Query 009567
Match_columns 532
No_of_seqs 405 out of 2306
Neff 6.1
Searched_HMMs 46136
Date Thu Mar 28 14:40:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009567.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009567hhsearch_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 1.6E-65 3.5E-70 541.9 38.7 315 216-531 58-414 (415)
2 PRK07406 RNA polymerase sigma 100.0 9.6E-63 2.1E-67 517.1 38.7 312 216-528 61-372 (373)
3 PRK05949 RNA polymerase sigma 100.0 5.4E-62 1.2E-66 505.1 39.2 312 215-529 15-326 (327)
4 TIGR02997 Sig70-cyanoRpoD RNA 100.0 2.7E-61 5.9E-66 494.2 37.1 298 218-516 1-298 (298)
5 PRK07405 RNA polymerase sigma 100.0 7.1E-61 1.5E-65 495.1 38.9 311 216-529 6-316 (317)
6 COG0568 RpoD DNA-directed RNA 100.0 5.3E-60 1.1E-64 485.9 32.4 313 217-529 8-342 (342)
7 PRK05901 RNA polymerase sigma 100.0 9.3E-60 2E-64 509.0 33.7 301 216-529 209-509 (509)
8 PRK07921 RNA polymerase sigma 100.0 1.5E-58 3.3E-63 478.5 34.9 299 217-528 25-323 (324)
9 PRK09210 RNA polymerase sigma 100.0 8E-55 1.7E-59 458.3 33.1 276 214-529 92-367 (367)
10 PRK05658 RNA polymerase sigma 100.0 1.7E-52 3.6E-57 467.2 31.1 274 219-529 345-618 (619)
11 TIGR02393 RpoD_Cterm RNA polym 100.0 2.5E-48 5.5E-53 385.9 28.8 238 292-529 1-238 (238)
12 PRK06596 RNA polymerase factor 100.0 6.2E-45 1.4E-49 371.1 32.8 264 214-521 10-282 (284)
13 PRK07500 rpoH2 RNA polymerase 100.0 9.1E-45 2E-49 370.8 32.9 264 218-523 6-281 (289)
14 PRK05657 RNA polymerase sigma 100.0 1.2E-44 2.5E-49 375.5 33.7 272 216-527 51-322 (325)
15 TIGR02392 rpoH_proteo alternat 100.0 3.5E-44 7.6E-49 362.9 32.0 258 219-520 2-269 (270)
16 PRK07122 RNA polymerase sigma 100.0 1.8E-43 3.9E-48 356.9 30.8 221 291-520 40-264 (264)
17 PRK07408 RNA polymerase sigma 100.0 8.4E-42 1.8E-46 343.1 30.6 227 289-522 23-254 (256)
18 TIGR02394 rpoS_proteo RNA poly 100.0 6.1E-41 1.3E-45 341.6 33.9 271 214-524 9-279 (285)
19 TIGR02850 spore_sigG RNA polym 100.0 9.6E-40 2.1E-44 327.5 31.2 243 227-519 10-254 (254)
20 PRK05911 RNA polymerase sigma 100.0 6E-40 1.3E-44 329.9 28.9 227 288-521 20-255 (257)
21 COG1191 FliA DNA-directed RNA 100.0 6E-39 1.3E-43 319.0 29.1 221 290-521 23-246 (247)
22 PRK08215 sporulation sigma fac 100.0 2.3E-38 4.9E-43 318.1 31.6 243 227-519 13-257 (258)
23 PRK06288 RNA polymerase sigma 100.0 3.6E-37 7.9E-42 311.2 30.6 250 227-522 6-263 (268)
24 TIGR02941 Sigma_B RNA polymera 100.0 1.6E-36 3.5E-41 303.9 31.0 244 231-519 8-253 (255)
25 TIGR02885 spore_sigF RNA polym 100.0 1.5E-36 3.2E-41 299.6 28.8 223 287-519 7-231 (231)
26 TIGR02980 SigBFG RNA polymeras 100.0 4.1E-36 8.9E-41 295.5 28.2 221 290-519 2-226 (227)
27 PRK07670 RNA polymerase sigma 100.0 2.9E-35 6.2E-40 294.5 31.1 225 289-520 20-250 (251)
28 PRK08583 RNA polymerase sigma 100.0 1.7E-34 3.6E-39 289.7 31.0 243 231-521 8-255 (257)
29 PRK05572 sporulation sigma fac 100.0 2.3E-34 5E-39 288.2 31.2 244 225-520 6-251 (252)
30 TIGR02479 FliA_WhiG RNA polyme 100.0 9.2E-35 2E-39 285.7 27.0 217 296-519 1-223 (224)
31 PRK12427 flagellar biosynthesi 100.0 1.5E-34 3.4E-39 286.5 28.3 209 293-518 17-230 (231)
32 PRK06986 fliA flagellar biosyn 100.0 2.8E-33 6E-38 277.5 28.4 225 288-521 5-234 (236)
33 PRK05803 sporulation sigma fac 100.0 6.6E-28 1.4E-32 238.8 26.2 210 219-521 17-229 (233)
34 TIGR02846 spore_sigmaK RNA pol 99.9 4.3E-24 9.4E-29 210.9 25.8 199 228-519 25-226 (227)
35 PRK08301 sporulation sigma fac 99.9 6E-24 1.3E-28 210.2 25.5 180 289-521 50-232 (234)
36 TIGR02835 spore_sigmaE RNA pol 99.9 5E-23 1.1E-27 204.2 25.5 180 289-521 50-232 (234)
37 PRK08295 RNA polymerase factor 99.9 1.3E-22 2.9E-27 195.9 22.6 195 277-523 9-206 (208)
38 TIGR02859 spore_sigH RNA polym 99.9 1E-21 2.2E-26 188.2 21.5 191 277-519 4-197 (198)
39 PRK05602 RNA polymerase sigma 99.9 7.7E-22 1.7E-26 188.0 20.5 176 277-524 5-181 (186)
40 TIGR02948 SigW_bacill RNA poly 99.9 2.4E-21 5.2E-26 183.7 20.3 180 280-521 6-186 (187)
41 PRK09648 RNA polymerase sigma 99.9 4.1E-21 8.9E-26 183.4 21.9 171 281-520 13-188 (189)
42 PRK09641 RNA polymerase sigma 99.9 2.9E-21 6.2E-26 183.2 20.6 180 280-521 6-186 (187)
43 PRK12513 RNA polymerase sigma 99.9 1.8E-21 3.9E-26 186.6 19.2 181 277-524 11-192 (194)
44 PRK09646 RNA polymerase sigma 99.9 2.7E-21 5.8E-26 185.9 20.4 176 278-521 16-192 (194)
45 PRK09652 RNA polymerase sigma 99.9 1E-20 2.2E-25 177.4 19.9 172 287-520 6-177 (182)
46 TIGR02952 Sig70_famx2 RNA poly 99.9 1.1E-20 2.5E-25 176.2 19.6 163 288-519 8-170 (170)
47 PRK12519 RNA polymerase sigma 99.9 1.3E-20 2.9E-25 180.5 19.2 175 278-520 15-190 (194)
48 PRK13919 putative RNA polymera 99.9 1.9E-20 4.2E-25 178.0 19.8 176 278-521 9-185 (186)
49 PRK06759 RNA polymerase factor 99.9 1.4E-20 3.1E-25 173.2 17.8 151 290-518 3-153 (154)
50 PRK12514 RNA polymerase sigma 99.9 2.7E-20 5.9E-25 176.1 20.1 173 278-520 5-178 (179)
51 PRK06811 RNA polymerase factor 99.9 3.1E-20 6.8E-25 177.8 20.4 175 277-521 3-181 (189)
52 TIGR02939 RpoE_Sigma70 RNA pol 99.9 3.9E-20 8.4E-25 175.9 20.8 181 278-520 6-187 (190)
53 PRK11922 RNA polymerase sigma 99.9 4.2E-20 9.1E-25 182.8 20.9 173 288-521 27-199 (231)
54 PRK11923 algU RNA polymerase s 99.9 5.9E-20 1.3E-24 175.8 21.2 180 279-520 7-187 (193)
55 PRK12524 RNA polymerase sigma 99.9 5.3E-20 1.1E-24 177.3 20.7 177 277-523 11-188 (196)
56 PRK09640 RNA polymerase sigma 99.8 2.3E-20 4.9E-25 178.5 17.1 173 276-520 7-183 (188)
57 TIGR02984 Sig-70_plancto1 RNA 99.8 1.3E-19 2.9E-24 171.9 21.9 180 288-520 4-189 (189)
58 PRK12537 RNA polymerase sigma 99.8 6.5E-20 1.4E-24 174.5 19.8 172 278-519 9-181 (182)
59 PRK12538 RNA polymerase sigma 99.8 5.5E-20 1.2E-24 182.8 20.0 174 278-523 49-223 (233)
60 PRK12534 RNA polymerase sigma 99.8 7.2E-20 1.6E-24 174.4 19.2 172 281-520 14-186 (187)
61 PRK12526 RNA polymerase sigma 99.8 1.2E-19 2.5E-24 176.6 20.8 171 287-522 34-204 (206)
62 PRK11924 RNA polymerase sigma 99.8 1.2E-19 2.7E-24 169.7 20.0 168 287-522 9-176 (179)
63 PRK12542 RNA polymerase sigma 99.8 8.3E-20 1.8E-24 174.0 18.3 175 287-528 5-179 (185)
64 PRK12515 RNA polymerase sigma 99.8 2.2E-19 4.7E-24 171.7 20.6 177 277-524 7-184 (189)
65 TIGR02937 sigma70-ECF RNA poly 99.8 2.5E-19 5.3E-24 161.2 19.1 157 292-519 2-158 (158)
66 PRK12531 RNA polymerase sigma 99.8 3E-19 6.5E-24 171.7 19.6 176 282-523 17-193 (194)
67 PRK09638 RNA polymerase sigma 99.8 2.2E-19 4.7E-24 169.1 18.2 172 277-520 3-175 (176)
68 PRK09643 RNA polymerase sigma 99.8 4.7E-19 1E-23 170.4 20.3 172 277-521 12-184 (192)
69 TIGR02985 Sig70_bacteroi1 RNA 99.8 2.6E-19 5.6E-24 164.4 17.4 160 292-519 2-161 (161)
70 PRK12543 RNA polymerase sigma 99.8 4.6E-19 1E-23 168.2 19.2 166 288-523 4-169 (179)
71 TIGR02954 Sig70_famx3 RNA poly 99.8 4.9E-19 1.1E-23 166.0 18.9 167 277-520 1-168 (169)
72 PRK09645 RNA polymerase sigma 99.8 8.3E-19 1.8E-23 164.9 19.3 165 288-523 6-170 (173)
73 PRK12522 RNA polymerase sigma 99.8 9E-19 2E-23 165.0 19.3 167 291-521 3-169 (173)
74 PRK12536 RNA polymerase sigma 99.8 6.1E-19 1.3E-23 167.6 17.8 170 280-522 9-180 (181)
75 TIGR02989 Sig-70_gvs1 RNA poly 99.8 6.5E-19 1.4E-23 162.8 17.5 158 292-519 2-159 (159)
76 PRK09415 RNA polymerase factor 99.8 1.1E-18 2.5E-23 165.6 19.1 164 289-521 14-177 (179)
77 TIGR03001 Sig-70_gmx1 RNA poly 99.8 1.6E-18 3.5E-23 173.5 20.7 180 277-525 24-215 (244)
78 PRK12520 RNA polymerase sigma 99.8 1.1E-18 2.5E-23 167.0 18.7 182 292-524 3-184 (191)
79 PRK12539 RNA polymerase sigma 99.8 2E-18 4.4E-23 164.5 19.5 170 279-522 8-182 (184)
80 PRK12512 RNA polymerase sigma 99.8 2.7E-18 5.9E-23 163.1 20.1 166 282-522 12-182 (184)
81 TIGR02999 Sig-70_X6 RNA polyme 99.8 2.4E-18 5.2E-23 163.0 18.9 171 280-519 5-182 (183)
82 TIGR02895 spore_sigI RNA polym 99.8 3.6E-18 7.9E-23 168.1 20.2 118 286-403 4-126 (218)
83 PRK12518 RNA polymerase sigma 99.8 2.3E-18 5E-23 162.0 18.0 166 287-523 7-172 (175)
84 PRK12533 RNA polymerase sigma 99.8 4.5E-18 9.8E-23 167.3 20.6 172 287-522 14-185 (216)
85 PRK12529 RNA polymerase sigma 99.8 3.3E-18 7.2E-23 162.5 18.6 166 287-520 9-176 (178)
86 COG1595 RpoE DNA-directed RNA 99.8 6.5E-18 1.4E-22 160.9 20.5 171 284-522 8-178 (182)
87 PRK09642 RNA polymerase sigma 99.8 2.8E-18 6.1E-23 159.3 16.8 157 298-523 2-158 (160)
88 PRK09649 RNA polymerase sigma 99.8 4.2E-18 9.1E-23 162.9 17.8 169 281-523 13-182 (185)
89 TIGR02947 SigH_actino RNA poly 99.8 2.7E-18 5.8E-23 164.7 16.1 172 290-521 10-181 (193)
90 PRK09644 RNA polymerase sigma 99.8 6.2E-18 1.4E-22 158.1 18.0 158 293-523 3-160 (165)
91 PRK12516 RNA polymerase sigma 99.8 6.8E-18 1.5E-22 162.0 18.7 161 289-523 8-168 (187)
92 TIGR02983 SigE-fam_strep RNA p 99.8 7.2E-18 1.6E-22 156.7 17.5 158 288-521 3-160 (162)
93 PRK12523 RNA polymerase sigma 99.8 6.6E-18 1.4E-22 159.1 17.3 162 289-521 8-169 (172)
94 PRK09647 RNA polymerase sigma 99.8 1.3E-17 2.9E-22 162.2 20.0 166 289-524 26-191 (203)
95 PRK12528 RNA polymerase sigma 99.8 1.3E-17 2.9E-22 155.1 18.3 157 291-518 4-160 (161)
96 PRK12547 RNA polymerase sigma 99.8 2.3E-17 5E-22 154.4 19.2 159 290-522 5-163 (164)
97 PRK12532 RNA polymerase sigma 99.8 1.9E-17 4E-22 159.1 18.8 181 294-524 8-189 (195)
98 TIGR02943 Sig70_famx1 RNA poly 99.8 1.9E-17 4.1E-22 158.9 18.6 178 294-522 5-182 (188)
99 PRK09639 RNA polymerase sigma 99.8 2.7E-17 5.9E-22 153.2 19.1 161 290-522 2-162 (166)
100 PRK12541 RNA polymerase sigma 99.8 2.6E-17 5.7E-22 153.1 18.6 157 289-518 3-159 (161)
101 PRK12545 RNA polymerase sigma 99.8 2.7E-17 5.8E-22 159.4 18.9 180 295-524 12-192 (201)
102 PRK12530 RNA polymerase sigma 99.8 3.1E-17 6.7E-22 157.4 18.9 177 294-523 10-186 (189)
103 PRK12544 RNA polymerase sigma 99.8 3.1E-17 6.8E-22 160.0 18.9 181 293-523 20-200 (206)
104 PRK08241 RNA polymerase factor 99.8 4.6E-17 1E-21 169.5 20.5 187 281-518 8-200 (339)
105 TIGR02950 SigM_subfam RNA poly 99.8 1.4E-17 3E-22 153.1 14.4 152 298-519 2-153 (154)
106 PRK12535 RNA polymerase sigma 99.8 6.2E-17 1.3E-21 156.6 19.3 170 282-523 15-185 (196)
107 TIGR02960 SigX5 RNA polymerase 99.8 5.6E-17 1.2E-21 167.4 20.2 182 289-521 3-192 (324)
108 PRK07037 extracytoplasmic-func 99.7 6.5E-17 1.4E-21 150.4 18.5 159 295-522 2-160 (163)
109 PRK12540 RNA polymerase sigma 99.7 6.6E-17 1.4E-21 154.5 18.5 160 291-524 5-164 (182)
110 PRK12527 RNA polymerase sigma 99.7 9E-17 2E-21 149.2 17.7 155 298-522 2-156 (159)
111 PRK09637 RNA polymerase sigma 99.7 1.4E-16 2.9E-21 152.1 19.0 154 293-521 3-156 (181)
112 PRK09651 RNA polymerase sigma 99.7 1.4E-16 3.1E-21 150.3 18.5 164 289-523 8-171 (172)
113 PRK12517 RNA polymerase sigma 99.7 1.6E-16 3.6E-21 152.5 18.2 162 286-522 18-179 (188)
114 TIGR02959 SigZ RNA polymerase 99.7 2E-16 4.4E-21 149.1 17.7 149 298-521 2-150 (170)
115 PRK12546 RNA polymerase sigma 99.7 2.5E-16 5.5E-21 151.5 18.5 156 291-521 8-163 (188)
116 PRK12511 RNA polymerase sigma 99.7 4.1E-16 8.8E-21 149.2 17.3 157 293-522 6-162 (182)
117 PRK12525 RNA polymerase sigma 99.7 9.8E-16 2.1E-20 143.9 18.8 160 290-520 8-167 (168)
118 PRK09047 RNA polymerase factor 99.7 8.4E-16 1.8E-20 142.3 16.6 156 313-524 2-159 (161)
119 PRK09636 RNA polymerase sigma 99.7 1.8E-15 4E-20 154.9 17.7 161 291-521 4-165 (293)
120 PRK06704 RNA polymerase factor 99.6 1.1E-14 2.4E-19 144.5 17.3 158 282-521 9-166 (228)
121 TIGR02957 SigX4 RNA polymerase 99.6 1.3E-14 2.8E-19 148.0 17.5 156 295-520 1-157 (281)
122 PRK09635 sigI RNA polymerase s 99.6 1.5E-14 3.2E-19 148.5 18.0 162 291-520 5-167 (290)
123 TIGR03209 P21_Cbot clostridium 99.5 4.7E-13 1E-17 122.1 14.4 136 293-505 1-141 (142)
124 PRK09191 two-component respons 99.5 4.2E-13 9.1E-18 132.9 12.9 137 292-521 2-138 (261)
125 PRK08311 putative RNA polymera 99.5 4.4E-12 9.5E-17 126.7 19.3 90 279-368 5-97 (237)
126 PF07638 Sigma70_ECF: ECF sigm 99.4 6.4E-11 1.4E-15 113.7 19.2 174 280-520 5-184 (185)
127 PF04545 Sigma70_r4: Sigma-70, 99.2 2.1E-11 4.6E-16 92.6 7.2 50 464-517 1-50 (50)
128 PF04542 Sigma70_r2: Sigma-70 99.2 2.9E-11 6.3E-16 96.6 7.9 70 296-365 1-70 (71)
129 PF04539 Sigma70_r3: Sigma-70 99.1 2.7E-10 5.9E-15 94.1 7.6 77 375-451 1-77 (78)
130 PF08281 Sigma70_r4_2: Sigma-7 98.9 3.7E-09 8E-14 81.3 7.2 54 458-515 1-54 (54)
131 PRK06930 positive control sigm 98.6 1.2E-07 2.7E-12 90.3 9.7 71 448-522 95-165 (170)
132 PRK00118 putative DNA-binding 98.4 9.7E-07 2.1E-11 77.6 8.9 61 460-524 10-70 (104)
133 cd06171 Sigma70_r4 Sigma70, re 98.3 2.5E-06 5.5E-11 63.5 6.8 53 460-516 3-55 (55)
134 TIGR00721 tfx DNA-binding prot 98.2 3.4E-06 7.4E-11 77.6 7.0 57 466-527 5-61 (137)
135 PRK03975 tfx putative transcri 98.2 4.3E-06 9.3E-11 77.3 7.2 51 466-521 5-55 (141)
136 PRK04217 hypothetical protein; 98.1 8.3E-06 1.8E-10 72.4 6.4 55 466-524 41-95 (110)
137 PF00140 Sigma70_r1_2: Sigma-7 98.0 1.6E-06 3.5E-11 62.1 0.9 34 217-250 1-34 (37)
138 TIGR01636 phage_rinA phage tra 98.0 3.6E-05 7.8E-10 70.6 8.9 63 456-520 71-133 (134)
139 PF04297 UPF0122: Putative hel 97.9 4.6E-05 1E-09 66.6 8.5 57 461-521 10-67 (101)
140 PRK05658 RNA polymerase sigma 97.9 0.0038 8.3E-08 70.9 25.0 34 216-249 102-135 (619)
141 smart00421 HTH_LUXR helix_turn 97.9 3.5E-05 7.7E-10 58.3 5.7 46 466-516 2-47 (58)
142 PF00196 GerE: Bacterial regul 97.7 6.9E-05 1.5E-09 58.5 5.9 47 466-517 2-48 (58)
143 cd06170 LuxR_C_like C-terminal 97.7 0.00012 2.6E-09 55.5 6.1 45 468-517 1-45 (57)
144 PF07374 DUF1492: Protein of u 97.5 0.00045 9.7E-09 60.3 8.7 55 457-515 44-99 (100)
145 PF04967 HTH_10: HTH DNA bindi 97.5 0.00031 6.8E-09 54.4 6.8 48 468-515 1-51 (53)
146 TIGR03879 near_KaiC_dom probab 97.5 0.00021 4.6E-09 58.9 6.1 47 460-510 8-55 (73)
147 TIGR01321 TrpR trp operon repr 97.5 0.00017 3.6E-09 62.2 5.3 50 459-508 23-76 (94)
148 PRK15201 fimbriae regulatory p 97.4 0.00034 7.3E-09 66.8 6.5 47 466-517 132-178 (198)
149 PRK15411 rcsA colanic acid cap 97.4 0.00033 7.2E-09 68.5 6.3 46 467-517 137-182 (207)
150 PRK10840 transcriptional regul 97.3 0.00039 8.5E-09 67.3 6.2 46 466-516 149-194 (216)
151 PRK13870 transcriptional regul 97.3 0.00041 8.8E-09 69.4 6.2 46 467-517 173-218 (234)
152 PRK11475 DNA-binding transcrip 97.3 0.00044 9.6E-09 67.9 6.3 46 466-516 133-178 (207)
153 PRK13719 conjugal transfer tra 97.3 0.00046 1E-08 68.1 6.2 50 462-516 138-187 (217)
154 TIGR03020 EpsA transcriptional 97.3 0.00049 1.1E-08 69.6 6.4 48 465-517 188-235 (247)
155 TIGR03541 reg_near_HchA LuxR f 97.3 0.00049 1.1E-08 68.6 6.2 48 465-517 169-216 (232)
156 PRK10188 DNA-binding transcrip 97.2 0.00055 1.2E-08 68.7 6.4 45 467-516 179-223 (240)
157 PRK10100 DNA-binding transcrip 97.2 0.00063 1.4E-08 67.2 6.3 48 465-517 153-200 (216)
158 COG2197 CitB Response regulato 97.2 0.00068 1.5E-08 66.7 6.0 46 466-516 147-192 (211)
159 COG4566 TtrR Response regulato 97.1 0.002 4.4E-08 62.2 8.2 60 456-520 131-190 (202)
160 PF02001 DUF134: Protein of un 97.1 0.0014 3E-08 57.9 6.6 53 467-523 41-93 (106)
161 COG2771 CsgD DNA-binding HTH d 97.0 0.0019 4.2E-08 50.4 6.5 48 466-518 3-50 (65)
162 PF13936 HTH_38: Helix-turn-he 97.0 0.001 2.2E-08 49.4 4.0 41 466-510 3-43 (44)
163 PRK09483 response regulator; P 97.0 0.0014 3.1E-08 62.3 6.0 46 466-516 147-192 (217)
164 PRK15369 two component system 96.7 0.0031 6.7E-08 58.5 6.3 46 466-516 148-193 (211)
165 TIGR01637 phage_arpU phage tra 96.7 0.011 2.4E-07 53.7 9.4 62 457-520 68-130 (132)
166 COG3413 Predicted DNA binding 96.6 0.0045 9.8E-08 61.0 6.8 53 467-519 155-210 (215)
167 PRK01381 Trp operon repressor; 96.6 0.0025 5.3E-08 55.5 4.0 48 458-505 22-73 (99)
168 PRK10651 transcriptional regul 96.5 0.0043 9.3E-08 58.3 5.9 46 466-516 154-199 (216)
169 COG1356 tfx Transcriptional re 96.5 0.002 4.3E-08 58.1 3.2 48 467-519 8-55 (143)
170 PRK09390 fixJ response regulat 96.5 0.0077 1.7E-07 55.6 7.1 54 460-518 134-187 (202)
171 COG2739 Uncharacterized protei 96.3 0.018 3.9E-07 50.1 7.4 48 466-517 16-63 (105)
172 PRK15320 transcriptional activ 96.2 0.0089 1.9E-07 58.2 5.9 50 463-517 160-209 (251)
173 COG1342 Predicted DNA-binding 96.1 0.016 3.4E-07 50.0 6.3 52 467-522 33-84 (99)
174 PRK10403 transcriptional regul 96.0 0.013 2.8E-07 54.9 5.9 46 466-516 152-197 (215)
175 PRK10360 DNA-binding transcrip 95.7 0.016 3.6E-07 54.0 5.1 46 466-516 136-181 (196)
176 PRK09958 DNA-binding transcrip 95.7 0.023 5E-07 53.4 6.1 47 465-516 141-187 (204)
177 PRK09935 transcriptional regul 95.7 0.023 5E-07 53.3 6.1 45 467-516 149-193 (210)
178 COG4941 Predicted RNA polymera 95.5 0.35 7.6E-06 50.9 14.4 49 466-518 119-167 (415)
179 PRK04841 transcriptional regul 95.4 0.026 5.6E-07 66.1 6.4 46 466-516 837-882 (903)
180 PF00325 Crp: Bacterial regula 95.2 0.026 5.7E-07 39.3 3.4 27 487-517 2-28 (32)
181 PRK13558 bacterio-opsin activa 95.1 0.042 9.1E-07 62.4 6.8 55 465-519 605-662 (665)
182 PF13613 HTH_Tnp_4: Helix-turn 95.1 0.058 1.3E-06 41.5 5.5 50 467-519 2-51 (53)
183 TIGR02531 yecD_yerC TrpR-relat 95.0 0.053 1.1E-06 46.5 5.5 38 465-508 34-71 (88)
184 PF13384 HTH_23: Homeodomain-l 94.9 0.026 5.7E-07 42.3 3.0 33 474-511 9-41 (50)
185 PF12645 HTH_16: Helix-turn-he 94.7 0.14 2.9E-06 41.4 7.0 56 282-337 4-65 (65)
186 PF13412 HTH_24: Winged helix- 94.7 0.091 2E-06 39.1 5.6 41 468-511 1-41 (48)
187 PF01726 LexA_DNA_bind: LexA D 94.3 0.068 1.5E-06 43.1 4.4 45 465-509 1-48 (65)
188 PF05263 DUF722: Protein of un 94.2 0.15 3.3E-06 46.7 7.0 54 458-513 72-125 (130)
189 PF04539 Sigma70_r3: Sigma-70 93.9 0.12 2.6E-06 42.3 5.2 38 249-286 4-41 (78)
190 PRK15418 transcriptional regul 93.6 0.098 2.1E-06 54.9 5.2 36 474-513 20-55 (318)
191 PF02796 HTH_7: Helix-turn-hel 93.5 0.099 2.2E-06 38.8 3.6 32 472-508 11-42 (45)
192 cd00569 HTH_Hin_like Helix-tur 93.5 0.17 3.7E-06 33.4 4.6 36 468-507 6-41 (42)
193 PF06530 Phage_antitermQ: Phag 93.2 0.57 1.2E-05 42.5 8.8 55 465-523 60-114 (125)
194 TIGR02393 RpoD_Cterm RNA polym 93.2 1.2 2.7E-05 44.3 12.1 35 250-284 88-122 (238)
195 PRK09210 RNA polymerase sigma 92.9 1.5 3.3E-05 46.8 12.9 130 250-416 217-347 (367)
196 PF13730 HTH_36: Helix-turn-he 92.6 0.42 9E-06 36.4 6.1 47 467-517 2-51 (55)
197 PRK07921 RNA polymerase sigma 92.5 2.2 4.7E-05 45.0 13.3 130 250-416 174-304 (324)
198 PF13404 HTH_AsnC-type: AsnC-t 92.4 0.37 7.9E-06 35.5 5.3 40 468-510 1-40 (42)
199 PF09862 DUF2089: Protein of u 92.4 0.36 7.7E-06 43.3 6.2 50 464-517 30-79 (113)
200 PHA00675 hypothetical protein 92.2 0.27 5.8E-06 40.9 4.8 40 466-509 21-61 (78)
201 PRK10430 DNA-binding transcrip 92.0 0.31 6.8E-06 48.0 6.0 48 467-514 158-205 (239)
202 PRK05901 RNA polymerase sigma 92.0 2.7 5.7E-05 47.1 13.7 130 250-416 359-489 (509)
203 PF13518 HTH_28: Helix-turn-he 91.8 0.37 8.1E-06 35.9 4.9 27 486-512 11-37 (52)
204 COG1191 FliA DNA-directed RNA 91.5 5.9 0.00013 40.3 14.4 147 219-416 88-234 (247)
205 PF06056 Terminase_5: Putative 91.4 0.39 8.5E-06 37.9 4.8 26 486-511 12-37 (58)
206 smart00351 PAX Paired Box doma 90.8 0.62 1.4E-05 42.2 6.1 42 468-513 18-59 (125)
207 PF10668 Phage_terminase: Phag 90.7 0.47 1E-05 37.8 4.5 26 485-510 20-45 (60)
208 PF04218 CENP-B_N: CENP-B N-te 90.7 0.32 6.8E-06 37.6 3.5 40 467-510 6-45 (53)
209 PRK07598 RNA polymerase sigma 90.6 6.5 0.00014 42.9 14.7 37 379-415 112-148 (415)
210 COG3355 Predicted transcriptio 90.5 0.92 2E-05 41.4 6.9 53 459-517 16-68 (126)
211 PF02650 HTH_WhiA: WhiA C-term 90.3 0.59 1.3E-05 39.8 5.2 45 464-511 34-80 (85)
212 COG2909 MalT ATP-dependent tra 90.3 0.32 7E-06 56.5 4.7 45 467-516 831-875 (894)
213 PF08279 HTH_11: HTH domain; 90.3 0.51 1.1E-05 35.9 4.4 38 471-510 1-38 (55)
214 PF12802 MarR_2: MarR family; 90.3 0.6 1.3E-05 36.1 4.9 43 467-510 2-44 (62)
215 COG2390 DeoR Transcriptional r 89.5 0.48 1E-05 49.9 4.9 35 475-513 18-52 (321)
216 PF01022 HTH_5: Bacterial regu 89.3 0.92 2E-05 33.7 5.0 37 470-510 2-38 (47)
217 PRK00423 tfb transcription ini 89.3 18 0.00039 37.8 16.4 178 294-515 119-304 (310)
218 PF01325 Fe_dep_repress: Iron 88.9 0.69 1.5E-05 36.6 4.3 46 468-517 2-48 (60)
219 PHA02591 hypothetical protein; 88.7 0.87 1.9E-05 38.0 4.8 24 486-509 58-81 (83)
220 PRK11083 DNA-binding response 88.7 0.64 1.4E-05 44.0 4.8 50 467-517 154-208 (228)
221 PRK05911 RNA polymerase sigma 88.5 3.4 7.3E-05 41.8 10.1 34 251-284 112-145 (257)
222 PRK07408 RNA polymerase sigma 88.2 1.3 2.9E-05 44.7 7.0 35 250-284 114-148 (256)
223 PRK10710 DNA-binding transcrip 87.7 0.79 1.7E-05 44.0 4.8 50 467-517 160-214 (240)
224 PF12840 HTH_20: Helix-turn-he 87.7 1.8 4E-05 33.8 6.0 37 470-509 10-46 (61)
225 cd00131 PAX Paired Box domain 87.5 1.5 3.2E-05 40.0 6.1 41 468-512 18-58 (128)
226 PHA02547 55 RNA polymerase sig 87.5 1.9 4.1E-05 41.2 6.9 65 296-360 42-109 (179)
227 PRK07406 RNA polymerase sigma 87.2 9.1 0.0002 41.2 12.9 34 250-283 224-257 (373)
228 TIGR02885 spore_sigF RNA polym 87.2 2.3 5E-05 41.9 7.8 32 253-284 101-132 (231)
229 PF13463 HTH_27: Winged helix 87.0 1.1 2.4E-05 35.2 4.5 41 468-510 1-41 (68)
230 PF03444 HrcA_DNA-bdg: Winged 86.9 1.4 3.1E-05 36.9 5.1 42 467-508 1-44 (78)
231 PRK05949 RNA polymerase sigma 86.9 9.7 0.00021 40.1 12.7 35 250-284 179-213 (327)
232 PRK07122 RNA polymerase sigma 86.8 8.7 0.00019 39.1 12.0 35 250-284 128-162 (264)
233 PRK06288 RNA polymerase sigma 86.5 13 0.00028 37.7 13.1 35 250-284 119-153 (268)
234 smart00344 HTH_ASNC helix_turn 86.5 1.6 3.5E-05 37.7 5.6 41 468-511 1-41 (108)
235 PRK15479 transcriptional regul 86.4 1.2 2.5E-05 42.0 5.1 49 467-516 148-201 (221)
236 TIGR02147 Fsuc_second hypothet 86.3 17 0.00036 37.5 13.7 84 394-482 137-227 (271)
237 PF13542 HTH_Tnp_ISL3: Helix-t 85.8 1.9 4.1E-05 32.3 5.0 34 473-511 18-51 (52)
238 TIGR02997 Sig70-cyanoRpoD RNA 85.7 14 0.0003 38.2 13.0 35 250-284 162-196 (298)
239 PRK12423 LexA repressor; Provi 85.6 1.5 3.2E-05 42.8 5.5 47 467-517 3-52 (202)
240 TIGR02850 spore_sigG RNA polym 85.3 11 0.00023 38.0 11.6 35 252-286 123-157 (254)
241 TIGR02154 PhoB phosphate regul 85.3 0.66 1.4E-05 43.8 2.8 50 467-517 154-208 (226)
242 PRK10336 DNA-binding transcrip 85.1 1.2 2.5E-05 42.1 4.4 49 467-516 149-202 (219)
243 PF01371 Trp_repressor: Trp re 84.6 1.3 2.7E-05 38.0 3.8 41 466-506 25-68 (87)
244 PF12728 HTH_17: Helix-turn-he 84.4 1.1 2.4E-05 33.6 3.1 24 488-511 2-25 (51)
245 TIGR03787 marine_sort_RR prote 84.3 1.4 3.1E-05 42.0 4.6 50 467-517 156-207 (227)
246 TIGR01610 phage_O_Nterm phage 84.3 4.1 8.9E-05 35.0 7.0 49 465-517 20-73 (95)
247 PF13744 HTH_37: Helix-turn-he 84.3 1.9 4.2E-05 35.8 4.8 45 475-523 23-72 (80)
248 smart00550 Zalpha Z-DNA-bindin 84.2 2.3 4.9E-05 34.4 5.0 41 472-517 8-48 (68)
249 PRK07670 RNA polymerase sigma 84.1 13 0.00029 37.2 11.7 35 251-285 111-145 (251)
250 PRK07405 RNA polymerase sigma 83.9 12 0.00025 39.3 11.5 34 250-283 169-202 (317)
251 PF09339 HTH_IclR: IclR helix- 83.9 1.4 3.1E-05 33.4 3.5 32 478-509 9-40 (52)
252 cd06571 Bac_DnaA_C C-terminal 83.8 3.4 7.3E-05 35.1 6.2 40 486-529 43-84 (90)
253 PF01978 TrmB: Sugar-specific 83.8 1.1 2.4E-05 35.8 3.0 44 467-517 5-48 (68)
254 PF00356 LacI: Bacterial regul 83.7 1.1 2.4E-05 33.6 2.8 22 489-510 1-22 (46)
255 COG3415 Transposase and inacti 83.6 2.1 4.5E-05 39.7 5.1 27 486-512 20-46 (138)
256 PF13022 HTH_Tnp_1_2: Helix-tu 83.5 5.7 0.00012 37.0 7.9 64 461-524 4-73 (142)
257 PF01047 MarR: MarR family; I 83.4 2.2 4.9E-05 32.6 4.6 41 468-511 1-41 (59)
258 TIGR00498 lexA SOS regulatory 83.1 2 4.2E-05 41.6 5.0 48 466-517 2-52 (199)
259 PRK10046 dpiA two-component re 83.0 1.2 2.6E-05 43.5 3.5 39 467-509 161-199 (225)
260 smart00345 HTH_GNTR helix_turn 82.9 2.1 4.5E-05 32.3 4.2 30 484-517 16-46 (60)
261 PF01726 LexA_DNA_bind: LexA D 82.9 3.9 8.4E-05 32.9 5.8 40 378-417 9-49 (65)
262 PRK11179 DNA-binding transcrip 82.7 2.7 5.9E-05 39.1 5.7 41 467-510 6-46 (153)
263 PF01710 HTH_Tnp_IS630: Transp 82.3 14 0.0003 33.1 9.8 28 486-517 70-97 (119)
264 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 82.3 3.3 7.1E-05 31.8 4.9 39 467-509 4-42 (50)
265 PRK07500 rpoH2 RNA polymerase 82.2 29 0.00063 35.8 13.5 26 393-418 244-269 (289)
266 TIGR01764 excise DNA binding d 82.1 1.6 3.5E-05 31.6 3.1 24 488-511 2-25 (49)
267 cd04762 HTH_MerR-trunc Helix-T 81.8 1.7 3.7E-05 31.3 3.2 25 488-512 1-25 (49)
268 PRK13413 mpi multiple promoter 81.8 2.5 5.3E-05 41.0 5.2 34 472-510 162-195 (200)
269 PF01418 HTH_6: Helix-turn-hel 81.8 2.8 6.1E-05 34.5 4.8 51 458-508 4-55 (77)
270 CHL00148 orf27 Ycf27; Reviewed 81.8 2 4.3E-05 41.2 4.5 50 467-517 161-217 (240)
271 PRK00215 LexA repressor; Valid 81.6 2.7 5.8E-05 40.8 5.4 44 467-510 1-47 (205)
272 PF13011 LZ_Tnp_IS481: leucine 81.4 3.6 7.8E-05 35.1 5.3 44 466-512 7-50 (85)
273 PRK11564 stationary phase indu 80.7 4 8.6E-05 44.2 6.9 51 467-517 10-60 (426)
274 PF13551 HTH_29: Winged helix- 80.4 3.2 6.8E-05 35.6 4.9 26 486-511 10-36 (112)
275 PRK11169 leucine-responsive tr 79.8 3 6.5E-05 39.3 4.9 40 468-510 12-51 (164)
276 cd04761 HTH_MerR-SF Helix-Turn 79.0 1.6 3.4E-05 32.1 2.2 25 488-512 1-25 (49)
277 COG1654 BirA Biotin operon rep 78.9 5.2 0.00011 33.7 5.4 33 482-518 14-46 (79)
278 COG1522 Lrp Transcriptional re 78.9 4.9 0.00011 36.7 6.0 42 466-510 4-45 (154)
279 PF08822 DUF1804: Protein of u 78.5 4.5 9.8E-05 38.6 5.6 42 469-513 4-45 (165)
280 PF13545 HTH_Crp_2: Crp-like h 78.4 2.9 6.2E-05 33.6 3.8 28 486-517 27-54 (76)
281 TIGR02479 FliA_WhiG RNA polyme 78.3 31 0.00068 33.7 11.8 35 250-284 84-118 (224)
282 PF01381 HTH_3: Helix-turn-hel 77.9 2.3 5.1E-05 32.0 2.9 25 486-510 8-32 (55)
283 PHA01976 helix-turn-helix prot 77.5 4.2 9.1E-05 32.0 4.4 25 486-510 14-38 (67)
284 PF08220 HTH_DeoR: DeoR-like h 77.3 4.1 8.8E-05 31.7 4.2 25 485-509 12-36 (57)
285 TIGR02787 codY_Gpos GTP-sensin 77.3 10 0.00023 38.4 8.0 56 458-517 167-224 (251)
286 smart00420 HTH_DEOR helix_turn 77.2 6 0.00013 28.9 4.9 25 486-510 13-37 (53)
287 smart00342 HTH_ARAC helix_turn 77.1 34 0.00073 26.9 10.4 23 394-416 1-23 (84)
288 PHA00542 putative Cro-like pro 77.1 4 8.7E-05 34.2 4.3 26 486-511 30-55 (82)
289 COG2522 Predicted transcriptio 76.6 4.4 9.6E-05 36.7 4.7 24 486-509 21-44 (119)
290 TIGR03697 NtcA_cyano global ni 76.4 3.2 6.9E-05 39.1 4.0 29 486-518 142-170 (193)
291 smart00418 HTH_ARSR helix_turn 76.4 4.4 9.5E-05 30.4 4.1 25 486-510 9-33 (66)
292 PF07750 GcrA: GcrA cell cycle 76.0 3.4 7.3E-05 39.3 4.0 37 470-510 5-42 (162)
293 PF13551 HTH_29: Winged helix- 75.7 8.4 0.00018 32.9 6.2 23 396-418 14-36 (112)
294 TIGR02337 HpaR homoprotocatech 75.6 14 0.0003 32.5 7.6 45 466-517 24-68 (118)
295 PF14394 DUF4423: Domain of un 75.6 7.6 0.00016 37.2 6.4 109 393-521 38-154 (171)
296 PF00392 GntR: Bacterial regul 75.4 4.1 8.8E-05 32.1 3.8 30 484-517 20-50 (64)
297 PF02954 HTH_8: Bacterial regu 75.2 4.5 9.8E-05 29.4 3.7 37 470-509 4-40 (42)
298 smart00419 HTH_CRP helix_turn_ 75.2 4.2 9E-05 29.4 3.5 28 486-517 7-34 (48)
299 TIGR00122 birA_repr_reg BirA b 75.0 6.6 0.00014 31.3 5.0 25 486-510 12-36 (69)
300 PF13560 HTH_31: Helix-turn-he 74.9 3.8 8.3E-05 32.2 3.5 25 486-510 13-37 (64)
301 cd00092 HTH_CRP helix_turn_hel 74.6 8.2 0.00018 29.9 5.4 28 486-517 24-51 (67)
302 PF08765 Mor: Mor transcriptio 74.4 6.5 0.00014 34.6 5.2 41 471-517 62-102 (108)
303 PF13411 MerR_1: MerR HTH fami 74.2 1.6 3.5E-05 34.6 1.1 25 488-512 1-25 (69)
304 TIGR03070 couple_hipB transcri 74.1 5.8 0.00013 29.6 4.2 25 486-510 14-38 (58)
305 TIGR02941 Sigma_B RNA polymera 73.9 36 0.00079 34.0 11.2 33 251-283 118-150 (255)
306 PRK05572 sporulation sigma fac 73.9 36 0.00077 34.1 11.1 32 251-282 120-151 (252)
307 PRK10072 putative transcriptio 73.7 5.1 0.00011 34.9 4.2 32 475-510 38-69 (96)
308 cd07377 WHTH_GntR Winged helix 73.3 6.6 0.00014 30.1 4.5 26 488-517 26-51 (66)
309 TIGR03830 CxxCG_CxxCG_HTH puta 73.2 11 0.00024 33.3 6.5 47 459-511 56-102 (127)
310 PF00046 Homeobox: Homeobox do 73.0 6.4 0.00014 30.0 4.2 51 467-517 6-57 (57)
311 COG0856 Orotate phosphoribosyl 71.8 5.1 0.00011 38.7 4.0 39 474-517 10-48 (203)
312 COG1476 Predicted transcriptio 71.7 6.2 0.00013 32.3 4.0 25 486-510 13-37 (68)
313 PRK09954 putative kinase; Prov 71.5 7.7 0.00017 40.9 5.9 42 468-512 1-42 (362)
314 TIGR02612 mob_myst_A mobile my 71.2 9.6 0.00021 35.9 5.7 52 468-523 23-80 (150)
315 PRK08215 sporulation sigma fac 71.1 43 0.00094 33.6 10.9 33 252-284 126-158 (258)
316 PF06971 Put_DNA-bind_N: Putat 71.0 11 0.00024 28.9 5.1 45 369-413 3-47 (50)
317 smart00346 HTH_ICLR helix_turn 70.9 9.9 0.00021 31.5 5.3 26 486-511 19-44 (91)
318 TIGR02844 spore_III_D sporulat 70.5 9.1 0.0002 32.3 4.9 24 486-509 18-41 (80)
319 PRK13918 CRP/FNR family transc 70.5 5.2 0.00011 38.0 3.9 28 486-517 148-175 (202)
320 cd01104 HTH_MlrA-CarA Helix-Tu 70.1 5.6 0.00012 31.3 3.4 23 488-510 1-23 (68)
321 PRK03573 transcriptional regul 70.0 15 0.00032 33.4 6.7 49 460-510 19-69 (144)
322 PF00376 MerR: MerR family reg 69.9 2.9 6.2E-05 30.1 1.5 23 489-511 1-23 (38)
323 PRK06030 hypothetical protein; 69.7 14 0.0003 33.7 6.3 40 486-529 68-107 (124)
324 cd00090 HTH_ARSR Arsenical Res 69.5 13 0.00028 28.6 5.4 37 470-510 7-43 (78)
325 COG5484 Uncharacterized conser 69.2 6 0.00013 40.2 4.1 25 486-510 18-42 (279)
326 PF08280 HTH_Mga: M protein tr 69.0 5.2 0.00011 31.3 3.0 37 471-510 6-42 (59)
327 smart00347 HTH_MARR helix_turn 68.8 12 0.00027 30.9 5.5 44 467-517 7-50 (101)
328 COG0568 RpoD DNA-directed RNA 68.6 55 0.0012 35.0 11.3 34 249-282 189-222 (342)
329 PRK00082 hrcA heat-inducible t 68.0 7.7 0.00017 41.1 5.0 65 466-531 2-80 (339)
330 PRK11512 DNA-binding transcrip 67.5 28 0.00061 31.7 8.0 48 460-510 28-77 (144)
331 PRK10870 transcriptional repre 67.4 30 0.00065 33.0 8.4 50 460-510 43-94 (176)
332 TIGR01884 cas_HTH CRISPR locus 67.2 14 0.00031 35.9 6.3 44 464-510 137-180 (203)
333 PRK11753 DNA-binding transcrip 67.2 23 0.00051 33.7 7.8 27 487-517 168-194 (211)
334 COG2973 TrpR Trp operon repres 67.0 13 0.00027 32.6 5.0 39 467-505 37-78 (103)
335 cd04764 HTH_MlrA-like_sg1 Heli 66.9 7.1 0.00015 30.8 3.4 23 488-510 1-23 (67)
336 PF01527 HTH_Tnp_1: Transposas 66.9 6.1 0.00013 31.7 3.1 27 486-512 22-48 (76)
337 TIGR00647 MG103 conserved hypo 66.9 12 0.00026 38.7 5.9 45 464-511 224-274 (279)
338 COG5625 Predicted transcriptio 66.8 8.3 0.00018 33.9 3.9 70 459-528 8-79 (113)
339 PRK11302 DNA-binding transcrip 66.2 9.8 0.00021 38.5 5.2 51 458-510 4-57 (284)
340 PRK09413 IS2 repressor TnpA; R 66.1 13 0.00029 33.2 5.4 35 474-512 20-54 (121)
341 PF08535 KorB: KorB domain; I 66.1 5.8 0.00012 33.8 2.9 24 486-509 2-25 (93)
342 COG2944 Predicted transcriptio 66.0 17 0.00037 32.2 5.9 40 465-510 41-80 (104)
343 PRK11161 fumarate/nitrate redu 65.8 7.1 0.00015 38.2 3.9 27 487-517 184-210 (235)
344 PRK06986 fliA flagellar biosyn 65.7 95 0.0021 30.6 12.0 32 252-283 98-129 (236)
345 PF05043 Mga: Mga helix-turn-h 65.3 5.1 0.00011 33.4 2.4 32 485-516 28-59 (87)
346 TIGR02980 SigBFG RNA polymeras 65.2 53 0.0012 32.1 10.0 31 253-283 94-124 (227)
347 PF02082 Rrf2: Transcriptional 65.1 11 0.00024 31.2 4.4 24 486-509 24-47 (83)
348 smart00422 HTH_MERR helix_turn 64.7 5.1 0.00011 31.6 2.2 25 488-512 1-25 (70)
349 PF12116 SpoIIID: Stage III sp 64.6 10 0.00022 32.0 3.9 44 472-517 6-49 (82)
350 TIGR01889 Staph_reg_Sar staphy 64.3 19 0.0004 31.5 5.9 44 467-510 22-66 (109)
351 PF14493 HTH_40: Helix-turn-he 63.6 17 0.00037 30.8 5.3 29 486-514 12-40 (91)
352 cd04763 HTH_MlrA-like Helix-Tu 63.5 8.9 0.00019 30.4 3.4 23 488-510 1-23 (68)
353 PF11662 DUF3263: Protein of u 63.4 26 0.00056 29.4 6.1 48 466-513 1-48 (77)
354 PRK15482 transcriptional regul 63.4 12 0.00027 38.1 5.3 50 459-510 5-57 (285)
355 COG1510 Predicted transcriptio 63.3 7.1 0.00015 37.5 3.2 29 485-517 39-67 (177)
356 PRK11337 DNA-binding transcrip 63.0 19 0.00041 36.8 6.6 52 457-510 15-69 (292)
357 TIGR02607 antidote_HigA addict 62.8 16 0.00035 29.4 4.9 25 486-510 17-41 (78)
358 PRK10161 transcriptional regul 61.8 9 0.0002 36.5 3.8 50 467-517 154-208 (229)
359 PRK10955 DNA-binding transcrip 61.6 6 0.00013 37.6 2.4 46 467-517 156-210 (232)
360 PRK04984 fatty acid metabolism 61.4 12 0.00026 36.9 4.6 30 484-517 27-57 (239)
361 PF05225 HTH_psq: helix-turn-h 61.4 20 0.00044 26.6 4.7 23 488-510 17-39 (45)
362 PRK11557 putative DNA-binding 61.1 17 0.00036 36.8 5.8 48 461-510 3-53 (278)
363 COG1508 RpoN DNA-directed RNA 60.9 1.3E+02 0.0027 33.4 12.5 47 463-509 294-352 (444)
364 KOG0484 Transcription factor P 60.6 13 0.00028 33.0 4.0 57 460-520 19-77 (125)
365 smart00354 HTH_LACI helix_turn 60.6 8.8 0.00019 30.9 2.9 23 488-510 1-23 (70)
366 PRK09391 fixK transcriptional 60.5 10 0.00023 37.3 4.0 28 487-518 179-206 (230)
367 PRK09863 putative frv operon r 59.5 19 0.0004 40.8 6.3 46 468-517 2-47 (584)
368 PF08784 RPA_C: Replication pr 59.3 15 0.00032 31.6 4.3 43 467-509 44-87 (102)
369 COG3093 VapI Plasmid maintenan 59.3 14 0.00031 32.6 4.1 35 474-510 12-46 (104)
370 PRK09726 antitoxin HipB; Provi 59.3 15 0.00033 30.9 4.3 25 486-510 24-48 (88)
371 COG1318 Predicted transcriptio 58.9 9.7 0.00021 36.6 3.2 28 486-513 60-87 (182)
372 TIGR02395 rpoN_sigma RNA polym 58.4 1.1E+02 0.0024 33.6 11.8 94 393-507 317-416 (429)
373 TIGR01387 cztR_silR_copR heavy 57.9 15 0.00034 34.2 4.6 49 467-516 147-200 (218)
374 PRK10402 DNA-binding transcrip 57.7 24 0.00052 34.5 6.0 47 468-518 149-196 (226)
375 COG1405 SUA7 Transcription ini 57.5 2.4E+02 0.0053 29.3 15.0 26 486-511 250-275 (285)
376 PRK03902 manganese transport t 57.5 20 0.00043 32.8 5.0 25 485-509 20-44 (142)
377 smart00342 HTH_ARAC helix_turn 57.4 18 0.0004 28.5 4.3 26 487-512 1-26 (84)
378 PRK01905 DNA-binding protein F 57.3 43 0.00092 27.7 6.5 37 471-510 37-73 (77)
379 COG2512 Predicted membrane-ass 57.3 15 0.00032 37.6 4.6 46 466-517 191-236 (258)
380 PRK11050 manganese transport r 57.3 17 0.00038 33.8 4.7 26 485-510 49-74 (152)
381 cd00086 homeodomain Homeodomai 57.2 28 0.0006 26.2 5.1 51 467-517 6-57 (59)
382 PF00165 HTH_AraC: Bacterial r 57.1 16 0.00034 26.2 3.4 25 486-510 7-31 (42)
383 PF13556 HTH_30: PucR C-termin 57.0 31 0.00066 26.9 5.3 35 486-520 11-45 (59)
384 PHA00738 putative HTH transcri 56.8 24 0.00053 31.4 5.2 37 470-509 12-48 (108)
385 PRK11414 colanic acid/biofilm 56.7 14 0.0003 36.1 4.1 31 483-517 30-60 (221)
386 PRK09863 putative frv operon r 56.6 57 0.0012 37.0 9.5 102 394-516 17-121 (584)
387 COG2345 Predicted transcriptio 56.6 20 0.00043 35.9 5.2 25 486-510 24-48 (218)
388 PRK10411 DNA-binding transcrip 56.4 20 0.00044 36.0 5.3 41 470-513 4-44 (240)
389 PF01710 HTH_Tnp_IS630: Transp 56.2 16 0.00034 32.7 4.0 24 486-509 17-40 (119)
390 cd04768 HTH_BmrR-like Helix-Tu 55.9 8.5 0.00018 33.1 2.2 26 488-513 1-26 (96)
391 TIGR03338 phnR_burk phosphonat 55.7 15 0.00032 35.5 4.1 30 484-517 31-60 (212)
392 TIGR02812 fadR_gamma fatty aci 55.5 17 0.00037 35.8 4.6 30 484-517 26-56 (235)
393 PRK11517 transcriptional regul 55.3 21 0.00046 33.5 5.1 49 467-516 147-200 (223)
394 PRK09392 ftrB transcriptional 55.2 13 0.00028 36.3 3.7 28 487-518 173-200 (236)
395 smart00862 Trans_reg_C Transcr 55.1 42 0.00091 26.6 6.1 50 467-517 5-60 (78)
396 PRK10141 DNA-binding transcrip 54.5 34 0.00073 30.9 5.8 49 462-517 7-56 (117)
397 PRK09990 DNA-binding transcrip 54.5 18 0.0004 36.0 4.6 37 475-517 20-57 (251)
398 PRK03837 transcriptional regul 54.2 19 0.00042 35.4 4.7 30 484-517 33-63 (241)
399 COG1846 MarR Transcriptional r 54.1 27 0.00058 29.7 5.1 40 468-510 20-59 (126)
400 PRK09706 transcriptional repre 53.6 20 0.00043 32.5 4.3 25 486-510 17-41 (135)
401 PRK14082 hypothetical protein; 53.4 45 0.00097 27.1 5.6 56 290-347 8-63 (65)
402 PRK09464 pdhR transcriptional 53.3 20 0.00042 35.8 4.7 38 474-517 22-60 (254)
403 PRK10643 DNA-binding transcrip 53.1 19 0.00041 33.7 4.3 49 467-516 149-202 (222)
404 TIGR02702 SufR_cyano iron-sulf 53.1 28 0.0006 33.9 5.5 26 486-511 14-39 (203)
405 PRK10421 DNA-binding transcrip 52.7 20 0.00044 35.8 4.6 38 474-517 14-52 (253)
406 TIGR02698 CopY_TcrY copper tra 52.6 36 0.00078 31.0 5.9 44 467-513 1-48 (130)
407 COG3877 Uncharacterized protei 52.6 31 0.00068 30.7 5.1 47 465-515 39-85 (122)
408 smart00530 HTH_XRE Helix-turn- 52.5 24 0.00052 24.6 3.9 25 486-510 9-33 (56)
409 PRK10225 DNA-binding transcrip 52.2 21 0.00045 35.8 4.6 38 474-517 21-59 (257)
410 PF04703 FaeA: FaeA-like prote 52.0 15 0.00032 29.5 2.8 25 486-510 14-38 (62)
411 cd04775 HTH_Cfa-like Helix-Tur 52.0 10 0.00023 32.9 2.1 26 488-513 2-27 (102)
412 PRK13509 transcriptional repre 51.9 24 0.00052 35.7 5.0 26 485-510 17-42 (251)
413 PF06322 Phage_NinH: Phage Nin 51.8 22 0.00048 28.5 3.6 27 475-508 11-37 (64)
414 PRK11534 DNA-binding transcrip 51.6 22 0.00047 34.8 4.6 38 474-517 19-56 (224)
415 PF06413 Neugrin: Neugrin; In 51.2 24 0.00053 35.4 4.9 42 467-509 10-51 (225)
416 cd01392 HTH_LacI Helix-turn-he 51.2 10 0.00022 28.1 1.7 21 491-511 1-21 (52)
417 PF12844 HTH_19: Helix-turn-he 51.1 25 0.00055 27.2 4.0 25 486-510 11-35 (64)
418 cd00383 trans_reg_C Effector d 50.9 34 0.00074 28.2 5.1 50 467-517 23-77 (95)
419 cd01105 HTH_GlnR-like Helix-Tu 50.6 12 0.00026 31.6 2.3 25 488-512 2-26 (88)
420 TIGR02944 suf_reg_Xantho FeS a 50.6 26 0.00056 31.4 4.6 30 484-517 22-51 (130)
421 cd01107 HTH_BmrR Helix-Turn-He 50.4 12 0.00026 32.8 2.3 26 488-513 1-26 (108)
422 TIGR00738 rrf2_super rrf2 fami 50.3 31 0.00067 30.7 5.0 25 485-509 23-47 (132)
423 COG1321 TroR Mn-dependent tran 50.1 29 0.00063 32.7 5.0 42 468-509 4-46 (154)
424 cd04773 HTH_TioE_rpt2 Second H 50.1 12 0.00025 32.9 2.2 25 488-512 1-25 (108)
425 PF14502 HTH_41: Helix-turn-he 49.9 31 0.00067 26.4 4.0 30 485-518 4-33 (48)
426 PRK13239 alkylmercury lyase; P 49.5 34 0.00074 33.9 5.5 29 391-419 33-61 (206)
427 TIGR00180 parB_part ParB-like 49.4 33 0.00072 32.9 5.4 43 466-510 101-143 (187)
428 cd04782 HTH_BltR Helix-Turn-He 49.4 12 0.00027 32.1 2.2 25 488-512 1-25 (97)
429 PF09012 FeoC: FeoC like trans 49.4 13 0.00028 29.9 2.1 26 485-510 12-37 (69)
430 PF04963 Sigma54_CBD: Sigma-54 49.2 41 0.00088 32.7 6.0 60 466-529 28-94 (194)
431 PRK09744 DNA-binding transcrip 49.2 23 0.0005 29.5 3.5 19 489-507 12-30 (75)
432 PF07037 DUF1323: Putative tra 49.1 19 0.00041 32.7 3.3 23 488-510 1-23 (122)
433 smart00389 HOX Homeodomain. DN 49.0 29 0.00062 25.9 4.0 47 468-514 7-54 (56)
434 TIGR02394 rpoS_proteo RNA poly 48.6 2.9E+02 0.0063 28.1 12.5 31 255-285 139-169 (285)
435 cd04772 HTH_TioE_rpt1 First He 48.4 14 0.00029 32.1 2.3 25 488-512 1-25 (99)
436 PF13443 HTH_26: Cro/C1-type H 48.2 18 0.00038 28.0 2.7 26 486-511 9-34 (63)
437 cd04765 HTH_MlrA-like_sg2 Heli 48.2 21 0.00046 31.0 3.4 23 488-510 1-23 (99)
438 PF07900 DUF1670: Protein of u 48.1 1.8E+02 0.0038 29.3 10.1 37 380-417 92-128 (220)
439 PRK11014 transcriptional repre 48.0 36 0.00079 31.1 5.2 30 484-517 22-51 (141)
440 COG1737 RpiR Transcriptional r 47.9 39 0.00085 34.6 6.0 51 457-509 5-58 (281)
441 PRK12469 RNA polymerase factor 47.7 2.1E+02 0.0045 32.1 11.8 127 348-507 331-466 (481)
442 cd00093 HTH_XRE Helix-turn-hel 47.7 36 0.00079 23.8 4.2 25 486-510 11-35 (58)
443 PRK05932 RNA polymerase factor 47.7 1.7E+02 0.0038 32.4 11.3 24 393-416 342-365 (455)
444 cd04789 HTH_Cfa Helix-Turn-Hel 47.7 14 0.0003 32.2 2.2 26 488-513 2-27 (102)
445 cd04788 HTH_NolA-AlbR Helix-Tu 47.7 14 0.00029 31.8 2.1 26 488-513 1-26 (96)
446 PRK11523 DNA-binding transcrip 47.6 28 0.0006 34.8 4.7 30 484-517 28-58 (253)
447 PRK13777 transcriptional regul 47.2 42 0.0009 32.7 5.6 40 466-508 41-80 (185)
448 cd04766 HTH_HspR Helix-Turn-He 47.1 14 0.0003 31.3 2.1 26 488-513 2-27 (91)
449 TIGR02431 pcaR_pcaU beta-ketoa 47.1 33 0.00072 34.2 5.2 26 484-509 21-46 (248)
450 cd04780 HTH_MerR-like_sg5 Heli 47.1 14 0.00031 31.8 2.2 25 488-512 1-25 (95)
451 cd01109 HTH_YyaN Helix-Turn-He 47.1 14 0.00031 32.5 2.2 26 488-513 1-26 (113)
452 smart00352 POU Found in Pit-Oc 46.9 36 0.00077 28.5 4.4 32 475-510 16-53 (75)
453 PF12298 Bot1p: Eukaryotic mit 46.9 40 0.00086 32.5 5.4 38 468-508 17-54 (172)
454 cd01106 HTH_TipAL-Mta Helix-Tu 46.8 14 0.00031 31.9 2.2 25 488-512 1-25 (103)
455 cd00592 HTH_MerR-like Helix-Tu 46.6 15 0.00032 31.4 2.2 25 488-512 1-25 (100)
456 COG1481 Uncharacterized protei 46.6 39 0.00084 35.5 5.6 43 465-510 251-295 (308)
457 cd04777 HTH_MerR-like_sg1 Heli 46.6 15 0.00032 32.0 2.3 26 488-513 1-26 (107)
458 PRK13503 transcriptional activ 46.5 1.1E+02 0.0025 30.3 9.0 30 388-417 181-210 (278)
459 PRK09834 DNA-binding transcrip 46.3 33 0.00071 34.7 5.0 41 473-517 12-52 (263)
460 cd01282 HTH_MerR-like_sg3 Heli 46.3 15 0.00032 32.5 2.2 26 488-513 1-26 (112)
461 PRK06424 transcription factor; 46.3 29 0.00064 32.4 4.3 25 486-510 96-120 (144)
462 cd04769 HTH_MerR2 Helix-Turn-H 46.2 15 0.00032 32.6 2.2 27 488-514 1-27 (116)
463 PF00292 PAX: 'Paired box' dom 46.2 43 0.00094 30.6 5.2 32 474-510 25-56 (125)
464 PF08006 DUF1700: Protein of u 46.2 55 0.0012 31.2 6.3 57 454-510 3-63 (181)
465 cd04774 HTH_YfmP Helix-Turn-He 46.1 15 0.00032 31.7 2.1 26 488-513 1-26 (96)
466 cd01108 HTH_CueR Helix-Turn-He 46.1 14 0.00031 33.3 2.2 27 488-514 1-27 (127)
467 TIGR02044 CueR Cu(I)-responsiv 45.6 15 0.00032 33.2 2.2 26 488-513 1-26 (127)
468 PF04552 Sigma54_DBD: Sigma-54 45.2 7.1 0.00015 37.1 0.0 48 460-509 24-71 (160)
469 PRK13890 conjugal transfer pro 45.0 33 0.00071 30.9 4.3 25 486-510 17-41 (120)
470 COG4367 Uncharacterized protei 44.9 54 0.0012 28.3 5.2 40 467-509 2-45 (97)
471 cd04783 HTH_MerR1 Helix-Turn-H 44.4 16 0.00034 32.9 2.2 27 488-514 1-27 (126)
472 PRK14101 bifunctional glucokin 44.4 54 0.0012 37.7 6.9 52 457-510 343-397 (638)
473 PRK12427 flagellar biosynthesi 44.3 38 0.00083 33.6 5.1 34 251-284 103-136 (231)
474 PRK08583 RNA polymerase sigma 44.2 1.8E+02 0.004 29.0 10.1 25 393-417 220-244 (257)
475 PRK06266 transcription initiat 44.1 71 0.0015 30.8 6.7 47 460-510 13-59 (178)
476 TIGR02395 rpoN_sigma RNA polym 44.1 23 0.0005 38.9 3.7 46 464-509 283-340 (429)
477 PF05331 DUF742: Protein of un 43.9 37 0.00079 30.6 4.3 40 466-510 39-78 (114)
478 TIGR03826 YvyF flagellar opero 43.8 91 0.002 29.0 7.0 50 375-424 27-76 (137)
479 PRK09764 DNA-binding transcrip 43.7 34 0.00075 33.9 4.7 29 485-517 26-55 (240)
480 PRK13502 transcriptional activ 43.7 3.5E+02 0.0075 27.0 13.2 25 393-417 191-215 (282)
481 cd01279 HTH_HspR-like Helix-Tu 43.7 17 0.00036 31.5 2.1 24 488-511 2-25 (98)
482 PRK14999 histidine utilization 43.6 35 0.00075 33.9 4.7 28 486-517 34-62 (241)
483 cd04770 HTH_HMRTR Helix-Turn-H 43.5 17 0.00038 32.3 2.3 27 488-514 1-27 (123)
484 PF10078 DUF2316: Uncharacteri 43.4 50 0.0011 28.5 4.9 24 486-509 22-45 (89)
485 PRK09943 DNA-binding transcrip 43.4 34 0.00073 32.6 4.4 25 486-510 19-43 (185)
486 PRK10434 srlR DNA-bindng trans 43.4 31 0.00066 35.0 4.3 38 470-510 5-42 (256)
487 cd04768 HTH_BmrR-like Helix-Tu 43.4 2.1E+02 0.0045 24.4 8.9 34 486-519 56-89 (96)
488 cd01111 HTH_MerD Helix-Turn-He 43.3 18 0.00038 31.9 2.2 26 488-513 1-26 (107)
489 PF14549 P22_Cro: DNA-binding 43.0 34 0.00074 27.2 3.6 19 489-507 11-29 (60)
490 PF12085 DUF3562: Protein of u 43.0 48 0.001 27.0 4.4 41 488-531 8-48 (66)
491 TIGR02018 his_ut_repres histid 42.9 36 0.00078 33.5 4.6 28 486-517 23-51 (230)
492 TIGR02325 C_P_lyase_phnF phosp 42.9 29 0.00062 34.1 3.9 27 487-517 32-58 (238)
493 cd04784 HTH_CadR-PbrR Helix-Tu 42.9 18 0.00038 32.6 2.2 27 488-514 1-27 (127)
494 PRK08359 transcription factor; 42.7 34 0.00074 33.1 4.2 35 486-520 97-138 (176)
495 PF12324 HTH_15: Helix-turn-he 42.7 67 0.0015 27.0 5.4 44 349-421 22-65 (77)
496 COG4709 Predicted membrane pro 42.3 67 0.0014 31.5 6.1 58 455-512 4-65 (195)
497 PRK10219 DNA-binding transcrip 42.2 67 0.0014 27.5 5.7 26 486-511 20-45 (107)
498 cd04781 HTH_MerR-like_sg6 Heli 42.1 18 0.0004 32.2 2.2 26 488-513 1-26 (120)
499 cd04787 HTH_HMRTR_unk Helix-Tu 42.0 18 0.0004 32.8 2.2 25 488-512 1-25 (133)
500 TIGR02404 trehalos_R_Bsub treh 41.7 31 0.00066 34.0 3.9 27 487-517 24-50 (233)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=1.6e-65 Score=541.88 Aligned_cols=315 Identities=38% Similarity=0.651 Sum_probs=299.1
Q ss_pred CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHH--------------------HHHHHHHHHhhhCCCCcHHHHHHHc
Q 009567 216 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR--------------------LEKEKSKLQSQFGREPTLIEWAKAI 275 (532)
Q Consensus 216 ~~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~--------------------le~~~~~l~~~~g~~pt~~ewA~aa 275 (532)
..|+++.||++|++.|+||++||++|+++||.++. |++++..|+..+|++||..|||.++
T Consensus 58 ~~d~v~~yl~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~~~ 137 (415)
T PRK07598 58 STDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTA 137 (415)
T ss_pred CCChHHHHHHhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHHHh
Confidence 57899999999999999999999999999999999 9999999999999999999999555
Q ss_pred ----------------------cCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhh
Q 009567 276 ----------------------GLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSV 333 (532)
Q Consensus 276 ----------------------g~~~~~L~~~l~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAi 333 (532)
||++++|+..++.|..|+++||.+|+++|++||++|.++|++++||||||++|||+|+
T Consensus 138 ~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~rav 217 (415)
T PRK07598 138 DISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAV 217 (415)
T ss_pred CCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHH
Confidence 4566666777788999999999999999999999999999999999999999999999
Q ss_pred hhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHH
Q 009567 334 EKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLER 413 (532)
Q Consensus 334 ekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ 413 (532)
++|||++|++|+|||+||||++|.+++++++|+||+|.|+.+.+++++++...+.+++||.|+.+|||+.+||++++|+.
T Consensus 218 ekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~ 297 (415)
T PRK07598 218 EKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVRE 297 (415)
T ss_pred HHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHH
Q 009567 414 LIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEV 493 (532)
Q Consensus 414 ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EI 493 (532)
++.....++|||.+++++++..+.+.+.++. .+|++.+....+...|..+|..|||+||.||.+||||+||+++|++||
T Consensus 298 ~l~~~~~~~SLd~~vg~~~d~~l~d~l~~~~-~~pee~~~~~~l~~~L~~~L~~L~~reR~VI~LRygl~d~~~~Tl~EI 376 (415)
T PRK07598 298 VLLRVPRSVSLETKVGKDKDTELGDLLETDD-ISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEI 376 (415)
T ss_pred HHHHccCCcccccccCCCccccHHHhccCCC-CCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCCCHHHH
Confidence 9999999999999999888888888877543 578888888899999999999999999999999999999999999999
Q ss_pred HHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhhhh
Q 009567 494 GNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLL 531 (532)
Q Consensus 494 Ae~LgISrerVRqie~rALkKLR~~l~~~~l~~yldll 531 (532)
|+.||||+++||+++++|++|||+.-....+++|++.|
T Consensus 377 A~~LGvS~erVRqie~rAl~KLR~~~~~~~l~~y~~~~ 414 (415)
T PRK07598 377 GRALDLSRERVRQIESKALQKLRQPKRRNRIRDYLELL 414 (415)
T ss_pred HHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHHHhc
Confidence 99999999999999999999999999999999999765
No 2
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=9.6e-63 Score=517.09 Aligned_cols=312 Identities=37% Similarity=0.728 Sum_probs=300.3
Q ss_pred CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHH
Q 009567 216 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 295 (532)
Q Consensus 216 ~~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~ 295 (532)
..|++..||++|+++|+||++||++|+++|++++.+++.+.+|+...|++|+..+||.++|++..+|..+++.|..|++.
T Consensus 61 ~~d~l~~Yl~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~ 140 (373)
T PRK07406 61 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEK 140 (373)
T ss_pred CCCHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHH
Confidence 35789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHH
Q 009567 296 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 375 (532)
Q Consensus 296 LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~ 375 (532)
||.+|+++|+++|++|.++|.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++|++++++||+|.|+..
T Consensus 141 Li~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~~ 220 (373)
T PRK07406 141 MVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYE 220 (373)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHH
Q 009567 376 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ 455 (532)
Q Consensus 376 ~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~ 455 (532)
.+++++++...+.+.+|+.||.+|||+.+|+++++|..++.....++|||.+++++++..+.+++++.. .+|++.+...
T Consensus 221 ~~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d~l~d~~-~~pee~~~~~ 299 (373)
T PRK07406 221 TISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADG-ETPEDDVAKN 299 (373)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHHhcCCCC-CCHHHHHHHH
Confidence 999999999999999999999999999999999999999888888999999998777778889888763 4788888888
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhh
Q 009567 456 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYA 528 (532)
Q Consensus 456 ~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~yl 528 (532)
.+...|..+|..||++||.||.+||||+|++++|++|||+.||||++||||++.+|++|||.......++.|+
T Consensus 300 ~~~~~L~~aL~~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~~~~~~~l~~~~ 372 (373)
T PRK07406 300 LLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 372 (373)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHh
Confidence 8999999999999999999999999999889999999999999999999999999999999999999998886
No 3
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00 E-value=5.4e-62 Score=505.05 Aligned_cols=312 Identities=40% Similarity=0.669 Sum_probs=298.3
Q ss_pred CCChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHH
Q 009567 215 DRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSRE 294 (532)
Q Consensus 215 ~~~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are 294 (532)
...|++..||++|+++|+||++||++|+++|+.++.++..+..|+..+|++|+..+||.+++|++.+|+..++.|+.|++
T Consensus 15 ~~~d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~ 94 (327)
T PRK05949 15 FSADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQ 94 (327)
T ss_pred CCCCHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHH
Confidence 35689999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHH
Q 009567 295 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY 374 (532)
Q Consensus 295 ~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~ 374 (532)
.||..|+++|+++|++|.+++.+++||+|||++|||+++++|||++|++|+|||+||||++|.+++.+++++||+|.|+.
T Consensus 95 ~Li~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~~ 174 (327)
T PRK05949 95 KMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHIT 174 (327)
T ss_pred HHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHH
Q 009567 375 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK 454 (532)
Q Consensus 375 ~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~ 454 (532)
..+++++++...+.+++||+|+.+|||+.+|+++++|..++.....++|||.+++++++.++.+.++|.. .+|++.+..
T Consensus 175 ~~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~~-~~pe~~~~~ 253 (327)
T PRK05949 175 EKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEG-PSPDQYITQ 253 (327)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCCC-CCHHHHHHH
Confidence 9999999999999999999999999999999999999999998899999999998877778888888765 588988888
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 009567 455 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 529 (532)
Q Consensus 455 ~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~yld 529 (532)
..+...|..+|+.||++||.||.+||||+|++++|++|||+.||||+++|||++.+|++|||+. ...++.|+.
T Consensus 254 ~~~~~~L~~~L~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~~--~~~l~~~~~ 326 (327)
T PRK05949 254 ELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRRR--RANVKEYLA 326 (327)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence 8899999999999999999999999999999999999999999999999999999999999994 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=2.7e-61 Score=494.16 Aligned_cols=298 Identities=44% Similarity=0.755 Sum_probs=286.1
Q ss_pred hHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHH
Q 009567 218 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI 297 (532)
Q Consensus 218 d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI 297 (532)
|++..||++++++|+||++||.+|+++++.++.++..+.+|+.+.|++||..+||+++|+++.+|...++.|..|++.||
T Consensus 1 ~~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv 80 (298)
T TIGR02997 1 DLVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMI 80 (298)
T ss_pred CcHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHH
Confidence 46788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHH
Q 009567 298 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL 377 (532)
Q Consensus 298 ~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l 377 (532)
.+|+++|++||++|.++|.+++|||||||+|||+|+++|||++|++|+|||+||||++|.+++.+++++||+|.++...+
T Consensus 81 ~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~~~~~~~ 160 (298)
T TIGR02997 81 KANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKL 160 (298)
T ss_pred HHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHH
Q 009567 378 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 457 (532)
Q Consensus 378 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~~l 457 (532)
++++++...+.+.+|+.|+.+|||+.+|+++++|..++.....++|||.+++++++.++.+.+++. ..+|++.+....+
T Consensus 161 ~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~-~~~pe~~~~~~~~ 239 (298)
T TIGR02997 161 NKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDD-GESPEEQVERESL 239 (298)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccCC-CCCHHHHHHHHHH
Confidence 999999999999999999999999999999999999999888999999999776666777877774 4578888888888
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567 458 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 458 ~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR 516 (532)
...|..+|+.||++||+||.+||||+|++++|++|||+.||||++||||++++|++|||
T Consensus 240 ~~~L~~~L~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr 298 (298)
T TIGR02997 240 RQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298 (298)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 99999999999999999999999999999999999999999999999999999999996
No 5
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=7.1e-61 Score=495.10 Aligned_cols=311 Identities=38% Similarity=0.641 Sum_probs=297.1
Q ss_pred CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHH
Q 009567 216 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 295 (532)
Q Consensus 216 ~~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~ 295 (532)
.+|++..||++|+++|+||++||.+|+++|++++.+++++..|+..+|++|+..+||.++++++..|...++.|..|++.
T Consensus 6 ~~~~~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~ 85 (317)
T PRK07405 6 STDLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRK 85 (317)
T ss_pred CCcHHHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHH
Confidence 35789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHH
Q 009567 296 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 375 (532)
Q Consensus 296 LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~ 375 (532)
||..|+++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+|||+||||++|.++|.+++++||+|.|+..
T Consensus 86 L~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~~ 165 (317)
T PRK07405 86 MVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITE 165 (317)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHH
Q 009567 376 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ 455 (532)
Q Consensus 376 ~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~ 455 (532)
.+++++++...+...+|+.|+.+|||+.+|+++++|..++.....++|||.+++++++..+.+.++|.. .+|++.+...
T Consensus 166 ~~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~~-~~pe~~~~~~ 244 (317)
T PRK07405 166 KLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTG-ASPEDFATQS 244 (317)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCCC-CCHHHHHHHH
Confidence 999999999999999999999999999999999999999988888999999998777778888888764 5789888888
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 009567 456 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 529 (532)
Q Consensus 456 ~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~yld 529 (532)
.++..|..+|+.||++||.||.+||||+|++++|++|||+.||||++||||++.+|++|||+. ...+..|++
T Consensus 245 ~~~~~l~~al~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~--~~~l~~~~~ 316 (317)
T PRK07405 245 SLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKR--KANIQEYLA 316 (317)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence 899999999999999999999999999999999999999999999999999999999999995 456777764
No 6
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=100.00 E-value=5.3e-60 Score=485.90 Aligned_cols=313 Identities=36% Similarity=0.656 Sum_probs=289.1
Q ss_pred ChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHh-hhCCCCcHH---------------HHHHHccCCH-
Q 009567 217 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS-QFGREPTLI---------------EWAKAIGLSC- 279 (532)
Q Consensus 217 ~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~-~~g~~pt~~---------------ewA~aag~~~- 279 (532)
.|.+..|+.+++..+++++++|.++...++....+......|.. ..|..|+.. +|+.....++
T Consensus 8 ~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Ee 87 (342)
T COG0568 8 ADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEEE 87 (342)
T ss_pred hhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHHH
Confidence 57889999999999999999999999999887777667777776 677888876 6665555544
Q ss_pred HHHHHHHhhcH---HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHH
Q 009567 280 RDLKSELHSGN---SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 356 (532)
Q Consensus 280 ~~L~~~l~~g~---~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI 356 (532)
..|..++..|. .|+.+||.+|+|||++||++|.|+|+++.||||||+||||+|+++|||++||+|||||+||||++|
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 56777777773 699999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 009567 357 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 436 (532)
Q Consensus 357 ~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l 436 (532)
.++|.+++|+||+|.|+.+.+++++++.+.+.+++|++|+.+|||+.+|+++++|..++.....++|||.|++++++..+
T Consensus 168 ~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~ded~~l 247 (342)
T COG0568 168 TRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSEL 247 (342)
T ss_pred HHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCCCcccHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999988899
Q ss_pred hhhcccCCCCChhHHHHHHHHHHHHHHHHhc-CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567 437 QEITADTGVEIPDISVQKQLMRQHVRNLLTL-LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 515 (532)
Q Consensus 437 ~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~-L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKL 515 (532)
+|+++|+...+|++.+....+.+.+...|.. |+|+|+.||++|||++|+++.|++|||+.+|||++|||||+.+|++||
T Consensus 248 ~d~leD~~~~~p~~~~~~~~~~~~~~~~L~~~Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~isrERvRQIE~kAl~KL 327 (342)
T COG0568 248 GDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAKALRKL 327 (342)
T ss_pred HHHhhcCCcCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCcchHHHHHHHhCCcHHHHHHHHHHHHHHH
Confidence 9999999888999999999999999999999 999999999999999999999999999999999999999999999999
Q ss_pred HH-HhhcCchhhhhh
Q 009567 516 KQ-SLGGKASYGYAD 529 (532)
Q Consensus 516 R~-~l~~~~l~~yld 529 (532)
|. ......+++|++
T Consensus 328 r~~~~~~~~~~~~l~ 342 (342)
T COG0568 328 RRHPERSALLRSYLD 342 (342)
T ss_pred HHhhhhhhHHHHhhC
Confidence 94 445555677864
No 7
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=100.00 E-value=9.3e-60 Score=508.99 Aligned_cols=301 Identities=35% Similarity=0.613 Sum_probs=277.2
Q ss_pred CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHH
Q 009567 216 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 295 (532)
Q Consensus 216 ~~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~ 295 (532)
..|++..||++|+++|+||++||++|+++|+.+...+.. +. ...+|+. ....+|+..++.|..|++.
T Consensus 209 ~~d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~---~~-------~~~~~~~---~~~~~l~~~~~~g~~Ar~~ 275 (509)
T PRK05901 209 TADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEEL---LA-------EGEKLDP---ELRRDLQWIGRDGKRAKNH 275 (509)
T ss_pred cccHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhh---hh-------hcccchh---hhhhhhhhhccchHHHHHH
Confidence 468999999999999999999999999999875332221 11 1122442 2457788889999999999
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHH
Q 009567 296 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 375 (532)
Q Consensus 296 LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~ 375 (532)
||.+|+|||++||++|.++|++++||||||+||||+|+++|||++|++|+|||+||||++|.++|++++|+||+|.|+..
T Consensus 276 LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~~~~e 355 (509)
T PRK05901 276 LLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE 355 (509)
T ss_pred HHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHH
Q 009567 376 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ 455 (532)
Q Consensus 376 ~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~ 455 (532)
.++++.++...+.+.+||.||.+|||+.+|+++++|..++.....++|||.+++++++..+.+++.|.....|++.+...
T Consensus 356 ~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~~p~~~~~~~ 435 (509)
T PRK05901 356 TINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSFT 435 (509)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCCCCCHHHHHHHH
Confidence 99999999999999999999999999999999999999999888999999999887777889999998777899989888
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 009567 456 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 529 (532)
Q Consensus 456 ~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~yld 529 (532)
.++..|..+|..|+++||.||.+||||++++++|++|||+.||||++|||||+.+||+|||.......|+.|++
T Consensus 436 ~l~~~L~~aL~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~~~~~~l~~~l~ 509 (509)
T PRK05901 436 LLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDFLD 509 (509)
T ss_pred HHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999975
No 8
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=100.00 E-value=1.5e-58 Score=478.45 Aligned_cols=299 Identities=36% Similarity=0.632 Sum_probs=275.8
Q ss_pred ChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHH
Q 009567 217 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL 296 (532)
Q Consensus 217 ~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~L 296 (532)
+|++..||++++++|+||++||.+|+++|+.+..++.. |+..+|.... ...++...++.|..|++.|
T Consensus 25 ~~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~~L 91 (324)
T PRK07921 25 ADLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARRHL 91 (324)
T ss_pred CChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHHHH
Confidence 57899999999999999999999999999986655542 2233343111 4567888999999999999
Q ss_pred HHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHH
Q 009567 297 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTL 376 (532)
Q Consensus 297 I~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~ 376 (532)
|..|+++|+++|++|.++|.+++||+|||++|||+|+++|||++|++|+|||+||||++|.+++++++++||+|.|+...
T Consensus 92 v~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~~~ 171 (324)
T PRK07921 92 LEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ 171 (324)
T ss_pred HHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHH
Q 009567 377 LSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQL 456 (532)
Q Consensus 377 l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~~ 456 (532)
+++++++...+.+.+|+.||.+|||+.+|+++++|..++.....++|||.+++++++.++.++++|+...+|++.+....
T Consensus 172 ~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~~ 251 (324)
T PRK07921 172 VNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGL 251 (324)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCCCCCHHHHHHHHH
Confidence 99999999999999999999999999999999999999988888999999998777778899999876678888888888
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhh
Q 009567 457 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYA 528 (532)
Q Consensus 457 l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~yl 528 (532)
++..|..+|..|+++|+.||.+||||+|++++|++|||+.||||++|||||+.+|++|||.......|+.|+
T Consensus 252 ~~~~l~~~L~~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~~~~~~l~~~~ 323 (324)
T PRK07921 252 LHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSYA 323 (324)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHHHHHHHHhh
Confidence 999999999999999999999999999999999999999999999999999999999999998888888885
No 9
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=8e-55 Score=458.27 Aligned_cols=276 Identities=37% Similarity=0.712 Sum_probs=262.7
Q ss_pred CCCChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHH
Q 009567 214 FDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSR 293 (532)
Q Consensus 214 ~~~~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Ar 293 (532)
...+|+++.||++|+++|+||++||.+|+.+++. | +..|+
T Consensus 92 ~~~~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~---------------G-------------------------d~~A~ 131 (367)
T PRK09210 92 VKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEE---------------G-------------------------DEEAK 131 (367)
T ss_pred cccCcHHHHHHHHhhccCCCCHHHHHHHHHHHHh---------------h-------------------------HHHHH
Confidence 3457899999999999999999999999988764 2 35899
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhH
Q 009567 294 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI 373 (532)
Q Consensus 294 e~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~ 373 (532)
+.||..|+++|+++|++|.++|.+++||+|||++|||+|+++|||.+|++|+|||+||||++|.++|++++|+||+|.|+
T Consensus 132 ~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~ 211 (367)
T PRK09210 132 QRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 211 (367)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHH
Q 009567 374 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ 453 (532)
Q Consensus 374 ~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~ 453 (532)
...++++.++.+.+.+++||.||.+|||+.+|+++++|..++.....++|||.+++++++..+.++++|....+|++.+.
T Consensus 212 ~~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~~~~p~~~~~ 291 (367)
T PRK09210 212 VETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAA 291 (367)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCCCCCHHHHHH
Confidence 99999999999999999999999999999999999999999998888999999998877778999999887778999999
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 009567 454 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 529 (532)
Q Consensus 454 ~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~yld 529 (532)
...++..|..+|..||++||.||.+||||+||+++|++|||+.||||++|||||+.+||+|||.+.....|+.|++
T Consensus 292 ~~~~~~~l~~~l~~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~~~~~~~l~~~~~ 367 (367)
T PRK09210 292 YELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 367 (367)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhChHHHhHHHHhhC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999874
No 10
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=1.7e-52 Score=467.19 Aligned_cols=274 Identities=34% Similarity=0.633 Sum_probs=252.3
Q ss_pred HHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHH
Q 009567 219 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 298 (532)
Q Consensus 219 ~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~ 298 (532)
.+..||.++...+.||++|+..++++++. |+ .....|+++||.
T Consensus 345 ~lq~~L~~ie~~~~Ls~eElk~l~~~i~~---------------g~----------------------~~~~~a~~~Li~ 387 (619)
T PRK05658 345 KLQQELEAIEEETGLTIEELKEINRQISK---------------GE----------------------AKARRAKKEMVE 387 (619)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHHhc---------------cc----------------------hhhhHHHHHHHH
Confidence 34556666666666777776666666653 22 112378999999
Q ss_pred HHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHH
Q 009567 299 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS 378 (532)
Q Consensus 299 ~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ 378 (532)
+|+|||++||++|.++|++++||||||+||||+|+++|||++|++|+|||+||||++|.++|++++|+||+|.|+...++
T Consensus 388 ~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~irip~~~~~~~~ 467 (619)
T PRK05658 388 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 467 (619)
T ss_pred HHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCceecCHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHHH
Q 009567 379 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMR 458 (532)
Q Consensus 379 ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~~l~ 458 (532)
+++++...+.+++||+||.+|||+.+|+++++|..++.....++|||.|++++++..+.++++|....+|++.+....++
T Consensus 468 k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~~~~~l~d~i~d~~~~~p~~~~~~~~~~ 547 (619)
T PRK05658 468 KLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLR 547 (619)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCCCCCchhhhcCCCCCCChHHHHHHHHHH
Confidence 99999999999999999999999999999999999999888999999999888888899999998888899999888999
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 009567 459 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 529 (532)
Q Consensus 459 ~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~yld 529 (532)
..|..+|..||++|+.||++||||++++++|++|||+.||||++|||||+.+|++|||.+.....|+.|+|
T Consensus 548 ~~l~~~l~~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr~~~~~~~l~~~~~ 618 (619)
T PRK05658 548 EATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRSFLD 618 (619)
T ss_pred HHHHHHHHcCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHhchHHHHHHHHHhc
Confidence 99999999999999999999999998899999999999999999999999999999999999999999987
No 11
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=100.00 E-value=2.5e-48 Score=385.86 Aligned_cols=238 Identities=39% Similarity=0.753 Sum_probs=227.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccch
Q 009567 292 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 371 (532)
Q Consensus 292 Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~ 371 (532)
|+++||.+|+++|+++|++|.++|.+++||+|||++||++|+++|||++|++|+|||+||||++|.++++++.+.+|+|.
T Consensus 1 a~~~Li~~~~~lv~~ia~~~~~~~~~~eDLiQeG~igL~~A~~~fd~~~g~~FstYA~~~Ir~~I~~~l~~~~~~vrip~ 80 (238)
T TIGR02393 1 AKKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80 (238)
T ss_pred CHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCChHHHhHHHHHHHHHHHHHHcCCcEEeCH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHH
Q 009567 372 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 451 (532)
Q Consensus 372 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~ 451 (532)
++...++++.++...+.+++|++||.+|||+.+|+++++|..++......+|||.+++++++.++.+.++|+...+|++.
T Consensus 81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~p~~~ 160 (238)
T TIGR02393 81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESPDDY 160 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcccHHHHhcCCCCCChHHH
Confidence 99999999999999999999999999999999999999999998888789999999977766678888888877789888
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 009567 452 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 529 (532)
Q Consensus 452 ~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~yld 529 (532)
+...++...|..+|..||++||.||.++|||++++++|++|||+.||||+++|+|++.+|++|||..+....++.|+|
T Consensus 161 ~~~~~~~~~l~~~l~~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~~~~~~~~~~ 238 (238)
T TIGR02393 161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKSFLD 238 (238)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHHHhHHHHhhC
Confidence 888888999999999999999999999999998899999999999999999999999999999999999999999975
No 12
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=6.2e-45 Score=371.08 Aligned_cols=264 Identities=27% Similarity=0.470 Sum_probs=225.6
Q ss_pred CCCChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHH
Q 009567 214 FDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSR 293 (532)
Q Consensus 214 ~~~~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Ar 293 (532)
..+.+++..|+++++++|+||.++|.+|+.+++. .++..|+
T Consensus 10 ~~~~~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~---------------------------------------~Gd~~a~ 50 (284)
T PRK06596 10 LSPEGNLDAYIQAVNKIPMLTAEEEYMLAKRLRE---------------------------------------HGDLEAA 50 (284)
T ss_pred CCCccHHHHHHHHHhccCCCCHHHHHHHHHHHHH---------------------------------------cCCHHHH
Confidence 3456799999999999999999999999887532 2346899
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhH
Q 009567 294 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI 373 (532)
Q Consensus 294 e~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~ 373 (532)
+.||..|+++|+++|++|.+.+.+++||+|||++||++|+++|||++|++|+|||+|||+++|.+++++++++|++|.+.
T Consensus 51 ~~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~p~~~ 130 (284)
T PRK06596 51 KQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTK 130 (284)
T ss_pred HHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeeeccchH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999998889999976
Q ss_pred HH--HHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHh-cCCCcccCCCCCCCCC--cchhhhcccCCCCCh
Q 009567 374 YT--LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI-TRMPLSMQQPVWADQD--TTFQEITADTGVEIP 448 (532)
Q Consensus 374 ~~--~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~-~~~~iSLD~~v~~d~~--~~l~d~i~d~~~~~p 448 (532)
.. ...++.+....+. .+++|+.+|||+.+|+++++|..++.. ....+|||.+++++++ .++.+.++|.. .+|
T Consensus 131 ~~~~~~~~~~~~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~~-~~p 207 (284)
T PRK06596 131 AQRKLFFNLRKAKKRLG--WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDKS-SDP 207 (284)
T ss_pred HHHHHHHHHHHHHHHhc--cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcCCCC-CCc
Confidence 42 3344444444443 458999999999999999999998753 3468999999865532 45778888764 467
Q ss_pred hHHHHHH----HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567 449 DISVQKQ----LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 521 (532)
Q Consensus 449 ee~~~~~----~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~ 521 (532)
++.++.. .++..|..+|+.||++||.||.+|||. + +++|++|||+.||||++||||++++|++|||..+..
T Consensus 208 ~~~~~~~~~~~~~~~~L~~al~~L~~rEr~VL~lry~~-~-~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~l~~ 282 (284)
T PRK06596 208 ADVLEEDNWEDQRRALLADALEGLDERSRDIIEARWLD-D-DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEA 282 (284)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC-C-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 7666554 357789999999999999999999973 2 799999999999999999999999999999998764
No 13
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=9.1e-45 Score=370.77 Aligned_cols=264 Identities=26% Similarity=0.451 Sum_probs=226.9
Q ss_pred hHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHH
Q 009567 218 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI 297 (532)
Q Consensus 218 d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI 297 (532)
+..+.||+++.++|+||+++|.+|+++++. .++..|++.||
T Consensus 6 ~~~~~y~~~~~~~~~l~~~~e~~L~~~~~~---------------------------------------~gd~~A~~~Lv 46 (289)
T PRK07500 6 SADRSMIRSAMKAPYLEREEEHALAYRWKD---------------------------------------HRDEDALHRII 46 (289)
T ss_pred hHHHHHHHHHhcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHH
Confidence 466789999999999999999999997642 23468999999
Q ss_pred HHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHH--
Q 009567 298 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT-- 375 (532)
Q Consensus 298 ~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~-- 375 (532)
..|+++|+++|++|.+++.+++||+|||++|||+|+++|||++|.+|+|||+||||++|.++++++++++|+|.+...
T Consensus 47 ~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~~~~~~~ 126 (289)
T PRK07500 47 SAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKA 126 (289)
T ss_pred HHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCccHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999988654
Q ss_pred HHHHHHHHHHHHHH---hcCCCCCHHHHHHHhCCCHHHHHHHHH-hcCCCcccCCCCCCCCCc--chhhhcccCCCCChh
Q 009567 376 LLSKVLEAKRLYIQ---EGNHSPDKEDLARRVGITVEKLERLIF-ITRMPLSMQQPVWADQDT--TFQEITADTGVEIPD 449 (532)
Q Consensus 376 ~l~ki~ka~~~l~~---~~gr~Pt~eEIA~~lgis~e~v~~ll~-~~~~~iSLD~~v~~d~~~--~l~d~i~d~~~~~pe 449 (532)
...++++.+..+.+ .+|+.|+.+|||+.+|+++++|..+.. ....++|||.+++++++. ++.+.+.|+.. +|+
T Consensus 127 ~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~i~d~~~-~pe 205 (289)
T PRK07500 127 LFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDSP-LPD 205 (289)
T ss_pred HHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCCCcccHHHhccCCCC-Cch
Confidence 33445555555444 689999999999999999999988753 345789999998765443 57888887653 566
Q ss_pred HHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 009567 450 ISVQK----QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 523 (532)
Q Consensus 450 e~~~~----~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~ 523 (532)
+.+.. .+....|..+|..||++||.||.+||+. ++++|++|||+.||||+++|+|++++|++|||..+..+.
T Consensus 206 ~~~~~~~~~~~~~~~l~~al~~L~~rer~vl~lr~~~--~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~~~~ 281 (289)
T PRK07500 206 EQVESSIDGERRRRWLTQALQTLNERELRIIRERRLR--EDGATLEALGEELGISKERVRQIEARALEKLRRALLSQS 281 (289)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 65443 3456678999999999999999999962 379999999999999999999999999999999987654
No 14
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=100.00 E-value=1.2e-44 Score=375.53 Aligned_cols=272 Identities=35% Similarity=0.567 Sum_probs=253.8
Q ss_pred CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHH
Q 009567 216 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 295 (532)
Q Consensus 216 ~~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~ 295 (532)
..|.++.|+++|+..|+||+++|..|+.+++. ++..|++.
T Consensus 51 ~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~----------------------------------------Gd~~A~~~ 90 (325)
T PRK05657 51 VLDATQLYLNEIGYSPLLTAEEEVYFARRALR----------------------------------------GDFAARQR 90 (325)
T ss_pred cccHHHHHHHHHhcCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHH
Confidence 46788999999999999999999999987763 34689999
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHH
Q 009567 296 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 375 (532)
Q Consensus 296 LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~ 375 (532)
||..|.++|+++|++|.+++.+++||+|||++|+|+++++||+.+|++|+|||+||||++|.++++++.+.|++|.++..
T Consensus 91 Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~~~~~ 170 (325)
T PRK05657 91 MIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVK 170 (325)
T ss_pred HHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHH
Q 009567 376 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ 455 (532)
Q Consensus 376 ~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~ 455 (532)
.++.+.++...+.+.+|+.|+.+|||..+|+++++|..++.......|+|.++..+...++.+.+.+....+|+..+...
T Consensus 171 ~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~ 250 (325)
T PRK05657 171 ELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDD 250 (325)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCCcchhhhccCCCCCCHHHHHHHH
Confidence 99989999999999999999999999999999999999998877889999998777767788888887666888888888
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhh
Q 009567 456 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGY 527 (532)
Q Consensus 456 ~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~y 527 (532)
+....|..+|..||+++|.||.+||||.+.+++|++|||+.||||+++|++++++|+++||+.+...++..+
T Consensus 251 e~~~~L~~aL~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~~~~~~~~ 322 (325)
T PRK05657 251 DMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQGLSIE 322 (325)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhCccchh
Confidence 888999999999999999999999999888999999999999999999999999999999999998887543
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=3.5e-44 Score=362.87 Aligned_cols=258 Identities=28% Similarity=0.501 Sum_probs=217.8
Q ss_pred HHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHH
Q 009567 219 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 298 (532)
Q Consensus 219 ~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~ 298 (532)
++..||++++.+|+|++++|.+|+.++.. .++..|++.||.
T Consensus 2 ~~~~yl~~~~~~~~l~~~~e~~l~~~~~~---------------------------------------~gd~~a~~~Lv~ 42 (270)
T TIGR02392 2 SLDAYIRAVNRIPMLTPEEEYQLAKRLRE---------------------------------------HGDLDAAKKLVL 42 (270)
T ss_pred hHHHHHHHHhcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHHH
Confidence 57789999999999999999999886431 234689999999
Q ss_pred HHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHH--HH
Q 009567 299 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY--TL 376 (532)
Q Consensus 299 ~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~--~~ 376 (532)
.|+++|+++|++|.+++.+++||+|||++||++|+++|||++|++|+|||+||||++|.+++++.++++|+|.+.. ..
T Consensus 43 ~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir~p~~~~~~~~ 122 (270)
T TIGR02392 43 SHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKL 122 (270)
T ss_pred HhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCceecCchHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999888899998654 33
Q ss_pred HHHHHHHHHHHHHhcCCCC-CHHHHHHHhCCCHHHHHHHHHhc-CCCcccCCCCCCCCC--cchhhhcccCCCCChhHHH
Q 009567 377 LSKVLEAKRLYIQEGNHSP-DKEDLARRVGITVEKLERLIFIT-RMPLSMQQPVWADQD--TTFQEITADTGVEIPDISV 452 (532)
Q Consensus 377 l~ki~ka~~~l~~~~gr~P-t~eEIA~~lgis~e~v~~ll~~~-~~~iSLD~~v~~d~~--~~l~d~i~d~~~~~pee~~ 452 (532)
..++.++...+. +++.| +.+|||+.+|+++++|..+.... ...+|||.+++++++ ..+.+.+.|.. .+|++.+
T Consensus 123 ~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~l~d~~-~~pe~~~ 199 (270)
T TIGR02392 123 FFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKT-SDPEDTL 199 (270)
T ss_pred HHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCCccccHHHHhcCCC-CChHHHH
Confidence 445555544442 33556 69999999999999999986533 347999999866543 25677777765 3677666
Q ss_pred HHH----HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567 453 QKQ----LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 520 (532)
Q Consensus 453 ~~~----~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~ 520 (532)
... .++..|..+|..||++||.||.+||+. ++++|++|||+.||||+++|+|++.+|++|||..+.
T Consensus 200 ~~~~~~~~~~~~L~~al~~L~~rer~vl~l~y~~--~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~l~ 269 (270)
T TIGR02392 200 EEEQWEELQRQALANALGSLDARSRRIIEARWLD--DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAALA 269 (270)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhcC--CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 543 356789999999999999999999962 368999999999999999999999999999999764
No 16
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=1.8e-43 Score=356.86 Aligned_cols=221 Identities=24% Similarity=0.391 Sum_probs=201.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 009567 291 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 370 (532)
Q Consensus 291 ~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP 370 (532)
.++++||.+|+|||++||++|.++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++++++.++||+|
T Consensus 40 ~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I~~~lr~~~~~ir~P 119 (264)
T PRK07122 40 RQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVP 119 (264)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHcCCccccC
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCCcccCCCCCCCCCc--chhhhcccCCCC
Q 009567 371 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWADQDT--TFQEITADTGVE 446 (532)
Q Consensus 371 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~--~~~~iSLD~~v~~d~~~--~l~d~i~d~~~~ 446 (532)
.++...+++++++...+.+++|+.||.+|||+.+|+++++|..++.. ...++|||.+++++++. .+.+.++
T Consensus 120 r~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~d~~~----- 194 (264)
T PRK07122 120 RRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDARAIADTLG----- 194 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCCCCcccchhccC-----
Confidence 99999999999999999999999999999999999999999998864 45689999998654332 3333332
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567 447 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 520 (532)
Q Consensus 447 ~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~ 520 (532)
+++..++..+....|..+|..||+++|.||.++|+ +++|++|||+.||||.++|++++++|+++||..++
T Consensus 195 ~~~~~~e~~~~~~~l~~~l~~L~~rer~vl~l~y~----~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l~ 264 (264)
T PRK07122 195 DVDAGLDQIENREALRPLLAALPERERTVLVLRFF----ESMTQTQIAERVGISQMHVSRLLAKTLARLRDQLE 264 (264)
T ss_pred CcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcC
Confidence 34555666677888999999999999999999998 89999999999999999999999999999999763
No 17
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=8.4e-42 Score=343.09 Aligned_cols=227 Identities=25% Similarity=0.408 Sum_probs=201.5
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhCC-CCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcccc
Q 009567 289 GNSSREKLINANLRLVVHVAKQYQGR-GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 367 (532)
Q Consensus 289 g~~Are~LI~~nlrLV~sIAkrY~~~-g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~I 367 (532)
+..|++.||..|+++|+++|++|.+. +.+++||+|||+||||+|+++|||++|++|+|||+|||+++|.++++++.++|
T Consensus 23 d~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~~v 102 (256)
T PRK07408 23 SIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTV 102 (256)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcCCee
Confidence 45899999999999999999999875 67799999999999999999999999999999999999999999999999999
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHH--hcCCCcccCCCCCCCCCc--chhhhcccC
Q 009567 368 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF--ITRMPLSMQQPVWADQDT--TFQEITADT 443 (532)
Q Consensus 368 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~--~~~~~iSLD~~v~~d~~~--~l~d~i~d~ 443 (532)
|+|.++...+++++++...+.+.+|++|+.+|||+.+|+++++|..+.. .....+|||.+++++++. .+.+.++++
T Consensus 103 r~pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~~~d~ 182 (256)
T PRK07408 103 RIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDEDGSTSLGDLLPDP 182 (256)
T ss_pred eeCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCCCccccccccCCc
Confidence 9999999999999999999999999999999999999999999999865 345688999988654332 455666655
Q ss_pred CCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567 444 GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 522 (532)
Q Consensus 444 ~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~ 522 (532)
... +.. ...+....|..+|..||+++|.||.++|+ +++|++|||+.||+|.++|++++.+|++|||..+...
T Consensus 183 ~~~-~~~--~~~~~~~~l~~~l~~L~~~~r~vl~l~y~----~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~~~ 254 (256)
T PRK07408 183 RYR-SFQ--LAQEDRIRLQQALAQLEERTREVLEFVFL----HDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQPE 254 (256)
T ss_pred ccc-hhh--hhHHHHHHHHHHHHcCCHHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhcc
Confidence 432 111 23345667999999999999999999998 8999999999999999999999999999999988654
No 18
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=100.00 E-value=6.1e-41 Score=341.58 Aligned_cols=271 Identities=35% Similarity=0.572 Sum_probs=248.5
Q ss_pred CCCChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHH
Q 009567 214 FDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSR 293 (532)
Q Consensus 214 ~~~~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Ar 293 (532)
....|.+++||.+|+.+|.||.++|.+|+..++. | +..|+
T Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~---------------g-------------------------d~~a~ 48 (285)
T TIGR02394 9 TRVADVTQLYLREIGFKPLLTAEEEIAYARRALA---------------G-------------------------DFEAR 48 (285)
T ss_pred cCcchHHHHHHHHHhccCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHH
Confidence 3467899999999999999999999999887664 3 36899
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhH
Q 009567 294 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI 373 (532)
Q Consensus 294 e~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~ 373 (532)
+.||..|.++|+++|++|.+++.+.+||+|||++|||+|+++||+.+|++|+||+.|||+.+|.+++.++.+.+++|.++
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 HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHH
Q 009567 374 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ 453 (532)
Q Consensus 374 ~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~ 453 (532)
...++.+.+..+.+.+..|+.|+.+++|..+|++++++..++......+|+|.++..+...++.+.+.++...+|++.+.
T Consensus 129 ~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~~~~pe~~~~ 208 (285)
T TIGR02394 129 IKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLVQ 208 (285)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchhhhhcCCCCCCHHHHHH
Confidence 99999988888888888999999999999999999999999988888899998876665555666666666567888888
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 009567 454 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 524 (532)
Q Consensus 454 ~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l 524 (532)
..+....|..+|..||+++|.||.++|||.+.+++|++|||+.||+|.++|++++++|+++||+.+...++
T Consensus 209 ~~e~~~~L~~al~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~~~~~ 279 (285)
T TIGR02394 209 NDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERDGV 279 (285)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 88889999999999999999999999988888999999999999999999999999999999999987654
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=9.6e-40 Score=327.50 Aligned_cols=243 Identities=27% Similarity=0.444 Sum_probs=215.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHH
Q 009567 227 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH 306 (532)
Q Consensus 227 i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~~nlrLV~s 306 (532)
.+++|+||++||.+|+.+++. ++..|++.|+..|.++|++
T Consensus 10 ~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~~~~~v~~ 49 (254)
T TIGR02850 10 TSKLPVLKNQEMRELFIRMQS----------------------------------------GDTTAREKLINGNLRLVLS 49 (254)
T ss_pred ccCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHHH
Confidence 468899999999999877653 2368999999999999999
Q ss_pred HHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHH
Q 009567 307 VAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL 386 (532)
Q Consensus 307 IAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~ 386 (532)
+|++|.+++.+++||+|||++|||+++++|||.+|.+|+||++|||++.|.++++++. .||+|.++...++++.++...
T Consensus 50 ~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~-~ir~p~~~~~~~~~~~~~~~~ 128 (254)
T TIGR02850 50 VIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDK 128 (254)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CccCchHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999965 889999999999999999999
Q ss_pred HHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCc--chhhhcccCCCCChhHHHHHHHHHHHHHHH
Q 009567 387 YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQEITADTGVEIPDISVQKQLMRQHVRNL 464 (532)
Q Consensus 387 l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~--~l~d~i~d~~~~~pee~~~~~~l~~~L~~~ 464 (532)
+.+++|+.|+.+|||+.+|+++++|..++.....+.|||.++.++++. ++.+.+.|+.. .++ ....+..|..+
T Consensus 129 l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~~~d~~~-~~~----~~~~~~~l~~~ 203 (254)
T TIGR02850 129 LISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEKN-KDS----QWLEGIALKEA 203 (254)
T ss_pred HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCCCCcchhhhhcCCccc-cHH----HHHhHHHHHHH
Confidence 999999999999999999999999999998888889999988644432 45666666432 122 22344578999
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567 465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519 (532)
Q Consensus 465 L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l 519 (532)
+..||+++|.||.++|+ +++|++|||+.||+|+++|++++.+|++|||..+
T Consensus 204 l~~L~~rer~vi~~~~~----~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~~~ 254 (254)
T TIGR02850 204 MKRLNEREKMILNMRFF----EGKTQMEVAEEIGISQAQVSRLEKAALKHMRKYV 254 (254)
T ss_pred HHcCCHHHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence 99999999999999997 8999999999999999999999999999999853
No 20
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=100.00 E-value=6e-40 Score=329.91 Aligned_cols=227 Identities=26% Similarity=0.391 Sum_probs=204.9
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHhhC---CCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhc
Q 009567 288 SGNSSREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS 364 (532)
Q Consensus 288 ~g~~Are~LI~~nlrLV~sIAkrY~~---~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~ 364 (532)
++..|++.||..|+|+|+++|++|.+ .+++++||+|||+||||+|+++|||++|++|+|||+||||++|.+++++..
T Consensus 20 ~~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~ 99 (257)
T PRK05911 20 QEIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQD 99 (257)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 34589999999999999999999862 356799999999999999999999999999999999999999999999986
Q ss_pred cccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcC--CCcccCCCCCC--CC--Ccchhh
Q 009567 365 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQPVWA--DQ--DTTFQE 438 (532)
Q Consensus 365 r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~--~~iSLD~~v~~--d~--~~~l~d 438 (532)
+ +|+++...++++.++...+.+.+|+.|+.+|||+.+|+++++|..++.... .++|||.++.. ++ +.++.+
T Consensus 100 ~---~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~~~~~~~~~l~~ 176 (257)
T PRK05911 100 W---VPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQSDDEAGLALEE 176 (257)
T ss_pred C---CCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCCCCCccccchhh
Confidence 4 899999999999999999999999999999999999999999999886554 46899987643 21 235678
Q ss_pred hcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567 439 ITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 518 (532)
Q Consensus 439 ~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~ 518 (532)
.++|.....|++.+...+....|..+|..||++||.||.++|+ +++|++|||+.||+|+++|++++.+|+++||+.
T Consensus 177 ~l~d~~~~~~~~~~~~~~~~~~l~~al~~L~~~er~vi~l~y~----e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 252 (257)
T PRK05911 177 RIADERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYYY----EELVLKEIGKILGVSESRVSQIHSKALLKLRAT 252 (257)
T ss_pred hccCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 8888766678888888888889999999999999999999998 999999999999999999999999999999998
Q ss_pred hhc
Q 009567 519 LGG 521 (532)
Q Consensus 519 l~~ 521 (532)
+..
T Consensus 253 l~~ 255 (257)
T PRK05911 253 LSA 255 (257)
T ss_pred HHh
Confidence 754
No 21
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=100.00 E-value=6e-39 Score=319.01 Aligned_cols=221 Identities=27% Similarity=0.508 Sum_probs=202.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCC-CHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccc
Q 009567 290 NSSREKLINANLRLVVHVAKQYQGRGI-SLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 368 (532)
Q Consensus 290 ~~Are~LI~~nlrLV~sIAkrY~~~g~-~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IR 368 (532)
..++ .||+.|+|||.+||++|.+++. +++||+|-|+|||++|+++|||++|.+|+|||...|+++|.+++|++. .++
T Consensus 23 ~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~LR~~~-~v~ 100 (247)
T COG1191 23 EEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKND-SVK 100 (247)
T ss_pred HHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHHHHhCC-Ccc
Confidence 5788 9999999999999999998877 999999999999999999999999999999999999999999999999 999
Q ss_pred cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcC--CCcccCCCCCCCCCcchhhhcccCCCC
Q 009567 369 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQPVWADQDTTFQEITADTGVE 446 (532)
Q Consensus 369 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~--~~iSLD~~v~~d~~~~l~d~i~d~~~~ 446 (532)
+|+.+....+++..+...+.+++||+||.+|||+.+|++.+++...+.... ..+|+|..+..+++.. .++...
T Consensus 101 vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d~~-----~~~~~~ 175 (247)
T COG1191 101 VPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDD-----VDDQIE 175 (247)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccccc-----hhhccc
Confidence 999999999999999999999999999999999999999999999987664 6788887765544433 223345
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567 447 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 521 (532)
Q Consensus 447 ~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~ 521 (532)
+|.+.++..+....|.+++..|++|||.||.+||. +++|++|||+.||||+.+|+|++++|++|||..+..
T Consensus 176 ~~~~~~~~~~~~~~l~~ai~~L~EREk~Vl~l~y~----eelt~kEI~~~LgISes~VSql~kkai~kLr~~l~~ 246 (247)
T COG1191 176 NPDDGVEKEELLEILKEAIEPLPEREKLVLVLRYK----EELTQKEIAEVLGISESRVSRLHKKAIKKLRKELNK 246 (247)
T ss_pred cchhHHHHHHHHHHHHHHHHccCHHHHHHHHHHHH----hccCHHHHHHHhCccHHHHHHHHHHHHHHHHHHhcc
Confidence 77778888888888999999999999999999998 999999999999999999999999999999998754
No 22
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=100.00 E-value=2.3e-38 Score=318.13 Aligned_cols=243 Identities=27% Similarity=0.463 Sum_probs=215.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHH
Q 009567 227 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH 306 (532)
Q Consensus 227 i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~~nlrLV~s 306 (532)
..++|+|+++|+..|+.+++. ++..|++.||..|.++|++
T Consensus 13 ~~~~~~l~~~~~~~l~~~~~~----------------------------------------gd~~a~~~l~~~~~~~v~~ 52 (258)
T PRK08215 13 TSKLPVLKNEEMRELFERMQN----------------------------------------GDKEAREKLINGNLRLVLS 52 (258)
T ss_pred CCCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHHHHHHHH
Confidence 467889999999998887653 3468999999999999999
Q ss_pred HHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHH
Q 009567 307 VAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL 386 (532)
Q Consensus 307 IAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~ 386 (532)
+|++|.+++.+.+||+|||++|||+++++|||.+|++|+||+++||++.|.++++++. .||+|.++.....++.++...
T Consensus 53 ~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~~-~vrip~~~~~~~~~~~~~~~~ 131 (258)
T PRK08215 53 VIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREK 131 (258)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-ceEecHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999985 889999999999999999999
Q ss_pred HHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCc--chhhhcccCCCCChhHHHHHHHHHHHHHHH
Q 009567 387 YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQEITADTGVEIPDISVQKQLMRQHVRNL 464 (532)
Q Consensus 387 l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~--~l~d~i~d~~~~~pee~~~~~~l~~~L~~~ 464 (532)
+.+++|+.|+.+|||+.+|+++++|..++.....+.|||.++.++++. ++.+.++++.. .++ .......+..+
T Consensus 132 l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~-~~~----~~~~~~~l~~~ 206 (258)
T PRK08215 132 LINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDEKN-KDE----NWLEEIALKEA 206 (258)
T ss_pred HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchhhhhhccCccc-cHH----HHHhHHHHHHH
Confidence 999999999999999999999999999988777888999988655433 34555555431 222 22334578899
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567 465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519 (532)
Q Consensus 465 L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l 519 (532)
+..||++++.||.++|+ +++|++|||+.||+|.++|++++++|+++||+.+
T Consensus 207 l~~L~~~er~vi~~~~~----~~~t~~eIA~~lgis~~~V~~~~~~al~kLr~~l 257 (258)
T PRK08215 207 MKKLNDREKLILNLRFF----QGKTQMEVAEEIGISQAQVSRLEKAALKHMRKYI 257 (258)
T ss_pred HHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999997 8999999999999999999999999999999876
No 23
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=100.00 E-value=3.6e-37 Score=311.16 Aligned_cols=250 Identities=20% Similarity=0.353 Sum_probs=221.8
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHH
Q 009567 227 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH 306 (532)
Q Consensus 227 i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~~nlrLV~s 306 (532)
.+++|+||.++|.+|+..++. .++..+++.|+..|.++|+.
T Consensus 6 ~~~~~~~~~~~e~~l~~~~~~---------------------------------------~~d~~a~~~l~~~y~~lv~~ 46 (268)
T PRK06288 6 SGKIPKYAQQDETELWREYKK---------------------------------------TGDPKIREYLILKYSPLVKY 46 (268)
T ss_pred cCCCccccchHHHHHHHHHHH---------------------------------------cCCHHHHHHHHHHHHHHHHH
Confidence 378999999999999987653 23468999999999999999
Q ss_pred HHHHhh-C--CCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHH
Q 009567 307 VAKQYQ-G--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEA 383 (532)
Q Consensus 307 IAkrY~-~--~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka 383 (532)
+|++|. + .+.+++||+|||++|||+++++||+.+|++|+||++|||++.|.+++++. +++|.++....++++++
T Consensus 47 ~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~---~~~p~~~~~~~~~i~~~ 123 (268)
T PRK06288 47 VAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSI---DWIPRSVRQKARQIERA 123 (268)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhc---CccCHHHHHHHHHHHHH
Confidence 999986 3 56789999999999999999999999999999999999999999999865 46899999999999999
Q ss_pred HHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCCcccCCCCCCCC---CcchhhhcccCCCCChhHHHHHHHHH
Q 009567 384 KRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQ---DTTFQEITADTGVEIPDISVQKQLMR 458 (532)
Q Consensus 384 ~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~--~~~iSLD~~v~~d~---~~~l~d~i~d~~~~~pee~~~~~~l~ 458 (532)
...+.+.+|+.||.+|||+.+|++.+++..++... ...+|||.++..++ ..++.+.++++...+|++.+...+..
T Consensus 124 ~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~l~~~~~~~~~~~pe~~~~~~e~~ 203 (268)
T PRK06288 124 IAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLESPAALNPDEIAEREEIK 203 (268)
T ss_pred HHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccCCCcccchhhhhccCCCCCCHHHHHHHHHHH
Confidence 99999999999999999999999999999988644 45789988764222 23566777777667888888888888
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567 459 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 522 (532)
Q Consensus 459 ~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~ 522 (532)
..|..+|..||+++|.||.++|+ +++|++|||+.||+|.++|++++.+|+++||.++...
T Consensus 204 ~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~~~ 263 (268)
T PRK06288 204 RVIVEAIKTLPEREKKVLILYYY----EDLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLAEI 263 (268)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999998 8999999999999999999999999999999998643
No 24
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=100.00 E-value=1.6e-36 Score=303.93 Aligned_cols=244 Identities=23% Similarity=0.356 Sum_probs=215.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHH
Q 009567 231 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQ 310 (532)
Q Consensus 231 ~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~~nlrLV~sIAkr 310 (532)
|.||++||.+|+.+++. .++..|++.|+..|.++|+.+|++
T Consensus 8 ~~l~~~~~~~li~~~~~---------------------------------------~gd~~a~~~l~~~y~~~v~~~a~~ 48 (255)
T TIGR02941 8 TNLTKEDVIQWIAEFQQ---------------------------------------NQNGEAQEKLVDHYQNLVYSIAYK 48 (255)
T ss_pred CCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHHHHhHHHHHHHHHH
Confidence 66899999888887653 123689999999999999999999
Q ss_pred hhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHh
Q 009567 311 YQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQE 390 (532)
Q Consensus 311 Y~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~ 390 (532)
|.+++.+.+||+|||++|||+++++||++.|.+|+||+++||++.|.+++++..+.+++|.++....++++++...+.+.
T Consensus 49 ~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~iri~~~~~~~~~~~~~~~~~l~~~ 128 (255)
T TIGR02941 49 YSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDH 128 (255)
T ss_pred HhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHHHHHHHHHHhcC
Q 009567 391 GNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLL 468 (532)
Q Consensus 391 ~gr~Pt~eEIA~~lgis~e~v~~ll~~~--~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L 468 (532)
+|+.|+.+|+|+.+|++.+++..++... ....|||.++..+++......+ + ...+|++.+...+....+..+|+.|
T Consensus 129 ~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~-~-~~~~~~~~~~~~e~~~~l~~~l~~L 206 (255)
T TIGR02941 129 LQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSDGSTVARL-D-SVGEVEDGYDQTERRMVLEKILPIL 206 (255)
T ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCCCcccccc-c-ccCCcchHHHHHHHHHHHHHHHHcC
Confidence 9999999999999999999998887653 4578999988765443322221 1 1224666677777778899999999
Q ss_pred CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567 469 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519 (532)
Q Consensus 469 ~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l 519 (532)
|+++|.||.++|+ +++|++|||+.||+|.++|++++.+|+++||..+
T Consensus 207 ~~~~r~ii~l~~~----~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~ 253 (255)
T TIGR02941 207 SEREKSIIHCTFE----ENLSQKETGERLGISQMHVSRLQRQAISKLKEAA 253 (255)
T ss_pred CHHHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 9999999999998 8999999999999999999999999999999865
No 25
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=100.00 E-value=1.5e-36 Score=299.58 Aligned_cols=223 Identities=29% Similarity=0.469 Sum_probs=199.3
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccc
Q 009567 287 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 366 (532)
Q Consensus 287 ~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~ 366 (532)
.++..|++.|+..|.++|+++|++|.+++.+++||+|||++|||+++++|||.+|.+|+||++|||++.|.++++++. .
T Consensus 7 ~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~~~-~ 85 (231)
T TIGR02885 7 NGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDG-I 85 (231)
T ss_pred cCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-C
Confidence 345689999999999999999999999999999999999999999999999999999999999999999999999986 8
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCc--chhhhcccCC
Q 009567 367 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQEITADTG 444 (532)
Q Consensus 367 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~--~l~d~i~d~~ 444 (532)
|++|.++....+++.++...+..++|+.||.+|||+.+|++++++..++.......|||.+++++++. ++.+.+.++.
T Consensus 86 i~~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~~ 165 (231)
T TIGR02885 86 IKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLDQIADKG 165 (231)
T ss_pred eECCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCCCcchhhhhcCCCC
Confidence 99999999999999999999999999999999999999999999999988888889999988655432 3556666543
Q ss_pred CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567 445 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519 (532)
Q Consensus 445 ~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l 519 (532)
. +++. ...+..+..+++.||+++++||.++|+ +++|++|||+.||||+++|++++++|++|||..+
T Consensus 166 ~--~~~~---~~~~~~l~~~l~~L~~~e~~i~~~~~~----~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~l 231 (231)
T TIGR02885 166 S--EDSD---WLEKIALKEAISKLDERERQIIMLRYF----KDKTQTEVANMLGISQVQVSRLEKKVLKKMKEKL 231 (231)
T ss_pred c--cHHh---HHHHHHHHHHHHcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHhC
Confidence 2 2222 223557889999999999999999998 8999999999999999999999999999999864
No 26
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=100.00 E-value=4.1e-36 Score=295.51 Aligned_cols=221 Identities=28% Similarity=0.452 Sum_probs=199.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcccccc
Q 009567 290 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 369 (532)
Q Consensus 290 ~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRl 369 (532)
..|++.||..|.++|+++|++|.+++.+.+||+|||++|||+|+++||+++|.+|+||+++||++.|.++++++.+.+++
T Consensus 2 ~~a~~~lv~~y~~~v~~~a~~~~~~~~~~eDl~Qe~~i~l~~a~~~f~~~~~~~F~ty~~~~i~~~~~~~~r~~~~~~ri 81 (227)
T TIGR02980 2 KEAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVRV 81 (227)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCcHHHHHHHHHHHHHHHHHHcCCceec
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCC--CcccCCCCCCCCC--cchhhhcccCCC
Q 009567 370 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRM--PLSMQQPVWADQD--TTFQEITADTGV 445 (532)
Q Consensus 370 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~--~iSLD~~v~~d~~--~~l~d~i~d~~~ 445 (532)
|.++...+++++++...+.+.+|+.|+.+|+|+.+|++.+++..++..... ..|||.++.++++ ..+.+.+.
T Consensus 82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~~---- 157 (227)
T TIGR02980 82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTLG---- 157 (227)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCcccccccC----
Confidence 999999999999999999999999999999999999999999998876554 8999998863322 12233322
Q ss_pred CChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567 446 EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519 (532)
Q Consensus 446 ~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l 519 (532)
+++..+...+....|..+|..||+++++||.++|+ +++|++|||+.||+|.++|+++.++|+++||+.+
T Consensus 158 -~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~y~----~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~l 226 (227)
T TIGR02980 158 -DEDDALETVEDRLALKPLLAALPERERRILLLRFF----EDKTQSEIAERLGISQMHVSRLLRRALKKLREQL 226 (227)
T ss_pred -CcchHHHhHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 34455556667778999999999999999999998 8999999999999999999999999999999865
No 27
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=2.9e-35 Score=294.54 Aligned_cols=225 Identities=24% Similarity=0.369 Sum_probs=202.3
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhC---CCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcc
Q 009567 289 GNSSREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR 365 (532)
Q Consensus 289 g~~Are~LI~~nlrLV~sIAkrY~~---~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r 365 (532)
+..|++.||..|.++|+++|++|.+ ++.+.+||+|||++|||+++++|||.+|.+|+||+++||++.|.++++++.
T Consensus 20 d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~d~lR~~~- 98 (251)
T PRK07670 20 DPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKED- 98 (251)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC-
Confidence 4589999999999999999999975 678999999999999999999999999999999999999999999999876
Q ss_pred ccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHH--hcCCCcccCCCCCCCCCc-chhhhccc
Q 009567 366 TIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF--ITRMPLSMQQPVWADQDT-TFQEITAD 442 (532)
Q Consensus 366 ~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~--~~~~~iSLD~~v~~d~~~-~l~d~i~d 442 (532)
++|.++...+++++++...+.+.+|+.|+.+|||+.+|++.++|..++. ....+.|||.++.++++. .+...+.+
T Consensus 99 --~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~ 176 (251)
T PRK07670 99 --WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDDGENVSVTIRD 176 (251)
T ss_pred --CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccCCCCcchhhhhhcC
Confidence 6999999999999999999999999999999999999999999999876 345689999988655443 23344455
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567 443 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 520 (532)
Q Consensus 443 ~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~ 520 (532)
....+|++.+...+....|..+|..||+++|+||.++|+ +++|++|||+.||+|.++|++++++|+++||.++.
T Consensus 177 ~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~ 250 (251)
T PRK07670 177 DKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFYK----EELTLTEIGQVLNLSTSRISQIHSKALFKLKKLLE 250 (251)
T ss_pred cCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 555678888888888889999999999999999999998 99999999999999999999999999999999875
No 28
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=100.00 E-value=1.7e-34 Score=289.66 Aligned_cols=243 Identities=24% Similarity=0.355 Sum_probs=214.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHH
Q 009567 231 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQ 310 (532)
Q Consensus 231 ~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~~nlrLV~sIAkr 310 (532)
|.|+++||.+|..+++. .++..|++.||..|.++|+++|++
T Consensus 8 ~~l~~~e~~~li~~~~~---------------------------------------~gd~~a~~~l~~~~~~~v~~~a~~ 48 (257)
T PRK08583 8 TKLTKEEVNKWIAEYQE---------------------------------------NQDEEAQEKLVKHYKNLVESLAYK 48 (257)
T ss_pred CcCChHHHHHHHHHHHH---------------------------------------cCCHHHHHHHHHHHHHHHHHHHHH
Confidence 77999999888876653 134689999999999999999999
Q ss_pred hhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHh
Q 009567 311 YQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQE 390 (532)
Q Consensus 311 Y~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~ 390 (532)
|.+++.+.+||+||||+|||+++++||+.+|.+|+||+++||++.|.++++++.+.+++|.++....+++.++...+...
T Consensus 49 ~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~~~i~r~~~~~~~~~~~~~~~~~~~ 128 (257)
T PRK08583 49 YSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTE 128 (257)
T ss_pred HhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHHHHHHhcCCCcCCCHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999998999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCCcccCCCCCCCCCc---chhhhcccCCCCChhHHHHHHHHHHHHHHHH
Q 009567 391 GNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQDT---TFQEITADTGVEIPDISVQKQLMRQHVRNLL 465 (532)
Q Consensus 391 ~gr~Pt~eEIA~~lgis~e~v~~ll~~~--~~~iSLD~~v~~d~~~---~l~d~i~d~~~~~pee~~~~~~l~~~L~~~L 465 (532)
.++.|+.+++|+.+|++.+++..+.... ....|+|.+++.+++. .+.+.. ..|++.+...+....+..+|
T Consensus 129 ~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~-----~~~e~~~~~~~~~~~l~~~l 203 (257)
T PRK08583 129 LQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDGSTVTLLDIV-----GQQEDGYELTEQRMILEKIL 203 (257)
T ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCCCCccchHhhhc-----CCcchhHHHHHHHHHHHHHH
Confidence 9999999999999999999998876643 3578899887654332 122222 24566666667777899999
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 521 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~ 521 (532)
..||+++|+||.++|+ +++|++|||+.||||.++|+++.++|+++||..+..
T Consensus 204 ~~L~~~~r~vl~l~~~----~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l~~ 255 (257)
T PRK08583 204 PVLSDREKSIIQCTFI----ENLSQKETGERLGISQMHVSRLQRQAIKKLREAAFL 255 (257)
T ss_pred HhCCHHHHHHHHHHHh----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 9999999999999998 899999999999999999999999999999998764
No 29
>PRK05572 sporulation sigma factor SigF; Validated
Probab=100.00 E-value=2.3e-34 Score=288.17 Aligned_cols=244 Identities=28% Similarity=0.430 Sum_probs=213.3
Q ss_pred hcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHH
Q 009567 225 WGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLV 304 (532)
Q Consensus 225 ~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~~nlrLV 304 (532)
+.-...|.||.+++.+|...++. ++..|++.|+..|.++|
T Consensus 6 ~~~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~y~~~v 45 (252)
T PRK05572 6 KNKKKKPQLKDEENKELIKKSQD----------------------------------------GDQEARDTLVEKNLRLV 45 (252)
T ss_pred ccCcCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHH
Confidence 34567899999999888776542 23689999999999999
Q ss_pred HHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHH
Q 009567 305 VHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAK 384 (532)
Q Consensus 305 ~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~ 384 (532)
+++|++|.+++.+.+||+|||++++|+++++|++.+|.+|.||+++||++.|.+++++.. .|++|.++....++++++.
T Consensus 46 ~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~~~-~~r~~~~~~~~~~~~~~~~ 124 (252)
T PRK05572 46 WSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDK 124 (252)
T ss_pred HHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CCCCCHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999998889999999999999999999874 7899999999999999999
Q ss_pred HHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCc--chhhhcccCCCCChhHHHHHHHHHHHHH
Q 009567 385 RLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQEITADTGVEIPDISVQKQLMRQHVR 462 (532)
Q Consensus 385 ~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~--~l~d~i~d~~~~~pee~~~~~~l~~~L~ 462 (532)
..+..++|+.|+.+|+|+.+|++++++..+......+.||+.++.+++.. ++.+.+.++.. + .......|.
T Consensus 125 ~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~~~---~----~~~~~~~l~ 197 (252)
T PRK05572 125 DELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITLLDQIADQSE---E----DWFDKIALK 197 (252)
T ss_pred HHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCCCCcchhhhhcCCCch---h----hHHHHHHHH
Confidence 99999999999999999999999999999888877889999887654332 23344443321 1 123356788
Q ss_pred HHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567 463 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 520 (532)
Q Consensus 463 ~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~ 520 (532)
.++..||+++++||.++|+ +++|++|||+.+|+|.++|++++++|+++||..+.
T Consensus 198 ~~l~~L~~~~~~v~~l~~~----~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l~ 251 (252)
T PRK05572 198 EAIRELDERERLIVYLRYF----KDKTQSEVAKRLGISQVQVSRLEKKILKQMKEKLD 251 (252)
T ss_pred HHHHcCCHHHHHHHHHHHh----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999997 89999999999999999999999999999998774
No 30
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=100.00 E-value=9.2e-35 Score=285.74 Aligned_cols=217 Identities=23% Similarity=0.419 Sum_probs=196.0
Q ss_pred HHHHHHHHHHHHHHHhhC---CCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchh
Q 009567 296 LINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 372 (532)
Q Consensus 296 LI~~nlrLV~sIAkrY~~---~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~ 372 (532)
|+..|.++|+++|++|.+ ++.+++||+|||++|||+++++|||++|++|+||+++||++.|.+++++.. ++|.+
T Consensus 1 L~~~~~~lv~~~a~~~~~~~~~~~~~eDl~Qe~~~~l~~a~~~fd~~~~~~f~t~~~~~i~~~~~~~lr~~~---~~p~~ 77 (224)
T TIGR02479 1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLD---WVPRS 77 (224)
T ss_pred CHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHHcC---ccCHH
Confidence 588999999999999986 789999999999999999999999999999999999999999999998865 58999
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCCcccCCCCCCC-CCcchhhhcccCCCCChh
Q 009567 373 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWAD-QDTTFQEITADTGVEIPD 449 (532)
Q Consensus 373 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~--~~~~iSLD~~v~~d-~~~~l~d~i~d~~~~~pe 449 (532)
....++++.++...+.+.+|+.|+.+|+|+.+|+++++|..++.. ....+|+|....++ +..++.+.++++...+|+
T Consensus 78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (224)
T TIGR02479 78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDKSEDPE 157 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhccccccCCHH
Confidence 999999999999999999999999999999999999999999864 34567888766543 334566667665666888
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567 450 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519 (532)
Q Consensus 450 e~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l 519 (532)
+.+...+....|..+|+.||+++|+||.++|+ +++|++|||+.||+|.++|++++++|+++||.++
T Consensus 158 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~y~----~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 223 (224)
T TIGR02479 158 EELEREELREALAEAIESLSEREQLVLSLYYY----EELNLKEIGEVLGLTESRVSQIHSQALKKLRAKL 223 (224)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHc
Confidence 88888888899999999999999999999998 8999999999999999999999999999999875
No 31
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=100.00 E-value=1.5e-34 Score=286.49 Aligned_cols=209 Identities=21% Similarity=0.335 Sum_probs=179.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhC---CCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcccccc
Q 009567 293 REKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 369 (532)
Q Consensus 293 re~LI~~nlrLV~sIAkrY~~---~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRl 369 (532)
...|+..|+|+|.++|++|.+ .+.+.+||+|||++|||+|+++|||.+| +|+||++||||++|.+++++..+ +
T Consensus 17 ~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~~---~ 92 (231)
T PRK12427 17 EGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELDW---R 92 (231)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcCC---C
Confidence 346788899999999999875 4679999999999999999999998666 89999999999999999998653 6
Q ss_pred chhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCCcccCCCCCCCCCcchhhhcccCCCCC
Q 009567 370 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWADQDTTFQEITADTGVEI 447 (532)
Q Consensus 370 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~--~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~ 447 (532)
|+++....++++++...+.+++|+.|+.+|||+.+|+++++|..++.. .....|||.+++++++.. .+.+ ..
T Consensus 93 ~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~---~~~~---~~ 166 (231)
T PRK12427 93 PRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAHND---ILQS---RD 166 (231)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCccc---ccCC---CC
Confidence 888899999999999999999999999999999999999999998764 456899999986654322 2221 12
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567 448 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 518 (532)
Q Consensus 448 pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~ 518 (532)
+++.. .....|..++..||+++|.||.++|+ +++|++|||+.||||.++|+|++++|++|||..
T Consensus 167 ~~~~~---~~~~~l~~~l~~L~~~er~vi~l~~~----~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr~~ 230 (231)
T PRK12427 167 LEENI---IIEDNLKQALSQLDEREQLILHLYYQ----HEMSLKEIALVLDLTEARICQLNKKIAQKIKSF 230 (231)
T ss_pred HHHHH---HHHHHHHHHHHcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 33222 24557899999999999999999998 899999999999999999999999999999964
No 32
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=100.00 E-value=2.8e-33 Score=277.49 Aligned_cols=225 Identities=23% Similarity=0.410 Sum_probs=198.6
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHhh---CCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhc
Q 009567 288 SGNSSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS 364 (532)
Q Consensus 288 ~g~~Are~LI~~nlrLV~sIAkrY~---~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~ 364 (532)
.|.-+++.|+..|.++|+++|++|. +++.+.+||+|||++|||+++++|||++|.+|+||+++||++.|.++++++.
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 4678999999999999999999997 6789999999999999999999999999999999999999999999999986
Q ss_pred cccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCCcccCCCCCCCCCcchhhhccc
Q 009567 365 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQDTTFQEITAD 442 (532)
Q Consensus 365 r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~--~~~iSLD~~v~~d~~~~l~d~i~d 442 (532)
+ +|.++.....++.++...+.+.+|++|+.+|||+.+|++.++|..++... ...+|++..++++++. +.. ..+
T Consensus 85 ~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~-~~~-~~~ 159 (236)
T PRK06986 85 W---VPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDS-ILV-TED 159 (236)
T ss_pred C---CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCcc-ccc-ccC
Confidence 4 68888888888889999999999999999999999999999999988753 3567888877554432 222 223
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567 443 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 521 (532)
Q Consensus 443 ~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~ 521 (532)
+...+|++.+...+....|..+|..||+++|.||.++|. +++|++|||+.||||.++|++++.+|+++||+.+..
T Consensus 160 ~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~~ 234 (236)
T PRK06986 160 HQDEDPLQQLEDEELREALVEAIESLPEREQLVLSLYYQ----EELNLKEIGAVLGVSESRVSQIHSQAIKRLRARLGE 234 (236)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHhc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 334567788888888889999999999999999999998 899999999999999999999999999999998764
No 33
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=99.96 E-value=6.6e-28 Score=238.78 Aligned_cols=210 Identities=25% Similarity=0.451 Sum_probs=171.7
Q ss_pred HHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHH
Q 009567 219 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 298 (532)
Q Consensus 219 ~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~ 298 (532)
.|..|+.+++..|+||+++|..|+..++. ++..|++.|+.
T Consensus 17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~----------------------------------------gd~~a~~~l~~ 56 (233)
T PRK05803 17 FLVSYVKNNSFPQPLSEEEERKYLELMKE----------------------------------------GDEEARNILIE 56 (233)
T ss_pred HHHHHHHHhcccCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHH
Confidence 56789999999999999999888776542 34689999999
Q ss_pred HHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHH
Q 009567 299 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS 378 (532)
Q Consensus 299 ~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ 378 (532)
.|.++|+++|.+|.+++.+.+||+|||++++|+++++||+++|.+|.||+++|+++.+.+++++..+..
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 999999999999999999999999999999999999999998999999999999999999998754210
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCC---CCcchhhhcccCCCCChhHHHHHH
Q 009567 379 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWAD---QDTTFQEITADTGVEIPDISVQKQ 455 (532)
Q Consensus 379 ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d---~~~~l~d~i~d~~~~~pee~~~~~ 455 (532)
...+++.+.+.+ ....+.+...+. .+++++.+...
T Consensus 126 -----------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 163 (233)
T PRK05803 126 -----------------------------------------KEVSLQDPIGVDKEGNEISLIDILGSE-EDDVIEQVELK 163 (233)
T ss_pred -----------------------------------------cCCCccccccCCCCcCcccHHHHccCC-CCCHHHHHHHH
Confidence 011111111111 112233333332 23567777777
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567 456 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 521 (532)
Q Consensus 456 ~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~ 521 (532)
...+.|..+|..||+++|+||.++|++.+.+++|++|||+.||+|.++|++++.+|+++||+.+..
T Consensus 164 ~~~~~l~~~l~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~~ 229 (233)
T PRK05803 164 MEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKELYR 229 (233)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 777889999999999999999999987666999999999999999999999999999999998764
No 34
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=99.93 E-value=4.3e-24 Score=210.86 Aligned_cols=199 Identities=28% Similarity=0.527 Sum_probs=156.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHH
Q 009567 228 ETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHV 307 (532)
Q Consensus 228 ~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~~nlrLV~sI 307 (532)
+..+.|++.+|..|+..++. ++..|++.|+..|.++|+++
T Consensus 25 ~~~~~~~~~~~~~li~~~~~----------------------------------------gd~~af~~l~~~y~~~v~~~ 64 (227)
T TIGR02846 25 SFPQPLSEEEEKKYLDRLKE----------------------------------------GDEEARNVLIERNLRLVAHI 64 (227)
T ss_pred hCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHHHH
Confidence 45666888888888776653 33689999999999999999
Q ss_pred HHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHH
Q 009567 308 AKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLY 387 (532)
Q Consensus 308 AkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l 387 (532)
|.+|.++..+.+||+||+++++|+++++|+++.+.+|.||+++|+++.+.+++++..+..+
T Consensus 65 ~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~Rk~~r~~~------------------- 125 (227)
T TIGR02846 65 VKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHLRALKKTKG------------------- 125 (227)
T ss_pred HHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHHHHHhcccc-------------------
Confidence 9999999999999999999999999999999988899999999999999999987642110
Q ss_pred HHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCC---CCcchhhhcccCCCCChhHHHHHHHHHHHHHHH
Q 009567 388 IQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWAD---QDTTFQEITADTGVEIPDISVQKQLMRQHVRNL 464 (532)
Q Consensus 388 ~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d---~~~~l~d~i~d~~~~~pee~~~~~~l~~~L~~~ 464 (532)
..+++.....+ ....+.+...+ ....+++.+...+..+.|..+
T Consensus 126 ---------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~ 171 (227)
T TIGR02846 126 ---------------------------------EVSLQDPIGVDKEGNEISLIDILGS-DGDSVIEQVELNLEIKKLYKK 171 (227)
T ss_pred ---------------------------------ceeccccccCCcccCcccHHHHhcC-CCCChHHHHHHHHHHHHHHHH
Confidence 01111111000 01112222222 123556666666666789999
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567 465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519 (532)
Q Consensus 465 L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l 519 (532)
|+.||+++|+||.++|.++..+++|++|||+.||+|.++|++++++|+++||+.+
T Consensus 172 i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~~ 226 (227)
T TIGR02846 172 LSVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYKEL 226 (227)
T ss_pred HHhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 9999999999999999765558999999999999999999999999999999875
No 35
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=99.93 E-value=6e-24 Score=210.23 Aligned_cols=180 Identities=28% Similarity=0.536 Sum_probs=139.9
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccc
Q 009567 289 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 368 (532)
Q Consensus 289 g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IR 368 (532)
+..|++.|+..|.++|+.+|++|.+++.+.+|++||+|+++|+++++|++..+++|.||+++++++.+.++++++.+..
T Consensus 50 d~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~d~lRk~~~~~- 128 (234)
T PRK08301 50 DEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNNKVK- 128 (234)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHHHHHHhccc-
Confidence 3589999999999999999999999999999999999999999999999988889999999999999999998764210
Q ss_pred cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCC--C-CcchhhhcccCCC
Q 009567 369 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWAD--Q-DTTFQEITADTGV 445 (532)
Q Consensus 369 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d--~-~~~l~d~i~d~~~ 445 (532)
...+++.+...+ . ...+.+...+. .
T Consensus 129 ---------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~-~ 156 (234)
T PRK08301 129 ---------------------------------------------------AEVSFDEPLNIDWDGNELLLSDVLGTD-N 156 (234)
T ss_pred ---------------------------------------------------cccccccccccccCCCcccHHHhccCc-c
Confidence 001112111100 0 01111222211 1
Q ss_pred CChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567 446 EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 521 (532)
Q Consensus 446 ~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~ 521 (532)
..++...........|..+|+.||+++|+||.++|+|...+++|++|||+.||||.++|+++.++|+++||+.+..
T Consensus 157 ~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l~~ 232 (234)
T PRK08301 157 DIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEINK 232 (234)
T ss_pred cchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 2333344445556679999999999999999999965444899999999999999999999999999999998753
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=5e-23 Score=204.18 Aligned_cols=180 Identities=30% Similarity=0.545 Sum_probs=140.9
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccc
Q 009567 289 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 368 (532)
Q Consensus 289 g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IR 368 (532)
+..|++.|+..|.+.|+.+|++|.+++.+.+|++||+++++|+++++|++..+++|.||++.++++.+.++++++.+...
T Consensus 50 d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~d~~Rk~~r~~~ 129 (234)
T TIGR02835 50 DESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILMYLRRNNKTRS 129 (234)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhccccC
Confidence 46899999999999999999999999999999999999999999999999888899999999999999999987653100
Q ss_pred cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCC---CCCCcchhhhcccCCC
Q 009567 369 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVW---ADQDTTFQEITADTGV 445 (532)
Q Consensus 369 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~---~d~~~~l~d~i~d~~~ 445 (532)
..+++.++. .+......+.. ++..
T Consensus 130 ----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~-~~~~ 156 (234)
T TIGR02835 130 ----------------------------------------------------EVSFDEPLNVDWDGNELLLSDVL-GTDS 156 (234)
T ss_pred ----------------------------------------------------cccccccccCCCCCCcchHHHhc-CCCC
Confidence 011111110 00001111111 1111
Q ss_pred CChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567 446 EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 521 (532)
Q Consensus 446 ~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~ 521 (532)
+.+++.+........|..+|..||+++|.||.++|++.+++++|++|||+.||+|..+|+++..+|+++||+.+..
T Consensus 157 ~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l~~ 232 (234)
T TIGR02835 157 DIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKEINR 232 (234)
T ss_pred CcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhhc
Confidence 2333444555556779999999999999999999976555899999999999999999999999999999998754
No 37
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=99.91 E-value=1.3e-22 Score=195.94 Aligned_cols=195 Identities=22% Similarity=0.329 Sum_probs=150.9
Q ss_pred CCHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHH
Q 009567 277 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 355 (532)
Q Consensus 277 ~~~~~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~a 355 (532)
++++.+...++.| ..|++.|+..|.++|+.+|.+|.+++.+.+|++||++++||+++.+||+.+|.+|.||++.++++.
T Consensus 9 ~~~~~l~~~~~~~d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n~ 88 (208)
T PRK08295 9 LEDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQ 88 (208)
T ss_pred CChHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHH
Confidence 4556666666555 499999999999999999999999999999999999999999999999988789999999999999
Q ss_pred HHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCC-CCCc
Q 009567 356 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWA-DQDT 434 (532)
Q Consensus 356 I~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~-d~~~ 434 (532)
+.+++++..+..+.+. ....|.+.++.+ +.+.
T Consensus 89 ~~d~~r~~~r~~~~~~-----------------------------------------------~~~~s~~~~~~~~~~~~ 121 (208)
T PRK08295 89 IITAIKTANRQKHIPL-----------------------------------------------NSYVSLDKPIYDEESDR 121 (208)
T ss_pred HHHHHHHhhhhccccc-----------------------------------------------cceeecCCcccCCccch
Confidence 9999876542111110 011233333222 2222
Q ss_pred chhhhcccCCCCChhHHHHHHHHHHHH-HHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567 435 TFQEITADTGVEIPDISVQKQLMRQHV-RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 513 (532)
Q Consensus 435 ~l~d~i~d~~~~~pee~~~~~~l~~~L-~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALk 513 (532)
.+.+.+.++...+|+..+...+....+ ..++..||+++|+||.+ |. +++|.+|||+.||+|.++|+....||++
T Consensus 122 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l-~~----e~~s~~EIA~~lgis~~tV~~~l~rar~ 196 (208)
T PRK08295 122 TLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLEL-YL----DGKSYQEIAEELNRHVKSIDNALQRVKR 196 (208)
T ss_pred hHHHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHH-HH----ccCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 344444444445677666555555555 45679999999999999 76 8999999999999999999999999999
Q ss_pred HHHHHhhcCc
Q 009567 514 RLKQSLGGKA 523 (532)
Q Consensus 514 KLR~~l~~~~ 523 (532)
+||+++....
T Consensus 197 ~Lr~~l~~~~ 206 (208)
T PRK08295 197 KLEKYLENRE 206 (208)
T ss_pred HHHHHHHhhc
Confidence 9999987653
No 38
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=99.89 E-value=1e-21 Score=188.19 Aligned_cols=191 Identities=23% Similarity=0.323 Sum_probs=146.0
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHH
Q 009567 277 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 355 (532)
Q Consensus 277 ~~~~~L~~~l~~g~-~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~a 355 (532)
|++..|...++.|+ .|++.|+..|.+.|+.+|+++.++..+.+||+||+++++|+++.+|++..|..|.||++.+|++.
T Consensus 4 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~~ 83 (198)
T TIGR02859 4 LEDEEIVELARQGNTHALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTRQ 83 (198)
T ss_pred cchHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHHH
Confidence 45677777777765 99999999999999999999999999999999999999999999999988789999999999999
Q ss_pred HHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCC-CCCc
Q 009567 356 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWA-DQDT 434 (532)
Q Consensus 356 I~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~-d~~~ 434 (532)
+.++++...+..+.+. ....|++.+... +++.
T Consensus 84 ~~~~~r~~~~~~~~~~-----------------------------------------------~~~~~~~~~~~~~~~~~ 116 (198)
T TIGR02859 84 IITAIKTATRQKHIPL-----------------------------------------------NSYVSLNKPIYDEESDR 116 (198)
T ss_pred HHHHHHHHHHhcccch-----------------------------------------------hhhcCcccccccccccc
Confidence 9888865431111000 011233332211 1122
Q ss_pred chhhhcccCCCCChhHHHHHHHHHHHHHHHHhcC-CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567 435 TFQEITADTGVEIPDISVQKQLMRQHVRNLLTLL-NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 513 (532)
Q Consensus 435 ~l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L-~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALk 513 (532)
++.+.+.+....+|++.+...+....|..+|..| ++.++.|+. +|. +++|++|||+.||+|.++|+...+||++
T Consensus 117 ~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~-~~~----~~~s~~eIA~~l~~s~~tV~~~l~r~r~ 191 (198)
T TIGR02859 117 TLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQ-SYL----DGKSYQEIACDLNRHVKSIDNALQRVKR 191 (198)
T ss_pred hHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHH-HHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3334333223346777777777778899999985 566666665 465 8999999999999999999999999999
Q ss_pred HHHHHh
Q 009567 514 RLKQSL 519 (532)
Q Consensus 514 KLR~~l 519 (532)
+||+.+
T Consensus 192 ~L~~~l 197 (198)
T TIGR02859 192 KLEKYL 197 (198)
T ss_pred HHHHhc
Confidence 999876
No 39
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=99.89 E-value=7.7e-22 Score=187.99 Aligned_cols=176 Identities=16% Similarity=0.250 Sum_probs=144.0
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHH
Q 009567 277 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 355 (532)
Q Consensus 277 ~~~~~L~~~l~~g~-~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~a 355 (532)
++++.|...++.|+ .|++.|+..|.++|+.+|++|.+++.+.+|++||+|+++|+++.+|++. +.+|.+|++..+++.
T Consensus 5 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n~ 83 (186)
T PRK05602 5 DPDEELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLNL 83 (186)
T ss_pred ccHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHHH
Confidence 45666777666665 9999999999999999999999999999999999999999999999986 457999999999999
Q ss_pred HHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 009567 356 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 435 (532)
Q Consensus 356 I~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~ 435 (532)
+.++++++.+. +.+. . .
T Consensus 84 ~~d~~R~~~~~--------------------------------------------------------~~~~-~---~--- 100 (186)
T PRK05602 84 CYDRLRRRREV--------------------------------------------------------PVED-A---P--- 100 (186)
T ss_pred HHHHHHhcCCC--------------------------------------------------------Cccc-c---c---
Confidence 99998765310 0000 0 0
Q ss_pred hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567 436 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 515 (532)
Q Consensus 436 l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKL 515 (532)
+ ..+. ...++..+...+....+..+|..||+++|+||.++|. +++|++|||+.||+|..+|++..+||+++|
T Consensus 101 --~-~~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~L 172 (186)
T PRK05602 101 --D-VPDP-APGPDAGLEARQRARRVEQALAALPERQREAIVLQYY----QGLSNIEAAAVMDISVDALESLLARGRRAL 172 (186)
T ss_pred --c-cCCC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHh----cCCCHHHHHHHhCcCHHHHHHHHHHHHHHH
Confidence 0 0011 1135555555666678999999999999999999998 899999999999999999999999999999
Q ss_pred HHHhhcCch
Q 009567 516 KQSLGGKAS 524 (532)
Q Consensus 516 R~~l~~~~l 524 (532)
|+.+...+.
T Consensus 173 r~~l~~~~~ 181 (186)
T PRK05602 173 RAQLADLPG 181 (186)
T ss_pred HHHHHhccc
Confidence 999987654
No 40
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=99.88 E-value=2.4e-21 Score=183.75 Aligned_cols=180 Identities=17% Similarity=0.253 Sum_probs=140.1
Q ss_pred HHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHH
Q 009567 280 RDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK 358 (532)
Q Consensus 280 ~~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~ 358 (532)
+.|...+..| ..|+..|+..|.++|+.+|++|.+++.+.+|++||+++++|+++.+|++.. .|.+|++..+++.+.+
T Consensus 6 ~~li~~~~~gd~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~~ 83 (187)
T TIGR02948 6 KKRIKEVRKGDENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLTID 83 (187)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHHH
Confidence 3344455544 599999999999999999999999999999999999999999999999865 5999999999999999
Q ss_pred HHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhh
Q 009567 359 AIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQE 438 (532)
Q Consensus 359 ~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d 438 (532)
++++..+... ++.....++...+.+
T Consensus 84 ~~rk~~~~~~-------------------------------------------------------~~~~~~~~~~~~~~~ 108 (187)
T TIGR02948 84 RLRKRKPDFY-------------------------------------------------------LDDEVQGTDGLTMES 108 (187)
T ss_pred HHHhhccccc-------------------------------------------------------ccccccCcccccccc
Confidence 9876432100 000000000111111
Q ss_pred hcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567 439 ITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 518 (532)
Q Consensus 439 ~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~ 518 (532)
...+. .+.|++.+...+....+..+|..|||++|.||.++|. +++|++|||+.||+|.++|++.+.||+++||..
T Consensus 109 ~~~~~-~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 109 QLAAD-EAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYM----EDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred ccccC-cCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 11111 2356666666677778999999999999999999988 899999999999999999999999999999998
Q ss_pred hhc
Q 009567 519 LGG 521 (532)
Q Consensus 519 l~~ 521 (532)
+..
T Consensus 184 l~~ 186 (187)
T TIGR02948 184 LRH 186 (187)
T ss_pred hhc
Confidence 753
No 41
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=99.88 E-value=4.1e-21 Score=183.42 Aligned_cols=171 Identities=23% Similarity=0.317 Sum_probs=137.9
Q ss_pred HHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCC----CCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHH
Q 009567 281 DLKSELHSG-NSSREKLINANLRLVVHVAKQYQGR----GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 355 (532)
Q Consensus 281 ~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~----g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~a 355 (532)
.|...+..| ..|++.|+..|.+.|+.+|.++.++ +.+.+|++||+++++|+++.+|++. +..|.+|++..+++.
T Consensus 13 ~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~n~ 91 (189)
T PRK09648 13 ALVAEAVAGDRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAAHK 91 (189)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHHHH
Confidence 355555555 4999999999999999999998765 3689999999999999999999864 457999999999999
Q ss_pred HHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 009567 356 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 435 (532)
Q Consensus 356 I~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~ 435 (532)
+.++++++.+.... ..+. +
T Consensus 92 ~~d~~r~~~r~~~~-----------------------------------------------------~~~~-~------- 110 (189)
T PRK09648 92 VADAHRAAGRDKAV-----------------------------------------------------PTEE-V------- 110 (189)
T ss_pred HHHHHHHhCCCccc-----------------------------------------------------cccc-c-------
Confidence 99999876531100 0000 0
Q ss_pred hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567 436 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 515 (532)
Q Consensus 436 l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKL 515 (532)
.+... ...+|++.+...+..+.|..+|..||+++|+||.++|+ +++|++|||+.||+|..+|++...||+++|
T Consensus 111 -~~~~~--~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~L 183 (189)
T PRK09648 111 -PERPS--DDAGPEERALRSESSNRMRELLDTLPEKQREILILRVV----VGLSAEETAEAVGSTPGAVRVAQHRALARL 183 (189)
T ss_pred -ccccc--cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 00000 11256666666777788999999999999999999998 899999999999999999999999999999
Q ss_pred HHHhh
Q 009567 516 KQSLG 520 (532)
Q Consensus 516 R~~l~ 520 (532)
|+.+.
T Consensus 184 r~~l~ 188 (189)
T PRK09648 184 RAEIE 188 (189)
T ss_pred HHHhc
Confidence 99864
No 42
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=99.88 E-value=2.9e-21 Score=183.20 Aligned_cols=180 Identities=15% Similarity=0.233 Sum_probs=141.7
Q ss_pred HHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHH
Q 009567 280 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK 358 (532)
Q Consensus 280 ~~L~~~l~~g~-~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~ 358 (532)
+.|...++.|+ .+++.++..|.++|+++|+++.++..+++|++||++++||+++++|++.. .|.+|++..+++.+.+
T Consensus 6 ~~li~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~~~d 83 (187)
T PRK09641 6 KRLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNLTID 83 (187)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHHHHH
Confidence 44555555554 99999999999999999999999999999999999999999999999853 7999999999999999
Q ss_pred HHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhh
Q 009567 359 AIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQE 438 (532)
Q Consensus 359 ~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d 438 (532)
++++..+.. +++.....++.....+
T Consensus 84 ~~R~~~~~~-------------------------------------------------------~~~~~~~~~~~~~~~~ 108 (187)
T PRK09641 84 RLRKRKPDY-------------------------------------------------------YLDAEVAGTEGLTMYS 108 (187)
T ss_pred HHHhcCccc-------------------------------------------------------cccccccCCcchhhhc
Confidence 988754210 0011110111111111
Q ss_pred hcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567 439 ITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 518 (532)
Q Consensus 439 ~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~ 518 (532)
.+.+. ..+|++.+...+....+..+|..||+++++||.++|. ++++++|||+.||||.++|++..+||+++||+.
T Consensus 109 ~~~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~----~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 109 QLAAD-DALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYI----EDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred ccccC-cCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHh----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 11111 2246666677777778999999999999999999998 899999999999999999999999999999998
Q ss_pred hhc
Q 009567 519 LGG 521 (532)
Q Consensus 519 l~~ 521 (532)
+..
T Consensus 184 l~~ 186 (187)
T PRK09641 184 LRH 186 (187)
T ss_pred Hhc
Confidence 753
No 43
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=99.88 E-value=1.8e-21 Score=186.65 Aligned_cols=181 Identities=18% Similarity=0.241 Sum_probs=146.0
Q ss_pred CCHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHH
Q 009567 277 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 355 (532)
Q Consensus 277 ~~~~~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~a 355 (532)
+++..+...+..| ..|++.|+..|.+.|+++|+++.++..+.+|++||+++++|+++++|++. ..|.+|++.++++.
T Consensus 11 ~~~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~--~~f~~wl~~i~~n~ 88 (194)
T PRK12513 11 ASDEALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPR--ARFRTWLYQIARNL 88 (194)
T ss_pred CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CchHHHHHHHHHHH
Confidence 3456667666666 49999999999999999999999999999999999999999999999974 36999999999999
Q ss_pred HHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 009567 356 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 435 (532)
Q Consensus 356 I~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~ 435 (532)
+.+++++..+....+. +. +. .
T Consensus 89 ~~~~~R~~~~~~~~~~-----------------------------------------------------~~----~~--~ 109 (194)
T PRK12513 89 LIDHWRRHGARQAPSL-----------------------------------------------------DA----DE--Q 109 (194)
T ss_pred HHHHHHHhcccccccc-----------------------------------------------------cc----ch--h
Confidence 9999987653211100 00 00 0
Q ss_pred hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567 436 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 515 (532)
Q Consensus 436 l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKL 515 (532)
+ ....+ ....|+..+...+....+..+|..||+++|.||.++|. +++|++|||+.||+|.++|+++..||+++|
T Consensus 110 ~-~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~L 183 (194)
T PRK12513 110 L-HALAD-DGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREH----GDLELEEIAELTGVPEETVKSRLRYALQKL 183 (194)
T ss_pred h-hhcCC-CCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeehc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 0 00011 12256666666677788999999999999999999998 899999999999999999999999999999
Q ss_pred HHHhhcCch
Q 009567 516 KQSLGGKAS 524 (532)
Q Consensus 516 R~~l~~~~l 524 (532)
|..+...++
T Consensus 184 r~~l~~~~~ 192 (194)
T PRK12513 184 RELLAEEVA 192 (194)
T ss_pred HHHHHHhhc
Confidence 999876554
No 44
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=99.88 E-value=2.7e-21 Score=185.94 Aligned_cols=176 Identities=16% Similarity=0.189 Sum_probs=139.7
Q ss_pred CHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHH
Q 009567 278 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 356 (532)
Q Consensus 278 ~~~~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI 356 (532)
+...|...+..| ..|++.|+..|.++|+++|.+|.++..+.+|++||+++++|+++++||+.+| .|.+|++..+++.+
T Consensus 16 ~~~~li~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n~~ 94 (194)
T PRK09646 16 DLDALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHRRA 94 (194)
T ss_pred cHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHHHH
Confidence 345566665555 4999999999999999999999999999999999999999999999998765 69999999999999
Q ss_pred HHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 009567 357 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 436 (532)
Q Consensus 357 ~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l 436 (532)
.++++++.+..+. +..... .
T Consensus 95 ~d~~r~~~~~~~~-------------------------------------------------------~~~~~~---~-- 114 (194)
T PRK09646 95 VDRVRSEQAASQR-------------------------------------------------------EVRYGA---R-- 114 (194)
T ss_pred HHHHHhhcccccc-------------------------------------------------------cccccc---c--
Confidence 9999876521100 000000 0
Q ss_pred hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567 437 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 437 ~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR 516 (532)
+. +.....+++.+...+..+.|..+|..||+++|+||.++|. +++|++|||+.||+|..+|+++++||+++||
T Consensus 115 -~~--~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr 187 (194)
T PRK09646 115 -NV--DPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYY----GGLTYREVAERLAVPLGTVKTRMRDGLIRLR 187 (194)
T ss_pred -cc--cccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCChHhHHHHHHHHHHHHH
Confidence 00 0011123344444555678999999999999999999998 8999999999999999999999999999999
Q ss_pred HHhhc
Q 009567 517 QSLGG 521 (532)
Q Consensus 517 ~~l~~ 521 (532)
..+..
T Consensus 188 ~~l~~ 192 (194)
T PRK09646 188 DCLGV 192 (194)
T ss_pred HHhcc
Confidence 98854
No 45
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=99.87 E-value=1e-20 Score=177.42 Aligned_cols=172 Identities=19% Similarity=0.236 Sum_probs=137.2
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccc
Q 009567 287 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 366 (532)
Q Consensus 287 ~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~ 366 (532)
.++..|++.|+..|.++|+.++++|.+++.+.+|++||++++||+++++|+ .+.+|.+|++..+++.+.+++++..+.
T Consensus 6 ~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~r~~~~~ 83 (182)
T PRK09652 6 RGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYLRKQGRR 83 (182)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHHHcccCC
Confidence 345689999999999999999999999999999999999999999999999 456899999999999999998775432
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCC
Q 009567 367 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE 446 (532)
Q Consensus 367 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~ 446 (532)
...+ +++ ..+.++....+...+ ..
T Consensus 84 ~~~~----------------------------------------------------~~~--~~~~~~~~~~~~~~~--~~ 107 (182)
T PRK09652 84 PPAS----------------------------------------------------DVD--AEEAEDFDLADALRD--IS 107 (182)
T ss_pred CCcc----------------------------------------------------ccc--ccccccccccccccc--cc
Confidence 1100 000 000000011111111 12
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567 447 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 520 (532)
Q Consensus 447 ~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~ 520 (532)
+|++.+...+....+..+|..|||++|+||.++|. .++|.+|||+.||+|..+|++.+.+|+++||+.+.
T Consensus 108 ~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 177 (182)
T PRK09652 108 TPENELLSAELEQRVRAAIESLPEELRTAITLREI----EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQ 177 (182)
T ss_pred ChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 56666777777788999999999999999999987 89999999999999999999999999999999875
No 46
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=99.87 E-value=1.1e-20 Score=176.23 Aligned_cols=163 Identities=20% Similarity=0.344 Sum_probs=134.3
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcccc
Q 009567 288 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 367 (532)
Q Consensus 288 ~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~I 367 (532)
++..|++.|+..|.+.+++++.++.++..+.+|++||+++.+|+++++|+...+ .|.+|++..+++.+.++++++.+..
T Consensus 8 ~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R~~~~~~ 86 (170)
T TIGR02952 8 REEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFRGSKRHP 86 (170)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 446999999999999999999999988899999999999999999999997555 8999999999999999998765311
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCC
Q 009567 368 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 447 (532)
Q Consensus 368 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~ 447 (532)
.. +.+. ..+... ...+
T Consensus 87 ~~-----------------------------------------------------~~~~---------~~~~~~--~~~~ 102 (170)
T TIGR02952 87 LF-----------------------------------------------------SLDV---------FKELLS--NEPN 102 (170)
T ss_pred CC-----------------------------------------------------cHHH---------HhhcCC--CCCC
Confidence 00 0000 000000 1124
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567 448 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519 (532)
Q Consensus 448 pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l 519 (532)
|++.+...+....+..+|..|||++|+||.++|. +|+|++|||+.||+|..+|++...||+++||+.+
T Consensus 103 ~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~l 170 (170)
T TIGR02952 103 PEEAILKEEANEKLLKALKILTPKQQHVIALRFG----QNLPIAEVARILGKTEGAVKILQFRAIKKLARQM 170 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence 5666666667788999999999999999999998 8999999999999999999999999999999864
No 47
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=1.3e-20 Score=180.48 Aligned_cols=175 Identities=23% Similarity=0.288 Sum_probs=137.7
Q ss_pred CHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHH
Q 009567 278 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 356 (532)
Q Consensus 278 ~~~~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI 356 (532)
+...|...+..| ..|++.|+..|.+.|+.+++++.++..+.+|++||+++++|+. ..|++..+ .|.||++.++++.+
T Consensus 15 ~~~~l~~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~ 92 (194)
T PRK12519 15 SDAELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRA 92 (194)
T ss_pred cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHH
Confidence 345566655555 5999999999999999999999999899999999999999976 67887654 79999999999999
Q ss_pred HHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 009567 357 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 436 (532)
Q Consensus 357 ~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l 436 (532)
.++++++.+..... .+. +. .
T Consensus 93 ~d~~Rk~~~~~~~~---------------------------~~~------------------------~~--------~- 112 (194)
T PRK12519 93 IDRLRSRRSRQRLL---------------------------ERW------------------------QQ--------E- 112 (194)
T ss_pred HHHHHhcccccchh---------------------------hhh------------------------hh--------h-
Confidence 99998765311000 000 00 0
Q ss_pred hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567 437 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 437 ~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR 516 (532)
...+.....+++.+...+....|..+|..||+++++||.++|. +++|++|||+.||+|.++|++++.||+++||
T Consensus 113 --~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 186 (194)
T PRK12519 113 --LLGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYY----EGLSQSEIAKRLGIPLGTVKARARQGLLKLR 186 (194)
T ss_pred --hcccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 0000011245555555666677899999999999999999998 8999999999999999999999999999999
Q ss_pred HHhh
Q 009567 517 QSLG 520 (532)
Q Consensus 517 ~~l~ 520 (532)
+.+.
T Consensus 187 ~~l~ 190 (194)
T PRK12519 187 ELLQ 190 (194)
T ss_pred HHHH
Confidence 9875
No 48
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=99.86 E-value=1.9e-20 Score=178.00 Aligned_cols=176 Identities=18% Similarity=0.270 Sum_probs=135.2
Q ss_pred CHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHH
Q 009567 278 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 356 (532)
Q Consensus 278 ~~~~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI 356 (532)
++..+...++.| ..|++.|+..|.+.|+.++++|.+++.+.+|++||+++++|+++++|++.. ..|.+|++..+++.+
T Consensus 9 ~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~-~~~~~wl~~ia~n~~ 87 (186)
T PRK13919 9 SDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRR-GSARAWLLALAHHAA 87 (186)
T ss_pred CHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCccc-cchHHHHHHHHHHHH
Confidence 456666666555 499999999999999999999999999999999999999999999998754 369999999999999
Q ss_pred HHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 009567 357 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 436 (532)
Q Consensus 357 ~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l 436 (532)
.+++++..+..+ ..+.+ ......
T Consensus 88 ~d~~rk~~~~~~----------------------------------------------------~~~~~-----~~~~~~ 110 (186)
T PRK13919 88 VDHVRRRAARPQ----------------------------------------------------PLEPD-----EREPEA 110 (186)
T ss_pred HHHHHhhhcccc----------------------------------------------------ccccc-----cccccc
Confidence 999977542100 00000 000000
Q ss_pred hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567 437 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 437 ~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR 516 (532)
.+ .+ .+............|..+|..||+++|+||.++|. +++|++|||+.||+|..+|+..++||+++||
T Consensus 111 ~~-~~-----~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr 180 (186)
T PRK13919 111 FD-LP-----GPGLDEEGHLDRTRLGRALKALSPEERRVIEVLYY----QGYTHREAAQLLGLPLGTLKTRARRALSRLK 180 (186)
T ss_pred cc-CC-----CccccHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 00 00 11111122233456889999999999999999998 9999999999999999999999999999999
Q ss_pred HHhhc
Q 009567 517 QSLGG 521 (532)
Q Consensus 517 ~~l~~ 521 (532)
..+..
T Consensus 181 ~~l~~ 185 (186)
T PRK13919 181 EVLRE 185 (186)
T ss_pred HHhcC
Confidence 98753
No 49
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=99.86 E-value=1.4e-20 Score=173.18 Aligned_cols=151 Identities=20% Similarity=0.237 Sum_probs=123.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcccccc
Q 009567 290 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 369 (532)
Q Consensus 290 ~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRl 369 (532)
..|++.|+..|.++|+.+++++ +...+.+|++|||++++|+++++|++..| .|.+|++..+++.+.++++++.+..
T Consensus 3 ~~af~~l~~~y~~~l~~~~~~~-~~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~~~~-- 78 (154)
T PRK06759 3 PATFTEAVVLYEGLIVNQIKKL-GIYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFAVQ-- 78 (154)
T ss_pred cccHHHHHHHHHHHHHHHHHHh-CCcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHHhhc--
Confidence 4689999999999999999886 56678999999999999999999998766 7999999999999999998753100
Q ss_pred chhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChh
Q 009567 370 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD 449 (532)
Q Consensus 370 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pe 449 (532)
. .. . .+ +.|+
T Consensus 79 ----------------------~---------------------------~~-~------~~--------------~~~~ 88 (154)
T PRK06759 79 ----------------------E---------------------------KC-V------CV--------------GEYE 88 (154)
T ss_pred ----------------------c---------------------------cc-c------cc--------------CCCc
Confidence 0 00 0 00 0111
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567 450 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 518 (532)
Q Consensus 450 e~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~ 518 (532)
+.....+....|..+|..||+++|+||.++|+ +++|.+|||+.||+|..+|+++..||+++||+.
T Consensus 89 ~~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~~----~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 89 DHFHFEDVEMKVKDFMSVLDEKEKYIIFERFF----VGKTMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred ccccHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 12222334567899999999999999999998 999999999999999999999999999999974
No 50
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=2.7e-20 Score=176.11 Aligned_cols=173 Identities=14% Similarity=0.158 Sum_probs=137.7
Q ss_pred CHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHH
Q 009567 278 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 356 (532)
Q Consensus 278 ~~~~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI 356 (532)
+...|...+..| ..|+..|+..|.+.|+.+|.+|.++..+.+|++||+++++|+++++|++.. ..|.||++..+++.+
T Consensus 5 ~~~~li~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~-~~~~~wl~~ia~n~~ 83 (179)
T PRK12514 5 DIEKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSG-LSPMTWLITIARNHA 83 (179)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHH
Confidence 344555555555 589999999999999999999999999999999999999999999999754 369999999999999
Q ss_pred HHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 009567 357 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 436 (532)
Q Consensus 357 ~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l 436 (532)
.+++++..+.. . .++. .
T Consensus 84 ~d~~R~~~~~~-~-----------------------------------------------------~~~~------~--- 100 (179)
T PRK12514 84 IDRLRARKAVA-V-----------------------------------------------------DIDE------A--- 100 (179)
T ss_pred HHHHHhcCCcc-c-----------------------------------------------------cccc------c---
Confidence 99997654210 0 0000 0
Q ss_pred hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567 437 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 437 ~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR 516 (532)
.+ ..+. ...|++.+...+....|..+|..||+++|+||.++|. +|+|++|||+.||+|..+|++.+.||+++||
T Consensus 101 ~~-~~~~-~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 174 (179)
T PRK12514 101 HD-LADP-SPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYL----EGLSYKELAERHDVPLNTMRTWLRRSLLKLR 174 (179)
T ss_pred hh-cccc-CCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCChHHHHHHHHHHHHHHH
Confidence 00 0001 1245555554555567899999999999999999998 8999999999999999999999999999999
Q ss_pred HHhh
Q 009567 517 QSLG 520 (532)
Q Consensus 517 ~~l~ 520 (532)
+++.
T Consensus 175 ~~l~ 178 (179)
T PRK12514 175 ECLS 178 (179)
T ss_pred HHhc
Confidence 9874
No 51
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=99.86 E-value=3.1e-20 Score=177.82 Aligned_cols=175 Identities=14% Similarity=0.181 Sum_probs=141.6
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCC---CCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHH
Q 009567 277 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRG---ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV 352 (532)
Q Consensus 277 ~~~~~L~~~l~~g~-~Are~LI~~nlrLV~sIAkrY~~~g---~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wI 352 (532)
++++.|+..+..|+ .|++.|+..|.+.|+.++.++.+++ .+.+|++||+++++|+++++|++..+ .|.||++..+
T Consensus 3 ~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~ia 81 (189)
T PRK06811 3 INEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAIS 81 (189)
T ss_pred CcHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHH
Confidence 45667777777765 8999999999999999999998863 46899999999999999999997654 7999999999
Q ss_pred HHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCC
Q 009567 353 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQ 432 (532)
Q Consensus 353 r~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~ 432 (532)
++.+.++++++.+.... .+.+.
T Consensus 82 rn~~~d~~rk~~~~~~~----------------------------------------------------~~~~~------ 103 (189)
T PRK06811 82 KYKAIDYKRKLTKNNEI----------------------------------------------------DSIDE------ 103 (189)
T ss_pred HHHHHHHHHHhcccccc----------------------------------------------------ccchh------
Confidence 99999999876531100 00000
Q ss_pred CcchhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567 433 DTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 512 (532)
Q Consensus 433 ~~~l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rAL 512 (532)
. .. ....+|++.+...+....|..+|..|||++|.||.++|. +++|.+|||+.||+|..+|++.+.||+
T Consensus 104 ~------~~-~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIAe~lgis~~~V~~~l~Ra~ 172 (189)
T PRK06811 104 F------IL-ISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYL----LGEKIEEIAKKLGLTRSAIDNRLSRGR 172 (189)
T ss_pred h------hh-cccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----ccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 0 00 011245666666677778999999999999999999997 899999999999999999999999999
Q ss_pred HHHHHHhhc
Q 009567 513 YRLKQSLGG 521 (532)
Q Consensus 513 kKLR~~l~~ 521 (532)
++||...-+
T Consensus 173 ~~Lr~~~~~ 181 (189)
T PRK06811 173 KKLQKNKLN 181 (189)
T ss_pred HHHHHcccC
Confidence 999986543
No 52
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=99.86 E-value=3.9e-20 Score=175.86 Aligned_cols=181 Identities=16% Similarity=0.210 Sum_probs=141.2
Q ss_pred CHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHH
Q 009567 278 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 356 (532)
Q Consensus 278 ~~~~L~~~l~~g~-~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI 356 (532)
++..|...+..|+ .+++.|+..|.+.|+.+|+++.+...+.+|++||+++++|+++++|++. ..|.+|++...++.+
T Consensus 6 ~d~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~~ 83 (190)
T TIGR02939 6 LDLELVERVQRGEKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNTA 83 (190)
T ss_pred cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHHH
Confidence 4556666666554 8999999999999999999999999999999999999999999999975 369999999999999
Q ss_pred HHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 009567 357 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 436 (532)
Q Consensus 357 ~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l 436 (532)
.+++++..+..... ..+.+. ...+
T Consensus 84 ~~~~r~~~r~~~~~--------------------------------------------------~~~~~~------~~~~ 107 (190)
T TIGR02939 84 KNHLVAQGRRPPTS--------------------------------------------------DVEIED------AEHF 107 (190)
T ss_pred HHHHHHhccCCCcc--------------------------------------------------cccccc------hhhh
Confidence 99887554211000 000000 0000
Q ss_pred hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567 437 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 437 ~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR 516 (532)
.+........+|++.+...+....|..+|..||+++|+||.++|. +++|++|||+.||+|..+|++..+||+++||
T Consensus 108 ~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr 183 (190)
T TIGR02939 108 EGADRLREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLREL----EGLSYEDIARIMDCPVGTVRSRIFRAREAIA 183 (190)
T ss_pred cccccccccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhhh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 000000011256666666677788999999999999999999997 8999999999999999999999999999999
Q ss_pred HHhh
Q 009567 517 QSLG 520 (532)
Q Consensus 517 ~~l~ 520 (532)
+++.
T Consensus 184 ~~l~ 187 (190)
T TIGR02939 184 IRLR 187 (190)
T ss_pred HHhh
Confidence 9886
No 53
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=4.2e-20 Score=182.84 Aligned_cols=173 Identities=18% Similarity=0.235 Sum_probs=137.9
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcccc
Q 009567 288 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 367 (532)
Q Consensus 288 ~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~I 367 (532)
++..|++.|+..|.+.|+++|+++.+.+.+.+|++||+++++|+++++|++. ..|.+|++..+++.+.+++++..+..
T Consensus 27 gd~~a~~~l~~~y~~~l~~~a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~Rk~~r~~ 104 (231)
T PRK11922 27 GDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNEALGRLRRRRRLV 104 (231)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHHHHHHHHhhcccc
Confidence 3468999999999999999999999999999999999999999999999985 47999999999999999988765322
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCC
Q 009567 368 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 447 (532)
Q Consensus 368 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~ 447 (532)
.++. . . +..... ++ ...... ....+
T Consensus 105 ~~~~----------------------------~----------------------~-~~~~~~-~~--~~~~~~-~~~~~ 129 (231)
T PRK11922 105 NLAE----------------------------M----------------------V-MASTIA-GG--ERTPLA-DPAED 129 (231)
T ss_pred cchh----------------------------c----------------------c-cccccc-cc--cccccC-cccCC
Confidence 1100 0 0 000000 00 000011 11235
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567 448 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 521 (532)
Q Consensus 448 pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~ 521 (532)
|++.+...+..+.|..+|..||+++|+||.++|. +++|++|||+.||+|.++|++.+.||+++||+.+..
T Consensus 130 ~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~~ 199 (231)
T PRK11922 130 PERAAARREIRALLERAIDALPDAFRAVFVLRVV----EELSVEETAQALGLPEETVKTRLHRARRLLRESLAR 199 (231)
T ss_pred hHHHHHHHHHHHHHHHHHHhCCHHHhhhheeehh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 6677777777888999999999999999999987 899999999999999999999999999999999865
No 54
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=99.85 E-value=5.9e-20 Score=175.85 Aligned_cols=180 Identities=15% Similarity=0.203 Sum_probs=140.5
Q ss_pred HHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHH
Q 009567 279 CRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR 357 (532)
Q Consensus 279 ~~~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~ 357 (532)
++.|...++.| ..+++.|+..|.+.|+.+++++.++..+.+|++||+++++|+++.+|++.. .|.+|++..+++.+.
T Consensus 7 ~~~ll~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~~ 84 (193)
T PRK11923 7 DQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTAK 84 (193)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHHH
Confidence 44555555555 599999999999999999999999989999999999999999999999864 499999999999999
Q ss_pred HHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchh
Q 009567 358 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ 437 (532)
Q Consensus 358 ~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~ 437 (532)
++++++.+.... ....++.....++.
T Consensus 85 d~~rk~~~~~~~--------------------------------------------------~~~~~~~~~~~~~~---- 110 (193)
T PRK11923 85 NHLVSRGRRPPD--------------------------------------------------SDVSSEDAEFYDGD---- 110 (193)
T ss_pred HHHHHhcCCCcc--------------------------------------------------ccccccchhhhccc----
Confidence 998765421100 00000000000000
Q ss_pred hhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 438 EITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 438 d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
..+. ....|++.+...+..+.+..+|..||+++|.||.++|. +|+|.+|||+.||+|..+|++...||+++||.
T Consensus 111 ~~~~--~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 184 (193)
T PRK11923 111 HALK--DIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREF----DGLSYEDIASVMQCPVGTVRSRIFRAREAIDK 184 (193)
T ss_pred cccc--CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 0011 12356666667777788999999999999999999987 89999999999999999999999999999999
Q ss_pred Hhh
Q 009567 518 SLG 520 (532)
Q Consensus 518 ~l~ 520 (532)
++.
T Consensus 185 ~l~ 187 (193)
T PRK11923 185 ALQ 187 (193)
T ss_pred HHH
Confidence 886
No 55
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=5.3e-20 Score=177.26 Aligned_cols=177 Identities=19% Similarity=0.211 Sum_probs=143.0
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHH
Q 009567 277 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 355 (532)
Q Consensus 277 ~~~~~L~~~l~~g~-~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~a 355 (532)
+++..|+..+..|+ .|++.|+..|.+.|+.+|.++.++..+.+|++||+++++|+.+.+|++.. ..|.+|++..+++.
T Consensus 11 ~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~n~ 89 (196)
T PRK12524 11 VSDEALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVCNL 89 (196)
T ss_pred cCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHHHHH
Confidence 35667777776664 99999999999999999999999999999999999999999999998533 47999999999999
Q ss_pred HHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 009567 356 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 435 (532)
Q Consensus 356 I~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~ 435 (532)
+.++++++.+.. ..++. . .
T Consensus 90 ~~d~~Rk~~~~~------------------------------------------------------~~~~~-~---~--- 108 (196)
T PRK12524 90 CTDRLRRRRRAS------------------------------------------------------VDLDD-A---P--- 108 (196)
T ss_pred HHHHHHhhcCCC------------------------------------------------------CCccc-c---c---
Confidence 999987653200 00000 0 0
Q ss_pred hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567 436 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 515 (532)
Q Consensus 436 l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKL 515 (532)
+. .+. ...+++.+...+....|..+|+.||+++|+||.|+|. ++++++|||+.||||..+|+++++||+++|
T Consensus 109 --~~-~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~~----~g~s~~eIA~~lgis~~tV~~~l~Ra~~~L 180 (196)
T PRK12524 109 --EP-ADA-APGAEEALIEGDRMRALDAALAALPERQRQAVVLRHI----EGLSNPEIAEVMEIGVEAVESLTARGKRAL 180 (196)
T ss_pred --cc-ccc-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 00 011 1235555666667778999999999999999999998 899999999999999999999999999999
Q ss_pred HHHhhcCc
Q 009567 516 KQSLGGKA 523 (532)
Q Consensus 516 R~~l~~~~ 523 (532)
|.++...+
T Consensus 181 r~~l~~~~ 188 (196)
T PRK12524 181 AALLAGQR 188 (196)
T ss_pred HHHHHhcc
Confidence 99987543
No 56
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=99.85 E-value=2.3e-20 Score=178.52 Aligned_cols=173 Identities=20% Similarity=0.290 Sum_probs=136.5
Q ss_pred cCCHHHHHHHHhh----cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHH
Q 009567 276 GLSCRDLKSELHS----GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 351 (532)
Q Consensus 276 g~~~~~L~~~l~~----g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~w 351 (532)
.++++.|+..++. +..|++.|+..|.+.|+++|.+|.++..+.+|++||+++.+|+++++|++. ..|.+|++.+
T Consensus 7 ~~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~~--~~~~~wl~~i 84 (188)
T PRK09640 7 ELNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLYSI 84 (188)
T ss_pred CCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcCC--CcchHHHHHH
Confidence 4667778877764 469999999999999999999999999999999999999999999999863 4799999999
Q ss_pred HHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCC
Q 009567 352 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWAD 431 (532)
Q Consensus 352 Ir~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d 431 (532)
+++.+.+++++..+.... . .+...
T Consensus 85 a~n~~~d~~R~~~~~~~~--------------------------~---------------------------~~~~~--- 108 (188)
T PRK09640 85 TYNECITQYRKERRKRRL--------------------------M---------------------------DALSL--- 108 (188)
T ss_pred HHHHHHHHHHHhcccccC--------------------------c---------------------------chhhh---
Confidence 999999999864421000 0 00000
Q ss_pred CCcchhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009567 432 QDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 511 (532)
Q Consensus 432 ~~~~l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rA 511 (532)
+...++. ++.....+....|..+|..||+++|+||.++|. +++|++|||+.||||..+|+..+.||
T Consensus 109 ------~~~~~~~----~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra 174 (188)
T PRK09640 109 ------DPLEEAS----EEKAPKPEERGGLDRWLVHVNPIDREILVLRFV----AELEFQEIADIMHMGLSATKMRYKRA 174 (188)
T ss_pred ------ccccccc----ccccccHHHHHHHHHHHHhcChhheeeeeeHHh----cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 0000000 000111233456899999999999999999998 89999999999999999999999999
Q ss_pred HHHHHHHhh
Q 009567 512 LYRLKQSLG 520 (532)
Q Consensus 512 LkKLR~~l~ 520 (532)
+++||..+.
T Consensus 175 ~~~Lr~~l~ 183 (188)
T PRK09640 175 LDKLREKFA 183 (188)
T ss_pred HHHHHHHHH
Confidence 999999874
No 57
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=99.85 E-value=1.3e-19 Score=171.87 Aligned_cols=180 Identities=19% Similarity=0.196 Sum_probs=138.8
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHhhC----CCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhh
Q 009567 288 SGNSSREKLINANLRLVVHVAKQYQG----RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 363 (532)
Q Consensus 288 ~g~~Are~LI~~nlrLV~sIAkrY~~----~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~ 363 (532)
++..|++.|+..|.+.|+.+|++|.+ +..+.+|++||+++.+|+++.+|++..+.+|.+|++..+++.+.+++++.
T Consensus 4 ~~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~~ 83 (189)
T TIGR02984 4 GDQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRRH 83 (189)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHHH
Confidence 44699999999999999999999853 56789999999999999999999986667899999999999999998764
Q ss_pred cc-ccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCC-CCCCcchhhhcc
Q 009567 364 SR-TIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVW-ADQDTTFQEITA 441 (532)
Q Consensus 364 ~r-~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~-~d~~~~l~d~i~ 441 (532)
.+ -.+ .+ ....+++.+.. ++....+.+.+.
T Consensus 84 ~~~~~r-------------------------~~-----------------------~~~~~~~~~~~~~~~~~~~~~~~~ 115 (189)
T TIGR02984 84 LGAQKR-------------------------DI-----------------------RREQSLDAGGRLDESSVRLAAQLA 115 (189)
T ss_pred HHHHhh-------------------------hc-----------------------ccccCCCcccccCCcchhHHHHcc
Confidence 20 000 00 00112222111 111122333333
Q ss_pred cCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567 442 DTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 520 (532)
Q Consensus 442 d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~ 520 (532)
+. ..+|++.+...+....|..+|..|||++|+||.++|+ +++|++|||+.||||.++|++..+||+++||+.+.
T Consensus 116 ~~-~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~~----~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~l~ 189 (189)
T TIGR02984 116 AD-GPSPSQVAARREAAVRLAQALAKLPEDYREVILLRHL----EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQILE 189 (189)
T ss_pred CC-CCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhC
Confidence 32 3356777777777788999999999999999999998 89999999999999999999999999999998763
No 58
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=6.5e-20 Score=174.47 Aligned_cols=172 Identities=13% Similarity=0.164 Sum_probs=136.9
Q ss_pred CHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHH
Q 009567 278 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 356 (532)
Q Consensus 278 ~~~~L~~~l~~g~-~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI 356 (532)
+...|...+.+|+ .|++.|+..|.+.|+.++.++.++..+.+|++||+|+.+|+.+++|++.. ..|.+|++..+++.+
T Consensus 9 ~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~-~~~~~wL~~iarn~~ 87 (182)
T PRK12537 9 DYEACLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPAR-GSARGWIYSVTRHLA 87 (182)
T ss_pred hHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCccc-ccHHHHHHHHHHHHH
Confidence 4455666666554 99999999999999999999999999999999999999999999998644 379999999999999
Q ss_pred HHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 009567 357 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 436 (532)
Q Consensus 357 ~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l 436 (532)
.+++++..+...+ +. ..
T Consensus 88 ~d~~r~~~~~~~~-------------------------------------------------------~~-----~~--- 104 (182)
T PRK12537 88 LNVLRDTRREVVL-------------------------------------------------------DD-----DA--- 104 (182)
T ss_pred HHHHHhccccCcc-------------------------------------------------------cc-----ch---
Confidence 9999876421100 00 00
Q ss_pred hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567 437 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 437 ~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR 516 (532)
.+...+ ...+++..........+..+|+.||+++|+||.++|. +++|++|||+.||||.++|+....||+++||
T Consensus 105 ~~~~~~--~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr 178 (182)
T PRK12537 105 EETAQT--LHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYV----DGCSHAEIAQRLGAPLGTVKAWIKRSLKALR 178 (182)
T ss_pred hhhccc--ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCChhhHHHHHHHHHHHHH
Confidence 000000 1123333344445567899999999999999999998 9999999999999999999999999999999
Q ss_pred HHh
Q 009567 517 QSL 519 (532)
Q Consensus 517 ~~l 519 (532)
.++
T Consensus 179 ~~l 181 (182)
T PRK12537 179 ECM 181 (182)
T ss_pred HHh
Confidence 986
No 59
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=5.5e-20 Score=182.78 Aligned_cols=174 Identities=14% Similarity=0.222 Sum_probs=139.7
Q ss_pred CHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHH
Q 009567 278 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 356 (532)
Q Consensus 278 ~~~~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI 356 (532)
++..|...+..| ..|++.|+..|.+.|+.+++++.++..+.+|++||+|+.+|+.+++|++..+ .|.+|++..+++.+
T Consensus 49 ~d~~Li~~~~~gd~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~~ 127 (233)
T PRK12538 49 EDEELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNRC 127 (233)
T ss_pred cHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHHH
Confidence 445566666555 4899999999999999999999999999999999999999999999987544 79999999999999
Q ss_pred HHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 009567 357 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 436 (532)
Q Consensus 357 ~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l 436 (532)
.++++++.+. . ++. . .+
T Consensus 128 id~~Rk~~~~-~-------------------------------------------------------~~~-~-~~----- 144 (233)
T PRK12538 128 IDLRRKPRTE-N-------------------------------------------------------VDA-V-PE----- 144 (233)
T ss_pred HHHHHhhccc-c-------------------------------------------------------ccc-c-cc-----
Confidence 9988753210 0 000 0 00
Q ss_pred hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567 437 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 437 ~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR 516 (532)
. .+ ....+++.+...+....|..+|..||+++|+||.|+|. +++|++|||+.||+|.++|+++++||+++||
T Consensus 145 --~-~~-~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~~----eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr 216 (233)
T PRK12538 145 --V-AD-GKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSYH----ENMSNGEIAEVMDTTVAAVESLLKRGRQQLR 216 (233)
T ss_pred --c-cc-CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 0 00 01133444555566678999999999999999999998 9999999999999999999999999999999
Q ss_pred HHhhcCc
Q 009567 517 QSLGGKA 523 (532)
Q Consensus 517 ~~l~~~~ 523 (532)
+.+...+
T Consensus 217 ~~l~~~~ 223 (233)
T PRK12538 217 DLLRRHE 223 (233)
T ss_pred HHHHHhh
Confidence 9987554
No 60
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=7.2e-20 Score=174.39 Aligned_cols=172 Identities=15% Similarity=0.161 Sum_probs=135.8
Q ss_pred HHHHHHh-hcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHH
Q 009567 281 DLKSELH-SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA 359 (532)
Q Consensus 281 ~L~~~l~-~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ 359 (532)
.+...+. ++..+++.|+..|.++|+.+|.+|.++..+.+|++||+++++|+++++|++.++ .|.+|++..+++.+.++
T Consensus 14 ~l~~~~~~~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~~d~ 92 (187)
T PRK12534 14 RLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKAIDH 92 (187)
T ss_pred HHHHHHHcCCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHHH
Confidence 3444444 445999999999999999999999999999999999999999999999998654 58899999999999999
Q ss_pred HHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhh
Q 009567 360 IFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEI 439 (532)
Q Consensus 360 ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~ 439 (532)
+++..+... ..+++. ....
T Consensus 93 ~R~~~~~~~----------------------------------------------------~~~~~~---------~~~~ 111 (187)
T PRK12534 93 LRANAPQRR----------------------------------------------------NVALDD---------AGEL 111 (187)
T ss_pred HHhcccccc----------------------------------------------------cccccc---------hhhh
Confidence 876542100 000000 0000
Q ss_pred cccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567 440 TADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519 (532)
Q Consensus 440 i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l 519 (532)
. +. ..++++.....+....|..+|..||++++.|+.++|. +++|++|||+.||+|.++|+++++||+++||..+
T Consensus 112 ~-~~-~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 185 (187)
T PRK12534 112 R-AA-DASPLERTERASTRRRIDHCLAELEPPRSELIRTAFF----EGITYEELAARTDTPIGTVKSWIRRGLAKLKACL 185 (187)
T ss_pred c-cc-cCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Confidence 0 00 1123344445566678999999999999999999998 8999999999999999999999999999999987
Q ss_pred h
Q 009567 520 G 520 (532)
Q Consensus 520 ~ 520 (532)
.
T Consensus 186 ~ 186 (187)
T PRK12534 186 E 186 (187)
T ss_pred c
Confidence 4
No 61
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=1.2e-19 Score=176.60 Aligned_cols=171 Identities=12% Similarity=0.156 Sum_probs=133.0
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccc
Q 009567 287 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 366 (532)
Q Consensus 287 ~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~ 366 (532)
.++..+++.|+..|.+.|+.++.++.++..+.+|++||+++.+|++++.|++.++ .|.||++.++++.+.+++++..+.
T Consensus 34 ~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d~~Rk~~~~ 112 (206)
T PRK12526 34 SRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFDMLRKIKAK 112 (206)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHHHHHHhccc
Confidence 3456999999999999999999999999889999999999999999999998665 599999999999999999876531
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCC
Q 009567 367 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE 446 (532)
Q Consensus 367 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~ 446 (532)
.... .. . +...+.+.+.+. ..
T Consensus 113 ~~~~-----------------------------------------------------~~----~-~~~~~~~~~~~~-~~ 133 (206)
T PRK12526 113 KEQN-----------------------------------------------------LG----D-DIWPIEQALAES-QS 133 (206)
T ss_pred cccc-----------------------------------------------------cc----c-ccchhhhhcccc-cC
Confidence 1000 00 0 000000111111 11
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567 447 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 522 (532)
Q Consensus 447 ~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~ 522 (532)
.+. ..........|..+|..||+++|+||.++|+ +++|++|||+.||+|.++|+..++||+++||+.+...
T Consensus 134 ~~~-~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~ 204 (206)
T PRK12526 134 ESE-EFSDHLMDKQILSYIEKLPEAQQTVVKGVYF----QELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQMGEQ 204 (206)
T ss_pred chH-HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence 122 2223334457899999999999999999998 9999999999999999999999999999999998654
No 62
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=1.2e-19 Score=169.68 Aligned_cols=168 Identities=16% Similarity=0.176 Sum_probs=138.6
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccc
Q 009567 287 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 366 (532)
Q Consensus 287 ~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~ 366 (532)
.++..|++.|+..|.+.|+++|+++.++..+.+|++||++++||++.++|+ .+..|.+|++..+++.+.+++++..+.
T Consensus 9 ~~~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~~r~~~~~ 86 (179)
T PRK11924 9 TGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDLLRRRRRE 86 (179)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHHHHhcccc
Confidence 344699999999999999999999999999999999999999999999998 345899999999999999998765421
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCC
Q 009567 367 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE 446 (532)
Q Consensus 367 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~ 446 (532)
... ..+ .. . +...+....
T Consensus 87 ~~~-----------------------------------------------------~~~-~~---~-----~~~~~~~~~ 104 (179)
T PRK11924 87 KAV-----------------------------------------------------LSD-DA---L-----EPEFAETAE 104 (179)
T ss_pred ccc-----------------------------------------------------Ccc-cc---c-----ccccCCccC
Confidence 100 000 00 0 000000224
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567 447 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 522 (532)
Q Consensus 447 ~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~ 522 (532)
+|++.+...+....+..+|..||++++.||.++|. +++|..|||+.||+|+.+|+++..+|+++||+.+..+
T Consensus 105 ~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~~~ 176 (179)
T PRK11924 105 TPEAALLAKDDLARIDRCLDALPVKQREVFLLRYV----EGLSYREIAEILGVPVGTVKSRLRRARQLLRECLEAQ 176 (179)
T ss_pred CHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 67778888888889999999999999999999998 8999999999999999999999999999999988754
No 63
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=8.3e-20 Score=174.02 Aligned_cols=175 Identities=17% Similarity=0.201 Sum_probs=139.0
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccc
Q 009567 287 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 366 (532)
Q Consensus 287 ~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~ 366 (532)
.++..|++.|+..|.+.++.+|.++.++..+.+|++||+++.+|+++++|++..+..|.||++..+++.+.++++++.+.
T Consensus 5 ~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~~~ 84 (185)
T PRK12542 5 NNDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNKRH 84 (185)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 34569999999999999999999999999999999999999999999999875555899999999999999999876421
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCC
Q 009567 367 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE 446 (532)
Q Consensus 367 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~ 446 (532)
... . +. . .. +.... ..+
T Consensus 85 ~~~------------------~------------------------------------~~-~---~~----~~~~~-~~~ 101 (185)
T PRK12542 85 ETF------------------L------------------------------------EE-Y---ER----ESIEA-VDE 101 (185)
T ss_pred hhh------------------h------------------------------------hh-c---cc----cchhh-hhc
Confidence 000 0 00 0 00 00000 001
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhh
Q 009567 447 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYG 526 (532)
Q Consensus 447 ~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~ 526 (532)
.+++..........|..+|..|||++|+||.++|. +++|++|||+.||+|..+|+..+.||+++||..+....-..
T Consensus 102 ~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~~~ 177 (185)
T PRK12542 102 NIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVF----YNLTYQEISSVMGITEANVRKQFERARKRVQNMIGGIQHDE 177 (185)
T ss_pred cHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccchHH
Confidence 23333333444567899999999999999999998 89999999999999999999999999999999998887777
Q ss_pred hh
Q 009567 527 YA 528 (532)
Q Consensus 527 yl 528 (532)
|+
T Consensus 178 ~~ 179 (185)
T PRK12542 178 FK 179 (185)
T ss_pred HH
Confidence 74
No 64
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=2.2e-19 Score=171.70 Aligned_cols=177 Identities=19% Similarity=0.270 Sum_probs=143.4
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHH
Q 009567 277 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 355 (532)
Q Consensus 277 ~~~~~L~~~l~~g~-~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~a 355 (532)
++++.|...+..|+ .|++.|+..|.+.++.++.++.++..+.+|++||+++.+|++.++|++. ..|.+|++..+++.
T Consensus 7 ~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n~ 84 (189)
T PRK12515 7 TTDEMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARFK 84 (189)
T ss_pred cCHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHHH
Confidence 46667777666554 8999999999999999999999999999999999999999999999974 47999999999999
Q ss_pred HHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 009567 356 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 435 (532)
Q Consensus 356 I~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~ 435 (532)
+.+++++..+.. +.. +.
T Consensus 85 ~~d~~r~~~~~~--------------------------------------------------------~~~----~~--- 101 (189)
T PRK12515 85 ALSALRRRKHEE--------------------------------------------------------IDD----EA--- 101 (189)
T ss_pred HHHHHHccCCCC--------------------------------------------------------Ccc----cc---
Confidence 999987543100 000 00
Q ss_pred hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567 436 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 515 (532)
Q Consensus 436 l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKL 515 (532)
.....+ ...+|+......+....+..+|..||+++|+||.++|. +++|++|||+.||+|..+|++...||+++|
T Consensus 102 -~~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~tV~~~l~Rar~~L 175 (189)
T PRK12515 102 -AAAIED-GADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYY----HEKSVEEVGEIVGIPESTVKTRMFYARKKL 175 (189)
T ss_pred -ccccCC-CCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 000111 12245555566666778999999999999999999998 899999999999999999999999999999
Q ss_pred HHHhhcCch
Q 009567 516 KQSLGGKAS 524 (532)
Q Consensus 516 R~~l~~~~l 524 (532)
|..+...+.
T Consensus 176 r~~l~~~~~ 184 (189)
T PRK12515 176 AELLKAAGV 184 (189)
T ss_pred HHHHHHhcc
Confidence 999887654
No 65
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=99.83 E-value=2.5e-19 Score=161.18 Aligned_cols=157 Identities=24% Similarity=0.389 Sum_probs=131.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccch
Q 009567 292 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 371 (532)
Q Consensus 292 Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~ 371 (532)
|++.++..|.++|+++++++.+++.+.+|++|||+++++++++.|++. .+|.+|+.+++++.+.++++++.+ . +.
T Consensus 2 a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~-~--~~ 76 (158)
T TIGR02937 2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR-L--RR 76 (158)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhcc-C--Cc
Confidence 789999999999999999999999999999999999999999999998 689999999999999999988764 1 10
Q ss_pred hHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHH
Q 009567 372 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 451 (532)
Q Consensus 372 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~ 451 (532)
.. . .. .... .....++..
T Consensus 77 ~~---------------------------------------------------~------~~----~~~~-~~~~~~~~~ 94 (158)
T TIGR02937 77 EL---------------------------------------------------D------LL----EELL-DSDPSPEEE 94 (158)
T ss_pred ch---------------------------------------------------h------hh----hhcc-cccCCHHHH
Confidence 00 0 00 0000 111245556
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567 452 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519 (532)
Q Consensus 452 ~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l 519 (532)
.........|..++..||++++.||.++|+ .|+|..|||+.+|+|+.+|+++..+++++||+.+
T Consensus 95 ~~~~~~~~~l~~~l~~L~~~~~~ii~~~~~----~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~l 158 (158)
T TIGR02937 95 LEQEEEREALREALEKLPEREREVLVLRYL----EGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158 (158)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 666677778999999999999999999987 7999999999999999999999999999999864
No 66
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=99.83 E-value=3e-19 Score=171.72 Aligned_cols=176 Identities=12% Similarity=0.148 Sum_probs=134.1
Q ss_pred HHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHH
Q 009567 282 LKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI 360 (532)
Q Consensus 282 L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~i 360 (532)
++..+..| ..|++.|+..|.+.|+.+|.++.++..+.+|++||+++.+|+..++|++.++ .|.+|++..+++.+.+++
T Consensus 17 li~~~~~~d~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn~~ld~~ 95 (194)
T PRK12531 17 CMEKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRNLCFDLL 95 (194)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHHHHHHHH
Confidence 45555555 5999999999999999999999999889999999999999999999997554 699999999999999999
Q ss_pred HhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhc
Q 009567 361 FQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEIT 440 (532)
Q Consensus 361 r~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i 440 (532)
++..+.... . ..+... .+.. ....+
T Consensus 96 Rk~~~~~~~-------------------------~---------------------------~~~~~~-~~~~--~~~~~ 120 (194)
T PRK12531 96 RKQKGKDLH-------------------------I---------------------------HADDIW-PSDY--YPPDL 120 (194)
T ss_pred HHhcccccc-------------------------c---------------------------chhhcc-cccc--ccccc
Confidence 875421000 0 000000 0000 00000
Q ss_pred ccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567 441 ADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 520 (532)
Q Consensus 441 ~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~ 520 (532)
.+ ...++.. .....+..++..||+++|+||.++|. +++|.+|||+.||||.++|+..+++|+++||..+.
T Consensus 121 ~~--~~~~e~~----~~~~~l~~~l~~Lp~~~r~v~~l~~~----eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~ 190 (194)
T PRK12531 121 VD--HYSPEQD----MLKEQVMKFLDRLPKAQRDVLQAVYL----EELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSMD 190 (194)
T ss_pred cc--ccCHHHH----HHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHhh
Confidence 00 0122222 23356888999999999999999998 99999999999999999999999999999999987
Q ss_pred cCc
Q 009567 521 GKA 523 (532)
Q Consensus 521 ~~~ 523 (532)
...
T Consensus 191 ~~~ 193 (194)
T PRK12531 191 AES 193 (194)
T ss_pred hcc
Confidence 654
No 67
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=99.83 E-value=2.2e-19 Score=169.14 Aligned_cols=172 Identities=13% Similarity=0.192 Sum_probs=133.8
Q ss_pred CCHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHH
Q 009567 277 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 355 (532)
Q Consensus 277 ~~~~~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~a 355 (532)
|++..+...+..| ..|++.|+..|.+.|+.+|++|.++..+.+|++||+++++|+++++|++. .+|.+|++..+++.
T Consensus 3 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n~ 80 (176)
T PRK09638 3 MDEKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASRL 80 (176)
T ss_pred ccHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHH
Confidence 3455565555555 49999999999999999999999999999999999999999999999874 47999999999999
Q ss_pred HHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 009567 356 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 435 (532)
Q Consensus 356 I~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~ 435 (532)
+.+++++..+..... +.+ .+.
T Consensus 81 ~~d~~r~~~~~~~~~---------------------------~~~-----------------------~~~--------- 101 (176)
T PRK09638 81 YKDHLRKQKREKLRL---------------------------QRA-----------------------KEE--------- 101 (176)
T ss_pred HHHHHHHhccccchh---------------------------hhc-----------------------ccc---------
Confidence 999998754211000 000 000
Q ss_pred hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567 436 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 515 (532)
Q Consensus 436 l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKL 515 (532)
..+. ... +..........|..+|..||+++|+||.++|. +++|++|||+.||+|..+|+....||+++|
T Consensus 102 ----~~~~--~~~-~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~l~is~~~V~~~l~ra~~~l 170 (176)
T PRK09638 102 ----TLRK--EKW-EAAIKGAEWSEMLDALSKLDPEFRAPVILKHY----YGYTYEEIAKMLNIPEGTVKSRVHHGIKQL 170 (176)
T ss_pred ----cCCc--cch-HHHHHhhhHHHHHHHHHcCCHHHhheeeehhh----cCCCHHHHHHHHCCChhHHHHHHHHHHHHH
Confidence 0000 000 11122233456889999999999999999987 899999999999999999999999999999
Q ss_pred HHHhh
Q 009567 516 KQSLG 520 (532)
Q Consensus 516 R~~l~ 520 (532)
|+.+.
T Consensus 171 ~~~l~ 175 (176)
T PRK09638 171 RKEWG 175 (176)
T ss_pred HHHhc
Confidence 99774
No 68
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=99.83 E-value=4.7e-19 Score=170.36 Aligned_cols=172 Identities=16% Similarity=0.163 Sum_probs=138.7
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHH
Q 009567 277 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 355 (532)
Q Consensus 277 ~~~~~L~~~l~~g~-~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~a 355 (532)
+++..+...+..|+ .+++.|+..|.+.|++++.++.++..+.+|++||+++.+|+++++|++. ..|.+|++..+++.
T Consensus 12 ~~~~~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~--~~f~~wL~~i~rn~ 89 (192)
T PRK09643 12 RSDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGD--AAVSSWLHRIVVNA 89 (192)
T ss_pred cCHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCC--CccHHHHHHHHHHH
Confidence 35666766666554 9999999999999999999999999999999999999999999999975 36999999999999
Q ss_pred HHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 009567 356 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 435 (532)
Q Consensus 356 I~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~ 435 (532)
+.+++++..+..+. +++. ..
T Consensus 90 ~~d~~Rk~~~~~~~-----------------------------------------------------~~~~----~~--- 109 (192)
T PRK09643 90 CLDRLRRAKARPTV-----------------------------------------------------PLDD----VY--- 109 (192)
T ss_pred HHHHHHccccCCCC-----------------------------------------------------Cccc----cc---
Confidence 99999875421100 0000 00
Q ss_pred hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567 436 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 515 (532)
Q Consensus 436 l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKL 515 (532)
+. . ..+++.+...+....|..+|..||+++|+||.++|. +++|++|||+.||+|..+|+....||+++|
T Consensus 110 --~~-~----~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~~----~g~s~~EIA~~lg~s~~tV~~rl~rar~~L 178 (192)
T PRK09643 110 --PV-A----QLERDPTARVETALAVQRALMRLPVEQRAALVAVDM----QGYSVADAARMLGVAEGTVKSRCARGRARL 178 (192)
T ss_pred --cc-c----CCcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 00 0 012223344455667999999999999999999998 899999999999999999999999999999
Q ss_pred HHHhhc
Q 009567 516 KQSLGG 521 (532)
Q Consensus 516 R~~l~~ 521 (532)
|+.+..
T Consensus 179 r~~l~~ 184 (192)
T PRK09643 179 AELLGY 184 (192)
T ss_pred HHHHHH
Confidence 998864
No 69
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=99.83 E-value=2.6e-19 Score=164.44 Aligned_cols=160 Identities=18% Similarity=0.188 Sum_probs=129.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccch
Q 009567 292 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 371 (532)
Q Consensus 292 Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~ 371 (532)
|++.|+..|.+.|+.+++++.++..+.+|++||+++++|+++.+|++. .+|.+|++.++++.+.+++++..+....
T Consensus 2 a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~--~~~~~wl~~i~r~~~~d~~r~~~~~~~~-- 77 (161)
T TIGR02985 2 AFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEV--ESFKAYLFTIVKNRSLNYLRHKQVEEKY-- 77 (161)
T ss_pred hHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc--ccHHHHHHHHHHHHHHHHHHHHHhHhHH--
Confidence 789999999999999999999998999999999999999999999874 4799999999999999998775421000
Q ss_pred hHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHH
Q 009567 372 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 451 (532)
Q Consensus 372 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~ 451 (532)
...+ . ++.. ......++++.
T Consensus 78 -------------------------~~~~------------------------~----~~~~-------~~~~~~~~~~~ 97 (161)
T TIGR02985 78 -------------------------QEEI------------------------L----EIEV-------DELSENDPEEE 97 (161)
T ss_pred -------------------------HHHH------------------------H----hhcc-------cccCCCCcHHH
Confidence 0000 0 0000 00011245556
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567 452 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519 (532)
Q Consensus 452 ~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l 519 (532)
+...+....|..++..||+++++||.++|. +++|..|||+.||+|+++|+++..+|+++||+.+
T Consensus 98 ~~~~e~~~~l~~~l~~L~~~~r~il~l~~~----~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~l 161 (161)
T TIGR02985 98 LEAKELQLIIYKAIEKLPEQCRKIFILSRF----EGKSYKEIAEELGISVKTVEYHISKALKELRKEL 161 (161)
T ss_pred HHHHHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 666677778999999999999999999987 8999999999999999999999999999999864
No 70
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=99.82 E-value=4.6e-19 Score=168.18 Aligned_cols=166 Identities=16% Similarity=0.197 Sum_probs=132.9
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcccc
Q 009567 288 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 367 (532)
Q Consensus 288 ~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~I 367 (532)
++..|++.|+..|.+.|+.++++|.++..+.+|++||+++.+|+++.+|++.. .|.+|++..+++.+.++++...+..
T Consensus 4 ~d~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~~~~~ 81 (179)
T PRK12543 4 GDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKRWRRF 81 (179)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhhcccc
Confidence 34589999999999999999999999999999999999999999999999864 6999999999998888876543110
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCC
Q 009567 368 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 447 (532)
Q Consensus 368 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~ 447 (532)
+. ++... +.. + ......
T Consensus 82 ~~------------------------------------------------------~~~~~-~~~-----~---~~~~~~ 98 (179)
T PRK12543 82 RI------------------------------------------------------FEKAE-EQR-----K---PVSIDF 98 (179)
T ss_pred cc------------------------------------------------------ccccc-ccc-----c---cccccC
Confidence 00 00000 000 0 001113
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 009567 448 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 523 (532)
Q Consensus 448 pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~ 523 (532)
|+. +...+....|..+|..|||++|+||.++|. +++|++|||+.||||..+|+..++||+++||+.+....
T Consensus 99 ~~~-~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~~----e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~ 169 (179)
T PRK12543 99 SED-VLSKESNQELIELIHKLPYKLRQVIILRYL----HDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIEE 169 (179)
T ss_pred hHH-HHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444 555666778999999999999999999998 99999999999999999999999999999999987643
No 71
>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=99.82 E-value=4.9e-19 Score=166.01 Aligned_cols=167 Identities=18% Similarity=0.213 Sum_probs=132.3
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHH
Q 009567 277 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 355 (532)
Q Consensus 277 ~~~~~L~~~l~~g~-~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~a 355 (532)
|+++.+...+..|+ .|++.++..|.+.|++++.++.++..+.+|++||+++.+|+..++|++. .+|.+|++..+++.
T Consensus 1 ~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~--~~~~~wl~~i~~n~ 78 (169)
T TIGR02954 1 MNDEELVKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHP--KYFNTWLTRILINE 78 (169)
T ss_pred CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCc--cccHHHHHHHHHHH
Confidence 34556666665554 9999999999999999999999999999999999999999999999975 36999999999999
Q ss_pred HHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 009567 356 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 435 (532)
Q Consensus 356 I~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~ 435 (532)
+.+++++..+... ++.....+
T Consensus 79 ~~d~~R~~~~~~~-------------------------------------------------------~~~~~~~~---- 99 (169)
T TIGR02954 79 CIDLLKKKKKVIP-------------------------------------------------------FDPNTSIE---- 99 (169)
T ss_pred HHHHHHhcCCcCc-------------------------------------------------------cccccccc----
Confidence 9999876542100 00000000
Q ss_pred hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567 436 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 515 (532)
Q Consensus 436 l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKL 515 (532)
+. .++. .. .....+..+|..||+++|+||.++|. +|+|.+|||+.||||..+|+....||+++|
T Consensus 100 ------~~---~~~~--~~-~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eiA~~lgis~~tv~~~l~Ra~~~L 163 (169)
T TIGR02954 100 ------KG---ECET--HA-DSRLDLYKAIDTLNDKYQTAIILRYY----HDLTIKEIAEVMNKPEGTVKTYLHRALKKL 163 (169)
T ss_pred ------cc---hhhh--ch-HHHHHHHHHHHhCCHHHhHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 00 0000 00 11236888999999999999999998 899999999999999999999999999999
Q ss_pred HHHhh
Q 009567 516 KQSLG 520 (532)
Q Consensus 516 R~~l~ 520 (532)
|..+.
T Consensus 164 r~~l~ 168 (169)
T TIGR02954 164 KKRLE 168 (169)
T ss_pred HHHhc
Confidence 99874
No 72
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=99.82 E-value=8.3e-19 Score=164.90 Aligned_cols=165 Identities=14% Similarity=0.126 Sum_probs=131.2
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcccc
Q 009567 288 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 367 (532)
Q Consensus 288 ~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~I 367 (532)
.+..+++.|+..|.+.|+.+|.++.++..+.+|++||.|+.+|+..++|++.. ..|.+|++..+++.+.++++++.+..
T Consensus 6 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~Rk~~~~~ 84 (173)
T PRK09645 6 AEAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSARARP 84 (173)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHHHHHHHhhcccc
Confidence 34689999999999999999999999888999999999999999999997532 47999999999999999998654210
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCC
Q 009567 368 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 447 (532)
Q Consensus 368 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~ 447 (532)
.. ..+ +.. + .++. .
T Consensus 85 ~~-----------------------------------------------------~~~------~~~---~-~~~~---~ 98 (173)
T PRK09645 85 VE-----------------------------------------------------GGD------DVL---G-VPEQ---S 98 (173)
T ss_pred cc-----------------------------------------------------ccc------ccc---c-CCCC---C
Confidence 00 000 000 0 0000 1
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 009567 448 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 523 (532)
Q Consensus 448 pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~ 523 (532)
+++.+........|..+|+.||+++|+||.|+|. +++|.+|||+.||+|..+|+..++||+++||+.+...+
T Consensus 99 ~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~ 170 (173)
T PRK09645 99 APDEVDRALDRLLVADALAQLSPEHRAVLVRSYY----RGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQERG 170 (173)
T ss_pred CchHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhccc
Confidence 2222333334457889999999999999999998 99999999999999999999999999999999987654
No 73
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=99.82 E-value=9e-19 Score=165.00 Aligned_cols=167 Identities=16% Similarity=0.193 Sum_probs=130.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 009567 291 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 370 (532)
Q Consensus 291 ~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP 370 (532)
..++.|+..|.++|+.+|++|.++..+++|++||+++.+|+++++|++.. +|.+|++..+++.+.++++++.+....+
T Consensus 3 ~~~~~l~~~y~~~i~~~~~~~~~~~~daeDvvQe~~i~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~Rk~~~~~~~~ 80 (173)
T PRK12522 3 EKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE--NYKKWITTICVRTFYDFYRKKKRWKDRI 80 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcCCcc--chHHHHHHHHHHHHHHHHHHhccccccc
Confidence 45899999999999999999999999999999999999999999999853 7999999999999999998765321000
Q ss_pred hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhH
Q 009567 371 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI 450 (532)
Q Consensus 371 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee 450 (532)
... .+. + ...+.........++.
T Consensus 81 ~~~--------------------------------------------------~~~----~---~~~~~~~~~~~~~~~~ 103 (173)
T PRK12522 81 LDL--------------------------------------------------FHK----E---DGGEIEFADDVNISEE 103 (173)
T ss_pred ccc--------------------------------------------------cch----h---hhhhhccccCCCChHH
Confidence 000 000 0 0000000001112333
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567 451 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 521 (532)
Q Consensus 451 ~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~ 521 (532)
....+..+.+..+|..||+++++|+.++|. +++|++|||+.||+|..+|+..+.||+++||+.+..
T Consensus 104 -~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~ 169 (173)
T PRK12522 104 -FIQKVEAEMIREVIQLLNEKYKTVLVLYYY----EQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEG 169 (173)
T ss_pred -HHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 444556778999999999999999999998 999999999999999999999999999999998754
No 74
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=6.1e-19 Score=167.64 Aligned_cols=170 Identities=15% Similarity=0.146 Sum_probs=130.5
Q ss_pred HHHHHHHh-hcHHHHHHHHHHHHHHHHHHHHHhhC-CCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHH
Q 009567 280 RDLKSELH-SGNSSREKLINANLRLVVHVAKQYQG-RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR 357 (532)
Q Consensus 280 ~~L~~~l~-~g~~Are~LI~~nlrLV~sIAkrY~~-~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~ 357 (532)
..+...+. ++..|++.|+..|.+.|+.++.++.+ ...+.+|++||+++.||+.++.|++. ..|.+|++..++|.+.
T Consensus 9 ~~~~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~~~ 86 (181)
T PRK12536 9 RALLLRGLAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYKLM 86 (181)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHHHH
Confidence 33444444 45599999999999999999998765 57899999999999999999999974 4699999999999999
Q ss_pred HHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchh
Q 009567 358 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ 437 (532)
Q Consensus 358 ~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~ 437 (532)
+++++..+... .+....+ ..
T Consensus 87 d~~Rk~~~~~~-------------------------------------------------------~~~~~~~-----~~ 106 (181)
T PRK12536 87 DFLRSRARREA-------------------------------------------------------LHDPLDD-----ES 106 (181)
T ss_pred HHHHHHhcccc-------------------------------------------------------ccCCccc-----hh
Confidence 99987542100 0000000 00
Q ss_pred hhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 438 EITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 438 d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
+...+. .++. .+....+..+|..||+++|.||.++|. +++|.+|||+.||+|+++|+...++|+++||+
T Consensus 107 ~~~~~~---~~~~----~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 107 ELFATS---DDEA----AEARRDLGKLLEQLPDRQRLPIVHVKL----EGLSVAETAQLTGLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred hhcCCC---Ccch----HHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 000011 1111 123446889999999999999999998 99999999999999999999999999999999
Q ss_pred HhhcC
Q 009567 518 SLGGK 522 (532)
Q Consensus 518 ~l~~~ 522 (532)
.+...
T Consensus 176 ~l~~~ 180 (181)
T PRK12536 176 KIRGE 180 (181)
T ss_pred HhcCC
Confidence 88653
No 75
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=99.81 E-value=6.5e-19 Score=162.83 Aligned_cols=158 Identities=18% Similarity=0.218 Sum_probs=125.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccch
Q 009567 292 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 371 (532)
Q Consensus 292 Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~ 371 (532)
|++.++..|.+.|+.+|+++.++..+.+|++||+++.+|+++++|++.. .|.+|++..+++.+.++++++.+.... .
T Consensus 2 ~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~~-~ 78 (159)
T TIGR02989 2 AFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRLV-F 78 (159)
T ss_pred HHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhcccccc-c
Confidence 7899999999999999999999999999999999999999999999763 599999999999999999876532100 0
Q ss_pred hHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHH
Q 009567 372 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 451 (532)
Q Consensus 372 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~ 451 (532)
.++. .+.+.+.. ++.+.
T Consensus 79 -------------------------~~~~------------------------------------~~~~~~~~--~~~~~ 95 (159)
T TIGR02989 79 -------------------------DDEL------------------------------------LEALAAEA--EATEA 95 (159)
T ss_pred -------------------------CHHH------------------------------------HHHHHhhc--ccchH
Confidence 0000 00000000 11111
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567 452 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519 (532)
Q Consensus 452 ~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l 519 (532)
.........|..+++.||++++.||.++|. +|+|.+|||+.||||.++|+...+||+++||+++
T Consensus 96 ~~~~~~~~~l~~~i~~L~~~~r~v~~l~~~----~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~~~ 159 (159)
T TIGR02989 96 DRSEDELQALEGCLEKLPERQRELLQLRYQ----RGVSLTALAEQLGRTVNAVYKALSRLRVRLRDCV 159 (159)
T ss_pred hhHHHHHHHHHHHHHHCCHHHHHHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcC
Confidence 222334467889999999999999999987 8999999999999999999999999999999853
No 76
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=99.81 E-value=1.1e-18 Score=165.64 Aligned_cols=164 Identities=16% Similarity=0.180 Sum_probs=134.0
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccc
Q 009567 289 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 368 (532)
Q Consensus 289 g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IR 368 (532)
+..|++.|+..|.+.|++++.++.++..+.+|++||+++.+|+++++|++. ..|.+|++..+++.+.+++++..+-..
T Consensus 14 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~--~~~~awl~~ia~n~~~d~~Rk~~~~~~ 91 (179)
T PRK09415 14 KEDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGK--SSLKTWLYRIAINHCKDYLKSWHNKKV 91 (179)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--cccHHHHHHHHHHHHHHHHHhhccccc
Confidence 358999999999999999999999998999999999999999999999874 369999999999999999887532100
Q ss_pred cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCCh
Q 009567 369 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP 448 (532)
Q Consensus 369 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~p 448 (532)
. +.+. ...... ....+|
T Consensus 92 ~-----------------------------------------------------~~~~--------~~~~~~--~~~~~~ 108 (179)
T PRK09415 92 I-----------------------------------------------------VTED--------IFTYME--SQKESV 108 (179)
T ss_pred c-----------------------------------------------------cccc--------cccccc--ccccCc
Confidence 0 0000 000000 011245
Q ss_pred hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567 449 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 521 (532)
Q Consensus 449 ee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~ 521 (532)
++.+...+....|..+|..||+++|+||.++|. +|+|++|||+.||||.++|++.+.||+++||+.+..
T Consensus 109 e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l~~ 177 (179)
T PRK09415 109 EEEVIQNAEDERLASAVMSLPIKYREVIYLFYY----EELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEE 177 (179)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 666666677778999999999999999999998 899999999999999999999999999999998764
No 77
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=99.81 E-value=1.6e-18 Score=173.49 Aligned_cols=180 Identities=16% Similarity=0.195 Sum_probs=141.1
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHH-------hhhhhCCcCCCchhhHH
Q 009567 277 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMK-------SVEKFKPQAGCRFASYA 348 (532)
Q Consensus 277 ~~~~~L~~~l~~g~-~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLik-------AiekFDp~kG~rFSTYA 348 (532)
.++..|...++.|+ .|+..|+..|.+.|+.++.++.++..+.+|++||.|+.+|. .+.+|++. ..|.||+
T Consensus 24 ~~d~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~--~~~~tWL 101 (244)
T TIGR03001 24 AADLYLACACAQGEPAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGR--GPLLSWV 101 (244)
T ss_pred ccHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCC--CchHhHH
Confidence 46677888777776 99999999999999999999999999999999999999994 78889864 3699999
Q ss_pred HHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCC
Q 009567 349 YWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPV 428 (532)
Q Consensus 349 ~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v 428 (532)
+..++|.+.++++++.+...+ +
T Consensus 102 ~~Ia~N~~id~lRk~~r~~~~-------------------------------------------------------~--- 123 (244)
T TIGR03001 102 RIVATRIALELQAQERRHSPV-------------------------------------------------------E--- 123 (244)
T ss_pred HHHHHHHHHHHHHHhcccCcc-------------------------------------------------------c---
Confidence 999999999999765421100 0
Q ss_pred CCCCCcchhhhcccCCCCChhHHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHH
Q 009567 429 WADQDTTFQEITADTGVEIPDISVQK----QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERV 504 (532)
Q Consensus 429 ~~d~~~~l~d~i~d~~~~~pee~~~~----~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerV 504 (532)
+++ ...+. .+. ..+|++.+.. .+....|..+|+.||+++|+||.++|. +++|++|||++||||.++|
T Consensus 124 -~~~--~~~~~-~~~-~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~----eg~S~~EIA~~Lgis~~TV 194 (244)
T TIGR03001 124 -EPT--ELAAL-PAP-GSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHFV----DGLSMDRIGAMYQVHRSTV 194 (244)
T ss_pred -ccc--ccccc-cCC-CCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHH
Confidence 000 00000 011 1134433332 235567999999999999999999998 9999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhcCchh
Q 009567 505 RQLESRALYRLKQSLGGKASY 525 (532)
Q Consensus 505 Rqie~rALkKLR~~l~~~~l~ 525 (532)
+..+.||+++||+.+.+....
T Consensus 195 k~rl~RAr~~Lr~~l~~~~~~ 215 (244)
T TIGR03001 195 SRWVAQARERLLERTRRRLAE 215 (244)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999998775443
No 78
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=1.1e-18 Score=167.01 Aligned_cols=182 Identities=16% Similarity=0.158 Sum_probs=136.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccch
Q 009567 292 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 371 (532)
Q Consensus 292 Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~ 371 (532)
+++.|+..|.+.|+.+|.++.++..+.+|++||.++.+|+.+++|++. .+|.+|++..+++.+.++++++.+....+.
T Consensus 3 ~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~--~~~~~WL~~ia~n~~~d~~Rk~~r~~~~~~ 80 (191)
T PRK12520 3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQ--SSLKTYLVGILKHKIIDAIRSGRREVRLSL 80 (191)
T ss_pred chHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--ccHHHHHHHHHHHHHHHHHHhhcCcCcccc
Confidence 688999999999999999999999999999999999999999999864 369999999999999999987653221100
Q ss_pred hHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHH
Q 009567 372 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 451 (532)
Q Consensus 372 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~ 451 (532)
.... ....+++ ++... . .+ ......++. ..+|++.
T Consensus 81 ~~~~------------------~~~~~~~-----------------------~~~~~-~-~~-~~~~~~~~~-~~~~~~~ 115 (191)
T PRK12520 81 DDAD------------------EQSDDDL-----------------------FDALF-A-AD-GHYREPPSD-WGDPDAA 115 (191)
T ss_pred cccc------------------cchhhhh-----------------------hhhhc-c-cc-cccccCccc-cCCHHHH
Confidence 0000 0000000 00000 0 00 000001111 2356776
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 009567 452 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 524 (532)
Q Consensus 452 ~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l 524 (532)
+...+....|..+|..||+++|+||.|+|. +++|++|||+.||+|.++|++.+.||+++||+++...+.
T Consensus 116 ~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~ 184 (191)
T PRK12520 116 LSRREFFEVLQACVDRLPPRTGRVFMMREW----LELETEEICQELQITATNAWVLLYRARMRLRECLDLHWF 184 (191)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 777777788999999999999999999998 899999999999999999999999999999999987653
No 79
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=2e-18 Score=164.50 Aligned_cols=170 Identities=16% Similarity=0.181 Sum_probs=130.7
Q ss_pred HHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHH----hhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHH
Q 009567 279 CRDLKSELHSG-NSSREKLINANLRLVVHVAKQ----YQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR 353 (532)
Q Consensus 279 ~~~L~~~l~~g-~~Are~LI~~nlrLV~sIAkr----Y~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr 353 (532)
...|...+..| ..|++.|+..|.+.|+.+|++ +.++..+.+|++||+++.+|++++.|++.. .|.+|++..++
T Consensus 8 ~~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~~ 85 (184)
T PRK12539 8 LKALMLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIAR 85 (184)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHHH
Confidence 34455555555 599999999999999999874 557788999999999999999999999753 69999999999
Q ss_pred HHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCC
Q 009567 354 QTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD 433 (532)
Q Consensus 354 ~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~ 433 (532)
+.+.+++++..+.. . ..+.+. ..
T Consensus 86 n~~~d~~R~~~~~~-~---------------------------------------------------~~~~~~-----~~ 108 (184)
T PRK12539 86 YKLIDHLRRTRASL-A---------------------------------------------------DVPIDD-----AD 108 (184)
T ss_pred HHHHHHHHHHhccc-c---------------------------------------------------ccChhh-----hc
Confidence 99999988754210 0 000000 00
Q ss_pred cchhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567 434 TTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 513 (532)
Q Consensus 434 ~~l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALk 513 (532)
... +.+.....+....|..++..||+++|+|+.++|. +|+|++|||+.||+|..+|+....||++
T Consensus 109 ----~~~-------~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~ra~~ 173 (184)
T PRK12539 109 ----ELV-------AHDDHAAVESTLDLGRLLARLPEKMRLAIQAVKL----EGLSVAEAATRSGMSESAVKVSVHRGLK 173 (184)
T ss_pred ----ccc-------CCcHHhhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 000 0001112233457899999999999999999998 8999999999999999999999999999
Q ss_pred HHHHHhhcC
Q 009567 514 RLKQSLGGK 522 (532)
Q Consensus 514 KLR~~l~~~ 522 (532)
+||+.+...
T Consensus 174 ~Lr~~l~~~ 182 (184)
T PRK12539 174 ALAALIGRE 182 (184)
T ss_pred HHHHHHhhc
Confidence 999988643
No 80
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=2.7e-18 Score=163.11 Aligned_cols=166 Identities=19% Similarity=0.241 Sum_probs=128.5
Q ss_pred HHHHHh-hcHHHHHHHHHHHHHHHHHHHHHhhCC----CCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHH
Q 009567 282 LKSELH-SGNSSREKLINANLRLVVHVAKQYQGR----GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 356 (532)
Q Consensus 282 L~~~l~-~g~~Are~LI~~nlrLV~sIAkrY~~~----g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI 356 (532)
+...+. ++..|++.|+..|.+.|+.+|.++.++ ..+.+|++||+++.+|...++|++. ..|.+|++..+++.+
T Consensus 12 l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn~~ 89 (184)
T PRK12512 12 LMRSANAGDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARNKL 89 (184)
T ss_pred HHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHHHH
Confidence 333444 456999999999999999999998763 3689999999999999999999874 479999999999999
Q ss_pred HHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 009567 357 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 436 (532)
Q Consensus 357 ~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l 436 (532)
.++++++.+.... +++. +
T Consensus 90 ~d~~Rr~~~~~~~-----------------------------------------------------~~~~---------~ 107 (184)
T PRK12512 90 IDALRRRGRRVFV-----------------------------------------------------DIDD---------F 107 (184)
T ss_pred HHHHHhhcccccC-----------------------------------------------------Cchh---------c
Confidence 9998765421110 0000 0
Q ss_pred hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567 437 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 437 ~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR 516 (532)
.+.+++.. +.+ ......+..+|+.||+++|+||.++|. +++|++|||+.||+|..+|+...++|+++||
T Consensus 108 ~~~~~~~~---~~~----~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr 176 (184)
T PRK12512 108 AETLPAEP---ATE----TLPAGDVGRHLETLPPRQRDVVQSISV----EGASIKETAAKLSMSEGAVRVALHRGLAALA 176 (184)
T ss_pred cccccccc---hhh----HHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 00011100 001 122346788999999999999999998 8999999999999999999999999999999
Q ss_pred HHhhcC
Q 009567 517 QSLGGK 522 (532)
Q Consensus 517 ~~l~~~ 522 (532)
..+.+.
T Consensus 177 ~~l~~~ 182 (184)
T PRK12512 177 AKFRSE 182 (184)
T ss_pred HHhhcC
Confidence 998764
No 81
>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=99.80 E-value=2.4e-18 Score=163.03 Aligned_cols=171 Identities=19% Similarity=0.265 Sum_probs=125.6
Q ss_pred HHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCC-----CHhhHHHHHHHHHHH-hhhhhCCcCCCchhhHHHHHH
Q 009567 280 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGI-----SLHDLLQEGSMGLMK-SVEKFKPQAGCRFASYAYWWV 352 (532)
Q Consensus 280 ~~L~~~l~~g~-~Are~LI~~nlrLV~sIAkrY~~~g~-----~~eDLiQEG~iGLik-AiekFDp~kG~rFSTYA~~wI 352 (532)
..|...++.|+ .|++.|+..|.+.|+.+|.+|.++.. +.+|++||+|+.+|+ ...+|++. ..|.+|++.++
T Consensus 5 ~~li~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~i~ 82 (183)
T TIGR02999 5 TELLQQWQNGDAAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAKAM 82 (183)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHHHH
Confidence 34555555554 89999999999999999999998877 899999999999998 78889764 36999999999
Q ss_pred HHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCC
Q 009567 353 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQ 432 (532)
Q Consensus 353 r~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~ 432 (532)
++.+.+++++..+..+. . . ..+...
T Consensus 83 ~n~~~d~~R~~~~~~~~----------------------~---------------------------~--~~~~~~---- 107 (183)
T TIGR02999 83 RRILVDHARRRRAQKRG----------------------G---------------------------G--AVRVPL---- 107 (183)
T ss_pred HHHHHHHHHHHHHHhcc----------------------C---------------------------C--cccccc----
Confidence 99999998765321000 0 0 000000
Q ss_pred CcchhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567 433 DTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 512 (532)
Q Consensus 433 ~~~l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rAL 512 (532)
.+..++. .++.. ......+.+...|..||+++|+||.|+|. +++|++|||+.||+|..+|+..+.||+
T Consensus 108 ----~~~~~~~---~~~~~-~~~~~l~~~~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar 175 (183)
T TIGR02999 108 ----DEVLPDA---EADLD-EELLDLDDALDKLAQVDPRQAEVVELRFF----AGLTVEEIAELLGVSVRTVERDWRFAR 175 (183)
T ss_pred ----ccccCCC---CccHH-HHHHHHHHHHHHhhcCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 0000000 11111 11111223444567799999999999998 999999999999999999999999999
Q ss_pred HHHHHHh
Q 009567 513 YRLKQSL 519 (532)
Q Consensus 513 kKLR~~l 519 (532)
++||+.+
T Consensus 176 ~~Lr~~l 182 (183)
T TIGR02999 176 AWLADEL 182 (183)
T ss_pred HHHHHHh
Confidence 9999976
No 82
>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=99.80 E-value=3.6e-18 Score=168.14 Aligned_cols=118 Identities=18% Similarity=0.265 Sum_probs=105.0
Q ss_pred HhhcHHHHHHHHHHHHHHHHHHHHHhhCCC--CCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhh
Q 009567 286 LHSGNSSREKLINANLRLVVHVAKQYQGRG--ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 363 (532)
Q Consensus 286 l~~g~~Are~LI~~nlrLV~sIAkrY~~~g--~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~ 363 (532)
++.|+..++.||..|.|+|.++|++|.++. .+.+|++|+|++|||+|+++|||++|.+|.|||.+||++.|.+++|+.
T Consensus 4 ~~~gd~~~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dylRk~ 83 (218)
T TIGR02895 4 IQPGNEEREELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYIRKN 83 (218)
T ss_pred hhcCChHHHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHhc
Confidence 345554599999999999999999998775 589999999999999999999999999999999999999999999987
Q ss_pred c---cccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHH
Q 009567 364 S---RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARR 403 (532)
Q Consensus 364 ~---r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~ 403 (532)
. +.+++|....+....+..+...+..+.++.|+.+||+..
T Consensus 84 ~k~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~ 126 (218)
T TIGR02895 84 QKYQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEY 126 (218)
T ss_pred ccccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHH
Confidence 7 567899776666777788888899999999999999754
No 83
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=2.3e-18 Score=161.98 Aligned_cols=166 Identities=17% Similarity=0.162 Sum_probs=127.7
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccc
Q 009567 287 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 366 (532)
Q Consensus 287 ~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~ 366 (532)
.++..+++.|+..|.+.|+.+++++.+. .+.+|++||+++.+|+.++.|++. ..|.+|++..+++.+.+++++..+.
T Consensus 7 ~gd~~a~~~l~~~~~~~l~~~~~~~~~~-~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~~~~ 83 (175)
T PRK12518 7 RGDRQSFRQLYRRYQQKVRSTLYQLCGR-ELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARRQFAQR 83 (175)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHcCH-hHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHHHhhcc
Confidence 3446999999999999999999998753 688999999999999999999974 4699999999999999998764321
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCC
Q 009567 367 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE 446 (532)
Q Consensus 367 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~ 446 (532)
-.. .+... .... ....
T Consensus 84 ~~~------------------------------------------------------~~~~~-~~~~------~~~~--- 99 (175)
T PRK12518 84 PSR------------------------------------------------------IQDDS-LNDQ------PSRP--- 99 (175)
T ss_pred ccc------------------------------------------------------hhccc-cccc------ccCC---
Confidence 000 00000 0000 0000
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 009567 447 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 523 (532)
Q Consensus 447 ~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~ 523 (532)
.++......+....+..+|+.||+++|+||.++|+ +|+|++|||+.||+|..+|+....||+++||+.+...+
T Consensus 100 ~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~~~~ 172 (175)
T PRK12518 100 SDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHDL----EDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQQG 172 (175)
T ss_pred CCcHHHHHHHHHHHHHHHHHhCCHHHeeeeeehHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 11112222233456889999999999999999998 89999999999999999999999999999999987654
No 84
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=4.5e-18 Score=167.29 Aligned_cols=172 Identities=18% Similarity=0.167 Sum_probs=136.7
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccc
Q 009567 287 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 366 (532)
Q Consensus 287 ~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~ 366 (532)
.....++..|+..|.+.++.++.++.++..+.+|++||+|+.+|+.+++|++. .|.+|++..++|.+.++++++.+.
T Consensus 14 ~~~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~~~~ 90 (216)
T PRK12533 14 AARGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRRANA 90 (216)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhhccc
Confidence 34468999999999999999999999999999999999999999999999853 499999999999999998876421
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCC
Q 009567 367 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE 446 (532)
Q Consensus 367 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~ 446 (532)
... ........ ...... . ++...
T Consensus 91 ~~~-----------------------------------------------------~~~~~~~~--~~~~~~-~-~~~~~ 113 (216)
T PRK12533 91 HEV-----------------------------------------------------AAPDTLDD--ADSLDD-W-QPAGE 113 (216)
T ss_pred ccc-----------------------------------------------------cccccccc--cccccc-c-ccCCC
Confidence 100 00000000 000000 0 11123
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567 447 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 522 (532)
Q Consensus 447 ~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~ 522 (532)
+|++.+...+....|..+|..||+++|+||.|+|. +++|++|||+.||||.++|+++++||+++||+.+...
T Consensus 114 ~~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~----eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~ 185 (216)
T PRK12533 114 DPLALLLRAEDVRLVNAALAKLPVEYREVLVLREL----EDMSYREIAAIADVPVGTVMSRLARARRRLAALLGGA 185 (216)
T ss_pred CHHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHccc
Confidence 56667777777788999999999999999999998 8999999999999999999999999999999998654
No 85
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=3.3e-18 Score=162.47 Aligned_cols=166 Identities=9% Similarity=0.023 Sum_probs=130.1
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHHhhC--CCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhc
Q 009567 287 HSGNSSREKLINANLRLVVHVAKQYQG--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS 364 (532)
Q Consensus 287 ~~g~~Are~LI~~nlrLV~sIAkrY~~--~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~ 364 (532)
.++..+++.|+..|.+.|+.++..+.+ +..+.+|++||.|+.+|+..++|++.....|.||++..+++.+.++++++.
T Consensus 9 ~~d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~Rk~~ 88 (178)
T PRK12529 9 SADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRRRQS 88 (178)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHHHHH
Confidence 455699999999999999998766665 357899999999999999999998544457999999999999999887543
Q ss_pred cccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCC
Q 009567 365 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTG 444 (532)
Q Consensus 365 r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~ 444 (532)
+.. .. .+. ..+ ..+..
T Consensus 89 ~~~------------------~~------------------------------------~~~---------~~~-~~~~~ 104 (178)
T PRK12529 89 LEL------------------AW------------------------------------LEA---------LAT-LPEPL 104 (178)
T ss_pred HHh------------------hh------------------------------------hhH---------hhh-ccCcC
Confidence 100 00 000 000 00011
Q ss_pred CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567 445 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 520 (532)
Q Consensus 445 ~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~ 520 (532)
..+|++.+...+....|..+|..||+++|.||.|+|. +++|++|||+.||+|.++|+...++|+.+|++.+.
T Consensus 105 ~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~~~ 176 (178)
T PRK12529 105 HPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATL----DGMKQKDIAQALDIALPTVKKYIHQAYVTCLSLMP 176 (178)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhCC
Confidence 1255655655666678999999999999999999998 99999999999999999999999999999998753
No 86
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=99.79 E-value=6.5e-18 Score=160.90 Aligned_cols=171 Identities=20% Similarity=0.285 Sum_probs=136.1
Q ss_pred HHHhhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhh
Q 009567 284 SELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 363 (532)
Q Consensus 284 ~~l~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~ 363 (532)
....++..++..++..|.+.++.+++++.++..+.+||+||+++.+|+++..| .. +..|.||++.+++|.+.+++++.
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~~R~~ 85 (182)
T COG1595 8 EALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDRLRKR 85 (182)
T ss_pred HHHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHHHHHHh
Confidence 34455669999999999999999999999988899999999999999999999 33 34799999999999999999887
Q ss_pred ccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccC
Q 009567 364 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADT 443 (532)
Q Consensus 364 ~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~ 443 (532)
.+.... .+ +.+ ......+.
T Consensus 86 ~r~~~~------------------------------------------------------~~-----~~~--~~~~~~~~ 104 (182)
T COG1595 86 KRRRAR------------------------------------------------------VE-----EAD--LLPEEADP 104 (182)
T ss_pred cccccc------------------------------------------------------cc-----ccc--ccccccCc
Confidence 643211 00 000 00000000
Q ss_pred CCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567 444 GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 522 (532)
Q Consensus 444 ~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~ 522 (532)
..+.+ +.+...+....|..+|..||+++|++|.++|+ +|+|++|||+.||||.++|+..+++|+++||..+...
T Consensus 105 ~~~~~-~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~----~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~~~ 178 (182)
T COG1595 105 APDLA-ELLLAEEELERLRRALARLPPRQREAFLLRYL----EGLSYEEIAEILGISVGTVKSRLHRARKKLREQLEEA 178 (182)
T ss_pred ccccc-hHHHHHHHHHHHHHHHHhCCHHHhHHhhhHhh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence 00011 24555667778999999999999999999998 9999999999999999999999999999999988754
No 87
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=99.79 E-value=2.8e-18 Score=159.30 Aligned_cols=157 Identities=13% Similarity=0.044 Sum_probs=125.9
Q ss_pred HHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHH
Q 009567 298 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL 377 (532)
Q Consensus 298 ~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l 377 (532)
..|.+.|+.+|.++.++..+.+|++||+++.+|+++++|++. .|.+|++..+++.+.+++++..+..+.
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 568999999999999999999999999999999999999863 499999999999999999875421000
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHH
Q 009567 378 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 457 (532)
Q Consensus 378 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~~l 457 (532)
..+. . .. .+... ...+|++.+...+.
T Consensus 71 --------------------------------------------~~~~----~-~~---~~~~~--~~~~~~~~~~~~e~ 96 (160)
T PRK09642 71 --------------------------------------------LSLC----K-ET---EENIK--SSHNIEDLLLTKEQ 96 (160)
T ss_pred --------------------------------------------cccc----h-hh---hhhcc--CCCChHHHHHHHHH
Confidence 0000 0 00 00000 11245555666667
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 009567 458 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 523 (532)
Q Consensus 458 ~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~ 523 (532)
...|..+|+.||+++|+||.++|. +++|.+|||+.||+|.++|+....||+++||+.+....
T Consensus 97 ~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 158 (160)
T PRK09642 97 KLLIAQKLRELPENYRDVVLAHYL----EEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKEEE 158 (160)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhhc
Confidence 778999999999999999999998 99999999999999999999999999999999986554
No 88
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=99.79 E-value=4.2e-18 Score=162.85 Aligned_cols=169 Identities=17% Similarity=0.122 Sum_probs=128.5
Q ss_pred HHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHH
Q 009567 281 DLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA 359 (532)
Q Consensus 281 ~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ 359 (532)
.|...+..| ..|++.|+..|.+.++.++. +.++..+.+|++||.|+.+|+..++|++. ..|.+|++..+++.+.++
T Consensus 13 ~l~~~~~~gd~~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~~~d~ 89 (185)
T PRK09649 13 ALALSAAKGNGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVADH 89 (185)
T ss_pred HHHHHHHccCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHHHHHH
Confidence 355555544 59999999999999999995 67888899999999999999999999964 469999999999999999
Q ss_pred HHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhh
Q 009567 360 IFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEI 439 (532)
Q Consensus 360 ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~ 439 (532)
+++..+..+. +.+. .. +.
T Consensus 90 ~Rk~~~~~~~-----------------------------------------------------~~~~-----~~----~~ 107 (185)
T PRK09649 90 IRHVRSRPRT-----------------------------------------------------TRGA-----RP----EH 107 (185)
T ss_pred HHHhcccccc-----------------------------------------------------cccc-----ch----hh
Confidence 9875421100 0000 00 00
Q ss_pred cccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567 440 TADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519 (532)
Q Consensus 440 i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l 519 (532)
..+. +......+....|..+|..||+++|+||.|+|. +++|++|||+.||+|.++|+..+.||+++||+.+
T Consensus 108 ~~~~-----~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~~ 178 (185)
T PRK09649 108 LIDG-----DRHARGFEDLVEVTTMIADLTTDQREALLLTQL----LGLSYADAAAVCGCPVGTIRSRVARARDALLADA 178 (185)
T ss_pred ccCh-----hhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 0000 000011112245788999999999999999998 9999999999999999999999999999999966
Q ss_pred hcCc
Q 009567 520 GGKA 523 (532)
Q Consensus 520 ~~~~ 523 (532)
....
T Consensus 179 ~~~~ 182 (185)
T PRK09649 179 EPDD 182 (185)
T ss_pred Cccc
Confidence 5443
No 89
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=99.79 E-value=2.7e-18 Score=164.71 Aligned_cols=172 Identities=18% Similarity=0.199 Sum_probs=130.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcccccc
Q 009567 290 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 369 (532)
Q Consensus 290 ~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRl 369 (532)
..+++.|+..|.+.|+.+|.++.++..+.+|++||.|+.+|+.+.+|++. ..|.+|++..++|.+.++++++.+....
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 48899999999999999999999998999999999999999999999864 4699999999999999999876531100
Q ss_pred chhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChh
Q 009567 370 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD 449 (532)
Q Consensus 370 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pe 449 (532)
. ..+++. .. .+. .... ........++
T Consensus 88 ~-------------------------~~~~~~-----------~~--------~~~----~~~~------~~~~~~~~~e 113 (193)
T TIGR02947 88 S-------------------------DDDDIE-----------DW--------QLA----KAAS------HTSNGLRSAE 113 (193)
T ss_pred c-------------------------cchhhh-----------hh--------hhc----cccc------cccccccchh
Confidence 0 000000 00 000 0000 0000111233
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567 450 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 521 (532)
Q Consensus 450 e~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~ 521 (532)
...........|..+|..||+++|+||.|+|. +++|++|||+.||+|..+|+.++.||+++||+.+..
T Consensus 114 ~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 181 (193)
T TIGR02947 114 LEALDGLPDQDIKDALQGLPEEFRQAVYLADV----EGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVD 181 (193)
T ss_pred HHHHhhhhHHHHHHHHHhCCHHHhhheeehhh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 33333344567899999999999999999998 999999999999999999999999999999998864
No 90
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=99.78 E-value=6.2e-18 Score=158.09 Aligned_cols=158 Identities=15% Similarity=0.107 Sum_probs=130.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchh
Q 009567 293 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 372 (532)
Q Consensus 293 re~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~ 372 (532)
++.|+..|.+.|+.+|+++.++..+.+|++||+++.+|+++++|++. .|.+|++..+++.+.+++++..+....
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~--- 76 (165)
T PRK09644 3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFV--- 76 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhcccc---
Confidence 57899999999999999999999999999999999999999999863 599999999999999999876421100
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHH
Q 009567 373 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV 452 (532)
Q Consensus 373 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~ 452 (532)
..+++ +.+. ..+|++.+
T Consensus 77 -----------------------~~~~~-------------------------------------~~~~---~~~~~~~~ 93 (165)
T PRK09644 77 -----------------------GTDEI-------------------------------------EAIQ---AESTEEYV 93 (165)
T ss_pred -----------------------chhHH-------------------------------------hhhc---ccChHHHH
Confidence 00000 0000 01355555
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 009567 453 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 523 (532)
Q Consensus 453 ~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~ 523 (532)
...+....+..+|..||+++|+||.++|. +++|.+|||+.||+|..+|+..+.||+++||+.+....
T Consensus 94 ~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~~ 160 (165)
T PRK09644 94 VAKNSYEKLIQIIHTLPVIEAQAILLCDV----HELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEEK 160 (165)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHhHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Confidence 55666678999999999999999999998 99999999999999999999999999999999987544
No 91
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=6.8e-18 Score=162.03 Aligned_cols=161 Identities=20% Similarity=0.197 Sum_probs=128.3
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccc
Q 009567 289 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 368 (532)
Q Consensus 289 g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IR 368 (532)
+..++..|+..|.+.++.+|.++.++..+.+|++||.++.+|+..++|+.. ..|.+|++..+++.+.++++++.+...
T Consensus 8 ~~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~awL~~Ia~n~~~d~~R~~~~~~~ 85 (187)
T PRK12516 8 GTPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVG--TNMKAWLFTILRNEFYSQMRKRGREVQ 85 (187)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCc--ccHHHHHHHHHHHHHHHHHHhhcCCcc
Confidence 458999999999999999999999999999999999999999999999864 359999999999999999887542100
Q ss_pred cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCCh
Q 009567 369 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP 448 (532)
Q Consensus 369 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~p 448 (532)
. .+.. +.+... . .+
T Consensus 86 ~------------------------------------------------------~~~~--------~~~~~~-~---~~ 99 (187)
T PRK12516 86 D------------------------------------------------------TDGM--------FTEQLA-V---HP 99 (187)
T ss_pred c------------------------------------------------------cccc--------cccccC-C---Cc
Confidence 0 0000 000000 0 01
Q ss_pred hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 009567 449 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 523 (532)
Q Consensus 449 ee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~ 523 (532)
+. ........|..+|..||+++|+||.|+|. +++|++|||+.||+|.++|+..+.||+++||+.+...+
T Consensus 100 ~~--~~~~~~~~l~~~L~~Lp~~~r~i~~L~~~----~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~~~ 168 (187)
T PRK12516 100 SQ--YGTLDLQDFRAALDQLPDDQREAIILVGA----SGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQIEG 168 (187)
T ss_pred ch--hhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence 10 01112346889999999999999999998 99999999999999999999999999999999998654
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=99.78 E-value=7.2e-18 Score=156.70 Aligned_cols=158 Identities=19% Similarity=0.211 Sum_probs=127.5
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcccc
Q 009567 288 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 367 (532)
Q Consensus 288 ~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~I 367 (532)
++..+++.|+..|.+.|+.+|.++.++..+.+|++||+++.+|+..++|+. ...|.+|++..+++.+.+++++..+.
T Consensus 3 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~~~d~~rk~~~~- 79 (162)
T TIGR02983 3 ATEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNLARSRWRRRRLL- 79 (162)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHHHHHHHHhhccc-
Confidence 456999999999999999999999999999999999999999999999964 34799999999999999998765420
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCC
Q 009567 368 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 447 (532)
Q Consensus 368 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~ 447 (532)
.+ . +... ++..
T Consensus 80 ~~-----------------------------------------------------~-~~~~------------~~~~--- 90 (162)
T TIGR02983 80 EL-----------------------------------------------------P-TREL------------PDAA--- 90 (162)
T ss_pred cc-----------------------------------------------------c-cccc------------Cccc---
Confidence 00 0 0000 0000
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567 448 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 521 (532)
Q Consensus 448 pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~ 521 (532)
++.........+.|..+|..||+++|+||.++|. +++|.+|||+.||+|.++|++...||+++||+.+..
T Consensus 91 ~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 160 (162)
T TIGR02983 91 APDPAPDVALRAALARALRRLPARQRAVVVLRYY----EDLSEAQVAEALGISVGTVKSRLSRALARLRELLEE 160 (162)
T ss_pred CCccchhHHHHHHHHHHHHhCCHHHHHHhhhHHH----hcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 0001122334567889999999999999999997 899999999999999999999999999999998764
No 93
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=99.78 E-value=6.6e-18 Score=159.14 Aligned_cols=162 Identities=14% Similarity=0.084 Sum_probs=127.3
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccc
Q 009567 289 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 368 (532)
Q Consensus 289 g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IR 368 (532)
+..++..|+..|.+.|+.++.++.++..+.+|++||+++.+|+. ..|+.. ..|.+|++.++++.+.++++++.+..
T Consensus 8 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~~~~- 83 (172)
T PRK12523 8 HSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAALEQ- 83 (172)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHHHHH-
Confidence 34999999999999999999999999999999999999999986 446543 36999999999999999998754100
Q ss_pred cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCCh
Q 009567 369 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP 448 (532)
Q Consensus 369 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~p 448 (532)
.. ..++ .. ........|
T Consensus 84 -----------------~~---------~~~~------------------------~~-------------~~~~~~~~~ 100 (172)
T PRK12523 84 -----------------AY---------LAEL------------------------AL-------------VPEAEQPSP 100 (172)
T ss_pred -----------------HH---------HHHH------------------------hh-------------cccccCCCh
Confidence 00 0000 00 000001134
Q ss_pred hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567 449 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 521 (532)
Q Consensus 449 ee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~ 521 (532)
+......+....+..+|..||+++|+||.|+|. +++|++|||+.||+|.++|++.+.+|+++||..+..
T Consensus 101 ~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l~~ 169 (172)
T PRK12523 101 EEQHLILEDLKAIDRLLGKLSSKARAAFLYNRL----DGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIALYG 169 (172)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 444444444457999999999999999999998 999999999999999999999999999999998764
No 94
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=99.78 E-value=1.3e-17 Score=162.24 Aligned_cols=166 Identities=20% Similarity=0.290 Sum_probs=135.9
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccc
Q 009567 289 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 368 (532)
Q Consensus 289 g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IR 368 (532)
+..+++.|+..|.+.++.++.++.++..+.+|++||+++.+|+...+|++ + .|.+|++..+++.+.+++++..+ .+
T Consensus 26 d~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~~-~~ 101 (203)
T PRK09647 26 TMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRAR-IR 101 (203)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhccc-Cc
Confidence 35899999999999999999999999999999999999999999999985 3 69999999999999999987542 10
Q ss_pred cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCCh
Q 009567 369 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP 448 (532)
Q Consensus 369 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~p 448 (532)
. ..++ .+ + +... ....+|
T Consensus 102 ~----------------------------------------------------~~~~------~~--~-~~~~-~~~~~~ 119 (203)
T PRK09647 102 M----------------------------------------------------EALP------ED--Y-DRVP-GDEPNP 119 (203)
T ss_pred c----------------------------------------------------cccc------cc--c-cccC-CCCCCH
Confidence 0 0000 00 0 0001 112245
Q ss_pred hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 009567 449 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 524 (532)
Q Consensus 449 ee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l 524 (532)
+..+...+....|..+|..||+++|+||.++|+ ++++++|||+.||+|..+|++.+.||+++||+.+...+-
T Consensus 120 ~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~~----~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~~~~ 191 (203)
T PRK09647 120 EQIYHDARLDPDLQAALDSLPPEFRAAVVLCDI----EGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAAHAP 191 (203)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhch
Confidence 556666777778999999999999999999998 999999999999999999999999999999999876543
No 95
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=99.77 E-value=1.3e-17 Score=155.07 Aligned_cols=157 Identities=15% Similarity=0.084 Sum_probs=124.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 009567 291 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 370 (532)
Q Consensus 291 ~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP 370 (532)
.|++.|+..|.+.|+.++.++.++..+.+|++||+++.+|+..+.|++ ..|.+|.+.++++.+.+++++..+..
T Consensus 4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~---~~~~~wl~~i~~n~~~d~~R~~~~~~--- 77 (161)
T PRK12528 4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQI---IEPRAFLTTIAKRVLCNHYRRQDLER--- 77 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhccccccc---cCHHHHHHHHHHHHHHHHHHHHHHHH---
Confidence 689999999999999999999999899999999999999999988865 26999999999999999987643100
Q ss_pred hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhH
Q 009567 371 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI 450 (532)
Q Consensus 371 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee 450 (532)
.. .+++ + + .++.....++.
T Consensus 78 ---------------~~---------~~~~------------------------~------------~-~~~~~~~~~~~ 96 (161)
T PRK12528 78 ---------------AY---------LEAL------------------------A------------Q-LPERVAPSEEE 96 (161)
T ss_pred ---------------hh---------HHHh------------------------h------------c-cccccCCCHHH
Confidence 00 0000 0 0 00001112333
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567 451 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 518 (532)
Q Consensus 451 ~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~ 518 (532)
.....+....|..+|..||+++|+||.|+|. +|+|.+|||+.||+|.++|+..+.+|+++||..
T Consensus 97 ~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~----~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~ 160 (161)
T PRK12528 97 RAIILETLVELDQLLDGLPPLVKRAFLLAQV----DGLGYGEIATELGISLATVKRYLNKAAMRCYFA 160 (161)
T ss_pred HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhc
Confidence 3333344567899999999999999999998 999999999999999999999999999999864
No 96
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=99.77 E-value=2.3e-17 Score=154.44 Aligned_cols=159 Identities=17% Similarity=0.152 Sum_probs=126.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcccccc
Q 009567 290 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 369 (532)
Q Consensus 290 ~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRl 369 (532)
...+..++..|.+.|+.+|+++.++..+.+|++||+++.+|+..++|++. ..|.+|++..+++.+.+++++..+....
T Consensus 5 ~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~~~~~~~ 82 (164)
T PRK12547 5 SKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMG--TNLKAWLFTILRNEFYSQMRKRGREVQD 82 (164)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCc--ccHHHHHHHHHHHHHHHHHHhhcccccc
Confidence 46789999999999999999999999999999999999999999999864 3599999999999999998875421000
Q ss_pred chhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChh
Q 009567 370 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD 449 (532)
Q Consensus 370 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pe 449 (532)
.+...... .+ ..++
T Consensus 83 ------------------------------------------------------~~~~~~~~---------~~---~~~~ 96 (164)
T PRK12547 83 ------------------------------------------------------SDGVFTAR---------VA---VHPA 96 (164)
T ss_pred ------------------------------------------------------cccccccc---------CC---CCch
Confidence 00000000 00 0111
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567 450 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 522 (532)
Q Consensus 450 e~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~ 522 (532)
. ........+..+|..||+++|+||.++|. +++|++|||+.||+|.++|++.+.||+++||..+.-.
T Consensus 97 ~--~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 163 (164)
T PRK12547 97 Q--YGSLDLQDFKKALNLLSADQREAIILIGA----SGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLKVD 163 (164)
T ss_pred h--hhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence 1 11122456889999999999999999998 8999999999999999999999999999999988643
No 97
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=99.77 E-value=1.9e-17 Score=159.14 Aligned_cols=181 Identities=18% Similarity=0.143 Sum_probs=132.3
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCC-HhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchh
Q 009567 294 EKLINANLRLVVHVAKQYQGRGIS-LHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 372 (532)
Q Consensus 294 e~LI~~nlrLV~sIAkrY~~~g~~-~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~ 372 (532)
+..+..|.+.|+.+|+++.++..+ .+|++||+++.+|+++++|++. .+|.+|++..+++.+.++++++.+.......
T Consensus 8 ~~~~~~~~~~l~~~a~~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~~ 85 (195)
T PRK12532 8 DAELIESRKLLLHFARLQLPDHPDLAEDLVQETLLSAYSAGDSFQGR--ALVNSWLFAILKNKIIDALRQIGRQRKVFTL 85 (195)
T ss_pred hhhHHHHHHHHHHHHHHHcCChhhhHHHHHHHHHHHHHHhccccccc--chHHHHHHHHHHHHHHHHHHHhccccccccc
Confidence 456778999999999999998888 9999999999999999999864 4799999999999999999876532110000
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHH
Q 009567 373 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV 452 (532)
Q Consensus 373 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~ 452 (532)
. ..+.+ ... ..+.. .. ++....+... ....+|+..+
T Consensus 86 ~----------------------~~~~~-----------~~~------~~~~~---~~-~~~~~~~~~~-~~~~~~e~~~ 121 (195)
T PRK12532 86 L----------------------DDELL-----------DEA------FESHF---SQ-NGHWTPEGQP-QHWNTPEKSL 121 (195)
T ss_pred c----------------------ccccc-----------chh------hhhhh---cc-ccccccccCc-cccCCHHHHH
Confidence 0 00000 000 00000 00 0000000000 1123567777
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 009567 453 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 524 (532)
Q Consensus 453 ~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l 524 (532)
...+....+..+|..||+++|+||.|+|. +++|++|||+.||+|..+|+..++||+++||+++....+
T Consensus 122 ~~~e~~~~l~~~l~~L~~~~r~i~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~ 189 (195)
T PRK12532 122 NNNEFQKILQSCLYNLPENTARVFTLKEI----LGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKWF 189 (195)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHhhhHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 77777778999999999999999999998 999999999999999999999999999999999976543
No 98
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=99.77 E-value=1.9e-17 Score=158.89 Aligned_cols=178 Identities=12% Similarity=0.132 Sum_probs=132.7
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhH
Q 009567 294 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI 373 (532)
Q Consensus 294 e~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~ 373 (532)
.+.+..|.+.|+.+|+++.++..+.+|++||+++.+|+..++|++. .+|.+|++..+++.+.++++++.+....+. +
T Consensus 5 ~~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~~-~ 81 (188)
T TIGR02943 5 PQELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVSD-L 81 (188)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCccc-c
Confidence 3577889999999999999999999999999999999999999975 479999999999999999987653211100 0
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHH
Q 009567 374 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ 453 (532)
Q Consensus 374 ~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~ 453 (532)
. ++. ..-.++... ...+.......++ ....|+..+.
T Consensus 82 ------------------~-----~~~-------------------~~~~~~~~~-~~~~~~~~~~~~~-~~~~~e~~~~ 117 (188)
T TIGR02943 82 ------------------D-----DEL-------------------DDEAFNALF-TQNGHWAQHGQPQ-HWNTPEKQLE 117 (188)
T ss_pred ------------------c-----ccc-------------------ccchhhhhh-ccccchhcccccc-ccCCHHHHHH
Confidence 0 000 000000000 0000000011111 1235666777
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567 454 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 522 (532)
Q Consensus 454 ~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~ 522 (532)
..+....+..+|..||+++|+||.++|. +++|++|||+.||+|.++|++++.||+++||+++...
T Consensus 118 ~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~ 182 (188)
T TIGR02943 118 NKEFWEVFEACLYHLPEQTARVFMMREV----LGFESDEICQELEISTSNCHVLLYRARLSLRACLSIN 182 (188)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 7777788999999999999999999998 8999999999999999999999999999999998754
No 99
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=99.77 E-value=2.7e-17 Score=153.24 Aligned_cols=161 Identities=19% Similarity=0.179 Sum_probs=129.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcccccc
Q 009567 290 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 369 (532)
Q Consensus 290 ~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRl 369 (532)
+.+++.|+..|.+.|+.+|+++.++..+.+|++||+++.+|++ .|+. +..|.+|++..+++.+.+++++..+..+.
T Consensus 2 ~~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~~~~~ 77 (166)
T PRK09639 2 DETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKRRRAR 77 (166)
T ss_pred chHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhcccccc
Confidence 3689999999999999999999999999999999999999999 6764 34799999999999999999875521110
Q ss_pred chhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChh
Q 009567 370 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD 449 (532)
Q Consensus 370 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pe 449 (532)
. +. .....+. + ....|+
T Consensus 78 ~------------------------------------------------------~~------~~~~~~~--~-~~~~~e 94 (166)
T PRK09639 78 I------------------------------------------------------LG------EFQWQEV--D-NEPSPE 94 (166)
T ss_pred c------------------------------------------------------cc------hhhhhhc--c-CCCChH
Confidence 0 00 0000000 1 122566
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567 450 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 522 (532)
Q Consensus 450 e~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~ 522 (532)
+.....+....+..+|..||+++|.||.++| +|+|++|||+.||+|..+|+..+.||+++||+.+...
T Consensus 95 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-----~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~~~ 162 (166)
T PRK09639 95 EIWIRKEEITKVQEVLAKMTERDRTVLLLRF-----SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQM 162 (166)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 6666666677899999999999999999999 5899999999999999999999999999999988643
No 100
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=99.77 E-value=2.6e-17 Score=153.09 Aligned_cols=157 Identities=14% Similarity=0.118 Sum_probs=124.0
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccc
Q 009567 289 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 368 (532)
Q Consensus 289 g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IR 368 (532)
...+++.++..|.+.|+.++.++.++..+.+|++||+++.+|+..++|++. .|.||++..+++.+.+++++..+...
T Consensus 3 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~~ 79 (161)
T PRK12541 3 RKQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEKKYKT 79 (161)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhcccccc
Confidence 357899999999999999999999999999999999999999999999863 59999999999999999987653100
Q ss_pred cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCCh
Q 009567 369 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP 448 (532)
Q Consensus 369 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~p 448 (532)
+ ..+ + ...+.....+
T Consensus 80 ~-----------------------------------------------------~~~-------~-----~~~~~~~~~~ 94 (161)
T PRK12541 80 T-----------------------------------------------------TIE-------E-----FHLPNVPSTE 94 (161)
T ss_pred c-----------------------------------------------------chh-------h-----hhccCCCCcH
Confidence 0 000 0 0000000112
Q ss_pred hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567 449 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 518 (532)
Q Consensus 449 ee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~ 518 (532)
++.....+. ..+..+|..||+++|.||.|+|. +++|.+|||+.||+|..+|++...||+++||+.
T Consensus 95 ~~~~~~~~~-~~~~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 95 HEYFIKHEI-ASWLDSLSSLPLERRNVLLLRDY----YGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HHHHHHhHH-HHHHHHHHHCCHHHHHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 222222222 34567899999999999999998 899999999999999999999999999999975
No 101
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=99.76 E-value=2.7e-17 Score=159.41 Aligned_cols=180 Identities=14% Similarity=0.157 Sum_probs=130.5
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHH
Q 009567 295 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY 374 (532)
Q Consensus 295 ~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~ 374 (532)
.++..|.+.++.+|+++.++..+.+|++||.|+.+|+.+++|++. ..|.+|++..+++.+.++++++.+...++..
T Consensus 12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~-- 87 (201)
T PRK12545 12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQ--SAHKTWVFGILRNKLIDTLRARQRTVNLSAL-- 87 (201)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhcccc--chHHHHHHHHHHHHHHHHHHhhccccccccc--
Confidence 458889999999999999999999999999999999999999975 3699999999999999999876532111000
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch-hhhcccCCCCChhHHHH
Q 009567 375 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF-QEITADTGVEIPDISVQ 453 (532)
Q Consensus 375 ~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l-~d~i~d~~~~~pee~~~ 453 (532)
..++. ....++...... ...+ .+..++ ....+++...
T Consensus 88 ----------------------~~~~~------------------~~~~~~~~~~~~-~~~~~~~~~~~-~~~~~~~~~~ 125 (201)
T PRK12545 88 ----------------------DAELD------------------GEALLDRELFKD-NGHWAAHAKPR-PWPKPETILQ 125 (201)
T ss_pred ----------------------ccccc------------------hhhhhhhhhhcc-cccccccccCc-CCCCHHHHHH
Confidence 00000 000000000000 0000 000011 1124555555
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 009567 454 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 524 (532)
Q Consensus 454 ~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l 524 (532)
..+....+..+|..||+++|+||.|+|+ +++|++|||+.||+|.++|+..+.||+++||+++...++
T Consensus 126 ~~~~~~~l~~~L~~Lp~~~r~v~~L~~~----eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~~ 192 (201)
T PRK12545 126 QQQFWTLFETCLDHLPEQIGRVFMMREF----LDFEIDDICTELTLTANHCSVLLYRARTRLRTCLSEKGL 192 (201)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 5556667899999999999999999998 999999999999999999999999999999999975543
No 102
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=99.76 E-value=3.1e-17 Score=157.38 Aligned_cols=177 Identities=16% Similarity=0.109 Sum_probs=131.0
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhH
Q 009567 294 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI 373 (532)
Q Consensus 294 e~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~ 373 (532)
+..|..|.+.++.+|.++.++..+.+|++||+|+.+|+..++|++. .+|.+|++..+++.+.++++++.+...... .
T Consensus 10 ~~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~-~ 86 (189)
T PRK12530 10 SLEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQ--SALKTWIFAILKNKIIDLIRYRKRFVNESE-L 86 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCC--ccHHHHHHHHHHHHHHHHHHhhccCCCccc-c
Confidence 3457778999999999999998999999999999999999999875 369999999999999999987653211000 0
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHH
Q 009567 374 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ 453 (532)
Q Consensus 374 ~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~ 453 (532)
. ++. .+.... +.......+.........|+..+.
T Consensus 87 ------------------~-----~~~-------------------~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~ 120 (189)
T PRK12530 87 ------------------I-----EED-------------------SPNSFF----DEKGHWKPEYYEPSEWQEVENTVY 120 (189)
T ss_pred ------------------c-----ccc-------------------cchhhh----cccccccccccCCccccCHHHHHH
Confidence 0 000 000000 000000000000111235666666
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 009567 454 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 523 (532)
Q Consensus 454 ~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~ 523 (532)
..+....|..+|+.||+++|+||.|+|. +++|++|||+.||+|.++|+.+++||+++||+++....
T Consensus 121 ~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~ 186 (189)
T PRK12530 121 KEEFWLIFEACLNHLPAQQARVFMMREY----LELSSEQICQECDISTSNLHVLLYRARLQLQACLSKNW 186 (189)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHhHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6777788999999999999999999998 89999999999999999999999999999999986543
No 103
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=99.76 E-value=3.1e-17 Score=160.01 Aligned_cols=181 Identities=18% Similarity=0.216 Sum_probs=134.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchh
Q 009567 293 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 372 (532)
Q Consensus 293 re~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~ 372 (532)
-..++..|.+.|+.+|+++.++....+|++||+++.+|+.+.+|++. .+|.+|++..+++.+.+++++..+....+..
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 36788999999999999999999999999999999999999999864 4699999999999999999876542111100
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHH
Q 009567 373 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV 452 (532)
Q Consensus 373 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~ 452 (532)
. . ....+ ..+..+. + ................|+..+
T Consensus 98 ~------------------~--~~~~~---------~~~~~~~--------------~-~~~~~~~~~~~~~~~~~e~~~ 133 (206)
T PRK12544 98 L------------------R--DEEEE---------EDFEELF--------------D-ESGHWQKDERPQAWGNPEESL 133 (206)
T ss_pred c------------------c--ccchh---------hHHHHhh--------------c-ccccccccccccccCCHHHHH
Confidence 0 0 00000 0000000 0 000000000011123567667
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 009567 453 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 523 (532)
Q Consensus 453 ~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~ 523 (532)
...+....+..+|..||+++|+||.++|. +++|++|||+.||+|..+|+..+.||+++||+.+....
T Consensus 134 ~~~e~~~~l~~~L~~L~~~~r~v~~L~~~----~g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~~ 200 (206)
T PRK12544 134 EQEQFWRIFEACLDGLPAKYARVFMMREF----IELETNEICHAVDLSVSNLNVLLYRARLRLRECLENKW 200 (206)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 77777778899999999999999999998 89999999999999999999999999999999987543
No 104
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=99.76 E-value=4.6e-17 Score=169.48 Aligned_cols=187 Identities=18% Similarity=0.200 Sum_probs=135.9
Q ss_pred HHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHH
Q 009567 281 DLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA 359 (532)
Q Consensus 281 ~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ 359 (532)
+|+..++.| ..+++.|+..|.+.|+.+|.++.++..+.+|++||.++.+|+.+++|++. ..|.+|++...+|.+.++
T Consensus 8 ~l~~~~~~gd~~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~ 85 (339)
T PRK08241 8 ALLARAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATNVCLDA 85 (339)
T ss_pred HHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHHHHHHH
Confidence 455555555 49999999999999999999999999999999999999999999999853 469999999999999999
Q ss_pred HHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhh
Q 009567 360 IFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEI 439 (532)
Q Consensus 360 ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~ 439 (532)
++++.+... +.. .+ .+. .........+....+.+.
T Consensus 86 ~Rk~~~~~~-~~~------------------~~-~~~-------------------------~~~~~~~~~~~~~~~~~~ 120 (339)
T PRK08241 86 LEGRARRPL-PTD------------------LG-APA-------------------------ADPVDELVERPEVPWLEP 120 (339)
T ss_pred HHhhccccC-ccc------------------cC-CCc-------------------------CcccccccccccccccCC
Confidence 987643100 000 00 000 000000000000001111
Q ss_pred cccC----CCCChhHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009567 440 TADT----GVEIPDISVQKQL-MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR 514 (532)
Q Consensus 440 i~d~----~~~~pee~~~~~~-l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkK 514 (532)
+.+. ...+|++.+...+ ....|..+|..||+++|+||.|+|. +++|++|||++||+|..+|++++.||+++
T Consensus 121 ~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~RAr~~ 196 (339)
T PRK08241 121 YPDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLILRDV----LGWSAAEVAELLDTSVAAVNSALQRARAT 196 (339)
T ss_pred CCcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhHHh----hCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 1110 1235665555444 3456889999999999999999998 99999999999999999999999999999
Q ss_pred HHHH
Q 009567 515 LKQS 518 (532)
Q Consensus 515 LR~~ 518 (532)
||+.
T Consensus 197 Lr~~ 200 (339)
T PRK08241 197 LAER 200 (339)
T ss_pred Hhhc
Confidence 9993
No 105
>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=99.75 E-value=1.4e-17 Score=153.13 Aligned_cols=152 Identities=18% Similarity=0.206 Sum_probs=122.3
Q ss_pred HHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHH
Q 009567 298 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL 377 (532)
Q Consensus 298 ~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l 377 (532)
..|.+.|+.++.++.++..+.+|++||+++.+|+.+++|++ .+|.+|++..+++.+.+++++..+....+
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~~------- 71 (154)
T TIGR02950 2 REYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTID------- 71 (154)
T ss_pred chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhcccc-------
Confidence 57899999999999998889999999999999999999997 37999999999999999987654211000
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHH
Q 009567 378 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 457 (532)
Q Consensus 378 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~~l 457 (532)
.+. +.+... .....|++.+...+.
T Consensus 72 -------------------~~~------------------------------------~~~~~~-~~~~~~~~~~~~~~~ 95 (154)
T TIGR02950 72 -------------------DDA------------------------------------IGDLEQ-HPVESPEHHLLIKIE 95 (154)
T ss_pred -------------------Hhh------------------------------------hhhccc-cccCChhHHHHHHHH
Confidence 000 000000 011245555555566
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567 458 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519 (532)
Q Consensus 458 ~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l 519 (532)
...|..+|..||+++++||.++|+ +|+|++|||+.||+|..+|++...||+++||+.+
T Consensus 96 ~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~l 153 (154)
T TIGR02950 96 QEEITHHLSRLPENYRTVLILREF----KEFSYKEIAELLNLSLAKVKSNLFRARKELKKLL 153 (154)
T ss_pred HHHHHHHHHhCCHhheeeeeehhh----ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 678999999999999999999988 8999999999999999999999999999999875
No 106
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=99.75 E-value=6.2e-17 Score=156.59 Aligned_cols=170 Identities=17% Similarity=0.110 Sum_probs=129.6
Q ss_pred HHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHH
Q 009567 282 LKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI 360 (532)
Q Consensus 282 L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~i 360 (532)
|+..+..| ..+++.|+..|.+.++.+++ +.++..+.+|++||.|+.+|+..++|++. ..|.+|++..+++.+.+++
T Consensus 15 l~~~~~~~d~~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~ 91 (196)
T PRK12535 15 LALAAGRGDRAALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAAR--SSARTWLLSLARRVWVDNI 91 (196)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCc--ccHHHHHHHHHHHHHHHHH
Confidence 44444444 59999999999999999975 67888899999999999999999999864 3699999999999999999
Q ss_pred HhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhc
Q 009567 361 FQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEIT 440 (532)
Q Consensus 361 r~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i 440 (532)
++..+..+. ..+ .. . ...+
T Consensus 92 Rk~~~~~~~-----------------------------------------------------~~~-~~-~----~~~~-- 110 (196)
T PRK12535 92 RHDMARPRK-----------------------------------------------------SAT-EY-E----DAAA-- 110 (196)
T ss_pred HhhccCCCc-----------------------------------------------------ccc-cc-c----cccc--
Confidence 875421110 000 00 0 0000
Q ss_pred ccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567 441 ADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 520 (532)
Q Consensus 441 ~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~ 520 (532)
.. ..++..... .....+..+|+.||+++|+||.++|. +++|++|||+.||+|.++|++.+.||+++||+.+.
T Consensus 111 --~~-~~~~~~~~~-~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~ 182 (196)
T PRK12535 111 --TT-ASNETTGSW-SEWIDVRTLIDALPPERREALILTQV----LGYTYEEAAKIADVRVGTIRSRVARARADLIAATA 182 (196)
T ss_pred --cc-CCcchhHHH-HHHHHHHHHHHcCCHHHHHHhhhHHH----hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 00 111111111 12346889999999999999999998 89999999999999999999999999999999987
Q ss_pred cCc
Q 009567 521 GKA 523 (532)
Q Consensus 521 ~~~ 523 (532)
...
T Consensus 183 ~~~ 185 (196)
T PRK12535 183 TGQ 185 (196)
T ss_pred ccc
Confidence 654
No 107
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=99.75 E-value=5.6e-17 Score=167.45 Aligned_cols=182 Identities=17% Similarity=0.187 Sum_probs=134.0
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccc
Q 009567 289 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 368 (532)
Q Consensus 289 g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IR 368 (532)
+..|++.|+..|.+.++.+|.++.++..+.+|++||.++.+|+.+++|++. ..|.+|++..++|.+.++++++.+...
T Consensus 3 d~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~~~ 80 (324)
T TIGR02960 3 DGAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQRRPR 80 (324)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhccCCcC
Confidence 458999999999999999999999999999999999999999999999864 469999999999999999987553110
Q ss_pred cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcc-------
Q 009567 369 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITA------- 441 (532)
Q Consensus 369 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~------- 441 (532)
.... .. + ........ ..+......+.+.
T Consensus 81 ~~~~------------------~~--~------------------------~~~~~~~~-~~~~~~~~~~~~~~~~~~~~ 115 (324)
T TIGR02960 81 PVGL------------------GA--P------------------------SADGTAAA-SEAAEVTWLEPLPDLTLDLD 115 (324)
T ss_pred cccc------------------CC--C------------------------CCcccccc-cccccccccCCCCccccccc
Confidence 0000 00 0 00000000 0000000000000
Q ss_pred cCCCCChhHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567 442 DTGVEIPDISVQKQL-MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 520 (532)
Q Consensus 442 d~~~~~pee~~~~~~-l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~ 520 (532)
.....+|++.+...+ +...+..+|..||+++|+||.|+|. +++|++|||+.||+|.++|++++.||+++||+++.
T Consensus 116 ~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 191 (324)
T TIGR02960 116 DPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDV----LGWRAAETAELLGTSTASVNSALQRARATLDEVGP 191 (324)
T ss_pred cCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcc
Confidence 011235665555444 4556889999999999999999998 89999999999999999999999999999999987
Q ss_pred c
Q 009567 521 G 521 (532)
Q Consensus 521 ~ 521 (532)
.
T Consensus 192 ~ 192 (324)
T TIGR02960 192 S 192 (324)
T ss_pred c
Confidence 4
No 108
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=99.75 E-value=6.5e-17 Score=150.41 Aligned_cols=159 Identities=14% Similarity=0.214 Sum_probs=124.9
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHH
Q 009567 295 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY 374 (532)
Q Consensus 295 ~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~ 374 (532)
.++..|.+.++.+|.++.++..+.+|++||+++.+|+....|++. .|.+|++..+++.+.++++++.+....
T Consensus 2 ~~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn~~~d~~R~~~~~~~~----- 73 (163)
T PRK07037 2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRNLAIDHYRRQALENKY----- 73 (163)
T ss_pred hHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHHHHHHHHHhhcccccc-----
Confidence 367788999999999999999999999999999999998877763 488999999999999999875421000
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHH
Q 009567 375 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK 454 (532)
Q Consensus 375 ~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~ 454 (532)
+ ..+.... .. .+. ..+|+..+..
T Consensus 74 ------------------------------------------------~------~~~~~~~-~~-~~~-~~~~~~~~~~ 96 (163)
T PRK07037 74 ------------------------------------------------H------GDEEDGL-DV-PSP-EASPEAALIN 96 (163)
T ss_pred ------------------------------------------------c------ccccccc-cc-CCC-CCCHHHHHHH
Confidence 0 0000000 00 011 1245555555
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567 455 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 522 (532)
Q Consensus 455 ~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~ 522 (532)
.+..+.+..+|..|||++|+||.++|. +++|.+|||+.||+|.++|+....||+++||+.+...
T Consensus 97 ~~~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l~~~ 160 (163)
T PRK07037 97 RDTLRHVADALSELPARTRYAFEMYRL----HGETQKDIARELGVSPTLVNFMIRDALVHCRKCLDAC 160 (163)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence 566678899999999999999999998 8999999999999999999999999999999988654
No 109
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=99.75 E-value=6.6e-17 Score=154.54 Aligned_cols=160 Identities=18% Similarity=0.220 Sum_probs=126.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 009567 291 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 370 (532)
Q Consensus 291 ~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP 370 (532)
.++..++..|.+.|+.+|.++.++..+.+|++||.++.+|+..++|++.. .|.+|++..+++.+.++++++.+....
T Consensus 5 ~~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~~~~~- 81 (182)
T PRK12540 5 DSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGS--NLPAWLFTILRNLFRSDYRKRRREVED- 81 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCc--hHHHHHHHHHHHHHHHHHHhccccccc-
Confidence 56788999999999999999999999999999999999999999998753 699999999999999998765421000
Q ss_pred hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhH
Q 009567 371 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI 450 (532)
Q Consensus 371 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee 450 (532)
.+. ...+... . .++.
T Consensus 82 -----------------------------------------------------~~~--------~~~~~~~-~---~~~~ 96 (182)
T PRK12540 82 -----------------------------------------------------ADG--------SYAKTLK-S---QPGQ 96 (182)
T ss_pred -----------------------------------------------------ccc--------ccccccc-C---CCch
Confidence 000 0000000 0 1111
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 009567 451 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 524 (532)
Q Consensus 451 ~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l 524 (532)
.. ......|..+|+.||+++|+||.++|. +++|.+|||+.||+|..+|++.++||+++||+.+.....
T Consensus 97 ~~--~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~~ 164 (182)
T PRK12540 97 NA--HLEFEEFRAALDKLPQDQREALILVGA----SGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDGA 164 (182)
T ss_pred HH--HHHHHHHHHHHHhCCHHHHHHhhHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 11 112346889999999999999999998 999999999999999999999999999999999986553
No 110
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=99.74 E-value=9e-17 Score=149.21 Aligned_cols=155 Identities=12% Similarity=0.090 Sum_probs=123.8
Q ss_pred HHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHH
Q 009567 298 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL 377 (532)
Q Consensus 298 ~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l 377 (532)
..|.+.++.++.++.++..+.+|++||.++.+|+..+.|++ .+|.||++..+++.+.++++++.+...
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~---~~~~~wL~~ia~n~~~d~~R~~~~~~~--------- 69 (159)
T PRK12527 2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQI---EHPRAFLYRTALNLVVDRHRRHRVRQA--------- 69 (159)
T ss_pred hhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhccccccc---cchHHHHHHHHHHHHHHHHHHHhcccc---------
Confidence 56888899999999998889999999999999999999875 279999999999999999886531000
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHH
Q 009567 378 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 457 (532)
Q Consensus 378 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~~l 457 (532)
.+++. . .+. ......+|++.+...+.
T Consensus 70 --------------------------------------------~~~~~-~-~~~--------~~~~~~~~~~~~~~~~~ 95 (159)
T PRK12527 70 --------------------------------------------EPLEV-L-DEE--------ERLHSPSPQTRLDLGQR 95 (159)
T ss_pred --------------------------------------------cchhh-h-hcc--------ccccCCCHHHHHHHHHH
Confidence 00000 0 000 00011246666666667
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567 458 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 522 (532)
Q Consensus 458 ~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~ 522 (532)
...|..+|..||+++++||.|+|+ +++|.+|||+.||+|.++|+..+.||+++||+.+...
T Consensus 96 ~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~~~ 156 (159)
T PRK12527 96 LALLQRALAELPPACRDSFLLRKL----EGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQW 156 (159)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 778999999999999999999998 9999999999999999999999999999999998754
No 111
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=99.74 E-value=1.4e-16 Score=152.15 Aligned_cols=154 Identities=21% Similarity=0.194 Sum_probs=126.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchh
Q 009567 293 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 372 (532)
Q Consensus 293 re~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~ 372 (532)
++.|+..|.+.|+.+|.++.++..+.+|++||.++.+|+.+..|++. .+|.+|++..+++.+.++++++.+...++
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~~--~~~~~wL~~i~~n~~~d~~Rk~~~~~~~~-- 78 (181)
T PRK09637 3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNTIIDFYRKKNRSEELP-- 78 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhccc--cchHHHHHHHHHHHHHHHHHhccccCCcc--
Confidence 57899999999999999999999999999999999999999999853 47999999999999999998765211000
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHH
Q 009567 373 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV 452 (532)
Q Consensus 373 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~ 452 (532)
.+ +...+ .+++..
T Consensus 79 ---------------------------------------------------------~~------~~~~~----~~~~~~ 91 (181)
T PRK09637 79 ---------------------------------------------------------DD------LLFED----EEREEN 91 (181)
T ss_pred ---------------------------------------------------------hh------hhccC----CChhHH
Confidence 00 00000 111222
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567 453 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 521 (532)
Q Consensus 453 ~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~ 521 (532)
...+....+..+|..||+++|+||.++|. ++++.+|||+.||+|..+|+....||+++||+.+..
T Consensus 92 ~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (181)
T PRK09637 92 AKKELAPCLRPFIDALPEKYAEALRLTEL----EGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156 (181)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 33445667899999999999999999998 999999999999999999999999999999998864
No 112
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=99.73 E-value=1.4e-16 Score=150.33 Aligned_cols=164 Identities=15% Similarity=0.071 Sum_probs=126.6
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccc
Q 009567 289 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 368 (532)
Q Consensus 289 g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IR 368 (532)
+..|++.++..|.+.++.++.++.++..+.+|++||.++.+|+. ..|++-. .|.+|++..+++.+.+++++..+...
T Consensus 8 ~~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~~~~~ 84 (172)
T PRK09651 8 ASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNALEKA 84 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 35899999999999999999999999999999999999999998 3565432 58999999999999999876431000
Q ss_pred cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCCh
Q 009567 369 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP 448 (532)
Q Consensus 369 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~p 448 (532)
. .+.+ + . +.+....+|
T Consensus 85 ----------------------~-----~~~~------------------------~------------~-~~~~~~~~~ 100 (172)
T PRK09651 85 ----------------------Y-----LEML------------------------A------------L-MPEGGAPSP 100 (172)
T ss_pred ----------------------h-----hhHH------------------------h------------h-ccccCCCCh
Confidence 0 0000 0 0 000011133
Q ss_pred hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 009567 449 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 523 (532)
Q Consensus 449 ee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~ 523 (532)
+......+....|..+|..||+++|+||.++|+ +++|++|||+.||+|.++|+....||+++|+...-..|
T Consensus 101 ~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~~~~~~ 171 (172)
T PRK09651 101 EERESQLETLQLLDSMLDGLNGKTREAFLLSQL----DGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLFRLEYG 171 (172)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHhHHhhhhhc----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHcC
Confidence 444444445567899999999999999999998 99999999999999999999999999999998765443
No 113
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=99.73 E-value=1.6e-16 Score=152.47 Aligned_cols=162 Identities=19% Similarity=0.154 Sum_probs=125.7
Q ss_pred HhhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcc
Q 009567 286 LHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR 365 (532)
Q Consensus 286 l~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r 365 (532)
+..+..+++.++..|.+.|+.+|.++.++..+.+|++||.|+.+|+.++.|++. ..|.+|++..+++.+.+..++..+
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 345679999999999999999999999999999999999999999999999864 369999999998876554432210
Q ss_pred ccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCC
Q 009567 366 TIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGV 445 (532)
Q Consensus 366 ~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~ 445 (532)
. ....+ .. ...+...
T Consensus 96 ~------------------------------------------------------~~~~~-------~~----~~~~~~~ 110 (188)
T PRK12517 96 D------------------------------------------------------LVDIE-------DD----SIEDDAS 110 (188)
T ss_pred C------------------------------------------------------ccCcc-------cc----cccCccc
Confidence 0 00000 00 0011111
Q ss_pred CChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567 446 EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 522 (532)
Q Consensus 446 ~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~ 522 (532)
..++.. ...+.|..+|..||+++|.||.++|+ ++++++|||+.||||..+|+.++.||+++||..+...
T Consensus 111 ~~~e~~----~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 179 (188)
T PRK12517 111 HSSEEE----MEQEWLRRQIAKLDPEYREPLLLQVI----GGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALEKP 179 (188)
T ss_pred cChhHH----HHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 123322 22356889999999999999999998 9999999999999999999999999999999998643
No 114
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=99.72 E-value=2e-16 Score=149.15 Aligned_cols=149 Identities=21% Similarity=0.217 Sum_probs=120.9
Q ss_pred HHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHH
Q 009567 298 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL 377 (532)
Q Consensus 298 ~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l 377 (532)
..|.+.++.++.++.++..+.+|++||+++.+|+++++|++. .+|.+|++..+++.+.+++++..+...++
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 468889999999999999999999999999999999999963 57999999999999999998765311000
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHH
Q 009567 378 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 457 (532)
Q Consensus 378 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~~l 457 (532)
+. ... . .++++.....+.
T Consensus 73 -----------------------------------------------~~------------~~~-~--~~~~~~~~~~e~ 90 (170)
T TIGR02959 73 -----------------------------------------------ES------------LLA-A--DSAREETFVKEL 90 (170)
T ss_pred -----------------------------------------------hh------------hcc-c--CCccHHHHHHHH
Confidence 00 000 0 011222333445
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567 458 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 521 (532)
Q Consensus 458 ~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~ 521 (532)
...|..+|..||+++|.||.++|. +++|.+|||+.||+|..+|++.+.||+++||..+..
T Consensus 91 ~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 150 (170)
T TIGR02959 91 SQCIPPMIKELPDEYREAIRLTEL----EGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLET 150 (170)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 567899999999999999999998 999999999999999999999999999999998863
No 115
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=99.72 E-value=2.5e-16 Score=151.46 Aligned_cols=156 Identities=19% Similarity=0.206 Sum_probs=121.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 009567 291 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 370 (532)
Q Consensus 291 ~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP 370 (532)
.+++.|+. |.+.|+.+|+.+.++..+.+|++||.++.+|+.+..|+.. ..|.+|++..+++.+.+++++..+...
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 55666666 7799999999999999999999999999999999999864 469999999999999999877542100
Q ss_pred hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhH
Q 009567 371 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI 450 (532)
Q Consensus 371 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee 450 (532)
..+. ...+...+ .+..
T Consensus 83 ----------------------------------------------------~~~~--------~~~~~~~~----~~~~ 98 (188)
T PRK12546 83 ----------------------------------------------------DPEG--------VHAASLAV----KPAH 98 (188)
T ss_pred ----------------------------------------------------Cccc--------cccccccc----CCcc
Confidence 0000 00000000 0100
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567 451 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 521 (532)
Q Consensus 451 ~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~ 521 (532)
........+..+|..||+++|+||.|+|. +++|.+|||+.||||..+|+..+.||+++||+.+..
T Consensus 99 --~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~----~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~ 163 (188)
T PRK12546 99 --DGRLAMSDFRAAFAQLPDEQREALILVGA----SGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQL 163 (188)
T ss_pred --hhHHHHHHHHHHHHhCCHHHhHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 01122346889999999999999999998 899999999999999999999999999999998865
No 116
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=99.70 E-value=4.1e-16 Score=149.18 Aligned_cols=157 Identities=13% Similarity=0.167 Sum_probs=122.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchh
Q 009567 293 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 372 (532)
Q Consensus 293 re~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~ 372 (532)
++..+..+++.|+.+|.++.++..+.+|++||.|+.+|+....|++. .+|.+|++..+++.+.++++++.+.....
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 45557889999999999999998999999999999999999999864 36999999999999999998764211000
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHH
Q 009567 373 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV 452 (532)
Q Consensus 373 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~ 452 (532)
+++ . +. .+.....+.
T Consensus 82 -------------------------~~~------------------------~------------~~-~~~~~~~~~--- 96 (182)
T PRK12511 82 -------------------------DEL------------------------A------------VL-ADASLPAAQ--- 96 (182)
T ss_pred -------------------------cch------------------------h------------hc-cccCCCcch---
Confidence 000 0 00 000000111
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567 453 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 522 (532)
Q Consensus 453 ~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~ 522 (532)
........|..+|..||+++|+||.|+|. +++|++|||+.||||.++|+....||+++||..+...
T Consensus 97 ~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~~~ 162 (182)
T PRK12511 97 EHAVRLAQIRDAFFDLPEEQRAALHLVAI----EGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEEGT 162 (182)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhc
Confidence 11123456889999999999999999998 8999999999999999999999999999999988644
No 117
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=99.70 E-value=9.8e-16 Score=143.95 Aligned_cols=160 Identities=14% Similarity=0.117 Sum_probs=126.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcccccc
Q 009567 290 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 369 (532)
Q Consensus 290 ~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRl 369 (532)
..++..++..|.+.++.+|.++.++..+.+|++||.++.+|+..+.++. ..|.+|.+..+++.+.+++++...
T Consensus 8 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~---- 80 (168)
T PRK12525 8 NTLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDL---- 80 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHH----
Confidence 3789999999999999999999999999999999999999986665542 369999999999999988875320
Q ss_pred chhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChh
Q 009567 370 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD 449 (532)
Q Consensus 370 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pe 449 (532)
.+ ... + +.+ + .+.....+|+
T Consensus 81 --------~~------~~~---------~------------------------~~~------------~-~~~~~~~~~~ 100 (168)
T PRK12525 81 --------ER------AYL---------Q------------------------SLA------------E-APEAVQPSPE 100 (168)
T ss_pred --------HH------HHH---------H------------------------HHh------------c-ccccccCChH
Confidence 00 000 0 000 0 0001112455
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567 450 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 520 (532)
Q Consensus 450 e~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~ 520 (532)
+..........|..+|..||+++|+||.|+|. +++|++|||+.||+|..+|+....+|+++||..+.
T Consensus 101 ~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~----eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~~~ 167 (168)
T PRK12525 101 EQWMVIETLLAIDRLLDGLSGKARAAFLMSQL----EGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQGFQ 167 (168)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhc
Confidence 55555566678999999999999999999998 99999999999999999999999999999998763
No 118
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=99.69 E-value=8.4e-16 Score=142.32 Aligned_cols=156 Identities=17% Similarity=0.183 Sum_probs=113.1
Q ss_pred CCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcC
Q 009567 313 GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGN 392 (532)
Q Consensus 313 ~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~g 392 (532)
++..+.+|++||+|+.+|+..+. ++ +..|.+|++..+++.+.++++++.+..+...
T Consensus 2 ~~~~~AeDivQe~fl~~~~~~~~-~~--~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~--------------------- 57 (161)
T PRK09047 2 RDDDAALDIVQDAMIKLAEKYGD-RP--AAEWPPLFQRILQNRIHDWFRRQKVRNTWVS--------------------- 57 (161)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhh-cc--cCchHHHHHHHHHHHHHHHHHhhcccccccc---------------------
Confidence 34456899999999999999886 33 4579999999999999999987652110000
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCC--CCChhHHHHHHHHHHHHHHHHhcCCH
Q 009567 393 HSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTG--VEIPDISVQKQLMRQHVRNLLTLLNP 470 (532)
Q Consensus 393 r~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~--~~~pee~~~~~~l~~~L~~~L~~L~~ 470 (532)
...++.... ++++....+.+.+.. ..+|++.+...+....|..+|..||+
T Consensus 58 ---------------------------~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~ 109 (161)
T PRK09047 58 ---------------------------LFSSFSDDD-DDDDFDPLETLDSADEGAESPADKLERAQVLQLIEEAIQKLPA 109 (161)
T ss_pred ---------------------------ccccccccc-ccccccHHHHhccccccCCCHHHHHHHHHHHHHHHHHHHhCCH
Confidence 000000000 001111112222211 23577777777778889999999999
Q ss_pred HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 009567 471 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 524 (532)
Q Consensus 471 rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l 524 (532)
++|+||.|+|+ +++|++|||+.||+|..+|+.+..||+++||+.+...++
T Consensus 110 ~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~~ 159 (161)
T PRK09047 110 RQREAFLLRYW----EDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEAKGI 159 (161)
T ss_pred HHHHHHHHHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcCc
Confidence 99999999998 999999999999999999999999999999999986654
No 119
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=99.67 E-value=1.8e-15 Score=154.85 Aligned_cols=161 Identities=16% Similarity=0.095 Sum_probs=123.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 009567 291 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 370 (532)
Q Consensus 291 ~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP 370 (532)
.....++..|.+.++.+|+++.++..+.+|++||.++. |.....|+ ...|.+|++..++|.+.+++++..+....
T Consensus 4 ~~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~---~~~~~~WL~~Ia~n~~~d~lR~~~~~~~~- 78 (293)
T PRK09636 4 ADAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQ---IRDPRAWLTRVVTRLCLDRLRSARHRRET- 78 (293)
T ss_pred cHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhccccc---ccCHHHHHHHHHHHHHHHHHHhhhccccc-
Confidence 34678999999999999999999999999999999999 66667775 34799999999999999999865421000
Q ss_pred hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhH
Q 009567 371 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI 450 (532)
Q Consensus 371 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee 450 (532)
. ....+..+ ..+.. ..|++
T Consensus 79 --------------------~----------------------------~~~~~~e~------------~~~~~-~~~~~ 97 (293)
T PRK09636 79 --------------------Y----------------------------VGPWLPEP------------VVEEL-DDPLE 97 (293)
T ss_pred --------------------c----------------------------cCCcCCcC------------CCCCC-CChHH
Confidence 0 00000000 00111 12333
Q ss_pred HH-HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567 451 SV-QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 521 (532)
Q Consensus 451 ~~-~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~ 521 (532)
.. ........+..+|+.|||++|.||.|+|. +++|++|||+.||+|..+|+++.+||+++||+.+..
T Consensus 98 ~~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~~----~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~~ 165 (293)
T PRK09636 98 AVVAAEDLSLALMLALERLSPLERAAFLLHDV----FGVPFDEIASTLGRSPAACRQLASRARKHVRAARPR 165 (293)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCC
Confidence 33 34455567899999999999999999998 899999999999999999999999999999997653
No 120
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=99.62 E-value=1.1e-14 Score=144.48 Aligned_cols=158 Identities=18% Similarity=0.178 Sum_probs=122.1
Q ss_pred HHHHHhhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHH
Q 009567 282 LKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIF 361 (532)
Q Consensus 282 L~~~l~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir 361 (532)
|...+..+..+++.++..| +.++.++.++.++..+.+||+||.++.+|+. |+.. ..|.+|++..++|.+.++++
T Consensus 9 ~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~--~~~~~WL~~IarN~~id~~R 82 (228)
T PRK06704 9 LKNHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNK--DICMTLVYKIARNRWLDQIK 82 (228)
T ss_pred HhcccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCcc--ccHHHHHHHHHHHHHHHHHh
Confidence 4444555668888888888 7899999999999999999999999999876 5543 25999999999999999987
Q ss_pred hhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcc
Q 009567 362 QHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITA 441 (532)
Q Consensus 362 ~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~ 441 (532)
++.+.-. +. ++ ..
T Consensus 83 k~k~~~~-------------------------------------------------------~~----~~--~~------ 95 (228)
T PRK06704 83 SKSVHEK-------------------------------------------------------IR----DQ--IT------ 95 (228)
T ss_pred ccccccc-------------------------------------------------------cc----cc--cc------
Confidence 6542000 00 00 00
Q ss_pred cCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567 442 DTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 521 (532)
Q Consensus 442 d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~ 521 (532)
...+.... ....+.+..+|+.||+++|.||.|+|. +++|++|||+.||+|.++|+..+.||+++||+.+..
T Consensus 96 ---~~~~~~~~--~~~~~~l~~~L~~Lp~~~R~v~lL~~~----eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~ 166 (228)
T PRK06704 96 ---FEEPHEKI--ADLHEMVGKVLSSLNVQQSAILLLKDV----FQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEE 166 (228)
T ss_pred ---cCChHHHH--HHHHHHHHHHHHhCCHHHhhHhhhHHh----hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 00111111 123356888999999999999999998 899999999999999999999999999999998865
No 121
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=99.62 E-value=1.3e-14 Score=147.97 Aligned_cols=156 Identities=21% Similarity=0.141 Sum_probs=118.7
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHH
Q 009567 295 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY 374 (532)
Q Consensus 295 ~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~ 374 (532)
+++..|.+.++.+|+++.++..+.+|++||+++.+++. .|+. ...|.+|.+.++++.+.+++++..+.-..
T Consensus 1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~--~~~~~awL~~Ia~n~~ld~lR~~~~~~~~----- 71 (281)
T TIGR02957 1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQ--IENPKAYLTKVVTRRCIDVLRSARARREV----- 71 (281)
T ss_pred ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Cccc--ccCHHHHHHHHHHHHHHHHHHHhhhcccc-----
Confidence 36889999999999999999999999999999997765 4543 23699999999999999999765310000
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHH
Q 009567 375 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK 454 (532)
Q Consensus 375 ~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~ 454 (532)
. ....+..+ ..+. ...|++....
T Consensus 72 --------------------~------------------------~~~~~~e~------------~~~~-~~~~~~~~~~ 94 (281)
T TIGR02957 72 --------------------Y------------------------VGPWLPEP------------LLTT-SADPAESVEL 94 (281)
T ss_pred --------------------c------------------------CCCCCCcc------------cCCC-CCChHHHHHH
Confidence 0 00000000 0000 1234444433
Q ss_pred -HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567 455 -QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 520 (532)
Q Consensus 455 -~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~ 520 (532)
+.+...+..+|+.|||+||.||.|+|. .++|++|||+.||+|..+|+++.+||+++||+...
T Consensus 95 ~e~~~~~l~~~l~~L~~~~R~v~~L~~~----~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~ 157 (281)
T TIGR02957 95 AESLSMAYLLLLERLSPLERAVFVLREV----FDYPYEEIASIVGKSEANCRQLVSRARRHLDARRP 157 (281)
T ss_pred HHHHHHHHHHHHhhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 345567888999999999999999998 89999999999999999999999999999999764
No 122
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=99.62 E-value=1.5e-14 Score=148.45 Aligned_cols=162 Identities=17% Similarity=0.086 Sum_probs=123.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 009567 291 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 370 (532)
Q Consensus 291 ~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP 370 (532)
..+..++..|.+.++.+|+++.++..+.||++||.++.+|++...+ . ..|.+|++...++.+.+++++..+.-..
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 5678899999999999999999999999999999999999987543 1 3599999999999999999864310000
Q ss_pred hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhH
Q 009567 371 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI 450 (532)
Q Consensus 371 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee 450 (532)
....+.. .. + +..++ ..+|++
T Consensus 80 --------------------------------------------------~~~~~~~--~~-~----~~~~~--~~~~~~ 100 (290)
T PRK09635 80 --------------------------------------------------PQDIAAW--HD-G----DASVS--SVDPAD 100 (290)
T ss_pred --------------------------------------------------ccccccc--Cc-c----ccCCC--CCCcHH
Confidence 0000000 00 0 00001 113333
Q ss_pred -HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567 451 -SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 520 (532)
Q Consensus 451 -~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~ 520 (532)
.....+....+..+|+.|||++|.||.|+|. .++|++|||+.||+|..+|+++.+||+++||....
T Consensus 101 ~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~~----~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~~ 167 (290)
T PRK09635 101 RVTLDDEVRLALLIMLERLGPAERVVFVLHEI----FGLPYQQIATTIGSQASTCRQLAHRARRKINESRI 167 (290)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHH----hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhCC
Confidence 3344555678899999999999999999998 89999999999999999999999999999998643
No 123
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=99.49 E-value=4.7e-13 Score=122.13 Aligned_cols=136 Identities=12% Similarity=0.139 Sum_probs=99.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhh-----hCCcCCCchhhHHHHHHHHHHHHHHHhhcccc
Q 009567 293 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEK-----FKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 367 (532)
Q Consensus 293 re~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiek-----FDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~I 367 (532)
++.++..|.++++.+|++|.+. +| +||.++.+|..+.+ |++. ..|.||.+..+++.+.++++++.+..
T Consensus 1 f~~~~~~y~~~l~~~~~~~~~~----~~-~qdvf~~~w~~~~~~~~~~~~~~--~~~~~wL~~iarN~~id~~Rk~~~~~ 73 (142)
T TIGR03209 1 FEEIYMNFKNTIDIFTRKYNLY----YD-YNDILYHLWIILKKIDLNKFNTE--NDLEKYISTSLKRYCLDICNKKNRDK 73 (142)
T ss_pred ChHHHHHHHHHHHHHHHHhcch----hh-HHHHHHHHHHHHHHhhhhhcCch--hHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 3679999999999999999662 34 49999999999875 5432 47999999999999999998654210
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCC
Q 009567 368 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 447 (532)
Q Consensus 368 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~ 447 (532)
+. . ...++ .+ ... .
T Consensus 74 ~~-----------------~--------~~~~~-------------------------------~~---------~~~-~ 87 (142)
T TIGR03209 74 KI-----------------I--------YNSEI-------------------------------TD---------IKL-S 87 (142)
T ss_pred hh-----------------h--------hhhhh-------------------------------hc---------ccc-c
Confidence 00 0 00000 00 000 1
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHH
Q 009567 448 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVR 505 (532)
Q Consensus 448 pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVR 505 (532)
+.+.....+....+..+|+.||+++|+||.|+|. +++|++|||+.||+|.++|+
T Consensus 88 ~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~----~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 88 LINVYSSNDLEFEFNDLISILPNKQKKIIYMKFF----EDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred hhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHhhc
Confidence 1122233344556889999999999999999998 99999999999999999997
No 124
>PRK09191 two-component response regulator; Provisional
Probab=99.47 E-value=4.2e-13 Score=132.92 Aligned_cols=137 Identities=17% Similarity=0.123 Sum_probs=110.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccch
Q 009567 292 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 371 (532)
Q Consensus 292 Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~ 371 (532)
++..|+..|.+.|+.+|.++.++..+.+|++||+++.+|+...+|++. ..|.+|++.++++.....
T Consensus 2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~~------------ 67 (261)
T PRK09191 2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSSA------------ 67 (261)
T ss_pred chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhccc------------
Confidence 578899999999999999999999999999999999999999999874 458999887665321000
Q ss_pred hHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHH
Q 009567 372 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 451 (532)
Q Consensus 372 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~ 451 (532)
.. ... .. ..+..
T Consensus 68 -------------------------------------------------------~~-~~~---------~~--~~~~~- 79 (261)
T PRK09191 68 -------------------------------------------------------GA-NDP---------EP--GSPFE- 79 (261)
T ss_pred -------------------------------------------------------cc-cCC---------CC--CCCch-
Confidence 00 000 00 01111
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567 452 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 521 (532)
Q Consensus 452 ~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~ 521 (532)
..+..+|..||+++|+||.++|. +++|++|||+.||+|.++|+....+|+++||..+..
T Consensus 80 -------~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~~ 138 (261)
T PRK09191 80 -------ARAERRLAGLTPLPRQAFLLTAL----EGFSVEEAAEILGVDPAEAEALLDDARAEIARQVAT 138 (261)
T ss_pred -------HHHHHHHHhCCHHHhHHHHHHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCCC
Confidence 15888999999999999999998 999999999999999999999999999999987653
No 125
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=99.46 E-value=4.4e-12 Score=126.71 Aligned_cols=90 Identities=20% Similarity=0.328 Sum_probs=78.8
Q ss_pred HHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCC--CHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHH
Q 009567 279 CRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGI--SLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 355 (532)
Q Consensus 279 ~~~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~--~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~a 355 (532)
.+.++..++.| ..|++.|+..|.++|+++|.++.++.. +.+|++|||++++|+++++|++++|..|.+|+..+|++.
T Consensus 5 ~~~Li~~~~~gD~~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn~ 84 (237)
T PRK08311 5 LEDILEKIKNGDEELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKRR 84 (237)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence 34455556655 489999999999999999999998765 489999999999999999999999888999999999999
Q ss_pred HHHHHHhhccccc
Q 009567 356 IRKAIFQHSRTIR 368 (532)
Q Consensus 356 I~~~ir~~~r~IR 368 (532)
+.++++++.+...
T Consensus 85 ~iDylRk~~~~~~ 97 (237)
T PRK08311 85 LIDYFRKESKHNL 97 (237)
T ss_pred HHHHHHHhhcccc
Confidence 9999998776433
No 126
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=99.35 E-value=6.4e-11 Score=113.71 Aligned_cols=174 Identities=20% Similarity=0.309 Sum_probs=118.3
Q ss_pred HHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCC---CCCHhh--HHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHH
Q 009567 280 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGR---GISLHD--LLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR 353 (532)
Q Consensus 280 ~~L~~~l~~g~-~Are~LI~~nlrLV~sIAkrY~~~---g~~~eD--LiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr 353 (532)
.+|+..++.|+ .|.+.|+..|++-++.+|+++.+. +.+.+| |++|.++.++..-...+++....|..|+...++
T Consensus 5 t~ll~~~~~GD~~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~~~~~r 84 (185)
T PF07638_consen 5 TELLDRWRQGDEAALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALLARIMR 84 (185)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHHHHHHH
Confidence 34566666665 999999999999999999987643 344554 467777777663333233333468888888888
Q ss_pred HHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCC
Q 009567 354 QTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD 433 (532)
Q Consensus 354 ~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~ 433 (532)
+.+.++.+.+.+..| +|.. ...+|+...
T Consensus 85 r~lid~~R~~~a~KR----------------------g~~~-------------------------~~~~l~~~~----- 112 (185)
T PF07638_consen 85 RKLIDHARRRQAQKR----------------------GGDQ-------------------------VRVELDERA----- 112 (185)
T ss_pred HHHHHHHHHHHHHhc----------------------CCCC-------------------------cccchhhhh-----
Confidence 888888776542111 1100 011122111
Q ss_pred cchhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567 434 TTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 513 (532)
Q Consensus 434 ~~l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALk 513 (532)
.+...+.|+..+ ++.+.+..+.. |+|+++++|.++|. .|+|.+|||+.||||..+|+.....|..
T Consensus 113 -------~~~~~~~~~~~~---~l~e~l~~L~~-l~~~~~~~v~l~~~----~Gls~~EIA~~lgiS~~tV~r~l~~aR~ 177 (185)
T PF07638_consen 113 -------DSGDEPSPEELL---ELEEALERLLA-LDPRQRRVVELRFF----EGLSVEEIAERLGISERTVRRRLRRARA 177 (185)
T ss_pred -------ccccCCCHHHHH---HHHHHHHHHHc-cCHHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 001112444433 23444555555 99999999999987 8999999999999999999999999999
Q ss_pred HHHHHhh
Q 009567 514 RLKQSLG 520 (532)
Q Consensus 514 KLR~~l~ 520 (532)
+|+..+.
T Consensus 178 ~l~~~l~ 184 (185)
T PF07638_consen 178 WLRRELR 184 (185)
T ss_pred HHHHHhc
Confidence 9998764
No 127
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=99.24 E-value=2.1e-11 Score=92.60 Aligned_cols=50 Identities=36% Similarity=0.628 Sum_probs=46.3
Q ss_pred HHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 464 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 464 ~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
+|+.|||+|++||.++|+ +++|++|||+.||+|+++|+++..+|++|||+
T Consensus 1 Al~~L~~~er~vi~~~y~----~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 1 ALDQLPPREREVIRLRYF----EGLTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp HHCTS-HHHHHHHHHHHT----ST-SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred ChhhCCHHHHHHHHHHhc----CCCCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 588999999999999998 99999999999999999999999999999985
No 128
>PF04542 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR007627 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [, ]. The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation [, ].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1OR7_B 1H3L_B 2Z2S_C 2Q1Z_C 2O7G_B 1SMY_F 1IW7_P 2BE5_F 2A6E_F 2CW0_F ....
Probab=99.23 E-value=2.9e-11 Score=96.64 Aligned_cols=70 Identities=23% Similarity=0.432 Sum_probs=67.0
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcc
Q 009567 296 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR 365 (532)
Q Consensus 296 LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r 365 (532)
|++.|.++|+.++++|.+++.+.+|++||++++||+++++||+++|..|.+|++..+++.+.++++++.|
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 6889999999999999999999999999999999999999999999899999999999999999998764
No 129
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=99.09 E-value=2.7e-10 Score=94.05 Aligned_cols=77 Identities=30% Similarity=0.491 Sum_probs=66.3
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHH
Q 009567 375 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 451 (532)
Q Consensus 375 ~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~ 451 (532)
+++++|.+++..|.+++||.||.+|||+.|||++++|..++...+.++||+.+++.+++.++.+++.|+...+|++.
T Consensus 1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d~~~~~P~e~ 77 (78)
T PF04539_consen 1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIEDDDAPSPEEE 77 (78)
T ss_dssp HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-SSS--HHHH
T ss_pred ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecCCCCCChhhc
Confidence 36789999999999999999999999999999999999999999999999999998888999999999988888764
No 130
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=98.92 E-value=3.7e-09 Score=81.27 Aligned_cols=54 Identities=30% Similarity=0.440 Sum_probs=46.4
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567 458 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 515 (532)
Q Consensus 458 ~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKL 515 (532)
++.|..+|..|||++|.||.++|. +++|++|||+.+|+|.++|++...+|+++|
T Consensus 1 r~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIa~~l~~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 1 REALQQALAQLPERQREIFLLRYF----QGMSYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp HHHHHHHHHCS-HHHHHHHHHHHT----S---HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH----HCcCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 357889999999999999999998 999999999999999999999999999987
No 131
>PRK06930 positive control sigma-like factor; Validated
Probab=98.65 E-value=1.2e-07 Score=90.28 Aligned_cols=71 Identities=18% Similarity=0.285 Sum_probs=62.5
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567 448 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 522 (532)
Q Consensus 448 pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~ 522 (532)
+.+.....+....|..++..||+++|+||.++|+ +++|++|||+.||+|.++|+.+..||+++|+..+...
T Consensus 95 ~~~~~~~~e~~~~l~~al~~L~~rer~V~~L~~~----eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~ 165 (170)
T PRK06930 95 EPESVISEWDKIRIEDALSVLTEREKEVYLMHRG----YGLSYSEIADYLNIKKSTVQSMIERAEKKIARQINES 165 (170)
T ss_pred ChhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 3334444556678999999999999999999998 9999999999999999999999999999999988754
No 132
>PRK00118 putative DNA-binding protein; Validated
Probab=98.44 E-value=9.7e-07 Score=77.56 Aligned_cols=61 Identities=21% Similarity=0.146 Sum_probs=55.4
Q ss_pred HHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 009567 460 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 524 (532)
Q Consensus 460 ~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l 524 (532)
.+.-....||+++++|+.++|. +++|.+|||+.+|+|+.+|+.+..+|+++||+++..-++
T Consensus 10 l~d~~~~~L~ekqRevl~L~y~----eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~ 70 (104)
T PRK00118 10 LFDFYGSLLTEKQRNYMELYYL----DDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHL 70 (104)
T ss_pred HHHHHhccCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence 4445668999999999999998 999999999999999999999999999999999887654
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=98.28 E-value=2.5e-06 Score=63.45 Aligned_cols=53 Identities=38% Similarity=0.589 Sum_probs=49.4
Q ss_pred HHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567 460 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 460 ~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR 516 (532)
.+..++..|++.++.++.++|. +++|..+||+.+|+|..+|+++..++..+||
T Consensus 3 ~~~~~~~~l~~~~~~~~~~~~~----~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 3 RLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred HHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 5778899999999999999997 8999999999999999999999999988874
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=98.20 E-value=3.4e-06 Score=77.64 Aligned_cols=57 Identities=19% Similarity=0.269 Sum_probs=49.6
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhh
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGY 527 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~y 527 (532)
..||++|++||.+++ +|+|++|||+.||+|+.+|++++++|+++|+.......+-.+
T Consensus 5 ~~Lte~qr~VL~Lr~-----~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l~~~ 61 (137)
T TIGR00721 5 TFLTERQIKVLELRE-----KGLSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDFVKF 61 (137)
T ss_pred CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHHHHH
Confidence 459999999999975 799999999999999999999999999999986555444433
No 135
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=98.18 E-value=4.3e-06 Score=77.32 Aligned_cols=51 Identities=24% Similarity=0.399 Sum_probs=47.3
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 521 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~ 521 (532)
..|+|+|++||.+++ +++|++|||+.||+|+.+|+.++++|+++||+....
T Consensus 5 ~~Lt~rqreVL~lr~-----~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t 55 (141)
T PRK03975 5 SFLTERQIEVLRLRE-----RGLTQQEIADILGTSRANVSSIEKRARENIEKARET 55 (141)
T ss_pred cCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 469999999999975 799999999999999999999999999999997654
No 136
>PRK04217 hypothetical protein; Provisional
Probab=98.06 E-value=8.3e-06 Score=72.41 Aligned_cols=55 Identities=20% Similarity=0.136 Sum_probs=50.9
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 524 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l 524 (532)
..|++.|++|+.++|. +++|++|||+.+|||+.+|++++.+|+++|++.+.....
T Consensus 41 ~~Lt~eereai~l~~~----eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~~ 95 (110)
T PRK04217 41 IFMTYEEFEALRLVDY----EGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGRE 95 (110)
T ss_pred ccCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 5799999999999997 899999999999999999999999999999999876544
No 137
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPro: IPR009042 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....
Probab=98.02 E-value=1.6e-06 Score=62.14 Aligned_cols=34 Identities=41% Similarity=0.464 Sum_probs=30.0
Q ss_pred ChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHH
Q 009567 217 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR 250 (532)
Q Consensus 217 ~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~ 250 (532)
+|+++.||++|+++|+||++||++|+++|+.+..
T Consensus 1 ~D~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~~ 34 (37)
T PF00140_consen 1 SDSLRLYLKEIGRYPLLTAEEEIELARRIRKGDE 34 (37)
T ss_dssp HHHHHHHHHHHHHS-EETTHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHH
Confidence 3799999999999999999999999999998543
No 138
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.
Probab=97.96 E-value=3.6e-05 Score=70.59 Aligned_cols=63 Identities=19% Similarity=0.295 Sum_probs=55.3
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567 456 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 520 (532)
Q Consensus 456 ~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~ 520 (532)
...+.|..+|+.|++.+|.||.++|+ .+..+|..+||..||+|+.+|.++..+|+.+|+..+.
T Consensus 71 ~~~~~I~~~l~~Ld~~er~II~~rY~--~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~lG 133 (134)
T TIGR01636 71 RNRDAIENCLNEADEQTRVIIQELYM--KKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEELG 133 (134)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHc--cCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhC
Confidence 34567899999999999999999996 2234699999999999999999999999999998753
No 139
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=97.93 E-value=4.6e-05 Score=66.58 Aligned_cols=57 Identities=28% Similarity=0.367 Sum_probs=44.8
Q ss_pred HHHHH-hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567 461 VRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 521 (532)
Q Consensus 461 L~~~L-~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~ 521 (532)
|.... .-|+++|++++.++|. +++|+.|||+.+||||..|...++||.++|...=..
T Consensus 10 L~d~Yg~LLT~kQ~~~l~lyy~----eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~yE~k 67 (101)
T PF04297_consen 10 LFDFYGELLTEKQREILELYYE----EDLSLSEIAEELGISRQAVYDSIKRAEKKLEEYEEK 67 (101)
T ss_dssp HHHHHGGGS-HHHHHHHHHHCT----S---HHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHCCHHHHHHHHHHHc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 44444 4599999999999998 999999999999999999999999999999775443
No 140
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=97.87 E-value=0.0038 Score=70.95 Aligned_cols=34 Identities=32% Similarity=0.493 Sum_probs=31.4
Q ss_pred CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHH
Q 009567 216 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLI 249 (532)
Q Consensus 216 ~~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~ 249 (532)
.+||+++||++|+..||||+|+|++++++|..+.
T Consensus 102 t~DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~ 135 (619)
T PRK05658 102 TDDPVRMYLREMGTVELLTREGEIEIAKRIEAGE 135 (619)
T ss_pred CCChHHHHHHHhccCcCCCcHHHHHHHHHHHHHH
Confidence 5799999999999999999999999999998643
No 141
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=97.85 E-value=3.5e-05 Score=58.30 Aligned_cols=46 Identities=26% Similarity=0.400 Sum_probs=41.4
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR 516 (532)
..|+++|+.|+.+.+ .++|.+|||+.+|+|+.+|+++..+++++|.
T Consensus 2 ~~l~~~e~~i~~~~~-----~g~s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 2 ASLTPREREVLRLLA-----EGLTNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 468999999998754 6899999999999999999999999988885
No 142
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=97.74 E-value=6.9e-05 Score=58.52 Aligned_cols=47 Identities=23% Similarity=0.317 Sum_probs=41.2
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
..|+++|.+|+.+.. .|+|.+|||+.+|||..+|+.+..++++||.-
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 579999999999987 79999999999999999999999999999853
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=97.66 E-value=0.00012 Score=55.50 Aligned_cols=45 Identities=29% Similarity=0.487 Sum_probs=40.3
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
|+++|++|+.+.+ .++|.+|||+.+|+|+.+|+.+..+++++|+.
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 6899999998855 68999999999999999999999999888754
No 144
>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This entry is represented by Streptococcus phage 7201, Orf19. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several hypothetical, highly conserved Streptococcal and related phage proteins. The function of this family is unknown.
Probab=97.54 E-value=0.00045 Score=60.27 Aligned_cols=55 Identities=22% Similarity=0.439 Sum_probs=49.8
Q ss_pred HHHHHHHHHhcCC-HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567 457 MRQHVRNLLTLLN-PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 515 (532)
Q Consensus 457 l~~~L~~~L~~L~-~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKL 515 (532)
.+..+..+++.|+ +.+|.||.++|. .+++..+|++.||+|+.++-.+..+|++.|
T Consensus 44 ~k~ei~~~I~~l~d~~~r~iL~~~Yi----~~~~~~~I~~~l~~S~~t~yr~~~~Al~~L 99 (100)
T PF07374_consen 44 EKLEIRRAINKLEDPDERLILRMRYI----NKLTWEQIAEELNISRRTYYRIHKKALKEL 99 (100)
T ss_pred HHHHHHHHHHHccChhHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence 3456888888886 899999999998 789999999999999999999999999986
No 145
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=97.54 E-value=0.00031 Score=54.41 Aligned_cols=48 Identities=27% Similarity=0.428 Sum_probs=42.3
Q ss_pred CCHHHHHHHHHHhccc--C-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567 468 LNPKERCIVRLRFGIE--D-GKPKSLSEVGNIFGLSKERVRQLESRALYRL 515 (532)
Q Consensus 468 L~~rER~VL~LRyGL~--~-~e~~Tl~EIAe~LgISrerVRqie~rALkKL 515 (532)
|+++|++||..-|-.+ + ...-|+.|||+.||||+.++..++.+|.+||
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 7899999999876443 3 4688999999999999999999999999987
No 146
>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=97.53 E-value=0.00021 Score=58.90 Aligned_cols=47 Identities=19% Similarity=0.213 Sum_probs=41.6
Q ss_pred HHHHHHhcCCHHHHHHHHHH-hcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 460 HVRNLLTLLNPKERCIVRLR-FGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 460 ~L~~~L~~L~~rER~VL~LR-yGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.+.+-|..||++.+.++.|. |. +++|++|||+.||+|..+|+.++++
T Consensus 8 ~~~~~l~~l~~~~r~af~L~R~~----eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 8 KLAERLTWVDSLAEAAAALAREE----AGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred hHHHHHhcCCHHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 45667899999999999995 44 8999999999999999999998775
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=97.50 E-value=0.00017 Score=62.24 Aligned_cols=50 Identities=22% Similarity=0.240 Sum_probs=43.5
Q ss_pred HHHHHHH-hcCCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHHHHH
Q 009567 459 QHVRNLL-TLLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLE 508 (532)
Q Consensus 459 ~~L~~~L-~~L~~rER~VL~LRyGL~~---~e~~Tl~EIAe~LgISrerVRqie 508 (532)
+.+..+| ..|+|+|+.+|..|||+.+ ..++|++|||+.+|||+.+|.+..
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 3566677 5599999999999999987 689999999999999999997653
No 148
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=97.40 E-value=0.00034 Score=66.83 Aligned_cols=47 Identities=23% Similarity=0.352 Sum_probs=43.8
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
..|+++|++|+.+.- +|+|.+|||+.||+|..||+....++++||.-
T Consensus 132 ~~LSpRErEVLrLLA-----qGkTnKEIAe~L~IS~rTVkth~srImkKLgV 178 (198)
T PRK15201 132 RHFSVTERHLLKLIA-----SGYHLSETAALLSLSEEQTKSLRRSIMRKLHV 178 (198)
T ss_pred CCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 469999999999986 89999999999999999999999999999954
No 149
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=97.36 E-value=0.00033 Score=68.52 Aligned_cols=46 Identities=11% Similarity=0.237 Sum_probs=43.4
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
.|++||++||.+.- +|+|.+|||+.||+|..||+.+..+.++||.-
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 49999999999987 89999999999999999999999999999963
No 150
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=97.32 E-value=0.00039 Score=67.31 Aligned_cols=46 Identities=22% Similarity=0.291 Sum_probs=43.3
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR 516 (532)
..|++||++|+.+.- +|+|.+|||+.||+|..||+.+..+.++||-
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 469999999999987 7999999999999999999999999999994
No 151
>PRK13870 transcriptional regulator TraR; Provisional
Probab=97.30 E-value=0.00041 Score=69.43 Aligned_cols=46 Identities=26% Similarity=0.364 Sum_probs=43.2
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
.|++||++||.+-= +|+|..|||.+||||..||..++++|++||-.
T Consensus 173 ~LT~RE~E~L~W~A-----~GKT~~EIa~ILgISe~TV~~Hl~na~~KLga 218 (234)
T PRK13870 173 WLDPKEATYLRWIA-----VGKTMEEIADVEGVKYNSVRVKLREAMKRFDV 218 (234)
T ss_pred CCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 59999999999986 89999999999999999999999999999943
No 152
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=97.30 E-value=0.00044 Score=67.91 Aligned_cols=46 Identities=20% Similarity=0.342 Sum_probs=43.5
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR 516 (532)
..|++||++||.+.- +|+|.+|||+.|+||..||+.+..+.++||.
T Consensus 133 ~~LT~RE~eVL~ll~-----~G~snkeIA~~L~iS~~TV~~h~~~I~~KLg 178 (207)
T PRK11475 133 RMLSPTEREILRFMS-----RGYSMPQIAEQLERNIKTIRAHKFNVMSKLG 178 (207)
T ss_pred CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 469999999999987 7999999999999999999999999999994
No 153
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=97.28 E-value=0.00046 Score=68.06 Aligned_cols=50 Identities=8% Similarity=-0.050 Sum_probs=46.5
Q ss_pred HHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567 462 RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 462 ~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR 516 (532)
.++...|+|+|++|+.+.- +|+|.+|||+.|++|..||+....+.++||.
T Consensus 138 ~~~~~~LS~RE~eVL~Lia-----~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLg 187 (217)
T PRK13719 138 LEAKNKVTKYQNDVFILYS-----FGFSHEYIAQLLNITVGSSKNKISEILKFFG 187 (217)
T ss_pred hhccCCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 5567899999999999986 7999999999999999999999999999994
No 154
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=97.27 E-value=0.00049 Score=69.56 Aligned_cols=48 Identities=21% Similarity=0.261 Sum_probs=44.5
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 465 L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
+..|+++|++|+.+.. +|+|.+|||++||||..||+....++++||.-
T Consensus 188 ~~~LT~RE~evl~l~a-----~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v 235 (247)
T TIGR03020 188 AGLITAREAEILAWVR-----DGKTNEEIAAILGISSLTVKNHLQHIFKKLDV 235 (247)
T ss_pred ccCCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence 4579999999999976 89999999999999999999999999999964
No 155
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=97.25 E-value=0.00049 Score=68.55 Aligned_cols=48 Identities=19% Similarity=0.267 Sum_probs=44.5
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 465 L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
...|+++|++||.+.. +|+|..|||++||||..+|+.++.++++||+.
T Consensus 169 ~~~Lt~re~evl~~~a-----~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~ 216 (232)
T TIGR03541 169 AGVLSEREREVLAWTA-----LGRRQADIAAILGISERTVENHLRSARRKLGV 216 (232)
T ss_pred hccCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence 3579999999999975 79999999999999999999999999999974
No 156
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=97.24 E-value=0.00055 Score=68.71 Aligned_cols=45 Identities=16% Similarity=0.258 Sum_probs=43.0
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR 516 (532)
.|++||++||.+.. +|+|..|||.+||||..||+.++.++++||-
T Consensus 179 ~LT~rE~evl~~~a-----~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~ 223 (240)
T PRK10188 179 NFSKREKEILKWTA-----EGKTSAEIAMILSISENTVNFHQKNMQKKFN 223 (240)
T ss_pred CCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 69999999999996 8999999999999999999999999999995
No 157
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=97.20 E-value=0.00063 Score=67.24 Aligned_cols=48 Identities=17% Similarity=0.127 Sum_probs=44.5
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 465 L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
+..|+++|++|+.+.. +|+|.+|||+.|++|..||+.+..++++||.-
T Consensus 153 ~~~Lt~rE~~Vl~l~~-----~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v 200 (216)
T PRK10100 153 SALLTHREKEILNKLR-----IGASNNEIARSLFISENTVKTHLYNLFKKIAV 200 (216)
T ss_pred cCCCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 3469999999999998 79999999999999999999999999999954
No 158
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=97.16 E-value=0.00068 Score=66.70 Aligned_cols=46 Identities=30% Similarity=0.371 Sum_probs=43.3
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR 516 (532)
..|++||++|+++.- +|+|.+|||+.|++|..||+.+..+.++||.
T Consensus 147 ~~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~ 192 (211)
T COG2197 147 ELLTPRELEVLRLLA-----EGLSNKEIAEELNLSEKTVKTHVSNILRKLG 192 (211)
T ss_pred CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHhHHHHHHHHHHHHcC
Confidence 479999999999876 7999999999999999999999999999994
No 159
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=97.09 E-value=0.002 Score=62.23 Aligned_cols=60 Identities=17% Similarity=0.231 Sum_probs=53.4
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567 456 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 520 (532)
Q Consensus 456 ~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~ 520 (532)
.....+...+.+|+||||+|+..-- .|+..++||..||||.-||..+..+.++||+..--
T Consensus 131 ~~~~~~~~~l~tLT~RERqVl~~vV-----~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~Sl 190 (202)
T COG4566 131 DRQAAIRARLATLTPRERQVLDLVV-----RGLMNKQIAFDLGISERTVELHRANVMEKMQARSL 190 (202)
T ss_pred HHHHHHHHHHHhcCHHHHHHHHHHH-----cCcccHHHHHHcCCchhhHHHHHHHHHHHHhhccH
Confidence 3446788999999999999999887 79999999999999999999999999999986543
No 160
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=97.09 E-value=0.0014 Score=57.88 Aligned_cols=53 Identities=19% Similarity=0.164 Sum_probs=48.7
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 523 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~ 523 (532)
.|+..|-+.|+|.+. +++|.+|.|+.||||+.|+..++..|.+|+-..|....
T Consensus 41 ~L~~dElEAiRL~D~----egl~QeeaA~~MgVSR~T~~ril~~ARkKiA~ALv~Gk 93 (106)
T PF02001_consen 41 VLTVDELEAIRLVDY----EGLSQEEAAERMGVSRPTFQRILESARKKIADALVEGK 93 (106)
T ss_pred EeeHHHHHHHHHHHH----cCCCHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHCCC
Confidence 578889999999998 99999999999999999999999999999999886544
No 161
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=97.05 E-value=0.0019 Score=50.43 Aligned_cols=48 Identities=33% Similarity=0.432 Sum_probs=43.4
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 518 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~ 518 (532)
..|+++|.+|+.+.- .|+|..|||..+|+|..+|+....++.+||.-.
T Consensus 3 ~~Lt~rE~~v~~l~~-----~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~ 50 (65)
T COG2771 3 ADLTPREREILRLVA-----QGKSNKEIARILGISEETVKTHLRNIYRKLGVK 50 (65)
T ss_pred ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 468999999998876 689999999999999999999999999998653
No 162
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=96.97 E-value=0.001 Score=49.37 Aligned_cols=41 Identities=24% Similarity=0.339 Sum_probs=24.3
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
..|++.||..|...+- +|+|..+||+.||+|++||...++|
T Consensus 3 ~~Lt~~eR~~I~~l~~----~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEALLE----QGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHHHHC----S---HHHHHHHTT--HHHHHHHHHH
T ss_pred cchhhhHHHHHHHHHH----cCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 4689999999998875 8999999999999999999988776
No 163
>PRK09483 response regulator; Provisional
Probab=96.96 E-value=0.0014 Score=62.25 Aligned_cols=46 Identities=22% Similarity=0.300 Sum_probs=42.5
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR 516 (532)
..|+++|++|+.+.. +|+|.+|||+.|++|..||+.+..+.++||-
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 469999999998765 7999999999999999999999999999983
No 164
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=96.74 E-value=0.0031 Score=58.51 Aligned_cols=46 Identities=22% Similarity=0.358 Sum_probs=42.4
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR 516 (532)
..|+++|++|+.+. . +++|.+|||+.+++|..||+....++++||.
T Consensus 148 ~~lt~~e~~vl~l~-~----~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 148 PLLTPRERQILKLI-T----EGYTNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred cCCCHHHHHHHHHH-H----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 45999999999984 4 8899999999999999999999999999995
No 165
>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=96.70 E-value=0.011 Score=53.73 Aligned_cols=62 Identities=21% Similarity=0.244 Sum_probs=53.5
Q ss_pred HHHHHHHHH-hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567 457 MRQHVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 520 (532)
Q Consensus 457 l~~~L~~~L-~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~ 520 (532)
....+..++ ..|++.+|+||..+|. . .++++.-+|+..+|+|+.+...+.++|+.++-..+.
T Consensus 68 ~~~~i~~ai~~~l~~~~r~Il~~~Yl-~-~~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~l~ 130 (132)
T TIGR01637 68 EARAIVNAIVNQLDEISRQILYDKYL-E-PDQKYDYQIMMELGYSHRQYYRIKKRALLRFATLYG 130 (132)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHc-C-ccccchHHHHHHhCCcHHHHHHHHHHHHHHHHHHhC
Confidence 345677777 9999999999999997 2 137899999999999999999999999999987664
No 166
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=96.62 E-value=0.0045 Score=60.98 Aligned_cols=53 Identities=23% Similarity=0.350 Sum_probs=46.1
Q ss_pred cCCHHHHHHHHHHhccc--C-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567 467 LLNPKERCIVRLRFGIE--D-GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~--~-~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l 519 (532)
.|+++|++||+.-|-++ + ....+++|||+.||||+.++.+++.+|.+||=..+
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~~~ 210 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIEAY 210 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 69999999999877543 3 47789999999999999999999999999996643
No 167
>PRK01381 Trp operon repressor; Provisional
Probab=96.59 E-value=0.0025 Score=55.51 Aligned_cols=48 Identities=27% Similarity=0.312 Sum_probs=40.8
Q ss_pred HHHHHHHHhc-CCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHH
Q 009567 458 RQHVRNLLTL-LNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVR 505 (532)
Q Consensus 458 ~~~L~~~L~~-L~~rER~VL~LRyGL~~---~e~~Tl~EIAe~LgISrerVR 505 (532)
.+.+..+|.. |+|+|+..|..||++.. ..++|++||++.+|||..+|.
T Consensus 22 ~~~~~~~l~~llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTIT 73 (99)
T PRK01381 22 EDLHLPLLTLLLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATIT 73 (99)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeeh
Confidence 3456666755 99999999999999876 457999999999999998885
No 168
>PRK10651 transcriptional regulator NarL; Provisional
Probab=96.55 E-value=0.0043 Score=58.31 Aligned_cols=46 Identities=20% Similarity=0.294 Sum_probs=42.6
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR 516 (532)
..|+++|++|+.+.. ++++.++||+.+++|..||+.+..++++||.
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 459999999999866 7899999999999999999999999999994
No 169
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=96.53 E-value=0.002 Score=58.06 Aligned_cols=48 Identities=25% Similarity=0.359 Sum_probs=44.5
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l 519 (532)
-|+++|-.||.||- +|+|.+|||++||-|+..|+-++++|+.++.+.-
T Consensus 8 flte~qikvl~lRe-----kG~tQ~eIA~~L~TTraNvSaIEkrA~enIekar 55 (143)
T COG1356 8 FLTEQQIKVLVLRE-----KGLTQSEIARILKTTRANVSAIEKRALENIEKAR 55 (143)
T ss_pred eeehhheeeeehhh-----ccccHHHHHHHHccchhhHHHHHHHHHHHHHHHH
Confidence 48899999999998 7999999999999999999999999999998753
No 170
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=96.49 E-value=0.0077 Score=55.55 Aligned_cols=54 Identities=13% Similarity=0.189 Sum_probs=47.4
Q ss_pred HHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567 460 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 518 (532)
Q Consensus 460 ~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~ 518 (532)
.+...+..|+++|++|+.+.+ .+++.++||+.+|+|..+|+....++++||+..
T Consensus 134 ~~~~~~~~l~~~e~~vl~~~~-----~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~ 187 (202)
T PRK09390 134 DIRARIASLSERERQVMDGLV-----AGLSNKVIARDLDISPRTVEVYRANVMTKMQAG 187 (202)
T ss_pred HHHHHHHhhhhhHHHHHHHHH-----ccCchHHHHHHcCCCHHHHHHHHHHHHHHHccc
Confidence 355667889999999999754 689999999999999999999999999999653
No 171
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=96.26 E-value=0.018 Score=50.15 Aligned_cols=48 Identities=25% Similarity=0.328 Sum_probs=43.7
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
.-|+.+|+..+.++|. +++|+.|||+.++|||..|...++|.-+.|-.
T Consensus 16 sLLT~KQ~~Y~~lyy~----dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~ 63 (105)
T COG2739 16 SLLTKKQKNYLELYYL----DDLSLSEIAEEFNVSRQAIYDNIKRTEKILED 63 (105)
T ss_pred HHHhHHHHHHHHHHHH----hhccHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence 5589999999999998 89999999999999999999999998776644
No 172
>PRK15320 transcriptional activator SprB; Provisional
Probab=96.21 E-value=0.0089 Score=58.25 Aligned_cols=50 Identities=22% Similarity=0.308 Sum_probs=44.8
Q ss_pred HHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 463 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 463 ~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
++--.|+++|.+|+.+-- +|+|.+|||+.|++|..+|+...++.+.||.-
T Consensus 160 ~~~~~LSdREIEVL~LLA-----kG~SNKEIAekL~LS~KTVSTYKnRLLeKLgA 209 (251)
T PRK15320 160 NLPPGVTQAKYALLILLS-----SGHPAIELAKKFGLGTKTVSIYRKKVMYRLGM 209 (251)
T ss_pred cCCCCCCHHHHHHHHHHH-----cCCCHHHHHHHhccchhhHHHHHHHHHHHcCC
Confidence 334689999999999887 79999999999999999999999999999843
No 173
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=96.13 E-value=0.016 Score=50.02 Aligned_cols=52 Identities=19% Similarity=0.148 Sum_probs=47.2
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 522 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~ 522 (532)
.|+..|-+.|+|... ++++.+|-|..||||+.|+-..+..|++|+-..+...
T Consensus 33 ~lt~eElEAlRLvD~----~~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~aLveG 84 (99)
T COG1342 33 ILTIEELEALRLVDY----EGLTQEEAALRMGISRQTFWRLLTSARKKVADALVEG 84 (99)
T ss_pred eecHHHHHHHHHHhH----hhccHHHHHHHhcccHHHHHHHHHHHHHHHHHHHhcC
Confidence 367778899999988 8999999999999999999999999999999988654
No 174
>PRK10403 transcriptional regulator NarP; Provisional
Probab=96.00 E-value=0.013 Score=54.87 Aligned_cols=46 Identities=15% Similarity=0.230 Sum_probs=42.2
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR 516 (532)
..|+++|.+|+.+.. +++|.+|||+.+|+|..||+.+..++++||.
T Consensus 152 ~~Lt~~e~~vl~~~~-----~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 152 SVLTERELDVLHELA-----QGLSNKQIASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred ccCCHHHHHHHHHHH-----CCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 459999999998875 7899999999999999999999999999984
No 175
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=95.68 E-value=0.016 Score=54.00 Aligned_cols=46 Identities=20% Similarity=0.255 Sum_probs=42.4
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR 516 (532)
..|+++|++|+.+.. +++|.++||+.+++|..+|+.+..+.++||.
T Consensus 136 ~~Lt~~E~~il~~l~-----~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 136 DPLTKRERQVAEKLA-----QGMAVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred cCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 469999999999976 6899999999999999999999999999985
No 176
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=95.66 E-value=0.023 Score=53.36 Aligned_cols=47 Identities=21% Similarity=0.320 Sum_probs=42.8
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567 465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 465 L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR 516 (532)
+..|+++|++|+.+.. .+.|.+|||+.+++|..+|+.+..+.++||.
T Consensus 141 ~~~lt~~E~~vl~~l~-----~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~ 187 (204)
T PRK09958 141 LDSLSKQEISVMRYIL-----DGKDNNDIAEKMFISNKTVSTYKSRLMEKLE 187 (204)
T ss_pred cccCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 3569999999999887 6889999999999999999999999999983
No 177
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=95.66 E-value=0.023 Score=53.26 Aligned_cols=45 Identities=24% Similarity=0.242 Sum_probs=40.7
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR 516 (532)
.|+++|.+|+.+.. +++|.+|||+.+++|..+|+....++++||.
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 48999999998754 6799999999999999999999999999984
No 178
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=95.52 E-value=0.35 Score=50.87 Aligned_cols=49 Identities=24% Similarity=0.323 Sum_probs=46.4
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 518 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~ 518 (532)
-.|++.+|-.+.||.. -|+|..|||..|=|+..++-|.+.||.++++..
T Consensus 119 Pal~~~~riALtLR~v----~GLs~~eIArAFLv~e~am~QRivRAK~ri~~a 167 (415)
T COG4941 119 PALPPEQRIALTLRLV----GGLSTAEIARAFLVPEAAMAQRIVRAKARIREA 167 (415)
T ss_pred CCCChhhHHHHHHHHH----cCCcHHHHHHHHcCCcHHHHHHHHHHHHHHHhc
Confidence 6699999999999998 799999999999999999999999999999974
No 179
>PRK04841 transcriptional regulator MalT; Provisional
Probab=95.37 E-value=0.026 Score=66.14 Aligned_cols=46 Identities=11% Similarity=0.172 Sum_probs=43.3
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR 516 (532)
..|+++|++|+.+.. +|+|.+|||+.|+||..||+.+.++.++||.
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 459999999999977 8999999999999999999999999999995
No 180
>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=95.18 E-value=0.026 Score=39.27 Aligned_cols=27 Identities=30% Similarity=0.643 Sum_probs=20.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 487 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 487 ~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
++|.+|||+.+|+|+++|+ |++++|++
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 4799999999999999996 66777765
No 181
>PRK13558 bacterio-opsin activator; Provisional
Probab=95.08 E-value=0.042 Score=62.39 Aligned_cols=55 Identities=13% Similarity=0.070 Sum_probs=45.9
Q ss_pred HhcCCHHHHHHHHHHhccc---CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567 465 LTLLNPKERCIVRLRFGIE---DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519 (532)
Q Consensus 465 L~~L~~rER~VL~LRyGL~---~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l 519 (532)
...|+++|+++|..-|..+ -..+-|..|||+.||||+.++.+++.+|.+||=..+
T Consensus 605 ~~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l~~~~ 662 (665)
T PRK13558 605 ENDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKLVGAF 662 (665)
T ss_pred hhhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4689999999999988621 123449999999999999999999999999986543
No 182
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=95.06 E-value=0.058 Score=41.46 Aligned_cols=50 Identities=18% Similarity=0.242 Sum_probs=43.0
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l 519 (532)
.|+..++-++.+.|. ..+.|++.+|..+|||+++|.++.+..+.-|...+
T Consensus 2 kLs~~d~lll~L~~L---R~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l 51 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYL---RLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVL 51 (53)
T ss_pred CCCHHHHHHHHHHHH---HcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhc
Confidence 578888888888775 37899999999999999999999999888776654
No 183
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=94.97 E-value=0.053 Score=46.45 Aligned_cols=38 Identities=13% Similarity=0.239 Sum_probs=31.6
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 009567 465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE 508 (532)
Q Consensus 465 L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie 508 (532)
++.|++| .+|+.+.- .++|..|||+.+|||+.||..+.
T Consensus 34 ~~~Ls~R-~~I~~ll~-----~G~S~~eIA~~LgISrsTIyRi~ 71 (88)
T TIGR02531 34 IQSLAQR-LQVAKMLK-----QGKTYSDIEAETGASTATISRVK 71 (88)
T ss_pred HHhhhHH-HHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHH
Confidence 3468999 78887754 67999999999999999998843
No 184
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=94.86 E-value=0.026 Score=42.25 Aligned_cols=33 Identities=27% Similarity=0.326 Sum_probs=22.9
Q ss_pred HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009567 474 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 511 (532)
Q Consensus 474 ~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rA 511 (532)
+||.++. +++|..+||+.||||+.+|+++.++-
T Consensus 9 ~ii~l~~-----~G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 9 QIIRLLR-----EGWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp -HHHHHH-----HT--HHHHHHHHTS-HHHHHHHHT--
T ss_pred HHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 3555555 68999999999999999999987663
No 185
>PF12645 HTH_16: Helix-turn-helix domain; InterPro: IPR024760 This domain appears to be a helix-turn-helix domain, suggesting a transcriptional regulatory protein. Some proteins with this domain are annotated as conjugative transposon proteins.
Probab=94.73 E-value=0.14 Score=41.42 Aligned_cols=56 Identities=18% Similarity=0.286 Sum_probs=44.7
Q ss_pred HHHHHhhcHHHHHHHHHHHHHHHHHHHHHh----hC--CCCCHhhHHHHHHHHHHHhhhhhC
Q 009567 282 LKSELHSGNSSREKLINANLRLVVHVAKQY----QG--RGISLHDLLQEGSMGLMKSVEKFK 337 (532)
Q Consensus 282 L~~~l~~g~~Are~LI~~nlrLV~sIAkrY----~~--~g~~~eDLiQEG~iGLikAiekFD 337 (532)
+..+.+|+..|.++++..|.|++.+.+.+- .+ ++.--+|+-|+-...|++++-+|+
T Consensus 4 I~~A~~GD~~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~ 65 (65)
T PF12645_consen 4 IKAAKQGDPEAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE 65 (65)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence 444555667999999999999999998772 22 133349999999999999999996
No 186
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=94.71 E-value=0.091 Score=39.13 Aligned_cols=41 Identities=17% Similarity=0.255 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009567 468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 511 (532)
Q Consensus 468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rA 511 (532)
|++.++.||.+-+- +.+.|..|||+.+|+|..+|+++.++-
T Consensus 1 l~~~~~~Il~~l~~---~~~~t~~ela~~~~is~~tv~~~l~~L 41 (48)
T PF13412_consen 1 LDETQRKILNYLRE---NPRITQKELAEKLGISRSTVNRYLKKL 41 (48)
T ss_dssp --HHHHHHHHHHHH---CTTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH---cCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 57788888876553 366999999999999999998766543
No 187
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=94.31 E-value=0.068 Score=43.11 Aligned_cols=45 Identities=18% Similarity=0.417 Sum_probs=29.3
Q ss_pred HhcCCHHHHHHHHH--HhcccCCCCCCHHHHHHHhCCC-HHHHHHHHH
Q 009567 465 LTLLNPKERCIVRL--RFGIEDGKPKSLSEVGNIFGLS-KERVRQLES 509 (532)
Q Consensus 465 L~~L~~rER~VL~L--RyGL~~~e~~Tl~EIAe~LgIS-rerVRqie~ 509 (532)
+..|+++|++||.. .|.-..|-+-|.+|||+.||++ ..+|.+.+.
T Consensus 1 M~~LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~ 48 (65)
T PF01726_consen 1 MKELTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLK 48 (65)
T ss_dssp -----HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHH
Confidence 35799999999987 3333456788999999999997 999976554
No 188
>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=94.24 E-value=0.15 Score=46.71 Aligned_cols=54 Identities=17% Similarity=0.334 Sum_probs=45.1
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567 458 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 513 (532)
Q Consensus 458 ~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALk 513 (532)
+..|...++.|.+.++.||.+||+ ...++|..+||..|++|..+++.+...-..
T Consensus 72 k~~id~~~~~l~de~k~Ii~lry~--~r~~~TW~~IA~~l~i~erta~r~~~~fK~ 125 (130)
T PF05263_consen 72 KEAIDRWLETLIDEEKRIIKLRYD--RRSRRTWYQIAQKLHISERTARRWRDRFKN 125 (130)
T ss_pred HHHHHHHHHhhCHHHHHHHHHHHc--ccccchHHHHHHHhCccHHHHHHHHHHHHH
Confidence 456788889999999999999998 334699999999999999999876654433
No 189
>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=93.89 E-value=0.12 Score=42.30 Aligned_cols=38 Identities=32% Similarity=0.613 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHH
Q 009567 249 IRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL 286 (532)
Q Consensus 249 ~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l 286 (532)
.++.+++.+|+..+||+||.+|.|+..|++.+.+...+
T Consensus 4 ~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l 41 (78)
T PF04539_consen 4 RKIERARRELEQELGREPTDEEIAEELGISVEEVRELL 41 (78)
T ss_dssp HHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHH
Confidence 35667889999999999999999999999988775544
No 190
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=93.61 E-value=0.098 Score=54.85 Aligned_cols=36 Identities=22% Similarity=0.344 Sum_probs=32.5
Q ss_pred HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567 474 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 513 (532)
Q Consensus 474 ~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALk 513 (532)
+|-.|+|. +++|.+|||+.|||||.+|.+++.+|++
T Consensus 20 ~vA~lYY~----~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~ 55 (318)
T PRK15418 20 RIAWFYYH----DGLTQSEIGERLGLTRLKVSRLLEKGRQ 55 (318)
T ss_pred HHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 46678887 9999999999999999999999999876
No 191
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=93.49 E-value=0.099 Score=38.81 Aligned_cols=32 Identities=25% Similarity=0.296 Sum_probs=23.6
Q ss_pred HHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 009567 472 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE 508 (532)
Q Consensus 472 ER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie 508 (532)
..+|+.|+- +|+|..+||+.+|||+.+|..++
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 355666665 67999999999999999998775
No 192
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=93.47 E-value=0.17 Score=33.39 Aligned_cols=36 Identities=19% Similarity=0.335 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHH
Q 009567 468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL 507 (532)
Q Consensus 468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqi 507 (532)
+++.++..+...|- .+.|..+||+.+|+|+.+|..+
T Consensus 6 ~~~~~~~~i~~~~~----~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 6 LTPEQIEEARRLLA----AGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHh
Confidence 45555655655554 5779999999999999999875
No 193
>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=93.19 E-value=0.57 Score=42.54 Aligned_cols=55 Identities=18% Similarity=0.123 Sum_probs=49.2
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 009567 465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 523 (532)
Q Consensus 465 L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~ 523 (532)
|..-.|.+-++|.++|. .++|...||..+++|...||+...+|-.-+..++.-.+
T Consensus 60 L~~~~~~~~~ll~~~Yv----~g~s~r~IA~~~~~s~~~ir~~l~~ae~~i~g~l~~~~ 114 (125)
T PF06530_consen 60 LKKRDPEEYDLLILYYV----YGWSKRQIARKLKCSEGKIRKRLQRAEGFIDGCLSMLT 114 (125)
T ss_pred HHccCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHhhhhHhhhhHHhh
Confidence 45588999999999999 89999999999999999999999999999988765433
No 194
>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=93.16 E-value=1.2 Score=44.25 Aligned_cols=35 Identities=31% Similarity=0.574 Sum_probs=28.9
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHH
Q 009567 250 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 284 (532)
Q Consensus 250 ~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~ 284 (532)
++.+....|...+|++||.+|.|+..|++.+.+..
T Consensus 88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~ 122 (238)
T TIGR02393 88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVRE 122 (238)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 34456778888899999999999999999877743
No 195
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=92.88 E-value=1.5 Score=46.84 Aligned_cols=130 Identities=18% Similarity=0.278 Sum_probs=73.1
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHH-HHH
Q 009567 250 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEG-SMG 328 (532)
Q Consensus 250 ~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG-~iG 328 (532)
++.+...+|...+|++||..|.|+..|++.+.+...+... .. .+++++.+.++ -..
T Consensus 217 ~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~-------------------~~----~~SLd~~~~~~~~~~ 273 (367)
T PRK09210 217 KLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIA-------------------QE----PVSLETPIGEEDDSH 273 (367)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHh-------------------cC----CCCcCCCCCCCCcch
Confidence 4456677888889999999999999999988775433211 00 11111111110 011
Q ss_pred HHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCH
Q 009567 329 LMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITV 408 (532)
Q Consensus 329 LikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~ 408 (532)
|...+. |+.............++..+.+++. .+|..-...+.. .+.-..|.+-|.+|||+.+|+|.
T Consensus 274 l~d~i~--d~~~~~p~~~~~~~~~~~~l~~~l~------~L~~rEr~Vl~l------rygl~~~~~~tl~EIa~~lgvs~ 339 (367)
T PRK09210 274 LGDFIE--DQDATSPADHAAYELLKEQLEDVLD------TLTDREENVLRL------RFGLDDGRTRTLEEVGKVFGVTR 339 (367)
T ss_pred hhhhcc--CCCCCCHHHHHHHHHHHHHHHHHHH------hCCHHHHHHHHH------HhccCCCCCccHHHHHHHHCCCH
Confidence 111111 1111223444455566666666663 344433222211 11112346789999999999999
Q ss_pred HHHHHHHH
Q 009567 409 EKLERLIF 416 (532)
Q Consensus 409 e~v~~ll~ 416 (532)
++|+.+..
T Consensus 340 erVrQi~~ 347 (367)
T PRK09210 340 ERIRQIEA 347 (367)
T ss_pred HHHHHHHH
Confidence 99998854
No 196
>PF13730 HTH_36: Helix-turn-helix domain
Probab=92.57 E-value=0.42 Score=36.42 Aligned_cols=47 Identities=19% Similarity=0.289 Sum_probs=35.1
Q ss_pred cCCHHHHHHHHHHhcccCCCCC---CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPK---SLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~---Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
.|++.++.|+....-+.++.+. |.+.||+.+|+|+.+|+ ++++.|.+
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~----~~i~~L~~ 51 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQ----RAIKELEE 51 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 5888888888775555433332 89999999999999996 56666654
No 197
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=92.55 E-value=2.2 Score=45.01 Aligned_cols=130 Identities=18% Similarity=0.218 Sum_probs=69.6
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHH-HHHH
Q 009567 250 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQE-GSMG 328 (532)
Q Consensus 250 ~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQE-G~iG 328 (532)
++.++..+|...+|++||..|.|+..|++.+.+...... + ..-.++++.+.+ +...
T Consensus 174 ~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~-------------------~----~~~~SLd~~~~~~~~~~ 230 (324)
T PRK07921 174 KLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEH-------------------S----RDPVSLDMPVGSDEEAP 230 (324)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHH-------------------c----CCCceecCCCCCCCCch
Confidence 455677888889999999999999999998776432210 0 011111111111 0011
Q ss_pred HHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCH
Q 009567 329 LMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITV 408 (532)
Q Consensus 329 LikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~ 408 (532)
|...+.. +........+...-.+..+..++. .+|.+-...+.. .+.-.++.+-|.+|||+.+|+|.
T Consensus 231 l~d~l~d--~~~~~pe~~~~~~~~~~~l~~~L~------~L~eREr~Vl~~------rygl~~~~~~Tl~eIa~~lgvS~ 296 (324)
T PRK07921 231 LGDFIED--SEATSAENAVIAGLLHTDIRSVLA------TLDEREQQVIRL------RFGLDDGQPRTLDQIGKLFGLSR 296 (324)
T ss_pred HHHHhcC--CCCCCHHHHHHHHHHHHHHHHHHH------hCCHHHHHHHHH------HHhcCCCCCcCHHHHHHHHCCCH
Confidence 2222221 111112333333344444555542 234332222211 11112345679999999999999
Q ss_pred HHHHHHHH
Q 009567 409 EKLERLIF 416 (532)
Q Consensus 409 e~v~~ll~ 416 (532)
++|+.+..
T Consensus 297 eRVrQIe~ 304 (324)
T PRK07921 297 ERVRQIER 304 (324)
T ss_pred HHHHHHHH
Confidence 99998854
No 198
>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=92.43 E-value=0.37 Score=35.50 Aligned_cols=40 Identities=33% Similarity=0.422 Sum_probs=27.4
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
|++-.+.||...-. +...|+.+||+.+|+|..+|.+.+.+
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 34556677766543 25789999999999999999877654
No 199
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=92.39 E-value=0.36 Score=43.26 Aligned_cols=50 Identities=20% Similarity=0.299 Sum_probs=42.7
Q ss_pred HHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 464 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 464 ~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
.+..|++.+..-|....- ..=+++|+++.||||-.|||..+.+.+++|.-
T Consensus 30 ~~~~L~~E~~~Fi~~Fi~----~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 30 WFARLSPEQLEFIKLFIK----NRGNLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred hhhcCCHHHHHHHHHHHH----hcCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 367899998888877654 34499999999999999999999999999965
No 200
>PHA00675 hypothetical protein
Probab=92.23 E-value=0.27 Score=40.92 Aligned_cols=40 Identities=18% Similarity=0.089 Sum_probs=31.5
Q ss_pred hcCCHHHHHHHHHHh-cccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 466 TLLNPKERCIVRLRF-GIEDGKPKSLSEVGNIFGLSKERVRQLES 509 (532)
Q Consensus 466 ~~L~~rER~VL~LRy-GL~~~e~~Tl~EIAe~LgISrerVRqie~ 509 (532)
..|++.+-+.|+.++ - .+.|+.+||..||||+++|.+|..
T Consensus 21 AKLt~~qV~~IR~l~~r----~G~s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 21 AKLTDAEVERIRELHEV----EGMSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred cccCHHHHHHHHHHHHh----cCccHHHHHHHhCCCHHHHHHHHc
Confidence 356666666666655 4 678999999999999999999865
No 201
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=91.97 E-value=0.31 Score=47.99 Aligned_cols=48 Identities=15% Similarity=0.070 Sum_probs=36.8
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR 514 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkK 514 (532)
.|+++|.+++.....=..++++|.+|||+.||+|..||+.+..++...
T Consensus 158 ~Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~ 205 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVNC 205 (239)
T ss_pred CCCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHhC
Confidence 488999877654331112389999999999999999999998887543
No 202
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=91.96 E-value=2.7 Score=47.06 Aligned_cols=130 Identities=17% Similarity=0.282 Sum_probs=71.4
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHH-HHHH
Q 009567 250 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQE-GSMG 328 (532)
Q Consensus 250 ~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQE-G~iG 328 (532)
++.+.+.+|...+|++||.+|.|+..|++.+.+....+. ...-+++++.+.+ +...
T Consensus 359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~-----------------------~~~~~SLD~~i~~d~~~~ 415 (509)
T PRK05901 359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKY-----------------------NREPISLDKTIGKEGDSQ 415 (509)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh-----------------------cCCCcccccccccCCccc
Confidence 455677888899999999999999999987776443211 1112222222211 1111
Q ss_pred HHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCH
Q 009567 329 LMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITV 408 (532)
Q Consensus 329 LikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~ 408 (532)
+...+. |+........+..+..+..+..++. .||.+-...+.. .+.-..+..-|..|||..+|||.
T Consensus 416 l~d~l~--D~~~~~p~~~~~~~~l~~~L~~aL~------~L~eREr~VI~l------RyGL~~~e~~TL~EIa~~lGVSr 481 (509)
T PRK05901 416 FGDFIE--DSEAVSPVDAVSFTLLQDQLQEVLE------TLSEREAGVIRM------RFGLTDGQPKTLDEIGQVYGVTR 481 (509)
T ss_pred HHHhcc--CCCCCCHHHHHHHHHHHHHHHHHHh------hCCHHHHHHHHH------HhhccCCCCCCHHHHHHHHCCCH
Confidence 211111 1111122333344445555555553 234332222221 11112246789999999999999
Q ss_pred HHHHHHHH
Q 009567 409 EKLERLIF 416 (532)
Q Consensus 409 e~v~~ll~ 416 (532)
++|+.+..
T Consensus 482 ERVRQIe~ 489 (509)
T PRK05901 482 ERIRQIES 489 (509)
T ss_pred HHHHHHHH
Confidence 99998854
No 203
>PF13518 HTH_28: Helix-turn-helix domain
Probab=91.82 E-value=0.37 Score=35.95 Aligned_cols=27 Identities=26% Similarity=0.382 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESRAL 512 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~rAL 512 (532)
++.|+.+||..+|||+.+|+++..+-.
T Consensus 11 ~g~s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 11 EGESVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred cCCCHHHHHHHHCCCHhHHHHHHHHHH
Confidence 456999999999999999998876644
No 204
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=91.46 E-value=5.9 Score=40.31 Aligned_cols=147 Identities=20% Similarity=0.207 Sum_probs=81.1
Q ss_pred HHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHH
Q 009567 219 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 298 (532)
Q Consensus 219 ~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~ 298 (532)
.+..||++-. +.--+.--.+++.+ +..+..+|+..+|++||..|.|+..|++.+++...+..+.
T Consensus 88 ei~d~LR~~~--~v~vpR~~~~~~~~------i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~-------- 151 (247)
T COG1191 88 EILDYLRKND--SVKVPRSLRELGRR------IEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAIN-------- 151 (247)
T ss_pred HHHHHHHhCC--CccCcHHHHHHHHH------HHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhc--------
Confidence 4567888877 11122333444444 4457788999999999999999999999887754433322
Q ss_pred HHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHH
Q 009567 299 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS 378 (532)
Q Consensus 299 ~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ 378 (532)
.....++--.....+.+ + + +...+..+..+-.|-..+.+..++. .+|..-...+
T Consensus 152 --~~~~~sld~~~~~~~d~--~------------~---~~~~~~~~~~~~~~~~~~~l~~ai~------~L~EREk~Vl- 205 (247)
T COG1191 152 --GSQLLSLDEDVLKDDDD--D------------V---DDQIENPDDGVEKEELLEILKEAIE------PLPEREKLVL- 205 (247)
T ss_pred --cccccchhhhhcccccc--c------------h---hhccccchhHHHHHHHHHHHHHHHH------ccCHHHHHHH-
Confidence 11222222211111111 0 0 1112233444555555566665553 2232111111
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 379 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF 416 (532)
Q Consensus 379 ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~ 416 (532)
.-...-+-|..|||+.+|||..+|..+..
T Consensus 206 ---------~l~y~eelt~kEI~~~LgISes~VSql~k 234 (247)
T COG1191 206 ---------VLRYKEELTQKEIAEVLGISESRVSRLHK 234 (247)
T ss_pred ---------HHHHHhccCHHHHHHHhCccHHHHHHHHH
Confidence 01112256789999999999999987754
No 205
>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=91.43 E-value=0.39 Score=37.90 Aligned_cols=26 Identities=19% Similarity=0.331 Sum_probs=24.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESRA 511 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~rA 511 (532)
+|++..|||+.||+++.+|.....+-
T Consensus 12 ~G~~~~eIA~~Lg~~~~TV~~W~~r~ 37 (58)
T PF06056_consen 12 QGWSIKEIAEELGVPRSTVYSWKDRY 37 (58)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHHhh
Confidence 89999999999999999999988763
No 206
>smart00351 PAX Paired Box domain.
Probab=90.78 E-value=0.62 Score=42.17 Aligned_cols=42 Identities=14% Similarity=0.051 Sum_probs=32.6
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567 468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 513 (532)
Q Consensus 468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALk 513 (532)
++..+|.=|...|- ++.|..+||+.||||+.+|..+.++...
T Consensus 18 ~s~~~R~riv~~~~----~G~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 18 LPDEERQRIVELAQ----NGVRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred CCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 45555555555554 6889999999999999999999888643
No 207
>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=90.70 E-value=0.47 Score=37.82 Aligned_cols=26 Identities=23% Similarity=0.468 Sum_probs=23.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 485 GKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 485 ~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
+..+++.+||+.||||..+||....+
T Consensus 20 ~g~i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 20 NGKIKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred CCCccHHHHHHHHCCCHHHHHHHhhh
Confidence 36899999999999999999987654
No 208
>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=90.67 E-value=0.32 Score=37.57 Aligned_cols=40 Identities=20% Similarity=0.305 Sum_probs=26.9
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.|+..|+.=|.-+|- .|.+..+||..|||++++|+.|...
T Consensus 6 ~LTl~eK~~iI~~~e----~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 6 SLTLEEKLEIIKRLE----EGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp S--HHHHHHHHHHHH----CTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred cCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 456666555555554 6779999999999999999998865
No 209
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=90.56 E-value=6.5 Score=42.94 Aligned_cols=37 Identities=22% Similarity=0.399 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHH
Q 009567 379 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLI 415 (532)
Q Consensus 379 ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll 415 (532)
.+.+.+..+..++|++||.+|.|..+|+++..++..+
T Consensus 112 ~l~~~~~~l~~~~g~~pt~~ewa~~~~~~~~~l~~~l 148 (415)
T PRK07598 112 RLIEVRERLTSELGHRPSLERWAKTADISLADLKPTL 148 (415)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCcHHHHHHhh
Confidence 3455667888999999999999988887766666554
No 210
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=90.50 E-value=0.92 Score=41.42 Aligned_cols=53 Identities=21% Similarity=0.290 Sum_probs=42.7
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 459 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 459 ~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
..+..++-.|++.+-+|+.... ..+.++|..|||+.+|+++++|. ||+++|=.
T Consensus 16 ~dvl~c~~GLs~~Dv~v~~~LL--~~~~~~tvdelae~lnr~rStv~----rsl~~L~~ 68 (126)
T COG3355 16 EDVLKCVYGLSELDVEVYKALL--EENGPLTVDELAEILNRSRSTVY----RSLQNLLE 68 (126)
T ss_pred HHHHHHHhCCcHHHHHHHHHHH--hhcCCcCHHHHHHHHCccHHHHH----HHHHHHHH
Confidence 3567788899999999987654 12379999999999999999994 77777744
No 211
>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA. It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.
Probab=90.33 E-value=0.59 Score=39.83 Aligned_cols=45 Identities=29% Similarity=0.322 Sum_probs=33.7
Q ss_pred HHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHh--CCCHHHHHHHHHHH
Q 009567 464 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIF--GLSKERVRQLESRA 511 (532)
Q Consensus 464 ~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~L--gISrerVRqie~rA 511 (532)
.+..||+..+++..+|.- ....|+.|+|+.| .||++.|..+..+.
T Consensus 34 ~~~~l~~~l~~~a~lRl~---~Pd~SL~EL~~~~~~~iSKSgvnhrlrKl 80 (85)
T PF02650_consen 34 GLDKLPEKLREFAELRLE---NPDASLKELGELLEPPISKSGVNHRLRKL 80 (85)
T ss_dssp -GGGS-HHHHHHHHHHHH----TTS-HHHHHHTT--T--HHHHHHHHHHH
T ss_pred ccccCCHHHHHHHHHHHH---CccccHHHHHHHHcCcCcHHHHHHHHHHH
Confidence 358999999999999974 4789999999999 99999998765543
No 212
>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]
Probab=90.32 E-value=0.32 Score=56.52 Aligned_cols=45 Identities=18% Similarity=0.100 Sum_probs=42.7
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR 516 (532)
-|+.||++|+.+.| .|+|.+|||+.+.||-.||+....+...||.
T Consensus 831 ~Ls~RE~eVL~Lia-----~G~SN~eIa~~L~isl~TVKtH~rniy~KLg 875 (894)
T COG2909 831 PLSQRELEVLGLIA-----QGLSNEEIAQELFISLTTVKTHIRNIYQKLG 875 (894)
T ss_pred CccHHHHHHHHHHH-----ccCCHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 39999999999999 7999999999999999999999999999984
No 213
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=90.29 E-value=0.51 Score=35.91 Aligned_cols=38 Identities=21% Similarity=0.438 Sum_probs=26.8
Q ss_pred HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 471 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 471 rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
|++.||.+.+ ..+.+.|.+|||+.||||+.+|+..+..
T Consensus 1 R~~~il~~L~--~~~~~it~~eLa~~l~vS~rTi~~~i~~ 38 (55)
T PF08279_consen 1 RQKQILKLLL--ESKEPITAKELAEELGVSRRTIRRDIKE 38 (55)
T ss_dssp HHHHHHHHHH--HTTTSBEHHHHHHHCTS-HHHHHHHHHH
T ss_pred CHHHHHHHHH--HcCCCcCHHHHHHHhCCCHHHHHHHHHH
Confidence 4556666542 2335699999999999999999865543
No 214
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=90.27 E-value=0.6 Score=36.08 Aligned_cols=43 Identities=23% Similarity=0.287 Sum_probs=32.1
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.|++.+..||..-+.-+ +.+.|..|||+.+|+++.+|.++.++
T Consensus 2 glt~~q~~vL~~l~~~~-~~~~t~~~la~~l~~~~~~vs~~v~~ 44 (62)
T PF12802_consen 2 GLTPSQFRVLMALARHP-GEELTQSELAERLGISKSTVSRIVKR 44 (62)
T ss_dssp TSTHHHHHHHHHHHHST-TSGEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHHCC-CCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 47888888888766522 23489999999999999999765544
No 215
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=89.51 E-value=0.48 Score=49.87 Aligned_cols=35 Identities=23% Similarity=0.290 Sum_probs=30.7
Q ss_pred HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567 475 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 513 (532)
Q Consensus 475 VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALk 513 (532)
+-.++|- +++|..|||+.||||+.+|+..+.+|.+
T Consensus 18 ~A~lYY~----~gltQ~eIA~~LgiSR~~v~rlL~~Ar~ 52 (321)
T COG2390 18 AAWLYYV----EGLTQSEIAERLGISRATVSRLLAKARE 52 (321)
T ss_pred HHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4557776 9999999999999999999988888865
No 216
>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=89.28 E-value=0.92 Score=33.74 Aligned_cols=37 Identities=27% Similarity=0.390 Sum_probs=27.3
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 470 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 470 ~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
|.-..|+.+-.. .+++..||++.+|+|+.+|++....
T Consensus 2 ~~R~~Il~~L~~----~~~~~~el~~~l~~s~~~vs~hL~~ 38 (47)
T PF01022_consen 2 PTRLRILKLLSE----GPLTVSELAEELGLSQSTVSHHLKK 38 (47)
T ss_dssp HHHHHHHHHHTT----SSEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHh----CCCchhhHHHhccccchHHHHHHHH
Confidence 444556655543 6899999999999999999876543
No 217
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=89.25 E-value=18 Score=37.79 Aligned_cols=178 Identities=13% Similarity=0.148 Sum_probs=92.7
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhH
Q 009567 294 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI 373 (532)
Q Consensus 294 e~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~ 373 (532)
++-+...+..+..++.+. ++ .+-+.|....+++.+.....-+|.....++.-.|.-+++ .
T Consensus 119 er~l~~a~~~I~~~~~~L---~L--p~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR----~----------- 178 (310)
T PRK00423 119 ERNLAFALSELDRIASQL---GL--PRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACR----R----------- 178 (310)
T ss_pred hHHHHHHHHHHHHHHHHc---CC--CHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHH----H-----------
Confidence 344444556666666655 23 356777777777777666777887776666655544432 1
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchh-hhcccCCCCChhHHH
Q 009567 374 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ-EITADTGVEIPDISV 452 (532)
Q Consensus 374 ~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~-d~i~d~~~~~pee~~ 452 (532)
.+-+-|..||+..++++..++..........+.++.+.. +...+. .+...-.. +....
T Consensus 179 -----------------~~~prtl~eI~~~~~v~~k~i~~~~~~l~k~L~~~~~~~--~p~~~i~r~~~~L~L--~~~v~ 237 (310)
T PRK00423 179 -----------------CKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPT--DPIDYVPRFASELGL--SGEVQ 237 (310)
T ss_pred -----------------cCCCcCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCC--CHHHHHHHHHHHcCC--CHHHH
Confidence 223456788888888888888665443333233322221 111111 11111111 11111
Q ss_pred HHHHHHHHHHHHHh-cC----CHHH--HHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567 453 QKQLMRQHVRNLLT-LL----NPKE--RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 515 (532)
Q Consensus 453 ~~~~l~~~L~~~L~-~L----~~rE--R~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKL 515 (532)
.. ....+..+.+ .| +|.- --+|.+-.-+ .|.+.|++|||...|||..+|++..+.-.+.|
T Consensus 238 ~~--A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~-~g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l 304 (310)
T PRK00423 238 KK--AIEILQKAKEKGLTSGKGPTGLAAAAIYIASLL-LGERRTQREVAEVAGVTEVTVRNRYKELAEKL 304 (310)
T ss_pred HH--HHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHH-hCCCCCHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 11 1112222221 11 1211 1112221111 24889999999999999999997776666554
No 218
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=88.91 E-value=0.69 Score=36.62 Aligned_cols=46 Identities=22% Similarity=0.407 Sum_probs=33.0
Q ss_pred CCHHHHHHHHHHhccc-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 468 LNPKERCIVRLRFGIE-DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 468 L~~rER~VL~LRyGL~-~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
|++....-|...|.|. ++.+-+..+||+.||||+.+|. .++++|.+
T Consensus 2 Lt~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt----~ml~~L~~ 48 (60)
T PF01325_consen 2 LTESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVT----EMLKRLAE 48 (60)
T ss_dssp CSCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHH----HHHHHHHH
T ss_pred CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHH----HHHHHHHH
Confidence 5555556666666554 5688999999999999999996 45556644
No 219
>PHA02591 hypothetical protein; Provisional
Probab=88.68 E-value=0.87 Score=38.04 Aligned_cols=24 Identities=21% Similarity=0.436 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLES 509 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~ 509 (532)
.|+|.++||+.||+|.++||++..
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHh
Confidence 689999999999999999999865
No 220
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=88.66 E-value=0.64 Score=44.04 Aligned_cols=50 Identities=14% Similarity=0.050 Sum_probs=43.2
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCC-----HHHHHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLS-----KERVRQLESRALYRLKQ 517 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgIS-----rerVRqie~rALkKLR~ 517 (532)
.|+++|.+|+.+..- +.|.++|.+||++.++.+ ..+|+.+..+.++||..
T Consensus 154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~l~~Kl~~ 208 (228)
T PRK11083 154 TLTRYEFLLLKTLLL-SPGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLRA 208 (228)
T ss_pred ecCHHHHHHHHHHHh-CCCceECHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhcc
Confidence 599999999988763 345679999999999986 78999999999999964
No 221
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=88.51 E-value=3.4 Score=41.85 Aligned_cols=34 Identities=26% Similarity=0.423 Sum_probs=27.2
Q ss_pred HHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHH
Q 009567 251 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 284 (532)
Q Consensus 251 le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~ 284 (532)
+......|...+|++||..|.|+..|++.+.+..
T Consensus 112 l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~ 145 (257)
T PRK05911 112 LADAMDSLRQSLGKEPTDGELCEYLNISQQELSG 145 (257)
T ss_pred HHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHH
Confidence 3345566778889999999999999999877743
No 222
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=88.21 E-value=1.3 Score=44.68 Aligned_cols=35 Identities=29% Similarity=0.497 Sum_probs=29.2
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHH
Q 009567 250 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 284 (532)
Q Consensus 250 ~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~ 284 (532)
++.+...+|...+|++||..|.|+..|++.+.+..
T Consensus 114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~ 148 (256)
T PRK07408 114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQE 148 (256)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHH
Confidence 44566778888999999999999999999877643
No 223
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional
Probab=87.74 E-value=0.79 Score=43.95 Aligned_cols=50 Identities=18% Similarity=0.120 Sum_probs=44.3
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~Lg-----ISrerVRqie~rALkKLR~ 517 (532)
.|+++|++|+.+... +.|++.|.++|++.+. ++..+|+....+.++||..
T Consensus 160 ~Lt~~e~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~lr~kl~~ 214 (240)
T PRK10710 160 DLTPAEFRLLKTLSH-EPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLES 214 (240)
T ss_pred ecCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCcCcCCCccCHHHHHHHHHHHhhc
Confidence 599999999998764 5567899999999998 9999999999999999963
No 224
>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=87.71 E-value=1.8 Score=33.80 Aligned_cols=37 Identities=27% Similarity=0.373 Sum_probs=27.7
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 470 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 509 (532)
Q Consensus 470 ~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~ 509 (532)
|.-+.||.+-. .+.++|..|||+.+|++..+|++.+.
T Consensus 10 p~R~~Il~~L~---~~~~~t~~ela~~l~~~~~t~s~hL~ 46 (61)
T PF12840_consen 10 PTRLRILRLLA---SNGPMTVSELAEELGISQSTVSYHLK 46 (61)
T ss_dssp HHHHHHHHHHH---HCSTBEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHh---cCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 66666776651 13899999999999999999976543
No 225
>cd00131 PAX Paired Box domain
Probab=87.46 E-value=1.5 Score=39.98 Aligned_cols=41 Identities=12% Similarity=0.017 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567 468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 512 (532)
Q Consensus 468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rAL 512 (532)
|+...|.-|...|- +++|..+||+.||||+.+|..+.++-.
T Consensus 18 lS~d~R~rIv~~~~----~G~s~~~iA~~~~Vs~~tV~r~i~r~~ 58 (128)
T cd00131 18 LPDSIRQRIVELAQ----SGIRPCDISRQLRVSHGCVSKILNRYY 58 (128)
T ss_pred CCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 44444444444454 789999999999999999998888754
No 226
>PHA02547 55 RNA polymerase sigma factor; Provisional
Probab=87.45 E-value=1.9 Score=41.21 Aligned_cols=65 Identities=12% Similarity=0.136 Sum_probs=46.5
Q ss_pred HHHHHHHHHHHHHHHhhCCCCC---HhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHH
Q 009567 296 LINANLRLVVHVAKQYQGRGIS---LHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI 360 (532)
Q Consensus 296 LI~~nlrLV~sIAkrY~~~g~~---~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~i 360 (532)
+=.+-+..+..++++|.-+|.. -+|+|.+|.-..++.++.|||++...+-.|.+..+-++..+-|
T Consensus 42 ig~~imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI 109 (179)
T PHA02547 42 IGLAIMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRI 109 (179)
T ss_pred HHHHHHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHH
Confidence 3344555666666666555555 4999999999999999999999987776676665555544444
No 227
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=87.23 E-value=9.1 Score=41.21 Aligned_cols=34 Identities=32% Similarity=0.584 Sum_probs=28.7
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHH
Q 009567 250 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 283 (532)
Q Consensus 250 ~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~ 283 (532)
++.+....|...+|++||..|.|+..|++.+.+.
T Consensus 224 ~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~ 257 (373)
T PRK07406 224 RIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLR 257 (373)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence 4556677888889999999999999999977764
No 228
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=87.18 E-value=2.3 Score=41.92 Aligned_cols=32 Identities=38% Similarity=0.579 Sum_probs=26.3
Q ss_pred HHHHHHHhhhCCCCcHHHHHHHccCCHHHHHH
Q 009567 253 KEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 284 (532)
Q Consensus 253 ~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~ 284 (532)
+....|...+|++||..|.|+..|++.+.+..
T Consensus 101 ~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~ 132 (231)
T TIGR02885 101 YMKEELSKELGREPTINELAEALGVSPEEIVM 132 (231)
T ss_pred HHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHH
Confidence 45567777889999999999999999877643
No 229
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=86.97 E-value=1.1 Score=35.18 Aligned_cols=41 Identities=20% Similarity=0.332 Sum_probs=26.2
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
|++.|..||..-. ..+.++|..+|++.+|+++.+|...+++
T Consensus 1 lt~~q~~vL~~l~--~~~~~~t~~~l~~~~~~~~~~vs~~i~~ 41 (68)
T PF13463_consen 1 LTRPQWQVLRALA--HSDGPMTQSDLAERLGISKSTVSRIIKK 41 (68)
T ss_dssp --HHHHHHHHHHT----TS-BEHHHHHHHTT--HHHHHHHHHH
T ss_pred CCHHHHHHHHHHH--ccCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 4666777766555 2458999999999999999999754443
No 230
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=86.91 E-value=1.4 Score=36.93 Aligned_cols=42 Identities=24% Similarity=0.400 Sum_probs=34.6
Q ss_pred cCCHHHHHHHHHHhc--ccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFG--IEDGKPKSLSEVGNIFGLSKERVRQLE 508 (532)
Q Consensus 467 ~L~~rER~VL~LRyG--L~~~e~~Tl~EIAe~LgISrerVRqie 508 (532)
.|++++++||...-- ...|++-.-++||+.+|+|..+||+..
T Consensus 1 ~Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M 44 (78)
T PF03444_consen 1 MLTERQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEM 44 (78)
T ss_pred CCCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHH
Confidence 388999999876432 346799999999999999999999764
No 231
>PRK05949 RNA polymerase sigma factor; Validated
Probab=86.88 E-value=9.7 Score=40.15 Aligned_cols=35 Identities=26% Similarity=0.461 Sum_probs=28.6
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHH
Q 009567 250 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 284 (532)
Q Consensus 250 ~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~ 284 (532)
++.+....+...+|++||..|.|+..|++.+.+..
T Consensus 179 ~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~ 213 (327)
T PRK05949 179 KIKKTQRELSQKLGRSATPAEIAKELELEPSQIRE 213 (327)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence 44556677778899999999999999999877644
No 232
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=86.79 E-value=8.7 Score=39.10 Aligned_cols=35 Identities=29% Similarity=0.554 Sum_probs=28.7
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHH
Q 009567 250 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 284 (532)
Q Consensus 250 ~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~ 284 (532)
++.+...+|...+|++||..|.|+..|++.+.+..
T Consensus 128 ~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~ 162 (264)
T PRK07122 128 RLGRATAELSQRLGRAPTASELAAELGMDREEVVE 162 (264)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 34456677888899999999999999999877754
No 233
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=86.53 E-value=13 Score=37.67 Aligned_cols=35 Identities=29% Similarity=0.532 Sum_probs=28.7
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHH
Q 009567 250 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 284 (532)
Q Consensus 250 ~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~ 284 (532)
++.+....|+..+|++||..+.|...|++.+.+..
T Consensus 119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~ 153 (268)
T PRK06288 119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYNS 153 (268)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHH
Confidence 45566777888899999999999999998776643
No 234
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=86.45 E-value=1.6 Score=37.66 Aligned_cols=41 Identities=27% Similarity=0.252 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009567 468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 511 (532)
Q Consensus 468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rA 511 (532)
|++.++.||....- +...|..+||+.+|+|+.+|+....+-
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 46778888876543 247899999999999999998655443
No 235
>PRK15479 transcriptional regulatory protein TctD; Provisional
Probab=86.43 E-value=1.2 Score=42.04 Aligned_cols=49 Identities=18% Similarity=0.233 Sum_probs=41.6
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLK 516 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~Lg-----ISrerVRqie~rALkKLR 516 (532)
.|+++|.+|+.+..- +-|...|.++|++.+. +|..+|+.+..+.++||.
T Consensus 148 ~Lt~~E~~il~~l~~-~~~~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl~ 201 (221)
T PRK15479 148 ALTPREQALLTVLMY-RRTRPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKLQ 201 (221)
T ss_pred ecCHHHHHHHHHHHh-CCCCcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhcC
Confidence 599999999987652 3346679999999986 999999999999999985
No 236
>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=86.33 E-value=17 Score=37.51 Aligned_cols=84 Identities=23% Similarity=0.326 Sum_probs=45.9
Q ss_pred CCCHHHHHHHhC--CCHHHHHHHHHhcCC--CcccCCCCCCCCCcchhh-hcccCCCCChhHHH--HHHHHHHHHHHHHh
Q 009567 394 SPDKEDLARRVG--ITVEKLERLIFITRM--PLSMQQPVWADQDTTFQE-ITADTGVEIPDISV--QKQLMRQHVRNLLT 466 (532)
Q Consensus 394 ~Pt~eEIA~~lg--is~e~v~~ll~~~~~--~iSLD~~v~~d~~~~l~d-~i~d~~~~~pee~~--~~~~l~~~L~~~L~ 466 (532)
.+++++||+.++ ||.++|+..+..... -+--+. ++.-...+ .+.... +.+...+ ...++.+.-.++|+
T Consensus 137 ~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~----~g~y~~t~~~l~~~~-~~~~~avr~~h~q~l~lA~~al~ 211 (271)
T TIGR02147 137 ADDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNE----DGFYKQTDKAVSTGD-EVIPLAVRQYQKQMIDLAKEALD 211 (271)
T ss_pred CCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECC----CCcEEeecceeecCC-ccchHHHHHHHHHHHHHHHHHHH
Confidence 567889999999 999999988764321 111111 11000011 111111 1222211 12233444567788
Q ss_pred cCCHHHHHHHHHHhcc
Q 009567 467 LLNPKERCIVRLRFGI 482 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL 482 (532)
..|+.+|.+=.+-+|+
T Consensus 212 ~~p~~eR~~S~lT~~i 227 (271)
T TIGR02147 212 ALPPSERDVSTVTFGI 227 (271)
T ss_pred hCCccccccceeeEec
Confidence 9999999977776664
No 237
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=85.84 E-value=1.9 Score=32.33 Aligned_cols=34 Identities=26% Similarity=0.408 Sum_probs=26.8
Q ss_pred HHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009567 473 RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 511 (532)
Q Consensus 473 R~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rA 511 (532)
..|+.+.. +..|.++||+.+|||..+|+.+..+.
T Consensus 18 ~~i~~~~~-----~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 18 QYILKLLR-----ESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHHHHHHh-----hcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 34555554 34699999999999999999988764
No 238
>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=85.72 E-value=14 Score=38.21 Aligned_cols=35 Identities=26% Similarity=0.496 Sum_probs=28.5
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHH
Q 009567 250 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 284 (532)
Q Consensus 250 ~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~ 284 (532)
++.+.+..+...+|++||..+.|...|++.+.+..
T Consensus 162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~ 196 (298)
T TIGR02997 162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRE 196 (298)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 44556667778899999999999999999877753
No 239
>PRK12423 LexA repressor; Provisional
Probab=85.62 E-value=1.5 Score=42.84 Aligned_cols=47 Identities=30% Similarity=0.513 Sum_probs=35.6
Q ss_pred cCCHHHHHHHHHHhc--ccCCCCCCHHHHHHHhC-CCHHHHHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFG--IEDGKPKSLSEVGNIFG-LSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 467 ~L~~rER~VL~LRyG--L~~~e~~Tl~EIAe~Lg-ISrerVRqie~rALkKLR~ 517 (532)
.|++++++|+..--- ..+|-+-|..|||+.|| +|+.+|+ ++|++|++
T Consensus 3 ~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~----~~l~~L~~ 52 (202)
T PRK12423 3 TLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVAR----KHVQALAE 52 (202)
T ss_pred cCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHH----HHHHHHHH
Confidence 489999999886432 22344679999999999 5999998 46667766
No 240
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=85.26 E-value=11 Score=37.98 Aligned_cols=35 Identities=29% Similarity=0.346 Sum_probs=28.2
Q ss_pred HHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHH
Q 009567 252 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL 286 (532)
Q Consensus 252 e~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l 286 (532)
.+...++...+|++||.+|.|+..|++.+.+...+
T Consensus 123 ~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~ 157 (254)
T TIGR02850 123 LQVRDKLISENSKEPTVSEIAKELKVPQEEVVFAL 157 (254)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 34566777888999999999999999988775443
No 241
>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB. PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself. It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.
Probab=85.25 E-value=0.66 Score=43.77 Aligned_cols=50 Identities=16% Similarity=0.114 Sum_probs=42.4
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHH-----HHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEV-----GNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EI-----Ae~LgISrerVRqie~rALkKLR~ 517 (532)
.|+++|.+|+.+... +-|+++|.++| |..++++..+|+....+.++||..
T Consensus 154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~l~~Kl~~ 208 (226)
T TIGR02154 154 SLGPTEFRLLHFFMT-HPERVYSREQLLDRVWGRDVYVEERTVDVHIRRLRKALNP 208 (226)
T ss_pred EcCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCCCCCCCCccHHHHHHHHHHhhcc
Confidence 599999999988764 33467888888 778999999999999999999963
No 242
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=85.12 E-value=1.2 Score=42.06 Aligned_cols=49 Identities=16% Similarity=0.180 Sum_probs=41.8
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLK 516 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~Lg-----ISrerVRqie~rALkKLR 516 (532)
.|+++|.+|+.+..- +.|..+|.++|++.+. ++..+|+.+..+.++||.
T Consensus 149 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl~ 202 (219)
T PRK10336 149 TLKPKEFALLELLMR-NAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLG 202 (219)
T ss_pred ecCHHHHHHHHHHHh-CCCccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhcC
Confidence 499999999987652 3346699999999996 999999999999999985
No 243
>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=84.64 E-value=1.3 Score=38.01 Aligned_cols=41 Identities=22% Similarity=0.327 Sum_probs=30.3
Q ss_pred hcCCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHHH
Q 009567 466 TLLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQ 506 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~---~e~~Tl~EIAe~LgISrerVRq 506 (532)
.-++|.|+.-|..|+-+-. .+++|+.||++.+|+|..+|.+
T Consensus 25 dL~T~~E~~~l~~R~~va~~lL~~g~syreIa~~tgvS~aTItR 68 (87)
T PF01371_consen 25 DLCTPDELEALAQRWQVAKELLDEGKSYREIAEETGVSIATITR 68 (87)
T ss_dssp HHSSHHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHH
T ss_pred HhCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHH
Confidence 3467777776666554322 1689999999999999999963
No 244
>PF12728 HTH_17: Helix-turn-helix domain
Probab=84.36 E-value=1.1 Score=33.63 Aligned_cols=24 Identities=17% Similarity=0.376 Sum_probs=21.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRA 511 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rA 511 (532)
+|.+|+|+.||||+.+|+++..+.
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcC
Confidence 689999999999999999987643
No 245
>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator. This model describes a family of DNA-binding response regulator proteins, associated with an adjacent histidine kinase (TIGR03785) to form a two-component system. This system co-occurs with, and often is adjacent to, a proteobacterial variant form of the protein sorting transpeptidase called sortase (TIGR03784), and a single target protein for the sortase. We give this protein the gene symbol pdsR, for Proteobacterial Dedicated Sortase system Response regulator.
Probab=84.32 E-value=1.4 Score=41.97 Aligned_cols=50 Identities=14% Similarity=0.087 Sum_probs=42.0
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHH--HHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEV--GNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EI--Ae~LgISrerVRqie~rALkKLR~ 517 (532)
.|+++|.+||.+..- +.|..+|.++| +..++++..+|+.+..+.++||..
T Consensus 156 ~Lt~~E~~il~~l~~-~~g~v~s~~~i~~~~~~~~~~~tv~~~v~rlr~Kl~~ 207 (227)
T TIGR03787 156 DLTVTEFWMVHALAK-HPGHVKSRQQLMDAAKIVVDDSTITSHIKRIRKKFQA 207 (227)
T ss_pred cCCHHHHHHHHHHHh-CCCccccHHHHHHHhhhcCCccCHHHHHHHHHHHhcc
Confidence 499999999988762 22355699999 888999999999999999999963
No 246
>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=84.29 E-value=4.1 Score=35.03 Aligned_cols=49 Identities=18% Similarity=0.244 Sum_probs=37.0
Q ss_pred HhcCCHHHHHHHHHH----hccc-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 465 LTLLNPKERCIVRLR----FGIE-DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 465 L~~L~~rER~VL~LR----yGL~-~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
...+++++..+|... ||.. ...+.|..|||+.+|+++++|+ |++++|.+
T Consensus 20 ~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVs----r~L~~Le~ 73 (95)
T TIGR01610 20 GADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVS----DAIKSLAR 73 (95)
T ss_pred hCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 467899999987743 3322 2378999999999999999996 66666654
No 247
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=84.28 E-value=1.9 Score=35.80 Aligned_cols=45 Identities=29% Similarity=0.341 Sum_probs=29.9
Q ss_pred HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH-----HHHHHHHHHhhcCc
Q 009567 475 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES-----RALYRLKQSLGGKA 523 (532)
Q Consensus 475 VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~-----rALkKLR~~l~~~~ 523 (532)
|..++-- .++|..|+|+.+|+|+.+|+++++ -.+.+|...+..-+
T Consensus 23 i~~~~~~----~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aLG 72 (80)
T PF13744_consen 23 IRELREE----RGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEALG 72 (80)
T ss_dssp HHHHHHC----CT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHTT
T ss_pred HHHHHHH----cCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHcC
Confidence 4444444 789999999999999999999985 24666666555443
No 248
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=84.21 E-value=2.3 Score=34.38 Aligned_cols=41 Identities=22% Similarity=0.384 Sum_probs=27.1
Q ss_pred HHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 472 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 472 ER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
+..||.+... .++++.|..|||+.+||++.+|++ .|.+|.+
T Consensus 8 ~~~IL~~L~~-~g~~~~ta~eLa~~lgl~~~~v~r----~L~~L~~ 48 (68)
T smart00550 8 EEKILEFLEN-SGDETSTALQLAKNLGLPKKEVNR----VLYSLEK 48 (68)
T ss_pred HHHHHHHHHH-CCCCCcCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence 3444444332 122369999999999999999875 4555544
No 249
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=84.08 E-value=13 Score=37.16 Aligned_cols=35 Identities=23% Similarity=0.363 Sum_probs=27.9
Q ss_pred HHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHH
Q 009567 251 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 285 (532)
Q Consensus 251 le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~ 285 (532)
+++....+...+|++|+..++|+..|++.+.+...
T Consensus 111 ~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~ 145 (251)
T PRK07670 111 VEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEAT 145 (251)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHH
Confidence 34455667778899999999999999998777543
No 250
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=83.88 E-value=12 Score=39.34 Aligned_cols=34 Identities=26% Similarity=0.522 Sum_probs=28.3
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHH
Q 009567 250 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 283 (532)
Q Consensus 250 ~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~ 283 (532)
++.+....+...+|++||..|.|++.|++.+.+.
T Consensus 169 ~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~ 202 (317)
T PRK07405 169 KIKKAQRQLSQQLGRAATIGELAEELELTPKQVR 202 (317)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHH
Confidence 4556777888889999999999999999876664
No 251
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=83.87 E-value=1.4 Score=33.38 Aligned_cols=32 Identities=38% Similarity=0.516 Sum_probs=23.3
Q ss_pred HHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 478 LRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 509 (532)
Q Consensus 478 LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~ 509 (532)
+.+.-..+.++|+.|||+.+|+++.+|..+..
T Consensus 9 L~~l~~~~~~~t~~eia~~~gl~~stv~r~L~ 40 (52)
T PF09339_consen 9 LEALAESGGPLTLSEIARALGLPKSTVHRLLQ 40 (52)
T ss_dssp HHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 33433455778999999999999999976543
No 252
>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=83.85 E-value=3.4 Score=35.12 Aligned_cols=40 Identities=20% Similarity=0.256 Sum_probs=28.0
Q ss_pred CCCCHHHHHHHhC-CCHHHHHHHHHHHHHHHHHHhhc-Cchhhhhh
Q 009567 486 KPKSLSEVGNIFG-LSKERVRQLESRALYRLKQSLGG-KASYGYAD 529 (532)
Q Consensus 486 e~~Tl~EIAe~Lg-ISrerVRqie~rALkKLR~~l~~-~~l~~yld 529 (532)
-++|+.+||+.|| .+.++|..... ++.+.+.. ..++..++
T Consensus 43 ~~~s~~~Ig~~fg~r~hStV~~a~~----ri~~~~~~d~~~~~~v~ 84 (90)
T cd06571 43 TGLSLPEIGRAFGGRDHSTVLHAVR----KIEELLEEDPELKEDVE 84 (90)
T ss_pred hCCCHHHHHHHhCCCCHhHHHHHHH----HHHHHHHhCHHHHHHHH
Confidence 4799999999999 99999975554 44444433 34444443
No 253
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=83.80 E-value=1.1 Score=35.76 Aligned_cols=44 Identities=25% Similarity=0.349 Sum_probs=32.8
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
.|++.|..|+..-. ...+.|..|||+.+|+++.+|+ +++++|.+
T Consensus 5 gLs~~E~~vy~~Ll---~~~~~t~~eIa~~l~i~~~~v~----~~L~~L~~ 48 (68)
T PF01978_consen 5 GLSENEAKVYLALL---KNGPATAEEIAEELGISRSTVY----RALKSLEE 48 (68)
T ss_dssp CHHHHHHHHHHHHH---HHCHEEHHHHHHHHTSSHHHHH----HHHHHHHH
T ss_pred CcCHHHHHHHHHHH---HcCCCCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 46777888776543 1268999999999999999996 55555544
No 254
>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=83.69 E-value=1.1 Score=33.64 Aligned_cols=22 Identities=18% Similarity=0.356 Sum_probs=19.9
Q ss_pred CHHHHHHHhCCCHHHHHHHHHH
Q 009567 489 SLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 489 Tl~EIAe~LgISrerVRqie~r 510 (532)
|++|||+..|||..+|+..++.
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~ 22 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNG 22 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTT
T ss_pred CHHHHHHHHCcCHHHHHHHHhC
Confidence 7899999999999999987764
No 255
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=83.56 E-value=2.1 Score=39.74 Aligned_cols=27 Identities=26% Similarity=0.208 Sum_probs=24.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESRAL 512 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~rAL 512 (532)
+|+|.+|||++||||.++|..+.++-.
T Consensus 20 ~G~S~re~Ak~~gvs~sTvy~wv~r~~ 46 (138)
T COG3415 20 EGLSCREAAKRFGVSISTVYRWVRRYR 46 (138)
T ss_pred cCccHHHHHHHhCccHHHHHHHHHHhc
Confidence 799999999999999999999888754
No 256
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=83.51 E-value=5.7 Score=36.95 Aligned_cols=64 Identities=19% Similarity=0.326 Sum_probs=36.8
Q ss_pred HHHHHhcCCHHHHHHHHHH----hcccCCCCCCHHHHHHHhCCCHHHHHHHHH--HHHHHHHHHhhcCch
Q 009567 461 VRNLLTLLNPKERCIVRLR----FGIEDGKPKSLSEVGNIFGLSKERVRQLES--RALYRLKQSLGGKAS 524 (532)
Q Consensus 461 L~~~L~~L~~rER~VL~LR----yGL~~~e~~Tl~EIAe~LgISrerVRqie~--rALkKLR~~l~~~~l 524 (532)
+..+=..|++.|+....+. |...+|+.+|+.|||+.+||++.++-++.+ +++-.....+....+
T Consensus 4 ~~~le~~L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~~~~Fiey~n~la~~~~ 73 (142)
T PF13022_consen 4 LKELEAKLTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQQNKAFIEYKNELADRFL 73 (142)
T ss_dssp HHHHHTTS-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHHH-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHcCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHhcCHHHHHHHHHHHHHHH
Confidence 4445578999988843332 222245789999999999999999999884 444444444443333
No 257
>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=83.38 E-value=2.2 Score=32.64 Aligned_cols=41 Identities=24% Similarity=0.416 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009567 468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 511 (532)
Q Consensus 468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rA 511 (532)
|+..|-.||..-+- ..+.|..|||+.+|+++.+|.++.++-
T Consensus 1 lt~~q~~iL~~l~~---~~~~~~~~la~~~~~~~~~~t~~i~~L 41 (59)
T PF01047_consen 1 LTPSQFRILRILYE---NGGITQSELAEKLGISRSTVTRIIKRL 41 (59)
T ss_dssp STHHHHHHHHHHHH---HSSEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH---cCCCCHHHHHHHHCCChhHHHHHHHHH
Confidence 45666666666553 257999999999999999997665543
No 258
>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=83.07 E-value=2 Score=41.58 Aligned_cols=48 Identities=21% Similarity=0.337 Sum_probs=36.3
Q ss_pred hcCCHHHHHHHHHHhc--ccCCCCCCHHHHHHHhCCC-HHHHHHHHHHHHHHHHH
Q 009567 466 TLLNPKERCIVRLRFG--IEDGKPKSLSEVGNIFGLS-KERVRQLESRALYRLKQ 517 (532)
Q Consensus 466 ~~L~~rER~VL~LRyG--L~~~e~~Tl~EIAe~LgIS-rerVRqie~rALkKLR~ 517 (532)
..|+++|++||.+-.- ..++.+.|.+|||+.+|++ +.+|+. .+++|.+
T Consensus 2 ~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~----~l~~L~~ 52 (199)
T TIGR00498 2 KPLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEE----HLKALER 52 (199)
T ss_pred CccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHH----HHHHHHH
Confidence 3589999999987652 2245678999999999998 999974 4455544
No 259
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=82.97 E-value=1.2 Score=43.47 Aligned_cols=39 Identities=18% Similarity=0.232 Sum_probs=28.9
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 509 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~ 509 (532)
.|+++ +|+.+.- .+..++|.+|||+.||||+.||+.+..
T Consensus 161 ~Lt~r--~Vl~~~~--~g~~g~s~~eIa~~l~iS~~Tv~~~~~ 199 (225)
T PRK10046 161 PLTLN--AVRKLFK--EPGVQHTAETVAQALTISRTTARRYLE 199 (225)
T ss_pred HHHHH--HHHHHHH--cCCCCcCHHHHHHHhCccHHHHHHHHH
Confidence 35554 5665543 122479999999999999999998875
No 260
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=82.90 E-value=2.1 Score=32.31 Aligned_cols=30 Identities=37% Similarity=0.493 Sum_probs=24.0
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 484 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 484 ~~e~~-Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
.|... |..|||+.+|+|+.+|+ +++++|.+
T Consensus 16 ~~~~l~s~~~la~~~~vs~~tv~----~~l~~L~~ 46 (60)
T smart00345 16 PGDKLPSERELAAQLGVSRTTVR----EALSRLEA 46 (60)
T ss_pred CCCcCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 34556 99999999999999997 56666655
No 261
>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=82.87 E-value=3.9 Score=32.94 Aligned_cols=40 Identities=28% Similarity=0.472 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHhCCC-HHHHHHHHHh
Q 009567 378 SKVLEAKRLYIQEGNHSPDKEDLARRVGIT-VEKLERLIFI 417 (532)
Q Consensus 378 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis-~e~v~~ll~~ 417 (532)
.++-.....+..+.|..||..|||+.+|++ ...|...+..
T Consensus 9 ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~ 49 (65)
T PF01726_consen 9 KEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKA 49 (65)
T ss_dssp HHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 344455566777899999999999999997 8888877654
No 262
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=82.67 E-value=2.7 Score=39.09 Aligned_cols=41 Identities=15% Similarity=0.261 Sum_probs=32.5
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.|++.++.||..--- +...|+.|||+.+|+|+.+|+.+..+
T Consensus 6 ~lD~~D~~Il~~Lq~---d~R~s~~eiA~~lglS~~tV~~Ri~r 46 (153)
T PRK11179 6 QIDNLDRGILEALME---NARTPYAELAKQFGVSPGTIHVRVEK 46 (153)
T ss_pred ccCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 377888888877543 25789999999999999999865543
No 263
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=82.32 E-value=14 Score=33.06 Aligned_cols=28 Identities=32% Similarity=0.432 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
.+.|+.|||+.||||..+|. ++|++|.-
T Consensus 70 pd~tl~Ela~~l~Vs~~ti~----~~Lkrlg~ 97 (119)
T PF01710_consen 70 PDATLRELAERLGVSPSTIW----RALKRLGI 97 (119)
T ss_pred CCcCHHHHHHHcCCCHHHHH----HHHHHcCc
Confidence 78999999999999999986 56666643
No 264
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=82.31 E-value=3.3 Score=31.84 Aligned_cols=39 Identities=21% Similarity=0.242 Sum_probs=25.6
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 509 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~ 509 (532)
.|++.|+--|....- .++++.|||..+|-|+..|+..++
T Consensus 4 ~Lt~~Eqaqid~m~q----lG~s~~~isr~i~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 4 TLTDAEQAQIDVMHQ----LGMSLREISRRIGRSRTCIRRYLK 42 (50)
T ss_dssp ---HHHHHHHHHHHH----TT--HHHHHHHHT--HHHHHHHHH
T ss_pred cCCHHHHHHHHHHHH----hchhHHHHHHHhCccHHHHHHHhc
Confidence 467777766666665 689999999999999999987754
No 265
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=82.18 E-value=29 Score=35.82 Aligned_cols=26 Identities=19% Similarity=0.332 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhc
Q 009567 393 HSPDKEDLARRVGITVEKLERLIFIT 418 (532)
Q Consensus 393 r~Pt~eEIA~~lgis~e~v~~ll~~~ 418 (532)
..-|.+|||+.+|+|.++|..+....
T Consensus 244 ~~~t~~EIa~~lgvs~~~V~q~~~~A 269 (289)
T PRK07500 244 DGATLEALGEELGISKERVRQIEARA 269 (289)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 45689999999999999999886543
No 266
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=82.13 E-value=1.6 Score=31.62 Aligned_cols=24 Identities=25% Similarity=0.407 Sum_probs=21.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRA 511 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rA 511 (532)
+|.+|+|+.||||+.+|+++.+..
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcC
Confidence 589999999999999999988654
No 267
>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=81.85 E-value=1.7 Score=31.25 Aligned_cols=25 Identities=16% Similarity=0.300 Sum_probs=22.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRAL 512 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rAL 512 (532)
+|..|+|+.+|||+.+|+++.....
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 5889999999999999999988764
No 268
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=81.80 E-value=2.5 Score=41.01 Aligned_cols=34 Identities=26% Similarity=0.293 Sum_probs=27.5
Q ss_pred HHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 472 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 472 ER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
++.|..++- .++|..+||+.||||+.+|.++.+.
T Consensus 162 ~~~i~~~~~-----~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 162 EEKIKKLLD-----KGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred HHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 345666644 6899999999999999999988763
No 269
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=81.79 E-value=2.8 Score=34.55 Aligned_cols=51 Identities=20% Similarity=0.251 Sum_probs=34.6
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhc-ccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 009567 458 RQHVRNLLTLLNPKERCIVRLRFG-IEDGKPKSLSEVGNIFGLSKERVRQLE 508 (532)
Q Consensus 458 ~~~L~~~L~~L~~rER~VL~LRyG-L~~~e~~Tl~EIAe~LgISrerVRqie 508 (532)
...|......|++.|+.|..+..- .+.-..+|..|||+..|||..+|.+..
T Consensus 4 ~~~i~~~~~~ls~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~ 55 (77)
T PF01418_consen 4 LEKIRSQYNSLSPTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRFC 55 (77)
T ss_dssp HHHHHHHGGGS-HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHhhCCHHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHH
Confidence 456777789999999998865432 011257999999999999999996543
No 270
>CHL00148 orf27 Ycf27; Reviewed
Probab=81.75 E-value=2 Score=41.16 Aligned_cols=50 Identities=18% Similarity=0.115 Sum_probs=42.7
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHh-------CCCHHHHHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-------GLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~L-------gISrerVRqie~rALkKLR~ 517 (532)
.|+++|.+|+.+... +.|+++|.+||++.+ +++..+|+.+..+.++||..
T Consensus 161 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l~~~~~~~~~~~~tv~~~i~~lr~KL~~ 217 (240)
T CHL00148 161 RLTGMEFSLLELLIS-KSGEIFSRATILKEVWGYTPERHIDTRVVDVHISRLRAKLED 217 (240)
T ss_pred EcCHHHHHHHHHHHH-CCCEEEcHHHHHHHhcCCCcccCCCcccHHHHHHHHHHHhcc
Confidence 499999999987652 344789999999999 48999999999999999964
No 271
>PRK00215 LexA repressor; Validated
Probab=81.64 E-value=2.7 Score=40.82 Aligned_cols=44 Identities=25% Similarity=0.320 Sum_probs=33.7
Q ss_pred cCCHHHHHHHHHHh--cccCCCCCCHHHHHHHhCC-CHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRF--GIEDGKPKSLSEVGNIFGL-SKERVRQLESR 510 (532)
Q Consensus 467 ~L~~rER~VL~LRy--GL~~~e~~Tl~EIAe~LgI-SrerVRqie~r 510 (532)
.|+++|++||.+-. ....+.+.|+.|||+.+|+ ++.+|..++.+
T Consensus 1 ~lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~ 47 (205)
T PRK00215 1 MLTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKA 47 (205)
T ss_pred CCCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 37889999987543 2234578899999999999 99999755443
No 272
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=81.40 E-value=3.6 Score=35.12 Aligned_cols=44 Identities=18% Similarity=0.209 Sum_probs=36.9
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 512 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rAL 512 (532)
..|+|.-|..|..+.. .++++..++|+.||||+.+++++..|=.
T Consensus 7 A~Lt~~gR~~lv~~vv---~~g~~~a~aA~~~gVS~~Ta~kW~~Ryr 50 (85)
T PF13011_consen 7 ARLTPRGRLRLVRRVV---EQGWPVAHAAAEFGVSRRTAYKWLARYR 50 (85)
T ss_pred CCCCHHHHHHHHHHHH---HcCCcHHHHHHHhCCCHHHHHHHHHHHH
Confidence 3689999988888774 1589999999999999999999887744
No 273
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=80.68 E-value=4 Score=44.18 Aligned_cols=51 Identities=16% Similarity=0.203 Sum_probs=42.8
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
.+++.||..+.+.+.|...++.|+.++|+.|+||++||.+-+++..+.|.+
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 478889888888777777789999999999999999999877766666655
No 274
>PF13551 HTH_29: Winged helix-turn helix
Probab=80.37 E-value=3.2 Score=35.59 Aligned_cols=26 Identities=19% Similarity=0.349 Sum_probs=23.1
Q ss_pred CCC-CHHHHHHHhCCCHHHHHHHHHHH
Q 009567 486 KPK-SLSEVGNIFGLSKERVRQLESRA 511 (532)
Q Consensus 486 e~~-Tl~EIAe~LgISrerVRqie~rA 511 (532)
++. |..+||+.+|+|+.+|.++.++-
T Consensus 10 ~g~~~~~~ia~~lg~s~~Tv~r~~~~~ 36 (112)
T PF13551_consen 10 EGVSTIAEIARRLGISRRTVYRWLKRY 36 (112)
T ss_pred cCCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence 677 69999999999999999988773
No 275
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=79.76 E-value=3 Score=39.34 Aligned_cols=40 Identities=23% Similarity=0.147 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
|++.++.||..-- .+...|+.|||+.+|+|+.+|+.+..+
T Consensus 12 lD~~D~~IL~~Lq---~d~R~s~~eiA~~lglS~~tv~~Ri~r 51 (164)
T PRK11169 12 LDRIDRNILNELQ---KDGRISNVELSKRVGLSPTPCLERVRR 51 (164)
T ss_pred HHHHHHHHHHHhc---cCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 5677888887543 235789999999999999999876544
No 276
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=79.03 E-value=1.6 Score=32.07 Aligned_cols=25 Identities=24% Similarity=0.404 Sum_probs=22.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRAL 512 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rAL 512 (532)
+|..|+|+.+|||..+|+.++.+.+
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999988775
No 277
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=78.87 E-value=5.2 Score=33.66 Aligned_cols=33 Identities=18% Similarity=0.309 Sum_probs=27.1
Q ss_pred ccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567 482 IEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 518 (532)
Q Consensus 482 L~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~ 518 (532)
+.++...|-++||+.||+||.+| .+.+++||+.
T Consensus 14 ~~~~~~~SGe~La~~LgiSRtaV----wK~Iq~Lr~~ 46 (79)
T COG1654 14 LLTGNFVSGEKLAEELGISRTAV----WKHIQQLREE 46 (79)
T ss_pred HcCCCcccHHHHHHHHCccHHHH----HHHHHHHHHh
Confidence 34557899999999999998888 5777888864
No 278
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=78.86 E-value=4.9 Score=36.72 Aligned_cols=42 Identities=31% Similarity=0.285 Sum_probs=33.4
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
..|++.++.||...-. | -..|+.|||+.+|+|+.+|+.+..+
T Consensus 4 ~~lD~~D~~IL~~L~~--d-~r~~~~eia~~lglS~~~v~~Ri~~ 45 (154)
T COG1522 4 MKLDDIDRRILRLLQE--D-ARISNAELAERVGLSPSTVLRRIKR 45 (154)
T ss_pred ccccHHHHHHHHHHHH--h-CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4578888888887543 3 4599999999999999999876554
No 279
>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=78.52 E-value=4.5 Score=38.63 Aligned_cols=42 Identities=21% Similarity=0.202 Sum_probs=34.2
Q ss_pred CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567 469 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 513 (532)
Q Consensus 469 ~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALk 513 (532)
|+.-|.-++..|.+ +++|++.+|..+|||..|+|.+..+|..
T Consensus 4 ~~e~R~~~R~~YV~---~~~sLe~aA~~~gVs~~TarrWK~~Ak~ 45 (165)
T PF08822_consen 4 PQETRDAVRRAYVF---DRLSLEQAAAKCGVSYATARRWKREAKA 45 (165)
T ss_pred cHHHHHHHHHHHHh---CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34456666776763 6799999999999999999999999864
No 280
>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=78.37 E-value=2.9 Score=33.62 Aligned_cols=28 Identities=39% Similarity=0.666 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
-++|.++||..+|+|+++|. +.+++|++
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~----r~l~~l~~ 54 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVS----RILKRLKD 54 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHH----HHHHHHHH
T ss_pred ecCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 46899999999999999985 66777766
No 281
>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=78.31 E-value=31 Score=33.74 Aligned_cols=35 Identities=31% Similarity=0.635 Sum_probs=28.4
Q ss_pred HHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHH
Q 009567 250 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 284 (532)
Q Consensus 250 ~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~ 284 (532)
++.+...+|...+|++|+.+|.|+..|++.+.+..
T Consensus 84 ~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~ 118 (224)
T TIGR02479 84 KLERAIRELEARLGREPTEEEIAEELGMDLKEYRQ 118 (224)
T ss_pred HHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHH
Confidence 45556777888899999999999999998776643
No 282
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=77.94 E-value=2.3 Score=31.99 Aligned_cols=25 Identities=24% Similarity=0.426 Sum_probs=21.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.++|.+|+|+.+|+|+.+|+.+++.
T Consensus 8 ~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 8 KGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred cCCCHHHHHHHhCCCcchhHHHhcC
Confidence 6899999999999999999999875
No 283
>PHA01976 helix-turn-helix protein
Probab=77.49 E-value=4.2 Score=31.97 Aligned_cols=25 Identities=16% Similarity=0.238 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.++|..|+|+.+|||+.+|+++++.
T Consensus 14 ~glt~~~lA~~~gvs~~~v~~~e~g 38 (67)
T PHA01976 14 RAWSAPELSRRAGVRHSLIYDFEAD 38 (67)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 7899999999999999999999864
No 284
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=77.33 E-value=4.1 Score=31.71 Aligned_cols=25 Identities=24% Similarity=0.318 Sum_probs=21.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 485 GKPKSLSEVGNIFGLSKERVRQLES 509 (532)
Q Consensus 485 ~e~~Tl~EIAe~LgISrerVRqie~ 509 (532)
....|.+|+|+.||||..|||.-+.
T Consensus 12 ~~~~s~~ela~~~~VS~~TiRRDl~ 36 (57)
T PF08220_consen 12 KGKVSVKELAEEFGVSEMTIRRDLN 36 (57)
T ss_pred cCCEEHHHHHHHHCcCHHHHHHHHH
Confidence 3678999999999999999986543
No 285
>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=77.30 E-value=10 Score=38.38 Aligned_cols=56 Identities=21% Similarity=0.248 Sum_probs=45.3
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhcccCC--CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 458 RQHVRNLLTLLNPKERCIVRLRFGIEDG--KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 458 ~~~L~~~L~~L~~rER~VL~LRyGL~~~--e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
+..+.-++..|+--|.+.+...+-.-++ .-.+..+||+.+|||+..|+ +|+++|..
T Consensus 167 ka~Vq~Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ir----eAlrkLE~ 224 (251)
T TIGR02787 167 KAAVQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIV----NALRKLES 224 (251)
T ss_pred HHHHHHHHHhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 3456778999999999988887765544 46899999999999999886 67777765
No 286
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=77.24 E-value=6 Score=28.89 Aligned_cols=25 Identities=20% Similarity=0.376 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.+.|..+|++.+|+|+.+|++.+..
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~ 37 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNK 37 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4699999999999999999766543
No 287
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=77.12 E-value=34 Score=26.90 Aligned_cols=23 Identities=35% Similarity=0.496 Sum_probs=19.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Q 009567 394 SPDKEDLARRVGITVEKLERLIF 416 (532)
Q Consensus 394 ~Pt~eEIA~~lgis~e~v~~ll~ 416 (532)
+++.++||+.+|++...+..++.
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~ 23 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFK 23 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Confidence 36889999999999999988765
No 288
>PHA00542 putative Cro-like protein
Probab=77.09 E-value=4 Score=34.19 Aligned_cols=26 Identities=12% Similarity=0.102 Sum_probs=23.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESRA 511 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~rA 511 (532)
.++|..++|+.+|||+.+|.+++...
T Consensus 30 ~glTq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 30 AGWSQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHcCC
Confidence 68999999999999999999998654
No 289
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=76.57 E-value=4.4 Score=36.69 Aligned_cols=24 Identities=25% Similarity=0.336 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLES 509 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~ 509 (532)
+|+|..+||+.||+|+..|+|+++
T Consensus 21 eG~Sq~~iA~LLGltqaAVS~Yls 44 (119)
T COG2522 21 EGLSQYRIAKLLGLTQAAVSQYLS 44 (119)
T ss_pred cCCcHHHHHHHhCCCHHHHHHHHc
Confidence 689999999999999999999875
No 290
>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=76.44 E-value=3.2 Score=39.06 Aligned_cols=29 Identities=17% Similarity=0.244 Sum_probs=24.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 518 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~ 518 (532)
-++|.+|||..+|+|+++|. |++++|++.
T Consensus 142 ~~~t~~~iA~~lG~tretvs----R~l~~l~~~ 170 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTIT----RLLGDLRKK 170 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHH----HHHHHHHHC
Confidence 36899999999999999995 788888774
No 291
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=76.41 E-value=4.4 Score=30.43 Aligned_cols=25 Identities=24% Similarity=0.373 Sum_probs=21.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
++.|..+|++.+|+|+.+|+.+.++
T Consensus 9 ~~~~~~~i~~~l~is~~~v~~~l~~ 33 (66)
T smart00418 9 GELCVCELAEILGLSQSTVSHHLKK 33 (66)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHH
Confidence 6889999999999999999766544
No 292
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=75.99 E-value=3.4 Score=39.35 Aligned_cols=37 Identities=19% Similarity=0.202 Sum_probs=29.4
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHhC-CCHHHHHHHHHH
Q 009567 470 PKERCIVRLRFGIEDGKPKSLSEVGNIFG-LSKERVRQLESR 510 (532)
Q Consensus 470 ~rER~VL~LRyGL~~~e~~Tl~EIAe~Lg-ISrerVRqie~r 510 (532)
+..-+.|.-.+. +|+|..|||+.|| ||++.|--..+|
T Consensus 5 de~~~~L~~lw~----~G~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 5 DERVERLRKLWA----EGLSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred HHHHHHHHHHHH----cCCCHHHHHHHhCCcchhhhhhhhhc
Confidence 344455555565 8999999999999 999999877776
No 293
>PF13551 HTH_29: Winged helix-turn helix
Probab=75.68 E-value=8.4 Score=32.90 Aligned_cols=23 Identities=26% Similarity=0.377 Sum_probs=21.1
Q ss_pred CHHHHHHHhCCCHHHHHHHHHhc
Q 009567 396 DKEDLARRVGITVEKLERLIFIT 418 (532)
Q Consensus 396 t~eEIA~~lgis~e~v~~ll~~~ 418 (532)
+..++|..+|++...|..++...
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~ 36 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRY 36 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHH
Confidence 79999999999999999998764
No 294
>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=75.61 E-value=14 Score=32.54 Aligned_cols=45 Identities=16% Similarity=0.184 Sum_probs=34.6
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
..|++.+..||...+. +.+.|..|||+.+|+++.+|. +.+++|-+
T Consensus 24 ~~lt~~q~~iL~~l~~---~~~~t~~ela~~~~~~~~tvs----~~l~~Le~ 68 (118)
T TIGR02337 24 HGLTEQQWRILRILAE---QGSMEFTQLANQACILRPSLT----GILARLER 68 (118)
T ss_pred cCCCHHHHHHHHHHHH---cCCcCHHHHHHHhCCCchhHH----HHHHHHHH
Confidence 4689999888876542 368999999999999999996 45555543
No 295
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=75.58 E-value=7.6 Score=37.18 Aligned_cols=109 Identities=16% Similarity=0.204 Sum_probs=58.4
Q ss_pred CCCCHHHHHHHh--CCCHHHHHHHHHhcCC--CcccCCCCCCCCCcchhh-hcccCCCCChhHHHHHH---HHHHHHHHH
Q 009567 393 HSPDKEDLARRV--GITVEKLERLIFITRM--PLSMQQPVWADQDTTFQE-ITADTGVEIPDISVQKQ---LMRQHVRNL 464 (532)
Q Consensus 393 r~Pt~eEIA~~l--gis~e~v~~ll~~~~~--~iSLD~~v~~d~~~~l~d-~i~d~~~~~pee~~~~~---~l~~~L~~~ 464 (532)
-.++..+||+.+ +|+.++++..+..... -+--+.. +.....+ .+. ...+.+.. ..+. .+.+.-.++
T Consensus 38 ~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~----g~y~~t~~~l~-~~~~~~~~-avr~~h~q~~~lA~~a 111 (171)
T PF14394_consen 38 FAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGD----GKYVQTDKSLT-TSSEIPSE-AVRSYHKQMLELAQEA 111 (171)
T ss_pred CCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCC----CcEEEecceee-CCCCCcHH-HHHHHHHHHHHHHHHH
Confidence 356899999999 9999999998865322 1111111 0000011 111 11112222 2222 233344567
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567 465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 521 (532)
Q Consensus 465 L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~ 521 (532)
|+..|+.+|.+=.+-+|++ ..+++ .|+..+...++++......
T Consensus 112 l~~~p~~~R~~s~~T~~vs---~~~~~-----------ki~~~i~~fRk~i~~i~~~ 154 (171)
T PF14394_consen 112 LDRVPPEERDFSGLTMSVS---REDYE-----------KIKKEIREFRKKIIAIAEE 154 (171)
T ss_pred HHhCCccccceeeeEEEeC---HHHHH-----------HHHHHHHHHHHHHHHHHhc
Confidence 7888899998877777642 22333 3445555666666655544
No 296
>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=75.41 E-value=4.1 Score=32.11 Aligned_cols=30 Identities=37% Similarity=0.533 Sum_probs=22.4
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 484 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 484 ~~e~~-Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
.|+.+ |..+||+.||+|+.+|| +|+..|..
T Consensus 20 ~g~~lps~~~la~~~~vsr~tvr----~al~~L~~ 50 (64)
T PF00392_consen 20 PGDRLPSERELAERYGVSRTTVR----EALRRLEA 50 (64)
T ss_dssp TTSBE--HHHHHHHHTS-HHHHH----HHHHHHHH
T ss_pred CCCEeCCHHHHHHHhccCCcHHH----HHHHHHHH
Confidence 34778 99999999999999997 56666644
No 297
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=75.23 E-value=4.5 Score=29.44 Aligned_cols=37 Identities=14% Similarity=0.225 Sum_probs=24.5
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 470 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 509 (532)
Q Consensus 470 ~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~ 509 (532)
+-|+.+|.-..-- .+.+..+.|+.||||+.+++..+.
T Consensus 4 ~~E~~~i~~aL~~---~~gn~~~aA~~Lgisr~tL~~klk 40 (42)
T PF02954_consen 4 EFEKQLIRQALER---CGGNVSKAARLLGISRRTLYRKLK 40 (42)
T ss_dssp HHHHHHHHHHHHH---TTT-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHHH---hCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4456666554431 345889999999999999987654
No 298
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=75.20 E-value=4.2 Score=29.41 Aligned_cols=28 Identities=36% Similarity=0.665 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
-+.|..|||+.+|+|+.+|+ +++++|.+
T Consensus 7 ~~~s~~~la~~l~~s~~tv~----~~l~~L~~ 34 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVS----RTLKRLEK 34 (48)
T ss_pred eccCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 46899999999999999995 55566654
No 299
>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=75.03 E-value=6.6 Score=31.33 Aligned_cols=25 Identities=24% Similarity=0.388 Sum_probs=20.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
...|..|||+.+|+|+.+|++...+
T Consensus 12 ~~~~~~eLa~~l~vS~~tv~~~l~~ 36 (69)
T TIGR00122 12 NPFSGEKLGEALGMSRTAVNKHIQT 36 (69)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4678999999999999999765443
No 300
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=74.90 E-value=3.8 Score=32.17 Aligned_cols=25 Identities=20% Similarity=0.340 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.++|..++|+.+|+|.++|+++++.
T Consensus 13 ~gls~~~lA~~~g~s~s~v~~iE~G 37 (64)
T PF13560_consen 13 AGLSQAQLADRLGVSQSTVSRIERG 37 (64)
T ss_dssp HTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 5799999999999999999999864
No 301
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=74.61 E-value=8.2 Score=29.91 Aligned_cols=28 Identities=32% Similarity=0.590 Sum_probs=23.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
.+.|..|||+.+|+|+.+|+ +.+++|++
T Consensus 24 ~~~s~~ela~~~g~s~~tv~----r~l~~L~~ 51 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVS----RTLKELEE 51 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 57999999999999999996 55556655
No 302
>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=74.43 E-value=6.5 Score=34.60 Aligned_cols=41 Identities=24% Similarity=0.420 Sum_probs=26.8
Q ss_pred HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 471 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 471 rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
+.++|... | .+++..|+|..+|+|..+|++|+++..++-+.
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 44556654 3 47899999999999999999999988776654
No 303
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=74.16 E-value=1.6 Score=34.56 Aligned_cols=25 Identities=28% Similarity=0.514 Sum_probs=22.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRAL 512 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rAL 512 (532)
||..|+|+.+|||..+||.++.+.+
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 4789999999999999999998766
No 304
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=74.06 E-value=5.8 Score=29.62 Aligned_cols=25 Identities=12% Similarity=0.279 Sum_probs=23.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.++|..++|+.+|+|+.+|+.+++.
T Consensus 14 ~gltq~~lA~~~gvs~~~vs~~e~g 38 (58)
T TIGR03070 14 LGLTQADLADLAGVGLRFIRDVENG 38 (58)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 5799999999999999999999864
No 305
>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=73.93 E-value=36 Score=34.02 Aligned_cols=33 Identities=30% Similarity=0.528 Sum_probs=26.4
Q ss_pred HHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHH
Q 009567 251 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 283 (532)
Q Consensus 251 le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~ 283 (532)
+......+...+|++|+..+.|...|++.+.+.
T Consensus 118 ~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~ 150 (255)
T TIGR02941 118 IKKAIDELTDHLQRSPKIIEIADHLGLSEEEVL 150 (255)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence 334566777888999999999999999877664
No 306
>PRK05572 sporulation sigma factor SigF; Validated
Probab=73.87 E-value=36 Score=34.12 Aligned_cols=32 Identities=34% Similarity=0.687 Sum_probs=25.2
Q ss_pred HHHHHHHHHhhhCCCCcHHHHHHHccCCHHHH
Q 009567 251 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDL 282 (532)
Q Consensus 251 le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L 282 (532)
+.+....+....|++|+..+.|+..|++.+.+
T Consensus 120 ~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v 151 (252)
T PRK05572 120 IRKDKDELSKELGREPTIEELAEYLGVTPEEV 151 (252)
T ss_pred HHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHH
Confidence 33455667777899999999999999887765
No 307
>PRK10072 putative transcriptional regulator; Provisional
Probab=73.68 E-value=5.1 Score=34.85 Aligned_cols=32 Identities=28% Similarity=0.479 Sum_probs=27.0
Q ss_pred HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 475 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 475 VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
|-.+|.. .++|..|+|+.+|||..+|++++..
T Consensus 38 ik~LR~~----~glTQ~elA~~lGvS~~TVs~WE~G 69 (96)
T PRK10072 38 FEQLRKG----TGLKIDDFARVLGVSVAMVKEWESR 69 (96)
T ss_pred HHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 4455665 6899999999999999999999863
No 308
>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=73.34 E-value=6.6 Score=30.08 Aligned_cols=26 Identities=35% Similarity=0.465 Sum_probs=21.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
.|.++||+.+|+|+++|+ +++++|.+
T Consensus 26 ~~~~~la~~~~is~~~v~----~~l~~L~~ 51 (66)
T cd07377 26 PSERELAEELGVSRTTVR----EALRELEA 51 (66)
T ss_pred CCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 459999999999999997 56666655
No 309
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=73.22 E-value=11 Score=33.33 Aligned_cols=47 Identities=21% Similarity=0.257 Sum_probs=35.6
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009567 459 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 511 (532)
Q Consensus 459 ~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rA 511 (532)
+.....-..+.+.+-.-++..+ ++|..++|+.+|+|+.+|+++++..
T Consensus 56 ~~~~~~~~~~~~~~i~~~r~~~------gltq~~lA~~lg~~~~tis~~e~g~ 102 (127)
T TIGR03830 56 DFYRKVDGLLTPPEIRRIRKKL------GLSQREAAELLGGGVNAFSRYERGE 102 (127)
T ss_pred HHHHHccCCcCHHHHHHHHHHc------CCCHHHHHHHhCCCHHHHHHHHCCC
Confidence 3334444667887766666665 5899999999999999999998753
No 310
>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=73.01 E-value=6.4 Score=29.96 Aligned_cols=51 Identities=12% Similarity=0.137 Sum_probs=39.5
Q ss_pred cCCHHHHHHHHHHhcccCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDG-KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~-e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
.+++.+..+|.-.|.-+.. ......+||..+||+...|..+...-..+.|+
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 4678888899888874321 22356889999999999999999887777653
No 311
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=71.78 E-value=5.1 Score=38.70 Aligned_cols=39 Identities=21% Similarity=0.202 Sum_probs=32.8
Q ss_pred HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 474 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 474 ~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
..+.|.- .|+|-.|||+.||+|++|++-+..|+.++...
T Consensus 10 kA~eLk~-----~Glt~gEIAdELNvSreTa~WL~~r~~~~~~~ 48 (203)
T COG0856 10 KARELKS-----KGLTTGEIADELNVSRETATWLLTRAFKKESV 48 (203)
T ss_pred HHHHHHH-----CCCcHHHhhhhhhhhHHHHHHHHhhhhhccCC
Confidence 3455655 79999999999999999999999998877643
No 312
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=71.68 E-value=6.2 Score=32.31 Aligned_cols=25 Identities=16% Similarity=0.331 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.++|..|.|+.+|||+.||-.+++.
T Consensus 13 ~~ltQ~elA~~vgVsRQTi~~iEkg 37 (68)
T COG1476 13 LGLTQEELAKLVGVSRQTIIAIEKG 37 (68)
T ss_pred hCcCHHHHHHHcCcCHHHHHHHHcC
Confidence 4799999999999999999998864
No 313
>PRK09954 putative kinase; Provisional
Probab=71.52 E-value=7.7 Score=40.89 Aligned_cols=42 Identities=19% Similarity=0.264 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567 468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 512 (532)
Q Consensus 468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rAL 512 (532)
|+++++.||.+..- +...|..|||+.||||+.+|+.++.+-.
T Consensus 1 ~~~~~~~il~~l~~---~~~~s~~~la~~l~~s~~~v~~~i~~L~ 42 (362)
T PRK09954 1 MNNREKEILAILRR---NPLIQQNEIADILQISRSRVAAHIMDLM 42 (362)
T ss_pred CChHHHHHHHHHHH---CCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 46677788776552 2579999999999999999987766533
No 314
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=71.24 E-value=9.6 Score=35.87 Aligned_cols=52 Identities=23% Similarity=0.303 Sum_probs=37.8
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH------HHHHHHHHhhcCc
Q 009567 468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR------ALYRLKQSLGGKA 523 (532)
Q Consensus 468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r------ALkKLR~~l~~~~ 523 (532)
.+|..-.|=.+|-. .|+|..++|+.+|||+.+|.++++. .+..|.+....-+
T Consensus 23 ~~p~~~~Ir~~R~~----lGmTq~eLAerlGVS~~tIs~iE~G~~~~~psl~~L~kIA~aLg 80 (150)
T TIGR02612 23 QTPKEGWVRAIRKA----LGMSGAQLAGRLGVTPQRVEALEKSELSGTVTLKTLRAAAEALD 80 (150)
T ss_pred ccCcHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCCCHHHHHHHHHHcC
Confidence 35554456666665 7899999999999999999999985 3455555444333
No 315
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=71.06 E-value=43 Score=33.64 Aligned_cols=33 Identities=24% Similarity=0.307 Sum_probs=27.1
Q ss_pred HHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHH
Q 009567 252 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 284 (532)
Q Consensus 252 e~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~ 284 (532)
.+...++...+|++|+..|.|...|++.+.+..
T Consensus 126 ~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~ 158 (258)
T PRK08215 126 LQVREKLINENSKEPTVEEIAKELEVPREEVVF 158 (258)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHH
Confidence 345567777889999999999999999887754
No 316
>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=71.03 E-value=11 Score=28.88 Aligned_cols=45 Identities=22% Similarity=0.330 Sum_probs=31.5
Q ss_pred cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHH
Q 009567 369 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLER 413 (532)
Q Consensus 369 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ 413 (532)
||......+-.+.+.-..+..++-...+..+||+.+|+++..|+.
T Consensus 3 Ip~~ti~RL~~Y~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 3 IPKATIRRLPLYLRYLEQLKEEGVERVSSQELAEALGITPAQVRK 47 (50)
T ss_dssp -SHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHcCCeeECHHHHHHHHCCCHHHhcc
Confidence 455555555556666677777777788999999999999999975
No 317
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=70.85 E-value=9.9 Score=31.45 Aligned_cols=26 Identities=27% Similarity=0.349 Sum_probs=22.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESRA 511 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~rA 511 (532)
.+.|..|||+.+|+++.+|+.+...-
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L 44 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTL 44 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 58999999999999999998665543
No 318
>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=70.49 E-value=9.1 Score=32.28 Aligned_cols=24 Identities=25% Similarity=0.447 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLES 509 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~ 509 (532)
...|+++||+.+|||+.||+..+.
T Consensus 18 ~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 18 TKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHhc
Confidence 467999999999999999998664
No 319
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=70.45 E-value=5.2 Score=38.03 Aligned_cols=28 Identities=18% Similarity=0.237 Sum_probs=24.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
-+.|.++||..+|+|+++|. |+|++|++
T Consensus 148 ~~~t~~~iA~~lG~tretvs----R~l~~l~~ 175 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVT----KVIGELSR 175 (202)
T ss_pred ecCCHHHHHHHhCccHHHHH----HHHHHHHH
Confidence 36799999999999999995 77777776
No 320
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=70.09 E-value=5.6 Score=31.29 Aligned_cols=23 Identities=26% Similarity=0.488 Sum_probs=21.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~r 510 (532)
+|..|+|+.+|||..++|.++++
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 57899999999999999999875
No 321
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=70.00 E-value=15 Score=33.41 Aligned_cols=49 Identities=8% Similarity=0.047 Sum_probs=34.9
Q ss_pred HHHHHH--hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 460 HVRNLL--TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 460 ~L~~~L--~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.+...+ -.|++.+-.||..-+- .+++.|..|||+.+|+++.+|.+...+
T Consensus 19 ~~~~~l~~~glt~~q~~vL~~l~~--~~~~~t~~eLa~~l~~~~~tvt~~v~~ 69 (144)
T PRK03573 19 LIDHRLKPLELTQTHWVTLHNIHQ--LPPEQSQIQLAKAIGIEQPSLVRTLDQ 69 (144)
T ss_pred HHHHHHHhcCCCHHHHHHHHHHHH--cCCCCCHHHHHHHhCCChhhHHHHHHH
Confidence 344444 3688888888766542 225689999999999999999754443
No 322
>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=69.91 E-value=2.9 Score=30.11 Aligned_cols=23 Identities=26% Similarity=0.538 Sum_probs=19.3
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHH
Q 009567 489 SLSEVGNIFGLSKERVRQLESRA 511 (532)
Q Consensus 489 Tl~EIAe~LgISrerVRqie~rA 511 (532)
|..|+|+.+|||..++|.++...
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 46799999999999999998765
No 323
>PRK06030 hypothetical protein; Provisional
Probab=69.66 E-value=14 Score=33.73 Aligned_cols=40 Identities=15% Similarity=0.081 Sum_probs=28.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 529 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~yld 529 (532)
-++|+.+||+.||-+.+||..-.+ +.++.+.+..++..++
T Consensus 68 ~~~sl~~IG~~FGRDHSTV~haik----kIe~~~~d~~lk~~v~ 107 (124)
T PRK06030 68 LGWPMNEVALAFGRDRTTVGHACH----TVEDLRDDAAFDARVS 107 (124)
T ss_pred cCCCHHHHHHHHCCChhHHHHHHH----HHHHHhhCHHHHHHHH
Confidence 578999999999999999976555 4444444555555544
No 324
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=69.48 E-value=13 Score=28.63 Aligned_cols=37 Identities=30% Similarity=0.457 Sum_probs=25.4
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 470 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 470 ~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
..+..|+...+- .+.+..||++.+|+++.+|+....+
T Consensus 7 ~~~~~il~~l~~----~~~~~~ei~~~~~i~~~~i~~~l~~ 43 (78)
T cd00090 7 PTRLRILRLLLE----GPLTVSELAERLGLSQSTVSRHLKK 43 (78)
T ss_pred hHHHHHHHHHHH----CCcCHHHHHHHHCcCHhHHHHHHHH
Confidence 344455554332 2399999999999999999755443
No 325
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=69.22 E-value=6 Score=40.19 Aligned_cols=25 Identities=20% Similarity=0.444 Sum_probs=23.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
++|.+.+||+.||||+.+|+.+..|
T Consensus 18 ~gmk~~dIAeklGvspntiksWKrr 42 (279)
T COG5484 18 KGMKLKDIAEKLGVSPNTIKSWKRR 42 (279)
T ss_pred hhccHHHHHHHhCCChHHHHHHHHh
Confidence 7899999999999999999998876
No 326
>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=69.02 E-value=5.2 Score=31.29 Aligned_cols=37 Identities=14% Similarity=0.215 Sum_probs=26.6
Q ss_pred HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 471 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 471 rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
|+.++|.+-+. ....|+.|+|+.+|+|..+|++.+..
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 34455555553 47899999999999999999865543
No 327
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=68.81 E-value=12 Score=30.88 Aligned_cols=44 Identities=32% Similarity=0.501 Sum_probs=33.9
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
.|+..+..||.+-+. ..++|..+|++.+++|+.+|+ +++++|.+
T Consensus 7 ~l~~~~~~il~~l~~---~~~~~~~~la~~~~~s~~~i~----~~l~~L~~ 50 (101)
T smart00347 7 GLTPTQFLVLRILYE---EGPLSVSELAKRLGVSPSTVT----RVLDRLEK 50 (101)
T ss_pred CCCHHHHHHHHHHHH---cCCcCHHHHHHHHCCCchhHH----HHHHHHHH
Confidence 467778888877764 246999999999999999986 55555554
No 328
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=68.62 E-value=55 Score=34.96 Aligned_cols=34 Identities=35% Similarity=0.523 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHH
Q 009567 249 IRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDL 282 (532)
Q Consensus 249 ~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L 282 (532)
-+|.+++.+|...+|++|+.++.|+..|++...+
T Consensus 189 nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V 222 (342)
T COG0568 189 NKLRRVKRELLQELGREPTPEEIAEELGVSPDKV 222 (342)
T ss_pred HHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHH
Confidence 3556678888888999999999999999986644
No 329
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=68.00 E-value=7.7 Score=41.13 Aligned_cols=65 Identities=23% Similarity=0.283 Sum_probs=45.1
Q ss_pred hcCCHHHHHHHHH--HhcccCCCCCCHHHHHHH--hCCCHHHHHHHHHHHHHHHHHHhh----------cCchhhhhhhh
Q 009567 466 TLLNPKERCIVRL--RFGIEDGKPKSLSEVGNI--FGLSKERVRQLESRALYRLKQSLG----------GKASYGYADLL 531 (532)
Q Consensus 466 ~~L~~rER~VL~L--RyGL~~~e~~Tl~EIAe~--LgISrerVRqie~rALkKLR~~l~----------~~~l~~yldll 531 (532)
..|++|+++|+.. ...+..+++-+.+++++. +|+|..|||.... .|.++--..+ ..+++.|+|-|
T Consensus 2 ~~l~~R~~~Il~~IV~~yi~~~~pv~s~~l~~~~~l~~S~aTIR~dm~-~Le~~G~l~~~h~sagrIPT~kGYR~YVd~L 80 (339)
T PRK00082 2 SMLDERQREILRAIVEDYIATGEPVGSKTLSKRYGLGVSSATIRNDMA-DLEELGLLEKPHTSSGRIPTDKGYRYFVDHL 80 (339)
T ss_pred CccCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHhCCCCChHHHHHHHH-HHHhCCCcCCCcCCCCCCcCHHHHHHHHHHh
Confidence 3588999999962 112344599999999977 9999999998766 3555422111 13577787765
No 330
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=67.55 E-value=28 Score=31.69 Aligned_cols=48 Identities=6% Similarity=0.020 Sum_probs=36.0
Q ss_pred HHHHHH--hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 460 HVRNLL--TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 460 ~L~~~L--~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.+...+ ..|++.|-.||..-+. ..+.|..|||+.+|+++.+|..++.+
T Consensus 28 ~~~~~l~~~glt~~q~~vL~~l~~---~~~~t~~eLa~~l~i~~~tvsr~l~~ 77 (144)
T PRK11512 28 LLNEYLSPLDITAAQFKVLCSIRC---AACITPVELKKVLSVDLGALTRMLDR 77 (144)
T ss_pred HHHHHhcccCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 344444 3689999988886542 35799999999999999999754443
No 331
>PRK10870 transcriptional repressor MprA; Provisional
Probab=67.36 E-value=30 Score=33.04 Aligned_cols=50 Identities=12% Similarity=0.118 Sum_probs=36.0
Q ss_pred HHHHHHh--cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 460 HVRNLLT--LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 460 ~L~~~L~--~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.+...+. .|++-+-.||...+. .++.+.|..|||+.+|+++.+|.++..+
T Consensus 43 ~~~~~l~~~gLt~~q~~iL~~L~~-~~~~~it~~eLa~~l~l~~~tvsr~v~r 94 (176)
T PRK10870 43 NRNKMLKAQGINETLFMALITLES-QENHSIQPSELSCALGSSRTNATRIADE 94 (176)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHhc-CCCCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4455553 488888788776653 2236789999999999999999655443
No 332
>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=67.24 E-value=14 Score=35.90 Aligned_cols=44 Identities=18% Similarity=0.189 Sum_probs=34.6
Q ss_pred HHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 464 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 464 ~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
....|++++..|+.+..- ..+.|..|||+.+|+|+.+|++...+
T Consensus 137 ~~~~ls~~~~~IL~~l~~---~g~~s~~eia~~l~is~stv~r~L~~ 180 (203)
T TIGR01884 137 LLAGLSREELKVLEVLKA---EGEKSVKNIAKKLGKSLSTISRHLRE 180 (203)
T ss_pred hhcCCCHHHHHHHHHHHH---cCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 456799999888876642 23679999999999999999865554
No 333
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=67.20 E-value=23 Score=33.67 Aligned_cols=27 Identities=37% Similarity=0.493 Sum_probs=23.2
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 487 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 487 ~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
+.|.++||..+|+|+++|+ |++++|++
T Consensus 168 ~~t~~~lA~~lG~tr~tvs----R~l~~l~~ 194 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVG----RVLKMLED 194 (211)
T ss_pred CCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 6889999999999999996 66777766
No 334
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=66.96 E-value=13 Score=32.63 Aligned_cols=39 Identities=28% Similarity=0.376 Sum_probs=31.4
Q ss_pred cCCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHH
Q 009567 467 LLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVR 505 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~---~e~~Tl~EIAe~LgISrerVR 505 (532)
-|+|.||+-+-.|+-+-. ...+|.+||+..||+|-.+|-
T Consensus 37 lLTpdEReal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtIT 78 (103)
T COG2973 37 LLTPDEREALGTRVRIVEELLRGELSQREIAQKLGVSIATIT 78 (103)
T ss_pred HcCHhHHHHHHHHHHHHHHHHhccccHHHHHHHhCcchhhhc
Confidence 388889888887775532 258999999999999998884
No 335
>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=66.95 E-value=7.1 Score=30.84 Aligned_cols=23 Identities=26% Similarity=0.473 Sum_probs=21.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~r 510 (532)
+|..|+|+.+|||..++|.++.+
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 57899999999999999999876
No 336
>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=66.88 E-value=6.1 Score=31.73 Aligned_cols=27 Identities=22% Similarity=0.306 Sum_probs=24.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESRAL 512 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~rAL 512 (532)
.+.|..+||..+||++.+++++.....
T Consensus 22 ~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 22 SGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp HHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCceEeeecccccccccccHHHHHHh
Confidence 579999999999999999999998876
No 337
>TIGR00647 MG103 conserved hypothetical protein.
Probab=66.88 E-value=12 Score=38.75 Aligned_cols=45 Identities=16% Similarity=0.194 Sum_probs=37.8
Q ss_pred HHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC------CCHHHHHHHHHHH
Q 009567 464 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG------LSKERVRQLESRA 511 (532)
Q Consensus 464 ~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~Lg------ISrerVRqie~rA 511 (532)
.++.||+.-+++..+|.- ..+.|++|+|+.|. ||++.|..+..+.
T Consensus 224 gl~~Lp~~L~~~a~lRl~---~Pd~SL~ELgell~~~~~~~isKSgvnhRlrKl 274 (279)
T TIGR00647 224 GFEKLPLNFQRICLLKID---HPDWSLEQIAEFFASKYKVKISRSGIQHRLRKL 274 (279)
T ss_pred CcccCCHHHHHHHHHHHh---CcccCHHHHHHHhccCCCCCcCHHHHHHHHHHH
Confidence 357899999999999974 47899999999994 9999998766543
No 338
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=66.82 E-value=8.3 Score=33.94 Aligned_cols=70 Identities=23% Similarity=0.275 Sum_probs=49.3
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH--HHHHHHhhcCchhhhh
Q 009567 459 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL--YRLKQSLGGKASYGYA 528 (532)
Q Consensus 459 ~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rAL--kKLR~~l~~~~l~~yl 528 (532)
..+..+|..++-+--+|+.+.+.+.-+.++-..||+..||||.-+||-....-+ --|+..+...+.-.|+
T Consensus 8 ~~l~~~L~~~glk~~eI~IY~lLve~~~~mri~ei~rEl~is~rtvr~~v~~l~rrGll~relvqkgWvGYi 79 (113)
T COG5625 8 RKLGKALEAIGLKKNEIRIYSLLVEKGRGMRIREIQRELGISERTVRAAVAVLLRRGLLARELVQKGWVGYI 79 (113)
T ss_pred HHHHHHHHHcCCCcchhhhhhHHHHhcCCchHHHHHHHHhHHHHHHHHHHHHHHHhhHHHHHHHhccceeeE
Confidence 346666766655555566666666666899999999999999999998777766 3356555555544443
No 339
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=66.24 E-value=9.8 Score=38.48 Aligned_cols=51 Identities=14% Similarity=0.225 Sum_probs=40.4
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhcccCC---CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 458 RQHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 458 ~~~L~~~L~~L~~rER~VL~LRyGL~~~---e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.+.|...+..|++.|+.|..+.. +.. ..+|..|||+..|+|..+|-+..++
T Consensus 4 ~~~i~~~~~~Lt~~e~~Ia~yil--~n~~~v~~~si~~lA~~~~vS~aTv~Rf~kk 57 (284)
T PRK11302 4 LEKIQSRLEHLSKSERKVAEVIL--ASPQTAIHSSIATLAKMANVSEPTVNRFCRS 57 (284)
T ss_pred HHHHHHHHhhCCHHHHHHHHHHH--hCHHHHHhcCHHHHHHHhCCCHHHHHHHHHH
Confidence 34677888999999999987543 332 3589999999999999999766554
No 340
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=66.11 E-value=13 Score=33.21 Aligned_cols=35 Identities=17% Similarity=0.196 Sum_probs=28.0
Q ss_pred HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567 474 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 512 (532)
Q Consensus 474 ~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rAL 512 (532)
+++...+- .+.|..+||..+|||..+|.++..+..
T Consensus 20 ~aV~~~~~----~g~sv~evA~e~gIs~~tl~~W~r~y~ 54 (121)
T PRK09413 20 AIVQQSFE----PGMTVSLVARQHGVAASQLFLWRKQYQ 54 (121)
T ss_pred HHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHh
Confidence 34444443 689999999999999999999987753
No 341
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=66.07 E-value=5.8 Score=33.82 Aligned_cols=24 Identities=17% Similarity=0.108 Sum_probs=17.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLES 509 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~ 509 (532)
.|+|..|||+.+|.|+..|.+++.
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 342
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=66.01 E-value=17 Score=32.18 Aligned_cols=40 Identities=28% Similarity=0.392 Sum_probs=36.0
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 465 L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
...|++.|-..|+-.++ +|..+-|..||+|.++|+.++..
T Consensus 41 ~~~ls~~eIk~iRe~~~------lSQ~vFA~~L~vs~~Tv~~WEqG 80 (104)
T COG2944 41 VKTLSPTEIKAIREKLG------LSQPVFARYLGVSVSTVRKWEQG 80 (104)
T ss_pred CCCCCHHHHHHHHHHhC------CCHHHHHHHHCCCHHHHHHHHcC
Confidence 36799999999988875 89999999999999999999975
No 343
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=65.83 E-value=7.1 Score=38.17 Aligned_cols=27 Identities=30% Similarity=0.566 Sum_probs=23.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 487 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 487 ~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
+.|.++||..+|+|+++|. |.+++|++
T Consensus 184 ~lt~~~iA~~lG~sr~tvs----R~l~~l~~ 210 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETIS----RLLGRFQK 210 (235)
T ss_pred cccHHHHHHHhCCcHHHHH----HHHHHHHH
Confidence 6899999999999999996 56677766
No 344
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=65.68 E-value=95 Score=30.63 Aligned_cols=32 Identities=34% Similarity=0.571 Sum_probs=25.7
Q ss_pred HHHHHHHHhhhCCCCcHHHHHHHccCCHHHHH
Q 009567 252 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 283 (532)
Q Consensus 252 e~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~ 283 (532)
......+...+|++|+..++|+..|++.+.+.
T Consensus 98 ~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~ 129 (236)
T PRK06986 98 AQAIRQLEQELGREPTDTEVAEKLGLSLEEYR 129 (236)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHH
Confidence 34556666778999999999999999877664
No 345
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=65.33 E-value=5.1 Score=33.37 Aligned_cols=32 Identities=13% Similarity=0.082 Sum_probs=22.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567 485 GKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 485 ~e~~Tl~EIAe~LgISrerVRqie~rALkKLR 516 (532)
+++.|+.++|+.++||++++.+..++.-+.|+
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 37899999999999999999765554444443
No 346
>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=65.21 E-value=53 Score=32.07 Aligned_cols=31 Identities=32% Similarity=0.592 Sum_probs=25.4
Q ss_pred HHHHHHHhhhCCCCcHHHHHHHccCCHHHHH
Q 009567 253 KEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 283 (532)
Q Consensus 253 ~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~ 283 (532)
+....+....|++|+..|.|+..|++.+.+.
T Consensus 94 ~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~ 124 (227)
T TIGR02980 94 KATEELTQRLGRSPTIAEIAEELGVSEEEVV 124 (227)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHhCCCHHHHH
Confidence 3455677778999999999999999877664
No 347
>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=65.05 E-value=11 Score=31.22 Aligned_cols=24 Identities=29% Similarity=0.481 Sum_probs=18.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLES 509 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~ 509 (532)
.+.|.+|||+.+|+|+..|+++..
T Consensus 24 ~~~s~~eiA~~~~i~~~~l~kil~ 47 (83)
T PF02082_consen 24 KPVSSKEIAERLGISPSYLRKILQ 47 (83)
T ss_dssp C-BEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHH
Confidence 458999999999999999986543
No 348
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=64.65 E-value=5.1 Score=31.59 Aligned_cols=25 Identities=28% Similarity=0.412 Sum_probs=22.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRAL 512 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rAL 512 (532)
+|..|+|+.+|||..+||.++...+
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~~gl 25 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYERIGL 25 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999977554
No 349
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=64.59 E-value=10 Score=32.03 Aligned_cols=44 Identities=25% Similarity=0.398 Sum_probs=28.6
Q ss_pred HHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 472 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 472 ER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
||-|-.-.|.++ ...|.++.|..||||++||..-...=|.++-.
T Consensus 6 eR~i~i~~yIi~--~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in~ 49 (82)
T PF12116_consen 6 ERVIEIANYIIE--TKATVRQAAKVFGVSKSTVHKDVTERLPKINP 49 (82)
T ss_dssp HHHHHHHHHHHH--H---HHHHHHHHTS-HHHHHHHHTTHHHHH-H
T ss_pred HHHHHHHHHHHH--cccHHHHHHHHHCCcHHHHHHHHHHHHHhcCH
Confidence 455555566655 47899999999999999998877655555543
No 350
>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=64.28 E-value=19 Score=31.50 Aligned_cols=44 Identities=11% Similarity=0.064 Sum_probs=34.3
Q ss_pred cCCHHHHHHHHHHhcc-cCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGI-EDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL-~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.|++.|-.||..-+-+ ..+.+.|..|||+.+++++.+|...+.+
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~ 66 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKK 66 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHH
Confidence 6899999998765521 1236799999999999999999765544
No 351
>PF14493 HTH_40: Helix-turn-helix domain
Probab=63.61 E-value=17 Score=30.79 Aligned_cols=29 Identities=21% Similarity=0.245 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESRALYR 514 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~rALkK 514 (532)
+|+|+.|||+.-|++.+||..++.++...
T Consensus 12 ~G~si~eIA~~R~L~~sTI~~HL~~~~~~ 40 (91)
T PF14493_consen 12 KGLSIEEIAKIRGLKESTIYGHLAELIES 40 (91)
T ss_pred cCCCHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence 79999999999999999999998887654
No 352
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=63.52 E-value=8.9 Score=30.44 Aligned_cols=23 Identities=22% Similarity=0.355 Sum_probs=20.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~r 510 (532)
+|..|+|+.+|||..++|.++..
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 47899999999999999999775
No 353
>PF11662 DUF3263: Protein of unknown function (DUF3263); InterPro: IPR021678 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=63.44 E-value=26 Score=29.45 Aligned_cols=48 Identities=19% Similarity=0.131 Sum_probs=37.1
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 513 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALk 513 (532)
+.|+++++.||-+---.....+-+-+.|-+.||+|.-+--|.++..+.
T Consensus 1 ~~Ls~~d~~iL~fE~~ww~~~GaKe~aIre~fGls~~rYyq~Ln~LiD 48 (77)
T PF11662_consen 1 EGLSDRDRAILDFERRWWRHGGAKEEAIREEFGLSPTRYYQRLNALID 48 (77)
T ss_pred CCCCHHHHHHHHHHHHhCcCCCCcHHHHHHHHCCCHHHHHHHHHHHhC
Confidence 368999999998632222224668899999999999999999887654
No 354
>PRK15482 transcriptional regulator MurR; Provisional
Probab=63.43 E-value=12 Score=38.09 Aligned_cols=50 Identities=16% Similarity=0.260 Sum_probs=40.1
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhcccCC---CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 459 QHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 459 ~~L~~~L~~L~~rER~VL~LRyGL~~~---e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
..|......|++.|+.|..+. |++. ..+|..|||+..|+|..+|-+.-++
T Consensus 5 ~~i~~~~~~Lt~~e~~Ia~yI--l~n~~~v~~~si~elA~~~~vS~aTv~Rf~kk 57 (285)
T PRK15482 5 TKIRNAESEFTENEQKIADFL--RANVSELKSVSSRKMAKQLGISQSSIVKFAQK 57 (285)
T ss_pred HHHHHHHhhcCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHH
Confidence 467778899999999998754 4432 4589999999999999999766554
No 355
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=63.30 E-value=7.1 Score=37.55 Aligned_cols=29 Identities=34% Similarity=0.590 Sum_probs=25.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 485 GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 485 ~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
.+|+|+.||++.+|+|+++|+ .++++|..
T Consensus 39 ~~Pmtl~Ei~E~lg~Sks~vS----~~lkkL~~ 67 (177)
T COG1510 39 RKPLTLDEIAEALGMSKSNVS----MGLKKLQD 67 (177)
T ss_pred CCCccHHHHHHHHCCCcchHH----HHHHHHHh
Confidence 489999999999999999997 46777755
No 356
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=63.05 E-value=19 Score=36.79 Aligned_cols=52 Identities=15% Similarity=0.306 Sum_probs=41.4
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHhcccCC---CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 457 MRQHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 457 l~~~L~~~L~~L~~rER~VL~LRyGL~~~---e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
+...|+..+..|++.|+.|..+.. ++. ..+|..+||+..|||..+|-+..++
T Consensus 15 i~~~i~~~~~~Lt~~e~~Ia~yil--~~~~~v~~~si~~lA~~~~vS~aTi~Rf~kk 69 (292)
T PRK11337 15 LGPYIRMKQEGLTPLESRVVEWLL--KPGDLSEATALKDIAEALAVSEAMIVKVAKK 69 (292)
T ss_pred HHHHHHHHHhhcCHHHHHHHHHHH--hCHHHHHhcCHHHHHHHhCCChHHHHHHHHH
Confidence 345788889999999999987553 332 4589999999999999999766554
No 357
>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=62.75 E-value=16 Score=29.42 Aligned_cols=25 Identities=12% Similarity=0.275 Sum_probs=23.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.++|..++|+.+|+|+.+|+++++.
T Consensus 17 ~~~t~~~lA~~~gis~~tis~~~~g 41 (78)
T TIGR02607 17 LGLSIRALAKALGVSRSTLSRIVNG 41 (78)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 6899999999999999999999864
No 358
>PRK10161 transcriptional regulator PhoB; Provisional
Probab=61.79 E-value=9 Score=36.49 Aligned_cols=50 Identities=14% Similarity=0.055 Sum_probs=40.2
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHH-----HhCCCHHHHHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGN-----IFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe-----~LgISrerVRqie~rALkKLR~ 517 (532)
.|+++|.+|+.+.. -+-|++.|.++|.. .++++..+|+.+..+.++||..
T Consensus 154 ~Lt~~E~~ll~~l~-~~~~~~~s~~~l~~~~~~~~~~~~~~tv~~~i~rlr~Kl~~ 208 (229)
T PRK10161 154 EMGPTEFKLLHFFM-THPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEP 208 (229)
T ss_pred EcCHHHHHHHHHHH-hCCCceEcHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhcc
Confidence 59999999997765 24457888777644 6688999999999999999963
No 359
>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional
Probab=61.55 E-value=6 Score=37.60 Aligned_cols=46 Identities=13% Similarity=0.018 Sum_probs=38.3
Q ss_pred cCCHHHHHHHHHHhcccCCCCCC---------HHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKS---------LSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~T---------l~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
.|+++|.+|+.+.. .+.+ ..+||..++++..+|+.+..+.++||..
T Consensus 156 ~Lt~~E~~~l~~l~-----~~~~~v~sr~~l~~~~~~~~~~~~~~tv~~~i~~lr~Kl~~ 210 (232)
T PRK10955 156 ELTGTEFTLLYLLA-----QHLGQVVSREHLSQEVLGKRLTPFDRAIDMHISNLRRKLPD 210 (232)
T ss_pred cCCHHHHHHHHHHH-----hCCCceEcHHHHHHHHhCCCCCCCCcCHHHHHHHHHHhccc
Confidence 59999999998876 3443 4778888899999999999999999963
No 360
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=61.39 E-value=12 Score=36.94 Aligned_cols=30 Identities=23% Similarity=0.460 Sum_probs=25.6
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 484 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 484 ~~e~~-Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
.|+.+ |-.|+|+.||||+.+|| .||+.|..
T Consensus 27 pG~~LPsE~eLae~~gVSRt~VR----eAL~~L~~ 57 (239)
T PRK04984 27 PGSILPAERELSELIGVTRTTLR----EVLQRLAR 57 (239)
T ss_pred CCCcCCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 45788 79999999999999998 67777765
No 361
>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=61.36 E-value=20 Score=26.64 Aligned_cols=23 Identities=13% Similarity=0.325 Sum_probs=17.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~r 510 (532)
+|+.+.|+.+||++.+++.+...
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 362
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=61.15 E-value=17 Score=36.81 Aligned_cols=48 Identities=17% Similarity=0.221 Sum_probs=38.1
Q ss_pred HHHHHhcCCHHHHHHHHHHhcccCC---CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 461 VRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 461 L~~~L~~L~~rER~VL~LRyGL~~~---e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
|......|++.|+.|..+.. +.. ..+|..|+|+..|+|..+|.+..++
T Consensus 3 i~~~~~~Lt~~e~~ia~yil--~n~~~v~~~si~elA~~~~vS~aTv~Rf~kk 53 (278)
T PRK11557 3 IRQRYPGLAQSDRKLADYLL--LQPDTARHLSSQQLANEAGVSQSSVVKFAQK 53 (278)
T ss_pred hhHhhhhCCHHHHHHHHHHH--hCHHHHHhcCHHHHHHHhCCCHHHHHHHHHH
Confidence 55667889999999987554 332 3599999999999999999866554
No 363
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=60.90 E-value=1.3e+02 Score=33.41 Aligned_cols=47 Identities=19% Similarity=0.376 Sum_probs=33.1
Q ss_pred HHHhcCCHHHHHHHH-------HHhccc-CC----CCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 463 NLLTLLNPKERCIVR-------LRFGIE-DG----KPKSLSEVGNIFGLSKERVRQLES 509 (532)
Q Consensus 463 ~~L~~L~~rER~VL~-------LRyGL~-~~----e~~Tl~EIAe~LgISrerVRqie~ 509 (532)
-++..|..|++.++. +-+++. +| .++++++||+.+|+..+||++...
T Consensus 294 wLiksL~qR~~TLlkV~~~Iv~~Q~~Ff~~g~~~l~PL~LrdvA~~i~~HESTISRai~ 352 (444)
T COG1508 294 WLIKSLEQREETLLKVAEEIVEYQKAFFEGGEEALKPLVLRDVADEIGMHESTISRAIT 352 (444)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCCcccHHHHHHHhCccHHHHHHHHh
Confidence 345777777776554 322222 22 689999999999999999987654
No 364
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=60.59 E-value=13 Score=32.95 Aligned_cols=57 Identities=14% Similarity=0.194 Sum_probs=47.4
Q ss_pred HHHHHH--hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567 460 HVRNLL--TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 520 (532)
Q Consensus 460 ~L~~~L--~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~ 520 (532)
.|+.-+ ..|.+-||-...-+|- +-+|-+|||-.+.++..||..+...-..|.|+.-+
T Consensus 19 RIRTTFTS~QLkELErvF~ETHYP----DIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 19 RIRTTFTSAQLKELERVFAETHYP----DIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred hhhhhhhHHHHHHHHHHHHhhcCC----cchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence 344433 5688888888888996 89999999999999999999999988888887543
No 365
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=60.59 E-value=8.8 Score=30.93 Aligned_cols=23 Identities=22% Similarity=0.416 Sum_probs=20.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~r 510 (532)
.|.+|||+.+|||+.+|+.+.+.
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~ 23 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNG 23 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCC
Confidence 37899999999999999987654
No 366
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=60.52 E-value=10 Score=37.28 Aligned_cols=28 Identities=36% Similarity=0.587 Sum_probs=23.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567 487 PKSLSEVGNIFGLSKERVRQLESRALYRLKQS 518 (532)
Q Consensus 487 ~~Tl~EIAe~LgISrerVRqie~rALkKLR~~ 518 (532)
+.|.++||..+|+|+++|. |++++|++.
T Consensus 179 ~lt~~~IA~~lGisretls----R~L~~L~~~ 206 (230)
T PRK09391 179 PMSRRDIADYLGLTIETVS----RALSQLQDR 206 (230)
T ss_pred cCCHHHHHHHHCCCHHHHH----HHHHHHHHC
Confidence 5799999999999999995 677788763
No 367
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=59.47 E-value=19 Score=40.84 Aligned_cols=46 Identities=24% Similarity=0.266 Sum_probs=37.4
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
|++|+.+||.+-- + ++.|..++|+.||||..|||+-++..-.-|++
T Consensus 2 l~~R~~~iL~~L~---~-~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~ 47 (584)
T PRK09863 2 LNERELKIVDLLE---Q-QDRSGGELAQQLGVSRRTIVRDIAYINFTLNG 47 (584)
T ss_pred hHHHHHHHHHHHH---c-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 6788889987642 2 58999999999999999999988776666665
No 368
>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=59.34 E-value=15 Score=31.65 Aligned_cols=43 Identities=16% Similarity=0.244 Sum_probs=31.0
Q ss_pred cCCHHHHHHHHHHhc-ccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFG-IEDGKPKSLSEVGNIFGLSKERVRQLES 509 (532)
Q Consensus 467 ~L~~rER~VL~LRyG-L~~~e~~Tl~EIAe~LgISrerVRqie~ 509 (532)
.|++..++|+.+.-. -...++.+..+|++.|+++...||+.+.
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~ 87 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALD 87 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHH
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHH
Confidence 688888888887655 3445899999999999999999986543
No 369
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=59.30 E-value=14 Score=32.64 Aligned_cols=35 Identities=17% Similarity=0.302 Sum_probs=27.9
Q ss_pred HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 474 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 474 ~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
+||+-.|. +.-++|..+.|+.|||++.+|..+++.
T Consensus 12 EiL~eefl--ep~glt~~~lA~~lgV~r~~is~ling 46 (104)
T COG3093 12 EILREEFL--EPLGLTQTELAEALGVTRNTISELING 46 (104)
T ss_pred HHHHHHHh--ccccCCHHHHHHHhCCCHHHHHHHHcC
Confidence 46666665 223699999999999999999998764
No 370
>PRK09726 antitoxin HipB; Provisional
Probab=59.25 E-value=15 Score=30.86 Aligned_cols=25 Identities=16% Similarity=0.330 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.++|..|+|+.+|||+.+|+++++.
T Consensus 24 ~gltq~elA~~~gvs~~tis~~e~g 48 (88)
T PRK09726 24 NGWTQSELAKKIGIKQATISNFENN 48 (88)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 5799999999999999999999884
No 371
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=58.88 E-value=9.7 Score=36.62 Aligned_cols=28 Identities=18% Similarity=0.227 Sum_probs=24.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESRALY 513 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~rALk 513 (532)
-++|..|||+.+|.|+.+||++....-+
T Consensus 60 ag~Ti~EIAeelG~TeqTir~hlkgetk 87 (182)
T COG1318 60 AGMTISEIAEELGRTEQTVRNHLKGETK 87 (182)
T ss_pred ccCcHHHHHHHhCCCHHHHHHHHhcchh
Confidence 4799999999999999999998765433
No 372
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=58.45 E-value=1.1e+02 Score=33.57 Aligned_cols=94 Identities=13% Similarity=0.211 Sum_probs=50.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCC-CChhHHHHHHHHHHHHHHHHhcCCHH
Q 009567 393 HSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGV-EIPDISVQKQLMRQHVRNLLTLLNPK 471 (532)
Q Consensus 393 r~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~-~~pee~~~~~~l~~~L~~~L~~L~~r 471 (532)
++-+..+||+.+|+.+.+|..+.... .+..|.|- -.+..++...-. .+....+.....+..|..++..=+
T Consensus 317 kPLtlkdiA~~lglheSTVSRav~~K----yi~tp~Gi---~~lk~FFs~~~~~~~~g~~~S~~~Ik~~I~~lI~~E~-- 387 (429)
T TIGR02395 317 KPLTLREVAEELGLHESTISRAINNK----YLQTPRGV---FELKYFFSRGVQTDSGEGEVSSTAIKALIKELIAAED-- 387 (429)
T ss_pred cCCcHHHHHHHhCCCccchhhhhcCc----eEecCCce---EEHHHhcCCccCCCCCCCccCHHHHHHHHHHHHHhcC--
Confidence 45689999999999999998876421 12222110 112222221100 000011223334444444443222
Q ss_pred HHHHHHHHhcccCCCCCCHHHHHHHh-----CCCHHHHHHH
Q 009567 472 ERCIVRLRFGIEDGKPKSLSEVGNIF-----GLSKERVRQL 507 (532)
Q Consensus 472 ER~VL~LRyGL~~~e~~Tl~EIAe~L-----gISrerVRqi 507 (532)
...++|-++|++.| .|+|-||-++
T Consensus 388 ------------~~~PlSD~~I~~~L~~~Gi~IaRRTVaKY 416 (429)
T TIGR02395 388 ------------KRKPLSDQKIAELLKEKGIKIARRTVAKY 416 (429)
T ss_pred ------------CCCCCCHHHHHHHHHhcCCCeehHHHHHH
Confidence 23789999999999 7788777654
No 373
>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=57.90 E-value=15 Score=34.18 Aligned_cols=49 Identities=14% Similarity=0.121 Sum_probs=40.8
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-----GLSKERVRQLESRALYRLK 516 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~L-----gISrerVRqie~rALkKLR 516 (532)
.|+++|.+|+.+... +.|+..|.++|...+ ..+..+|..++.+.++||.
T Consensus 147 ~Lt~~E~~il~~l~~-~~~~~~sr~~i~~~~~~~~~~~~~~~~~~~i~~lr~kl~ 200 (218)
T TIGR01387 147 TLTRKEFQLLWLLMR-RTGEVLPRTVIASLVWGMNFDSDTNVVDVAIRRLRAKVD 200 (218)
T ss_pred eCCHHHHHHHHHHHh-CCCeeEcHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhhc
Confidence 599999999988763 445679999999998 4567899999998888885
No 374
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=57.73 E-value=24 Score=34.54 Aligned_cols=47 Identities=15% Similarity=0.142 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHhccc-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567 468 LNPKERCIVRLRFGIE-DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 518 (532)
Q Consensus 468 L~~rER~VL~LRyGL~-~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~ 518 (532)
++.++|-+-.+...-+ +.-+.|.+|||..+|+|+++|. |+|++|++.
T Consensus 149 ~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvs----R~L~~L~~~ 196 (226)
T PRK10402 149 FPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLL----YVLAQFIQD 196 (226)
T ss_pred ChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHH----HHHHHHHHC
Confidence 3566665554432111 1234689999999999999995 778888773
No 375
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=57.47 E-value=2.4e+02 Score=29.32 Aligned_cols=26 Identities=15% Similarity=0.309 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESRA 511 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~rA 511 (532)
...|.+|||...|||..|||+..+.-
T Consensus 250 ~~~tq~eva~v~~vtevTIrnrykel 275 (285)
T COG1405 250 ERRTQKEVAKVAGVTEVTIRNRYKEL 275 (285)
T ss_pred CchHHHHHHHHhCCeeeHHHHHHHHH
Confidence 78999999999999999999988433
No 376
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=57.46 E-value=20 Score=32.78 Aligned_cols=25 Identities=8% Similarity=0.185 Sum_probs=21.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 485 GKPKSLSEVGNIFGLSKERVRQLES 509 (532)
Q Consensus 485 ~e~~Tl~EIAe~LgISrerVRqie~ 509 (532)
+...+..+||+.||||..+|+..+.
T Consensus 20 ~~~~~~~ela~~l~vs~~svs~~l~ 44 (142)
T PRK03902 20 KGYARVSDIAEALSVHPSSVTKMVQ 44 (142)
T ss_pred CCCcCHHHHHHHhCCChhHHHHHHH
Confidence 3577999999999999999986543
No 377
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=57.40 E-value=18 Score=28.45 Aligned_cols=26 Identities=19% Similarity=0.471 Sum_probs=22.4
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567 487 PKSLSEVGNIFGLSKERVRQLESRAL 512 (532)
Q Consensus 487 ~~Tl~EIAe~LgISrerVRqie~rAL 512 (532)
+.|+.+||+.+|+|...+.++..+..
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~ 26 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKET 26 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHh
Confidence 46899999999999999988887655
No 378
>PRK01905 DNA-binding protein Fis; Provisional
Probab=57.34 E-value=43 Score=27.65 Aligned_cols=37 Identities=11% Similarity=0.201 Sum_probs=25.1
Q ss_pred HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 471 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 471 rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
-|+.+|...+-- .+-+..+.|+.+|||+.+++...++
T Consensus 37 ~E~~~i~~aL~~---~~gn~s~aAr~LGIsrstL~rklkk 73 (77)
T PRK01905 37 VEKPLLEVVMEQ---AGGNQSLAAEYLGINRNTLRKKLQQ 73 (77)
T ss_pred HHHHHHHHHHHH---cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 355555544421 2347899999999999998765543
No 379
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=57.25 E-value=15 Score=37.61 Aligned_cols=46 Identities=35% Similarity=0.391 Sum_probs=36.2
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
..|++.|++||.+--+ .|...+++||-+.+|+|+.+|. |++++|-+
T Consensus 191 ~~L~~~e~~il~~i~~--~GGri~Q~eL~r~lglsktTvs----R~L~~LEk 236 (258)
T COG2512 191 YDLNEDEKEILDLIRE--RGGRITQAELRRALGLSKTTVS----RILRRLEK 236 (258)
T ss_pred CCCCHHHHHHHHHHHH--hCCEEeHHHHHHhhCCChHHHH----HHHHHHHh
Confidence 5689999999987654 3356899999999999999996 55555543
No 380
>PRK11050 manganese transport regulator MntR; Provisional
Probab=57.25 E-value=17 Score=33.82 Aligned_cols=26 Identities=15% Similarity=0.233 Sum_probs=21.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 485 GKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 485 ~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
+.+.+..|||+.+|||+.+|+..+.+
T Consensus 49 ~~~~t~~eLA~~l~is~stVsr~l~~ 74 (152)
T PRK11050 49 VGEARQVDIAARLGVSQPTVAKMLKR 74 (152)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 36899999999999999999754443
No 381
>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=57.22 E-value=28 Score=26.18 Aligned_cols=51 Identities=16% Similarity=0.198 Sum_probs=38.6
Q ss_pred cCCHHHHHHHHHHhcccCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDG-KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~-e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
.+++.+..+|.-.|.-+.. ......+||..+|++...|+.+...-..+.+.
T Consensus 6 ~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 6 RFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 4677778888888865332 33457899999999999999998887776553
No 382
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=57.13 E-value=16 Score=26.24 Aligned_cols=25 Identities=16% Similarity=0.274 Sum_probs=18.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.++|+.+||+.+|+|+...++..++
T Consensus 7 ~~~~l~~iA~~~g~S~~~f~r~Fk~ 31 (42)
T PF00165_consen 7 QKLTLEDIAEQAGFSPSYFSRLFKK 31 (42)
T ss_dssp SS--HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 6799999999999998888766554
No 383
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=56.98 E-value=31 Score=26.87 Aligned_cols=35 Identities=11% Similarity=0.121 Sum_probs=26.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 520 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~ 520 (532)
.+.+..+.|+.|+|.++||+.++.++-+.+.-.+.
T Consensus 11 ~~~n~~~tA~~L~iHrNTl~yRl~ki~~l~g~dl~ 45 (59)
T PF13556_consen 11 NNGNISKTARALHIHRNTLRYRLKKIEELLGLDLD 45 (59)
T ss_dssp TTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--TT
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCcCCC
Confidence 57899999999999999999998888777655444
No 384
>PHA00738 putative HTH transcription regulator
Probab=56.77 E-value=24 Score=31.45 Aligned_cols=37 Identities=22% Similarity=0.033 Sum_probs=27.4
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 470 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 509 (532)
Q Consensus 470 ~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~ 509 (532)
|.-+.||.+-. .+++++..||++.+++|+.+|++.++
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 44455665433 23679999999999999999987653
No 385
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=56.68 E-value=14 Score=36.13 Aligned_cols=31 Identities=29% Similarity=0.383 Sum_probs=26.3
Q ss_pred cCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 483 EDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 483 ~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
..|+.++..++|+.||||+..|| .||+.|..
T Consensus 30 ~pG~~L~e~~La~~lgVSRtpVR----EAL~~L~~ 60 (221)
T PRK11414 30 KPGARLITKNLAEQLGMSITPVR----EALLRLVS 60 (221)
T ss_pred CCCCccCHHHHHHHHCCCchhHH----HHHHHHHH
Confidence 35688899999999999999998 67777765
No 386
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=56.63 E-value=57 Score=36.97 Aligned_cols=102 Identities=15% Similarity=0.176 Sum_probs=57.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhcCCC---cccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCH
Q 009567 394 SPDKEDLARRVGITVEKLERLIFITRMP---LSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNP 470 (532)
Q Consensus 394 ~Pt~eEIA~~lgis~e~v~~ll~~~~~~---iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~ 470 (532)
..|..+||+.+|+|...|+.-+..-... ..+. .+....+-.+ .. .++. .+...+..-++
T Consensus 17 ~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~-~i~~~~Gy~l----~~---~~~~----------~~~~~~~~~~~ 78 (584)
T PRK09863 17 DRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIG-SISGSAKYHL----EI---LNRR----------SLFQLLQKSDN 78 (584)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchh-heecCCceEE----Ee---CCHH----------HHHHHHhcCCH
Confidence 6789999999999999987654422110 0000 0000011111 00 0111 11122222233
Q ss_pred HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567 471 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 471 rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR 516 (532)
|+..+.++..+ .++.++.++|+.|.||+.||.+-..+.-+.+.
T Consensus 79 -e~~~il~~Ll~--~~~~~~~~La~~l~vS~sTi~~dl~~v~~~l~ 121 (584)
T PRK09863 79 -EDRLLLLRLLL--NTFTPMAQLASALNLSRTWVAERLPRLNQRYE 121 (584)
T ss_pred -HHHHHHHHHHH--cCCccHHHHHHHhCCCHHHHHHHHHHHHHhhh
Confidence 44444444433 36899999999999999999887777776665
No 387
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=56.60 E-value=20 Score=35.85 Aligned_cols=25 Identities=28% Similarity=0.347 Sum_probs=22.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.+.|..|||+.||||...||+.+..
T Consensus 24 g~~sa~elA~~Lgis~~avR~HL~~ 48 (218)
T COG2345 24 GPVSADELAEELGISPMAVRRHLDD 48 (218)
T ss_pred CCccHHHHHHHhCCCHHHHHHHHHH
Confidence 6999999999999999999987654
No 388
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=56.44 E-value=20 Score=35.97 Aligned_cols=41 Identities=17% Similarity=0.250 Sum_probs=31.8
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567 470 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 513 (532)
Q Consensus 470 ~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALk 513 (532)
+|++.|+.+-. .....+.+||++.||||..|||+.+..--.
T Consensus 4 ~R~~~Il~~l~---~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 4 ARQQAIVDLLL---NHTSLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred HHHHHHHHHHH---HcCCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 56666666543 235889999999999999999998886544
No 389
>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=56.25 E-value=16 Score=32.69 Aligned_cols=24 Identities=33% Similarity=0.458 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLES 509 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~ 509 (532)
.+.|..++|..||||+.+|..+..
T Consensus 17 ~g~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 17 KGKSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred ccchHHHHHHHhCcHHHHHHHHHH
Confidence 678999999999999999998876
No 390
>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=55.89 E-value=8.5 Score=33.06 Aligned_cols=26 Identities=19% Similarity=0.448 Sum_probs=22.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRALY 513 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rALk 513 (532)
+|..|+|+.+|||..++|.++...+=
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~~Gll 26 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDIGLF 26 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999987543
No 391
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=55.66 E-value=15 Score=35.48 Aligned_cols=30 Identities=27% Similarity=0.420 Sum_probs=25.8
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 484 DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 484 ~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
.|+.++..++|+.||||+..|| .||+.|..
T Consensus 31 pG~~L~e~~La~~lgVSRtpVR----eAL~~L~~ 60 (212)
T TIGR03338 31 PGAKLNESDIAARLGVSRGPVR----EAFRALEE 60 (212)
T ss_pred CCCEecHHHHHHHhCCChHHHH----HHHHHHHH
Confidence 4588899999999999999997 67777765
No 392
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=55.53 E-value=17 Score=35.76 Aligned_cols=30 Identities=23% Similarity=0.460 Sum_probs=26.0
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 484 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 484 ~~e~~-Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
.|+.+ |-.++|+.||||+..|| .||.+|..
T Consensus 26 pG~~LpsE~~La~~lgVSRtpVR----EAL~~Le~ 56 (235)
T TIGR02812 26 PGSILPAERELSELIGVTRTTLR----EVLQRLAR 56 (235)
T ss_pred CCCcCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 45888 89999999999999997 68888865
No 393
>PRK11517 transcriptional regulatory protein YedW; Provisional
Probab=55.31 E-value=21 Score=33.50 Aligned_cols=49 Identities=14% Similarity=0.078 Sum_probs=40.4
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-----GLSKERVRQLESRALYRLK 516 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~L-----gISrerVRqie~rALkKLR 516 (532)
.|+++|.+|+.+..- +-|+..|..+|...+ ..+..+|+.++.|.++||.
T Consensus 147 ~Lt~~E~~il~~l~~-~~g~~~s~~~i~~~~w~~~~~~~~~tv~~~i~rlr~Kl~ 200 (223)
T PRK11517 147 TLTRKEFQLLWLLAS-RAGEIIPRTVIASEIWGINFDSDTNTVDVAIRRLRAKVD 200 (223)
T ss_pred eCCHHHHHHHHHHHh-CCCccCCHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhhc
Confidence 599999999988662 445778999999986 4467899999999888885
No 394
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=55.22 E-value=13 Score=36.35 Aligned_cols=28 Identities=21% Similarity=0.379 Sum_probs=22.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567 487 PKSLSEVGNIFGLSKERVRQLESRALYRLKQS 518 (532)
Q Consensus 487 ~~Tl~EIAe~LgISrerVRqie~rALkKLR~~ 518 (532)
++|.++||..+|+++++|. |++++|++.
T Consensus 173 ~~t~~~iA~~lG~tretvs----R~l~~L~~~ 200 (236)
T PRK09392 173 PYEKRVLASYLGMTPENLS----RAFAALASH 200 (236)
T ss_pred eCCHHHHHHHhCCChhHHH----HHHHHHHhC
Confidence 5778999999999999985 666667653
No 395
>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=55.11 E-value=42 Score=26.56 Aligned_cols=50 Identities=22% Similarity=0.231 Sum_probs=36.4
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHh------CCCHHHHHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF------GLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~L------gISrerVRqie~rALkKLR~ 517 (532)
.|+++|..+|.+.. ...|...|.++|.+.+ ..+..+|++...+..++|..
T Consensus 5 ~Lt~~e~~lL~~L~-~~~~~~vs~~~l~~~lw~~~~~~~~~~~l~~~i~~LR~~l~~ 60 (78)
T smart00862 5 KLTPKEFRLLELLL-RNPGRVVSREELLEAVWGDDDDDVDDNTLDVHISRLRKKLED 60 (78)
T ss_pred ecCHHHHHHHHHHH-hCCCCccCHHHHHHHHcCCCCCCCccchHHHHHHHHHHHHhc
Confidence 47889999775544 3455789999999975 35677787777777777754
No 396
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=54.54 E-value=34 Score=30.86 Aligned_cols=49 Identities=16% Similarity=0.226 Sum_probs=33.9
Q ss_pred HHHHhcCCHHHH-HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 462 RNLLTLLNPKER-CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 462 ~~~L~~L~~rER-~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
...+..|.+.-| .||.+-. ++.+++..||++.+|+|+.+|++.+ +.|++
T Consensus 7 ~~~fkaLadptRl~IL~~L~---~~~~~~v~ela~~l~lsqstvS~HL----~~L~~ 56 (117)
T PRK10141 7 LQLFKILSDETRLGIVLLLR---ESGELCVCDLCTALDQSQPKISRHL----ALLRE 56 (117)
T ss_pred HHHHHHhCCHHHHHHHHHHH---HcCCcCHHHHHHHHCcCHHHHHHHH----HHHHH
Confidence 355666665544 5665433 2257999999999999999998654 45554
No 397
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=54.46 E-value=18 Score=35.96 Aligned_cols=37 Identities=24% Similarity=0.306 Sum_probs=28.8
Q ss_pred HHHHHhcccCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 475 IVRLRFGIEDGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 475 VL~LRyGL~~~e~~-Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
|+.-.| ..|+.+ |-.++|+.||||+..|| .||+.|..
T Consensus 20 I~~g~l--~pG~~LPsE~eLa~~~gVSRtpVR----EAL~~L~~ 57 (251)
T PRK09990 20 IVDGVL--KVGQALPSERRLCEKLGFSRSALR----EGLTVLRG 57 (251)
T ss_pred HHcCCC--CCCCcCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 444443 355788 89999999999999997 68888865
No 398
>PRK03837 transcriptional regulator NanR; Provisional
Probab=54.17 E-value=19 Score=35.41 Aligned_cols=30 Identities=37% Similarity=0.496 Sum_probs=25.6
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 484 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 484 ~~e~~-Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
.|+.+ +..++|+.||||+..|| .||..|..
T Consensus 33 pG~~Lp~E~~Lae~~gVSRt~VR----EAL~~L~~ 63 (241)
T PRK03837 33 PGDQLPSERELMAFFGVGRPAVR----EALQALKR 63 (241)
T ss_pred CCCCCCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 45778 89999999999999998 67777764
No 399
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=54.08 E-value=27 Score=29.72 Aligned_cols=40 Identities=20% Similarity=0.345 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
|++.+..||...+.. .+.+..+||+.+++++.+|.++..+
T Consensus 20 lt~~q~~~L~~l~~~---~~~~~~~la~~l~i~~~~vt~~l~~ 59 (126)
T COG1846 20 LTPPQYQVLLALYEA---GGITVKELAERLGLDRSTVTRLLKR 59 (126)
T ss_pred CCHHHHHHHHHHHHh---CCCcHHHHHHHHCCCHHHHHHHHHH
Confidence 999999999887762 2222299999999999999755443
No 400
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=53.61 E-value=20 Score=32.53 Aligned_cols=25 Identities=16% Similarity=0.104 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.++|..++|+.+|||+.+|+++++.
T Consensus 17 ~gltq~~lA~~~gvs~~~is~~E~g 41 (135)
T PRK09706 17 LKLSQRSLAKAVKVSHVSISQWERD 41 (135)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 6899999999999999999999865
No 401
>PRK14082 hypothetical protein; Provisional
Probab=53.37 E-value=45 Score=27.05 Aligned_cols=56 Identities=16% Similarity=0.105 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhH
Q 009567 290 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASY 347 (532)
Q Consensus 290 ~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTY 347 (532)
....+.++..+.+.+.+-..+ -.-.+.+||-||--+.+++.+..++...+--|.-|
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 356678899888866654432 12246799999999999999999988766556554
No 402
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=53.33 E-value=20 Score=35.81 Aligned_cols=38 Identities=24% Similarity=0.372 Sum_probs=28.9
Q ss_pred HHHHHHhcccCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 474 CIVRLRFGIEDGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 474 ~VL~LRyGL~~~e~~-Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
.|+.-.| ..|+.+ |-.++|+.||||+..|| .||+.|..
T Consensus 22 ~I~~g~l--~pG~~LpsE~eLa~~lgVSRtpVR----EAL~~L~~ 60 (254)
T PRK09464 22 LILEGTL--RPGEKLPPERELAKQFDVSRPSLR----EAIQRLEA 60 (254)
T ss_pred HHHcCCC--CCCCcCCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 3444443 345777 89999999999999997 67888765
No 403
>PRK10643 DNA-binding transcriptional regulator BasR; Provisional
Probab=53.09 E-value=19 Score=33.72 Aligned_cols=49 Identities=14% Similarity=0.059 Sum_probs=35.7
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHH-----HhCCCHHHHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGN-----IFGLSKERVRQLESRALYRLK 516 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe-----~LgISrerVRqie~rALkKLR 516 (532)
.|+++|.+|+.+..- ..|...|-++|.+ .++++..+|+.+.++.++||.
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 599999999987652 2224444455544 268999999999999999985
No 404
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=53.06 E-value=28 Score=33.87 Aligned_cols=26 Identities=12% Similarity=0.176 Sum_probs=23.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESRA 511 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~rA 511 (532)
.+.|..|||+.+|||+.+|++++.+-
T Consensus 14 ~~~t~~eLA~~lgis~~tV~~~L~~L 39 (203)
T TIGR02702 14 GQATAAALAEALAISPQAVRRHLKDL 39 (203)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46999999999999999999998865
No 405
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=52.74 E-value=20 Score=35.79 Aligned_cols=38 Identities=24% Similarity=0.329 Sum_probs=28.9
Q ss_pred HHHHHHhcccCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 474 CIVRLRFGIEDGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 474 ~VL~LRyGL~~~e~~-Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
.|+.-.| ..|+.+ +..|+|+.||||+..|| .||+.|..
T Consensus 14 ~I~~g~l--~pG~~LpsE~eLae~~gVSRtpVR----EAL~~Le~ 52 (253)
T PRK10421 14 LIEEKNL--EAGMKLPAERQLAMQLGVSRNSLR----EALAKLVS 52 (253)
T ss_pred HHHcCCC--CCCCcCCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 3444443 345788 79999999999999997 68888865
No 406
>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=52.59 E-value=36 Score=30.97 Aligned_cols=44 Identities=14% Similarity=0.185 Sum_probs=34.1
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHh----CCCHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF----GLSKERVRQLESRALY 513 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~L----gISrerVRqie~rALk 513 (532)
.|++.|.+|+...+- ..+.|..||.+.| |+++.||+..+.|-.+
T Consensus 1 ~Lt~~E~~VM~vlW~---~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~ 48 (130)
T TIGR02698 1 SISDAEWEVMRVVWT---LGETTSRDIIRILAEKKDWSDSTIKTLLGRLVD 48 (130)
T ss_pred CCCHHHHHHHHHHHc---CCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHH
Confidence 378999999877653 2478999977776 7999999887776555
No 407
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.57 E-value=31 Score=30.66 Aligned_cols=47 Identities=23% Similarity=0.241 Sum_probs=38.9
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567 465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 515 (532)
Q Consensus 465 L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKL 515 (532)
.+.|++.+-+.+.+++- -.=+++||-..+|+|--+||......|++|
T Consensus 39 F~~Lt~d~LeFv~lf~r----~RGnlKEvEr~lg~sYptvR~kld~vlram 85 (122)
T COG3877 39 FEYLTSDQLEFVELFLR----CRGNLKEVERELGISYPTVRTKLDEVLRAM 85 (122)
T ss_pred ccccCHhHhHHHHHHHH----HccCHHHHHHHHCCccHHHHHHHHHHHHHc
Confidence 46678888888888775 334899999999999999999888888776
No 408
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=52.53 E-value=24 Score=24.64 Aligned_cols=25 Identities=20% Similarity=0.388 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.++|..++|+.+|++..+|.+++..
T Consensus 9 ~~~s~~~la~~~~i~~~~i~~~~~~ 33 (56)
T smart00530 9 KGLTQEELAEKLGVSRSTLSRIENG 33 (56)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 6789999999999999999987764
No 409
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=52.18 E-value=21 Score=35.76 Aligned_cols=38 Identities=21% Similarity=0.400 Sum_probs=28.9
Q ss_pred HHHHHHhcccCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 474 CIVRLRFGIEDGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 474 ~VL~LRyGL~~~e~~-Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
.|+.-.|. .|+.+ |-.++|+.||||+..|| .||+.|..
T Consensus 21 ~I~~g~l~--pG~~LpsE~eLa~~~gVSRtpVR----EAL~~L~~ 59 (257)
T PRK10225 21 LIIKTPYN--PGERLPPEREIAEMLDVTRTVVR----EALIMLEI 59 (257)
T ss_pred HHHhCCCC--CCCcCcCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 34444443 45788 69999999999999998 68888865
No 410
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=51.99 E-value=15 Score=29.53 Aligned_cols=25 Identities=24% Similarity=0.352 Sum_probs=20.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.+.|-.|||+.+|+|+.+||.++..
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 6899999999999999999977643
No 411
>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=51.98 E-value=10 Score=32.89 Aligned_cols=26 Identities=23% Similarity=0.384 Sum_probs=23.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRALY 513 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rALk 513 (532)
+|..|+|+.+|||..++|.++..++-
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~~Gll 27 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESIGLI 27 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 68999999999999999999988664
No 412
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=51.93 E-value=24 Score=35.67 Aligned_cols=26 Identities=15% Similarity=0.093 Sum_probs=22.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 485 GKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 485 ~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
....+.+|+++.||||..|||+.+..
T Consensus 17 ~~~~~~~ela~~l~vS~~TirRdL~~ 42 (251)
T PRK13509 17 LGFVTVEKVIERLGISPATARRDINK 42 (251)
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 36789999999999999999977554
No 413
>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=51.77 E-value=22 Score=28.55 Aligned_cols=27 Identities=22% Similarity=0.463 Sum_probs=23.0
Q ss_pred HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 009567 475 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE 508 (532)
Q Consensus 475 VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie 508 (532)
+|.--|| +..|+|..|++++.+||+..
T Consensus 11 lLi~~~G-------nqtEvaR~l~c~R~TVrKY~ 37 (64)
T PF06322_consen 11 LLIETYG-------NQTEVARRLGCNRATVRKYS 37 (64)
T ss_pred HHHHHhC-------cHHHHHHHhcccHHHHHHHh
Confidence 4566777 88999999999999999764
No 414
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=51.59 E-value=22 Score=34.76 Aligned_cols=38 Identities=24% Similarity=0.299 Sum_probs=29.3
Q ss_pred HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 474 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 474 ~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
.|+.-.| ..|+.++..++|+.||||+..|| .||.+|..
T Consensus 19 ~I~~g~l--~pG~~L~e~eLae~lgVSRtpVR----EAL~~L~~ 56 (224)
T PRK11534 19 DIIRGNF--QPDEKLRMSLLTSRYALGVGPLR----EALSQLVA 56 (224)
T ss_pred HHHhCCC--CCCCcCCHHHHHHHHCCChHHHH----HHHHHHHH
Confidence 4555544 24588899999999999999997 67777755
No 415
>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=51.23 E-value=24 Score=35.38 Aligned_cols=42 Identities=17% Similarity=0.204 Sum_probs=33.0
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 509 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~ 509 (532)
.|+..+.+-|++.+-. +-+.+|...+|+.|+||.+.||.|++
T Consensus 10 ~Ls~~~~~~ir~L~~~-~p~~~t~~~Lae~F~vspe~irrILk 51 (225)
T PF06413_consen 10 KLSREAMEQIRYLHKE-DPEEWTVERLAESFKVSPEAIRRILK 51 (225)
T ss_pred CCCHHHHHHHHHHHHh-CccccCHHHHHhhCCCCHHHHHHHHh
Confidence 5677777777765542 33568999999999999999999875
No 416
>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=51.19 E-value=10 Score=28.10 Aligned_cols=21 Identities=14% Similarity=0.248 Sum_probs=18.3
Q ss_pred HHHHHHhCCCHHHHHHHHHHH
Q 009567 491 SEVGNIFGLSKERVRQLESRA 511 (532)
Q Consensus 491 ~EIAe~LgISrerVRqie~rA 511 (532)
++||+.+|||+.+|+++++.-
T Consensus 1 ~~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 1 KDIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred CcHHHHHCcCHHHHHHHHcCC
Confidence 379999999999999998754
No 417
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=51.07 E-value=25 Score=27.17 Aligned_cols=25 Identities=16% Similarity=0.405 Sum_probs=20.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.++|..++|+.+|+++.++.++++.
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 6899999999999999999999965
No 418
>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=50.92 E-value=34 Score=28.24 Aligned_cols=50 Identities=22% Similarity=0.157 Sum_probs=36.3
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHH
Q 009567 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~Lg-----ISrerVRqie~rALkKLR~ 517 (532)
.|+++|..+|.+.+ ...|+..|.++|.+.+. .+...+++.+.+..+||..
T Consensus 23 ~Lt~~e~~lL~~L~-~~~~~~vs~~~l~~~lw~~~~~~~~~~l~~~I~rLRkkl~~ 77 (95)
T cd00383 23 ELTPKEFELLELLA-RNPGRVLSREQLLEAVWGDDYDVDDRTVDVHISRLRKKLED 77 (95)
T ss_pred EeCHHHHHHHHHHH-hCCCCcCCHHHHHHHhcCCCCCCCcccHHHHHHHHHHHhcc
Confidence 47899999887765 45668999999999884 5666676666665555543
No 419
>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=50.65 E-value=12 Score=31.59 Aligned_cols=25 Identities=28% Similarity=0.498 Sum_probs=22.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRAL 512 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rAL 512 (532)
+|..|+|+.+|||..++|.++...+
T Consensus 2 ~ti~evA~~~gvs~~tLR~ye~~Gl 26 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEEKGL 26 (88)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 6899999999999999999988765
No 420
>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=50.57 E-value=26 Score=31.40 Aligned_cols=30 Identities=30% Similarity=0.468 Sum_probs=23.7
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 484 DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 484 ~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
++.+.|..|||+.+|+|+..|+++ +++|++
T Consensus 22 ~~~~~s~~eia~~l~is~~~v~~~----l~~L~~ 51 (130)
T TIGR02944 22 DSQPYSAAEIAEQTGLNAPTVSKI----LKQLSL 51 (130)
T ss_pred CCCCccHHHHHHHHCcCHHHHHHH----HHHHHH
Confidence 346799999999999999999754 445554
No 421
>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=50.41 E-value=12 Score=32.82 Aligned_cols=26 Identities=19% Similarity=0.273 Sum_probs=23.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRALY 513 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rALk 513 (532)
+|..|+|+.+|||..++|.++..++=
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~~GLi 26 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKIGLL 26 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCC
Confidence 57899999999999999999998654
No 422
>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=50.28 E-value=31 Score=30.73 Aligned_cols=25 Identities=20% Similarity=0.367 Sum_probs=21.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 485 GKPKSLSEVGNIFGLSKERVRQLES 509 (532)
Q Consensus 485 ~e~~Tl~EIAe~LgISrerVRqie~ 509 (532)
+.+.|.+|||+.+|+++..|+++..
T Consensus 23 ~~~~s~~eia~~~~i~~~~v~~il~ 47 (132)
T TIGR00738 23 EGPVSVKEIAERQGISRSYLEKILR 47 (132)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHH
Confidence 3589999999999999999976543
No 423
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=50.15 E-value=29 Score=32.68 Aligned_cols=42 Identities=10% Similarity=0.127 Sum_probs=28.8
Q ss_pred CCHHHHHHHHHHhccc-CCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 468 LNPKERCIVRLRFGIE-DGKPKSLSEVGNIFGLSKERVRQLES 509 (532)
Q Consensus 468 L~~rER~VL~LRyGL~-~~e~~Tl~EIAe~LgISrerVRqie~ 509 (532)
+++....-|...|.+. ++......+||+.|||++.+|.++++
T Consensus 4 ~s~~~edYL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~ 46 (154)
T COG1321 4 LSETEEDYLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLK 46 (154)
T ss_pred cchHHHHHHHHHHHHHhccCcccHHHHHHHhCCCcHHHHHHHH
Confidence 4444444444444333 44678999999999999999976544
No 424
>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=50.05 E-value=12 Score=32.94 Aligned_cols=25 Identities=20% Similarity=0.521 Sum_probs=22.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRAL 512 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rAL 512 (532)
+|..|+|+.+|||..++|.++...+
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gl 25 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKEGL 25 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999988765
No 425
>PF14502 HTH_41: Helix-turn-helix domain
Probab=49.86 E-value=31 Score=26.39 Aligned_cols=30 Identities=27% Similarity=0.441 Sum_probs=25.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567 485 GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 518 (532)
Q Consensus 485 ~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~ 518 (532)
..-.|..|.++.|++|+.+| ..||+.|.+.
T Consensus 4 dRi~tI~e~~~~~~vs~Gti----Q~Alk~Le~~ 33 (48)
T PF14502_consen 4 DRIPTISEYSEKFGVSRGTI----QNALKFLEEN 33 (48)
T ss_pred cccCCHHHHHHHhCcchhHH----HHHHHHHHHC
Confidence 35679999999999999999 4788888763
No 426
>PRK13239 alkylmercury lyase; Provisional
Probab=49.51 E-value=34 Score=33.92 Aligned_cols=29 Identities=21% Similarity=0.237 Sum_probs=26.0
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhcC
Q 009567 391 GNHSPDKEDLARRVGITVEKLERLIFITR 419 (532)
Q Consensus 391 ~gr~Pt~eEIA~~lgis~e~v~~ll~~~~ 419 (532)
.|+.|+..+||+.+|+++++|+.++....
T Consensus 33 ~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 33 KGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 57899999999999999999999987643
No 427
>TIGR00180 parB_part ParB-like partition proteins. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Probab=49.43 E-value=33 Score=32.93 Aligned_cols=43 Identities=19% Similarity=0.191 Sum_probs=32.4
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
..|++-|+-....+.. .. .++|.++||+.+|+|+.+|+++..-
T Consensus 101 ~~lt~~e~a~~~~~l~-~~-~g~s~~~iA~~lg~s~~~V~r~l~l 143 (187)
T TIGR00180 101 EDLSPIEEAQAYKRLL-EK-FSMTQEDLAKKIGKSRAHITNLLRL 143 (187)
T ss_pred cCCCHHHHHHHHHHHH-HH-hCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4788888766554432 21 4789999999999999999987654
No 428
>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=49.41 E-value=12 Score=32.07 Aligned_cols=25 Identities=20% Similarity=0.339 Sum_probs=22.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRAL 512 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rAL 512 (532)
+|..|+|+.+|||..++|.++..++
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gl 25 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDKIGL 25 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 4789999999999999999988765
No 429
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=49.37 E-value=13 Score=29.88 Aligned_cols=26 Identities=31% Similarity=0.417 Sum_probs=19.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 485 GKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 485 ~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
+...|+.|||..||+|++.|+.++..
T Consensus 12 ~~~~S~~eLa~~~~~s~~~ve~mL~~ 37 (69)
T PF09012_consen 12 RGRVSLAELAREFGISPEAVEAMLEQ 37 (69)
T ss_dssp S-SEEHHHHHHHTT--HHHHHHHHHH
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 36789999999999999999877654
No 430
>PF04963 Sigma54_CBD: Sigma-54 factor, core binding domain; InterPro: IPR007046 This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme []. The centre of this domain contains a very weak similarity to a helix-turn-helix motif, which may represent a DNA binding domain.; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent; PDB: 2K9L_A 2K9M_A.
Probab=49.16 E-value=41 Score=32.71 Aligned_cols=60 Identities=27% Similarity=0.308 Sum_probs=36.0
Q ss_pred hcCCHHHHHHHHHHhcccCC---CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH----hhcCchhhhhh
Q 009567 466 TLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLESRALYRLKQS----LGGKASYGYAD 529 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~---e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~----l~~~~l~~yld 529 (532)
..|++.++.|...--+--|. =..++.+||+.+|++.+.|. ++++.|+.. +.+..++++|.
T Consensus 28 ~~l~~~~~~ia~~lI~~LD~~GyL~~~~~eia~~l~~~~~~v~----~~l~~lQ~leP~GigAr~l~EcLl 94 (194)
T PF04963_consen 28 SPLSEEEREIAEYLIDNLDDDGYLTESLEEIAEELGVSEEEVE----KALELLQSLEPAGIGARDLQECLL 94 (194)
T ss_dssp H---TCCHHHHHHHCCCBTTTSTCSS-HHHHHHHCTS-HHHHH----HHHHHHHTTSS--TTTS-TTHHHH
T ss_pred cccCHHHHHHHHHHHHcCCCCCccCCCHHHHHHHhCCCHHHHH----HHHHHHHcCCCCccCcCCHHHHHH
Confidence 46889888887765443233 34699999999999999985 666677652 23445555543
No 431
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=49.16 E-value=23 Score=29.47 Aligned_cols=19 Identities=21% Similarity=0.240 Sum_probs=18.4
Q ss_pred CHHHHHHHhCCCHHHHHHH
Q 009567 489 SLSEVGNIFGLSKERVRQL 507 (532)
Q Consensus 489 Tl~EIAe~LgISrerVRqi 507 (532)
+...+|+.||||.+.|+|+
T Consensus 12 s~~kvA~aLGIs~~AVsQW 30 (75)
T PRK09744 12 SKTKLANAAGVRLASVAAW 30 (75)
T ss_pred cHHHHHHHHCCCHHHHHHH
Confidence 8899999999999999998
No 432
>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=49.11 E-value=19 Score=32.67 Aligned_cols=23 Identities=13% Similarity=0.338 Sum_probs=20.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~r 510 (532)
||-+|+|+.+|+|+.+|..+..+
T Consensus 1 MT~eELA~~tG~srQTINrWvRk 23 (122)
T PF07037_consen 1 MTPEELAELTGYSRQTINRWVRK 23 (122)
T ss_pred CCHHHHHHHhCccHHHHHHHHHh
Confidence 68999999999999999988754
No 433
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=49.01 E-value=29 Score=25.94 Aligned_cols=47 Identities=15% Similarity=0.171 Sum_probs=36.1
Q ss_pred CCHHHHHHHHHHhcccCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009567 468 LNPKERCIVRLRFGIEDG-KPKSLSEVGNIFGLSKERVRQLESRALYR 514 (532)
Q Consensus 468 L~~rER~VL~LRyGL~~~-e~~Tl~EIAe~LgISrerVRqie~rALkK 514 (532)
+++.+..+|.-.|..+.. ......+||..+|++...|..+......+
T Consensus 7 ~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~ 54 (56)
T smart00389 7 FTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAK 54 (56)
T ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhc
Confidence 678888888888864432 23457899999999999999988776554
No 434
>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=48.59 E-value=2.9e+02 Score=28.14 Aligned_cols=31 Identities=26% Similarity=0.470 Sum_probs=23.9
Q ss_pred HHHHHhhhCCCCcHHHHHHHccCCHHHHHHH
Q 009567 255 KSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 285 (532)
Q Consensus 255 ~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~ 285 (532)
...+....|++|+..+.|...|++...+...
T Consensus 139 ~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~ 169 (285)
T TIGR02394 139 ARQLEKKLGREPSVEEIAELLDKPVEDVSRV 169 (285)
T ss_pred HHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 3345566799999999999999987766543
No 435
>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=48.35 E-value=14 Score=32.05 Aligned_cols=25 Identities=32% Similarity=0.421 Sum_probs=22.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRAL 512 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rAL 512 (532)
++..|+|+.+|||..++|.++...+
T Consensus 1 y~i~e~A~~~gvs~~tlR~Ye~~Gl 25 (99)
T cd04772 1 YRTVDLARAIGLSPQTVRNYESLGL 25 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 4789999999999999999987655
No 436
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=48.22 E-value=18 Score=27.95 Aligned_cols=26 Identities=8% Similarity=0.218 Sum_probs=19.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESRA 511 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~rA 511 (532)
.++|..++|+..|||+.+|..+.+.-
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 57899999999999999999988865
No 437
>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=48.17 E-value=21 Score=30.95 Aligned_cols=23 Identities=35% Similarity=0.507 Sum_probs=21.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~r 510 (532)
+|..|+|+.+|||..++|.++..
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~~ 23 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 57899999999999999999876
No 438
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=48.11 E-value=1.8e+02 Score=29.29 Aligned_cols=37 Identities=22% Similarity=0.259 Sum_probs=27.2
Q ss_pred HHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHh
Q 009567 380 VLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 417 (532)
Q Consensus 380 i~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~ 417 (532)
|.+...+...++| -.|.+++|-.||+|+..|...+..
T Consensus 92 IvRl~~EAy~Qgg-lLT~~Dla~LL~~S~~TI~~~i~~ 128 (220)
T PF07900_consen 92 IVRLTNEAYDQGG-LLTQEDLAMLLGISPRTISKDIKE 128 (220)
T ss_pred HHHHHHHHHHcCC-cccHHHHHHHHCCCHHHHHHHHHH
Confidence 3334444444555 899999999999999999887654
No 439
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=48.03 E-value=36 Score=31.08 Aligned_cols=30 Identities=27% Similarity=0.630 Sum_probs=24.5
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 484 DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 484 ~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
+|+..|.+|||+.+|||+..|| +++.+|++
T Consensus 22 ~g~~~s~~~ia~~~~is~~~vr----k~l~~L~~ 51 (141)
T PRK11014 22 EGRMTSISEVTEVYGVSRNHMV----KIINQLSR 51 (141)
T ss_pred CCCccCHHHHHHHHCcCHHHHH----HHHHHHHh
Confidence 4567899999999999998887 56666765
No 440
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=47.91 E-value=39 Score=34.62 Aligned_cols=51 Identities=20% Similarity=0.260 Sum_probs=40.1
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHhcccCC---CCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 457 MRQHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLES 509 (532)
Q Consensus 457 l~~~L~~~L~~L~~rER~VL~LRyGL~~~---e~~Tl~EIAe~LgISrerVRqie~ 509 (532)
+...|......|++.||.|-.+. |.+. ..+|.+|||+..|||+.+|-+..+
T Consensus 5 l~~~I~~~~~~Lt~~er~iA~yi--l~~~~~~~~~si~elA~~a~VS~aTv~Rf~~ 58 (281)
T COG1737 5 LLERIRERYDSLTKSERKIADYI--LANPDEVALLSIAELAERAGVSPATVVRFAR 58 (281)
T ss_pred HHHHHHHHHhcCCHHHHHHHHHH--HhCHHHHHHHHHHHHHHHhCCCHHHHHHHHH
Confidence 45578888999999999997654 3332 357999999999999999965443
No 441
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=47.75 E-value=2.1e+02 Score=32.09 Aligned_cols=127 Identities=13% Similarity=0.223 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcC---CCCCHHHHHHHhCCCHHHHHHHHHhcCCCccc
Q 009567 348 AYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGN---HSPDKEDLARRVGITVEKLERLIFITRMPLSM 424 (532)
Q Consensus 348 A~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~g---r~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSL 424 (532)
|.|.|+.-=.|. ..+......|-+....+...|. ++-+..+||+.+|+.+.+|..+..
T Consensus 331 A~wli~si~qR~-----------~TllkV~~~Iv~~Q~~Ff~~G~~~LkPLtlkdVAe~lglHeSTVSRa~~-------- 391 (481)
T PRK12469 331 ARWLIRNAQQRF-----------DTIQRVAECIVARQRDFFRYGEIALKPLVLRDVAEELGLHESTISRATG-------- 391 (481)
T ss_pred HHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHhCCcccCcCCcHHHHHHHhCCCcchhhHHhc--------
Q ss_pred CCCCCCCCCc-chhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHh-----C
Q 009567 425 QQPVWADQDT-TFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-----G 498 (532)
Q Consensus 425 D~~v~~d~~~-~l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~L-----g 498 (532)
+.-+....+. .+-.++...-.......+.....+..|..+++.=+++ +++|-++|++.| .
T Consensus 392 ~KY~~tp~GifeLK~FFs~~v~~~~g~~~Ss~~Ik~~Ik~lI~~Ed~~--------------kPLSD~~I~~~L~~~GI~ 457 (481)
T PRK12469 392 NKYMATPRGTFEFKHFFPRKLEAAGGGECSAAAVRALIKEMIAAEQAG--------------DPLSDVALAEMLAGRGVL 457 (481)
T ss_pred CceeecCCceEeHHHhhccccCCCCCccccHHHHHHHHHHHHHhcCCC--------------CCCCHHHHHHHHHhcCCC
Q ss_pred CCHHHHHHH
Q 009567 499 LSKERVRQL 507 (532)
Q Consensus 499 ISrerVRqi 507 (532)
|+|-||-++
T Consensus 458 IARRTVAKY 466 (481)
T PRK12469 458 IARRTVAKY 466 (481)
T ss_pred eechhHHHH
No 442
>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=47.74 E-value=36 Score=23.84 Aligned_cols=25 Identities=20% Similarity=0.405 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.++|..++|..+|+|+.+|.+++..
T Consensus 11 ~~~s~~~~a~~~~~~~~~v~~~~~g 35 (58)
T cd00093 11 KGLTQEELAEKLGVSRSTISRIENG 35 (58)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 5789999999999999999987764
No 443
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=47.74 E-value=1.7e+02 Score=32.37 Aligned_cols=24 Identities=17% Similarity=0.256 Sum_probs=20.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 393 HSPDKEDLARRVGITVEKLERLIF 416 (532)
Q Consensus 393 r~Pt~eEIA~~lgis~e~v~~ll~ 416 (532)
++-+..+||+.+|+.+.+|..+..
T Consensus 342 kPLtlkdvAe~lglheSTVSRav~ 365 (455)
T PRK05932 342 KPLVLKDIAEELGMHESTISRATT 365 (455)
T ss_pred cCccHHHHHHHhCCCccchhhhhc
Confidence 456899999999999999988764
No 444
>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=47.72 E-value=14 Score=32.17 Aligned_cols=26 Identities=23% Similarity=0.313 Sum_probs=23.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRALY 513 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rALk 513 (532)
+|..|+|+.+|||..++|.++...+-
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~~Gll 27 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKLGLI 27 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 68999999999999999999887654
No 445
>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=47.66 E-value=14 Score=31.80 Aligned_cols=26 Identities=19% Similarity=0.270 Sum_probs=22.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRALY 513 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rALk 513 (532)
|+..|+|+.+|||..++|.++...+-
T Consensus 1 m~i~eva~~~gvs~~tlR~ye~~Gll 26 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDHIGLL 26 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999987653
No 446
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=47.58 E-value=28 Score=34.79 Aligned_cols=30 Identities=20% Similarity=0.174 Sum_probs=25.2
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 484 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 484 ~~e~~-Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
.|+.+ |-.++|+.||||+..|| .||+.|..
T Consensus 28 pG~~LpsE~eLae~~gVSRtpVR----EAL~~L~~ 58 (253)
T PRK11523 28 VGDKLPAERFIADEKNVSRTVVR----EAIIMLEV 58 (253)
T ss_pred CCCCCCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 45788 58999999999999997 68888865
No 447
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=47.21 E-value=42 Score=32.65 Aligned_cols=40 Identities=20% Similarity=0.155 Sum_probs=32.7
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE 508 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie 508 (532)
-.|++.|..||...+. ..+.|..+||+.+++++.+|..+.
T Consensus 41 ~gLt~~q~~iL~~L~~---~~~itq~eLa~~l~l~~sTvtr~l 80 (185)
T PRK13777 41 YDLNINEHHILWIAYH---LKGASISEIAKFGVMHVSTAFNFS 80 (185)
T ss_pred CCCCHHHHHHHHHHHh---CCCcCHHHHHHHHCCCHhhHHHHH
Confidence 4689999999876654 368999999999999999986543
No 448
>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=47.13 E-value=14 Score=31.29 Aligned_cols=26 Identities=19% Similarity=0.286 Sum_probs=22.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRALY 513 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rALk 513 (532)
+|..|+|+.+|||..+||.++...+-
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~~Gli 27 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYERLGLL 27 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCCc
Confidence 68899999999999999999876543
No 449
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=47.10 E-value=33 Score=34.21 Aligned_cols=26 Identities=19% Similarity=0.350 Sum_probs=22.2
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 484 DGKPKSLSEVGNIFGLSKERVRQLES 509 (532)
Q Consensus 484 ~~e~~Tl~EIAe~LgISrerVRqie~ 509 (532)
.+.++|+.|||+.+|+++++|..+..
T Consensus 21 ~~~~~~l~eia~~lglpksT~~RlL~ 46 (248)
T TIGR02431 21 ERPRLTLTDVAEATGLTRAAARRFLL 46 (248)
T ss_pred CCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34789999999999999999976554
No 450
>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=47.06 E-value=14 Score=31.77 Aligned_cols=25 Identities=20% Similarity=0.262 Sum_probs=22.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRAL 512 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rAL 512 (532)
|+..|+|+.+|||..+||-++...+
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye~~GL 25 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLREGL 25 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999988765
No 451
>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=47.06 E-value=14 Score=32.49 Aligned_cols=26 Identities=31% Similarity=0.446 Sum_probs=23.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRALY 513 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rALk 513 (532)
+|..|+|+.+|||..++|.++..++-
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye~~gll 26 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEKEGLL 26 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999987764
No 452
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=46.92 E-value=36 Score=28.46 Aligned_cols=32 Identities=19% Similarity=0.283 Sum_probs=25.9
Q ss_pred HHHHHhcccCCCCCCHHHHHHHhC------CCHHHHHHHHHH
Q 009567 475 IVRLRFGIEDGKPKSLSEVGNIFG------LSKERVRQLESR 510 (532)
Q Consensus 475 VL~LRyGL~~~e~~Tl~EIAe~Lg------ISrerVRqie~r 510 (532)
+...|-- -++|..++|+.+| +|..+|.++++.
T Consensus 16 lk~~R~~----lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~ 53 (75)
T smart00352 16 FKQRRIK----LGFTQADVGLALGALYGPDFSQTTICRFEAL 53 (75)
T ss_pred HHHHHHH----cCCCHHHHHHHhcccccCcCCHHHHHHHHhc
Confidence 4445554 6899999999999 599999998863
No 453
>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes. This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].
Probab=46.86 E-value=40 Score=32.52 Aligned_cols=38 Identities=24% Similarity=0.280 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 009567 468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE 508 (532)
Q Consensus 468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie 508 (532)
|++.-|+-|.-.+- .+++|+++||..+||+..||.-|+
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 45555555555553 267799999999999999996554
No 454
>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=46.76 E-value=14 Score=31.88 Aligned_cols=25 Identities=20% Similarity=0.339 Sum_probs=22.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRAL 512 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rAL 512 (532)
+|..|+|+.+|||..++|.++...+
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~~Gl 25 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDEIGL 25 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999988765
No 455
>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=46.60 E-value=15 Score=31.36 Aligned_cols=25 Identities=28% Similarity=0.542 Sum_probs=22.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRAL 512 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rAL 512 (532)
+|..|+|+.+|||..+|+.++...+
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~~Gl 25 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEEKGL 25 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999988765
No 456
>COG1481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.58 E-value=39 Score=35.48 Aligned_cols=43 Identities=30% Similarity=0.299 Sum_probs=36.1
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCC--CHHHHHHHHHH
Q 009567 465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGL--SKERVRQLESR 510 (532)
Q Consensus 465 L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgI--SrerVRqie~r 510 (532)
++.||++-+++-.+|.- ..+.|++|||+.+.. |++.|..+..|
T Consensus 251 l~~lpe~l~e~a~LRl~---hpd~SLeeLg~~l~~~iSKSGvnHrlrk 295 (308)
T COG1481 251 LEKLPEKLREAALLRLE---HPDASLEELGELLEPPISKSGVNHRLRK 295 (308)
T ss_pred hhhCCHHHHHHHHHhhc---ChhhhHHHHHHHhcCcccHHHHHHHHHH
Confidence 58899999999999873 588999999999987 88888765544
No 457
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=46.56 E-value=15 Score=32.04 Aligned_cols=26 Identities=12% Similarity=0.179 Sum_probs=23.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRALY 513 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rALk 513 (532)
|+..|+|+.+|||..++|-.+...|=
T Consensus 1 m~Ige~a~~~gvs~~tlRyYe~~GLl 26 (107)
T cd04777 1 MKIGKFAKKNNITIDTVRHYIDLGLL 26 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCc
Confidence 57899999999999999999998874
No 458
>PRK13503 transcriptional activator RhaS; Provisional
Probab=46.49 E-value=1.1e+02 Score=30.33 Aligned_cols=30 Identities=17% Similarity=0.154 Sum_probs=24.0
Q ss_pred HHhcCCCCCHHHHHHHhCCCHHHHHHHHHh
Q 009567 388 IQEGNHSPDKEDLARRVGITVEKLERLIFI 417 (532)
Q Consensus 388 ~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~ 417 (532)
.+......|.+++|+.+|+++..+..+...
T Consensus 181 ~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk~ 210 (278)
T PRK13503 181 EDHFAEEVNWEALADQFSLSLRTLHRQLKQ 210 (278)
T ss_pred HHhhcCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 334445789999999999999999888653
No 459
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=46.29 E-value=33 Score=34.71 Aligned_cols=41 Identities=22% Similarity=0.261 Sum_probs=27.2
Q ss_pred HHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 473 RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 473 R~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
|-+-.|.+.-..+.++|+.||++.+|+++.+|.+ .++.|..
T Consensus 12 ral~iL~~l~~~~~~ls~~eia~~lgl~kstv~R----lL~tL~~ 52 (263)
T PRK09834 12 RGLMVLRALNRLDGGATVGLLAELTGLHRTTVRR----LLETLQE 52 (263)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence 3333343332334569999999999999999964 4555543
No 460
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=46.28 E-value=15 Score=32.48 Aligned_cols=26 Identities=23% Similarity=0.339 Sum_probs=23.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRALY 513 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rALk 513 (532)
++..|+|+.+|||..++|.++..+|=
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye~~GLl 26 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEEQGLL 26 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCC
Confidence 57899999999999999999987654
No 461
>PRK06424 transcription factor; Provisional
Probab=46.27 E-value=29 Score=32.41 Aligned_cols=25 Identities=12% Similarity=0.056 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.++|..|+|+.+|+++.+|+++++.
T Consensus 96 ~GLSQ~eLA~~iGvs~stIskiE~G 120 (144)
T PRK06424 96 LSMSQADLAAKIFERKNVIASIERG 120 (144)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 6899999999999999999999973
No 462
>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=46.23 E-value=15 Score=32.64 Aligned_cols=27 Identities=19% Similarity=0.336 Sum_probs=24.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRALYR 514 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rALkK 514 (532)
||..|+|+.+|||..++|.++..++=.
T Consensus 1 ~~ige~a~~~gvs~~tLryYe~~GLi~ 27 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEEKGLLP 27 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 588999999999999999999887654
No 463
>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=46.21 E-value=43 Score=30.64 Aligned_cols=32 Identities=22% Similarity=0.210 Sum_probs=23.7
Q ss_pred HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 474 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 474 ~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.||.|.. .+.+-.+||..|+||...|++|+.|
T Consensus 25 rIvela~-----~G~rp~~Isr~l~Vs~gcVsKIl~R 56 (125)
T PF00292_consen 25 RIVELAK-----EGVRPCDISRQLRVSHGCVSKILSR 56 (125)
T ss_dssp HHHHHHH-----TT--HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHhh-----hcCCHHHHHHHHccchhHHHHHHHH
Confidence 4666665 6899999999999999999988876
No 464
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=46.21 E-value=55 Score=31.16 Aligned_cols=57 Identities=23% Similarity=0.248 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHhc--ccC--CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 454 KQLMRQHVRNLLTLLNPKERCIVRLRFG--IED--GKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 454 ~~~l~~~L~~~L~~L~~rER~VL~LRyG--L~~--~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
+++..+.|+..|+.||+.|++=+.-.|- +++ .+|+|-+||.+.||=+++-++++...
T Consensus 3 k~efL~~L~~~L~~lp~~e~~e~l~~Y~e~f~d~~~~G~sEeeii~~LG~P~~iA~~i~~~ 63 (181)
T PF08006_consen 3 KNEFLNELEKYLKKLPEEEREEILEYYEEYFDDAGEEGKSEEEIIAELGSPKEIAREILAE 63 (181)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHcCCHHHHHHHHHHh
Confidence 3455667889999999998877665552 222 35799999999999999999888754
No 465
>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=46.10 E-value=15 Score=31.71 Aligned_cols=26 Identities=27% Similarity=0.402 Sum_probs=22.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRALY 513 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rALk 513 (532)
++..|+|+.+|||..++|.++...+-
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye~~Gll 26 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEEIGLV 26 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999876543
No 466
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=46.07 E-value=14 Score=33.26 Aligned_cols=27 Identities=26% Similarity=0.379 Sum_probs=23.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRALYR 514 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rALkK 514 (532)
||..|+|+.+|||..++|.++...+-.
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~~GLl~ 27 (127)
T cd01108 1 MNIGEAAKLTGLSAKMIRYYEEIGLIP 27 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 588999999999999999999887653
No 467
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=45.63 E-value=15 Score=33.15 Aligned_cols=26 Identities=27% Similarity=0.494 Sum_probs=23.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRALY 513 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rALk 513 (532)
|+..|+|+.+|||..++|.++...+-
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~~GLl 26 (127)
T TIGR02044 1 MNIGQVAKLTGLSSKMIRYYEEKGLI 26 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999987664
No 468
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=45.18 E-value=7.1 Score=37.12 Aligned_cols=48 Identities=13% Similarity=0.212 Sum_probs=0.0
Q ss_pred HHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 460 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 509 (532)
Q Consensus 460 ~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~ 509 (532)
.|..+...|=..|..-|.. |-..-.++|+++||+.+|++.+||+....
T Consensus 24 TL~~v~~~iv~~Q~~ff~~--g~~~l~PLt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 24 TLLRVAQAIVERQKDFFLG--GPGALKPLTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp --------------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHhc--CcccCcCCCHHHHHHHhCCCHhHHHHHHc
Confidence 3445555566666665442 21122799999999999999999987554
No 469
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=45.02 E-value=33 Score=30.87 Aligned_cols=25 Identities=16% Similarity=0.183 Sum_probs=23.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.++|.+|+|+.+|||+++|.++++.
T Consensus 17 ~Glsq~eLA~~~Gis~~~is~iE~g 41 (120)
T PRK13890 17 RHMTKKELSERSGVSISFLSDLTTG 41 (120)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 6799999999999999999999874
No 470
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.92 E-value=54 Score=28.27 Aligned_cols=40 Identities=18% Similarity=0.341 Sum_probs=28.4
Q ss_pred cCCHHHHHHH----HHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 467 LLNPKERCIV----RLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 509 (532)
Q Consensus 467 ~L~~rER~VL----~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~ 509 (532)
.|+|.|+++- ...|-| -++|.++||..||+|...|..++.
T Consensus 2 SLn~eq~~~Tk~elqan~el---~~LS~~~iA~~Ln~t~~~lekil~ 45 (97)
T COG4367 2 SLNPEQKQRTKQELQANFEL---CPLSDEEIATALNWTEVKLEKILQ 45 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhh---ccccHHHHHHHhCCCHHHHHHHHH
Confidence 3555555443 334433 589999999999999999877764
No 471
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=44.44 E-value=16 Score=32.88 Aligned_cols=27 Identities=22% Similarity=0.410 Sum_probs=23.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRALYR 514 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rALkK 514 (532)
+|..|+|+.+|||..+||.++...+-.
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~~GLl~ 27 (126)
T cd04783 1 LTIGELAKAAGVNVETIRYYQRRGLLP 27 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 578999999999999999999877654
No 472
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=44.39 E-value=54 Score=37.68 Aligned_cols=52 Identities=15% Similarity=0.273 Sum_probs=41.4
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHhcccCC---CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 457 MRQHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 457 l~~~L~~~L~~L~~rER~VL~LRyGL~~~---e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
+.+.|...+..|++.||.|..+.. ... ..+|..|||+..|+|..+|-+..++
T Consensus 343 l~~~I~~~~~~Lt~~E~~IA~yIl--~n~~~v~~~si~eLA~~~~vS~aTV~Rf~kk 397 (638)
T PRK14101 343 VFERIRQMRDALTPAERRVADLAL--NHPRSIINDPIVDIARKADVSQPTVIRFCRS 397 (638)
T ss_pred HHHHHHHHHhhcCHHHHHHHHHHH--hCHHHHHhccHHHHHHHhCCCHHHHHHHHHH
Confidence 445788889999999999987543 332 3579999999999999999766554
No 473
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=44.28 E-value=38 Score=33.65 Aligned_cols=34 Identities=15% Similarity=0.392 Sum_probs=28.1
Q ss_pred HHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHH
Q 009567 251 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 284 (532)
Q Consensus 251 le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~ 284 (532)
+......|...+|++||..|.|+..|++.+++..
T Consensus 103 i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~ 136 (231)
T PRK12427 103 TNDAIREIAKRLGHEPNFEEISAELNLTAEEYQE 136 (231)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHH
Confidence 3456677888899999999999999999877744
No 474
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=44.24 E-value=1.8e+02 Score=28.99 Aligned_cols=25 Identities=20% Similarity=0.320 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHh
Q 009567 393 HSPDKEDLARRVGITVEKLERLIFI 417 (532)
Q Consensus 393 r~Pt~eEIA~~lgis~e~v~~ll~~ 417 (532)
..-+..|||+.+|+++..|...+..
T Consensus 220 ~g~s~~eIA~~l~is~~tV~~~~~r 244 (257)
T PRK08583 220 ENLSQKETGERLGISQMHVSRLQRQ 244 (257)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3568999999999999999887653
No 475
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=44.12 E-value=71 Score=30.84 Aligned_cols=47 Identities=9% Similarity=0.132 Sum_probs=30.3
Q ss_pred HHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 460 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 460 ~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.+..++.. ++.-..||..-. .. ...|-+|||+.|||+...||+++.+
T Consensus 13 ~l~~~~~~-~~~~~~Vl~~L~--~~-g~~tdeeLA~~Lgi~~~~VRk~L~~ 59 (178)
T PRK06266 13 VLFEIMEG-DEEGFEVLKALI--KK-GEVTDEEIAEQTGIKLNTVRKILYK 59 (178)
T ss_pred HHHHHhcC-CccHhHHHHHHH--Hc-CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 34444432 444455555322 22 4799999999999999999866543
No 476
>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=44.07 E-value=23 Score=38.87 Aligned_cols=46 Identities=24% Similarity=0.453 Sum_probs=31.6
Q ss_pred HHhcCCHHHHHHHHH---------HhcccCC---CCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 464 LLTLLNPKERCIVRL---------RFGIEDG---KPKSLSEVGNIFGLSKERVRQLES 509 (532)
Q Consensus 464 ~L~~L~~rER~VL~L---------RyGL~~~---e~~Tl~EIAe~LgISrerVRqie~ 509 (532)
++..|.-|...+++. -|+..|. .++|+++||+.+|++.+||++..+
T Consensus 283 li~~i~~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdiA~~lglheSTVSRav~ 340 (429)
T TIGR02395 283 LIKALEQREETLLKVAEAIVEHQKDFFLGGPAALKPLTLREVAEELGLHESTISRAIN 340 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccCcCCcHHHHHHHhCCCccchhhhhc
Confidence 345566666655432 2222222 799999999999999999987654
No 477
>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=43.86 E-value=37 Score=30.59 Aligned_cols=40 Identities=35% Similarity=0.470 Sum_probs=35.5
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
..|.+.++.|+.+.- .+.|..|||..++++-.-||.+..-
T Consensus 39 ~~l~pE~~~Il~lC~-----~~~SVAEiAA~L~lPlgVvrVLvsD 78 (114)
T PF05331_consen 39 AGLGPEHRAILELCR-----RPLSVAEIAARLGLPLGVVRVLVSD 78 (114)
T ss_pred CCCCHHHHHHHHHHC-----CCccHHHHHHhhCCCchhhhhhHHH
Confidence 578999999999987 5999999999999999999887653
No 478
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=43.84 E-value=91 Score=28.98 Aligned_cols=50 Identities=10% Similarity=0.170 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccc
Q 009567 375 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSM 424 (532)
Q Consensus 375 ~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSL 424 (532)
..-..+.+++.-|...-++..|..||++.+|++++.|..++...+-.++-
T Consensus 27 ~~e~~f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGRL~~~~ 76 (137)
T TIGR03826 27 EEEREFEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGRLQLKH 76 (137)
T ss_pred HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCCeeccC
Confidence 33344444555555556667899999999999999999999877655443
No 479
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=43.73 E-value=34 Score=33.91 Aligned_cols=29 Identities=34% Similarity=0.492 Sum_probs=23.8
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 485 GKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 485 ~e~~-Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
|+.+ |-.|+|+.+|||+.||| +|+..|..
T Consensus 26 G~~LPsE~eL~~~~~VSR~TvR----~Al~~L~~ 55 (240)
T PRK09764 26 GDALPTESALQTEFGVSRVTVR----QALRQLVE 55 (240)
T ss_pred CCcCCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 3555 89999999999999998 67777754
No 480
>PRK13502 transcriptional activator RhaR; Provisional
Probab=43.72 E-value=3.5e+02 Score=27.04 Aligned_cols=25 Identities=4% Similarity=-0.045 Sum_probs=21.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHh
Q 009567 393 HSPDKEDLARRVGITVEKLERLIFI 417 (532)
Q Consensus 393 r~Pt~eEIA~~lgis~e~v~~ll~~ 417 (532)
...+.+++|..+|+|+..+..+...
T Consensus 191 ~~~~~~~lA~~~~iS~~~L~r~fk~ 215 (282)
T PRK13502 191 CPFALDAFCQQEQCSERVLRQQFRA 215 (282)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3568899999999999999888763
No 481
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=43.65 E-value=17 Score=31.45 Aligned_cols=24 Identities=13% Similarity=0.329 Sum_probs=21.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRA 511 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rA 511 (532)
+|..|+|+.+|||..++|.++...
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye~~G 25 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDRLG 25 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCC
Confidence 689999999999999999997755
No 482
>PRK14999 histidine utilization repressor; Provisional
Probab=43.60 E-value=35 Score=33.86 Aligned_cols=28 Identities=29% Similarity=0.387 Sum_probs=23.3
Q ss_pred CCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 486 KPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 486 e~~-Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
+.+ |-.|+|+.+|||+.||| +||..|..
T Consensus 34 ~~LPsE~eLa~~~gVSR~TVR----~Al~~L~~ 62 (241)
T PRK14999 34 DRIPSEAELVAQYGFSRMTIN----RALRELTD 62 (241)
T ss_pred CcCCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 445 99999999999999998 57777754
No 483
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=43.53 E-value=17 Score=32.31 Aligned_cols=27 Identities=22% Similarity=0.356 Sum_probs=24.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRALYR 514 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rALkK 514 (532)
+|..|+|+.+|||..++|-++...|-.
T Consensus 1 ~~I~eva~~~gvs~~tLRyYe~~GLl~ 27 (123)
T cd04770 1 MKIGELAKAAGVSPDTIRYYERIGLLP 27 (123)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 588999999999999999999887654
No 484
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=43.39 E-value=50 Score=28.47 Aligned_cols=24 Identities=25% Similarity=0.306 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLES 509 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~ 509 (532)
-++|.++||..||+|.+.|.+++.
T Consensus 22 ~~ls~~~ia~dL~~s~~~le~vL~ 45 (89)
T PF10078_consen 22 SGLSLEQIAADLGTSPEHLEQVLN 45 (89)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHc
Confidence 579999999999999999987764
No 485
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=43.38 E-value=34 Score=32.65 Aligned_cols=25 Identities=16% Similarity=0.290 Sum_probs=23.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
.++|++|+|+.+|+|+.+|+++++.
T Consensus 19 ~glt~~elA~~~gis~~~is~~E~g 43 (185)
T PRK09943 19 QGLSQRRAAELSGLTHSAISTIEQD 43 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 6799999999999999999999974
No 486
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=43.37 E-value=31 Score=34.99 Aligned_cols=38 Identities=13% Similarity=0.164 Sum_probs=28.4
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567 470 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510 (532)
Q Consensus 470 ~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r 510 (532)
+|...|+.+-- .....+..|+|+.||||+.|||+-+..
T Consensus 5 eR~~~Il~~L~---~~~~v~v~eLa~~l~VS~~TIRRDL~~ 42 (256)
T PRK10434 5 QRQAAILEYLQ---KQGKTSVEELAQYFDTTGTTIRKDLVI 42 (256)
T ss_pred HHHHHHHHHHH---HcCCEEHHHHHHHHCCCHHHHHHHHHH
Confidence 45566665533 224689999999999999999977554
No 487
>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=43.37 E-value=2.1e+02 Score=24.40 Aligned_cols=34 Identities=15% Similarity=0.178 Sum_probs=26.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l 519 (532)
-|+++++|.+.+......+..+...-+..|+..+
T Consensus 56 ~G~~l~~I~~~l~~~~~~~~~~l~~~~~~l~~~i 89 (96)
T cd04768 56 LGFSLAEIKELLDTEMEELTAMLLEKKQAIQQKI 89 (96)
T ss_pred cCCCHHHHHHHHhcCcHHHHHHHHHHHHHHHHHH
Confidence 5899999999999876667776666666666654
No 488
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=43.29 E-value=18 Score=31.91 Aligned_cols=26 Identities=31% Similarity=0.261 Sum_probs=23.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRALY 513 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rALk 513 (532)
+|..|+|+.+|||..+||.++..++-
T Consensus 1 y~Ige~A~~~gvs~~tlR~ye~~GLl 26 (107)
T cd01111 1 YSISQLALDAGVSVHIVRDYLLRGLL 26 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999987654
No 489
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=43.04 E-value=34 Score=27.21 Aligned_cols=19 Identities=26% Similarity=0.401 Sum_probs=17.4
Q ss_pred CHHHHHHHhCCCHHHHHHH
Q 009567 489 SLSEVGNIFGLSKERVRQL 507 (532)
Q Consensus 489 Tl~EIAe~LgISrerVRqi 507 (532)
+...+|+.||||+.+|.++
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 490
>PF12085 DUF3562: Protein of unknown function (DUF3562); InterPro: IPR021945 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 62 to 84 amino acids in length. This protein has two completely conserved residues (A and Y) that may be functionally important.
Probab=42.95 E-value=48 Score=27.03 Aligned_cols=41 Identities=17% Similarity=0.292 Sum_probs=32.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhhhh
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLL 531 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~yldll 531 (532)
-.+++||+..|++.+.|++.....+..|+.- -...+|+-+|
T Consensus 8 e~i~~iA~~t~~P~e~V~~my~dt~~~l~~~---ARV~DYl~lf 48 (66)
T PF12085_consen 8 EVIRSIAEETGTPAETVRRMYDDTMRELSSG---ARVHDYLPLF 48 (66)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHHHHcC---CchhhhHHHH
Confidence 3578999999999999999999988888653 3455666554
No 491
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=42.94 E-value=36 Score=33.46 Aligned_cols=28 Identities=32% Similarity=0.335 Sum_probs=23.4
Q ss_pred CCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 486 KPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 486 e~~-Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
+.+ |-.|+|+.+|||+.||| +|+..|..
T Consensus 23 ~~LPsE~eLa~~~~VSR~TVR----~Al~~L~~ 51 (230)
T TIGR02018 23 HRIPSEHELVAQYGCSRMTVN----RALRELTD 51 (230)
T ss_pred CcCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 444 99999999999999998 67777755
No 492
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=42.90 E-value=29 Score=34.11 Aligned_cols=27 Identities=26% Similarity=0.432 Sum_probs=23.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 487 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 487 ~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
=-|-.|+|+.+|||+.||| +||..|..
T Consensus 32 LPsE~eLa~~~~VSR~TvR----~Al~~L~~ 58 (238)
T TIGR02325 32 LPAEMQLAERFGVNRHTVR----RAIAALVE 58 (238)
T ss_pred CcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 3499999999999999998 67777765
No 493
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=42.88 E-value=18 Score=32.60 Aligned_cols=27 Identities=26% Similarity=0.336 Sum_probs=23.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRALYR 514 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rALkK 514 (532)
|+..|+|+.+|||..++|.++...|=.
T Consensus 1 m~IgevA~~~gvs~~tLRyYe~~GLl~ 27 (127)
T cd04784 1 MKIGELAKKTGCSVETIRYYEKEGLLP 27 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 578999999999999999999887653
No 494
>PRK08359 transcription factor; Validated
Probab=42.75 E-value=34 Score=33.11 Aligned_cols=35 Identities=20% Similarity=0.284 Sum_probs=28.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH-------HHHHHHHHhh
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESR-------ALYRLKQSLG 520 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~r-------ALkKLR~~l~ 520 (532)
.++|++|+|+.+|+++.+|+.|+.. .+.+|-+.+.
T Consensus 97 kglSQeeLA~~lgvs~stI~~iE~G~~~Ps~~~l~kLak~l~ 138 (176)
T PRK08359 97 SGLSYEELSHEVGLSVNDLRRIAHGEYEPTIKEAKKLERYFK 138 (176)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCCCcCCCHHHHHHHHHHhC
Confidence 6899999999999999999999763 4555555544
No 495
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=42.73 E-value=67 Score=26.99 Aligned_cols=44 Identities=16% Similarity=0.303 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCC
Q 009567 349 YWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMP 421 (532)
Q Consensus 349 ~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~ 421 (532)
.+|+...+.+.+.. |+..+.++||..+|++.++|..++......
T Consensus 22 ~~~L~r~LLr~LA~-----------------------------G~PVt~~~LA~a~g~~~e~v~~~L~~~p~t 65 (77)
T PF12324_consen 22 FAWLLRPLLRLLAK-----------------------------GQPVTVEQLAAALGWPVEEVRAALAAMPDT 65 (77)
T ss_dssp HHHHHHHHHHHHTT-----------------------------TS-B-HHHHHHHHT--HHHHHHHHHH-TTS
T ss_pred cHHHHHHHHHHHHc-----------------------------CCCcCHHHHHHHHCCCHHHHHHHHHhCCCc
No 496
>COG4709 Predicted membrane protein [Function unknown]
Probab=42.30 E-value=67 Score=31.49 Aligned_cols=58 Identities=19% Similarity=0.157 Sum_probs=45.4
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHhc--cc--CCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567 455 QLMRQHVRNLLTLLNPKERCIVRLRFG--IE--DGKPKSLSEVGNIFGLSKERVRQLESRAL 512 (532)
Q Consensus 455 ~~l~~~L~~~L~~L~~rER~VL~LRyG--L~--~~e~~Tl~EIAe~LgISrerVRqie~rAL 512 (532)
.+....|+..|+.||+.+|.=+...|- ++ +..++|-.||+..||=+.+-.+++..+..
T Consensus 4 ~efL~eL~~yL~~Lp~~~r~e~m~dyeehF~~a~~~GksE~EI~~~LG~P~eiA~ei~s~~~ 65 (195)
T COG4709 4 TEFLNELEQYLEGLPREERREIMYDYEEHFREAQEAGKSEEEIAKDLGDPKEIAAEILSERG 65 (195)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhhhhcCCCHHHHHHHhCCHHHHHHHHHHHcc
Confidence 345567899999999999887766542 12 23689999999999999999988877654
No 497
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=42.17 E-value=67 Score=27.53 Aligned_cols=26 Identities=19% Similarity=0.238 Sum_probs=23.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009567 486 KPKSLSEVGNIFGLSKERVRQLESRA 511 (532)
Q Consensus 486 e~~Tl~EIAe~LgISrerVRqie~rA 511 (532)
++.|+++||+.+|+|+.+..++.++.
T Consensus 20 ~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 20 QPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 78999999999999999998887775
No 498
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. 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, an
Probab=42.12 E-value=18 Score=32.20 Aligned_cols=26 Identities=27% Similarity=0.400 Sum_probs=23.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRALY 513 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rALk 513 (532)
||..|+|+.+|||..++|.+++..+-
T Consensus 1 m~IgevA~~~gvs~~tlRyYe~~GLl 26 (120)
T cd04781 1 LDIAEVARQSGLPASTLRYYEEKGLI 26 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999987654
No 499
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=42.02 E-value=18 Score=32.84 Aligned_cols=25 Identities=24% Similarity=0.352 Sum_probs=22.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567 488 KSLSEVGNIFGLSKERVRQLESRAL 512 (532)
Q Consensus 488 ~Tl~EIAe~LgISrerVRqie~rAL 512 (532)
|+..|+|+.+|||..++|.++..+|
T Consensus 1 m~IgE~A~~~gvs~~TLRyYE~~GL 25 (133)
T cd04787 1 MKVKELANAAGVTPDTVRFYTRIGL 25 (133)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999987654
No 500
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=41.70 E-value=31 Score=33.98 Aligned_cols=27 Identities=37% Similarity=0.454 Sum_probs=23.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567 487 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517 (532)
Q Consensus 487 ~~Tl~EIAe~LgISrerVRqie~rALkKLR~ 517 (532)
=-|-.|+|+.||||+.||| +|+..|..
T Consensus 24 LPsE~eLa~~~gVSR~TVR----~Al~~L~~ 50 (233)
T TIGR02404 24 LPSEHELMDQYGASRETVR----KALNLLTE 50 (233)
T ss_pred CcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 3489999999999999997 67777755
Done!