Query 010327
Match_columns 513
No_of_seqs 333 out of 1824
Neff 6.1
Searched_HMMs 46136
Date Thu Mar 28 23:14:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010327.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010327hhsearch_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 4E-64 8.7E-69 528.6 36.0 314 195-512 54-411 (415)
2 PRK07406 RNA polymerase sigma 100.0 3.3E-60 7.1E-65 495.5 36.0 310 200-513 62-373 (373)
3 PRK05949 RNA polymerase sigma 100.0 7.8E-60 1.7E-64 486.5 36.1 309 198-512 15-325 (327)
4 TIGR02997 Sig70-cyanoRpoD RNA 100.0 1.8E-58 3.8E-63 471.1 35.3 296 201-500 1-298 (298)
5 PRK07405 RNA polymerase sigma 100.0 4.5E-58 9.8E-63 471.9 36.0 309 198-512 5-315 (317)
6 COG0568 RpoD DNA-directed RNA 100.0 3E-58 6.5E-63 470.6 29.7 313 197-512 5-341 (342)
7 PRK05901 RNA polymerase sigma 100.0 7.4E-58 1.6E-62 491.8 31.6 304 193-512 203-508 (509)
8 PRK07921 RNA polymerase sigma 100.0 4.1E-56 8.9E-61 458.0 32.1 298 199-512 24-323 (324)
9 PRK09210 RNA polymerase sigma 100.0 6.1E-54 1.3E-58 449.3 31.5 273 197-512 92-366 (367)
10 PRK05658 RNA polymerase sigma 100.0 1.5E-50 3.3E-55 449.2 29.2 237 273-512 379-617 (619)
11 TIGR02393 RpoD_Cterm RNA polym 100.0 7.5E-47 1.6E-51 373.5 25.6 235 275-512 1-237 (238)
12 PRK05657 RNA polymerase sigma 100.0 2.5E-44 5.4E-49 371.2 30.0 269 198-509 50-320 (325)
13 PRK06596 RNA polymerase factor 100.0 1.9E-43 4.1E-48 358.5 29.3 258 200-504 13-281 (284)
14 PRK07500 rpoH2 RNA polymerase 100.0 2.9E-43 6.4E-48 357.9 29.2 262 198-504 3-278 (289)
15 PRK07122 RNA polymerase sigma 100.0 7.3E-43 1.6E-47 350.7 26.2 221 273-502 39-262 (264)
16 TIGR02392 rpoH_proteo alternat 100.0 2.2E-42 4.8E-47 348.0 28.9 255 202-503 2-268 (270)
17 TIGR02394 rpoS_proteo RNA poly 100.0 2.1E-40 4.6E-45 336.0 29.7 265 199-506 11-277 (285)
18 PRK07408 RNA polymerase sigma 100.0 2E-40 4.3E-45 331.5 27.4 227 269-504 20-252 (256)
19 PRK05911 RNA polymerase sigma 100.0 1E-39 2.3E-44 326.6 25.5 228 270-503 19-253 (257)
20 TIGR02850 spore_sigG RNA polym 100.0 3.8E-39 8.2E-44 321.6 28.7 241 210-502 10-253 (254)
21 COG1191 FliA DNA-directed RNA 100.0 1.3E-38 2.7E-43 315.1 25.6 225 267-503 17-244 (247)
22 PRK08215 sporulation sigma fac 100.0 1.1E-37 2.3E-42 311.7 27.7 240 211-502 14-256 (258)
23 PRK06288 RNA polymerase sigma 100.0 1.9E-36 4.2E-41 304.3 28.0 249 211-504 7-261 (268)
24 TIGR02885 spore_sigF RNA polym 100.0 3.2E-36 6.9E-41 295.8 26.3 224 267-502 4-230 (231)
25 TIGR02941 Sigma_B RNA polymera 100.0 2.4E-35 5.1E-40 294.0 28.4 225 271-503 26-253 (255)
26 TIGR02980 SigBFG RNA polymeras 100.0 4.2E-35 9.1E-40 286.9 25.4 222 272-502 1-225 (227)
27 PRK07670 RNA polymerase sigma 100.0 2.6E-34 5.7E-39 286.2 26.7 229 269-503 17-249 (251)
28 PRK12427 flagellar biosynthesi 100.0 3.9E-34 8.6E-39 282.2 25.8 212 275-501 16-229 (231)
29 TIGR02479 FliA_WhiG RNA polyme 100.0 3.5E-34 7.6E-39 280.3 24.9 218 279-502 1-222 (224)
30 PRK05572 sporulation sigma fac 100.0 1E-33 2.2E-38 282.2 27.7 242 208-503 6-250 (252)
31 PRK08583 RNA polymerase sigma 100.0 2.9E-33 6.4E-38 279.3 27.2 227 270-504 25-254 (257)
32 PRK06986 fliA flagellar biosyn 100.0 7.8E-33 1.7E-37 273.0 24.9 226 271-503 5-232 (236)
33 PRK05803 sporulation sigma fac 100.0 5.1E-27 1.1E-31 231.3 22.8 207 202-504 17-228 (233)
34 PRK08301 sporulation sigma fac 99.9 1.8E-23 3.9E-28 205.8 22.9 180 268-503 46-230 (234)
35 TIGR02846 spore_sigmaK RNA pol 99.9 2.7E-23 5.7E-28 204.2 23.0 179 268-502 42-225 (227)
36 TIGR02835 spore_sigmaE RNA pol 99.9 3.4E-22 7.5E-27 197.2 21.8 184 265-503 43-230 (234)
37 PRK08295 RNA polymerase factor 99.9 3.7E-21 8.1E-26 184.9 19.6 186 264-504 14-203 (208)
38 PRK09648 RNA polymerase sigma 99.9 1.6E-20 3.5E-25 178.5 19.7 171 265-503 15-187 (189)
39 PRK05602 RNA polymerase sigma 99.9 1.4E-20 3E-25 178.5 18.0 170 263-505 9-178 (186)
40 TIGR02952 Sig70_famx2 RNA poly 99.9 2.6E-20 5.6E-25 172.9 19.3 167 265-502 2-169 (170)
41 TIGR02859 spore_sigH RNA polym 99.9 2.1E-20 4.6E-25 178.1 18.9 185 263-502 8-196 (198)
42 PRK12513 RNA polymerase sigma 99.9 1.2E-20 2.6E-25 180.1 17.0 176 262-506 14-190 (194)
43 PRK09652 RNA polymerase sigma 99.9 1.7E-20 3.7E-25 175.1 17.4 173 267-503 3-176 (182)
44 TIGR02948 SigW_bacill RNA poly 99.9 2.4E-20 5.3E-25 176.0 17.7 177 263-503 7-184 (187)
45 PRK09646 RNA polymerase sigma 99.8 3.3E-20 7.2E-25 177.5 18.1 170 265-504 21-191 (194)
46 PRK06759 RNA polymerase factor 99.8 3.3E-20 7.2E-25 170.0 16.9 152 272-502 2-153 (154)
47 PRK09641 RNA polymerase sigma 99.8 7.2E-20 1.6E-24 172.8 18.9 176 264-503 8-184 (187)
48 PRK11922 RNA polymerase sigma 99.8 6.8E-20 1.5E-24 180.4 18.9 174 269-505 25-199 (231)
49 PRK12519 RNA polymerase sigma 99.8 9.9E-20 2.1E-24 173.6 18.1 170 264-503 19-189 (194)
50 PRK06811 RNA polymerase factor 99.8 1.1E-19 2.5E-24 173.1 18.4 174 263-505 7-181 (189)
51 PRK13919 putative RNA polymera 99.8 1.6E-19 3.4E-24 170.9 18.3 171 264-503 13-183 (186)
52 TIGR02939 RpoE_Sigma70 RNA pol 99.8 4.1E-19 8.8E-24 168.0 19.2 177 264-504 10-187 (190)
53 PRK11924 RNA polymerase sigma 99.8 3.5E-19 7.5E-24 165.8 18.3 170 265-504 4-174 (179)
54 PRK09640 RNA polymerase sigma 99.8 2.2E-19 4.9E-24 170.8 16.3 159 271-503 23-182 (188)
55 PRK11923 algU RNA polymerase s 99.8 8.4E-19 1.8E-23 167.0 20.0 176 264-503 10-186 (193)
56 PRK12514 RNA polymerase sigma 99.8 4.5E-19 9.6E-24 167.0 17.9 169 264-503 9-177 (179)
57 PRK12524 RNA polymerase sigma 99.8 5.2E-19 1.1E-23 169.5 18.5 171 263-504 15-185 (196)
58 PRK12538 RNA polymerase sigma 99.8 4.2E-19 9.1E-24 175.6 18.0 169 263-504 52-220 (233)
59 TIGR02984 Sig-70_plancto1 RNA 99.8 6.4E-19 1.4E-23 166.4 18.4 180 270-502 3-187 (189)
60 PRK12531 RNA polymerase sigma 99.8 5.4E-19 1.2E-23 169.1 17.9 174 265-506 18-192 (194)
61 PRK12542 RNA polymerase sigma 99.8 1.7E-19 3.7E-24 171.0 14.1 169 269-506 4-173 (185)
62 PRK12534 RNA polymerase sigma 99.8 4.2E-19 9.1E-24 168.3 16.5 170 265-503 16-185 (187)
63 PRK12526 RNA polymerase sigma 99.8 7.1E-19 1.5E-23 170.2 18.2 173 265-504 29-202 (206)
64 PRK12537 RNA polymerase sigma 99.8 6.9E-19 1.5E-23 166.6 17.6 168 263-502 12-180 (182)
65 PRK12515 RNA polymerase sigma 99.8 9.6E-19 2.1E-23 166.4 17.4 172 263-506 11-182 (189)
66 TIGR02937 sigma70-ECF RNA poly 99.8 1.4E-18 3E-23 155.6 17.0 155 275-502 2-157 (158)
67 PRK12536 RNA polymerase sigma 99.8 2E-18 4.3E-23 163.3 17.6 167 264-504 11-178 (181)
68 PRK09643 RNA polymerase sigma 99.8 2.9E-18 6.3E-23 164.1 18.4 167 263-504 16-183 (192)
69 PRK12543 RNA polymerase sigma 99.8 2E-18 4.4E-23 163.0 17.0 164 270-504 3-166 (179)
70 TIGR02985 Sig70_bacteroi1 RNA 99.8 2.3E-18 4.9E-23 157.4 16.5 158 275-502 2-160 (161)
71 PRK09638 RNA polymerase sigma 99.8 1.9E-18 4.1E-23 161.9 16.1 166 264-503 8-174 (176)
72 TIGR02895 spore_sigI RNA polym 99.8 4.7E-18 1E-22 166.5 18.3 120 267-388 3-126 (218)
73 PRK12512 RNA polymerase sigma 99.8 6E-18 1.3E-22 160.0 18.5 167 265-505 13-181 (184)
74 PRK09415 RNA polymerase factor 99.8 4.1E-18 8.9E-23 161.0 17.3 163 270-503 12-175 (179)
75 TIGR02954 Sig70_famx3 RNA poly 99.8 4.7E-18 1E-22 158.6 17.4 163 263-503 5-167 (169)
76 PRK09649 RNA polymerase sigma 99.8 4.8E-18 1E-22 161.7 17.1 169 264-508 14-183 (185)
77 PRK09645 RNA polymerase sigma 99.8 6.3E-18 1.4E-22 158.1 17.3 163 270-504 5-167 (173)
78 PRK12522 RNA polymerase sigma 99.8 6.3E-18 1.4E-22 158.5 17.3 164 274-503 3-167 (173)
79 PRK12539 RNA polymerase sigma 99.8 8.7E-18 1.9E-22 159.3 18.4 169 264-504 11-180 (184)
80 TIGR03001 Sig-70_gmx1 RNA poly 99.8 5.8E-18 1.2E-22 168.7 17.9 179 262-511 27-217 (244)
81 TIGR02989 Sig-70_gvs1 RNA poly 99.8 6E-18 1.3E-22 155.6 16.6 157 274-502 1-158 (159)
82 PRK12518 RNA polymerase sigma 99.8 6.9E-18 1.5E-22 158.0 15.7 168 265-504 2-169 (175)
83 TIGR02999 Sig-70_X6 RNA polyme 99.8 1.2E-17 2.6E-22 157.4 17.0 168 264-502 7-181 (183)
84 PRK12520 RNA polymerase sigma 99.8 1.3E-17 2.9E-22 158.9 16.8 180 275-507 3-183 (191)
85 PRK12529 RNA polymerase sigma 99.8 1.3E-17 2.8E-22 157.6 16.3 168 268-503 7-175 (178)
86 COG1595 RpoE DNA-directed RNA 99.8 3E-17 6.4E-22 155.6 18.8 170 265-504 6-176 (182)
87 PRK09647 RNA polymerase sigma 99.8 2.9E-17 6.2E-22 159.1 17.8 165 270-505 24-188 (203)
88 PRK12533 RNA polymerase sigma 99.8 4.2E-17 9E-22 159.7 18.9 169 270-504 14-183 (216)
89 TIGR02947 SigH_actino RNA poly 99.8 1.6E-17 3.5E-22 158.5 15.0 173 270-504 7-180 (193)
90 TIGR02983 SigE-fam_strep RNA p 99.7 3.1E-17 6.7E-22 151.7 15.9 157 270-503 2-158 (162)
91 PRK12516 RNA polymerase sigma 99.7 4.3E-17 9.2E-22 155.7 16.8 159 271-505 7-166 (187)
92 PRK12541 RNA polymerase sigma 99.7 6.1E-17 1.3E-21 149.9 17.3 158 271-502 2-159 (161)
93 PRK09642 RNA polymerase sigma 99.7 2.8E-17 6E-22 151.9 14.4 153 281-504 2-155 (160)
94 PRK12523 RNA polymerase sigma 99.7 5.2E-17 1.1E-21 152.3 15.5 163 269-503 5-167 (172)
95 PRK12528 RNA polymerase sigma 99.7 1E-16 2.2E-21 148.4 17.2 157 274-502 4-160 (161)
96 PRK09644 RNA polymerase sigma 99.7 6.3E-17 1.4E-21 150.6 15.9 154 276-504 3-157 (165)
97 PRK08241 RNA polymerase factor 99.7 1.4E-16 3.1E-21 165.0 19.4 187 263-502 8-200 (339)
98 PRK12535 RNA polymerase sigma 99.7 1.4E-16 3.1E-21 153.3 17.7 167 264-504 15-182 (196)
99 PRK09639 RNA polymerase sigma 99.7 1.3E-16 2.9E-21 147.9 16.7 158 273-504 2-160 (166)
100 TIGR02943 Sig70_famx1 RNA poly 99.7 1.1E-16 2.4E-21 152.8 16.5 177 277-506 5-182 (188)
101 PRK12547 RNA polymerase sigma 99.7 1.8E-16 3.8E-21 147.7 16.8 156 273-504 5-161 (164)
102 PRK12532 RNA polymerase sigma 99.7 1.8E-16 4E-21 151.5 16.7 180 277-508 8-189 (195)
103 TIGR02960 SigX5 RNA polymerase 99.7 2.3E-16 5E-21 162.1 18.4 182 271-504 2-191 (324)
104 PRK12545 RNA polymerase sigma 99.7 1.7E-16 3.8E-21 153.0 16.4 178 278-506 12-190 (201)
105 TIGR02950 SigM_subfam RNA poly 99.7 9E-17 1.9E-21 147.0 13.1 150 281-502 2-152 (154)
106 PRK12530 RNA polymerase sigma 99.7 2.6E-16 5.7E-21 150.2 16.7 173 277-504 10-183 (189)
107 PRK12544 RNA polymerase sigma 99.7 5.3E-16 1.1E-20 150.6 16.9 180 276-507 20-200 (206)
108 PRK07037 extracytoplasmic-func 99.7 5E-16 1.1E-20 143.7 15.9 155 278-503 2-157 (163)
109 PRK09637 RNA polymerase sigma 99.7 7.5E-16 1.6E-20 146.3 16.9 152 276-504 3-155 (181)
110 PRK09651 RNA polymerase sigma 99.7 9.9E-16 2.1E-20 143.9 17.1 159 271-501 7-165 (172)
111 PRK12540 RNA polymerase sigma 99.7 8.6E-16 1.9E-20 146.1 16.5 158 274-507 5-163 (182)
112 PRK12527 RNA polymerase sigma 99.7 6.9E-16 1.5E-20 142.6 15.1 152 281-504 2-154 (159)
113 PRK12517 RNA polymerase sigma 99.7 1.1E-15 2.4E-20 146.0 16.4 160 269-504 18-177 (188)
114 TIGR02959 SigZ RNA polymerase 99.7 1.4E-15 3E-20 142.7 16.1 146 281-503 2-148 (170)
115 PRK12546 RNA polymerase sigma 99.7 1.7E-15 3.7E-20 144.9 16.4 156 273-504 7-162 (188)
116 PRK12511 RNA polymerase sigma 99.7 2.8E-15 6E-20 142.7 16.6 153 276-503 6-159 (182)
117 PRK12525 RNA polymerase sigma 99.7 3.7E-15 7.9E-20 139.4 16.5 159 273-503 8-166 (168)
118 PRK09636 RNA polymerase sigma 99.6 4.3E-15 9.4E-20 151.3 16.3 159 274-503 4-163 (293)
119 PRK09047 RNA polymerase factor 99.6 7.3E-15 1.6E-19 135.4 13.9 152 299-505 2-156 (161)
120 PRK06704 RNA polymerase factor 99.6 2.1E-14 4.6E-19 141.8 15.6 158 263-503 7-164 (228)
121 TIGR02957 SigX4 RNA polymerase 99.6 3.1E-14 6.7E-19 144.5 16.0 155 278-503 1-156 (281)
122 PRK09635 sigI RNA polymerase s 99.6 4.9E-14 1.1E-18 143.9 16.5 160 274-502 5-165 (290)
123 PRK09191 two-component respons 99.5 7.8E-13 1.7E-17 130.4 14.1 136 275-504 2-137 (261)
124 TIGR03209 P21_Cbot clostridium 99.4 1.4E-12 3E-17 118.4 12.1 136 276-490 1-142 (142)
125 PRK08311 putative RNA polymera 99.4 1.1E-11 2.3E-16 123.3 17.3 80 265-347 9-90 (237)
126 PF07638 Sigma70_ECF: ECF sigm 99.4 1.9E-11 4.1E-16 116.8 15.9 175 263-503 6-183 (185)
127 PF04545 Sigma70_r4: Sigma-70, 99.2 4.3E-11 9.4E-16 90.4 6.7 50 448-501 1-50 (50)
128 PF04542 Sigma70_r2: Sigma-70 99.1 1.8E-10 4E-15 91.5 7.9 66 279-347 1-66 (71)
129 PF04539 Sigma70_r3: Sigma-70 99.0 1.5E-09 3.1E-14 89.2 7.1 75 360-434 1-76 (78)
130 PF08281 Sigma70_r4_2: Sigma-7 98.9 3.3E-09 7.1E-14 81.1 7.3 54 442-499 1-54 (54)
131 PRK06930 positive control sigm 98.5 5.6E-07 1.2E-11 85.3 8.9 65 436-504 99-163 (170)
132 cd06171 Sigma70_r4 Sigma70, re 98.3 2.5E-06 5.4E-11 63.2 7.1 54 443-500 2-55 (55)
133 PRK00118 putative DNA-binding 98.2 3.2E-06 6.8E-11 73.9 6.9 57 444-504 10-66 (104)
134 TIGR00721 tfx DNA-binding prot 98.1 4.3E-06 9.2E-11 76.6 6.2 54 451-509 6-59 (137)
135 PRK03975 tfx putative transcri 98.1 7E-06 1.5E-10 75.5 6.0 50 450-504 5-54 (141)
136 PF04297 UPF0122: Putative hel 98.0 3.4E-05 7.3E-10 67.0 8.1 55 444-502 9-64 (101)
137 PRK04217 hypothetical protein; 97.9 1.4E-05 3E-10 70.6 5.3 55 450-508 41-95 (110)
138 smart00421 HTH_LUXR helix_turn 97.9 4.4E-05 9.6E-10 57.5 6.3 50 450-504 2-51 (58)
139 TIGR01636 phage_rinA phage tra 97.8 0.00011 2.5E-09 66.9 9.9 61 440-502 71-131 (134)
140 PF07374 DUF1492: Protein of u 97.7 0.00011 2.5E-09 63.6 8.0 56 440-499 43-99 (100)
141 PF00140 Sigma70_r1_2: Sigma-7 97.7 1.1E-05 2.3E-10 57.6 1.2 33 200-232 1-33 (37)
142 PF00196 GerE: Bacterial regul 97.7 0.0001 2.3E-09 57.2 6.3 52 450-506 2-53 (58)
143 cd06170 LuxR_C_like C-terminal 97.7 0.00017 3.7E-09 54.4 6.9 49 452-505 1-49 (57)
144 TIGR03879 near_KaiC_dom probab 97.5 0.00018 4E-09 58.9 5.6 46 445-494 9-55 (73)
145 TIGR01321 TrpR trp operon repr 97.5 0.00012 2.7E-09 62.7 4.7 50 443-492 23-76 (94)
146 PF04967 HTH_10: HTH DNA bindi 97.5 0.00034 7.3E-09 53.9 6.6 48 452-499 1-51 (53)
147 PRK15201 fimbriae regulatory p 97.3 0.00066 1.4E-08 64.5 7.0 52 451-507 133-184 (198)
148 PRK15411 rcsA colanic acid cap 97.3 0.00048 1E-08 67.0 6.1 50 451-505 137-186 (207)
149 PRK10840 transcriptional regul 97.2 0.00056 1.2E-08 65.9 6.1 52 450-506 149-200 (216)
150 TIGR03020 EpsA transcriptional 97.2 0.00065 1.4E-08 68.3 6.6 54 449-507 188-241 (247)
151 PRK11475 DNA-binding transcrip 97.2 0.00055 1.2E-08 66.9 6.0 52 450-506 133-184 (207)
152 TIGR03541 reg_near_HchA LuxR f 97.2 0.00072 1.6E-08 67.0 6.8 53 449-506 169-221 (232)
153 PRK13719 conjugal transfer tra 97.2 0.00088 1.9E-08 65.8 6.7 56 446-506 138-193 (217)
154 PRK10100 DNA-binding transcrip 97.2 0.0008 1.7E-08 66.1 6.5 52 450-506 154-205 (216)
155 PF13936 HTH_38: Helix-turn-he 97.1 0.00064 1.4E-08 50.2 4.0 41 450-494 3-43 (44)
156 PRK13870 transcriptional regul 97.1 0.00095 2.1E-08 66.4 6.1 51 451-506 173-223 (234)
157 PRK10188 DNA-binding transcrip 97.1 0.001 2.3E-08 66.3 6.3 52 451-507 179-230 (240)
158 COG2771 CsgD DNA-binding HTH d 97.0 0.0027 5.9E-08 49.3 6.8 54 450-508 3-56 (65)
159 COG4566 TtrR Response regulato 97.0 0.0027 5.8E-08 61.1 7.9 65 440-509 131-195 (202)
160 COG2197 CitB Response regulato 96.9 0.0019 4E-08 63.3 6.3 52 450-506 147-198 (211)
161 PF02001 DUF134: Protein of un 96.8 0.0023 4.9E-08 56.2 5.6 48 451-502 41-88 (106)
162 PRK09483 response regulator; P 96.8 0.0021 4.6E-08 60.7 5.9 50 450-504 147-196 (217)
163 PRK05658 RNA polymerase sigma 96.8 0.0028 6.1E-08 71.6 7.8 38 195-232 98-135 (619)
164 COG3413 Predicted DNA binding 96.8 0.0028 6.1E-08 62.1 6.7 51 451-501 155-208 (215)
165 PF12645 HTH_16: Helix-turn-he 96.7 0.0067 1.5E-07 48.7 6.9 60 264-323 3-65 (65)
166 PRK01381 Trp operon repressor; 96.7 0.0016 3.4E-08 56.4 3.3 50 441-490 21-74 (99)
167 COG2739 Uncharacterized protei 96.6 0.0036 7.7E-08 54.1 5.0 46 452-501 18-63 (105)
168 PRK09390 fixJ response regulat 96.6 0.0082 1.8E-07 55.1 7.7 59 444-507 134-192 (202)
169 PRK15369 two component system 96.5 0.0073 1.6E-07 55.7 6.9 50 450-504 148-197 (211)
170 COG1356 tfx Transcriptional re 96.4 0.0019 4E-08 57.9 2.5 49 452-505 9-57 (143)
171 TIGR01637 phage_arpU phage tra 96.4 0.016 3.4E-07 52.4 8.6 57 442-502 69-128 (132)
172 PRK10651 transcriptional regul 96.4 0.0072 1.6E-07 56.5 6.3 52 450-506 154-205 (216)
173 PRK10403 transcriptional regul 95.9 0.016 3.5E-07 53.9 6.3 55 450-509 152-206 (215)
174 PRK15320 transcriptional activ 95.9 0.014 3E-07 56.6 5.7 51 447-502 160-210 (251)
175 COG1342 Predicted DNA-binding 95.8 0.016 3.5E-07 49.6 5.1 48 451-502 33-80 (99)
176 PRK10360 DNA-binding transcrip 95.8 0.025 5.4E-07 52.5 6.8 55 450-509 136-190 (196)
177 PRK13558 bacterio-opsin activa 95.4 0.026 5.5E-07 63.8 6.5 52 449-500 605-659 (665)
178 PRK09935 transcriptional regul 95.3 0.034 7.3E-07 51.9 6.0 49 451-504 149-197 (210)
179 PRK09958 DNA-binding transcrip 95.2 0.037 8.1E-07 51.6 6.0 51 449-504 141-191 (204)
180 PF04539 Sigma70_r3: Sigma-70 95.2 0.043 9.4E-07 44.7 5.4 40 231-270 3-42 (78)
181 COG4941 Predicted RNA polymera 95.2 0.49 1.1E-05 49.5 14.0 58 440-501 109-166 (415)
182 TIGR02531 yecD_yerC TrpR-relat 95.1 0.044 9.6E-07 46.6 5.4 37 450-492 35-71 (88)
183 PRK04841 transcriptional regul 95.0 0.046 1E-06 63.7 6.9 53 450-507 837-889 (903)
184 PF05263 DUF722: Protein of un 94.9 0.1 2.2E-06 47.6 7.3 57 441-499 71-127 (130)
185 PF13613 HTH_Tnp_4: Helix-turn 94.7 0.069 1.5E-06 40.8 5.0 48 451-501 2-49 (53)
186 PF13384 HTH_23: Homeodomain-l 94.7 0.028 6.1E-07 41.8 2.8 33 458-495 9-41 (50)
187 PF02796 HTH_7: Helix-turn-hel 94.5 0.038 8.2E-07 40.8 3.1 33 456-493 11-43 (45)
188 PRK09210 RNA polymerase sigma 94.1 0.48 1E-05 50.3 11.7 130 233-402 217-348 (367)
189 PF13412 HTH_24: Winged helix- 94.1 0.13 2.9E-06 38.0 5.3 41 452-495 1-41 (48)
190 cd00569 HTH_Hin_like Helix-tur 94.0 0.1 2.2E-06 34.4 4.2 36 452-491 6-41 (42)
191 PRK15418 transcriptional regul 94.0 0.072 1.6E-06 55.5 4.9 36 458-497 20-55 (318)
192 PF01726 LexA_DNA_bind: LexA D 93.7 0.079 1.7E-06 42.5 3.7 45 449-493 1-48 (65)
193 PF00325 Crp: Bacterial regula 93.6 0.073 1.6E-06 36.8 2.8 26 471-500 2-27 (32)
194 TIGR02393 RpoD_Cterm RNA polym 93.4 1.1 2.3E-05 44.5 11.9 36 233-268 88-123 (238)
195 PF09862 DUF2089: Protein of u 93.4 0.18 4E-06 44.8 5.7 50 448-501 30-79 (113)
196 PRK05901 RNA polymerase sigma 93.2 1 2.2E-05 50.1 12.4 37 233-269 359-395 (509)
197 PRK07921 RNA polymerase sigma 93.1 1.1 2.4E-05 46.9 12.0 36 233-268 174-209 (324)
198 PF06530 Phage_antitermQ: Phag 92.7 0.53 1.1E-05 42.5 7.8 52 447-502 58-109 (125)
199 PF04218 CENP-B_N: CENP-B N-te 92.3 0.13 2.9E-06 39.4 2.9 40 451-494 6-45 (53)
200 PF13404 HTH_AsnC-type: AsnC-t 92.2 0.36 7.8E-06 35.3 5.0 39 453-494 2-40 (42)
201 PF10668 Phage_terminase: Phag 92.1 0.25 5.4E-06 39.1 4.3 39 454-494 7-45 (60)
202 PF06056 Terminase_5: Putative 91.8 0.32 7E-06 38.1 4.6 26 470-495 12-37 (58)
203 PF13730 HTH_36: Helix-turn-he 91.7 0.51 1.1E-05 35.7 5.6 46 451-500 2-50 (55)
204 PF13518 HTH_28: Helix-turn-he 91.7 0.26 5.6E-06 36.6 3.9 27 470-496 11-37 (52)
205 PRK07598 RNA polymerase sigma 91.6 1.4 3E-05 47.8 10.7 37 364-400 112-148 (415)
206 PRK10430 DNA-binding transcrip 91.5 0.35 7.7E-06 47.4 5.7 48 451-498 158-205 (239)
207 smart00351 PAX Paired Box doma 91.2 0.49 1.1E-05 42.6 5.8 42 452-497 18-59 (125)
208 PRK07408 RNA polymerase sigma 90.7 0.97 2.1E-05 45.4 8.1 37 233-269 114-150 (256)
209 COG2390 DeoR Transcriptional r 90.5 0.34 7.4E-06 50.7 4.7 35 459-497 18-52 (321)
210 PRK07406 RNA polymerase sigma 90.3 2.7 5.9E-05 44.9 11.5 36 233-268 224-259 (373)
211 PF01726 LexA_DNA_bind: LexA D 90.2 0.86 1.9E-05 36.5 5.8 43 360-402 6-49 (65)
212 PHA00675 hypothetical protein 90.1 0.56 1.2E-05 38.8 4.6 41 450-493 21-61 (78)
213 PF08279 HTH_11: HTH domain; 90.0 0.47 1E-05 35.9 4.0 39 455-495 1-39 (55)
214 PRK05911 RNA polymerase sigma 89.8 3.9 8.5E-05 41.1 11.7 36 234-269 112-147 (257)
215 PF02650 HTH_WhiA: WhiA C-term 89.7 0.65 1.4E-05 39.3 4.9 44 449-495 35-80 (85)
216 PRK05949 RNA polymerase sigma 89.5 8.6 0.00019 40.3 14.2 37 233-269 179-215 (327)
217 PHA02591 hypothetical protein; 89.2 0.62 1.4E-05 38.7 4.3 24 470-493 58-81 (83)
218 PF12802 MarR_2: MarR family; 89.1 0.78 1.7E-05 35.2 4.7 43 451-494 2-44 (62)
219 PF01022 HTH_5: Bacterial regu 89.1 0.79 1.7E-05 33.9 4.5 37 454-494 2-38 (47)
220 COG1191 FliA DNA-directed RNA 88.8 7.8 0.00017 39.2 12.7 38 232-269 110-147 (247)
221 COG2909 MalT ATP-dependent tra 88.7 0.55 1.2E-05 54.4 5.0 50 452-506 832-881 (894)
222 PRK06288 RNA polymerase sigma 88.6 10 0.00023 38.1 13.8 37 233-269 119-155 (268)
223 PRK07122 RNA polymerase sigma 88.2 6.4 0.00014 39.8 11.9 36 234-269 129-164 (264)
224 cd00131 PAX Paired Box domain 87.9 1.2 2.6E-05 40.3 5.8 42 452-497 18-59 (128)
225 TIGR02885 spore_sigF RNA polym 87.4 3.9 8.4E-05 40.1 9.5 34 236-269 101-134 (231)
226 TIGR02850 spore_sigG RNA polym 86.7 8.4 0.00018 38.5 11.7 36 235-270 123-158 (254)
227 PF01418 HTH_6: Helix-turn-hel 86.6 1.5 3.2E-05 36.0 5.1 52 442-493 4-56 (77)
228 PF12840 HTH_20: Helix-turn-he 86.5 2.3 5E-05 33.0 5.9 37 454-493 10-46 (61)
229 PF13542 HTH_Tnp_ISL3: Helix-t 86.1 1.7 3.7E-05 32.4 4.8 25 471-495 27-51 (52)
230 COG3355 Predicted transcriptio 86.0 2.7 5.8E-05 38.2 6.8 51 444-500 17-67 (126)
231 PRK10046 dpiA two-component re 86.0 0.77 1.7E-05 44.6 3.7 39 451-493 161-199 (225)
232 PF13463 HTH_27: Winged helix 85.9 1.5 3.2E-05 34.3 4.6 42 452-495 1-42 (68)
233 PF00356 LacI: Bacterial regul 85.8 0.78 1.7E-05 34.3 2.8 22 473-494 1-22 (46)
234 PHA02547 55 RNA polymerase sig 85.8 2.6 5.7E-05 40.1 6.8 62 283-347 46-110 (179)
235 smart00344 HTH_ASNC helix_turn 85.7 1.7 3.6E-05 37.4 5.3 41 452-495 1-41 (108)
236 PF01047 MarR: MarR family; I 85.6 1.3 2.8E-05 33.8 4.0 41 452-495 1-41 (59)
237 PF01710 HTH_Tnp_IS630: Transp 85.3 9.2 0.0002 34.0 9.9 28 469-500 69-96 (119)
238 smart00550 Zalpha Z-DNA-bindin 85.2 2 4.3E-05 34.5 5.1 23 471-493 22-44 (68)
239 PF01325 Fe_dep_repress: Iron 84.9 1.2 2.5E-05 35.1 3.5 45 452-500 2-47 (60)
240 PF01978 TrmB: Sugar-specific 84.8 0.61 1.3E-05 37.0 1.9 40 451-493 5-44 (68)
241 PF01371 Trp_repressor: Trp re 84.4 1.2 2.5E-05 38.0 3.5 46 452-498 27-75 (87)
242 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 84.2 2 4.2E-05 32.9 4.3 39 451-493 4-42 (50)
243 PF12728 HTH_17: Helix-turn-he 84.1 1.1 2.4E-05 33.4 3.0 24 472-495 2-25 (51)
244 PF03444 HrcA_DNA-bdg: Winged 84.0 1.9 4.1E-05 36.0 4.5 43 451-493 1-45 (78)
245 PRK07405 RNA polymerase sigma 84.0 10 0.00022 39.6 11.1 36 233-268 169-204 (317)
246 PRK07670 RNA polymerase sigma 83.9 14 0.00031 36.7 11.8 37 234-270 111-147 (251)
247 TIGR02997 Sig70-cyanoRpoD RNA 83.9 15 0.00034 37.6 12.3 35 234-268 163-197 (298)
248 smart00342 HTH_ARAC helix_turn 83.7 12 0.00025 29.5 9.1 73 379-494 1-74 (84)
249 PRK12423 LexA repressor; Provi 83.6 1.6 3.4E-05 42.4 4.6 48 450-501 2-52 (202)
250 PRK07500 rpoH2 RNA polymerase 83.4 9.7 0.00021 39.1 10.5 26 378-403 244-269 (289)
251 PF13011 LZ_Tnp_IS481: leucine 83.4 2.5 5.4E-05 35.8 5.1 43 451-496 8-50 (85)
252 PRK00423 tfb transcription ini 83.1 42 0.00091 34.9 15.2 177 280-500 122-305 (310)
253 TIGR00498 lexA SOS regulatory 82.5 1.8 4E-05 41.5 4.6 44 450-493 2-48 (199)
254 cd04762 HTH_MerR-trunc Helix-T 82.4 1.3 2.8E-05 31.7 2.7 25 472-496 1-25 (49)
255 PRK11083 DNA-binding response 82.3 1.9 4.2E-05 40.5 4.6 50 451-501 154-208 (228)
256 PRK13413 mpi multiple promoter 82.3 2.2 4.7E-05 41.2 5.0 35 455-494 161-195 (200)
257 TIGR01610 phage_O_Nterm phage 82.2 4.8 0.00011 34.4 6.6 49 449-501 20-73 (95)
258 TIGR02479 FliA_WhiG RNA polyme 82.1 21 0.00044 34.8 11.9 37 233-269 84-120 (224)
259 TIGR01764 excise DNA binding d 81.9 1.6 3.5E-05 31.4 3.1 24 472-495 2-25 (49)
260 PRK11179 DNA-binding transcrip 81.9 2.8 6.1E-05 38.8 5.4 41 451-494 6-46 (153)
261 PRK10710 DNA-binding transcrip 81.8 2 4.4E-05 40.9 4.6 50 451-501 160-214 (240)
262 COG3415 Transposase and inacti 81.7 2.5 5.4E-05 39.0 4.8 28 469-496 19-46 (138)
263 PRK10336 DNA-binding transcrip 81.4 1.9 4.2E-05 40.3 4.3 50 451-501 149-203 (219)
264 smart00345 HTH_GNTR helix_turn 81.3 2.7 5.8E-05 31.5 4.2 28 470-501 18-46 (60)
265 PF02954 HTH_8: Bacterial regu 81.1 2.1 4.6E-05 31.0 3.4 38 454-494 4-41 (42)
266 PF08220 HTH_DeoR: DeoR-like h 80.9 2.4 5.3E-05 32.8 3.9 35 456-493 2-36 (57)
267 PRK15479 transcriptional regul 80.6 2.7 5.8E-05 39.3 4.9 50 451-501 148-202 (221)
268 TIGR02337 HpaR homoprotocatech 80.2 6.9 0.00015 34.2 7.1 48 443-493 15-64 (118)
269 cd04761 HTH_MerR-SF Helix-Turn 80.0 1.4 3E-05 32.2 2.1 25 472-496 1-25 (49)
270 PRK11169 leucine-responsive tr 79.7 2.9 6.3E-05 39.2 4.8 40 452-494 12-51 (164)
271 PF13744 HTH_37: Helix-turn-he 79.5 2.7 5.9E-05 34.7 4.0 31 459-493 23-53 (80)
272 PF09339 HTH_IclR: IclR helix- 79.5 2.5 5.4E-05 31.8 3.5 25 469-493 16-40 (52)
273 smart00420 HTH_DEOR helix_turn 79.3 4 8.7E-05 29.6 4.5 25 470-494 13-37 (53)
274 COG0856 Orotate phosphoribosyl 78.9 2.6 5.6E-05 40.5 4.0 41 458-503 10-50 (203)
275 PF13551 HTH_29: Winged helix- 78.3 3.8 8.3E-05 34.9 4.8 25 470-494 10-35 (112)
276 PF01381 HTH_3: Helix-turn-hel 78.3 2.2 4.8E-05 31.9 2.9 25 470-494 8-32 (55)
277 COG1522 Lrp Transcriptional re 78.2 4 8.6E-05 37.1 5.1 42 450-494 4-45 (154)
278 TIGR02147 Fsuc_second hypothet 78.0 41 0.0009 34.5 12.8 97 378-482 136-240 (271)
279 PRK05572 sporulation sigma fac 77.9 29 0.00063 34.6 11.6 32 235-266 121-152 (252)
280 PHA01976 helix-turn-helix prot 77.9 3.5 7.6E-05 32.2 4.0 26 469-494 13-38 (67)
281 PHA00542 putative Cro-like pro 77.7 3.1 6.6E-05 34.7 3.8 26 470-495 30-55 (82)
282 PRK00215 LexA repressor; Valid 77.1 3.9 8.5E-05 39.4 5.0 44 452-495 2-48 (205)
283 TIGR03787 marine_sort_RR prote 76.9 3.7 8E-05 38.8 4.7 50 451-501 156-207 (227)
284 PF13551 HTH_29: Winged helix- 76.6 6.7 0.00015 33.3 5.8 24 381-404 14-37 (112)
285 PF13411 MerR_1: MerR HTH fami 76.6 1.3 2.8E-05 34.9 1.2 25 472-496 1-25 (69)
286 PRK08215 sporulation sigma fac 76.5 35 0.00076 34.1 11.8 33 236-268 127-159 (258)
287 PF13560 HTH_31: Helix-turn-he 76.4 3.2 6.9E-05 32.4 3.4 26 469-494 12-37 (64)
288 smart00419 HTH_CRP helix_turn_ 75.9 3.8 8.3E-05 29.4 3.5 27 471-501 8-34 (48)
289 PRK13239 alkylmercury lyase; P 75.9 5.3 0.00011 39.3 5.4 29 376-404 33-61 (206)
290 TIGR02787 codY_Gpos GTP-sensin 75.6 10 0.00022 38.3 7.4 56 442-501 167-224 (251)
291 cd06571 Bac_DnaA_C C-terminal 75.6 7.3 0.00016 32.8 5.6 32 470-501 43-75 (90)
292 COG2522 Predicted transcriptio 75.5 4.6 0.0001 36.3 4.5 24 470-493 21-44 (119)
293 TIGR02844 spore_III_D sporulat 75.5 5.3 0.00011 33.5 4.6 35 455-493 7-41 (80)
294 PF08280 HTH_Mga: M protein tr 75.4 4.3 9.3E-05 31.6 3.8 37 455-494 6-42 (59)
295 TIGR02154 PhoB phosphate regul 75.2 1.9 4E-05 40.5 2.1 51 451-502 154-209 (226)
296 TIGR00122 birA_repr_reg BirA b 75.0 6.3 0.00014 31.3 4.8 25 470-494 12-36 (69)
297 TIGR02941 Sigma_B RNA polymera 74.8 47 0.001 33.0 12.2 33 235-267 119-151 (255)
298 PRK11511 DNA-binding transcrip 74.4 34 0.00074 30.5 10.0 40 363-402 9-48 (127)
299 cd00092 HTH_CRP helix_turn_hel 74.3 5 0.00011 31.0 4.0 29 469-501 23-51 (67)
300 PF07750 GcrA: GcrA cell cycle 74.2 3.6 7.7E-05 39.0 3.7 38 453-494 4-42 (162)
301 PRK11512 DNA-binding transcrip 73.8 14 0.00029 33.6 7.4 48 444-494 28-77 (144)
302 TIGR01884 cas_HTH CRISPR locus 73.7 7.8 0.00017 37.5 6.0 44 448-494 137-180 (203)
303 TIGR03070 couple_hipB transcri 73.2 5.3 0.00011 29.7 3.8 25 470-494 14-38 (58)
304 PF00046 Homeobox: Homeobox do 73.1 6.6 0.00014 29.7 4.3 50 451-500 6-56 (57)
305 PF13022 HTH_Tnp_1_2: Helix-tu 73.0 9.7 0.00021 35.3 6.0 50 445-494 4-57 (142)
306 COG1510 Predicted transcriptio 73.0 4 8.8E-05 39.0 3.7 30 469-502 39-68 (177)
307 TIGR02980 SigBFG RNA polymeras 72.7 38 0.00083 32.9 10.7 31 236-266 94-124 (227)
308 PF00376 MerR: MerR family reg 72.4 2.3 4.9E-05 30.4 1.5 24 473-496 1-24 (38)
309 PRK11302 DNA-binding transcrip 72.3 9.2 0.0002 38.5 6.4 53 442-494 4-57 (284)
310 PF08765 Mor: Mor transcriptio 71.9 7.8 0.00017 33.9 5.0 43 455-503 62-104 (108)
311 TIGR02612 mob_myst_A mobile my 71.7 7.4 0.00016 36.4 5.1 39 452-494 23-61 (150)
312 TIGR03830 CxxCG_CxxCG_HTH puta 71.6 11 0.00025 33.1 6.1 41 449-495 62-102 (127)
313 PF12324 HTH_15: Helix-turn-he 71.5 9.4 0.0002 31.8 5.0 28 376-403 35-62 (77)
314 cd00090 HTH_ARSR Arsenical Res 71.5 9.2 0.0002 29.3 5.0 37 454-494 7-43 (78)
315 PRK10072 putative transcriptio 71.4 5.3 0.00011 34.6 3.8 26 469-494 44-69 (96)
316 PF13545 HTH_Crp_2: Crp-like h 71.1 4.6 9.9E-05 32.2 3.2 27 471-501 28-54 (76)
317 smart00347 HTH_MARR helix_turn 71.1 9 0.00019 31.5 5.1 44 451-501 7-50 (101)
318 PRK11337 DNA-binding transcrip 71.1 11 0.00023 38.4 6.6 54 440-493 14-68 (292)
319 COG1476 Predicted transcriptio 71.0 5.8 0.00013 32.3 3.7 25 470-494 13-37 (68)
320 smart00418 HTH_ARSR helix_turn 70.9 7.9 0.00017 28.8 4.3 26 469-494 8-33 (66)
321 PF08822 DUF1804: Protein of u 70.6 8.8 0.00019 36.5 5.3 41 454-497 5-45 (165)
322 cd01104 HTH_MlrA-CarA Helix-Tu 70.6 5.3 0.00011 31.2 3.4 23 472-494 1-23 (68)
323 PRK11564 stationary phase indu 70.5 8.9 0.00019 41.3 6.2 51 451-501 10-60 (426)
324 cd07377 WHTH_GntR Winged helix 69.8 8.9 0.00019 29.2 4.5 26 472-501 26-51 (66)
325 TIGR03697 NtcA_cyano global ni 69.6 5 0.00011 37.5 3.6 28 471-502 143-170 (193)
326 CHL00148 orf27 Ycf27; Reviewed 69.5 6.2 0.00013 37.5 4.3 50 451-501 161-217 (240)
327 PRK09413 IS2 repressor TnpA; R 69.2 10 0.00022 33.8 5.3 34 459-496 21-54 (121)
328 PF08535 KorB: KorB domain; I 69.2 4.7 0.0001 34.1 3.0 24 470-493 2-25 (93)
329 cd04764 HTH_MlrA-like_sg1 Heli 68.8 6.1 0.00013 31.0 3.4 24 472-495 1-24 (67)
330 PRK15482 transcriptional regul 68.5 12 0.00027 37.9 6.4 52 443-494 5-57 (285)
331 COG2345 Predicted transcriptio 67.8 9.4 0.0002 37.9 5.1 26 469-494 23-48 (218)
332 PF01527 HTH_Tnp_1: Transposas 67.7 4.6 9.9E-05 32.3 2.5 28 469-496 21-48 (76)
333 PF14493 HTH_40: Helix-turn-he 67.7 8.3 0.00018 32.5 4.2 31 469-499 11-41 (91)
334 PRK11557 putative DNA-binding 67.4 10 0.00023 38.1 5.6 50 445-494 3-53 (278)
335 COG1654 BirA Biotin operon rep 67.2 11 0.00023 31.6 4.6 30 468-501 16-45 (79)
336 PRK10219 DNA-binding transcrip 67.0 55 0.0012 27.9 9.3 38 365-402 7-44 (107)
337 PRK03573 transcriptional regul 66.7 23 0.00049 32.0 7.2 49 444-494 19-69 (144)
338 PRK10870 transcriptional repre 66.5 28 0.0006 33.1 8.0 51 443-494 42-94 (176)
339 COG2944 Predicted transcriptio 66.5 12 0.00025 33.0 4.9 40 449-494 41-80 (104)
340 PRK01905 DNA-binding protein F 66.2 22 0.00047 29.2 6.3 36 456-494 38-73 (77)
341 PRK00135 scpB segregation and 66.0 38 0.00082 32.9 8.8 104 369-485 9-118 (188)
342 PRK06986 fliA flagellar biosyn 66.0 90 0.0019 30.6 11.8 34 236-269 99-132 (236)
343 smart00422 HTH_MERR helix_turn 66.0 4.6 9.9E-05 31.7 2.1 25 472-496 1-25 (70)
344 smart00354 HTH_LACI helix_turn 65.8 6.1 0.00013 31.7 2.8 22 472-493 1-22 (70)
345 COG2973 TrpR Trp operon repres 65.8 11 0.00024 32.8 4.5 45 452-500 38-85 (103)
346 PF14394 DUF4423: Domain of un 65.5 13 0.00028 35.4 5.5 97 377-481 37-141 (171)
347 PRK09863 putative frv operon r 65.3 42 0.00092 37.8 10.5 104 378-500 16-121 (584)
348 COG1737 RpiR Transcriptional r 65.2 14 0.00029 37.8 6.0 53 441-493 5-58 (281)
349 TIGR00647 MG103 conserved hypo 65.1 13 0.00028 38.3 5.7 44 449-495 225-274 (279)
350 cd00086 homeodomain Homeodomai 65.1 16 0.00035 27.3 5.0 51 451-501 6-57 (59)
351 TIGR01889 Staph_reg_Sar staphy 64.9 16 0.00035 31.7 5.6 44 451-494 22-66 (109)
352 COG4367 Uncharacterized protei 64.4 15 0.00033 31.3 5.0 55 451-512 2-60 (97)
353 cd04763 HTH_MlrA-like Helix-Tu 64.3 8.3 0.00018 30.4 3.3 23 472-494 1-23 (68)
354 smart00346 HTH_ICLR helix_turn 64.2 15 0.00032 30.2 5.0 26 470-495 19-44 (91)
355 PF02082 Rrf2: Transcriptional 63.9 12 0.00026 30.9 4.3 25 470-494 24-48 (83)
356 PF04963 Sigma54_CBD: Sigma-54 63.6 2.2 4.8E-05 41.3 -0.1 94 380-499 53-146 (194)
357 PRK06596 RNA polymerase factor 63.3 93 0.002 31.8 11.7 25 378-402 247-271 (284)
358 COG5484 Uncharacterized conser 63.2 8.3 0.00018 39.0 3.8 26 469-494 17-42 (279)
359 TIGR02607 antidote_HigA addict 63.1 14 0.00031 29.5 4.6 26 469-494 16-41 (78)
360 PF00165 HTH_AraC: Bacterial r 62.8 11 0.00024 26.9 3.4 27 469-495 6-32 (42)
361 PF00392 GntR: Bacterial regul 62.3 9.1 0.0002 29.9 3.2 28 469-500 21-49 (64)
362 COG1508 RpoN DNA-directed RNA 61.4 31 0.00067 37.8 8.0 55 439-493 283-352 (444)
363 PRK10141 DNA-binding transcrip 61.3 20 0.00044 32.1 5.6 45 446-493 7-52 (117)
364 COG3877 Uncharacterized protei 60.3 17 0.00036 32.1 4.6 49 449-501 39-87 (122)
365 PF06971 Put_DNA-bind_N: Putat 59.9 20 0.00044 27.3 4.6 46 354-399 3-48 (50)
366 PRK14101 bifunctional glucokin 59.9 20 0.00044 40.9 6.7 55 440-494 342-397 (638)
367 PRK10411 DNA-binding transcrip 59.8 15 0.00033 36.6 5.1 41 454-497 4-44 (240)
368 COG1318 Predicted transcriptio 58.9 9.6 0.00021 36.4 3.2 26 470-495 60-85 (182)
369 PF04703 FaeA: FaeA-like prote 58.9 9.4 0.0002 30.4 2.7 25 470-494 14-38 (62)
370 PF01710 HTH_Tnp_IS630: Transp 58.1 12 0.00026 33.3 3.6 25 469-493 16-40 (119)
371 PF11662 DUF3263: Protein of u 57.7 35 0.00075 28.5 5.9 47 451-497 2-48 (77)
372 PF08784 RPA_C: Replication pr 57.5 17 0.00036 31.1 4.3 43 451-493 44-87 (102)
373 PF12844 HTH_19: Helix-turn-he 57.5 11 0.00023 29.2 2.8 26 469-494 10-35 (64)
374 PF12116 SpoIIID: Stage III sp 57.1 11 0.00024 31.6 2.9 42 456-499 6-47 (82)
375 PRK12427 flagellar biosynthesi 56.8 25 0.00053 34.8 6.0 36 234-269 103-138 (231)
376 COG1846 MarR Transcriptional r 56.6 20 0.00043 30.4 4.7 40 452-494 20-59 (126)
377 smart00389 HOX Homeodomain. DN 56.6 25 0.00055 26.1 4.7 48 451-498 6-54 (56)
378 PRK13918 CRP/FNR family transc 56.3 12 0.00025 35.4 3.4 27 471-501 149-175 (202)
379 PF00440 TetR_N: Bacterial reg 56.0 13 0.00028 27.2 2.9 23 469-491 14-36 (47)
380 COG4367 Uncharacterized protei 56.0 28 0.0006 29.8 5.1 39 367-405 10-49 (97)
381 cd04768 HTH_BmrR-like Helix-Tu 56.0 8.3 0.00018 32.9 2.1 26 472-497 1-26 (96)
382 PF05225 HTH_psq: helix-turn-h 55.9 28 0.0006 25.7 4.6 23 472-494 17-39 (45)
383 PRK10572 DNA-binding transcrip 55.7 2.3E+02 0.0049 28.4 14.4 38 365-402 185-222 (290)
384 PRK09726 antitoxin HipB; Provi 55.7 16 0.00035 30.6 3.8 25 470-494 24-48 (88)
385 PF13556 HTH_30: PucR C-termin 55.0 27 0.00059 27.0 4.7 34 469-502 10-43 (59)
386 PF06322 Phage_NinH: Phage Nin 54.9 18 0.00038 28.9 3.5 27 459-492 11-37 (64)
387 PRK13777 transcriptional regul 54.7 49 0.0011 32.0 7.4 40 451-493 42-81 (185)
388 KOG0484 Transcription factor P 54.5 15 0.00033 32.3 3.4 52 450-505 27-78 (125)
389 smart00530 HTH_XRE Helix-turn- 54.2 16 0.00034 25.5 3.1 25 470-494 9-33 (56)
390 PF05043 Mga: Mga helix-turn-h 54.1 8.5 0.00018 31.8 1.8 33 469-501 28-60 (87)
391 cd04775 HTH_Cfa-like Helix-Tur 53.6 9.3 0.0002 33.0 2.1 26 472-497 2-27 (102)
392 TIGR00180 parB_part ParB-like 53.6 21 0.00044 34.2 4.6 43 450-494 101-143 (187)
393 cd01392 HTH_LacI Helix-turn-he 53.5 8.8 0.00019 28.3 1.7 20 475-494 1-20 (52)
394 TIGR02944 suf_reg_Xantho FeS a 53.4 20 0.00044 31.9 4.3 25 469-493 23-47 (130)
395 cd01107 HTH_BmrR Helix-Turn-He 52.9 10 0.00022 33.1 2.2 26 472-497 1-26 (108)
396 cd04773 HTH_TioE_rpt2 Second H 52.5 10 0.00022 33.2 2.1 25 472-496 1-25 (108)
397 PRK09706 transcriptional repre 52.5 18 0.00039 32.6 3.9 26 469-494 16-41 (135)
398 PRK04984 fatty acid metabolism 52.3 19 0.00041 35.3 4.3 29 469-501 28-57 (239)
399 PRK09744 DNA-binding transcrip 52.0 19 0.00041 29.8 3.4 19 473-491 12-30 (75)
400 TIGR03826 YvyF flagellar opero 51.8 34 0.00074 31.6 5.5 50 359-408 26-75 (137)
401 PRK09391 fixK transcriptional 51.6 16 0.00034 35.9 3.5 28 471-502 179-206 (230)
402 PF13443 HTH_26: Cro/C1-type H 51.5 14 0.00031 28.3 2.7 26 470-495 9-34 (63)
403 PF02042 RWP-RK: RWP-RK domain 51.3 33 0.00072 26.4 4.5 29 459-493 9-37 (52)
404 smart00352 POU Found in Pit-Oc 51.2 23 0.00049 29.4 3.8 25 469-493 22-52 (75)
405 PRK10434 srlR DNA-bindng trans 50.8 22 0.00047 35.9 4.5 42 454-499 5-46 (256)
406 PF12793 SgrR_N: Sugar transpo 50.8 23 0.0005 31.5 4.2 34 460-494 9-42 (115)
407 cd04766 HTH_HspR Helix-Turn-He 50.8 11 0.00024 31.7 2.0 26 472-497 2-27 (91)
408 cd04782 HTH_BltR Helix-Turn-He 50.7 11 0.00025 32.1 2.1 25 472-496 1-25 (97)
409 cd04789 HTH_Cfa Helix-Turn-Hel 50.5 12 0.00025 32.4 2.2 26 472-497 2-27 (102)
410 cd01105 HTH_GlnR-like Helix-Tu 50.4 12 0.00026 31.4 2.2 25 472-496 2-26 (88)
411 PRK13509 transcriptional repre 50.4 24 0.00052 35.4 4.7 38 454-494 5-42 (251)
412 PF07037 DUF1323: Putative tra 50.2 18 0.00038 32.7 3.3 23 472-494 1-23 (122)
413 PRK13503 transcriptional activ 50.1 1.3E+02 0.0028 29.8 10.0 36 367-402 175-210 (278)
414 PRK10955 DNA-binding transcrip 50.1 12 0.00026 35.3 2.4 46 451-501 156-210 (232)
415 cd04772 HTH_TioE_rpt1 First He 50.1 12 0.00026 32.2 2.2 26 472-497 1-26 (99)
416 TIGR00738 rrf2_super rrf2 fami 50.1 31 0.00067 30.6 5.0 26 469-494 23-48 (132)
417 cd04788 HTH_NolA-AlbR Helix-Tu 50.0 12 0.00025 32.0 2.1 26 472-497 1-26 (96)
418 PF06413 Neugrin: Neugrin; In 49.9 26 0.00056 35.0 4.8 42 451-493 10-51 (225)
419 cd00093 HTH_XRE Helix-turn-hel 49.7 27 0.00058 24.4 3.8 25 470-494 11-35 (58)
420 PF12298 Bot1p: Eukaryotic mit 49.7 31 0.00068 33.0 5.1 39 452-493 17-55 (172)
421 TIGR02698 CopY_TcrY copper tra 49.6 41 0.0009 30.4 5.7 44 451-497 1-48 (130)
422 COG2512 Predicted membrane-ass 49.6 23 0.00049 36.1 4.4 42 450-493 191-232 (258)
423 PHA00738 putative HTH transcri 49.6 35 0.00075 30.3 4.9 37 454-493 12-48 (108)
424 cd04774 HTH_YfmP Helix-Turn-He 49.4 12 0.00026 32.1 2.1 26 472-497 1-26 (96)
425 PRK03902 manganese transport t 49.3 30 0.00064 31.4 4.8 26 469-494 20-45 (142)
426 cd04765 HTH_MlrA-like_sg2 Heli 49.3 20 0.00042 31.0 3.4 23 472-494 1-23 (99)
427 cd01109 HTH_YyaN Helix-Turn-He 49.1 12 0.00027 32.7 2.2 26 472-497 1-26 (113)
428 TIGR02394 rpoS_proteo RNA poly 49.1 2.6E+02 0.0057 28.3 12.2 32 238-269 139-170 (285)
429 PRK11753 DNA-binding transcrip 49.1 18 0.0004 34.2 3.6 28 471-502 168-195 (211)
430 PRK11161 fumarate/nitrate redu 48.9 18 0.00038 35.2 3.4 28 471-502 184-211 (235)
431 PF00292 PAX: 'Paired box' dom 48.8 30 0.00065 31.5 4.6 33 458-495 25-57 (125)
432 cd04780 HTH_MerR-like_sg5 Heli 48.4 13 0.00028 31.8 2.1 25 472-496 1-25 (95)
433 PRK06424 transcription factor; 48.2 22 0.00049 33.0 3.8 26 469-494 95-120 (144)
434 PRK10681 DNA-binding transcrip 48.0 26 0.00056 35.2 4.6 41 454-498 7-47 (252)
435 TIGR02812 fadR_gamma fatty aci 48.0 24 0.00052 34.5 4.3 30 468-501 26-56 (235)
436 cd01106 HTH_TipAL-Mta Helix-Tu 47.9 13 0.00029 31.9 2.2 25 472-496 1-25 (103)
437 PF02787 CPSase_L_D3: Carbamoy 47.9 1.9E+02 0.004 26.1 9.6 24 471-494 72-95 (123)
438 cd01282 HTH_MerR-like_sg3 Heli 47.9 13 0.00029 32.6 2.2 26 472-497 1-26 (112)
439 cd00592 HTH_MerR-like Helix-Tu 47.7 14 0.0003 31.4 2.2 25 472-496 1-25 (100)
440 cd04769 HTH_MerR2 Helix-Turn-H 47.4 14 0.00029 32.7 2.2 27 472-498 1-27 (116)
441 PRK11414 colanic acid/biofilm 47.4 21 0.00046 34.6 3.8 30 468-501 31-60 (221)
442 cd01279 HTH_HspR-like Helix-Tu 47.1 13 0.00029 31.8 2.0 25 472-496 2-26 (98)
443 PRK14082 hypothetical protein; 47.1 64 0.0014 26.0 5.6 56 272-332 7-62 (65)
444 PRK09990 DNA-binding transcrip 47.0 25 0.00055 34.7 4.3 38 458-501 19-57 (251)
445 cd04777 HTH_MerR-like_sg1 Heli 46.8 14 0.00031 31.9 2.2 26 472-497 1-26 (107)
446 PRK15121 right oriC-binding tr 46.7 2.5E+02 0.0053 28.4 11.5 41 362-402 4-44 (289)
447 TIGR03338 phnR_burk phosphonat 46.6 23 0.00049 34.0 3.8 29 469-501 32-60 (212)
448 cd04783 HTH_MerR1 Helix-Turn-H 46.5 14 0.0003 33.1 2.1 27 472-498 1-27 (126)
449 PRK08359 transcription factor; 46.4 25 0.00054 33.8 3.9 26 469-494 96-121 (176)
450 PF10078 DUF2316: Uncharacteri 46.4 38 0.00083 29.0 4.6 39 452-493 3-45 (89)
451 TIGR00270 conserved hypothetic 46.3 26 0.00056 32.9 3.9 26 469-494 80-105 (154)
452 PF05732 RepL: Firmicute plasm 46.2 46 0.00099 31.5 5.6 54 445-502 46-102 (165)
453 PRK13890 conjugal transfer pro 46.1 24 0.00053 31.5 3.6 26 469-494 16-41 (120)
454 PF08279 HTH_11: HTH domain; 46.1 43 0.00093 25.0 4.5 24 380-403 16-39 (55)
455 PF04967 HTH_10: HTH DNA bindi 46.0 27 0.00058 27.0 3.3 26 378-403 22-47 (53)
456 COG3093 VapI Plasmid maintenan 46.0 30 0.00064 30.5 3.9 35 458-494 12-46 (104)
457 COG1405 SUA7 Transcription ini 45.9 3.6E+02 0.0078 27.9 14.0 28 470-497 250-277 (285)
458 COG1349 GlpR Transcriptional r 45.9 21 0.00046 35.9 3.6 38 453-493 4-41 (253)
459 smart00342 HTH_ARAC helix_turn 45.7 31 0.00068 26.9 3.9 26 471-496 1-26 (84)
460 cd04770 HTH_HMRTR Helix-Turn-H 45.6 15 0.00033 32.5 2.2 27 472-498 1-27 (123)
461 PRK11534 DNA-binding transcrip 45.6 28 0.0006 33.8 4.2 39 457-501 18-56 (224)
462 PF14549 P22_Cro: DNA-binding 45.5 28 0.00061 27.5 3.4 19 473-491 11-29 (60)
463 cd01111 HTH_MerD Helix-Turn-He 45.5 15 0.00033 32.1 2.2 26 472-497 1-26 (107)
464 PRK11050 manganese transport r 45.5 31 0.00066 32.0 4.3 26 469-494 49-74 (152)
465 PF09012 FeoC: FeoC like trans 45.4 19 0.00042 28.6 2.6 26 469-494 12-37 (69)
466 PRK13705 plasmid-partitioning 45.0 26 0.00057 37.6 4.3 56 441-496 3-64 (388)
467 PRK11014 transcriptional repre 45.0 29 0.00062 31.6 4.0 29 469-501 23-51 (141)
468 PRK10421 DNA-binding transcrip 44.8 29 0.00062 34.5 4.3 38 458-501 14-52 (253)
469 PF04545 Sigma70_r4: Sigma-70, 44.6 39 0.00084 24.9 4.0 27 376-402 17-43 (50)
470 COG1321 TroR Mn-dependent tran 44.5 33 0.00072 32.1 4.4 42 452-493 4-46 (154)
471 PRK10161 transcriptional regul 44.5 25 0.00055 33.2 3.7 50 451-501 154-208 (229)
472 PRK09943 DNA-binding transcrip 44.3 28 0.00061 33.0 4.0 26 469-494 18-43 (185)
473 PF07037 DUF1323: Putative tra 44.3 43 0.00093 30.3 4.7 23 381-403 2-24 (122)
474 TIGR02395 rpoN_sigma RNA polym 44.1 28 0.00061 38.0 4.4 47 447-493 282-340 (429)
475 PRK03837 transcriptional regul 44.0 31 0.00068 33.7 4.4 38 458-501 25-63 (241)
476 PF00325 Crp: Bacterial regula 43.8 27 0.00059 24.2 2.7 22 381-402 4-25 (32)
477 cd04767 HTH_HspR-like_MBC Heli 43.8 16 0.00036 32.9 2.1 27 472-498 2-28 (120)
478 PRK10643 DNA-binding transcrip 43.6 26 0.00056 32.6 3.6 47 451-500 149-202 (222)
479 PRK12469 RNA polymerase factor 43.3 34 0.00073 38.0 4.9 46 448-493 334-391 (481)
480 PRK10906 DNA-binding transcrip 43.2 34 0.00075 34.4 4.6 37 454-493 5-41 (252)
481 cd00092 HTH_CRP helix_turn_hel 43.1 70 0.0015 24.4 5.4 24 379-402 25-48 (67)
482 TIGR02392 rpoH_proteo alternat 43.1 1.9E+02 0.0042 29.1 10.0 26 377-402 234-259 (270)
483 cd04781 HTH_MerR-like_sg6 Heli 42.9 17 0.00038 32.2 2.2 26 472-497 1-26 (120)
484 COG2963 Transposase and inacti 42.9 47 0.001 28.9 4.9 44 451-498 7-52 (116)
485 PRK09464 pdhR transcriptional 42.8 32 0.0007 34.0 4.3 38 458-501 22-60 (254)
486 PRK10225 DNA-binding transcrip 42.7 32 0.0007 34.2 4.3 38 458-501 21-59 (257)
487 cd04776 HTH_GnyR Helix-Turn-He 42.4 18 0.00039 32.2 2.2 25 472-496 1-25 (118)
488 PRK04424 fatty acid biosynthes 42.3 38 0.00082 32.5 4.5 37 454-493 7-43 (185)
489 TIGR02404 trehalos_R_Bsub treh 42.2 27 0.00057 34.2 3.5 26 472-501 25-50 (233)
490 PF13542 HTH_Tnp_ISL3: Helix-t 42.1 61 0.0013 23.8 4.7 27 376-402 24-50 (52)
491 PF13412 HTH_24: Winged helix- 42.1 72 0.0016 23.1 5.1 24 379-402 17-40 (48)
492 PF08006 DUF1700: Protein of u 42.1 56 0.0012 30.9 5.6 58 438-495 3-64 (181)
493 PRK06030 hypothetical protein; 42.0 68 0.0015 29.1 5.8 41 455-499 57-97 (124)
494 PRK08583 RNA polymerase sigma 42.0 2.4E+02 0.0052 27.9 10.5 31 237-267 121-151 (257)
495 PF05331 DUF742: Protein of un 42.0 40 0.00087 30.1 4.3 39 450-493 39-77 (114)
496 TIGR02325 C_P_lyase_phnF phosp 41.9 25 0.00054 34.3 3.3 26 472-501 33-58 (238)
497 PF04552 Sigma54_DBD: Sigma-54 41.8 8.6 0.00019 36.3 0.0 47 445-493 25-71 (160)
498 PRK10402 DNA-binding transcrip 41.6 50 0.0011 32.0 5.4 47 452-502 149-196 (226)
499 PF12085 DUF3562: Protein of u 41.0 53 0.0011 26.6 4.3 34 472-505 8-41 (66)
500 COG1481 Uncharacterized protei 40.5 53 0.0011 34.3 5.4 43 449-494 251-295 (308)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=4e-64 Score=528.64 Aligned_cols=314 Identities=31% Similarity=0.489 Sum_probs=290.6
Q ss_pred hhcCCCChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHH--------------------HHHHHHHHHHHhCCCCCHHHH
Q 010327 195 EYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKV--------------------FVQVKEQLQKDLGREPTDVEL 254 (513)
Q Consensus 195 ~~~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~--------------------l~~~~~~l~~~l~r~p~~~e~ 254 (513)
..+.++|+|+.||++|+++|+||++||+.|+++||.++. |+++++.|+..+|++|+..||
T Consensus 54 ~~~~~~d~v~~yl~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ew 133 (415)
T PRK07598 54 RNRRSTDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERW 133 (415)
T ss_pred cCCCCCChHHHHHHhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHH
Confidence 445678999999999999999999999999999999998 889999999999999999999
Q ss_pred HHHcc----------------------CCHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHH
Q 010327 255 AEATN----------------------MSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGV 312 (513)
Q Consensus 255 A~~~~----------------------~s~e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~ 312 (513)
|.++| ++.++|.+.+..|..|+++||.+|++||+++|++|. ++|++++||||||+
T Consensus 134 a~~~~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~---~~g~~~eDLiQEG~ 210 (415)
T PRK07598 134 AKTADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQ---NRGLELLDLVQEGT 210 (415)
T ss_pred HHHhCCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHc---cCCCCHHHHHHHHH
Confidence 95554 556666666677899999999999999999999998 78999999999999
Q ss_pred HHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCC
Q 010327 313 KGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNI 391 (513)
Q Consensus 313 iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgi 391 (513)
+|||+|+++|||++|++|||||+||||++|.++++ ++++||+|.|+.+.+++++++...|.+++||.||.+|||+.+||
T Consensus 211 iGL~ravekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~i 290 (415)
T PRK07598 211 LGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEM 290 (415)
T ss_pred HHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCC
Confidence 99999999999999999999999999999999999 99999999999999999999999999999999999999999999
Q ss_pred CHHHHHHHHHhccCcccccCCCCCchhh-hhccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCC
Q 010327 392 SPERYREVMKASKPILSLHSRHGVTQEE-FINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKG 470 (513)
Q Consensus 392 s~e~v~~~l~~~~~~~SLd~~~~~~~~e-~~d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~ 470 (513)
++++|+.++.....++|||.+++++++. +.+.+. ++..+|++.....++...|..+|+.|||+|+.||.|||||+|++
T Consensus 291 s~~~vr~~l~~~~~~~SLd~~vg~~~d~~l~d~l~-~~~~~pee~~~~~~l~~~L~~~L~~L~~reR~VI~LRygl~d~~ 369 (415)
T PRK07598 291 TPTQVREVLLRVPRSVSLETKVGKDKDTELGDLLE-TDDISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGH 369 (415)
T ss_pred CHHHHHHHHHHccCCcccccccCCCccccHHHhcc-CCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCC
Confidence 9999999999999999999998766554 444443 44456787788888999999999999999999999999999999
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhcc
Q 010327 471 DRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 512 (513)
Q Consensus 471 ~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~~yl 512 (513)
++|++|||+.||||+++||+++++|++|||++.+...|++|+
T Consensus 370 ~~Tl~EIA~~LGvS~erVRqie~rAl~KLR~~~~~~~l~~y~ 411 (415)
T PRK07598 370 TYSLAEIGRALDLSRERVRQIESKALQKLRQPKRRNRIRDYL 411 (415)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHH
Confidence 999999999999999999999999999999999999999996
No 2
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=3.3e-60 Score=495.49 Aligned_cols=310 Identities=34% Similarity=0.539 Sum_probs=291.7
Q ss_pred CChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHHHH
Q 010327 200 TDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKL 279 (513)
Q Consensus 200 ~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~~L 279 (513)
.|.+..||++|+++|+||++||..|++.++.+..++..+.+|+...|++|+..+||.+.|++...|.+.+..|..|++.|
T Consensus 62 ~d~l~~Yl~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~L 141 (373)
T PRK07406 62 EDSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKM 141 (373)
T ss_pred CCHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHHH
Confidence 58899999999999999999999999999999999999999999999999999999999999999999999889999999
Q ss_pred HHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccccch
Q 010327 280 IKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGL 358 (513)
Q Consensus 280 I~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~~ 358 (513)
|.+|+++|+++|++|. +++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++|+ ++++||+|.|+
T Consensus 142 i~~~l~lV~~iA~ry~---~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~ 218 (373)
T PRK07406 142 VQSNLRLVVSIAKKYM---NRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHL 218 (373)
T ss_pred HHHHHHHHHHHHHHHc---CCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHH
Confidence 9999999999999998 7899999999999999999999999999999999999999999999999 89999999999
Q ss_pred hHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh-hhhccccCCCCCCchhhhH
Q 010327 359 ESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVENENQRQ 437 (513)
Q Consensus 359 ~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~-e~~d~l~d~~~~~~ee~~~ 437 (513)
...+++++++...|.+++||.||.+|||+.+|+++++|..++.....++|||.+.+.+++ .+.+.+.++ ..+|++...
T Consensus 219 ~~~~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d~l~d~-~~~pee~~~ 297 (373)
T PRK07406 219 YETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEAD-GETPEDDVA 297 (373)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHHhcCCC-CCCHHHHHH
Confidence 999999999999999999999999999999999999999999988999999999765444 344555443 355777778
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhccC
Q 010327 438 PALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 513 (513)
Q Consensus 438 ~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~~yl~ 513 (513)
...+...|..+|+.||++|+.||.+||||+|++++|++|||+.||||+++|||++.+|++|||++.....|..|+.
T Consensus 298 ~~~~~~~L~~aL~~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~~~~~~~l~~~~~ 373 (373)
T PRK07406 298 KNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYIR 373 (373)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHhC
Confidence 8888999999999999999999999999998889999999999999999999999999999999999999999874
No 3
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00 E-value=7.8e-60 Score=486.51 Aligned_cols=309 Identities=33% Similarity=0.541 Sum_probs=287.7
Q ss_pred CCCChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHH
Q 010327 198 YSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARN 277 (513)
Q Consensus 198 ~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~ 277 (513)
.+.|.+..||++|+++|+||++||..|++.++.+..+++.++.|+..+|++|+..+||.+++++...|...+.+|..|++
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 34699999999999999999999999999999999999999999999999999999999999999888888888889999
Q ss_pred HHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcccccccc
Q 010327 278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPF 356 (513)
Q Consensus 278 ~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~ 356 (513)
.||.+|+++|+++|++|. +++.+++|||||||+|||+|+++|||++|++|+|||+||||++|.+++. ++++||+|.
T Consensus 95 ~Li~~~~~~V~~iA~~y~---~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~ 171 (327)
T PRK05949 95 KMIEANLRLVVAIAKKYQ---KRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPI 171 (327)
T ss_pred HHHHHHHHHHHHHHHHHc---cCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCH
Confidence 999999999999999998 7899999999999999999999999999999999999999999999999 999999999
Q ss_pred chhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh-hhhccccCCCCCCchhh
Q 010327 357 GLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVENENQ 435 (513)
Q Consensus 357 ~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~-e~~d~l~d~~~~~~ee~ 435 (513)
|+...+++++++...+..++||.||.+|||+.+|+++++|..++.....++|||.+.+++++ .+.+.+.+. ..+|++.
T Consensus 172 ~~~~~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~-~~~pe~~ 250 (327)
T PRK05949 172 HITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDE-GPSPDQY 250 (327)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCC-CCCHHHH
Confidence 99999999999999999999999999999999999999999999999999999999865544 344444443 3567877
Q ss_pred hHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhcc
Q 010327 436 RQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 512 (513)
Q Consensus 436 ~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~~yl 512 (513)
.....+...|..+|+.|||+|+.||.+||||+|++++|++|||+.||||+++|||++.+|++|||+ ....|..|+
T Consensus 251 ~~~~~~~~~L~~~L~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~--~~~~l~~~~ 325 (327)
T PRK05949 251 ITQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRR--RRANVKEYL 325 (327)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH--HHHHHHHHH
Confidence 888888999999999999999999999999999999999999999999999999999999999998 346677775
No 4
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=100.00 E-value=1.8e-58 Score=471.10 Aligned_cols=296 Identities=38% Similarity=0.613 Sum_probs=277.0
Q ss_pred ChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHHHHH
Q 010327 201 DLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLI 280 (513)
Q Consensus 201 d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~~LI 280 (513)
|.+..|+++|+.+|+||++||..|++.++.+..+++.++.|+.++|++|+..+||+++|++...+...+..|..|++.||
T Consensus 1 ~~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv 80 (298)
T TIGR02997 1 DLVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMI 80 (298)
T ss_pred CcHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHH
Confidence 46789999999999999999999999999999999999999999999999999999999999888888888899999999
Q ss_pred HHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccccchh
Q 010327 281 KHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLE 359 (513)
Q Consensus 281 ~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~~~ 359 (513)
.+|+++|+++|++|. ++|.+++|||||||+|||+|+++|||++|++|+|||+||||++|.+++. +.+++|+|.++.
T Consensus 81 ~~~lrlV~~iA~~y~---~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~~~~ 157 (298)
T TIGR02997 81 KANLRLVVSVAKKYQ---NRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHIT 157 (298)
T ss_pred HHhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcHHHH
Confidence 999999999999999 7899999999999999999999999999999999999999999999999 899999999999
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh-hhhccccCCCCCCchhhhHH
Q 010327 360 SVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVENENQRQP 438 (513)
Q Consensus 360 ~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~-e~~d~l~d~~~~~~ee~~~~ 438 (513)
..+++++++...+.+.+|+.||.+|||+.+|+++++|..++.....++|||.+.+++++ .+.+.+.+ ...+|++....
T Consensus 158 ~~~~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~-~~~~pe~~~~~ 236 (298)
T TIGR02997 158 EKLNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLED-DGESPEEQVER 236 (298)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccC-CCCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999998755433 33343444 34567777788
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010327 439 ALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 500 (513)
Q Consensus 439 ~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR 500 (513)
.++...|..+|+.|||+|+.||.+||||+|++++|++|||+.||||+++|||++.+|++|||
T Consensus 237 ~~~~~~L~~~L~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr 298 (298)
T TIGR02997 237 ESLRQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298 (298)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 88888999999999999999999999999999999999999999999999999999999997
No 5
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=4.5e-58 Score=471.88 Aligned_cols=309 Identities=33% Similarity=0.543 Sum_probs=286.5
Q ss_pred CCCChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHH
Q 010327 198 YSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARN 277 (513)
Q Consensus 198 ~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~ 277 (513)
.++|.+..||++|+.+|+||++||..|++.++.+..+++.+..|++++|++|+..+||.+++++...|...+.+|..|++
T Consensus 5 ~~~~~~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~ 84 (317)
T PRK07405 5 TSTDLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKR 84 (317)
T ss_pred CCCcHHHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHH
Confidence 34688999999999999999999999999999999999999999999999999999999999999888888887889999
Q ss_pred HHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcccccccc
Q 010327 278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPF 356 (513)
Q Consensus 278 ~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~ 356 (513)
.||.+|+++|+++|++|. +++.+++||+||||+|||+|+++|||++|++|+|||+||||++|.++|. ++++||+|.
T Consensus 85 ~L~~~~~~~V~~~a~~~~---~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~ 161 (317)
T PRK07405 85 KMVEANLRLVVSVAKKYL---KRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPI 161 (317)
T ss_pred HHHHHHHHHHHHHHHHHc---CCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCCh
Confidence 999999999999999999 7899999999999999999999999999999999999999999999999 999999999
Q ss_pred chhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh-hhhccccCCCCCCchhh
Q 010327 357 GLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVENENQ 435 (513)
Q Consensus 357 ~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~-e~~d~l~d~~~~~~ee~ 435 (513)
|+...+++++++...+...+|+.||.+|||+.+|++++++..+++....++|||.+.+++++ .+.+.+.+. ..+|++.
T Consensus 162 ~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~-~~~pe~~ 240 (317)
T PRK07405 162 HITEKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDT-GASPEDF 240 (317)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCC-CCCHHHH
Confidence 99999999999999999999999999999999999999999999888889999998765544 344444443 3567887
Q ss_pred hHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhcc
Q 010327 436 RQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 512 (513)
Q Consensus 436 ~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~~yl 512 (513)
....++...|..+|+.|||+|+.||.+||||+|++++|++|||+.||||+++|||++.+|++|||+. ...|..|+
T Consensus 241 ~~~~~~~~~l~~al~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~--~~~l~~~~ 315 (317)
T PRK07405 241 ATQSSLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKR--KANIQEYL 315 (317)
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHH
Confidence 8888889999999999999999999999999999999999999999999999999999999999984 45666664
No 6
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=100.00 E-value=3e-58 Score=470.59 Aligned_cols=313 Identities=35% Similarity=0.537 Sum_probs=282.6
Q ss_pred cCCCChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHH-HhCCCCCHH---------------HHHHHccC
Q 010327 197 SYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQK-DLGREPTDV---------------ELAEATNM 260 (513)
Q Consensus 197 ~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~-~l~r~p~~~---------------e~A~~~~~ 260 (513)
..++|.+..|+.+++..++++.+++..+.+.++....+......+.. .+++.|+.. +|+.....
T Consensus 5 ~~~~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 84 (342)
T COG0568 5 RLSADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTP 84 (342)
T ss_pred ccchhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccCh
Confidence 45789999999999999999999999999999888877666667655 677777765 44443333
Q ss_pred CH-HHHH-HHHHH--hHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHH
Q 010327 261 SA-AQVK-KCLEV--GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLF 336 (513)
Q Consensus 261 s~-e~L~-~~~~g--d~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~ 336 (513)
+. ..|. .+..| +..|+.+||.+|++||++||++|. ++|++|.||||||+||||+|+++|||++||+|||||+|
T Consensus 85 ~Ee~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~---~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~w 161 (342)
T COG0568 85 EEEKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYT---GRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATW 161 (342)
T ss_pred HHHHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhh---cCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHH
Confidence 32 2333 34455 677999999999999999999999 89999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCC
Q 010327 337 WIRHAIIRSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGV 415 (513)
Q Consensus 337 wIR~aI~raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~ 415 (513)
|||++|.++|. +.++||+|.|+.+.++++.++.++|.+++|++|+.+|||+.+|+++++|+.++.....++|||.++++
T Consensus 162 WIrqaI~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~ 241 (342)
T COG0568 162 WIRQAITRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGD 241 (342)
T ss_pred HHHHHHHHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCC
Confidence 99999999999 99999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred chh-hhhccccCCCCCCchhhhHHHHHHHHHHHHHhc-CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 416 TQE-EFINGITDVDGVENENQRQPALLRLALDDVLDS-LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 416 ~~~-e~~d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~-L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
+++ .+.+.+.|+...+|++.+....+.+.+...|.. |+|+|+.||++||||+|+.+.|++|||+.+|||+++||||+.
T Consensus 242 ded~~l~d~leD~~~~~p~~~~~~~~~~~~~~~~L~~~Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~isrERvRQIE~ 321 (342)
T COG0568 242 DEDSELGDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEA 321 (342)
T ss_pred CcccHHHHHhhcCCcCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCcchHHHHHHHhCCcHHHHHHHHH
Confidence 655 466888888777899999999999999999999 999999999999999999999999999999999999999999
Q ss_pred HHHHHHh-Ccchhhhhhhcc
Q 010327 494 KGLMKLK-HPTRVDYLRQHM 512 (513)
Q Consensus 494 rALkKLR-~~~~~~~L~~yl 512 (513)
+|++||| ++.+...+++|+
T Consensus 322 kAl~KLr~~~~~~~~~~~~l 341 (342)
T COG0568 322 KALRKLRRHPERSALLRSYL 341 (342)
T ss_pred HHHHHHHHhhhhhhHHHHhh
Confidence 9999999 888888788886
No 7
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=100.00 E-value=7.4e-58 Score=491.79 Aligned_cols=304 Identities=32% Similarity=0.474 Sum_probs=271.4
Q ss_pred HHhhcCCCChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHh
Q 010327 193 VREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVG 272 (513)
Q Consensus 193 ~~~~~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd 272 (513)
....+...|.+..||++|+.+|+||++||..|++.++.+..+++. +. ...+|+.. ....+++.+..+
T Consensus 203 ~~~~~~~~d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~---~~-------~~~~~~~~---~~~~l~~~~~~g 269 (509)
T PRK05901 203 DAKLTATADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEEL---LA-------EGEKLDPE---LRRDLQWIGRDG 269 (509)
T ss_pred hhhccccccHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhh---hh-------hcccchhh---hhhhhhhhccch
Confidence 445667789999999999999999999999999999876433321 11 11223322 345577788889
Q ss_pred HHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccc
Q 010327 273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSF 351 (513)
Q Consensus 273 ~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~ 351 (513)
..|+++||.+|+|||+++|++|. ++|++++||||||+||||+|+++|||++|++|||||+||||++|.++|. +.++
T Consensus 270 ~~Ar~~LI~sNLrLVvsIAkrY~---~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~ 346 (509)
T PRK05901 270 KRAKNHLLEANLRLVVSLAKRYT---NRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQART 346 (509)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCc
Confidence 99999999999999999999998 7899999999999999999999999999999999999999999999999 8999
Q ss_pred cccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh-hhhccccCCCCC
Q 010327 352 TRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGV 430 (513)
Q Consensus 352 iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~-e~~d~l~d~~~~ 430 (513)
||+|.|+.+.++++.++..+|.+.+||.||.+|||+.||+++++|..++.....++|||.+.+.+++ .+.+.+.+....
T Consensus 347 IRvP~~~~e~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~ 426 (509)
T PRK05901 347 IRIPVHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAV 426 (509)
T ss_pred eecCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCCCC
Confidence 9999999999999999999999999999999999999999999999999999999999999765444 355666666666
Q ss_pred CchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhh
Q 010327 431 ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQ 510 (513)
Q Consensus 431 ~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~~ 510 (513)
.|++.+....++..|..+|..|+++|+.||.+||||++++++|++|||+.||||+++||||+.+||.|||++.+...|+.
T Consensus 427 ~p~~~~~~~~l~~~L~~aL~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~~~~~~l~~ 506 (509)
T PRK05901 427 SPVDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRD 506 (509)
T ss_pred CHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 77887888889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cc
Q 010327 511 HM 512 (513)
Q Consensus 511 yl 512 (513)
|+
T Consensus 507 ~l 508 (509)
T PRK05901 507 FL 508 (509)
T ss_pred hh
Confidence 86
No 8
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=100.00 E-value=4.1e-56 Score=458.03 Aligned_cols=298 Identities=32% Similarity=0.443 Sum_probs=264.2
Q ss_pred CCChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHHH
Q 010327 199 STDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNK 278 (513)
Q Consensus 199 ~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~~ 278 (513)
..|.+..||++|+.+|+||++||..|++.++.+..++.. |...+|.... ....+...+..|..|++.
T Consensus 24 ~~~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~~ 90 (324)
T PRK07921 24 AADLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARRH 90 (324)
T ss_pred CCChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHHH
Confidence 358899999999999999999999999999866544332 1122221110 234577778888999999
Q ss_pred HHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccccc
Q 010327 279 LIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFG 357 (513)
Q Consensus 279 LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~ 357 (513)
||.+|+++|+++|++|. +++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++|+ +.+.||+|.|
T Consensus 91 Lv~~~~~lV~~iA~r~~---~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~ 167 (324)
T PRK07921 91 LLEANLRLVVSLAKRYT---GRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVH 167 (324)
T ss_pred HHHHHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHH
Confidence 99999999999999999 7899999999999999999999999999999999999999999999999 8999999999
Q ss_pred hhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh-hhhccccCCCCCCchhhh
Q 010327 358 LESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVENENQR 436 (513)
Q Consensus 358 ~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~-e~~d~l~d~~~~~~ee~~ 436 (513)
+.+.+++++++...|.+++||.||.+|||+.+|+++++|..++.....++|||.+.+++++ .+.+.+.+....+|++..
T Consensus 168 ~~~~~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~pe~~~ 247 (324)
T PRK07921 168 LVEQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAV 247 (324)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCCCCCHHHHH
Confidence 9999999999999999999999999999999999999999999988899999999765444 355566665555677777
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhcc
Q 010327 437 QPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 512 (513)
Q Consensus 437 ~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~~yl 512 (513)
...++...|..+|..|+++|+.||.+||||+|++++|++|||+.||||+++||||+.+||+|||.......|..|+
T Consensus 248 ~~~~~~~~l~~~L~~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~~~~~~l~~~~ 323 (324)
T PRK07921 248 IAGLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSYA 323 (324)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHHHHHHHHhh
Confidence 8888899999999999999999999999999889999999999999999999999999999999998888898886
No 9
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=6.1e-54 Score=449.33 Aligned_cols=273 Identities=34% Similarity=0.557 Sum_probs=254.8
Q ss_pred cCCCChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHH
Q 010327 197 SYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAAR 276 (513)
Q Consensus 197 ~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar 276 (513)
....|++.+||++|+..|+||++||..|++.+ ..|+..|+
T Consensus 92 ~~~~d~~~~yl~~i~~~~~l~~~ee~~L~~~~----------------------------------------~~Gd~~A~ 131 (367)
T PRK09210 92 VKINDPVRMYLKEIGRVPLLTAEEEIELAKRI----------------------------------------EEGDEEAK 131 (367)
T ss_pred cccCcHHHHHHHHhhccCCCCHHHHHHHHHHH----------------------------------------HhhHHHHH
Confidence 34579999999999999999999999997665 35788999
Q ss_pred HHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccc
Q 010327 277 NKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVP 355 (513)
Q Consensus 277 ~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP 355 (513)
+.||.+|+++|+++|++|. +++.+++||+||||+|||+|+++|||.+|++|+|||+||||++|.++|. +.+++|+|
T Consensus 132 ~~Li~~~~~lV~~iA~~~~---~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip 208 (367)
T PRK09210 132 QRLAEANLRLVVSIAKRYV---GRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIP 208 (367)
T ss_pred HHHHHHHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceecc
Confidence 9999999999999999998 7899999999999999999999999999999999999999999999999 99999999
Q ss_pred cchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh-hhhccccCCCCCCchh
Q 010327 356 FGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVENEN 434 (513)
Q Consensus 356 ~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~-e~~d~l~d~~~~~~ee 434 (513)
.|+++.++++.++.+.|..++||.||.+|||+.||+++++|+.++.....++|||.+.+.+++ .+.+.+.+....+|++
T Consensus 209 ~~~~~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~~~~p~~ 288 (367)
T PRK09210 209 VHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPAD 288 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCCCCCHHH
Confidence 999999999999999999999999999999999999999999999999899999999765533 4556666666667888
Q ss_pred hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhcc
Q 010327 435 QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 512 (513)
Q Consensus 435 ~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~~yl 512 (513)
......++..|..+|..||++|+.||.+||||+|++++|++|||+.||||+++|||++.+||+|||++.+...|+.|+
T Consensus 289 ~~~~~~~~~~l~~~l~~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~~~~~~~l~~~~ 366 (367)
T PRK09210 289 HAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFL 366 (367)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhChHHHhHHHHhh
Confidence 888889999999999999999999999999999999999999999999999999999999999999999999999986
No 10
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=1.5e-50 Score=449.24 Aligned_cols=237 Identities=36% Similarity=0.593 Sum_probs=223.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccc
Q 010327 273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSF 351 (513)
Q Consensus 273 ~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~ 351 (513)
..|+++||.+|++||++||++|. ++|++++||||||+||||+|+++|||++|++|||||+||||++|.++|+ +.++
T Consensus 379 ~~a~~~Li~~nlrlV~~iA~ky~---~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~ 455 (619)
T PRK05658 379 RRAKKEMVEANLRLVISIAKKYT---NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 455 (619)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHh---hCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCc
Confidence 47899999999999999999998 7899999999999999999999999999999999999999999999999 8999
Q ss_pred cccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh-hhhccccCCCCC
Q 010327 352 TRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGV 430 (513)
Q Consensus 352 iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~-e~~d~l~d~~~~ 430 (513)
||+|.|+.+.++++.++...|.+++||.||.+|||+.||+++++|+.++.....++|||.+++++++ .+.+.+.+....
T Consensus 456 irip~~~~~~~~k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~~~~~l~d~i~d~~~~ 535 (619)
T PRK05658 456 IRIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAE 535 (619)
T ss_pred eecCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCCCCCchhhhcCCCCCC
Confidence 9999999999999999999999999999999999999999999999999999999999999765544 355666666666
Q ss_pred CchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhh
Q 010327 431 ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQ 510 (513)
Q Consensus 431 ~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~~ 510 (513)
+|++......++..|..+|..||++|+.||++||||++..++|++|||+.||||+++|||++.+||+|||++.+...|+.
T Consensus 536 ~p~~~~~~~~~~~~l~~~l~~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr~~~~~~~l~~ 615 (619)
T PRK05658 536 LPIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRS 615 (619)
T ss_pred ChHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHhchHHHHHHHH
Confidence 77887888889999999999999999999999999998899999999999999999999999999999999999999999
Q ss_pred cc
Q 010327 511 HM 512 (513)
Q Consensus 511 yl 512 (513)
|+
T Consensus 616 ~~ 617 (619)
T PRK05658 616 FL 617 (619)
T ss_pred Hh
Confidence 86
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=7.5e-47 Score=373.48 Aligned_cols=235 Identities=34% Similarity=0.570 Sum_probs=218.2
Q ss_pred HHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccc
Q 010327 275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTR 353 (513)
Q Consensus 275 Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iR 353 (513)
|+++||.+|+++|+++|++|. +++.+++||+|||++||++|+++|||++|++|+|||+||||++|.+++. +.+.++
T Consensus 1 a~~~Li~~~~~lv~~ia~~~~---~~~~~~eDLiQeG~igL~~A~~~fd~~~g~~FstYA~~~Ir~~I~~~l~~~~~~vr 77 (238)
T TIGR02393 1 AKKQLVESNLRLVVSIAKKYT---NRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIR 77 (238)
T ss_pred CHHHHHHHhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHhCCCCCCChHHHhHHHHHHHHHHHHHHcCCcEE
Confidence 578999999999999999998 7899999999999999999999999999999999999999999999999 889999
Q ss_pred cccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh-hhhccccCCCCCCc
Q 010327 354 VPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVEN 432 (513)
Q Consensus 354 lP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~-e~~d~l~d~~~~~~ 432 (513)
+|.++.+.++++.++...|.+++|+.||.+|||+.||++++++..++......+|||.+.+.+++ .+.+.+.++...+|
T Consensus 78 ip~~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~p 157 (238)
T TIGR02393 78 IPVHMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESP 157 (238)
T ss_pred eCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcccHHHHhcCCCCCCh
Confidence 99999999999999999999999999999999999999999999999888889999998765444 34455666555667
Q ss_pred hhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhcc
Q 010327 433 ENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 512 (513)
Q Consensus 433 ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~~yl 512 (513)
++.....++...|..+|+.||++|+.||.++|||++++++|++|||+.||||.++|+|++.+|++|||+....+.|+.|+
T Consensus 158 ~~~~~~~~~~~~l~~~l~~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~~~~~~~~~ 237 (238)
T TIGR02393 158 DDYAAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKSFL 237 (238)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHHHhHHHHhh
Confidence 77777888889999999999999999999999999999999999999999999999999999999999999889898885
No 12
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=100.00 E-value=2.5e-44 Score=371.16 Aligned_cols=269 Identities=29% Similarity=0.445 Sum_probs=243.9
Q ss_pred CCCChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHH
Q 010327 198 YSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARN 277 (513)
Q Consensus 198 ~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~ 277 (513)
...|.+++|+++|+..|+||+++|..|...+ ..|+..|++
T Consensus 50 ~~~~~~~~y~~~~~~~~~l~~~ee~~li~~~----------------------------------------~~Gd~~A~~ 89 (325)
T PRK05657 50 RVLDATQLYLNEIGYSPLLTAEEEVYFARRA----------------------------------------LRGDFAARQ 89 (325)
T ss_pred ccccHHHHHHHHHhcCCCCCHHHHHHHHHHH----------------------------------------HcCCHHHHH
Confidence 4679999999999999999999999886554 468899999
Q ss_pred HHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcccccccc
Q 010327 278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPF 356 (513)
Q Consensus 278 ~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~ 356 (513)
.||..|.++|+++|++|. +++.+++||+||||+|||+++++||+.+|++|+|||+||||++|.+++. +.+.+++|.
T Consensus 90 ~Li~~y~~~V~~~a~~~~---~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~ 166 (325)
T PRK05657 90 RMIESNLRLVVKIAKRYL---NRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPV 166 (325)
T ss_pred HHHHHhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCH
Confidence 999999999999999998 7889999999999999999999999999999999999999999999998 889999999
Q ss_pred chhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh-hhhccccCCCCCCchhh
Q 010327 357 GLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVENENQ 435 (513)
Q Consensus 357 ~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~-e~~d~l~d~~~~~~ee~ 435 (513)
++...++.+.++...|...+|+.||.+|||+.+|+++++|..++.......|||.+...+.. .+.+.+.+....+|++.
T Consensus 167 ~~~~~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~~~l~d~l~d~~~~~pe~~ 246 (325)
T PRK05657 167 HVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDT 246 (325)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCCcchhhhccCCCCCCHHHH
Confidence 99999999999999999999999999999999999999999999988888999988654433 34455555544567777
Q ss_pred hHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhh
Q 010327 436 RQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLR 509 (513)
Q Consensus 436 ~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~ 509 (513)
....+....|..+|..||+++|.||.++|||.+++++|++|||+.||||.++|++++++|+++||+......+.
T Consensus 247 ~~~~e~~~~L~~aL~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~~~~~~ 320 (325)
T PRK05657 247 TQDDDMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQGLS 320 (325)
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhCccc
Confidence 78888888999999999999999999999999999999999999999999999999999999999876655543
No 13
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=1.9e-43 Score=358.45 Aligned_cols=258 Identities=24% Similarity=0.285 Sum_probs=213.9
Q ss_pred CChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHHHH
Q 010327 200 TDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKL 279 (513)
Q Consensus 200 ~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~~L 279 (513)
.+.+..|+++++..|+||.++|..|+... ...||..|++.|
T Consensus 13 ~~~~~~y~~~~~~~~~l~~~~e~~l~~~~---------------------------------------~~~Gd~~a~~~L 53 (284)
T PRK06596 13 EGNLDAYIQAVNKIPMLTAEEEYMLAKRL---------------------------------------REHGDLEAAKQL 53 (284)
T ss_pred ccHHHHHHHHHhccCCCCHHHHHHHHHHH---------------------------------------HHcCCHHHHHHH
Confidence 47899999999999999999998886653 135889999999
Q ss_pred HHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccccch
Q 010327 280 IKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGL 358 (513)
Q Consensus 280 I~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~~ 358 (513)
|.+|+++|+++|++|. +.+.+++||+|||++||++|+++|||++|++|+|||+|||+++|.++++ +.+.+++|.+.
T Consensus 54 v~~~~~lV~~ia~~~~---~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~p~~~ 130 (284)
T PRK06596 54 VLSHLRFVVHIARGYR---GYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTK 130 (284)
T ss_pred HHHhHHHHHHHHHHhc---CCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeeeccchH
Confidence 9999999999999998 7899999999999999999999999999999999999999999999999 66778999875
Q ss_pred hH--HHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHh-ccCcccccCCCCCchh---hhhccccCCCCCCc
Q 010327 359 ES--VRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA-SKPILSLHSRHGVTQE---EFINGITDVDGVEN 432 (513)
Q Consensus 359 ~~--~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~-~~~~~SLd~~~~~~~~---e~~d~l~d~~~~~~ 432 (513)
.. ....+.+...++. .+++||.+|||+.||+++++|..++.. ...++|||.+.+++++ .+.+.+.+. ..+|
T Consensus 131 ~~~~~~~~~~~~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~-~~~p 207 (284)
T PRK06596 131 AQRKLFFNLRKAKKRLG--WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDK-SSDP 207 (284)
T ss_pred HHHHHHHHHHHHHHHhc--cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcCCC-CCCc
Confidence 42 2333444444443 349999999999999999999998753 3478999998654322 244455544 3445
Q ss_pred hhhhHHH----HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010327 433 ENQRQPA----LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 504 (513)
Q Consensus 433 ee~~~~~----~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~ 504 (513)
++..+.. ++...|..+|+.||++|+.||.+|||.+ +++|++|||+.||||+++|+|++.+|++|||+...
T Consensus 208 ~~~~~~~~~~~~~~~~L~~al~~L~~rEr~VL~lry~~~--~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~l~ 281 (284)
T PRK06596 208 ADVLEEDNWEDQRRALLADALEGLDERSRDIIEARWLDD--DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIE 281 (284)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCC--CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5544433 4678899999999999999999999642 68999999999999999999999999999997543
No 14
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=2.9e-43 Score=357.87 Aligned_cols=262 Identities=26% Similarity=0.293 Sum_probs=220.7
Q ss_pred CCCChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHH
Q 010327 198 YSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARN 277 (513)
Q Consensus 198 ~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~ 277 (513)
...++++.|++++..+|+||+++|..|++.++ ..||..|++
T Consensus 3 ~~~~~~~~y~~~~~~~~~l~~~~e~~L~~~~~---------------------------------------~~gd~~A~~ 43 (289)
T PRK07500 3 ADASADRSMIRSAMKAPYLEREEEHALAYRWK---------------------------------------DHRDEDALH 43 (289)
T ss_pred cchhHHHHHHHHHhcCCCCCHHHHHHHHHHHH---------------------------------------HCCCHHHHH
Confidence 35688999999999999999999999977651 247899999
Q ss_pred HHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcccccccc
Q 010327 278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPF 356 (513)
Q Consensus 278 ~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~ 356 (513)
.||..|+++|+++|++|. +++.+++||+||||+|||+|+++|||.+|++|+|||+|||+++|.++++ +.+.+|+|.
T Consensus 44 ~Lv~~~~~lV~~~a~~~~---~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~ 120 (289)
T PRK07500 44 RIISAHMRLVISMAGKFR---RFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGT 120 (289)
T ss_pred HHHHHhHHHHHHHHHHHc---CCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCc
Confidence 999999999999999998 7789999999999999999999999999999999999999999999999 788999999
Q ss_pred chhH--HHHHHHHHHHHHHH---HhCCCCCHHHHHHhcCCCHHHHHHHHH-hccCcccccCCCCCchh---hhhccccCC
Q 010327 357 GLES--VRGEIQRAKLELLF---ELKRVPTDEEIIQGVNISPERYREVMK-ASKPILSLHSRHGVTQE---EFINGITDV 427 (513)
Q Consensus 357 ~~~~--~~~ki~ka~~~L~~---elgR~PT~eELA~~lgis~e~v~~~l~-~~~~~~SLd~~~~~~~~---e~~d~l~d~ 427 (513)
+... ...++.+....+.. .+|+.||.+|||+.||+++++|..++. ....++|||.+.+++++ .+.+.+.++
T Consensus 121 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~i~d~ 200 (289)
T PRK07500 121 SSAQKALFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDD 200 (289)
T ss_pred cHHHHHHHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCCCcccHHHhccCC
Confidence 8655 33455555555554 689999999999999999999988753 45579999998765433 245555554
Q ss_pred CCCCchhhhH----HHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 428 DGVENENQRQ----PALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 428 ~~~~~ee~~~----~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
. .+|++... ..++...|..+|+.||++|+.||.++|+. .+++|++|||+.||||+++|+|++.+|+++||...
T Consensus 201 ~-~~pe~~~~~~~~~~~~~~~l~~al~~L~~rer~vl~lr~~~--~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l 277 (289)
T PRK07500 201 S-PLPDEQVESSIDGERRRRWLTQALQTLNERELRIIRERRLR--EDGATLEALGEELGISKERVRQIEARALEKLRRAL 277 (289)
T ss_pred C-CCchHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3 34554433 23456789999999999999999999952 47999999999999999999999999999999765
Q ss_pred h
Q 010327 504 R 504 (513)
Q Consensus 504 ~ 504 (513)
.
T Consensus 278 ~ 278 (289)
T PRK07500 278 L 278 (289)
T ss_pred H
Confidence 4
No 15
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=7.3e-43 Score=350.69 Aligned_cols=221 Identities=24% Similarity=0.306 Sum_probs=195.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccc
Q 010327 273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSF 351 (513)
Q Consensus 273 ~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~ 351 (513)
..++++||.+|++||+++|++|. ++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++++ +..+
T Consensus 39 ~~~r~~Lv~~~l~LV~~iA~~y~---~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I~~~lr~~~~~ 115 (264)
T PRK07122 39 QRQRDRIVTRCLPLADHIARRFD---GRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWS 115 (264)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHcCCc
Confidence 45899999999999999999998 6799999999999999999999999999999999999999999999999 7889
Q ss_pred cccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHh--ccCcccccCCCCCchhhhhccccCCCC
Q 010327 352 TRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA--SKPILSLHSRHGVTQEEFINGITDVDG 429 (513)
Q Consensus 352 iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~--~~~~~SLd~~~~~~~~e~~d~l~d~~~ 429 (513)
||+|.++.+..++++++..+|.+++|+.||.+|||+.||+++++|.+++.. ...++|||.+.+++++.. ..+.+. .
T Consensus 116 ir~Pr~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~-~~~~d~-~ 193 (264)
T PRK07122 116 VKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDA-RAIADT-L 193 (264)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCCCCc-ccchhc-c
Confidence 999999999999999999999999999999999999999999999998865 456899999865432210 111111 1
Q ss_pred CCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 430 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 430 ~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
.+++...+..+....|..+|+.||++|+.||.++| ++++|++|||+.||||.++|++++.+|+++||..
T Consensus 194 ~~~~~~~e~~~~~~~l~~~l~~L~~rer~vl~l~y----~~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 262 (264)
T PRK07122 194 GDVDAGLDQIENREALRPLLAALPERERTVLVLRF----FESMTQTQIAERVGISQMHVSRLLAKTLARLRDQ 262 (264)
T ss_pred CCcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHh----cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 22344456667788899999999999999999999 6899999999999999999999999999999964
No 16
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=100.00 E-value=2.2e-42 Score=348.03 Aligned_cols=255 Identities=25% Similarity=0.314 Sum_probs=208.7
Q ss_pred hHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHHHHHH
Q 010327 202 LVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIK 281 (513)
Q Consensus 202 ~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~~LI~ 281 (513)
.+..|+++|+.+|+|++++|..|+..+ ...||..|++.||.
T Consensus 2 ~~~~yl~~~~~~~~l~~~~e~~l~~~~---------------------------------------~~~gd~~a~~~Lv~ 42 (270)
T TIGR02392 2 SLDAYIRAVNRIPMLTPEEEYQLAKRL---------------------------------------REHGDLDAAKKLVL 42 (270)
T ss_pred hHHHHHHHHhcCCCCCHHHHHHHHHHH---------------------------------------HHCCCHHHHHHHHH
Confidence 467899999999999999998886653 13588999999999
Q ss_pred HHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccccchh-
Q 010327 282 HNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLE- 359 (513)
Q Consensus 282 ~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~~~- 359 (513)
+|+++|+++|++|. +++.+++||+|||++|||+|+++|||++|++|+|||+|||+++|.++++ +...+|+|.+..
T Consensus 43 ~~~~lV~~~a~~~~---~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir~p~~~~~ 119 (270)
T TIGR02392 43 SHLRFVVKIARGYR---GYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQ 119 (270)
T ss_pred HhHHHHHHHHHHHc---CCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCceecCchHHH
Confidence 99999999999998 7899999999999999999999999999999999999999999999999 666789997643
Q ss_pred -HHHHHHHHHHHHHHHHhCCCC-CHHHHHHhcCCCHHHHHHHHHh-ccCcccccCCCCCchh---hhhccccCCCCCCch
Q 010327 360 -SVRGEIQRAKLELLFELKRVP-TDEEIIQGVNISPERYREVMKA-SKPILSLHSRHGVTQE---EFINGITDVDGVENE 433 (513)
Q Consensus 360 -~~~~ki~ka~~~L~~elgR~P-T~eELA~~lgis~e~v~~~l~~-~~~~~SLd~~~~~~~~---e~~d~l~d~~~~~~e 433 (513)
....++.+....+. .++.| +.+|||+.||+++++|..++.. ...++|||.+.+++++ .+.+.+.++. .+|+
T Consensus 120 ~~~~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~l~d~~-~~pe 196 (270)
T TIGR02392 120 RKLFFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKT-SDPE 196 (270)
T ss_pred HHHHHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCCccccHHHHhcCCC-CChH
Confidence 33444454444432 22566 6999999999999999998653 3357999998755332 2344454443 3455
Q ss_pred hhhHH----HHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 434 NQRQP----ALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 434 e~~~~----~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
+.... ..+...|..+|..||++|+.||.++||. .+++|++|||+.||||.++|+|++.+||+|||...
T Consensus 197 ~~~~~~~~~~~~~~~L~~al~~L~~rer~vl~l~y~~--~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~l 268 (270)
T TIGR02392 197 DTLEEEQWEELQRQALANALGSLDARSRRIIEARWLD--DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAAL 268 (270)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhcC--CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 54433 3466789999999999999999999953 35899999999999999999999999999999753
No 17
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=100.00 E-value=2.1e-40 Score=335.98 Aligned_cols=265 Identities=29% Similarity=0.443 Sum_probs=238.1
Q ss_pred CCChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHHH
Q 010327 199 STDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNK 278 (513)
Q Consensus 199 ~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~~ 278 (513)
-+|++++||++|..+|.||.+++..|...+ .+|+..|++.
T Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~li~~~----------------------------------------~~gd~~a~~~ 50 (285)
T TIGR02394 11 VADVTQLYLREIGFKPLLTAEEEIAYARRA----------------------------------------LAGDFEARKV 50 (285)
T ss_pred cchHHHHHHHHHhccCCCCHHHHHHHHHHH----------------------------------------HcCCHHHHHH
Confidence 379999999999999999999998885554 4688999999
Q ss_pred HHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccccc
Q 010327 279 LIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFG 357 (513)
Q Consensus 279 LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~ 357 (513)
|+..|.++|+++|++|. +++.+++||+||||+|||+|+++||+..|++|+||++|||+.++++++. +.+.+++|.+
T Consensus 51 L~~~y~~~v~~~a~~~~---~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain~~i~~~~~~~~~p~~ 127 (285)
T TIGR02394 51 MIESNLRLVVSIAKHYV---NRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVH 127 (285)
T ss_pred HHHHhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHHHHHHHcCCceeCcHH
Confidence 99999999999999998 7899999999999999999999999999999999999999999999999 8889999999
Q ss_pred hhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh-hhhccccCCCCCCchhhh
Q 010327 358 LESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVENENQR 436 (513)
Q Consensus 358 ~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~-e~~d~l~d~~~~~~ee~~ 436 (513)
+...++.+.+..+.+...+|+.|+.+++|+.+|++++++..++.......|+|.+...+.. .+.+.+.+....+|++..
T Consensus 128 ~~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~~~~pe~~~ 207 (285)
T TIGR02394 128 VIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLV 207 (285)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchhhhhcCCCCCCHHHHH
Confidence 9999999999888888999999999999999999999999999988888999986544332 233344444445577777
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010327 437 QPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 506 (513)
Q Consensus 437 ~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~ 506 (513)
...+....|..+|..||+++|.||.++|||.+++++|++|||+.||||.++|++++++|+++||+.....
T Consensus 208 ~~~e~~~~L~~al~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~~~ 277 (285)
T TIGR02394 208 QNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERD 277 (285)
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 8888889999999999999999999999999999999999999999999999999999999999866543
No 18
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=2e-40 Score=331.51 Aligned_cols=227 Identities=29% Similarity=0.382 Sum_probs=196.0
Q ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-
Q 010327 269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT- 347 (513)
Q Consensus 269 ~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~- 347 (513)
..|+..|++.||.+|+++|+++|++|.. ..+.+++||+|||+||||+|+++|||++|++|+|||+|||+++|.++++
T Consensus 20 ~~gd~~a~~~Lv~~~~~lV~~ia~~~~~--~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~ 97 (256)
T PRK07408 20 QNPSIALRNQLVELNLGLVRKEAHRWSN--QCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRD 97 (256)
T ss_pred HCCCHHHHHHHHHHhHHHHHHHHHHHhc--cCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 3678899999999999999999999973 2366799999999999999999999999999999999999999999999
Q ss_pred hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHh--ccCcccccCCCCCchhh---hhc
Q 010327 348 VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA--SKPILSLHSRHGVTQEE---FIN 422 (513)
Q Consensus 348 ~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~--~~~~~SLd~~~~~~~~e---~~d 422 (513)
+..+||+|.++.+.++++.++..+|.+++|+.||.+|||+.||+++++|..++.. ....+|||.+...+++. +.+
T Consensus 98 ~~~~vr~pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d 177 (256)
T PRK07408 98 KSPTVRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDEDGSTSLGD 177 (256)
T ss_pred cCCeeeeCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCCCcccccc
Confidence 8899999999999999999999999999999999999999999999999998753 45688999986543332 223
Q ss_pred cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
.+.+... .+ .....+....|..+|..||++++.||.++| ++++|++|||+.||||.++|++++.+|+++||+.
T Consensus 178 ~~~d~~~-~~--~~~~~~~~~~l~~~l~~L~~~~r~vl~l~y----~~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~ 250 (256)
T PRK07408 178 LLPDPRY-RS--FQLAQEDRIRLQQALAQLEERTREVLEFVF----LHDLTQKEAAERLGISPVTVSRRVKKGLDQLKKL 250 (256)
T ss_pred ccCCccc-ch--hhhhHHHHHHHHHHHHcCCHHHHHHHHHHH----HCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3333221 11 112345567799999999999999999999 6899999999999999999999999999999976
Q ss_pred ch
Q 010327 503 TR 504 (513)
Q Consensus 503 ~~ 504 (513)
..
T Consensus 251 l~ 252 (256)
T PRK07408 251 LQ 252 (256)
T ss_pred hh
Confidence 54
No 19
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=100.00 E-value=1e-39 Score=326.56 Aligned_cols=228 Identities=26% Similarity=0.354 Sum_probs=199.7
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhc
Q 010327 270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS 349 (513)
Q Consensus 270 ~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~ 349 (513)
.|+..|++.||.+|+++|+++|++|...+..+++++||+|||++|||+|+++|||++|++|+|||+||||++|.++++..
T Consensus 19 ~~~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~ 98 (257)
T PRK05911 19 TQEIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQ 98 (257)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhc
Confidence 57889999999999999999999986444456789999999999999999999999999999999999999999999932
Q ss_pred cccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhcc--CcccccCCCCC--chh---hhhc
Q 010327 350 SFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASK--PILSLHSRHGV--TQE---EFIN 422 (513)
Q Consensus 350 r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~--~~~SLd~~~~~--~~~---e~~d 422 (513)
.++|.++.+..+++..+...|.+.+||.||.+|||+.+|+++++|..++.... .++|||.+... +++ .+.+
T Consensus 99 --~~~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~~~~~~~~~l~~ 176 (257)
T PRK05911 99 --DWVPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQSDDEAGLALEE 176 (257)
T ss_pred --CCCCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCCCCCccccchhh
Confidence 24899999999999999999999999999999999999999999999987654 46899986532 111 2344
Q ss_pred cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
.+.+.....|++.....++...|..+|+.|||+|+.||.++| ++++|++|||+.||||.++|++++.+|+++||+.
T Consensus 177 ~l~d~~~~~~~~~~~~~~~~~~l~~al~~L~~~er~vi~l~y----~e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 252 (257)
T PRK05911 177 RIADERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYY----YEELVLKEIGKILGVSESRVSQIHSKALLKLRAT 252 (257)
T ss_pred hccCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 555554445666777778888999999999999999999999 6899999999999999999999999999999975
Q ss_pred c
Q 010327 503 T 503 (513)
Q Consensus 503 ~ 503 (513)
.
T Consensus 253 l 253 (257)
T PRK05911 253 L 253 (257)
T ss_pred H
Confidence 4
No 20
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=100.00 E-value=3.8e-39 Score=321.64 Aligned_cols=241 Identities=27% Similarity=0.353 Sum_probs=210.6
Q ss_pred cCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Q 010327 210 MKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLF 289 (513)
Q Consensus 210 i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~~LI~~nlrLV~s 289 (513)
...+|+||++|+..|+..+ ..||..|++.|+..|+++|++
T Consensus 10 ~~~~~~l~~~~~~~li~~~----------------------------------------~~gd~~a~~~L~~~~~~~v~~ 49 (254)
T TIGR02850 10 TSKLPVLKNQEMRELFIRM----------------------------------------QSGDTTAREKLINGNLRLVLS 49 (254)
T ss_pred ccCCCCCCHHHHHHHHHHH----------------------------------------HcCCHHHHHHHHHHhHHHHHH
Confidence 4578999999998775544 357889999999999999999
Q ss_pred HHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhccccccccchhHHHHHHHHHH
Q 010327 290 VIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAK 369 (513)
Q Consensus 290 IAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~iRlP~~~~~~~~ki~ka~ 369 (513)
+|++|. +++.+++||+||||+|||+|+++|||.+|.+|+||++|||+++|.++++....+|+|.++.+..+++.++.
T Consensus 50 ~a~~~~---~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~~ir~p~~~~~~~~~~~~~~ 126 (254)
T TIGR02850 50 VIQRFN---NRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVR 126 (254)
T ss_pred HHHHHh---CCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCCCccCchHHHHHHHHHHHHH
Confidence 999998 77899999999999999999999999999999999999999999999996568999999999999999999
Q ss_pred HHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh---hhhccccCCCCCCchhhhHHHHHHHHHH
Q 010327 370 LELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE---EFINGITDVDGVENENQRQPALLRLALD 446 (513)
Q Consensus 370 ~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~---e~~d~l~d~~~~~~ee~~~~~~l~~~L~ 446 (513)
.++..++|+.||.+|||+.||++++++..++.....+.|||.+...+++ .+.+.+.++.. +. ........|.
T Consensus 127 ~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~~~d~~~--~~---~~~~~~~~l~ 201 (254)
T TIGR02850 127 DKLISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEKN--KD---SQWLEGIALK 201 (254)
T ss_pred HHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCCCCcchhhhhcCCccc--cH---HHHHhHHHHH
Confidence 9999999999999999999999999999999988888999987643322 13334433321 11 2234556789
Q ss_pred HHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 447 DVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 447 ~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
.+|+.|+++++.||.++| ++++|++|||+.||+|.++|++++.+|+++||+.
T Consensus 202 ~~l~~L~~rer~vi~~~~----~~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~~ 253 (254)
T TIGR02850 202 EAMKRLNEREKMILNMRF----FEGKTQMEVAEEIGISQAQVSRLEKAALKHMRKY 253 (254)
T ss_pred HHHHcCCHHHHHHHHHHH----cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 999999999999999999 5799999999999999999999999999999963
No 21
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=100.00 E-value=1.3e-38 Score=315.11 Aligned_cols=225 Identities=32% Similarity=0.429 Sum_probs=198.0
Q ss_pred HHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCC-cHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHH
Q 010327 267 KCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGP-RFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRS 345 (513)
Q Consensus 267 ~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~-~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~ra 345 (513)
...+|+..++ .||++|+|||.++|++|. +++. .++||+|-|+|||++|+++|||++|.+|+|||...|+++|.++
T Consensus 17 ~~~~g~~~~~-~Li~~ylpLV~~ia~k~~---~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~ 92 (247)
T COG1191 17 YYAEGDEEAR-RLIERYLPLVKSIARKFE---NRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDY 92 (247)
T ss_pred HHHhcCHHHH-HHHHHHHHHHHHHHHHHH---hcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHH
Confidence 3456889999 999999999999999999 4444 9999999999999999999999999999999999999999999
Q ss_pred HHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhcc--CcccccCCCCCchhhhhcc
Q 010327 346 MTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASK--PILSLHSRHGVTQEEFING 423 (513)
Q Consensus 346 I~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~--~~~SLd~~~~~~~~e~~d~ 423 (513)
++....+++|+.+++..+++..+..+|..++||+||++|||+.||++.++|..++...+ ..+|+|.....+++..
T Consensus 93 LR~~~~v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d~~--- 169 (247)
T COG1191 93 LRKNDSVKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDD--- 169 (247)
T ss_pred HHhCCCccCcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccccc---
Confidence 99433999999999999999999999999999999999999999999999999998765 6677777554332221
Q ss_pred ccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 424 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 424 l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
.++...++++..+..++...|..++..|+++|+.||.+|| ++++|++|||+.||||.++|+|++.+|+++||...
T Consensus 170 -~~~~~~~~~~~~~~~~~~~~l~~ai~~L~EREk~Vl~l~y----~eelt~kEI~~~LgISes~VSql~kkai~kLr~~l 244 (247)
T COG1191 170 -VDDQIENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRY----KEELTQKEIAEVLGISESRVSRLHKKAIKKLRKEL 244 (247)
T ss_pred -hhhccccchhHHHHHHHHHHHHHHHHccCHHHHHHHHHHH----HhccCHHHHHHHhCccHHHHHHHHHHHHHHHHHHh
Confidence 1222334556677778888888888899999999999999 89999999999999999999999999999999654
No 22
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=100.00 E-value=1.1e-37 Score=311.69 Aligned_cols=240 Identities=29% Similarity=0.382 Sum_probs=209.1
Q ss_pred CCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Q 010327 211 KIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFV 290 (513)
Q Consensus 211 ~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~~LI~~nlrLV~sI 290 (513)
..+|+|+++|+..|+..+ ..||..|++.||..|+++|+++
T Consensus 14 ~~~~~l~~~~~~~l~~~~----------------------------------------~~gd~~a~~~l~~~~~~~v~~~ 53 (258)
T PRK08215 14 SKLPVLKNEEMRELFERM----------------------------------------QNGDKEAREKLINGNLRLVLSV 53 (258)
T ss_pred CCCCCCCHHHHHHHHHHH----------------------------------------HcCCHHHHHHHHHHHHHHHHHH
Confidence 467899999888775544 3578899999999999999999
Q ss_pred HHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhccccccccchhHHHHHHHHHHH
Q 010327 291 IKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAKL 370 (513)
Q Consensus 291 Akky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~iRlP~~~~~~~~ki~ka~~ 370 (513)
|++|. +++.+++||+|||++|||+|+++||+.+|.+|+||++|||+++|.++++....+|+|.++.....++.++..
T Consensus 54 a~~~~---~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~~~vrip~~~~~~~~~~~~~~~ 130 (258)
T PRK08215 54 IQRFN---NRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVRE 130 (258)
T ss_pred HHHHh---CCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCCceEecHHHHHHHHHHHHHHH
Confidence 99998 778999999999999999999999999999999999999999999999955688999999999999999999
Q ss_pred HHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhh---hhccccCCCCCCchhhhHHHHHHHHHHH
Q 010327 371 ELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEE---FINGITDVDGVENENQRQPALLRLALDD 447 (513)
Q Consensus 371 ~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e---~~d~l~d~~~~~~ee~~~~~~l~~~L~~ 447 (513)
++..++|+.||.+|||+.||++++++..++.....+.|||.+...+++. +.+.+.+... ..+.......|..
T Consensus 131 ~l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~l~~ 205 (258)
T PRK08215 131 KLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDEKN-----KDENWLEEIALKE 205 (258)
T ss_pred HHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchhhhhhccCccc-----cHHHHHhHHHHHH
Confidence 9999999999999999999999999999998888888999886443321 2233333211 1223345567889
Q ss_pred HHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 448 VLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 448 aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
+|+.||++++.||.++| ++++|++|||+.||+|.++|++++.+|+++||+.
T Consensus 206 ~l~~L~~~er~vi~~~~----~~~~t~~eIA~~lgis~~~V~~~~~~al~kLr~~ 256 (258)
T PRK08215 206 AMKKLNDREKLILNLRF----FQGKTQMEVAEEIGISQAQVSRLEKAALKHMRKY 256 (258)
T ss_pred HHHcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999 6899999999999999999999999999999964
No 23
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=100.00 E-value=1.9e-36 Score=304.35 Aligned_cols=249 Identities=23% Similarity=0.349 Sum_probs=214.9
Q ss_pred CCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Q 010327 211 KIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFV 290 (513)
Q Consensus 211 ~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~~LI~~nlrLV~sI 290 (513)
|.+|+||+++|..|+..++ ..||..|++.|+..|.++|+.+
T Consensus 7 ~~~~~~~~~~e~~l~~~~~---------------------------------------~~~d~~a~~~l~~~y~~lv~~~ 47 (268)
T PRK06288 7 GKIPKYAQQDETELWREYK---------------------------------------KTGDPKIREYLILKYSPLVKYV 47 (268)
T ss_pred CCCccccchHHHHHHHHHH---------------------------------------HcCCHHHHHHHHHHHHHHHHHH
Confidence 6789999999999877652 2468899999999999999999
Q ss_pred HHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhccccccccchhHHHHHHHHHHH
Q 010327 291 IKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAKL 370 (513)
Q Consensus 291 Akky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~iRlP~~~~~~~~ki~ka~~ 370 (513)
|++|......+.+++||+||||+|||+|+++||+.+|++|+||++|||++.|.++++. .+++|.++....+++.++..
T Consensus 48 a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~--~~~~p~~~~~~~~~i~~~~~ 125 (268)
T PRK06288 48 AGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRS--IDWIPRSVRQKARQIERAIA 125 (268)
T ss_pred HHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHh--cCccCHHHHHHHHHHHHHHH
Confidence 9998632235778999999999999999999999999999999999999999999982 35689999999999999999
Q ss_pred HHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhc--cCcccccCCCCC--chh--hhhccccCCCCCCchhhhHHHHHHHH
Q 010327 371 ELLFELKRVPTDEEIIQGVNISPERYREVMKAS--KPILSLHSRHGV--TQE--EFINGITDVDGVENENQRQPALLRLA 444 (513)
Q Consensus 371 ~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~--~~~~SLd~~~~~--~~~--e~~d~l~d~~~~~~ee~~~~~~l~~~ 444 (513)
.|.+++|+.||.+|||+.+|++.+++..++... ...+|||..... +.+ .+.+.+.+....+|++.....+....
T Consensus 126 ~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~l~~~~~~~~~~~pe~~~~~~e~~~~ 205 (268)
T PRK06288 126 MLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLESPAALNPDEIAEREEIKRV 205 (268)
T ss_pred HHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccCCCcccchhhhhccCCCCCCHHHHHHHHHHHHH
Confidence 999999999999999999999999999998654 456888876531 111 23444555555667777778888889
Q ss_pred HHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010327 445 LDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 504 (513)
Q Consensus 445 L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~ 504 (513)
|..+|+.||++++.||.++| ++++|++|||+.||+|.++|++++.+|+++||....
T Consensus 206 l~~~l~~L~~~~r~vl~l~~----~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~ 261 (268)
T PRK06288 206 IVEAIKTLPEREKKVLILYY----YEDLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLA 261 (268)
T ss_pred HHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999 789999999999999999999999999999997643
No 24
>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=3.2e-36 Score=295.77 Aligned_cols=224 Identities=30% Similarity=0.401 Sum_probs=197.1
Q ss_pred HHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHH
Q 010327 267 KCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSM 346 (513)
Q Consensus 267 ~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI 346 (513)
++..|+..|++.|+..|.++|+++|++|. +++.+++||+|||++|||+++++|||..|.+|+||++|||++.|.+++
T Consensus 4 ~~~~gd~~a~~~l~~~y~~~v~~~a~~~~---~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~l 80 (231)
T TIGR02885 4 LAQNGDKEARDKLIECNLRLVWSIVKRFL---NRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFL 80 (231)
T ss_pred HHHcCCHHHHHHHHHHhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHH
Confidence 34578999999999999999999999998 778999999999999999999999999999999999999999999999
Q ss_pred HhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh---hhhcc
Q 010327 347 TVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE---EFING 423 (513)
Q Consensus 347 ~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~---e~~d~ 423 (513)
+....+++|.++....+++.++...|..++|+.||.+|||+.+|++++++..++.....+.|||....++++ .+++.
T Consensus 81 r~~~~i~~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~ 160 (231)
T TIGR02885 81 RDDGIIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLDQ 160 (231)
T ss_pred HhCCCeECCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCCCcchhhhh
Confidence 955689999999999999999999999999999999999999999999999999888888999987654332 12333
Q ss_pred ccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 424 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 424 l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
+.++.. + .........|..+|+.||++|+.||.++| ++++|++|||+.||+|+++|++++++|+++||..
T Consensus 161 ~~~~~~--~---~~~~~~~~~l~~~l~~L~~~e~~i~~~~~----~~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~ 230 (231)
T TIGR02885 161 IADKGS--E---DSDWLEKIALKEAISKLDERERQIIMLRY----FKDKTQTEVANMLGISQVQVSRLEKKVLKKMKEK 230 (231)
T ss_pred cCCCCc--c---HHhHHHHHHHHHHHHcCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHh
Confidence 333211 1 12334566788999999999999999999 5799999999999999999999999999999963
No 25
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=100.00 E-value=2.4e-35 Score=294.04 Aligned_cols=225 Identities=25% Similarity=0.301 Sum_probs=197.5
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hc
Q 010327 271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VS 349 (513)
Q Consensus 271 gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~ 349 (513)
||..|++.|+..|.++|+.+|++|. +++.+.+||+||||+|||+|+++||++.|..|+||+++||++.|.++++ +.
T Consensus 26 gd~~a~~~l~~~y~~~v~~~a~~~~---~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~~~~lr~~~ 102 (255)
T TIGR02941 26 QNGEAQEKLVDHYQNLVYSIAYKYS---KGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKT 102 (255)
T ss_pred CCHHHHHHHHHHhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHHHHHHHHcC
Confidence 6789999999999999999999998 7889999999999999999999999999999999999999999999999 67
Q ss_pred cccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhc--cCcccccCCCCCchhhhhccccCC
Q 010327 350 SFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKAS--KPILSLHSRHGVTQEEFINGITDV 427 (513)
Q Consensus 350 r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~--~~~~SLd~~~~~~~~e~~d~l~d~ 427 (513)
..+++|.++.+..++++++...+...+|+.||.+|+|+.+|++.+++..++... ....|||.++..+++.......+.
T Consensus 103 ~~iri~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~ 182 (255)
T TIGR02941 103 WSVHVPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSDGSTVARLDS 182 (255)
T ss_pred CCcCCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCCCcccccccc
Confidence 789999999999999999999999999999999999999999999999887754 467888887654333211111111
Q ss_pred CCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 428 DGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 428 ~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
..++++.....+....|..+|+.||++++.||.++| ++++|++|||+.||||.++|++++.+|+++||...
T Consensus 183 -~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~ii~l~~----~~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~ 253 (255)
T TIGR02941 183 -VGEVEDGYDQTERRMVLEKILPILSEREKSIIHCTF----EENLSQKETGERLGISQMHVSRLQRQAISKLKEAA 253 (255)
T ss_pred -cCCcchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH----cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 122455566677778899999999999999999999 68999999999999999999999999999999753
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=4.2e-35 Score=286.94 Aligned_cols=222 Identities=31% Similarity=0.396 Sum_probs=194.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcc
Q 010327 272 GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSS 350 (513)
Q Consensus 272 d~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r 350 (513)
|..|++.||..|.++|+++|++|. +++.+.+||+|||++|||+|+++||+++|.+|+||++|||++.|.++++ +..
T Consensus 1 ~~~a~~~lv~~y~~~v~~~a~~~~---~~~~~~eDl~Qe~~i~l~~a~~~f~~~~~~~F~ty~~~~i~~~~~~~~r~~~~ 77 (227)
T TIGR02980 1 DKEAREKLVELNLPLVRSIARRFR---NRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTW 77 (227)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHhcCcccCCCcHHHHHHHHHHHHHHHHHHcCC
Confidence 457999999999999999999998 6788999999999999999999999999999999999999999999999 667
Q ss_pred ccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccC--cccccCCCCCchhhhhccccCCC
Q 010327 351 FTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKP--ILSLHSRHGVTQEEFINGITDVD 428 (513)
Q Consensus 351 ~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~--~~SLd~~~~~~~~e~~d~l~d~~ 428 (513)
.+++|.++.+..++++++...+.+.+|+.||.+|||+.+|++++++..++..... ..|||.+..++++. ...+.+ .
T Consensus 78 ~~ri~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~-~~~~~d-~ 155 (227)
T TIGR02980 78 AVRVPRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGD-PIALLD-T 155 (227)
T ss_pred ceecCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCC-Cccccc-c
Confidence 9999999999999999999999999999999999999999999999998887654 88999876522211 111111 1
Q ss_pred CCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 429 GVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 429 ~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
..++++..+..+....|..+|..||++|+.||.++| ++++|++|||+.||+|.++|++++.+|+++||+.
T Consensus 156 ~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~y----~~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~ 225 (227)
T TIGR02980 156 LGDEDDALETVEDRLALKPLLAALPERERRILLLRF----FEDKTQSEIAERLGISQMHVSRLLRRALKKLREQ 225 (227)
T ss_pred cCCcchHHHhHHHHHHHHHHHHcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 122344455667778899999999999999999999 6899999999999999999999999999999964
No 27
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=2.6e-34 Score=286.20 Aligned_cols=229 Identities=25% Similarity=0.329 Sum_probs=198.8
Q ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHh
Q 010327 269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV 348 (513)
Q Consensus 269 ~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~ 348 (513)
..||..|++.||..|.++|+++|.+|..++.++.+.+||+||||+|||+++++||+.+|.+|+||++|||++.|.++++.
T Consensus 17 ~~~d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~d~lR~ 96 (251)
T PRK07670 17 EERDPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRK 96 (251)
T ss_pred HcCCHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHh
Confidence 35689999999999999999999999743346889999999999999999999999999999999999999999999993
Q ss_pred ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHh--ccCcccccCCCCCchhh--hhccc
Q 010327 349 SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA--SKPILSLHSRHGVTQEE--FINGI 424 (513)
Q Consensus 349 ~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~--~~~~~SLd~~~~~~~~e--~~d~l 424 (513)
. .++|.++.+.+++++++...+.+.+|+.|+.+|||+.+|+++++|..++.. .....|||.+..++++. +...+
T Consensus 97 ~--~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~ 174 (251)
T PRK07670 97 E--DWLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDDGENVSVTI 174 (251)
T ss_pred c--CCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccCCCCcchhhhhh
Confidence 2 269999999999999999999999999999999999999999999999764 45778999886433322 22233
Q ss_pred cCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 425 TDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 425 ~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
.+....++++.....+....|..+|+.||+++|.||.++| ++++|++|||+.||+|.++|++++.+|+++||...
T Consensus 175 ~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 249 (251)
T PRK07670 175 RDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFY----KEELTLTEIGQVLNLSTSRISQIHSKALFKLKKLL 249 (251)
T ss_pred cCcCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 3444445666667777788899999999999999999999 79999999999999999999999999999999643
No 28
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=100.00 E-value=3.9e-34 Score=282.18 Aligned_cols=212 Identities=21% Similarity=0.281 Sum_probs=180.8
Q ss_pred HHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhcccccc
Q 010327 275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRV 354 (513)
Q Consensus 275 Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~iRl 354 (513)
....|+..|++||.++|++|......+.+.+||+|||++|||+|+++||+..| +|+|||+|||+++|.++++.. .++
T Consensus 16 ~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~--~~~ 92 (231)
T PRK12427 16 EEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELREL--DWR 92 (231)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhc--CCC
Confidence 45688999999999999999865556789999999999999999999998666 899999999999999999932 247
Q ss_pred ccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHh--ccCcccccCCCCCchhhhhccccCCCCCCc
Q 010327 355 PFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA--SKPILSLHSRHGVTQEEFINGITDVDGVEN 432 (513)
Q Consensus 355 P~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~--~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ 432 (513)
|.++....++++++...|.+++|+.||.+|||+.||+++++|.+++.. .....|||.+.+.++.. +.+ + ..++
T Consensus 93 ~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~--~~~-~--~~~~ 167 (231)
T PRK12427 93 PRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAHN--DIL-Q--SRDL 167 (231)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCcc--ccc-C--CCCH
Confidence 888999999999999999999999999999999999999999998764 45789999986543321 111 1 1112
Q ss_pred hhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 433 ENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 433 ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
+ +.......|..+|..||++++.||.++| ++++|++|||+.||||.++|+|++.+|+++||.
T Consensus 168 ~---~~~~~~~~l~~~l~~L~~~er~vi~l~~----~~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr~ 229 (231)
T PRK12427 168 E---ENIIIEDNLKQALSQLDEREQLILHLYY----QHEMSLKEIALVLDLTEARICQLNKKIAQKIKS 229 (231)
T ss_pred H---HHHHHHHHHHHHHHcCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHh
Confidence 2 2334566789999999999999999999 689999999999999999999999999999985
No 29
>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=3.5e-34 Score=280.27 Aligned_cols=218 Identities=28% Similarity=0.411 Sum_probs=190.3
Q ss_pred HHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhccccccccch
Q 010327 279 LIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGL 358 (513)
Q Consensus 279 LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~iRlP~~~ 358 (513)
|+..|.++|+++|++|..+++++.+++||+|||++|||+|+++|||++|++|+||+++||++.+.++++.. .++|.++
T Consensus 1 L~~~~~~lv~~~a~~~~~~~~~~~~~eDl~Qe~~~~l~~a~~~fd~~~~~~f~t~~~~~i~~~~~~~lr~~--~~~p~~~ 78 (224)
T TIGR02479 1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRL--DWVPRSL 78 (224)
T ss_pred CHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHHc--CccCHHH
Confidence 68899999999999998544478999999999999999999999999999999999999999999999832 3699999
Q ss_pred hHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhc--cCcccccCCCCCc--hhhhhccccCCCCCCchh
Q 010327 359 ESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKAS--KPILSLHSRHGVT--QEEFINGITDVDGVENEN 434 (513)
Q Consensus 359 ~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~--~~~~SLd~~~~~~--~~e~~d~l~d~~~~~~ee 434 (513)
...++++.++..+|.+++|+.|+.+|||+.+|+++++|..++... ...+|+|....+. ...+.+.+.++...++++
T Consensus 79 ~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~~ 158 (224)
T TIGR02479 79 RQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDKSEDPEE 158 (224)
T ss_pred HHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhccccccCCHHH
Confidence 999999999999999999999999999999999999999998643 4567888754432 122333444444556777
Q ss_pred hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 435 QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 435 ~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
.....+....|..+|+.||++++.||.++| .+++|++|||+.||+|.++|++++.+|+++||..
T Consensus 159 ~~~~~~~~~~l~~~l~~L~~~~r~il~l~y----~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 159 ELEREELREALAEAIESLSEREQLVLSLYY----YEELNLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----hCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 777888888999999999999999999999 7899999999999999999999999999999964
No 30
>PRK05572 sporulation sigma factor SigF; Validated
Probab=100.00 E-value=1e-33 Score=282.17 Aligned_cols=242 Identities=29% Similarity=0.404 Sum_probs=208.5
Q ss_pred HhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHHHHHHHHHHHH
Q 010327 208 KKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLV 287 (513)
Q Consensus 208 ~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~~LI~~nlrLV 287 (513)
+.-+..|.||.+++..|...+ ..|+..|++.|+..|.++|
T Consensus 6 ~~~~~~~~l~~~~~~~li~~~----------------------------------------~~gd~~a~~~L~~~y~~~v 45 (252)
T PRK05572 6 KNKKKKPQLKDEENKELIKKS----------------------------------------QDGDQEARDTLVEKNLRLV 45 (252)
T ss_pred ccCcCCCCCCHHHHHHHHHHH----------------------------------------HcCCHHHHHHHHHHhHHHH
Confidence 345678999998887774433 3578899999999999999
Q ss_pred HHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhccccccccchhHHHHHHHH
Q 010327 288 LFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQR 367 (513)
Q Consensus 288 ~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~iRlP~~~~~~~~ki~k 367 (513)
+.+|++|. +++.+++||+||||+++|+++++|++.+|.+|+||+++||++.|.++++..+.+++|.++....+++++
T Consensus 46 ~~~a~~~~---~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~~~~~r~~~~~~~~~~~~~~ 122 (252)
T PRK05572 46 WSVVQRFL---NRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDGTVKVSRSLKETANKIRK 122 (252)
T ss_pred HHHHHHHc---cCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHH
Confidence 99999998 788999999999999999999999999888999999999999999999966789999999999999999
Q ss_pred HHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhh---hhccccCCCCCCchhhhHHHHHHHH
Q 010327 368 AKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEE---FINGITDVDGVENENQRQPALLRLA 444 (513)
Q Consensus 368 a~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e---~~d~l~d~~~~~~ee~~~~~~l~~~ 444 (513)
+...+..++||.|+.+|+|+.+|++++++..++.....+.||+.+..+++.. ..+.+.++. .........
T Consensus 123 ~~~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~~-------~~~~~~~~~ 195 (252)
T PRK05572 123 DKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITLLDQIADQS-------EEDWFDKIA 195 (252)
T ss_pred HHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCCCCcchhhhhcCCCc-------hhhHHHHHH
Confidence 9999999999999999999999999999999988888888998775433221 112222211 122345678
Q ss_pred HHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 445 LDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 445 L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
|..+|+.||++++.||.++| ++++|++|||+.||+|.++|++++.+|+++||...
T Consensus 196 l~~~l~~L~~~~~~v~~l~~----~~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l 250 (252)
T PRK05572 196 LKEAIRELDERERLIVYLRY----FKDKTQSEVAKRLGISQVQVSRLEKKILKQMKEKL 250 (252)
T ss_pred HHHHHHcCCHHHHHHHHHHH----hCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 89999999999999999999 68999999999999999999999999999999643
No 31
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=100.00 E-value=2.9e-33 Score=279.29 Aligned_cols=227 Identities=25% Similarity=0.299 Sum_probs=196.7
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-h
Q 010327 270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-V 348 (513)
Q Consensus 270 ~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~ 348 (513)
.||..|++.|+..|.++|+++|++|. +++.+++||+||||++||+++++||+..|.+|+||+++||++.|.++++ +
T Consensus 25 ~gd~~a~~~l~~~~~~~v~~~a~~~~---~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~~~~lr~~ 101 (257)
T PRK08583 25 NQDEEAQEKLVKHYKNLVESLAYKYS---KGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDK 101 (257)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHHHHHHhc
Confidence 37889999999999999999999998 7788999999999999999999999999989999999999999999999 6
Q ss_pred ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhc--cCcccccCCCCCchhhhhccccC
Q 010327 349 SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKAS--KPILSLHSRHGVTQEEFINGITD 426 (513)
Q Consensus 349 ~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~--~~~~SLd~~~~~~~~e~~d~l~d 426 (513)
...+++|.++.+..+++..+...+...++|.|+.+|+|+.+|++.+++...+... ....|+|.+.+.+++.....+.+
T Consensus 102 ~~~~~i~r~~~~~~~~~~~~~~~~~~~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~ 181 (257)
T PRK08583 102 TWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDGSTVTLLD 181 (257)
T ss_pred CCCcCCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCCCCccchHhh
Confidence 7789999999999999999999999999999999999999999999998887654 35678887764433221111111
Q ss_pred CCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010327 427 VDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 504 (513)
Q Consensus 427 ~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~ 504 (513)
...++++.....+....|..+|..||++++.||.++| ++++|++|||+.||||.++|++++++|+++||....
T Consensus 182 -~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l~ 254 (257)
T PRK08583 182 -IVGQQEDGYELTEQRMILEKILPVLSDREKSIIQCTF----IENLSQKETGERLGISQMHVSRLQRQAIKKLREAAF 254 (257)
T ss_pred -hcCCcchhHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----hCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 1123455556667778899999999999999999999 689999999999999999999999999999997543
No 32
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=100.00 E-value=7.8e-33 Score=272.97 Aligned_cols=226 Identities=24% Similarity=0.358 Sum_probs=193.6
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhcc
Q 010327 271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSS 350 (513)
Q Consensus 271 gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r 350 (513)
.|.-+++.|+..|.++|+++|++|..+++++.+++||+||||+|||+++++|||+.|.+|+||+++||++.+.+++++..
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 45678999999999999999999974445788999999999999999999999999999999999999999999999322
Q ss_pred ccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhc--cCcccccCCCCCchhhhhccccCCC
Q 010327 351 FTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKAS--KPILSLHSRHGVTQEEFINGITDVD 428 (513)
Q Consensus 351 ~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~--~~~~SLd~~~~~~~~e~~d~l~d~~ 428 (513)
++|.++.....++.++...+.+.+|+.||.+|||+.+|++.++|..++... ...+|++...+.+++.+. ...++.
T Consensus 85 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~-~~~~~~ 161 (236)
T PRK06986 85 --WVPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDSIL-VTEDHQ 161 (236)
T ss_pred --CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCcccc-cccCCC
Confidence 368888888888999999999999999999999999999999999998764 356678877554433322 122233
Q ss_pred CCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 429 GVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 429 ~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
..++++.....+....|..+|+.||++++.||.++| .+++|++|||+.||||.++|++++.+|+++||+..
T Consensus 162 ~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 162 DEDPLQQLEDEELREALVEAIESLPEREQLVLSLYY----QEELNLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHh----ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 345666677777888999999999999999999999 78999999999999999999999999999999753
No 33
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=99.95 E-value=5.1e-27 Score=231.30 Aligned_cols=207 Identities=30% Similarity=0.382 Sum_probs=164.4
Q ss_pred hHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHHHHHH
Q 010327 202 LVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIK 281 (513)
Q Consensus 202 ~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~~LI~ 281 (513)
++..|+.++++.|+||++++..|...+ ..|+..|++.|+.
T Consensus 17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~----------------------------------------~~gd~~a~~~l~~ 56 (233)
T PRK05803 17 FLVSYVKNNSFPQPLSEEEERKYLELM----------------------------------------KEGDEEARNILIE 56 (233)
T ss_pred HHHHHHHHhcccCCCCHHHHHHHHHHH----------------------------------------HcCCHHHHHHHHH
Confidence 677899999999999999988775444 3578899999999
Q ss_pred HHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccccchhH
Q 010327 282 HNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLES 360 (513)
Q Consensus 282 ~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~~~~ 360 (513)
.|.++|+++|.+|. +++.+.+||+|||+++||+++++||+++|.+|.||+++|+++.+.++++ ..+..
T Consensus 57 ~y~~~l~~~a~~~~---~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~~~-------- 125 (233)
T PRK05803 57 RNLRLVAHIVKKFE---NTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTK-------- 125 (233)
T ss_pred HhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhccc--------
Confidence 99999999999998 7889999999999999999999999998889999999999999999988 32110
Q ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCc--h--hhhhccccCCCCCCchhhh
Q 010327 361 VRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVT--Q--EEFINGITDVDGVENENQR 436 (513)
Q Consensus 361 ~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~--~--~e~~d~l~d~~~~~~ee~~ 436 (513)
...+++.....+ + ..+.+...+ ...++++..
T Consensus 126 --------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~ 160 (233)
T PRK05803 126 --------------------------------------------KEVSLQDPIGVDKEGNEISLIDILGS-EEDDVIEQV 160 (233)
T ss_pred --------------------------------------------cCCCccccccCCCCcCcccHHHHccC-CCCCHHHHH
Confidence 001111111000 0 011111111 122345555
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010327 437 QPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 504 (513)
Q Consensus 437 ~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~ 504 (513)
........|..+|+.||+++|+||.++|++.+++++|++|||+.||||.++|++++.+|+++||....
T Consensus 161 ~~~~~~~~l~~~l~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~ 228 (233)
T PRK05803 161 ELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKELY 228 (233)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 66667778999999999999999999998877799999999999999999999999999999997654
No 34
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=99.92 E-value=1.8e-23 Score=205.82 Aligned_cols=180 Identities=26% Similarity=0.409 Sum_probs=137.8
Q ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH
Q 010327 268 CLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT 347 (513)
Q Consensus 268 ~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~ 347 (513)
+..||..|++.|+..|.++|+.+|++|. +++.+.+|++||+|+++|+++++|++..+++|.||+++++++.+.++++
T Consensus 46 ~~~gd~~af~~l~~~y~~~l~~~a~~~~---~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~d~lR 122 (234)
T PRK08301 46 LPKGDEAVRSLLIERNLRLVVYIARKFE---NTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLR 122 (234)
T ss_pred HHccCHHHHHHHHHHhHHHHHHHHHHhh---cCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHHHH
Confidence 4568899999999999999999999998 7788999999999999999999999988889999999999999999998
Q ss_pred -hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCC--chh-h-hhc
Q 010327 348 -VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGV--TQE-E-FIN 422 (513)
Q Consensus 348 -~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~--~~~-e-~~d 422 (513)
+.+.. ...+++..... ++. . ..+
T Consensus 123 k~~~~~----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~ 150 (234)
T PRK08301 123 RNNKVK----------------------------------------------------AEVSFDEPLNIDWDGNELLLSD 150 (234)
T ss_pred HHhccc----------------------------------------------------cccccccccccccCCCcccHHH
Confidence 32110 00111111000 000 0 001
Q ss_pred cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
...+ ....+............|..+|++||+++|.||.++|+|...+++|++|||+.||||.++|++++++|+++||+.
T Consensus 151 ~~~~-~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 151 VLGT-DNDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred hccC-cccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 1111 111122233344556679999999999999999999987667899999999999999999999999999999975
Q ss_pred c
Q 010327 503 T 503 (513)
Q Consensus 503 ~ 503 (513)
.
T Consensus 230 l 230 (234)
T PRK08301 230 I 230 (234)
T ss_pred H
Confidence 3
No 35
>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=99.92 E-value=2.7e-23 Score=204.23 Aligned_cols=179 Identities=35% Similarity=0.438 Sum_probs=137.5
Q ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH
Q 010327 268 CLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT 347 (513)
Q Consensus 268 ~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~ 347 (513)
+..|+..|++.|+..|.++|+++|.+|. ++..+.+||+||+|+++|+++++|+++.+..|.||+++++++.+.++++
T Consensus 42 ~~~gd~~af~~l~~~y~~~v~~~~~~~~---~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~R 118 (227)
T TIGR02846 42 LKEGDEEARNVLIERNLRLVAHIVKKFS---NTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHLR 118 (227)
T ss_pred HHcCCHHHHHHHHHHhHHHHHHHHHHhc---CCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHHH
Confidence 3568899999999999999999999998 6788999999999999999999999988888999999999999999998
Q ss_pred -hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCC--ch--hhhhc
Q 010327 348 -VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGV--TQ--EEFIN 422 (513)
Q Consensus 348 -~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~--~~--~e~~d 422 (513)
..+..+ ..+++..... +. ....+
T Consensus 119 k~~r~~~----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~ 146 (227)
T TIGR02846 119 ALKKTKG----------------------------------------------------EVSLQDPIGVDKEGNEISLID 146 (227)
T ss_pred HHhcccc----------------------------------------------------ceeccccccCCcccCcccHHH
Confidence 321100 0011110000 00 00111
Q ss_pred cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
... .....+++.....+....|..+|+.||+++|+||.++|.++.++++|++|||+.||+|.++|++++++|+++||+.
T Consensus 147 ~~~-~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~ 225 (227)
T TIGR02846 147 ILG-SDGDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYKE 225 (227)
T ss_pred Hhc-CCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 111 1122244444555666779999999999999999999955444899999999999999999999999999999964
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=99.90 E-value=3.4e-22 Score=197.20 Aligned_cols=184 Identities=26% Similarity=0.402 Sum_probs=139.0
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHH
Q 010327 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR 344 (513)
Q Consensus 265 L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~r 344 (513)
+..+..|+..|++.|+..|.+.|+++|.+|. +++.+.+||+||+|+++|+++++|++..+++|+||++.++++.+.+
T Consensus 43 ~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~---~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~d 119 (234)
T TIGR02835 43 LQKLTQGDESAKSTLIERNLRLVVYIARKFE---NTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILM 119 (234)
T ss_pred HHHHHcCCHHHHHHHHHHhHHHHHHHHHHhc---cCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHH
Confidence 3444678899999999999999999999998 7888999999999999999999999888888999999999999999
Q ss_pred HHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCC---Cchhhh
Q 010327 345 SMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHG---VTQEEF 420 (513)
Q Consensus 345 aI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~---~~~~e~ 420 (513)
+++ +.+... ..+++.... .++...
T Consensus 120 ~~Rk~~r~~~----------------------------------------------------~~~~~~~~~~~~~~~~~~ 147 (234)
T TIGR02835 120 YLRRNNKTRS----------------------------------------------------EVSFDEPLNVDWDGNELL 147 (234)
T ss_pred HHHHhccccC----------------------------------------------------cccccccccCCCCCCcch
Confidence 998 322100 001111100 000000
Q ss_pred hccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010327 421 INGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 500 (513)
Q Consensus 421 ~d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR 500 (513)
.....+.+...+++..........|..+|+.||++++.||.++|.|.+++++|++|||+.||||..+|++++.+|+++||
T Consensus 148 ~~~~~~~~~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR 227 (234)
T TIGR02835 148 LSDVLGTDSDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLK 227 (234)
T ss_pred HHHhcCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 00111111111223334445566799999999999999999999665558999999999999999999999999999999
Q ss_pred Ccc
Q 010327 501 HPT 503 (513)
Q Consensus 501 ~~~ 503 (513)
+..
T Consensus 228 ~~l 230 (234)
T TIGR02835 228 KEI 230 (234)
T ss_pred HHh
Confidence 754
No 37
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=99.87 E-value=3.7e-21 Score=184.93 Aligned_cols=186 Identities=18% Similarity=0.228 Sum_probs=138.2
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHH
Q 010327 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (513)
Q Consensus 264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~ 343 (513)
.+..+..|+..|++.|+..|.++|+.+|.+|. ++..+.+||+||+|++||+++++|++.++.+|.||++.++++.+.
T Consensus 14 l~~~~~~~d~~a~~~l~~~y~~~v~~~~~~~~---~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n~~~ 90 (208)
T PRK08295 14 LVELARSGDKEALEYLIEKYKNFVRAKARSYF---LIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQII 90 (208)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHH
Confidence 34556789999999999999999999999998 788999999999999999999999998877999999999999999
Q ss_pred HHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCch--hhh
Q 010327 344 RSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ--EEF 420 (513)
Q Consensus 344 raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~--~e~ 420 (513)
++++ ..+..+.+. ....|++.....+. ..+
T Consensus 91 d~~r~~~r~~~~~~-----------------------------------------------~~~~s~~~~~~~~~~~~~~ 123 (208)
T PRK08295 91 TAIKTANRQKHIPL-----------------------------------------------NSYVSLDKPIYDEESDRTL 123 (208)
T ss_pred HHHHHhhhhccccc-----------------------------------------------cceeecCCcccCCccchhH
Confidence 8887 222111110 00112222111101 111
Q ss_pred hccccCCCCCCchhhhHHHHHHHHH-HHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010327 421 INGITDVDGVENENQRQPALLRLAL-DDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 499 (513)
Q Consensus 421 ~d~l~d~~~~~~ee~~~~~~l~~~L-~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKL 499 (513)
.+.+.++...+|++.....+....+ ..+++.||+.++.||.+ | .+++|++|||+.||+|.++|+..+.+|+++|
T Consensus 124 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l-~----~e~~s~~EIA~~lgis~~tV~~~l~rar~~L 198 (208)
T PRK08295 124 LDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLEL-Y----LDGKSYQEIAEELNRHVKSIDNALQRVKRKL 198 (208)
T ss_pred HHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHH-H----HccCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 1212222223455444444444445 56779999999999999 7 5899999999999999999999999999999
Q ss_pred hCcch
Q 010327 500 KHPTR 504 (513)
Q Consensus 500 R~~~~ 504 (513)
|....
T Consensus 199 r~~l~ 203 (208)
T PRK08295 199 EKYLE 203 (208)
T ss_pred HHHHH
Confidence 97654
No 38
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=99.86 E-value=1.6e-20 Score=178.48 Aligned_cols=171 Identities=17% Similarity=0.168 Sum_probs=134.5
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhcc-CCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHH
Q 010327 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDF-ANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (513)
Q Consensus 265 L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~-~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~ 343 (513)
+.....|+..|++.|+..|.+.|+.+|.++..+. +...+.+|++||+|++||+++.+|++. +..|.+|++..+++.+.
T Consensus 15 ~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~n~~~ 93 (189)
T PRK09648 15 VAEAVAGDRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAAHKVA 93 (189)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHHHHHH
Confidence 5566789999999999999999999999987321 124689999999999999999999864 45799999999999999
Q ss_pred HHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010327 344 RSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN 422 (513)
Q Consensus 344 raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d 422 (513)
++++ +.+....+ .+ ...+
T Consensus 94 d~~r~~~r~~~~~-----------------------------------------------------~~--------~~~~ 112 (189)
T PRK09648 94 DAHRAAGRDKAVP-----------------------------------------------------TE--------EVPE 112 (189)
T ss_pred HHHHHhCCCcccc-----------------------------------------------------cc--------cccc
Confidence 9888 32210000 00 0000
Q ss_pred cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
.. + ...++++.....+....|..+|..||+++|.||.++| ++++|++|||+.||||..+|++.+.||+++||+.
T Consensus 113 ~~-~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 113 RP-S-DDAGPEERALRSESSNRMRELLDTLPEKQREILILRV----VVGLSAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred cc-c-cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 00 1 1123455555666777899999999999999999999 7899999999999999999999999999999965
Q ss_pred c
Q 010327 503 T 503 (513)
Q Consensus 503 ~ 503 (513)
.
T Consensus 187 l 187 (189)
T PRK09648 187 I 187 (189)
T ss_pred h
Confidence 3
No 39
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=99.86 E-value=1.4e-20 Score=178.48 Aligned_cols=170 Identities=12% Similarity=0.130 Sum_probs=136.6
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010327 263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI 342 (513)
Q Consensus 263 e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI 342 (513)
..+..+..|+..|++.|+..|.++|+.+|.+|. +++.+.+|++||+|++||+++.+|++. +..|.+|++..+++.+
T Consensus 9 ~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n~~ 84 (186)
T PRK05602 9 ELLARVAAGDPAAFRVLVARKLPRLLALATRML---GDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLNLC 84 (186)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHHHH
Confidence 345667889999999999999999999999998 778899999999999999999999986 4579999999999999
Q ss_pred HHHHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010327 343 IRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN 422 (513)
Q Consensus 343 ~raI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d 422 (513)
.++++..+.. + .+. ..+
T Consensus 85 ~d~~R~~~~~--~-----------------------------------------------------~~~-----~~~--- 101 (186)
T PRK05602 85 YDRLRRRREV--P-----------------------------------------------------VED-----APD--- 101 (186)
T ss_pred HHHHHhcCCC--C-----------------------------------------------------ccc-----ccc---
Confidence 8888721100 0 000 000
Q ss_pred cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
..+ ....++......+....+..+|+.||++++.||.++| ++++|++|||+.||+|..+|++.+++|+++||+.
T Consensus 102 -~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 175 (186)
T PRK05602 102 -VPD-PAPGPDAGLEARQRARRVEQALAALPERQREAIVLQY----YQGLSNIEAAAVMDISVDALESLLARGRRALRAQ 175 (186)
T ss_pred -cCC-CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHH----hcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 001 1112344444556667799999999999999999999 7999999999999999999999999999999976
Q ss_pred chh
Q 010327 503 TRV 505 (513)
Q Consensus 503 ~~~ 505 (513)
...
T Consensus 176 l~~ 178 (186)
T PRK05602 176 LAD 178 (186)
T ss_pred HHh
Confidence 543
No 40
>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=99.86 E-value=2.6e-20 Score=172.95 Aligned_cols=167 Identities=17% Similarity=0.179 Sum_probs=134.4
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHH
Q 010327 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR 344 (513)
Q Consensus 265 L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~r 344 (513)
+.+..+||..|++.|+..|.+.+++++.++. ++..+++|++||+|+.+|++.++|+...+ .|.+|++..+++.+.+
T Consensus 2 i~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d 77 (170)
T TIGR02952 2 LERAQDREEDAFARIYETYSDRVYRYIYYRV---GCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVND 77 (170)
T ss_pred hHHHHccCHHHHHHHHHHHHHHHHHHHHHHH---CChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHH
Confidence 3456779999999999999999999999887 67789999999999999999999997555 7999999999999999
Q ss_pred HHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhcc
Q 010327 345 SMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING 423 (513)
Q Consensus 345 aI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~ 423 (513)
+++ +.+.... +++ .....
T Consensus 78 ~~R~~~~~~~~-----------------------------------------------------~~~--------~~~~~ 96 (170)
T TIGR02952 78 YFRGSKRHPLF-----------------------------------------------------SLD--------VFKEL 96 (170)
T ss_pred HHHhcCCCCCC-----------------------------------------------------cHH--------HHhhc
Confidence 998 3221000 000 00000
Q ss_pred ccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 424 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 424 l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
.. ...++++.....+....+..+|..|||+++.||.++| .+++|++|||+.||||.++|++.+.||+++||+.
T Consensus 97 ~~--~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~ 169 (170)
T TIGR02952 97 LS--NEPNPEEAILKEEANEKLLKALKILTPKQQHVIALRF----GQNLPIAEVARILGKTEGAVKILQFRAIKKLARQ 169 (170)
T ss_pred CC--CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 00 1123455555566677899999999999999999999 7899999999999999999999999999999964
No 41
>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=99.86 E-value=2.1e-20 Score=178.13 Aligned_cols=185 Identities=18% Similarity=0.229 Sum_probs=136.8
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010327 263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI 342 (513)
Q Consensus 263 e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI 342 (513)
+.+..+..|+..|++.|+..|.+.|+.+|.++. ++..+++||+||+|+.+|+++.+|++..+..|+||++.+|++.+
T Consensus 8 ~l~~~~~~~d~~a~~~l~~~~~~~l~~~a~~~~---~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~~~ 84 (198)
T TIGR02859 8 EIVELARQGNTHALEYLINKYKNFVRAKARSYF---LIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTRQI 84 (198)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHc---cccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHHHH
Confidence 345566788999999999999999999999998 67889999999999999999999999887799999999999998
Q ss_pred HHHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCC--chhh
Q 010327 343 IRSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGV--TQEE 419 (513)
Q Consensus 343 ~raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~--~~~e 419 (513)
.++++ ..+..+.+ .....|++.+... .+++
T Consensus 85 ~~~~r~~~~~~~~~-----------------------------------------------~~~~~~~~~~~~~~~~~~~ 117 (198)
T TIGR02859 85 ITAIKTATRQKHIP-----------------------------------------------LNSYVSLNKPIYDEESDRT 117 (198)
T ss_pred HHHHHHHHHhcccc-----------------------------------------------hhhhcCcccccccccccch
Confidence 88877 21111100 0011222222111 1111
Q ss_pred hhccccCCCCCCchhhhHHHHHHHHHHHHHhcC-CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010327 420 FINGITDVDGVENENQRQPALLRLALDDVLDSL-KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 498 (513)
Q Consensus 420 ~~d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L-~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkK 498 (513)
+.+.+.+....++++.....+....|..+|+.| ++.++.|+. +| .+++|++|||+.||+|.++|+..+++|+++
T Consensus 118 ~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~-~~----~~~~s~~eIA~~l~~s~~tV~~~l~r~r~~ 192 (198)
T TIGR02859 118 LLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQ-SY----LDGKSYQEIACDLNRHVKSIDNALQRVKRK 192 (198)
T ss_pred HHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHH-HH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 222222122234566666667777889999995 666666665 46 589999999999999999999999999999
Q ss_pred HhCc
Q 010327 499 LKHP 502 (513)
Q Consensus 499 LR~~ 502 (513)
||+.
T Consensus 193 L~~~ 196 (198)
T TIGR02859 193 LEKY 196 (198)
T ss_pred HHHh
Confidence 9964
No 42
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=1.2e-20 Score=180.11 Aligned_cols=176 Identities=20% Similarity=0.196 Sum_probs=140.4
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHH
Q 010327 262 AAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHA 341 (513)
Q Consensus 262 ~e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~a 341 (513)
.+.+..+..||..|++.|+..|.+.|+++|.++. ++..+.+|++||+|+++|++.++|++.. .|.+|++..+++.
T Consensus 14 ~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~---~~~~daeDlvQe~fi~l~~~~~~~~~~~--~f~~wl~~i~~n~ 88 (194)
T PRK12513 14 EALMLRYRAGDAAAFEALYARHRTGLYRFLLRLA---RDRALAEDIFQETWLRVIRARAQYQPRA--RFRTWLYQIARNL 88 (194)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHHHHhcCCCC--chHHHHHHHHHHH
Confidence 3457777889999999999999999999999998 7788999999999999999999999743 6999999999999
Q ss_pred HHHHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhh
Q 010327 342 IIRSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEF 420 (513)
Q Consensus 342 I~raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~ 420 (513)
+.++++ ..+..+.+ .+. +...
T Consensus 89 ~~~~~R~~~~~~~~~-----------------------------------------------------~~~-----~~~~ 110 (194)
T PRK12513 89 LIDHWRRHGARQAPS-----------------------------------------------------LDA-----DEQL 110 (194)
T ss_pred HHHHHHHhccccccc-----------------------------------------------------ccc-----chhh
Confidence 999988 32211110 000 0000
Q ss_pred hccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010327 421 INGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 500 (513)
Q Consensus 421 ~d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR 500 (513)
.... ....+++...+..+....|..+|+.||++++.||.++| .+++|++|||+.||+|.++|++++.+|+++||
T Consensus 111 -~~~~-~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr 184 (194)
T PRK12513 111 -HALA-DDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLRE----HGDLELEEIAELTGVPEETVKSRLRYALQKLR 184 (194)
T ss_pred -hhcC-CCCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeeh----ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 0001 11223455556667778899999999999999999999 78999999999999999999999999999999
Q ss_pred Ccchhh
Q 010327 501 HPTRVD 506 (513)
Q Consensus 501 ~~~~~~ 506 (513)
......
T Consensus 185 ~~l~~~ 190 (194)
T PRK12513 185 ELLAEE 190 (194)
T ss_pred HHHHHh
Confidence 765543
No 43
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=99.85 E-value=1.7e-20 Score=175.09 Aligned_cols=173 Identities=16% Similarity=0.108 Sum_probs=134.9
Q ss_pred HHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHH
Q 010327 267 KCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSM 346 (513)
Q Consensus 267 ~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI 346 (513)
++.+||..|++.|+..|.++|+.++++|. +++.+.+|++||++++||++++.|+ .+.+|.+|++..+++.+.+.+
T Consensus 3 ~~~~gd~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~ 77 (182)
T PRK09652 3 RVQRGDRAAFALLVRRYQPRVKRLLSRLT---RDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYL 77 (182)
T ss_pred hhhcCCHHHHHHHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHH
Confidence 45679999999999999999999999998 6788999999999999999999999 455899999999999999988
Q ss_pred Hh-ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhcccc
Q 010327 347 TV-SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGIT 425 (513)
Q Consensus 347 ~~-~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~ 425 (513)
++ .+....+ ..+.+.. ++....+..
T Consensus 78 r~~~~~~~~~--------------------------------------------------~~~~~~~---~~~~~~~~~- 103 (182)
T PRK09652 78 RKQGRRPPAS--------------------------------------------------DVDAEEA---EDFDLADAL- 103 (182)
T ss_pred HcccCCCCcc--------------------------------------------------ccccccc---ccccccccc-
Confidence 83 2211000 0000000 000001111
Q ss_pred CCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 426 DVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 426 d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
+ ...++++.....+....+..+|..|||+++.||.++| ..++|++|||+.||+|..+|++.+.+|+++||+..
T Consensus 104 ~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 104 R-DISTPENELLSAELEQRVRAAIESLPEELRTAITLRE----IEGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred c-cccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 1 1123555556666778899999999999999999998 68999999999999999999999999999999754
No 44
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=99.85 E-value=2.4e-20 Score=175.96 Aligned_cols=177 Identities=19% Similarity=0.209 Sum_probs=136.9
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010327 263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI 342 (513)
Q Consensus 263 e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI 342 (513)
..+..+.+|+..|+..|+..|.++|+.+|.+|. +++.+++|++||+|+++|+++..|++.. .|.+|++..+++.+
T Consensus 7 ~li~~~~~gd~~a~~~l~~~y~~~v~~~~~~~~---~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~ 81 (187)
T TIGR02948 7 KRIKEVRKGDENAFADLVDLYKDKIYQLCYRML---GNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLT 81 (187)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHH
Confidence 346677889999999999999999999999998 7788999999999999999999999865 69999999999999
Q ss_pred HHHHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCC-CCchhhhh
Q 010327 343 IRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRH-GVTQEEFI 421 (513)
Q Consensus 343 ~raI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~-~~~~~e~~ 421 (513)
.++++..+. . . .++... ..+.....
T Consensus 82 ~~~~rk~~~-~-~----------------------------------------------------~~~~~~~~~~~~~~~ 107 (187)
T TIGR02948 82 IDRLRKRKP-D-F----------------------------------------------------YLDDEVQGTDGLTME 107 (187)
T ss_pred HHHHHhhcc-c-c----------------------------------------------------cccccccCccccccc
Confidence 988872110 0 0 000000 00000001
Q ss_pred ccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 422 NGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 422 d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
+...+ ...++++.....+....+..+|+.|||+++.||.++| .+++|++|||+.||+|.++|++.+.||+++||.
T Consensus 108 ~~~~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 108 SQLAA-DEAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKY----MEDLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred ccccc-CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 11111 1223445555556667799999999999999999998 689999999999999999999999999999996
Q ss_pred cc
Q 010327 502 PT 503 (513)
Q Consensus 502 ~~ 503 (513)
..
T Consensus 183 ~l 184 (187)
T TIGR02948 183 QL 184 (187)
T ss_pred Hh
Confidence 54
No 45
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=99.85 E-value=3.3e-20 Score=177.50 Aligned_cols=170 Identities=15% Similarity=0.190 Sum_probs=134.1
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHH
Q 010327 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR 344 (513)
Q Consensus 265 L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~r 344 (513)
+.....|+..|++.|+..|.++|+.+|.+|. ++..+.+|++||+|+++|+++++||+.+| .|.+|++..+++.+.+
T Consensus 21 i~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~---~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~d 96 (194)
T PRK09646 21 LRRVARGDQDAFAELYDRTSSRVYGLVRRVL---RDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHRRAVD 96 (194)
T ss_pred HHHHHccCHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHHHHHH
Confidence 4556778999999999999999999999999 78899999999999999999999998765 6999999999999999
Q ss_pred HHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhcc
Q 010327 345 SMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING 423 (513)
Q Consensus 345 aI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~ 423 (513)
.++ +.+..+.- .+.. .. +
T Consensus 97 ~~r~~~~~~~~~---------------------------------------------------~~~~-------~~--~- 115 (194)
T PRK09646 97 RVRSEQAASQRE---------------------------------------------------VRYG-------AR--N- 115 (194)
T ss_pred HHHhhccccccc---------------------------------------------------cccc-------cc--c-
Confidence 888 32110000 0000 00 0
Q ss_pred ccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 424 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 424 l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
. +.....+++.....+....|..+|..||++++.||.++| .+++|++|||+.||+|..+|++++++|+++||...
T Consensus 116 ~-~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 116 V-DPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAY----YGGLTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred c-cccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 0 000111233333445567899999999999999999999 78999999999999999999999999999999765
Q ss_pred h
Q 010327 504 R 504 (513)
Q Consensus 504 ~ 504 (513)
.
T Consensus 191 ~ 191 (194)
T PRK09646 191 G 191 (194)
T ss_pred c
Confidence 3
No 46
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=99.85 E-value=3.3e-20 Score=169.95 Aligned_cols=152 Identities=22% Similarity=0.246 Sum_probs=122.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhccc
Q 010327 272 GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSF 351 (513)
Q Consensus 272 d~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~ 351 (513)
+..|++.|+..|.++|+++++++. ...+++|++||+++++|++++.|++..| .|.+|++..+++.+.+++++...
T Consensus 2 ~~~af~~l~~~y~~~l~~~~~~~~----~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~~ 76 (154)
T PRK06759 2 KPATFTEAVVLYEGLIVNQIKKLG----IYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFA 76 (154)
T ss_pred CcccHHHHHHHHHHHHHHHHHHhC----CcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHHh
Confidence 457899999999999999998864 4568999999999999999999998766 69999999999999998882100
Q ss_pred cccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCC
Q 010327 352 TRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVE 431 (513)
Q Consensus 352 iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~ 431 (513)
. . +... . + ..
T Consensus 77 -------------------~--~-----------------------------------~~~~--~---------~---~~ 86 (154)
T PRK06759 77 -------------------V--Q-----------------------------------EKCV--C---------V---GE 86 (154)
T ss_pred -------------------h--c-----------------------------------cccc--c---------c---CC
Confidence 0 0 0000 0 0 00
Q ss_pred chhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 432 NENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 432 ~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
+++.....+....|..+|.+||++++.||.++| .+++|.+|||+.||+|..+|++++.+|+++||+.
T Consensus 87 ~~~~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~----~~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 87 YEDHFHFEDVEMKVKDFMSVLDEKEKYIIFERF----FVGKTMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred CcccccHHHHHHHHHHHHHhCCHHHHHHHHHHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 111222334456789999999999999999999 7899999999999999999999999999999963
No 47
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=99.84 E-value=7.2e-20 Score=172.76 Aligned_cols=176 Identities=16% Similarity=0.160 Sum_probs=136.8
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHH
Q 010327 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (513)
Q Consensus 264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~ 343 (513)
.+.....|+..|+..|+..|.++|+.+|.+|. ++..+++|++||++++||+++++|++.. .|.+|++..+++.+.
T Consensus 8 li~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~~~ 82 (187)
T PRK09641 8 LIKQVKKGDQNAFAELVDLYKDKIYQLCYRML---GNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNLTI 82 (187)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHHHH
Confidence 45566789999999999999999999999998 7888999999999999999999999853 699999999999999
Q ss_pred HHHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCC-chhhhhc
Q 010327 344 RSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGV-TQEEFIN 422 (513)
Q Consensus 344 raI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~-~~~e~~d 422 (513)
+++++.+.. .+++..... +.....+
T Consensus 83 d~~R~~~~~------------------------------------------------------~~~~~~~~~~~~~~~~~ 108 (187)
T PRK09641 83 DRLRKRKPD------------------------------------------------------YYLDAEVAGTEGLTMYS 108 (187)
T ss_pred HHHHhcCcc------------------------------------------------------ccccccccCCcchhhhc
Confidence 988832100 000000000 0000111
Q ss_pred cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
...+ ...++++.....+....|..+|+.||++++.||.++| ..++|++|||+.||||.++|++.++||+++||..
T Consensus 109 ~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~----~~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 109 QLAA-DDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKY----IEDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred cccc-CcCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHH----hhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 1111 1223455555666677899999999999999999999 6899999999999999999999999999999965
Q ss_pred c
Q 010327 503 T 503 (513)
Q Consensus 503 ~ 503 (513)
.
T Consensus 184 l 184 (187)
T PRK09641 184 L 184 (187)
T ss_pred H
Confidence 4
No 48
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=6.8e-20 Score=180.44 Aligned_cols=174 Identities=16% Similarity=0.135 Sum_probs=134.8
Q ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-
Q 010327 269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT- 347 (513)
Q Consensus 269 ~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~- 347 (513)
..|+..|++.|+..|.++|+++|.++. ++..+.+||+||+|++||++++.|++. ..|.+|++..+++.+.++++
T Consensus 25 ~~gd~~a~~~l~~~y~~~l~~~a~~~~---~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~Rk 99 (231)
T PRK11922 25 LAGDEAAFEALMRRHNRRLYRTARAIL---RNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNEALGRLRR 99 (231)
T ss_pred HcCCHHHHHHHHHHHHHHHHHHHHHHh---CChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHHHHHHHHh
Confidence 568899999999999999999999998 678899999999999999999999975 36999999999999998887
Q ss_pred hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCC
Q 010327 348 VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDV 427 (513)
Q Consensus 348 ~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~ 427 (513)
..+...++ + ... .....++.... ...
T Consensus 100 ~~r~~~~~----------------------------~------------------------~~~-~~~~~~~~~~~-~~~ 125 (231)
T PRK11922 100 RRRLVNLA----------------------------E------------------------MVM-ASTIAGGERTP-LAD 125 (231)
T ss_pred hcccccch----------------------------h------------------------ccc-ccccccccccc-cCc
Confidence 32211100 0 000 00000000000 111
Q ss_pred CCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010327 428 DGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV 505 (513)
Q Consensus 428 ~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~ 505 (513)
...++++.....+..+.|..+|+.||+++++||.++| .+++|++|||+.||+|.++|++.+.+|+++||+....
T Consensus 126 ~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~~ 199 (231)
T PRK11922 126 PAEDPERAAARREIRALLERAIDALPDAFRAVFVLRV----VEELSVEETAQALGLPEETVKTRLHRARRLLRESLAR 199 (231)
T ss_pred ccCChHHHHHHHHHHHHHHHHHHhCCHHHhhhheeeh----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 1233555566677778899999999999999999998 7899999999999999999999999999999986543
No 49
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=9.9e-20 Score=173.57 Aligned_cols=170 Identities=23% Similarity=0.218 Sum_probs=132.6
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHH
Q 010327 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (513)
Q Consensus 264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~ 343 (513)
.+.....||..|++.|+..|.+.|+.+++++. ++..+.+|++||+|+++|+. ..|++..+ .|.||++.++++.+.
T Consensus 19 l~~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~---~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~~ 93 (194)
T PRK12519 19 LFSALKAGQSAALGVLYDRHAGLVYGLALKIL---GNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRAI 93 (194)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHHH
Confidence 45566789999999999999999999999998 67788999999999999976 67887655 799999999999999
Q ss_pred HHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010327 344 RSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN 422 (513)
Q Consensus 344 raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d 422 (513)
++++ +.+..... +. ......
T Consensus 94 d~~Rk~~~~~~~~------------------------------------------------------~~----~~~~~~- 114 (194)
T PRK12519 94 DRLRSRRSRQRLL------------------------------------------------------ER----WQQELL- 114 (194)
T ss_pred HHHHhcccccchh------------------------------------------------------hh----hhhhhc-
Confidence 9988 32100000 00 000000
Q ss_pred cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
.+....++++.....+....|..+|..||++++.||.++| .+++|++|||+.||+|.++|++++.||+++||+.
T Consensus 115 --~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 115 --GEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAY----YEGLSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred --ccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhh----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 0001122344444555566789999999999999999999 7899999999999999999999999999999965
Q ss_pred c
Q 010327 503 T 503 (513)
Q Consensus 503 ~ 503 (513)
.
T Consensus 189 l 189 (194)
T PRK12519 189 L 189 (194)
T ss_pred H
Confidence 3
No 50
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=99.84 E-value=1.1e-19 Score=173.10 Aligned_cols=174 Identities=13% Similarity=0.138 Sum_probs=136.5
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010327 263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI 342 (513)
Q Consensus 263 e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI 342 (513)
..+.....|+..|++.|+..|.++|+.++.++..+.....+.+|++||++++||+++++|+++.+ .|.||++..+++.+
T Consensus 7 ~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~iarn~~ 85 (189)
T PRK06811 7 NFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAISKYKA 85 (189)
T ss_pred HHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHHHHHH
Confidence 34666778999999999999999999999999832112357999999999999999999997655 79999999999999
Q ss_pred HHHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhh
Q 010327 343 IRSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFI 421 (513)
Q Consensus 343 ~raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~ 421 (513)
.++++ +.+..... +.+ +..
T Consensus 86 ~d~~rk~~~~~~~~----------------------------------------------------~~~-------~~~- 105 (189)
T PRK06811 86 IDYKRKLTKNNEID----------------------------------------------------SID-------EFI- 105 (189)
T ss_pred HHHHHHhccccccc----------------------------------------------------cch-------hhh-
Confidence 99988 32210000 000 000
Q ss_pred ccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 422 NGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 422 d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
.+ ...++++.....+....|..+|..|||+++.||.++| .+++|++|||+.||+|..+|++.+.||+++||.
T Consensus 106 ---~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 106 ---LI-SEESIENEIILKENKEEILKLINDLEKLDREIFIRRY----LLGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred ---hc-ccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 00 1122444455566667799999999999999999998 689999999999999999999999999999998
Q ss_pred cchh
Q 010327 502 PTRV 505 (513)
Q Consensus 502 ~~~~ 505 (513)
...+
T Consensus 178 ~~~~ 181 (189)
T PRK06811 178 NKLN 181 (189)
T ss_pred cccC
Confidence 6544
No 51
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=99.83 E-value=1.6e-19 Score=170.88 Aligned_cols=171 Identities=19% Similarity=0.202 Sum_probs=130.6
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHH
Q 010327 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (513)
Q Consensus 264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~ 343 (513)
.+.....|+..|++.|+..|.+.|+.++++|. +++.+.+|++||+|+.+|+++++|++..+ .|.+|++..+++.+.
T Consensus 13 l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~---~~~~~aeDlvQe~~i~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~ 88 (186)
T PRK13919 13 LLALVARGEEEALRALFRRYAGAFLALARRMG---LDGAAAEDVVQEVFIRVWKKAKEFDPRRG-SARAWLLALAHHAAV 88 (186)
T ss_pred HHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHh---cCHHHHHHHHHHHHHHHHHhhhccCcccc-chHHHHHHHHHHHHH
Confidence 35556789999999999999999999999998 67889999999999999999999987543 599999999999999
Q ss_pred HHHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhcc
Q 010327 344 RSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING 423 (513)
Q Consensus 344 raI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~ 423 (513)
+++++....... ++. ...+. ..
T Consensus 89 d~~rk~~~~~~~-----------------------------------------------------~~~----~~~~~-~~ 110 (186)
T PRK13919 89 DHVRRRAARPQP-----------------------------------------------------LEP----DEREP-EA 110 (186)
T ss_pred HHHHhhhccccc-----------------------------------------------------ccc----ccccc-cc
Confidence 988831100000 000 00000 00
Q ss_pred ccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 424 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 424 l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
.+. .+++......+....|..+|+.||++++.||.++| .+++|++|||+.||+|..+|+..++||+++||...
T Consensus 111 -~~~--~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l 183 (186)
T PRK13919 111 -FDL--PGPGLDEEGHLDRTRLGRALKALSPEERRVIEVLY----YQGYTHREAAQLLGLPLGTLKTRARRALSRLKEVL 183 (186)
T ss_pred -ccC--CCccccHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 000 01111112233456789999999999999999999 79999999999999999999999999999999643
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=99.83 E-value=4.1e-19 Score=168.04 Aligned_cols=177 Identities=12% Similarity=0.087 Sum_probs=135.5
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHH
Q 010327 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (513)
Q Consensus 264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~ 343 (513)
.+.....|+..|+..|+..|.+.|+.+|.++. ++..+.+||+||+|++||+++++|++. ..|.+|++...++.+.
T Consensus 10 l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~~~ 84 (190)
T TIGR02939 10 LVERVQRGEKQAFDLLVRKYQHKVVALVGRYV---RDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNTAK 84 (190)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---CCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHHHH
Confidence 45566789999999999999999999999998 778899999999999999999999975 3699999999999988
Q ss_pred HHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010327 344 RSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN 422 (513)
Q Consensus 344 raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d 422 (513)
+.++ +.+..... ..+.+. .+....
T Consensus 85 ~~~r~~~r~~~~~--------------------------------------------------~~~~~~-----~~~~~~ 109 (190)
T TIGR02939 85 NHLVAQGRRPPTS--------------------------------------------------DVEIED-----AEHFEG 109 (190)
T ss_pred HHHHHhccCCCcc--------------------------------------------------cccccc-----hhhhcc
Confidence 8776 32211000 000000 000000
Q ss_pred cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
........++++.....+....|..+|+.||++++.||.++| .+++|++|||+.||+|..+|++.+++|+++||+.
T Consensus 110 ~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 110 ADRLREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLRE----LEGLSYEDIARIMDCPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred cccccccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhh----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 000001123455555666777899999999999999999999 7899999999999999999999999999999976
Q ss_pred ch
Q 010327 503 TR 504 (513)
Q Consensus 503 ~~ 504 (513)
.+
T Consensus 186 l~ 187 (190)
T TIGR02939 186 LR 187 (190)
T ss_pred hh
Confidence 53
No 53
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=99.83 E-value=3.5e-19 Score=165.84 Aligned_cols=170 Identities=15% Similarity=0.044 Sum_probs=137.1
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHH
Q 010327 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR 344 (513)
Q Consensus 265 L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~r 344 (513)
+..+..|+..|++.|+..|.+.|+.+|+++. ++..+.+|++||+++.||.+.+.|+ .+..|.+|++..+++.+.+
T Consensus 4 ~~~~~~~~~~a~~~l~~~y~~~l~~~~~~~~---~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d 78 (179)
T PRK11924 4 MPVDATGDKEAFSELFRPHAPDLLRYARRQL---GDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYD 78 (179)
T ss_pred HHHHHccCHHHHHHHHHHHHHHHHHHHHHHh---CCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHH
Confidence 3445789999999999999999999999998 7888999999999999999999998 3457999999999999998
Q ss_pred HHHh-ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhcc
Q 010327 345 SMTV-SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING 423 (513)
Q Consensus 345 aI~~-~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~ 423 (513)
++++ .+..... .+. .. ..
T Consensus 79 ~~r~~~~~~~~~-----------------------------------------------------~~~-----~~---~~ 97 (179)
T PRK11924 79 LLRRRRREKAVL-----------------------------------------------------SDD-----AL---EP 97 (179)
T ss_pred HHHhcccccccC-----------------------------------------------------ccc-----cc---cc
Confidence 8873 2110000 000 00 00
Q ss_pred ccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 424 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 424 l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
..+....++++.....+....|..+|..||++++.||.++| ..++|+.|||+.||+|+.+|++.+.+|+++||+..
T Consensus 98 ~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l 173 (179)
T PRK11924 98 EFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRY----VEGLSYREIAEILGVPVGTVKSRLRRARQLLRECL 173 (179)
T ss_pred ccCCccCCHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 00002334666677778888999999999999999999999 68999999999999999999999999999999754
Q ss_pred h
Q 010327 504 R 504 (513)
Q Consensus 504 ~ 504 (513)
.
T Consensus 174 ~ 174 (179)
T PRK11924 174 E 174 (179)
T ss_pred H
Confidence 4
No 54
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=99.82 E-value=2.2e-19 Score=170.79 Aligned_cols=159 Identities=18% Similarity=0.226 Sum_probs=125.7
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHh-c
Q 010327 271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-S 349 (513)
Q Consensus 271 gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~-~ 349 (513)
||..|++.|+..|.+.|+++|.+|. ++..+.+|++||+|+.||+++++|++. ..|.+|++.++++.+.+.++. .
T Consensus 23 gd~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeDlvQe~f~~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~~ 97 (188)
T PRK09640 23 HVTRAYEELMRRYQRTLFNVCARYL---GNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLYSITYNECITQYRKER 97 (188)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHh---CCHhhHHHHHHHHHHHHHHHHHHhcCC--CcchHHHHHHHHHHHHHHHHHhc
Confidence 6999999999999999999999998 778899999999999999999999863 479999999999999998882 1
Q ss_pred cccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCC
Q 010327 350 SFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDG 429 (513)
Q Consensus 350 r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~ 429 (513)
+..... .+ ...+...+.
T Consensus 98 ~~~~~~-----------------------------------------------------~~--------~~~~~~~~~-- 114 (188)
T PRK09640 98 RKRRLM-----------------------------------------------------DA--------LSLDPLEEA-- 114 (188)
T ss_pred ccccCc-----------------------------------------------------ch--------hhhcccccc--
Confidence 100000 00 000000000
Q ss_pred CCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 430 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 430 ~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
.++.....+....|..+|+.||++++.||.++| .+++|++|||+.||||..+|+..+.||+++||...
T Consensus 115 --~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 182 (188)
T PRK09640 115 --SEEKAPKPEERGGLDRWLVHVNPIDREILVLRF----VAELEFQEIADIMHMGLSATKMRYKRALDKLREKF 182 (188)
T ss_pred --cccccccHHHHHHHHHHHHhcChhheeeeeeHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 001111224456789999999999999999999 78999999999999999999999999999999753
No 55
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=99.82 E-value=8.4e-19 Score=167.03 Aligned_cols=176 Identities=12% Similarity=0.050 Sum_probs=135.0
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHH
Q 010327 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (513)
Q Consensus 264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~ 343 (513)
.+..+..|+..|++.|+..|.+.|+.++.+|. ++..+.+|++||+|+++|+++..|++.. .|.+|++...++.+.
T Consensus 10 ll~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~---~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~~ 84 (193)
T PRK11923 10 LVERVQRGDKRAFDLLVLKYQHKILGLIVRFV---HDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTAK 84 (193)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---CCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHHH
Confidence 35556778999999999999999999999998 6778999999999999999999999864 489999999999888
Q ss_pred HHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010327 344 RSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN 422 (513)
Q Consensus 344 raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d 422 (513)
++++ +.+..... ..+++.. +.+..
T Consensus 85 d~~rk~~~~~~~~--------------------------------------------------~~~~~~~-----~~~~~ 109 (193)
T PRK11923 85 NHLVSRGRRPPDS--------------------------------------------------DVSSEDA-----EFYDG 109 (193)
T ss_pred HHHHHhcCCCccc--------------------------------------------------cccccch-----hhhcc
Confidence 8887 32210000 0000000 00000
Q ss_pred cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
.....+..+|++.....+....+..+|..||++++.||.++| .+++|++|||+.||+|..+|++...||+++||..
T Consensus 110 ~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 185 (193)
T PRK11923 110 DHALKDIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLRE----FDGLSYEDIASVMQCPVGTVRSRIFRAREAIDKA 185 (193)
T ss_pred cccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 000001123455555667778899999999999999999998 7999999999999999999999999999999965
Q ss_pred c
Q 010327 503 T 503 (513)
Q Consensus 503 ~ 503 (513)
.
T Consensus 186 l 186 (193)
T PRK11923 186 L 186 (193)
T ss_pred H
Confidence 4
No 56
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=99.82 E-value=4.5e-19 Score=166.98 Aligned_cols=169 Identities=14% Similarity=0.149 Sum_probs=132.6
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHH
Q 010327 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (513)
Q Consensus 264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~ 343 (513)
.+..+..|+..|+..|+..|.+.|+.+|.+|. ++..+.+|++||+|+++|+++++|++..+ .|.||++..+++.+.
T Consensus 9 li~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeD~~Qe~fl~~~~~~~~~~~~~~-~~~~wl~~ia~n~~~ 84 (179)
T PRK12514 9 LIVRVSLGDRDAFSSLYDATSAKLFGICLRVL---KDRSEAEEALQDVYVKIWTKADRFAVSGL-SPMTWLITIARNHAI 84 (179)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHH---cCHHHHHHHHHHHHHHHHHhHHhcCcccc-cHHHHHHHHHHHHHH
Confidence 35556789999999999999999999999998 77889999999999999999999997543 599999999999999
Q ss_pred HHHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhcc
Q 010327 344 RSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING 423 (513)
Q Consensus 344 raI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~ 423 (513)
+++++.+....+ ++. ...
T Consensus 85 d~~R~~~~~~~~-----------------------------------------------------~~~-----~~~---- 102 (179)
T PRK12514 85 DRLRARKAVAVD-----------------------------------------------------IDE-----AHD---- 102 (179)
T ss_pred HHHHhcCCcccc-----------------------------------------------------ccc-----chh----
Confidence 988731100000 000 000
Q ss_pred ccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 424 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 424 l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
..+ ...++++.....+....|..+|..||++++.||.++| .+++|++|||+.||+|..+|++.+.||+++||+..
T Consensus 103 ~~~-~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 177 (179)
T PRK12514 103 LAD-PSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAY----LEGLSYKELAERHDVPLNTMRTWLRRSLLKLRECL 177 (179)
T ss_pred ccc-cCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCChHHHHHHHHHHHHHHHHHh
Confidence 000 1112344343344445788999999999999999999 78999999999999999999999999999999753
No 57
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=99.82 E-value=5.2e-19 Score=169.48 Aligned_cols=171 Identities=18% Similarity=0.102 Sum_probs=136.2
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010327 263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI 342 (513)
Q Consensus 263 e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI 342 (513)
..+.++..|+..|++.|+..|.+.|+.+|.++. ++..+.+|++||+++.+|+..+.|++.. ..|.+|++..+++.+
T Consensus 15 ~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~---~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~n~~ 90 (196)
T PRK12524 15 ALLVLYANGDPAAARALTLRLAPRALAVATRVL---GDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVCNLC 90 (196)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHHHHHH
Confidence 456667889999999999999999999999998 7888999999999999999999998533 469999999999999
Q ss_pred HHHHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010327 343 IRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN 422 (513)
Q Consensus 343 ~raI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d 422 (513)
.+.+++.+... ..++.. .+
T Consensus 91 ~d~~Rk~~~~~-----------------------------------------------------~~~~~~-----~~--- 109 (196)
T PRK12524 91 TDRLRRRRRAS-----------------------------------------------------VDLDDA-----PE--- 109 (196)
T ss_pred HHHHHhhcCCC-----------------------------------------------------CCcccc-----cc---
Confidence 98887211000 000000 00
Q ss_pred cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
. .+ ...++++.....+....|..+|+.||++++.||.|+| .+++|++|||+.||||..+|+++++||+++||..
T Consensus 110 ~-~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~----~~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 110 P-AD-AAPGAEEALIEGDRMRALDAALAALPERQRQAVVLRH----IEGLSNPEIAEVMEIGVEAVESLTARGKRALAAL 183 (196)
T ss_pred c-cc-cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 0 01 1122344455556677899999999999999999999 7899999999999999999999999999999975
Q ss_pred ch
Q 010327 503 TR 504 (513)
Q Consensus 503 ~~ 504 (513)
..
T Consensus 184 l~ 185 (196)
T PRK12524 184 LA 185 (196)
T ss_pred HH
Confidence 54
No 58
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=99.82 E-value=4.2e-19 Score=175.59 Aligned_cols=169 Identities=15% Similarity=0.160 Sum_probs=134.5
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010327 263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI 342 (513)
Q Consensus 263 e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI 342 (513)
+.+..+..||..|++.|+..|.+.|+.++.++. ++..+.+|++||+|+.+|+..++|++..+ .|.+|++..+++.+
T Consensus 52 ~Li~~~~~gd~~af~~L~~~y~~~l~~~~~~~~---~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~~ 127 (233)
T PRK12538 52 ELLDRLATDDEAAFRLLVERHIDRAYAIALRIV---GNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNRC 127 (233)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHHH
Confidence 345667789999999999999999999999998 67789999999999999999999986544 69999999999999
Q ss_pred HHHHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010327 343 IRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN 422 (513)
Q Consensus 343 ~raI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d 422 (513)
.+++++.+... ++. ..+
T Consensus 128 id~~Rk~~~~~-------------------------------------------------------~~~-----~~~--- 144 (233)
T PRK12538 128 IDLRRKPRTEN-------------------------------------------------------VDA-----VPE--- 144 (233)
T ss_pred HHHHHhhcccc-------------------------------------------------------ccc-----ccc---
Confidence 88776211000 000 000
Q ss_pred cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
. .+ ....+++.....+....|..+|..||+++|+||.|+| .+++|++|||+.||+|.++|+++++||+++||+.
T Consensus 145 ~-~~-~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~----~eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~ 218 (233)
T PRK12538 145 V-AD-GKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSY----HENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDL 218 (233)
T ss_pred c-cc-CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 0 00 0112333344556667899999999999999999999 7999999999999999999999999999999976
Q ss_pred ch
Q 010327 503 TR 504 (513)
Q Consensus 503 ~~ 504 (513)
..
T Consensus 219 l~ 220 (233)
T PRK12538 219 LR 220 (233)
T ss_pred HH
Confidence 54
No 59
>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=99.82 E-value=6.4e-19 Score=166.36 Aligned_cols=180 Identities=15% Similarity=0.123 Sum_probs=135.0
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHchhc-cCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHh
Q 010327 270 EVGRAARNKLIKHNLRLVLFVIKKYFQD-FANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV 348 (513)
Q Consensus 270 ~gd~~Ar~~LI~~nlrLV~sIAkky~~~-~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~ 348 (513)
.|+..|++.|+..|.+.|+.+|++|... +++..+.+|++||+++.+|+++..|++..+..|.+|++..+++.+.+++++
T Consensus 3 ~~~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~ 82 (189)
T TIGR02984 3 GGDQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRR 82 (189)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHH
Confidence 5789999999999999999999987521 235678999999999999999999997666689999999999999988872
Q ss_pred c--cccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCC-Cc-hhhhhccc
Q 010327 349 S--SFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHG-VT-QEEFINGI 424 (513)
Q Consensus 349 ~--r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~-~~-~~e~~d~l 424 (513)
. +..+.+ ....+++.... .+ ...+.+.+
T Consensus 83 ~~~~~~r~~------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~ 114 (189)
T TIGR02984 83 HLGAQKRDI------------------------------------------------RREQSLDAGGRLDESSVRLAAQL 114 (189)
T ss_pred HHHHHhhhc------------------------------------------------ccccCCCcccccCCcchhHHHHc
Confidence 1 000000 00112221110 00 11112222
Q ss_pred cCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 425 TDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 425 ~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
.+ ...++++.....+....|..+|..|||+++.||.++| ..++|++|||..||||.++|++.+++|+++||+.
T Consensus 115 ~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~----~~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~ 187 (189)
T TIGR02984 115 AA-DGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRH----LEGLSFAEVAERMDRSEGAVSMLWVRGLARLRQI 187 (189)
T ss_pred cC-CCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 22 2234555556666677899999999999999999999 6899999999999999999999999999999964
No 60
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=99.82 E-value=5.4e-19 Score=169.10 Aligned_cols=174 Identities=14% Similarity=0.120 Sum_probs=132.2
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHH
Q 010327 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR 344 (513)
Q Consensus 265 L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~r 344 (513)
+.+...|+..|++.|+..|.+.|+.+|.++. ++..+.+|++||+|+.+|+..++|++..+ .|.+|++..+++.+.+
T Consensus 18 i~~~~~~d~~af~~l~~~y~~~l~~~~~~~~---~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn~~ld 93 (194)
T PRK12531 18 MEKVKSRDKQAFALVFSYYAPKLKQFAMKHV---GNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRNLCFD 93 (194)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHHHHHH
Confidence 5667789999999999999999999999998 67788999999999999999999997544 6999999999999999
Q ss_pred HHHh-ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhcc
Q 010327 345 SMTV-SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING 423 (513)
Q Consensus 345 aI~~-~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~ 423 (513)
++++ .+..... +.+... ........
T Consensus 94 ~~Rk~~~~~~~~----------------------------------------------------~~~~~~--~~~~~~~~ 119 (194)
T PRK12531 94 LLRKQKGKDLHI----------------------------------------------------HADDIW--PSDYYPPD 119 (194)
T ss_pred HHHHhccccccc----------------------------------------------------chhhcc--cccccccc
Confidence 8883 2100000 000000 00000000
Q ss_pred ccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 424 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 424 l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
.. ....++ .......+..+|.+||++++.||.++| .+++|++|||+.||||.++|+..+++|+++||...
T Consensus 120 ~~--~~~~~e----~~~~~~~l~~~l~~Lp~~~r~v~~l~~----~eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 120 LV--DHYSPE----QDMLKEQVMKFLDRLPKAQRDVLQAVY----LEELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred cc--cccCHH----HHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 00 001111 223345688999999999999999999 79999999999999999999999999999999765
Q ss_pred hhh
Q 010327 504 RVD 506 (513)
Q Consensus 504 ~~~ 506 (513)
..+
T Consensus 190 ~~~ 192 (194)
T PRK12531 190 DAE 192 (194)
T ss_pred hhc
Confidence 543
No 61
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=1.7e-19 Score=171.01 Aligned_cols=169 Identities=15% Similarity=0.144 Sum_probs=130.5
Q ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHh
Q 010327 269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV 348 (513)
Q Consensus 269 ~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~ 348 (513)
..||..|+..|+..|.+.++.+|.++. ++..+.+|++||.|+.+|++.++|++..+..|.||++..+++.+.+++++
T Consensus 4 ~~gd~~a~~~l~~~y~~~l~~~~~~~~---~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk 80 (185)
T PRK12542 4 TNNDYEKMEELYELYEQKVYYVAYSIL---NNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRK 80 (185)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHH
Confidence 468899999999999999999999998 67788999999999999999999986544579999999999999998882
Q ss_pred -ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCC
Q 010327 349 -SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDV 427 (513)
Q Consensus 349 -~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~ 427 (513)
.+... +. +. . .. .....
T Consensus 81 ~~~~~~------------------~~------------------------------------~~-~---~~---~~~~~- 98 (185)
T PRK12542 81 NKRHET------------------FL------------------------------------EE-Y---ER---ESIEA- 98 (185)
T ss_pred hhhhhh------------------hh------------------------------------hh-c---cc---cchhh-
Confidence 11000 00 00 0 00 00000
Q ss_pred CCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010327 428 DGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 506 (513)
Q Consensus 428 ~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~ 506 (513)
....+++.....+....|..+|..|||++++||.|+| .+++|++|||+.||+|.++|+..+.||+++||+.....
T Consensus 99 ~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~ 173 (185)
T PRK12542 99 VDENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKV----FYNLTYQEISSVMGITEANVRKQFERARKRVQNMIGGI 173 (185)
T ss_pred hhccHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHccc
Confidence 0011222223334456789999999999999999998 78999999999999999999999999999999865443
No 62
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=4.2e-19 Score=168.31 Aligned_cols=170 Identities=20% Similarity=0.210 Sum_probs=133.3
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHH
Q 010327 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR 344 (513)
Q Consensus 265 L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~r 344 (513)
+.....|+..+++.|+..|.++|+++|.+|. ++..+.+|++||+|+.+|++.++|++..+ .|.+|++..+++.+.+
T Consensus 16 ~~~~~~~~~~~~~~l~~~y~~~l~~~~~~~~---~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~~d 91 (187)
T PRK12534 16 LTATAGGDRHAFEALYRQTSPKLFGVCLRMI---PQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKAID 91 (187)
T ss_pred HHHHHcCCHHHHHHHHHHhhHHHHHHHHHHh---cCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHH
Confidence 5556678999999999999999999999998 77889999999999999999999998654 5889999999999998
Q ss_pred HHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccc
Q 010327 345 SMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGI 424 (513)
Q Consensus 345 aI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l 424 (513)
++++....+ . ..+++. ....
T Consensus 92 ~~R~~~~~~-~--------------------------------------------------~~~~~~-----~~~~---- 111 (187)
T PRK12534 92 HLRANAPQR-R--------------------------------------------------NVALDD-----AGEL---- 111 (187)
T ss_pred HHHhccccc-c--------------------------------------------------cccccc-----hhhh----
Confidence 887311000 0 000000 0000
Q ss_pred cCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 425 TDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 425 ~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
.+ ...++++.....+....|..+|+.||++++.|+.++| .+++|++|||+.||+|.++|++++++|+++||...
T Consensus 112 ~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 185 (187)
T PRK12534 112 RA-ADASPLERTERASTRRRIDHCLAELEPPRSELIRTAF----FEGITYEELAARTDTPIGTVKSWIRRGLAKLKACL 185 (187)
T ss_pred cc-ccCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Confidence 00 0112333334456677899999999999999999999 79999999999999999999999999999999643
No 63
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=7.1e-19 Score=170.20 Aligned_cols=173 Identities=12% Similarity=0.120 Sum_probs=131.9
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHH
Q 010327 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR 344 (513)
Q Consensus 265 L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~r 344 (513)
+.....|+..|++.|+..|.++|+.++.++. ++..+.+|++||+|+.+|++++.|++.++ .|.||++.++++.+.+
T Consensus 29 ~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~---~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d 104 (206)
T PRK12526 29 ILVAISRDKQAFTHLFQFFAPKIKRFGIKQL---GNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFD 104 (206)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---CCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHH
Confidence 3445679999999999999999999999998 67788999999999999999999997665 5999999999999999
Q ss_pred HHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhcc
Q 010327 345 SMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING 423 (513)
Q Consensus 345 aI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~ 423 (513)
+++ +.+..... ++ .+.....+.
T Consensus 105 ~~Rk~~~~~~~~-----------------------------------------------------~~----~~~~~~~~~ 127 (206)
T PRK12526 105 MLRKIKAKKEQN-----------------------------------------------------LG----DDIWPIEQA 127 (206)
T ss_pred HHHHhccccccc-----------------------------------------------------cc----cccchhhhh
Confidence 988 32210000 00 000000000
Q ss_pred ccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 424 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 424 l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
+.+. .. .............|..+|..||++++.||.++| ++++|++|||+.||+|..+|+..+++|+++||...
T Consensus 128 ~~~~-~~-~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 128 LAES-QS-ESEEFSDHLMDKQILSYIEKLPEAQQTVVKGVY----FQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred cccc-cC-chHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 0111 11 111222333446789999999999999999999 79999999999999999999999999999999765
Q ss_pred h
Q 010327 504 R 504 (513)
Q Consensus 504 ~ 504 (513)
.
T Consensus 202 ~ 202 (206)
T PRK12526 202 G 202 (206)
T ss_pred h
Confidence 4
No 64
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=6.9e-19 Score=166.58 Aligned_cols=168 Identities=16% Similarity=0.131 Sum_probs=133.0
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010327 263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI 342 (513)
Q Consensus 263 e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI 342 (513)
+.+..+..|+..|++.|+..|.+.|+.++.++. ++..+.+|++||+|+.+|+..++|++..+ .|.+|++..+++.+
T Consensus 12 ~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~---~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wL~~iarn~~ 87 (182)
T PRK12537 12 ACLLACARGDRRALQALYQQESARLLGVARRIV---RDRALAEDIVHDAFIKIWTGAASFDPARG-SARGWIYSVTRHLA 87 (182)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---CCHhHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHH
Confidence 346667789999999999999999999999998 78889999999999999999999986443 69999999999999
Q ss_pred HHHHHh-ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhh
Q 010327 343 IRSMTV-SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFI 421 (513)
Q Consensus 343 ~raI~~-~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~ 421 (513)
.++++. .+... .+. .. .
T Consensus 88 ~d~~r~~~~~~~-------------------------------------------------------~~~----~~---~ 105 (182)
T PRK12537 88 LNVLRDTRREVV-------------------------------------------------------LDD----DA---E 105 (182)
T ss_pred HHHHHhccccCc-------------------------------------------------------ccc----ch---h
Confidence 998883 11000 000 00 0
Q ss_pred ccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 422 NGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 422 d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
+...+ ..++++..........|..+|+.||+++++||.++| .+++|++|||+.||||.++|+..+.+|+++||.
T Consensus 106 ~~~~~--~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 106 ETAQT--LHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAY----VDGCSHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred hhccc--ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 00000 111222333444556789999999999999999999 799999999999999999999999999999996
Q ss_pred c
Q 010327 502 P 502 (513)
Q Consensus 502 ~ 502 (513)
.
T Consensus 180 ~ 180 (182)
T PRK12537 180 C 180 (182)
T ss_pred H
Confidence 5
No 65
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=9.6e-19 Score=166.42 Aligned_cols=172 Identities=16% Similarity=0.154 Sum_probs=137.0
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010327 263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI 342 (513)
Q Consensus 263 e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI 342 (513)
+.+.....||..|++.|+..|.+.++.++.++. ++..+.+|++||+|+.+|++.+.|++. ..|.+|++..+++.+
T Consensus 11 ~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n~~ 85 (189)
T PRK12515 11 MLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLV---RDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARFKA 85 (189)
T ss_pred HHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHHHH
Confidence 456677889999999999999999999999998 678899999999999999999999964 379999999999999
Q ss_pred HHHHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010327 343 IRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN 422 (513)
Q Consensus 343 ~raI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d 422 (513)
.+++++.+...+ .. +...
T Consensus 86 ~d~~r~~~~~~~-------------------------------------------------------~~-------~~~~ 103 (189)
T PRK12515 86 LSALRRRKHEEI-------------------------------------------------------DD-------EAAA 103 (189)
T ss_pred HHHHHccCCCCC-------------------------------------------------------cc-------cccc
Confidence 988873110000 00 0000
Q ss_pred cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
...+ ...++++.....+....+..+|+.||+++++||.++| .+++|++|||+.||+|..+|++.+.||+++||+.
T Consensus 104 ~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (189)
T PRK12515 104 AIED-GADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVY----YHEKSVEEVGEIVGIPESTVKTRMFYARKKLAEL 178 (189)
T ss_pred ccCC-CCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 0111 1123444445556667899999999999999999999 7999999999999999999999999999999986
Q ss_pred chhh
Q 010327 503 TRVD 506 (513)
Q Consensus 503 ~~~~ 506 (513)
....
T Consensus 179 l~~~ 182 (189)
T PRK12515 179 LKAA 182 (189)
T ss_pred HHHh
Confidence 5543
No 66
>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=99.80 E-value=1.4e-18 Score=155.59 Aligned_cols=155 Identities=23% Similarity=0.279 Sum_probs=126.5
Q ss_pred HHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccc
Q 010327 275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTR 353 (513)
Q Consensus 275 Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iR 353 (513)
|++.|+..|.++|.++++++. .++.+.+|++|||+++||++++.|++. ..|.+|+.+++++.+.++++ +.+
T Consensus 2 a~~~l~~~~~~~v~~~~~~~~---~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~--- 73 (158)
T TIGR02937 2 AFEELYERYLPLLYRYARRYL---GDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR--- 73 (158)
T ss_pred HHHHHHHHHHHHHHHHHHHHh---CCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhcc---
Confidence 789999999999999999998 677889999999999999999999998 68999999999999999998 322
Q ss_pred cccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCch
Q 010327 354 VPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENE 433 (513)
Q Consensus 354 lP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~e 433 (513)
.+... . ... .. ......++
T Consensus 74 ~~~~~---------------------------------------------------~------~~~---~~-~~~~~~~~ 92 (158)
T TIGR02937 74 LRREL---------------------------------------------------D------LLE---EL-LDSDPSPE 92 (158)
T ss_pred CCcch---------------------------------------------------h------hhh---hc-ccccCCHH
Confidence 11000 0 000 00 01112344
Q ss_pred hhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 434 NQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 434 e~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
+..........|..+|+.||+.++.||.++| ..++|..|||+.||+|+++|+++..+++++||+.
T Consensus 93 ~~~~~~~~~~~l~~~l~~L~~~~~~ii~~~~----~~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~ 157 (158)
T TIGR02937 93 EELEQEEEREALREALEKLPEREREVLVLRY----LEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157 (158)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 4555666777899999999999999999998 5799999999999999999999999999999963
No 67
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=2e-18 Score=163.30 Aligned_cols=167 Identities=16% Similarity=0.136 Sum_probs=129.5
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHH
Q 010327 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (513)
Q Consensus 264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~ 343 (513)
.+..+..||..|++.|+..|.+.|+.++.++.. .+..+.+||+||+|+.||+.++.|++. ..|.+|++..+++.+.
T Consensus 11 ~~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~--~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~~~ 86 (181)
T PRK12536 11 LLLRGLAGDAAAYRQFLSELAAHLRGFLRRRLP--QLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYKLM 86 (181)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcC--CChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHHHH
Confidence 467778899999999999999999999987651 346799999999999999999999974 3699999999999999
Q ss_pred HHHHh-ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010327 344 RSMTV-SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN 422 (513)
Q Consensus 344 raI~~-~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d 422 (513)
+++++ .+... .+.... +..+
T Consensus 87 d~~Rk~~~~~~-------------------------------------------------------~~~~~~----~~~~ 107 (181)
T PRK12536 87 DFLRSRARREA-------------------------------------------------------LHDPLD----DESE 107 (181)
T ss_pred HHHHHHhcccc-------------------------------------------------------ccCCcc----chhh
Confidence 99883 21100 000000 0000
Q ss_pred cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
...+. .++ ..+....+..+|..||++++.||.++| .+++|++|||+.||+|.++|+..+++|+++||+.
T Consensus 108 ~~~~~---~~~----~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 108 LFATS---DDE----AAEARRDLGKLLEQLPDRQRLPIVHVK----LEGLSVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred hcCCC---Ccc----hHHHHHHHHHHHHHCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 00000 011 123445689999999999999999998 7999999999999999999999999999999976
Q ss_pred ch
Q 010327 503 TR 504 (513)
Q Consensus 503 ~~ 504 (513)
..
T Consensus 177 l~ 178 (181)
T PRK12536 177 IR 178 (181)
T ss_pred hc
Confidence 54
No 68
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=99.80 E-value=2.9e-18 Score=164.10 Aligned_cols=167 Identities=13% Similarity=0.096 Sum_probs=134.0
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010327 263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI 342 (513)
Q Consensus 263 e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI 342 (513)
+.+.....|+..+++.|+..|.+.|++++.++. ++..+.+|++||+|+.+|+++++|++.. .|.+|++..+++.+
T Consensus 16 ~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~---~~~~~AeDlvQEvfl~l~~~~~~~~~~~--~f~~wL~~i~rn~~ 90 (192)
T PRK09643 16 ELLAAHVAGDRYAFGELFRRHHRRLWAVARRTS---GTREDAADALQDAMLSAHRAAGSFRGDA--AVSSWLHRIVVNAC 90 (192)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHc---CCHhhHHHHHHHHHHHHHHHHHhcCCCC--ccHHHHHHHHHHHH
Confidence 456667789999999999999999999999998 7788999999999999999999999653 69999999999999
Q ss_pred HHHHHh-ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhh
Q 010327 343 IRSMTV-SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFI 421 (513)
Q Consensus 343 ~raI~~-~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~ 421 (513)
.+++++ .+.... +++. ..
T Consensus 91 ~d~~Rk~~~~~~~-----------------------------------------------------~~~~-----~~--- 109 (192)
T PRK09643 91 LDRLRRAKARPTV-----------------------------------------------------PLDD-----VY--- 109 (192)
T ss_pred HHHHHccccCCCC-----------------------------------------------------Cccc-----cc---
Confidence 999883 211000 0000 00
Q ss_pred ccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 422 NGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 422 d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
... ..+++.....+....|..+|+.||+++++||.|+| .+++|++|||+.||+|..+|+..+.+|+++||.
T Consensus 110 -~~~----~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~----~~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~ 180 (192)
T PRK09643 110 -PVA----QLERDPTARVETALAVQRALMRLPVEQRAALVAVD----MQGYSVADAARMLGVAEGTVKSRCARGRARLAE 180 (192)
T ss_pred -ccc----CCcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 000 01122234445567799999999999999999999 799999999999999999999999999999997
Q ss_pred cch
Q 010327 502 PTR 504 (513)
Q Consensus 502 ~~~ 504 (513)
...
T Consensus 181 ~l~ 183 (192)
T PRK09643 181 LLG 183 (192)
T ss_pred HHH
Confidence 543
No 69
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=2e-18 Score=162.99 Aligned_cols=164 Identities=16% Similarity=0.087 Sum_probs=129.0
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhc
Q 010327 270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS 349 (513)
Q Consensus 270 ~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~ 349 (513)
.|+..|++.|+..|.+.|+.++..|. ++..+.+|++||+|+.+|+++..|++.. .|.+|++..+++.+.++++..
T Consensus 3 ~~d~~af~~l~~~~~~~l~~~~~~~~---~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~ 77 (179)
T PRK12543 3 SGDQEAFSEIYDVTIQEVYKTVHFLV---EDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKR 77 (179)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhh
Confidence 57889999999999999999999998 7888999999999999999999999864 699999999998888776621
Q ss_pred cccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCC
Q 010327 350 SFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDG 429 (513)
Q Consensus 350 r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~ 429 (513)
..... .++.. .+..+. ...
T Consensus 78 ~~~~~-----------------------------------------------------~~~~~-----~~~~~~---~~~ 96 (179)
T PRK12543 78 WRRFR-----------------------------------------------------IFEKA-----EEQRKP---VSI 96 (179)
T ss_pred ccccc-----------------------------------------------------ccccc-----cccccc---ccc
Confidence 10000 00000 000000 001
Q ss_pred CCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010327 430 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 504 (513)
Q Consensus 430 ~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~ 504 (513)
..++. ....+....|..+|..|||++|.||.++| .+++|++|||+.||||..+|+..+.+|+++||+...
T Consensus 97 ~~~~~-~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~----~e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 166 (179)
T PRK12543 97 DFSED-VLSKESNQELIELIHKLPYKLRQVIILRY----LHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQ 166 (179)
T ss_pred cChHH-HHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 12333 45556677899999999999999999998 799999999999999999999999999999998654
No 70
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=99.79 E-value=2.3e-18 Score=157.42 Aligned_cols=158 Identities=15% Similarity=0.161 Sum_probs=124.8
Q ss_pred HHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccc
Q 010327 275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTR 353 (513)
Q Consensus 275 Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iR 353 (513)
|++.|+..|.+.|+.+++++. ++..+.+|++||+++++|+++.+|++.. +|.+|++.++++.+.++++ ..+..
T Consensus 2 a~~~l~~~~~~~l~~~~~~~~---~~~~~aeD~~Qe~~~~~~~~~~~~~~~~--~~~~wl~~i~r~~~~d~~r~~~~~~- 75 (161)
T TIGR02985 2 AFEQLYRRYYPKLCAFAYRYV---KDEEEAEDIVQDVFVKLWENRETLEEVE--SFKAYLFTIVKNRSLNYLRHKQVEE- 75 (161)
T ss_pred hHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhHHhccccc--cHHHHHHHHHHHHHHHHHHHHHhHh-
Confidence 789999999999999999998 6788899999999999999999998643 7999999999999999887 21100
Q ss_pred cccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCch
Q 010327 354 VPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENE 433 (513)
Q Consensus 354 lP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~e 433 (513)
.....+ .. . .. ......+++
T Consensus 76 -------------~~~~~~-------------------------------------~~-------~-~~--~~~~~~~~~ 95 (161)
T TIGR02985 76 -------------KYQEEI-------------------------------------LE-------I-EV--DELSENDPE 95 (161)
T ss_pred -------------HHHHHH-------------------------------------Hh-------h-cc--cccCCCCcH
Confidence 000000 00 0 00 000111244
Q ss_pred hhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 434 NQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 434 e~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
+.....+....|..+|..||++++.||.++| .+++|..|||+.||+|+++|++++.+|+++||+.
T Consensus 96 ~~~~~~e~~~~l~~~l~~L~~~~r~il~l~~----~~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~ 160 (161)
T TIGR02985 96 EELEAKELQLIIYKAIEKLPEQCRKIFILSR----FEGKSYKEIAEELGISVKTVEYHISKALKELRKE 160 (161)
T ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 4455566777899999999999999999988 6899999999999999999999999999999963
No 71
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=99.79 E-value=1.9e-18 Score=161.94 Aligned_cols=166 Identities=16% Similarity=0.117 Sum_probs=129.8
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHH
Q 010327 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (513)
Q Consensus 264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~ 343 (513)
.+....+||..|++.|+..|.+.|+.+|.+|. ++..+.+|++||+|+++|++++.|++. .+|.+|++..+++.+.
T Consensus 8 l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n~~~ 82 (176)
T PRK09638 8 LIQKAKKGDDAALTTLFQQHYSFLYKYLLKLT---LDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASRLYK 82 (176)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHc---CCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHH
Confidence 35566789999999999999999999999998 778889999999999999999999874 4799999999999999
Q ss_pred HHHHh-ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010327 344 RSMTV-SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN 422 (513)
Q Consensus 344 raI~~-~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d 422 (513)
++++. .+..... +. ..+
T Consensus 83 d~~r~~~~~~~~~---------------------------~~-----------------------~~~------------ 100 (176)
T PRK09638 83 DHLRKQKREKLRL---------------------------QR-----------------------AKE------------ 100 (176)
T ss_pred HHHHHhccccchh---------------------------hh-----------------------ccc------------
Confidence 99883 2110000 00 000
Q ss_pred cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
...+.. .. +..........|..+|..||++++.||.++| ..++|++|||+.||+|..+|++.+.+|+++||+.
T Consensus 101 ~~~~~~--~~-~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~ 173 (176)
T PRK09638 101 ETLRKE--KW-EAAIKGAEWSEMLDALSKLDPEFRAPVILKH----YYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKE 173 (176)
T ss_pred ccCCcc--ch-HHHHHhhhHHHHHHHHHcCCHHHhheeeehh----hcCCCHHHHHHHHCCChhHHHHHHHHHHHHHHHH
Confidence 000000 00 1112233445688999999999999999998 7899999999999999999999999999999974
Q ss_pred c
Q 010327 503 T 503 (513)
Q Consensus 503 ~ 503 (513)
.
T Consensus 174 l 174 (176)
T PRK09638 174 W 174 (176)
T ss_pred h
Confidence 3
No 72
>TIGR02895 spore_sigI RNA polymerase sigma-I factor. Members of this sigma factor protein family are strictly limited to endospore-forming species in the Firmicutes lineage of bacteria, but are not universally present among such species. Sigma-I was shown to be induced by heat shock (PubMed:11157964) in Bacillus subtilis and is suggested by its phylogenetic profile to be connected to the program of sporulation (PubMed:16311624).
Probab=99.79 E-value=4.7e-18 Score=166.51 Aligned_cols=120 Identities=12% Similarity=0.166 Sum_probs=104.5
Q ss_pred HHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHH
Q 010327 267 KCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSM 346 (513)
Q Consensus 267 ~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI 346 (513)
.+..||.. ++.||..|.|+|.++|.+|..+. .+.+.+||+|+|++|||+|+++|||++|.+|.|||.+||++.|.+++
T Consensus 3 ~~~~gd~~-~e~LI~~Y~plI~~~a~~~~~~~-~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dyl 80 (218)
T TIGR02895 3 PIQPGNEE-REELIRQYKPFIAKIVSSVCGRY-IDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYI 80 (218)
T ss_pred hhhcCChH-HHHHHHHhHHHHHHHHHHHHccC-CCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHH
Confidence 34567777 99999999999999999997321 13589999999999999999999999999999999999999999999
Q ss_pred H-hc---cccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHh
Q 010327 347 T-VS---SFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQG 388 (513)
Q Consensus 347 ~-~~---r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~ 388 (513)
+ .. ..+++|....+....+..+..++..++++.|+.+||+..
T Consensus 81 Rk~~k~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~ 126 (218)
T TIGR02895 81 RKNQKYQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEY 126 (218)
T ss_pred HhcccccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHH
Confidence 9 44 466888777776778888888999999999999999764
No 73
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=99.79 E-value=6e-18 Score=159.98 Aligned_cols=167 Identities=16% Similarity=0.185 Sum_probs=128.2
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccC-CCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHH
Q 010327 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFA-NGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (513)
Q Consensus 265 L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~-~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~ 343 (513)
+..+..|+..|++.|+..|.+.|+.+|.++..+.+ +..+.+|++||+|+.+|...+.|+.. ..|.+|++..+++.+.
T Consensus 13 ~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn~~~ 90 (184)
T PRK12512 13 MRSANAGDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARNKLI 90 (184)
T ss_pred HHHHHccCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHHHHH
Confidence 55567799999999999999999999999874211 34689999999999999999999863 3699999999999999
Q ss_pred HHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010327 344 RSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN 422 (513)
Q Consensus 344 raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d 422 (513)
++++ +.+....+ ++ ++.+
T Consensus 91 d~~Rr~~~~~~~~-----------------------------------------------------~~--------~~~~ 109 (184)
T PRK12512 91 DALRRRGRRVFVD-----------------------------------------------------ID--------DFAE 109 (184)
T ss_pred HHHHhhcccccCC-----------------------------------------------------ch--------hccc
Confidence 9887 22110000 00 0000
Q ss_pred cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
...+.. .. .......+..+|+.||+++++||.++| .+++|++|||+.||+|..+|+...++|+++||..
T Consensus 110 ~~~~~~---~~----~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12512 110 TLPAEP---AT----ETLPAGDVGRHLETLPPRQRDVVQSIS----VEGASIKETAAKLSMSEGAVRVALHRGLAALAAK 178 (184)
T ss_pred cccccc---hh----hHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 001100 00 112345688899999999999999998 7899999999999999999999999999999976
Q ss_pred chh
Q 010327 503 TRV 505 (513)
Q Consensus 503 ~~~ 505 (513)
.++
T Consensus 179 l~~ 181 (184)
T PRK12512 179 FRS 181 (184)
T ss_pred hhc
Confidence 543
No 74
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=99.79 E-value=4.1e-18 Score=161.03 Aligned_cols=163 Identities=15% Similarity=0.060 Sum_probs=130.1
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhc
Q 010327 270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS 349 (513)
Q Consensus 270 ~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~ 349 (513)
..+..|++.|+..|.+.|+.+|.++. ++..+.+|++||+|+.||+++++|++. ..|.+|++..+++.+.+++++.
T Consensus 12 ~~~~~a~~~l~~~~~~~l~~~~~~~~---~~~~~AeDlvQd~fl~l~~~~~~~~~~--~~~~awl~~ia~n~~~d~~Rk~ 86 (179)
T PRK09415 12 EDKEDLIDEIMNEYGQEVLQLVYSYV---KNKEVAEDLTQEIFVKCYKSLHTYKGK--SSLKTWLYRIAINHCKDYLKSW 86 (179)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHHHHHHHhcCCC--cccHHHHHHHHHHHHHHHHHhh
Confidence 45688999999999999999999998 778899999999999999999999864 3699999999999999988731
Q ss_pred -cccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCC
Q 010327 350 -SFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD 428 (513)
Q Consensus 350 -r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~ 428 (513)
+....+ .+. ..+... ..
T Consensus 87 ~~~~~~~-----------------------------------------------------~~~--------~~~~~~-~~ 104 (179)
T PRK09415 87 HNKKVIV-----------------------------------------------------TED--------IFTYME-SQ 104 (179)
T ss_pred ccccccc-----------------------------------------------------ccc--------cccccc-cc
Confidence 100000 000 000000 11
Q ss_pred CCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 429 GVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 429 ~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
..++++.....+....|..+|+.||+++++||.++| ++++|++|||+.||||..+|++.+.||+++||...
T Consensus 105 ~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l 175 (179)
T PRK09415 105 KESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFY----YEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGL 175 (179)
T ss_pred ccCcHHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 123455555566777899999999999999999999 78999999999999999999999999999999644
No 75
>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=99.79 E-value=4.7e-18 Score=158.58 Aligned_cols=163 Identities=24% Similarity=0.204 Sum_probs=128.6
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010327 263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI 342 (513)
Q Consensus 263 e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI 342 (513)
+.+..+..||..|++.|+..|.+.|++++.++. ++..+.+|++||+|+.+|+..+.|++.. .|.||++..+++.+
T Consensus 5 ~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeD~~Qe~~l~~~~~~~~~~~~~--~~~~wl~~i~~n~~ 79 (169)
T TIGR02954 5 ELVKKAKRGNKPAFESLIKKHKEKLYKTAFIYV---KNEHDALDVIQETVYKAYLSIDKLKHPK--YFNTWLTRILINEC 79 (169)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHHHHhccCcc--ccHHHHHHHHHHHH
Confidence 345667789999999999999999999999998 7888999999999999999999999753 69999999999999
Q ss_pred HHHHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010327 343 IRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN 422 (513)
Q Consensus 343 ~raI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d 422 (513)
.+++++... ..| ++...
T Consensus 80 ~d~~R~~~~-~~~-----------------------------------------------------~~~~~--------- 96 (169)
T TIGR02954 80 IDLLKKKKK-VIP-----------------------------------------------------FDPNT--------- 96 (169)
T ss_pred HHHHHhcCC-cCc-----------------------------------------------------ccccc---------
Confidence 998873110 000 00000
Q ss_pred cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
... ...++. + ......|..+|+.||+++++||.++| .+++|.+|||+.||+|..+|+....+|+++||..
T Consensus 97 --~~~-~~~~~~--~-~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 97 --SIE-KGECET--H-ADSRLDLYKAIDTLNDKYQTAIILRY----YHDLTIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred --ccc-cchhhh--c-hHHHHHHHHHHHhCCHHHhHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 000 000010 0 11123688999999999999999999 7899999999999999999999999999999974
Q ss_pred c
Q 010327 503 T 503 (513)
Q Consensus 503 ~ 503 (513)
.
T Consensus 167 l 167 (169)
T TIGR02954 167 L 167 (169)
T ss_pred h
Confidence 3
No 76
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=99.78 E-value=4.8e-18 Score=161.66 Aligned_cols=169 Identities=17% Similarity=0.128 Sum_probs=129.2
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHH
Q 010327 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (513)
Q Consensus 264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~ 343 (513)
.+.++..|+..|++.|+..|.+.++.++. +. ++..+.+|++||.|+.+|+..++|++. ..|.+|++..+++.+.
T Consensus 14 l~~~~~~gd~~af~~l~~~~~~~l~~~~~-~~---~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~~~ 87 (185)
T PRK09649 14 LALSAAKGNGRALEAFIKATQQDVWRFVA-YL---SDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVA 87 (185)
T ss_pred HHHHHHccCHHHHHHHHHHHHHHHHHHHH-Hh---CCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHHHH
Confidence 35667789999999999999999999995 55 677899999999999999999999964 3699999999999999
Q ss_pred HHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010327 344 RSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN 422 (513)
Q Consensus 344 raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d 422 (513)
++++ +.+..+.. .+. ..+.
T Consensus 88 d~~Rk~~~~~~~~-----------------------------------------------------~~~----~~~~--- 107 (185)
T PRK09649 88 DHIRHVRSRPRTT-----------------------------------------------------RGA----RPEH--- 107 (185)
T ss_pred HHHHHhccccccc-----------------------------------------------------ccc----chhh---
Confidence 9888 22110000 000 0000
Q ss_pred cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
..+ ++......+....|..+|++||+++|.||.|+| ++++|++|||+.||+|.++|+..+.+|+++||+.
T Consensus 108 -~~~-----~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 177 (185)
T PRK09649 108 -LID-----GDRHARGFEDLVEVTTMIADLTTDQREALLLTQ----LLGLSYADAAAVCGCPVGTIRSRVARARDALLAD 177 (185)
T ss_pred -ccC-----hhhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 000 000011112234588899999999999999999 7999999999999999999999999999999986
Q ss_pred chhhhh
Q 010327 503 TRVDYL 508 (513)
Q Consensus 503 ~~~~~L 508 (513)
...+.|
T Consensus 178 ~~~~~~ 183 (185)
T PRK09649 178 AEPDDL 183 (185)
T ss_pred CCcccc
Confidence 655443
No 77
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=99.78 E-value=6.3e-18 Score=158.14 Aligned_cols=163 Identities=14% Similarity=0.141 Sum_probs=126.8
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhc
Q 010327 270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS 349 (513)
Q Consensus 270 ~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~ 349 (513)
.++..|++.|+..|.+.|+.+|.++. ++..+.+|++||.|+.+|+..++|++.. ..|.+|++..+++.+.+++++.
T Consensus 5 ~~~~~~~~~l~~~~~~~l~~~~~~~~---~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~Rk~ 80 (173)
T PRK09645 5 TAEAALMRALYDEHAAPLWRYALRLT---GDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSA 80 (173)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHHHHHHHhh
Confidence 36789999999999999999999998 6778899999999999999999997532 3699999999999999988831
Q ss_pred cccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCC
Q 010327 350 SFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDG 429 (513)
Q Consensus 350 r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~ 429 (513)
+... + ...+ +... ..+
T Consensus 81 ~~~~-~---------------------------------------------------~~~~--------~~~~-~~~--- 96 (173)
T PRK09645 81 RARP-V---------------------------------------------------EGGD--------DVLG-VPE--- 96 (173)
T ss_pred cccc-c---------------------------------------------------cccc--------cccc-CCC---
Confidence 1000 0 0000 0000 000
Q ss_pred CCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010327 430 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 504 (513)
Q Consensus 430 ~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~ 504 (513)
.++++..........|..+|+.||+++++||.|+| ++++|++|||+.||+|..+|+..+++|+++||+...
T Consensus 97 ~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~----~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 167 (173)
T PRK09645 97 QSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSY----YRGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQ 167 (173)
T ss_pred CCCchHHHHHhHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 11122233334455789999999999999999999 799999999999999999999999999999997654
No 78
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=6.3e-18 Score=158.47 Aligned_cols=164 Identities=11% Similarity=0.009 Sum_probs=126.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcccc
Q 010327 274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFT 352 (513)
Q Consensus 274 ~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~i 352 (513)
..++.|+..|.++|+.+|.+|. ++..+++|++||+++.||++.+.|++.. +|.+|++..+++.+.++++ +.+..
T Consensus 3 ~~~~~l~~~y~~~i~~~~~~~~---~~~~daeDvvQe~~i~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~Rk~~~~~ 77 (173)
T PRK12522 3 EKVEELIDIYKQQIYSLCYKLA---KTKEDAEDIFQETWIKVFSSRHQLSYVE--NYKKWITTICVRTFYDFYRKKKRWK 77 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHHHHHHHHcCCcc--chHHHHHHHHHHHHHHHHHHhcccc
Confidence 4589999999999999999998 7889999999999999999999999754 7999999999999999988 32210
Q ss_pred ccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCc
Q 010327 353 RVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVEN 432 (513)
Q Consensus 353 RlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ 432 (513)
..+. +.. +.+...+.........+
T Consensus 78 ~~~~---------------------------------------------------~~~-----~~~~~~~~~~~~~~~~~ 101 (173)
T PRK12522 78 DRIL---------------------------------------------------DLF-----HKEDGGEIEFADDVNIS 101 (173)
T ss_pred cccc---------------------------------------------------ccc-----chhhhhhhccccCCCCh
Confidence 0000 000 00000000000111112
Q ss_pred hhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 433 ENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 433 ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
+. ....+..+.|..+|..||++++.||.|+| .+++|++|||+.||+|..+|+..+.||+++||+..
T Consensus 102 ~~-~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 167 (173)
T PRK12522 102 EE-FIQKVEAEMIREVIQLLNEKYKTVLVLYY----YEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHL 167 (173)
T ss_pred HH-HHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 22 44455677899999999999999999999 79999999999999999999999999999999654
No 79
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=8.7e-18 Score=159.33 Aligned_cols=169 Identities=16% Similarity=0.178 Sum_probs=128.6
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhcc-CCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010327 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDF-ANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI 342 (513)
Q Consensus 264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~-~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI 342 (513)
.+.+...||..|++.|+..|.+.|+.+|++...++ ++..+.+|++||+++.+|++.+.|++.. .|.+|++..+++.+
T Consensus 11 l~~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~~n~~ 88 (184)
T PRK12539 11 LMLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIARYKL 88 (184)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHHHHHH
Confidence 35566789999999999999999999987433211 5678999999999999999999999753 69999999999999
Q ss_pred HHHHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010327 343 IRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN 422 (513)
Q Consensus 343 ~raI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d 422 (513)
.++++.......+ .+++. . +
T Consensus 89 ~d~~R~~~~~~~~---------------------------------------------------~~~~~------~---~ 108 (184)
T PRK12539 89 IDHLRRTRASLAD---------------------------------------------------VPIDD------A---D 108 (184)
T ss_pred HHHHHHHhccccc---------------------------------------------------cChhh------h---c
Confidence 9988821100000 00000 0 0
Q ss_pred cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
... +.+.....+....|..+|..||+++++||.++| .+++|++|||+.||+|..+|+..+++|+++||+.
T Consensus 109 ~~~------~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 109 ELV------AHDDHAAVESTLDLGRLLARLPEKMRLAIQAVK----LEGLSVAEAATRSGMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred ccc------CCcHHhhHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 000 001112223456789999999999999999999 7899999999999999999999999999999975
Q ss_pred ch
Q 010327 503 TR 504 (513)
Q Consensus 503 ~~ 504 (513)
..
T Consensus 179 l~ 180 (184)
T PRK12539 179 IG 180 (184)
T ss_pred Hh
Confidence 43
No 80
>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=99.78 E-value=5.8e-18 Score=168.67 Aligned_cols=179 Identities=16% Similarity=0.151 Sum_probs=138.0
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHH-------HHhhcCCcCCCccchHH
Q 010327 262 AAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLIT-------AIDRFEPKRRFRLSTYG 334 (513)
Q Consensus 262 ~e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLir-------AvekFDp~kG~rFSTYA 334 (513)
...+..+..|+..|+..|+..|.+.|+.++.++. ++..+.+|++||.|+.+|. .+++|++. ..|.||+
T Consensus 27 ~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~---~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~--~~~~tWL 101 (244)
T TIGR03001 27 LYLACACAQGEPAALAALERHVLSKVPARLAGLR---PPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGR--GPLLSWV 101 (244)
T ss_pred HHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHhccchhhhhhccCCC--CchHhHH
Confidence 3456667889999999999999999999999997 6788999999999999994 78889864 3699999
Q ss_pred HHHHHHHHHHHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCC
Q 010327 335 LFWIRHAIIRSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRH 413 (513)
Q Consensus 335 ~~wIR~aI~raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~ 413 (513)
+..++|.+.++++ +.+... ++.
T Consensus 102 ~~Ia~N~~id~lRk~~r~~~-------------------------------------------------------~~~-- 124 (244)
T TIGR03001 102 RIVATRIALELQAQERRHSP-------------------------------------------------------VEE-- 124 (244)
T ss_pred HHHHHHHHHHHHHHhcccCc-------------------------------------------------------ccc--
Confidence 9999999999887 221100 000
Q ss_pred CCchhhhhccccCCCCCCchhhhHH----HHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHH
Q 010327 414 GVTQEEFINGITDVDGVENENQRQP----ALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVR 489 (513)
Q Consensus 414 ~~~~~e~~d~l~d~~~~~~ee~~~~----~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVR 489 (513)
.+...+ ..+ ...++++.... .+....|..+|++||+++|+||.|+| .+++|++|||+.||||.++|+
T Consensus 125 ---~~~~~~-~~~-~~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~----~eg~S~~EIA~~Lgis~~TVk 195 (244)
T TIGR03001 125 ---PTELAA-LPA-PGSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHF----VDGLSMDRIGAMYQVHRSTVS 195 (244)
T ss_pred ---cccccc-ccC-CCCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHH
Confidence 000000 001 11123332222 34567799999999999999999999 899999999999999999999
Q ss_pred HHHHHHHHHHhCcchhhhhhhc
Q 010327 490 KHEVKGLMKLKHPTRVDYLRQH 511 (513)
Q Consensus 490 qi~~rALkKLR~~~~~~~L~~y 511 (513)
..+.+|+++||+....+....|
T Consensus 196 ~rl~RAr~~Lr~~l~~~~~~~~ 217 (244)
T TIGR03001 196 RWVAQARERLLERTRRRLAERL 217 (244)
T ss_pred HHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999998877665554
No 81
>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=99.78 E-value=6e-18 Score=155.60 Aligned_cols=157 Identities=16% Similarity=0.212 Sum_probs=122.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcccc
Q 010327 274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFT 352 (513)
Q Consensus 274 ~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~i 352 (513)
+|++.++..|.++|+.+|+++. ++..+.+|++||+++.+|+++++|++.. .|.+|++..+++.+.++++ +.+..
T Consensus 1 ~~~~~~~~~~~~~l~~~~~~~~---~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~ 75 (159)
T TIGR02989 1 EAFAALLQRHQRSLRAFVRSLV---PDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDR 75 (159)
T ss_pred CHHHHHHHHhHHHHHHHHHHHc---CChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhcccc
Confidence 3789999999999999999998 7888999999999999999999999764 6999999999999999988 32210
Q ss_pred ccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCc
Q 010327 353 RVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVEN 432 (513)
Q Consensus 353 RlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ 432 (513)
. +. .+++ .+.. .+. .++
T Consensus 76 ~-~~-------------------------~~~~--------------------------------~~~~---~~~--~~~ 92 (159)
T TIGR02989 76 L-VF-------------------------DDEL--------------------------------LEAL---AAE--AEA 92 (159)
T ss_pred c-cc-------------------------CHHH--------------------------------HHHH---Hhh--ccc
Confidence 0 00 0000 0000 000 011
Q ss_pred hhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 433 ENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 433 ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
.+..........|..+++.||++++.||.++| .+++|.+|||+.||||..+|+...+||+++||+.
T Consensus 93 ~~~~~~~~~~~~l~~~i~~L~~~~r~v~~l~~----~~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~~ 158 (159)
T TIGR02989 93 TEADRSEDELQALEGCLEKLPERQRELLQLRY----QRGVSLTALAEQLGRTVNAVYKALSRLRVRLRDC 158 (159)
T ss_pred chHhhHHHHHHHHHHHHHHCCHHHHHHHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhc
Confidence 11122233456788999999999999999998 7899999999999999999999999999999974
No 82
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=99.77 E-value=6.9e-18 Score=157.97 Aligned_cols=168 Identities=13% Similarity=0.061 Sum_probs=127.2
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHH
Q 010327 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR 344 (513)
Q Consensus 265 L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~r 344 (513)
+..+..||..|++.|+..|.+.|+.++.++. + ..+.+|++||+|+.+|+.++.|++. ..|.+|++..+++.+.+
T Consensus 2 ~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~---~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d 75 (175)
T PRK12518 2 ILRCQRGDRQSFRQLYRRYQQKVRSTLYQLC---G-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATD 75 (175)
T ss_pred hhHHHcCCHHHHHHHHHHHHHHHHHHHHHHc---C-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHH
Confidence 3456789999999999999999999999976 3 4689999999999999999999974 46999999999999998
Q ss_pred HHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccc
Q 010327 345 SMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGI 424 (513)
Q Consensus 345 aI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l 424 (513)
++++....+ . ..+. ... .+..
T Consensus 76 ~~R~~~~~~-~----------------------------------------------------~~~~-----~~~-~~~~ 96 (175)
T PRK12518 76 ARRQFAQRP-S----------------------------------------------------RIQD-----DSL-NDQP 96 (175)
T ss_pred HHHHhhccc-c----------------------------------------------------chhc-----ccc-cccc
Confidence 877211000 0 0000 000 0000
Q ss_pred cCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010327 425 TDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 504 (513)
Q Consensus 425 ~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~ 504 (513)
.. ..+++.....+....+..+|+.||++++.||.|+| .+++|++|||+.||+|..+|++.+.||+++||+...
T Consensus 97 ~~---~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~ 169 (175)
T PRK12518 97 SR---PSDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHD----LEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQ 169 (175)
T ss_pred cC---CCCcHHHHHHHHHHHHHHHHHhCCHHHeeeeeehH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 00 01111122233445688999999999999999999 789999999999999999999999999999997654
No 83
>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=99.77 E-value=1.2e-17 Score=157.43 Aligned_cols=168 Identities=14% Similarity=0.122 Sum_probs=122.1
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCC-----cHHHHHHHHHHHHHH-HHhhcCCcCCCccchHHHHH
Q 010327 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGP-----RFQDLCQAGVKGLIT-AIDRFEPKRRFRLSTYGLFW 337 (513)
Q Consensus 264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~-----~~eDLIQEG~iGLir-AvekFDp~kG~rFSTYA~~w 337 (513)
.+..+..|+..|+..|+..|.+.|+.+|.+|. ++.. +.+|++||+|+.+|+ ..++|++. ..|.+|++.+
T Consensus 7 li~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~---~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~i 81 (183)
T TIGR02999 7 LLQQWQNGDAAARDQLFPQLYQELRRIARRQL---RRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAKA 81 (183)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---hcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHHH
Confidence 35556789999999999999999999999998 5555 899999999999998 78889754 3699999999
Q ss_pred HHHHHHHHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCc
Q 010327 338 IRHAIIRSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVT 416 (513)
Q Consensus 338 IR~aI~raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~ 416 (513)
+++.+.+.++ +.+..+.. . ..+..
T Consensus 82 ~~n~~~d~~R~~~~~~~~~-------------------------------------------------~--~~~~~---- 106 (183)
T TIGR02999 82 MRRILVDHARRRRAQKRGG-------------------------------------------------G--AVRVP---- 106 (183)
T ss_pred HHHHHHHHHHHHHHHhccC-------------------------------------------------C--ccccc----
Confidence 9999998887 21100000 0 00000
Q ss_pred hhhhhccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010327 417 QEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL 496 (513)
Q Consensus 417 ~~e~~d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rAL 496 (513)
.+...... .++.. +.......+...|++|||+++.||.|+| .+++|++|||+.||+|.++|+..+.||+
T Consensus 107 ----~~~~~~~~--~~~~~-~~~~~l~~~~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tVk~~l~Rar 175 (183)
T TIGR02999 107 ----LDEVLPDA--EADLD-EELLDLDDALDKLAQVDPRQAEVVELRF----FAGLTVEEIAELLGVSVRTVERDWRFAR 175 (183)
T ss_pred ----cccccCCC--CccHH-HHHHHHHHHHHHhhcCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 00000000 11111 1111122334456779999999999999 7999999999999999999999999999
Q ss_pred HHHhCc
Q 010327 497 MKLKHP 502 (513)
Q Consensus 497 kKLR~~ 502 (513)
++||+.
T Consensus 176 ~~Lr~~ 181 (183)
T TIGR02999 176 AWLADE 181 (183)
T ss_pred HHHHHH
Confidence 999964
No 84
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=99.76 E-value=1.3e-17 Score=158.88 Aligned_cols=180 Identities=14% Similarity=0.142 Sum_probs=130.2
Q ss_pred HHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccc
Q 010327 275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTR 353 (513)
Q Consensus 275 Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iR 353 (513)
+++.|+..|.+.|+.+|.++. ++..+.+|++||.|+.+|+.+++|++.. .|.+|++..+++.+.++++ +.+...
T Consensus 3 ~~~~l~~~~~~~l~~~a~~~~---~~~~~AeDivQevfl~~~~~~~~~~~~~--~~~~WL~~ia~n~~~d~~Rk~~r~~~ 77 (191)
T PRK12520 3 IAPAQLEALRPHLLRFARLQL---RDPALAEDAVSETLLAVLEHPERFAGQS--SLKTYLVGILKHKIIDAIRSGRREVR 77 (191)
T ss_pred chHHHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHhhhhhcccc--cHHHHHHHHHHHHHHHHHHhhcCcCc
Confidence 688999999999999999998 7788999999999999999999998543 6999999999999999988 332111
Q ss_pred cccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCch
Q 010327 354 VPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENE 433 (513)
Q Consensus 354 lP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~e 433 (513)
.+.... ......++ ++... ..+.......+ ...+++
T Consensus 78 ~~~~~~------------------~~~~~~~~-----------------------~~~~~--~~~~~~~~~~~-~~~~~~ 113 (191)
T PRK12520 78 LSLDDA------------------DEQSDDDL-----------------------FDALF--AADGHYREPPS-DWGDPD 113 (191)
T ss_pred cccccc------------------ccchhhhh-----------------------hhhhc--ccccccccCcc-ccCCHH
Confidence 110000 00000000 00000 00000000111 112355
Q ss_pred hhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010327 434 NQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY 507 (513)
Q Consensus 434 e~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~ 507 (513)
+.....+....|..+|..||+++|.||.|+| .+++|++|||+.||+|.++|++.+.||+++||+......
T Consensus 114 ~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 183 (191)
T PRK12520 114 AALSRREFFEVLQACVDRLPPRTGRVFMMRE----WLELETEEICQELQITATNAWVLLYRARMRLRECLDLHW 183 (191)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5555666677899999999999999999999 789999999999999999999999999999998765443
No 85
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=99.76 E-value=1.3e-17 Score=157.62 Aligned_cols=168 Identities=14% Similarity=0.087 Sum_probs=127.8
Q ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHHchhccC-CCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHH
Q 010327 268 CLEVGRAARNKLIKHNLRLVLFVIKKYFQDFA-NGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSM 346 (513)
Q Consensus 268 ~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~-~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI 346 (513)
...|+..|++.|+..|.+.|+.++..+.. . +..+.+|++||.|+.+|+..+.|++.....|.||++...++.+.+++
T Consensus 7 ~~~~d~~af~~ly~~~~~~l~~~~~~~~~--~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~ 84 (178)
T PRK12529 7 CLSADRDKVATLYRENHAWLRNWLAYRLR--SWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWR 84 (178)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHH
Confidence 45789999999999999999998766551 1 35689999999999999999999854445799999999999998877
Q ss_pred HhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccC
Q 010327 347 TVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITD 426 (513)
Q Consensus 347 ~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d 426 (513)
++.+. + . . ..+ .... ...
T Consensus 85 Rk~~~-~-~---------------~------------------------------------~~~--------~~~~-~~~ 102 (178)
T PRK12529 85 RRQSL-E-L---------------A------------------------------------WLE--------ALAT-LPE 102 (178)
T ss_pred HHHHH-H-h---------------h------------------------------------hhh--------Hhhh-ccC
Confidence 62110 0 0 0 000 0000 000
Q ss_pred CCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 427 VDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 427 ~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
....++++.....+....|..+|.+|||++|.||.|+| .+++|++|||+.||||.++|+..+.+|+.+|+..+
T Consensus 103 ~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~~ 175 (178)
T PRK12529 103 PLHPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMAT----LDGMKQKDIAQALDIALPTVKKYIHQAYVTCLSLM 175 (178)
T ss_pred cCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence 11123444445555567799999999999999999999 79999999999999999999999999999998653
No 86
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=99.76 E-value=3e-17 Score=155.57 Aligned_cols=170 Identities=18% Similarity=0.135 Sum_probs=133.0
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHH
Q 010327 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR 344 (513)
Q Consensus 265 L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~r 344 (513)
+.....++..++..++..+.+.++.++.++. ++..+.+||+||+|+.+|+++..| .. +..|.||++..++|.+.+
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD 80 (182)
T COG1595 6 LAEALRGDRAAFEELLERLRPRLRRLARRLL---GDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAID 80 (182)
T ss_pred HHHHHhcchHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHH
Confidence 4455688899999999999999999999999 666699999999999999999999 33 447999999999999999
Q ss_pred HHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhcc
Q 010327 345 SMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING 423 (513)
Q Consensus 345 aI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~ 423 (513)
.++ +.+..... +. .+....
T Consensus 81 ~~R~~~r~~~~~------------------------------------------------------~~------~~~~~~ 100 (182)
T COG1595 81 RLRKRKRRRARV------------------------------------------------------EE------ADLLPE 100 (182)
T ss_pred HHHHhccccccc------------------------------------------------------cc------cccccc
Confidence 998 33211100 00 000000
Q ss_pred ccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 424 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 424 l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
..+...... +.....+....|..+|..||+++|.+|.++| .+++|++|||+.||||.++|+..+++|+.+|+...
T Consensus 101 ~~~~~~~~~-~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~----~~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l 175 (182)
T COG1595 101 EADPAPDLA-ELLLAEEELERLRRALARLPPRQREAFLLRY----LEGLSYEEIAEILGISVGTVKSRLHRARKKLREQL 175 (182)
T ss_pred ccCcccccc-hHHHHHHHHHHHHHHHHhCCHHHhHHhhhHh----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 000000000 2345567778899999999999999999999 79999999999999999999999999999999765
Q ss_pred h
Q 010327 504 R 504 (513)
Q Consensus 504 ~ 504 (513)
.
T Consensus 176 ~ 176 (182)
T COG1595 176 E 176 (182)
T ss_pred h
Confidence 4
No 87
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=99.76 E-value=2.9e-17 Score=159.12 Aligned_cols=165 Identities=17% Similarity=0.199 Sum_probs=131.6
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhc
Q 010327 270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS 349 (513)
Q Consensus 270 ~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~ 349 (513)
.|+..+++.|+..|.+.++.++.++. ++..+.+|++||+|+.+|+...+|++ + .|.+|++..+++.+.+++++.
T Consensus 24 ~~d~~a~~~l~~~~~~~L~~~~~~~~---~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~ 97 (203)
T PRK09647 24 KATMPSWEELVRQHADRVYRLAYRLS---GNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRR 97 (203)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHh---CCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhc
Confidence 46889999999999999999999998 67789999999999999999999985 3 599999999999999998832
Q ss_pred cccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCC
Q 010327 350 SFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDG 429 (513)
Q Consensus 350 r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~ 429 (513)
...+.. .++ +++ +... ...
T Consensus 98 ~~~~~~----------------------------------------------------~~~-------~~~-~~~~-~~~ 116 (203)
T PRK09647 98 ARIRME----------------------------------------------------ALP-------EDY-DRVP-GDE 116 (203)
T ss_pred ccCccc----------------------------------------------------ccc-------ccc-cccC-CCC
Confidence 111000 000 000 0001 112
Q ss_pred CCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010327 430 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV 505 (513)
Q Consensus 430 ~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~ 505 (513)
.+++......++...|..+|+.||++++.||.|+| .+++|++|||+.||||..+|++.+.||+++||+....
T Consensus 117 ~~~~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~----~~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~ 188 (203)
T PRK09647 117 PNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCD----IEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAA 188 (203)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 23444455666777899999999999999999999 7899999999999999999999999999999975543
No 88
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=99.75 E-value=4.2e-17 Score=159.65 Aligned_cols=169 Identities=14% Similarity=0.079 Sum_probs=130.4
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-h
Q 010327 270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-V 348 (513)
Q Consensus 270 ~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~ 348 (513)
.....++..|+..|.+.++.++.++. ++..+.+|++||.|+.+|+.+++|++. .|.+|++..++|.+.+.++ +
T Consensus 14 ~~~~~~f~~l~~~~~~~l~~~~~~~~---~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~ 87 (216)
T PRK12533 14 AARGERFRQLVLPHLDAAYNLARWLC---GNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRR 87 (216)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHh---CCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhh
Confidence 34567999999999999999999998 778899999999999999999999853 4999999999999998887 3
Q ss_pred ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCC
Q 010327 349 SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD 428 (513)
Q Consensus 349 ~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~ 428 (513)
.+..... ..+. . ......+.. ++.
T Consensus 88 ~~~~~~~----------------------------------------------------~~~~-~--~~~~~~~~~-~~~ 111 (216)
T PRK12533 88 ANAHEVA----------------------------------------------------APDT-L--DDADSLDDW-QPA 111 (216)
T ss_pred ccccccc----------------------------------------------------cccc-c--ccccccccc-ccC
Confidence 2110000 0000 0 000000000 111
Q ss_pred CCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010327 429 GVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 504 (513)
Q Consensus 429 ~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~ 504 (513)
..++++.....+....|..+|+.||+++++||.|+| .+++|++|||+.||||.++|++++++|+++||+...
T Consensus 112 ~~~~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y----~eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~ 183 (216)
T PRK12533 112 GEDPLALLLRAEDVRLVNAALAKLPVEYREVLVLRE----LEDMSYREIAAIADVPVGTVMSRLARARRRLAALLG 183 (216)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHc
Confidence 223555556667778899999999999999999999 799999999999999999999999999999997553
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=99.75 E-value=1.6e-17 Score=158.51 Aligned_cols=173 Identities=14% Similarity=0.082 Sum_probs=127.5
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-h
Q 010327 270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-V 348 (513)
Q Consensus 270 ~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~ 348 (513)
.++..+++.|+..|.+.|+.+|.++. ++..+.+|++||.|+.+|+..+.|++. ..|.+|++..+++.+.++++ +
T Consensus 7 ~~~~~~f~~l~~~~~~~l~~~~~~~~---~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~ 81 (193)
T TIGR02947 7 TQRAQRFERDALEYLDQLYGAALRMT---RNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKA 81 (193)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHh
Confidence 45678999999999999999999998 677889999999999999999999864 36999999999999999888 3
Q ss_pred ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCC
Q 010327 349 SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD 428 (513)
Q Consensus 349 ~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~ 428 (513)
.+..... ..+++. .. .+. . ........
T Consensus 82 ~~~~~~~-------------------------~~~~~~-----------~~--------~~~--------~-~~~~~~~~ 108 (193)
T TIGR02947 82 QRRPQQS-------------------------DDDDIE-----------DW--------QLA--------K-AASHTSNG 108 (193)
T ss_pred cCCcccc-------------------------cchhhh-----------hh--------hhc--------c-cccccccc
Confidence 2210000 000000 00 000 0 00000000
Q ss_pred CCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010327 429 GVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 504 (513)
Q Consensus 429 ~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~ 504 (513)
...++......+....|..+|++||++++.||.|+| .+++|++|||+.||||..+|+.++.||+++||+...
T Consensus 109 ~~~~e~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 109 LRSAELEALDGLPDQDIKDALQGLPEEFRQAVYLAD----VEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred ccchhHHHHhhhhHHHHHHHHHhCCHHHhhheeehh----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 011222223334456788999999999999999999 799999999999999999999999999999997654
No 90
>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=99.75 E-value=3.1e-17 Score=151.70 Aligned_cols=157 Identities=17% Similarity=0.163 Sum_probs=125.1
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhc
Q 010327 270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS 349 (513)
Q Consensus 270 ~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~ 349 (513)
.|+..+++.|+..|.+.|+.+|..+. ++..+.+|++||+|+.+|++.++|+. ...|.+|++..+++.+.+++++.
T Consensus 2 ~~~~~~~~~l~~~~~~~l~~~~~~~~---~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~~~d~~rk~ 76 (162)
T TIGR02983 2 SATEEEFTAFVAARYPRLLRTAYLLT---GDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNLARSRWRRR 76 (162)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHHHHHHHHhh
Confidence 47899999999999999999999998 77889999999999999999999964 34799999999999998888721
Q ss_pred cccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCC
Q 010327 350 SFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDG 429 (513)
Q Consensus 350 r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~ 429 (513)
....++ + +.. ....
T Consensus 77 ~~~~~~------------------------------------------------------~-------~~~----~~~~- 90 (162)
T TIGR02983 77 RLLELP------------------------------------------------------T-------REL----PDAA- 90 (162)
T ss_pred cccccc------------------------------------------------------c-------ccc----Cccc-
Confidence 100000 0 000 0000
Q ss_pred CCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 430 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 430 ~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
+++.....+....|..+|..||++++.||.|+| .+++|.+|||+.||+|.++|++.+.+|+++||+..
T Consensus 91 --~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 91 --APDPAPDVALRAALARALRRLPARQRAVVVLRY----YEDLSEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred --CCccchhHHHHHHHHHHHHhCCHHHHHHhhhHH----HhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 011112334556788999999999999999999 78999999999999999999999999999999754
No 91
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=99.74 E-value=4.3e-17 Score=155.71 Aligned_cols=159 Identities=13% Similarity=0.094 Sum_probs=124.4
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHh-c
Q 010327 271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-S 349 (513)
Q Consensus 271 gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~-~ 349 (513)
+|..++..|+..|.+.++.+|.++. ++..+.+|++||.|+.+|+..++|+... .|.+|++..+++.+.+++++ .
T Consensus 7 ~~~~~f~~l~~~~~~~L~~~a~~~~---~~~~~AEDivQevfl~~~~~~~~~~~~~--~~~awL~~Ia~n~~~d~~R~~~ 81 (187)
T PRK12516 7 EGTPPFKRELLAALPSLRAFAVSLI---GRHDRADDLVQDTIMKAWAKQDHFEVGT--NMKAWLFTILRNEFYSQMRKRG 81 (187)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHc---CCHhHHHHHHHHHHHHHHHhhhccCCcc--cHHHHHHHHHHHHHHHHHHhhc
Confidence 5688999999999999999999998 7788999999999999999999998643 59999999999999998883 2
Q ss_pred cccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCC
Q 010327 350 SFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDG 429 (513)
Q Consensus 350 r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~ 429 (513)
+... ..+ +...+.. +.
T Consensus 82 ~~~~------------------------------------------------------~~~-------~~~~~~~-~~-- 97 (187)
T PRK12516 82 REVQ------------------------------------------------------DTD-------GMFTEQL-AV-- 97 (187)
T ss_pred CCcc------------------------------------------------------ccc-------ccccccc-CC--
Confidence 1000 000 0000000 00
Q ss_pred CCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010327 430 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV 505 (513)
Q Consensus 430 ~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~ 505 (513)
.++. ........|..+|+.||+++++||.|+| .+++|++|||+.||||.++|+.++.+|+++||+....
T Consensus 98 -~~~~--~~~~~~~~l~~~L~~Lp~~~r~i~~L~~----~~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~ 166 (187)
T PRK12516 98 -HPSQ--YGTLDLQDFRAALDQLPDDQREAIILVG----ASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQI 166 (187)
T ss_pred -Ccch--hhHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 0111 1112235688999999999999999999 7999999999999999999999999999999976553
No 92
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=99.74 E-value=6.1e-17 Score=149.89 Aligned_cols=158 Identities=15% Similarity=0.070 Sum_probs=121.5
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhcc
Q 010327 271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSS 350 (513)
Q Consensus 271 gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r 350 (513)
++..|++.++..|.+.|+.++.++. ++..+.+|++||+++.+|+..++|++. .|.||++..+++.+.+++++.+
T Consensus 2 ~~~~a~~~l~~~~~~~l~~~~~~~~---~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~ 75 (161)
T PRK12541 2 KRKQSLEEIYSEHMQDLFRYLLSLT---GDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEK 75 (161)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHh---cCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhcc
Confidence 4568999999999999999999998 778899999999999999999999863 5999999999999999888321
Q ss_pred ccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCC
Q 010327 351 FTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGV 430 (513)
Q Consensus 351 ~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~ 430 (513)
... . ... ++.. . .....
T Consensus 76 ~~~-~---------------------------------------------------~~~--------~~~~-~--~~~~~ 92 (161)
T PRK12541 76 KYK-T---------------------------------------------------TTI--------EEFH-L--PNVPS 92 (161)
T ss_pred ccc-c---------------------------------------------------cch--------hhhh-c--cCCCC
Confidence 000 0 000 0000 0 00000
Q ss_pred CchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 431 ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 431 ~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
++++.....+. ..+..+|..||++++.||.|+| .+++|++|||+.||+|..+|++.++||+++||..
T Consensus 93 ~~~~~~~~~~~-~~~~~~l~~L~~~~r~v~~l~~----~~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 93 TEHEYFIKHEI-ASWLDSLSSLPLERRNVLLLRD----YYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred cHHHHHHHhHH-HHHHHHHHHCCHHHHHHhhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 11222222233 3455789999999999999999 7899999999999999999999999999999964
No 93
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=99.74 E-value=2.8e-17 Score=151.88 Aligned_cols=153 Identities=15% Similarity=0.105 Sum_probs=119.6
Q ss_pred HHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccccchh
Q 010327 281 KHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLE 359 (513)
Q Consensus 281 ~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~~~ 359 (513)
+.|.+.|+.+|.++. ++..+.+|++||.|+.+|++.++|++. .|.+|++..+++.+.++++ +.+..+.
T Consensus 2 ~~y~~~l~~~~~~~~---~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n~~~d~~Rk~~~~~~~----- 70 (160)
T PRK09642 2 QTYRHYIFQVIFSIL---RHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATNHAIDYKRKKARENEE----- 70 (160)
T ss_pred chHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHHHHHHHHHHhcccccc-----
Confidence 578999999999998 778899999999999999999999863 4999999999999999888 3211000
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchhhhHHH
Q 010327 360 SVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPA 439 (513)
Q Consensus 360 ~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee~~~~~ 439 (513)
.++. .... +... ...++++.....
T Consensus 71 -----------------------------------------------~~~~----~~~~---~~~~--~~~~~~~~~~~~ 94 (160)
T PRK09642 71 -----------------------------------------------LSLC----KETE---ENIK--SSHNIEDLLLTK 94 (160)
T ss_pred -----------------------------------------------cccc----hhhh---hhcc--CCCChHHHHHHH
Confidence 0000 0000 0000 112244445555
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010327 440 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 504 (513)
Q Consensus 440 ~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~ 504 (513)
+....|..+|+.||+.++.||.|+| .+++|++|||+.||+|.++|++.+.+|+++||+...
T Consensus 95 e~~~~l~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (160)
T PRK09642 95 EQKLLIAQKLRELPENYRDVVLAHY----LEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWK 155 (160)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 6677899999999999999999999 799999999999999999999999999999997654
No 94
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=99.74 E-value=5.2e-17 Score=152.30 Aligned_cols=163 Identities=16% Similarity=0.118 Sum_probs=124.6
Q ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHh
Q 010327 269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV 348 (513)
Q Consensus 269 ~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~ 348 (513)
..|+..|+..|+..|.+.|+.++.++. ++..+.+|++||.|+.+|+. ..|... ..|.+|++..+++.+.++++.
T Consensus 5 ~~~~~~a~~~l~~~~~~~l~~~~~~~~---~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk 78 (172)
T PRK12523 5 QSPHSELVGALYRDHRGWLLAWLRRNV---ACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRR 78 (172)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHHc---CCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHH
Confidence 468899999999999999999999998 77889999999999999987 446543 369999999999999998882
Q ss_pred ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCC
Q 010327 349 SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD 428 (513)
Q Consensus 349 ~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~ 428 (513)
... . . ... .++ . . .....
T Consensus 79 ~~~---------------~-~-~~~---------~~~------------------------~-----------~-~~~~~ 96 (172)
T PRK12523 79 AAL---------------E-Q-AYL---------AEL------------------------A-----------L-VPEAE 96 (172)
T ss_pred HHH---------------H-H-HHH---------HHH------------------------h-----------h-ccccc
Confidence 110 0 0 000 000 0 0 00001
Q ss_pred CCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 429 GVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 429 ~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
...++......+....|..+|+.||++++.||.|+| .+++|++|||+.||+|.++|++.+.+|+++||...
T Consensus 97 ~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~----~~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l 167 (172)
T PRK12523 97 QPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNR----LDGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIAL 167 (172)
T ss_pred CCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 112333333334445799999999999999999999 79999999999999999999999999999998644
No 95
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=99.73 E-value=1e-16 Score=148.39 Aligned_cols=157 Identities=17% Similarity=0.147 Sum_probs=121.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhccccc
Q 010327 274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTR 353 (513)
Q Consensus 274 ~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~iR 353 (513)
.|++.|+..|.+.|+.++.++. ++..+.+|++||.|+.+|+..+.|++ ..|.+|.+.++++.+.+.++....
T Consensus 4 ~a~~~l~~~~~~~l~~~~~~~~---~~~~~AeDivQe~flk~~~~~~~~~~---~~~~~wl~~i~~n~~~d~~R~~~~-- 75 (161)
T PRK12528 4 ATVEGLYSAHHHWLTGWLRRRL---GCPQSAADLAQDTFVKVLVARETAQI---IEPRAFLTTIAKRVLCNHYRRQDL-- 75 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHc---CCcccHHHHHHHHHHHHHhccccccc---cCHHHHHHHHHHHHHHHHHHHHHH--
Confidence 6899999999999999999998 67789999999999999999888864 259999999999999988872110
Q ss_pred cccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCch
Q 010327 354 VPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENE 433 (513)
Q Consensus 354 lP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~e 433 (513)
.. ... .. + ....+.....++
T Consensus 76 ------------~~---~~~---------~~------------------------~------------~~~~~~~~~~~~ 95 (161)
T PRK12528 76 ------------ER---AYL---------EA------------------------L------------AQLPERVAPSEE 95 (161)
T ss_pred ------------HH---hhH---------HH------------------------h------------hccccccCCCHH
Confidence 00 000 00 0 000000111122
Q ss_pred hhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 434 NQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 434 e~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
......+....|..+|..||++++.||.|+| .+++|++|||+.||+|.++|+..+.+|+++||..
T Consensus 96 ~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~----~~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~ 160 (161)
T PRK12528 96 ERAIILETLVELDQLLDGLPPLVKRAFLLAQ----VDGLGYGEIATELGISLATVKRYLNKAAMRCYFA 160 (161)
T ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhc
Confidence 2233334456789999999999999999999 7999999999999999999999999999999853
No 96
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=99.73 E-value=6.3e-17 Score=150.57 Aligned_cols=154 Identities=16% Similarity=0.117 Sum_probs=123.9
Q ss_pred HHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHh-cccccc
Q 010327 276 RNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-SSFTRV 354 (513)
Q Consensus 276 r~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~-~r~iRl 354 (513)
++.|+..|.+.|+.+|.++. ++..+.+|++||.|+.+|++++.|++. .|.+|++..+++.+.+++++ .+...+
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~---~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~ 76 (165)
T PRK09644 3 IEEIYKMYINDVYRYLFSLT---KSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFV 76 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhcccc
Confidence 57899999999999999998 778899999999999999999999863 59999999999999999883 110000
Q ss_pred ccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchh
Q 010327 355 PFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENEN 434 (513)
Q Consensus 355 P~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee 434 (513)
. .+ . .+.+.. .++++
T Consensus 77 ~--------------------------~~-----------------------------------~-~~~~~~---~~~~~ 91 (165)
T PRK09644 77 G--------------------------TD-----------------------------------E-IEAIQA---ESTEE 91 (165)
T ss_pred c--------------------------hh-----------------------------------H-Hhhhcc---cChHH
Confidence 0 00 0 000000 12444
Q ss_pred hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010327 435 QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 504 (513)
Q Consensus 435 ~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~ 504 (513)
.....+....|..+|..||+++++||.++| .+++|++|||+.||+|..+|+..+.||+++||+...
T Consensus 92 ~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 157 (165)
T PRK09644 92 YVVAKNSYEKLIQIIHTLPVIEAQAILLCD----VHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLK 157 (165)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHhHH----HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 444556667899999999999999999998 789999999999999999999999999999997654
No 97
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=99.73 E-value=1.4e-16 Score=164.96 Aligned_cols=187 Identities=17% Similarity=0.163 Sum_probs=134.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010327 263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI 342 (513)
Q Consensus 263 e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI 342 (513)
+.+.++..|+..|++.|+..|.+.|+.+|.++. ++..+.+|++||.|+.+|+.+++|++. ..|.+|++...+|.+
T Consensus 8 ~l~~~~~~gd~~af~~l~~~y~~~l~~~~~~~~---~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~ 82 (339)
T PRK08241 8 ALLARAAAGDRDAFAALVEPHRRELLAHCYRML---GSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATNVC 82 (339)
T ss_pred HHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHh---CChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHHHH
Confidence 457778899999999999999999999999998 677899999999999999999999853 369999999999999
Q ss_pred HHHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhh
Q 010327 343 IRSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFI 421 (513)
Q Consensus 343 ~raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~ 421 (513)
.++++ +.+. ..+.. .+. +..++ .+.........+.
T Consensus 83 ~d~~Rk~~~~-~~~~~------------------~~~-~~~~~------------------------~~~~~~~~~~~~~ 118 (339)
T PRK08241 83 LDALEGRARR-PLPTD------------------LGA-PAADP------------------------VDELVERPEVPWL 118 (339)
T ss_pred HHHHHhhccc-cCccc------------------cCC-CcCcc------------------------ccccccccccccc
Confidence 99888 3211 00000 000 00000 0000000000011
Q ss_pred ccccCC----CCCCchhhhHHHH-HHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010327 422 NGITDV----DGVENENQRQPAL-LRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL 496 (513)
Q Consensus 422 d~l~d~----~~~~~ee~~~~~~-l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rAL 496 (513)
+.+.+. ...++++.....+ ....|..+|++||+++|.||.|+| .+++|++|||+.||+|..+|+++++||+
T Consensus 119 ~~~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~RAr 194 (339)
T PRK08241 119 EPYPDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLILRD----VLGWSAAEVAELLDTSVAAVNSALQRAR 194 (339)
T ss_pred CCCCcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhHH----hhCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 111110 0223444333333 455688999999999999999999 7999999999999999999999999999
Q ss_pred HHHhCc
Q 010327 497 MKLKHP 502 (513)
Q Consensus 497 kKLR~~ 502 (513)
++||+.
T Consensus 195 ~~Lr~~ 200 (339)
T PRK08241 195 ATLAER 200 (339)
T ss_pred HHHhhc
Confidence 999983
No 98
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=99.73 E-value=1.4e-16 Score=153.28 Aligned_cols=167 Identities=16% Similarity=0.118 Sum_probs=127.1
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHH
Q 010327 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (513)
Q Consensus 264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~ 343 (513)
.+..+..|+..|++.|+..|.+.++.+++ +. ++..+.+|++||.|+.||+..++|++. ..|.+|++..+++.+.
T Consensus 15 l~~~~~~~d~~a~~~l~~~y~~~l~~~~~-~~---~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~Iarn~~i 88 (196)
T PRK12535 15 LALAAGRGDRAALTEFIRETQDDVWRLLA-HL---GGHDIADDLTQETYLRVMSALPRFAAR--SSARTWLLSLARRVWV 88 (196)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHH-Hh---CCHHHHHHHHHHHHHHHHHHhhhcCCc--ccHHHHHHHHHHHHHH
Confidence 35667789999999999999999999975 45 577899999999999999999999863 3699999999999999
Q ss_pred HHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010327 344 RSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN 422 (513)
Q Consensus 344 raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d 422 (513)
++++ ..+..+.. .+. .....
T Consensus 89 d~~Rk~~~~~~~~-----------------------------------------------------~~~-----~~~~~- 109 (196)
T PRK12535 89 DNIRHDMARPRKS-----------------------------------------------------ATE-----YEDAA- 109 (196)
T ss_pred HHHHhhccCCCcc-----------------------------------------------------ccc-----ccccc-
Confidence 9988 32110000 000 00000
Q ss_pred cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
+. ...++... .......|..+|+.||+++++||.|+| ++++|++|||+.||+|..+|+..++||+++||+.
T Consensus 110 ---~~-~~~~~~~~-~~~~~~~l~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~ 180 (196)
T PRK12535 110 ---AT-TASNETTG-SWSEWIDVRTLIDALPPERREALILTQ----VLGYTYEEAAKIADVRVGTIRSRVARARADLIAA 180 (196)
T ss_pred ---cc-cCCcchhH-HHHHHHHHHHHHHcCCHHHHHHhhhHH----HhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 00 01111111 112234688999999999999999999 8999999999999999999999999999999965
Q ss_pred ch
Q 010327 503 TR 504 (513)
Q Consensus 503 ~~ 504 (513)
..
T Consensus 181 l~ 182 (196)
T PRK12535 181 TA 182 (196)
T ss_pred hc
Confidence 43
No 99
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=99.73 E-value=1.3e-16 Score=147.87 Aligned_cols=158 Identities=14% Similarity=0.077 Sum_probs=123.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccc
Q 010327 273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSF 351 (513)
Q Consensus 273 ~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~ 351 (513)
..+++.|+..|.+.|+.+|.++. ++..+.+|++||+|+.+|++ .|+. +..|.+|++..+++.+.++++ ..+.
T Consensus 2 ~~~f~~l~~~y~~~l~~~~~~~~---~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~~ 74 (166)
T PRK09639 2 DETFEDLFEQYYPDVVQQIFYIV---KDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKRR 74 (166)
T ss_pred chHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhccc
Confidence 36899999999999999999998 67889999999999999999 6764 347999999999999999888 3211
Q ss_pred cccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCC
Q 010327 352 TRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVE 431 (513)
Q Consensus 352 iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~ 431 (513)
.+.. +. ..+.. .+ +....
T Consensus 75 ~~~~------------------------------------------------------~~-----~~~~~-~~--~~~~~ 92 (166)
T PRK09639 75 RARI------------------------------------------------------LG-----EFQWQ-EV--DNEPS 92 (166)
T ss_pred cccc------------------------------------------------------cc-----hhhhh-hc--cCCCC
Confidence 1000 00 00000 00 11223
Q ss_pred chhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010327 432 NENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 504 (513)
Q Consensus 432 ~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~ 504 (513)
+++.....+....|..+|..||++++.||.++| +++|++|||+.||+|..+|+..+.+|+++||....
T Consensus 93 ~e~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-----~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~ 160 (166)
T PRK09639 93 PEEIWIRKEEITKVQEVLAKMTERDRTVLLLRF-----SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYE 160 (166)
T ss_pred hHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 455555556666789999999999999999999 58999999999999999999999999999997654
No 100
>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=99.72 E-value=1.1e-16 Score=152.77 Aligned_cols=177 Identities=15% Similarity=0.128 Sum_probs=127.2
Q ss_pred HHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccc
Q 010327 277 NKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVP 355 (513)
Q Consensus 277 ~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP 355 (513)
.+++..|.+.|+.+|.++. ++..+.+|++||+|+.+|+..++|++. ..|.+|++..+++.+.++++ +.+....+
T Consensus 5 ~~~~~~~~~~l~~~~~~~~---~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~ 79 (188)
T TIGR02943 5 PQELEQLRRDLLRFARLQL---RDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVS 79 (188)
T ss_pred HHHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCcc
Confidence 4578889999999999998 778899999999999999999999965 37999999999999999988 32211110
Q ss_pred cchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchhh
Q 010327 356 FGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQ 435 (513)
Q Consensus 356 ~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee~ 435 (513)
. + .++. . .. .++... .+.+.............++..
T Consensus 80 ~-~-----------------------~~~~----~--~~-------------~~~~~~-~~~~~~~~~~~~~~~~~~e~~ 115 (188)
T TIGR02943 80 D-L-----------------------DDEL----D--DE-------------AFNALF-TQNGHWAQHGQPQHWNTPEKQ 115 (188)
T ss_pred c-c-----------------------cccc----c--cc-------------hhhhhh-ccccchhccccccccCCHHHH
Confidence 0 0 0000 0 00 000000 000000001111112234555
Q ss_pred hHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010327 436 RQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 506 (513)
Q Consensus 436 ~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~ 506 (513)
....+....|..+|..||+++++||.++| .+++|++|||+.||+|.++|++++.||+++||+.....
T Consensus 116 ~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~ 182 (188)
T TIGR02943 116 LENKEFWEVFEACLYHLPEQTARVFMMRE----VLGFESDEICQELEISTSNCHVLLYRARLSLRACLSIN 182 (188)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 56666677899999999999999999999 79999999999999999999999999999999866543
No 101
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=99.72 E-value=1.8e-16 Score=147.69 Aligned_cols=156 Identities=12% Similarity=0.058 Sum_probs=121.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHh-ccc
Q 010327 273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-SSF 351 (513)
Q Consensus 273 ~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~-~r~ 351 (513)
...+..|+..|.+.|+.+|.++. ++..+.+|++||+|+.+|+..+.|++.. .|.+|++..+++.+.+.++. .+.
T Consensus 5 ~~~f~~~~~~~~~~l~~~a~~~~---~~~~~AeDivQe~fl~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~ 79 (164)
T PRK12547 5 SKNFKQELLLALPALRAFAVSLS---SKHDKAEDLVQDTLMKAWAKQDSFEMGT--NLKAWLFTILRNEFYSQMRKRGRE 79 (164)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHc---CCHhhHHHHHHHHHHHHHHhhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhccc
Confidence 46789999999999999999998 7888999999999999999999998543 59999999999999998882 210
Q ss_pred cccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCC
Q 010327 352 TRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVE 431 (513)
Q Consensus 352 iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~ 431 (513)
+ . +. ....... .+ ..
T Consensus 80 ---~-------------------------~----------------------------~~-----~~~~~~~-~~---~~ 94 (164)
T PRK12547 80 ---V-------------------------Q----------------------------DS-----DGVFTAR-VA---VH 94 (164)
T ss_pred ---c-------------------------c----------------------------cc-----ccccccc-CC---CC
Confidence 0 0 00 0000000 00 00
Q ss_pred chhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010327 432 NENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 504 (513)
Q Consensus 432 ~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~ 504 (513)
++. ........|..+|..||+.+++||.|+| .+++|++|||+.||||.++|++.+.||+++||....
T Consensus 95 ~~~--~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 161 (164)
T PRK12547 95 PAQ--YGSLDLQDFKKALNLLSADQREAIILIG----ASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLK 161 (164)
T ss_pred chh--hhHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHh
Confidence 111 1122345688999999999999999999 799999999999999999999999999999997554
No 102
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=99.72 E-value=1.8e-16 Score=151.49 Aligned_cols=180 Identities=16% Similarity=0.137 Sum_probs=126.6
Q ss_pred HHHHHHHHHHHHHHHHHchhccCCCCc-HHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcccccc
Q 010327 277 NKLIKHNLRLVLFVIKKYFQDFANGPR-FQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRV 354 (513)
Q Consensus 277 ~~LI~~nlrLV~sIAkky~~~~~~g~~-~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRl 354 (513)
+..+..|.+.|+.+|.++. ++..+ .+|++||+|+.+|++.++|++. ..|.+|++..+++.+.++++ +.+....
T Consensus 8 ~~~~~~~~~~l~~~a~~~~---~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~~ 82 (195)
T PRK12532 8 DAELIESRKLLLHFARLQL---PDHPDLAEDLVQETLLSAYSAGDSFQGR--ALVNSWLFAILKNKIIDALRQIGRQRKV 82 (195)
T ss_pred hhhHHHHHHHHHHHHHHHc---CChhhhHHHHHHHHHHHHHHhccccccc--chHHHHHHHHHHHHHHHHHHHhcccccc
Confidence 3567788999999999998 66777 9999999999999999999864 37999999999999999988 3221110
Q ss_pred ccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchh
Q 010327 355 PFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENEN 434 (513)
Q Consensus 355 P~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee 434 (513)
.... ..+.+ .... .+... .+.....+. ......+++.
T Consensus 83 ~~~~----------------------~~~~~-----------~~~~------~~~~~---~~~~~~~~~-~~~~~~~~e~ 119 (195)
T PRK12532 83 FTLL----------------------DDELL-----------DEAF------ESHFS---QNGHWTPEG-QPQHWNTPEK 119 (195)
T ss_pred cccc----------------------ccccc-----------chhh------hhhhc---ccccccccc-CccccCCHHH
Confidence 0000 00000 0000 00000 000000000 0111223555
Q ss_pred hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhh
Q 010327 435 QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL 508 (513)
Q Consensus 435 ~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L 508 (513)
.....+....+..+|..||+++++||.|+| .+++|++|||+.||+|..+|++.++||+++||+......+
T Consensus 120 ~~~~~e~~~~l~~~l~~L~~~~r~i~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~ 189 (195)
T PRK12532 120 SLNNNEFQKILQSCLYNLPENTARVFTLKE----ILGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKWF 189 (195)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHhhhHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 556667777899999999999999999999 7999999999999999999999999999999987665543
No 103
>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=99.72 E-value=2.3e-16 Score=162.09 Aligned_cols=182 Identities=17% Similarity=0.112 Sum_probs=129.5
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhcc
Q 010327 271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSS 350 (513)
Q Consensus 271 gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r 350 (513)
|+..|++.|+..|.+.|+.+|.++. ++..+.+|++||.|+.+|+..++|++. ..|.+|++..++|.+.+++++.+
T Consensus 2 gd~~af~~l~~~~~~~l~~~a~~~~---~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~ 76 (324)
T TIGR02960 2 VDGAAFTALAEPHRRELLAHCYRML---GSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQ 76 (324)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHhc---CChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhcc
Confidence 6789999999999999999999998 778899999999999999999999864 36999999999999999988321
Q ss_pred ccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhcccc-----
Q 010327 351 FTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGIT----- 425 (513)
Q Consensus 351 ~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~----- 425 (513)
....+. .+. ...................+.+.
T Consensus 77 ~~~~~~--------------------------~~~-----------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 113 (324)
T TIGR02960 77 RRPRPV--------------------------GLG-----------------APSADGTAAASEAAEVTWLEPLPDLTLD 113 (324)
T ss_pred CCcCcc--------------------------ccC-----------------CCCCcccccccccccccccCCCCccccc
Confidence 100000 000 00000000000000000000000
Q ss_pred --CCCCCCchhhhHHHH-HHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 426 --DVDGVENENQRQPAL-LRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 426 --d~~~~~~ee~~~~~~-l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
.....++++.....+ +...|..+|++||+++|.||.|+| .+++|++|||+.||+|.++|+++++||+++||+.
T Consensus 114 ~~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 189 (324)
T TIGR02960 114 LDDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRD----VLGWRAAETAELLGTSTASVNSALQRARATLDEV 189 (324)
T ss_pred cccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 011123444333333 456688999999999999999999 7899999999999999999999999999999986
Q ss_pred ch
Q 010327 503 TR 504 (513)
Q Consensus 503 ~~ 504 (513)
..
T Consensus 190 l~ 191 (324)
T TIGR02960 190 GP 191 (324)
T ss_pred cc
Confidence 54
No 104
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=99.71 E-value=1.7e-16 Score=152.96 Aligned_cols=178 Identities=13% Similarity=0.075 Sum_probs=123.9
Q ss_pred HHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcccccccc
Q 010327 278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPF 356 (513)
Q Consensus 278 ~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~ 356 (513)
.++..|.+.++.+|.++. ++..+.+|++||.|+.+|+..++|++.. .|.+|++..+++.+.++++ +.+...++.
T Consensus 12 ~~~~~~~~~l~~~~~~~~---~d~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~IarN~~~d~~Rk~~r~~~~~~ 86 (201)
T PRK12545 12 AYLAQLRHDLLRFARLQL---RDADAAEDAVQEALAAAWSQAGRFAGQS--AHKTWVFGILRNKLIDTLRARQRTVNLSA 86 (201)
T ss_pred HHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHhhhhccccc--hHHHHHHHHHHHHHHHHHHhhcccccccc
Confidence 448889999999999998 7778999999999999999999999753 6999999999999999988 322111100
Q ss_pred chhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchhhh
Q 010327 357 GLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQR 436 (513)
Q Consensus 357 ~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee~~ 436 (513)
+ ..++. ....++.........+......+...++++..
T Consensus 87 ---------------~---------~~~~~------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 124 (201)
T PRK12545 87 ---------------L---------DAELD------------------GEALLDRELFKDNGHWAAHAKPRPWPKPETIL 124 (201)
T ss_pred ---------------c---------ccccc------------------hhhhhhhhhhcccccccccccCcCCCCHHHHH
Confidence 0 00000 00000000000000000000011112234444
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010327 437 QPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 506 (513)
Q Consensus 437 ~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~ 506 (513)
...+....|..+|..||+++|.||.|+| ++++|++|||+.||+|.++|+..+.||+++||+.....
T Consensus 125 ~~~~~~~~l~~~L~~Lp~~~r~v~~L~~----~eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~ 190 (201)
T PRK12545 125 QQQQFWTLFETCLDHLPEQIGRVFMMRE----FLDFEIDDICTELTLTANHCSVLLYRARTRLRTCLSEK 190 (201)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455556788999999999999999999 79999999999999999999999999999999866543
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=99.71 E-value=9e-17 Score=147.02 Aligned_cols=150 Identities=15% Similarity=0.117 Sum_probs=117.0
Q ss_pred HHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccccchh
Q 010327 281 KHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLE 359 (513)
Q Consensus 281 ~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~~~ 359 (513)
..|.+.|+.++.++. ++..+.+|++||+++.+|+++++|++ .+|.||++..+++.+.++++ +.+....+
T Consensus 2 ~~~~~~l~~~~~~~~---~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~~---- 71 (154)
T TIGR02950 2 REYMHDVFRYLYRLT---KDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTID---- 71 (154)
T ss_pred chHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhcccc----
Confidence 578899999999998 67789999999999999999999997 37999999999999998887 32100000
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchhhhHHH
Q 010327 360 SVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPA 439 (513)
Q Consensus 360 ~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee~~~~~ 439 (513)
. +. ......+...++++.....
T Consensus 72 -----------------------~----------------------------------~~-~~~~~~~~~~~~~~~~~~~ 93 (154)
T TIGR02950 72 -----------------------D----------------------------------DA-IGDLEQHPVESPEHHLLIK 93 (154)
T ss_pred -----------------------H----------------------------------hh-hhhccccccCChhHHHHHH
Confidence 0 00 0000000111244444455
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 440 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 440 ~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
+....|..+|..||+.++.||.++| .+++|++|||+.||+|..+|++..++|+++||+.
T Consensus 94 ~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~ 152 (154)
T TIGR02950 94 IEQEEITHHLSRLPENYRTVLILRE----FKEFSYKEIAELLNLSLAKVKSNLFRARKELKKL 152 (154)
T ss_pred HHHHHHHHHHHhCCHhheeeeeehh----hccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5667799999999999999999998 6899999999999999999999999999999963
No 106
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=99.71 E-value=2.6e-16 Score=150.22 Aligned_cols=173 Identities=16% Similarity=0.103 Sum_probs=123.8
Q ss_pred HHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccc
Q 010327 277 NKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVP 355 (513)
Q Consensus 277 ~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP 355 (513)
...|..|.+.++.+|.+|. ++..+.+|++||.|+.+|+..+.|++.. .|.+|++..+++.+.++++ +.+.....
T Consensus 10 ~~~~~~~~~~l~~~~~~~~---~d~~~AeDivQe~flk~~~~~~~~~~~~--~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~ 84 (189)
T PRK12530 10 SLEIEEIRLQMLKFATLQL---KDADLAEDVVQEALVSAYKNADSFKGQS--ALKTWIFAILKNKIIDLIRYRKRFVNES 84 (189)
T ss_pred HHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHHHHhchhccCCc--cHHHHHHHHHHHHHHHHHHhhccCCCcc
Confidence 3457778899999999998 6778999999999999999999998653 6999999999999999888 32211000
Q ss_pred cchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchhh
Q 010327 356 FGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQ 435 (513)
Q Consensus 356 ~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee~ 435 (513)
.. . ++ ........ .......+........+++..
T Consensus 85 -~~--------------~---------~~-------------------~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~ 118 (189)
T PRK12530 85 -EL--------------I---------EE-------------------DSPNSFFD---EKGHWKPEYYEPSEWQEVENT 118 (189)
T ss_pred -cc--------------c---------cc-------------------ccchhhhc---ccccccccccCCccccCHHHH
Confidence 00 0 00 00000000 000000000001111234445
Q ss_pred hHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010327 436 RQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 504 (513)
Q Consensus 436 ~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~ 504 (513)
....+....|..+|++||+++|+||.|+| .+++|++|||+.||+|.++|+.+++||+++||+...
T Consensus 119 ~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 183 (189)
T PRK12530 119 VYKEEFWLIFEACLNHLPAQQARVFMMRE----YLELSSEQICQECDISTSNLHVLLYRARLQLQACLS 183 (189)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHhHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 55667777899999999999999999999 789999999999999999999999999999997654
No 107
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=99.69 E-value=5.3e-16 Score=150.62 Aligned_cols=180 Identities=13% Similarity=0.134 Sum_probs=128.3
Q ss_pred HHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcccccc
Q 010327 276 RNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRV 354 (513)
Q Consensus 276 r~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRl 354 (513)
-..|+..|.+.|+.+|.++. ++..+.+|++||.|+.+|+.++.|++. .+|.+|++..+++.+.++++ ..+....
T Consensus 20 ~~~~~~~~~~~l~~~~~~~~---~d~~~AEDivQEvfikl~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~~~~~~ 94 (206)
T PRK12544 20 DPVFLEDLRKQMIKFATLQL---SDLHLAEDAVQEALIGALKNADSFAGR--AAFKTWVFAILKNKIIDLLRQKKRHVSA 94 (206)
T ss_pred hHHHHHHHHHHHHHHHHHHh---CCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhhcccccc
Confidence 36788999999999999999 778899999999999999999999864 36999999999999999998 3321111
Q ss_pred ccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchh
Q 010327 355 PFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENEN 434 (513)
Q Consensus 355 P~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee 434 (513)
+... . +... ...+..+. + ...............+|+.
T Consensus 95 ~~~~------------------~--~~~~---------~~~~~~~~---------~-----~~~~~~~~~~~~~~~~~e~ 131 (206)
T PRK12544 95 SSLL------------------R--DEEE---------EEDFEELF---------D-----ESGHWQKDERPQAWGNPEE 131 (206)
T ss_pred cccc------------------c--ccch---------hhHHHHhh---------c-----ccccccccccccccCCHHH
Confidence 1000 0 0000 00000000 0 0000000000111123455
Q ss_pred hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010327 435 QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY 507 (513)
Q Consensus 435 ~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~ 507 (513)
.....+....+..+|..||++++.||.++| ++++|++|||+.||+|..+|++.++||+++||+......
T Consensus 132 ~~~~~e~~~~l~~~L~~L~~~~r~v~~L~~----~~g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~~ 200 (206)
T PRK12544 132 SLEQEQFWRIFEACLDGLPAKYARVFMMRE----FIELETNEICHAVDLSVSNLNVLLYRARLRLRECLENKW 200 (206)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 555566667789999999999999999999 799999999999999999999999999999998765433
No 108
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=99.69 E-value=5e-16 Score=143.73 Aligned_cols=155 Identities=14% Similarity=0.114 Sum_probs=118.0
Q ss_pred HHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcccccccc
Q 010327 278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPF 356 (513)
Q Consensus 278 ~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~ 356 (513)
.++..|.+.++.+|.++. ++..+.+|++||+++.+|+....|++. .|.+|++..+++.+.++++ +......
T Consensus 2 ~~~~~~~~~l~~~~~~~~---~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn~~~d~~R~~~~~~~~-- 73 (163)
T PRK07037 2 DVFVDNRSMLVKIAARIV---GCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRNLAIDHYRRQALENKY-- 73 (163)
T ss_pred hHHHHHHHHHHHHHHHHc---CCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHHHHHHHHHhhcccccc--
Confidence 357788899999999998 678899999999999999998877753 4789999999999998887 3210000
Q ss_pred chhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchhhh
Q 010327 357 GLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQR 436 (513)
Q Consensus 357 ~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee~~ 436 (513)
+ + .+.+. .. .... ..+++...
T Consensus 74 ---------------------------------------------------~-~----~~~~~-~~-~~~~-~~~~~~~~ 94 (163)
T PRK07037 74 ---------------------------------------------------H-G----DEEDG-LD-VPSP-EASPEAAL 94 (163)
T ss_pred ---------------------------------------------------c-c----ccccc-cc-cCCC-CCCHHHHH
Confidence 0 0 00000 00 0111 12244444
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 437 QPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 437 ~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
...+..+.|..+|+.|||+++.||.++| .+++|.+|||+.||+|.++|+..+.+|+++||+..
T Consensus 95 ~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 95 INRDTLRHVADALSELPARTRYAFEMYR----LHGETQKDIARELGVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4555667789999999999999999999 78999999999999999999999999999999754
No 109
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=99.69 E-value=7.5e-16 Score=146.30 Aligned_cols=152 Identities=16% Similarity=0.151 Sum_probs=122.1
Q ss_pred HHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcccccc
Q 010327 276 RNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRV 354 (513)
Q Consensus 276 r~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRl 354 (513)
++.|+..|.+.|+.+|.++. ++..+.+|++||.++.+|+.+..|++. ..|.+|++..+++.+.++++ +.+...+
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~---~~~~~aeDi~QEvflkl~~~~~~~~~~--~~~~~wL~~i~~n~~~d~~Rk~~~~~~~ 77 (181)
T PRK09637 3 LESIWSEYKAQLKAFLHSRV---SNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNTIIDFYRKKNRSEEL 77 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHh---CChhhHHHHHHHHHHHHHHhHHHhccc--cchHHHHHHHHHHHHHHHHHhccccCCc
Confidence 57899999999999999998 788999999999999999999999853 47999999999999999988 3211000
Q ss_pred ccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchh
Q 010327 355 PFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENEN 434 (513)
Q Consensus 355 P~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee 434 (513)
+ .+... .+ ++++
T Consensus 78 ~-------------------------------------------------------------~~~~~---~~----~~~~ 89 (181)
T PRK09637 78 P-------------------------------------------------------------DDLLF---ED----EERE 89 (181)
T ss_pred c-------------------------------------------------------------hhhhc---cC----CChh
Confidence 0 00000 00 0112
Q ss_pred hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010327 435 QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 504 (513)
Q Consensus 435 ~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~ 504 (513)
.....+....+..+|+.||++++.||.++| .+++++.|||+.||+|..+|+..+.+|+++||+...
T Consensus 90 ~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (181)
T PRK09637 90 ENAKKELAPCLRPFIDALPEKYAEALRLTE----LEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLE 155 (181)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 223345567799999999999999999999 799999999999999999999999999999997543
No 110
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=99.69 E-value=9.9e-16 Score=143.89 Aligned_cols=159 Identities=13% Similarity=0.096 Sum_probs=120.8
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhcc
Q 010327 271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSS 350 (513)
Q Consensus 271 gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r 350 (513)
.+..|++.++..|.+.++.++.++. ++..+.+||+||.|+.+|+. ..|++-. .|.+|++..+++.+.+++++.+
T Consensus 7 ~~~~af~~l~~~~~~~l~~~~~~~~---~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~ 80 (172)
T PRK09651 7 TASLTFESLYGTHHGWLKSWLTRKL---QSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNA 80 (172)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHc---CCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHH
Confidence 4578999999999999999999998 77889999999999999998 4565432 5889999999999988887211
Q ss_pred ccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCC
Q 010327 351 FTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGV 430 (513)
Q Consensus 351 ~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~ 430 (513)
... .. .+ ... .+.+....
T Consensus 81 ~~~-----------------~~------------------------------------~~-----~~~----~~~~~~~~ 98 (172)
T PRK09651 81 LEK-----------------AY------------------------------------LE-----MLA----LMPEGGAP 98 (172)
T ss_pred HHh-----------------hh------------------------------------hh-----HHh----hccccCCC
Confidence 000 00 00 000 00000111
Q ss_pred CchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 431 ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 431 ~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
+++......+....|..+|+.|||++++||.++| ++++|++|||+.||+|..+|+..+.+|+++|+.
T Consensus 99 ~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~ 165 (172)
T PRK09651 99 SPEERESQLETLQLLDSMLDGLNGKTREAFLLSQ----LDGLTYSEIAHKLGVSVSSVKKYVAKATEHCLL 165 (172)
T ss_pred ChHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhhh----ccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 2333333444556789999999999999999999 799999999999999999999999999999985
No 111
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=99.68 E-value=8.6e-16 Score=146.13 Aligned_cols=158 Identities=14% Similarity=0.095 Sum_probs=121.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcccc
Q 010327 274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFT 352 (513)
Q Consensus 274 ~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~i 352 (513)
.+...++..|.+.|+.+|.++. ++..+.+|++||.|+.+|+..+.|++.. .|.+|++..+++.+.+.++ +.+..
T Consensus 5 ~~~~~~~~~~~~~l~~~~~~~~---~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~~~ 79 (182)
T PRK12540 5 DSLRDDILAAVPSLRAFAISLS---GNGDRADDLVQETLLRALANIDSFQPGS--NLPAWLFTILRNLFRSDYRKRRREV 79 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHhHHhcCCCc--hHHHHHHHHHHHHHHHHHHhccccc
Confidence 5678899999999999999998 7788999999999999999999998653 6999999999999988877 22100
Q ss_pred ccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCc
Q 010327 353 RVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVEN 432 (513)
Q Consensus 353 RlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ 432 (513)
.. .+ +...... + . .+
T Consensus 80 ~~------------------------------------------------------~~-------~~~~~~~-~-~--~~ 94 (182)
T PRK12540 80 ED------------------------------------------------------AD-------GSYAKTL-K-S--QP 94 (182)
T ss_pred cc------------------------------------------------------cc-------ccccccc-c-C--CC
Confidence 00 00 0000000 0 0 01
Q ss_pred hhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010327 433 ENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY 507 (513)
Q Consensus 433 ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~ 507 (513)
+.. .......|..+|+.||+++++||.|+| .+++|++|||+.||+|..+|++.++||+++||+......
T Consensus 95 ~~~--~~~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~ 163 (182)
T PRK12540 95 GQN--AHLEFEEFRAALDKLPQDQREALILVG----ASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDG 163 (182)
T ss_pred chH--HHHHHHHHHHHHHhCCHHHHHHhhHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 111 112234688999999999999999999 799999999999999999999999999999998766443
No 112
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=99.68 E-value=6.9e-16 Score=142.59 Aligned_cols=152 Identities=13% Similarity=0.090 Sum_probs=116.9
Q ss_pred HHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccccchh
Q 010327 281 KHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLE 359 (513)
Q Consensus 281 ~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~~~ 359 (513)
..|.+.++.++.++. ++..+.+|++||.|+.||+..+.|++. +|.||++..+++.+.++++ +.....
T Consensus 2 ~~~~~~l~~~~~~~~---~~~~~aeDi~Qevf~~l~~~~~~~~~~---~~~~wL~~ia~n~~~d~~R~~~~~~~------ 69 (159)
T PRK12527 2 ENYYRELVRFLSARL---GNRQAAEDVAHDAYLRVLERSSSAQIE---HPRAFLYRTALNLVVDRHRRHRVRQA------ 69 (159)
T ss_pred hhHHHHHHHHHHHHc---CCHhhHHHHHHHHHHHHHhcccccccc---chHHHHHHHHHHHHHHHHHHHhcccc------
Confidence 467788888888888 677889999999999999999998752 6899999999999999887 211000
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchhhhHHH
Q 010327 360 SVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPA 439 (513)
Q Consensus 360 ~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee~~~~~ 439 (513)
.+++. ..+. ......++++.....
T Consensus 70 -----------------------------------------------~~~~~--------~~~~-~~~~~~~~~~~~~~~ 93 (159)
T PRK12527 70 -----------------------------------------------EPLEV--------LDEE-ERLHSPSPQTRLDLG 93 (159)
T ss_pred -----------------------------------------------cchhh--------hhcc-ccccCCCHHHHHHHH
Confidence 00000 0000 000112345555555
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010327 440 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 504 (513)
Q Consensus 440 ~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~ 504 (513)
+....|..+|.+||++++.||.|+| ++++|++|||+.||+|.++|+..+.+|+++||+...
T Consensus 94 ~~~~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~ 154 (159)
T PRK12527 94 QRLALLQRALAELPPACRDSFLLRK----LEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMR 154 (159)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 6667899999999999999999999 799999999999999999999999999999997644
No 113
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=99.68 E-value=1.1e-15 Score=146.03 Aligned_cols=160 Identities=14% Similarity=0.135 Sum_probs=122.7
Q ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHh
Q 010327 269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV 348 (513)
Q Consensus 269 ~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~ 348 (513)
+.++..+++.++..|.+.|+.+|.++. ++..+.+|++||.|+.+|+.++.|++. ..|.+|++..+++.+.+..++
T Consensus 18 ~~~~~~~f~~l~~~y~~~l~~~~~~~~---~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~ 92 (188)
T PRK12517 18 MLSKQRRYEALVKALHADIYRYAYWLC---KDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFER 92 (188)
T ss_pred hhccHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHH
Confidence 466899999999999999999999998 778899999999999999999999864 368999998888866544331
Q ss_pred ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCC
Q 010327 349 SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD 428 (513)
Q Consensus 349 ~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~ 428 (513)
... ...+.+ +. ...+..
T Consensus 93 ~~~-----------------------------------------------------~~~~~~-------~~---~~~~~~ 109 (188)
T PRK12517 93 KQF-----------------------------------------------------DLVDIE-------DD---SIEDDA 109 (188)
T ss_pred hcc-----------------------------------------------------CccCcc-------cc---cccCcc
Confidence 000 000000 00 000111
Q ss_pred CCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010327 429 GVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 504 (513)
Q Consensus 429 ~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~ 504 (513)
..+++. ......|..+|..||++++.||.++| .+++|++|||+.||||..+|+.++.||+++||....
T Consensus 110 ~~~~e~----~~~~~~l~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (188)
T PRK12517 110 SHSSEE----EMEQEWLRRQIAKLDPEYREPLLLQV----IGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALE 177 (188)
T ss_pred ccChhH----HHHHHHHHHHHHhCCHHHHHHHHHHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 111221 22335688999999999999999999 789999999999999999999999999999997654
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=99.67 E-value=1.4e-15 Score=142.74 Aligned_cols=146 Identities=16% Similarity=0.135 Sum_probs=115.8
Q ss_pred HHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHh-ccccccccchh
Q 010327 281 KHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-SSFTRVPFGLE 359 (513)
Q Consensus 281 ~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~-~r~iRlP~~~~ 359 (513)
..|.+.++.++.++. ++..+.+|++||+|+.+|++++.|++. ..|.+|++..+++.+.++++. .+...++
T Consensus 2 ~~~~~~l~~~~~~~~---~~~~~AeDlvQe~fl~l~~~~~~~~~~--~~f~~wl~~iarn~~~d~~Rk~~~~~~~~---- 72 (170)
T TIGR02959 2 DEFRSELKAFIKSRV---SDASDVEDLLQEVFIKIHRNLPSLKDG--QKIQSWLYQIARNTIIDFYRSKSRSVELP---- 72 (170)
T ss_pred chHHHHHHHHHHHHc---CCHhhHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhccCccccc----
Confidence 467888999999998 778899999999999999999999963 479999999999999999883 2110000
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchhhhHHH
Q 010327 360 SVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPA 439 (513)
Q Consensus 360 ~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee~~~~~ 439 (513)
+... .. .++++.....
T Consensus 73 ----------------------------------------------------------~~~~----~~--~~~~~~~~~~ 88 (170)
T TIGR02959 73 ----------------------------------------------------------ESLL----AA--DSAREETFVK 88 (170)
T ss_pred ----------------------------------------------------------hhhc----cc--CCccHHHHHH
Confidence 0000 00 0112222334
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 440 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 440 ~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
+....|..+|+.||++++.||.++| .+++|++|||+.||+|..+|++.+.+|+++||...
T Consensus 89 e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 89 ELSQCIPPMIKELPDEYREAIRLTE----LEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4556789999999999999999999 78999999999999999999999999999999754
No 115
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=99.67 E-value=1.7e-15 Score=144.93 Aligned_cols=156 Identities=13% Similarity=0.095 Sum_probs=118.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhcccc
Q 010327 273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT 352 (513)
Q Consensus 273 ~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~i 352 (513)
..+++.|.. |.+.|+++|..+. ++..+.+|++||.|+.+|+.+..|+.. ..|.+|++..+++.+.+.+++..
T Consensus 7 ~~~~~~l~~-~~~~l~~~a~~~l---~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~-- 78 (188)
T PRK12546 7 RDPRDELVE-HLPALRAFAISLT---RNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHK-- 78 (188)
T ss_pred hhHHHHHHH-HHHHHHHHHHHHc---CChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhc--
Confidence 456667766 6799999999998 788999999999999999999999864 36999999999999998877311
Q ss_pred ccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCc
Q 010327 353 RVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVEN 432 (513)
Q Consensus 353 RlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ 432 (513)
+.+ . ..+ ....+...+. +
T Consensus 79 r~~-------------------------~--------------------------~~~-------~~~~~~~~~~----~ 96 (188)
T PRK12546 79 REV-------------------------P--------------------------DPE-------GVHAASLAVK----P 96 (188)
T ss_pred ccc-------------------------c--------------------------Ccc-------cccccccccC----C
Confidence 000 0 000 0000000000 0
Q ss_pred hhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010327 433 ENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 504 (513)
Q Consensus 433 ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~ 504 (513)
. .........+..+|+.|||+++.||.|+| .+++|.+|||+.||||..+|+..+.+|+++||+...
T Consensus 97 ~--~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~----~~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~ 162 (188)
T PRK12546 97 A--HDGRLAMSDFRAAFAQLPDEQREALILVG----ASGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQ 162 (188)
T ss_pred c--chhHHHHHHHHHHHHhCCHHHhHHhhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 0 01122234688999999999999999999 799999999999999999999999999999997554
No 116
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=99.66 E-value=2.8e-15 Score=142.74 Aligned_cols=153 Identities=12% Similarity=0.073 Sum_probs=116.9
Q ss_pred HHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcccccc
Q 010327 276 RNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRV 354 (513)
Q Consensus 276 r~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRl 354 (513)
+...+..+++.|+.+|.++. ++..+.+|++||.|+.+|+....|++. ..|.+|++..+++.+.++++ +.+....
T Consensus 6 ~~~~~~~~~~~l~~~~~~~~---~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~~~~~ 80 (182)
T PRK12511 6 KRFDVLDQLVPLRRYARSLT---RDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRVEARR 80 (182)
T ss_pred hhhhHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhcccccc
Confidence 44557788999999999998 778899999999999999999999864 36999999999999999888 3211000
Q ss_pred ccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchh
Q 010327 355 PFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENEN 434 (513)
Q Consensus 355 P~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee 434 (513)
. ++ ... ..+.....+.
T Consensus 81 ~---------------------------~~--------------------------------~~~----~~~~~~~~~~- 96 (182)
T PRK12511 81 A---------------------------DE--------------------------------LAV----LADASLPAAQ- 96 (182)
T ss_pred c---------------------------cc--------------------------------hhh----ccccCCCcch-
Confidence 0 00 000 0000000011
Q ss_pred hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 435 QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 435 ~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
........|..+|.+||+++++||.|+| .+++|++|||+.||||.++|+..+.+|+++||...
T Consensus 97 --~~~~~~~~l~~~l~~Lp~~~R~v~~L~~----~eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~ 159 (182)
T PRK12511 97 --EHAVRLAQIRDAFFDLPEEQRAALHLVA----IEGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFE 159 (182)
T ss_pred --HHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 1122345688999999999999999999 79999999999999999999999999999999644
No 117
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=99.65 E-value=3.7e-15 Score=139.38 Aligned_cols=159 Identities=14% Similarity=0.078 Sum_probs=121.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhcccc
Q 010327 273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT 352 (513)
Q Consensus 273 ~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~i 352 (513)
..++..++..|.+.++++|.+|. ++..+.+|++||.|+.+|+..+.++. ..|.+|++..+++.+.++++..+.
T Consensus 8 ~~~~~~~~~~~~~~l~~~~~~~~---~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~- 80 (168)
T PRK12525 8 NTLIGQMFQQDYDWLCKKLSRQL---GCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDL- 80 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHc---CCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHH-
Confidence 46789999999999999999998 67789999999999999986555542 269999999999999887772110
Q ss_pred ccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCc
Q 010327 353 RVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVEN 432 (513)
Q Consensus 353 RlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ 432 (513)
.+. ... +.+ + .......++
T Consensus 81 -------------~~~---~~~---------------------------------~~~-----------~-~~~~~~~~~ 99 (168)
T PRK12525 81 -------------ERA---YLQ---------------------------------SLA-----------E-APEAVQPSP 99 (168)
T ss_pred -------------HHH---HHH---------------------------------HHh-----------c-ccccccCCh
Confidence 000 000 000 0 000011234
Q ss_pred hhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 433 ENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 433 ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
++.....+....|..+|+.||++++.||.|+| .+++|++|||+.||+|..+|+..+.+|+++||...
T Consensus 100 ~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~----~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~~ 166 (168)
T PRK12525 100 EEQWMVIETLLAIDRLLDGLSGKARAAFLMSQ----LEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQGF 166 (168)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhh
Confidence 44444555567899999999999999999998 79999999999999999999999999999999653
No 118
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=99.64 E-value=4.3e-15 Score=151.32 Aligned_cols=159 Identities=14% Similarity=0.037 Sum_probs=119.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhccccc
Q 010327 274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTR 353 (513)
Q Consensus 274 ~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~iR 353 (513)
.....|+..|.+.++.+|+++. ++..+.+|++||.|+. |.....|+ ...|.+|++..+++.+.+++++.+..+
T Consensus 4 ~~~~~l~~~~~~~l~~~a~~~~---~~~~dAEDlvQe~fl~-~~~~~~~~---~~~~~~WL~~Ia~n~~~d~lR~~~~~~ 76 (293)
T PRK09636 4 ADAAAEFEPLRPHLLSVAYRML---GSVADAEDIVQEAWLR-WNNADRAQ---IRDPRAWLTRVVTRLCLDRLRSARHRR 76 (293)
T ss_pred cHHHHHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHH-HHhccccc---ccCHHHHHHHHHHHHHHHHHHhhhccc
Confidence 3467899999999999999998 7788999999999999 66667776 246999999999999999888211000
Q ss_pred cccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCch
Q 010327 354 VPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENE 433 (513)
Q Consensus 354 lP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~e 433 (513)
. .... ..+.+...+.. .+++
T Consensus 77 -~---------------------------------------------------~~~~-------~~~~e~~~~~~-~~~~ 96 (293)
T PRK09636 77 -E---------------------------------------------------TYVG-------PWLPEPVVEEL-DDPL 96 (293)
T ss_pred -c---------------------------------------------------cccC-------CcCCcCCCCCC-CChH
Confidence 0 0000 00000011111 1233
Q ss_pred h-hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 434 N-QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 434 e-~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
+ ......+...+..+|++|||++|.||.|+| ..++|++|||+.||+|..+|+++++||+++||+..
T Consensus 97 ~~~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~----~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~ 163 (293)
T PRK09636 97 EAVVAAEDLSLALMLALERLSPLERAAFLLHD----VFGVPFDEIASTLGRSPAACRQLASRARKHVRAAR 163 (293)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 2 233445566789999999999999999999 78999999999999999999999999999999854
No 119
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=99.61 E-value=7.3e-15 Score=135.35 Aligned_cols=152 Identities=11% Similarity=0.084 Sum_probs=106.0
Q ss_pred CCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccccchhHHHHHHHHHHHHHHHHhC
Q 010327 299 ANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELK 377 (513)
Q Consensus 299 ~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elg 377 (513)
++..+.+|++||.|+.+|+..+.+ + +..|.+|++..+++.+.++++ +.+......
T Consensus 2 ~~~~~AeDivQe~fl~~~~~~~~~-~--~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~--------------------- 57 (161)
T PRK09047 2 RDDDAALDIVQDAMIKLAEKYGDR-P--AAEWPPLFQRILQNRIHDWFRRQKVRNTWVS--------------------- 57 (161)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhhc-c--cCchHHHHHHHHHHHHHHHHHhhcccccccc---------------------
Confidence 345679999999999999998863 3 446999999999999999988 321100000
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCC--CCCchhhhHHHHHHHHHHHHHhcCCHH
Q 010327 378 RVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD--GVENENQRQPALLRLALDDVLDSLKPK 455 (513)
Q Consensus 378 R~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~--~~~~ee~~~~~~l~~~L~~aL~~L~~r 455 (513)
...++......+..+..+.+.+.. ..++++.....+....|..+|+.||++
T Consensus 58 ---------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~ 110 (161)
T PRK09047 58 ---------------------------LFSSFSDDDDDDDFDPLETLDSADEGAESPADKLERAQVLQLIEEAIQKLPAR 110 (161)
T ss_pred ---------------------------cccccccccccccccHHHHhccccccCCCHHHHHHHHHHHHHHHHHHHhCCHH
Confidence 000000000000011111111111 133555566667778899999999999
Q ss_pred HHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010327 456 ESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV 505 (513)
Q Consensus 456 Er~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~ 505 (513)
++.||.|+| ++++|++|||+.||||..+|+.++.+|+++||+....
T Consensus 111 ~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 156 (161)
T PRK09047 111 QREAFLLRY----WEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEA 156 (161)
T ss_pred HHHHHHHHH----HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999 7999999999999999999999999999999976543
No 120
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=99.59 E-value=2.1e-14 Score=141.81 Aligned_cols=158 Identities=18% Similarity=0.127 Sum_probs=121.1
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010327 263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI 342 (513)
Q Consensus 263 e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI 342 (513)
..|.+...++..+++.+++.| +.++.++.++. ++..+.+||+||.|+.+|+. |+.. ..|.+|++...++.+
T Consensus 7 ~~~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~---~d~~dAEDlvQE~flk~~~~---~~~~--~~~~~WL~~IarN~~ 77 (228)
T PRK06704 7 HILKNHIDMNHSNINFLIEQY-GELKRYCTFLT---KNKWDGEDLAQETVCKVLQK---YSNK--DICMTLVYKIARNRW 77 (228)
T ss_pred HHHhcccCCCHHHHHHHHHHH-HHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHH---cCcc--ccHHHHHHHHHHHHH
Confidence 356777888999999998888 68999999988 77889999999999999986 5543 248999999999999
Q ss_pred HHHHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010327 343 IRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN 422 (513)
Q Consensus 343 ~raI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d 422 (513)
.+.+++.... + .+. +.
T Consensus 78 id~~Rk~k~~--~----------------------------------------------------~~~-------~~--- 93 (228)
T PRK06704 78 LDQIKSKSVH--E----------------------------------------------------KIR-------DQ--- 93 (228)
T ss_pred HHHHhccccc--c----------------------------------------------------ccc-------cc---
Confidence 9888721100 0 000 00
Q ss_pred cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
.... .++.. ..+....+..+|+.||+++|.||.|+| .+++|++|||+.||+|.++|++.+.||+++||+.
T Consensus 94 -~~~~---~~~~~--~~~~~~~l~~~L~~Lp~~~R~v~lL~~----~eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~ 163 (228)
T PRK06704 94 -ITFE---EPHEK--IADLHEMVGKVLSSLNVQQSAILLLKD----VFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTV 163 (228)
T ss_pred -cccC---ChHHH--HHHHHHHHHHHHHhCCHHHhhHhhhHH----hhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 0000 01111 122345688999999999999999999 7899999999999999999999999999999975
Q ss_pred c
Q 010327 503 T 503 (513)
Q Consensus 503 ~ 503 (513)
.
T Consensus 164 l 164 (228)
T PRK06704 164 S 164 (228)
T ss_pred H
Confidence 4
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=99.58 E-value=3.1e-14 Score=144.46 Aligned_cols=155 Identities=14% Similarity=0.047 Sum_probs=114.7
Q ss_pred HHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhccccccccc
Q 010327 278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFG 357 (513)
Q Consensus 278 ~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~iRlP~~ 357 (513)
+++..|.+.++.+|+++. ++..+.+|++||.|+.+++. .|+. ...|.+|++..+++.+.++++..+..+..
T Consensus 1 ~l~~~~~~~l~~~a~r~l---g~~~dAEDvvQE~flk~~~~--~~~~--~~~~~awL~~Ia~n~~ld~lR~~~~~~~~-- 71 (281)
T TIGR02957 1 EEFEALRPLLFSLAYRML---GSVADAEDIVQETFLRWQEA--DRAQ--IENPKAYLTKVVTRRCIDVLRSARARREV-- 71 (281)
T ss_pred ChHHHHHHHHHHHHHHHh---CCHhHHHHHHHHHHHHHHhC--Cccc--ccCHHHHHHHHHHHHHHHHHHHhhhcccc--
Confidence 368899999999999998 77889999999999997775 4543 23699999999999999988821100000
Q ss_pred hhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchhhhH
Q 010327 358 LESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQ 437 (513)
Q Consensus 358 ~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee~~~ 437 (513)
..+ + .+.+...+ ...++++...
T Consensus 72 --------------------------------------------------~~~-~------~~~e~~~~-~~~~~~~~~~ 93 (281)
T TIGR02957 72 --------------------------------------------------YVG-P------WLPEPLLT-TSADPAESVE 93 (281)
T ss_pred --------------------------------------------------cCC-C------CCCcccCC-CCCChHHHHH
Confidence 000 0 00000001 1122333332
Q ss_pred -HHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 438 -PALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 438 -~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
...+...+..+|++|||+||.||.|+| ..++|++|||+.||+|..+|+++++||+++||+..
T Consensus 94 ~~e~~~~~l~~~l~~L~~~~R~v~~L~~----~~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~ 156 (281)
T TIGR02957 94 LAESLSMAYLLLLERLSPLERAVFVLRE----VFDYPYEEIASIVGKSEANCRQLVSRARRHLDARR 156 (281)
T ss_pred HHHHHHHHHHHHHhhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 334556788899999999999999999 78999999999999999999999999999999743
No 122
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=99.57 E-value=4.9e-14 Score=143.87 Aligned_cols=160 Identities=13% Similarity=0.070 Sum_probs=119.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhccccc
Q 010327 274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTR 353 (513)
Q Consensus 274 ~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~iR 353 (513)
..+..++..|.+.++++|.++. ++..+.||++||.|+.+|++...+. ..|.+|++...++.+.++++..+..+
T Consensus 5 ~~~~~l~~~~~~~L~~~a~r~l---gs~~dAEDvvQE~flr~~~~~~~~~----~~~~aWL~~Ia~n~~id~lRk~~~rr 77 (290)
T PRK09635 5 DPVSAAWRAHRAYLVDLAFRMV---GDIGVAEDMVQEAFSRLLRAPVGDI----DDERGWLIVVTSRLCLDHIKSASTRR 77 (290)
T ss_pred cHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHhcCcccc----ccHHHHHHHHHHHHHHHHHhhhhccC
Confidence 4678899999999999999999 7888999999999999999865431 25899999999999999887311100
Q ss_pred cccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCch
Q 010327 354 VPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENE 433 (513)
Q Consensus 354 lP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~e 433 (513)
.. ....+... .+ +... ...+++
T Consensus 78 ~~--------------------------------------------------~~~~~~~~---~~---~~~~--~~~~~~ 99 (290)
T PRK09635 78 ER--------------------------------------------------PQDIAAWH---DG---DASV--SSVDPA 99 (290)
T ss_pred cC--------------------------------------------------cccccccC---cc---ccCC--CCCCcH
Confidence 00 00000000 00 0000 111232
Q ss_pred h-hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 434 N-QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 434 e-~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
+ .....+....+..+|+.|||+++.||.|+| ..++|++|||+.||+|..+|+++++||+++||..
T Consensus 100 ~~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~----~~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~ 165 (290)
T PRK09635 100 DRVTLDDEVRLALLIMLERLGPAERVVFVLHE----IFGLPYQQIATTIGSQASTCRQLAHRARRKINES 165 (290)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHH----HhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 2 234455667889999999999999999999 7899999999999999999999999999999974
No 123
>PRK09191 two-component response regulator; Provisional
Probab=99.46 E-value=7.8e-13 Score=130.37 Aligned_cols=136 Identities=8% Similarity=-0.041 Sum_probs=108.7
Q ss_pred HHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhcccccc
Q 010327 275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRV 354 (513)
Q Consensus 275 Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~iRl 354 (513)
++..|+..|.+.|+.+|.++. ++..+.+|++||+|+.+|+....|++. ..|.+|++.++++.....
T Consensus 2 ~~~~l~~~~~~~l~~~~~~~~---~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~~--------- 67 (261)
T PRK09191 2 SLSQRIAPHLPYLRRYARALT---GSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSSA--------- 67 (261)
T ss_pred chHHHHHHHhHHHHHHHHHhc---CChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhccc---------
Confidence 478899999999999999998 678899999999999999999999864 358888887654421000
Q ss_pred ccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchh
Q 010327 355 PFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENEN 434 (513)
Q Consensus 355 P~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee 434 (513)
... .... . .+..
T Consensus 68 ---------------------------------------------------------~~~--------~~~~-~--~~~~ 79 (261)
T PRK09191 68 ---------------------------------------------------------GAN--------DPEP-G--SPFE 79 (261)
T ss_pred ---------------------------------------------------------ccc--------CCCC-C--CCch
Confidence 000 0000 0 0110
Q ss_pred hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010327 435 QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 504 (513)
Q Consensus 435 ~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~ 504 (513)
..+..+|+.||+++|.||.|+| .+++|++|||+.||+|.++|+....+|+++|+....
T Consensus 80 --------~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~ 137 (261)
T PRK09191 80 --------ARAERRLAGLTPLPRQAFLLTA----LEGFSVEEAAEILGVDPAEAEALLDDARAEIARQVA 137 (261)
T ss_pred --------HHHHHHHHhCCHHHhHHHHHHH----HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCC
Confidence 1688999999999999999999 799999999999999999999999999999997554
No 124
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=99.42 E-value=1.4e-12 Score=118.39 Aligned_cols=136 Identities=18% Similarity=0.230 Sum_probs=97.6
Q ss_pred HHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhh-----cCCcCCCccchHHHHHHHHHHHHHHH-hc
Q 010327 276 RNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDR-----FEPKRRFRLSTYGLFWIRHAIIRSMT-VS 349 (513)
Q Consensus 276 r~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvek-----FDp~kG~rFSTYA~~wIR~aI~raI~-~~ 349 (513)
++.|+..|.++++.+|++|. . .+| +||.++.+|....+ |++. ..|.||++..+++.+.+.++ +.
T Consensus 1 f~~~~~~y~~~l~~~~~~~~---~----~~~-~qdvf~~~w~~~~~~~~~~~~~~--~~~~~wL~~iarN~~id~~Rk~~ 70 (142)
T TIGR03209 1 FEEIYMNFKNTIDIFTRKYN---L----YYD-YNDILYHLWIILKKIDLNKFNTE--NDLEKYISTSLKRYCLDICNKKN 70 (142)
T ss_pred ChHHHHHHHHHHHHHHHHhc---c----hhh-HHHHHHHHHHHHHHhhhhhcCch--hHHHHHHHHHHHHHHHHHHHHHh
Confidence 36799999999999999997 2 224 49999999999875 5532 46999999999999999888 21
Q ss_pred cccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCC
Q 010327 350 SFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDG 429 (513)
Q Consensus 350 r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~ 429 (513)
+... ... + .+..+ ..
T Consensus 71 ~~~~------------------~~~-----------------------------------~-------~~~~~----~~- 85 (142)
T TIGR03209 71 RDKK------------------IIY-----------------------------------N-------SEITD----IK- 85 (142)
T ss_pred hhhh------------------hhh-----------------------------------h-------hhhhc----cc-
Confidence 1000 000 0 00000 00
Q ss_pred CCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHH
Q 010327 430 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRK 490 (513)
Q Consensus 430 ~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRq 490 (513)
..+++.....+....|..+|+.||+.+|+||.|+| .+++|++|||+.||+|.++|+.
T Consensus 86 ~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~----~~~~s~~EIA~~l~is~~tV~~ 142 (142)
T TIGR03209 86 LSLINVYSSNDLEFEFNDLISILPNKQKKIIYMKF----FEDMKEIDIAKKLHISRQSVYK 142 (142)
T ss_pred cchhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHhhcC
Confidence 00112223334455688999999999999999999 7999999999999999999973
No 125
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=99.40 E-value=1.1e-11 Score=123.32 Aligned_cols=80 Identities=15% Similarity=0.207 Sum_probs=73.4
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCC--cHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010327 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGP--RFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI 342 (513)
Q Consensus 265 L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~--~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI 342 (513)
+..+..||..|++.|+..|.++|+++|.+|. ++.. +.+|++|||++++|+|+++|++++|..|.+|+..+|++.+
T Consensus 9 i~~~~~gD~~AfeeLi~~Y~p~I~~~a~~~~---~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn~~ 85 (237)
T PRK08311 9 LEKIKNGDEELREELIEEYKPFIAKVVSSVC---GRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKRRL 85 (237)
T ss_pred HHHHHCCCHHHHHHHHHHHHHHHHHHHHHHh---cccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence 4556789999999999999999999999998 4443 5899999999999999999999988889999999999999
Q ss_pred HHHHH
Q 010327 343 IRSMT 347 (513)
Q Consensus 343 ~raI~ 347 (513)
.++++
T Consensus 86 iDylR 90 (237)
T PRK08311 86 IDYFR 90 (237)
T ss_pred HHHHH
Confidence 99999
No 126
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=99.36 E-value=1.9e-11 Score=116.79 Aligned_cols=175 Identities=19% Similarity=0.184 Sum_probs=118.2
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHH--HHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHH
Q 010327 263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQD--LCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRH 340 (513)
Q Consensus 263 e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eD--LIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~ 340 (513)
+.|.++.+||..|.+.|+..|++-++.+|+++......+.+.+| |++|.|+.++..-...+.+.-..|..|+...+++
T Consensus 6 ~ll~~~~~GD~~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~~~~~rr 85 (185)
T PF07638_consen 6 ELLDRWRQGDEAALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALLARIMRR 85 (185)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHHHHHHHH
Confidence 45777889999999999999999999999987654344555555 4677777776633322333333588888888888
Q ss_pred HHHHHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhh
Q 010327 341 AIIRSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEE 419 (513)
Q Consensus 341 aI~raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e 419 (513)
.+.+.++ +....|-. . ....+|+...
T Consensus 86 ~lid~~R~~~a~KRg~----------------------~-------------------------~~~~~l~~~~------ 112 (185)
T PF07638_consen 86 KLIDHARRRQAQKRGG----------------------D-------------------------QVRVELDERA------ 112 (185)
T ss_pred HHHHHHHHHHHHhcCC----------------------C-------------------------Ccccchhhhh------
Confidence 8888777 32211110 0 0001111100
Q ss_pred hhccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010327 420 FINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 499 (513)
Q Consensus 420 ~~d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKL 499 (513)
+ +.+...++. ..++.+.+..+.. |+|++..+|.++| +.|+|.+|||+.||||..+|++....|..+|
T Consensus 113 --~---~~~~~~~~~---~~~l~e~l~~L~~-l~~~~~~~v~l~~----~~Gls~~EIA~~lgiS~~tV~r~l~~aR~~l 179 (185)
T PF07638_consen 113 --D---SGDEPSPEE---LLELEEALERLLA-LDPRQRRVVELRF----FEGLSVEEIAERLGISERTVRRRLRRARAWL 179 (185)
T ss_pred --c---cccCCCHHH---HHHHHHHHHHHHc-cCHHHHHHHHHHH----HCCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 0 001122222 2345555655555 9999999999998 7899999999999999999999999999999
Q ss_pred hCcc
Q 010327 500 KHPT 503 (513)
Q Consensus 500 R~~~ 503 (513)
+...
T Consensus 180 ~~~l 183 (185)
T PF07638_consen 180 RREL 183 (185)
T ss_pred HHHh
Confidence 8643
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=99.19 E-value=4.3e-11 Score=90.40 Aligned_cols=50 Identities=46% Similarity=0.587 Sum_probs=46.1
Q ss_pred HHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 448 VLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 448 aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
+|+.|||+|+.||.++| ++++|+.|||+.||+|.++|++++.+|+++||+
T Consensus 1 Al~~L~~~er~vi~~~y----~~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 1 ALDQLPPREREVIRLRY----FEGLTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp HHCTS-HHHHHHHHHHH----TST-SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred ChhhCCHHHHHHHHHHh----cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 68899999999999999 799999999999999999999999999999984
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=99.13 E-value=1.8e-10 Score=91.53 Aligned_cols=66 Identities=21% Similarity=0.312 Sum_probs=63.4
Q ss_pred HHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH
Q 010327 279 LIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT 347 (513)
Q Consensus 279 LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~ 347 (513)
|++.|.++|+.++.+|. +++.+.+|++||++++||+++++||++.|..|.+|++..+++.+.+.++
T Consensus 1 L~~~~~~~l~~~~~~~~---~~~~~~eD~~qe~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~r 66 (71)
T PF04542_consen 1 LYERYYPLLYRYARRYT---GDPEDAEDLVQEAFIKLWRAIDSYDPDRGDSFRAWLFRIARNRILDYLR 66 (71)
T ss_dssp HHHHTHHHHHHHHHTCT---TCSSHHHHHHHHHHHHHHHHHHHTSTTSSSHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHh---CCHhhHHHHhhHHHHHHHhhhhcccccccCCHHHHHHHHHHHHHHHHHH
Confidence 78999999999999998 7788999999999999999999999999988999999999999999998
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=98.97 E-value=1.5e-09 Score=89.21 Aligned_cols=75 Identities=37% Similarity=0.415 Sum_probs=60.2
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh-hhhccccCCCCCCchh
Q 010327 360 SVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVENEN 434 (513)
Q Consensus 360 ~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~-e~~d~l~d~~~~~~ee 434 (513)
+++++|.++..+|.+++||.||.+|||+.|||++++|+.++...+.++||+.+...+++ .+.+.+.|....+|++
T Consensus 1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d~~~~~P~e 76 (78)
T PF04539_consen 1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIEDDDAPSPEE 76 (78)
T ss_dssp HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-SSS--HHH
T ss_pred ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecCCCCCChhh
Confidence 46789999999999999999999999999999999999999999999999998876644 4666677776766665
No 130
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=98.93 E-value=3.3e-09 Score=81.11 Aligned_cols=54 Identities=28% Similarity=0.329 Sum_probs=46.3
Q ss_pred HHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010327 442 RLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 499 (513)
Q Consensus 442 ~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKL 499 (513)
++.|..+|..|||+++.||.++| .+++|+.|||+.+|+|.++|++.+.+|+++|
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 REALQQALAQLPERQREIFLLRY----FQGMSYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp HHHHHHHHHCS-HHHHHHHHHHH----TS---HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHHHH----HHCcCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 35788999999999999999999 7999999999999999999999999999987
No 131
>PRK06930 positive control sigma-like factor; Validated
Probab=98.47 E-value=5.6e-07 Score=85.34 Aligned_cols=65 Identities=20% Similarity=0.187 Sum_probs=58.5
Q ss_pred hHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010327 436 RQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 504 (513)
Q Consensus 436 ~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~ 504 (513)
....+....|..+|+.|||+++.||.++| .+++|++|||+.||+|.++|++++.+|+++|+....
T Consensus 99 ~~~~e~~~~l~~al~~L~~rer~V~~L~~----~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~ 163 (170)
T PRK06930 99 VISEWDKIRIEDALSVLTEREKEVYLMHR----GYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQIN 163 (170)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 34455667899999999999999999998 689999999999999999999999999999997554
No 132
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=98.30 E-value=2.5e-06 Score=63.16 Aligned_cols=54 Identities=39% Similarity=0.467 Sum_probs=49.9
Q ss_pred HHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010327 443 LALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 500 (513)
Q Consensus 443 ~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR 500 (513)
..+..++..||+.++.++.++| .+++|..+||+.||+|..+|+++..++..+|+
T Consensus 2 ~~~~~~~~~l~~~~~~~~~~~~----~~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 2 ERLEEALDKLPEREREVILLRF----GEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred HHHHHHHHhCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 3577889999999999999999 68999999999999999999999999998875
No 133
>PRK00118 putative DNA-binding protein; Validated
Probab=98.22 E-value=3.2e-06 Score=73.92 Aligned_cols=57 Identities=25% Similarity=0.233 Sum_probs=51.3
Q ss_pred HHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010327 444 ALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 504 (513)
Q Consensus 444 ~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~ 504 (513)
.++-....||++++.|+.++| .+++|..|||+.||+|+.+|++++.+|+++||+...
T Consensus 10 l~d~~~~~L~ekqRevl~L~y----~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~ 66 (104)
T PRK00118 10 LFDFYGSLLTEKQRNYMELYY----LDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEE 66 (104)
T ss_pred HHHHHhccCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 444566789999999999999 789999999999999999999999999999997554
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=98.13 E-value=4.3e-06 Score=76.57 Aligned_cols=54 Identities=19% Similarity=0.164 Sum_probs=47.5
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhh
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLR 509 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~ 509 (513)
-||++|++||.+++ +++|++|||+.||+|+++|++++++|+++|+.....-.+-
T Consensus 6 ~Lte~qr~VL~Lr~-----~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l~ 59 (137)
T TIGR00721 6 FLTERQIKVLELRE-----KGLSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDFV 59 (137)
T ss_pred CCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHHH
Confidence 49999999999976 7999999999999999999999999999999755444443
No 135
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=98.05 E-value=7e-06 Score=75.50 Aligned_cols=50 Identities=26% Similarity=0.213 Sum_probs=45.9
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010327 450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 504 (513)
Q Consensus 450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~ 504 (513)
..|||+|++||.+++ +++|++|||+.||+|+.+|++++++|+++||+...
T Consensus 5 ~~Lt~rqreVL~lr~-----~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~ 54 (141)
T PRK03975 5 SFLTERQIEVLRLRE-----RGLTQQEIADILGTSRANVSSIEKRARENIEKARE 54 (141)
T ss_pred cCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 469999999999965 79999999999999999999999999999997543
No 136
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=97.96 E-value=3.4e-05 Score=67.04 Aligned_cols=55 Identities=29% Similarity=0.330 Sum_probs=43.6
Q ss_pred HHHHHHhc-CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 444 ALDDVLDS-LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 444 ~L~~aL~~-L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
.|.+.... ||++|+.++.++| .+++|+.|||+.+|||+.+|.....||.++|...
T Consensus 9 ~L~d~Yg~LLT~kQ~~~l~lyy----~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~y 64 (101)
T PF04297_consen 9 LLFDFYGELLTEKQREILELYY----EEDLSLSEIAEELGISRQAVYDSIKRAEKKLEEY 64 (101)
T ss_dssp HHHHHHGGGS-HHHHHHHHHHC----TS---HHHHHHHCTS-HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHCCHHHHHHHHHHH----ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34445544 9999999999999 7999999999999999999999999999999753
No 137
>PRK04217 hypothetical protein; Provisional
Probab=97.93 E-value=1.4e-05 Score=70.60 Aligned_cols=55 Identities=15% Similarity=-0.040 Sum_probs=49.5
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhh
Q 010327 450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL 508 (513)
Q Consensus 450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L 508 (513)
..|++.|++||.++| .+++|++|||+.||||..+|++++.+|.++|+.......+
T Consensus 41 ~~Lt~eereai~l~~----~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~~ 95 (110)
T PRK04217 41 IFMTYEEFEALRLVD----YEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGRE 95 (110)
T ss_pred ccCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 479999999999999 7899999999999999999999999999999986654443
No 138
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=97.86 E-value=4.4e-05 Score=57.45 Aligned_cols=50 Identities=36% Similarity=0.358 Sum_probs=44.5
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010327 450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 504 (513)
Q Consensus 450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~ 504 (513)
..|++.|+.|+.+.+ .++|..|||+.||+|+.+|+++..+++++|.-...
T Consensus 2 ~~l~~~e~~i~~~~~-----~g~s~~eia~~l~is~~tv~~~~~~~~~kl~~~~~ 51 (58)
T smart00421 2 ASLTPREREVLRLLA-----EGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSR 51 (58)
T ss_pred CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCH
Confidence 468999999997754 68999999999999999999999999999986554
No 139
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.
Probab=97.84 E-value=0.00011 Score=66.92 Aligned_cols=61 Identities=18% Similarity=0.194 Sum_probs=53.0
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 440 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 440 ~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
.....|..+|+.|++.++.||.++|. . ...+|+.+||..||+|..+|+++..+|+.+|+..
T Consensus 71 ~~~~~I~~~l~~Ld~~er~II~~rY~-~-~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~ 131 (134)
T TIGR01636 71 RNRDAIENCLNEADEQTRVIIQELYM-K-KRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEE 131 (134)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHc-c-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 45667999999999999999999993 1 1235999999999999999999999999999854
No 140
>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=97.75 E-value=0.00011 Score=63.62 Aligned_cols=56 Identities=32% Similarity=0.485 Sum_probs=50.5
Q ss_pred HHHHHHHHHHhcCC-HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010327 440 LLRLALDDVLDSLK-PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 499 (513)
Q Consensus 440 ~l~~~L~~aL~~L~-~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKL 499 (513)
..+..+..++++|. +.++.||.++| ...+++.+||..||+|+.++..++.+|++.|
T Consensus 43 ~~k~ei~~~I~~l~d~~~r~iL~~~Y----i~~~~~~~I~~~l~~S~~t~yr~~~~Al~~L 99 (100)
T PF07374_consen 43 KEKLEIRRAINKLEDPDERLILRMRY----INKLTWEQIAEELNISRRTYYRIHKKALKEL 99 (100)
T ss_pred HHHHHHHHHHHHccChhHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence 44566888999985 89999999999 7899999999999999999999999999876
No 141
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPro: IPR009042 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....
Probab=97.74 E-value=1.1e-05 Score=57.58 Aligned_cols=33 Identities=21% Similarity=0.245 Sum_probs=29.2
Q ss_pred CChHHHHHHhcCCCCCCChHHHHHHHHHHhHhH
Q 010327 200 TDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMK 232 (513)
Q Consensus 200 ~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~ 232 (513)
+|.+..||++|+.+|+||++||..|++.|+.+.
T Consensus 1 ~D~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~ 33 (37)
T PF00140_consen 1 SDSLRLYLKEIGRYPLLTAEEEIELARRIRKGD 33 (37)
T ss_dssp HHHHHHHHHHHHHS-EETTHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhH
Confidence 378999999999999999999999999997654
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=97.70 E-value=0.0001 Score=57.17 Aligned_cols=52 Identities=31% Similarity=0.319 Sum_probs=44.8
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010327 450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 506 (513)
Q Consensus 450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~ 506 (513)
+.|+++|.+||.+.. .++|.+|||..||||..+|+.+..++++||.-..+.+
T Consensus 2 ~~LT~~E~~vl~~l~-----~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~~~~ 53 (58)
T PF00196_consen 2 PSLTERELEVLRLLA-----QGMSNKEIAEELGISEKTVKSHRRRIMKKLGVKNRAE 53 (58)
T ss_dssp GSS-HHHHHHHHHHH-----TTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-SSHHH
T ss_pred CccCHHHHHHHHHHH-----hcCCcchhHHhcCcchhhHHHHHHHHHHHhCCCCHHH
Confidence 579999999999987 7999999999999999999999999999998766544
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=0.00017 Score=54.37 Aligned_cols=49 Identities=35% Similarity=0.366 Sum_probs=43.9
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010327 452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV 505 (513)
Q Consensus 452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~ 505 (513)
|+++|+.|+.+.+ .++|.+|||+.||+|+.+|+.+..+++++|.-....
T Consensus 1 l~~~e~~i~~~~~-----~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~~~~~ 49 (57)
T cd06170 1 LTPREREVLRLLA-----EGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRT 49 (57)
T ss_pred CCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCCCHH
Confidence 6899999998855 689999999999999999999999999999976543
No 144
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=97.52 E-value=0.00018 Score=58.89 Aligned_cols=46 Identities=22% Similarity=0.204 Sum_probs=41.0
Q ss_pred HHHHHhcCCHHHHHHHhHH-hcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 445 LDDVLDSLKPKESLVIRQR-FGLDGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 445 L~~aL~~L~~rEr~VL~lR-yGL~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
+..-|+.||++.+.++.|. | .+++|++|||+.||+|..+|+.++.+
T Consensus 9 ~~~~l~~l~~~~r~af~L~R~----~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 9 LAERLTWVDSLAEAAAALARE----EAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHhcCCHHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 5567889999999999994 4 58999999999999999999999874
No 145
>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=97.52 E-value=0.00012 Score=62.67 Aligned_cols=50 Identities=20% Similarity=0.268 Sum_probs=43.1
Q ss_pred HHHHHHHh-cCCHHHHHHHhHHhcCCC---CCCCCHHHHHHHhCCCHHHHHHHH
Q 010327 443 LALDDVLD-SLKPKESLVIRQRFGLDG---KGDRTLGEIAGNLNISREMVRKHE 492 (513)
Q Consensus 443 ~~L~~aL~-~L~~rEr~VL~lRyGL~~---~~~~Tl~EIA~~LgISrerVRqi~ 492 (513)
+.+..+|. -|+|+|+.+|.+||||.+ ..++|+.|||+.+|||+.+|.+..
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 34666774 499999999999999987 678999999999999999998654
No 146
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=97.51 E-value=0.00034 Score=53.91 Aligned_cols=48 Identities=27% Similarity=0.373 Sum_probs=41.4
Q ss_pred CCHHHHHHHhHHh--cCCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010327 452 LKPKESLVIRQRF--GLDGK-GDRTLGEIAGNLNISREMVRKHEVKGLMKL 499 (513)
Q Consensus 452 L~~rEr~VL~lRy--GL~~~-~~~Tl~EIA~~LgISrerVRqi~~rALkKL 499 (513)
|+++|++||..-| |..+. .+-|+.|||+.||||.+++..++.+|.+||
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 7899999998855 43332 468999999999999999999999999987
No 147
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=97.28 E-value=0.00066 Score=64.51 Aligned_cols=52 Identities=19% Similarity=0.194 Sum_probs=47.5
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY 507 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~ 507 (513)
.||++|++||.+.- +|+|.+|||+.|++|..||+....++++||.-..+.+.
T Consensus 133 ~LSpRErEVLrLLA-----qGkTnKEIAe~L~IS~rTVkth~srImkKLgV~SRaEL 184 (198)
T PRK15201 133 HFSVTERHLLKLIA-----SGYHLSETAALLSLSEEQTKSLRRSIMRKLHVKTEQQF 184 (198)
T ss_pred CCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHH
Confidence 59999999999987 89999999999999999999999999999987666543
No 148
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=97.26 E-value=0.00048 Score=67.04 Aligned_cols=50 Identities=24% Similarity=0.268 Sum_probs=46.2
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV 505 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~ 505 (513)
.|+|+|++||.+.- +|+|.+|||+.||+|..||+.+..+.++||.-..+.
T Consensus 137 ~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v~nr~ 186 (207)
T PRK15411 137 SLSRTESSMLRMWM-----AGQGTIQISDQMNIKAKTVSSHKGNIKRKIKTHNKQ 186 (207)
T ss_pred cCCHHHHHHHHHHH-----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCCCcHH
Confidence 59999999999987 899999999999999999999999999999865553
No 149
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=97.22 E-value=0.00056 Score=65.87 Aligned_cols=52 Identities=31% Similarity=0.328 Sum_probs=46.7
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010327 450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 506 (513)
Q Consensus 450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~ 506 (513)
..|+++|++||.+.- +|+|.+|||+.||+|..||+.+..+.++||--..+.+
T Consensus 149 ~~Lt~rE~evl~~~~-----~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~v~~~~~ 200 (216)
T PRK10840 149 KRLSPKESEVLRLFA-----EGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIA 200 (216)
T ss_pred ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHH
Confidence 359999999999987 7999999999999999999999999999997654443
No 150
>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=97.22 E-value=0.00065 Score=68.27 Aligned_cols=54 Identities=24% Similarity=0.202 Sum_probs=48.8
Q ss_pred HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010327 449 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY 507 (513)
Q Consensus 449 L~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~ 507 (513)
+..||++|++||.+.. +++|.+|||+.||||..||+....++++||.-..+.+.
T Consensus 188 ~~~LT~RE~evl~l~a-----~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~nr~qA 241 (247)
T TIGR03020 188 AGLITAREAEILAWVR-----DGKTNEEIAAILGISSLTVKNHLQHIFKKLDVRNRAQA 241 (247)
T ss_pred ccCCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCCCCHHHH
Confidence 4579999999999976 79999999999999999999999999999997766554
No 151
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=97.21 E-value=0.00055 Score=66.87 Aligned_cols=52 Identities=21% Similarity=0.279 Sum_probs=47.0
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010327 450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 506 (513)
Q Consensus 450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~ 506 (513)
..||++|++||.+.- +|+|.+|||+.|+||..||+.+..+.++||--..+.+
T Consensus 133 ~~LT~RE~eVL~ll~-----~G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv~n~~e 184 (207)
T PRK11475 133 RMLSPTEREILRFMS-----RGYSMPQIAEQLERNIKTIRAHKFNVMSKLGVSSDAG 184 (207)
T ss_pred CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHH
Confidence 469999999999987 7999999999999999999999999999997655443
No 152
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=97.21 E-value=0.00072 Score=67.02 Aligned_cols=53 Identities=26% Similarity=0.204 Sum_probs=47.7
Q ss_pred HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010327 449 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 506 (513)
Q Consensus 449 L~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~ 506 (513)
...||++|++||.+.. +++|..|||++||||..+|+.++.++++||.-..+.+
T Consensus 169 ~~~Lt~re~evl~~~a-----~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~~~~ 221 (232)
T TIGR03541 169 AGVLSEREREVLAWTA-----LGRRQADIAAILGISERTVENHLRSARRKLGVATTAQ 221 (232)
T ss_pred hccCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCHHH
Confidence 3469999999999965 7999999999999999999999999999999766544
No 153
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=97.16 E-value=0.00088 Score=65.78 Aligned_cols=56 Identities=14% Similarity=-0.043 Sum_probs=50.6
Q ss_pred HHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010327 446 DDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 506 (513)
Q Consensus 446 ~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~ 506 (513)
..+...|+|+|++||.+.- +|+|.+|||+.|++|..||+.+..+.++||--..+.+
T Consensus 138 ~~~~~~LS~RE~eVL~Lia-----~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv~sR~e 193 (217)
T PRK13719 138 LEAKNKVTKYQNDVFILYS-----FGFSHEYIAQLLNITVGSSKNKISEILKFFGISSRDE 193 (217)
T ss_pred hhccCCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHH
Confidence 4566789999999999987 7999999999999999999999999999998766654
No 154
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=97.16 E-value=0.0008 Score=66.13 Aligned_cols=52 Identities=23% Similarity=0.210 Sum_probs=47.7
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010327 450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 506 (513)
Q Consensus 450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~ 506 (513)
..||++|++||.+.. +++|.+|||+.|++|..||+.+..++++||.-..+.+
T Consensus 154 ~~Lt~rE~~Vl~l~~-----~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v~nr~e 205 (216)
T PRK10100 154 ALLTHREKEILNKLR-----IGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQ 205 (216)
T ss_pred CCCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHH
Confidence 469999999999998 6999999999999999999999999999998766654
No 155
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=97.12 E-value=0.00064 Score=50.20 Aligned_cols=41 Identities=27% Similarity=0.328 Sum_probs=24.8
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
.+|++.|+..|...+ ..++|..+||+.||+|++||...+.|
T Consensus 3 ~~Lt~~eR~~I~~l~----~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEALL----EQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHHHH----CS---HHHHHHHTT--HHHHHHHHHH
T ss_pred cchhhhHHHHHHHHH----HcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 469999999999888 78999999999999999999988776
No 156
>PRK13870 transcriptional regulator TraR; Provisional
Probab=97.07 E-value=0.00095 Score=66.42 Aligned_cols=51 Identities=22% Similarity=0.244 Sum_probs=46.5
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 506 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~ 506 (513)
.||+||++||.+-= +|+|..|||.+||||..||..++..|.+||--..+.+
T Consensus 173 ~LT~RE~E~L~W~A-----~GKT~~EIa~ILgISe~TV~~Hl~na~~KLga~nr~q 223 (234)
T PRK13870 173 WLDPKEATYLRWIA-----VGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAH 223 (234)
T ss_pred CCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHH
Confidence 49999999999986 8999999999999999999999999999997665544
No 157
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=97.06 E-value=0.001 Score=66.34 Aligned_cols=52 Identities=23% Similarity=0.288 Sum_probs=47.1
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY 507 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~ 507 (513)
.|+++|++||.+.. .|+|..|||.+||||..||+.++.++++||--..+.+.
T Consensus 179 ~LT~rE~evl~~~a-----~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~~~nr~q~ 230 (240)
T PRK10188 179 NFSKREKEILKWTA-----EGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQI 230 (240)
T ss_pred CCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHH
Confidence 59999999999997 79999999999999999999999999999986655443
No 158
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=96.99 E-value=0.0027 Score=49.32 Aligned_cols=54 Identities=31% Similarity=0.359 Sum_probs=47.3
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhh
Q 010327 450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL 508 (513)
Q Consensus 450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L 508 (513)
..|+++|.+|+.+.- .++|..|||..+|+|..+|+....++..||.-..+...+
T Consensus 3 ~~Lt~rE~~v~~l~~-----~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~~r~~~~ 56 (65)
T COG2771 3 ADLTPREREILRLVA-----QGKSNKEIARILGISEETVKTHLRNIYRKLGVKNRVELV 56 (65)
T ss_pred ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHH
Confidence 359999999998876 579999999999999999999999999999876665443
No 159
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=96.98 E-value=0.0027 Score=61.11 Aligned_cols=65 Identities=23% Similarity=0.256 Sum_probs=56.7
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhh
Q 010327 440 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLR 509 (513)
Q Consensus 440 ~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~ 509 (513)
.....+...|.+|+|+||+|+...- .++..++||..||||..||..+..+.+.||+.....+-++
T Consensus 131 ~~~~~~~~~l~tLT~RERqVl~~vV-----~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~SlaeLvr 195 (202)
T COG4566 131 DRQAAIRARLATLTPRERQVLDLVV-----RGLMNKQIAFDLGISERTVELHRANVMEKMQARSLAELVR 195 (202)
T ss_pred HHHHHHHHHHHhcCHHHHHHHHHHH-----cCcccHHHHHHcCCchhhHHHHHHHHHHHHhhccHHHHHH
Confidence 4456788899999999999999886 7899999999999999999999999999999766655444
No 160
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=96.90 E-value=0.0019 Score=63.27 Aligned_cols=52 Identities=33% Similarity=0.360 Sum_probs=47.2
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010327 450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 506 (513)
Q Consensus 450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~ 506 (513)
..||+||++||++.- +|+|.+|||+.|++|..||+.+.++.++||.-..+.+
T Consensus 147 ~~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~v~~Rte 198 (211)
T COG2197 147 ELLTPRELEVLRLLA-----EGLSNKEIAEELNLSEKTVKTHVSNILRKLGVRNRTE 198 (211)
T ss_pred CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHhHHHHHHHHHHHHcCCCCHHH
Confidence 469999999999986 7999999999999999999999999999998766544
No 161
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=96.82 E-value=0.0023 Score=56.24 Aligned_cols=48 Identities=19% Similarity=0.091 Sum_probs=44.6
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
.|+..|-+.|+|.+ ++++|++|.|+.||||+.|+..++..|.+|+-..
T Consensus 41 ~L~~dElEAiRL~D----~egl~QeeaA~~MgVSR~T~~ril~~ARkKiA~A 88 (106)
T PF02001_consen 41 VLTVDELEAIRLVD----YEGLSQEEAAERMGVSRPTFQRILESARKKIADA 88 (106)
T ss_pred EeeHHHHHHHHHHH----HcCCCHHHHHHHcCCcHHHHHHHHHHHHHHHHHH
Confidence 58889999999998 7899999999999999999999999999999754
No 162
>PRK09483 response regulator; Provisional
Probab=96.82 E-value=0.0021 Score=60.74 Aligned_cols=50 Identities=22% Similarity=0.237 Sum_probs=44.8
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010327 450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 504 (513)
Q Consensus 450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~ 504 (513)
..|+++|++||.+.. .++|.+|||+.|++|..||+.+..+.++||--..+
T Consensus 147 ~~Lt~rE~~vl~~~~-----~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~v~~~ 196 (217)
T PRK09483 147 ASLSERELQIMLMIT-----KGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGD 196 (217)
T ss_pred cccCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCH
Confidence 469999999998865 78999999999999999999999999999965444
No 163
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=96.81 E-value=0.0028 Score=71.62 Aligned_cols=38 Identities=16% Similarity=0.156 Sum_probs=34.5
Q ss_pred hhcCCCChHHHHHHhcCCCCCCChHHHHHHHHHHhHhH
Q 010327 195 EYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMK 232 (513)
Q Consensus 195 ~~~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~ 232 (513)
+++.++|+|+|||++||.+||||.|+|+.+|++|+.+.
T Consensus 98 ~~~rt~DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~ 135 (619)
T PRK05658 98 EIGRTDDPVRMYLREMGTVELLTREGEIEIAKRIEAGE 135 (619)
T ss_pred ccCCCCChHHHHHHHhccCcCCCcHHHHHHHHHHHHHH
Confidence 45668999999999999999999999999999998664
No 164
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=96.79 E-value=0.0028 Score=62.08 Aligned_cols=51 Identities=24% Similarity=0.310 Sum_probs=43.9
Q ss_pred cCCHHHHHHHhHHh--cCCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 451 SLKPKESLVIRQRF--GLDGK-GDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 451 ~L~~rEr~VL~lRy--GL~~~-~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
.|+++|++||+.-| |..+. ...|++|||+.||||.+++.+++.+|.+||=.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~ 208 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIE 208 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 59999999999865 44333 45899999999999999999999999999854
No 165
>PF12645 HTH_16: Helix-turn-helix domain; InterPro: IPR024760 This domain appears to be a helix-turn-helix domain, suggesting a transcriptional regulatory protein. Some proteins with this domain are annotated as conjugative transposon proteins.
Probab=96.69 E-value=0.0067 Score=48.69 Aligned_cols=60 Identities=25% Similarity=0.230 Sum_probs=48.6
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhc-c--CCCCcHHHHHHHHHHHHHHHHhhcC
Q 010327 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQD-F--ANGPRFQDLCQAGVKGLITAIDRFE 323 (513)
Q Consensus 264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~-~--~~g~~~eDLIQEG~iGLirAvekFD 323 (513)
.|.++.+||..|.++++.+|.+++.+++.+-..+ . ..+.--+||-|+-...|+.++-+|+
T Consensus 3 vI~~A~~GD~~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~ 65 (65)
T PF12645_consen 3 VIKAAKQGDPEAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE 65 (65)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence 4677899999999999999999999988762211 0 1234449999999999999999996
No 166
>PRK01381 Trp operon repressor; Provisional
Probab=96.65 E-value=0.0016 Score=56.35 Aligned_cols=50 Identities=18% Similarity=0.224 Sum_probs=41.6
Q ss_pred HHHHHHHHHhc-CCHHHHHHHhHHhcCCC---CCCCCHHHHHHHhCCCHHHHHH
Q 010327 441 LRLALDDVLDS-LKPKESLVIRQRFGLDG---KGDRTLGEIAGNLNISREMVRK 490 (513)
Q Consensus 441 l~~~L~~aL~~-L~~rEr~VL~lRyGL~~---~~~~Tl~EIA~~LgISrerVRq 490 (513)
..+.+..+|.. |+|.|+.+|..||++.. ..++|+.|||+.+|||..+|.+
T Consensus 21 ~~~~~~~~l~~llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITR 74 (99)
T PRK01381 21 EEDLHLPLLTLLLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATITR 74 (99)
T ss_pred cHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehh
Confidence 34456666766 89999999999999965 4579999999999999998873
No 167
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=96.59 E-value=0.0036 Score=54.11 Aligned_cols=46 Identities=24% Similarity=0.307 Sum_probs=42.4
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
|+.+|+..+.++| ..++|+.|||+.++||+++|...+.|.-+.|-.
T Consensus 18 LT~KQ~~Y~~lyy----~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~ 63 (105)
T COG2739 18 LTKKQKNYLELYY----LDDLSLSEIAEEFNVSRQAIYDNIKRTEKILED 63 (105)
T ss_pred HhHHHHHHHHHHH----HhhccHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence 8999999999999 789999999999999999999999998776643
No 168
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=96.56 E-value=0.0082 Score=55.08 Aligned_cols=59 Identities=19% Similarity=0.195 Sum_probs=51.0
Q ss_pred HHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010327 444 ALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY 507 (513)
Q Consensus 444 ~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~ 507 (513)
.+...+..|+++|++||.+.+ .+++.++||+.+|+|..+|+.+..++++||+...+.+-
T Consensus 134 ~~~~~~~~l~~~e~~vl~~~~-----~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~~~~~~ 192 (202)
T PRK09390 134 DIRARIASLSERERQVMDGLV-----AGLSNKVIARDLDISPRTVEVYRANVMTKMQAGSLSEL 192 (202)
T ss_pred HHHHHHHhhhhhHHHHHHHHH-----ccCchHHHHHHcCCCHHHHHHHHHHHHHHHccccHHHH
Confidence 455667889999999999755 67899999999999999999999999999987766543
No 169
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=96.49 E-value=0.0073 Score=55.67 Aligned_cols=50 Identities=26% Similarity=0.290 Sum_probs=45.0
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010327 450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 504 (513)
Q Consensus 450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~ 504 (513)
..|+++|++||.+.- +++|.++||+.|++|..||+.+..++++||.-..+
T Consensus 148 ~~lt~~e~~vl~l~~-----~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~~~ 197 (211)
T PRK15369 148 PLLTPRERQILKLIT-----EGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKV 197 (211)
T ss_pred cCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCH
Confidence 459999999999843 78999999999999999999999999999986554
No 170
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=96.44 E-value=0.0019 Score=57.92 Aligned_cols=49 Identities=24% Similarity=0.222 Sum_probs=45.4
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010327 452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV 505 (513)
Q Consensus 452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~ 505 (513)
|+++|-.||.||- +|+|.+|||++||-|+..|+-++.+|+.++.+..+.
T Consensus 9 lte~qikvl~lRe-----kG~tQ~eIA~~L~TTraNvSaIEkrA~enIekarnT 57 (143)
T COG1356 9 LTEQQIKVLVLRE-----KGLTQSEIARILKTTRANVSAIEKRALENIEKARNT 57 (143)
T ss_pred eehhheeeeehhh-----ccccHHHHHHHHccchhhHHHHHHHHHHHHHHHHHH
Confidence 8999999999997 899999999999999999999999999999876543
No 171
>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=96.43 E-value=0.016 Score=52.40 Aligned_cols=57 Identities=11% Similarity=0.166 Sum_probs=50.1
Q ss_pred HHHHHHHH-hcCCHHHHHHHhHHhcCCCCC--CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 442 RLALDDVL-DSLKPKESLVIRQRFGLDGKG--DRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 442 ~~~L~~aL-~~L~~rEr~VL~lRyGL~~~~--~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
...+..++ +.|++.+|.||.++| .. .++..+|+..||+|+.+...+..+|+.+|-..
T Consensus 69 ~~~i~~ai~~~l~~~~r~Il~~~Y----l~~~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~ 128 (132)
T TIGR01637 69 ARAIVNAIVNQLDEISRQILYDKY----LEPDQKYDYQIMMELGYSHRQYYRIKKRALLRFATL 128 (132)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHH----cCccccchHHHHHHhCCcHHHHHHHHHHHHHHHHHH
Confidence 34566777 999999999999999 44 78999999999999999999999999988643
No 172
>PRK10651 transcriptional regulator NarL; Provisional
Probab=96.38 E-value=0.0072 Score=56.46 Aligned_cols=52 Identities=27% Similarity=0.337 Sum_probs=46.3
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010327 450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 506 (513)
Q Consensus 450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~ 506 (513)
..|+++|++|+.+.. ++++.++||..|++|..||+.+..+.++||.-..+.+
T Consensus 154 ~~Lt~rE~~vl~~l~-----~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~~~~~~ 205 (216)
T PRK10651 154 NQLTPRERDILKLIA-----QGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVE 205 (216)
T ss_pred ccCCHHHHHHHHHHH-----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCHHH
Confidence 459999999999876 7899999999999999999999999999997655543
No 173
>PRK10403 transcriptional regulator NarP; Provisional
Probab=95.95 E-value=0.016 Score=53.91 Aligned_cols=55 Identities=29% Similarity=0.222 Sum_probs=47.8
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhh
Q 010327 450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLR 509 (513)
Q Consensus 450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~ 509 (513)
..|+++|.+|+.+.. .++|.++||+.+|+|..||+.+..+.++||.-..+.+...
T Consensus 152 ~~Lt~~e~~vl~~~~-----~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~~~~~~~~ 206 (215)
T PRK10403 152 SVLTERELDVLHELA-----QGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAATI 206 (215)
T ss_pred ccCCHHHHHHHHHHH-----CCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCHHHHHH
Confidence 359999999998876 6799999999999999999999999999997766655433
No 174
>PRK15320 transcriptional activator SprB; Provisional
Probab=95.93 E-value=0.014 Score=56.60 Aligned_cols=51 Identities=10% Similarity=0.068 Sum_probs=45.6
Q ss_pred HHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 447 DVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 447 ~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
.+--.|+++|.+||.+-- +|+|.+|||+.|++|..+|+....+.+.||.-.
T Consensus 160 ~~~~~LSdREIEVL~LLA-----kG~SNKEIAekL~LS~KTVSTYKnRLLeKLgAk 210 (251)
T PRK15320 160 NLPPGVTQAKYALLILLS-----SGHPAIELAKKFGLGTKTVSIYRKKVMYRLGMD 210 (251)
T ss_pred cCCCCCCHHHHHHHHHHH-----cCCCHHHHHHHhccchhhHHHHHHHHHHHcCCC
Confidence 334579999999999886 799999999999999999999999999999753
No 175
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=95.84 E-value=0.016 Score=49.64 Aligned_cols=48 Identities=21% Similarity=0.067 Sum_probs=43.7
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
.|+..|-+.|+|.. +.++|++|-|..||||+.|+-+.+..|++|.-..
T Consensus 33 ~lt~eElEAlRLvD----~~~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~a 80 (99)
T COG1342 33 ILTIEELEALRLVD----YEGLTQEEAALRMGISRQTFWRLLTSARKKVADA 80 (99)
T ss_pred eecHHHHHHHHHHh----HhhccHHHHHHHhcccHHHHHHHHHHHHHHHHHH
Confidence 47888999999988 7899999999999999999999999999998643
No 176
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=95.79 E-value=0.025 Score=52.50 Aligned_cols=55 Identities=27% Similarity=0.320 Sum_probs=48.1
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhh
Q 010327 450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLR 509 (513)
Q Consensus 450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~ 509 (513)
..|+++|.+|+.+.. +++|.++||+.|++|..+|+.+..+.++||.-..+.+-..
T Consensus 136 ~~Lt~~E~~il~~l~-----~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~~~~~~~l~~ 190 (196)
T PRK10360 136 DPLTKRERQVAEKLA-----QGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELAR 190 (196)
T ss_pred cCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHHHH
Confidence 369999999999976 5799999999999999999999999999998766655443
No 177
>PRK13558 bacterio-opsin activator; Provisional
Probab=95.44 E-value=0.026 Score=63.80 Aligned_cols=52 Identities=17% Similarity=0.172 Sum_probs=43.3
Q ss_pred HhcCCHHHHHHHhHHhcCC--C-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010327 449 LDSLKPKESLVIRQRFGLD--G-KGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 500 (513)
Q Consensus 449 L~~L~~rEr~VL~lRyGL~--~-~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR 500 (513)
...|+++|+++|..-|-.+ + -.+-|++|||+.||||++++.+++++|.+||=
T Consensus 605 ~~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l~ 659 (665)
T PRK13558 605 ENDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKLV 659 (665)
T ss_pred hhhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 3579999999999977221 1 12349999999999999999999999999984
No 178
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=95.34 E-value=0.034 Score=51.89 Aligned_cols=49 Identities=24% Similarity=0.209 Sum_probs=43.2
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 504 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~ 504 (513)
.|+++|..|+.+.. +++|.+|||+.|++|..+|+.+..++++||.-..+
T Consensus 149 ~lt~re~~vl~~l~-----~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~~~~~ 197 (210)
T PRK09935 149 VLSNREVTILRYLV-----SGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSI 197 (210)
T ss_pred cCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCH
Confidence 48999999998754 67999999999999999999999999999975443
No 179
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=95.24 E-value=0.037 Score=51.64 Aligned_cols=51 Identities=27% Similarity=0.305 Sum_probs=45.1
Q ss_pred HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010327 449 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 504 (513)
Q Consensus 449 L~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~ 504 (513)
+..|+++|.+|+.+.. .+.|.++||+.+++|..+|+.+..+.++||--..+
T Consensus 141 ~~~lt~~E~~vl~~l~-----~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~~~~~ 191 (204)
T PRK09958 141 LDSLSKQEISVMRYIL-----DGKDNNDIAEKMFISNKTVSTYKSRLMEKLECKSL 191 (204)
T ss_pred cccCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCH
Confidence 3569999999999887 67899999999999999999999999999964443
No 180
>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=95.18 E-value=0.043 Score=44.68 Aligned_cols=40 Identities=35% Similarity=0.671 Sum_probs=31.3
Q ss_pred hHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHH
Q 010327 231 MKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLE 270 (513)
Q Consensus 231 ~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~ 270 (513)
+..+.++..+|+..+||+|+.+|+|..+|++.+.+..++.
T Consensus 3 l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~ 42 (78)
T PF04539_consen 3 LRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQ 42 (78)
T ss_dssp HHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHH
Confidence 3456778889999999999999999999999988877653
No 181
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=95.16 E-value=0.49 Score=49.54 Aligned_cols=58 Identities=19% Similarity=0.321 Sum_probs=49.8
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 440 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 440 ~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
.++...--+---|++.+|-.|.+|. ..++|..|||..|=|+..++-|.+.||..+++.
T Consensus 109 ~LRLiFvccHPal~~~~riALtLR~----v~GLs~~eIArAFLv~e~am~QRivRAK~ri~~ 166 (415)
T COG4941 109 RLRLIFVCCHPALPPEQRIALTLRL----VGGLSTAEIARAFLVPEAAMAQRIVRAKARIRE 166 (415)
T ss_pred hHHhhhhhcCCCCChhhHHHHHHHH----HcCCcHHHHHHHHcCCcHHHHHHHHHHHHHHHh
Confidence 3444344444559999999999999 789999999999999999999999999999996
No 182
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=95.13 E-value=0.044 Score=46.63 Aligned_cols=37 Identities=16% Similarity=0.196 Sum_probs=31.4
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 010327 450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHE 492 (513)
Q Consensus 450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~ 492 (513)
+.|++| ..|+.+.- .++|..+||+.+|||+.||.++.
T Consensus 35 ~~Ls~R-~~I~~ll~-----~G~S~~eIA~~LgISrsTIyRi~ 71 (88)
T TIGR02531 35 QSLAQR-LQVAKMLK-----QGKTYSDIEAETGASTATISRVK 71 (88)
T ss_pred HhhhHH-HHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHH
Confidence 358899 78877765 57899999999999999999844
No 183
>PRK04841 transcriptional regulator MalT; Provisional
Probab=94.97 E-value=0.046 Score=63.70 Aligned_cols=53 Identities=21% Similarity=0.277 Sum_probs=47.7
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010327 450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY 507 (513)
Q Consensus 450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~ 507 (513)
..||++|.+|+.+.. +++|.+|||..|+||..||+.++.+...||.-..+.+.
T Consensus 837 ~~lt~~e~~v~~~~~-----~g~~~~~ia~~l~~s~~tv~~h~~~~~~kl~v~~r~~~ 889 (903)
T PRK04841 837 SPLTQREWQVLGLIY-----SGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEA 889 (903)
T ss_pred CCCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHH
Confidence 349999999999977 89999999999999999999999999999987666543
No 184
>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=94.86 E-value=0.1 Score=47.65 Aligned_cols=57 Identities=26% Similarity=0.345 Sum_probs=47.1
Q ss_pred HHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010327 441 LRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 499 (513)
Q Consensus 441 l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKL 499 (513)
....|..+++.|.+.++.||.+||+- ..++|+.+||..|++|..+++.....-...+
T Consensus 71 ~k~~id~~~~~l~de~k~Ii~lry~~--r~~~TW~~IA~~l~i~erta~r~~~~fK~~i 127 (130)
T PF05263_consen 71 QKEAIDRWLETLIDEEKRIIKLRYDR--RSRRTWYQIAQKLHISERTARRWRDRFKNDI 127 (130)
T ss_pred HHHHHHHHHHhhCHHHHHHHHHHHcc--cccchHHHHHHHhCccHHHHHHHHHHHHHHh
Confidence 45567888999999999999999952 3469999999999999999998876654433
No 185
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=94.70 E-value=0.069 Score=40.80 Aligned_cols=48 Identities=17% Similarity=0.168 Sum_probs=41.7
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
+|+..++.++.+.|- ..+.|++++|..+|||+++|+++.+..+.-|-.
T Consensus 2 kLs~~d~lll~L~~L---R~~~~~~~La~~FgIs~stvsri~~~~~~~L~~ 49 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYL---RLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQ 49 (53)
T ss_pred CCCHHHHHHHHHHHH---HcCCcHhHHhhheeecHHHHHHHHHHHHHHHHH
Confidence 688899999888763 678999999999999999999999998877654
No 186
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=94.69 E-value=0.028 Score=41.84 Aligned_cols=33 Identities=27% Similarity=0.256 Sum_probs=23.0
Q ss_pred HHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010327 458 LVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG 495 (513)
Q Consensus 458 ~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA 495 (513)
.||.+.. +++|..+||+.||||+.+|+++..+-
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 58999999999999999999987663
No 187
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=94.55 E-value=0.038 Score=40.82 Aligned_cols=33 Identities=18% Similarity=0.118 Sum_probs=24.0
Q ss_pred HHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 456 ESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 456 Er~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
..+|+.|+- .++|..+||+.||||+.+|.+++.
T Consensus 11 ~~~i~~l~~-----~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 11 IEEIKELYA-----EGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHHH-----TT--HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHh
Confidence 455666665 679999999999999999998763
No 188
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=94.14 E-value=0.48 Score=50.35 Aligned_cols=130 Identities=22% Similarity=0.297 Sum_probs=72.1
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHH
Q 010327 233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGV 312 (513)
Q Consensus 233 ~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~ 312 (513)
.+......|...+|++|+.+|+|..+|++.+.+..++.... . .+++-... +.+ +|
T Consensus 217 ~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~----~--------~~SLd~~~----~~~---~~------ 271 (367)
T PRK09210 217 KLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQ----E--------PVSLETPI----GEE---DD------ 271 (367)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhc----C--------CCCcCCCC----CCC---Cc------
Confidence 34556677888999999999999999999988876543211 0 01110000 000 01
Q ss_pred HHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhccccccccchhHHHHHHHHHHHHHHHH--hCCCCCHHHHHHhcC
Q 010327 313 KGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAKLELLFE--LKRVPTDEEIIQGVN 390 (513)
Q Consensus 313 iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~iRlP~~~~~~~~ki~ka~~~L~~e--lgR~PT~eELA~~lg 390 (513)
..|...+. |+.............++..+..++.. +|.. .+..-.+..- -|..-|.+|||+.+|
T Consensus 272 ~~l~d~i~--d~~~~~p~~~~~~~~~~~~l~~~l~~-----L~~r--------Er~Vl~lrygl~~~~~~tl~EIa~~lg 336 (367)
T PRK09210 272 SHLGDFIE--DQDATSPADHAAYELLKEQLEDVLDT-----LTDR--------EENVLRLRFGLDDGRTRTLEEVGKVFG 336 (367)
T ss_pred chhhhhcc--CCCCCCHHHHHHHHHHHHHHHHHHHh-----CCHH--------HHHHHHHHhccCCCCCccHHHHHHHHC
Confidence 01111111 11112223344455666667666651 3311 1111122211 237789999999999
Q ss_pred CCHHHHHHHHHh
Q 010327 391 ISPERYREVMKA 402 (513)
Q Consensus 391 is~e~v~~~l~~ 402 (513)
+|.++|+++...
T Consensus 337 vs~erVrQi~~~ 348 (367)
T PRK09210 337 VTRERIRQIEAK 348 (367)
T ss_pred CCHHHHHHHHHH
Confidence 999999988543
No 189
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=94.09 E-value=0.13 Score=38.01 Aligned_cols=41 Identities=24% Similarity=0.167 Sum_probs=30.2
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010327 452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG 495 (513)
Q Consensus 452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA 495 (513)
|++.++.||..-+- ..+.|..|||+.+|+|..+|+++..+-
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 56788888877662 456999999999999999999876653
No 190
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=93.99 E-value=0.1 Score=34.39 Aligned_cols=36 Identities=25% Similarity=0.385 Sum_probs=28.2
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHH
Q 010327 452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKH 491 (513)
Q Consensus 452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi 491 (513)
+++.++..+...| ..+.|..+||+.+|+|+.+|..+
T Consensus 6 ~~~~~~~~i~~~~----~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 6 LTPEQIEEARRLL----AAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHh
Confidence 5556666665556 45779999999999999999875
No 191
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=93.96 E-value=0.072 Score=55.53 Aligned_cols=36 Identities=22% Similarity=0.204 Sum_probs=32.7
Q ss_pred HHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010327 458 LVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 497 (513)
Q Consensus 458 ~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALk 497 (513)
.|-.||| .+++|.+|||++||+||.+|.+++.+|.+
T Consensus 20 ~vA~lYY----~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~ 55 (318)
T PRK15418 20 RIAWFYY----HDGLTQSEIGERLGLTRLKVSRLLEKGRQ 55 (318)
T ss_pred HHHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4567888 79999999999999999999999999976
No 192
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=93.73 E-value=0.079 Score=42.47 Aligned_cols=45 Identities=20% Similarity=0.243 Sum_probs=28.2
Q ss_pred HhcCCHHHHHHHhHH--hcCCCCCCCCHHHHHHHhCCC-HHHHHHHHH
Q 010327 449 LDSLKPKESLVIRQR--FGLDGKGDRTLGEIAGNLNIS-REMVRKHEV 493 (513)
Q Consensus 449 L~~L~~rEr~VL~lR--yGL~~~~~~Tl~EIA~~LgIS-rerVRqi~~ 493 (513)
|..|+++|++||... |-...+.+-|+.|||+.||++ .++|.+.+.
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 457999999998763 212223467999999999997 999987664
No 193
>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=93.64 E-value=0.073 Score=36.85 Aligned_cols=26 Identities=38% Similarity=0.431 Sum_probs=18.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010327 471 DRTLGEIAGNLNISREMVRKHEVKGLMKLK 500 (513)
Q Consensus 471 ~~Tl~EIA~~LgISrerVRqi~~rALkKLR 500 (513)
++|.+|||..+|+|+++|++ ++++|+
T Consensus 2 ~mtr~diA~~lG~t~ETVSR----~l~~l~ 27 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSR----ILKKLE 27 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHH----HHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHHH----HHHHHH
Confidence 47899999999999999985 555555
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=93.38 E-value=1.1 Score=44.51 Aligned_cols=36 Identities=44% Similarity=0.712 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010327 233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC 268 (513)
Q Consensus 233 ~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~ 268 (513)
.+......+...+|++|+.+|+|..+|++.+.+..+
T Consensus 88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~ 123 (238)
T TIGR02393 88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVREI 123 (238)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 344556778889999999999999999998887654
No 195
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=93.37 E-value=0.18 Score=44.83 Aligned_cols=50 Identities=28% Similarity=0.256 Sum_probs=44.2
Q ss_pred HHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 448 VLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 448 aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
.+..|++.+..-|.... ...=+++|+++.||||..|||..+.+.+.+|-.
T Consensus 30 ~~~~L~~E~~~Fi~~Fi----~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 30 WFARLSPEQLEFIKLFI----KNRGNLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred hhhcCCHHHHHHHHHHH----HhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 46789999998887776 445599999999999999999999999999987
No 196
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=93.24 E-value=1 Score=50.08 Aligned_cols=37 Identities=30% Similarity=0.527 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010327 233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL 269 (513)
Q Consensus 233 ~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~ 269 (513)
.+...+.+|...+|++|+.+|+|..+|++.+.+..++
T Consensus 359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~ 395 (509)
T PRK05901 359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQ 395 (509)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 4455677788899999999999999999988776653
No 197
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=93.08 E-value=1.1 Score=46.91 Aligned_cols=36 Identities=33% Similarity=0.593 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010327 233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC 268 (513)
Q Consensus 233 ~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~ 268 (513)
.+......|...+|++|+..|+|..+|++.+.+..+
T Consensus 174 ~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~ 209 (324)
T PRK07921 174 KLARIKRELHQQLGREATDEELAEESGIPEEKIADL 209 (324)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 445566778889999999999999999998777654
No 198
>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=92.69 E-value=0.53 Score=42.50 Aligned_cols=52 Identities=17% Similarity=0.091 Sum_probs=46.1
Q ss_pred HHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 447 DVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 447 ~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
..|.+-.|.+-.+|.++| ..++|...||..+++|...||+.+.+|-.-+...
T Consensus 58 ~~L~~~~~~~~~ll~~~Y----v~g~s~r~IA~~~~~s~~~ir~~l~~ae~~i~g~ 109 (125)
T PF06530_consen 58 ARLKKRDPEEYDLLILYY----VYGWSKRQIARKLKCSEGKIRKRLQRAEGFIDGC 109 (125)
T ss_pred HHHHccCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHhhhhHhhh
Confidence 334557999999999999 6899999999999999999999999998888765
No 199
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=92.33 E-value=0.13 Score=39.43 Aligned_cols=40 Identities=28% Similarity=0.322 Sum_probs=28.9
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
.|+..|+.=|..+| ..+.+..+||..|||+.++|+.|...
T Consensus 6 ~LTl~eK~~iI~~~----e~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 6 SLTLEEKLEIIKRL----EEGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp S--HHHHHHHHHHH----HCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred cCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 47777777666667 56779999999999999999999865
No 200
>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=92.21 E-value=0.36 Score=35.32 Aligned_cols=39 Identities=23% Similarity=0.368 Sum_probs=26.9
Q ss_pred CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 453 KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 453 ~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
++-.+.||..--. ....|+.+||+.+|+|..+|.+...+
T Consensus 2 D~~D~~Il~~Lq~---d~r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 2 DELDRKILRLLQE---DGRRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp -HHHHHHHHHHHH----TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CHHHHHHHHHHHH---cCCccHHHHHHHHCcCHHHHHHHHHH
Confidence 4455666665442 35799999999999999999987654
No 201
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=92.07 E-value=0.25 Score=39.12 Aligned_cols=39 Identities=23% Similarity=0.336 Sum_probs=28.5
Q ss_pred HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 454 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 454 ~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
|.--..+.++... ...+++.+||+.||||..+||....+
T Consensus 7 p~rdkA~e~y~~~--~g~i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 7 PNRDKAFEIYKES--NGKIKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred cCHHHHHHHHHHh--CCCccHHHHHHHHCCCHHHHHHHhhh
Confidence 3333445555422 45899999999999999999988654
No 202
>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=91.83 E-value=0.32 Score=38.15 Aligned_cols=26 Identities=23% Similarity=0.270 Sum_probs=24.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010327 470 GDRTLGEIAGNLNISREMVRKHEVKG 495 (513)
Q Consensus 470 ~~~Tl~EIA~~LgISrerVRqi~~rA 495 (513)
++++..|||+.||+++.+|.....+-
T Consensus 12 ~G~~~~eIA~~Lg~~~~TV~~W~~r~ 37 (58)
T PF06056_consen 12 QGWSIKEIAEELGVPRSTVYSWKDRY 37 (58)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHHhh
Confidence 79999999999999999999988764
No 203
>PF13730 HTH_36: Helix-turn-helix domain
Probab=91.74 E-value=0.51 Score=35.73 Aligned_cols=46 Identities=24% Similarity=0.362 Sum_probs=33.6
Q ss_pred cCCHHHHHHHhHHhcCCCCCC---CCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010327 451 SLKPKESLVIRQRFGLDGKGD---RTLGEIAGNLNISREMVRKHEVKGLMKLK 500 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~---~Tl~EIA~~LgISrerVRqi~~rALkKLR 500 (513)
.|++.++.|+..-.-+.+..+ .|.+.||+.+|+|+.+|+ ++++.|.
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~----~~i~~L~ 50 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQ----RAIKELE 50 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHH----HHHHHHH
Confidence 588999988776544432222 399999999999999998 4555554
No 204
>PF13518 HTH_28: Helix-turn-helix domain
Probab=91.73 E-value=0.26 Score=36.62 Aligned_cols=27 Identities=26% Similarity=0.254 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010327 470 GDRTLGEIAGNLNISREMVRKHEVKGL 496 (513)
Q Consensus 470 ~~~Tl~EIA~~LgISrerVRqi~~rAL 496 (513)
++.|+.+||..+|||+.+|+++..+-.
T Consensus 11 ~g~s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 11 EGESVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred cCCCHHHHHHHHCCCHhHHHHHHHHHH
Confidence 456999999999999999998887653
No 205
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=91.57 E-value=1.4 Score=47.80 Aligned_cols=37 Identities=19% Similarity=0.226 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHH
Q 010327 364 EIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVM 400 (513)
Q Consensus 364 ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l 400 (513)
.+.+....|..++|+.||.+|.|..+|+++.+++..+
T Consensus 112 ~l~~~~~~l~~~~g~~pt~~ewa~~~~~~~~~l~~~l 148 (415)
T PRK07598 112 RLIEVRERLTSELGHRPSLERWAKTADISLADLKPTL 148 (415)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCcHHHHHHhh
Confidence 4566677899999999999999988877766655443
No 206
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=91.52 E-value=0.35 Score=47.35 Aligned_cols=48 Identities=23% Similarity=0.165 Sum_probs=37.0
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 498 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkK 498 (513)
.|+++|.+++.....-....++|.+|||+.||+|..||+.+..++...
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 488999777654331011478999999999999999999999988554
No 207
>smart00351 PAX Paired Box domain.
Probab=91.17 E-value=0.49 Score=42.63 Aligned_cols=42 Identities=19% Similarity=0.059 Sum_probs=34.0
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010327 452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 497 (513)
Q Consensus 452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALk 497 (513)
|+..+|.-|...| .++.|..+||+.||||+.+|.++..+...
T Consensus 18 ~s~~~R~riv~~~----~~G~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 18 LPDEERQRIVELA----QNGVRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred CCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 5555666666666 46889999999999999999999998754
No 208
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=90.72 E-value=0.97 Score=45.44 Aligned_cols=37 Identities=32% Similarity=0.554 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010327 233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL 269 (513)
Q Consensus 233 ~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~ 269 (513)
.+.....+|...+|++|+..|+|..+|++.+.+..+.
T Consensus 114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~ 150 (256)
T PRK07408 114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIK 150 (256)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHH
Confidence 4455677888899999999999999999988776543
No 209
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=90.45 E-value=0.34 Score=50.67 Aligned_cols=35 Identities=29% Similarity=0.203 Sum_probs=31.1
Q ss_pred HHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010327 459 VIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 497 (513)
Q Consensus 459 VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALk 497 (513)
+-.+|| .+++|..|||+.||||+.+|++++.+|.+
T Consensus 18 ~A~lYY----~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~ 52 (321)
T COG2390 18 AAWLYY----VEGLTQSEIAERLGISRATVSRLLAKARE 52 (321)
T ss_pred HHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 445788 79999999999999999999999999865
No 210
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=90.34 E-value=2.7 Score=44.90 Aligned_cols=36 Identities=25% Similarity=0.490 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010327 233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC 268 (513)
Q Consensus 233 ~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~ 268 (513)
.+......|...+|++|+.+|+|..+|++.+.+..+
T Consensus 224 ~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~ 259 (373)
T PRK07406 224 RIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFI 259 (373)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 445566778889999999999999999998777543
No 211
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=90.19 E-value=0.86 Score=36.53 Aligned_cols=43 Identities=21% Similarity=0.195 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCC-HHHHHHHHHh
Q 010327 360 SVRGEIQRAKLELLFELKRVPTDEEIIQGVNIS-PERYREVMKA 402 (513)
Q Consensus 360 ~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis-~e~v~~~l~~ 402 (513)
+.-.++-.+..++..+.|..||..|||+.+|++ ...+...+..
T Consensus 6 ~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~ 49 (65)
T PF01726_consen 6 ERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKA 49 (65)
T ss_dssp HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 344556666777888899999999999999997 8888887765
No 212
>PHA00675 hypothetical protein
Probab=90.09 E-value=0.56 Score=38.82 Aligned_cols=41 Identities=17% Similarity=0.100 Sum_probs=31.4
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
..|++-+-+.|+..+- ..+.|+.+||..||||+++|.+|.+
T Consensus 21 AKLt~~qV~~IR~l~~---r~G~s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 21 AKLTDAEVERIRELHE---VEGMSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred cccCHHHHHHHHHHHH---hcCccHHHHHHHhCCCHHHHHHHHc
Confidence 3566666666655541 2577999999999999999999875
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=90.02 E-value=0.47 Score=35.92 Aligned_cols=39 Identities=21% Similarity=0.332 Sum_probs=27.5
Q ss_pred HHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010327 455 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG 495 (513)
Q Consensus 455 rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA 495 (513)
|+..||.+-+ ....+.|.+|||+.||||+.+|++.+..-
T Consensus 1 R~~~il~~L~--~~~~~it~~eLa~~l~vS~rTi~~~i~~L 39 (55)
T PF08279_consen 1 RQKQILKLLL--ESKEPITAKELAEELGVSRRTIRRDIKEL 39 (55)
T ss_dssp HHHHHHHHHH--HTTTSBEHHHHHHHCTS-HHHHHHHHHHH
T ss_pred CHHHHHHHHH--HcCCCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 4556666643 11345999999999999999999776543
No 214
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=89.85 E-value=3.9 Score=41.13 Aligned_cols=36 Identities=33% Similarity=0.559 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010327 234 FVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL 269 (513)
Q Consensus 234 l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~ 269 (513)
+......+...+|++|+.+|+|..+|++.+.+...+
T Consensus 112 l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~ 147 (257)
T PRK05911 112 LADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWF 147 (257)
T ss_pred HHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHH
Confidence 344555677889999999999999999988775543
No 215
>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=89.73 E-value=0.65 Score=39.31 Aligned_cols=44 Identities=30% Similarity=0.240 Sum_probs=34.1
Q ss_pred HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHh--CCCHHHHHHHHHHH
Q 010327 449 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNL--NISREMVRKHEVKG 495 (513)
Q Consensus 449 L~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~L--gISrerVRqi~~rA 495 (513)
++.||+..+++..+|.- ..+.|+.|+|+.| .||.+.|.-+..+-
T Consensus 35 ~~~l~~~l~~~a~lRl~---~Pd~SL~EL~~~~~~~iSKSgvnhrlrKl 80 (85)
T PF02650_consen 35 LDKLPEKLREFAELRLE---NPDASLKELGELLEPPISKSGVNHRLRKL 80 (85)
T ss_dssp GGGS-HHHHHHHHHHHH----TTS-HHHHHHTT--T--HHHHHHHHHHH
T ss_pred cccCCHHHHHHHHHHHH---CccccHHHHHHHHcCcCcHHHHHHHHHHH
Confidence 57899999999999884 5789999999999 99999998877654
No 216
>PRK05949 RNA polymerase sigma factor; Validated
Probab=89.47 E-value=8.6 Score=40.31 Aligned_cols=37 Identities=24% Similarity=0.486 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010327 233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL 269 (513)
Q Consensus 233 ~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~ 269 (513)
.+......+...+|++|+..|+|..+|++.+.+..++
T Consensus 179 ~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~ 215 (327)
T PRK05949 179 KIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYL 215 (327)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 3445556677889999999999999999987776543
No 217
>PHA02591 hypothetical protein; Provisional
Probab=89.20 E-value=0.62 Score=38.65 Aligned_cols=24 Identities=29% Similarity=0.209 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 470 GDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 470 ~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
.|+|.++||..||+|.++|+++..
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHh
Confidence 589999999999999999999875
No 218
>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=89.12 E-value=0.78 Score=35.25 Aligned_cols=43 Identities=26% Similarity=0.286 Sum_probs=32.3
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
.|++.|..||..-+.-++ .+.|..|||+.+++++.+|.++..+
T Consensus 2 glt~~q~~vL~~l~~~~~-~~~t~~~la~~l~~~~~~vs~~v~~ 44 (62)
T PF12802_consen 2 GLTPSQFRVLMALARHPG-EELTQSELAERLGISKSTVSRIVKR 44 (62)
T ss_dssp TSTHHHHHHHHHHHHSTT-SGEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHHCCC-CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 378888888887664221 2389999999999999999876654
No 219
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=89.09 E-value=0.79 Score=33.92 Aligned_cols=37 Identities=27% Similarity=0.391 Sum_probs=28.1
Q ss_pred HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 454 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 454 ~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
|.-..||.+-. .++++..||++.+|+|+++|++.+..
T Consensus 2 ~~R~~Il~~L~----~~~~~~~el~~~l~~s~~~vs~hL~~ 38 (47)
T PF01022_consen 2 PTRLRILKLLS----EGPLTVSELAEELGLSQSTVSHHLKK 38 (47)
T ss_dssp HHHHHHHHHHT----TSSEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHH----hCCCchhhHHHhccccchHHHHHHHH
Confidence 34455666655 47899999999999999999987654
No 220
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=88.75 E-value=7.8 Score=39.18 Aligned_cols=38 Identities=32% Similarity=0.561 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010327 232 KVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL 269 (513)
Q Consensus 232 ~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~ 269 (513)
..+..+...|+.++||+|++.|+|...|++.+++..++
T Consensus 110 ~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~ 147 (247)
T COG1191 110 RRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEAL 147 (247)
T ss_pred HHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHH
Confidence 34567778899999999999999999999987776544
No 221
>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]
Probab=88.71 E-value=0.55 Score=54.41 Aligned_cols=50 Identities=28% Similarity=0.177 Sum_probs=46.1
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010327 452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 506 (513)
Q Consensus 452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~ 506 (513)
||.||.+|+.+.| .|+|.+|||++|.||-.||+.+.+.--.||.-..+.+
T Consensus 832 Ls~RE~eVL~Lia-----~G~SN~eIa~~L~isl~TVKtH~rniy~KLgV~~Rtq 881 (894)
T COG2909 832 LSQRELEVLGLIA-----QGLSNEEIAQELFISLTTVKTHIRNIYQKLGVANRTQ 881 (894)
T ss_pred ccHHHHHHHHHHH-----ccCCHHHHHHHHHHHHHHHHHHHHHHHHHhCcchHHH
Confidence 8999999999999 7999999999999999999999999999997655544
No 222
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=88.62 E-value=10 Score=38.15 Aligned_cols=37 Identities=27% Similarity=0.418 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010327 233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL 269 (513)
Q Consensus 233 ~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~ 269 (513)
.+......|+..+|++|+..|+|...|++.+.+..+.
T Consensus 119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~ 155 (268)
T PRK06288 119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLL 155 (268)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHH
Confidence 4455666788899999999999999999987765543
No 223
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=88.21 E-value=6.4 Score=39.82 Aligned_cols=36 Identities=33% Similarity=0.478 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010327 234 FVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL 269 (513)
Q Consensus 234 l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~ 269 (513)
+......+...+|++|+..|+|..+|++.+.+..++
T Consensus 129 i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~ 164 (264)
T PRK07122 129 LGRATAELSQRLGRAPTASELAAELGMDREEVVEGL 164 (264)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 344566777889999999999999999988776544
No 224
>cd00131 PAX Paired Box domain
Probab=87.90 E-value=1.2 Score=40.34 Aligned_cols=42 Identities=17% Similarity=0.022 Sum_probs=32.9
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010327 452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 497 (513)
Q Consensus 452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALk 497 (513)
||...|.-|...| .+++|..+||+.||||+.+|..+..+-..
T Consensus 18 lS~d~R~rIv~~~----~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e 59 (128)
T cd00131 18 LPDSIRQRIVELA----QSGIRPCDISRQLRVSHGCVSKILNRYYE 59 (128)
T ss_pred CCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 5555555555556 47899999999999999999999888653
No 225
>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=87.40 E-value=3.9 Score=40.11 Aligned_cols=34 Identities=50% Similarity=0.656 Sum_probs=27.4
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010327 236 QVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL 269 (513)
Q Consensus 236 ~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~ 269 (513)
...+.+...+|+.|+..|+|...|++.+.+...+
T Consensus 101 ~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~ 134 (231)
T TIGR02885 101 YMKEELSKELGREPTINELAEALGVSPEEIVMAL 134 (231)
T ss_pred HHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHH
Confidence 4456677889999999999999999987775543
No 226
>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=86.75 E-value=8.4 Score=38.53 Aligned_cols=36 Identities=28% Similarity=0.447 Sum_probs=29.0
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHH
Q 010327 235 VQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLE 270 (513)
Q Consensus 235 ~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~ 270 (513)
......+..++|++|+.+|+|...|++.+.+..++.
T Consensus 123 ~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~~ 158 (254)
T TIGR02850 123 LQVRDKLISENSKEPTVSEIAKELKVPQEEVVFALD 158 (254)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 344566778899999999999999999888766543
No 227
>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=86.57 E-value=1.5 Score=36.03 Aligned_cols=52 Identities=15% Similarity=0.146 Sum_probs=36.3
Q ss_pred HHHHHHHHhcCCHHHHHHHhHHhc-CCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 442 RLALDDVLDSLKPKESLVIRQRFG-LDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 442 ~~~L~~aL~~L~~rEr~VL~lRyG-L~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
...|....+.|++.|+.|.....- .+....+|..|||+..|||..+|.+...
T Consensus 4 ~~~i~~~~~~ls~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~k 56 (77)
T PF01418_consen 4 LEKIRSQYNSLSPTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCK 56 (77)
T ss_dssp HHHHHHHGGGS-HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHhhCCHHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHH
Confidence 456777788999999999766441 0123479999999999999999987654
No 228
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=86.53 E-value=2.3 Score=33.04 Aligned_cols=37 Identities=30% Similarity=0.376 Sum_probs=28.1
Q ss_pred HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 454 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 454 ~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
|.-..||.+-.+ ..++|..|||+.+|++.++|+..+.
T Consensus 10 p~R~~Il~~L~~---~~~~t~~ela~~l~~~~~t~s~hL~ 46 (61)
T PF12840_consen 10 PTRLRILRLLAS---NGPMTVSELAEELGISQSTVSYHLK 46 (61)
T ss_dssp HHHHHHHHHHHH---CSTBEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHhc---CCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 666666666522 5899999999999999999987654
No 229
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=86.14 E-value=1.7 Score=32.41 Aligned_cols=25 Identities=24% Similarity=0.320 Sum_probs=22.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHH
Q 010327 471 DRTLGEIAGNLNISREMVRKHEVKG 495 (513)
Q Consensus 471 ~~Tl~EIA~~LgISrerVRqi~~rA 495 (513)
..|+++||+.+|||..+|+.+..+.
T Consensus 27 ~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 27 SRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 3699999999999999999998764
No 230
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=85.96 E-value=2.7 Score=38.24 Aligned_cols=51 Identities=25% Similarity=0.247 Sum_probs=39.6
Q ss_pred HHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010327 444 ALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 500 (513)
Q Consensus 444 ~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR 500 (513)
.+-.+.-.|++.+-+|+..-.- ...+.|..|||+.||.|+++|. ||+++|=
T Consensus 17 dvl~c~~GLs~~Dv~v~~~LL~--~~~~~tvdelae~lnr~rStv~----rsl~~L~ 67 (126)
T COG3355 17 DVLKCVYGLSELDVEVYKALLE--ENGPLTVDELAEILNRSRSTVY----RSLQNLL 67 (126)
T ss_pred HHHHHHhCCcHHHHHHHHHHHh--hcCCcCHHHHHHHHCccHHHHH----HHHHHHH
Confidence 3556666799999998766541 2468999999999999999987 6666664
No 231
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=85.96 E-value=0.77 Score=44.59 Aligned_cols=39 Identities=23% Similarity=0.135 Sum_probs=29.4
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
.|+++ +|+.+.- .|..++|.+|||+.||||+.||+.+..
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 45665 5665543 223479999999999999999999875
No 232
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=85.88 E-value=1.5 Score=34.30 Aligned_cols=42 Identities=26% Similarity=0.246 Sum_probs=27.6
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010327 452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG 495 (513)
Q Consensus 452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA 495 (513)
|++.|..||..-. ....++|..+||+.++++..+|++.+.+-
T Consensus 1 lt~~q~~vL~~l~--~~~~~~t~~~l~~~~~~~~~~vs~~i~~L 42 (68)
T PF13463_consen 1 LTRPQWQVLRALA--HSDGPMTQSDLAERLGISKSTVSRIIKKL 42 (68)
T ss_dssp --HHHHHHHHHHT----TS-BEHHHHHHHTT--HHHHHHHHHHH
T ss_pred CCHHHHHHHHHHH--ccCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 5677777776655 23578999999999999999998555443
No 233
>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=85.84 E-value=0.78 Score=34.30 Aligned_cols=22 Identities=23% Similarity=0.271 Sum_probs=19.7
Q ss_pred CHHHHHHHhCCCHHHHHHHHHH
Q 010327 473 TLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 473 Tl~EIA~~LgISrerVRqi~~r 494 (513)
|++|||+..|||..+|+..++.
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 7899999999999999987754
No 234
>PHA02547 55 RNA polymerase sigma factor; Provisional
Probab=85.79 E-value=2.6 Score=40.06 Aligned_cols=62 Identities=11% Similarity=0.160 Sum_probs=45.3
Q ss_pred HHHHHHHHHHHchhccCCCCc---HHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH
Q 010327 283 NLRLVLFVIKKYFQDFANGPR---FQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT 347 (513)
Q Consensus 283 nlrLV~sIAkky~~~~~~g~~---~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~ 347 (513)
.+..+..++++|. -.+.. -+|+|.+|.-..++.++.|||++...+-.|.+..+-++..+-|.
T Consensus 46 imkIa~glS~r~n---F~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~ 110 (179)
T PHA02547 46 IMKIAEGLSRRPN---FSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIK 110 (179)
T ss_pred HHHHHhccccCCc---cccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHH
Confidence 3444444555543 23433 68999999999999999999999877877777777777666555
No 235
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=85.69 E-value=1.7 Score=37.38 Aligned_cols=41 Identities=15% Similarity=0.191 Sum_probs=31.7
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010327 452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG 495 (513)
Q Consensus 452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA 495 (513)
|++.++.||....- ....|+.+||+.+|+|+.+|++...+-
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 46677888866542 246899999999999999999766543
No 236
>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=85.59 E-value=1.3 Score=33.82 Aligned_cols=41 Identities=29% Similarity=0.383 Sum_probs=31.3
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010327 452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG 495 (513)
Q Consensus 452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA 495 (513)
|++.|-.||..-+- ..+.|..+||+.+++++.+|.++..+-
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 56677777777653 457999999999999999998776554
No 237
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=85.28 E-value=9.2 Score=33.98 Aligned_cols=28 Identities=32% Similarity=0.458 Sum_probs=22.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 500 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR 500 (513)
..+.|+.|||+.||||.++|. ++|++|.
T Consensus 69 ~pd~tl~Ela~~l~Vs~~ti~----~~Lkrlg 96 (119)
T PF01710_consen 69 NPDATLRELAERLGVSPSTIW----RALKRLG 96 (119)
T ss_pred CCCcCHHHHHHHcCCCHHHHH----HHHHHcC
Confidence 368999999999999988887 5555554
No 238
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=85.16 E-value=2 Score=34.49 Aligned_cols=23 Identities=22% Similarity=0.238 Sum_probs=20.2
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Q 010327 471 DRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 471 ~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
+.|..|||+.+||+..+|++++.
T Consensus 22 ~~ta~eLa~~lgl~~~~v~r~L~ 44 (68)
T smart00550 22 TSTALQLAKNLGLPKKEVNRVLY 44 (68)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHH
Confidence 59999999999999999886554
No 239
>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=84.88 E-value=1.2 Score=35.11 Aligned_cols=45 Identities=24% Similarity=0.295 Sum_probs=31.0
Q ss_pred CCHHHHHHHhHHhcCC-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010327 452 LKPKESLVIRQRFGLD-GKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 500 (513)
Q Consensus 452 L~~rEr~VL~lRyGL~-~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR 500 (513)
|++....-|...|-|. +....+..+||+.||+|+.+|.. ++++|.
T Consensus 2 Lt~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~----ml~~L~ 47 (60)
T PF01325_consen 2 LTESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTE----MLKRLA 47 (60)
T ss_dssp CSCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHH----HHHHHH
T ss_pred CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHH----HHHHHH
Confidence 4555555555555553 45678999999999999999985 455554
No 240
>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=84.83 E-value=0.61 Score=37.01 Aligned_cols=40 Identities=33% Similarity=0.310 Sum_probs=30.7
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
.|++.|..|+..-.- ..+.|..|||+.+|+|+.+|+..+.
T Consensus 5 gLs~~E~~vy~~Ll~---~~~~t~~eIa~~l~i~~~~v~~~L~ 44 (68)
T PF01978_consen 5 GLSENEAKVYLALLK---NGPATAEEIAEELGISRSTVYRALK 44 (68)
T ss_dssp CHHHHHHHHHHHHHH---HCHEEHHHHHHHHTSSHHHHHHHHH
T ss_pred CcCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 367788888755431 3689999999999999999985543
No 241
>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=84.37 E-value=1.2 Score=37.99 Aligned_cols=46 Identities=20% Similarity=0.265 Sum_probs=32.4
Q ss_pred CCHHHHHHHhHHhcCCC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010327 452 LKPKESLVIRQRFGLDG---KGDRTLGEIAGNLNISREMVRKHEVKGLMK 498 (513)
Q Consensus 452 L~~rEr~VL~lRyGL~~---~~~~Tl~EIA~~LgISrerVRqi~~rALkK 498 (513)
|+|.|..-|..|+-+-. .+++|+.||++.+|+|..+|.+. +++|+.
T Consensus 27 ~T~~E~~~l~~R~~va~~lL~~g~syreIa~~tgvS~aTItRv-sr~Lk~ 75 (87)
T PF01371_consen 27 CTPDELEALAQRWQVAKELLDEGKSYREIAEETGVSIATITRV-SRCLKY 75 (87)
T ss_dssp SSHHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHH-HHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHH-HHHHHc
Confidence 67777766665553321 26899999999999999999753 445443
No 242
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=84.20 E-value=2 Score=32.86 Aligned_cols=39 Identities=23% Similarity=0.211 Sum_probs=26.3
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
.|++-|+.-|-... ..++|+.|||..+|-|+..|+..+.
T Consensus 4 ~Lt~~Eqaqid~m~----qlG~s~~~isr~i~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 4 TLTDAEQAQIDVMH----QLGMSLREISRRIGRSRTCIRRYLK 42 (50)
T ss_dssp ---HHHHHHHHHHH----HTT--HHHHHHHHT--HHHHHHHHH
T ss_pred cCCHHHHHHHHHHH----HhchhHHHHHHHhCccHHHHHHHhc
Confidence 47777777777766 4689999999999999999998743
No 243
>PF12728 HTH_17: Helix-turn-helix domain
Probab=84.12 E-value=1.1 Score=33.36 Aligned_cols=24 Identities=38% Similarity=0.338 Sum_probs=21.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKG 495 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rA 495 (513)
+|.+|+|+.||||+.+|+++..+.
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcC
Confidence 589999999999999999998654
No 244
>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=84.03 E-value=1.9 Score=36.00 Aligned_cols=43 Identities=16% Similarity=0.173 Sum_probs=34.4
Q ss_pred cCCHHHHHHHhHHhcC--CCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 451 SLKPKESLVIRQRFGL--DGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL--~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
.|+++|+.||...--+ ..+++-.-++||+.+++|..+||+...
T Consensus 1 ~Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~ 45 (78)
T PF03444_consen 1 MLTERQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMA 45 (78)
T ss_pred CCCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHH
Confidence 3899999998764322 345788999999999999999998764
No 245
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=84.00 E-value=10 Score=39.55 Aligned_cols=36 Identities=33% Similarity=0.448 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010327 233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC 268 (513)
Q Consensus 233 ~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~ 268 (513)
.+......+...+|+.|+..|+|..+|++.+.+...
T Consensus 169 ~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~ 204 (317)
T PRK07405 169 KIKKAQRQLSQQLGRAATIGELAEELELTPKQVREY 204 (317)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 445566677788999999999999999987766544
No 246
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=83.94 E-value=14 Score=36.73 Aligned_cols=37 Identities=22% Similarity=0.274 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHH
Q 010327 234 FVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLE 270 (513)
Q Consensus 234 l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~ 270 (513)
+.+....+...+|++|+..++|...|++.+.+..++.
T Consensus 111 ~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~ 147 (251)
T PRK07670 111 VEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMN 147 (251)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 3445566777899999999999999999888776543
No 247
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=83.85 E-value=15 Score=37.64 Aligned_cols=35 Identities=34% Similarity=0.641 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010327 234 FVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC 268 (513)
Q Consensus 234 l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~ 268 (513)
+......+...+|+.|+..|+|..+|++.+.+..+
T Consensus 163 ~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~ 197 (298)
T TIGR02997 163 IKKVQRELSQKLGRTPSEAEIAEALELEPEQVREL 197 (298)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 34445667778999999999999999998887654
No 248
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=83.74 E-value=12 Score=29.45 Aligned_cols=73 Identities=18% Similarity=0.179 Sum_probs=45.3
Q ss_pred CCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHH
Q 010327 379 VPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESL 458 (513)
Q Consensus 379 ~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~ 458 (513)
++|.++||+.+|++...+..++..... .++.+... ...+. .
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~~------------------------~s~~~~~~----~~r~~-----------~ 41 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKETG------------------------TTPKQYLR----DRRLE-----------R 41 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHhC------------------------cCHHHHHH----HHHHH-----------H
Confidence 378899999999999988887654210 11111110 11121 1
Q ss_pred HHhHHhcCCCCCCCCHHHHHHHhCC-CHHHHHHHHHH
Q 010327 459 VIRQRFGLDGKGDRTLGEIAGNLNI-SREMVRKHEVK 494 (513)
Q Consensus 459 VL~lRyGL~~~~~~Tl~EIA~~LgI-SrerVRqi~~r 494 (513)
++.+.. ..+.|+.+||..+|+ |.....+...+
T Consensus 42 a~~~l~----~~~~~~~~ia~~~g~~s~~~f~r~Fk~ 74 (84)
T smart00342 42 ARRLLR----DTDLSVTEIALRVGFSSQSYFSRAFKK 74 (84)
T ss_pred HHHHHH----cCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 222222 237899999999999 98877766544
No 249
>PRK12423 LexA repressor; Provisional
Probab=83.58 E-value=1.6 Score=42.44 Aligned_cols=48 Identities=27% Similarity=0.343 Sum_probs=33.8
Q ss_pred hcCCHHHHHHHhHHhcC--CCCCCCCHHHHHHHhC-CCHHHHHHHHHHHHHHHhC
Q 010327 450 DSLKPKESLVIRQRFGL--DGKGDRTLGEIAGNLN-ISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 450 ~~L~~rEr~VL~lRyGL--~~~~~~Tl~EIA~~Lg-ISrerVRqi~~rALkKLR~ 501 (513)
..|++++++|+..---. .++-.-|..|||+.|| +|+.+|+. +|+.|.+
T Consensus 2 ~~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~----~l~~L~~ 52 (202)
T PRK12423 2 DTLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARK----HVQALAE 52 (202)
T ss_pred CcCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHH----HHHHHHH
Confidence 35899999998763311 1223469999999999 59999995 4555544
No 250
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=83.44 E-value=9.7 Score=39.10 Aligned_cols=26 Identities=27% Similarity=0.266 Sum_probs=22.3
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHHhc
Q 010327 378 RVPTDEEIIQGVNISPERYREVMKAS 403 (513)
Q Consensus 378 R~PT~eELA~~lgis~e~v~~~l~~~ 403 (513)
..-|..|||+.||+|.++|+.++..+
T Consensus 244 ~~~t~~EIa~~lgvs~~~V~q~~~~A 269 (289)
T PRK07500 244 DGATLEALGEELGISKERVRQIEARA 269 (289)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56799999999999999999887543
No 251
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=83.41 E-value=2.5 Score=35.83 Aligned_cols=43 Identities=19% Similarity=0.236 Sum_probs=37.0
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL 496 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rAL 496 (513)
.|+|.-+..|..+.- .++++..++|+.||||+.+++++..|=.
T Consensus 8 ~Lt~~gR~~lv~~vv---~~g~~~a~aA~~~gVS~~Ta~kW~~Ryr 50 (85)
T PF13011_consen 8 RLTPRGRLRLVRRVV---EQGWPVAHAAAEFGVSRRTAYKWLARYR 50 (85)
T ss_pred CCCHHHHHHHHHHHH---HcCCcHHHHHHHhCCCHHHHHHHHHHHH
Confidence 589999999888762 3589999999999999999999988754
No 252
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=83.10 E-value=42 Score=34.87 Aligned_cols=177 Identities=14% Similarity=0.013 Sum_probs=88.9
Q ss_pred HHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhccccccccchh
Q 010327 280 IKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLE 359 (513)
Q Consensus 280 I~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~iRlP~~~~ 359 (513)
+...+..+..++.... +.+-+.|...-+++-+.....-+|.....++.-.|.-+ .+
T Consensus 122 l~~a~~~I~~~~~~L~--------Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiA----CR------------ 177 (310)
T PRK00423 122 LAFALSELDRIASQLG--------LPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAA----CR------------ 177 (310)
T ss_pred HHHHHHHHHHHHHHcC--------CCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHH----HH------------
Confidence 3444455556655553 33667777777877776666667766544443333222 22
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchhhhHHH
Q 010327 360 SVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPA 439 (513)
Q Consensus 360 ~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee~~~~~ 439 (513)
..|-+-|..||+..++++..++....+.....+.++.+.. +..+++..+.+.-..+ .+.. .
T Consensus 178 ---------------~~~~prtl~eI~~~~~v~~k~i~~~~~~l~k~L~~~~~~~-~p~~~i~r~~~~L~L~-~~v~--~ 238 (310)
T PRK00423 178 ---------------RCKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPT-DPIDYVPRFASELGLS-GEVQ--K 238 (310)
T ss_pred ---------------HcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCC-CHHHHHHHHHHHcCCC-HHHH--H
Confidence 1233456778888888888777655443322222222221 1122222221111111 1111 1
Q ss_pred HHHHHHHHHHhc-C----CHHH--HHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010327 440 LLRLALDDVLDS-L----KPKE--SLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 500 (513)
Q Consensus 440 ~l~~~L~~aL~~-L----~~rE--r~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR 500 (513)
.....+..+.+. | +|.- ..+|.+-.-+. +.+.|++|||...|||..+|++....-.+.|-
T Consensus 239 ~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~-g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l~ 305 (310)
T PRK00423 239 KAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLL-GERRTQREVAEVAGVTEVTVRNRYKELAEKLD 305 (310)
T ss_pred HHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHh-CCCCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 111222222211 1 2221 11222211112 35799999999999999999988777666554
No 253
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=82.55 E-value=1.8 Score=41.52 Aligned_cols=44 Identities=14% Similarity=0.114 Sum_probs=33.6
Q ss_pred hcCCHHHHHHHhHHhc--CCCCCCCCHHHHHHHhCCC-HHHHHHHHH
Q 010327 450 DSLKPKESLVIRQRFG--LDGKGDRTLGEIAGNLNIS-REMVRKHEV 493 (513)
Q Consensus 450 ~~L~~rEr~VL~lRyG--L~~~~~~Tl~EIA~~LgIS-rerVRqi~~ 493 (513)
..|+++|+.||..-.- ..++.+.|..|||+.||++ +.+|+.++.
T Consensus 2 ~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~ 48 (199)
T TIGR00498 2 KPLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLK 48 (199)
T ss_pred CccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHH
Confidence 3589999999887541 2234568999999999998 999985543
No 254
>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=82.45 E-value=1.3 Score=31.70 Aligned_cols=25 Identities=28% Similarity=0.244 Sum_probs=22.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGL 496 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rAL 496 (513)
+|..|+|+.||||+.+|+++...+.
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 5889999999999999999988764
No 255
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=82.35 E-value=1.9 Score=40.47 Aligned_cols=50 Identities=14% Similarity=0.018 Sum_probs=42.7
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCC-----HHHHHHHHHHHHHHHhC
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNIS-----REMVRKHEVKGLMKLKH 501 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgIS-----rerVRqi~~rALkKLR~ 501 (513)
.|+++|.+||.+..- +.+..+|.++|++.++.+ ..+|+.+..+.++||..
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 599999999988762 223469999999999986 78999999999999974
No 256
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=82.33 E-value=2.2 Score=41.15 Aligned_cols=35 Identities=23% Similarity=0.209 Sum_probs=28.0
Q ss_pred HHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 455 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 455 rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
.++.|..++. .++|+.+||+.||||+++|.++...
T Consensus 161 ~~~~i~~~~~-----~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 161 KEEKIKKLLD-----KGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred hHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 3455666644 5799999999999999999998863
No 257
>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=82.18 E-value=4.8 Score=34.37 Aligned_cols=49 Identities=22% Similarity=0.210 Sum_probs=36.0
Q ss_pred HhcCCHHHHHHHhHH----hcCC-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 449 LDSLKPKESLVIRQR----FGLD-GKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 449 L~~L~~rEr~VL~lR----yGL~-~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
...|++++..+|... ||.. .....|..|||+.+|+|+++|+ ++|++|.+
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 356899999987642 4422 2457999999999999999988 55555543
No 258
>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=82.13 E-value=21 Score=34.84 Aligned_cols=37 Identities=32% Similarity=0.530 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010327 233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL 269 (513)
Q Consensus 233 ~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~ 269 (513)
.+......+...+|++|+.+|+|..+|++.+.+..+.
T Consensus 84 ~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~ 120 (224)
T TIGR02479 84 KLERAIRELEARLGREPTEEEIAEELGMDLKEYRQAL 120 (224)
T ss_pred HHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHH
Confidence 4455667788889999999999999999987776644
No 259
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=81.94 E-value=1.6 Score=31.39 Aligned_cols=24 Identities=29% Similarity=0.339 Sum_probs=21.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKG 495 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rA 495 (513)
+|.+|+|+.||||+.+|+++....
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcC
Confidence 589999999999999999998665
No 260
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=81.93 E-value=2.8 Score=38.77 Aligned_cols=41 Identities=10% Similarity=0.169 Sum_probs=32.5
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
.|++.++.||..--- ....|+.+||+.+|+|+.+|+....+
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 377788888776541 35789999999999999999977654
No 261
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional
Probab=81.83 E-value=2 Score=40.86 Aligned_cols=50 Identities=14% Similarity=0.131 Sum_probs=43.8
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHhC
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN-----ISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~Lg-----ISrerVRqi~~rALkKLR~ 501 (513)
.|+++|.+|+.+... +.+...|.++|++.+. +|..+|+.+..+.++||..
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 599999999998773 3345799999999998 9999999999999999974
No 262
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=81.70 E-value=2.5 Score=39.04 Aligned_cols=28 Identities=14% Similarity=0.007 Sum_probs=25.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVKGL 496 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~rAL 496 (513)
.+++|..|||++||||.++|.....+--
T Consensus 19 ~~G~S~re~Ak~~gvs~sTvy~wv~r~~ 46 (138)
T COG3415 19 GEGLSCREAAKRFGVSISTVYRWVRRYR 46 (138)
T ss_pred HcCccHHHHHHHhCccHHHHHHHHHHhc
Confidence 3799999999999999999999888754
No 263
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=81.42 E-value=1.9 Score=40.27 Aligned_cols=50 Identities=22% Similarity=0.154 Sum_probs=41.9
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHhC
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN-----ISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~Lg-----ISrerVRqi~~rALkKLR~ 501 (513)
.|+++|.+||.+.. -+.+..+|.++|+..+. ++..+|+.+..+..+||..
T Consensus 149 ~Lt~~E~~il~~l~-~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl~~ 203 (219)
T PRK10336 149 TLKPKEFALLELLM-RNAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLGS 203 (219)
T ss_pred ecCHHHHHHHHHHH-hCCCccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhcCC
Confidence 49999999998765 12234589999999996 9999999999999999963
No 264
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=81.30 E-value=2.7 Score=31.51 Aligned_cols=28 Identities=32% Similarity=0.469 Sum_probs=22.4
Q ss_pred CCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 470 GDR-TLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 470 ~~~-Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
... |..|||+.||+|+.+|+ +++++|.+
T Consensus 18 ~~l~s~~~la~~~~vs~~tv~----~~l~~L~~ 46 (60)
T smart00345 18 DKLPSERELAAQLGVSRTTVR----EALSRLEA 46 (60)
T ss_pred CcCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 445 99999999999999998 55555654
No 265
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=81.10 E-value=2.1 Score=31.00 Aligned_cols=38 Identities=26% Similarity=0.269 Sum_probs=25.9
Q ss_pred HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 454 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 454 ~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
+-|+.+|...+- ..+.+..+.|+.||||+.+++..+.+
T Consensus 4 ~~E~~~i~~aL~---~~~gn~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 4 EFEKQLIRQALE---RCGGNVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp HHHHHHHHHHHH---HTTT-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHH---HhCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 446666665442 24568999999999999999876643
No 266
>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=80.94 E-value=2.4 Score=32.76 Aligned_cols=35 Identities=17% Similarity=0.283 Sum_probs=25.7
Q ss_pred HHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 456 ESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 456 Er~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
+..|+.+-. .....|.+|+|+.||||..|||+-+.
T Consensus 2 ~~~Il~~l~---~~~~~s~~ela~~~~VS~~TiRRDl~ 36 (57)
T PF08220_consen 2 QQQILELLK---EKGKVSVKELAEEFGVSEMTIRRDLN 36 (57)
T ss_pred HHHHHHHHH---HcCCEEHHHHHHHHCcCHHHHHHHHH
Confidence 344554432 24578999999999999999996554
No 267
>PRK15479 transcriptional regulatory protein TctD; Provisional
Probab=80.64 E-value=2.7 Score=39.30 Aligned_cols=50 Identities=14% Similarity=0.094 Sum_probs=41.8
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHhC
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN-----ISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~Lg-----ISrerVRqi~~rALkKLR~ 501 (513)
.|+++|.+|+.+..- +-+...|.++|++.+. +|..+|..+..+.++||..
T Consensus 148 ~Lt~~E~~il~~l~~-~~~~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl~~ 202 (221)
T PRK15479 148 ALTPREQALLTVLMY-RRTRPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKLQG 202 (221)
T ss_pred ecCHHHHHHHHHHHh-CCCCcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhcCC
Confidence 599999999987651 1124579999999986 9999999999999999964
No 268
>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=80.16 E-value=6.9 Score=34.24 Aligned_cols=48 Identities=15% Similarity=0.151 Sum_probs=35.9
Q ss_pred HHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 443 LALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 443 ~~L~~aL~--~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
..+...+. .|++.|..||...+. ..+.|..|||+.+|+++.+|.++..
T Consensus 15 ~~~~~~l~~~~lt~~q~~iL~~l~~---~~~~t~~ela~~~~~~~~tvs~~l~ 64 (118)
T TIGR02337 15 SFFRPILAQHGLTEQQWRILRILAE---QGSMEFTQLANQACILRPSLTGILA 64 (118)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHH---cCCcCHHHHHHHhCCCchhHHHHHH
Confidence 34444443 589999988876652 4679999999999999999875443
No 269
>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=79.97 E-value=1.4 Score=32.17 Aligned_cols=25 Identities=36% Similarity=0.404 Sum_probs=22.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGL 496 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rAL 496 (513)
+|..|+|+.+|||..+|+.++.+.+
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999988775
No 270
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=79.70 E-value=2.9 Score=39.18 Aligned_cols=40 Identities=10% Similarity=0.098 Sum_probs=31.3
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
|++.++.||..-- .....|+.|||+.+|+|+.+|+++..+
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 5667777876543 135789999999999999999977654
No 271
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=79.55 E-value=2.7 Score=34.68 Aligned_cols=31 Identities=29% Similarity=0.253 Sum_probs=23.2
Q ss_pred HHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 459 VIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 459 VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
|...+- ..++|..|+|+.||+|+++|+++++
T Consensus 23 i~~~~~----~~~ltQ~e~A~~lgisq~~vS~l~~ 53 (80)
T PF13744_consen 23 IRELRE----ERGLTQAELAERLGISQPRVSRLEN 53 (80)
T ss_dssp HHHHHH----CCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHHH----HcCCCHHHHHHHHCCChhHHHHHHc
Confidence 444555 5789999999999999999999885
No 272
>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=79.53 E-value=2.5 Score=31.84 Aligned_cols=25 Identities=32% Similarity=0.383 Sum_probs=20.9
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
..++|+.|||+.+|+++++|..++.
T Consensus 16 ~~~~t~~eia~~~gl~~stv~r~L~ 40 (52)
T PF09339_consen 16 GGPLTLSEIARALGLPKSTVHRLLQ 40 (52)
T ss_dssp BSCEEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 4568999999999999999997764
No 273
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=79.32 E-value=4 Score=29.65 Aligned_cols=25 Identities=28% Similarity=0.391 Sum_probs=21.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 470 GDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 470 ~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
.+.|..+|++.||+|+.+|++.+..
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~ 37 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNK 37 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4689999999999999999876644
No 274
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=78.88 E-value=2.6 Score=40.45 Aligned_cols=41 Identities=29% Similarity=0.269 Sum_probs=34.5
Q ss_pred HHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 458 LVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 458 ~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
..+.|.- .++|..|||+.||+|++|++-+..|+..+...+.
T Consensus 10 kA~eLk~-----~Glt~gEIAdELNvSreTa~WL~~r~~~~~~~~~ 50 (203)
T COG0856 10 KARELKS-----KGLTTGEIADELNVSRETATWLLTRAFKKESVPA 50 (203)
T ss_pred HHHHHHH-----CCCcHHHhhhhhhhhHHHHHHHHhhhhhccCCCC
Confidence 3445554 6899999999999999999999999988876655
No 275
>PF13551 HTH_29: Winged helix-turn helix
Probab=78.32 E-value=3.8 Score=34.86 Aligned_cols=25 Identities=36% Similarity=0.391 Sum_probs=22.7
Q ss_pred CCC-CHHHHHHHhCCCHHHHHHHHHH
Q 010327 470 GDR-TLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 470 ~~~-Tl~EIA~~LgISrerVRqi~~r 494 (513)
++. |..+||+.+|||+.+|.++..+
T Consensus 10 ~g~~~~~~ia~~lg~s~~Tv~r~~~~ 35 (112)
T PF13551_consen 10 EGVSTIAEIARRLGISRRTVYRWLKR 35 (112)
T ss_pred cCCCcHHHHHHHHCcCHHHHHHHHHH
Confidence 567 6999999999999999999887
No 276
>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=78.27 E-value=2.2 Score=31.92 Aligned_cols=25 Identities=28% Similarity=0.308 Sum_probs=21.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 470 GDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 470 ~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
.++|..|+|+.+|+|+.+|+++++.
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 5789999999999999999999875
No 277
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=78.19 E-value=4 Score=37.14 Aligned_cols=42 Identities=14% Similarity=0.135 Sum_probs=33.7
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
..|++.++.||...-. ....|+.|||+.+|+|..+|+.+..+
T Consensus 4 ~~lD~~D~~IL~~L~~---d~r~~~~eia~~lglS~~~v~~Ri~~ 45 (154)
T COG1522 4 MKLDDIDRRILRLLQE---DARISNAELAERVGLSPSTVLRRIKR 45 (154)
T ss_pred ccccHHHHHHHHHHHH---hCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4578888888877441 34599999999999999999987665
No 278
>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=77.96 E-value=41 Score=34.46 Aligned_cols=97 Identities=19% Similarity=0.250 Sum_probs=56.1
Q ss_pred CCCCHHHHHHhcC--CCHHHHHHHHHhccC--cccccCCCCCchhhhh---ccccCCCCCCchh-hhHHHHHHHHHHHHH
Q 010327 378 RVPTDEEIIQGVN--ISPERYREVMKASKP--ILSLHSRHGVTQEEFI---NGITDVDGVENEN-QRQPALLRLALDDVL 449 (513)
Q Consensus 378 R~PT~eELA~~lg--is~e~v~~~l~~~~~--~~SLd~~~~~~~~e~~---d~l~d~~~~~~ee-~~~~~~l~~~L~~aL 449 (513)
-.+++++||+.++ ||.+++++.+..... .+--+. ++.+. ..+.......+.- ...+.++-+.-.++|
T Consensus 136 ~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~-----~g~y~~t~~~l~~~~~~~~~avr~~h~q~l~lA~~al 210 (271)
T TIGR02147 136 FADDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNE-----DGFYKQTDKAVSTGDEVIPLAVRQYQKQMIDLAKEAL 210 (271)
T ss_pred CCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECC-----CCcEEeecceeecCCccchHHHHHHHHHHHHHHHHHH
Confidence 4567889999999 999999998875321 111111 11111 1111111111211 112333334446778
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhC
Q 010327 450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN 482 (513)
Q Consensus 450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~Lg 482 (513)
+..|+.+|.+=.+-+|+ ...++++|.+.+.
T Consensus 211 ~~~p~~eR~~S~lT~~i---~~~~~~~i~~~i~ 240 (271)
T TIGR02147 211 DALPPSERDVSTVTFGI---SEEAYKEIVKKIQ 240 (271)
T ss_pred HhCCccccccceeeEec---CHHHHHHHHHHHH
Confidence 89999999988888875 4557777777663
No 279
>PRK05572 sporulation sigma factor SigF; Validated
Probab=77.94 E-value=29 Score=34.56 Aligned_cols=32 Identities=44% Similarity=0.573 Sum_probs=25.2
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHccCCHHHHH
Q 010327 235 VQVKEQLQKDLGREPTDVELAEATNMSAAQVK 266 (513)
Q Consensus 235 ~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~ 266 (513)
......+..++|+.|+..|+|...|++.+.+.
T Consensus 121 ~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~ 152 (252)
T PRK05572 121 RKDKDELSKELGREPTIEELAEYLGVTPEEVV 152 (252)
T ss_pred HHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHH
Confidence 34455677778999999999999999877663
No 280
>PHA01976 helix-turn-helix protein
Probab=77.86 E-value=3.5 Score=32.22 Aligned_cols=26 Identities=8% Similarity=0.179 Sum_probs=23.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
..++|..++|+.+|||+.+|+++++.
T Consensus 13 ~~glt~~~lA~~~gvs~~~v~~~e~g 38 (67)
T PHA01976 13 ARAWSAPELSRRAGVRHSLIYDFEAD 38 (67)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 46899999999999999999999864
No 281
>PHA00542 putative Cro-like protein
Probab=77.69 E-value=3.1 Score=34.68 Aligned_cols=26 Identities=12% Similarity=0.107 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010327 470 GDRTLGEIAGNLNISREMVRKHEVKG 495 (513)
Q Consensus 470 ~~~Tl~EIA~~LgISrerVRqi~~rA 495 (513)
.++|..++|+.+|||+.+|.+++...
T Consensus 30 ~glTq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 30 AGWSQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHcCC
Confidence 57899999999999999999998654
No 282
>PRK00215 LexA repressor; Validated
Probab=77.07 E-value=3.9 Score=39.43 Aligned_cols=44 Identities=18% Similarity=0.065 Sum_probs=33.5
Q ss_pred CCHHHHHHHhHHh--cCCCCCCCCHHHHHHHhCC-CHHHHHHHHHHH
Q 010327 452 LKPKESLVIRQRF--GLDGKGDRTLGEIAGNLNI-SREMVRKHEVKG 495 (513)
Q Consensus 452 L~~rEr~VL~lRy--GL~~~~~~Tl~EIA~~LgI-SrerVRqi~~rA 495 (513)
|+++|.+||.+-. -.....+.|+.|||+.+|+ |+++|..++.+=
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L 48 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKAL 48 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 7889999986543 1122457899999999999 999999776543
No 283
>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=76.91 E-value=3.7 Score=38.84 Aligned_cols=50 Identities=10% Similarity=0.094 Sum_probs=41.7
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHH--HHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEI--AGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EI--A~~LgISrerVRqi~~rALkKLR~ 501 (513)
.|+++|.+||.+..- +.+.-.|.++| |..++++..+|+.+..+.++||..
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 499999999988761 11223599999 888999999999999999999974
No 284
>PF13551 HTH_29: Winged helix-turn helix
Probab=76.58 E-value=6.7 Score=33.32 Aligned_cols=24 Identities=25% Similarity=0.207 Sum_probs=21.5
Q ss_pred CHHHHHHhcCCCHHHHHHHHHhcc
Q 010327 381 TDEEIIQGVNISPERYREVMKASK 404 (513)
Q Consensus 381 T~eELA~~lgis~e~v~~~l~~~~ 404 (513)
|..++|..+|++...|..+++...
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~ 37 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYR 37 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHH
Confidence 799999999999999999987643
No 285
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=76.56 E-value=1.3 Score=34.86 Aligned_cols=25 Identities=36% Similarity=0.420 Sum_probs=23.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGL 496 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rAL 496 (513)
||..|+|+.+|||.++||.++.+.+
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 5789999999999999999999877
No 286
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=76.54 E-value=35 Score=34.12 Aligned_cols=33 Identities=30% Similarity=0.406 Sum_probs=27.1
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010327 236 QVKEQLQKDLGREPTDVELAEATNMSAAQVKKC 268 (513)
Q Consensus 236 ~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~ 268 (513)
.....+...+|++|+..|+|...|++.+.+...
T Consensus 127 ~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~ 159 (258)
T PRK08215 127 QVREKLINENSKEPTVEEIAKELEVPREEVVFA 159 (258)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHH
Confidence 445567778999999999999999998887554
No 287
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=76.41 E-value=3.2 Score=32.44 Aligned_cols=26 Identities=19% Similarity=0.307 Sum_probs=21.3
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
..++|..++|+.+|+|.++|+++++-
T Consensus 12 ~~gls~~~lA~~~g~s~s~v~~iE~G 37 (64)
T PF13560_consen 12 RAGLSQAQLADRLGVSQSTVSRIERG 37 (64)
T ss_dssp CHTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 45789999999999999999999863
No 288
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=75.92 E-value=3.8 Score=29.42 Aligned_cols=27 Identities=37% Similarity=0.432 Sum_probs=22.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 471 DRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 471 ~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
+.|..+||+.+|+|+++|+ +++++|..
T Consensus 8 ~~s~~~la~~l~~s~~tv~----~~l~~L~~ 34 (48)
T smart00419 8 PLTRQEIAELLGLTRETVS----RTLKRLEK 34 (48)
T ss_pred ccCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 6899999999999999986 55555554
No 289
>PRK13239 alkylmercury lyase; Provisional
Probab=75.88 E-value=5.3 Score=39.31 Aligned_cols=29 Identities=14% Similarity=0.102 Sum_probs=26.7
Q ss_pred hCCCCCHHHHHHhcCCCHHHHHHHHHhcc
Q 010327 376 LKRVPTDEEIIQGVNISPERYREVMKASK 404 (513)
Q Consensus 376 lgR~PT~eELA~~lgis~e~v~~~l~~~~ 404 (513)
.||.||..+||+.+|+++++++.+|....
T Consensus 33 ~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 33 KGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 69999999999999999999999998754
No 290
>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=75.64 E-value=10 Score=38.28 Aligned_cols=56 Identities=21% Similarity=0.272 Sum_probs=43.7
Q ss_pred HHHHHHHHhcCCHHHHHHHhHHhcCCCC--CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 442 RLALDDVLDSLKPKESLVIRQRFGLDGK--GDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 442 ~~~L~~aL~~L~~rEr~VL~lRyGL~~~--~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
+..++-++..||--|.+.+...+-.=+. .-.+..+||+.+|||+..|+ .|+++|..
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 4457788999999999888876644222 46899999999999998887 66677754
No 291
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=75.59 E-value=7.3 Score=32.84 Aligned_cols=32 Identities=19% Similarity=0.031 Sum_probs=28.8
Q ss_pred CCCCHHHHHHHhC-CCHHHHHHHHHHHHHHHhC
Q 010327 470 GDRTLGEIAGNLN-ISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 470 ~~~Tl~EIA~~Lg-ISrerVRqi~~rALkKLR~ 501 (513)
.++|+.+||+.|| .+.++|.....+--++|..
T Consensus 43 ~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~ 75 (90)
T cd06571 43 TGLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE 75 (90)
T ss_pred hCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh
Confidence 4899999999999 9999999888888887775
No 292
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=75.51 E-value=4.6 Score=36.34 Aligned_cols=24 Identities=17% Similarity=0.057 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 470 GDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 470 ~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
+++|..+||+.||+|+..|+|.++
T Consensus 21 eG~Sq~~iA~LLGltqaAVS~Yls 44 (119)
T COG2522 21 EGLSQYRIAKLLGLTQAAVSQYLS 44 (119)
T ss_pred cCCcHHHHHHHhCCCHHHHHHHHc
Confidence 489999999999999999999875
No 293
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=75.48 E-value=5.3 Score=33.48 Aligned_cols=35 Identities=17% Similarity=0.119 Sum_probs=26.0
Q ss_pred HHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 455 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 455 rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
|...|+.+-- . ...|+++||+.+|||..+|+..+.
T Consensus 7 R~~~I~e~l~---~-~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 7 RVLEIGKYIV---E-TKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred HHHHHHHHHH---H-CCCCHHHHHHHhCCCHHHHHHHhc
Confidence 4445554433 2 467999999999999999998653
No 294
>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=75.42 E-value=4.3 Score=31.57 Aligned_cols=37 Identities=22% Similarity=0.234 Sum_probs=27.7
Q ss_pred HHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 455 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 455 rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
|+-.+|.+-+. ...+|+.|+|+.+|+|..+|++....
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 45566666663 46789999999999999999876543
No 295
>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=75.23 E-value=1.9 Score=40.46 Aligned_cols=51 Identities=14% Similarity=0.075 Sum_probs=42.2
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHH-----HHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEI-----AGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EI-----A~~LgISrerVRqi~~rALkKLR~~ 502 (513)
.|+++|.+||.+-.. +.++..|.++| |..+++|..+|+.+..+.++||...
T Consensus 154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~l~~Kl~~~ 209 (226)
T TIGR02154 154 SLGPTEFRLLHFFMT-HPERVYSREQLLDRVWGRDVYVEERTVDVHIRRLRKALNPF 209 (226)
T ss_pred EcCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCCCCCCCCccHHHHHHHHHHhhccC
Confidence 599999999988762 12246788888 7889999999999999999999743
No 296
>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=75.00 E-value=6.3 Score=31.25 Aligned_cols=25 Identities=24% Similarity=0.242 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 470 GDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 470 ~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
...|..+||+.+|+|+.+|++...+
T Consensus 12 ~~~~~~eLa~~l~vS~~tv~~~l~~ 36 (69)
T TIGR00122 12 NPFSGEKLGEALGMSRTAVNKHIQT 36 (69)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4578999999999999999976654
No 297
>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=74.76 E-value=47 Score=33.00 Aligned_cols=33 Identities=24% Similarity=0.415 Sum_probs=26.5
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHH
Q 010327 235 VQVKEQLQKDLGREPTDVELAEATNMSAAQVKK 267 (513)
Q Consensus 235 ~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~ 267 (513)
......++..+|+.|+..++|...|++.+.+..
T Consensus 119 ~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~ 151 (255)
T TIGR02941 119 KKAIDELTDHLQRSPKIIEIADHLGLSEEEVLE 151 (255)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 345567788889999999999999998776644
No 298
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=74.39 E-value=34 Score=30.54 Aligned_cols=40 Identities=13% Similarity=-0.036 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHh
Q 010327 363 GEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA 402 (513)
Q Consensus 363 ~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~ 402 (513)
..+.++...+...+...++.++||+.+|+++..+..+...
T Consensus 9 ~~i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 9 ITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3455666667777888899999999999999998887654
No 299
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=74.35 E-value=5 Score=30.96 Aligned_cols=29 Identities=34% Similarity=0.378 Sum_probs=22.9
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
..++|..|||+.+|+|+++|++ .+++|.+
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r----~l~~L~~ 51 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSR----TLKELEE 51 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence 3579999999999999999975 4455554
No 300
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=74.18 E-value=3.6 Score=38.96 Aligned_cols=38 Identities=18% Similarity=0.235 Sum_probs=31.2
Q ss_pred CHHHHHHHhHHhcCCCCCCCCHHHHHHHhC-CCHHHHHHHHHH
Q 010327 453 KPKESLVIRQRFGLDGKGDRTLGEIAGNLN-ISREMVRKHEVK 494 (513)
Q Consensus 453 ~~rEr~VL~lRyGL~~~~~~Tl~EIA~~Lg-ISrerVRqi~~r 494 (513)
++..-+.|.-.+ .+++|..|||..|| ||++.|--..+|
T Consensus 4 tde~~~~L~~lw----~~G~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 4 TDERVERLRKLW----AEGLSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred CHHHHHHHHHHH----HcCCCHHHHHHHhCCcchhhhhhhhhc
Confidence 455556666666 58999999999999 999999887776
No 301
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=73.83 E-value=14 Score=33.62 Aligned_cols=48 Identities=13% Similarity=0.049 Sum_probs=36.4
Q ss_pred HHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 444 ALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 444 ~L~~aL~--~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
.+...+. .|++.|-.||..-+. .++.|..|||+.+|+++.+|..+..+
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 3444443 489999999887652 45799999999999999999865543
No 302
>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=73.70 E-value=7.8 Score=37.52 Aligned_cols=44 Identities=23% Similarity=0.320 Sum_probs=35.6
Q ss_pred HHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 448 VLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 448 aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
.+..|++++..||.+-.- ..+.|..|||+.+|+|+++|++++.+
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 355799999999877651 24689999999999999999976655
No 303
>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=73.17 E-value=5.3 Score=29.69 Aligned_cols=25 Identities=16% Similarity=0.122 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 470 GDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 470 ~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
.++|..++|+.+|+|+++|+++++.
T Consensus 14 ~gltq~~lA~~~gvs~~~vs~~e~g 38 (58)
T TIGR03070 14 LGLTQADLADLAGVGLRFIRDVENG 38 (58)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 5789999999999999999999864
No 304
>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=73.12 E-value=6.6 Score=29.69 Aligned_cols=50 Identities=16% Similarity=0.147 Sum_probs=39.4
Q ss_pred cCCHHHHHHHhHHhcCCCCC-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010327 451 SLKPKESLVIRQRFGLDGKG-DRTLGEIAGNLNISREMVRKHEVKGLMKLK 500 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~-~~Tl~EIA~~LgISrerVRqi~~rALkKLR 500 (513)
.+++.+..+|...|..+.+. .....+||..+|||...|......-..+.|
T Consensus 6 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k 56 (57)
T PF00046_consen 6 RFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEK 56 (57)
T ss_dssp SSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhC
Confidence 47888999999999654322 245789999999999999999887776655
No 305
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=73.02 E-value=9.7 Score=35.27 Aligned_cols=50 Identities=20% Similarity=0.228 Sum_probs=30.3
Q ss_pred HHHHHhcCCHHHHHHHhHH----hcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 445 LDDVLDSLKPKESLVIRQR----FGLDGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 445 L~~aL~~L~~rEr~VL~lR----yGL~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
+..+=.+|++.|+....+- |-..+++..|+.|||+.+|||+++..++.+.
T Consensus 4 ~~~le~~L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~ 57 (142)
T PF13022_consen 4 LKELEAKLTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQQ 57 (142)
T ss_dssp HHHHHTTS-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHcCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHhc
Confidence 3444467999988843331 1112346799999999999999999999853
No 306
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=72.96 E-value=4 Score=38.96 Aligned_cols=30 Identities=40% Similarity=0.436 Sum_probs=25.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
.+++|+.||++.+|+|+++|+ .++++|...
T Consensus 39 ~~Pmtl~Ei~E~lg~Sks~vS----~~lkkL~~~ 68 (177)
T COG1510 39 RKPLTLDEIAEALGMSKSNVS----MGLKKLQDW 68 (177)
T ss_pred CCCccHHHHHHHHCCCcchHH----HHHHHHHhc
Confidence 579999999999999999988 466666643
No 307
>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=72.71 E-value=38 Score=32.91 Aligned_cols=31 Identities=39% Similarity=0.568 Sum_probs=25.6
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHccCCHHHHH
Q 010327 236 QVKEQLQKDLGREPTDVELAEATNMSAAQVK 266 (513)
Q Consensus 236 ~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~ 266 (513)
.....+...+|+.|+..|+|..+|++.+.+.
T Consensus 94 ~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~ 124 (227)
T TIGR02980 94 KATEELTQRLGRSPTIAEIAEELGVSEEEVV 124 (227)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHhCCCHHHHH
Confidence 3456677888999999999999999987664
No 308
>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=72.37 E-value=2.3 Score=30.42 Aligned_cols=24 Identities=42% Similarity=0.571 Sum_probs=20.3
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHH
Q 010327 473 TLGEIAGNLNISREMVRKHEVKGL 496 (513)
Q Consensus 473 Tl~EIA~~LgISrerVRqi~~rAL 496 (513)
|..|+|+.+|||..++|..+...|
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~Gl 24 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYEREGL 24 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHTTS
T ss_pred CHHHHHHHHCCCHHHHHHHHHCCC
Confidence 467999999999999999998763
No 309
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=72.31 E-value=9.2 Score=38.45 Aligned_cols=53 Identities=15% Similarity=0.105 Sum_probs=40.9
Q ss_pred HHHHHHHHhcCCHHHHHHHhHHhcCC-CCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 442 RLALDDVLDSLKPKESLVIRQRFGLD-GKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 442 ~~~L~~aL~~L~~rEr~VL~lRyGL~-~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
...|...+..||+.|+.|......-. ....+|..|||+..|+|..+|-+..++
T Consensus 4 ~~~i~~~~~~Lt~~e~~Ia~yil~n~~~v~~~si~~lA~~~~vS~aTv~Rf~kk 57 (284)
T PRK11302 4 LEKIQSRLEHLSKSERKVAEVILASPQTAIHSSIATLAKMANVSEPTVNRFCRS 57 (284)
T ss_pred HHHHHHHHhhCCHHHHHHHHHHHhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHH
Confidence 35677888899999999987765210 113489999999999999999876553
No 310
>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=71.89 E-value=7.8 Score=33.92 Aligned_cols=43 Identities=12% Similarity=0.175 Sum_probs=26.8
Q ss_pred HHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010327 455 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 503 (513)
Q Consensus 455 rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~ 503 (513)
+.+.|.. .| .+++..++|..+|+|..+|++|+.+....-+...
T Consensus 62 R~~~I~~-~f-----~G~n~~eLA~kyglS~r~I~~Ii~~~~~~~~~~~ 104 (108)
T PF08765_consen 62 RNREIRR-EF-----NGMNVRELARKYGLSERQIYRIIKRVRRRERRRR 104 (108)
T ss_dssp HHHHHHH-H-------SS-HHHHHHHHT--HHHHHHHHHHHHH------
T ss_pred HHHHHHH-Hh-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHhh
Confidence 4455554 34 3789999999999999999999999887766543
No 311
>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=71.74 E-value=7.4 Score=36.40 Aligned_cols=39 Identities=26% Similarity=0.250 Sum_probs=31.1
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
.+|..-.|=.+|- ..++|..++|+.+|||+.+|.++++.
T Consensus 23 ~~p~~~~Ir~~R~----~lGmTq~eLAerlGVS~~tIs~iE~G 61 (150)
T TIGR02612 23 QTPKEGWVRAIRK----ALGMSGAQLAGRLGVTPQRVEALEKS 61 (150)
T ss_pred ccCcHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 3545444555566 46899999999999999999999984
No 312
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=71.56 E-value=11 Score=33.10 Aligned_cols=41 Identities=22% Similarity=0.119 Sum_probs=33.2
Q ss_pred HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010327 449 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG 495 (513)
Q Consensus 449 L~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA 495 (513)
-..+.+.+-.-++..+ ++|..++|+.+|+|+.+|+++++..
T Consensus 62 ~~~~~~~~i~~~r~~~------gltq~~lA~~lg~~~~tis~~e~g~ 102 (127)
T TIGR03830 62 DGLLTPPEIRRIRKKL------GLSQREAAELLGGGVNAFSRYERGE 102 (127)
T ss_pred cCCcCHHHHHHHHHHc------CCCHHHHHHHhCCCHHHHHHHHCCC
Confidence 3457887766666666 6799999999999999999988643
No 313
>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=71.51 E-value=9.4 Score=31.80 Aligned_cols=28 Identities=18% Similarity=0.145 Sum_probs=21.2
Q ss_pred hCCCCCHHHHHHhcCCCHHHHHHHHHhc
Q 010327 376 LKRVPTDEEIIQGVNISPERYREVMKAS 403 (513)
Q Consensus 376 lgR~PT~eELA~~lgis~e~v~~~l~~~ 403 (513)
.|++.|.+.||..+|++.++|..++...
T Consensus 35 ~G~PVt~~~LA~a~g~~~e~v~~~L~~~ 62 (77)
T PF12324_consen 35 KGQPVTVEQLAAALGWPVEEVRAALAAM 62 (77)
T ss_dssp TTS-B-HHHHHHHHT--HHHHHHHHHH-
T ss_pred cCCCcCHHHHHHHHCCCHHHHHHHHHhC
Confidence 3899999999999999999999998764
No 314
>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=71.48 E-value=9.2 Score=29.29 Aligned_cols=37 Identities=30% Similarity=0.466 Sum_probs=26.4
Q ss_pred HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 454 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 454 ~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
..+..|+...+ ..+.+..||++.+|+|..+|+....+
T Consensus 7 ~~~~~il~~l~----~~~~~~~ei~~~~~i~~~~i~~~l~~ 43 (78)
T cd00090 7 PTRLRILRLLL----EGPLTVSELAERLGLSQSTVSRHLKK 43 (78)
T ss_pred hHHHHHHHHHH----HCCcCHHHHHHHHCcCHhHHHHHHHH
Confidence 34555555444 22399999999999999999766544
No 315
>PRK10072 putative transcriptional regulator; Provisional
Probab=71.36 E-value=5.3 Score=34.57 Aligned_cols=26 Identities=23% Similarity=0.327 Sum_probs=23.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
..++|..++|+.+|||..+|+++++.
T Consensus 44 ~~glTQ~elA~~lGvS~~TVs~WE~G 69 (96)
T PRK10072 44 GTGLKIDDFARVLGVSVAMVKEWESR 69 (96)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 45899999999999999999999863
No 316
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=71.13 E-value=4.6 Score=32.22 Aligned_cols=27 Identities=44% Similarity=0.455 Sum_probs=22.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 471 DRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 471 ~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
++|.++||..+|+|+++|. +.+++|++
T Consensus 28 ~lt~~~iA~~~g~sr~tv~----r~l~~l~~ 54 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVS----RILKRLKD 54 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHH----HHHHHHHH
T ss_pred cCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 5899999999999999887 45555654
No 317
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=71.08 E-value=9 Score=31.52 Aligned_cols=44 Identities=30% Similarity=0.480 Sum_probs=33.9
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
.|+..+..||..-+. ..++|..+||+.+++|..+|++ ++++|.+
T Consensus 7 ~l~~~~~~il~~l~~---~~~~~~~~la~~~~~s~~~i~~----~l~~L~~ 50 (101)
T smart00347 7 GLTPTQFLVLRILYE---EGPLSVSELAKRLGVSPSTVTR----VLDRLEK 50 (101)
T ss_pred CCCHHHHHHHHHHHH---cCCcCHHHHHHHHCCCchhHHH----HHHHHHH
Confidence 477888888888774 3469999999999999988884 4555543
No 318
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=71.06 E-value=11 Score=38.38 Aligned_cols=54 Identities=24% Similarity=0.172 Sum_probs=42.1
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhHHhcCC-CCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 440 LLRLALDDVLDSLKPKESLVIRQRFGLD-GKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 440 ~l~~~L~~aL~~L~~rEr~VL~lRyGL~-~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
.+...|...+..|++.|+.|.....--. ....+|..+||+..|+|..+|-+..+
T Consensus 14 ~i~~~i~~~~~~Lt~~e~~Ia~yil~~~~~v~~~si~~lA~~~~vS~aTi~Rf~k 68 (292)
T PRK11337 14 GLGPYIRMKQEGLTPLESRVVEWLLKPGDLSEATALKDIAEALAVSEAMIVKVAK 68 (292)
T ss_pred hHHHHHHHHHhhcCHHHHHHHHHHHhCHHHHHhcCHHHHHHHhCCChHHHHHHHH
Confidence 3455788889999999999987765210 12358999999999999999987654
No 319
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=71.01 E-value=5.8 Score=32.25 Aligned_cols=25 Identities=24% Similarity=0.142 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 470 GDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 470 ~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
.++|.+|.|+.+|||+.||-.++.-
T Consensus 13 ~~ltQ~elA~~vgVsRQTi~~iEkg 37 (68)
T COG1476 13 LGLTQEELAKLVGVSRQTIIAIEKG 37 (68)
T ss_pred hCcCHHHHHHHcCcCHHHHHHHHcC
Confidence 4789999999999999999998864
No 320
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=70.87 E-value=7.9 Score=28.83 Aligned_cols=26 Identities=31% Similarity=0.409 Sum_probs=22.3
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
..+.|..+|++.+|+|+.+|++++.+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~ 33 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKK 33 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHH
Confidence 35789999999999999998877655
No 321
>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=70.65 E-value=8.8 Score=36.49 Aligned_cols=41 Identities=12% Similarity=0.144 Sum_probs=33.4
Q ss_pred HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010327 454 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 497 (513)
Q Consensus 454 ~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALk 497 (513)
+.=|.-++..|= ++.+|++.+|..+|||..|+|++...|..
T Consensus 5 ~e~R~~~R~~YV---~~~~sLe~aA~~~gVs~~TarrWK~~Ak~ 45 (165)
T PF08822_consen 5 QETRDAVRRAYV---FDRLSLEQAAAKCGVSYATARRWKREAKA 45 (165)
T ss_pred HHHHHHHHHHHH---hCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 444566666662 47899999999999999999999998864
No 322
>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=70.57 E-value=5.3 Score=31.23 Aligned_cols=23 Identities=26% Similarity=0.390 Sum_probs=21.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~r 494 (513)
+|..|+|+.+|||..++|.+..+
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 58899999999999999999875
No 323
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=70.54 E-value=8.9 Score=41.27 Aligned_cols=51 Identities=8% Similarity=-0.025 Sum_probs=42.9
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
.+++.||..+.+.+-|...++.|+.++|+.|+||++|+.+-+.+..+.|.+
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 478888888777766666678999999999999999999988888777755
No 324
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=69.84 E-value=8.9 Score=29.16 Aligned_cols=26 Identities=35% Similarity=0.477 Sum_probs=21.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
.|..+||..+|+|+++|+ +++++|.+
T Consensus 26 ~~~~~la~~~~is~~~v~----~~l~~L~~ 51 (66)
T cd07377 26 PSERELAEELGVSRTTVR----EALRELEA 51 (66)
T ss_pred CCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 469999999999999998 56666654
No 325
>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=69.62 E-value=5 Score=37.52 Aligned_cols=28 Identities=18% Similarity=0.185 Sum_probs=23.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 471 DRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 471 ~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
++|.+|||..+|+|+++|. |+|++|++.
T Consensus 143 ~~t~~~iA~~lG~tretvs----R~l~~l~~~ 170 (193)
T TIGR03697 143 RLSHQAIAEAIGSTRVTIT----RLLGDLRKK 170 (193)
T ss_pred CCCHHHHHHHhCCcHHHHH----HHHHHHHHC
Confidence 5899999999999999988 667777754
No 326
>CHL00148 orf27 Ycf27; Reviewed
Probab=69.52 E-value=6.2 Score=37.50 Aligned_cols=50 Identities=16% Similarity=0.094 Sum_probs=42.4
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHh-------CCCHHHHHHHHHHHHHHHhC
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNL-------NISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~L-------gISrerVRqi~~rALkKLR~ 501 (513)
.|+++|.+|+.+... +.+.+.|.++|++.+ +++..+|..+..+-++||..
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 499999999987762 123579999999999 48999999999999999975
No 327
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=69.23 E-value=10 Score=33.75 Aligned_cols=34 Identities=12% Similarity=0.138 Sum_probs=28.2
Q ss_pred HHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010327 459 VIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL 496 (513)
Q Consensus 459 VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rAL 496 (513)
++...+ ..++|+.+||..+|||..+|.++..+..
T Consensus 21 aV~~~~----~~g~sv~evA~e~gIs~~tl~~W~r~y~ 54 (121)
T PRK09413 21 IVQQSF----EPGMTVSLVARQHGVAASQLFLWRKQYQ 54 (121)
T ss_pred HHHHHH----cCCCCHHHHHHHHCcCHHHHHHHHHHHh
Confidence 444445 5689999999999999999999988754
No 328
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=69.16 E-value=4.7 Score=34.15 Aligned_cols=24 Identities=38% Similarity=0.256 Sum_probs=17.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 470 GDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 470 ~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
.++|..|||+.+|.|++.|.+++.
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 378999999999999999998764
No 329
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=68.82 E-value=6.1 Score=31.03 Aligned_cols=24 Identities=17% Similarity=0.169 Sum_probs=21.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKG 495 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rA 495 (513)
+|..|+|+.+|||..++|.+..+.
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~g 24 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKEF 24 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhc
Confidence 578999999999999999998763
No 330
>PRK15482 transcriptional regulator MurR; Provisional
Probab=68.54 E-value=12 Score=37.88 Aligned_cols=52 Identities=13% Similarity=0.082 Sum_probs=40.2
Q ss_pred HHHHHHHhcCCHHHHHHHhHHhcC-CCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 443 LALDDVLDSLKPKESLVIRQRFGL-DGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 443 ~~L~~aL~~L~~rEr~VL~lRyGL-~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
..|......||+.|+.|.....-= +....+|..|||+..|+|..+|-+.-++
T Consensus 5 ~~i~~~~~~Lt~~e~~Ia~yIl~n~~~v~~~si~elA~~~~vS~aTv~Rf~kk 57 (285)
T PRK15482 5 TKIRNAESEFTENEQKIADFLRANVSELKSVSSRKMAKQLGISQSSIVKFAQK 57 (285)
T ss_pred HHHHHHHhhcCHHHHHHHHHHHhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHH
Confidence 467788889999999998776510 0113499999999999999999876543
No 331
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=67.85 E-value=9.4 Score=37.91 Aligned_cols=26 Identities=35% Similarity=0.410 Sum_probs=23.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
..++|..|||++||||..+||+++..
T Consensus 23 ~g~~sa~elA~~Lgis~~avR~HL~~ 48 (218)
T COG2345 23 SGPVSADELAEELGISPMAVRRHLDD 48 (218)
T ss_pred cCCccHHHHHHHhCCCHHHHHHHHHH
Confidence 46899999999999999999988754
No 332
>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=67.72 E-value=4.6 Score=32.28 Aligned_cols=28 Identities=14% Similarity=0.170 Sum_probs=24.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVKGL 496 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~rAL 496 (513)
..+.|+.+||..+||++++++++.....
T Consensus 21 ~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 21 ESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp HHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HCCCceEeeecccccccccccHHHHHHh
Confidence 3579999999999999999999999886
No 333
>PF14493 HTH_40: Helix-turn-helix domain
Probab=67.72 E-value=8.3 Score=32.51 Aligned_cols=31 Identities=13% Similarity=0.065 Sum_probs=27.9
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVKGLMKL 499 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~rALkKL 499 (513)
.+++|+.|||+.-|++.+||..++.++...=
T Consensus 11 ~~G~si~eIA~~R~L~~sTI~~HL~~~~~~g 41 (91)
T PF14493_consen 11 QKGLSIEEIAKIRGLKESTIYGHLAELIESG 41 (91)
T ss_pred HcCCCHHHHHHHcCCCHHHHHHHHHHHHHhC
Confidence 3789999999999999999999999987653
No 334
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=67.36 E-value=10 Score=38.09 Aligned_cols=50 Identities=12% Similarity=0.072 Sum_probs=38.9
Q ss_pred HHHHHhcCCHHHHHHHhHHhcCC-CCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 445 LDDVLDSLKPKESLVIRQRFGLD-GKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 445 L~~aL~~L~~rEr~VL~lRyGL~-~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
|......|++.|+.|......-. ....+|..|+|+..|+|..+|.+..++
T Consensus 3 i~~~~~~Lt~~e~~ia~yil~n~~~v~~~si~elA~~~~vS~aTv~Rf~kk 53 (278)
T PRK11557 3 IRQRYPGLAQSDRKLADYLLLQPDTARHLSSQQLANEAGVSQSSVVKFAQK 53 (278)
T ss_pred hhHhhhhCCHHHHHHHHHHHhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHH
Confidence 56677899999999987765211 112499999999999999999877643
No 335
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=67.25 E-value=11 Score=31.62 Aligned_cols=30 Identities=27% Similarity=0.257 Sum_probs=24.3
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 468 GKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 468 ~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
++...|-++||+.||||+.+|- +.++.||+
T Consensus 16 ~~~~~SGe~La~~LgiSRtaVw----K~Iq~Lr~ 45 (79)
T COG1654 16 TGNFVSGEKLAEELGISRTAVW----KHIQQLRE 45 (79)
T ss_pred CCCcccHHHHHHHHCccHHHHH----HHHHHHHH
Confidence 3567899999999999988877 56667774
No 336
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=67.04 E-value=55 Score=27.87 Aligned_cols=38 Identities=8% Similarity=-0.028 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHh
Q 010327 365 IQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA 402 (513)
Q Consensus 365 i~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~ 402 (513)
+.++...+...+...++.++||+.+|+|...+..+.+.
T Consensus 7 ~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~ 44 (107)
T PRK10219 7 IQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRT 44 (107)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 44555566667788899999999999999998887654
No 337
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=66.69 E-value=23 Score=31.99 Aligned_cols=49 Identities=12% Similarity=0.171 Sum_probs=35.5
Q ss_pred HHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 444 ALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 444 ~L~~aL~--~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
.+...+. .|++.|-.||..-+-. .++.|..|||+.+|+++++|.+...+
T Consensus 19 ~~~~~l~~~glt~~q~~vL~~l~~~--~~~~t~~eLa~~l~~~~~tvt~~v~~ 69 (144)
T PRK03573 19 LIDHRLKPLELTQTHWVTLHNIHQL--PPEQSQIQLAKAIGIEQPSLVRTLDQ 69 (144)
T ss_pred HHHHHHHhcCCCHHHHHHHHHHHHc--CCCCCHHHHHHHhCCChhhHHHHHHH
Confidence 3444443 4899998888766521 24689999999999999999855544
No 338
>PRK10870 transcriptional repressor MprA; Provisional
Probab=66.53 E-value=28 Score=33.08 Aligned_cols=51 Identities=10% Similarity=0.046 Sum_probs=37.2
Q ss_pred HHHHHHHhc--CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 443 LALDDVLDS--LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 443 ~~L~~aL~~--L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
..+...|.. |++-+-.||...+. .+..+.|..|||+.+|+++.+|.++..+
T Consensus 42 ~~~~~~l~~~gLt~~q~~iL~~L~~-~~~~~it~~eLa~~l~l~~~tvsr~v~r 94 (176)
T PRK10870 42 ENRNKMLKAQGINETLFMALITLES-QENHSIQPSELSCALGSSRTNATRIADE 94 (176)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHhc-CCCCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 344555644 89988888877762 1234689999999999999999765544
No 339
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=66.49 E-value=12 Score=33.02 Aligned_cols=40 Identities=30% Similarity=0.373 Sum_probs=36.0
Q ss_pred HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 449 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 449 L~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
...|++.|-..|+-.+ ++|..+-|..||+|.++|+.++..
T Consensus 41 ~~~ls~~eIk~iRe~~------~lSQ~vFA~~L~vs~~Tv~~WEqG 80 (104)
T COG2944 41 VKTLSPTEIKAIREKL------GLSQPVFARYLGVSVSTVRKWEQG 80 (104)
T ss_pred CCCCCHHHHHHHHHHh------CCCHHHHHHHHCCCHHHHHHHHcC
Confidence 3569999999999998 679999999999999999999975
No 340
>PRK01905 DNA-binding protein Fis; Provisional
Probab=66.19 E-value=22 Score=29.22 Aligned_cols=36 Identities=19% Similarity=0.210 Sum_probs=25.5
Q ss_pred HHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 456 ESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 456 Er~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
|+.+|...+- ..+-+..+.|+.||||+.+++....+
T Consensus 38 E~~~i~~aL~---~~~gn~s~aAr~LGIsrstL~rklkk 73 (77)
T PRK01905 38 EKPLLEVVME---QAGGNQSLAAEYLGINRNTLRKKLQQ 73 (77)
T ss_pred HHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 5555544441 23457999999999999998876654
No 341
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=66.03 E-value=38 Score=32.86 Aligned_cols=104 Identities=16% Similarity=0.052 Sum_probs=63.3
Q ss_pred HHHHHHHhCCC-CCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchhhhHHHHHHHHHHH
Q 010327 369 KLELLFELKRV-PTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDD 447 (513)
Q Consensus 369 ~~~L~~elgR~-PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee~~~~~~l~~~L~~ 447 (513)
...+...-|.+ -|..+||+.+|++.+.+..++..-.....-+.. + +......+ .-......+....+..
T Consensus 9 iEA~LF~sg~pgls~~~La~~l~~~~~~v~~~l~~L~~~y~~~~~-g------i~i~~~~~---~y~l~tk~e~~~~v~~ 78 (188)
T PRK00135 9 IEALLFVSGEEGLSLEQLAEILELEPTEVQQLLEELQEKYEGDDR-G------LKLIEFND---VYKLVTKEENADYLQK 78 (188)
T ss_pred HHHHHHHcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhCCC-C------EEEEEECC---EEEEEEcHHHHHHHHH
Confidence 34455556776 799999999999999988887654322111100 0 00000000 0111123334444555
Q ss_pred HHh-----cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCH
Q 010327 448 VLD-----SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISR 485 (513)
Q Consensus 448 aL~-----~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISr 485 (513)
++. .|+.-.-++|...+- .++.|-.||++..|++.
T Consensus 79 ~~~~~~~~~LS~aaLEtLaiIay---~qPiTr~eI~~irGv~~ 118 (188)
T PRK00135 79 LVKTPIKQSLSQAALEVLAIIAY---KQPITRIEIDEIRGVNS 118 (188)
T ss_pred HhcccccCCCCHHHHHHHHHHHH---cCCcCHHHHHHHHCCCH
Confidence 443 599999999887542 68999999999999985
No 342
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=66.02 E-value=90 Score=30.62 Aligned_cols=34 Identities=44% Similarity=0.676 Sum_probs=26.6
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010327 236 QVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL 269 (513)
Q Consensus 236 ~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~ 269 (513)
.....+...+|++|+..++|..+|++.+.+..+.
T Consensus 99 ~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~ 132 (236)
T PRK06986 99 QAIRQLEQELGREPTDTEVAEKLGLSLEEYREML 132 (236)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHH
Confidence 3445566788999999999999999987765543
No 343
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=65.98 E-value=4.6 Score=31.67 Aligned_cols=25 Identities=36% Similarity=0.397 Sum_probs=22.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGL 496 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rAL 496 (513)
+|..|+|+.+|||..+++.++...+
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~~gl 25 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYERIGL 25 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999987665
No 344
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=65.83 E-value=6.1 Score=31.67 Aligned_cols=22 Identities=18% Similarity=0.203 Sum_probs=19.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~ 493 (513)
.|+.|||+.+|||.++|+.+++
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln 22 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLN 22 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHC
Confidence 3789999999999999998764
No 345
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=65.77 E-value=11 Score=32.76 Aligned_cols=45 Identities=29% Similarity=0.431 Sum_probs=33.9
Q ss_pred CCHHHHHHHhHHhcCCC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010327 452 LKPKESLVIRQRFGLDG---KGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 500 (513)
Q Consensus 452 L~~rEr~VL~lRyGL~~---~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR 500 (513)
|+|.||+-+-.|+-+-. ..++|..||+..||+|..+|- |+-.-|+
T Consensus 38 LTpdEReal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtIT----RGSN~LK 85 (103)
T COG2973 38 LTPDEREALGTRVRIVEELLRGELSQREIAQKLGVSIATIT----RGSNSLK 85 (103)
T ss_pred cCHhHHHHHHHHHHHHHHHHhccccHHHHHHHhCcchhhhc----cchhhhc
Confidence 78889888877775421 248999999999999988775 4445555
No 346
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=65.46 E-value=13 Score=35.38 Aligned_cols=97 Identities=14% Similarity=0.240 Sum_probs=54.3
Q ss_pred CCCCCHHHHHHhc--CCCHHHHHHHHHhccC--cccccCCCCCchhhhh---ccccCCCCCCchh-hhHHHHHHHHHHHH
Q 010327 377 KRVPTDEEIIQGV--NISPERYREVMKASKP--ILSLHSRHGVTQEEFI---NGITDVDGVENEN-QRQPALLRLALDDV 448 (513)
Q Consensus 377 gR~PT~eELA~~l--gis~e~v~~~l~~~~~--~~SLd~~~~~~~~e~~---d~l~d~~~~~~ee-~~~~~~l~~~L~~a 448 (513)
+-.+++.+||+.+ +||.+++++.+..... .+--+.. +.+. ..+.......+.- ...+..+.+.-.++
T Consensus 37 ~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~-----g~y~~t~~~l~~~~~~~~~avr~~h~q~~~lA~~a 111 (171)
T PF14394_consen 37 PFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGD-----GKYVQTDKSLTTSSEIPSEAVRSYHKQMLELAQEA 111 (171)
T ss_pred CCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCC-----CcEEEecceeeCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 3456899999999 9999999998876321 1111111 1111 1111111111111 11222333334567
Q ss_pred HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHh
Q 010327 449 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNL 481 (513)
Q Consensus 449 L~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~L 481 (513)
|+..|+.+|.+=.+-+|+ ...++++|.+.+
T Consensus 112 l~~~p~~~R~~s~~T~~v---s~~~~~ki~~~i 141 (171)
T PF14394_consen 112 LDRVPPEERDFSGLTMSV---SREDYEKIKKEI 141 (171)
T ss_pred HHhCCccccceeeeEEEe---CHHHHHHHHHHH
Confidence 788899999998888875 345666666655
No 347
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=65.33 E-value=42 Score=37.76 Aligned_cols=104 Identities=14% Similarity=0.093 Sum_probs=58.7
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHHhccCcccccC--CCCCchhhhhccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHH
Q 010327 378 RVPTDEEIIQGVNISPERYREVMKASKPILSLHS--RHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPK 455 (513)
Q Consensus 378 R~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~--~~~~~~~e~~d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~r 455 (513)
...|..+||+.+|+|..+++.-+..-...+.-.. ......+-. +.. .+. ..+...+..-++
T Consensus 16 ~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~~i~~~~Gy~---l~~-----~~~--------~~~~~~~~~~~~- 78 (584)
T PRK09863 16 QDRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIGSISGSAKYH---LEI-----LNR--------RSLFQLLQKSDN- 78 (584)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchhheecCCceE---EEe-----CCH--------HHHHHHHhcCCH-
Confidence 4679999999999999998776553221100000 000000000 000 000 111122222333
Q ss_pred HHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010327 456 ESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 500 (513)
Q Consensus 456 Er~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR 500 (513)
|+..+.++.-+ ..+.++.++|+.|.||++||.+-+.+.-+.|.
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 33334444433 36899999999999999999999888887776
No 348
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=65.19 E-value=14 Score=37.80 Aligned_cols=53 Identities=17% Similarity=0.128 Sum_probs=41.0
Q ss_pred HHHHHHHHHhcCCHHHHHHHhHHhcCC-CCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 441 LRLALDDVLDSLKPKESLVIRQRFGLD-GKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 441 l~~~L~~aL~~L~~rEr~VL~lRyGL~-~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
+...|...++.|++.|+.|-.+..-=. ....+|..|||+..|||+.+|-+..+
T Consensus 5 l~~~I~~~~~~Lt~~er~iA~yil~~~~~~~~~si~elA~~a~VS~aTv~Rf~~ 58 (281)
T COG1737 5 LLERIRERYDSLTKSERKIADYILANPDEVALLSIAELAERAGVSPATVVRFAR 58 (281)
T ss_pred HHHHHHHHHhcCCHHHHHHHHHHHhCHHHHHHHHHHHHHHHhCCCHHHHHHHHH
Confidence 456788899999999999977655110 11248999999999999999986654
No 349
>TIGR00647 MG103 conserved hypothetical protein.
Probab=65.15 E-value=13 Score=38.30 Aligned_cols=44 Identities=20% Similarity=0.175 Sum_probs=37.9
Q ss_pred HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhC------CCHHHHHHHHHHH
Q 010327 449 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN------ISREMVRKHEVKG 495 (513)
Q Consensus 449 L~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~Lg------ISrerVRqi~~rA 495 (513)
++.||+.-+++..+|.- ..+.|++|+|+.|. ||++.|.-+..+-
T Consensus 225 l~~Lp~~L~~~a~lRl~---~Pd~SL~ELgell~~~~~~~isKSgvnhRlrKl 274 (279)
T TIGR00647 225 FEKLPLNFQRICLLKID---HPDWSLEQIAEFFASKYKVKISRSGIQHRLRKL 274 (279)
T ss_pred cccCCHHHHHHHHHHHh---CcccCHHHHHHHhccCCCCCcCHHHHHHHHHHH
Confidence 57899999999999883 57899999999994 9999998877654
No 350
>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=65.09 E-value=16 Score=27.33 Aligned_cols=51 Identities=18% Similarity=0.221 Sum_probs=40.0
Q ss_pred cCCHHHHHHHhHHhcCCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 451 SLKPKESLVIRQRFGLDGK-GDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~-~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
.+++.+..+|...|..+.+ ......+||..+|+|...|......-..+.+.
T Consensus 6 ~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 6 RFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 4678888888888865443 23468899999999999999998887776654
No 351
>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=64.90 E-value=16 Score=31.69 Aligned_cols=44 Identities=27% Similarity=0.248 Sum_probs=33.9
Q ss_pred cCCHHHHHHHhHHhcC-CCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 451 SLKPKESLVIRQRFGL-DGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL-~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
.|++.|-.||..-+-+ ...++.|..+||..+++++++|.+...+
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 5899999998665411 1135799999999999999999866554
No 352
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.45 E-value=15 Score=31.32 Aligned_cols=55 Identities=25% Similarity=0.238 Sum_probs=35.5
Q ss_pred cCCHHHHHHH----hHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhcc
Q 010327 451 SLKPKESLVI----RQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 512 (513)
Q Consensus 451 ~L~~rEr~VL----~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~~yl 512 (513)
.|+|.|+.+- ...|- ...+|.++||..||+|...|..++.-. .++...=.|++|+
T Consensus 2 SLn~eq~~~Tk~elqan~e---l~~LS~~~iA~~Ln~t~~~lekil~~t----qr~~dvW~lRd~l 60 (97)
T COG4367 2 SLNPEQKQRTKQELQANFE---LCPLSDEEIATALNWTEVKLEKILQVT----QRPADVWRLRDFL 60 (97)
T ss_pred CCCHHHHHHHHHHHHHhhh---hccccHHHHHHHhCCCHHHHHHHHHHh----hccchhHHHHHHH
Confidence 3566665553 33443 357899999999999999998877543 2233334455554
No 353
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=64.29 E-value=8.3 Score=30.42 Aligned_cols=23 Identities=30% Similarity=0.352 Sum_probs=21.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~r 494 (513)
+|..|+|+.+|||..++|.++..
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 47899999999999999999876
No 354
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=64.16 E-value=15 Score=30.22 Aligned_cols=26 Identities=27% Similarity=0.305 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010327 470 GDRTLGEIAGNLNISREMVRKHEVKG 495 (513)
Q Consensus 470 ~~~Tl~EIA~~LgISrerVRqi~~rA 495 (513)
.+.|..|||+.+|+|+.+|++++..-
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L 44 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTL 44 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 47999999999999999999877543
No 355
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=63.89 E-value=12 Score=30.88 Aligned_cols=25 Identities=36% Similarity=0.270 Sum_probs=19.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 470 GDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 470 ~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
...|.+|||+.+|+|+..|+++..+
T Consensus 24 ~~~s~~eiA~~~~i~~~~l~kil~~ 48 (83)
T PF02082_consen 24 KPVSSKEIAERLGISPSYLRKILQK 48 (83)
T ss_dssp C-BEHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3489999999999999999976543
No 356
>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=63.62 E-value=2.2 Score=41.27 Aligned_cols=94 Identities=19% Similarity=0.240 Sum_probs=30.0
Q ss_pred CCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHH
Q 010327 380 PTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLV 459 (513)
Q Consensus 380 PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~V 459 (513)
.+.++||..++++.+++..++..-+. +|-. +...-+ .+..+.-++...- . ++.-..|
T Consensus 53 ~~~~eia~~l~~~~~~v~~~l~~lQ~---leP~----------------GigAr~--l~EcLllQl~~~~-~-~~~~~~i 109 (194)
T PF04963_consen 53 ESLEEIAEELGVSEEEVEKALELLQS---LEPA----------------GIGARD--LQECLLLQLERKG-P-PDLAYRI 109 (194)
T ss_dssp S-HHHHHHHCTS-HHHHHHHHHHHHT---TSS------------------TTTS---TTHHHHHHHHHS--S---TTHHH
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHc---CCCC----------------ccCcCC--HHHHHHHHHhccC-C-cHHHHHH
Confidence 57899999999999999999877542 2211 111100 1112222222111 1 2233344
Q ss_pred HhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010327 460 IRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 499 (513)
Q Consensus 460 L~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKL 499 (513)
|.-++ +......++.||+.+|+|.+.|...... +++|
T Consensus 110 l~~~l--~~l~~~~~~~ia~~l~~s~~~v~~~~~~-Ir~L 146 (194)
T PF04963_consen 110 LENHL--ELLANKDYKKIAKKLGISEEEVQEAIEL-IRTL 146 (194)
T ss_dssp HHHHH--HHHHH----------------------------
T ss_pred HHHHH--HHHHHhhhcccccccccccccccccccc-cccc
Confidence 44433 2233467889999999999999876654 4444
No 357
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=63.32 E-value=93 Score=31.79 Aligned_cols=25 Identities=28% Similarity=0.344 Sum_probs=22.1
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHHh
Q 010327 378 RVPTDEEIIQGVNISPERYREVMKA 402 (513)
Q Consensus 378 R~PT~eELA~~lgis~e~v~~~l~~ 402 (513)
..-|..|||+.+|+|.++|+++...
T Consensus 247 ~~~Tl~EIA~~lgvS~~rVrqi~~~ 271 (284)
T PRK06596 247 DKSTLQELAAEYGVSAERVRQIEKN 271 (284)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 5679999999999999999988654
No 358
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=63.15 E-value=8.3 Score=38.99 Aligned_cols=26 Identities=19% Similarity=0.302 Sum_probs=23.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
.++|.+.+||+.||||+.+|+.+..+
T Consensus 17 l~gmk~~dIAeklGvspntiksWKrr 42 (279)
T COG5484 17 LKGMKLKDIAEKLGVSPNTIKSWKRR 42 (279)
T ss_pred HhhccHHHHHHHhCCChHHHHHHHHh
Confidence 37799999999999999999998775
No 359
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=63.14 E-value=14 Score=29.55 Aligned_cols=26 Identities=15% Similarity=0.142 Sum_probs=23.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
..++|..++|+.+|+|+.+|+++++.
T Consensus 16 ~~~~t~~~lA~~~gis~~tis~~~~g 41 (78)
T TIGR02607 16 PLGLSIRALAKALGVSRSTLSRIVNG 41 (78)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 46789999999999999999998863
No 360
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=62.83 E-value=11 Score=26.90 Aligned_cols=27 Identities=22% Similarity=0.156 Sum_probs=19.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVKG 495 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~rA 495 (513)
..++|+.+||..+|+|....+++..+.
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 467999999999999988887766543
No 361
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=62.28 E-value=9.1 Score=29.89 Aligned_cols=28 Identities=29% Similarity=0.385 Sum_probs=20.6
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010327 469 KGDR-TLGEIAGNLNISREMVRKHEVKGLMKLK 500 (513)
Q Consensus 469 ~~~~-Tl~EIA~~LgISrerVRqi~~rALkKLR 500 (513)
++.. |..+||+.||||+.+|+ +|+..|.
T Consensus 21 g~~lps~~~la~~~~vsr~tvr----~al~~L~ 49 (64)
T PF00392_consen 21 GDRLPSERELAERYGVSRTTVR----EALRRLE 49 (64)
T ss_dssp TSBE--HHHHHHHHTS-HHHHH----HHHHHHH
T ss_pred CCEeCCHHHHHHHhccCCcHHH----HHHHHHH
Confidence 4567 99999999999999998 5555554
No 362
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=61.36 E-value=31 Score=37.82 Aligned_cols=55 Identities=15% Similarity=0.269 Sum_probs=37.6
Q ss_pred HHHHHHHH---HHHhcCCHHHHHHHhH------------HhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 439 ALLRLALD---DVLDSLKPKESLVIRQ------------RFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 439 ~~l~~~L~---~aL~~L~~rEr~VL~l------------RyGL~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
..+++.++ .++..|..|++.++.- .+|-.--.++++++||+.+|++.+||++...
T Consensus 283 ~~L~~~lq~A~wLiksL~qR~~TLlkV~~~Iv~~Q~~Ff~~g~~~l~PL~LrdvA~~i~~HESTISRai~ 352 (444)
T COG1508 283 DFLKEKLQEAKWLIKSLEQREETLLKVAEEIVEYQKAFFEGGEEALKPLVLRDVADEIGMHESTISRAIT 352 (444)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCCcccHHHHHHHhCccHHHHHHHHh
Confidence 34444443 4467788888776542 2332233579999999999999999997654
No 363
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=61.26 E-value=20 Score=32.06 Aligned_cols=45 Identities=11% Similarity=0.162 Sum_probs=31.8
Q ss_pred HHHHhcCCHHHH-HHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 446 DDVLDSLKPKES-LVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 446 ~~aL~~L~~rEr-~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
..++.-|.+.-| .||.+-. +.++++..||++.+|+|+.+|++++.
T Consensus 7 ~~~fkaLadptRl~IL~~L~---~~~~~~v~ela~~l~lsqstvS~HL~ 52 (117)
T PRK10141 7 LQLFKILSDETRLGIVLLLR---ESGELCVCDLCTALDQSQPKISRHLA 52 (117)
T ss_pred HHHHHHhCCHHHHHHHHHHH---HcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 355566654444 5555443 13579999999999999999997753
No 364
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.26 E-value=17 Score=32.14 Aligned_cols=49 Identities=18% Similarity=0.171 Sum_probs=41.6
Q ss_pred HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 449 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 449 L~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
++.|++.|-+-+.+++ .-.=+++||-..+|+|.-+||..+...|++|--
T Consensus 39 F~~Lt~d~LeFv~lf~----r~RGnlKEvEr~lg~sYptvR~kld~vlramgy 87 (122)
T COG3877 39 FEYLTSDQLEFVELFL----RCRGNLKEVERELGISYPTVRTKLDEVLRAMGY 87 (122)
T ss_pred ccccCHhHhHHHHHHH----HHccCHHHHHHHHCCccHHHHHHHHHHHHHcCC
Confidence 4568888888888887 344589999999999999999999999988864
No 365
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=59.88 E-value=20 Score=27.30 Aligned_cols=46 Identities=17% Similarity=0.107 Sum_probs=30.4
Q ss_pred cccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHH
Q 010327 354 VPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREV 399 (513)
Q Consensus 354 lP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~ 399 (513)
+|......+-...++...|..+.-..-+..+||+.+|++..+|+.=
T Consensus 3 Ip~~ti~RL~~Y~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRKD 48 (50)
T PF06971_consen 3 IPKATIRRLPLYLRYLEQLKEEGVERVSSQELAEALGITPAQVRKD 48 (50)
T ss_dssp -SHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHcCCeeECHHHHHHHHCCCHHHhccc
Confidence 4555555555556666666665555688899999999999999864
No 366
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=59.88 E-value=20 Score=40.86 Aligned_cols=55 Identities=16% Similarity=0.151 Sum_probs=42.6
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhHHhcCC-CCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 440 LLRLALDDVLDSLKPKESLVIRQRFGLD-GKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 440 ~l~~~L~~aL~~L~~rEr~VL~lRyGL~-~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
.+.+.|...++.||+.|+.|..+..--. ....+|..|||+..|+|..+|-+..++
T Consensus 342 ~l~~~I~~~~~~Lt~~E~~IA~yIl~n~~~v~~~si~eLA~~~~vS~aTV~Rf~kk 397 (638)
T PRK14101 342 AVFERIRQMRDALTPAERRVADLALNHPRSIINDPIVDIARKADVSQPTVIRFCRS 397 (638)
T ss_pred HHHHHHHHHHhhcCHHHHHHHHHHHhCHHHHHhccHHHHHHHhCCCHHHHHHHHHH
Confidence 3556788999999999999987755110 123489999999999999999876543
No 367
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=59.78 E-value=15 Score=36.63 Aligned_cols=41 Identities=17% Similarity=0.252 Sum_probs=32.4
Q ss_pred HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010327 454 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 497 (513)
Q Consensus 454 ~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALk 497 (513)
+|++.|+.+-.. ....|..|||+.||||..|||+.+..--.
T Consensus 4 ~R~~~Il~~l~~---~~~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 4 ARQQAIVDLLLN---HTSLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred HHHHHHHHHHHH---cCCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 566777666442 45799999999999999999999886543
No 368
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=58.91 E-value=9.6 Score=36.42 Aligned_cols=26 Identities=31% Similarity=0.363 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010327 470 GDRTLGEIAGNLNISREMVRKHEVKG 495 (513)
Q Consensus 470 ~~~Tl~EIA~~LgISrerVRqi~~rA 495 (513)
-+||..|||+.+|.|..+||+++.-.
T Consensus 60 ag~Ti~EIAeelG~TeqTir~hlkge 85 (182)
T COG1318 60 AGMTISEIAEELGRTEQTVRNHLKGE 85 (182)
T ss_pred ccCcHHHHHHHhCCCHHHHHHHHhcc
Confidence 48999999999999999999987643
No 369
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=58.90 E-value=9.4 Score=30.42 Aligned_cols=25 Identities=32% Similarity=0.183 Sum_probs=20.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 470 GDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 470 ~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
.+.|..|||+.+|+|..+||.++..
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 5899999999999999999988654
No 370
>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=58.14 E-value=12 Score=33.26 Aligned_cols=25 Identities=20% Similarity=0.299 Sum_probs=22.9
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
..+.|..++|..|+||+.+|..+..
T Consensus 16 ~~g~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 16 EKGKSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred HccchHHHHHHHhCcHHHHHHHHHH
Confidence 4688999999999999999999876
No 371
>PF11662 DUF3263: Protein of unknown function (DUF3263); InterPro: IPR021678 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=57.66 E-value=35 Score=28.49 Aligned_cols=47 Identities=9% Similarity=0.008 Sum_probs=36.1
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 497 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALk 497 (513)
.|+++++.||-+----....+-+-+.|-+.||+|.-+-.|.++.-+.
T Consensus 2 ~Ls~~d~~iL~fE~~ww~~~GaKe~aIre~fGls~~rYyq~Ln~LiD 48 (77)
T PF11662_consen 2 GLSDRDRAILDFERRWWRHGGAKEEAIREEFGLSPTRYYQRLNALID 48 (77)
T ss_pred CCCHHHHHHHHHHHHhCcCCCCcHHHHHHHHCCCHHHHHHHHHHHhC
Confidence 58999999997632112234668899999999999999999887653
No 372
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=57.49 E-value=17 Score=31.14 Aligned_cols=43 Identities=26% Similarity=0.239 Sum_probs=30.9
Q ss_pred cCCHHHHHHHhHHhc-CCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 451 SLKPKESLVIRQRFG-LDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 451 ~L~~rEr~VL~lRyG-L~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
.|++.++.||...-. -...++.++.+|++.|+++...|++.+.
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 688888888877654 3446789999999999999999996654
No 373
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=57.45 E-value=11 Score=29.16 Aligned_cols=26 Identities=31% Similarity=0.320 Sum_probs=20.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
..++|+.++|+.+|++++++.++++.
T Consensus 10 ~~~lt~~~~a~~~~i~~~~i~~~e~g 35 (64)
T PF12844_consen 10 EKGLTQKDLAEKLGISRSTISKIENG 35 (64)
T ss_dssp HCT--HHHHHHHHTS-HHHHHHHHTT
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 35789999999999999999999865
No 374
>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=57.12 E-value=11 Score=31.64 Aligned_cols=42 Identities=19% Similarity=0.267 Sum_probs=26.7
Q ss_pred HHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010327 456 ESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 499 (513)
Q Consensus 456 Er~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKL 499 (513)
||.|-...|-+ ....|..+.|..||||.+||.+-...=|.++
T Consensus 6 eR~i~i~~yIi--~~~aTVR~~Ak~FGvSKSTVHkDvteRL~~i 47 (82)
T PF12116_consen 6 ERVIEIANYII--ETKATVRQAAKVFGVSKSTVHKDVTERLPKI 47 (82)
T ss_dssp HHHHHHHHHHH--HH---HHHHHHHHTS-HHHHHHHHTTHHHHH
T ss_pred HHHHHHHHHHH--HcccHHHHHHHHHCCcHHHHHHHHHHHHHhc
Confidence 44444445544 2478999999999999999998776555444
No 375
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=56.84 E-value=25 Score=34.83 Aligned_cols=36 Identities=25% Similarity=0.391 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010327 234 FVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL 269 (513)
Q Consensus 234 l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~ 269 (513)
+......++..+|++|+.+|+|...|++.+.+....
T Consensus 103 i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~ 138 (231)
T PRK12427 103 TNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYL 138 (231)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 345566788889999999999999999988775544
No 376
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=56.62 E-value=20 Score=30.39 Aligned_cols=40 Identities=25% Similarity=0.368 Sum_probs=31.3
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
|++.|..||...+-. .+.+..+||+.+++++++|.++..+
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 999999999887732 2233399999999999999866554
No 377
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=56.60 E-value=25 Score=26.09 Aligned_cols=48 Identities=19% Similarity=0.200 Sum_probs=37.0
Q ss_pred cCCHHHHHHHhHHhcCCCCC-CCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010327 451 SLKPKESLVIRQRFGLDGKG-DRTLGEIAGNLNISREMVRKHEVKGLMK 498 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~-~~Tl~EIA~~LgISrerVRqi~~rALkK 498 (513)
.+++.+..+|...|..+.+. .....+||..+|+|...|.........+
T Consensus 6 ~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~ 54 (56)
T smart00389 6 SFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAK 54 (56)
T ss_pred cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhc
Confidence 37888889998888654332 3468899999999999999987766544
No 378
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=56.29 E-value=12 Score=35.38 Aligned_cols=27 Identities=30% Similarity=0.270 Sum_probs=22.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 471 DRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 471 ~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
+.|.++||..+|+|+++|. |.|++|++
T Consensus 149 ~~t~~~iA~~lG~tretvs----R~l~~l~~ 175 (202)
T PRK13918 149 YATHDELAAAVGSVRETVT----KVIGELSR 175 (202)
T ss_pred cCCHHHHHHHhCccHHHHH----HHHHHHHH
Confidence 5799999999999999998 56666764
No 379
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=56.04 E-value=13 Score=27.21 Aligned_cols=23 Identities=13% Similarity=0.151 Sum_probs=21.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHH
Q 010327 469 KGDRTLGEIAGNLNISREMVRKH 491 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi 491 (513)
+...|+.+||+..|||+..+.+.
T Consensus 14 ~~~~s~~~Ia~~~gvs~~~~y~~ 36 (47)
T PF00440_consen 14 YEAVSIRDIARRAGVSKGSFYRY 36 (47)
T ss_dssp TTTSSHHHHHHHHTSCHHHHHHH
T ss_pred HHhCCHHHHHHHHccchhhHHHH
Confidence 68899999999999999998765
No 380
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=56.00 E-value=28 Score=29.81 Aligned_cols=39 Identities=23% Similarity=0.363 Sum_probs=28.9
Q ss_pred HHHHHHHHHhC-CCCCHHHHHHhcCCCHHHHHHHHHhccC
Q 010327 367 RAKLELLFELK-RVPTDEEIIQGVNISPERYREVMKASKP 405 (513)
Q Consensus 367 ka~~~L~~elg-R~PT~eELA~~lgis~e~v~~~l~~~~~ 405 (513)
....+|...+. ..-|++|||..||+|+..++.++...+.
T Consensus 10 ~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil~~tqr 49 (97)
T COG4367 10 RTKQELQANFELCPLSDEEIATALNWTEVKLEKILQVTQR 49 (97)
T ss_pred HHHHHHHHhhhhccccHHHHHHHhCCCHHHHHHHHHHhhc
Confidence 34445554433 3458899999999999999999987654
No 381
>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=55.97 E-value=8.3 Score=32.91 Aligned_cols=26 Identities=31% Similarity=0.377 Sum_probs=23.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGLM 497 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rALk 497 (513)
+|..|+|+.+|||..++|-++..++-
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~~Gll 26 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDIGLF 26 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 58899999999999999999988653
No 382
>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=55.87 E-value=28 Score=25.71 Aligned_cols=23 Identities=13% Similarity=0.237 Sum_probs=17.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~r 494 (513)
+|+.+.|+.+||++++++.....
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 99999999999999999966553
No 383
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=55.70 E-value=2.3e+02 Score=28.40 Aligned_cols=38 Identities=21% Similarity=0.204 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHh
Q 010327 365 IQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA 402 (513)
Q Consensus 365 i~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~ 402 (513)
+.++...+...+....+++++|+.+|+|+..+..+.+.
T Consensus 185 i~~~~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk~ 222 (290)
T PRK10572 185 VREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQ 222 (290)
T ss_pred HHHHHHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 34444455566778899999999999999998887654
No 384
>PRK09726 antitoxin HipB; Provisional
Probab=55.66 E-value=16 Score=30.55 Aligned_cols=25 Identities=20% Similarity=0.304 Sum_probs=22.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 470 GDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 470 ~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
.++|..++|+.+|||+.+|+++++.
T Consensus 24 ~gltq~elA~~~gvs~~tis~~e~g 48 (88)
T PRK09726 24 NGWTQSELAKKIGIKQATISNFENN 48 (88)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 4789999999999999999999874
No 385
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=54.97 E-value=27 Score=26.99 Aligned_cols=34 Identities=21% Similarity=0.147 Sum_probs=27.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
..+.+..+.|+.|+|.+.||+..+.+.-..+--.
T Consensus 10 ~~~~n~~~tA~~L~iHrNTl~yRl~ki~~l~g~d 43 (59)
T PF13556_consen 10 ENNGNISKTARALHIHRNTLRYRLKKIEELLGLD 43 (59)
T ss_dssp HTTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCcC
Confidence 4578999999999999999999999988877543
No 386
>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=54.89 E-value=18 Score=28.90 Aligned_cols=27 Identities=30% Similarity=0.485 Sum_probs=22.4
Q ss_pred HHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 010327 459 VIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHE 492 (513)
Q Consensus 459 VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~ 492 (513)
+|..-|| +..|+|..|+|++.+|++..
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 4556675 68899999999999999864
No 387
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=54.72 E-value=49 Score=31.97 Aligned_cols=40 Identities=13% Similarity=0.058 Sum_probs=33.3
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
.|++.|..||..-+. ..+.|..+||+.++++.++|.++..
T Consensus 42 gLt~~q~~iL~~L~~---~~~itq~eLa~~l~l~~sTvtr~l~ 81 (185)
T PRK13777 42 DLNINEHHILWIAYH---LKGASISEIAKFGVMHVSTAFNFSK 81 (185)
T ss_pred CCCHHHHHHHHHHHh---CCCcCHHHHHHHHCCCHhhHHHHHH
Confidence 499999999977763 4689999999999999999876444
No 388
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=54.49 E-value=15 Score=32.34 Aligned_cols=52 Identities=19% Similarity=0.193 Sum_probs=45.7
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010327 450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV 505 (513)
Q Consensus 450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~ 505 (513)
.+|.+-|+....-+| -.-+|-+|||-.+.++..+|..+...-..|.|+..+.
T Consensus 27 ~QLkELErvF~ETHY----PDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~ 78 (125)
T KOG0484|consen 27 AQLKELERVFAETHY----PDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERA 78 (125)
T ss_pred HHHHHHHHHHHhhcC----CcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHH
Confidence 468888998888898 6779999999999999999999999999999986554
No 389
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=54.16 E-value=16 Score=25.50 Aligned_cols=25 Identities=28% Similarity=0.296 Sum_probs=22.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 470 GDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 470 ~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
.++|..++|+.+|+|..+|++++..
T Consensus 9 ~~~s~~~la~~~~i~~~~i~~~~~~ 33 (56)
T smart00530 9 KGLTQEELAEKLGVSRSTLSRIENG 33 (56)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 5789999999999999999987653
No 390
>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=54.13 E-value=8.5 Score=31.83 Aligned_cols=33 Identities=24% Similarity=0.186 Sum_probs=27.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
.+..|+.++|+.++||++++.+...+.-+.|+.
T Consensus 28 ~~~~s~~~la~~~~iS~sti~~~i~~l~~~l~~ 60 (87)
T PF05043_consen 28 NEYVSIEDLAEELFISRSTIYRDIKKLNKYLKK 60 (87)
T ss_dssp -SEEEHHHHHHHHT--HHHHHHHHHHHHHHHHC
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 468899999999999999999999988888874
No 391
>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=53.57 E-value=9.3 Score=32.98 Aligned_cols=26 Identities=27% Similarity=0.464 Sum_probs=23.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGLM 497 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rALk 497 (513)
+|..|+|+.+|||..++|-++..++-
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~~Gll 27 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESIGLI 27 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 68999999999999999999998764
No 392
>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=53.55 E-value=21 Score=34.20 Aligned_cols=43 Identities=23% Similarity=0.252 Sum_probs=32.6
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
..|++-|+.....+. +. ..++|..+||+.+|+|+.+|++++.-
T Consensus 101 ~~lt~~e~a~~~~~l-~~-~~g~s~~~iA~~lg~s~~~V~r~l~l 143 (187)
T TIGR00180 101 EDLSPIEEAQAYKRL-LE-KFSMTQEDLAKKIGKSRAHITNLLRL 143 (187)
T ss_pred cCCCHHHHHHHHHHH-HH-HhCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 368888877755543 11 14789999999999999999988754
No 393
>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=53.46 E-value=8.8 Score=28.28 Aligned_cols=20 Identities=20% Similarity=0.109 Sum_probs=17.4
Q ss_pred HHHHHHhCCCHHHHHHHHHH
Q 010327 475 GEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 475 ~EIA~~LgISrerVRqi~~r 494 (513)
.+||+.+|||..+|+++++.
T Consensus 1 ~~lA~~~gvs~~tvs~~l~g 20 (52)
T cd01392 1 KDIARAAGVSVATVSRVLNG 20 (52)
T ss_pred CcHHHHHCcCHHHHHHHHcC
Confidence 37999999999999998764
No 394
>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=53.42 E-value=20 Score=31.93 Aligned_cols=25 Identities=20% Similarity=0.110 Sum_probs=21.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
....|..|||+.+|+|+.+|++++.
T Consensus 23 ~~~~s~~eia~~l~is~~~v~~~l~ 47 (130)
T TIGR02944 23 SQPYSAAEIAEQTGLNAPTVSKILK 47 (130)
T ss_pred CCCccHHHHHHHHCcCHHHHHHHHH
Confidence 4579999999999999999986654
No 395
>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=52.89 E-value=10 Score=33.06 Aligned_cols=26 Identities=35% Similarity=0.397 Sum_probs=23.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGLM 497 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rALk 497 (513)
+|..|+|+.+|||.+++|-++..+|-
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~~GLi 26 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKIGLL 26 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCC
Confidence 57899999999999999999998764
No 396
>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=52.55 E-value=10 Score=33.18 Aligned_cols=25 Identities=36% Similarity=0.550 Sum_probs=23.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGL 496 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rAL 496 (513)
||..|+|+.+|||..++|.++..++
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gl 25 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKEGL 25 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999998875
No 397
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=52.51 E-value=18 Score=32.61 Aligned_cols=26 Identities=12% Similarity=0.120 Sum_probs=23.3
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
..++|..++|+.+|||+++|+++++.
T Consensus 16 ~~gltq~~lA~~~gvs~~~is~~E~g 41 (135)
T PRK09706 16 QLKLSQRSLAKAVKVSHVSISQWERD 41 (135)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 35789999999999999999998865
No 398
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=52.27 E-value=19 Score=35.33 Aligned_cols=29 Identities=17% Similarity=0.231 Sum_probs=24.3
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 469 KGDR-TLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 469 ~~~~-Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
++.+ |-.++|+.||||+.+|| .||..|..
T Consensus 28 G~~LPsE~eLae~~gVSRt~VR----eAL~~L~~ 57 (239)
T PRK04984 28 GSILPAERELSELIGVTRTTLR----EVLQRLAR 57 (239)
T ss_pred CCcCCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 4567 79999999999999999 67777764
No 399
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=52.02 E-value=19 Score=29.81 Aligned_cols=19 Identities=11% Similarity=0.088 Sum_probs=18.2
Q ss_pred CHHHHHHHhCCCHHHHHHH
Q 010327 473 TLGEIAGNLNISREMVRKH 491 (513)
Q Consensus 473 Tl~EIA~~LgISrerVRqi 491 (513)
|...+|+.||||.+.|+|+
T Consensus 12 s~~kvA~aLGIs~~AVsQW 30 (75)
T PRK09744 12 SKTKLANAAGVRLASVAAW 30 (75)
T ss_pred cHHHHHHHHCCCHHHHHHH
Confidence 7889999999999999998
No 400
>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=51.81 E-value=34 Score=31.60 Aligned_cols=50 Identities=18% Similarity=0.168 Sum_probs=38.2
Q ss_pred hHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCccc
Q 010327 359 ESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILS 408 (513)
Q Consensus 359 ~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~S 408 (513)
.+.-....++...|...-++..|+.||++.+|++++.|..+++..+-.++
T Consensus 26 ~~~e~~f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGRL~~~ 75 (137)
T TIGR03826 26 EEEEREFEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGRLQLK 75 (137)
T ss_pred HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCCeecc
Confidence 33444555666666666678899999999999999999999988765444
No 401
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=51.56 E-value=16 Score=35.85 Aligned_cols=28 Identities=25% Similarity=0.341 Sum_probs=22.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 471 DRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 471 ~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
+.|.++||..+|+|+++|. |++++|++.
T Consensus 179 ~lt~~~IA~~lGisretls----R~L~~L~~~ 206 (230)
T PRK09391 179 PMSRRDIADYLGLTIETVS----RALSQLQDR 206 (230)
T ss_pred cCCHHHHHHHHCCCHHHHH----HHHHHHHHC
Confidence 5799999999999999988 556667653
No 402
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=51.50 E-value=14 Score=28.29 Aligned_cols=26 Identities=19% Similarity=0.114 Sum_probs=19.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010327 470 GDRTLGEIAGNLNISREMVRKHEVKG 495 (513)
Q Consensus 470 ~~~Tl~EIA~~LgISrerVRqi~~rA 495 (513)
.++|..++|+..|||+.+|+++.+.-
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 46799999999999999999998854
No 403
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=51.31 E-value=33 Score=26.44 Aligned_cols=29 Identities=21% Similarity=0.259 Sum_probs=23.2
Q ss_pred HHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 459 VIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 459 VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
-|..+| .++++|.|+.|||+...++++..
T Consensus 9 ~L~~~f------hlp~~eAA~~Lgv~~T~LKr~CR 37 (52)
T PF02042_consen 9 DLSQYF------HLPIKEAAKELGVSVTTLKRRCR 37 (52)
T ss_pred HHHHHh------CCCHHHHHHHhCCCHHHHHHHHH
Confidence 455666 68999999999999888877654
No 404
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=51.21 E-value=23 Score=29.42 Aligned_cols=25 Identities=20% Similarity=0.193 Sum_probs=22.5
Q ss_pred CCCCCHHHHHHHhC------CCHHHHHHHHH
Q 010327 469 KGDRTLGEIAGNLN------ISREMVRKHEV 493 (513)
Q Consensus 469 ~~~~Tl~EIA~~Lg------ISrerVRqi~~ 493 (513)
.-++|..++|+.+| +|..+|+++++
T Consensus 22 ~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es 52 (75)
T smart00352 22 KLGFTQADVGLALGALYGPDFSQTTICRFEA 52 (75)
T ss_pred HcCCCHHHHHHHhcccccCcCCHHHHHHHHh
Confidence 35889999999999 69999999886
No 405
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=50.84 E-value=22 Score=35.87 Aligned_cols=42 Identities=17% Similarity=0.278 Sum_probs=31.7
Q ss_pred HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010327 454 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 499 (513)
Q Consensus 454 ~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKL 499 (513)
+|+..|+.+-- .....+..|+|+.||||..|||+-+.. |.+-
T Consensus 5 eR~~~Il~~L~---~~~~v~v~eLa~~l~VS~~TIRRDL~~-Le~~ 46 (256)
T PRK10434 5 QRQAAILEYLQ---KQGKTSVEELAQYFDTTGTTIRKDLVI-LEHA 46 (256)
T ss_pred HHHHHHHHHHH---HcCCEEHHHHHHHHCCCHHHHHHHHHH-HHHC
Confidence 56666666543 134689999999999999999998776 4443
No 406
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=50.83 E-value=23 Score=31.53 Aligned_cols=34 Identities=32% Similarity=0.299 Sum_probs=25.3
Q ss_pred HhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 460 IRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 460 L~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
|...|+ +.....|+.|||+.|.||+..|+.++.+
T Consensus 9 L~~~~~-~~~~~vtl~elA~~l~cS~Rn~r~lLkk 42 (115)
T PF12793_consen 9 LWQHYG-GQPVEVTLDELAELLFCSRRNARTLLKK 42 (115)
T ss_pred HHHHcC-CCCcceeHHHHHHHhCCCHHHHHHHHHH
Confidence 334554 3344689999999999999999877654
No 407
>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=50.77 E-value=11 Score=31.69 Aligned_cols=26 Identities=19% Similarity=0.171 Sum_probs=23.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGLM 497 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rALk 497 (513)
+|..|+|+.+|||..+|+.++...+-
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~~Gli 27 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYERLGLL 27 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCCc
Confidence 58999999999999999999987654
No 408
>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=50.67 E-value=11 Score=32.11 Aligned_cols=25 Identities=32% Similarity=0.307 Sum_probs=22.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGL 496 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rAL 496 (513)
+|..|+|+.+|||..++|-++..++
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gl 25 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDKIGL 25 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999998875
No 409
>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=50.48 E-value=12 Score=32.44 Aligned_cols=26 Identities=35% Similarity=0.393 Sum_probs=23.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGLM 497 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rALk 497 (513)
+|..|+|+.+|||..++|-++..++-
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~~Gll 27 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKLGLI 27 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 68999999999999999999987653
No 410
>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=50.40 E-value=12 Score=31.39 Aligned_cols=25 Identities=32% Similarity=0.422 Sum_probs=23.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGL 496 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rAL 496 (513)
+|..|+|+.+|||..++|.++...+
T Consensus 2 ~ti~evA~~~gvs~~tLR~ye~~Gl 26 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEEKGL 26 (88)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 6899999999999999999988775
No 411
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=50.38 E-value=24 Score=35.45 Aligned_cols=38 Identities=18% Similarity=0.209 Sum_probs=28.9
Q ss_pred HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 454 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 454 ~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
+|+..|+.+-- .....+..|+|+.||||..|||+.+..
T Consensus 5 ~R~~~Il~~l~---~~~~~~~~ela~~l~vS~~TirRdL~~ 42 (251)
T PRK13509 5 QRHQILLELLA---QLGFVTVEKVIERLGISPATARRDINK 42 (251)
T ss_pred HHHHHHHHHHH---HcCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 34555554433 245799999999999999999999876
No 412
>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=50.19 E-value=18 Score=32.65 Aligned_cols=23 Identities=26% Similarity=0.200 Sum_probs=20.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~r 494 (513)
||-+|+|+.+|+|+.+|.++..+
T Consensus 1 MT~eELA~~tG~srQTINrWvRk 23 (122)
T PF07037_consen 1 MTPEELAELTGYSRQTINRWVRK 23 (122)
T ss_pred CCHHHHHHHhCccHHHHHHHHHh
Confidence 68999999999999999988764
No 413
>PRK13503 transcriptional activator RhaS; Provisional
Probab=50.14 E-value=1.3e+02 Score=29.78 Aligned_cols=36 Identities=11% Similarity=-0.015 Sum_probs=27.3
Q ss_pred HHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHh
Q 010327 367 RAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA 402 (513)
Q Consensus 367 ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~ 402 (513)
++...+........|.+++|+.+|+|+..+..+.+.
T Consensus 175 ~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk~ 210 (278)
T PRK13503 175 QLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQ 210 (278)
T ss_pred HHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 333444455667889999999999999998887654
No 414
>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional
Probab=50.13 E-value=12 Score=35.29 Aligned_cols=46 Identities=13% Similarity=-0.034 Sum_probs=38.8
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCC---------HHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRT---------LGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~T---------l~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
.|+++|.+||.+-. .+.+ ...+|..++++..+|+.+..+.++||..
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 3333 4778888999999999999999999974
No 415
>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=50.12 E-value=12 Score=32.17 Aligned_cols=26 Identities=27% Similarity=0.369 Sum_probs=22.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGLM 497 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rALk 497 (513)
+|..|+|+.+|||..++|.++..++-
T Consensus 1 y~i~e~A~~~gvs~~tlR~Ye~~Gll 26 (99)
T cd04772 1 YRTVDLARAIGLSPQTVRNYESLGLI 26 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCC
Confidence 47899999999999999999887653
No 416
>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=50.06 E-value=31 Score=30.56 Aligned_cols=26 Identities=31% Similarity=0.322 Sum_probs=22.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
..+.|..|||+.+|+|+..|+++...
T Consensus 23 ~~~~s~~eia~~~~i~~~~v~~il~~ 48 (132)
T TIGR00738 23 EGPVSVKEIAERQGISRSYLEKILRT 48 (132)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHHH
Confidence 34799999999999999999876543
No 417
>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=50.02 E-value=12 Score=32.01 Aligned_cols=26 Identities=23% Similarity=0.395 Sum_probs=23.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGLM 497 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rALk 497 (513)
|+..|+|+.+|||..++|.++..++-
T Consensus 1 m~i~eva~~~gvs~~tlR~ye~~Gll 26 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDHIGLL 26 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999987753
No 418
>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family contains mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation []. Homologues of neugrin are found in fungi suggesting they have a alternative role or more than one function.
Probab=49.92 E-value=26 Score=35.01 Aligned_cols=42 Identities=21% Similarity=0.217 Sum_probs=32.3
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
.|+..+.+-|++-+-.+ -+.+|...+|+.|+||++.||+|+.
T Consensus 10 ~Ls~~~~~~ir~L~~~~-p~~~t~~~Lae~F~vspe~irrILk 51 (225)
T PF06413_consen 10 KLSREAMEQIRYLHKED-PEEWTVERLAESFKVSPEAIRRILK 51 (225)
T ss_pred CCCHHHHHHHHHHHHhC-ccccCHHHHHhhCCCCHHHHHHHHh
Confidence 46777777776655322 2458999999999999999999875
No 419
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=49.68 E-value=27 Score=24.43 Aligned_cols=25 Identities=28% Similarity=0.314 Sum_probs=22.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 470 GDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 470 ~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
.++|..++|..+|+|+.+|.+++..
T Consensus 11 ~~~s~~~~a~~~~~~~~~v~~~~~g 35 (58)
T cd00093 11 KGLTQEELAEKLGVSRSTISRIENG 35 (58)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 4789999999999999999987664
No 420
>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=49.68 E-value=31 Score=33.01 Aligned_cols=39 Identities=13% Similarity=0.100 Sum_probs=29.0
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
|++.-|.-|...+- .+++|+++||..+||+..||.-|+.
T Consensus 17 lse~~r~~Iy~~~~---~~~~sv~~vS~~ygi~~~RV~AIvr 55 (172)
T PF12298_consen 17 LSEELREQIYEDVM---QDGKSVREVSQKYGIKIQRVEAIVR 55 (172)
T ss_pred CCHHHHHHHHHHHH---hCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 55555555555553 4677999999999999999976653
No 421
>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=49.61 E-value=41 Score=30.40 Aligned_cols=44 Identities=20% Similarity=0.157 Sum_probs=34.8
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHh----CCCHHHHHHHHHHHHH
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNL----NISREMVRKHEVKGLM 497 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~L----gISrerVRqi~~rALk 497 (513)
.|++.|..|+...+. .++.|..||.+.| |++..||...+.+=.+
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 488999999977663 3578999977776 7999999988777544
No 422
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=49.59 E-value=23 Score=36.13 Aligned_cols=42 Identities=19% Similarity=0.143 Sum_probs=34.1
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
..|++.|+.||.+--+- +...++.||-+.+|.|+.+|+++++
T Consensus 191 ~~L~~~e~~il~~i~~~--GGri~Q~eL~r~lglsktTvsR~L~ 232 (258)
T COG2512 191 YDLNEDEKEILDLIRER--GGRITQAELRRALGLSKTTVSRILR 232 (258)
T ss_pred CCCCHHHHHHHHHHHHh--CCEEeHHHHHHhhCCChHHHHHHHH
Confidence 46999999999886642 2358999999999999999985543
No 423
>PHA00738 putative HTH transcription regulator
Probab=49.55 E-value=35 Score=30.29 Aligned_cols=37 Identities=14% Similarity=-0.048 Sum_probs=27.1
Q ss_pred HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 454 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 454 ~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
|.=+.||.+-.. +++++..||++.|++|+.+|++++.
T Consensus 12 ptRr~IL~lL~~---~e~~~V~eLae~l~lSQptVS~HLK 48 (108)
T PHA00738 12 ILRRKILELIAE---NYILSASLISHTLLLSYTTVLRHLK 48 (108)
T ss_pred HHHHHHHHHHHH---cCCccHHHHHHhhCCCHHHHHHHHH
Confidence 344555554331 3469999999999999999998754
No 424
>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=49.36 E-value=12 Score=32.05 Aligned_cols=26 Identities=23% Similarity=0.408 Sum_probs=22.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGLM 497 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rALk 497 (513)
++..|+|+.+|||..++|.++..++-
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye~~Gll 26 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEEIGLV 26 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999886543
No 425
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=49.29 E-value=30 Score=31.42 Aligned_cols=26 Identities=31% Similarity=0.348 Sum_probs=21.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
....+..+||+.||+|..+|+..+.+
T Consensus 20 ~~~~~~~ela~~l~vs~~svs~~l~~ 45 (142)
T PRK03902 20 KGYARVSDIAEALSVHPSSVTKMVQK 45 (142)
T ss_pred CCCcCHHHHHHHhCCChhHHHHHHHH
Confidence 34679999999999999999966533
No 426
>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=49.28 E-value=20 Score=30.96 Aligned_cols=23 Identities=26% Similarity=0.440 Sum_probs=21.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~r 494 (513)
+|..|+|+.+|||..++|.++..
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~~ 23 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 57899999999999999999876
No 427
>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=49.14 E-value=12 Score=32.66 Aligned_cols=26 Identities=31% Similarity=0.460 Sum_probs=23.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGLM 497 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rALk 497 (513)
+|..|+|+.+|||..++|-++..++-
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye~~gll 26 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEKEGLL 26 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 58899999999999999999988764
No 428
>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=49.11 E-value=2.6e+02 Score=28.34 Aligned_cols=32 Identities=41% Similarity=0.601 Sum_probs=25.2
Q ss_pred HHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010327 238 KEQLQKDLGREPTDVELAEATNMSAAQVKKCL 269 (513)
Q Consensus 238 ~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~ 269 (513)
...+...+|++|+..++|...|++...+..++
T Consensus 139 ~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~ 170 (285)
T TIGR02394 139 ARQLEKKLGREPSVEEIAELLDKPVEDVSRVL 170 (285)
T ss_pred HHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 33456678999999999999999987776654
No 429
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=49.06 E-value=18 Score=34.20 Aligned_cols=28 Identities=36% Similarity=0.311 Sum_probs=23.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 471 DRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 471 ~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
..|.++||..+|+|+++|+ |++++|++.
T Consensus 168 ~~t~~~lA~~lG~tr~tvs----R~l~~l~~~ 195 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVG----RVLKMLEDQ 195 (211)
T ss_pred CCCHHHHHHHhCCCHHHHH----HHHHHHHHC
Confidence 6899999999999999988 556667654
No 430
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=48.86 E-value=18 Score=35.16 Aligned_cols=28 Identities=21% Similarity=0.388 Sum_probs=22.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 471 DRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 471 ~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
+.|.++||..+|+|+++|.++ +++|++.
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~----l~~l~~~ 211 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRL----LGRFQKS 211 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHH----HHHHHHC
Confidence 589999999999999999854 5566653
No 431
>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=48.77 E-value=30 Score=31.47 Aligned_cols=33 Identities=15% Similarity=0.071 Sum_probs=23.7
Q ss_pred HHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010327 458 LVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG 495 (513)
Q Consensus 458 ~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA 495 (513)
.||.|.. .+.+-.+||..|+||...|++++.|=
T Consensus 25 rIvela~-----~G~rp~~Isr~l~Vs~gcVsKIl~Ry 57 (125)
T PF00292_consen 25 RIVELAK-----EGVRPCDISRQLRVSHGCVSKILSRY 57 (125)
T ss_dssp HHHHHHH-----TT--HHHHHHHHT--HHHHHHHHHHH
T ss_pred HHHHHhh-----hcCCHHHHHHHHccchhHHHHHHHHH
Confidence 4555665 68999999999999999999998763
No 432
>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=48.41 E-value=13 Score=31.81 Aligned_cols=25 Identities=16% Similarity=0.235 Sum_probs=23.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGL 496 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rAL 496 (513)
|+..|+|+.+|||..+||-++..++
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye~~GL 25 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLREGL 25 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999998876
No 433
>PRK06424 transcription factor; Provisional
Probab=48.18 E-value=22 Score=32.99 Aligned_cols=26 Identities=8% Similarity=0.125 Sum_probs=23.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
..++|+.|+|+.+|++.++|+++++.
T Consensus 95 ~~GLSQ~eLA~~iGvs~stIskiE~G 120 (144)
T PRK06424 95 RLSMSQADLAAKIFERKNVIASIERG 120 (144)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 46899999999999999999999863
No 434
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=48.03 E-value=26 Score=35.19 Aligned_cols=41 Identities=12% Similarity=0.083 Sum_probs=30.8
Q ss_pred HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010327 454 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 498 (513)
Q Consensus 454 ~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkK 498 (513)
+|+..|+.+-- .....+..|+|+.||||.+|||+=+.. |.+
T Consensus 7 eR~~~I~~~l~---~~~~v~v~eLa~~~~VS~~TIRRDL~~-Le~ 47 (252)
T PRK10681 7 ERIGQLLQALK---RSDKLHLKDAAALLGVSEMTIRRDLNA-HSA 47 (252)
T ss_pred HHHHHHHHHHH---HcCCCcHHHHHHHhCCCHHHHHHHHHH-hhc
Confidence 46666665533 245789999999999999999998875 443
No 435
>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=48.01 E-value=24 Score=34.53 Aligned_cols=30 Identities=17% Similarity=0.205 Sum_probs=25.0
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 468 GKGDR-TLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 468 ~~~~~-Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
.++.+ |-.++|+.||||+..|| .||.+|..
T Consensus 26 pG~~LpsE~~La~~lgVSRtpVR----EAL~~Le~ 56 (235)
T TIGR02812 26 PGSILPAERELSELIGVTRTTLR----EVLQRLAR 56 (235)
T ss_pred CCCcCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 35668 89999999999999999 67777764
No 436
>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=47.93 E-value=13 Score=31.91 Aligned_cols=25 Identities=28% Similarity=0.317 Sum_probs=22.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGL 496 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rAL 496 (513)
+|..|+|+.+|||..++|.++...+
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~~Gl 25 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDEIGL 25 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999988775
No 437
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=47.92 E-value=1.9e+02 Score=26.08 Aligned_cols=24 Identities=25% Similarity=0.166 Sum_probs=18.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 471 DRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 471 ~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
|.|-..||..+|++.+.|+++...
T Consensus 72 GFsD~~IA~l~~~~e~~vr~~R~~ 95 (123)
T PF02787_consen 72 GFSDRQIARLWGVSEEEVRELRKE 95 (123)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCHHHHHhccCCCHHHHHHHHHH
Confidence 668899999999999999987654
No 438
>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=47.91 E-value=13 Score=32.58 Aligned_cols=26 Identities=31% Similarity=0.479 Sum_probs=23.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGLM 497 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rALk 497 (513)
|+..|+|+.+|||..++|-++..+|-
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye~~GLl 26 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEEQGLL 26 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCC
Confidence 57899999999999999999988754
No 439
>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=47.69 E-value=14 Score=31.38 Aligned_cols=25 Identities=44% Similarity=0.538 Sum_probs=22.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGL 496 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rAL 496 (513)
+|..|+|+.+|||..+|+.+....+
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~~Gl 25 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEEKGL 25 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999988765
No 440
>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=47.43 E-value=14 Score=32.67 Aligned_cols=27 Identities=30% Similarity=0.461 Sum_probs=24.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGLMK 498 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rALkK 498 (513)
||..|+|+.+|||..++|-.+..+|-.
T Consensus 1 ~~ige~a~~~gvs~~tLryYe~~GLi~ 27 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEEKGLLP 27 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 688999999999999999999987654
No 441
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=47.39 E-value=21 Score=34.58 Aligned_cols=30 Identities=23% Similarity=0.267 Sum_probs=25.0
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 468 GKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 468 ~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
.++.++..++|+.||||+..|| .||+.|..
T Consensus 31 pG~~L~e~~La~~lgVSRtpVR----EAL~~L~~ 60 (221)
T PRK11414 31 PGARLITKNLAEQLGMSITPVR----EALLRLVS 60 (221)
T ss_pred CCCccCHHHHHHHHCCCchhHH----HHHHHHHH
Confidence 3567888999999999999998 67777764
No 442
>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=47.11 E-value=13 Score=31.83 Aligned_cols=25 Identities=24% Similarity=0.236 Sum_probs=22.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGL 496 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rAL 496 (513)
+|..|+|+.+|||..++|.++...+
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye~~Gl 26 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDRLGL 26 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 6899999999999999999987664
No 443
>PRK14082 hypothetical protein; Provisional
Probab=47.09 E-value=64 Score=26.00 Aligned_cols=56 Identities=13% Similarity=-0.001 Sum_probs=41.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccch
Q 010327 272 GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLST 332 (513)
Q Consensus 272 d~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFST 332 (513)
+....+.+|..+.+.+.+-... .+...-+||-||--+.+++-+..++...+--|--
T Consensus 7 ~~~e~e~ii~~FepkIkKsL~~-----T~yqeREDLeQElk~Ki~eK~~~~~~~e~PGF~e 62 (65)
T PRK14082 7 DTEEIEHLIENFSPMIKKKLSN-----TSYQEREDLEQELKIKIIEKADMLLCQEVPGFWE 62 (65)
T ss_pred hHHHHHHHHHHccHHHHHHHhc-----CChhhHHHHHHHHHHHHHHHHHHhhcccCCcHHH
Confidence 4456678999999877653322 2445789999999999999999998766544533
No 444
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=46.99 E-value=25 Score=34.73 Aligned_cols=38 Identities=21% Similarity=0.317 Sum_probs=28.4
Q ss_pred HHHhHHhcCCCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 458 LVIRQRFGLDGKGDR-TLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 458 ~VL~lRyGL~~~~~~-Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
.|+...| ..++.+ |-.++|+.||||+..|| .||+.|..
T Consensus 19 ~I~~g~l--~pG~~LPsE~eLa~~~gVSRtpVR----EAL~~L~~ 57 (251)
T PRK09990 19 LIVDGVL--KVGQALPSERRLCEKLGFSRSALR----EGLTVLRG 57 (251)
T ss_pred HHHcCCC--CCCCcCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 3444444 235667 88999999999999999 67777764
No 445
>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=46.82 E-value=14 Score=31.92 Aligned_cols=26 Identities=31% Similarity=0.390 Sum_probs=23.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGLM 497 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rALk 497 (513)
||..|+|+.+|||..++|-.+..+|-
T Consensus 1 m~Ige~a~~~gvs~~tlRyYe~~GLl 26 (107)
T cd04777 1 MKIGKFAKKNNITIDTVRHYIDLGLL 26 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCc
Confidence 57899999999999999999998874
No 446
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=46.68 E-value=2.5e+02 Score=28.43 Aligned_cols=41 Identities=15% Similarity=0.082 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHh
Q 010327 362 RGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA 402 (513)
Q Consensus 362 ~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~ 402 (513)
...+.++...+...+...++.++||+.+|+|...+..+.+.
T Consensus 4 ~~~i~~~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F~~ 44 (289)
T PRK15121 4 AGIIRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKD 44 (289)
T ss_pred HHHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34566677777778888999999999999999999888654
No 447
>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=46.58 E-value=23 Score=34.00 Aligned_cols=29 Identities=28% Similarity=0.371 Sum_probs=24.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
++..+..++|+.||||+..|| .||..|..
T Consensus 32 G~~L~e~~La~~lgVSRtpVR----eAL~~L~~ 60 (212)
T TIGR03338 32 GAKLNESDIAARLGVSRGPVR----EAFRALEE 60 (212)
T ss_pred CCEecHHHHHHHhCCChHHHH----HHHHHHHH
Confidence 467899999999999999999 67777764
No 448
>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=46.55 E-value=14 Score=33.06 Aligned_cols=27 Identities=30% Similarity=0.495 Sum_probs=23.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGLMK 498 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rALkK 498 (513)
||..|+|+.+|||..+||-++..+|-.
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~~GLl~ 27 (126)
T cd04783 1 LTIGELAKAAGVNVETIRYYQRRGLLP 27 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 578999999999999999998877654
No 449
>PRK08359 transcription factor; Validated
Probab=46.41 E-value=25 Score=33.84 Aligned_cols=26 Identities=15% Similarity=0.210 Sum_probs=23.3
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
..++|++|+|+.+|+|+.+|++++.-
T Consensus 96 ~kglSQeeLA~~lgvs~stI~~iE~G 121 (176)
T PRK08359 96 KSGLSYEELSHEVGLSVNDLRRIAHG 121 (176)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 46899999999999999999999753
No 450
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=46.38 E-value=38 Score=29.01 Aligned_cols=39 Identities=23% Similarity=0.338 Sum_probs=28.4
Q ss_pred CCHHHHHH----HhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 452 LKPKESLV----IRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 452 L~~rEr~V----L~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
|++.|+.+ |.-.|- .-++|.++||..||+|.+.|.+++.
T Consensus 3 Ln~~Q~~~T~~ELq~nf~---~~~ls~~~ia~dL~~s~~~le~vL~ 45 (89)
T PF10078_consen 3 LNPEQRRATRQELQANFE---LSGLSLEQIAADLGTSPEHLEQVLN 45 (89)
T ss_pred CCHHHHHHHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 45555444 333443 2578999999999999999998875
No 451
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=46.26 E-value=26 Score=32.89 Aligned_cols=26 Identities=15% Similarity=0.239 Sum_probs=23.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
..++|++++|+.+|+|.++|+++++-
T Consensus 80 ~~glSqeeLA~~lgvs~s~IsriE~G 105 (154)
T TIGR00270 80 KRGWSQEQLAKKIQEKESLIKKIENA 105 (154)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 46899999999999999999999963
No 452
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=46.23 E-value=46 Score=31.55 Aligned_cols=54 Identities=28% Similarity=0.249 Sum_probs=35.2
Q ss_pred HHHHHhcCCHHHHHHHhHHhcCCCCC---CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 445 LDDVLDSLKPKESLVIRQRFGLDGKG---DRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 445 L~~aL~~L~~rEr~VL~lRyGL~~~~---~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
+..+++-+..+.-.||.+...--+.. -+|.++||+.+|+|+.+|. ++++.|.+.
T Consensus 46 i~~~l~l~g~k~~~Vl~~il~~~d~~N~v~~t~~~ia~~l~iS~~Tv~----r~ik~L~e~ 102 (165)
T PF05732_consen 46 IIKVLDLIGNKAFRVLMYILENMDKDNAVVATQKEIAEKLGISKPTVS----RAIKELEEK 102 (165)
T ss_pred HHHHhhhhchhHHHHHHHHHHhcCCCCeEEeeHHHHHHHhCCCHHHHH----HHHHHHHhC
Confidence 33455545555556655533221222 3799999999999988876 788888764
No 453
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=46.13 E-value=24 Score=31.50 Aligned_cols=26 Identities=12% Similarity=0.095 Sum_probs=23.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
..++|.+|+|+.+|||.++|.++++.
T Consensus 16 ~~Glsq~eLA~~~Gis~~~is~iE~g 41 (120)
T PRK13890 16 ERHMTKKELSERSGVSISFLSDLTTG 41 (120)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 35789999999999999999999864
No 454
>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=46.12 E-value=43 Score=24.97 Aligned_cols=24 Identities=21% Similarity=0.268 Sum_probs=20.0
Q ss_pred CCHHHHHHhcCCCHHHHHHHHHhc
Q 010327 380 PTDEEIIQGVNISPERYREVMKAS 403 (513)
Q Consensus 380 PT~eELA~~lgis~e~v~~~l~~~ 403 (513)
-|.++||+.+|+|...+...+..-
T Consensus 16 it~~eLa~~l~vS~rTi~~~i~~L 39 (55)
T PF08279_consen 16 ITAKELAEELGVSRRTIRRDIKEL 39 (55)
T ss_dssp BEHHHHHHHCTS-HHHHHHHHHHH
T ss_pred cCHHHHHHHhCCCHHHHHHHHHHH
Confidence 789999999999999998877653
No 455
>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=46.03 E-value=27 Score=26.96 Aligned_cols=26 Identities=27% Similarity=0.294 Sum_probs=22.6
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHHhc
Q 010327 378 RVPTDEEIIQGVNISPERYREVMKAS 403 (513)
Q Consensus 378 R~PT~eELA~~lgis~e~v~~~l~~~ 403 (513)
|.-|..|||+.+|||...+...++.+
T Consensus 22 R~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 22 RRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 67899999999999999988877653
No 456
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=45.97 E-value=30 Score=30.52 Aligned_cols=35 Identities=20% Similarity=0.214 Sum_probs=26.6
Q ss_pred HHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 458 LVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 458 ~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
+||.-.|. ..-++|..+.|+.|||++.+|..+.+-
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 45556662 112689999999999999999988753
No 457
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=45.94 E-value=3.6e+02 Score=27.91 Aligned_cols=28 Identities=18% Similarity=0.101 Sum_probs=23.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010327 470 GDRTLGEIAGNLNISREMVRKHEVKGLM 497 (513)
Q Consensus 470 ~~~Tl~EIA~~LgISrerVRqi~~rALk 497 (513)
...|.+|||+..|||..|||+....-..
T Consensus 250 ~~~tq~eva~v~~vtevTIrnrykel~~ 277 (285)
T COG1405 250 ERRTQKEVAKVAGVTEVTIRNRYKELAD 277 (285)
T ss_pred CchHHHHHHHHhCCeeeHHHHHHHHHHH
Confidence 6899999999999999999998844333
No 458
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=45.86 E-value=21 Score=35.90 Aligned_cols=38 Identities=16% Similarity=0.243 Sum_probs=30.0
Q ss_pred CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 453 KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 453 ~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
.+|.+.|+.+--- ....+.+|+|+.||||.+|||+=+.
T Consensus 4 ~eR~~~Il~~l~~---~g~v~v~eLa~~~~VS~~TIRRDL~ 41 (253)
T COG1349 4 EERHQKILELLKE---KGKVSVEELAELFGVSEMTIRRDLN 41 (253)
T ss_pred HHHHHHHHHHHHH---cCcEEHHHHHHHhCCCHHHHHHhHH
Confidence 4577888877551 3468999999999999999998543
No 459
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=45.73 E-value=31 Score=26.92 Aligned_cols=26 Identities=23% Similarity=0.213 Sum_probs=22.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010327 471 DRTLGEIAGNLNISREMVRKHEVKGL 496 (513)
Q Consensus 471 ~~Tl~EIA~~LgISrerVRqi~~rAL 496 (513)
+.|+.+||+.+|+|...+.++..+..
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~ 26 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKET 26 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHh
Confidence 36899999999999999988877653
No 460
>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=45.61 E-value=15 Score=32.48 Aligned_cols=27 Identities=30% Similarity=0.454 Sum_probs=24.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGLMK 498 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rALkK 498 (513)
||..|+|+.+|||..++|-++...|-.
T Consensus 1 ~~I~eva~~~gvs~~tLRyYe~~GLl~ 27 (123)
T cd04770 1 MKIGELAKAAGVSPDTIRYYERIGLLP 27 (123)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 588999999999999999999887765
No 461
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=45.57 E-value=28 Score=33.83 Aligned_cols=39 Identities=15% Similarity=0.242 Sum_probs=28.8
Q ss_pred HHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 457 SLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 457 r~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
..|+...| ..++..+..++|+.||||+..|| .||.+|..
T Consensus 18 ~~I~~g~l--~pG~~L~e~eLae~lgVSRtpVR----EAL~~L~~ 56 (224)
T PRK11534 18 NDIIRGNF--QPDEKLRMSLLTSRYALGVGPLR----EALSQLVA 56 (224)
T ss_pred HHHHhCCC--CCCCcCCHHHHHHHHCCChHHHH----HHHHHHHH
Confidence 34555554 23467889999999999999988 67777764
No 462
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=45.53 E-value=28 Score=27.52 Aligned_cols=19 Identities=21% Similarity=0.289 Sum_probs=17.2
Q ss_pred CHHHHHHHhCCCHHHHHHH
Q 010327 473 TLGEIAGNLNISREMVRKH 491 (513)
Q Consensus 473 Tl~EIA~~LgISrerVRqi 491 (513)
+...+|+.||||+.+|.++
T Consensus 11 ~~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 11 GQSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp SHHHHHHHHTS-HHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHh
Confidence 7889999999999999999
No 463
>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=45.51 E-value=15 Score=32.09 Aligned_cols=26 Identities=23% Similarity=0.443 Sum_probs=23.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGLM 497 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rALk 497 (513)
+|..|+|+.+|||..++|.++..++-
T Consensus 1 y~Ige~A~~~gvs~~tlR~ye~~GLl 26 (107)
T cd01111 1 YSISQLALDAGVSVHIVRDYLLRGLL 26 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999998764
No 464
>PRK11050 manganese transport regulator MntR; Provisional
Probab=45.50 E-value=31 Score=31.99 Aligned_cols=26 Identities=27% Similarity=0.319 Sum_probs=21.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
.++.+..|||+.||||+++|++.+.+
T Consensus 49 ~~~~t~~eLA~~l~is~stVsr~l~~ 74 (152)
T PRK11050 49 VGEARQVDIAARLGVSQPTVAKMLKR 74 (152)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 35789999999999999999865544
No 465
>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=45.39 E-value=19 Score=28.62 Aligned_cols=26 Identities=31% Similarity=0.401 Sum_probs=20.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
....|+.|||..||+|+++|+..+..
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 45789999999999999999977654
No 466
>PRK13705 plasmid-partitioning protein SopA; Provisional
Probab=45.03 E-value=26 Score=37.58 Aligned_cols=56 Identities=20% Similarity=0.249 Sum_probs=41.0
Q ss_pred HHHHHHHHHhcCCHHHHHHHhHHhcCC------CCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010327 441 LRLALDDVLDSLKPKESLVIRQRFGLD------GKGDRTLGEIAGNLNISREMVRKHEVKGL 496 (513)
Q Consensus 441 l~~~L~~aL~~L~~rEr~VL~lRyGL~------~~~~~Tl~EIA~~LgISrerVRqi~~rAL 496 (513)
+...++++++.++...+.+...-|+=+ ....++..|+|+.+|||..+||..+..++
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~k~~r~~~i~e~A~~~gvs~~tiR~ye~~gl 64 (388)
T PRK13705 3 LMETLNQCINAGHEMTKAIAIAQFNDDSPEARKITRRWRIGEAADLVGVSSQAIRDAEKAGR 64 (388)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCcCCCccccccCCCCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 345677777777777777776655111 01346889999999999999999987765
No 467
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=44.99 E-value=29 Score=31.56 Aligned_cols=29 Identities=17% Similarity=0.218 Sum_probs=23.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
++..|..+||+.+|||+..|+ +++.+|++
T Consensus 23 g~~~s~~~ia~~~~is~~~vr----k~l~~L~~ 51 (141)
T PRK11014 23 GRMTSISEVTEVYGVSRNHMV----KIINQLSR 51 (141)
T ss_pred CCccCHHHHHHHHCcCHHHHH----HHHHHHHh
Confidence 346799999999999988888 55666665
No 468
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=44.79 E-value=29 Score=34.49 Aligned_cols=38 Identities=24% Similarity=0.327 Sum_probs=28.2
Q ss_pred HHHhHHhcCCCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 458 LVIRQRFGLDGKGDR-TLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 458 ~VL~lRyGL~~~~~~-Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
.|+...| ..++.+ |-.|+|+.||||+..|| .||+.|..
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 4554444 234567 78999999999999998 67777764
No 469
>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=44.64 E-value=39 Score=24.87 Aligned_cols=27 Identities=30% Similarity=0.262 Sum_probs=22.4
Q ss_pred hCCCCCHHHHHHhcCCCHHHHHHHHHh
Q 010327 376 LKRVPTDEEIIQGVNISPERYREVMKA 402 (513)
Q Consensus 376 lgR~PT~eELA~~lgis~e~v~~~l~~ 402 (513)
+...-|..|||+.+|+|...|+.+...
T Consensus 17 y~~~~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 17 YFEGLTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp HTST-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred hcCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 466778999999999999999988654
No 470
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=44.53 E-value=33 Score=32.12 Aligned_cols=42 Identities=24% Similarity=0.187 Sum_probs=28.3
Q ss_pred CCHHHHHHHhHHhcCC-CCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 452 LKPKESLVIRQRFGLD-GKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 452 L~~rEr~VL~lRyGL~-~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
+++....-|...|-|. +.......+||+.||||+.+|.+.++
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 3444444444444332 34568999999999999999986543
No 471
>PRK10161 transcriptional regulator PhoB; Provisional
Probab=44.49 E-value=25 Score=33.20 Aligned_cols=50 Identities=12% Similarity=0.089 Sum_probs=39.5
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHH-----HHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTLGEI-----AGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EI-----A~~LgISrerVRqi~~rALkKLR~ 501 (513)
.|+++|.+||.+-.- ..++..|.++| |..++++..+|+.+..+.++||..
T Consensus 154 ~Lt~~E~~ll~~l~~-~~~~~~s~~~l~~~~~~~~~~~~~~tv~~~i~rlr~Kl~~ 208 (229)
T PRK10161 154 EMGPTEFKLLHFFMT-HPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEP 208 (229)
T ss_pred EcCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhcc
Confidence 599999999977652 22356787776 446788999999999999999974
No 472
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=44.30 E-value=28 Score=32.97 Aligned_cols=26 Identities=8% Similarity=0.023 Sum_probs=23.3
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010327 469 KGDRTLGEIAGNLNISREMVRKHEVK 494 (513)
Q Consensus 469 ~~~~Tl~EIA~~LgISrerVRqi~~r 494 (513)
..++|+.++|+.+|||+++|+++++.
T Consensus 18 ~~glt~~elA~~~gis~~~is~~E~g 43 (185)
T PRK09943 18 QQGLSQRRAAELSGLTHSAISTIEQD 43 (185)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 35789999999999999999999864
No 473
>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=44.26 E-value=43 Score=30.25 Aligned_cols=23 Identities=17% Similarity=0.180 Sum_probs=20.6
Q ss_pred CHHHHHHhcCCCHHHHHHHHHhc
Q 010327 381 TDEEIIQGVNISPERYREVMKAS 403 (513)
Q Consensus 381 T~eELA~~lgis~e~v~~~l~~~ 403 (513)
|.+|||+.+|++.+.|....+..
T Consensus 2 T~eELA~~tG~srQTINrWvRke 24 (122)
T PF07037_consen 2 TPEELAELTGYSRQTINRWVRKE 24 (122)
T ss_pred CHHHHHHHhCccHHHHHHHHHhc
Confidence 68999999999999999988753
No 474
>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=44.13 E-value=28 Score=37.99 Aligned_cols=47 Identities=17% Similarity=0.212 Sum_probs=32.7
Q ss_pred HHHhcCCHHHHHHHhH------------HhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 447 DVLDSLKPKESLVIRQ------------RFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 447 ~aL~~L~~rEr~VL~l------------RyGL~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
.++..|.-|...+++. .+|-..-.++|+++||+.+|++.+||++..+
T Consensus 282 ~li~~i~~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdiA~~lglheSTVSRav~ 340 (429)
T TIGR02395 282 WLIKALEQREETLLKVAEAIVEHQKDFFLGGPAALKPLTLREVAEELGLHESTISRAIN 340 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccCcCCcHHHHHHHhCCCccchhhhhc
Confidence 3445566666665532 2332234799999999999999999997653
No 475
>PRK03837 transcriptional regulator NanR; Provisional
Probab=43.98 E-value=31 Score=33.68 Aligned_cols=38 Identities=21% Similarity=0.320 Sum_probs=27.8
Q ss_pred HHHhHHhcCCCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 458 LVIRQRFGLDGKGDR-TLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 458 ~VL~lRyGL~~~~~~-Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
.|+...| ..++.. +..++|+.||||+..|| .||..|..
T Consensus 25 ~I~~g~l--~pG~~Lp~E~~Lae~~gVSRt~VR----EAL~~L~~ 63 (241)
T PRK03837 25 MIRSGEF--GPGDQLPSERELMAFFGVGRPAVR----EALQALKR 63 (241)
T ss_pred HHHhCCC--CCCCCCCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 3444444 224567 89999999999999999 67777763
No 476
>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=43.81 E-value=27 Score=24.19 Aligned_cols=22 Identities=18% Similarity=0.357 Sum_probs=17.5
Q ss_pred CHHHHHHhcCCCHHHHHHHHHh
Q 010327 381 TDEEIIQGVNISPERYREVMKA 402 (513)
Q Consensus 381 T~eELA~~lgis~e~v~~~l~~ 402 (513)
|-++||+.+|++.+.|..++..
T Consensus 4 tr~diA~~lG~t~ETVSR~l~~ 25 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVSRILKK 25 (32)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHH
T ss_pred CHHHHHHHhCCcHHHHHHHHHH
Confidence 4579999999999999988754
No 477
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=43.78 E-value=16 Score=32.86 Aligned_cols=27 Identities=41% Similarity=0.535 Sum_probs=23.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGLMK 498 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rALkK 498 (513)
+|..|+|+.+|||..++|.++...+-.
T Consensus 2 ysI~eVA~~~GVs~~TLR~wE~~GLl~ 28 (120)
T cd04767 2 YPIGVVAELLNIHPETLRIWERHGLIK 28 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 689999999999999999998876543
No 478
>PRK10643 DNA-binding transcriptional regulator BasR; Provisional
Probab=43.56 E-value=26 Score=32.55 Aligned_cols=47 Identities=21% Similarity=0.138 Sum_probs=35.6
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCH-HHHH-H-----HhCCCHHHHHHHHHHHHHHHh
Q 010327 451 SLKPKESLVIRQRFGLDGKGDRTL-GEIA-G-----NLNISREMVRKHEVKGLMKLK 500 (513)
Q Consensus 451 ~L~~rEr~VL~lRyGL~~~~~~Tl-~EIA-~-----~LgISrerVRqi~~rALkKLR 500 (513)
.|+++|.+|+.+..- ..++++ .||+ + .+++|..+|+.+..+.++||.
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 599999999987641 234443 4444 3 368999999999999999996
No 479
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=43.34 E-value=34 Score=37.98 Aligned_cols=46 Identities=13% Similarity=0.231 Sum_probs=33.7
Q ss_pred HHhcCCHHHHHHHhH------------HhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 448 VLDSLKPKESLVIRQ------------RFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 448 aL~~L~~rEr~VL~l------------RyGL~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
++..|..|.+.+++. .+|...-.++|+++||+.+|+..+||++...
T Consensus 334 li~si~qR~~TllkV~~~Iv~~Q~~Ff~~G~~~LkPLtlkdVAe~lglHeSTVSRa~~ 391 (481)
T PRK12469 334 LIRNAQQRFDTIQRVAECIVARQRDFFRYGEIALKPLVLRDVAEELGLHESTISRATG 391 (481)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCcCCcHHHHHHHhCCCcchhhHHhc
Confidence 456677777766542 2343345789999999999999999997653
No 480
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=43.15 E-value=34 Score=34.40 Aligned_cols=37 Identities=14% Similarity=0.233 Sum_probs=28.1
Q ss_pred HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 454 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 454 ~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
+|...|+.+-- .....+..|+|+.||||.+|||+-+.
T Consensus 5 ~R~~~Il~~l~---~~~~~~~~ela~~l~vS~~TiRRdL~ 41 (252)
T PRK10906 5 QRHDAIIELVK---QQGYVSTEELVEHFSVSPQTIRRDLN 41 (252)
T ss_pred HHHHHHHHHHH---HcCCEeHHHHHHHhCCCHHHHHHHHH
Confidence 46666665543 13468999999999999999999644
No 481
>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=43.14 E-value=70 Score=24.38 Aligned_cols=24 Identities=21% Similarity=0.246 Sum_probs=21.1
Q ss_pred CCCHHHHHHhcCCCHHHHHHHHHh
Q 010327 379 VPTDEEIIQGVNISPERYREVMKA 402 (513)
Q Consensus 379 ~PT~eELA~~lgis~e~v~~~l~~ 402 (513)
..+..+||+.+|++...+..+++.
T Consensus 25 ~~s~~ela~~~g~s~~tv~r~l~~ 48 (67)
T cd00092 25 PLTRQEIADYLGLTRETVSRTLKE 48 (67)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHH
Confidence 468899999999999999988764
No 482
>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=43.10 E-value=1.9e+02 Score=29.10 Aligned_cols=26 Identities=27% Similarity=0.308 Sum_probs=21.8
Q ss_pred CCCCCHHHHHHhcCCCHHHHHHHHHh
Q 010327 377 KRVPTDEEIIQGVNISPERYREVMKA 402 (513)
Q Consensus 377 gR~PT~eELA~~lgis~e~v~~~l~~ 402 (513)
+..-|..|||+.+|+|..+|+.+...
T Consensus 234 ~~~~t~~eIA~~lgvS~~~V~q~~~~ 259 (270)
T TIGR02392 234 DDKLTLQELAAEYGVSAERIRQIEKN 259 (270)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 34568999999999999999987654
No 483
>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=42.92 E-value=17 Score=32.17 Aligned_cols=26 Identities=27% Similarity=0.394 Sum_probs=23.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGLM 497 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rALk 497 (513)
||..|+|+.+|||..++|-++...|-
T Consensus 1 m~IgevA~~~gvs~~tlRyYe~~GLl 26 (120)
T cd04781 1 LDIAEVARQSGLPASTLRYYEEKGLI 26 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 58899999999999999999987653
No 484
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=42.85 E-value=47 Score=28.90 Aligned_cols=44 Identities=18% Similarity=0.246 Sum_probs=32.7
Q ss_pred cCCHHHH-HHHhHHhcCCCCCCCCHHHHHHHhCC-CHHHHHHHHHHHHHH
Q 010327 451 SLKPKES-LVIRQRFGLDGKGDRTLGEIAGNLNI-SREMVRKHEVKGLMK 498 (513)
Q Consensus 451 ~L~~rEr-~VL~lRyGL~~~~~~Tl~EIA~~LgI-SrerVRqi~~rALkK 498 (513)
..|+..+ +|+.+++ ..+.|+.+||..+|| +.+.++++.......
T Consensus 7 ~~s~EfK~~iv~~~~----~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~ 52 (116)
T COG2963 7 KYSPEFKLEAVALYL----RGGDTVSEVAREFGIVSATQLYKWRIQLQKG 52 (116)
T ss_pred cCCHHHHHHHHHHHH----hcCccHHHHHHHhCCCChHHHHHHHHHHHHc
Confidence 4555555 5566666 467899999999996 999988877766553
No 485
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=42.77 E-value=32 Score=34.04 Aligned_cols=38 Identities=18% Similarity=0.350 Sum_probs=27.9
Q ss_pred HHHhHHhcCCCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 458 LVIRQRFGLDGKGDR-TLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 458 ~VL~lRyGL~~~~~~-Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
.|+...| ..++.. |-.++|+.||||+..|| .||..|..
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 4444444 224566 89999999999999999 67777764
No 486
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=42.68 E-value=32 Score=34.17 Aligned_cols=38 Identities=29% Similarity=0.445 Sum_probs=28.2
Q ss_pred HHHhHHhcCCCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 458 LVIRQRFGLDGKGDR-TLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 458 ~VL~lRyGL~~~~~~-Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
.|+...|. .++.+ |-.++|+.||||+..|| .||..|..
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 44544442 24567 68999999999999999 67777764
No 487
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=42.42 E-value=18 Score=32.17 Aligned_cols=25 Identities=32% Similarity=0.478 Sum_probs=22.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGL 496 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rAL 496 (513)
+|..|+|+.+|||..++|-++..+|
T Consensus 1 ~~Igeva~~~gvs~~tlRyYe~~GL 25 (118)
T cd04776 1 YTISELAREFDVTPRTLRFYEDKGL 25 (118)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999988765
No 488
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=42.33 E-value=38 Score=32.51 Aligned_cols=37 Identities=14% Similarity=0.072 Sum_probs=27.6
Q ss_pred HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 454 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 454 ~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
+|++.|+.+-- ..+..+..++|+.||||.+|||+-+.
T Consensus 7 ~R~~~Il~~l~---~~~~~~~~~La~~~~vS~~TiRRDl~ 43 (185)
T PRK04424 7 ERQKALQELIE---ENPFITDEELAEKFGVSIQTIRLDRM 43 (185)
T ss_pred HHHHHHHHHHH---HCCCEEHHHHHHHHCcCHHHHHHHHH
Confidence 45666655433 14568999999999999999997654
No 489
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=42.17 E-value=27 Score=34.22 Aligned_cols=26 Identities=35% Similarity=0.365 Sum_probs=22.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
-|-.|+|+.||||+.||| +|+..|..
T Consensus 25 PsE~eLa~~~gVSR~TVR----~Al~~L~~ 50 (233)
T TIGR02404 25 PSEHELMDQYGASRETVR----KALNLLTE 50 (233)
T ss_pred cCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 589999999999999999 67777754
No 490
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=42.12 E-value=61 Score=23.82 Aligned_cols=27 Identities=11% Similarity=0.251 Sum_probs=22.3
Q ss_pred hCCCCCHHHHHHhcCCCHHHHHHHHHh
Q 010327 376 LKRVPTDEEIIQGVNISPERYREVMKA 402 (513)
Q Consensus 376 lgR~PT~eELA~~lgis~e~v~~~l~~ 402 (513)
+...+|..+||..+|++...|..++..
T Consensus 24 ~~~~~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 24 LRESRSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HhhcCCHHHHHHHHCCCHHHHHHHHHh
Confidence 334478999999999999999988753
No 491
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=42.12 E-value=72 Score=23.13 Aligned_cols=24 Identities=21% Similarity=0.249 Sum_probs=19.0
Q ss_pred CCCHHHHHHhcCCCHHHHHHHHHh
Q 010327 379 VPTDEEIIQGVNISPERYREVMKA 402 (513)
Q Consensus 379 ~PT~eELA~~lgis~e~v~~~l~~ 402 (513)
..|..|||+.+|+|...+...++.
T Consensus 17 ~~t~~ela~~~~is~~tv~~~l~~ 40 (48)
T PF13412_consen 17 RITQKELAEKLGISRSTVNRYLKK 40 (48)
T ss_dssp TS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHH
Confidence 388999999999999999888754
No 492
>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=42.05 E-value=56 Score=30.92 Aligned_cols=58 Identities=21% Similarity=0.235 Sum_probs=44.8
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHhHHhcC--C--CCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010327 438 PALLRLALDDVLDSLKPKESLVIRQRFGL--D--GKGDRTLGEIAGNLNISREMVRKHEVKG 495 (513)
Q Consensus 438 ~~~l~~~L~~aL~~L~~rEr~VL~lRyGL--~--~~~~~Tl~EIA~~LgISrerVRqi~~rA 495 (513)
+++.-..|+..|..||+.|++=+.-+|-= + +.+++|-+||.+.||=+++-++++...-
T Consensus 3 k~efL~~L~~~L~~lp~~e~~e~l~~Y~e~f~d~~~~G~sEeeii~~LG~P~~iA~~i~~~~ 64 (181)
T PF08006_consen 3 KNEFLNELEKYLKKLPEEEREEILEYYEEYFDDAGEEGKSEEEIIAELGSPKEIAREILAEY 64 (181)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHcCCHHHHHHHHHHhh
Confidence 34556678888999999998877666632 1 2357899999999999999999987543
No 493
>PRK06030 hypothetical protein; Provisional
Probab=42.04 E-value=68 Score=29.12 Aligned_cols=41 Identities=10% Similarity=-0.070 Sum_probs=30.2
Q ss_pred HHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010327 455 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 499 (513)
Q Consensus 455 rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKL 499 (513)
|+-.+...+- .-++|+.+||+.||-+.+||..-..+.-+.+
T Consensus 57 RqIAMYL~r~----~~~~sl~~IG~~FGRDHSTV~haikkIe~~~ 97 (124)
T PRK06030 57 RQIAMYVAHV----SLGWPMNEVALAFGRDRTTVGHACHTVEDLR 97 (124)
T ss_pred HHHHHHHHHH----HcCCCHHHHHHHHCCChhHHHHHHHHHHHHh
Confidence 4444444444 4689999999999999999998888555544
No 494
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=42.02 E-value=2.4e+02 Score=27.94 Aligned_cols=31 Identities=26% Similarity=0.414 Sum_probs=23.3
Q ss_pred HHHHHHHHhCCCCCHHHHHHHccCCHHHHHH
Q 010327 237 VKEQLQKDLGREPTDVELAEATNMSAAQVKK 267 (513)
Q Consensus 237 ~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~ 267 (513)
....+...+++.|+..++|...|++.+.+..
T Consensus 121 ~~~~~~~~~~r~~~~~e~a~~~~~~~~~~~~ 151 (257)
T PRK08583 121 AVDELTTELQRSPKISEIADRLGVSEEEVLE 151 (257)
T ss_pred HHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 3344666778999999999988888766543
No 495
>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=41.95 E-value=40 Score=30.14 Aligned_cols=39 Identities=21% Similarity=0.246 Sum_probs=34.8
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
..|.+.++.|+.+.- ...|..|||..|+++..-||-+..
T Consensus 39 ~~l~pE~~~Il~lC~-----~~~SVAEiAA~L~lPlgVvrVLvs 77 (114)
T PF05331_consen 39 AGLGPEHRAILELCR-----RPLSVAEIAARLGLPLGVVRVLVS 77 (114)
T ss_pred CCCCHHHHHHHHHHC-----CCccHHHHHHhhCCCchhhhhhHH
Confidence 579999999999987 499999999999999999987764
No 496
>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=41.93 E-value=25 Score=34.31 Aligned_cols=26 Identities=19% Similarity=0.340 Sum_probs=22.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGLMKLKH 501 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rALkKLR~ 501 (513)
-|-.|+|+.+|||+.||| +||..|..
T Consensus 33 PsE~eLa~~~~VSR~TvR----~Al~~L~~ 58 (238)
T TIGR02325 33 PAEMQLAERFGVNRHTVR----RAIAALVE 58 (238)
T ss_pred cCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 489999999999999999 67777764
No 497
>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=41.76 E-value=8.6 Score=36.33 Aligned_cols=47 Identities=17% Similarity=0.176 Sum_probs=0.0
Q ss_pred HHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010327 445 LDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493 (513)
Q Consensus 445 L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~ 493 (513)
|..+...|=..|..-|.. |-....++|+++||+.+|++.+||++...
T Consensus 25 L~~v~~~iv~~Q~~ff~~--g~~~l~PLt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 25 LLRVAQAIVERQKDFFLG--GPGALKPLTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp -------------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHhc--CcccCcCCCHHHHHHHhCCCHhHHHHHHc
Confidence 444445555566665442 32235799999999999999999997654
No 498
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=41.57 E-value=50 Score=32.03 Aligned_cols=47 Identities=11% Similarity=-0.027 Sum_probs=30.8
Q ss_pred CCHHHHHHHhHHhcC-CCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010327 452 LKPKESLVIRQRFGL-DGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502 (513)
Q Consensus 452 L~~rEr~VL~lRyGL-~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~ 502 (513)
++.++|.+-.+..-- .+.-+.|.++||..+|+|+++|. |+|++|++.
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 366666654443211 11234689999999999999988 566677653
No 499
>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=41.01 E-value=53 Score=26.63 Aligned_cols=34 Identities=24% Similarity=0.264 Sum_probs=30.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010327 472 RTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV 505 (513)
Q Consensus 472 ~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~ 505 (513)
-.+.+||+..+++.+.|++.....+..|+.-.+.
T Consensus 8 e~i~~iA~~t~~P~e~V~~my~dt~~~l~~~ARV 41 (66)
T PF12085_consen 8 EVIRSIAEETGTPAETVRRMYDDTMRELSSGARV 41 (66)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHHHHcCCch
Confidence 3578999999999999999999999999987764
No 500
>COG1481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.53 E-value=53 Score=34.32 Aligned_cols=43 Identities=26% Similarity=0.208 Sum_probs=35.8
Q ss_pred HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCC--CHHHHHHHHHH
Q 010327 449 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNI--SREMVRKHEVK 494 (513)
Q Consensus 449 L~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgI--SrerVRqi~~r 494 (513)
|+.||+..+++-.+|.- ..+.|++|||+.+.. |++.|.-+..|
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 47899999999999883 578999999999987 88888755544
Done!