||+..+++|+++|
T Consensus 132 ~~~--~~~~e~~~~~~e~~~e~~~~l~~aL-~~Lp~~~R~v~~L~~---~eg~S~~EIA~~Lgis~~TVk~rl~RAr~~L 205 (244)
T TIGR03001 132 PAP--GSDPELDLLRERYRQDFRQALREAL-AALSERERHLLRLHF---VDGLSMDRIGAMYQVHRSTVSRWVAQARERL 205 (244)
T ss_pred cCC--CCCHHHHHHHHhhHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 011 1134433332 23556789999 899999999999999 8999999999999999999999999999999
Q ss_pred HHHHHHhhHHHh
Q 010521 493 KHAARKKKMEAM 504 (508)
Q Consensus 493 R~~L~~~~l~~~ 504 (508)
|+.+++...+.|
T Consensus 206 r~~l~~~~~~~~ 217 (244)
T TIGR03001 206 LERTRRRLAERL 217 (244)
T ss_pred HHHHHHHHHHhc
Confidence 999988766554
No 70
>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=99.85 E-value=4.8e-20 Score=171.70 Aligned_cols=153 Identities=20% Similarity=0.190 Sum_probs=123.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.|++.|+..|.+.|+++|.++.++..+++|++||+++.+|+.+++|++.. +|.+|++..+++.+.+++++..+.
T Consensus 16 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~---- 89 (169)
T TIGR02954 16 PAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPK--YFNTWLTRILINECIDLLKKKKKV---- 89 (169)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCcc--ccHHHHHHHHHHHHHHHHHhcCCc----
Confidence 99999999999999999999999999999999999999999999999753 699999999999999888765320
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
.+++.. ... .+.
T Consensus 90 --------------------------------------------------~~~~~~----------~~~----~~~---- 101 (169)
T TIGR02954 90 --------------------------------------------------IPFDPN----------TSI----EKG---- 101 (169)
T ss_pred --------------------------------------------------Cccccc----------ccc----ccc----
Confidence 000000 000 000
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~ 497 (508)
++. .+. +....+..+| ..||+++|+||.++| ++|+|.+|||+.||+|.++|+..++||+++||+.+.
T Consensus 102 ~~~--~~~-~~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~l~ 168 (169)
T TIGR02954 102 ECE--THA-DSRLDLYKAI-DTLNDKYQTAIILRY---YHDLTIKEIAEVMNKPEGTVKTYLHRALKKLKKRLE 168 (169)
T ss_pred hhh--hch-HHHHHHHHHH-HhCCHHHhHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 011 011 1123688888 899999999999999 899999999999999999999999999999999874
No 71
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=6e-20 Score=173.39 Aligned_cols=158 Identities=19% Similarity=0.174 Sum_probs=124.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcC-CCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDN-MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~-~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~iri 342 (508)
.|++.|+..|.+.|+.++.++.+ +..+++|++||+|+++|+.++.|++.. +|.+|++..++|.+.+++++..+....
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 578999999999999999999999743 699999999999999998876421000
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCC
Q 010521 343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE 422 (508)
Q Consensus 343 p~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e 422 (508)
..+++. ..+...+
T Consensus 99 --------------------------------------------------~~~~~~-------------~~~~~~~---- 111 (181)
T PRK12536 99 --------------------------------------------------HDPLDD-------------ESELFAT---- 111 (181)
T ss_pred --------------------------------------------------cCCccc-------------hhhhcCC----
Confidence 000000 0000000
Q ss_pred CCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521 423 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 498 (508)
Q Consensus 423 ~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~ 498 (508)
..++ ..+....+.++| ..||++++.||.++| .+|+|.+|||+.||+|+++|+..+++|+++||+.+..
T Consensus 112 ~~~~----~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l~~ 179 (181)
T PRK12536 112 SDDE----AAEARRDLGKLL-EQLPDRQRLPIVHVK---LEGLSVAETAQLTGLSESAVKVGIHRGLKALAAKIRG 179 (181)
T ss_pred CCcc----hHHHHHHHHHHH-HHCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 0111 123445688999 899999999999999 8999999999999999999999999999999998864
No 72
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=99.85 E-value=4.1e-20 Score=175.54 Aligned_cols=177 Identities=18% Similarity=0.132 Sum_probs=137.8
Q ss_pred CCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHH
Q 010521 204 ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQR 283 (508)
Q Consensus 204 ~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAkr 283 (508)
|-.+.+++..|+.++++||. .|++.||..|.+.++.++.
T Consensus 4 ~~~~~~~~~~l~~~~~~gd~----------------------------------------~af~~l~~~~~~~l~~~~~- 42 (185)
T PRK09649 4 TASDDEAVTALALSAAKGNG----------------------------------------RALEAFIKATQQDVWRFVA- 42 (185)
T ss_pred cccccHHHHHHHHHHHccCH----------------------------------------HHHHHHHHHHHHHHHHHHH-
Confidence 44556778889999999997 9999999999999999995
Q ss_pred hcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHc
Q 010521 284 YDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK 363 (508)
Q Consensus 284 Y~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~~~ 363 (508)
+.++..+++|++||+|+.+|+.+++|++. ..|.+|++..++|.+.+++++..+.....
T Consensus 43 ~~~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~~~d~~Rk~~~~~~~~-------------------- 100 (185)
T PRK09649 43 YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVADHIRHVRSRPRTT-------------------- 100 (185)
T ss_pred HhCCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHHHHHHHHHhccccccc--------------------
Confidence 68888899999999999999999999864 36999999999999999988653210000
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHHHHH
Q 010521 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLII 443 (508)
Q Consensus 364 Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~L~ 443 (508)
.+. . .+.+.+ +.......+....+..+|
T Consensus 101 --------------------------------~~~---------~----~~~~~~------~~~~~~~~e~~~~l~~~l- 128 (185)
T PRK09649 101 --------------------------------RGA---------R----PEHLID------GDRHARGFEDLVEVTTMI- 128 (185)
T ss_pred --------------------------------ccc---------c----hhhccC------hhhhhhhHHHHHHHHHHH-
Confidence 000 0 000000 000011112234578889
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 498 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~ 498 (508)
..||+++|.||.|+| ++|+|++|||+.||+|.++|++.++||+++||+.+..
T Consensus 129 ~~Lp~~~r~v~~L~~---~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~~~~ 180 (185)
T PRK09649 129 ADLTTDQREALLLTQ---LLGLSYADAAAVCGCPVGTIRSRVARARDALLADAEP 180 (185)
T ss_pred HhCCHHHhHHhhhHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCc
Confidence 899999999999999 8999999999999999999999999999999986543
No 73
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=99.85 E-value=6.1e-20 Score=171.43 Aligned_cols=164 Identities=15% Similarity=0.084 Sum_probs=130.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccc
Q 010521 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 341 (508)
Q Consensus 262 ~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~ir 341 (508)
++.|++.|+..|.+.++.+|.+++++..++||++||+|+.+|+..++|++.. ..|.+|++..++|.+.+++++..+...
T Consensus 7 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~Rk~~~~~~ 85 (173)
T PRK09645 7 EAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSARARPV 85 (173)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHHHHHHHhhccccc
Confidence 3489999999999999999999999989999999999999999999997533 369999999999999998876532100
Q ss_pred ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccC
Q 010521 342 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRV 421 (508)
Q Consensus 342 ip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~ 421 (508)
...+ +.. + .++
T Consensus 86 ----------------------------------------------------~~~~----------~~~---~-~~~--- 96 (173)
T PRK09645 86 ----------------------------------------------------EGGD----------DVL---G-VPE--- 96 (173)
T ss_pred ----------------------------------------------------cccc----------ccc---c-CCC---
Confidence 0000 000 0 000
Q ss_pred CCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521 422 ENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 500 (508)
Q Consensus 422 e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~ 500 (508)
..+.+.+...+....|..+| +.||+++|+||.|+| ++|+|++|||+.||+|.++|+.+++||+++||+.|...+
T Consensus 97 -~~~~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~L~~---~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~ 170 (173)
T PRK09645 97 -QSAPDEVDRALDRLLVADAL-AQLSPEHRAVLVRSY---YRGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQERG 170 (173)
T ss_pred -CCCchHHHHHhHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhccc
Confidence 11222333444456788999 899999999999999 899999999999999999999999999999999987543
No 74
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=99.85 E-value=5e-20 Score=173.79 Aligned_cols=164 Identities=15% Similarity=0.165 Sum_probs=133.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccc
Q 010521 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 341 (508)
Q Consensus 262 ~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~ir 341 (508)
++.|+++|+..|.+.|+++|.++.++..+++|++||+|+.+|+++.+|++.. .|.+|++..+++.+.+++++..+...
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 3489999999999999999999999999999999999999999999998643 69999999999999998877532100
Q ss_pred ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccC
Q 010521 342 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRV 421 (508)
Q Consensus 342 ip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~ 421 (508)
.+ .+. .......+
T Consensus 92 ~~----------------------------------------------------~~~------------~~~~~~~~--- 104 (179)
T PRK09415 92 IV----------------------------------------------------TED------------IFTYMESQ--- 104 (179)
T ss_pred cc----------------------------------------------------ccc------------cccccccc---
Confidence 00 000 00000001
Q ss_pred CCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521 422 ENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 498 (508)
Q Consensus 422 e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~ 498 (508)
.++|++.+...+....|..+| ..||+++|+||.|+| ++|+|++|||+.||+|.++|++++.||+++||..+..
T Consensus 105 ~~~~e~~~~~~e~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l~~ 177 (179)
T PRK09415 105 KESVEEEVIQNAEDERLASAV-MSLPIKYREVIYLFY---YEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEE 177 (179)
T ss_pred ccCcHHHHHHHHHHHHHHHHH-HhCCHHHhhHhHhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 135666666777788899999 899999999999999 7999999999999999999999999999999998754
No 75
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=99.85 E-value=1.9e-20 Score=170.69 Aligned_cols=161 Identities=20% Similarity=0.212 Sum_probs=129.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.|+++|+..|.+.|+.+++++.++..+++|++||+++++|+.+.+|++.. +|.+|++.++|+.+.+++++..+...
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 37899999999999999999999989999999999999999999998643 79999999999999988876642000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
.... +.. . .. .....+
T Consensus 77 ------------~~~~------------------------------------~~~-------~-~~--------~~~~~~ 92 (161)
T TIGR02985 77 ------------YQEE------------------------------------ILE-------I-EV--------DELSEN 92 (161)
T ss_pred ------------HHHH------------------------------------HHh-------h-cc--------cccCCC
Confidence 0000 000 0 00 000012
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
+|++.+...+....|..++ ..||++++.||.++| .+|+|..|||+.||+|+++|++++++|+++||+.|
T Consensus 93 ~~~~~~~~~e~~~~l~~~l-~~L~~~~r~il~l~~---~~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~l 161 (161)
T TIGR02985 93 DPEEELEAKELQLIIYKAI-EKLPEQCRKIFILSR---FEGKSYKEIAEELGISVKTVEYHISKALKELRKEL 161 (161)
T ss_pred CcHHHHHHHHHHHHHHHHH-HHCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 4555666677778899999 899999999999988 79999999999999999999999999999999754
No 76
>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=99.85 E-value=7.5e-20 Score=172.13 Aligned_cols=160 Identities=16% Similarity=0.108 Sum_probs=119.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCC-----CHHHHHHHHHHHHHH-hhhccCCCCCCcchhHHHHHHHHHHHHHHHHhc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGA-----DMADLVQGGLIGLLR-GIEKFDSSKGFKISTYVYWWIRQGVSRALVENS 337 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~-----d~EDLiQEG~IgLir-AiekFDperG~rFsTYA~~wIR~~I~~~Ird~~ 337 (508)
.|++.|+..|.+.++.+|.+|.++.. +++|++||+|+.+|+ ...+|++. ..|.+|++.+++|.+.+++++..
T Consensus 17 ~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~~ 94 (183)
T TIGR02999 17 AARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAKAMRRILVDHARRRR 94 (183)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999877 899999999999998 78889754 26999999999999988887653
Q ss_pred ccccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccc
Q 010521 338 RTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIA 417 (508)
Q Consensus 338 R~irip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~ 417 (508)
+..+.. ...+ ..+.+..+
T Consensus 95 ~~~~~~--------------------------------------------------~~~~------------~~~~~~~~ 112 (183)
T TIGR02999 95 AQKRGG--------------------------------------------------GAVR------------VPLDEVLP 112 (183)
T ss_pred HHhccC--------------------------------------------------Cccc------------cccccccC
Confidence 200000 0000 00000000
Q ss_pred cccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 418 DNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 418 d~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
...++. .+.....+.+...| ..||+++|.||.|+| ++|+|++|||+.||+|.+||+.+++||+++||+.|
T Consensus 113 ----~~~~~~-~~~~~~l~~~~~~l-~~Lp~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 182 (183)
T TIGR02999 113 ----DAEADL-DEELLDLDDALDKL-AQVDPRQAEVVELRF---FAGLTVEEIAELLGVSVRTVERDWRFARAWLADEL 182 (183)
T ss_pred ----CCCccH-HHHHHHHHHHHHHh-hcCCHHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 001111 11112223344456 679999999999999 89999999999999999999999999999999876
No 77
>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=4.8e-20 Score=164.57 Aligned_cols=157 Identities=27% Similarity=0.385 Sum_probs=130.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccc
Q 010521 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN 344 (508)
Q Consensus 265 A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~ 344 (508)
|++.|+..|.++|+++++++..++.+.+|++||+++++|++++.|++. .+|.+|++.++++.+.+++++..+ .+.
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 789999999999999999999999999999999999999999999997 589999999999999999987753 110
Q ss_pred cHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCC
Q 010521 345 HLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENN 424 (508)
Q Consensus 345 ~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~ 424 (508)
.. ... . .+.+ ..++
T Consensus 77 ~~--------------------------------------------------~~~----------~----~~~~--~~~~ 90 (158)
T TIGR02937 77 EL--------------------------------------------------DLL----------E----ELLD--SDPS 90 (158)
T ss_pred ch--------------------------------------------------hhh----------h----hccc--ccCC
Confidence 00 000 0 0000 0224
Q ss_pred ccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 425 PWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 425 Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
|++..........|..+| ..||+.++.||.++| ..|+|..|||+.+|+|+.+|+++..+++++||+.+
T Consensus 91 ~~~~~~~~~~~~~l~~~l-~~L~~~~~~ii~~~~---~~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~l 158 (158)
T TIGR02937 91 PEEELEQEEEREALREAL-EKLPEREREVLVLRY---LEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158 (158)
T ss_pred HHHHHHHHHHHHHHHHHH-HhCCHHHHHHHhhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 555666677778899999 899999999999998 68999999999999999999999999999999753
No 78
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=1.4e-19 Score=171.29 Aligned_cols=158 Identities=18% Similarity=0.198 Sum_probs=124.8
Q ss_pred HHHHHHHHHHHHHHHHHHH----HhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccc
Q 010521 264 LAREKLVMSNVRLVMSIAQ----RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRT 339 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAk----rY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~ 339 (508)
.|++.|+..|.+.|+.+|+ ++.++..+++|++||+++.+|+.++.|++.. .|.+|++..+++.+.+++++..+.
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 4557889999999999999999999999753 699999999999999888765320
Q ss_pred ccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccc
Q 010521 340 LRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADN 419 (508)
Q Consensus 340 irip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~ 419 (508)
. . ..+.+. ....
T Consensus 99 ~-~--------------------------------------------------~~~~~~-------------~~~~---- 110 (184)
T PRK12539 99 L-A--------------------------------------------------DVPIDD-------------ADEL---- 110 (184)
T ss_pred c-c--------------------------------------------------ccChhh-------------hccc----
Confidence 0 0 000000 0000
Q ss_pred cCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521 420 RVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 499 (508)
Q Consensus 420 ~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~ 499 (508)
.+.+.....+....+..+| ..||+++|.||.|+| ++|+|++|||+.||+|.++|++++++|+++||+.+...
T Consensus 111 ----~~~~~~~~~e~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~ 182 (184)
T PRK12539 111 ----VAHDDHAAVESTLDLGRLL-ARLPEKMRLAIQAVK---LEGLSVAEAATRSGMSESAVKVSVHRGLKALAALIGRE 182 (184)
T ss_pred ----cCCcHHhhHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHhhc
Confidence 0001112234456788999 899999999999999 79999999999999999999999999999999988653
No 79
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=5.1e-20 Score=175.14 Aligned_cols=182 Identities=14% Similarity=0.110 Sum_probs=136.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
-+++.|+..|.+.|+.+|.+++++..++||++||+|+.+|+.+++|++.. +|.+|++..++|.+.+++++..+.....
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 37899999999999999999999999999999999999999999998543 6999999999999999988765421111
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
..... .....++ ++.. .. .+. .....++. ..
T Consensus 80 ~~~~~-----------------~~~~~~~-----------------------~~~~-----~~-~~~-~~~~~~~~--~~ 110 (191)
T PRK12520 80 LDDAD-----------------EQSDDDL-----------------------FDAL-----FA-ADG-HYREPPSD--WG 110 (191)
T ss_pred ccccc-----------------cchhhhh-----------------------hhhh-----cc-ccc-ccccCccc--cC
Confidence 00000 0000000 0000 00 000 00001111 13
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 500 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~ 500 (508)
+|++.+...+....|..+| ..||+++|.||.|+| ++|+|++|||+.||+|.+||++.++||+++||+++...+
T Consensus 111 ~~~~~~~~~~~~~~l~~~l-~~Lp~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 183 (191)
T PRK12520 111 DPDAALSRREFFEVLQACV-DRLPPRTGRVFMMRE---WLELETEEICQELQITATNAWVLLYRARMRLRECLDLHW 183 (191)
T ss_pred CHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5666666777778899999 899999999999999 899999999999999999999999999999999998776
No 80
>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=99.84 E-value=4e-20 Score=169.71 Aligned_cols=159 Identities=15% Similarity=0.158 Sum_probs=126.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
+|++.++..|.+.|+.+|+++.++..++||++||+++.+|+++++|++.. .|.+|++..+++.+.++++++.+... +
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 37899999999999999999999999999999999999999999999754 69999999999999999987653110 0
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
.. ++ ..+.+.+. .
T Consensus 78 ~~------------------------~~----------------------------------------~~~~~~~~---~ 90 (159)
T TIGR02989 78 FD------------------------DE----------------------------------------LLEALAAE---A 90 (159)
T ss_pred cC------------------------HH----------------------------------------HHHHHHhh---c
Confidence 00 00 00000000 0
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
+|.+..........+..+| +.||++++.||.++| .+|+|.+|||+.||+|+++|+..++||+++||..+
T Consensus 91 ~~~~~~~~~~~~~~l~~~i-~~L~~~~r~v~~l~~---~~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~~~ 159 (159)
T TIGR02989 91 EATEADRSEDELQALEGCL-EKLPERQRELLQLRY---QRGVSLTALAEQLGRTVNAVYKALSRLRVRLRDCV 159 (159)
T ss_pred ccchHhhHHHHHHHHHHHH-HHCCHHHHHHHHHHH---hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcC
Confidence 1222223344456788999 899999999999998 79999999999999999999999999999999753
No 81
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=8.8e-20 Score=170.72 Aligned_cols=166 Identities=14% Similarity=0.151 Sum_probs=131.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
..+++|+..|.++|+.+|++|.++..+++|++||+++.+|+++++|++.. +|.+|++..++|.+.++++++.+....+
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 7999999999999999988765311000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccc-cccccCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSY-IADNRVE 422 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~-i~d~~~e 422 (508)
... .+. ....+. ..+. .
T Consensus 81 ~~~-------------------------------------------------~~~-----------~~~~~~~~~~~--~ 98 (173)
T PRK12522 81 LDL-------------------------------------------------FHK-----------EDGGEIEFADD--V 98 (173)
T ss_pred ccc-------------------------------------------------cch-----------hhhhhhccccC--C
Confidence 000 000 000000 0010 1
Q ss_pred CCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521 423 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 498 (508)
Q Consensus 423 ~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~ 498 (508)
..|+. ....+..+.+..+| ..||++++.||.|+| .+|+|++|||+.||+|.++|+..++||+++||+.+..
T Consensus 99 ~~~~~-~~~~~~~~~l~~~l-~~L~~~~r~i~~l~~---~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~ 169 (173)
T PRK12522 99 NISEE-FIQKVEAEMIREVI-QLLNEKYKTVLVLYY---YEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEG 169 (173)
T ss_pred CChHH-HHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 12333 44556678899999 899999999999999 8999999999999999999999999999999998864
No 82
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=1.4e-19 Score=170.77 Aligned_cols=157 Identities=17% Similarity=0.201 Sum_probs=124.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcC----CCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDN----MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRT 339 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~----~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~ 339 (508)
.|++.|+..|.+.|+.+|.++++ +..+++|++||+++.+|...++|++. ..|.+|++..+|+.+.+++++..+.
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 34689999999999999999999864 3699999999999999888765321
Q ss_pred ccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccc
Q 010521 340 LRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADN 419 (508)
Q Consensus 340 irip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~ 419 (508)
... .++. ..+.+++.
T Consensus 100 ~~~----------------------------------------------------~~~~-------------~~~~~~~~ 114 (184)
T PRK12512 100 VFV----------------------------------------------------DIDD-------------FAETLPAE 114 (184)
T ss_pred ccC----------------------------------------------------Cchh-------------cccccccc
Confidence 000 0000 00001110
Q ss_pred cCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521 420 RVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 499 (508)
Q Consensus 420 ~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~ 499 (508)
.+. .....+.+.++| ..||+++++||.++| .+|+|++|||+.||+|..+|+..+++|+++||..+.+.
T Consensus 115 ----~~~----~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~~~ 182 (184)
T PRK12512 115 ----PAT----ETLPAGDVGRHL-ETLPPRQRDVVQSIS---VEGASIKETAAKLSMSEGAVRVALHRGLAALAAKFRSE 182 (184)
T ss_pred ----chh----hHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Confidence 000 122345678888 899999999999999 79999999999999999999999999999999988753
No 83
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=7.6e-20 Score=170.86 Aligned_cols=162 Identities=15% Similarity=0.134 Sum_probs=125.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.|++.|+..|.+.|+.+++++.+ ..+++|++||+|+.+|+.++.|++. ..|.+|++..+++.+.+++++..+...
T Consensus 11 ~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~~~~~~-- 85 (175)
T PRK12518 11 QSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARRQFAQRPS-- 85 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHHHhhcccc--
Confidence 99999999999999999999875 4789999999999999999999974 369999999999988888775432000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
. .+. ...... ... .
T Consensus 86 -~--------------------------------------------------~~~-------~~~~~~----~~~----~ 99 (175)
T PRK12518 86 -R--------------------------------------------------IQD-------DSLNDQ----PSR----P 99 (175)
T ss_pred -c--------------------------------------------------hhc-------cccccc----ccC----C
Confidence 0 000 000000 000 0
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 500 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~ 500 (508)
.+.......+....+.++| +.||+++|.||.|+| ++|+|++|||+.||+|.++|++.++||+++||+.+.+.+
T Consensus 100 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~~---~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~~~~ 172 (175)
T PRK12518 100 SDTPDLMQLHYQDLVQQGL-QTLSLEHRAVLVLHD---LEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQQG 172 (175)
T ss_pred CCcHHHHHHHHHHHHHHHH-HhCCHHHeeeeeehH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 1111223334445688889 899999999999999 899999999999999999999999999999999997654
No 84
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=99.83 E-value=8.5e-20 Score=168.36 Aligned_cols=156 Identities=12% Similarity=0.081 Sum_probs=125.5
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHH
Q 010521 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 350 (508)
Q Consensus 271 e~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l 350 (508)
+.|.+.|+.+|.+++++..+++|++||+|+.+|+++++|++. .|.+|++..++|.+.+++++..+....
T Consensus 2 ~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n~~~d~~Rk~~~~~~~-------- 70 (160)
T PRK09642 2 QTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATNHAIDYKRKKARENEE-------- 70 (160)
T ss_pred chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHHHHHHHHHHhcccccc--------
Confidence 579999999999999999999999999999999999999863 499999999999999998776421000
Q ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHH
Q 010521 351 GLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVD 430 (508)
Q Consensus 351 ~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve 430 (508)
..+.. + ..+.+.. ..+|++.+.
T Consensus 71 -------------------------------------------~~~~~---------~---~~~~~~~---~~~~~~~~~ 92 (160)
T PRK09642 71 -------------------------------------------LSLCK---------E---TEENIKS---SHNIEDLLL 92 (160)
T ss_pred -------------------------------------------cccch---------h---hhhhccC---CCChHHHHH
Confidence 00000 0 0000000 124555666
Q ss_pred HHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521 431 DWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 499 (508)
Q Consensus 431 ~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~ 499 (508)
..+....|..+| +.||+++|.||.|+| .+|+|++|||+.||+|.++|+++++||+++||+.+...
T Consensus 93 ~~e~~~~l~~~l-~~Lp~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 157 (160)
T PRK09642 93 TKEQKLLIAQKL-RELPENYRDVVLAHY---LEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKEE 157 (160)
T ss_pred HHHHHHHHHHHH-HhCCHHHHHHHHHHH---HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhh
Confidence 667778899999 899999999999999 89999999999999999999999999999999999654
No 85
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=99.83 E-value=4.2e-19 Score=167.89 Aligned_cols=169 Identities=22% Similarity=0.208 Sum_probs=135.4
Q ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhc
Q 010521 258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS 337 (508)
Q Consensus 258 ~l~e~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~ 337 (508)
.+..+..++..++..|.+.++.+|.++.++..++|||+||+|+.+|+++..| .. +..|.||++.+++|.+++.+++..
T Consensus 9 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~~R~~~ 86 (182)
T COG1595 9 ALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDRLRKRK 86 (182)
T ss_pred HHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHHHHHHhc
Confidence 3445568999999999999999999999988899999999999999999999 33 347999999999999999998775
Q ss_pred ccccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccc
Q 010521 338 RTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIA 417 (508)
Q Consensus 338 R~irip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~ 417 (508)
+.... .+. ....+...
T Consensus 87 r~~~~-----------------------------------------------------~~~-----------~~~~~~~~ 102 (182)
T COG1595 87 RRRAR-----------------------------------------------------VEE-----------ADLLPEEA 102 (182)
T ss_pred ccccc-----------------------------------------------------ccc-----------cccccccc
Confidence 42111 000 00000000
Q ss_pred cccCCCCcc-chHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 418 DNRVENNPW-HGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 418 d~~~e~~Pe-~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
+.. .+. +.+...+....|.++| ..||+++|.||.|+| ++|+|++|||+.||||.+||+..+++|+++||..+
T Consensus 103 ~~~---~~~~~~~~~~~~~~~l~~al-~~Lp~~~R~~~~l~~---~~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l 175 (182)
T COG1595 103 DPA---PDLAELLLAEEELERLRRAL-ARLPPRQREAFLLRY---LEGLSYEEIAEILGISVGTVKSRLHRARKKLREQL 175 (182)
T ss_pred Ccc---cccchHHHHHHHHHHHHHHH-HhCCHHHhHHhhhHh---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 000 111 2456677788999999 899999999999999 89999999999999999999999999999999998
Q ss_pred HHh
Q 010521 497 RKK 499 (508)
Q Consensus 497 ~~~ 499 (508)
...
T Consensus 176 ~~~ 178 (182)
T COG1595 176 EEA 178 (182)
T ss_pred hhc
Confidence 754
No 86
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=99.83 E-value=3.6e-19 Score=173.96 Aligned_cols=169 Identities=14% Similarity=0.097 Sum_probs=134.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q 010521 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (508)
Q Consensus 263 ~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~iri 342 (508)
..++..|+..|.+.++.++.++.++..++||++||+|+.+|+.+++|++. .|.+|++..++|.+.++++++.+....
T Consensus 17 ~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~~~~~~~ 93 (216)
T PRK12533 17 GERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRRANAHEV 93 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhhcccccc
Confidence 48999999999999999999999999999999999999999999999852 499999999999999988776421000
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCC
Q 010521 343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE 422 (508)
Q Consensus 343 p~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e 422 (508)
...+. ..+...... +.+. .
T Consensus 94 ---------------------------------------------------~~~~~-------~~~~~~~~~-~~~~--~ 112 (216)
T PRK12533 94 ---------------------------------------------------AAPDT-------LDDADSLDD-WQPA--G 112 (216)
T ss_pred ---------------------------------------------------ccccc-------ccccccccc-cccC--C
Confidence 00000 000000000 0111 2
Q ss_pred CCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521 423 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 499 (508)
Q Consensus 423 ~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~ 499 (508)
.+|++.+...+....|..+| ..||+++|.||.|+| ++++|++|||+.||||.++|+++++||+++||+.+...
T Consensus 113 ~~~e~~~~~~e~~~~l~~al-~~Lp~~~R~v~~L~y---~eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~ 185 (216)
T PRK12533 113 EDPLALLLRAEDVRLVNAAL-AKLPVEYREVLVLRE---LEDMSYREIAAIADVPVGTVMSRLARARRRLAALLGGA 185 (216)
T ss_pred CCHHHHHHHHHHHHHHHHHH-HcCCHHHHhHhhhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHccc
Confidence 35667777778888899999 899999999999999 89999999999999999999999999999999998644
No 87
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=99.83 E-value=4.8e-19 Score=170.18 Aligned_cols=164 Identities=16% Similarity=0.104 Sum_probs=127.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.|++.|+..|.+.++.++. +.++..++||++||+|+.+|+..++|++.. .|.+|++..+++.+.+++++..+..+..
T Consensus 25 ~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Iarn~~id~~Rk~~~~~~~~ 101 (196)
T PRK12535 25 AALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAARS--SARTWLLSLARRVWVDNIRHDMARPRKS 101 (196)
T ss_pred HHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhccCCCcc
Confidence 9999999999999999975 678888999999999999999999998632 6999999999999999988764210000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
.+. .... .+. ..
T Consensus 102 ----------------------------------------------------~~~----------~~~~----~~~--~~ 113 (196)
T PRK12535 102 ----------------------------------------------------ATE----------YEDA----AAT--TA 113 (196)
T ss_pred ----------------------------------------------------ccc----------cccc----ccc--cC
Confidence 000 0000 000 01
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHH
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEA 503 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~ 503 (508)
.|+... .......+..+| ..||+++|+||.|+| ++|+|++|||+.||+|.++|++.++||+++||+.|....+.+
T Consensus 114 ~~~~~~-~~~~~~~l~~~l-~~Lp~~~r~v~~l~~---~~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~~ 188 (196)
T PRK12535 114 SNETTG-SWSEWIDVRTLI-DALPPERREALILTQ---VLGYTYEEAAKIADVRVGTIRSRVARARADLIAATATGQASA 188 (196)
T ss_pred CcchhH-HHHHHHHHHHHH-HcCCHHHHHHhhhHH---HhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccccchh
Confidence 122111 122235788899 899999999999999 899999999999999999999999999999999997665544
No 88
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=99.82 E-value=3.9e-19 Score=169.53 Aligned_cols=160 Identities=13% Similarity=0.160 Sum_probs=127.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q 010521 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (508)
Q Consensus 263 ~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~iri 342 (508)
..++..|+..|.+.++.+|.+++++..++||++||+|+.+|+..++|+... .|.+|++..++|.+.++++++.+...
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 69999999999999988876642100
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCC
Q 010521 343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE 422 (508)
Q Consensus 343 p~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e 422 (508)
..+. .+.+...
T Consensus 86 ----------------------------------------------------~~~~------------~~~~~~~----- 96 (187)
T PRK12516 86 ----------------------------------------------------DTDG------------MFTEQLA----- 96 (187)
T ss_pred ----------------------------------------------------cccc------------ccccccC-----
Confidence 0000 0000000
Q ss_pred CCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521 423 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 500 (508)
Q Consensus 423 ~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~ 500 (508)
..|+. ........|..+| ..||+++|+||.|+| ++|+|++|||+.||+|.++|++++++|+++||+.+...+
T Consensus 97 ~~~~~--~~~~~~~~l~~~L-~~Lp~~~r~i~~L~~---~~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~~~ 168 (187)
T PRK12516 97 VHPSQ--YGTLDLQDFRAAL-DQLPDDQREAIILVG---ASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQIEG 168 (187)
T ss_pred CCcch--hhHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence 01111 1122235688999 899999999999999 899999999999999999999999999999999998654
No 89
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=99.82 E-value=4.9e-19 Score=164.64 Aligned_cols=161 Identities=16% Similarity=0.193 Sum_probs=127.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccc
Q 010521 261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (508)
Q Consensus 261 e~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~i 340 (508)
.++..|.+++..|.+.|+.+|+++.++..++||++||+|+.+|+...+|++.. .|.+|++..++|.+.+++++..+..
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 35689999999999999999999999999999999999999999999998543 6999999999999999887654210
Q ss_pred cccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCcccccccccc
Q 010521 341 RLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNR 420 (508)
Q Consensus 341 rip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~ 420 (508)
. . .+. . .. ...
T Consensus 81 ~---~--------------------------------------------------~~~-----------~-~~---~~~- 91 (164)
T PRK12547 81 Q---D--------------------------------------------------SDG-----------V-FT---ARV- 91 (164)
T ss_pred c---c--------------------------------------------------ccc-----------c-cc---ccC-
Confidence 0 0 000 0 00 000
Q ss_pred CCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521 421 VENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 499 (508)
Q Consensus 421 ~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~ 499 (508)
..+++. ........+..+| ..||+++|+||.|+| .+|+|++|||+.||+|.++|++.++||+++||..+...
T Consensus 92 -~~~~~~--~~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 163 (164)
T PRK12547 92 -AVHPAQ--YGSLDLQDFKKAL-NLLSADQREAIILIG---ASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLKVD 163 (164)
T ss_pred -CCCchh--hhHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence 001111 1122345688899 899999999999999 89999999999999999999999999999999988643
No 90
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=99.82 E-value=2.6e-19 Score=168.98 Aligned_cols=164 Identities=11% Similarity=-0.028 Sum_probs=127.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhcC--CCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcc
Q 010521 261 ECSLAREKLVMSNVRLVMSIAQRYDN--MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR 338 (508)
Q Consensus 261 e~~~A~e~LIe~yl~LV~sIAkrY~~--~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R 338 (508)
++..|++.|+..|.+.|+.++.++++ +..++||++||+|+.+|+..++|++.....|.||++..++|.+.+++++..+
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 44599999999999999998766665 4678999999999999999999975444579999999999988888765421
Q ss_pred cccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCcccccccc
Q 010521 339 TLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIAD 418 (508)
Q Consensus 339 ~irip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d 418 (508)
. . .. .+. ..+....
T Consensus 90 ~----------------~-~~------------------------------------~~~-------------~~~~~~~ 103 (178)
T PRK12529 90 E----------------L-AW------------------------------------LEA-------------LATLPEP 103 (178)
T ss_pred H----------------h-hh------------------------------------hhH-------------hhhccCc
Confidence 0 0 00 000 0000000
Q ss_pred ccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 419 NRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 419 ~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
. .++|++.+...+....|..+| ..||+++|.||.|+| .+|+|++|||+.||+|.+||+.++++|+.+++..+
T Consensus 104 ~--~~~~e~~~~~~~~~~~l~~~l-~~Lp~~~R~v~~L~~---~~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~~ 175 (178)
T PRK12529 104 L--HPSPEQQSVILETLHEIDALL-DTLRPRVKQAFLMAT---LDGMKQKDIAQALDIALPTVKKYIHQAYVTCLSLM 175 (178)
T ss_pred C--CCCHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence 0 124555566666677899999 899999999999999 89999999999999999999999999999998764
No 91
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=99.82 E-value=4.7e-19 Score=164.59 Aligned_cols=158 Identities=15% Similarity=0.114 Sum_probs=130.5
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccccc
Q 010521 266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH 345 (508)
Q Consensus 266 ~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~ 345 (508)
++.|+..|.+.|+.+|+++.++..+++|++||+|+.+|+.++.|++. .|.+|++..+++.+.+++++..+.....
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~~-- 77 (165)
T PRK09644 3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFVG-- 77 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhccccc--
Confidence 67899999999999999999999999999999999999999999863 5999999999999999988764310000
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCc
Q 010521 346 LHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNP 425 (508)
Q Consensus 346 ~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~P 425 (508)
.. .. +.+. ..+|
T Consensus 78 -----------------------~~----------------------------------------~~-~~~~----~~~~ 89 (165)
T PRK09644 78 -----------------------TD----------------------------------------EI-EAIQ----AEST 89 (165)
T ss_pred -----------------------hh----------------------------------------HH-hhhc----ccCh
Confidence 00 00 0000 1245
Q ss_pred cchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521 426 WHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 500 (508)
Q Consensus 426 e~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~ 500 (508)
++.+...+....+..+| ..||+++|+||.|+| .+|+|.+|||+.||+|.++|+++++||+++||+.+....
T Consensus 90 ~~~~~~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~~ 160 (165)
T PRK09644 90 EEYVVAKNSYEKLIQII-HTLPVIEAQAILLCD---VHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEEK 160 (165)
T ss_pred HHHHHHHHHHHHHHHHH-HhCCHHHHHHHHhHH---HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Confidence 55566667778899999 899999999999998 799999999999999999999999999999999987553
No 92
>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=99.82 E-value=4.4e-19 Score=163.74 Aligned_cols=156 Identities=18% Similarity=0.181 Sum_probs=126.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccc
Q 010521 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 341 (508)
Q Consensus 262 ~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~ir 341 (508)
+..+++.|+..|.+.|+.+|.+++++..+++|++||+|+.+|+.+++|+. ...|.+|++..+++.+.+++++..+. .
T Consensus 4 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~~~d~~rk~~~~-~ 80 (162)
T TIGR02983 4 TEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNLARSRWRRRRLL-E 80 (162)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHHHHHHHHhhccc-c
Confidence 44999999999999999999999999999999999999999999999964 33799999999999888887755310 0
Q ss_pred ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccC
Q 010521 342 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRV 421 (508)
Q Consensus 342 ip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~ 421 (508)
.. +.. +++.
T Consensus 81 ----------------------------------------------------~~-~~~----------------~~~~-- 89 (162)
T TIGR02983 81 ----------------------------------------------------LP-TRE----------------LPDA-- 89 (162)
T ss_pred ----------------------------------------------------cc-ccc----------------cCcc--
Confidence 00 000 0000
Q ss_pred CCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521 422 ENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497 (508)
Q Consensus 422 e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~ 497 (508)
.+.......+..+.|..+| ..||+++|.||.|+| .+|+|.+|||+.||+|.++|++.+.||+++||+.+.
T Consensus 90 --~~~~~~~~~~~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 159 (162)
T TIGR02983 90 --AAPDPAPDVALRAALARAL-RRLPARQRAVVVLRY---YEDLSEAQVAEALGISVGTVKSRLSRALARLRELLE 159 (162)
T ss_pred --cCCccchhHHHHHHHHHHH-HhCCHHHHHHhhhHH---HhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 0111122344556788899 899999999999999 899999999999999999999999999999999875
No 93
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=99.82 E-value=2.8e-19 Score=170.36 Aligned_cols=172 Identities=15% Similarity=0.175 Sum_probs=130.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q 010521 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (508)
Q Consensus 263 ~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~iri 342 (508)
..+|+.|+..|.+.|+.+|.+++++..+++|++||+|+.+|+.+.+|++. .+|.+|++..++|.+.++++++.+....
T Consensus 10 ~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~~~~~~~ 87 (193)
T TIGR02947 10 AQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKAQRRPQQ 87 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHhcCCccc
Confidence 48999999999999999999999999999999999999999999999864 3699999999999999998876431100
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCC
Q 010521 343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE 422 (508)
Q Consensus 343 p~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e 422 (508)
.. .+++. . ..+.. .... .... .
T Consensus 88 ~~------------------------~~~~~-----------~--------~~~~~--------~~~~------~~~~-~ 109 (193)
T TIGR02947 88 SD------------------------DDDIE-----------D--------WQLAK--------AASH------TSNG-L 109 (193)
T ss_pred cc------------------------chhhh-----------h--------hhhcc--------cccc------cccc-c
Confidence 00 00000 0 00000 0000 0000 0
Q ss_pred CCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521 423 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 498 (508)
Q Consensus 423 ~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~ 498 (508)
..|+......+....|..+| ..||+++|.||.|+| .+|+|++|||+.||+|.++|+.+++||+++||+.+..
T Consensus 110 ~~~e~~~~~~~~~~~l~~~l-~~Lp~~~r~i~~L~~---~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 181 (193)
T TIGR02947 110 RSAELEALDGLPDQDIKDAL-QGLPEEFRQAVYLAD---VEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVD 181 (193)
T ss_pred cchhHHHHhhhhHHHHHHHH-HhCCHHHhhheeehh---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 12333333344556788999 899999999999999 8999999999999999999999999999999999864
No 94
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=99.82 E-value=7.9e-19 Score=169.75 Aligned_cols=168 Identities=20% Similarity=0.248 Sum_probs=136.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccc
Q 010521 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 341 (508)
Q Consensus 262 ~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~ir 341 (508)
+..+++.|+..|.+.++.++.++.++..+++|++||+|+.+|+...+|++ + .|.+|++..+|+.+.+++++..+ .+
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 34899999999999999999999999999999999999999999999985 3 69999999999999999886532 00
Q ss_pred ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccC
Q 010521 342 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRV 421 (508)
Q Consensus 342 ip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~ 421 (508)
. ..++. + . +.....
T Consensus 102 ~---------------------------------------------------~~~~~---------~---~-~~~~~~-- 115 (203)
T PRK09647 102 M---------------------------------------------------EALPE---------D---Y-DRVPGD-- 115 (203)
T ss_pred c---------------------------------------------------ccccc---------c---c-cccCCC--
Confidence 0 00000 0 0 000111
Q ss_pred CCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010521 422 ENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM 501 (508)
Q Consensus 422 e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l 501 (508)
.++|+..+...+....|..+| ..||++++.||.|+| ++|++++|||+.||+|.++|++.+.||+++||+.+...+-
T Consensus 116 ~~~~~~~~~~~~~~~~l~~~L-~~L~~~~r~v~~L~~---~~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~~~~ 191 (203)
T PRK09647 116 EPNPEQIYHDARLDPDLQAAL-DSLPPEFRAAVVLCD---IEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAAHAP 191 (203)
T ss_pred CCCHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhch
Confidence 234555566677778899999 899999999999999 8999999999999999999999999999999999987655
Q ss_pred HH
Q 010521 502 EA 503 (508)
Q Consensus 502 ~~ 503 (508)
.+
T Consensus 192 ~~ 193 (203)
T PRK09647 192 HA 193 (203)
T ss_pred hc
Confidence 43
No 95
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=99.81 E-value=3.5e-19 Score=166.65 Aligned_cols=160 Identities=15% Similarity=0.111 Sum_probs=126.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.|+..|+..|.+.|+.+|.++.++..+++|++||+|+.+|+. ..|... ..|.+|++..++|.+.+++++..+.
T Consensus 10 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~~~---- 82 (172)
T PRK12523 10 ELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAALE---- 82 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHHHH----
Confidence 899999999999999999999999999999999999999986 446543 3699999999999999998876320
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
. .... . +... . .+. ..
T Consensus 83 -----------~--~~~~-----------------------~----------~~~~--------~--------~~~--~~ 98 (172)
T PRK12523 83 -----------Q--AYLA-----------------------E----------LALV--------P--------EAE--QP 98 (172)
T ss_pred -----------H--HHHH-----------------------H----------Hhhc--------c--------ccc--CC
Confidence 0 0000 0 0000 0 000 11
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 498 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~ 498 (508)
+|+......+....+..+| ..||+++|.||.|+| .+|+|++|||+.||+|.++|++++++|+++||..|..
T Consensus 99 ~~~~~~~~~~~~~~l~~~l-~~Lp~~~r~v~~L~~---~~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l~~ 169 (172)
T PRK12523 99 SPEEQHLILEDLKAIDRLL-GKLSSKARAAFLYNR---LDGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIALYG 169 (172)
T ss_pred ChHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 3444444445556799999 899999999999999 8999999999999999999999999999999998864
No 96
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=99.81 E-value=1.2e-18 Score=161.35 Aligned_cols=161 Identities=16% Similarity=0.129 Sum_probs=129.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q 010521 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (508)
Q Consensus 263 ~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~iri 342 (508)
+.|++.|+..|.+.++.+|.++.++..+++|++||+|+.+|++ .|+. +..|.+|++..+++.+.+++++..+....
T Consensus 2 ~~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~~~~~ 77 (166)
T PRK09639 2 DETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKRRRAR 77 (166)
T ss_pred chHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhcccccc
Confidence 3789999999999999999999999999999999999999999 6764 34799999999999999988776421100
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCC
Q 010521 343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE 422 (508)
Q Consensus 343 p~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e 422 (508)
.. +. ....+ + +. .
T Consensus 78 ~~----------------------------------------------------~~-----------~~~~~-~-~~--~ 90 (166)
T PRK09639 78 IL----------------------------------------------------GE-----------FQWQE-V-DN--E 90 (166)
T ss_pred cc----------------------------------------------------ch-----------hhhhh-c-cC--C
Confidence 00 00 00000 0 11 2
Q ss_pred CCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521 423 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 499 (508)
Q Consensus 423 ~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~ 499 (508)
.+|++.....+....+..+| ..||+++|.||.++| +|+|++|||+.||+|.++|++.+.+|+++||..+...
T Consensus 91 ~~~e~~~~~~~~~~~l~~~l-~~L~~~~r~il~l~~----~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~~~ 162 (166)
T PRK09639 91 PSPEEIWIRKEEITKVQEVL-AKMTERDRTVLLLRF----SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQM 162 (166)
T ss_pred CChHHHHHHHHHHHHHHHHH-HcCCHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 35666666667777899999 899999999999998 7899999999999999999999999999999998754
No 97
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=99.80 E-value=2.3e-18 Score=178.01 Aligned_cols=174 Identities=19% Similarity=0.154 Sum_probs=128.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.|+++|+..|.+.|+.+|.+++++..++||++||+|+.+|+.+++|++. ..|.+|++..++|.+.+++++..+... +
T Consensus 19 ~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~-~ 95 (339)
T PRK08241 19 DAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATNVCLDALEGRARRPL-P 95 (339)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHHHHHHHHHhhccccC-c
Confidence 9999999999999999999999999999999999999999999999853 369999999999999999887643100 0
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCC---CCCCccccccccc-
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNG---LPGETHHSYIADN- 419 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~---~~~~~l~d~i~d~- 419 (508)
..++.+.....++ .......+.+.+.
T Consensus 96 --------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 125 (339)
T PRK08241 96 --------------------------------------------------TDLGAPAADPVDELVERPEVPWLEPYPDAL 125 (339)
T ss_pred --------------------------------------------------cccCCCcCcccccccccccccccCCCCccc
Confidence 0000000000000 0000000111110
Q ss_pred --cCCCCccchHHHHH-HHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 420 --RVENNPWHGVDDWA-LKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 420 --~~e~~Pe~~ve~~e-l~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
....+|++.+...+ ....|..+| .+||+++|.||.|+| ++|+|++|||+.||+|.++|+++++||+++||+
T Consensus 126 ~~~~~~~~e~~~~~~e~~~~~l~~~l-~~Lp~~~R~v~~L~~---~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 126 LDPAAADPAARVVARESVRLAFVAAL-QHLPPRQRAVLILRD---VLGWSAAEVAELLDTSVAAVNSALQRARATLAE 199 (339)
T ss_pred ccccCCChHHHHHHHHHHHHHHHHHH-HhCCHHHhhhhhhHH---hhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhh
Confidence 00135665555444 345688899 899999999999999 899999999999999999999999999999998
No 98
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=1.4e-18 Score=160.68 Aligned_cols=157 Identities=15% Similarity=0.105 Sum_probs=123.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.|+++|+..|.+.|+.+|.++.++..++||++||+|+.+|+..+.|++ ..|.+|++.++++.+.+++++..+.
T Consensus 4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~---~~~~~wl~~i~~n~~~d~~R~~~~~---- 76 (161)
T PRK12528 4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQI---IEPRAFLTTIAKRVLCNHYRRQDLE---- 76 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhccccccc---cCHHHHHHHHHHHHHHHHHHHHHHH----
Confidence 799999999999999999999999999999999999999999988864 2599999999999999888765310
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
.. .. . .++. .++.. .+
T Consensus 77 -----------~~--~~---------~------------------------~~~~-----------------~~~~~-~~ 92 (161)
T PRK12528 77 -----------RA--YL---------E------------------------ALAQ-----------------LPERV-AP 92 (161)
T ss_pred -----------Hh--hH---------H------------------------Hhhc-----------------ccccc-CC
Confidence 00 00 0 0000 00000 11
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA 495 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~ 495 (508)
+++......+....|..+| ..||+++|.||.|+| .+|+|++|||+.||+|.+||++.+.+|+++||..
T Consensus 93 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~v~~L~~---~~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~ 160 (161)
T PRK12528 93 SEEERAIILETLVELDQLL-DGLPPLVKRAFLLAQ---VDGLGYGEIATELGISLATVKRYLNKAAMRCYFA 160 (161)
T ss_pred CHHHHHHHHHHHHHHHHHH-HHCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhc
Confidence 2333333344556788999 899999999999999 8999999999999999999999999999999975
No 99
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=1.9e-18 Score=164.93 Aligned_cols=181 Identities=15% Similarity=0.169 Sum_probs=132.2
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCC-HHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccccc
Q 010521 267 EKLVMSNVRLVMSIAQRYDNMGAD-MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH 345 (508)
Q Consensus 267 e~LIe~yl~LV~sIAkrY~~~g~d-~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~ 345 (508)
++.+..|.+.|+.+|.++.++..+ ++|++||+|+.+|+++++|++. ..|.+|++..++|.+.++++++.+.......
T Consensus 8 ~~~~~~~~~~l~~~a~~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~~ 85 (195)
T PRK12532 8 DAELIESRKLLLHFARLQLPDHPDLAEDLVQETLLSAYSAGDSFQGR--ALVNSWLFAILKNKIIDALRQIGRQRKVFTL 85 (195)
T ss_pred hhhHHHHHHHHHHHHHHHcCChhhhHHHHHHHHHHHHHHhccccccc--chHHHHHHHHHHHHHHHHHHHhccccccccc
Confidence 456778999999999999999888 9999999999999999999864 3799999999999999999876431110000
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCc
Q 010521 346 LHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNP 425 (508)
Q Consensus 346 ~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~P 425 (508)
.. .+.+ ... ...... .++....+...+. ..+|
T Consensus 86 ~~---------------------~~~~-----------~~~------~~~~~~--------~~~~~~~~~~~~~--~~~~ 117 (195)
T PRK12532 86 LD---------------------DELL-----------DEA------FESHFS--------QNGHWTPEGQPQH--WNTP 117 (195)
T ss_pred cc---------------------cccc-----------chh------hhhhhc--------cccccccccCccc--cCCH
Confidence 00 0000 000 000000 0000000000011 1367
Q ss_pred cchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010521 426 WHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM 501 (508)
Q Consensus 426 e~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l 501 (508)
++.+...+....+..+| ..||+++|.||.|+| .+|+|++|||+.||+|.++|+++++||+++||+.+....+
T Consensus 118 e~~~~~~e~~~~l~~~l-~~L~~~~r~i~~L~~---~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~ 189 (195)
T PRK12532 118 EKSLNNNEFQKILQSCL-YNLPENTARVFTLKE---ILGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKWF 189 (195)
T ss_pred HHHHHHHHHHHHHHHHH-HhCCHHHHHHhhhHH---HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 77777777778899999 899999999999999 8999999999999999999999999999999999976543
No 100
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=2.4e-18 Score=164.01 Aligned_cols=176 Identities=11% Similarity=0.038 Sum_probs=129.5
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHH
Q 010521 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH 347 (508)
Q Consensus 268 ~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~ 347 (508)
.-+..|.+.++.+|.+++++..+++|++||+|+.+|+.+++|++.. +|.+|++..++|.+.++++++.+..... ...
T Consensus 11 ~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~~--~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~-~~~ 87 (189)
T PRK12530 11 LEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQS--ALKTWIFAILKNKIIDLIRYRKRFVNES-ELI 87 (189)
T ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCCc--cHHHHHHHHHHHHHHHHHHhhccCCCcc-ccc
Confidence 4467899999999999999999999999999999999999998653 6999999999999999988764311100 000
Q ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccc
Q 010521 348 ERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWH 427 (508)
Q Consensus 348 ~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~ 427 (508)
.+ . ....... ...........++. ..+|++
T Consensus 88 ----------------------~~----------~---------~~~~~~~-------~~~~~~~~~~~~~~--~~~~~~ 117 (189)
T PRK12530 88 ----------------------EE----------D---------SPNSFFD-------EKGHWKPEYYEPSE--WQEVEN 117 (189)
T ss_pred ----------------------cc----------c---------cchhhhc-------ccccccccccCCcc--ccCHHH
Confidence 00 0 0000000 00000000000111 124556
Q ss_pred hHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521 428 GVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 500 (508)
Q Consensus 428 ~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~ 500 (508)
.+...+....+..+| +.||+++|+||.|+| ++|+|++|||+.||+|.+||+.+++||+++||+++....
T Consensus 118 ~~~~~~~~~~l~~~l-~~Lp~~~R~v~~L~~---~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~ 186 (189)
T PRK12530 118 TVYKEEFWLIFEACL-NHLPAQQARVFMMRE---YLELSSEQICQECDISTSNLHVLLYRARLQLQACLSKNW 186 (189)
T ss_pred HHHHHHHHHHHHHHH-HhCCHHHHHHHhHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 666677778899999 899999999999999 899999999999999999999999999999999987543
No 101
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=2.3e-18 Score=165.76 Aligned_cols=181 Identities=15% Similarity=0.086 Sum_probs=129.4
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHH
Q 010521 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH 347 (508)
Q Consensus 268 ~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~ 347 (508)
.++..|.+.++.+|.+++++..+++|++||+|+.+|+.+++|++.. .|.+|++..++|.+.+++++..+...++...
T Consensus 12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~~- 88 (201)
T PRK12545 12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQS--AHKTWVFGILRNKLIDTLRARQRTVNLSALD- 88 (201)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhccccc--hHHHHHHHHHHHHHHHHHHhhcccccccccc-
Confidence 3488999999999999999999999999999999999999999753 6999999999999999998765311110000
Q ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccc
Q 010521 348 ERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWH 427 (508)
Q Consensus 348 ~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~ 427 (508)
.++.. ...++... ....+....+..++. ..+|++
T Consensus 89 ----------------------~~~~~------------------~~~~~~~~----~~~~~~~~~~~~~~~--~~~~~~ 122 (201)
T PRK12545 89 ----------------------AELDG------------------EALLDREL----FKDNGHWAAHAKPRP--WPKPET 122 (201)
T ss_pred ----------------------cccch------------------hhhhhhhh----hcccccccccccCcC--CCCHHH
Confidence 00000 00000000 000000000000011 124555
Q ss_pred hHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010521 428 GVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM 501 (508)
Q Consensus 428 ~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l 501 (508)
.....+....+..+| ..||+++|.||.|+| ++|+|++|||+.||+|.++|+..++||+++||+.+...++
T Consensus 123 ~~~~~~~~~~l~~~L-~~Lp~~~r~v~~L~~---~eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~~ 192 (201)
T PRK12545 123 ILQQQQFWTLFETCL-DHLPEQIGRVFMMRE---FLDFEIDDICTELTLTANHCSVLLYRARTRLRTCLSEKGL 192 (201)
T ss_pred HHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 555555666788899 899999999999999 8999999999999999999999999999999999975543
No 102
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=2.8e-18 Score=158.55 Aligned_cols=156 Identities=12% Similarity=0.080 Sum_probs=122.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q 010521 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (508)
Q Consensus 263 ~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~iri 342 (508)
..|+++++..|.+.|+.+|.++.++..+++|++||+++.+|+.+++|++. .|.||++..++|.+.+++++..+....
T Consensus 4 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~~~ 80 (161)
T PRK12541 4 KQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEKKYKTT 80 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhccccccc
Confidence 48999999999999999999999999999999999999999999999863 599999999999999998876431000
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCC
Q 010521 343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE 422 (508)
Q Consensus 343 p~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e 422 (508)
..+. ...+..
T Consensus 81 ----------------------------------------------------~~~~----------------~~~~~~-- 90 (161)
T PRK12541 81 ----------------------------------------------------TIEE----------------FHLPNV-- 90 (161)
T ss_pred ----------------------------------------------------chhh----------------hhccCC--
Confidence 0000 000000
Q ss_pred CCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010521 423 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA 495 (508)
Q Consensus 423 ~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~ 495 (508)
++|++..........+..+| ..||+++|.||.|+| .+|+|.+|||+.||+|.++|++.++||+++||+.
T Consensus 91 ~~~~~~~~~~~~~~~~~~~l-~~L~~~~r~v~~l~~---~~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 91 PSTEHEYFIKHEIASWLDSL-SSLPLERRNVLLLRD---YYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred CCcHHHHHHHhHHHHHHHHH-HHCCHHHHHHhhhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 11222222222334556788 899999999999999 8999999999999999999999999999999974
No 103
>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=99.80 E-value=2.3e-18 Score=164.10 Aligned_cols=176 Identities=12% Similarity=0.086 Sum_probs=131.2
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHH
Q 010521 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH 347 (508)
Q Consensus 268 ~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~ 347 (508)
+.+..|.+.|+.+|.+++++..+++|++||+|+.+|+...+|++. .+|.+|++..+++.+.+++++..+....+....
T Consensus 6 ~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~~~~~ 83 (188)
T TIGR02943 6 QELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVSDLDD 83 (188)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCcccccc
Confidence 567889999999999999999999999999999999999999864 379999999999999999987653211110000
Q ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccc
Q 010521 348 ERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWH 427 (508)
Q Consensus 348 ~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~ 427 (508)
.+. .-.++.. ....+....+..++. .++|+.
T Consensus 84 ------------------~~~------------------------~~~~~~~-----~~~~~~~~~~~~~~~--~~~~e~ 114 (188)
T TIGR02943 84 ------------------ELD------------------------DEAFNAL-----FTQNGHWAQHGQPQH--WNTPEK 114 (188)
T ss_pred ------------------ccc------------------------cchhhhh-----hccccchhccccccc--cCCHHH
Confidence 000 0000000 000000000111111 235666
Q ss_pred hHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521 428 GVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 498 (508)
Q Consensus 428 ~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~ 498 (508)
.+...+..+.+.++| ..||+++|+||.++| ++|+|++|||+.||+|.++|++++.||+++||+.+..
T Consensus 115 ~~~~~e~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~ 181 (188)
T TIGR02943 115 QLENKEFWEVFEACL-YHLPEQTARVFMMRE---VLGFESDEICQELEISTSNCHVLLYRARLSLRACLSI 181 (188)
T ss_pred HHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 777777778899999 899999999999999 8999999999999999999999999999999999974
No 104
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=99.79 E-value=3.3e-18 Score=165.79 Aligned_cols=180 Identities=14% Similarity=0.137 Sum_probs=132.6
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccccc
Q 010521 266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH 345 (508)
Q Consensus 266 ~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~ 345 (508)
-..|+..|.+.|+.+|++++++..+++|++||+|+.+|+.+.+|++. .+|.+|++..++|.+.+++++..+....+..
T Consensus 20 ~~~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfikl~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~~~~~~~~~ 97 (206)
T PRK12544 20 DPVFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGR--AAFKTWVFAILKNKIIDLLRQKKRHVSASSL 97 (206)
T ss_pred hHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhhccccccccc
Confidence 35788999999999999999999999999999999999999999864 3699999999999999999876531111100
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCc
Q 010521 346 LHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNP 425 (508)
Q Consensus 346 ~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~P 425 (508)
.. +... ...+.... +. ..........+ ...+|
T Consensus 98 ~~-------------------~~~~---------~~~~~~~~---------~~---------~~~~~~~~~~~--~~~~~ 129 (206)
T PRK12544 98 LR-------------------DEEE---------EEDFEELF---------DE---------SGHWQKDERPQ--AWGNP 129 (206)
T ss_pred cc-------------------ccch---------hhHHHHhh---------cc---------ccccccccccc--ccCCH
Confidence 00 0000 00000000 00 00000000011 12357
Q ss_pred cchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521 426 WHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 499 (508)
Q Consensus 426 e~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~ 499 (508)
++.+...+....+..+| ..||+++|+||.|+| ++|+|++|||+.||+|.++|++.++||+++||+.+...
T Consensus 130 e~~~~~~e~~~~l~~~L-~~L~~~~r~v~~L~~---~~g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~ 199 (206)
T PRK12544 130 EESLEQEQFWRIFEACL-DGLPAKYARVFMMRE---FIELETNEICHAVDLSVSNLNVLLYRARLRLRECLENK 199 (206)
T ss_pred HHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 76677777777888999 899999999999999 89999999999999999999999999999999999753
No 105
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=99.79 E-value=6.1e-18 Score=160.62 Aligned_cols=160 Identities=16% Similarity=0.179 Sum_probs=127.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.++..++..|++.|+++|.+++++..++||++||+|+.+|+..++|++.. .|.+|++..++|.+.++++++.+...
T Consensus 5 ~~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~~~~-- 80 (182)
T PRK12540 5 DSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGS--NLPAWLFTILRNLFRSDYRKRRREVE-- 80 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCc--hHHHHHHHHHHHHHHHHHHhcccccc--
Confidence 67889999999999999999999999999999999999999999998654 69999999999988888876542100
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
. .+. ...+.. ..
T Consensus 81 --------------------------------------------------~-~~~------------~~~~~~-----~~ 92 (182)
T PRK12540 81 --------------------------------------------------D-ADG------------SYAKTL-----KS 92 (182)
T ss_pred --------------------------------------------------c-ccc------------cccccc-----cC
Confidence 0 000 000000 01
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM 501 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l 501 (508)
.|+.. .......|..+| ..||+++|.||.|+| .+|+|++|||+.||+|.++|++.++||+++||+.+...+.
T Consensus 93 ~~~~~--~~~~~~~l~~~l-~~Lp~~~R~v~~L~~---~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~~ 164 (182)
T PRK12540 93 QPGQN--AHLEFEEFRAAL-DKLPQDQREALILVG---ASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDGA 164 (182)
T ss_pred CCchH--HHHHHHHHHHHH-HhCCHHHHHHhhHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 12111 112235688999 899999999999999 8999999999999999999999999999999999987654
No 106
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=99.78 E-value=7.4e-18 Score=159.80 Aligned_cols=154 Identities=19% Similarity=0.183 Sum_probs=126.1
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccccc
Q 010521 266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH 345 (508)
Q Consensus 266 ~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~ 345 (508)
++.|++.|.+.|+.+|.++.++..+++|++||+++.+|+.+..|++. .+|.+|++..+++.+.+++++..+...++
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 37999999999999999987664210000
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCc
Q 010521 346 LHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNP 425 (508)
Q Consensus 346 ~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~P 425 (508)
. + . ... +.+
T Consensus 79 ----------------------------------------------------~---------~-~----~~~-----~~~ 87 (181)
T PRK09637 79 ----------------------------------------------------D---------D-L----LFE-----DEE 87 (181)
T ss_pred ----------------------------------------------------h---------h-h----hcc-----CCC
Confidence 0 0 0 000 011
Q ss_pred cchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521 426 WHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 498 (508)
Q Consensus 426 e~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~ 498 (508)
++.....+....+..+| +.||+++|.||.++| .+|++.+|||+.||+|..+|+.++.||+++||+.+..
T Consensus 88 ~~~~~~~e~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (181)
T PRK09637 88 REENAKKELAPCLRPFI-DALPEKYAEALRLTE---LEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156 (181)
T ss_pred hhHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 22233445667788889 899999999999999 8999999999999999999999999999999998864
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=99.78 E-value=1.3e-18 Score=158.86 Aligned_cols=153 Identities=15% Similarity=0.160 Sum_probs=122.5
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHH
Q 010521 270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHER 349 (508)
Q Consensus 270 Ie~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~ 349 (508)
+..|.+.|+.++.++.++..+++|++||+++.+|+.+++|++ .+|.+|++..+++.+.+++++..+.....
T Consensus 1 y~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~~------ 71 (154)
T TIGR02950 1 YREYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTID------ 71 (154)
T ss_pred CchHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhcccc------
Confidence 357999999999999999899999999999999999999997 37999999999999988887654210000
Q ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchH
Q 010521 350 LGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGV 429 (508)
Q Consensus 350 l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~v 429 (508)
. +.+.+...+. ..+|++.+
T Consensus 72 --------------------~---------------------------------------~~~~~~~~~~--~~~~~~~~ 90 (154)
T TIGR02950 72 --------------------D---------------------------------------DAIGDLEQHP--VESPEHHL 90 (154)
T ss_pred --------------------H---------------------------------------hhhhhccccc--cCChhHHH
Confidence 0 0000000011 12455555
Q ss_pred HHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 430 DDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 430 e~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
...+....+.++| ..||++++.||.++| .+|+|++|||+.||+|..+|++.++||+++||+.+
T Consensus 91 ~~~~~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~l 153 (154)
T TIGR02950 91 LIKIEQEEITHHL-SRLPENYRTVLILRE---FKEFSYKEIAELLNLSLAKVKSNLFRARKELKKLL 153 (154)
T ss_pred HHHHHHHHHHHHH-HhCCHhheeeeeehh---hccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 6666677899999 899999999999998 79999999999999999999999999999999876
No 108
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=99.78 E-value=7.6e-18 Score=155.63 Aligned_cols=158 Identities=16% Similarity=0.203 Sum_probs=124.5
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHH
Q 010521 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH 347 (508)
Q Consensus 268 ~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~ 347 (508)
.++..|.+.++.+|.++.++..+++|++||+++++|+....|++. .|.+|++..+++.+.+++++..+...
T Consensus 2 ~~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn~~~d~~R~~~~~~~------ 72 (163)
T PRK07037 2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRNLAIDHYRRQALENK------ 72 (163)
T ss_pred hHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHHHHHHHHHhhccccc------
Confidence 357789999999999999999999999999999999998877653 47899999999998888876642100
Q ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccc
Q 010521 348 ERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWH 427 (508)
Q Consensus 348 ~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~ 427 (508)
.. ..+.... . ..+. ..+|++
T Consensus 73 ----------------------------------------------~~----------~~~~~~~-~-~~~~--~~~~~~ 92 (163)
T PRK07037 73 ----------------------------------------------YH----------GDEEDGL-D-VPSP--EASPEA 92 (163)
T ss_pred ----------------------------------------------cc----------ccccccc-c-cCCC--CCCHHH
Confidence 00 0000000 0 0011 124666
Q ss_pred hHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521 428 GVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 498 (508)
Q Consensus 428 ~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~ 498 (508)
.+...+..+.+..+| ..|||++|.||.++| .+|+|.+|||+.||+|.++|++.+.+|+++||+.+..
T Consensus 93 ~~~~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l~~ 159 (163)
T PRK07037 93 ALINRDTLRHVADAL-SELPARTRYAFEMYR---LHGETQKDIARELGVSPTLVNFMIRDALVHCRKCLDA 159 (163)
T ss_pred HHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 666667778889999 899999999999999 7999999999999999999999999999999998864
No 109
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=8.2e-18 Score=160.43 Aligned_cols=163 Identities=17% Similarity=0.155 Sum_probs=125.6
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcc
Q 010521 259 LMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR 338 (508)
Q Consensus 259 l~e~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R 338 (508)
+..+..+++.++..|.+.|+.+|.+++++..+++|++||+|+.+|+.++.|++. ..|.+|++..+++.+.+..++..+
T Consensus 18 ~~~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~~~~ 95 (188)
T PRK12517 18 MLSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFERKQF 95 (188)
T ss_pred hhccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHHhcc
Confidence 444669999999999999999999999999999999999999999999999864 369999999988865544332210
Q ss_pred cccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCcccccccc
Q 010521 339 TLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIAD 418 (508)
Q Consensus 339 ~irip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d 418 (508)
. ....+. . ...+
T Consensus 96 ~-----------------------------------------------------~~~~~~-----------~----~~~~ 107 (188)
T PRK12517 96 D-----------------------------------------------------LVDIED-----------D----SIED 107 (188)
T ss_pred C-----------------------------------------------------ccCccc-----------c----cccC
Confidence 0 000000 0 0011
Q ss_pred ccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521 419 NRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 498 (508)
Q Consensus 419 ~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~ 498 (508)
.. ..+|+. ....+.|..+| ..||+++|.||.++| .+|++++|||+.||+|.++|+.+++||+++||..+..
T Consensus 108 ~~-~~~~e~----~~~~~~l~~~l-~~Lp~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 178 (188)
T PRK12517 108 DA-SHSSEE----EMEQEWLRRQI-AKLDPEYREPLLLQV---IGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALEK 178 (188)
T ss_pred cc-ccChhH----HHHHHHHHHHH-HhCCHHHHHHHHHHH---HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 00 112322 22335688899 899999999999999 7999999999999999999999999999999999975
Q ss_pred hh
Q 010521 499 KK 500 (508)
Q Consensus 499 ~~ 500 (508)
..
T Consensus 179 ~~ 180 (188)
T PRK12517 179 PD 180 (188)
T ss_pred HH
Confidence 43
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=99.78 E-value=5.4e-18 Score=173.77 Aligned_cols=186 Identities=17% Similarity=0.121 Sum_probs=132.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q 010521 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (508)
Q Consensus 263 ~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~iri 342 (508)
..|++.|+..|.+.|+++|.+++++..++||++||+|+.+|+.+++|++. ..|.+|++..++|.+.+++++..+....
T Consensus 4 ~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~~~~ 81 (324)
T TIGR02960 4 GAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQRRPRP 81 (324)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhccCCcCc
Confidence 38999999999999999999999999999999999999999999999864 3699999999999999998876431000
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccc-cc-ccc
Q 010521 343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSY-IA-DNR 420 (508)
Q Consensus 343 p~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~-i~-d~~ 420 (508)
.... . + ......... ..........+.+. +. ...
T Consensus 82 ~~~~-----------------~--~------------------------~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~ 117 (324)
T TIGR02960 82 VGLG-----------------A--P------------------------SADGTAAAS-EAAEVTWLEPLPDLTLDLDDP 117 (324)
T ss_pred cccC-----------------C--C------------------------CCccccccc-ccccccccCCCCccccccccC
Confidence 0000 0 0 000000000 00000000000000 00 000
Q ss_pred CCCCccchHHHHH-HHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521 421 VENNPWHGVDDWA-LKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 498 (508)
Q Consensus 421 ~e~~Pe~~ve~~e-l~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~ 498 (508)
...+|++.+...+ +...+..+| ..||+++|.||.|+| .+|+|++|||+.||+|.++|+++++||+++||+.+..
T Consensus 118 ~~~~~~~~~~~~e~~~~~l~~~l-~~Lp~~~R~v~~L~~---~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 192 (324)
T TIGR02960 118 AAADPSVAAGSRESVRLAFVAAI-QYLPPRQRAVLLLRD---VLGWRAAETAELLGTSTASVNSALQRARATLDEVGPS 192 (324)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHH-HhCCHHHhhHhhhHH---HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccc
Confidence 1135655555444 445688899 899999999999999 8999999999999999999999999999999998874
No 111
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=99.77 E-value=1.2e-17 Score=156.58 Aligned_cols=162 Identities=15% Similarity=0.160 Sum_probs=124.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q 010521 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL 342 (508)
Q Consensus 263 ~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~iri 342 (508)
..|++.++..|.+.++.++.++.++..++||++||+|+.+|+. ..|++.. +|.+|++..+++.+.+++++..+.
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 3555332 588999999999888887754210
Q ss_pred cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCC
Q 010521 343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE 422 (508)
Q Consensus 343 p~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e 422 (508)
. .. .. .++. +.+.. .
T Consensus 83 ------------~---~~-----------------------~~---------~~~~-----------------~~~~~-~ 97 (172)
T PRK09651 83 ------------K---AY-----------------------LE---------MLAL-----------------MPEGG-A 97 (172)
T ss_pred ------------h---hh-----------------------hh---------HHhh-----------------ccccC-C
Confidence 0 00 00 0000 00000 1
Q ss_pred CCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521 423 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 499 (508)
Q Consensus 423 ~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~ 499 (508)
++|+......+....+..+| ..||+++|+||.|+| ++|+|++|||+.||+|.++|+..++||+++|+...-..
T Consensus 98 ~~~~~~~~~~e~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~~~~~ 170 (172)
T PRK09651 98 PSPEERESQLETLQLLDSML-DGLNGKTREAFLLSQ---LDGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLFRLEY 170 (172)
T ss_pred CChHHHHHHHHHHHHHHHHH-HhCCHHHhHHhhhhh---ccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHc
Confidence 23443444445567788999 899999999999999 89999999999999999999999999999999865443
No 112
>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=3e-17 Score=160.73 Aligned_cols=175 Identities=19% Similarity=0.234 Sum_probs=128.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCC--CCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhc---c
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMG--ADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS---R 338 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g--~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~---R 338 (508)
. +++||..|.|+|.++|.+|.++. .+.+|++|+|++|||+|+++|||++|.+|.+||.++|++.|.+++++.. +
T Consensus 10 ~-~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dylRk~~k~~~ 88 (218)
T TIGR02895 10 E-REELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYIRKNQKYQN 88 (218)
T ss_pred H-HHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHhcccccC
Confidence 5 99999999999999999998764 5899999999999999999999999999999999999999999999987 5
Q ss_pred cccccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHH------hCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCc
Q 010521 339 TLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEY------LNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGET 411 (508)
Q Consensus 339 ~irip~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~------Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~ 411 (508)
.+++|....+....+..+...+. +.++.|+.+||+.. .|++.+++.+
T Consensus 89 ~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~~~~L~~~gi~~~dLv~-------------------------- 142 (218)
T TIGR02895 89 LLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEYKKLLKQFGIEFVELVK-------------------------- 142 (218)
T ss_pred eeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCcHHHHhh--------------------------
Confidence 66888765554445555555553 67899999999865 3555544322
Q ss_pred cccccccccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHH
Q 010521 412 HHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQV 484 (508)
Q Consensus 412 l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi 484 (508)
..|-+.- .....-.+-..+. -++. ++..-+. ...+..+||+..++||+.|+.+.
T Consensus 143 -----------~sPkh~d-~r~~~i~ia~~~~--~~~~---l~~~l~~--kk~LP~k~l~~~~~v~rktier~ 196 (218)
T TIGR02895 143 -----------VSPKHRD-TRKKAIKIAKVIV--ENEE---LLEYLIR--KKKLPIKEIEERVRISRKTIERY 196 (218)
T ss_pred -----------cCCCCHH-HHHHHHHHHHHHh--cCHH---HHHHHHH--hCCCCHHHHHHHcCCCHHHHHHh
Confidence 1343322 2233333434441 2222 2222110 24689999999999999998654
No 113
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=99.77 E-value=1.1e-17 Score=154.24 Aligned_cols=155 Identities=13% Similarity=0.075 Sum_probs=123.2
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHH
Q 010521 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 350 (508)
Q Consensus 271 e~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l 350 (508)
..|.+.++.++.+++++..+++|++||+|+.+|+..+.|++ + +|.+|++..+++.+.+++++..+...
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~--~-~~~~wL~~ia~n~~~d~~R~~~~~~~--------- 69 (159)
T PRK12527 2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQI--E-HPRAFLYRTALNLVVDRHRRHRVRQA--------- 69 (159)
T ss_pred hhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhccccccc--c-chHHHHHHHHHHHHHHHHHHHhcccc---------
Confidence 57899999999999999899999999999999999999875 2 69999999999998888876531000
Q ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHH
Q 010521 351 GLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVD 430 (508)
Q Consensus 351 ~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve 430 (508)
.+++. +.+. .....++|++.+.
T Consensus 70 -------------------------------------------~~~~~-------------~~~~--~~~~~~~~~~~~~ 91 (159)
T PRK12527 70 -------------------------------------------EPLEV-------------LDEE--ERLHSPSPQTRLD 91 (159)
T ss_pred -------------------------------------------cchhh-------------hhcc--ccccCCCHHHHHH
Confidence 00000 0000 0000124566666
Q ss_pred HHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521 431 DWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 499 (508)
Q Consensus 431 ~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~ 499 (508)
..+....|..+| ..||++++.||.|+| ++|+|.+|||+.||+|.++|+..+.||+++||+.+...
T Consensus 92 ~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~~~ 156 (159)
T PRK12527 92 LGQRLALLQRAL-AELPPACRDSFLLRK---LEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQW 156 (159)
T ss_pred HHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 667777899999 899999999999999 89999999999999999999999999999999998754
No 114
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=99.76 E-value=2.4e-17 Score=157.49 Aligned_cols=156 Identities=17% Similarity=0.233 Sum_probs=121.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
++++.|+. |.+.|+++|.+++++..+++|++||+|+.+|+.+..|+.. ..|.+|++..++|.+.+++++..+...
T Consensus 8 ~~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r~~~-- 82 (188)
T PRK12546 8 DPRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKREVP-- 82 (188)
T ss_pred hHHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhccccc--
Confidence 56777766 7799999999999999999999999999999999999863 369999999999998888776542100
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
..+. ...+.. ..
T Consensus 83 ---------------------------------------------------~~~~------------~~~~~~-----~~ 94 (188)
T PRK12546 83 ---------------------------------------------------DPEG------------VHAASL-----AV 94 (188)
T ss_pred ---------------------------------------------------Cccc------------cccccc-----cc
Confidence 0000 000000 01
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 498 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~ 498 (508)
+|.. +.......+..+| ..||+++|.||.|+| .+|+|.+|||+.||+|..+|+++++||+++||+.+..
T Consensus 95 ~~~~--~~~~~~~~l~~~L-~~Lp~~~r~v~~L~~---~~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~ 163 (188)
T PRK12546 95 KPAH--DGRLAMSDFRAAF-AQLPDEQREALILVG---ASGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQL 163 (188)
T ss_pred CCcc--hhHHHHHHHHHHH-HhCCHHHhHHhhhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 1111 1122335688899 899999999999999 8999999999999999999999999999999998864
No 115
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=99.76 E-value=2e-17 Score=154.93 Aligned_cols=149 Identities=21% Similarity=0.256 Sum_probs=121.3
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHH
Q 010521 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 350 (508)
Q Consensus 271 e~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l 350 (508)
..|.+.++.++.++.++..+++|++||+|+.+|+++++|++. .+|.+|++..+++.+.+++++..+...++
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~~--~~f~~wl~~iarn~~~d~~Rk~~~~~~~~------- 72 (170)
T TIGR02959 2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDG--QKIQSWLYQIARNTIIDFYRSKSRSVELP------- 72 (170)
T ss_pred chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhccCccccc-------
Confidence 468999999999999999999999999999999999999863 47999999999999999988764310000
Q ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHH
Q 010521 351 GLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVD 430 (508)
Q Consensus 351 ~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve 430 (508)
+. .+.. ..|.+...
T Consensus 73 ----------------------------------------------~~----------------~~~~----~~~~~~~~ 86 (170)
T TIGR02959 73 ----------------------------------------------ES----------------LLAA----DSAREETF 86 (170)
T ss_pred ----------------------------------------------hh----------------hccc----CCccHHHH
Confidence 00 0000 01222333
Q ss_pred HHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521 431 DWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 498 (508)
Q Consensus 431 ~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~ 498 (508)
..+....+..+| ..||+++|.||.++| .+|+|++|||+.||+|..+|++.++||+++||..+..
T Consensus 87 ~~e~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 150 (170)
T TIGR02959 87 VKELSQCIPPMI-KELPDEYREAIRLTE---LEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLET 150 (170)
T ss_pred HHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 455567788999 899999999999999 8999999999999999999999999999999998863
No 116
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=99.75 E-value=4.3e-17 Score=154.90 Aligned_cols=158 Identities=16% Similarity=0.150 Sum_probs=122.7
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccccc
Q 010521 266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH 345 (508)
Q Consensus 266 ~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~ 345 (508)
....+..+++.|+.+|.++.++..+++|++||+|+.+|+....|++. .+|.+|++..+++.+.++++++.+.....
T Consensus 6 ~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~~~~~~-- 81 (182)
T PRK12511 6 KRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRVEARRA-- 81 (182)
T ss_pred hhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhccccccc--
Confidence 44457789999999999999999999999999999999999999864 36999999999999999987764210000
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCc
Q 010521 346 LHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNP 425 (508)
Q Consensus 346 ~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~P 425 (508)
+. +.+. .+.. .+.+
T Consensus 82 ---------------------------------------------------~~-------------~~~~-~~~~-~~~~ 95 (182)
T PRK12511 82 ---------------------------------------------------DE-------------LAVL-ADAS-LPAA 95 (182)
T ss_pred ---------------------------------------------------cc-------------hhhc-cccC-CCcc
Confidence 00 0000 0000 0011
Q ss_pred cchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521 426 WHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 500 (508)
Q Consensus 426 e~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~ 500 (508)
.........|..+| ..||+++|+||.|+| ++|+|++|||+.||+|.++|++.++||+++||+.+...+
T Consensus 96 ---~~~~~~~~~l~~~l-~~Lp~~~R~v~~L~~---~eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~~~~ 163 (182)
T PRK12511 96 ---QEHAVRLAQIRDAF-FDLPEEQRAALHLVA---IEGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEEGTG 163 (182)
T ss_pred ---hHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 11223446788899 899999999999999 899999999999999999999999999999999987544
No 117
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=99.74 E-value=6.2e-17 Score=151.08 Aligned_cols=159 Identities=14% Similarity=0.105 Sum_probs=125.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.++.+++..|.+.++.+|.+++++..+++|++||+|+.+|+....++. ..|.+|++..++|.+.+++++...
T Consensus 9 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~----- 80 (168)
T PRK12525 9 TLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDL----- 80 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHH-----
Confidence 789999999999999999999999999999999999999986555542 269999999999988887765421
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
++. ... +++. . +.. ..+
T Consensus 81 ----------~~~--~~~---------------------------------~~~~----------------~-~~~-~~~ 97 (168)
T PRK12525 81 ----------ERA--YLQ---------------------------------SLAE----------------A-PEA-VQP 97 (168)
T ss_pred ----------HHH--HHH---------------------------------HHhc----------------c-ccc-ccC
Confidence 000 000 0000 0 000 012
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~ 497 (508)
+|++.....+....|..+| +.||+++|.||.|+| .+|+|++|||+.||+|.+||+..+.+|++++|..+.
T Consensus 98 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~v~~L~~---~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~~~ 167 (168)
T PRK12525 98 SPEEQWMVIETLLAIDRLL-DGLSGKARAAFLMSQ---LEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQGFQ 167 (168)
T ss_pred ChHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhc
Confidence 5555555666678899999 899999999999998 899999999999999999999999999999998764
No 118
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=99.70 E-value=2.5e-16 Score=144.77 Aligned_cols=156 Identities=14% Similarity=0.100 Sum_probs=111.6
Q ss_pred CCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHcCC
Q 010521 286 NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGV 365 (508)
Q Consensus 286 ~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~~~Gr 365 (508)
++..+++|++||+|+.+|+..+.+ + +..|.+|++..++|.+.+++++..+.......
T Consensus 2 ~~~~~AeDivQe~fl~~~~~~~~~-~--~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~-------------------- 58 (161)
T PRK09047 2 RDDDAALDIVQDAMIKLAEKYGDR-P--AAEWPPLFQRILQNRIHDWFRRQKVRNTWVSL-------------------- 58 (161)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhhc-c--cCchHHHHHHHHHHHHHHHHHhhccccccccc--------------------
Confidence 345679999999999999998873 3 34699999999999999998876421000000
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccC-CCCccchHHHHHHHHHHHHHHHc
Q 010521 366 TPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRV-ENNPWHGVDDWALKDEVNKLIIV 444 (508)
Q Consensus 366 ~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~-e~~Pe~~ve~~el~e~L~~~L~~ 444 (508)
..++... .+.++....+.+.+... ..+|++.+...+....|..+| .
T Consensus 59 ---------------------------~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l-~ 105 (161)
T PRK09047 59 ---------------------------FSSFSDD-----DDDDDFDPLETLDSADEGAESPADKLERAQVLQLIEEAI-Q 105 (161)
T ss_pred ---------------------------ccccccc-----cccccccHHHHhccccccCCCHHHHHHHHHHHHHHHHHH-H
Confidence 0000000 00001111111211110 135677777777888899999 8
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 500 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~ 500 (508)
.||+++|.||.|+| ++|+|++|||+.||+|.++|+.+++||+++||+.+...+
T Consensus 106 ~Lp~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~ 158 (161)
T PRK09047 106 KLPARQREAFLLRY---WEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEAKG 158 (161)
T ss_pred hCCHHHHHHHHHHH---HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 99999999999999 899999999999999999999999999999999997654
No 119
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=99.70 E-value=2.7e-16 Score=159.84 Aligned_cols=160 Identities=14% Similarity=0.083 Sum_probs=122.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
..+.+++..|.+.++.+|++++++..++||++||+|+. |.....|++ ..|.+|++..++|.+.+++++..+...
T Consensus 4 ~~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~~---~~~~~WL~~Ia~n~~~d~lR~~~~~~~-- 77 (293)
T PRK09636 4 ADAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQI---RDPRAWLTRVVTRLCLDRLRSARHRRE-- 77 (293)
T ss_pred cHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhcccccc---cCHHHHHHHHHHHHHHHHHHhhhcccc--
Confidence 45778999999999999999999999999999999999 666677752 369999999999999998876532000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
.... ..+.+...+. ..
T Consensus 78 --------------------------------------------------~~~~------------~~~~e~~~~~--~~ 93 (293)
T PRK09636 78 --------------------------------------------------TYVG------------PWLPEPVVEE--LD 93 (293)
T ss_pred --------------------------------------------------cccC------------CcCCcCCCCC--CC
Confidence 0000 0000000011 11
Q ss_pred CccchHH-HHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521 424 NPWHGVD-DWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497 (508)
Q Consensus 424 ~Pe~~ve-~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~ 497 (508)
+|++... ..+....+..+| +.|||+||.||.|+| .+++|++|||+.||+|.++|+++++||+++||+.+.
T Consensus 94 ~~~~~~~~~~~~~~~l~~~l-~~L~~~~R~v~~L~~---~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~ 164 (293)
T PRK09636 94 DPLEAVVAAEDLSLALMLAL-ERLSPLERAAFLLHD---VFGVPFDEIASTLGRSPAACRQLASRARKHVRAARP 164 (293)
T ss_pred ChHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 3443332 344456688889 899999999999999 799999999999999999999999999999999754
No 120
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=99.69 E-value=6.5e-16 Score=152.38 Aligned_cols=149 Identities=17% Similarity=0.131 Sum_probs=116.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
.+++.+++.| +.++++|.++.++..++||++||+|+.+|+. |+.. + .|.+|++..++|.+.+.+++..+...
T Consensus 18 ~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~-~-~~~~WL~~IarN~~id~~Rk~k~~~~-- 89 (228)
T PRK06704 18 SNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNK-D-ICMTLVYKIARNRWLDQIKSKSVHEK-- 89 (228)
T ss_pred HHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCcc-c-cHHHHHHHHHHHHHHHHHhccccccc--
Confidence 7888888888 7899999999999999999999999999986 5533 2 58999999999988888876532000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
+.. .. . ..
T Consensus 90 ----------------------------------------------------~~~----------~~------~----~~ 97 (228)
T PRK06704 90 ----------------------------------------------------IRD----------QI------T----FE 97 (228)
T ss_pred ----------------------------------------------------ccc----------cc------c----cC
Confidence 000 00 0 00
Q ss_pred CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 498 (508)
Q Consensus 424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~ 498 (508)
+|.+.. .+..+.+..+| ..||+++|.||.|+| .+++|++|||+.||+|.++|+++++||+++||+.+..
T Consensus 98 ~~~~~~--~~~~~~l~~~L-~~Lp~~~R~v~lL~~---~eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~ 166 (228)
T PRK06704 98 EPHEKI--ADLHEMVGKVL-SSLNVQQSAILLLKD---VFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEE 166 (228)
T ss_pred ChHHHH--HHHHHHHHHHH-HhCCHHHhhHhhhHH---hhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 111111 22345678888 899999999999999 7999999999999999999999999999999998865
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=1.7e-15 Score=153.41 Aligned_cols=156 Identities=17% Similarity=0.087 Sum_probs=117.7
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHH
Q 010521 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH 347 (508)
Q Consensus 268 ~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~ 347 (508)
++++.|.+.++.+|++++++..++||++||+++.+++. .|+. ...|.+|++..++|.+.+++++..+...
T Consensus 1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~--~~~~~awL~~Ia~n~~ld~lR~~~~~~~------ 70 (281)
T TIGR02957 1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQ--IENPKAYLTKVVTRRCIDVLRSARARRE------ 70 (281)
T ss_pred ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Cccc--ccCHHHHHHHHHHHHHHHHHHHhhhccc------
Confidence 36889999999999999999999999999999997775 4543 2369999999999999998876532000
Q ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccc
Q 010521 348 ERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWH 427 (508)
Q Consensus 348 ~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~ 427 (508)
... . ..+.+...+. ..+|++
T Consensus 71 ----------------------------------------------~~~-~-----------~~~~e~~~~~--~~~~~~ 90 (281)
T TIGR02957 71 ----------------------------------------------VYV-G-----------PWLPEPLLTT--SADPAE 90 (281)
T ss_pred ----------------------------------------------ccC-C-----------CCCCcccCCC--CCChHH
Confidence 000 0 0000000000 124554
Q ss_pred hHHHH-HHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521 428 GVDDW-ALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497 (508)
Q Consensus 428 ~ve~~-el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~ 497 (508)
.++.. .+...+..+| ++|||+||.||.|+| .+++|++|||+.||+|..+|+++++||+++||....
T Consensus 91 ~~~~~e~~~~~l~~~l-~~L~~~~R~v~~L~~---~~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~ 157 (281)
T TIGR02957 91 SVELAESLSMAYLLLL-ERLSPLERAVFVLRE---VFDYPYEEIASIVGKSEANCRQLVSRARRHLDARRP 157 (281)
T ss_pred HHHHHHHHHHHHHHHH-hhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 44433 3445677888 899999999999999 799999999999999999999999999999998653
No 122
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=99.65 E-value=3e-15 Score=152.61 Aligned_cols=161 Identities=15% Similarity=0.045 Sum_probs=122.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip 343 (508)
..+..+++.|.+.++.+|++++++..++||++||+|+.+|++...+ . ..|.+|++...+|.+.+++++..+....
T Consensus 5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~-~---~~~~aWL~~Ia~n~~id~lRk~~~rr~~- 79 (290)
T PRK09635 5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD-I---DDERGWLIVVTSRLCLDHIKSASTRRER- 79 (290)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc-c---ccHHHHHHHHHHHHHHHHHhhhhccCcC-
Confidence 6789999999999999999999999999999999999999987653 1 2589999999999999888764320000
Q ss_pred ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521 344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423 (508)
Q Consensus 344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~ 423 (508)
....+. ... .+...+ ..
T Consensus 80 -------------------------------------------------~~~~~~---------~~~--~~~~~~---~~ 96 (290)
T PRK09635 80 -------------------------------------------------PQDIAA---------WHD--GDASVS---SV 96 (290)
T ss_pred -------------------------------------------------cccccc---------cCc--cccCCC---CC
Confidence 000000 000 000001 12
Q ss_pred Cccch-HHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 424 NPWHG-VDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 424 ~Pe~~-ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
+|++. ....+....+..+| ..|||+||.||.|+| ..++|++|||+.||+|..+|+++++||+++||...
T Consensus 97 ~~~~~~~~~~e~~~al~~~L-~~L~p~~R~vf~L~~---~~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~ 166 (290)
T PRK09635 97 DPADRVTLDDEVRLALLIML-ERLGPAERVVFVLHE---IFGLPYQQIATTIGSQASTCRQLAHRARRKINESR 166 (290)
T ss_pred CcHHHHHHHHHHHHHHHHHH-HhCCHHHHHHhhHHH---HhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence 34332 33455667788899 899999999999999 79999999999999999999999999999999854
No 123
>PRK09191 two-component response regulator; Provisional
Probab=99.56 E-value=3.4e-14 Score=139.69 Aligned_cols=136 Identities=11% Similarity=0.105 Sum_probs=110.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccc
Q 010521 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN 344 (508)
Q Consensus 265 A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~ 344 (508)
++..|+..|.+.++++|.++.++..+++|++||+|+.+|+...+|++.. .|.+|++.++++.. ....
T Consensus 2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~~--~~~~wl~~~~~~~~----~~~~------- 68 (261)
T PRK09191 2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEAS--SPRVGLYRLFHRLW----SSAG------- 68 (261)
T ss_pred chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCCc--chhhHHHHHHHHHh----cccc-------
Confidence 5889999999999999999999999999999999999999999998643 58999987665421 0000
Q ss_pred cHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCC
Q 010521 345 HLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENN 424 (508)
Q Consensus 345 ~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~ 424 (508)
. ... . ...
T Consensus 69 -----------------------------------------------------~---------~~~------~----~~~ 76 (261)
T PRK09191 69 -----------------------------------------------------A---------NDP------E----PGS 76 (261)
T ss_pred -----------------------------------------------------c---------cCC------C----CCC
Confidence 0 000 0 001
Q ss_pred ccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521 425 PWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497 (508)
Q Consensus 425 Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~ 497 (508)
+.. ..+.++| +.||+++|.||.|+| ++++|++|||+.||+|.++|+.+..+|+++||..+.
T Consensus 77 ~~~--------~~l~~~l-~~L~~~~r~v~~l~~---~~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~ 137 (261)
T PRK09191 77 PFE--------ARAERRL-AGLTPLPRQAFLLTA---LEGFSVEEAAEILGVDPAEAEALLDDARAEIARQVA 137 (261)
T ss_pred Cch--------HHHHHHH-HhCCHHHhHHHHHHH---HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCC
Confidence 111 1688889 899999999999999 899999999999999999999999999999997664
No 124
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=99.54 E-value=5.6e-14 Score=127.34 Aligned_cols=136 Identities=19% Similarity=0.210 Sum_probs=99.3
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhc-----cCCCCCCcchhHHHHHHHHHHHHHHHHhcccc
Q 010521 266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEK-----FDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340 (508)
Q Consensus 266 ~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiek-----FDperG~rFsTYA~~wIR~~I~~~Ird~~R~i 340 (508)
++.|+..|.++++.+|++|... +|+ ||.++.+|..+.+ |++. ..|.||++..++|.+.+++++..+..
T Consensus 1 f~~~~~~y~~~l~~~~~~~~~~----~~~-qdvf~~~w~~~~~~~~~~~~~~--~~~~~wL~~iarN~~id~~Rk~~~~~ 73 (142)
T TIGR03209 1 FEEIYMNFKNTIDIFTRKYNLY----YDY-NDILYHLWIILKKIDLNKFNTE--NDLEKYISTSLKRYCLDICNKKNRDK 73 (142)
T ss_pred ChHHHHHHHHHHHHHHHHhcch----hhH-HHHHHHHHHHHHHhhhhhcCch--hHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 4689999999999999999652 344 9999999999865 5532 36999999999999999987653200
Q ss_pred cccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCcccccccccc
Q 010521 341 RLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNR 420 (508)
Q Consensus 341 rip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~ 420 (508)
.. . . .+. . .+..
T Consensus 74 ~~--------------~-~------------------------------------~~~-------------~----~~~~ 85 (142)
T TIGR03209 74 KI--------------I-Y------------------------------------NSE-------------I----TDIK 85 (142)
T ss_pred hh--------------h-h------------------------------------hhh-------------h----hccc
Confidence 00 0 0 000 0 0000
Q ss_pred CCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHH
Q 010521 421 VENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVR 482 (508)
Q Consensus 421 ~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVr 482 (508)
..+.+.+...+....+.++| +.||+++|.||.|+| ++|+|++|||+.||+|.+||+
T Consensus 86 --~~~~~~~~~~~~~~~l~~~l-~~Lp~~~r~v~~l~~---~~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 86 --LSLINVYSSNDLEFEFNDLI-SILPNKQKKIIYMKF---FEDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred --cchhHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHhhc
Confidence 01112233344556788899 899999999999999 899999999999999999996
No 125
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=99.51 E-value=1.1e-12 Score=125.15 Aligned_cols=163 Identities=22% Similarity=0.257 Sum_probs=111.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCC---CCCHHH--HHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNM---GADMAD--LVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR 338 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~---g~d~ED--LiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R 338 (508)
.|++.|+..|++.++.+|+++... +.+.+| |++|+|+.++..-...+++....|..|+...+++.+.++++...+
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 999999999999999999987642 334444 577888877764333343333458888888888877777765542
Q ss_pred cccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCcccccccc
Q 010521 339 TLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIAD 418 (508)
Q Consensus 339 ~irip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d 418 (508)
..|-+.. ...+|+.. ..+
T Consensus 97 ~KRg~~~----------------------------------------------~~~~l~~~----------------~~~ 114 (185)
T PF07638_consen 97 QKRGGDQ----------------------------------------------VRVELDER----------------ADS 114 (185)
T ss_pred HhcCCCC----------------------------------------------cccchhhh----------------hcc
Confidence 1110000 00112211 000
Q ss_pred ccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521 419 NRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497 (508)
Q Consensus 419 ~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~ 497 (508)
.. .+.|+. ..++.+.+..+. . |+|+++.||.++| ++|+|.+|||+.||||+.||++....|..+|+..|.
T Consensus 115 ~~-~~~~~~---~~~l~e~l~~L~-~-l~~~~~~~v~l~~---~~Gls~~EIA~~lgiS~~tV~r~l~~aR~~l~~~l~ 184 (185)
T PF07638_consen 115 GD-EPSPEE---LLELEEALERLL-A-LDPRQRRVVELRF---FEGLSVEEIAERLGISERTVRRRLRRARAWLRRELR 184 (185)
T ss_pred cc-CCCHHH---HHHHHHHHHHHH-c-cCHHHHHHHHHHH---HCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence 00 123333 234556666655 4 9999999999998 899999999999999999999999999999998764
No 126
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=99.50 E-value=1.6e-12 Score=129.02 Aligned_cols=78 Identities=17% Similarity=0.207 Sum_probs=72.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCC--CHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccc
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDNMGA--DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR 341 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~~g~--d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~ir 341 (508)
.|++.|+..|.|+|+++|.+++++.. +.+|++|||++++|+++++|++++|.+|.+|++.+|++.+.++++++.+...
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 5999999999999999999999888789999999999999999998876433
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=99.27 E-value=1.4e-11 Score=97.82 Aligned_cols=70 Identities=27% Similarity=0.418 Sum_probs=66.7
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcc
Q 010521 269 LVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR 338 (508)
Q Consensus 269 LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R 338 (508)
|++.|.++|+++|.+|.+++.+.+|++||++++||+++++||++.+..|.+|++..+++.+.+.++++.|
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 6899999999999999999999999999999999999999999999889999999999999999988754
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=99.19 E-value=5.7e-11 Score=89.72 Aligned_cols=50 Identities=48% Similarity=0.679 Sum_probs=45.9
Q ss_pred HHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 441 LIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 441 ~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
+| +.|||+|+.||.++| ++++|+.|||+.||+|+++|+++..+|++|||+
T Consensus 1 Al-~~L~~~er~vi~~~y---~~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 1 AL-DQLPPREREVIRLRY---FEGLTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp HH-CTS-HHHHHHHHHHH---TST-SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred Ch-hhCCHHHHHHHHHHh---cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 46 899999999999999 899999999999999999999999999999995
No 129
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=98.91 E-value=3.7e-09 Score=80.78 Aligned_cols=53 Identities=28% Similarity=0.464 Sum_probs=45.4
Q ss_pred HHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 010521 436 DEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL 492 (508)
Q Consensus 436 e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKL 492 (508)
+.|..+| ..|||++|.||.++| .+|+|+.|||+.+|+|.++|++.+.+|+++|
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 8999999999999999999999999999987
No 130
>PRK06930 positive control sigma-like factor; Validated
Probab=98.67 E-value=1e-07 Score=90.40 Aligned_cols=71 Identities=17% Similarity=0.156 Sum_probs=62.9
Q ss_pred ccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521 425 PWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 499 (508)
Q Consensus 425 Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~ 499 (508)
|.+.....+....|..+| +.||+++|.||.++| .+|+|++|||+.||+|.++|++++.+|+++|+..+...
T Consensus 95 ~~~~~~~~e~~~~l~~al-~~L~~rer~V~~L~~---~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~ 165 (170)
T PRK06930 95 EPESVISEWDKIRIEDAL-SVLTEREKEVYLMHR---GYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQINES 165 (170)
T ss_pred ChhHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 444445566778899999 899999999999998 79999999999999999999999999999999988743
No 131
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=98.62 E-value=8.2e-08 Score=78.70 Aligned_cols=76 Identities=32% Similarity=0.364 Sum_probs=58.2
Q ss_pred HHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCcc
Q 010521 348 ERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPW 426 (508)
Q Consensus 348 ~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe 426 (508)
+++++++++++.|. ++||.|+.+|||+.||+++++|..++.....+.||+.+.+ .+++.++.+++.|... .+|+
T Consensus 1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~----~~~~~~l~~~i~d~~~-~~P~ 75 (78)
T PF04539_consen 1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVG----DEDDSTLGDFIEDDDA-PSPE 75 (78)
T ss_dssp HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCS----SSSSEEGGGSSB-SSS---HH
T ss_pred ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeec----CCCCCchhheecCCCC-CChh
Confidence 35788999999995 7899999999999999999999999999999999999753 3345678888888753 4676
Q ss_pred ch
Q 010521 427 HG 428 (508)
Q Consensus 427 ~~ 428 (508)
+.
T Consensus 76 e~ 77 (78)
T PF04539_consen 76 EE 77 (78)
T ss_dssp HH
T ss_pred hc
Confidence 43
No 132
>PRK00118 putative DNA-binding protein; Validated
Probab=98.50 E-value=5.4e-07 Score=78.71 Aligned_cols=55 Identities=22% Similarity=0.310 Sum_probs=52.1
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM 501 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l 501 (508)
..||++++.||.++| .+++|..|||+.+|+|++||++++.+|+++||+++.+.++
T Consensus 16 ~~L~ekqRevl~L~y---~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~ 70 (104)
T PRK00118 16 SLLTEKQRNYMELYY---LDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHL 70 (104)
T ss_pred ccCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence 799999999999999 7999999999999999999999999999999999987654
No 133
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=98.33 E-value=1.7e-06 Score=64.01 Aligned_cols=54 Identities=41% Similarity=0.605 Sum_probs=49.1
Q ss_pred HHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 436 DEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 436 e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
+.+..++ ..||+.++.++.++| .+++|..+||+.+|+|..+|++++.++..+||
T Consensus 2 ~~~~~~~-~~l~~~~~~~~~~~~---~~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 2 ERLEEAL-DKLPEREREVILLRF---GEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred HHHHHHH-HhCCHHHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 3566777 899999999999999 78999999999999999999999999988874
No 134
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=98.23 E-value=3.8e-06 Score=76.89 Aligned_cols=58 Identities=21% Similarity=0.326 Sum_probs=50.6
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhh
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAML 505 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~~l 505 (508)
..||++|++||.+++ +|+|++|||+.||+|+++|++++++|+++|+.......+-.++
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 469999999999975 8999999999999999999999999999999876655554443
No 135
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=98.21 E-value=4.6e-06 Score=76.71 Aligned_cols=52 Identities=31% Similarity=0.367 Sum_probs=48.0
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 499 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~ 499 (508)
..|||+|++||.+++ +|+|++|||+.||+|+++|++++++|+++||+...--
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 579999999999965 8999999999999999999999999999999987653
No 136
>PRK04217 hypothetical protein; Provisional
Probab=98.15 E-value=3.6e-06 Score=74.31 Aligned_cols=56 Identities=29% Similarity=0.258 Sum_probs=51.6
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKME 502 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~ 502 (508)
..|++.|++||.++| .+++|++|||+.||||++||++++.+|+++|+..+......
T Consensus 41 ~~Lt~eereai~l~~---~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~~~ 96 (110)
T PRK04217 41 IFMTYEEFEALRLVD---YEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGREL 96 (110)
T ss_pred ccCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhccce
Confidence 679999999999998 89999999999999999999999999999999999765543
No 137
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=98.14 E-value=1.3e-05 Score=69.65 Aligned_cols=56 Identities=34% Similarity=0.481 Sum_probs=45.1
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKME 502 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~ 502 (508)
.-|+++|+.++.++| .+++|+.|||+.+|||+.+|...+.||.++|...-.+.++-
T Consensus 16 ~LLT~kQ~~~l~lyy---~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~yE~kL~l~ 71 (101)
T PF04297_consen 16 ELLTEKQREILELYY---EEDLSLSEIAEELGISRQAVYDSIKRAEKKLEEYEEKLGLV 71 (101)
T ss_dssp GGS-HHHHHHHHHHC---TS---HHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHHH-HH
T ss_pred HHCCHHHHHHHHHHH---ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhhH
Confidence 459999999999999 89999999999999999999999999999998766655543
No 138
>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=97.96 E-value=3e-06 Score=60.47 Aligned_cols=33 Identities=30% Similarity=0.483 Sum_probs=30.9
Q ss_pred hhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCc
Q 010521 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS 223 (508)
Q Consensus 191 ~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~ 223 (508)
|+++.||++|+++|+||++||++|+++|+.|+.
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 689999999999999999999999999999996
No 139
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=97.84 E-value=4.3e-05 Score=57.42 Aligned_cols=46 Identities=37% Similarity=0.536 Sum_probs=41.7
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
..|++.|+.|+.+. ..|+|..|||+.+|+|+.+|+++..+++++|+
T Consensus 2 ~~l~~~e~~i~~~~----~~g~s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 2 ASLTPREREVLRLL----AEGLTNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCCCHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 46899999999774 48899999999999999999999999998886
No 140
>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=97.83 E-value=7.9e-05 Score=67.93 Aligned_cols=62 Identities=18% Similarity=0.238 Sum_probs=53.5
Q ss_pred HHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 433 ALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 433 el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
...+.|..+| +.|++.++.||.++|+ +...+|+.+||..||+|+.+|.++..+++.+|+..+
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-NEADEQTRVIIQELYM-KKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEEL 132 (134)
T ss_pred HHHHHHHHHH-HhCCHHHHHHHHHHHc-cCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 4556788888 8999999999999993 112359999999999999999999999999999765
No 141
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=97.73 E-value=7e-05 Score=58.11 Aligned_cols=47 Identities=28% Similarity=0.437 Sum_probs=41.4
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
+.|+++|.+|+.+.. .|+|..|||+.+|+|..||+....++++||.-
T Consensus 2 ~~LT~~E~~vl~~l~----~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 2 PSLTERELEVLRLLA----QGMSNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp GSS-HHHHHHHHHHH----TTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred CccCHHHHHHHHHHH----hcCCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 479999999999986 89999999999999999999999999999863
No 142
>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This entry is represented by Streptococcus phage 7201, Orf19. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several hypothetical, highly conserved Streptococcal and related phage proteins. The function of this family is unknown.
Probab=97.72 E-value=0.00013 Score=63.22 Aligned_cols=56 Identities=34% Similarity=0.506 Sum_probs=49.6
Q ss_pred HHHHHHHHHHHccCC-HHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 010521 433 ALKDEVNKLIIVTLG-EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL 492 (508)
Q Consensus 433 el~e~L~~~L~~~Lp-~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKL 492 (508)
.....+..+| +.|+ +.+|.||.++| .+++++.+||+.||+|+.++-.++.+|++.|
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 3446678888 6775 78999999999 8999999999999999999999999999876
No 143
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=97.70 E-value=9.4e-05 Score=55.78 Aligned_cols=45 Identities=33% Similarity=0.405 Sum_probs=40.9
Q ss_pred CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
|+++|+.|+.+.+ +++|.+|||+.+|+|+.+|+++..+++++|+.
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 78999999999999999999999999888875
No 144
>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=97.63 E-value=0.00018 Score=55.53 Aligned_cols=47 Identities=32% Similarity=0.487 Sum_probs=41.7
Q ss_pred CCHHHHHHHhHHhccCC----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 010521 446 LGEREREIIRLYYGLDK----ECLTWEDISKRIGLSRERVRQVGLVALEKL 492 (508)
Q Consensus 446 Lp~rER~VI~LryGLd~----eg~TleEIAe~LgIS~erVrqi~~rALkKL 492 (508)
|+++|++||..-|-+++ .+.|+.|||+.||||.+|+..++.+|.+||
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 78999999999776542 368999999999999999999999999886
No 145
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=97.63 E-value=0.00011 Score=60.28 Aligned_cols=47 Identities=13% Similarity=0.075 Sum_probs=40.6
Q ss_pred HHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 438 VNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 438 L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
+.+.| +.||++.+.++.|.+. .+++|++|||+.||+|..+|++++.+
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 44556 8999999999999531 58999999999999999999999875
No 146
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=97.46 E-value=0.0002 Score=69.56 Aligned_cols=46 Identities=17% Similarity=0.226 Sum_probs=43.6
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
.|++||++|+.+.- +|+|.+|||++||+|..||+....+.++||.-
T Consensus 137 ~LT~RE~eVL~lla----~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v 182 (207)
T PRK15411 137 SLSRTESSMLRMWM----AGQGTIQISDQMNIKAKTVSSHKGNIKRKIKT 182 (207)
T ss_pred cCCHHHHHHHHHHH----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence 49999999999985 99999999999999999999999999999973
No 147
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=97.45 E-value=0.00021 Score=61.35 Aligned_cols=50 Identities=18% Similarity=0.278 Sum_probs=41.1
Q ss_pred HHHHHHHHccCCHHHHHHHhHHhccCC----CCCCHHHHHHHHCCCHHHHHHHH
Q 010521 436 DEVNKLIIVTLGEREREIIRLYYGLDK----ECLTWEDISKRIGLSRERVRQVG 485 (508)
Q Consensus 436 e~L~~~L~~~Lp~rER~VI~LryGLd~----eg~TleEIAe~LgIS~erVrqi~ 485 (508)
+.+...|..-|+|+|+.+|.+||||-. .++|++|||+.+|||+.+|.+..
T Consensus 23 ~~l~~~l~~lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~s 76 (94)
T TIGR01321 23 DDMQLLLELILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGS 76 (94)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHH
Confidence 445555545699999999999999943 58999999999999999997543
No 148
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=97.43 E-value=0.0003 Score=66.89 Aligned_cols=47 Identities=17% Similarity=0.269 Sum_probs=44.3
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
..|+++|++|+.+.- +|+|.+|||+.|++|..||+....++++||.-
T Consensus 132 ~~LSpRErEVLrLLA----qGkTnKEIAe~L~IS~rTVkth~srImkKLgV 178 (198)
T PRK15201 132 RHFSVTERHLLKLIA----SGYHLSETAALLSLSEEQTKSLRRSIMRKLHV 178 (198)
T ss_pred CCCCHHHHHHHHHHH----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 579999999999985 99999999999999999999999999999974
No 149
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=97.39 E-value=0.0003 Score=68.66 Aligned_cols=46 Identities=22% Similarity=0.322 Sum_probs=43.7
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
..|++||++|+.+.- +|+|.+|||+.|++|..||+....+.++||.
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 8999999999999999999999999999994
No 150
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=97.37 E-value=0.00032 Score=68.78 Aligned_cols=50 Identities=10% Similarity=0.068 Sum_probs=46.1
Q ss_pred HHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 439 NKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 439 ~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
.+++ ..|+|+|++|+.+.- +|+|.+|||+.|++|..||+....+.++||.
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 4455 789999999999985 8999999999999999999999999999986
No 151
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=97.37 E-value=0.00032 Score=67.47 Aligned_cols=46 Identities=26% Similarity=0.371 Sum_probs=43.4
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
..|++||++|+.+.- +|+|.+|||+.|++|..||+....+.++||.
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 469999999999985 8999999999999999999999999999994
No 152
>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=97.28 E-value=0.00043 Score=68.53 Aligned_cols=47 Identities=30% Similarity=0.239 Sum_probs=44.2
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
..|+++|++||.+.. +|+|..|||+.||+|..||+..+.++++||+.
T Consensus 170 ~~Lt~re~evl~~~a----~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~ 216 (232)
T TIGR03541 170 GVLSEREREVLAWTA----LGRRQADIAAILGISERTVENHLRSARRKLGV 216 (232)
T ss_pred ccCCHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence 479999999999975 99999999999999999999999999999984
No 153
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=97.26 E-value=0.00046 Score=69.30 Aligned_cols=47 Identities=26% Similarity=0.237 Sum_probs=44.2
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
..|+++|++|+.+.. +|+|..|||+.||||..||+..+.++++||..
T Consensus 189 ~~LT~RE~evl~l~a----~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v 235 (247)
T TIGR03020 189 GLITAREAEILAWVR----DGKTNEEIAAILGISSLTVKNHLQHIFKKLDV 235 (247)
T ss_pred cCCCHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence 579999999999975 99999999999999999999999999999974
No 154
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=97.26 E-value=0.00066 Score=59.58 Aligned_cols=53 Identities=32% Similarity=0.338 Sum_probs=48.7
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 500 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~ 500 (508)
.|+..|-+.|+|.+ .+++|++|.|+.||||+.|+..++..|.+|+-..|-...
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 58889999999998 899999999999999999999999999999998886543
No 155
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=97.26 E-value=0.0012 Score=63.37 Aligned_cols=68 Identities=19% Similarity=0.243 Sum_probs=56.6
Q ss_pred HHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHh
Q 010521 432 WALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAM 504 (508)
Q Consensus 432 ~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~~ 504 (508)
......+...+ .+|+||||+|+.... .|+..++||..||||..||+....+.++||+..--..-++.|
T Consensus 130 ~~~~~~~~~~l-~tLT~RERqVl~~vV----~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~SlaeLvr~a 197 (202)
T COG4566 130 ADRQAAIRARL-ATLTPRERQVLDLVV----RGLMNKQIAFDLGISERTVELHRANVMEKMQARSLAELVRMA 197 (202)
T ss_pred HHHHHHHHHHH-HhcCHHHHHHHHHHH----cCcccHHHHHHcCCchhhHHHHHHHHHHHHhhccHHHHHHHH
Confidence 34456777788 899999999999885 899999999999999999999999999999875544444433
No 156
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=97.25 E-value=0.00047 Score=67.40 Aligned_cols=45 Identities=33% Similarity=0.403 Sum_probs=42.9
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
.|++||++|+++-- +|+|.+|||+.|++|..||+....+.++||.
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 59999999999974 9999999999999999999999999999996
No 157
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=97.24 E-value=0.00058 Score=67.08 Aligned_cols=47 Identities=19% Similarity=0.214 Sum_probs=44.2
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
..|+++|++|+.+.. +|+|.+|||+.|++|..||+....++++||.-
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 469999999999997 79999999999999999999999999999974
No 158
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=97.19 E-value=0.00048 Score=50.88 Aligned_cols=41 Identities=27% Similarity=0.320 Sum_probs=24.5
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
.+|++.||..|...+ .+|+|..+||+.||++++||...+.|
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 478999999998887 78999999999999999999988776
No 159
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=97.18 E-value=0.00068 Score=67.63 Aligned_cols=46 Identities=22% Similarity=0.243 Sum_probs=43.6
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
.|++||++||.+.. +|+|..|||++||||..||+..+.++++||-.
T Consensus 179 ~LT~rE~evl~~~a----~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~~ 224 (240)
T PRK10188 179 NFSKREKEILKWTA----EGKTSAEIAMILSISENTVNFHQKNMQKKFNA 224 (240)
T ss_pred CCCHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 69999999999986 99999999999999999999999999999963
No 160
>PRK13870 transcriptional regulator TraR; Provisional
Probab=97.18 E-value=0.00065 Score=67.52 Aligned_cols=45 Identities=22% Similarity=0.202 Sum_probs=42.8
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
.|++||++||.+-= +|+|..|||.+||||..||+..+..|++||-
T Consensus 173 ~LT~RE~E~L~W~A----~GKT~~EIa~ILgISe~TV~~Hl~na~~KLg 217 (234)
T PRK13870 173 WLDPKEATYLRWIA----VGKTMEEIADVEGVKYNSVRVKLREAMKRFD 217 (234)
T ss_pred CCCHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 59999999999985 9999999999999999999999999999995
No 161
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=97.02 E-value=0.0021 Score=49.92 Aligned_cols=47 Identities=32% Similarity=0.379 Sum_probs=43.1
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
..|+++|.+|+.+.- +|+|..|||..+|+|..||+....++..||.-
T Consensus 3 ~~Lt~rE~~v~~l~~----~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~ 49 (65)
T COG2771 3 ADLTPREREILRLVA----QGKSNKEIARILGISEETVKTHLRNIYRKLGV 49 (65)
T ss_pred ccCCHHHHHHHHHHH----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence 369999999998875 78999999999999999999999999999874
No 162
>PRK09483 response regulator; Provisional
Probab=97.00 E-value=0.0013 Score=62.04 Aligned_cols=46 Identities=26% Similarity=0.351 Sum_probs=42.8
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
..|+++|++|+.+.. +|+|.+|||+.|++|..||+...++.++||-
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 569999999998864 8999999999999999999999999999984
No 163
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=96.84 E-value=0.0025 Score=58.70 Aligned_cols=46 Identities=33% Similarity=0.435 Sum_probs=42.8
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
..|+++|++|+.+. .+|+|.+|||+.+++|..||+....++++||.
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 48999999999999999999999999999996
No 164
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=96.81 E-value=0.0062 Score=52.70 Aligned_cols=50 Identities=18% Similarity=0.312 Sum_probs=44.6
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
.-|+++|+..+.++| .+++|+.|||+.++||+++|...+.|+-+.|-..=
T Consensus 16 sLLT~KQ~~Y~~lyy---~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~YE 65 (105)
T COG2739 16 SLLTKKQKNYLELYY---LDDLSLSEIAEEFNVSRQAIYDNIKRTEKILEDYE 65 (105)
T ss_pred HHHhHHHHHHHHHHH---HhhccHHHHHHHhCccHHHHHHHHHHHHHHHHHHH
Confidence 348999999999999 88999999999999999999999999887776543
No 165
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=96.75 E-value=0.0031 Score=61.76 Aligned_cols=52 Identities=27% Similarity=0.405 Sum_probs=45.0
Q ss_pred cCCHHHHHHHhHHhccCC----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDK----ECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~----eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
.|+++|++||+.-|=.|+ ...+.+|||+.||||.+|+.+++.+|.+||=..+
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 599999999999886642 3589999999999999999999999999985443
No 166
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=96.72 E-value=0.036 Score=57.72 Aligned_cols=159 Identities=12% Similarity=0.034 Sum_probs=96.4
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccH
Q 010521 267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHL 346 (508)
Q Consensus 267 e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~ 346 (508)
+..+..-.+.++.---+|.++=.-+||.+|++|+..++...+=-|-+ .-..|++.--|+.-++.+++..+.-..|.+.
T Consensus 8 e~~~r~~~~r~~a~L~r~~rd~dlAEEa~~dA~~~Ale~WPr~G~P~--~PaAWL~~v~R~~aiD~~Rr~~~~~~~~~el 85 (415)
T COG4941 8 EAAARIERPRAMAALARYLRDLDLAEEALQDAFAAALERWPRAGPPR--NPAAWLIAVGRNRAIDRVRRRARRDAAPPEL 85 (415)
T ss_pred HHHHHHhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHhCcccCCCC--ChHHHHHHHHhhhHHHHHHHHHHhccCChhh
Confidence 34444455555555566777656789999999987665554433323 2456777777776666666654322222110
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCcc
Q 010521 347 HERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPW 426 (508)
Q Consensus 347 ~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe 426 (508)
.++.+ +.+....+...|.. -+
T Consensus 86 ----------------------------------------------~~~~e---------~~e~~~a~~~~d~~---i~- 106 (415)
T COG4941 86 ----------------------------------------------LLSDE---------DEEMEEAEALDDEH---IR- 106 (415)
T ss_pred ----------------------------------------------ccccc---------chhhhccccccccc---cc-
Confidence 00000 00000111111111 11
Q ss_pred chHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 427 HGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 427 ~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
.+....|.-+-.-.||+.+|--+.|+. ..|+|..|||..|=|+..++-|++.||.++++.
T Consensus 107 -----Dd~LRLiFvccHPal~~~~riALtLR~---v~GLs~~eIArAFLv~e~am~QRivRAK~ri~~ 166 (415)
T COG4941 107 -----DDRLRLIFVCCHPALPPEQRIALTLRL---VGGLSTAEIARAFLVPEAAMAQRIVRAKARIRE 166 (415)
T ss_pred -----hhhHHhhhhhcCCCCChhhHHHHHHHH---HcCCcHHHHHHHHcCCcHHHHHHHHHHHHHHHh
Confidence 112222222222579999999999998 789999999999999999999999999999985
No 167
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=96.66 E-value=0.0021 Score=72.53 Aligned_cols=58 Identities=22% Similarity=0.356 Sum_probs=47.1
Q ss_pred hhhhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHH
Q 010521 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREK 268 (508)
Q Consensus 189 ~~~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~ 268 (508)
..|+++|||++||++||||.++|+++|++|..|.. .+.+.+.+++-+...
T Consensus 102 t~DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~------------------------------~v~~al~~~P~~i~~ 151 (619)
T PRK05658 102 TDDPVRMYLREMGTVELLTREGEIEIAKRIEAGEN------------------------------IMIAALCESPLTIDA 151 (619)
T ss_pred CCChHHHHHHHhccCcCCCcHHHHHHHHHHHHHHH------------------------------HHHHHHHhCcHHHHH
Confidence 35899999999999999999999999999999996 455555566666666
Q ss_pred HHHHHHHH
Q 010521 269 LVMSNVRL 276 (508)
Q Consensus 269 LIe~yl~L 276 (508)
++.-|-.+
T Consensus 152 il~~~e~v 159 (619)
T PRK05658 152 ILEWYDRL 159 (619)
T ss_pred HHHHHHHH
Confidence 66666554
No 168
>PRK10651 transcriptional regulator NarL; Provisional
Probab=96.59 E-value=0.004 Score=58.08 Aligned_cols=46 Identities=28% Similarity=0.392 Sum_probs=43.0
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
..|+++|++|+.+.. +|++.++||+.+++|..||+....++++||.
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 469999999999865 8999999999999999999999999999996
No 169
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=96.52 E-value=0.0067 Score=55.51 Aligned_cols=55 Identities=20% Similarity=0.319 Sum_probs=47.6
Q ss_pred HHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 437 EVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 437 ~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
.+...+ ..|+++|+.|+.+.+ .+++.++||+.+|+|..+|+....++++||+..-
T Consensus 134 ~~~~~~-~~l~~~e~~vl~~~~----~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~~ 188 (202)
T PRK09390 134 DIRARI-ASLSERERQVMDGLV----AGLSNKVIARDLDISPRTVEVYRANVMTKMQAGS 188 (202)
T ss_pred HHHHHH-HhhhhhHHHHHHHHH----ccCchHHHHHHcCCCHHHHHHHHHHHHHHHcccc
Confidence 345556 789999999999754 7899999999999999999999999999997543
No 170
>PF12645 HTH_16: Helix-turn-helix domain; InterPro: IPR024760 This domain appears to be a helix-turn-helix domain, suggesting a transcriptional regulatory protein. Some proteins with this domain are annotated as conjugative transposon proteins.
Probab=96.52 E-value=0.0097 Score=47.78 Aligned_cols=47 Identities=26% Similarity=0.208 Sum_probs=40.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcC------CCCCHHHHHHHHHHHHHHhhhccC
Q 010521 264 LAREKLVMSNVRLVMSIAQRYDN------MGADMADLVQGGLIGLLRGIEKFD 310 (508)
Q Consensus 264 ~A~e~LIe~yl~LV~sIAkrY~~------~g~d~EDLiQEG~IgLirAiekFD 310 (508)
.|.++++.+|.|++.+.+.+-.. ++.--+|+-|+--..|++++.+|+
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 99999999999999999987221 244459999999999999999996
No 171
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=96.49 E-value=0.0024 Score=57.30 Aligned_cols=49 Identities=24% Similarity=0.316 Sum_probs=45.1
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
.-|+++|-.|+.||- .|.|++|||++||.|+..|+-++.+|+.++.+.-
T Consensus 7 tflte~qikvl~lRe----kG~tQ~eIA~~L~TTraNvSaIEkrA~enIekar 55 (143)
T COG1356 7 TFLTEQQIKVLVLRE----KGLTQSEIARILKTTRANVSAIEKRALENIEKAR 55 (143)
T ss_pred ceeehhheeeeehhh----ccccHHHHHHHHccchhhHHHHHHHHHHHHHHHH
Confidence 358999999999995 8999999999999999999999999999998754
No 172
>PRK01381 Trp operon repressor; Provisional
Probab=96.45 E-value=0.0032 Score=54.50 Aligned_cols=48 Identities=19% Similarity=0.254 Sum_probs=38.6
Q ss_pred HHHHHHHHHccCCHHHHHHHhHHhccCC---C-CCCHHHHHHHHCCCHHHHH
Q 010521 435 KDEVNKLIIVTLGEREREIIRLYYGLDK---E-CLTWEDISKRIGLSRERVR 482 (508)
Q Consensus 435 ~e~L~~~L~~~Lp~rER~VI~LryGLd~---e-g~TleEIAe~LgIS~erVr 482 (508)
.+.+...|..-|+|.|+..|..|+++-. + ++|++|||+.+|||..||.
T Consensus 22 ~~~~~~~l~~llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTIT 73 (99)
T PRK01381 22 EDLHLPLLTLLLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATIT 73 (99)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeeh
Confidence 3445555534499999999999999832 4 5999999999999999885
No 173
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=96.37 E-value=0.0079 Score=51.55 Aligned_cols=52 Identities=31% Similarity=0.293 Sum_probs=47.4
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 499 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~ 499 (508)
.|+..|-+.|+|.. +++++++|-|.+||||+.|+-+.+..|++|+-.+|-..
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 89999999999999999999999999999999887654
No 174
>PRK15320 transcriptional activator SprB; Provisional
Probab=96.31 E-value=0.0072 Score=58.59 Aligned_cols=46 Identities=13% Similarity=0.148 Sum_probs=43.2
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
-.|+++|.+|+.+-- +|+|.+|||+.|++|..||+....+.+.||.
T Consensus 163 ~~LSdREIEVL~LLA----kG~SNKEIAekL~LS~KTVSTYKnRLLeKLg 208 (251)
T PRK15320 163 PGVTQAKYALLILLS----SGHPAIELAKKFGLGTKTVSIYRKKVMYRLG 208 (251)
T ss_pred CCCCHHHHHHHHHHH----cCCCHHHHHHHhccchhhHHHHHHHHHHHcC
Confidence 578999999999875 8999999999999999999999999999986
No 175
>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=96.18 E-value=0.033 Score=50.26 Aligned_cols=61 Identities=20% Similarity=0.190 Sum_probs=49.9
Q ss_pred HHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521 436 DEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497 (508)
Q Consensus 436 e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~ 497 (508)
..+..++...|++.+|.||..+| |+.++++..+|+..||+|+.+...+..+|+.++-..+.
T Consensus 70 ~~i~~ai~~~l~~~~r~Il~~~Y-l~~~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~l~ 130 (132)
T TIGR01637 70 RAIVNAIVNQLDEISRQILYDKY-LEPDQKYDYQIMMELGYSHRQYYRIKKRALLRFATLYG 130 (132)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHH-cCccccchHHHHHHhCCcHHHHHHHHHHHHHHHHHHhC
Confidence 34444442589999999999999 22238999999999999999999999999999877653
No 176
>PRK10403 transcriptional regulator NarP; Provisional
Probab=95.98 E-value=0.012 Score=54.62 Aligned_cols=48 Identities=23% Similarity=0.246 Sum_probs=43.5
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA 495 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~ 495 (508)
..|+++|.+|+.+.. +|+|.++||+.+++|..||+..+.+.++||.-.
T Consensus 152 ~~Lt~~e~~vl~~~~----~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~ 199 (215)
T PRK10403 152 SVLTERELDVLHELA----QGLSNKQIASVLNISEQTVKVHIRNLLRKLNVR 199 (215)
T ss_pred ccCCHHHHHHHHHHH----CCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 359999999998875 889999999999999999999999999998643
No 177
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=95.83 E-value=0.02 Score=52.97 Aligned_cols=46 Identities=26% Similarity=0.342 Sum_probs=42.8
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
..|+++|++|+.+.. +|+|.++||+.+++|..||+....+.++||.
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 469999999999975 7899999999999999999999999999986
No 178
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=95.82 E-value=0.018 Score=53.58 Aligned_cols=45 Identities=27% Similarity=0.290 Sum_probs=41.0
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
.|+++|..|+.+.. +|+|.+|||+.|++|..||+....++++||.
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 58999999987654 7899999999999999999999999999986
No 179
>PRK13558 bacterio-opsin activator; Provisional
Probab=95.72 E-value=0.016 Score=65.25 Aligned_cols=52 Identities=23% Similarity=0.222 Sum_probs=44.2
Q ss_pred ccCCHHHHHHHhHHhccCC----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDK----ECLTWEDISKRIGLSRERVRQVGLVALEKLKHA 495 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~----eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~ 495 (508)
..|+++|+++|..-|-.++ .+.|.+|||+.||||++|+.+++.+|.+||=..
T Consensus 606 ~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l~~~ 661 (665)
T PRK13558 606 NDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKLVGA 661 (665)
T ss_pred hhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 5799999999999984331 234999999999999999999999999998543
No 180
>PRK04841 transcriptional regulator MalT; Provisional
Probab=95.71 E-value=0.016 Score=67.28 Aligned_cols=46 Identities=20% Similarity=0.288 Sum_probs=43.3
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
..|+++|++|+.+.. +|+|++|||+.|+||..||+..+.+...||.
T Consensus 837 ~~lt~~e~~v~~~~~----~g~~~~~ia~~l~~s~~tv~~h~~~~~~kl~ 882 (903)
T PRK04841 837 SPLTQREWQVLGLIY----SGYSNEQIAGELDVAATTIKTHIRNLYQKLG 882 (903)
T ss_pred CCCCHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 359999999999976 9999999999999999999999999999996
No 181
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=95.55 E-value=0.028 Score=52.41 Aligned_cols=46 Identities=22% Similarity=0.294 Sum_probs=42.7
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
..|+++|++|+.+.. .|.|.++||+.+++|..||+....+.++||.
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 469999999999876 7899999999999999999999999999984
No 182
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=95.34 E-value=0.016 Score=43.20 Aligned_cols=32 Identities=38% Similarity=0.412 Sum_probs=23.4
Q ss_pred HHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521 453 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 453 VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA 488 (508)
||.++. +|+|..+||+.||||+.||.++..+-
T Consensus 10 ii~l~~----~G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 10 IIRLLR----EGWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp HHHHHH----HT--HHHHHHHHTS-HHHHHHHHT--
T ss_pred HHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 666665 69999999999999999999987664
No 183
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=95.21 E-value=0.026 Score=39.11 Aligned_cols=27 Identities=41% Similarity=0.598 Sum_probs=19.4
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 464 CLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 464 g~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
++|.+|||+.+|++++||+ |++++|++
T Consensus 2 ~mtr~diA~~lG~t~ETVS----R~l~~l~~ 28 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVS----RILKKLER 28 (32)
T ss_dssp E--HHHHHHHHTS-HHHHH----HHHHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHH----HHHHHHHH
Confidence 3799999999999999997 55555553
No 184
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=95.17 E-value=0.046 Score=41.80 Aligned_cols=50 Identities=22% Similarity=0.326 Sum_probs=41.9
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
+|+..++-++.+.|- ..+.++++||..+|||++||+++.+..+.-|-..+
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 578888888877662 46899999999999999999999999888776543
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=95.10 E-value=0.056 Score=40.02 Aligned_cols=42 Identities=21% Similarity=0.343 Sum_probs=30.4
Q ss_pred CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
|++.++.||..-.- ..++|..|||+.+|+|..+|++++.+-.
T Consensus 1 l~~~~~~Il~~l~~--~~~~t~~ela~~~~is~~tv~~~l~~L~ 42 (48)
T PF13412_consen 1 LDETQRKILNYLRE--NPRITQKELAEKLGISRSTVNRYLKKLE 42 (48)
T ss_dssp --HHHHHHHHHHHH--CTTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH--cCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 57788888877651 3569999999999999999987766543
No 186
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=95.07 E-value=0.029 Score=58.43 Aligned_cols=36 Identities=31% Similarity=0.510 Sum_probs=33.0
Q ss_pred HHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010521 452 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALE 490 (508)
Q Consensus 452 ~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALk 490 (508)
.|-.||| .+++|+.|||++||+||.+|++++.+|++
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 3667888 89999999999999999999999999976
No 187
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=94.93 E-value=0.09 Score=47.93 Aligned_cols=56 Identities=23% Similarity=0.422 Sum_probs=44.5
Q ss_pred HHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 010521 435 KDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL 492 (508)
Q Consensus 435 ~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKL 492 (508)
.+.+...+ +.|.+.++.||.+||+- ..++|+.+||..|+++..|++.+...-...+
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 34555666 89999999999999952 1469999999999999999988776654433
No 188
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=94.83 E-value=0.064 Score=45.67 Aligned_cols=39 Identities=21% Similarity=0.345 Sum_probs=32.0
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA 488 (508)
+.|++| ..|+.+.- .|+|..+||+.+|||+.||.++ .++
T Consensus 35 ~~Ls~R-~~I~~ll~----~G~S~~eIA~~LgISrsTIyRi-~R~ 73 (88)
T TIGR02531 35 QSLAQR-LQVAKMLK----QGKTYSDIEAETGASTATISRV-KRC 73 (88)
T ss_pred HhhhHH-HHHHHHHH----CCCCHHHHHHHHCcCHHHHHHH-HHh
Confidence 467888 77777753 7899999999999999999984 444
No 189
>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=94.19 E-value=0.093 Score=34.51 Aligned_cols=37 Identities=22% Similarity=0.292 Sum_probs=28.9
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQV 484 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi 484 (508)
.+++.++..+...+ ..+.|..+||+.+|+++.+|.++
T Consensus 5 ~~~~~~~~~i~~~~---~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 5 KLTPEQIEEARRLL---AAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred cCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHh
Confidence 35566666665556 47789999999999999999875
No 190
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=94.18 E-value=0.076 Score=39.21 Aligned_cols=32 Identities=34% Similarity=0.456 Sum_probs=24.0
Q ss_pred HHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHH
Q 010521 450 EREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVG 485 (508)
Q Consensus 450 ER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~ 485 (508)
...|+.|+- +|+|..+||+.+|||+.||.+++
T Consensus 11 ~~~i~~l~~----~G~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 11 IEEIKELYA----EGMSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp HHHHHHHHH----TT--HHHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHH
Confidence 455777764 78999999999999999998765
No 191
>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 993W gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator. GpQ positively regulates expression of the phage late gene operons. Bacterial host RNA polymerase modified by antitermination proteins transcribes through termination sites that otherwise prevent expression of the regulated genes [, ].; GO: 0003677 DNA binding, 0060567 negative regulation of transcription termination, DNA-dependent
Probab=93.94 E-value=0.35 Score=43.62 Aligned_cols=55 Identities=15% Similarity=0.158 Sum_probs=49.2
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM 501 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l 501 (508)
.+-.|.+-.+|.+|| ..+.|...||..+++|...|++.+.+|-.-+...|...+.
T Consensus 61 ~~~~~~~~~ll~~~Y---v~g~s~r~IA~~~~~s~~~ir~~l~~ae~~i~g~l~~~~~ 115 (125)
T PF06530_consen 61 KKRDPEEYDLLILYY---VYGWSKRQIARKLKCSEGKIRKRLQRAEGFIDGCLSMLTI 115 (125)
T ss_pred HccCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHhhhhHhhhhHHhhh
Confidence 468899999999999 7899999999999999999999999999999988765443
No 192
>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=93.52 E-value=0.091 Score=42.74 Aligned_cols=36 Identities=33% Similarity=0.540 Sum_probs=28.0
Q ss_pred chhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhh
Q 010521 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (508)
Q Consensus 225 ~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~ 260 (508)
..++.+|...+||+|+.+++|..+||+.+++...+.
T Consensus 7 ~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~ 42 (78)
T PF04539_consen 7 ERARRELEQELGREPTDEEIAEELGISVEEVRELLQ 42 (78)
T ss_dssp HHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHH
Confidence 356778999999999999999999999998776654
No 193
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=92.84 E-value=0.21 Score=39.21 Aligned_cols=32 Identities=19% Similarity=0.251 Sum_probs=27.1
Q ss_pred HHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521 453 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 453 VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA 488 (508)
...|+. +|++..|||+.||+++.||.....+-
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 194
>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]
Probab=92.83 E-value=0.12 Score=59.67 Aligned_cols=45 Identities=27% Similarity=0.276 Sum_probs=42.8
Q ss_pred CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
|+.||++|+.+.| .|+|.+|||+++.||-.||+..+.....||.-
T Consensus 832 Ls~RE~eVL~Lia----~G~SN~eIa~~L~isl~TVKtH~rniy~KLgV 876 (894)
T COG2909 832 LSQRELEVLGLIA----QGLSNEEIAQELFISLTTVKTHIRNIYQKLGV 876 (894)
T ss_pred ccHHHHHHHHHHH----ccCCHHHHHHHHHHHHHHHHHHHHHHHHHhCc
Confidence 8999999999998 99999999999999999999999999999863
No 195
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=92.80 E-value=0.2 Score=40.23 Aligned_cols=43 Identities=21% Similarity=0.297 Sum_probs=27.5
Q ss_pred ccCCHHHHHHHhHHhc-c--CCCCCCHHHHHHHHCCC-HHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYG-L--DKECLTWEDISKRIGLS-RERVRQVGL 486 (508)
Q Consensus 444 ~~Lp~rER~VI~LryG-L--d~eg~TleEIAe~LgIS-~erVrqi~~ 486 (508)
..|+++|++|+...-. + ++-.-|.+|||+.||++ .++|.+.+.
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 5799999999876322 1 23467999999999996 999976654
No 196
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=92.50 E-value=0.31 Score=43.39 Aligned_cols=48 Identities=27% Similarity=0.342 Sum_probs=42.5
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
..|++.+..-|..+. ...=+++|+++.||||..|||.++.+.+++|.-
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 689999999887766 445699999999999999999999999999875
No 197
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=92.46 E-value=0.33 Score=35.54 Aligned_cols=40 Identities=28% Similarity=0.427 Sum_probs=26.8
Q ss_pred CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
|++..+.||..--. ....|+.+||+.+|+|..+|.+++.+
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 34556677766441 24589999999999999999877654
No 198
>PF13518 HTH_28: Helix-turn-helix domain
Probab=92.43 E-value=0.2 Score=37.17 Aligned_cols=34 Identities=26% Similarity=0.343 Sum_probs=27.1
Q ss_pred HHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 452 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 452 ~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
.||.++. ++.|..+||+.+|||+.+|.+++.+-.
T Consensus 4 ~iv~~~~----~g~s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 4 QIVELYL----EGESVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred HHHHHHH----cCCCHHHHHHHHCCCHhHHHHHHHHHH
Confidence 3555544 677999999999999999998877653
No 199
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=92.42 E-value=0.22 Score=48.75 Aligned_cols=46 Identities=9% Similarity=0.147 Sum_probs=36.0
Q ss_pred cCCHHHHHHHhHHh-ccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYY-GLDKECLTWEDISKRIGLSRERVRQVGLVALE 490 (508)
Q Consensus 445 ~Lp~rER~VI~Lry-GLd~eg~TleEIAe~LgIS~erVrqi~~rALk 490 (508)
.|++++.+++.... +...+|+|.+|||+.||+|..||+....++..
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 58888877664432 22247899999999999999999999987744
No 200
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=92.39 E-value=0.17 Score=52.96 Aligned_cols=35 Identities=40% Similarity=0.533 Sum_probs=31.2
Q ss_pred HHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010521 453 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALE 490 (508)
Q Consensus 453 VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALk 490 (508)
+-.+|| .+|+|+.|||++||||+.+|++.+.+|.+
T Consensus 18 ~A~lYY---~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~ 52 (321)
T COG2390 18 AAWLYY---VEGLTQSEIAERLGISRATVSRLLAKARE 52 (321)
T ss_pred HHHHHH---hcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 445777 79999999999999999999999998875
No 201
>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=92.23 E-value=0.23 Score=39.36 Aligned_cols=35 Identities=17% Similarity=0.354 Sum_probs=26.5
Q ss_pred HHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 452 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 452 ~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
..+.++... ...+++.+||+.||||..||+.+..+
T Consensus 11 kA~e~y~~~-~g~i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 11 KAFEIYKES-NGKIKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred HHHHHHHHh-CCCccHHHHHHHHCCCHHHHHHHhhh
Confidence 345554421 35799999999999999999988764
No 202
>smart00351 PAX Paired Box domain.
Probab=92.17 E-value=0.34 Score=43.61 Aligned_cols=41 Identities=22% Similarity=0.135 Sum_probs=32.8
Q ss_pred CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
++..+|.=|...| .+|.|..+||+.||||+.||.+++.+..
T Consensus 18 ~s~~~R~riv~~~---~~G~s~~~iA~~~gvs~~tV~kwi~r~~ 58 (125)
T smart00351 18 LPDEERQRIVELA---QNGVRPCDISRQLCVSHGCVSKILGRYY 58 (125)
T ss_pred CCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 5555555444555 4789999999999999999999998864
No 203
>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=92.10 E-value=0.16 Score=39.04 Aligned_cols=40 Identities=25% Similarity=0.216 Sum_probs=27.5
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
.|+-.|+.=|.-++ ..|.+..+||+.|||+++||+.|...
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 46666666444445 57889999999999999999998765
No 204
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=91.86 E-value=0.31 Score=37.48 Aligned_cols=44 Identities=18% Similarity=0.225 Sum_probs=32.6
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA 488 (508)
.|++.|..||..-+.-+..++|..|||+.+++++.+|.+++.+-
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 37788888887765422233899999999999999998776553
No 205
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=91.35 E-value=5.8 Score=40.07 Aligned_cols=63 Identities=22% Similarity=0.403 Sum_probs=45.7
Q ss_pred hhhhHHHHHHhhc--ccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhh
Q 010521 189 IQNRLKGYVKGVV--SEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (508)
Q Consensus 189 ~~~~~~~yl~~i~--~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e 261 (508)
+-+.+.+||+... ..| --..++.++ ...+..+|...+|++|+++++|..+|++.++....+..
T Consensus 85 I~Gei~d~LR~~~~v~vp----R~~~~~~~~------i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~ 149 (247)
T COG1191 85 IRGEILDYLRKNDSVKVP----RSLRELGRR------IEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLA 149 (247)
T ss_pred HHHHHHHHHHhCCCccCc----HHHHHHHHH------HHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHH
Confidence 4467788999877 444 334444444 34566789999999999999999999999875555443
No 206
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=91.32 E-value=2.9 Score=44.10 Aligned_cols=32 Identities=31% Similarity=0.509 Sum_probs=30.4
Q ss_pred hhHHHHHHhhcccCCCCHHHHHHHHHHHHcCC
Q 010521 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGL 222 (508)
Q Consensus 191 ~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd 222 (508)
+.+..|+..+...|+|+++||..|+++++.|+
T Consensus 67 ~~~~~~~~~~~~~~~l~~~Ee~~la~~~~~g~ 98 (342)
T COG0568 67 GRLSFYIRAIEAAPLLTPEEEKALARRLKRGE 98 (342)
T ss_pred hhHHHHHHHHhhhcccChHHHHHHHHHHHcCC
Confidence 58889999999999999999999999999997
No 207
>PHA00675 hypothetical protein
Probab=90.67 E-value=0.49 Score=39.20 Aligned_cols=41 Identities=17% Similarity=0.238 Sum_probs=32.3
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 486 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~ 486 (508)
.+|++.|-+.|+..+- .+|.|+.+||+.||||+++|.+|.+
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 5677777766655441 2788999999999999999998865
No 208
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=90.23 E-value=0.4 Score=40.77 Aligned_cols=46 Identities=15% Similarity=0.187 Sum_probs=34.2
Q ss_pred ccCCHHHHHHHhHHhccC----CCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLD----KECLTWEDISKRIGLSRERVRQVGLVALE 490 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd----~eg~TleEIAe~LgIS~erVrqi~~rALk 490 (508)
+-|+|.|+.-+..|+-+- .+|+|+.||++.+|+|..||.+ ..++|+
T Consensus 25 dL~T~~E~~~l~~R~~va~~lL~~g~syreIa~~tgvS~aTItR-vsr~Lk 74 (87)
T PF01371_consen 25 DLCTPDELEALAQRWQVAKELLDEGKSYREIAEETGVSIATITR-VSRCLK 74 (87)
T ss_dssp HHSSHHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHH-HHHHHH
T ss_pred HhCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHH-HHHHHH
Confidence 447888887776665442 2789999999999999999863 344444
No 209
>PF13730 HTH_36: Helix-turn-helix domain
Probab=90.05 E-value=1 Score=34.08 Aligned_cols=45 Identities=22% Similarity=0.355 Sum_probs=32.0
Q ss_pred cCCHHHHHHHhHHhcc-CCCC---CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGL-DKEC---LTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 445 ~Lp~rER~VI~LryGL-d~eg---~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
.|++.++.|+..-.-+ +.++ .|.+.||+.+|+|+.||. ++++.|.
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~----~~i~~L~ 50 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQ----RAIKELE 50 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHH----HHHHHHH
Confidence 5888888877654433 2222 389999999999999996 4555554
No 210
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=90.01 E-value=2.2 Score=45.39 Aligned_cols=129 Identities=19% Similarity=0.307 Sum_probs=68.4
Q ss_pred hhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHh
Q 010521 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRG 305 (508)
Q Consensus 226 ~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirA 305 (508)
.+..+|...+|++|+.+++|..+|++.++++..+.... -..++-.. -+.+ +| ..+...
T Consensus 220 ~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~------------~~~SLd~~---~~~~-~~------~~l~d~ 277 (367)
T PRK09210 220 RVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQ------------EPVSLETP---IGEE-DD------SHLGDF 277 (367)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhc------------CCCCcCCC---CCCC-Cc------chhhhh
Confidence 34567788899999999999999999988766543210 00000000 0111 11 011111
Q ss_pred hhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHH
Q 010521 306 IEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVR 384 (508)
Q Consensus 306 iekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~ 384 (508)
+. |+....+........++..+..+|. .+|..-...+. . .+. .-|.+-|.+|||+.+|+|.++|+
T Consensus 278 i~--d~~~~~p~~~~~~~~~~~~l~~~l~------~L~~rEr~Vl~----l--rygl~~~~~~tl~EIa~~lgvs~erVr 343 (367)
T PRK09210 278 IE--DQDATSPADHAAYELLKEQLEDVLD------TLTDREENVLR----L--RFGLDDGRTRTLEEVGKVFGVTRERIR 343 (367)
T ss_pred cc--CCCCCCHHHHHHHHHHHHHHHHHHH------hCCHHHHHHHH----H--HhccCCCCCccHHHHHHHHCCCHHHHH
Confidence 21 1111223344445555555555542 23322211110 0 000 12356799999999999999999
Q ss_pred HHHHHh
Q 010521 385 NATEAI 390 (508)
Q Consensus 385 ~~l~~~ 390 (508)
++...+
T Consensus 344 Qi~~~A 349 (367)
T PRK09210 344 QIEAKA 349 (367)
T ss_pred HHHHHH
Confidence 986543
No 211
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=89.79 E-value=1.7 Score=40.13 Aligned_cols=64 Identities=17% Similarity=0.201 Sum_probs=40.3
Q ss_pred HHccCCHHHHHHHhHH-----hccCCCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHHhhHHHhh
Q 010521 442 IIVTLGEREREIIRLY-----YGLDKECLTWEDISKRIGLSRERVRQVGL--VALEKLKHAARKKKMEAML 505 (508)
Q Consensus 442 L~~~Lp~rER~VI~Lr-----yGLd~eg~TleEIAe~LgIS~erVrqi~~--rALkKLR~~L~~~~l~~~l 505 (508)
|..+|++.|+....+- .+.+++..|+.|||+.+||+++|+-++.+ ++.....+.+....+..++
T Consensus 7 le~~L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~~~~Fiey~n~la~~~~~~~~ 77 (142)
T PF13022_consen 7 LEAKLTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQQNKAFIEYKNELADRFLSSHR 77 (142)
T ss_dssp HHTTS-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHHH-HHHHHHHHHHHHHHHHTTH
T ss_pred HHHHcCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHhH
Confidence 3378999998843332 22223569999999999999999999884 4566666666666666554
No 212
>cd00131 PAX Paired Box domain
Probab=89.76 E-value=0.78 Score=41.54 Aligned_cols=41 Identities=20% Similarity=0.101 Sum_probs=31.5
Q ss_pred CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
|+...|.-|.+.| .+|+|..+||+.||||+.+|..++.+-.
T Consensus 18 lS~d~R~rIv~~~---~~G~s~~~iA~~~~Vs~~tV~r~i~r~~ 58 (128)
T cd00131 18 LPDSIRQRIVELA---QSGIRPCDISRQLRVSHGCVSKILNRYY 58 (128)
T ss_pred CCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4554444333445 5899999999999999999999988754
No 213
>PHA02591 hypothetical protein; Provisional
Probab=89.75 E-value=0.58 Score=38.90 Aligned_cols=25 Identities=28% Similarity=0.357 Sum_probs=22.7
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGL 486 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~ 486 (508)
..|+|.++||+.||+++++|++...
T Consensus 57 eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 57 RKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 4689999999999999999999875
No 214
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=89.70 E-value=0.55 Score=47.15 Aligned_cols=60 Identities=25% Similarity=0.412 Sum_probs=40.1
Q ss_pred hhhhHHHHHHhhc---ccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHh
Q 010521 189 IQNRLKGYVKGVV---SEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (508)
Q Consensus 189 ~~~~~~~yl~~i~---~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~ 258 (508)
+.+.+..||+... +.| ......+.+++ .++.+|...+|++|+.+++|..+|++.+++...
T Consensus 87 Ir~~i~~~lr~~~~~vr~p----r~~~~~~~~~~------~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~ 149 (256)
T PRK07408 87 IRGEIQHYLRDKSPTVRIP----RRWQELQRQAK------KVRQELRQELGRQPTDQEIAQALDISLEEWQEI 149 (256)
T ss_pred HHHHHHHHHHHcCCeeeeC----HHHHHHHHHHH------HHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHH
Confidence 4456666776533 233 22233343332 356678889999999999999999998876554
No 215
>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=89.53 E-value=2.9 Score=41.36 Aligned_cols=32 Identities=28% Similarity=0.499 Sum_probs=26.9
Q ss_pred hHHHHHHhhCCCCchHHHHHHhccChHHHHHh
Q 010521 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (508)
Q Consensus 227 ~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~ 258 (508)
+..++...+|++|+.+++|..+|++.+++...
T Consensus 92 ~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~ 123 (238)
T TIGR02393 92 AERQLTQELGREPTDEELAERMGMPAEKVREI 123 (238)
T ss_pred HHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 45567788999999999999999998876554
No 216
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=89.34 E-value=4.7 Score=40.51 Aligned_cols=61 Identities=25% Similarity=0.283 Sum_probs=40.5
Q ss_pred hhhhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhh
Q 010521 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (508)
Q Consensus 189 ~~~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l 259 (508)
+.+.+..|++.....| ....+.+.++. .++..|...+|++|+.+++|..+|++.+++...+
T Consensus 87 Ir~~i~~~lr~~~~~p----r~~~~~~~~l~------~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~ 147 (257)
T PRK05911 87 IKAAIIDDLRKQDWVP----RSVHQKANKLA------DAMDSLRQSLGKEPTDGELCEYLNISQQELSGWF 147 (257)
T ss_pred HHHHHHHHHHhcCCCC----HHHHHHHHHHH------HHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHH
Confidence 4455566666655533 23333444443 2445678889999999999999999988765543
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=89.07 E-value=0.69 Score=36.39 Aligned_cols=41 Identities=27% Similarity=0.419 Sum_probs=28.9
Q ss_pred CCHHHHHHHhHHhcc--CCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521 446 LGEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGL 486 (508)
Q Consensus 446 Lp~rER~VI~LryGL--d~eg~TleEIAe~LgIS~erVrqi~~ 486 (508)
|++....-|...|-| +.+..+..+||+.||+|+.+|...+.
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 455555555555555 35679999999999999999975443
No 218
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=88.96 E-value=1.1 Score=33.23 Aligned_cols=37 Identities=22% Similarity=0.275 Sum_probs=27.9
Q ss_pred HHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 448 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 448 ~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
|.-..|+.+-. ..+++..||++.+|+|+++|++.+..
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 44455666655 47899999999999999999877654
No 219
>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=88.93 E-value=1.5 Score=34.07 Aligned_cols=43 Identities=19% Similarity=0.244 Sum_probs=31.9
Q ss_pred HHHHHHccCCHHHHHHHhHH-hccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521 438 VNKLIIVTLGEREREIIRLY-YGLDKECLTWEDISKRIGLSRERVRQVGL 486 (508)
Q Consensus 438 L~~~L~~~Lp~rER~VI~Lr-yGLd~eg~TleEIAe~LgIS~erVrqi~~ 486 (508)
+.++| .+|.-+.|+.+- - .+++|..|||+.+|++.++|++.+.
T Consensus 3 i~~aL---~~p~R~~Il~~L~~---~~~~t~~ela~~l~~~~~t~s~hL~ 46 (61)
T PF12840_consen 3 IFKAL---SDPTRLRILRLLAS---NGPMTVSELAEELGISQSTVSYHLK 46 (61)
T ss_dssp HHHHH---TSHHHHHHHHHHHH---CSTBEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHh---CCHHHHHHHHHHhc---CCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 44555 356666777665 3 6899999999999999999986654
No 220
>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=88.87 E-value=0.69 Score=34.96 Aligned_cols=38 Identities=26% Similarity=0.483 Sum_probs=26.3
Q ss_pred HHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 449 REREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 449 rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
|++.|+.+-+- ..++.|.+|||+.||||+.||++.+..
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 45566655421 134599999999999999999866554
No 221
>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=88.57 E-value=0.99 Score=37.65 Aligned_cols=41 Identities=29% Similarity=0.379 Sum_probs=33.6
Q ss_pred CCHHHHHHHhHHhcc---CCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521 446 LGEREREIIRLYYGL---DKECLTWEDISKRIGLSRERVRQVGL 486 (508)
Q Consensus 446 Lp~rER~VI~LryGL---d~eg~TleEIAe~LgIS~erVrqi~~ 486 (508)
|+++|+.||..-.-+ ..++..-++||+.+++|..|||+...
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 889999988764433 35688999999999999999998754
No 222
>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=87.97 E-value=0.97 Score=38.28 Aligned_cols=43 Identities=16% Similarity=0.139 Sum_probs=32.8
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHH--CCCHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRI--GLSRERVRQVGLVA 488 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~L--gIS~erVrqi~~rA 488 (508)
+.||+..+.+..+|.- ..+.|+.|+|+.+ .||.++|..+..+.
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 4689999999999 99999998776554
No 223
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=87.97 E-value=1.3 Score=36.64 Aligned_cols=39 Identities=23% Similarity=0.365 Sum_probs=27.7
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH-----HHHHHHHHHHHHhh
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGL-----VALEKLKHAARKKK 500 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~-----rALkKLR~~L~~~~ 500 (508)
..++|+.|+|+.+|+++++|+++++ -.+.+|.+.+...|
T Consensus 29 ~~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aLG 72 (80)
T PF13744_consen 29 ERGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEALG 72 (80)
T ss_dssp CCT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHTT
T ss_pred HcCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHcC
Confidence 5789999999999999999999984 24667776665543
No 224
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=87.74 E-value=1.3 Score=33.09 Aligned_cols=35 Identities=26% Similarity=0.430 Sum_probs=27.1
Q ss_pred HHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521 450 EREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 450 ER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA 488 (508)
++.|+.+.. +..|.++||+.+|+|..||..+..+.
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 44799999999999999999998764
No 225
>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=87.63 E-value=2.4 Score=36.25 Aligned_cols=42 Identities=29% Similarity=0.381 Sum_probs=32.6
Q ss_pred ccCCHHHHHHHhHH----hccC--CCCCCHHHHHHHHCCCHHHHHHHH
Q 010521 444 VTLGEREREIIRLY----YGLD--KECLTWEDISKRIGLSRERVRQVG 485 (508)
Q Consensus 444 ~~Lp~rER~VI~Lr----yGLd--~eg~TleEIAe~LgIS~erVrqi~ 485 (508)
..+++++..||..- ||.. ..++|..|||+.+|+++++|++.+
T Consensus 21 ~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L 68 (95)
T TIGR01610 21 ADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAI 68 (95)
T ss_pred CCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHH
Confidence 67899999977632 3432 367999999999999999996443
No 226
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=87.53 E-value=1.4 Score=35.41 Aligned_cols=24 Identities=25% Similarity=0.322 Sum_probs=20.8
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 464 CLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 464 g~TleEIAe~LgIS~erVrqi~~r 487 (508)
++|..|||+.+|++..+|++++.+
T Consensus 22 ~~ta~eLa~~lgl~~~~v~r~L~~ 45 (68)
T smart00550 22 TSTALQLAKNLGLPKKEVNRVLYS 45 (68)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHH
Confidence 599999999999999999766554
No 227
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=87.50 E-value=11 Score=41.91 Aligned_cols=32 Identities=28% Similarity=0.449 Sum_probs=27.0
Q ss_pred hHHHHHHhhCCCCchHHHHHHhccChHHHHHh
Q 010521 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (508)
Q Consensus 227 ~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~ 258 (508)
++.+|...+|++|+.+++|..+|++.++++..
T Consensus 363 ~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~ 394 (509)
T PRK05901 363 IERELLQELGREPTPEELAKEMGFTPEKVREI 394 (509)
T ss_pred HHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 45677788999999999999999998876554
No 228
>PHA02547 55 RNA polymerase sigma factor; Provisional
Probab=87.31 E-value=2.1 Score=40.68 Aligned_cols=65 Identities=14% Similarity=0.282 Sum_probs=47.9
Q ss_pred HHHHHHHHHHHHhcCCCCC---HHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHh
Q 010521 272 SNVRLVMSIAQRYDNMGAD---MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVEN 336 (508)
Q Consensus 272 ~yl~LV~sIAkrY~~~g~d---~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~ 336 (508)
+.+..+..+.++|--++.. -+|.|.+|.-.+++.++.|||++..-+-.|++..+-++..+.|...
T Consensus 45 ~imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~kE 112 (179)
T PHA02547 45 AIMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKKE 112 (179)
T ss_pred HHHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHHH
Confidence 3455555666666545554 7899999999999999999999987777777776666665555443
No 229
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=87.10 E-value=0.87 Score=42.78 Aligned_cols=50 Identities=12% Similarity=0.013 Sum_probs=41.7
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCC-----HHHHHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLS-----RERVRQVGLVALEKLKH 494 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS-----~erVrqi~~rALkKLR~ 494 (508)
.|+++|.+|+.+-.-=.+.++|.++|++.++.+ ..||+..+.+.++||+.
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 699999999988762112469999999999986 78999999999999963
No 230
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=86.99 E-value=1.1 Score=41.39 Aligned_cols=34 Identities=21% Similarity=0.165 Sum_probs=28.4
Q ss_pred HHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 453 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 453 VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
++..++ .+|+|.+|||+++|||.+||..++.+-.
T Consensus 13 ~~~~~~---~~G~S~re~Ak~~gvs~sTvy~wv~r~~ 46 (138)
T COG3415 13 VVDAVV---GEGLSCREAAKRFGVSISTVYRWVRRYR 46 (138)
T ss_pred HHHHHH---HcCccHHHHHHHhCccHHHHHHHHHHhc
Confidence 444554 4899999999999999999999888754
No 231
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=86.89 E-value=5.7 Score=41.62 Aligned_cols=32 Identities=28% Similarity=0.397 Sum_probs=26.8
Q ss_pred hHHHHHHhhCCCCchHHHHHHhccChHHHHHh
Q 010521 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (508)
Q Consensus 227 ~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~ 258 (508)
++.+|...+|++|+.+++|..+|++.+++...
T Consensus 178 ~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~ 209 (324)
T PRK07921 178 IKRELHQQLGREATDEELAEESGIPEEKIADL 209 (324)
T ss_pred HHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 45677788999999999999999998876544
No 232
>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=86.82 E-value=1.1 Score=34.15 Aligned_cols=42 Identities=21% Similarity=0.382 Sum_probs=30.9
Q ss_pred CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
|+..|-.||..-+- ..++|..+||+.+++++++|.++..+-.
T Consensus 1 lt~~q~~iL~~l~~--~~~~~~~~la~~~~~~~~~~t~~i~~L~ 42 (59)
T PF01047_consen 1 LTPSQFRILRILYE--NGGITQSELAEKLGISRSTVTRIIKRLE 42 (59)
T ss_dssp STHHHHHHHHHHHH--HSSEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH--cCCCCHHHHHHHHCCChhHHHHHHHHHH
Confidence 45667777766552 4679999999999999999987766543
No 233
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=86.75 E-value=1.4 Score=33.74 Aligned_cols=39 Identities=31% Similarity=0.390 Sum_probs=26.4
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 486 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~ 486 (508)
.|++.||.-|...+ ..|+++.|||+.+|-|+..|+..+.
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 57888888777766 5689999999999999999987653
No 234
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=86.67 E-value=3.2 Score=36.98 Aligned_cols=34 Identities=9% Similarity=0.122 Sum_probs=28.5
Q ss_pred HHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521 452 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 452 ~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA 488 (508)
.++...+ ..|.|..+||+.+|||..++.++....
T Consensus 20 ~aV~~~~---~~g~sv~evA~e~gIs~~tl~~W~r~y 53 (121)
T PRK09413 20 AIVQQSF---EPGMTVSLVARQHGVAASQLFLWRKQY 53 (121)
T ss_pred HHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3555555 578999999999999999999998764
No 235
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=86.39 E-value=26 Score=36.45 Aligned_cols=179 Identities=19% Similarity=0.104 Sum_probs=93.7
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccH
Q 010521 267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHL 346 (508)
Q Consensus 267 e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~ 346 (508)
++-+...+..|..++.+. ++. +-+.|....+++.+.....-+|.+...++.-.|.- +++.+
T Consensus 119 er~l~~a~~~I~~~~~~L---~Lp--~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYi----ACR~~---------- 179 (310)
T PRK00423 119 ERNLAFALSELDRIASQL---GLP--RSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYA----ACRRC---------- 179 (310)
T ss_pred hHHHHHHHHHHHHHHHHc---CCC--HHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHH----HHHHc----------
Confidence 344445556677777665 222 45666666777776655555776665554433333 33332
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCC-CCc
Q 010521 347 HERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE-NNP 425 (508)
Q Consensus 347 ~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e-~~P 425 (508)
|..-+..||++..+++..++......+.+.+.++.+. ....+++..-... .-|
T Consensus 180 -----------------~~prtl~eI~~~~~v~~k~i~~~~~~l~k~L~~~~~~---------~~p~~~i~r~~~~L~L~ 233 (310)
T PRK00423 180 -----------------KVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPP---------TDPIDYVPRFASELGLS 233 (310)
T ss_pred -----------------CCCcCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCC---------CCHHHHHHHHHHHcCCC
Confidence 3334677888888888888877766665544443321 0111222111000 012
Q ss_pred cchHHHHHHHHHHHHHHHccC----CHH--HHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 010521 426 WHGVDDWALKDEVNKLIIVTL----GER--EREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL 492 (508)
Q Consensus 426 e~~ve~~el~e~L~~~L~~~L----p~r--ER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKL 492 (508)
.+ +. ......+..+....| +|. -..+|.+-.-+.+.+.|++|||...||+..||++....-.+.|
T Consensus 234 ~~-v~-~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l 304 (310)
T PRK00423 234 GE-VQ-KKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKELAEKL 304 (310)
T ss_pred HH-HH-HHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 11 11 111222222221111 121 1222333221235679999999999999999998777666554
No 236
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=86.23 E-value=1.6 Score=37.41 Aligned_cols=41 Identities=22% Similarity=0.319 Sum_probs=31.7
Q ss_pred CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521 446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA 488 (508)
|++.++.|+..-.- ....|+.+||+.+|+|+.+|++.+.+-
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 46678888876541 246899999999999999998766554
No 237
>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=86.21 E-value=0.75 Score=34.40 Aligned_cols=34 Identities=29% Similarity=0.343 Sum_probs=25.8
Q ss_pred CHHHHHHHHCCCHHHHHHHHHH-------HHHHHHHHHHHh
Q 010521 466 TWEDISKRIGLSRERVRQVGLV-------ALEKLKHAARKK 499 (508)
Q Consensus 466 TleEIAe~LgIS~erVrqi~~r-------ALkKLR~~L~~~ 499 (508)
|++|||+..|+|..||+..++. ..+++...++..
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~~~~vs~~tr~rI~~~a~~l 41 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNGPPRVSEETRERILEAAEEL 41 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTTCSSSTHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHH
Confidence 7899999999999999998864 445555544443
No 238
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=86.03 E-value=0.97 Score=42.26 Aligned_cols=49 Identities=18% Similarity=0.131 Sum_probs=40.6
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRIG-----LSRERVRQVGLVALEKLK 493 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~Lg-----IS~erVrqi~~rALkKLR 493 (508)
.|+++|.+|+.+..-=.+..+|.++|++.+. ++..||+..+.+.++||.
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 239
>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=85.93 E-value=31 Score=37.63 Aligned_cols=25 Identities=16% Similarity=0.286 Sum_probs=22.1
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGL 486 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~ 486 (508)
..++|+++||+.+|++.+||++...
T Consensus 316 LkPLtlkdiA~~lglheSTVSRav~ 340 (429)
T TIGR02395 316 LKPLTLREVAEELGLHESTISRAIN 340 (429)
T ss_pred CcCCcHHHHHHHhCCCccchhhhhc
Confidence 3689999999999999999987654
No 240
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=85.73 E-value=1.5 Score=40.58 Aligned_cols=42 Identities=12% Similarity=0.219 Sum_probs=32.9
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA 488 (508)
.|++.++.||..--- ....|+.|||+.+|+|+.+|+.++.+-
T Consensus 6 ~lD~~D~~Il~~Lq~--d~R~s~~eiA~~lglS~~tV~~Ri~rL 47 (153)
T PRK11179 6 QIDNLDRGILEALME--NARTPYAELAKQFGVSPGTIHVRVEKM 47 (153)
T ss_pred ccCHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 578888888877541 235899999999999999998776553
No 241
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=85.61 E-value=2.9 Score=38.06 Aligned_cols=51 Identities=24% Similarity=0.343 Sum_probs=38.5
Q ss_pred HHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 010521 436 DEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL 492 (508)
Q Consensus 436 e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKL 492 (508)
+.+.+++ -.|++.+-+|+..-.- ...++|..|||+.+|++++||. +|+++|
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 5899999998866541 1368999999999999999995 555554
No 242
>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=85.61 E-value=1.9 Score=35.30 Aligned_cols=52 Identities=10% Similarity=0.199 Sum_probs=34.8
Q ss_pred HHHHHHHHHccCCHHHHHHHhHHhcc--CCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 435 KDEVNKLIIVTLGEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 435 ~e~L~~~L~~~Lp~rER~VI~LryGL--d~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
.+.|.... ..|++.|+.|.....-- +...+|..|||+..|||+.+|-+...+
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 44566666 89999999988664311 134699999999999999999765443
No 243
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=85.34 E-value=1.9 Score=37.33 Aligned_cols=46 Identities=22% Similarity=0.391 Sum_probs=35.7
Q ss_pred HHHHHHHHHHccCCHHHHHHHhHHhcc-C---CCCCCHHHHHHHHCCCHHHHH
Q 010521 434 LKDEVNKLIIVTLGEREREIIRLYYGL-D---KECLTWEDISKRIGLSRERVR 482 (508)
Q Consensus 434 l~e~L~~~L~~~Lp~rER~VI~LryGL-d---~eg~TleEIAe~LgIS~erVr 482 (508)
....|..++ |+|.||+-+..|+.+ . ...+|++||+..||+|..+|-
T Consensus 29 ~~~~lL~ll---LTpdEReal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtIT 78 (103)
T COG2973 29 LHQPLLTLL---LTPDEREALGTRVRIVEELLRGELSQREIAQKLGVSIATIT 78 (103)
T ss_pred HHHHHHHHH---cCHhHHHHHHHHHHHHHHHHhccccHHHHHHHhCcchhhhc
Confidence 344555555 899999988888765 1 257999999999999998883
No 244
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional
Probab=85.27 E-value=1.2 Score=42.30 Aligned_cols=49 Identities=10% Similarity=0.077 Sum_probs=42.4
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRIG-----LSRERVRQVGLVALEKLK 493 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~Lg-----IS~erVrqi~~rALkKLR 493 (508)
.|+++|+.|+.+...=.+++.|.++|++.+. ++..||+..+.+.++||.
T Consensus 160 ~Lt~~e~~il~~l~~~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~lr~kl~ 213 (240)
T PRK10710 160 DLTPAEFRLLKTLSHEPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLE 213 (240)
T ss_pred ecCHHHHHHHHHHHhCCCceEcHHHHHHHhcCcCcCCCccCHHHHHHHHHHHhh
Confidence 5999999999987631234799999999998 999999999999999996
No 245
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=85.05 E-value=0.84 Score=44.23 Aligned_cols=40 Identities=18% Similarity=0.118 Sum_probs=29.3
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 486 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~ 486 (508)
+.|+++ +|+.+.- -+..|+|.+|||+.||+|+.||+....
T Consensus 160 ~~Lt~r--~Vl~~~~-~g~~g~s~~eIa~~l~iS~~Tv~~~~~ 199 (225)
T PRK10046 160 DPLTLN--AVRKLFK-EPGVQHTAETVAQALTISRTTARRYLE 199 (225)
T ss_pred CHHHHH--HHHHHHH-cCCCCcCHHHHHHHhCccHHHHHHHHH
Confidence 345554 5665542 112369999999999999999998875
No 246
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=84.69 E-value=10 Score=33.65 Aligned_cols=27 Identities=26% Similarity=0.433 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 463 ECLTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 463 eg~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
.+.|+.|||+.||||.++|. ++|++|.
T Consensus 70 pd~tl~Ela~~l~Vs~~ti~----~~Lkrlg 96 (119)
T PF01710_consen 70 PDATLRELAERLGVSPSTIW----RALKRLG 96 (119)
T ss_pred CCcCHHHHHHHcCCCHHHHH----HHHHHcC
Confidence 67999999999999999996 4555544
No 247
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=84.61 E-value=1.5 Score=41.17 Aligned_cols=42 Identities=21% Similarity=0.226 Sum_probs=32.0
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA 488 (508)
.|++.++.||..-- .....|+.|||+.+|+|+.+|++++.+-
T Consensus 11 ~lD~~D~~IL~~Lq--~d~R~s~~eiA~~lglS~~tv~~Ri~rL 52 (164)
T PRK11169 11 DLDRIDRNILNELQ--KDGRISNVELSKRVGLSPTPCLERVRRL 52 (164)
T ss_pred hHHHHHHHHHHHhc--cCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46677888886543 0235899999999999999998776653
No 248
>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=84.50 E-value=1.8 Score=33.76 Aligned_cols=43 Identities=19% Similarity=0.285 Sum_probs=27.2
Q ss_pred CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
|+..|..||..-. -...++|..+||+.++++..+|.+.+.+..
T Consensus 1 lt~~q~~vL~~l~-~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~ 43 (68)
T PF13463_consen 1 LTRPQWQVLRALA-HSDGPMTQSDLAERLGISKSTVSRIIKKLE 43 (68)
T ss_dssp --HHHHHHHHHHT---TS-BEHHHHHHHTT--HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHH-ccCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4566777765543 125789999999999999999986655443
No 249
>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB. PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself. It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.
Probab=84.04 E-value=0.76 Score=43.02 Aligned_cols=49 Identities=12% Similarity=0.192 Sum_probs=40.6
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHH-----HHHHCCCHHHHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDI-----SKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEI-----Ae~LgIS~erVrqi~~rALkKLR 493 (508)
.|+++|.+|+.+-..--+.++|.++| |+.++++..||+..+.+.++||.
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 250
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=84.02 E-value=1.8 Score=41.61 Aligned_cols=37 Identities=19% Similarity=0.348 Sum_probs=29.0
Q ss_pred CHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 447 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 447 p~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
++.++.|+.++ .+|+|..+||+.||||++||.++...
T Consensus 159 ~~~~~~i~~~~----~~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 159 TGKEEKIKKLL----DKGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred chhHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 33445666664 37899999999999999999888753
No 251
>PRK15479 transcriptional regulatory protein TctD; Provisional
Probab=83.97 E-value=1.7 Score=40.58 Aligned_cols=49 Identities=14% Similarity=0.145 Sum_probs=40.3
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRIG-----LSRERVRQVGLVALEKLK 493 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~Lg-----IS~erVrqi~~rALkKLR 493 (508)
.|+++|.+|+.+..-=.+...|.++|++.+. +|..||+..+.+.++||.
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 5999999999876510123479999999996 999999999999999985
No 252
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=83.65 E-value=1.3 Score=42.34 Aligned_cols=38 Identities=24% Similarity=0.211 Sum_probs=31.7
Q ss_pred HHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 010521 451 REIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL 492 (508)
Q Consensus 451 R~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKL 492 (508)
+..+.|+- .|+|..|||++||+|++|++.+..|+.++.
T Consensus 9 ~kA~eLk~----~Glt~gEIAdELNvSreTa~WL~~r~~~~~ 46 (203)
T COG0856 9 KKARELKS----KGLTTGEIADELNVSRETATWLLTRAFKKE 46 (203)
T ss_pred HHHHHHHH----CCCcHHHhhhhhhhhHHHHHHHHhhhhhcc
Confidence 34555663 899999999999999999999999987654
No 253
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=83.37 E-value=17 Score=37.20 Aligned_cols=65 Identities=17% Similarity=0.156 Sum_probs=37.1
Q ss_pred HhhhhHHHHHHhhcccCCC-CHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHH
Q 010521 188 LIQNRLKGYVKGVVSEELL-THAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPEL 255 (508)
Q Consensus 188 ~~~~~~~~yl~~i~~~~lL-t~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L 255 (508)
++.+.+..||+.-...+.+ +......+..+++. ++....++...+|++|+.+++|..+|++.+++
T Consensus 100 ~Ir~~I~~~lr~~~~~iR~p~~~~~~~~~~~~~~---~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v 165 (289)
T PRK07500 100 WIRASIQDYILRNWSIVRGGTSSAQKALFFNLRR---LRARLAQADEELTKQEIHREIATALGVSLSDV 165 (289)
T ss_pred HHHHHHHHHHHHCCCceecCccHHHHHHHHHHHH---HHHHHHhhhcccCCCCCHHHHHHHhCcCHHHH
Confidence 4556777777664333221 22233334333332 11122222236899999999999999998764
No 254
>PF13551 HTH_29: Winged helix-turn helix
Probab=83.02 E-value=12 Score=31.73 Aligned_cols=23 Identities=22% Similarity=0.291 Sum_probs=21.4
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHh
Q 010521 368 SVDRIAEYLNMSQKKVRNATEAI 390 (508)
Q Consensus 368 t~eEIA~~Lgis~e~v~~~l~~~ 390 (508)
+..+||+.+|++..+|.+.+...
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~ 36 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRY 36 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHH
Confidence 79999999999999999998875
No 255
>PF12728 HTH_17: Helix-turn-helix domain
Probab=82.77 E-value=1.4 Score=32.80 Aligned_cols=24 Identities=25% Similarity=0.266 Sum_probs=21.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~rA 488 (508)
+|.+|+|+.||||+.||.++..+.
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcC
Confidence 689999999999999999988653
No 256
>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=82.72 E-value=0.96 Score=35.85 Aligned_cols=41 Identities=24% Similarity=0.272 Sum_probs=31.3
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
.|++.|..|+..-. ...++|..|||+.+|+++.+|...+.+
T Consensus 5 gLs~~E~~vy~~Ll--~~~~~t~~eIa~~l~i~~~~v~~~L~~ 45 (68)
T PF01978_consen 5 GLSENEAKVYLALL--KNGPATAEEIAEELGISRSTVYRALKS 45 (68)
T ss_dssp CHHHHHHHHHHHHH--HHCHEEHHHHHHHHTSSHHHHHHHHHH
T ss_pred CcCHHHHHHHHHHH--HcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 57788888775543 146799999999999999999755443
No 257
>PRK05949 RNA polymerase sigma factor; Validated
Probab=82.46 E-value=8.4 Score=40.36 Aligned_cols=34 Identities=15% Similarity=0.354 Sum_probs=26.9
Q ss_pred chhHHHHHHhhCCCCchHHHHHHhccChHHHHHh
Q 010521 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (508)
Q Consensus 225 ~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~ 258 (508)
..++.++...+|++|+.+++|..+|++.+++...
T Consensus 181 ~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~ 214 (327)
T PRK05949 181 KKTQRELSQKLGRSATPAEIAKELELEPSQIREY 214 (327)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 3345566778999999999999999998775553
No 258
>PF13551 HTH_29: Winged helix-turn helix
Probab=82.12 E-value=2.5 Score=35.98 Aligned_cols=33 Identities=30% Similarity=0.370 Sum_probs=26.6
Q ss_pred HHHhHHhccCCCCC-CHHHHHHHHCCCHHHHHHHHHHH
Q 010521 452 EIIRLYYGLDKECL-TWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 452 ~VI~LryGLd~eg~-TleEIAe~LgIS~erVrqi~~rA 488 (508)
.||.+.. +|. |..+||+.+|+|+.||.+++.+-
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 3555543 778 59999999999999999888774
No 259
>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=81.99 E-value=1.4 Score=31.45 Aligned_cols=25 Identities=20% Similarity=0.205 Sum_probs=22.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
+|..|+|+.+|||+.||+++...+.
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 5889999999999999999987753
No 260
>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator. This model describes a family of DNA-binding response regulator proteins, associated with an adjacent histidine kinase (TIGR03785) to form a two-component system. This system co-occurs with, and often is adjacent to, a proteobacterial variant form of the protein sorting transpeptidase called sortase (TIGR03784), and a single target protein for the sortase. We give this protein the gene symbol pdsR, for Proteobacterial Dedicated Sortase system Response regulator.
Probab=81.88 E-value=1.9 Score=40.70 Aligned_cols=47 Identities=9% Similarity=0.027 Sum_probs=40.3
Q ss_pred cCCHHHHHHHhHHhccCCCC--CCHHHH--HHHHCCCHHHHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKEC--LTWEDI--SKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg--~TleEI--Ae~LgIS~erVrqi~~rALkKLR 493 (508)
.|+++|..|+.+..- ..| +|.++| |..++++..||+..+.+.++||.
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 599999999988761 124 599999 88899999999999999999996
No 261
>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=81.57 E-value=4.1 Score=30.85 Aligned_cols=50 Identities=16% Similarity=0.256 Sum_probs=39.9
Q ss_pred cCCHHHHHHHhHHhccCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDK--ECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~--eg~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
.+++.+..+|...|..+. .....++||..+||+...|..+...-..+.|+
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 578888899999885421 22458899999999999999999988777663
No 262
>CHL00148 orf27 Ycf27; Reviewed
Probab=81.37 E-value=1.9 Score=40.95 Aligned_cols=50 Identities=18% Similarity=0.118 Sum_probs=41.8
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHH-------CCCHHHHHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRI-------GLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~L-------gIS~erVrqi~~rALkKLR~ 494 (508)
.|+++|.+|+.+...-.++++|.++|++.+ +++..+|+.++.+.++||..
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 599999999988752123579999999999 48999999999999999963
No 263
>PRK12423 LexA repressor; Provisional
Probab=80.96 E-value=2.8 Score=40.64 Aligned_cols=47 Identities=19% Similarity=0.290 Sum_probs=33.2
Q ss_pred ccCCHHHHHHHhHHhc-cC--CCCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYG-LD--KECLTWEDISKRIG-LSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 444 ~~Lp~rER~VI~LryG-Ld--~eg~TleEIAe~Lg-IS~erVrqi~~rALkKLR~ 494 (508)
..|+++|++|+..--. +. +-..|..|||+.|| +|+++|+. ++++|++
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 3589999998875331 11 12459999999999 59999984 5555554
No 264
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=80.94 E-value=1.9 Score=31.00 Aligned_cols=24 Identities=25% Similarity=0.357 Sum_probs=21.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~rA 488 (508)
+|.+|+|+.||||+.+|.++....
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcC
Confidence 689999999999999999988654
No 265
>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=80.91 E-value=3.2 Score=39.36 Aligned_cols=42 Identities=21% Similarity=0.242 Sum_probs=34.0
Q ss_pred CHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010521 447 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALE 490 (508)
Q Consensus 447 p~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALk 490 (508)
|+.-|.-++..|= ++++|++.+|...|||..|++++..+|..
T Consensus 4 ~~e~R~~~R~~YV--~~~~sLe~aA~~~gVs~~TarrWK~~Ak~ 45 (165)
T PF08822_consen 4 PQETRDAVRRAYV--FDRLSLEQAAAKCGVSYATARRWKREAKA 45 (165)
T ss_pred cHHHHHHHHHHHH--hCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3445566666661 37899999999999999999999999864
No 266
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=80.72 E-value=14 Score=40.26 Aligned_cols=38 Identities=16% Similarity=0.495 Sum_probs=30.7
Q ss_pred ccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhh
Q 010521 223 SLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (508)
Q Consensus 223 ~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~ 260 (508)
.+..++.+|...+|++|+.+++|..+||+.+.++..+.
T Consensus 263 ~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l~ 300 (415)
T PRK07598 263 KIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLL 300 (415)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 34445667778899999999999999999998776643
No 267
>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=80.43 E-value=4.2 Score=39.79 Aligned_cols=31 Identities=35% Similarity=0.536 Sum_probs=25.2
Q ss_pred HHHHHHhhCCCCchHHHHHHhccChHHHHHh
Q 010521 228 KLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (508)
Q Consensus 228 ~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~ 258 (508)
...+...+|++|+.+++|..+|++.+++...
T Consensus 103 ~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~ 133 (231)
T TIGR02885 103 KEELSKELGREPTINELAEALGVSPEEIVMA 133 (231)
T ss_pred HHHHHHHHCcCCCHHHHHHHHCcCHHHHHHH
Confidence 3456677899999999999999998876543
No 268
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=80.14 E-value=1.9 Score=32.35 Aligned_cols=26 Identities=15% Similarity=0.442 Sum_probs=21.5
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
..++|+.|+|+.+|+|+.+|++++..
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 35799999999999999999999875
No 269
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=79.71 E-value=27 Score=35.12 Aligned_cols=34 Identities=38% Similarity=0.470 Sum_probs=27.9
Q ss_pred chhHHHHHHhhCCCCchHHHHHHhccChHHHHHh
Q 010521 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (508)
Q Consensus 225 ~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~ 258 (508)
..++..|...+|++|+.+++|..+|++.+++...
T Consensus 121 ~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~ 154 (268)
T PRK06288 121 ERAIAMLEARLGRTPSDEEIADELGISLEEYNSL 154 (268)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHH
Confidence 3456678888999999999999999998775554
No 270
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=79.56 E-value=3.1 Score=37.45 Aligned_cols=31 Identities=29% Similarity=0.178 Sum_probs=25.9
Q ss_pred HHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 453 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 453 VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
...|+. +|+|+.+||+.||+|+.+|+|.+..
T Consensus 15 A~~L~e----eG~Sq~~iA~LLGltqaAVS~Yls~ 45 (119)
T COG2522 15 AKELIE----EGLSQYRIAKLLGLTQAAVSQYLSG 45 (119)
T ss_pred HHHHHH----cCCcHHHHHHHhCCCHHHHHHHHcc
Confidence 344554 6899999999999999999998753
No 271
>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=79.55 E-value=2.6 Score=32.64 Aligned_cols=24 Identities=13% Similarity=0.214 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q 010521 463 ECLTWEDISKRIGLSRERVRQVGL 486 (508)
Q Consensus 463 eg~TleEIAe~LgIS~erVrqi~~ 486 (508)
...|.+|+|+.||||..|||+-+.
T Consensus 13 ~~~s~~ela~~~~VS~~TiRRDl~ 36 (57)
T PF08220_consen 13 GKVSVKELAEEFGVSEMTIRRDLN 36 (57)
T ss_pred CCEEHHHHHHHHCcCHHHHHHHHH
Confidence 468999999999999999987654
No 272
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=79.34 E-value=4.4 Score=34.38 Aligned_cols=44 Identities=14% Similarity=0.027 Sum_probs=36.5
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
..|++.-|..|..+. + .++.+..+.|+.+|||+.|++++..|=.
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 468999888777765 1 2689999999999999999999987743
No 273
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=79.23 E-value=3.8 Score=37.21 Aligned_cols=43 Identities=23% Similarity=0.345 Sum_probs=33.8
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA 488 (508)
..|++.++.||..--. .-..|+.|||+.+|+|+.+|+.++.+-
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 3678888888877531 234899999999999999998776653
No 274
>PHA01976 helix-turn-helix protein
Probab=79.15 E-value=3.2 Score=32.46 Aligned_cols=26 Identities=12% Similarity=0.203 Sum_probs=23.6
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
..++|..|+|+.+|+|+.+|++++..
T Consensus 13 ~~glt~~~lA~~~gvs~~~v~~~e~g 38 (67)
T PHA01976 13 ARAWSAPELSRRAGVRHSLIYDFEAD 38 (67)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 46799999999999999999999864
No 275
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=78.58 E-value=4.4 Score=29.41 Aligned_cols=25 Identities=16% Similarity=0.205 Sum_probs=21.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 463 ECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 463 eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
.+.|..+|++.+|+++.+|++.+..
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~ 37 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNK 37 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4699999999999999999766644
No 276
>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=78.40 E-value=3.1 Score=30.10 Aligned_cols=38 Identities=18% Similarity=0.176 Sum_probs=25.3
Q ss_pred CHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521 447 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 486 (508)
Q Consensus 447 p~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~ 486 (508)
.+-|+.+|.-..- ..+-+..+.|+.||||+.++...+.
T Consensus 3 ~~~E~~~i~~aL~--~~~gn~~~aA~~Lgisr~tL~~klk 40 (42)
T PF02954_consen 3 EEFEKQLIRQALE--RCGGNVSKAARLLGISRRTLYRKLK 40 (42)
T ss_dssp HHHHHHHHHHHHH--HTTT-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHHH--HhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3446666665441 2356899999999999999987654
No 277
>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=78.29 E-value=1.7 Score=31.63 Aligned_cols=25 Identities=24% Similarity=0.333 Sum_probs=22.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
+|..|+|+.+||++.||+.+..+.+
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999987765
No 278
>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=77.68 E-value=2.2 Score=34.17 Aligned_cols=35 Identities=11% Similarity=0.178 Sum_probs=28.5
Q ss_pred HHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 452 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 452 ~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
.||..+. ..|.|..+||..+||+++++.++.....
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 3555554 4789999999999999999999998875
No 279
>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=77.49 E-value=5.5 Score=31.88 Aligned_cols=31 Identities=35% Similarity=0.579 Sum_probs=23.9
Q ss_pred HHHcCCCCCHHHHHHHhCCC-HHHHHHHHHHh
Q 010521 360 LEEKGVTPSVDRIAEYLNMS-QKKVRNATEAI 390 (508)
Q Consensus 360 l~~~Gr~Pt~eEIA~~Lgis-~e~v~~~l~~~ 390 (508)
+.+.|..||..|||+.+|+. ...|...+...
T Consensus 19 ~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~L 50 (65)
T PF01726_consen 19 IEENGYPPTVREIAEALGLKSTSTVQRHLKAL 50 (65)
T ss_dssp HHHHSS---HHHHHHHHTSSSHHHHHHHHHHH
T ss_pred HHHcCCCCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 35689999999999999996 98998887765
No 280
>PHA00542 putative Cro-like protein
Probab=77.48 E-value=3.2 Score=34.56 Aligned_cols=27 Identities=11% Similarity=0.102 Sum_probs=24.0
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~rA 488 (508)
..++|..++|+.+|||+.+|.+++...
T Consensus 29 ~~glTq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 29 RAGWSQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHHcCC
Confidence 467999999999999999999998653
No 281
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=76.99 E-value=1.3e+02 Score=33.52 Aligned_cols=25 Identities=16% Similarity=0.306 Sum_probs=22.1
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGL 486 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~ 486 (508)
..++|+++||+.+|+..+||++...
T Consensus 367 LkPLtlkdVAe~lglHeSTVSRa~~ 391 (481)
T PRK12469 367 LKPLVLRDVAEELGLHESTISRATG 391 (481)
T ss_pred CcCCcHHHHHHHhCCCcchhhHHhc
Confidence 3689999999999999999987654
No 282
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=76.83 E-value=3.6 Score=29.54 Aligned_cols=23 Identities=35% Similarity=0.458 Sum_probs=19.4
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Q 010521 464 CLTWEDISKRIGLSRERVRQVGL 486 (508)
Q Consensus 464 g~TleEIAe~LgIS~erVrqi~~ 486 (508)
++|..|||+.+|+|+.+|++.+.
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~ 30 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLK 30 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHH
Confidence 58999999999999999964443
No 283
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=76.66 E-value=1.3e+02 Score=33.27 Aligned_cols=25 Identities=16% Similarity=0.353 Sum_probs=22.1
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGL 486 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~ 486 (508)
..++|+++||+.+|+..+||++...
T Consensus 341 LkPLtlkdvAe~lglheSTVSRav~ 365 (455)
T PRK05932 341 LKPLVLKDIAEELGMHESTISRATT 365 (455)
T ss_pred CcCccHHHHHHHhCCCccchhhhhc
Confidence 3689999999999999999987654
No 284
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=76.61 E-value=3.9 Score=30.54 Aligned_cols=27 Identities=33% Similarity=0.634 Sum_probs=21.3
Q ss_pred CCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 463 ECL-TWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 463 eg~-TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
+.+ |..|||+.+|+|+.+|++ ++++|.
T Consensus 18 ~~l~s~~~la~~~~vs~~tv~~----~l~~L~ 45 (60)
T smart00345 18 DKLPSERELAAQLGVSRTTVRE----ALSRLE 45 (60)
T ss_pred CcCcCHHHHHHHHCCCHHHHHH----HHHHHH
Confidence 345 899999999999999974 455554
No 285
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=76.48 E-value=2.8 Score=31.17 Aligned_cols=25 Identities=24% Similarity=0.187 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 463 ECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 463 eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
.++|+.++|+.+|+|+++|++++..
T Consensus 14 ~gltq~~lA~~~gvs~~~vs~~e~g 38 (58)
T TIGR03070 14 LGLTQADLADLAGVGLRFIRDVENG 38 (58)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 5799999999999999999999864
No 286
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=76.20 E-value=1.3e+02 Score=33.15 Aligned_cols=24 Identities=17% Similarity=0.333 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q 010521 463 ECLTWEDISKRIGLSRERVRQVGL 486 (508)
Q Consensus 463 eg~TleEIAe~LgIS~erVrqi~~ 486 (508)
.++++++||+.+|++.+||++...
T Consensus 329 ~PL~LrdvA~~i~~HESTISRai~ 352 (444)
T COG1508 329 KPLVLRDVADEIGMHESTISRAIT 352 (444)
T ss_pred CcccHHHHHHHhCccHHHHHHHHh
Confidence 469999999999999999987654
No 287
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=76.02 E-value=35 Score=26.58 Aligned_cols=26 Identities=19% Similarity=0.194 Sum_probs=21.5
Q ss_pred CCCCHHHHHHHHCC-CHHHHHHHHHHH
Q 010521 463 ECLTWEDISKRIGL-SRERVRQVGLVA 488 (508)
Q Consensus 463 eg~TleEIAe~LgI-S~erVrqi~~rA 488 (508)
.+.++.+||..+|+ +.....+...+.
T Consensus 49 ~~~~~~~ia~~~g~~s~~~f~r~Fk~~ 75 (84)
T smart00342 49 TDLSVTEIALRVGFSSQSYFSRAFKKL 75 (84)
T ss_pred CCCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 36899999999999 988887766543
No 288
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=75.92 E-value=8 Score=32.61 Aligned_cols=31 Identities=19% Similarity=0.177 Sum_probs=25.1
Q ss_pred CCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHH
Q 010521 463 ECLTWEDISKRIG-LSRERVRQVGLVALEKLK 493 (508)
Q Consensus 463 eg~TleEIAe~Lg-IS~erVrqi~~rALkKLR 493 (508)
-++|+.+||+.|| .+.+||.....+.-++|.
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 289
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=75.90 E-value=3.8 Score=33.34 Aligned_cols=25 Identities=28% Similarity=0.368 Sum_probs=22.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 463 ECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 463 eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
-++|++|.|+.+|||+.|+-.++..
T Consensus 13 ~~ltQ~elA~~vgVsRQTi~~iEkg 37 (68)
T COG1476 13 LGLTQEELAKLVGVSRQTIIAIEKG 37 (68)
T ss_pred hCcCHHHHHHHcCcCHHHHHHHHcC
Confidence 4699999999999999999988764
No 290
>PRK10870 transcriptional repressor MprA; Provisional
Probab=75.77 E-value=18 Score=34.26 Aligned_cols=44 Identities=11% Similarity=0.082 Sum_probs=34.1
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA 488 (508)
.|++.|-.|+...+..+..+.|..|||+.+++++.+|.+++.+-
T Consensus 52 gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rL 95 (176)
T PRK10870 52 GINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADEL 95 (176)
T ss_pred CCCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 58888888887765222346899999999999999997766553
No 291
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=75.75 E-value=3.7 Score=32.05 Aligned_cols=26 Identities=19% Similarity=0.385 Sum_probs=21.3
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
..++|..++|+.+|+|.++|++++.-
T Consensus 12 ~~gls~~~lA~~~g~s~s~v~~iE~G 37 (64)
T PF13560_consen 12 RAGLSQAQLADRLGVSQSTVSRIERG 37 (64)
T ss_dssp CHTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 35799999999999999999999864
No 292
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=75.61 E-value=6.1 Score=31.32 Aligned_cols=26 Identities=19% Similarity=0.273 Sum_probs=21.6
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
....|..|||+.+|+|+.+|++.+.+
T Consensus 11 ~~~~~~~eLa~~l~vS~~tv~~~l~~ 36 (69)
T TIGR00122 11 DNPFSGEKLGEALGMSRTAVNKHIQT 36 (69)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 34578999999999999999866554
No 293
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=75.42 E-value=24 Score=37.74 Aligned_cols=31 Identities=23% Similarity=0.404 Sum_probs=25.8
Q ss_pred hHHHHHHhhCCCCchHHHHHHhccChHHHHH
Q 010521 227 HKLRLKERLGCEPSMEQLAASLRISRPELQS 257 (508)
Q Consensus 227 ~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~ 257 (508)
++..|...+|++|+.+++|..+|++.+++..
T Consensus 228 a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~ 258 (373)
T PRK07406 228 TTKVLSQEFGRKPTEEEIAESMEMTIEKLRF 258 (373)
T ss_pred HHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 3456777899999999999999999887643
No 294
>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=75.42 E-value=3.6 Score=38.43 Aligned_cols=27 Identities=26% Similarity=0.407 Sum_probs=22.7
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 464 CLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 464 g~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
++|.+|||..+|+|+++|. |++++|++
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 5899999999999999996 66666664
No 295
>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=75.26 E-value=3.3 Score=33.04 Aligned_cols=26 Identities=46% Similarity=0.659 Sum_probs=21.2
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 464 CLTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 464 g~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
++|.++||..+|+|+++|.+ .+++|+
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r----~l~~l~ 53 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSR----ILKRLK 53 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHH----HHHHHH
T ss_pred cCCHHHHHHHHCCCHHHHHH----HHHHHH
Confidence 58999999999999999864 455554
No 296
>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=75.20 E-value=5.6 Score=33.34 Aligned_cols=37 Identities=24% Similarity=0.186 Sum_probs=27.7
Q ss_pred HHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 448 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 448 ~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
+|+..|+.+-- ....|..+||+.+|+|+.||+..+..
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 45555555543 24579999999999999999987753
No 297
>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=75.19 E-value=13 Score=32.16 Aligned_cols=44 Identities=18% Similarity=0.094 Sum_probs=34.6
Q ss_pred cCCHHHHHHHhHHh--ccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYY--GLDKECLTWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 445 ~Lp~rER~VI~Lry--GLd~eg~TleEIAe~LgIS~erVrqi~~rA 488 (508)
.|++.|-.||..-+ .-+..+.|..|||+.+++++++|.+.+.+-
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~L 67 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKL 67 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHH
Confidence 79999999886644 112357999999999999999998766553
No 298
>PRK10072 putative transcriptional regulator; Provisional
Probab=75.14 E-value=4 Score=35.34 Aligned_cols=32 Identities=19% Similarity=0.202 Sum_probs=26.1
Q ss_pred HHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 453 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 453 VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
|-.+|. ..++|+.++|+.+|||..||++++..
T Consensus 38 ik~LR~---~~glTQ~elA~~lGvS~~TVs~WE~G 69 (96)
T PRK10072 38 FEQLRK---GTGLKIDDFARVLGVSVAMVKEWESR 69 (96)
T ss_pred HHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 334454 45799999999999999999999863
No 299
>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=75.11 E-value=12 Score=36.35 Aligned_cols=34 Identities=32% Similarity=0.456 Sum_probs=27.3
Q ss_pred hhHHHHHHhhCCCCchHHHHHHhccChHHHHHhh
Q 010521 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (508)
Q Consensus 226 ~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l 259 (508)
.++.+|...+|++|+.+++|..+|++.+.++..+
T Consensus 87 ~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~ 120 (224)
T TIGR02479 87 RAIRELEARLGREPTEEEIAEELGMDLKEYRQAL 120 (224)
T ss_pred HHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHH
Confidence 3455677789999999999999999988765543
No 300
>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=75.09 E-value=7.4 Score=29.80 Aligned_cols=37 Identities=27% Similarity=0.352 Sum_probs=26.8
Q ss_pred HHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 448 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 448 ~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
+.+..|+...+ ..+.+..||++.+|+++.+|+..+.+
T Consensus 7 ~~~~~il~~l~---~~~~~~~ei~~~~~i~~~~i~~~l~~ 43 (78)
T cd00090 7 PTRLRILRLLL---EGPLTVSELAERLGLSQSTVSRHLKK 43 (78)
T ss_pred hHHHHHHHHHH---HCCcCHHHHHHHHCcCHhHHHHHHHH
Confidence 44555665444 23499999999999999999765544
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=74.75 E-value=14 Score=32.23 Aligned_cols=42 Identities=12% Similarity=0.230 Sum_probs=33.6
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
..|++.|..||..-.. ..+.|..|||+.+|+++.+|.+.+.+
T Consensus 24 ~~lt~~q~~iL~~l~~--~~~~t~~ela~~~~~~~~tvs~~l~~ 65 (118)
T TIGR02337 24 HGLTEQQWRILRILAE--QGSMEFTQLANQACILRPSLTGILAR 65 (118)
T ss_pred cCCCHHHHHHHHHHHH--cCCcCHHHHHHHhCCCchhHHHHHHH
Confidence 4789999888876542 46799999999999999999755544
No 302
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=74.43 E-value=6.3 Score=29.35 Aligned_cols=27 Identities=19% Similarity=0.135 Sum_probs=22.7
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~rA 488 (508)
.++.|..+|++.+|+|+.+|+..+.+-
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L 34 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKL 34 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHH
Confidence 467899999999999999998776553
No 303
>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=74.28 E-value=6.6 Score=34.36 Aligned_cols=41 Identities=20% Similarity=0.389 Sum_probs=26.7
Q ss_pred HHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 449 REREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 449 rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
+.+.|... | +|++..++|.++|+|..+|.+|+.+...+-++
T Consensus 62 R~~~I~~~-f----~G~n~~eLA~kyglS~r~I~~Ii~~~~~~~~~ 102 (108)
T PF08765_consen 62 RNREIRRE-F----NGMNVRELARKYGLSERQIYRIIKRVRRRERR 102 (108)
T ss_dssp HHHHHHHH-------SS-HHHHHHHHT--HHHHHHHHHHHHH----
T ss_pred HHHHHHHH-h----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 44556554 3 58999999999999999999999988776554
No 304
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=73.98 E-value=10 Score=33.40 Aligned_cols=51 Identities=27% Similarity=0.304 Sum_probs=44.9
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~ 497 (508)
.+|.+-||-...-+| -+-+|-+|||-++.++..+|..+.+.-..|.|+.-+
T Consensus 27 ~QLkELErvF~ETHY---PDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 27 AQLKELERVFAETHY---PDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred HHHHHHHHHHHhhcC---CcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence 568888888888888 678999999999999999999999999999987543
No 305
>PRK14082 hypothetical protein; Provisional
Probab=73.62 E-value=12 Score=30.16 Aligned_cols=56 Identities=11% Similarity=0.024 Sum_probs=42.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhH
Q 010521 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320 (508)
Q Consensus 263 ~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTY 320 (508)
....+.++..+.|.+.+-... -.-.+.|||.||--+.+++-+..++...+.-|.-|
T Consensus 8 ~~e~e~ii~~FepkIkKsL~~--T~yqeREDLeQElk~Ki~eK~~~~~~~e~PGF~ef 63 (65)
T PRK14082 8 TEEIEHLIENFSPMIKKKLSN--TSYQEREDLEQELKIKIIEKADMLLCQEVPGFWEF 63 (65)
T ss_pred HHHHHHHHHHccHHHHHHHhc--CChhhHHHHHHHHHHHHHHHHHHhhcccCCcHHHh
Confidence 366788999999988763322 12357899999999999999999987765556544
No 306
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=73.14 E-value=5.1 Score=30.89 Aligned_cols=24 Identities=33% Similarity=0.396 Sum_probs=20.4
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q 010521 463 ECLTWEDISKRIGLSRERVRQVGL 486 (508)
Q Consensus 463 eg~TleEIAe~LgIS~erVrqi~~ 486 (508)
.++|..|||+.+|+|+.+|++++.
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~ 47 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLK 47 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHH
Confidence 469999999999999999965444
No 307
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=73.06 E-value=3.7 Score=30.88 Aligned_cols=25 Identities=24% Similarity=0.384 Sum_probs=20.4
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGL 486 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~ 486 (508)
..++|..|||+.+|+++++|.+++.
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 3568999999999999999976654
No 308
>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=73.03 E-value=6.8 Score=37.55 Aligned_cols=43 Identities=16% Similarity=0.197 Sum_probs=32.3
Q ss_pred ccCCHHHHHHHhHHhcc---CCCCCCHHHHHHHHCCC-HHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGL---DKECLTWEDISKRIGLS-RERVRQVGL 486 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGL---d~eg~TleEIAe~LgIS-~erVrqi~~ 486 (508)
..|+++|+.|+..-.-. +..+.|..|||+.+|++ ++||..++.
T Consensus 2 ~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~ 48 (199)
T TIGR00498 2 KPLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLK 48 (199)
T ss_pred CccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHH
Confidence 35899999998775411 12358899999999998 999975544
No 309
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=73.00 E-value=15 Score=38.17 Aligned_cols=35 Identities=17% Similarity=0.411 Sum_probs=26.9
Q ss_pred cchhHHHHHHhhCCCCchHHHHHHhccChHHHHHh
Q 010521 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (508)
Q Consensus 224 l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~ 258 (508)
+...+..+...+|++|+.+++|..+|++.+++...
T Consensus 170 l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~ 204 (317)
T PRK07405 170 IKKAQRQLSQQLGRAATIGELAEELELTPKQVREY 204 (317)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 34455566778999999999999999987765433
No 310
>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=72.94 E-value=5.3 Score=31.06 Aligned_cols=37 Identities=14% Similarity=0.331 Sum_probs=27.2
Q ss_pred HHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 449 REREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 449 rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
|+..++.+-+. ...+|+.|||+.+|+|..+|++.+..
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 45556666553 45799999999999999999876553
No 311
>PRK00215 LexA repressor; Validated
Probab=72.75 E-value=7.5 Score=37.42 Aligned_cols=43 Identities=21% Similarity=0.220 Sum_probs=32.1
Q ss_pred CCHHHHHHHhHHhc--c-CCCCCCHHHHHHHHCC-CHHHHHHHHHHH
Q 010521 446 LGEREREIIRLYYG--L-DKECLTWEDISKRIGL-SRERVRQVGLVA 488 (508)
Q Consensus 446 Lp~rER~VI~LryG--L-d~eg~TleEIAe~LgI-S~erVrqi~~rA 488 (508)
|+++|+.|+.+-.- . +..+.|+.|||+.+|+ +++||..++.+-
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L 48 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKAL 48 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 78889998865420 1 1346799999999999 999998666543
No 312
>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=72.70 E-value=3.4 Score=35.01 Aligned_cols=24 Identities=38% Similarity=0.302 Sum_probs=17.6
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q 010521 463 ECLTWEDISKRIGLSRERVRQVGL 486 (508)
Q Consensus 463 eg~TleEIAe~LgIS~erVrqi~~ 486 (508)
.|+|..|||+++|.|++.|.+++.
T Consensus 2 ~G~tq~eIA~~lGks~s~Vs~~l~ 25 (93)
T PF08535_consen 2 FGWTQEEIAKRLGKSRSWVSNHLA 25 (93)
T ss_dssp TT--HHHHHHHTT--HHHHHHHHG
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 479999999999999999998764
No 313
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=72.25 E-value=7.5 Score=37.60 Aligned_cols=42 Identities=14% Similarity=0.185 Sum_probs=34.1
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
..|++++..|+..-.. ..+.+..|||+.+|+|++||++.+.+
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 24689999999999999999866655
No 314
>PRK09954 putative kinase; Provisional
Probab=72.24 E-value=6.9 Score=40.93 Aligned_cols=41 Identities=22% Similarity=0.347 Sum_probs=32.1
Q ss_pred CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521 446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA 488 (508)
|+++++.||.+.. .....|..|||+.||+|+.+|+.++.+-
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 4677778887754 1235899999999999999998877654
No 315
>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=72.06 E-value=12 Score=33.00 Aligned_cols=40 Identities=15% Similarity=0.015 Sum_probs=31.6
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA 488 (508)
..+.+.+-.-++..+ ++|.+++|+.+|+++.+|+++++..
T Consensus 63 ~~~~~~~i~~~r~~~-----gltq~~lA~~lg~~~~tis~~e~g~ 102 (127)
T TIGR03830 63 GLLTPPEIRRIRKKL-----GLSQREAAELLGGGVNAFSRYERGE 102 (127)
T ss_pred CCcCHHHHHHHHHHc-----CCCHHHHHHHhCCCHHHHHHHHCCC
Confidence 566776655555554 5899999999999999999988753
No 316
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=71.85 E-value=1.9 Score=33.85 Aligned_cols=25 Identities=24% Similarity=0.343 Sum_probs=22.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
||..|+|+.+|||+.+|+.+..+.+
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 5789999999999999999987654
No 317
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=71.18 E-value=12 Score=31.28 Aligned_cols=30 Identities=20% Similarity=0.431 Sum_probs=23.9
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 461 DKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 461 d~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
++...|-++||+.||+||.+|- +.+++||.
T Consensus 16 ~~~~~SGe~La~~LgiSRtaVw----K~Iq~Lr~ 45 (79)
T COG1654 16 TGNFVSGEKLAEELGISRTAVW----KHIQQLRE 45 (79)
T ss_pred CCCcccHHHHHHHHCccHHHHH----HHHHHHHH
Confidence 3567999999999999999885 55566663
No 318
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=71.10 E-value=37 Score=33.74 Aligned_cols=34 Identities=18% Similarity=0.256 Sum_probs=27.6
Q ss_pred hHHHHHHhhCCCCchHHHHHHhccChHHHHHhhh
Q 010521 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (508)
Q Consensus 227 ~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~ 260 (508)
...++...+|++|+.+++|..+|++.++++..+.
T Consensus 114 ~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~ 147 (251)
T PRK07670 114 AIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMN 147 (251)
T ss_pred HHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 4455667889999999999999999888766544
No 319
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=71.08 E-value=11 Score=35.36 Aligned_cols=47 Identities=17% Similarity=0.258 Sum_probs=35.2
Q ss_pred HHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH------HHHHHHHHHHHhhHH
Q 010521 453 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV------ALEKLKHAARKKKME 502 (508)
Q Consensus 453 VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r------ALkKLR~~L~~~~l~ 502 (508)
|=.+|- .-|+|..++|+.+|||+.+|++++.. .+..|.+.....+..
T Consensus 30 Ir~~R~---~lGmTq~eLAerlGVS~~tIs~iE~G~~~~~psl~~L~kIA~aLgv~ 82 (150)
T TIGR02612 30 VRAIRK---ALGMSGAQLAGRLGVTPQRVEALEKSELSGTVTLKTLRAAAEALDCT 82 (150)
T ss_pred HHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCCCHHHHHHHHHHcCCC
Confidence 444454 46899999999999999999999985 455666666554443
No 320
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=70.90 E-value=4.9 Score=40.62 Aligned_cols=26 Identities=15% Similarity=0.328 Sum_probs=24.0
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
.+||.+.+||+.||||+.||+.+..|
T Consensus 17 l~gmk~~dIAeklGvspntiksWKrr 42 (279)
T COG5484 17 LKGMKLKDIAEKLGVSPNTIKSWKRR 42 (279)
T ss_pred HhhccHHHHHHHhCCChHHHHHHHHh
Confidence 47899999999999999999999876
No 321
>PF14493 HTH_40: Helix-turn-helix domain
Probab=70.10 E-value=10 Score=31.97 Aligned_cols=30 Identities=23% Similarity=0.240 Sum_probs=27.1
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGLVALEK 491 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~rALkK 491 (508)
.+|+|.+|||+.-|++.+||...+.++...
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 322
>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=69.95 E-value=17 Score=27.61 Aligned_cols=26 Identities=31% Similarity=0.512 Sum_probs=20.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
.|..+||+.+|+|+.+|+ +++++|..
T Consensus 26 ~~~~~la~~~~is~~~v~----~~l~~L~~ 51 (66)
T cd07377 26 PSERELAEELGVSRTTVR----EALRELEA 51 (66)
T ss_pred CCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 459999999999999997 45555543
No 323
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=69.87 E-value=11 Score=31.01 Aligned_cols=41 Identities=24% Similarity=0.345 Sum_probs=31.7
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
.|+..+..||.+-+. ..++|..+||+.+++++.+|++.+.+
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 577788888877662 24689999999999999998754443
No 324
>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=69.84 E-value=5.3 Score=37.77 Aligned_cols=26 Identities=27% Similarity=0.345 Sum_probs=23.5
Q ss_pred CCCCCHHHHHHHHC-CCHHHHHHHHHH
Q 010521 462 KECLTWEDISKRIG-LSRERVRQVGLV 487 (508)
Q Consensus 462 ~eg~TleEIAe~Lg-IS~erVrqi~~r 487 (508)
.+|+|..|||+.|| ||++.|--..+|
T Consensus 16 ~~G~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 16 AEGLSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred HcCCCHHHHHHHhCCcchhhhhhhhhc
Confidence 58999999999999 999999877766
No 325
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=69.83 E-value=4.6 Score=32.35 Aligned_cols=23 Identities=26% Similarity=0.289 Sum_probs=20.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~r 487 (508)
.|+.|||+.+|||+.||+.+++.
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~ 23 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNG 23 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCC
Confidence 37899999999999999987754
No 326
>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=69.44 E-value=5.1 Score=36.03 Aligned_cols=23 Identities=22% Similarity=0.277 Sum_probs=21.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~r 487 (508)
||.+|+|+.+|+++.||.+++.+
T Consensus 1 MT~eELA~~tG~srQTINrWvRk 23 (122)
T PF07037_consen 1 MTPEELAELTGYSRQTINRWVRK 23 (122)
T ss_pred CCHHHHHHHhCccHHHHHHHHHh
Confidence 78999999999999999998764
No 327
>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=69.35 E-value=48 Score=34.02 Aligned_cols=32 Identities=22% Similarity=0.462 Sum_probs=26.1
Q ss_pred hHHHHHHhhCCCCchHHHHHHhccChHHHHHh
Q 010521 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (508)
Q Consensus 227 ~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~ 258 (508)
.+.++...+|++|+.+++|..+|++.+++...
T Consensus 166 ~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~ 197 (298)
T TIGR02997 166 VQRELSQKLGRTPSEAEIAEALELEPEQVREL 197 (298)
T ss_pred HHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 34456677999999999999999998876554
No 328
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=69.09 E-value=11 Score=34.12 Aligned_cols=41 Identities=7% Similarity=0.087 Sum_probs=33.6
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
.|++.|..||..-+. .++.|..|||+.+|+++++|...+.+
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 688999888876541 46799999999999999999876654
No 329
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=68.83 E-value=6 Score=37.32 Aligned_cols=27 Identities=22% Similarity=0.403 Sum_probs=22.2
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 464 CLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 464 g~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
..|+++||..+|+|+++|+ |++++|++
T Consensus 149 ~~t~~~iA~~lG~tretvs----R~l~~l~~ 175 (202)
T PRK13918 149 YATHDELAAAVGSVRETVT----KVIGELSR 175 (202)
T ss_pred cCCHHHHHHHhCccHHHHH----HHHHHHHH
Confidence 5799999999999999996 55556553
No 330
>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=68.73 E-value=6.3 Score=30.77 Aligned_cols=23 Identities=17% Similarity=0.213 Sum_probs=20.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~r 487 (508)
+|..|+|+.+|||..|++.+..+
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 58899999999999999998865
No 331
>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=68.27 E-value=69 Score=32.83 Aligned_cols=97 Identities=13% Similarity=0.218 Sum_probs=51.8
Q ss_pred CCCCCHHHHHHHhC--CCHHHHHHHHHHhCc--cccccccCCCCCCCCCCCc-cc-cccccccCCCCccchH--HHHHHH
Q 010521 364 GVTPSVDRIAEYLN--MSQKKVRNATEAIGK--VFSLDREAFPSLNGLPGET-HH-SYIADNRVENNPWHGV--DDWALK 435 (508)
Q Consensus 364 Gr~Pt~eEIA~~Lg--is~e~v~~~l~~~~~--~~SLD~~~~~~~~~~~~~~-l~-d~i~d~~~e~~Pe~~v--e~~el~ 435 (508)
+..+++.+||+.++ ||.++|++.+....+ .+.-+. +|.- .. ..+.... +.|-..+ -+.+..
T Consensus 135 ~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~---------~g~y~~t~~~l~~~~--~~~~~avr~~h~q~l 203 (271)
T TIGR02147 135 PFADDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNE---------DGFYKQTDKAVSTGD--EVIPLAVRQYQKQMI 203 (271)
T ss_pred CCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECC---------CCcEEeecceeecCC--ccchHHHHHHHHHHH
Confidence 34557889999999 999999999887643 222221 1100 00 0111111 1121111 122333
Q ss_pred HHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHH
Q 010521 436 DEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRI 474 (508)
Q Consensus 436 e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~L 474 (508)
+.-.++| +..|+.+|.+-.+-+|++ .-++++|.+.+
T Consensus 204 ~lA~~al-~~~p~~eR~~S~lT~~i~--~~~~~~i~~~i 239 (271)
T TIGR02147 204 DLAKEAL-DALPPSERDVSTVTFGIS--EEAYKEIVKKI 239 (271)
T ss_pred HHHHHHH-HhCCccccccceeeEecC--HHHHHHHHHHH
Confidence 4455566 789999999877766532 33445544443
No 332
>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=67.72 E-value=11 Score=30.25 Aligned_cols=26 Identities=19% Similarity=0.253 Sum_probs=23.3
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
..++|..++|+.+|+|+.+|++++..
T Consensus 16 ~~~~t~~~lA~~~gis~~tis~~~~g 41 (78)
T TIGR02607 16 PLGLSIRALAKALGVSRSTLSRIVNG 41 (78)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 45799999999999999999999863
No 333
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=67.55 E-value=13 Score=28.81 Aligned_cols=42 Identities=14% Similarity=0.101 Sum_probs=30.4
Q ss_pred HHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521 453 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497 (508)
Q Consensus 453 VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~ 497 (508)
.+..++ ..+.+..+.|+.|+|.++||+.++.++-+.+...+.
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 467999999999999999999999998777655443
No 334
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=67.34 E-value=11 Score=37.80 Aligned_cols=62 Identities=11% Similarity=0.144 Sum_probs=45.2
Q ss_pred HHHHHHHHHccCCHHHHHHHhHHhcc--CCCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHH
Q 010521 435 KDEVNKLIIVTLGEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGLV----ALEKLKHAAR 497 (508)
Q Consensus 435 ~e~L~~~L~~~Lp~rER~VI~LryGL--d~eg~TleEIAe~LgIS~erVrqi~~r----ALkKLR~~L~ 497 (508)
.+.|...+ ..|++.|+.|......- ....+|..|||+..|+|..||-+--++ +..-||..+.
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 35566777 89999999998775421 113589999999999999999765543 5555555554
No 335
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=67.18 E-value=9.4 Score=32.07 Aligned_cols=35 Identities=20% Similarity=0.153 Sum_probs=24.6
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521 463 ECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497 (508)
Q Consensus 463 eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~ 497 (508)
...|.++.|..||||.+||.+-+..=|.++-..|.
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 46899999999999999999888776666655543
No 336
>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=66.67 E-value=13 Score=27.92 Aligned_cols=50 Identities=18% Similarity=0.192 Sum_probs=38.3
Q ss_pred cCCHHHHHHHhHHhccCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDK--ECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~--eg~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
.+++.+..+|.-.|..+. ......+||..+|++...|..+......+.+.
T Consensus 6 ~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 6 RFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 467778888888875421 23568899999999999999999887776553
No 337
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=66.63 E-value=5.7 Score=37.97 Aligned_cols=29 Identities=31% Similarity=0.603 Sum_probs=24.0
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 461 DKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 461 d~eg~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
..+++|+.||++.+|+|++.|++ ++++|.
T Consensus 38 s~~Pmtl~Ei~E~lg~Sks~vS~----~lkkL~ 66 (177)
T COG1510 38 SRKPLTLDEIAEALGMSKSNVSM----GLKKLQ 66 (177)
T ss_pred cCCCccHHHHHHHHCCCcchHHH----HHHHHH
Confidence 46899999999999999999975 555554
No 338
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=66.55 E-value=13 Score=37.81 Aligned_cols=65 Identities=15% Similarity=0.192 Sum_probs=47.8
Q ss_pred HHHHHHHHHHHccCCHHHHHHHhHHhccC--CCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHHH
Q 010521 433 ALKDEVNKLIIVTLGEREREIIRLYYGLD--KECLTWEDISKRIGLSRERVRQVGLV----ALEKLKHAARK 498 (508)
Q Consensus 433 el~e~L~~~L~~~Lp~rER~VI~LryGLd--~eg~TleEIAe~LgIS~erVrqi~~r----ALkKLR~~L~~ 498 (508)
.+.+.|...+ ..|++.|+.|.....--. ...+|..+||+..|||..||-+.-++ +...||..+..
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 3456777778 899999999987764211 23599999999999999999765443 56666666543
No 339
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=66.53 E-value=12 Score=32.96 Aligned_cols=39 Identities=26% Similarity=0.198 Sum_probs=35.5
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
..|++.|-..|+-.+ ++|+.+-|..||+|.+||+.++..
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 689999999998887 489999999999999999999975
No 340
>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=65.82 E-value=7.5 Score=34.55 Aligned_cols=25 Identities=24% Similarity=0.272 Sum_probs=23.2
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGL 486 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~ 486 (508)
..|.|..++|..++||+.||..+..
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 5789999999999999999999877
No 341
>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=65.41 E-value=13 Score=33.79 Aligned_cols=33 Identities=24% Similarity=0.225 Sum_probs=24.7
Q ss_pred HHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 451 REIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 451 R~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
+.||.|.. +|..-.+||..|+||.+.|++++.|
T Consensus 24 ~rIvela~----~G~rp~~Isr~l~Vs~gcVsKIl~R 56 (125)
T PF00292_consen 24 QRIVELAK----EGVRPCDISRQLRVSHGCVSKILSR 56 (125)
T ss_dssp HHHHHHHH----TT--HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHHhh----hcCCHHHHHHHHccchhHHHHHHHH
Confidence 34777776 7999999999999999999998876
No 342
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=65.24 E-value=14 Score=33.29 Aligned_cols=42 Identities=12% Similarity=0.040 Sum_probs=32.5
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
.|++.|..||..-+.. .++.|..|||+.+|+++++|.+.+.+
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 6888888877655411 24689999999999999999866654
No 343
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=64.54 E-value=6.8 Score=37.45 Aligned_cols=28 Identities=18% Similarity=0.223 Sum_probs=24.1
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010521 463 ECLTWEDISKRIGLSRERVRQVGLVALE 490 (508)
Q Consensus 463 eg~TleEIAe~LgIS~erVrqi~~rALk 490 (508)
-+||..|||+.+|.|+.|||+++.-.-+
T Consensus 60 ag~Ti~EIAeelG~TeqTir~hlkgetk 87 (182)
T COG1318 60 AGMTISEIAEELGRTEQTVRNHLKGETK 87 (182)
T ss_pred ccCcHHHHHHHhCCCHHHHHHHHhcchh
Confidence 4799999999999999999998765443
No 344
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=64.18 E-value=8.1 Score=37.49 Aligned_cols=27 Identities=26% Similarity=0.532 Sum_probs=21.9
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 464 CLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 464 g~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
++|+++||..+|+|+++|.++ +++|++
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 589999999999999999754 555553
No 345
>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=63.55 E-value=4.6 Score=28.86 Aligned_cols=23 Identities=22% Similarity=0.289 Sum_probs=19.1
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHH
Q 010521 466 TWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 466 TleEIAe~LgIS~erVrqi~~rA 488 (508)
|..|+|+.+|||..|+|.+....
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~G 23 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYEREG 23 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHTT
T ss_pred CHHHHHHHHCCCHHHHHHHHHCC
Confidence 46799999999999999988765
No 346
>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=63.54 E-value=18 Score=28.14 Aligned_cols=23 Identities=30% Similarity=0.500 Sum_probs=17.6
Q ss_pred CCC-CHHHHHHHHCCCHHHHHHHH
Q 010521 463 ECL-TWEDISKRIGLSRERVRQVG 485 (508)
Q Consensus 463 eg~-TleEIAe~LgIS~erVrqi~ 485 (508)
+.+ |..+||+.+|+|+.+|+..+
T Consensus 22 ~~lps~~~la~~~~vsr~tvr~al 45 (64)
T PF00392_consen 22 DRLPSERELAERYGVSRTTVREAL 45 (64)
T ss_dssp SBE--HHHHHHHHTS-HHHHHHHH
T ss_pred CEeCCHHHHHHHhccCCcHHHHHH
Confidence 556 99999999999999997443
No 347
>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=63.38 E-value=9.4 Score=29.96 Aligned_cols=23 Identities=22% Similarity=0.283 Sum_probs=20.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~r 487 (508)
+|..|+|+.+|||..|++.+..+
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 57899999999999999999775
No 348
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=62.69 E-value=12 Score=26.66 Aligned_cols=27 Identities=26% Similarity=0.298 Sum_probs=19.7
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~rA 488 (508)
.++.|+.+||+.+|+|+...++...+.
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 467999999999999999888776654
No 349
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=62.64 E-value=49 Score=32.46 Aligned_cols=32 Identities=28% Similarity=0.426 Sum_probs=25.3
Q ss_pred hHHHHHHhhCCCCchHHHHHHhccChHHHHHh
Q 010521 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (508)
Q Consensus 227 ~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~ 258 (508)
....+...+|++|+.+++|..+|++.+++...
T Consensus 100 ~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~ 131 (236)
T PRK06986 100 AIRQLEQELGREPTDTEVAEKLGLSLEEYREM 131 (236)
T ss_pred HHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHH
Confidence 34556667899999999999999998765543
No 350
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=62.59 E-value=23 Score=29.06 Aligned_cols=26 Identities=23% Similarity=0.376 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521 463 ECLTWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 463 eg~TleEIAe~LgIS~erVrqi~~rA 488 (508)
.++|..|||+.+|+++.+|++++..-
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L 44 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTL 44 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 47999999999999999998776553
No 351
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=62.55 E-value=9.6 Score=36.11 Aligned_cols=27 Identities=33% Similarity=0.500 Sum_probs=21.8
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 464 CLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 464 g~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
..|.++||..+|+|+++|++ ++++|++
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR----~l~~l~~ 194 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGR----VLKMLED 194 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHH----HHHHHHH
Confidence 57999999999999999964 4555553
No 352
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=62.36 E-value=19 Score=38.76 Aligned_cols=50 Identities=18% Similarity=0.128 Sum_probs=36.3
Q ss_pred cCCHHHHHHHhHHhcc-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 445 ~Lp~rER~VI~LryGL-d~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
.+++.||..+.+.+=| ..++.|+.++|+.|+||++|+.+-+.+..+.|..
T Consensus 10 ~~s~~ER~~~il~~LL~~~~~v~l~~Lae~l~VSrsTi~~DLk~l~~~L~~ 60 (426)
T PRK11564 10 VLSAPQRRCQILLMLFQPGLTVTLETFSQLNGVDDDTARQDIAETGREIQR 60 (426)
T ss_pred CCCHHHHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4677777665554323 4578999999999999999998866665555544
No 353
>TIGR00647 MG103 conserved hypothetical protein.
Probab=61.87 E-value=16 Score=37.55 Aligned_cols=43 Identities=19% Similarity=0.095 Sum_probs=36.7
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHC------CCHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIG------LSRERVRQVGLVA 488 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~Lg------IS~erVrqi~~rA 488 (508)
+.||+.-+++..+|. ...+.|++|+|+.|. ||.+.|..+..+.
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 246899999999994 9999998776654
No 354
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=61.74 E-value=6.3 Score=30.84 Aligned_cols=25 Identities=24% Similarity=0.323 Sum_probs=21.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
+|..|+|+.+|||+.+++.+....+
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~~gl 25 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYERIGL 25 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999998876544
No 355
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=61.73 E-value=15 Score=36.57 Aligned_cols=26 Identities=15% Similarity=0.181 Sum_probs=23.2
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
..++|..|||++||||..+||+.+..
T Consensus 23 ~g~~sa~elA~~Lgis~~avR~HL~~ 48 (218)
T COG2345 23 SGPVSADELAEELGISPMAVRRHLDD 48 (218)
T ss_pred cCCccHHHHHHHhCCCHHHHHHHHHH
Confidence 46899999999999999999988764
No 356
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=61.67 E-value=2.7e+02 Score=31.08 Aligned_cols=22 Identities=23% Similarity=0.342 Sum_probs=19.5
Q ss_pred CHHHHHHHhCCCHHHHHHHHHH
Q 010521 368 SVDRIAEYLNMSQKKVRNATEA 389 (508)
Q Consensus 368 t~eEIA~~Lgis~e~v~~~l~~ 389 (508)
+..+||+.+|+.+.+|.++...
T Consensus 371 tlkdVAe~lglHeSTVSRa~~~ 392 (481)
T PRK12469 371 VLRDVAEELGLHESTISRATGN 392 (481)
T ss_pred cHHHHHHHhCCCcchhhHHhcC
Confidence 7899999999999999987653
No 357
>PRK09726 antitoxin HipB; Provisional
Probab=61.46 E-value=12 Score=31.36 Aligned_cols=38 Identities=13% Similarity=0.226 Sum_probs=29.2
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH----HHHHHHHHHHhh
Q 010521 463 ECLTWEDISKRIGLSRERVRQVGLVA----LEKLKHAARKKK 500 (508)
Q Consensus 463 eg~TleEIAe~LgIS~erVrqi~~rA----LkKLR~~L~~~~ 500 (508)
.++|.+++|+.+|||+.+|+++++.- +.+|.+.+...+
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 57999999999999999999998843 355555554433
No 358
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=61.41 E-value=16 Score=41.02 Aligned_cols=46 Identities=22% Similarity=0.252 Sum_probs=37.2
Q ss_pred CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
|++|+..++.+-- .++.|..++|+.||||..||++-+...-.-|+.
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 5788888887642 367999999999999999999888766555555
No 359
>PRK10161 transcriptional regulator PhoB; Provisional
Probab=61.35 E-value=9 Score=36.25 Aligned_cols=50 Identities=10% Similarity=0.141 Sum_probs=38.9
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHH-----HHCCCHHHHHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISK-----RIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe-----~LgIS~erVrqi~~rALkKLR~ 494 (508)
.|+++|..|+.+-.---+++.|.++|.. .++++..||+..+.+.++||..
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 5999999999876522235788777654 5678999999999999999963
No 360
>PRK15482 transcriptional regulator MurR; Provisional
Probab=61.27 E-value=20 Score=36.21 Aligned_cols=61 Identities=13% Similarity=0.257 Sum_probs=44.4
Q ss_pred HHHHHHHHccCCHHHHHHHhHHhcc--CCCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHH
Q 010521 436 DEVNKLIIVTLGEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGLV----ALEKLKHAAR 497 (508)
Q Consensus 436 e~L~~~L~~~Lp~rER~VI~LryGL--d~eg~TleEIAe~LgIS~erVrqi~~r----ALkKLR~~L~ 497 (508)
..|.... ..|++.|+.|.....-- ....+|..|||+..|+|..||-+.-++ +...||..+.
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 79999999998775421 012599999999999999999665443 5566665554
No 361
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=60.09 E-value=23 Score=35.84 Aligned_cols=62 Identities=23% Similarity=0.295 Sum_probs=42.3
Q ss_pred HhhhhHHHHHHhhcc---cCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhh
Q 010521 188 LIQNRLKGYVKGVVS---EELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (508)
Q Consensus 188 ~~~~~~~~yl~~i~~---~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l 259 (508)
++.+.+..||++... .| ....++..+++. +...|...+|++|+.+++|..+|++.+++...+
T Consensus 100 ~Irg~I~~~lr~~~~~ir~P----r~~~~~~~~i~~------~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~ 164 (264)
T PRK07122 100 TIMGEVRRHFRDNSWSVKVP----RRLKELHLRLGR------ATAELSQRLGRAPTASELAAELGMDREEVVEGL 164 (264)
T ss_pred HHHHHHHHHHHHcCCccccC----HHHHHHHHHHHH------HHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 455677777776443 33 233344444443 345677789999999999999999988765543
No 362
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.05 E-value=19 Score=31.84 Aligned_cols=47 Identities=17% Similarity=0.234 Sum_probs=39.4
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
+.|++.|-+.+.+++ .--=+++||-+.+|+|.-|||..+...+++|-
T Consensus 40 ~~Lt~d~LeFv~lf~---r~RGnlKEvEr~lg~sYptvR~kld~vlramg 86 (122)
T COG3877 40 EYLTSDQLEFVELFL---RCRGNLKEVERELGISYPTVRTKLDEVLRAMG 86 (122)
T ss_pred cccCHhHhHHHHHHH---HHccCHHHHHHHHCCccHHHHHHHHHHHHHcC
Confidence 678888888888877 33458999999999999999999988887763
No 363
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=60.05 E-value=23 Score=34.96 Aligned_cols=61 Identities=23% Similarity=0.370 Sum_probs=39.7
Q ss_pred hhhhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhh
Q 010521 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (508)
Q Consensus 189 ~~~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l 259 (508)
+.+.+..||+.....| -.......+++ .+...+...+|++|+.+++|..+|++.+++...+
T Consensus 78 Ir~~il~~lr~~~~~~----r~vr~~~~~i~------~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~ 138 (231)
T PRK12427 78 IRGAILDELRELDWRP----RRLRQKTHKTN------DAIREIAKRLGHEPNFEEISAELNLTAEEYQEYL 138 (231)
T ss_pred HHHHHHHHHHhcCCCC----HHHHHHHHHHH------HHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 3345555666544332 22233444433 3456777889999999999999999988775544
No 364
>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=59.79 E-value=33 Score=34.73 Aligned_cols=53 Identities=32% Similarity=0.389 Sum_probs=39.0
Q ss_pred HHHHHHHHccCCHHHHHHHhHHhcc-CC-C-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 436 DEVNKLIIVTLGEREREIIRLYYGL-DK-E-CLTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 436 e~L~~~L~~~Lp~rER~VI~LryGL-d~-e-g~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
..+.-+| .+|+=-|.+.+...+-. +. + -.+..+||+++|||+..|+ +|+++|.
T Consensus 168 a~Vq~Ai-~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ir----eAlrkLE 223 (251)
T TIGR02787 168 AAVQMAI-NTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIV----NALRKLE 223 (251)
T ss_pred HHHHHHH-HhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHH----HHHHHHH
Confidence 3455567 88988888877766544 34 2 4799999999999999886 5555554
No 365
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=59.59 E-value=18 Score=30.62 Aligned_cols=41 Identities=17% Similarity=0.263 Sum_probs=32.2
Q ss_pred cCCHHHHHHHhHHhccCCCCCCH-HHHHHHHCCCHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTW-EDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~Tl-eEIAe~LgIS~erVrqi~~rA 488 (508)
.|++.|..|+...+ ..+-.. .+||+.+++++++|.+.+.+-
T Consensus 19 ~lt~~q~~~L~~l~---~~~~~~~~~la~~l~i~~~~vt~~l~~L 60 (126)
T COG1846 19 GLTPPQYQVLLALY---EAGGITVKELAERLGLDRSTVTRLLKRL 60 (126)
T ss_pred CCCHHHHHHHHHHH---HhCCCcHHHHHHHHCCCHHHHHHHHHHH
Confidence 38999999998776 333333 999999999999998776553
No 366
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=59.57 E-value=1e+02 Score=34.61 Aligned_cols=105 Identities=14% Similarity=0.116 Sum_probs=57.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHHHHHcc
Q 010521 366 TPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVT 445 (508)
Q Consensus 366 ~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~L~~~ 445 (508)
..|..+||+.+|+|..+|++-.......+.=..... ..... +-.+... ++ ..+...+ ..
T Consensus 17 ~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~~--i~~~~----Gy~l~~~----~~----------~~~~~~~-~~ 75 (584)
T PRK09863 17 DRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIGS--ISGSA----KYHLEIL----NR----------RSLFQLL-QK 75 (584)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchhh--eecCC----ceEEEeC----CH----------HHHHHHH-hc
Confidence 458999999999999999886665432110000000 00000 1111110 11 1111222 22
Q ss_pred CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
-++ |+..+.++.-+ .++.+..++|+.|.||++||.+-+.+..+.+.
T Consensus 76 ~~~-e~~~il~~Ll~-~~~~~~~~La~~l~vS~sTi~~dl~~v~~~l~ 121 (584)
T PRK09863 76 SDN-EDRLLLLRLLL-NTFTPMAQLASALNLSRTWVAERLPRLNQRYE 121 (584)
T ss_pred CCH-HHHHHHHHHHH-cCCccHHHHHHHhCCCHHHHHHHHHHHHHhhh
Confidence 233 33333333322 46799999999999999999887777766554
No 367
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=59.54 E-value=12 Score=38.00 Aligned_cols=43 Identities=26% Similarity=0.347 Sum_probs=34.2
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
..|++.|+.||.+--+- +...++.||.+.+|.|+.||.+++++
T Consensus 191 ~~L~~~e~~il~~i~~~-GGri~Q~eL~r~lglsktTvsR~L~~ 233 (258)
T COG2512 191 YDLNEDEKEILDLIRER-GGRITQAELRRALGLSKTTVSRILRR 233 (258)
T ss_pred CCCCHHHHHHHHHHHHh-CCEEeHHHHHHhhCCChHHHHHHHHH
Confidence 47999999999886531 13389999999999999999765543
No 368
>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=59.30 E-value=17 Score=34.78 Aligned_cols=43 Identities=28% Similarity=0.301 Sum_probs=32.4
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
..|++-|+.....+. ++..++|.++||+.+|+|+.+|++.+.-
T Consensus 101 ~~lt~~e~a~~~~~l-~~~~g~s~~~iA~~lg~s~~~V~r~l~l 143 (187)
T TIGR00180 101 EDLSPIEEAQAYKRL-LEKFSMTQEDLAKKIGKSRAHITNLLRL 143 (187)
T ss_pred cCCCHHHHHHHHHHH-HHHhCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 478888876654442 1124799999999999999999987754
No 369
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=59.07 E-value=12 Score=29.46 Aligned_cols=23 Identities=13% Similarity=0.114 Sum_probs=20.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~r 487 (508)
+|..|+|+.+|||..|++.+...
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 47899999999999999998765
No 370
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=58.91 E-value=25 Score=26.02 Aligned_cols=23 Identities=17% Similarity=0.270 Sum_probs=17.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~r 487 (508)
+|+.+.|+.+||+++|++.++..
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 371
>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional
Probab=58.69 E-value=6.9 Score=36.86 Aligned_cols=45 Identities=20% Similarity=0.082 Sum_probs=37.7
Q ss_pred cCCHHHHHHHhHHhccCCCCCC---------HHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLT---------WEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~T---------leEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
.|+++|.+|+.+-. ++.+ ...||..++++..||+..+.+.++||.
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 69999999998875 4443 477888889999999999999999986
No 372
>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=58.69 E-value=23 Score=33.88 Aligned_cols=38 Identities=24% Similarity=0.281 Sum_probs=26.6
Q ss_pred CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHH
Q 010521 446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVG 485 (508)
Q Consensus 446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~ 485 (508)
|++.-|.-|...+- .+|+|.++||..+||+..||.-|+
T Consensus 17 lse~~r~~Iy~~~~--~~~~sv~~vS~~ygi~~~RV~AIv 54 (172)
T PF12298_consen 17 LSEELREQIYEDVM--QDGKSVREVSQKYGIKIQRVEAIV 54 (172)
T ss_pred CCHHHHHHHHHHHH--hCCCCHHHHHHHhCCCHHHHHHHH
Confidence 55555553333331 478899999999999999995443
No 373
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=58.66 E-value=37 Score=32.28 Aligned_cols=29 Identities=31% Similarity=0.468 Sum_probs=24.8
Q ss_pred CCCCCHHHHHHHh--CCCHHHHHHHHHHhCc
Q 010521 364 GVTPSVDRIAEYL--NMSQKKVRNATEAIGK 392 (508)
Q Consensus 364 Gr~Pt~eEIA~~L--gis~e~v~~~l~~~~~ 392 (508)
+..+++.+||+.+ ++|.+++++.+....+
T Consensus 37 ~~~~d~~~iak~l~p~is~~ev~~sL~~L~~ 67 (171)
T PF14394_consen 37 PFAPDPEWIAKRLRPKISAEEVRDSLEFLEK 67 (171)
T ss_pred CCCCCHHHHHHHhcCCCCHHHHHHHHHHHHH
Confidence 4556899999999 9999999999887743
No 374
>PRK01905 DNA-binding protein Fis; Provisional
Probab=58.54 E-value=37 Score=27.86 Aligned_cols=37 Identities=11% Similarity=0.143 Sum_probs=25.8
Q ss_pred HHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 449 REREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 449 rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
-|+.+|...+- ..+-+..+.|+.||||+.+++..+.+
T Consensus 37 ~E~~~i~~aL~--~~~gn~s~aAr~LGIsrstL~rklkk 73 (77)
T PRK01905 37 VEKPLLEVVME--QAGGNQSLAAEYLGINRNTLRKKLQQ 73 (77)
T ss_pred HHHHHHHHHHH--HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 35665555441 23567999999999999998766543
No 375
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=58.53 E-value=15 Score=27.40 Aligned_cols=47 Identities=15% Similarity=0.158 Sum_probs=36.2
Q ss_pred cCCHHHHHHHhHHhccCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDK--ECLTWEDISKRIGLSRERVRQVGLVALEK 491 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~--eg~TleEIAe~LgIS~erVrqi~~rALkK 491 (508)
.+++.+..+|.-.|..+. ......+||..+|++...|..+......+
T Consensus 6 ~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~ 54 (56)
T smart00389 6 SFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAK 54 (56)
T ss_pred cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhc
Confidence 467888888888874431 23568899999999999999988876554
No 376
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=58.43 E-value=9.8 Score=29.23 Aligned_cols=26 Identities=19% Similarity=0.348 Sum_probs=19.9
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521 463 ECLTWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 463 eg~TleEIAe~LgIS~erVrqi~~rA 488 (508)
.++|..++|+..|+++.+++++.+.-
T Consensus 9 ~~it~~~La~~~gis~~tl~~~~~~~ 34 (63)
T PF13443_consen 9 RGITQKDLARKTGISRSTLSRILNGK 34 (63)
T ss_dssp TT--HHHHHHHHT--HHHHHHHHTTT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcc
Confidence 57899999999999999999998865
No 377
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=58.22 E-value=12 Score=36.52 Aligned_cols=27 Identities=33% Similarity=0.490 Sum_probs=22.2
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 464 CLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 464 g~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
..|.++||..+|+++++|+ |++++|++
T Consensus 179 ~lt~~~IA~~lGisretls----R~L~~L~~ 205 (230)
T PRK09391 179 PMSRRDIADYLGLTIETVS----RALSQLQD 205 (230)
T ss_pred cCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 4799999999999999996 55566654
No 378
>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=58.12 E-value=17 Score=29.93 Aligned_cols=24 Identities=21% Similarity=0.378 Sum_probs=19.3
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 464 CLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 464 g~TleEIAe~LgIS~erVrqi~~r 487 (508)
..|.+|||+.+|+++..|+++..+
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 389999999999999999876554
No 379
>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=57.91 E-value=7.8 Score=32.04 Aligned_cols=32 Identities=22% Similarity=0.212 Sum_probs=22.6
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
.+..|++++|+.++||++|+.+.+...-+.|+
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 57899999999999999999766555544443
No 380
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=57.86 E-value=18 Score=36.17 Aligned_cols=42 Identities=21% Similarity=0.324 Sum_probs=31.9
Q ss_pred CHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010521 447 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALE 490 (508)
Q Consensus 447 p~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALk 490 (508)
.+|++.|+.+-.. ....+..|||+.||||..|||+-+..--.
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 3566666666431 35689999999999999999998876543
No 381
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=57.60 E-value=38 Score=25.89 Aligned_cols=45 Identities=31% Similarity=0.440 Sum_probs=31.2
Q ss_pred cccccHHHHHHHHHHHHHHHHHcCCCC-CHHHHHHHhCCCHHHHHH
Q 010521 341 RLPNHLHERLGLIRNAKLRLEEKGVTP-SVDRIAEYLNMSQKKVRN 385 (508)
Q Consensus 341 rip~~~~~~l~kir~a~~~l~~~Gr~P-t~eEIA~~Lgis~e~v~~ 385 (508)
.||....+++-...+.-..+.+.|.+- +..+||+.+|++..+|+.
T Consensus 2 ~Ip~~ti~RL~~Y~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 2 KIPKATIRRLPLYLRYLEQLKEEGVERVSSQELAEALGITPAQVRK 47 (50)
T ss_dssp S-SHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHcCCeeECHHHHHHHHCCCHHHhcc
Confidence 356666666766666666676777644 689999999999999986
No 382
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=57.49 E-value=16 Score=32.25 Aligned_cols=33 Identities=24% Similarity=0.393 Sum_probs=26.9
Q ss_pred HHHhHHhccCCC--CCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 452 EIIRLYYGLDKE--CLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 452 ~VI~LryGLd~e--g~TleEIAe~LgIS~erVrqi~~r 487 (508)
+||.-.| .+ |+|..+.|+.|||++.+|..+++.
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 3566665 34 699999999999999999998764
No 383
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=57.44 E-value=11 Score=30.10 Aligned_cols=25 Identities=24% Similarity=0.134 Sum_probs=20.4
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 463 ECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 463 eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
.+.|..|||+.+|+|..+||.++..
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 6799999999999999999887653
No 384
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=57.02 E-value=14 Score=33.22 Aligned_cols=26 Identities=15% Similarity=0.101 Sum_probs=23.4
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
..++|..++|+.+|||+++|++++..
T Consensus 16 ~~gltq~~lA~~~gvs~~~is~~E~g 41 (135)
T PRK09706 16 QLKLSQRSLAKAVKVSHVSISQWERD 41 (135)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 35799999999999999999999865
No 385
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=56.94 E-value=2.3e+02 Score=28.87 Aligned_cols=26 Identities=15% Similarity=0.266 Sum_probs=22.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHh
Q 010521 365 VTPSVDRIAEYLNMSQKKVRNATEAI 390 (508)
Q Consensus 365 r~Pt~eEIA~~Lgis~e~v~~~l~~~ 390 (508)
.+-|..|||+.+|+|.++|+.+....
T Consensus 247 ~~~Tl~EIA~~lgvS~~rVrqi~~~A 272 (284)
T PRK06596 247 DKSTLQELAAEYGVSAERVRQIEKNA 272 (284)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 45689999999999999999987653
No 386
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=56.51 E-value=23 Score=36.11 Aligned_cols=63 Identities=21% Similarity=0.279 Sum_probs=44.3
Q ss_pred HHHHHHHHHHHccCCHHHHHHHhHHhcc-C-CCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHH
Q 010521 433 ALKDEVNKLIIVTLGEREREIIRLYYGL-D-KECLTWEDISKRIGLSRERVRQVGLV----ALEKLKHAA 496 (508)
Q Consensus 433 el~e~L~~~L~~~Lp~rER~VI~LryGL-d-~eg~TleEIAe~LgIS~erVrqi~~r----ALkKLR~~L 496 (508)
.+...|.... +.|++.||.|-..-.-- + ...+|..|||+..|||+.||-+--++ +...+|..+
T Consensus 4 ~l~~~I~~~~-~~Lt~~er~iA~yil~~~~~~~~~si~elA~~a~VS~aTv~Rf~~kLGf~Gf~efk~~l 72 (281)
T COG1737 4 NLLERIRERY-DSLTKSERKIADYILANPDEVALLSIAELAERAGVSPATVVRFARKLGFEGFSEFKLAL 72 (281)
T ss_pred hHHHHHHHHH-hcCCHHHHHHHHHHHhCHHHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCHHHHHHHH
Confidence 3456777777 89999999998765411 0 12489999999999999999665443 344444444
No 387
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=56.22 E-value=18 Score=36.32 Aligned_cols=59 Identities=15% Similarity=0.213 Sum_probs=42.7
Q ss_pred HHHHHHccCCHHHHHHHhHHhcc--CCCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHH
Q 010521 438 VNKLIIVTLGEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGLV----ALEKLKHAAR 497 (508)
Q Consensus 438 L~~~L~~~Lp~rER~VI~LryGL--d~eg~TleEIAe~LgIS~erVrqi~~r----ALkKLR~~L~ 497 (508)
|.+.. ..|++.|+.|......- ....+|..|+|+..|+|..||.+.-++ +..-||..+.
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 34445 78999999998776521 023599999999999999999766544 4555665554
No 388
>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=56.07 E-value=7.2 Score=28.75 Aligned_cols=21 Identities=29% Similarity=0.283 Sum_probs=18.3
Q ss_pred HHHHHHHCCCHHHHHHHHHHH
Q 010521 468 EDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 468 eEIAe~LgIS~erVrqi~~rA 488 (508)
++||+.+|||+.+|+++++.-
T Consensus 1 ~~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 1 KDIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred CcHHHHHCcCHHHHHHHHcCC
Confidence 379999999999999998754
No 389
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=56.05 E-value=14 Score=25.67 Aligned_cols=25 Identities=24% Similarity=0.458 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 463 ECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 463 eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
.++|..++|+.+|++..+|++++..
T Consensus 9 ~~~s~~~la~~~~i~~~~i~~~~~~ 33 (56)
T smart00530 9 KGLTQEELAEKLGVSRSTLSRIENG 33 (56)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 5689999999999999999988764
No 390
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=55.53 E-value=32 Score=26.79 Aligned_cols=26 Identities=23% Similarity=0.339 Sum_probs=22.7
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 464 CLTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 464 g~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
+.|+.+||+.+|+|...+.++..+..
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~ 26 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKET 26 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHh
Confidence 36899999999999999999888765
No 391
>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=55.46 E-value=17 Score=28.04 Aligned_cols=25 Identities=24% Similarity=0.484 Sum_probs=20.1
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 463 ECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 463 eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
.++|+.++|+.+|++++++.+++..
T Consensus 11 ~~lt~~~~a~~~~i~~~~i~~~e~g 35 (64)
T PF12844_consen 11 KGLTQKDLAEKLGISRSTISKIENG 35 (64)
T ss_dssp CT--HHHHHHHHTS-HHHHHHHHTT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 5799999999999999999999864
No 392
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=55.33 E-value=22 Score=32.23 Aligned_cols=25 Identities=12% Similarity=0.121 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 463 ECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 463 eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
...+..+||+.||+|..+|+..+.+
T Consensus 21 ~~~~~~ela~~l~vs~~svs~~l~~ 45 (142)
T PRK03902 21 GYARVSDIAEALSVHPSSVTKMVQK 45 (142)
T ss_pred CCcCHHHHHHHhCCChhHHHHHHHH
Confidence 5679999999999999999876643
No 393
>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=54.17 E-value=50 Score=25.52 Aligned_cols=48 Identities=23% Similarity=0.247 Sum_probs=37.2
Q ss_pred CCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhH
Q 010521 206 LTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECS 263 (508)
Q Consensus 206 Lt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~ 263 (508)
||+.|..-|..++..|=. ..-+.-+.+++|..+|+|...+...+..++
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 566676677777777766 345677889999999999998888877653
No 394
>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=54.10 E-value=46 Score=33.15 Aligned_cols=34 Identities=21% Similarity=0.298 Sum_probs=27.4
Q ss_pred hHHHHHHhhCCCCchHHHHHHhccChHHHHHhhh
Q 010521 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (508)
Q Consensus 227 ~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~ 260 (508)
++.++...+|++|+.+++|..+|++.+++...+.
T Consensus 125 ~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~~ 158 (254)
T TIGR02850 125 VRDKLISENSKEPTVSEIAKELKVPQEEVVFALD 158 (254)
T ss_pred HHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3456777899999999999999999887665543
No 395
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=54.03 E-value=33 Score=33.93 Aligned_cols=40 Identities=25% Similarity=0.299 Sum_probs=27.8
Q ss_pred HHHHHhHHhccCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 450 EREIIRLYYGLDKECL-TWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 450 ER~VI~LryGLd~eg~-TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
...|+.-.|. .++.+ |-.++|+.||||+.+|| .|+..|..
T Consensus 20 ~~~I~~g~l~-pG~~LpsE~eLa~~lgVSRtpVR----EAL~~L~~ 60 (254)
T PRK09464 20 EFLILEGTLR-PGEKLPPERELAKQFDVSRPSLR----EAIQRLEA 60 (254)
T ss_pred HHHHHcCCCC-CCCcCCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 3445554441 13556 89999999999999997 66666653
No 396
>PF14502 HTH_41: Helix-turn-helix domain
Probab=53.89 E-value=21 Score=27.12 Aligned_cols=27 Identities=30% Similarity=0.373 Sum_probs=22.9
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 464 CLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 464 g~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
=.|..|.++++++|+.|| +.||+.|..
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 577777764
No 397
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.73 E-value=26 Score=29.98 Aligned_cols=43 Identities=12% Similarity=0.155 Sum_probs=29.2
Q ss_pred cCCHHHHHHHhHHhccC--CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLD--KECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd--~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
.|++.|+.+-.--+.-+ .-.+|.++||..||+|...|..+++-
T Consensus 2 SLn~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil~~ 46 (97)
T COG4367 2 SLNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLEKILQV 46 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHHHHHHH
Confidence 35666655543322212 23699999999999999998877643
No 398
>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=53.69 E-value=30 Score=33.09 Aligned_cols=28 Identities=39% Similarity=0.510 Sum_probs=23.1
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
++.++..++|+.||||+.+|| .||..|.
T Consensus 32 G~~L~e~~La~~lgVSRtpVR----eAL~~L~ 59 (212)
T TIGR03338 32 GAKLNESDIAARLGVSRGPVR----EAFRALE 59 (212)
T ss_pred CCEecHHHHHHHhCCChHHHH----HHHHHHH
Confidence 466899999999999999997 5666654
No 399
>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=53.65 E-value=19 Score=33.27 Aligned_cols=49 Identities=18% Similarity=0.108 Sum_probs=39.4
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRI-----GLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~L-----gIS~erVrqi~~rALkKLR 493 (508)
.|+++|..|+.+-..-.++-.|.++|++.+ ..+..+|..++.+.++||.
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 699999999988763223458999999999 4567888888888888885
No 400
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=53.47 E-value=27 Score=33.68 Aligned_cols=42 Identities=14% Similarity=0.069 Sum_probs=34.1
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
-.|++.|..||..-+. .++.|..+||+.++++.+||.+++.+
T Consensus 41 ~gLt~~q~~iL~~L~~--~~~itq~eLa~~l~l~~sTvtr~l~r 82 (185)
T PRK13777 41 YDLNINEHHILWIAYH--LKGASISEIAKFGVMHVSTAFNFSKK 82 (185)
T ss_pred CCCCHHHHHHHHHHHh--CCCcCHHHHHHHHCCCHhhHHHHHHH
Confidence 3799999998877652 46899999999999999998765543
No 401
>PRK03837 transcriptional regulator NanR; Provisional
Probab=53.40 E-value=26 Score=34.20 Aligned_cols=38 Identities=29% Similarity=0.358 Sum_probs=26.7
Q ss_pred HHHHhHHhccCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 451 REIIRLYYGLDKECL-TWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 451 R~VI~LryGLd~eg~-TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
..|+.-.|. .++-+ +..+||+.||||+.+|| .|+..|.
T Consensus 24 ~~I~~g~l~-pG~~Lp~E~~Lae~~gVSRt~VR----EAL~~L~ 62 (241)
T PRK03837 24 QMIRSGEFG-PGDQLPSERELMAFFGVGRPAVR----EALQALK 62 (241)
T ss_pred HHHHhCCCC-CCCCCCCHHHHHHHhCCCHHHHH----HHHHHHH
Confidence 334544441 13557 89999999999999997 5666665
No 402
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=53.32 E-value=13 Score=37.33 Aligned_cols=37 Identities=22% Similarity=0.344 Sum_probs=29.8
Q ss_pred CHHHHHHHhHHhccCCC-CCCHHHHHHHHCCCHHHHHHHHH
Q 010521 447 GEREREIIRLYYGLDKE-CLTWEDISKRIGLSRERVRQVGL 486 (508)
Q Consensus 447 p~rER~VI~LryGLd~e-g~TleEIAe~LgIS~erVrqi~~ 486 (508)
.+|++.|+.+-- .+ -.+.+|+|+.||||..|||+=+.
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 457888887754 33 48999999999999999998554
No 403
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=53.23 E-value=2.3e+02 Score=28.48 Aligned_cols=94 Identities=18% Similarity=0.150 Sum_probs=53.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhC--ccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHHHHHc
Q 010521 367 PSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIV 444 (508)
Q Consensus 367 Pt~eEIA~~Lgis~e~v~~~l~~~~--~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~L~~ 444 (508)
....|+.+.++++..+++-.++... +.++-.. .+..+.-+-.+-+.. +. + + + .
T Consensus 116 ~~lsEl~~nl~i~R~TlRyhlriLe~~~li~a~~---------~~g~~~yfpa~~t~~--~~---e-------~---~-~ 170 (240)
T COG3398 116 FSLSELRANLYINRSTLRYHLRILESNPLIEAGR---------VGGALRYFPADMTYG--EA---E-------V---L-S 170 (240)
T ss_pred ccHHHHHHhcCCChHHHHHHHHHHHhCcchhhhc---------cCCceEEccCCCCcc--cc---h-------H---H-H
Confidence 3578999999999999887766542 2222111 112222222222111 11 1 1 1 1
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
-=++.+|.|+..-- ..+++|..+||..+|+|+.||+....+
T Consensus 171 Lkn~~~k~I~~eiq--~~~~~t~~~ia~~l~ls~aTV~~~lk~ 211 (240)
T COG3398 171 LKNETSKAIIYEIQ--ENKCNTNLLIAYELNLSVATVAYHLKK 211 (240)
T ss_pred hhchhHHHHHHHHh--cCCcchHHHHHHHcCccHHHHHHHHHH
Confidence 11344566665432 246799999999999999999876544
No 404
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=53.19 E-value=30 Score=32.79 Aligned_cols=56 Identities=30% Similarity=0.365 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHHHccCCHHHHHHHhHHhcc--C---CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 431 DWALKDEVNKLIIVTLGEREREIIRLYYGL--D---KECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 431 ~~el~e~L~~~L~~~Lp~rER~VI~LryGL--d---~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
+++-.+.|++.| +.||+.|++=+.-+|-= + .+|.|-+||.+.||=+++-++++...
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 456678899999 79999988865555522 1 24789999999999988888887754
No 405
>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=52.99 E-value=18 Score=34.25 Aligned_cols=86 Identities=20% Similarity=0.303 Sum_probs=19.5
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHh-----CccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHHHH
Q 010521 368 SVDRIAEYLNMSQKKVRNATEAI-----GKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLI 442 (508)
Q Consensus 368 t~eEIA~~Lgis~e~v~~~l~~~-----~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~L 442 (508)
+..+||+.+|+++.+|..+.... .++++|.. ++..... .+....+....+...|.++|
T Consensus 51 t~~~iA~~lgl~~STVSRav~~Ky~~t~~Gi~plk~----------------fF~~~~~-~~~~~~~S~~~ik~~i~~lI 113 (160)
T PF04552_consen 51 TMKDIADELGLHESTVSRAVKNKYIQTPRGIFPLKD----------------FFSRSVS-SGSGEEFSSEAIKARIKELI 113 (160)
T ss_dssp ----------------------------------S---------------------SS---SS-SS---TTH-HHHHHHH
T ss_pred CHHHHHHHhCCCHhHHHHHHcCceeecCCeeeeHHH----------------hcccccc-CCCCcccHHHHHHHHHHHHH
Confidence 68999999999999998875532 22333332 2222110 11111122233344454444
Q ss_pred HccCCHHHHHHHhHHhccCCCCCCHHHHHHHH-----CCCHHHHHHH
Q 010521 443 IVTLGEREREIIRLYYGLDKECLTWEDISKRI-----GLSRERVRQV 484 (508)
Q Consensus 443 ~~~Lp~rER~VI~LryGLd~eg~TleEIAe~L-----gIS~erVrqi 484 (508)
+.=++ ..++|-++|++.| .||+.||.+.
T Consensus 114 -~~Ed~-------------~~PlSD~~i~~~L~~~gi~isRRTVaKY 146 (160)
T PF04552_consen 114 -EEEDK-------------KKPLSDQEIAELLKEEGIKISRRTVAKY 146 (160)
T ss_dssp -TTS-T-------------TS---HHHHHHHHTTTTS---HHHHHHH
T ss_pred -HhcCC-------------CCCCCHHHHHHHHHHcCCCccHHHHHHH
Confidence 11000 2478999999999 7888888654
No 406
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=52.89 E-value=21 Score=29.64 Aligned_cols=26 Identities=19% Similarity=0.294 Sum_probs=22.6
Q ss_pred CCCCCHHHHHHHHC------CCHHHHHHHHHH
Q 010521 462 KECLTWEDISKRIG------LSRERVRQVGLV 487 (508)
Q Consensus 462 ~eg~TleEIAe~Lg------IS~erVrqi~~r 487 (508)
.-|+|+.++|+.+| +|+.+|++++.-
T Consensus 22 ~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~ 53 (75)
T smart00352 22 KLGFTQADVGLALGALYGPDFSQTTICRFEAL 53 (75)
T ss_pred HcCCCHHHHHHHhcccccCcCCHHHHHHHHhc
Confidence 35799999999999 599999998763
No 407
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=52.46 E-value=77 Score=26.93 Aligned_cols=27 Identities=15% Similarity=0.180 Sum_probs=24.7
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~rA 488 (508)
.++.|.++||+.+|+|+.+..++..+.
T Consensus 19 ~~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 19 DQPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 467999999999999999999988886
No 408
>PRK06030 hypothetical protein; Provisional
Probab=52.39 E-value=48 Score=30.09 Aligned_cols=39 Identities=10% Similarity=0.026 Sum_probs=27.7
Q ss_pred HHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 448 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 448 ~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
+|+-.+...+- .-++|+.+||+.||.+.+||..-..+.-
T Consensus 56 aRqIAMYL~r~---~~~~sl~~IG~~FGRDHSTV~haikkIe 94 (124)
T PRK06030 56 IRQIAMYVAHV---SLGWPMNEVALAFGRDRTTVGHACHTVE 94 (124)
T ss_pred HHHHHHHHHHH---HcCCCHHHHHHHHCCChhHHHHHHHHHH
Confidence 44444444443 4579999999999999999987666433
No 409
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=52.36 E-value=36 Score=33.70 Aligned_cols=39 Identities=26% Similarity=0.245 Sum_probs=27.2
Q ss_pred HHHHhHHhccCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 451 REIIRLYYGLDKECL-TWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 451 R~VI~LryGLd~eg~-TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
..|+.-.|. .++-+ +..|+|+.||||+..|| .||+.|..
T Consensus 13 ~~I~~g~l~-pG~~LpsE~eLae~~gVSRtpVR----EAL~~Le~ 52 (253)
T PRK10421 13 ALIEEKNLE-AGMKLPAERQLAMQLGVSRNSLR----EALAKLVS 52 (253)
T ss_pred HHHHcCCCC-CCCcCCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 345544441 13567 68999999999999997 66666653
No 410
>COG4709 Predicted membrane protein [Function unknown]
Probab=52.34 E-value=30 Score=33.61 Aligned_cols=58 Identities=19% Similarity=0.183 Sum_probs=45.2
Q ss_pred HHHHHHHHHHHHHccCCHHHHHHHhHHhcc---C--CCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 431 DWALKDEVNKLIIVTLGEREREIIRLYYGL---D--KECLTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 431 ~~el~e~L~~~L~~~Lp~rER~VI~LryGL---d--~eg~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
+.+...+|++.| +.||+.+|.=+...|-= + ..|.|-+||+..||-+.+-.+.+..+..
T Consensus 3 k~efL~eL~~yL-~~Lp~~~r~e~m~dyeehF~~a~~~GksE~EI~~~LG~P~eiA~ei~s~~~ 65 (195)
T COG4709 3 KTEFLNELEQYL-EGLPREERREIMYDYEEHFREAQEAGKSEEEIAKDLGDPKEIAAEILSERG 65 (195)
T ss_pred HHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHhhhhcCCCHHHHHHHhCCHHHHHHHHHHHcc
Confidence 456778899999 89999999866555422 1 2479999999999999988888776643
No 411
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=52.27 E-value=93 Score=34.00 Aligned_cols=89 Identities=18% Similarity=0.262 Sum_probs=51.4
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHh-----CccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHH
Q 010521 366 TPSVDRIAEYLNMSQKKVRNATEAI-----GKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNK 440 (508)
Q Consensus 366 ~Pt~eEIA~~Lgis~e~v~~~l~~~-----~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~ 440 (508)
+-+..+||+.+|+.+.+|.++.... .++++|-. |........++...+....++..|.+
T Consensus 318 PLtlkdiA~~lglheSTVSRav~~Kyi~tp~Gi~~lk~----------------FFs~~~~~~~~g~~~S~~~Ik~~I~~ 381 (429)
T TIGR02395 318 PLTLREVAEELGLHESTISRAINNKYLQTPRGVFELKY----------------FFSRGVQTDSGEGEVSSTAIKALIKE 381 (429)
T ss_pred CCcHHHHHHHhCCCccchhhhhcCceEecCCceEEHHH----------------hcCCccCCCCCCCccCHHHHHHHHHH
Confidence 3379999999999999998876532 22333322 22211100011112344556666666
Q ss_pred HHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHH-----CCCHHHHHHH
Q 010521 441 LIIVTLGEREREIIRLYYGLDKECLTWEDISKRI-----GLSRERVRQV 484 (508)
Q Consensus 441 ~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~L-----gIS~erVrqi 484 (508)
+| +.=++ ..++|-++|++.| .|+|.||-+.
T Consensus 382 lI-~~E~~-------------~~PlSD~~I~~~L~~~Gi~IaRRTVaKY 416 (429)
T TIGR02395 382 LI-AAEDK-------------RKPLSDQKIAELLKEKGIKIARRTVAKY 416 (429)
T ss_pred HH-HhcCC-------------CCCCCHHHHHHHHHhcCCCeehHHHHHH
Confidence 66 21111 2568888888888 6788888654
No 412
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=52.20 E-value=16 Score=35.49 Aligned_cols=26 Identities=15% Similarity=0.263 Sum_probs=20.9
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 464 CLTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 464 g~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
++|.++||..+|+++++|++ ++++|+
T Consensus 173 ~~t~~~iA~~lG~tretvsR----~l~~L~ 198 (236)
T PRK09392 173 PYEKRVLASYLGMTPENLSR----AFAALA 198 (236)
T ss_pred eCCHHHHHHHhCCChhHHHH----HHHHHH
Confidence 57889999999999999964 455554
No 413
>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=52.03 E-value=25 Score=25.73 Aligned_cols=23 Identities=26% Similarity=0.455 Sum_probs=20.9
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQV 484 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi 484 (508)
+++.|.++||+..|+|+.++.+.
T Consensus 14 ~~~~s~~~Ia~~~gvs~~~~y~~ 36 (47)
T PF00440_consen 14 YEAVSIRDIARRAGVSKGSFYRY 36 (47)
T ss_dssp TTTSSHHHHHHHHTSCHHHHHHH
T ss_pred HHhCCHHHHHHHHccchhhHHHH
Confidence 68899999999999999998764
No 414
>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=52.00 E-value=25 Score=24.56 Aligned_cols=26 Identities=23% Similarity=0.452 Sum_probs=22.7
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521 463 ECLTWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 463 eg~TleEIAe~LgIS~erVrqi~~rA 488 (508)
.++|..++|+.+|+++.+|.+++...
T Consensus 11 ~~~s~~~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 11 KGLTQEELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHcCC
Confidence 46899999999999999999887643
No 415
>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=51.63 E-value=4.9 Score=37.98 Aligned_cols=47 Identities=21% Similarity=0.301 Sum_probs=0.0
Q ss_pred HHHHHHHccCCHHHHHHHhHHhcc-CCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521 437 EVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGL 486 (508)
Q Consensus 437 ~L~~~L~~~Lp~rER~VI~LryGL-d~eg~TleEIAe~LgIS~erVrqi~~ 486 (508)
.|.... ..|=+.|..-|.. |- ...++|+++||+.+|++.+||++...
T Consensus 24 TL~~v~-~~iv~~Q~~ff~~--g~~~l~PLt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 24 TLLRVA-QAIVERQKDFFLG--GPGALKPLTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp ---------------------------------------------------
T ss_pred HHHHHH-HHHHHHHHHHHhc--CcccCcCCCHHHHHHHhCCCHhHHHHHHc
Confidence 344444 5566777776643 21 24689999999999999999987654
No 416
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=51.63 E-value=20 Score=29.70 Aligned_cols=20 Identities=15% Similarity=0.237 Sum_probs=19.0
Q ss_pred CHHHHHHHHCCCHHHHHHHH
Q 010521 466 TWEDISKRIGLSRERVRQVG 485 (508)
Q Consensus 466 TleEIAe~LgIS~erVrqi~ 485 (508)
+...+|+.||||.++|+|+-
T Consensus 12 s~~kvA~aLGIs~~AVsQWG 31 (75)
T PRK09744 12 SKTKLANAAGVRLASVAAWG 31 (75)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 89999999999999999994
No 417
>PRK06424 transcription factor; Provisional
Probab=51.49 E-value=19 Score=33.39 Aligned_cols=26 Identities=8% Similarity=0.123 Sum_probs=23.6
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
..|+|++|+|+.+|+++++|+++++.
T Consensus 95 ~~GLSQ~eLA~~iGvs~stIskiE~G 120 (144)
T PRK06424 95 RLSMSQADLAAKIFERKNVIASIERG 120 (144)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 46799999999999999999999863
No 418
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=51.48 E-value=39 Score=33.55 Aligned_cols=39 Identities=31% Similarity=0.333 Sum_probs=27.1
Q ss_pred HHHHhHHhccCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 451 REIIRLYYGLDKECL-TWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 451 R~VI~LryGLd~eg~-TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
..|+.-.|. .++.+ |-.++|+.||||+.+|| .|++.|..
T Consensus 20 ~~I~~g~l~-pG~~LpsE~eLa~~~gVSRtpVR----EAL~~L~~ 59 (257)
T PRK10225 20 DLIIKTPYN-PGERLPPEREIAEMLDVTRTVVR----EALIMLEI 59 (257)
T ss_pred HHHHhCCCC-CCCcCcCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 334544442 13567 68999999999999997 66666653
No 419
>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=51.45 E-value=46 Score=29.85 Aligned_cols=41 Identities=20% Similarity=0.103 Sum_probs=31.6
Q ss_pred HHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521 452 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496 (508)
Q Consensus 452 ~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L 496 (508)
+.+.||. -|+|..+||+.++||+++|-+...+-.+--.+.+
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 3555665 7899999999999999999988766555544444
No 420
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=51.37 E-value=23 Score=30.28 Aligned_cols=43 Identities=16% Similarity=0.300 Sum_probs=29.6
Q ss_pred cCCHHHHHHHhHHhc-c-CCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYG-L-DKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 445 ~Lp~rER~VI~LryG-L-d~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
.|++.++.|+...-. - ..+|++..+|++.|+++...|++.+..
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~ 88 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDF 88 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHH
Confidence 467777777766543 2 247899999999999999999866543
No 421
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=51.15 E-value=17 Score=35.30 Aligned_cols=44 Identities=11% Similarity=0.059 Sum_probs=28.6
Q ss_pred CHHHHHHHhHHhcc--CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 447 GEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 447 p~rER~VI~LryGL--d~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
+.++|-+-.+..-- +.-..|.++||+.+|+|+++|+ |++++|++
T Consensus 150 ~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvs----R~L~~L~~ 195 (226)
T PRK10402 150 PLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLL----YVLAQFIQ 195 (226)
T ss_pred hHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHH----HHHHHHHH
Confidence 55565544443200 1124689999999999999996 56666654
No 422
>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=50.85 E-value=53 Score=25.80 Aligned_cols=49 Identities=12% Similarity=0.148 Sum_probs=32.6
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHH------CCCHHHHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRI------GLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~L------gIS~erVrqi~~rALkKLR 493 (508)
.|+++|..+|.+-.--.+...|.++|.+.+ ..+..+|++.+.+..++|.
T Consensus 5 ~Lt~~e~~lL~~L~~~~~~~vs~~~l~~~lw~~~~~~~~~~~l~~~i~~LR~~l~ 59 (78)
T smart00862 5 KLTPKEFRLLELLLRNPGRVVSREELLEAVWGDDDDDVDDNTLDVHISRLRKKLE 59 (78)
T ss_pred ecCHHHHHHHHHHHhCCCCccCHHHHHHHHcCCCCCCCccchHHHHHHHHHHHHh
Confidence 588999997766542123468999999986 3455666666665555554
No 423
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=50.79 E-value=40 Score=33.28 Aligned_cols=38 Identities=24% Similarity=0.355 Sum_probs=27.0
Q ss_pred HHHHhHHhccCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 451 REIIRLYYGLDKECL-TWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 451 R~VI~LryGLd~eg~-TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
..|+.-.|- .++.+ +-.+||+.||||+..|| .||++|.
T Consensus 18 ~~I~~g~l~-pG~~LPsE~eLa~~~gVSRtpVR----EAL~~L~ 56 (251)
T PRK09990 18 RLIVDGVLK-VGQALPSERRLCEKLGFSRSALR----EGLTVLR 56 (251)
T ss_pred HHHHcCCCC-CCCcCcCHHHHHHHHCCCHHHHH----HHHHHHH
Confidence 334444441 13567 88999999999999997 6666665
No 424
>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=50.74 E-value=22 Score=26.85 Aligned_cols=36 Identities=11% Similarity=0.123 Sum_probs=29.7
Q ss_pred CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHH
Q 010521 446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVG 485 (508)
Q Consensus 446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~ 485 (508)
-|.-..+|+.|-+ +|.-.+++|+.|+|+..||-..+
T Consensus 7 kpgikeqIvema~----nG~GiRdtaRvL~I~~nTVlrtL 42 (46)
T PF12759_consen 7 KPGIKEQIVEMAF----NGSGIRDTARVLKISINTVLRTL 42 (46)
T ss_pred CccHHHHHHHHHh----cCCcchhhHhHhcchHHHHHHHH
Confidence 3555668999987 88999999999999999995443
No 425
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=50.68 E-value=78 Score=28.18 Aligned_cols=33 Identities=21% Similarity=0.194 Sum_probs=27.3
Q ss_pred HHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521 453 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 453 VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA 488 (508)
.|.-++ .++.|++++|+.+|+|+.++.++..+.
T Consensus 17 ~I~~~~---~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 17 WIEDNL---ESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHhc---CCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 334455 477999999999999999999988876
No 426
>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=50.55 E-value=23 Score=28.26 Aligned_cols=27 Identities=26% Similarity=0.582 Sum_probs=21.9
Q ss_pred HHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHH
Q 010521 453 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVG 485 (508)
Q Consensus 453 VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~ 485 (508)
.|...|| ++.|+|+.|++++.||++..
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 3445565 88999999999999998764
No 427
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=50.07 E-value=29 Score=34.84 Aligned_cols=38 Identities=21% Similarity=0.274 Sum_probs=28.3
Q ss_pred HHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 448 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 448 ~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
+|+..|+.+-- .....+..|||+.||||..|||+-+..
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 34555554432 124589999999999999999998776
No 428
>PRK10643 DNA-binding transcriptional regulator BasR; Provisional
Probab=49.76 E-value=17 Score=33.75 Aligned_cols=47 Identities=13% Similarity=-0.030 Sum_probs=35.2
Q ss_pred cCCHHHHHHHhHHhccCCCCCCH-HHHH-H-----HHCCCHHHHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTW-EDIS-K-----RIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~Tl-eEIA-e-----~LgIS~erVrqi~~rALkKLR 493 (508)
.|+++|.+|+.+..- ..|++. +||+ + .++++..||+....+.++||.
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 245552 5554 3 268899999999999999985
No 429
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=49.72 E-value=22 Score=31.75 Aligned_cols=26 Identities=19% Similarity=0.244 Sum_probs=23.3
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
..|+|.+|+|+.+|||++++.++++.
T Consensus 16 ~~Glsq~eLA~~~Gis~~~is~iE~g 41 (120)
T PRK13890 16 ERHMTKKELSERSGVSISFLSDLTTG 41 (120)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 35799999999999999999999864
No 430
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=49.59 E-value=38 Score=38.63 Aligned_cols=64 Identities=17% Similarity=0.154 Sum_probs=47.4
Q ss_pred HHHHHHHHHHHccCCHHHHHHHhHHhcc--CCCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHH
Q 010521 433 ALKDEVNKLIIVTLGEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGLV----ALEKLKHAAR 497 (508)
Q Consensus 433 el~e~L~~~L~~~Lp~rER~VI~LryGL--d~eg~TleEIAe~LgIS~erVrqi~~r----ALkKLR~~L~ 497 (508)
.+.+.|.... ..|++.||.|.....-- ....+|..|||+..++|..||-+.-++ ....||..+.
T Consensus 342 ~l~~~I~~~~-~~Lt~~E~~IA~yIl~n~~~v~~~si~eLA~~~~vS~aTV~Rf~kkLGf~Gf~efK~~L~ 411 (638)
T PRK14101 342 AVFERIRQMR-DALTPAERRVADLALNHPRSIINDPIVDIARKADVSQPTVIRFCRSLGCQGLSDFKLKLA 411 (638)
T ss_pred HHHHHHHHHH-hhcCHHHHHHHHHHHhCHHHHHhccHHHHHHHhCCCHHHHHHHHHHhCCCCHHHHHHHHH
Confidence 4566787878 89999999998775411 023589999999999999998765543 5666666554
No 431
>PF11662 DUF3263: Protein of unknown function (DUF3263); InterPro: IPR021678 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=48.98 E-value=62 Score=27.04 Aligned_cols=45 Identities=24% Similarity=0.208 Sum_probs=36.2
Q ss_pred cCCHHHHHHHhHH-hccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLY-YGLDKECLTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 445 ~Lp~rER~VI~Lr-yGLd~eg~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
.|+++++.||..- -+....|-.-+.|-+.||+|.-+--|.++..+
T Consensus 2 ~Ls~~d~~iL~fE~~ww~~~GaKe~aIre~fGls~~rYyq~Ln~Li 47 (77)
T PF11662_consen 2 GLSDRDRAILDFERRWWRHGGAKEEAIREEFGLSPTRYYQRLNALI 47 (77)
T ss_pred CCCHHHHHHHHHHHHhCcCCCCcHHHHHHHHCCCHHHHHHHHHHHh
Confidence 5899999999762 22234578899999999999999999888755
No 432
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=48.75 E-value=41 Score=32.57 Aligned_cols=29 Identities=28% Similarity=0.371 Sum_probs=23.5
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
++.++..+||+.||||+..|| .|++.|..
T Consensus 32 G~~L~e~~La~~lgVSRtpVR----EAL~~L~~ 60 (221)
T PRK11414 32 GARLITKNLAEQLGMSITPVR----EALLRLVS 60 (221)
T ss_pred CCccCHHHHHHHHCCCchhHH----HHHHHHHH
Confidence 466888999999999999997 66666653
No 433
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=48.64 E-value=23 Score=30.36 Aligned_cols=24 Identities=33% Similarity=0.368 Sum_probs=21.7
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q 010521 463 ECLTWEDISKRIGLSRERVRQVGL 486 (508)
Q Consensus 463 eg~TleEIAe~LgIS~erVrqi~~ 486 (508)
-|+|.++||..||+|.+.|.+++.
T Consensus 22 ~~ls~~~ia~dL~~s~~~le~vL~ 45 (89)
T PF10078_consen 22 SGLSLEQIAADLGTSPEHLEQVLN 45 (89)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHc
Confidence 479999999999999999988765
No 434
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=48.50 E-value=24 Score=35.53 Aligned_cols=38 Identities=11% Similarity=0.214 Sum_probs=29.3
Q ss_pred HHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 448 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 448 ~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
+|++.|+.+--- ....+..|+|+.||||+.|||+-+..
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 466666665430 23589999999999999999998776
No 435
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=48.25 E-value=37 Score=30.43 Aligned_cols=41 Identities=17% Similarity=0.198 Sum_probs=29.2
Q ss_pred ccCCHHHH-HHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521 444 VTLGERER-EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 486 (508)
Q Consensus 444 ~~Lp~rER-~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~ 486 (508)
..|.+.-| .||.+-. +.++++..||++.+|+|+.+|++.+.
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 34444444 5665543 13579999999999999999987754
No 436
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=48.21 E-value=2.1e+02 Score=28.53 Aligned_cols=29 Identities=14% Similarity=0.283 Sum_probs=25.2
Q ss_pred HcCCCCCHHHHHHHhCCCHHHHHHHHHHh
Q 010521 362 EKGVTPSVDRIAEYLNMSQKKVRNATEAI 390 (508)
Q Consensus 362 ~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~ 390 (508)
+.|--.|..++|-.||+|+.+|.+.....
T Consensus 101 ~QgglLT~~Dla~LL~~S~~TI~~~i~~y 129 (220)
T PF07900_consen 101 DQGGLLTQEDLAMLLGISPRTISKDIKEY 129 (220)
T ss_pred HcCCcccHHHHHHHHCCCHHHHHHHHHHH
Confidence 56888899999999999999999876655
No 437
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=48.02 E-value=53 Score=31.77 Aligned_cols=39 Identities=28% Similarity=0.338 Sum_probs=27.4
Q ss_pred HHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 450 EREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 450 ER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
...|+.-.|- .++.++.+++|+.||||+..|| .|+.+|.
T Consensus 17 ~~~I~~g~l~-pG~~L~e~eLae~lgVSRtpVR----EAL~~L~ 55 (224)
T PRK11534 17 KNDIIRGNFQ-PDEKLRMSLLTSRYALGVGPLR----EALSQLV 55 (224)
T ss_pred HHHHHhCCCC-CCCcCCHHHHHHHHCCChHHHH----HHHHHHH
Confidence 3445555441 1356889999999999999997 5666654
No 438
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=47.72 E-value=14 Score=31.52 Aligned_cols=25 Identities=28% Similarity=0.369 Sum_probs=22.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
+|..|+|+.+|||..|+|.++..++
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~~Gl 25 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDIGL 25 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999887754
No 439
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=47.65 E-value=2.4e+02 Score=27.36 Aligned_cols=99 Identities=20% Similarity=0.272 Sum_probs=62.6
Q ss_pred HcCCC-CCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHH
Q 010521 362 EKGVT-PSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNK 440 (508)
Q Consensus 362 ~~Gr~-Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~ 440 (508)
-.|.+ -+..+||+.++++..++..++........-+. .+-.+... .+-+....+.+....+.+
T Consensus 15 ~sg~pgls~~~La~~l~~~~~~v~~~l~~L~~~y~~~~---------~gi~i~~~-------~~~y~l~tk~e~~~~v~~ 78 (188)
T PRK00135 15 VSGEEGLSLEQLAEILELEPTEVQQLLEELQEKYEGDD---------RGLKLIEF-------NDVYKLVTKEENADYLQK 78 (188)
T ss_pred HcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhCC---------CCEEEEEE-------CCEEEEEEcHHHHHHHHH
Confidence 35665 58999999999999999888776543321111 01111110 112222333444555555
Q ss_pred HHH----ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCH
Q 010521 441 LII----VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSR 478 (508)
Q Consensus 441 ~L~----~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~ 478 (508)
++. ..|+.-.-++|...+. .++.|..||++..|++.
T Consensus 79 ~~~~~~~~~LS~aaLEtLaiIay--~qPiTr~eI~~irGv~~ 118 (188)
T PRK00135 79 LVKTPIKQSLSQAALEVLAIIAY--KQPITRIEIDEIRGVNS 118 (188)
T ss_pred HhcccccCCCCHHHHHHHHHHHH--cCCcCHHHHHHHHCCCH
Confidence 552 2599998888877541 57999999999999986
No 440
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=47.26 E-value=49 Score=29.94 Aligned_cols=44 Identities=16% Similarity=0.239 Sum_probs=33.7
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHH----CCCHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRI----GLSRERVRQVGLVALE 490 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~L----gIS~erVrqi~~rALk 490 (508)
.|++.|..|+..-. +.++.|..||.+.| +++..||...+.|-.+
T Consensus 1 ~Lt~~E~~VM~vlW--~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~ 48 (130)
T TIGR02698 1 SISDAEWEVMRVVW--TLGETTSRDIIRILAEKKDWSDSTIKTLLGRLVD 48 (130)
T ss_pred CCCHHHHHHHHHHH--cCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHH
Confidence 37889999886653 13578999977776 7999999888777554
No 441
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=47.16 E-value=27 Score=27.65 Aligned_cols=19 Identities=26% Similarity=0.358 Sum_probs=17.5
Q ss_pred CHHHHHHHHCCCHHHHHHH
Q 010521 466 TWEDISKRIGLSRERVRQV 484 (508)
Q Consensus 466 TleEIAe~LgIS~erVrqi 484 (508)
+...+|+.||||+.+|.++
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 442
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=47.14 E-value=32 Score=32.24 Aligned_cols=26 Identities=23% Similarity=0.203 Sum_probs=21.7
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
.......+||+.|||++.+|.+.+++
T Consensus 22 ~~~~~~~diA~~L~Vsp~sVt~ml~r 47 (154)
T COG1321 22 KGFARTKDIAERLKVSPPSVTEMLKR 47 (154)
T ss_pred cCcccHHHHHHHhCCCcHHHHHHHHH
Confidence 34589999999999999999766554
No 443
>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=47.13 E-value=53 Score=31.97 Aligned_cols=25 Identities=28% Similarity=0.416 Sum_probs=20.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
-|-.|+|+.+|||+.||| +|+..|.
T Consensus 33 PsE~eLa~~~~VSR~TvR----~Al~~L~ 57 (238)
T TIGR02325 33 PAEMQLAERFGVNRHTVR----RAIAALV 57 (238)
T ss_pred cCHHHHHHHHCCCHHHHH----HHHHHHH
Confidence 499999999999999997 5555554
No 444
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=47.02 E-value=26 Score=34.30 Aligned_cols=29 Identities=28% Similarity=0.472 Sum_probs=23.1
Q ss_pred CCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 462 KECL-TWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 462 ~eg~-TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
++.+ |-.|+|+.||||+.+|| .|+..|..
T Consensus 28 G~~LPsE~eLae~~gVSRt~VR----eAL~~L~~ 57 (239)
T PRK04984 28 GSILPAERELSELIGVTRTTLR----EVLQRLAR 57 (239)
T ss_pred CCcCCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 3567 79999999999999997 56666653
No 445
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=46.71 E-value=14 Score=31.81 Aligned_cols=26 Identities=23% Similarity=0.335 Sum_probs=22.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLVALE 490 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~rALk 490 (508)
+|..|+|+.+|||..|++.++..++-
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~~Gll 27 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESIGLI 27 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 68999999999999999998887543
No 446
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=46.61 E-value=23 Score=36.89 Aligned_cols=42 Identities=17% Similarity=0.089 Sum_probs=35.0
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA 488 (508)
.+|+..||.-|..-. ..++|..|||+.||..++||..-+.|.
T Consensus 6 ~hLT~~eR~~I~~l~---~~~~S~reIA~~LgRh~sTIsRElkRn 47 (318)
T COG2826 6 KHLTLFERYEIERLL---KAKMSIREIAKQLNRHHSTISRELKRN 47 (318)
T ss_pred hhCCHHHHHHHHHHH---HcCCCHHHHHHHhCCCcchhhHHHhcC
Confidence 478888888776654 579999999999999999998877654
No 447
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=46.10 E-value=27 Score=33.13 Aligned_cols=26 Identities=12% Similarity=0.189 Sum_probs=23.6
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
..++|++++|+.+|+|+++|+++++.
T Consensus 18 ~~glt~~elA~~~gis~~~is~~E~g 43 (185)
T PRK09943 18 QQGLSQRRAAELSGLTHSAISTIEQD 43 (185)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 35799999999999999999999974
No 448
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=46.10 E-value=15 Score=32.07 Aligned_cols=25 Identities=16% Similarity=0.311 Sum_probs=22.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
||..|+|+.+|||+.|++.+...++
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gl 25 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKEGL 25 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999987654
No 449
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=46.09 E-value=82 Score=27.43 Aligned_cols=42 Identities=29% Similarity=0.466 Sum_probs=32.8
Q ss_pred ccCCHHHHHHH----hHHhccC--CCCCCHHHHHHHHCCCHHHHHHHH
Q 010521 444 VTLGEREREII----RLYYGLD--KECLTWEDISKRIGLSRERVRQVG 485 (508)
Q Consensus 444 ~~Lp~rER~VI----~LryGLd--~eg~TleEIAe~LgIS~erVrqi~ 485 (508)
..|+.+|..|+ +.-||.+ .+-.|..+|++..|+++..|+..+
T Consensus 28 ~dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al 75 (100)
T PF04492_consen 28 ADLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKAL 75 (100)
T ss_pred ccccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHH
Confidence 67899988754 5567775 345899999999999999886443
No 450
>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=45.71 E-value=62 Score=30.65 Aligned_cols=53 Identities=21% Similarity=0.451 Sum_probs=34.4
Q ss_pred HHHHHHHccCCHHHHHHHhHHhc-cCCCC---CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 437 EVNKLIIVTLGEREREIIRLYYG-LDKEC---LTWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 437 ~L~~~L~~~Lp~rER~VI~LryG-Ld~eg---~TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
.+...+ +.+..+.-.|+.+-.. ++.++ +|+++||+.+|+|+.||. ++++.|..
T Consensus 45 ni~~~l-~l~g~k~~~Vl~~il~~~d~~N~v~~t~~~ia~~l~iS~~Tv~----r~ik~L~e 101 (165)
T PF05732_consen 45 NIIKVL-DLIGNKAFRVLMYILENMDKDNAVVATQKEIAEKLGISKPTVS----RAIKELEE 101 (165)
T ss_pred HHHHHh-hhhchhHHHHHHHHHHhcCCCCeEEeeHHHHHHHhCCCHHHHH----HHHHHHHh
Confidence 344555 5555555555544331 13332 799999999999999985 67777664
No 451
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=45.59 E-value=17 Score=30.58 Aligned_cols=25 Identities=24% Similarity=0.275 Sum_probs=22.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
+|..|+|+.+|||..|++.+..+.+
T Consensus 2 ~ti~evA~~~gvs~~tLR~ye~~Gl 26 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEEKGL 26 (88)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 6899999999999999999977654
No 452
>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=45.57 E-value=40 Score=29.79 Aligned_cols=24 Identities=21% Similarity=0.355 Sum_probs=20.9
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 464 CLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 464 g~TleEIAe~LgIS~erVrqi~~r 487 (508)
+.|.+|||+.+|+++.+|++++..
T Consensus 25 ~~s~~eia~~~~i~~~~v~~il~~ 48 (132)
T TIGR00738 25 PVSVKEIAERQGISRSYLEKILRT 48 (132)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHH
Confidence 789999999999999999866543
No 453
>PRK08359 transcription factor; Validated
Probab=45.39 E-value=27 Score=33.60 Aligned_cols=26 Identities=31% Similarity=0.567 Sum_probs=23.1
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
..++|++|+|+.+|+++.+|+.++.-
T Consensus 96 ~kglSQeeLA~~lgvs~stI~~iE~G 121 (176)
T PRK08359 96 KSGLSYEELSHEVGLSVNDLRRIAHG 121 (176)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 45799999999999999999988653
No 454
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=45.28 E-value=43 Score=29.13 Aligned_cols=43 Identities=14% Similarity=0.260 Sum_probs=32.5
Q ss_pred cCCHHHH-HHHhHHhccCCCCCCHHHHHHHHCC-CHHHHHHHHHHHHH
Q 010521 445 TLGERER-EIIRLYYGLDKECLTWEDISKRIGL-SRERVRQVGLVALE 490 (508)
Q Consensus 445 ~Lp~rER-~VI~LryGLd~eg~TleEIAe~LgI-S~erVrqi~~rALk 490 (508)
..|+..+ +|+.+++ ..|.|..+||+.+|| +.+.++++......
T Consensus 7 ~~s~EfK~~iv~~~~---~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~ 51 (116)
T COG2963 7 KYSPEFKLEAVALYL---RGGDTVSEVAREFGIVSATQLYKWRIQLQK 51 (116)
T ss_pred cCCHHHHHHHHHHHH---hcCccHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 4555555 5777777 568899999999996 99998876665444
No 455
>PRK11517 transcriptional regulatory protein YedW; Provisional
Probab=44.76 E-value=39 Score=31.49 Aligned_cols=49 Identities=18% Similarity=0.123 Sum_probs=38.3
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRI-----GLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~L-----gIS~erVrqi~~rALkKLR 493 (508)
.|+++|..|+.+-.-=-++-.|.++|.+.+ ..+..+|+.++.|.++||.
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 699999999988651112447999999997 4467899999888888885
No 456
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=44.72 E-value=32 Score=34.52 Aligned_cols=38 Identities=18% Similarity=0.233 Sum_probs=28.7
Q ss_pred HHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 448 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 448 ~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
+|+..|+.+--- ....+..|+|+.||||..|||+-+..
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 456666655321 24589999999999999999988775
No 457
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=44.62 E-value=31 Score=34.74 Aligned_cols=38 Identities=18% Similarity=0.253 Sum_probs=28.0
Q ss_pred HHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 448 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 448 ~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
+|++.|+.+-- .....+..|||+.|+||..|||+-+..
T Consensus 5 ~R~~~Il~~l~--~~~~~~~~ela~~l~vS~~TiRRdL~~ 42 (252)
T PRK10906 5 QRHDAIIELVK--QQGYVSTEELVEHFSVSPQTIRRDLND 42 (252)
T ss_pred HHHHHHHHHHH--HcCCEeHHHHHHHhCCCHHHHHHHHHH
Confidence 45666665543 023589999999999999999986543
No 458
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=44.47 E-value=16 Score=30.64 Aligned_cols=25 Identities=12% Similarity=0.134 Sum_probs=22.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
+|..|+|+.+|||+.|++.+...++
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~~Gl 26 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYERLGL 26 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 6899999999999999999987544
No 459
>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=44.46 E-value=34 Score=34.14 Aligned_cols=43 Identities=26% Similarity=0.236 Sum_probs=33.3
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 486 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~ 486 (508)
..|+..+.+-|++-+-.+-+.+|...+|+.|+||+++|++|+.
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 4677777776766553333458999999999999999999875
No 460
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=44.33 E-value=17 Score=31.62 Aligned_cols=26 Identities=23% Similarity=0.222 Sum_probs=22.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLVALE 490 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~rALk 490 (508)
++..|+|+.+|||..|+|.++..++-
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~~GLi 26 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKIGLL 26 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCC
Confidence 57899999999999999999887653
No 461
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=44.05 E-value=30 Score=32.43 Aligned_cols=26 Identities=15% Similarity=0.251 Sum_probs=23.6
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
..++|++++|+.+|+++++|+++++-
T Consensus 80 ~~glSqeeLA~~lgvs~s~IsriE~G 105 (154)
T TIGR00270 80 KRGWSQEQLAKKIQEKESLIKKIENA 105 (154)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 45799999999999999999999864
No 462
>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=44.01 E-value=56 Score=24.30 Aligned_cols=26 Identities=19% Similarity=0.371 Sum_probs=21.2
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHhC
Q 010521 366 TPSVDRIAEYLNMSQKKVRNATEAIG 391 (508)
Q Consensus 366 ~Pt~eEIA~~Lgis~e~v~~~l~~~~ 391 (508)
..+..+||+.+|+|..+|.+.+....
T Consensus 15 ~it~~eLa~~l~vS~rTi~~~i~~L~ 40 (55)
T PF08279_consen 15 PITAKELAEELGVSRRTIRRDIKELR 40 (55)
T ss_dssp SBEHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 36899999999999999998777653
No 463
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=43.93 E-value=60 Score=32.17 Aligned_cols=38 Identities=26% Similarity=0.151 Sum_probs=26.2
Q ss_pred HHHHhHHhccCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 451 REIIRLYYGLDKECL-TWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 451 R~VI~LryGLd~eg~-TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
..|+...|. .++.+ |-.+||+.||||+..|| .|++.|.
T Consensus 19 ~~I~~g~l~-pG~~LpsE~eLae~~gVSRtpVR----EAL~~L~ 57 (253)
T PRK11523 19 ERIEQGVYL-VGDKLPAERFIADEKNVSRTVVR----EAIIMLE 57 (253)
T ss_pred HHHHcCCCC-CCCCCCCHHHHHHHHCCCHHHHH----HHHHHHH
Confidence 334444431 13567 58899999999999997 6666665
No 464
>PHA00738 putative HTH transcription regulator
Probab=43.81 E-value=49 Score=29.41 Aligned_cols=37 Identities=24% Similarity=0.099 Sum_probs=26.9
Q ss_pred HHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521 448 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 486 (508)
Q Consensus 448 ~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~ 486 (508)
|.=+.||.+-. ..++++..||++.+++|+.+|++.+.
T Consensus 12 ptRr~IL~lL~--~~e~~~V~eLae~l~lSQptVS~HLK 48 (108)
T PHA00738 12 ILRRKILELIA--ENYILSASLISHTLLLSYTTVLRHLK 48 (108)
T ss_pred HHHHHHHHHHH--HcCCccHHHHHHhhCCCHHHHHHHHH
Confidence 34445555433 13569999999999999999998764
No 465
>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=43.59 E-value=59 Score=31.73 Aligned_cols=25 Identities=36% Similarity=0.429 Sum_probs=20.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLVALEKLK 493 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~rALkKLR 493 (508)
-|-.|+|+.+|||+.||| +|+..|.
T Consensus 25 PsE~eLa~~~gVSR~TVR----~Al~~L~ 49 (233)
T TIGR02404 25 PSEHELMDQYGASRETVR----KALNLLT 49 (233)
T ss_pred cCHHHHHHHHCCCHHHHH----HHHHHHH
Confidence 589999999999999997 4555554
No 466
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=43.51 E-value=32 Score=33.64 Aligned_cols=29 Identities=28% Similarity=0.472 Sum_probs=23.6
Q ss_pred CCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521 462 KECL-TWEDISKRIGLSRERVRQVGLVALEKLKH 494 (508)
Q Consensus 462 ~eg~-TleEIAe~LgIS~erVrqi~~rALkKLR~ 494 (508)
++-+ |-.++|+.||||+..|| .||.+|..
T Consensus 27 G~~LpsE~~La~~lgVSRtpVR----EAL~~Le~ 56 (235)
T TIGR02812 27 GSILPAERELSELIGVTRTTLR----EVLQRLAR 56 (235)
T ss_pred CCcCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 3567 79999999999999997 66666653
No 467
>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=43.31 E-value=18 Score=30.60 Aligned_cols=25 Identities=24% Similarity=0.299 Sum_probs=22.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
+|..|+|+.+||++.+|+.+...++
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~~Gl 25 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEEKGL 25 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999987654
No 468
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=42.85 E-value=18 Score=30.97 Aligned_cols=25 Identities=20% Similarity=0.514 Sum_probs=21.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
|+..|+|+.+|||..|++.+...++
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye~~Gl 25 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEEIGL 25 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999977643
No 469
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=42.54 E-value=19 Score=31.12 Aligned_cols=25 Identities=20% Similarity=0.363 Sum_probs=22.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
+|..|+|+.+|||..|+|.+...++
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~~Gl 26 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKLGL 26 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 6899999999999999998887654
No 470
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=42.51 E-value=19 Score=30.97 Aligned_cols=25 Identities=20% Similarity=0.264 Sum_probs=22.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
+|..|+|+.+|||..|++.+...++
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~~Gl 25 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDEIGL 25 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999887654
No 471
>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=42.44 E-value=40 Score=30.18 Aligned_cols=40 Identities=30% Similarity=0.374 Sum_probs=35.1
Q ss_pred ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
..|.+.++.|+.+.- ...|..|||..++++.+-|+-+..-
T Consensus 39 ~~l~pE~~~Il~lC~----~~~SVAEiAA~L~lPlgVvrVLvsD 78 (114)
T PF05331_consen 39 AGLGPEHRAILELCR----RPLSVAEIAARLGLPLGVVRVLVSD 78 (114)
T ss_pred CCCCHHHHHHHHHHC----CCccHHHHHHhhCCCchhhhhhHHH
Confidence 579999999999985 5899999999999999999876543
No 472
>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=42.33 E-value=59 Score=26.60 Aligned_cols=49 Identities=18% Similarity=0.135 Sum_probs=33.0
Q ss_pred cCCHHHHHHHhHHhccCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHH
Q 010521 445 TLGEREREIIRLYYGLDKECLTWEDISKRIG-----LSRERVRQVGLVALEKLK 493 (508)
Q Consensus 445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~Lg-----IS~erVrqi~~rALkKLR 493 (508)
.|+++|..+|.+-+-=.++..|.++|.+.+- .+..++.+.+.+..++|.
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 5899999988876522246789999999884 455555555554444443
No 473
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=42.23 E-value=19 Score=30.79 Aligned_cols=25 Identities=24% Similarity=0.308 Sum_probs=21.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
|+..|+|+.+|||..||+-++..++
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye~~GL 25 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLREGL 25 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999998877654
No 474
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=41.92 E-value=19 Score=30.68 Aligned_cols=25 Identities=20% Similarity=0.335 Sum_probs=22.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
+|..|+|+.+|||..|+|.+...++
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gl 25 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDKIGL 25 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 4789999999999999999987765
No 475
>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=41.89 E-value=31 Score=29.74 Aligned_cols=23 Identities=13% Similarity=0.235 Sum_probs=20.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~r 487 (508)
+|..|+|+.+|||..|++.+...
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~~ 23 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 47899999999999999999765
No 476
>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=41.88 E-value=33 Score=30.48 Aligned_cols=26 Identities=15% Similarity=0.213 Sum_probs=21.7
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
....|..|||+.+|+|+.+|++++..
T Consensus 23 ~~~~s~~eia~~l~is~~~v~~~l~~ 48 (130)
T TIGR02944 23 SQPYSAAEIAEQTGLNAPTVSKILKQ 48 (130)
T ss_pred CCCccHHHHHHHHCcCHHHHHHHHHH
Confidence 35689999999999999999766543
No 477
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=41.76 E-value=19 Score=30.65 Aligned_cols=25 Identities=20% Similarity=0.395 Sum_probs=22.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
|+..|+|+.+|||..|++.+...++
T Consensus 1 m~i~eva~~~gvs~~tlR~ye~~Gl 25 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDHIGL 25 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999887654
No 478
>PF04645 DUF603: Protein of unknown function, DUF603; InterPro: IPR006739 This family includes several uncharacterised proteins from Borrelia species.
Probab=41.67 E-value=34 Score=32.75 Aligned_cols=26 Identities=35% Similarity=0.432 Sum_probs=21.6
Q ss_pred CCC-CCHHHHHHHHCCCHHHHHHHHHH
Q 010521 462 KEC-LTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 462 ~eg-~TleEIAe~LgIS~erVrqi~~r 487 (508)
.+| ++..|||++||||+..|-...++
T Consensus 16 ~eg~L~d~~Ia~~lgvs~~nV~kmR~K 42 (181)
T PF04645_consen 16 KEGRLSDAEIAKELGVSRVNVWKMRQK 42 (181)
T ss_pred hcCCccHHHHHHHHCchHHHHHHHHHH
Confidence 466 99999999999999998765443
No 479
>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=41.57 E-value=20 Score=30.76 Aligned_cols=25 Identities=32% Similarity=0.449 Sum_probs=21.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
++..|+|+.+|||..|+|.+...++
T Consensus 1 y~i~e~A~~~gvs~~tlR~Ye~~Gl 25 (99)
T cd04772 1 YRTVDLARAIGLSPQTVRNYESLGL 25 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 4788999999999999998876644
No 480
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=41.49 E-value=41 Score=35.45 Aligned_cols=44 Identities=36% Similarity=0.468 Sum_probs=35.0
Q ss_pred ccCCHHHHHHHh------HHhccCCCCCCHHHHHHH--HCCCHHHHHHHHHHHHHH
Q 010521 444 VTLGEREREIIR------LYYGLDKECLTWEDISKR--IGLSRERVRQVGLVALEK 491 (508)
Q Consensus 444 ~~Lp~rER~VI~------LryGLd~eg~TleEIAe~--LgIS~erVrqi~~rALkK 491 (508)
..|++|++.|+. +.. .++.+.+++|+. +|+|..|||+.+.. |.+
T Consensus 2 ~~l~~R~~~Il~~IV~~yi~~---~~pv~s~~l~~~~~l~~S~aTIR~dm~~-Le~ 53 (339)
T PRK00082 2 SMLDERQREILRAIVEDYIAT---GEPVGSKTLSKRYGLGVSSATIRNDMAD-LEE 53 (339)
T ss_pred CccCHHHHHHHHHHHHHHHhc---CCCcCHHHHHHHhCCCCChHHHHHHHHH-HHh
Confidence 468999999996 333 578999999977 99999999987763 443
No 481
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=41.36 E-value=73 Score=30.54 Aligned_cols=39 Identities=23% Similarity=0.322 Sum_probs=28.6
Q ss_pred CHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 447 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 447 p~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
++.-..|+..-. ....+|-+|||+.|||+...||+++.+
T Consensus 21 ~~~~~~Vl~~L~--~~g~~tdeeLA~~Lgi~~~~VRk~L~~ 59 (178)
T PRK06266 21 DEEGFEVLKALI--KKGEVTDEEIAEQTGIKLNTVRKILYK 59 (178)
T ss_pred CccHhHHHHHHH--HcCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 544555665433 124699999999999999999977654
No 482
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=41.23 E-value=20 Score=31.43 Aligned_cols=25 Identities=20% Similarity=0.298 Sum_probs=22.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
|+..|+|+.+|||..|+|.++..++
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye~~GL 25 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEEQGL 25 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCC
Confidence 5789999999999999999988754
No 483
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=41.22 E-value=44 Score=34.51 Aligned_cols=39 Identities=15% Similarity=0.194 Sum_probs=29.5
Q ss_pred HHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 449 REREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 449 rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
+.+.|+.+-. +....+..+||+.+|+|+.+|++.+..-.
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 4555665543 13568999999999999999999887654
No 484
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=41.12 E-value=20 Score=31.30 Aligned_cols=25 Identities=24% Similarity=0.404 Sum_probs=22.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
+|..|+|+.+|||..|++.+...++
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye~~gl 25 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEKEGL 25 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999887654
No 485
>PHA02943 hypothetical protein; Provisional
Probab=41.11 E-value=40 Score=31.80 Aligned_cols=35 Identities=26% Similarity=0.387 Sum_probs=25.8
Q ss_pred HHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521 449 REREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 486 (508)
Q Consensus 449 rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~ 486 (508)
|-.+|+.+-- ..+.|..|||+.||+|-+.|+.++.
T Consensus 12 R~~eILE~Lk---~G~~TtseIAkaLGlS~~qa~~~Ly 46 (165)
T PHA02943 12 RMIKTLRLLA---DGCKTTSRIANKLGVSHSMARNALY 46 (165)
T ss_pred HHHHHHHHHh---cCCccHHHHHHHHCCCHHHHHHHHH
Confidence 3344555532 3568899999999999999987764
No 486
>PRK09480 slmA division inhibitor protein; Provisional
Probab=40.71 E-value=2.7e+02 Score=25.59 Aligned_cols=70 Identities=19% Similarity=0.018 Sum_probs=50.3
Q ss_pred CCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHh
Q 010521 236 GCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRG 305 (508)
Q Consensus 236 g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirA 305 (508)
|...+.+++|..+|++...+-.--...++-+..+++.+..-+............+..+.++..+-.++.-
T Consensus 28 G~~~ti~~Ia~~agvs~gt~Y~~F~~K~~L~~~v~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~ 97 (194)
T PRK09480 28 GERITTAKLAARVGVSEAALYRHFPSKARMFEGLIEFIEESLFSRINQILKDEKDTLARARLILLLLLGF 97 (194)
T ss_pred CCccCHHHHHHHhCCCHhHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHH
Confidence 5678999999999999999999999887777788877766555544444433345666666655555543
No 487
>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=40.38 E-value=75 Score=27.38 Aligned_cols=42 Identities=10% Similarity=0.008 Sum_probs=30.0
Q ss_pred CHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 010521 447 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL 492 (508)
Q Consensus 447 p~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKL 492 (508)
+.++-.+|.... +.-|+..-|+.||||+.+|.+.+.+.=..|
T Consensus 3 ~~~~l~~~~av~----~~gSis~AA~~L~iS~stvs~~I~~LE~~l 44 (99)
T TIGR00637 3 DPRRVALLKAIA----RMGSISQAAKDAGISYKSAWDYIRAMNNLS 44 (99)
T ss_pred CHHHHHHHHHHH----HhCCHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence 445555555554 567999999999999999986665544433
No 488
>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=40.14 E-value=63 Score=25.29 Aligned_cols=33 Identities=27% Similarity=0.332 Sum_probs=26.0
Q ss_pred HHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhC
Q 010521 359 RLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391 (508)
Q Consensus 359 ~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~ 391 (508)
.+.+.+...+..+||+.||+++..|.+++....
T Consensus 15 ~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~ 47 (60)
T PF01325_consen 15 ELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLA 47 (60)
T ss_dssp HHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHcCCCCccHHHHHHHHCCChHHHHHHHHHHH
Confidence 334466777899999999999999999988763
No 489
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=40.06 E-value=41 Score=32.22 Aligned_cols=37 Identities=22% Similarity=0.391 Sum_probs=27.2
Q ss_pred HHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521 448 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL 486 (508)
Q Consensus 448 ~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~ 486 (508)
+|++.|+.+--- ..-.+..++|+.||+|..|||+-+.
T Consensus 7 ~R~~~Il~~l~~--~~~~~~~~La~~~~vS~~TiRRDl~ 43 (185)
T PRK04424 7 ERQKALQELIEE--NPFITDEELAEKFGVSIQTIRLDRM 43 (185)
T ss_pred HHHHHHHHHHHH--CCCEEHHHHHHHHCcCHHHHHHHHH
Confidence 455556544331 2457999999999999999998765
No 490
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=40.04 E-value=4.4e+02 Score=27.25 Aligned_cols=28 Identities=18% Similarity=0.130 Sum_probs=23.9
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGLVAL 489 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~rAL 489 (508)
+...|++|||+..|||..||++....-.
T Consensus 249 ~~~~tq~eva~v~~vtevTIrnrykel~ 276 (285)
T COG1405 249 GERRTQKEVAKVAGVTEVTIRNRYKELA 276 (285)
T ss_pred CCchHHHHHHHHhCCeeeHHHHHHHHHH
Confidence 4679999999999999999999884433
No 491
>PRK11050 manganese transport regulator MntR; Provisional
Probab=40.03 E-value=81 Score=29.13 Aligned_cols=26 Identities=23% Similarity=0.184 Sum_probs=22.1
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
.++.+..|||+.+++++++|++.+.+
T Consensus 49 ~~~~t~~eLA~~l~is~stVsr~l~~ 74 (152)
T PRK11050 49 VGEARQVDIAARLGVSQPTVAKMLKR 74 (152)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 36799999999999999999866544
No 492
>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=39.93 E-value=40 Score=24.80 Aligned_cols=27 Identities=26% Similarity=0.261 Sum_probs=22.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHh
Q 010521 364 GVTPSVDRIAEYLNMSQKKVRNATEAI 390 (508)
Q Consensus 364 Gr~Pt~eEIA~~Lgis~e~v~~~l~~~ 390 (508)
...-|..|||+.+|+|..+|.......
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~~~~a 44 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRILKRA 44 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHHHHHH
Confidence 456689999999999999999876643
No 493
>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=39.77 E-value=21 Score=30.62 Aligned_cols=24 Identities=8% Similarity=0.163 Sum_probs=21.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLVA 488 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~rA 488 (508)
+|..|+|+.+|||..+++.+...+
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye~~G 25 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDRLG 25 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCC
Confidence 689999999999999999987654
No 494
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.69 E-value=78 Score=27.20 Aligned_cols=40 Identities=20% Similarity=0.232 Sum_probs=28.7
Q ss_pred HHHHHHHHHHc-C-CCCCHHHHHHHhCCCHHHHHHHHHHhCc
Q 010521 353 IRNAKLRLEEK-G-VTPSVDRIAEYLNMSQKKVRNATEAIGK 392 (508)
Q Consensus 353 ir~a~~~l~~~-G-r~Pt~eEIA~~Lgis~e~v~~~l~~~~~ 392 (508)
.++.+++|+++ . ..-++++||+.||+++.+++.++...++
T Consensus 8 ~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil~~tqr 49 (97)
T COG4367 8 KQRTKQELQANFELCPLSDEEIATALNWTEVKLEKILQVTQR 49 (97)
T ss_pred HHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHHHHHHHhhc
Confidence 34455556532 2 3347999999999999999999876544
No 495
>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=39.61 E-value=58 Score=25.89 Aligned_cols=32 Identities=25% Similarity=0.196 Sum_probs=25.1
Q ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHH
Q 010521 356 AKLRLEEKGVTPSVDRIAEYLNMSQKKVRNAT 387 (508)
Q Consensus 356 a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l 387 (508)
|+..+.+.+-.-+..+||+.||++..+|+..-
T Consensus 12 A~e~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 12 AFEIYKESNGKIKLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred HHHHHHHhCCCccHHHHHHHHCCCHHHHHHHh
Confidence 34444566777889999999999999998754
No 496
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=39.38 E-value=19 Score=30.80 Aligned_cols=37 Identities=19% Similarity=0.358 Sum_probs=27.3
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH-----HHHHHHHHHH
Q 010521 462 KECLTWEDISKRIGLSRERVRQVGLVA-----LEKLKHAARK 498 (508)
Q Consensus 462 ~eg~TleEIAe~LgIS~erVrqi~~rA-----LkKLR~~L~~ 498 (508)
..++++.+||+.+||++.+|+-....- +.||...|..
T Consensus 39 q~~l~Q~qiae~lgV~qprvS~l~~gk~~~fs~dkLvtml~~ 80 (91)
T COG5606 39 QAALSQAQIAELLGVTQPRVSDLARGKIQDFSIDKLVTMLAR 80 (91)
T ss_pred HHHHHHHHHHHHhCCCCchHHHHHhcchhHhhHHHHHHHHHH
Confidence 456899999999999999998766543 3445554443
No 497
>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=39.36 E-value=82 Score=29.53 Aligned_cols=39 Identities=23% Similarity=0.144 Sum_probs=27.8
Q ss_pred CHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521 447 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV 487 (508)
Q Consensus 447 p~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r 487 (508)
.+....|+..-+ ....+|-+|||+.||++...||+++.+
T Consensus 13 g~~~v~Vl~aL~--~~~~~tdEeLa~~Lgi~~~~VRk~L~~ 51 (158)
T TIGR00373 13 EEEVGLVLFSLG--IKGEFTDEEISLELGIKLNEVRKALYA 51 (158)
T ss_pred ChhHHHHHHHHh--ccCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 445555665432 134699999999999999999866554
No 498
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=39.33 E-value=22 Score=31.29 Aligned_cols=26 Identities=12% Similarity=0.219 Sum_probs=22.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010521 465 LTWEDISKRIGLSRERVRQVGLVALE 490 (508)
Q Consensus 465 ~TleEIAe~LgIS~erVrqi~~rALk 490 (508)
||..|+|+.+|||..|++-.+..++-
T Consensus 1 ~~ige~a~~~gvs~~tLryYe~~GLi 26 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEEKGLL 26 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 68899999999999999998877653
No 499
>PF11994 DUF3489: Protein of unknown function (DUF3489); InterPro: IPR021880 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.
Probab=39.32 E-value=85 Score=25.92 Aligned_cols=41 Identities=22% Similarity=0.238 Sum_probs=32.7
Q ss_pred HHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 010521 449 REREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEK 491 (508)
Q Consensus 449 rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkK 491 (508)
+|-.||.|-.- -+|.|..||++.+|--+.+||--+..+++|
T Consensus 11 Kqa~li~mL~r--p~GATi~ei~~atGWq~HTvRgalsg~~kK 51 (72)
T PF11994_consen 11 KQAQLIAMLRR--PEGATIAEICEATGWQPHTVRGALSGLLKK 51 (72)
T ss_pred HHHHHHHHHcC--CCCCCHHHHHHhhCCchhhHHHHHHHHHHH
Confidence 45556666441 578999999999999999999998888654
No 500
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=39.30 E-value=2.3e+02 Score=31.28 Aligned_cols=35 Identities=23% Similarity=0.345 Sum_probs=28.0
Q ss_pred HHHHHcCCCC-CHHHHHHHhCCCHHHHHHHHHHhCc
Q 010521 358 LRLEEKGVTP-SVDRIAEYLNMSQKKVRNATEAIGK 392 (508)
Q Consensus 358 ~~l~~~Gr~P-t~eEIA~~Lgis~e~v~~~l~~~~~ 392 (508)
..|.+.|.-. +.++||..+|++.+++..++...+.
T Consensus 129 ~~LD~~GyL~~~~~eia~~l~~~~~~v~~~l~~lQ~ 164 (455)
T PRK05932 129 DALDDEGYLTEDLEEIAESLGVELDEVEAVLKRIQS 164 (455)
T ss_pred HhCCCCCCCCCCHHHHHHHcCCCHHHHHHHHHHHhc
Confidence 3445678665 6899999999999999999887643
Done!