Query 009803
Match_columns 525
No_of_seqs 432 out of 2431
Neff 6.2
Searched_HMMs 46136
Date Thu Mar 28 17:31:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009803.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009803hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK07598 RNA polymerase sigma 100.0 1.6E-65 3.6E-70 540.6 38.3 312 210-523 58-412 (415)
2 PRK07406 RNA polymerase sigma 100.0 2.8E-63 6.1E-68 520.0 38.5 311 210-522 61-372 (373)
3 PRK05949 RNA polymerase sigma 100.0 5.5E-62 1.2E-66 504.1 38.6 310 210-523 16-326 (327)
4 TIGR02997 Sig70-cyanoRpoD RNA 100.0 2.4E-61 5.2E-66 493.8 35.6 297 212-510 1-298 (298)
5 PRK07405 RNA polymerase sigma 100.0 5.4E-61 1.2E-65 495.1 38.2 309 211-523 7-316 (317)
6 COG0568 RpoD DNA-directed RNA 100.0 1.2E-60 2.5E-65 489.5 30.7 312 211-523 8-342 (342)
7 PRK05901 RNA polymerase sigma 100.0 3.8E-60 8.3E-65 510.8 33.1 302 208-523 207-509 (509)
8 PRK07921 RNA polymerase sigma 100.0 3.8E-59 8.2E-64 482.0 34.9 300 210-523 24-324 (324)
9 PRK09210 RNA polymerase sigma 100.0 3.6E-55 7.8E-60 460.1 33.5 273 210-523 94-367 (367)
10 PRK05658 RNA polymerase sigma 100.0 2.7E-52 5.9E-57 464.7 31.9 270 216-523 349-618 (619)
11 TIGR02393 RpoD_Cterm RNA polym 100.0 4.5E-48 9.8E-53 383.5 27.3 238 286-523 1-238 (238)
12 PRK07500 rpoH2 RNA polymerase 100.0 2.8E-45 6E-50 373.9 31.8 262 212-516 6-280 (289)
13 PRK06596 RNA polymerase factor 100.0 4.3E-45 9.4E-50 371.6 32.0 261 210-515 12-282 (284)
14 PRK05657 RNA polymerase sigma 100.0 2.1E-44 4.6E-49 372.9 33.1 268 211-519 52-320 (325)
15 TIGR02392 rpoH_proteo alternat 100.0 1.8E-44 3.9E-49 364.4 30.9 257 213-514 2-269 (270)
16 PRK07122 RNA polymerase sigma 100.0 7.4E-44 1.6E-48 359.0 27.7 221 284-513 39-263 (264)
17 PRK07408 RNA polymerase sigma 100.0 3.3E-42 7.2E-47 345.4 30.6 227 282-515 22-253 (256)
18 TIGR02394 rpoS_proteo RNA poly 100.0 8E-41 1.7E-45 340.2 33.2 271 207-518 8-279 (285)
19 TIGR02850 spore_sigG RNA polym 100.0 7E-41 1.5E-45 335.2 29.7 242 221-512 10-253 (254)
20 PRK05911 RNA polymerase sigma 100.0 2.6E-40 5.6E-45 332.0 28.1 227 282-515 20-255 (257)
21 PRK08215 sporulation sigma fac 100.0 3.5E-39 7.6E-44 323.5 30.2 242 222-513 14-257 (258)
22 COG1191 FliA DNA-directed RNA 100.0 1.5E-38 3.2E-43 315.4 28.0 222 282-514 21-245 (247)
23 PRK06288 RNA polymerase sigma 100.0 5.1E-38 1.1E-42 316.9 30.1 249 221-515 6-262 (268)
24 TIGR02941 Sigma_B RNA polymera 100.0 2.8E-37 6E-42 309.0 30.4 245 224-513 7-253 (255)
25 TIGR02885 spore_sigF RNA polym 100.0 3.8E-37 8.3E-42 303.4 27.8 223 281-513 7-231 (231)
26 TIGR02980 SigBFG RNA polymeras 100.0 1.4E-36 3.1E-41 298.3 27.5 221 284-513 2-226 (227)
27 PRK07670 RNA polymerase sigma 100.0 5.3E-36 1.1E-40 299.4 29.9 226 282-514 19-250 (251)
28 PRK08583 RNA polymerase sigma 100.0 2.7E-35 5.8E-40 295.0 29.7 248 223-515 6-255 (257)
29 PRK05572 sporulation sigma fac 100.0 4.4E-35 9.6E-40 292.9 29.6 241 222-514 9-251 (252)
30 TIGR02479 FliA_WhiG RNA polyme 100.0 2.7E-35 5.9E-40 289.1 26.2 217 290-513 1-223 (224)
31 PRK12427 flagellar biosynthesi 100.0 1.5E-34 3.2E-39 286.2 26.9 210 286-512 16-230 (231)
32 PRK06986 fliA flagellar biosyn 100.0 7.4E-34 1.6E-38 281.2 27.9 225 282-515 5-234 (236)
33 PRK05803 sporulation sigma fac 100.0 3.3E-28 7.1E-33 240.6 25.7 209 213-515 17-229 (233)
34 PRK08301 sporulation sigma fac 99.9 5.7E-25 1.2E-29 217.2 24.0 180 282-514 49-231 (234)
35 TIGR02846 spore_sigmaK RNA pol 99.9 7.5E-25 1.6E-29 215.9 24.0 205 216-513 19-226 (227)
36 TIGR02835 spore_sigmaE RNA pol 99.9 5.7E-24 1.2E-28 210.6 24.0 180 282-514 49-231 (234)
37 PRK08295 RNA polymerase factor 99.9 6.4E-23 1.4E-27 197.9 21.5 189 277-517 16-206 (208)
38 PRK05602 RNA polymerase sigma 99.9 3.3E-22 7.3E-27 190.2 21.8 170 276-517 11-180 (186)
39 PRK09646 RNA polymerase sigma 99.9 3.5E-22 7.6E-27 191.8 21.2 174 274-515 18-192 (194)
40 TIGR02948 SigW_bacill RNA poly 99.9 4.7E-22 1E-26 188.4 20.3 180 273-514 6-185 (187)
41 PRK12513 RNA polymerase sigma 99.9 3.5E-22 7.7E-27 191.3 19.1 179 273-518 14-192 (194)
42 PRK09648 RNA polymerase sigma 99.9 1.2E-21 2.7E-26 186.8 22.7 165 281-514 20-188 (189)
43 TIGR02859 spore_sigH RNA polym 99.9 6.1E-22 1.3E-26 189.5 20.2 189 273-513 6-197 (198)
44 PRK09641 RNA polymerase sigma 99.9 1.3E-21 2.8E-26 185.3 21.4 175 278-514 11-185 (187)
45 PRK09652 RNA polymerase sigma 99.9 1.5E-21 3.2E-26 183.0 20.5 174 279-514 4-177 (182)
46 PRK11922 RNA polymerase sigma 99.9 1.3E-21 2.8E-26 193.4 20.6 193 222-515 7-199 (231)
47 TIGR02952 Sig70_famx2 RNA poly 99.9 2.7E-21 5.8E-26 180.2 20.3 165 280-513 6-170 (170)
48 PRK06759 RNA polymerase factor 99.9 1.2E-21 2.7E-26 180.1 17.0 151 284-512 3-153 (154)
49 PRK12519 RNA polymerase sigma 99.9 2.6E-21 5.5E-26 185.2 19.7 170 277-514 21-190 (194)
50 PRK12514 RNA polymerase sigma 99.9 5.3E-21 1.1E-25 180.7 20.8 169 276-514 10-178 (179)
51 PRK12524 RNA polymerase sigma 99.9 5.7E-21 1.2E-25 183.7 21.4 173 275-517 16-188 (196)
52 TIGR02939 RpoE_Sigma70 RNA pol 99.9 6.7E-21 1.5E-25 180.9 21.3 177 276-514 11-187 (190)
53 PRK06811 RNA polymerase factor 99.9 7.6E-21 1.6E-25 181.8 21.4 173 272-514 4-180 (189)
54 PRK13919 putative RNA polymera 99.9 6E-21 1.3E-25 181.2 19.8 170 277-514 15-184 (186)
55 PRK11923 algU RNA polymerase s 99.9 1.1E-20 2.3E-25 180.7 21.5 175 278-514 13-187 (193)
56 PRK12537 RNA polymerase sigma 99.9 7.9E-21 1.7E-25 180.5 20.4 169 275-513 13-181 (182)
57 PRK12534 RNA polymerase sigma 99.9 7.5E-21 1.6E-25 180.9 19.6 171 276-514 16-186 (187)
58 PRK12538 RNA polymerase sigma 99.9 9.4E-21 2E-25 187.9 20.6 165 281-517 59-223 (233)
59 PRK12542 RNA polymerase sigma 99.9 3.6E-21 7.9E-26 183.1 16.8 175 281-522 5-179 (185)
60 PRK09640 RNA polymerase sigma 99.9 4.3E-21 9.4E-26 183.2 16.8 172 271-514 8-183 (188)
61 PRK11924 RNA polymerase sigma 99.9 2.7E-20 5.8E-25 174.0 21.5 170 279-516 7-176 (179)
62 TIGR02984 Sig-70_plancto1 RNA 99.9 1.8E-20 3.9E-25 177.6 20.6 179 282-513 4-188 (189)
63 PRK12515 RNA polymerase sigma 99.9 2.3E-20 5.1E-25 178.1 21.0 174 274-518 11-184 (189)
64 PRK12526 RNA polymerase sigma 99.9 2.4E-20 5.1E-25 181.1 20.1 172 280-516 33-204 (206)
65 PRK12543 RNA polymerase sigma 99.9 3E-20 6.4E-25 176.1 19.7 165 282-516 4-168 (179)
66 PRK09645 RNA polymerase sigma 99.9 4.9E-20 1.1E-24 173.0 19.4 164 282-516 6-169 (173)
67 PRK09643 RNA polymerase sigma 99.8 7.9E-20 1.7E-24 175.5 20.6 171 272-515 13-184 (192)
68 TIGR02937 sigma70-ECF RNA poly 99.8 7E-20 1.5E-24 164.7 18.5 157 286-513 2-158 (158)
69 PRK09638 RNA polymerase sigma 99.8 4.3E-20 9.4E-25 173.7 17.8 166 277-514 10-175 (176)
70 TIGR02985 Sig70_bacteroi1 RNA 99.8 3.2E-20 6.9E-25 170.3 16.3 160 286-513 2-161 (161)
71 PRK12531 RNA polymerase sigma 99.8 6.6E-20 1.4E-24 176.0 19.1 175 277-517 19-193 (194)
72 TIGR02954 Sig70_famx3 RNA poly 99.8 1E-19 2.2E-24 170.4 19.6 162 276-514 7-168 (169)
73 PRK09415 RNA polymerase factor 99.8 1E-19 2.2E-24 172.6 19.0 165 282-515 13-177 (179)
74 PRK12536 RNA polymerase sigma 99.8 7.7E-20 1.7E-24 173.6 18.3 168 275-515 11-179 (181)
75 PRK12522 RNA polymerase sigma 99.8 1.1E-19 2.4E-24 171.0 19.1 167 285-515 3-169 (173)
76 TIGR03001 Sig-70_gmx1 RNA poly 99.8 2.2E-19 4.7E-24 179.4 22.1 183 270-521 23-217 (244)
77 PRK12520 RNA polymerase sigma 99.8 1.5E-19 3.3E-24 172.8 19.5 181 286-517 3-183 (191)
78 COG1595 RpoE DNA-directed RNA 99.8 2.8E-19 6.1E-24 170.0 20.5 172 277-516 7-178 (182)
79 PRK12539 RNA polymerase sigma 99.8 2.6E-19 5.7E-24 170.4 19.6 165 277-515 13-181 (184)
80 PRK12533 RNA polymerase sigma 99.8 4.1E-19 8.8E-24 174.4 20.8 171 282-516 15-185 (216)
81 TIGR02999 Sig-70_X6 RNA polyme 99.8 3.3E-19 7.2E-24 168.7 19.4 166 279-513 11-182 (183)
82 PRK12529 RNA polymerase sigma 99.8 2.2E-19 4.9E-24 170.2 18.1 165 281-513 9-175 (178)
83 TIGR02989 Sig-70_gvs1 RNA poly 99.8 1E-19 2.2E-24 168.0 15.4 157 286-512 2-158 (159)
84 PRK12518 RNA polymerase sigma 99.8 2E-19 4.3E-24 169.0 17.5 167 279-516 5-171 (175)
85 PRK12512 RNA polymerase sigma 99.8 5.6E-19 1.2E-23 167.6 19.8 163 278-515 15-181 (184)
86 PRK09649 RNA polymerase sigma 99.8 4E-19 8.8E-24 169.6 18.7 167 278-518 17-183 (185)
87 PRK09642 RNA polymerase sigma 99.8 2.8E-19 6E-24 165.8 16.9 156 292-516 2-157 (160)
88 PRK09647 RNA polymerase sigma 99.8 8.7E-19 1.9E-23 170.3 20.6 165 282-516 25-189 (203)
89 TIGR02947 SigH_actino RNA poly 99.8 2.7E-19 5.8E-24 171.4 16.7 173 283-515 9-181 (193)
90 PRK12516 RNA polymerase sigma 99.8 6.9E-19 1.5E-23 168.6 18.9 162 282-517 7-168 (187)
91 TIGR02983 SigE-fam_strep RNA p 99.8 5.6E-19 1.2E-23 164.0 17.2 159 281-515 2-160 (162)
92 PRK12523 RNA polymerase sigma 99.8 5.7E-19 1.2E-23 166.1 17.5 163 282-515 7-169 (172)
93 PRK09644 RNA polymerase sigma 99.8 7.3E-19 1.6E-23 164.1 18.0 157 287-516 3-159 (165)
94 PRK09639 RNA polymerase sigma 99.8 1E-18 2.2E-23 162.6 18.9 160 284-515 2-161 (166)
95 PRK12528 RNA polymerase sigma 99.8 1E-18 2.3E-23 162.3 18.0 158 284-512 3-160 (161)
96 PRK12541 RNA polymerase sigma 99.8 1.8E-18 3.9E-23 160.7 18.7 158 282-512 2-159 (161)
97 TIGR02943 Sig70_famx1 RNA poly 99.8 2.2E-18 4.8E-23 165.0 19.6 178 288-516 5-182 (188)
98 PRK12532 RNA polymerase sigma 99.8 2.2E-18 4.8E-23 165.3 19.6 181 288-518 8-189 (195)
99 PRK12530 RNA polymerase sigma 99.8 2.6E-18 5.6E-23 164.6 19.8 176 288-516 10-185 (189)
100 PRK12547 RNA polymerase sigma 99.8 2.4E-18 5.2E-23 160.8 19.1 158 284-515 5-162 (164)
101 PRK12545 RNA polymerase sigma 99.8 2.7E-18 5.9E-23 166.1 19.4 180 289-517 12-191 (201)
102 TIGR02960 SigX5 RNA polymerase 99.8 2.4E-18 5.1E-23 177.5 19.8 183 282-515 2-192 (324)
103 PRK12535 RNA polymerase sigma 99.8 3.7E-18 8E-23 164.8 19.7 168 277-516 17-184 (196)
104 PRK08241 RNA polymerase factor 99.8 5.1E-18 1.1E-22 176.4 21.7 186 275-511 9-199 (339)
105 PRK12544 RNA polymerase sigma 99.8 6.6E-18 1.4E-22 164.5 20.5 179 287-516 20-199 (206)
106 PRK07037 extracytoplasmic-func 99.8 7.3E-18 1.6E-22 156.6 19.2 158 289-515 2-159 (163)
107 TIGR02950 SigM_subfam RNA poly 99.8 1.3E-18 2.8E-23 159.8 13.3 152 292-513 2-153 (154)
108 PRK12527 RNA polymerase sigma 99.8 7.1E-18 1.5E-22 156.4 17.9 154 292-515 2-155 (159)
109 PRK12517 RNA polymerase sigma 99.8 1.1E-17 2.4E-22 160.3 19.5 161 281-516 19-179 (188)
110 PRK12540 RNA polymerase sigma 99.8 8.7E-18 1.9E-22 160.3 18.6 160 285-518 5-164 (182)
111 TIGR02895 spore_sigI RNA polym 99.8 1E-17 2.2E-22 164.6 19.5 115 282-397 7-126 (218)
112 PRK09637 RNA polymerase sigma 99.8 1.3E-17 2.7E-22 159.0 18.7 154 287-515 3-156 (181)
113 PRK09651 RNA polymerase sigma 99.8 1.3E-17 2.8E-22 157.2 17.7 162 283-515 8-169 (172)
114 PRK12546 RNA polymerase sigma 99.8 2.5E-17 5.4E-22 158.1 18.4 157 284-515 7-163 (188)
115 TIGR02959 SigZ RNA polymerase 99.8 2.6E-17 5.6E-22 155.0 17.8 149 292-515 2-150 (170)
116 PRK12511 RNA polymerase sigma 99.8 3.1E-17 6.6E-22 156.7 17.0 156 287-515 6-161 (182)
117 PRK12525 RNA polymerase sigma 99.7 6.7E-17 1.4E-21 151.7 18.1 159 284-513 8-166 (168)
118 PRK09636 RNA polymerase sigma 99.7 9.5E-17 2.1E-21 164.1 18.4 160 285-514 4-164 (293)
119 PRK09047 RNA polymerase factor 99.7 1.1E-16 2.3E-21 148.1 15.9 155 307-517 2-158 (161)
120 TIGR02957 SigX4 RNA polymerase 99.7 7.2E-16 1.6E-20 156.9 18.4 156 289-514 1-157 (281)
121 PRK06704 RNA polymerase factor 99.7 7.6E-16 1.7E-20 152.5 18.0 159 275-515 8-166 (228)
122 PRK09635 sigI RNA polymerase s 99.7 1.1E-15 2.4E-20 156.4 18.9 161 285-513 5-166 (290)
123 TIGR03209 P21_Cbot clostridium 99.6 6.5E-14 1.4E-18 127.6 13.6 136 287-499 1-141 (142)
124 PRK09191 two-component respons 99.5 1.1E-13 2.5E-18 136.9 14.3 136 286-514 2-137 (261)
125 PRK08311 putative RNA polymera 99.4 1.9E-11 4E-16 121.9 19.0 82 279-360 12-95 (237)
126 PF07638 Sigma70_ECF: ECF sigm 99.4 2.9E-11 6.2E-16 115.9 19.6 172 276-514 8-184 (185)
127 PF04542 Sigma70_r2: Sigma-70 99.3 1.2E-11 2.6E-16 98.7 7.8 70 290-359 1-70 (71)
128 PF04545 Sigma70_r4: Sigma-70, 99.3 1.7E-11 3.7E-16 92.8 7.2 50 458-511 1-50 (50)
129 PF04539 Sigma70_r3: Sigma-70 99.1 1E-10 2.2E-15 96.3 5.7 77 369-445 1-77 (78)
130 PF08281 Sigma70_r4_2: Sigma-7 98.9 2.5E-09 5.5E-14 82.0 7.1 53 453-509 2-54 (54)
131 PRK06930 positive control sigm 98.7 9E-08 1.9E-12 91.0 10.2 70 443-516 96-165 (170)
132 PRK00118 putative DNA-binding 98.5 8E-07 1.7E-11 77.8 9.3 61 453-517 9-69 (104)
133 cd06171 Sigma70_r4 Sigma70, re 98.3 2.2E-06 4.8E-11 63.7 6.8 54 453-510 2-55 (55)
134 PRK04217 hypothetical protein; 98.1 6.3E-06 1.4E-10 72.9 6.8 57 459-519 40-96 (110)
135 TIGR00721 tfx DNA-binding prot 98.1 8.7E-06 1.9E-10 74.7 7.5 58 460-522 5-62 (137)
136 PRK03975 tfx putative transcri 98.0 1.5E-05 3.2E-10 73.6 7.7 51 460-515 5-55 (141)
137 PF00140 Sigma70_r1_2: Sigma-7 98.0 2.4E-06 5.2E-11 61.0 1.9 31 212-243 2-33 (37)
138 PF04297 UPF0122: Putative hel 98.0 3.4E-05 7.3E-10 67.2 8.4 57 455-515 10-67 (101)
139 TIGR01636 phage_rinA phage tra 97.9 5E-05 1.1E-09 69.5 8.7 62 450-513 71-132 (134)
140 smart00421 HTH_LUXR helix_turn 97.8 4.9E-05 1.1E-09 57.4 5.7 47 460-511 2-48 (58)
141 TIGR03879 near_KaiC_dom probab 97.8 8.8E-05 1.9E-09 60.9 7.2 47 454-504 8-55 (73)
142 PRK05658 RNA polymerase sigma 97.7 0.0046 9.9E-08 70.2 21.7 32 210-242 102-134 (619)
143 PF07374 DUF1492: Protein of u 97.7 0.00026 5.6E-09 61.6 8.9 55 451-509 44-99 (100)
144 PF04967 HTH_10: HTH DNA bindi 97.7 0.00019 4.1E-09 55.4 7.0 48 462-509 1-51 (53)
145 cd06170 LuxR_C_like C-terminal 97.6 0.00019 4.2E-09 54.3 6.1 46 462-512 1-46 (57)
146 PF00196 GerE: Bacterial regul 97.4 0.00041 8.9E-09 53.9 6.0 47 460-511 2-48 (58)
147 TIGR01321 TrpR trp operon repr 97.2 0.00074 1.6E-08 58.1 5.4 49 453-501 23-75 (94)
148 PRK13719 conjugal transfer tra 97.1 0.00094 2E-08 65.7 6.2 51 456-511 138-188 (217)
149 TIGR03541 reg_near_HchA LuxR f 97.1 0.00094 2E-08 66.4 6.2 51 459-514 169-219 (232)
150 PRK15411 rcsA colanic acid cap 97.1 0.0011 2.3E-08 64.8 6.2 46 461-511 137-182 (207)
151 PRK15201 fimbriae regulatory p 97.0 0.0013 2.9E-08 62.6 6.5 47 460-511 132-178 (198)
152 TIGR03020 EpsA transcriptional 97.0 0.0011 2.4E-08 66.8 6.4 49 459-512 188-236 (247)
153 PRK10840 transcriptional regul 97.0 0.0012 2.7E-08 63.7 6.2 46 460-510 149-194 (216)
154 PRK11475 DNA-binding transcrip 97.0 0.0014 3E-08 64.2 6.3 47 459-510 132-178 (207)
155 PF02001 DUF134: Protein of un 97.0 0.0021 4.7E-08 56.5 6.6 53 461-517 41-93 (106)
156 PRK10100 DNA-binding transcrip 96.9 0.0015 3.3E-08 64.3 6.2 48 459-511 153-200 (216)
157 PRK10188 DNA-binding transcrip 96.9 0.0018 3.9E-08 64.9 6.4 47 461-512 179-225 (240)
158 PRK13870 transcriptional regul 96.9 0.0017 3.7E-08 64.8 6.2 47 461-512 173-219 (234)
159 COG2197 CitB Response regulato 96.9 0.0017 3.8E-08 63.7 5.9 47 460-511 147-193 (211)
160 PF13936 HTH_38: Helix-turn-he 96.8 0.0015 3.2E-08 48.4 3.8 41 460-504 3-43 (44)
161 COG3413 Predicted DNA binding 96.8 0.0031 6.7E-08 62.0 7.0 53 461-513 155-210 (215)
162 COG4566 TtrR Response regulato 96.7 0.0081 1.8E-07 58.0 8.8 64 451-519 132-195 (202)
163 COG2739 Uncharacterized protei 96.7 0.0034 7.3E-08 54.3 5.6 49 460-512 16-64 (105)
164 PRK15369 two component system 96.7 0.0037 8E-08 58.0 6.5 47 460-511 148-194 (211)
165 TIGR01637 phage_arpU phage tra 96.7 0.012 2.5E-07 53.4 9.2 63 450-514 67-130 (132)
166 PRK09483 response regulator; P 96.6 0.0037 8.1E-08 59.3 6.0 46 460-510 147-192 (217)
167 COG2771 CsgD DNA-binding HTH d 96.6 0.007 1.5E-07 47.1 6.5 50 460-514 3-52 (65)
168 COG4941 Predicted RNA polymera 96.5 0.068 1.5E-06 55.8 14.2 159 288-512 8-167 (415)
169 PF00325 Crp: Bacterial regula 96.3 0.0048 1E-07 42.7 3.5 27 481-511 2-28 (32)
170 PRK09390 fixJ response regulat 96.3 0.012 2.6E-07 54.2 7.0 56 454-514 134-189 (202)
171 PRK10651 transcriptional regul 96.2 0.0088 1.9E-07 56.1 5.8 47 460-511 154-200 (216)
172 COG1342 Predicted DNA-binding 96.1 0.017 3.6E-07 49.6 6.3 53 461-517 33-85 (99)
173 PRK01381 Trp operon repressor; 96.0 0.0088 1.9E-07 51.9 4.4 48 452-499 22-73 (99)
174 PRK13558 bacterio-opsin activa 95.5 0.028 6.2E-07 63.7 7.0 53 459-511 605-660 (665)
175 COG1356 tfx Transcriptional re 95.3 0.017 3.7E-07 52.0 3.6 50 461-515 8-57 (143)
176 PF01726 LexA_DNA_bind: LexA D 95.1 0.034 7.3E-07 44.7 4.4 45 459-503 1-48 (65)
177 PF13613 HTH_Tnp_4: Helix-turn 95.1 0.058 1.3E-06 41.3 5.5 49 461-512 2-50 (53)
178 PRK10360 DNA-binding transcrip 95.1 0.046 9.9E-07 50.9 5.9 49 460-513 136-184 (196)
179 PRK09935 transcriptional regul 95.0 0.048 1E-06 51.1 6.1 46 461-511 149-194 (210)
180 PRK10403 transcriptional regul 95.0 0.047 1E-06 51.0 5.8 49 460-513 152-200 (215)
181 PF13412 HTH_24: Winged helix- 94.9 0.081 1.8E-06 39.2 5.9 40 462-504 1-40 (48)
182 PRK15320 transcriptional activ 94.9 0.053 1.1E-06 52.8 5.9 66 440-511 144-209 (251)
183 PF05263 DUF722: Protein of un 94.8 0.16 3.5E-06 46.4 8.5 51 452-504 72-122 (130)
184 PF13384 HTH_23: Homeodomain-l 94.4 0.046 1E-06 40.8 3.4 32 469-505 10-41 (50)
185 PRK04841 transcriptional regul 94.3 0.071 1.5E-06 62.4 6.4 47 460-511 837-883 (903)
186 PRK09958 DNA-binding transcrip 94.3 0.095 2.1E-06 49.1 6.2 47 459-510 141-187 (204)
187 PF12645 HTH_16: Helix-turn-he 94.2 0.19 4.2E-06 40.4 6.8 56 276-331 4-65 (65)
188 PF06530 Phage_antitermQ: Phag 94.0 0.32 7E-06 44.0 8.6 52 459-514 60-111 (125)
189 PF13404 HTH_AsnC-type: AsnC-t 93.9 0.19 4E-06 36.9 5.6 40 462-504 1-40 (42)
190 PRK15418 transcriptional regul 93.9 0.087 1.9E-06 55.1 5.3 36 468-507 20-55 (318)
191 PF10668 Phage_terminase: Phag 93.7 0.14 3E-06 40.6 4.8 35 468-504 11-45 (60)
192 cd00569 HTH_Hin_like Helix-tur 93.6 0.17 3.8E-06 33.3 4.8 36 462-501 6-41 (42)
193 PF09862 DUF2089: Protein of u 93.4 0.24 5.2E-06 44.2 6.4 49 459-511 31-79 (113)
194 PF13730 HTH_36: Helix-turn-he 93.3 0.34 7.4E-06 36.8 6.5 47 461-511 2-51 (55)
195 TIGR02531 yecD_yerC TrpR-relat 93.3 0.18 3.9E-06 43.0 5.4 38 459-502 34-71 (88)
196 PF02796 HTH_7: Helix-turn-hel 93.1 0.13 2.8E-06 38.1 3.7 32 466-502 11-42 (45)
197 PRK09210 RNA polymerase sigma 93.1 1 2.2E-05 48.1 11.9 126 244-410 217-347 (367)
198 TIGR02393 RpoD_Cterm RNA polym 92.9 1.4 3.1E-05 43.7 12.1 34 245-278 89-122 (238)
199 PF08279 HTH_11: HTH domain; 92.8 0.26 5.7E-06 37.4 5.3 41 465-511 1-41 (55)
200 PRK05901 RNA polymerase sigma 92.8 1.2 2.6E-05 49.6 12.4 126 244-410 359-489 (509)
201 PHA00675 hypothetical protein 92.4 0.28 6.1E-06 40.6 5.1 40 460-503 21-61 (78)
202 PRK07921 RNA polymerase sigma 92.0 2.1 4.6E-05 45.0 12.5 35 244-278 174-208 (324)
203 PF04539 Sigma70_r3: Sigma-70 91.9 0.31 6.8E-06 39.7 4.9 37 243-279 4-40 (78)
204 PRK07598 RNA polymerase sigma 91.7 1.4 2.9E-05 48.0 10.8 39 371-409 110-148 (415)
205 PRK10430 DNA-binding transcrip 91.6 0.39 8.4E-06 47.2 6.2 47 461-507 158-204 (239)
206 PF01325 Fe_dep_repress: Iron 91.1 0.55 1.2E-05 37.1 5.3 46 462-511 2-48 (60)
207 PF13518 HTH_28: Helix-turn-he 91.1 0.43 9.4E-06 35.5 4.6 25 482-506 13-37 (52)
208 PF06056 Terminase_5: Putative 90.9 0.52 1.1E-05 37.0 5.0 29 473-505 9-37 (58)
209 PF04218 CENP-B_N: CENP-B N-te 90.6 0.36 7.8E-06 37.1 3.8 40 461-504 6-45 (53)
210 PF12802 MarR_2: MarR family; 90.6 0.71 1.5E-05 35.6 5.6 43 461-504 2-44 (62)
211 smart00351 PAX Paired Box doma 90.5 0.74 1.6E-05 41.6 6.3 41 462-506 18-58 (125)
212 COG1191 FliA DNA-directed RNA 90.0 3.7 8.1E-05 41.6 11.5 144 215-410 91-234 (247)
213 COG2390 DeoR Transcriptional r 90.0 0.44 9.5E-06 50.0 5.0 36 468-507 17-52 (321)
214 COG3355 Predicted transcriptio 89.8 1.2 2.7E-05 40.4 7.1 53 453-511 16-68 (126)
215 PHA02591 hypothetical protein; 89.3 0.81 1.7E-05 38.1 5.0 22 482-503 60-81 (83)
216 PF02650 HTH_WhiA: WhiA C-term 88.9 0.93 2E-05 38.5 5.3 43 459-504 35-79 (85)
217 PF09339 HTH_IclR: IclR helix- 88.7 0.67 1.5E-05 35.1 3.9 36 467-502 4-39 (52)
218 PF03444 HrcA_DNA-bdg: Winged 88.6 1 2.2E-05 37.6 5.3 41 461-502 1-44 (78)
219 TIGR01610 phage_O_Nterm phage 88.6 1.3 2.8E-05 38.0 6.2 49 459-511 20-73 (95)
220 smart00550 Zalpha Z-DNA-bindin 88.6 1.2 2.7E-05 35.8 5.7 41 466-511 8-48 (68)
221 PRK15479 transcriptional regul 88.2 0.79 1.7E-05 43.1 5.1 49 461-510 148-201 (221)
222 PRK12423 LexA repressor; Provi 88.2 0.94 2E-05 44.1 5.7 48 460-511 2-52 (202)
223 PRK07408 RNA polymerase sigma 88.2 1.8 3.8E-05 43.7 7.8 35 244-278 114-148 (256)
224 PF01978 TrmB: Sugar-specific 88.0 0.6 1.3E-05 37.2 3.5 44 461-511 5-48 (68)
225 PHA02547 55 RNA polymerase sig 88.0 1.8 3.8E-05 41.3 7.0 63 294-356 46-111 (179)
226 cd06571 Bac_DnaA_C C-terminal 87.9 1.8 4E-05 36.6 6.6 42 465-510 32-74 (90)
227 PF01047 MarR: MarR family; I 87.8 1.3 2.9E-05 33.8 5.2 40 462-504 1-40 (59)
228 smart00345 HTH_GNTR helix_turn 87.7 0.93 2E-05 34.2 4.2 29 479-511 17-46 (60)
229 PRK11083 DNA-binding response 87.6 0.84 1.8E-05 43.1 4.9 50 461-511 154-208 (228)
230 PF01371 Trp_repressor: Trp re 87.6 1.8 3.9E-05 36.9 6.2 45 461-508 26-75 (87)
231 PF13463 HTH_27: Winged helix 87.1 1.2 2.6E-05 34.9 4.7 43 462-510 1-43 (68)
232 COG2909 MalT ATP-dependent tra 87.1 0.75 1.6E-05 53.5 4.8 48 461-513 831-878 (894)
233 TIGR03787 marine_sort_RR prote 87.0 0.96 2.1E-05 43.1 4.9 50 461-511 156-207 (227)
234 PRK10710 DNA-binding transcrip 87.0 1 2.2E-05 43.2 5.1 50 461-511 160-214 (240)
235 PRK05911 RNA polymerase sigma 86.8 3.8 8.3E-05 41.3 9.3 32 247-278 114-145 (257)
236 cd00131 PAX Paired Box domain 86.8 1.8 4E-05 39.3 6.3 41 462-506 18-58 (128)
237 TIGR02885 spore_sigF RNA polym 86.7 2.2 4.9E-05 41.9 7.4 31 247-277 101-131 (231)
238 PRK10336 DNA-binding transcrip 86.6 1 2.3E-05 42.3 4.9 49 461-510 149-202 (219)
239 PRK07406 RNA polymerase sigma 86.6 7.7 0.00017 41.6 11.9 35 243-277 223-257 (373)
240 smart00344 HTH_ASNC helix_turn 86.6 1.7 3.6E-05 37.5 5.7 39 462-503 1-39 (108)
241 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 86.5 1.9 4E-05 33.0 5.1 38 461-502 4-41 (50)
242 PF01726 LexA_DNA_bind: LexA D 86.5 2 4.2E-05 34.5 5.6 39 372-410 9-48 (65)
243 PRK07122 RNA polymerase sigma 86.5 8.2 0.00018 39.2 11.6 34 245-278 129-162 (264)
244 PRK05949 RNA polymerase sigma 86.4 5.2 0.00011 42.0 10.4 34 245-278 180-213 (327)
245 TIGR02147 Fsuc_second hypothet 86.2 12 0.00025 38.5 12.4 98 386-490 135-238 (271)
246 TIGR00498 lexA SOS regulatory 86.1 1.4 3.1E-05 42.5 5.6 48 460-511 2-52 (199)
247 PRK11179 DNA-binding transcrip 85.8 1.8 3.9E-05 40.2 5.9 40 461-503 6-45 (153)
248 TIGR02850 spore_sigG RNA polym 85.4 10 0.00022 38.0 11.6 35 245-279 122-156 (254)
249 PF12728 HTH_17: Helix-turn-he 85.4 0.92 2E-05 33.9 3.0 24 482-505 2-25 (51)
250 PRK06288 RNA polymerase sigma 85.3 14 0.00031 37.3 12.6 34 244-277 119-152 (268)
251 PF13011 LZ_Tnp_IS481: leucine 85.2 2.4 5.1E-05 36.1 5.7 44 460-506 7-50 (85)
252 COG1522 Lrp Transcriptional re 85.2 1.4 3.1E-05 40.2 4.9 42 460-504 4-45 (154)
253 PF01022 HTH_5: Bacterial regu 84.9 2.6 5.6E-05 31.2 5.2 23 481-503 15-37 (47)
254 PF00356 LacI: Bacterial regul 84.7 0.96 2.1E-05 33.9 2.8 22 483-504 1-22 (46)
255 PF13545 HTH_Crp_2: Crp-like h 84.6 1.3 2.9E-05 35.5 3.9 28 480-511 27-54 (76)
256 PF01710 HTH_Tnp_IS630: Transp 84.5 7.9 0.00017 34.5 9.2 27 482-512 72-98 (119)
257 PRK00215 LexA repressor; Valid 84.3 1.9 4.2E-05 41.7 5.6 43 462-504 2-47 (205)
258 PRK10046 dpiA two-component re 84.2 1.1 2.4E-05 43.7 3.8 39 461-503 161-199 (225)
259 PF02954 HTH_8: Bacterial regu 84.1 1.9 4.2E-05 31.3 4.2 38 463-503 3-40 (42)
260 smart00419 HTH_CRP helix_turn_ 84.1 1.7 3.7E-05 31.4 4.0 27 481-511 8-34 (48)
261 TIGR02997 Sig70-cyanoRpoD RNA 84.0 13 0.00029 38.2 11.9 34 245-278 163-196 (298)
262 TIGR02787 codY_Gpos GTP-sensin 83.7 5.6 0.00012 40.2 8.5 55 453-511 168-224 (251)
263 TIGR03697 NtcA_cyano global ni 83.6 1.3 2.8E-05 41.6 4.0 29 480-512 142-170 (193)
264 PF12840 HTH_20: Helix-turn-he 83.5 5.2 0.00011 31.1 6.7 36 464-502 10-45 (61)
265 PRK11169 leucine-responsive tr 83.5 1.7 3.7E-05 40.8 4.7 40 462-504 12-51 (164)
266 PF08822 DUF1804: Protein of u 83.4 2.6 5.7E-05 40.0 5.8 42 463-507 4-45 (165)
267 COG3415 Transposase and inacti 83.3 2.3 5E-05 39.3 5.3 34 469-506 13-46 (138)
268 TIGR01764 excise DNA binding d 83.3 1.4 3E-05 31.9 3.1 24 482-505 2-25 (49)
269 smart00342 HTH_ARAC helix_turn 83.2 14 0.00031 29.0 9.5 23 388-410 1-23 (84)
270 TIGR02154 PhoB phosphate regul 82.9 0.97 2.1E-05 42.6 2.8 50 461-511 154-208 (226)
271 PF13022 HTH_Tnp_1_2: Helix-tu 82.8 6.6 0.00014 36.4 8.0 65 455-519 4-74 (142)
272 cd04762 HTH_MerR-trunc Helix-T 82.8 1.5 3.3E-05 31.5 3.2 25 482-506 1-25 (49)
273 PF08220 HTH_DeoR: DeoR-like h 82.7 2.9 6.3E-05 32.4 4.9 39 466-511 2-40 (57)
274 PRK07405 RNA polymerase sigma 82.5 14 0.00031 38.6 11.5 34 244-277 169-202 (317)
275 cd00092 HTH_CRP helix_turn_hel 82.5 4.2 9E-05 31.5 5.9 28 480-511 24-51 (67)
276 COG1654 BirA Biotin operon rep 82.4 3.6 7.9E-05 34.4 5.6 32 476-511 14-45 (79)
277 PF01418 HTH_6: Helix-turn-hel 81.3 3 6.4E-05 34.3 4.8 50 452-501 4-54 (77)
278 COG1510 Predicted transcriptio 81.2 1.5 3.3E-05 41.8 3.3 30 478-511 38-67 (177)
279 PRK07670 RNA polymerase sigma 81.0 18 0.00039 36.2 11.3 34 245-278 111-144 (251)
280 PF00392 GntR: Bacterial regul 80.3 2.4 5.3E-05 33.3 3.8 30 478-511 20-50 (64)
281 PF13542 HTH_Tnp_ISL3: Helix-t 80.1 4.7 0.0001 30.0 5.2 24 482-505 28-51 (52)
282 PF00046 Homeobox: Homeobox do 80.1 4.3 9.3E-05 30.8 5.0 51 461-511 6-57 (57)
283 cd07377 WHTH_GntR Winged helix 80.0 3.5 7.6E-05 31.6 4.6 26 482-511 26-51 (66)
284 cd04761 HTH_MerR-SF Helix-Turn 79.9 1.4 3.1E-05 32.2 2.2 25 482-506 1-25 (49)
285 smart00346 HTH_ICLR helix_turn 79.7 4.6 0.0001 33.4 5.5 25 480-504 19-43 (91)
286 PRK13918 CRP/FNR family transc 79.5 2.1 4.6E-05 40.6 3.9 28 480-511 148-175 (202)
287 smart00420 HTH_DEOR helix_turn 79.0 5.2 0.00011 29.1 5.0 22 481-502 14-35 (53)
288 CHL00148 orf27 Ycf27; Reviewed 78.9 3 6.4E-05 39.9 4.7 50 461-511 161-217 (240)
289 PRK00423 tfb transcription ini 78.8 39 0.00085 35.2 13.2 84 289-409 120-203 (310)
290 PF13744 HTH_37: Helix-turn-he 78.5 4.1 8.9E-05 33.7 4.8 42 469-514 23-69 (80)
291 PRK10072 putative transcriptio 78.4 3.5 7.6E-05 35.8 4.4 32 469-504 38-69 (96)
292 PRK11564 stationary phase indu 78.4 5.6 0.00012 43.0 7.1 51 461-511 10-60 (426)
293 PRK07500 rpoH2 RNA polymerase 78.3 19 0.0004 37.1 10.6 24 387-410 244-267 (289)
294 PF08280 HTH_Mga: M protein tr 78.2 4.1 8.8E-05 31.8 4.4 40 465-511 6-45 (59)
295 PHA01976 helix-turn-helix prot 78.2 4.2 9.1E-05 31.9 4.6 32 469-504 7-38 (67)
296 TIGR02479 FliA_WhiG RNA polyme 78.1 23 0.0005 34.6 10.8 35 244-278 84-118 (224)
297 COG1476 Predicted transcriptio 77.7 3.8 8.3E-05 33.4 4.1 32 469-504 6-37 (68)
298 PF02082 Rrf2: Transcriptional 77.4 4.5 9.8E-05 33.5 4.7 31 477-511 21-51 (83)
299 PF01527 HTH_Tnp_1: Transposas 76.5 3.9 8.5E-05 32.8 4.0 25 482-506 24-48 (76)
300 PF13411 MerR_1: MerR HTH fami 75.9 1.4 3.1E-05 34.7 1.3 25 482-506 1-25 (69)
301 PRK11161 fumarate/nitrate redu 75.8 3.1 6.6E-05 40.7 3.9 28 480-511 183-210 (235)
302 PRK11753 DNA-binding transcrip 75.7 14 0.00031 35.1 8.4 27 481-511 168-194 (211)
303 PRK12427 flagellar biosynthesi 75.5 26 0.00056 34.8 10.4 34 245-278 103-136 (231)
304 PF01381 HTH_3: Helix-turn-hel 75.5 4.1 8.9E-05 30.5 3.7 23 482-504 10-32 (55)
305 PF13560 HTH_31: Helix-turn-he 75.3 4.3 9.2E-05 31.8 3.8 23 482-504 15-37 (64)
306 TIGR02844 spore_III_D sporulat 75.1 5.1 0.00011 33.6 4.4 23 481-503 19-41 (80)
307 TIGR03070 couple_hipB transcri 75.1 5.7 0.00012 29.6 4.4 23 482-504 16-38 (58)
308 smart00347 HTH_MARR helix_turn 75.1 8.6 0.00019 31.8 5.9 44 461-511 7-50 (101)
309 TIGR02612 mob_myst_A mobile my 74.9 7.3 0.00016 36.5 5.9 49 462-514 23-77 (150)
310 TIGR00122 birA_repr_reg BirA b 74.9 7.9 0.00017 30.8 5.4 27 481-511 13-39 (69)
311 PHA00542 putative Cro-like pro 74.8 5.4 0.00012 33.3 4.5 24 482-505 32-55 (82)
312 PF14394 DUF4423: Domain of un 74.7 6.7 0.00015 37.4 5.7 111 386-514 37-153 (171)
313 TIGR02941 Sigma_B RNA polymera 74.3 24 0.00052 35.3 9.9 33 245-277 118-150 (255)
314 PRK13413 mpi multiple promoter 74.2 5.9 0.00013 38.3 5.3 32 467-503 163-194 (200)
315 COG1508 RpoN DNA-directed RNA 73.8 37 0.0008 37.3 11.6 46 457-502 294-351 (444)
316 TIGR02337 HpaR homoprotocatech 73.7 18 0.00038 31.7 7.8 44 460-510 24-67 (118)
317 PRK06030 hypothetical protein; 73.4 11 0.00023 34.3 6.4 37 464-504 56-92 (124)
318 PRK09954 putative kinase; Prov 73.4 6.5 0.00014 41.3 5.9 43 462-507 1-43 (362)
319 PRK09413 IS2 repressor TnpA; R 72.8 10 0.00022 33.8 6.2 25 482-506 30-54 (121)
320 PF13551 HTH_29: Winged helix- 72.7 5.9 0.00013 33.8 4.5 24 482-505 12-36 (112)
321 cd00090 HTH_ARSR Arsenical Res 72.6 12 0.00026 28.7 5.9 25 482-510 21-45 (78)
322 PRK05572 sporulation sigma fac 72.5 31 0.00068 34.4 10.3 32 245-276 120-151 (252)
323 PRK10402 DNA-binding transcrip 72.4 7.9 0.00017 37.8 5.8 46 462-511 149-195 (226)
324 PF12116 SpoIIID: Stage III sp 72.2 5.9 0.00013 33.2 4.0 47 465-513 5-51 (82)
325 PF07750 GcrA: GcrA cell cycle 72.2 5.1 0.00011 38.0 4.2 36 465-504 6-42 (162)
326 PF08765 Mor: Mor transcriptio 72.1 8.5 0.00018 33.8 5.3 41 465-511 62-102 (108)
327 PF00376 MerR: MerR family reg 72.0 2.7 5.7E-05 30.1 1.7 23 483-505 1-23 (38)
328 PRK08215 sporulation sigma fac 71.7 41 0.0009 33.7 10.9 33 246-278 126-158 (258)
329 PRK09391 fixK transcriptional 71.6 4.6 9.9E-05 39.7 4.0 27 481-511 179-205 (230)
330 PRK11014 transcriptional repre 71.0 10 0.00022 34.6 5.8 30 478-511 22-51 (141)
331 cd01104 HTH_MlrA-CarA Helix-Tu 70.9 5.2 0.00011 31.4 3.4 23 482-504 1-23 (68)
332 TIGR01884 cas_HTH CRISPR locus 70.6 12 0.00026 36.3 6.6 44 458-504 137-180 (203)
333 PRK01905 DNA-binding protein F 70.6 20 0.00043 29.5 6.9 36 465-503 37-72 (77)
334 PRK03573 transcriptional regul 70.4 15 0.00033 33.2 6.9 49 453-503 18-68 (144)
335 PRK11302 DNA-binding transcrip 70.0 9 0.0002 38.7 5.8 50 452-503 4-56 (284)
336 COG5484 Uncharacterized conser 70.0 6.2 0.00014 39.9 4.4 33 468-504 10-42 (279)
337 PRK09863 putative frv operon r 69.7 23 0.00051 39.9 9.6 103 387-510 16-121 (584)
338 smart00418 HTH_ARSR helix_turn 69.6 7.9 0.00017 28.9 4.1 24 481-504 10-33 (66)
339 COG2973 TrpR Trp operon repres 69.4 17 0.00038 31.6 6.4 37 461-499 37-78 (103)
340 PRK11337 DNA-binding transcrip 69.3 13 0.00028 37.9 6.8 51 451-503 15-68 (292)
341 COG2512 Predicted membrane-ass 69.2 7.4 0.00016 39.7 4.9 45 460-510 191-235 (258)
342 COG0856 Orotate phosphoribosyl 68.9 7.1 0.00015 37.6 4.3 30 482-511 19-48 (203)
343 PF05043 Mga: Mga helix-turn-h 68.7 4 8.8E-05 33.9 2.4 34 480-517 29-62 (87)
344 COG4367 Uncharacterized protei 68.6 9.9 0.00022 32.5 4.6 40 376-415 10-50 (97)
345 PRK10870 transcriptional repre 68.0 30 0.00065 32.9 8.6 50 454-504 43-94 (176)
346 cd04764 HTH_MlrA-like_sg1 Heli 68.0 6.7 0.00014 30.9 3.4 23 482-504 1-23 (67)
347 PF13551 HTH_29: Winged helix- 67.9 6.5 0.00014 33.5 3.7 23 390-412 14-36 (112)
348 PRK11512 DNA-binding transcrip 67.9 13 0.00029 33.8 5.9 46 455-503 29-76 (144)
349 TIGR03830 CxxCG_CxxCG_HTH puta 67.3 18 0.0004 31.8 6.6 44 456-505 59-102 (127)
350 PF12298 Bot1p: Eukaryotic mit 66.9 15 0.00033 35.2 6.2 39 461-502 16-54 (172)
351 PRK09392 ftrB transcriptional 66.8 6.1 0.00013 38.7 3.7 27 481-511 173-199 (236)
352 TIGR02980 SigBFG RNA polymeras 66.8 40 0.00086 32.9 9.4 30 248-277 95-124 (227)
353 PF14502 HTH_41: Helix-turn-he 66.7 10 0.00022 28.8 4.0 29 479-511 4-32 (48)
354 PF14493 HTH_40: Helix-turn-he 66.0 11 0.00025 31.7 4.7 27 482-508 14-40 (91)
355 PRK06986 fliA flagellar biosyn 66.0 69 0.0015 31.6 11.0 31 247-277 99-129 (236)
356 COG2345 Predicted transcriptio 65.9 11 0.00024 37.6 5.2 24 481-504 25-48 (218)
357 smart00422 HTH_MERR helix_turn 65.6 4.8 0.0001 31.7 2.2 25 482-506 1-25 (70)
358 PF05225 HTH_psq: helix-turn-h 65.5 10 0.00022 28.1 3.7 22 482-503 17-38 (45)
359 cd00086 homeodomain Homeodomai 65.4 20 0.00043 26.9 5.6 51 461-511 6-57 (59)
360 PRK15482 transcriptional regul 65.3 12 0.00026 38.1 5.6 49 453-503 5-56 (285)
361 TIGR00180 parB_part ParB-like 65.2 12 0.00026 35.9 5.3 43 460-504 101-143 (187)
362 cd04763 HTH_MlrA-like Helix-Tu 64.6 8.2 0.00018 30.5 3.4 23 482-504 1-23 (68)
363 TIGR02607 antidote_HigA addict 64.3 15 0.00033 29.4 5.0 23 482-504 19-41 (78)
364 TIGR02944 suf_reg_Xantho FeS a 64.2 12 0.00026 33.5 4.8 30 478-511 22-51 (130)
365 PRK11050 manganese transport r 63.7 27 0.00058 32.5 7.2 27 481-511 51-77 (152)
366 PRK04984 fatty acid metabolism 63.2 9.3 0.0002 37.6 4.2 30 478-511 27-57 (239)
367 smart00354 HTH_LACI helix_turn 63.0 7.5 0.00016 31.2 2.9 23 482-504 1-23 (70)
368 TIGR00647 MG103 conserved hypo 62.8 17 0.00037 37.6 6.0 43 459-504 225-273 (279)
369 PRK10141 DNA-binding transcrip 62.0 23 0.0005 31.8 6.1 49 456-511 7-56 (117)
370 TIGR03338 phnR_burk phosphonat 61.7 9.1 0.0002 36.9 3.8 30 478-511 31-60 (212)
371 TIGR02431 pcaR_pcaU beta-ketoa 61.5 15 0.00032 36.6 5.4 38 466-503 9-46 (248)
372 PRK10161 transcriptional regul 61.4 9.4 0.0002 36.3 3.8 50 461-511 154-208 (229)
373 PF13556 HTH_30: PucR C-termin 61.3 26 0.00056 27.2 5.6 33 482-514 13-45 (59)
374 COG2522 Predicted transcriptio 60.6 15 0.00033 33.1 4.7 22 482-503 23-44 (119)
375 PF04703 FaeA: FaeA-like prote 60.4 10 0.00022 30.3 3.1 24 480-503 14-37 (62)
376 COG2944 Predicted transcriptio 60.1 18 0.0004 31.9 4.9 40 459-504 41-80 (104)
377 PRK03902 manganese transport t 59.9 21 0.00046 32.5 5.7 22 481-502 22-43 (142)
378 PRK11414 colanic acid/biofilm 59.7 10 0.00022 37.0 3.7 37 469-511 24-60 (221)
379 PRK09726 antitoxin HipB; Provi 59.7 16 0.00035 30.6 4.5 23 482-504 26-48 (88)
380 PRK13239 alkylmercury lyase; P 59.6 17 0.00038 35.8 5.3 28 385-412 33-60 (206)
381 TIGR01387 cztR_silR_copR heavy 59.1 15 0.00033 34.2 4.7 50 461-511 147-201 (218)
382 smart00862 Trans_reg_C Transcr 59.0 33 0.00072 27.1 6.1 50 461-511 5-60 (78)
383 TIGR02812 fadR_gamma fatty aci 58.7 12 0.00027 36.7 4.2 30 478-511 26-56 (235)
384 smart00389 HOX Homeodomain. DN 58.6 20 0.00044 26.7 4.5 48 461-508 6-54 (56)
385 PRK11534 DNA-binding transcrip 58.5 12 0.00025 36.6 3.9 38 468-511 19-56 (224)
386 PRK06596 RNA polymerase factor 58.4 90 0.0019 32.0 10.6 24 387-410 247-270 (284)
387 PRK11557 putative DNA-binding 58.3 14 0.0003 37.3 4.6 47 455-503 3-52 (278)
388 PRK09990 DNA-binding transcrip 58.3 13 0.00028 37.0 4.3 37 469-511 20-57 (251)
389 PRK03837 transcriptional regul 57.9 13 0.00029 36.4 4.3 37 469-511 26-63 (241)
390 PRK09834 DNA-binding transcrip 57.8 18 0.00039 36.5 5.3 37 466-502 11-47 (263)
391 PRK10225 DNA-binding transcrip 57.8 13 0.00028 37.1 4.2 38 468-511 21-59 (257)
392 PRK09464 pdhR transcriptional 57.7 13 0.00029 36.9 4.3 38 468-511 22-60 (254)
393 KOG0484 Transcription factor P 57.1 18 0.00038 32.0 4.3 52 460-515 27-78 (125)
394 PRK11517 transcriptional regul 57.1 20 0.00044 33.6 5.2 49 461-510 147-200 (223)
395 PF06971 Put_DNA-bind_N: Putat 56.9 22 0.00048 27.2 4.3 46 363-408 3-48 (50)
396 PF08535 KorB: KorB domain; I 56.6 10 0.00022 32.2 2.7 22 482-503 4-25 (93)
397 TIGR00738 rrf2_super rrf2 fami 56.5 23 0.0005 31.5 5.2 25 478-502 22-46 (132)
398 PRK10411 DNA-binding transcrip 55.9 22 0.00049 35.6 5.5 41 464-507 4-44 (240)
399 PRK10421 DNA-binding transcrip 55.7 15 0.00032 36.7 4.2 38 468-511 14-52 (253)
400 TIGR02698 CopY_TcrY copper tra 55.7 30 0.00065 31.4 5.9 44 461-507 1-48 (130)
401 TIGR01889 Staph_reg_Sar staphy 55.7 33 0.00071 29.8 5.9 43 461-503 22-65 (109)
402 COG1321 TroR Mn-dependent tran 55.6 23 0.0005 33.2 5.2 26 478-503 21-46 (154)
403 TIGR02395 rpoN_sigma RNA polym 55.3 61 0.0013 35.5 9.2 24 387-410 317-340 (429)
404 COG1318 Predicted transcriptio 55.2 12 0.00026 35.9 3.2 26 482-507 62-87 (182)
405 COG3877 Uncharacterized protei 55.1 31 0.00067 30.6 5.4 48 459-510 39-86 (122)
406 PRK09706 transcriptional repre 55.0 20 0.00042 32.5 4.5 23 482-504 19-41 (135)
407 cd04768 HTH_BmrR-like Helix-Tu 54.9 9 0.0002 32.8 2.2 25 482-506 1-25 (96)
408 PF09012 FeoC: FeoC like trans 54.7 10 0.00022 30.4 2.3 24 481-504 14-37 (69)
409 PRK10163 DNA-binding transcrip 54.5 24 0.00052 35.8 5.6 26 478-503 37-62 (271)
410 PRK11569 transcriptional repre 54.5 21 0.00045 36.3 5.1 33 471-503 33-65 (274)
411 PRK14101 bifunctional glucokin 54.3 23 0.00051 40.5 6.0 51 451-503 343-396 (638)
412 COG1846 MarR Transcriptional r 54.2 28 0.00061 29.5 5.3 39 462-503 20-58 (126)
413 COG4367 Uncharacterized protei 54.1 41 0.00088 28.9 5.8 39 462-503 3-45 (97)
414 PRK10434 srlR DNA-bindng trans 53.8 22 0.00048 35.9 5.1 41 464-508 5-45 (256)
415 smart00342 HTH_ARAC helix_turn 53.5 26 0.00057 27.5 4.6 25 482-506 2-26 (84)
416 smart00530 HTH_XRE Helix-turn- 53.5 28 0.0006 24.2 4.4 23 482-504 11-33 (56)
417 PF00165 HTH_AraC: Bacterial r 52.9 21 0.00046 25.4 3.6 24 481-504 8-31 (42)
418 PF05732 RepL: Firmicute plasm 52.8 50 0.0011 31.4 7.0 53 455-511 46-101 (165)
419 smart00352 POU Found in Pit-Oc 52.5 27 0.00059 29.0 4.5 33 468-504 15-53 (75)
420 PF12844 HTH_19: Helix-turn-he 52.4 26 0.00056 27.0 4.3 23 482-504 13-35 (64)
421 cd04775 HTH_Cfa-like Helix-Tur 52.2 10 0.00022 32.8 2.1 26 482-507 2-27 (102)
422 PF01710 HTH_Tnp_IS630: Transp 52.1 27 0.00058 31.1 4.9 22 482-503 19-40 (119)
423 cd04773 HTH_TioE_rpt2 Second H 52.0 10 0.00023 33.1 2.2 25 482-506 1-25 (108)
424 cd01392 HTH_LacI Helix-turn-he 52.0 9.8 0.00021 28.1 1.7 20 486-505 2-21 (52)
425 PRK05932 RNA polymerase factor 52.0 81 0.0018 34.8 9.5 24 387-410 342-365 (455)
426 PF04552 Sigma54_DBD: Sigma-54 51.9 15 0.00033 34.7 3.4 23 388-410 49-71 (160)
427 PF08784 RPA_C: Replication pr 51.9 27 0.00059 29.9 4.7 42 461-502 44-86 (102)
428 PRK13509 transcriptional repre 51.5 28 0.00061 35.0 5.5 37 465-504 6-42 (251)
429 cd00383 trans_reg_C Effector d 51.5 37 0.0008 27.9 5.4 50 461-511 23-77 (95)
430 PF06413 Neugrin: Neugrin; In 51.3 26 0.00056 35.1 5.0 42 461-503 10-51 (225)
431 PRK10643 DNA-binding transcrip 51.3 22 0.00048 33.2 4.5 49 461-510 149-202 (222)
432 COG5625 Predicted transcriptio 51.3 26 0.00056 30.8 4.3 54 453-506 8-61 (113)
433 cd00093 HTH_XRE Helix-turn-hel 51.2 33 0.00071 24.0 4.5 23 482-504 13-35 (58)
434 COG3093 VapI Plasmid maintenan 51.2 26 0.00056 30.9 4.4 35 468-504 12-46 (104)
435 cd01107 HTH_BmrR Helix-Turn-He 50.9 12 0.00025 32.8 2.3 26 482-507 1-26 (108)
436 PHA00738 putative HTH transcri 50.8 34 0.00074 30.4 5.1 35 465-502 13-47 (108)
437 COG3711 BglG Transcriptional a 50.8 18 0.00038 39.7 4.2 47 464-511 84-130 (491)
438 PRK11523 DNA-binding transcrip 50.6 21 0.00045 35.6 4.3 37 469-511 21-58 (253)
439 COG1349 GlpR Transcriptional r 50.3 20 0.00043 36.2 4.2 37 463-502 4-40 (253)
440 PRK12469 RNA polymerase factor 50.2 21 0.00045 39.7 4.6 45 458-502 334-390 (481)
441 cd01105 HTH_GlnR-like Helix-Tu 50.0 12 0.00026 31.5 2.2 25 482-506 2-26 (88)
442 cd04766 HTH_HspR Helix-Turn-He 49.9 12 0.00027 31.5 2.2 26 482-507 2-27 (91)
443 TIGR00373 conserved hypothetic 49.9 35 0.00076 32.1 5.5 27 481-511 28-54 (158)
444 COG1737 RpiR Transcriptional r 49.8 28 0.0006 35.6 5.2 49 451-501 5-56 (281)
445 PRK04158 transcriptional repre 49.6 29 0.00062 35.4 5.1 56 452-511 170-227 (256)
446 TIGR02395 rpoN_sigma RNA polym 49.5 19 0.00041 39.4 4.1 44 459-502 284-339 (429)
447 cd04782 HTH_BltR Helix-Turn-He 49.4 13 0.00027 32.0 2.2 25 482-506 1-25 (97)
448 cd04765 HTH_MlrA-like_sg2 Heli 49.3 20 0.00043 31.0 3.4 23 482-504 1-23 (99)
449 PF10078 DUF2316: Uncharacteri 49.2 41 0.00088 28.9 5.2 22 482-503 24-45 (89)
450 PF07037 DUF1323: Putative tra 49.1 19 0.00041 32.5 3.3 23 482-504 1-23 (122)
451 PRK06424 transcription factor; 49.1 27 0.00058 32.5 4.5 32 469-504 89-120 (144)
452 PRK13777 transcriptional regul 49.0 39 0.00085 32.7 5.8 39 461-502 42-80 (185)
453 PRK10857 DNA-binding transcrip 48.8 43 0.00093 31.7 5.9 31 477-511 21-51 (164)
454 PRK06266 transcription initiat 48.8 58 0.0013 31.3 6.9 50 454-511 13-62 (178)
455 cd04788 HTH_NolA-AlbR Helix-Tu 48.6 13 0.00028 31.8 2.1 25 482-506 1-25 (96)
456 cd01279 HTH_HspR-like Helix-Tu 48.4 13 0.00029 32.0 2.2 24 482-505 2-25 (98)
457 cd04772 HTH_TioE_rpt1 First He 47.9 14 0.0003 31.9 2.3 25 482-506 1-25 (99)
458 cd04789 HTH_Cfa Helix-Turn-Hel 47.9 14 0.0003 32.1 2.2 26 482-507 2-27 (102)
459 TIGR02018 his_ut_repres histid 47.9 24 0.00052 34.6 4.2 26 482-511 26-51 (230)
460 COG1802 GntR Transcriptional r 47.9 15 0.00033 36.0 2.8 38 468-511 28-65 (230)
461 cd00592 HTH_MerR-like Helix-Tu 47.9 14 0.0003 31.5 2.2 25 482-506 1-25 (100)
462 cd01106 HTH_TipAL-Mta Helix-Tu 47.7 14 0.0003 31.9 2.2 25 482-506 1-25 (103)
463 TIGR03826 YvyF flagellar opero 47.7 56 0.0012 30.2 6.3 54 363-416 21-74 (137)
464 PRK09863 putative frv operon r 47.6 37 0.0008 38.4 6.2 46 462-511 2-47 (584)
465 PF00486 Trans_reg_C: Transcri 47.6 52 0.0011 25.9 5.5 51 461-512 5-60 (77)
466 cd01282 HTH_MerR-like_sg3 Heli 47.6 14 0.0003 32.6 2.2 26 482-507 1-26 (112)
467 PF00440 TetR_N: Bacterial reg 47.6 41 0.00088 24.6 4.4 21 481-501 16-36 (47)
468 cd04780 HTH_MerR-like_sg5 Heli 47.4 14 0.0003 31.7 2.2 25 482-506 1-25 (95)
469 PF00292 PAX: 'Paired box' dom 47.2 44 0.00096 30.5 5.4 32 468-504 25-56 (125)
470 PF11662 DUF3263: Protein of u 47.1 77 0.0017 26.5 6.4 45 461-507 2-48 (77)
471 PHA02943 hypothetical protein; 47.1 41 0.00089 31.8 5.2 22 482-503 25-46 (165)
472 PF04552 Sigma54_DBD: Sigma-54 47.0 6.4 0.00014 37.3 0.0 47 454-502 24-70 (160)
473 cd04774 HTH_YfmP Helix-Turn-He 47.0 14 0.0003 31.7 2.1 25 482-506 1-25 (96)
474 PRK09764 DNA-binding transcrip 47.0 25 0.00055 34.8 4.3 28 480-511 27-55 (240)
475 cd01109 HTH_YyaN Helix-Turn-He 46.9 14 0.00031 32.4 2.2 26 482-507 1-26 (113)
476 PRK14999 histidine utilization 46.8 26 0.00056 34.7 4.3 26 482-511 37-62 (241)
477 cd04774 HTH_YfmP Helix-Turn-He 46.6 1.2E+02 0.0025 26.0 7.8 88 390-513 2-92 (96)
478 PRK00082 hrcA heat-inducible t 46.5 29 0.00064 36.7 4.9 43 460-503 2-49 (339)
479 PRK10681 DNA-binding transcrip 46.4 32 0.00069 34.6 4.9 38 464-504 7-44 (252)
480 TIGR02325 C_P_lyase_phnF phosp 46.3 27 0.00059 34.2 4.4 26 482-511 33-58 (238)
481 PF10668 Phage_terminase: Phag 46.3 33 0.00071 27.3 3.9 32 379-410 13-44 (60)
482 PRK12469 RNA polymerase factor 46.1 1E+02 0.0022 34.4 9.1 37 374-410 352-391 (481)
483 cd01108 HTH_CueR Helix-Turn-He 46.1 14 0.00031 33.2 2.2 26 482-507 1-26 (127)
484 PF04545 Sigma70_r4: Sigma-70, 45.8 49 0.0011 24.4 4.7 26 385-410 17-42 (50)
485 PF00325 Crp: Bacterial regula 45.5 24 0.00052 24.5 2.7 21 390-410 4-24 (32)
486 COG4465 CodY Pleiotropic trans 45.5 82 0.0018 31.5 7.3 54 454-511 175-230 (261)
487 TIGR02010 IscR iron-sulfur clu 45.3 45 0.00098 30.2 5.3 30 478-511 22-51 (135)
488 PRK09943 DNA-binding transcrip 45.3 32 0.00069 32.7 4.5 23 482-504 21-43 (185)
489 PRK13705 plasmid-partitioning 45.3 29 0.00063 37.4 4.7 55 452-506 4-64 (388)
490 cd04769 HTH_MerR2 Helix-Turn-H 45.2 16 0.00034 32.4 2.2 27 482-508 1-27 (116)
491 PRK11886 bifunctional biotin-- 45.1 38 0.00081 35.2 5.4 39 465-506 5-43 (319)
492 TIGR02044 CueR Cu(I)-responsiv 45.1 15 0.00033 33.0 2.2 26 482-507 1-26 (127)
493 PF05930 Phage_AlpA: Prophage 45.1 27 0.00058 26.3 3.2 24 482-505 4-27 (51)
494 COG4709 Predicted membrane pro 45.1 61 0.0013 31.6 6.2 58 449-506 4-65 (195)
495 TIGR02404 trehalos_R_Bsub treh 44.9 29 0.00064 34.0 4.4 27 481-511 24-50 (233)
496 PRK05932 RNA polymerase factor 44.9 24 0.00052 38.9 4.1 45 458-502 308-364 (455)
497 PF08299 Bac_DnaA_C: Bacterial 44.9 50 0.0011 26.7 4.9 34 465-502 33-67 (70)
498 PF08281 Sigma70_r4_2: Sigma-7 44.8 74 0.0016 23.6 5.6 27 384-410 22-48 (54)
499 PRK04424 fatty acid biosynthes 44.6 42 0.0009 32.3 5.2 37 464-503 7-43 (185)
500 PRK00430 fis global DNA-bindin 44.5 40 0.00087 29.1 4.5 36 465-503 55-90 (95)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=1.6e-65 Score=540.57 Aligned_cols=312 Identities=39% Similarity=0.699 Sum_probs=295.0
Q ss_pred CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHH--------------------HHhHHHHHHhhcCCCCchHHhHHh
Q 009803 210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLK--------------------LEGLREVLSERCGGSPTFAQWAAA 268 (525)
Q Consensus 210 ~~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~--------------------le~~~~~l~~~~g~~pt~~ewa~a 268 (525)
..|+++ ||++| +++||||++||++|+++||.++. |++++..|++++|++||..+||.+
T Consensus 58 ~~d~v~~yl~~i-gr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~~ 136 (415)
T PRK07598 58 STDLVRLYLQEI-GRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKT 136 (415)
T ss_pred CCChHHHHHHhc-ccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHHH
Confidence 479999 99999 99999999999999999999999 899999999999999999999966
Q ss_pred hcCC----------------------HHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHh
Q 009803 269 AGVD----------------------QRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRG 326 (525)
Q Consensus 269 ~g~d----------------------~~~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirA 326 (525)
+|++ ...|.+.++.|..|+++||.+|+++|+++|++|.++|++++||||||++|||+|
T Consensus 137 ~~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~ra 216 (415)
T PRK07598 137 ADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERA 216 (415)
T ss_pred hCCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHH
Confidence 6554 555555567888999999999999999999999999999999999999999999
Q ss_pred hhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHH
Q 009803 327 AEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLH 406 (525)
Q Consensus 327 iekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~ 406 (525)
+++|||++|++|+||++||||++|.+++.+++++||+|.|+.+.+++++++++.+.+++||.||.+|||+.+|+++++|+
T Consensus 217 vekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr 296 (415)
T PRK07598 217 VEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVR 296 (415)
T ss_pred HHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHH
Q 009803 407 AVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQE 486 (525)
Q Consensus 407 ~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~E 486 (525)
.++.....++|||.+++++++..+.+.+.++ ..+|++.+....+...|..+|..||++||.||.||||++||.++|++|
T Consensus 297 ~~l~~~~~~~SLd~~vg~~~d~~l~d~l~~~-~~~pee~~~~~~l~~~L~~~L~~L~~reR~VI~LRygl~d~~~~Tl~E 375 (415)
T PRK07598 297 EVLLRVPRSVSLETKVGKDKDTELGDLLETD-DISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAE 375 (415)
T ss_pred HHHHHccCCcccccccCCCccccHHHhccCC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCCCHHH
Confidence 9999889999999999988888888877654 458999999999999999999999999999999999999999999999
Q ss_pred HHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhhhhhc
Q 009803 487 IGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 523 (525)
Q Consensus 487 IAe~LgIS~erVRqie~RALkKLR~~l~~~~L~~yl~ 523 (525)
||+.||||+++|||++++|++|||++-....|++|+.
T Consensus 376 IA~~LGvS~erVRqie~rAl~KLR~~~~~~~l~~y~~ 412 (415)
T PRK07598 376 IGRALDLSRERVRQIESKALQKLRQPKRRNRIRDYLE 412 (415)
T ss_pred HHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHHH
Confidence 9999999999999999999999999999999999986
No 2
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=2.8e-63 Score=519.99 Aligned_cols=311 Identities=48% Similarity=0.794 Sum_probs=299.3
Q ss_pred CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHH
Q 009803 210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD 288 (525)
Q Consensus 210 ~~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e 288 (525)
..|++. ||++| +++|+||++||++|+++|+.++.+++++.+|+...|+.|+..+||.++|++...|.+++..|..|++
T Consensus 61 ~~d~l~~Yl~~i-~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~ 139 (373)
T PRK07406 61 TEDSIRVYLQEI-GRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKE 139 (373)
T ss_pred CCCHHHHHHHHh-cccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHH
Confidence 368899 99999 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchH
Q 009803 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV 368 (525)
Q Consensus 289 ~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~ 368 (525)
.||.+|+++|+++|++|.++|.+++||+|||++|||+++++|||.+|++|+|||+||||++|.++|++++++||+|.|+.
T Consensus 140 ~Li~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~ 219 (373)
T PRK07406 140 KMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLY 219 (373)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHH
Q 009803 369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK 448 (525)
Q Consensus 369 ~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~ 448 (525)
..+++++++...|.+++|+.||.+|||+.+|+++++|..++.....++|||.+++++++..+.++++++. .+|++.+..
T Consensus 220 ~~~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d~l~d~~-~~pee~~~~ 298 (373)
T PRK07406 220 ETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADG-ETPEDDVAK 298 (373)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHHhcCCCC-CCHHHHHHH
Confidence 9999999999999999999999999999999999999999988889999999998777777888888763 478888888
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhhhhh
Q 009803 449 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYA 522 (525)
Q Consensus 449 ~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~~yl 522 (525)
..+...|..+|+.||++||.||.+|||++|++++|++|||+.||||++||||++.+|++|||+......|+.|+
T Consensus 299 ~~~~~~L~~aL~~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~~~~~~~l~~~~ 372 (373)
T PRK07406 299 NLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 372 (373)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHh
Confidence 99999999999999999999999999998888899999999999999999999999999999999999999986
No 3
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00 E-value=5.5e-62 Score=504.07 Aligned_cols=310 Identities=37% Similarity=0.688 Sum_probs=296.5
Q ss_pred CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHH
Q 009803 210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD 288 (525)
Q Consensus 210 ~~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e 288 (525)
..|++. ||++| +++|+||++||++|+++|+.++.++..+..|+...|+.|+..+|+.++++++..|...++.|..|++
T Consensus 16 ~~d~~~~yl~~i-~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~ 94 (327)
T PRK05949 16 SADMVRTYLHEI-GRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQ 94 (327)
T ss_pred CCCHHHHHHHHc-CCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHH
Confidence 468999 99999 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchH
Q 009803 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV 368 (525)
Q Consensus 289 ~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~ 368 (525)
.||.+|+++|+++|++|.+++.+++|||||||+|||+++++|||++|++|+|||+||||++|.+++.+++++||+|.|+.
T Consensus 95 ~Li~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~~ 174 (327)
T PRK05949 95 KMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHIT 174 (327)
T ss_pred HHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHH
Q 009803 369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK 448 (525)
Q Consensus 369 ~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~ 448 (525)
..+++++++.+.+.+++|+.||.+|||+.+|+++++|..++.....++|||.+++++++..+.+.++++. .+|++.+..
T Consensus 175 ~~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~~-~~pe~~~~~ 253 (327)
T PRK05949 175 EKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEG-PSPDQYITQ 253 (327)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCCC-CCHHHHHHH
Confidence 9999999999999999999999999999999999999999998899999999998777777788887765 589999999
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhhhhhc
Q 009803 449 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 523 (525)
Q Consensus 449 ~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~~yl~ 523 (525)
..+...|..+|+.||++||.||.+|||++|++++|++|||+.||||+++|||++++|++|||+. ...|+.|+.
T Consensus 254 ~~~~~~L~~~L~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~~--~~~l~~~~~ 326 (327)
T PRK05949 254 ELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRRR--RANVKEYLA 326 (327)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence 9999999999999999999999999999988999999999999999999999999999999994 467888875
No 4
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=100.00 E-value=2.4e-61 Score=493.79 Aligned_cols=297 Identities=45% Similarity=0.778 Sum_probs=284.0
Q ss_pred CHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHH
Q 009803 212 DPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKM 290 (525)
Q Consensus 212 d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~L 290 (525)
|++. ||++| +++|+||++||.+|+++|+.++.+++++..|+++.|++||..+||+++|++...|...++.|..|++.|
T Consensus 1 ~~~~~yl~~~-~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~L 79 (298)
T TIGR02997 1 DLVRLYLQEI-GRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKM 79 (298)
T ss_pred CcHHHHHHHc-cccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHH
Confidence 4677 99999 999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHH
Q 009803 291 ITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEA 370 (525)
Q Consensus 291 v~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~ 370 (525)
|.+|+++|+++|++|.++|.+++|||||||+|||+|+++|||.+|++|+||++||||++|.+++.+++++||+|.++...
T Consensus 80 v~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~~~~~~ 159 (298)
T TIGR02997 80 IKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEK 159 (298)
T ss_pred HHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHHHH
Q 009803 371 TYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKF 450 (525)
Q Consensus 371 ~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~~ 450 (525)
+++++++...+.+.+|+.||.+|||+.+|+++++|..++.....++|||.+++++++.++.+.+++. ..+|++.+....
T Consensus 160 ~~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~-~~~pe~~~~~~~ 238 (298)
T TIGR02997 160 LNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDD-GESPEEQVERES 238 (298)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccCC-CCCHHHHHHHHH
Confidence 9999999999999999999999999999999999999999888999999998766666677777764 458899999888
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803 451 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510 (525)
Q Consensus 451 ~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR 510 (525)
+...|..+|+.||++||.||.+|||++|++++|++|||+.||||++||||++++|++|||
T Consensus 239 ~~~~L~~~L~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr 298 (298)
T TIGR02997 239 LRQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298 (298)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 999999999999999999999999998888899999999999999999999999999996
No 5
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=5.4e-61 Score=495.09 Aligned_cols=309 Identities=41% Similarity=0.705 Sum_probs=295.2
Q ss_pred CCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHH
Q 009803 211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDK 289 (525)
Q Consensus 211 ~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~ 289 (525)
+|++. ||++| +++|+||++||++|+++|+.++.+++++..|++++|++|+..+||.++++++..|...+..|..|+++
T Consensus 7 ~~~~~~yl~~i-~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~ 85 (317)
T PRK07405 7 TDLVRTYLREI-GRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRK 85 (317)
T ss_pred CcHHHHHHHHc-cccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHH
Confidence 57899 99999 99999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHH
Q 009803 290 MITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVE 369 (525)
Q Consensus 290 Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~ 369 (525)
||..|+++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+|||+||||++|.++|.+++++||+|.|+..
T Consensus 86 L~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~~ 165 (317)
T PRK07405 86 MVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITE 165 (317)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHHH
Q 009803 370 ATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKK 449 (525)
Q Consensus 370 ~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~ 449 (525)
.+++++++.+.+...+|+.||.+|||+.+|+++++|..++.....++|||.+++++++..+.+.++++. .+|++.+...
T Consensus 166 ~~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~~-~~pe~~~~~~ 244 (317)
T PRK07405 166 KLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTG-ASPEDFATQS 244 (317)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCCC-CCHHHHHHHH
Confidence 999999999999999999999999999999999999999988888999999998777777788887764 5799999989
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhhhhhc
Q 009803 450 FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 523 (525)
Q Consensus 450 ~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~~yl~ 523 (525)
.+...|..+|+.||++||.||.+|||++|++++|++|||+.||||++||||++.+|++|||+. ...|..|+.
T Consensus 245 ~~~~~l~~al~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~--~~~l~~~~~ 316 (317)
T PRK07405 245 SLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKR--KANIQEYLA 316 (317)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence 999999999999999999999999999888999999999999999999999999999999995 457788875
No 6
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=100.00 E-value=1.2e-60 Score=489.49 Aligned_cols=312 Identities=42% Similarity=0.708 Sum_probs=288.1
Q ss_pred CCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHh-hcCCCCchH---------------HhHHhhcCCH
Q 009803 211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSE-RCGGSPTFA---------------QWAAAAGVDQ 273 (525)
Q Consensus 211 ~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~-~~g~~pt~~---------------ewa~a~g~d~ 273 (525)
.|.+. |+.++ +..+++++++|..+...++....+..+...|.. ..|..|+.. +|+.....++
T Consensus 8 ~d~~~~~l~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~E 86 (342)
T COG0568 8 ADAVRAYLDEI-GRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEE 86 (342)
T ss_pred hhHHHHHHHHh-cchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHH
Confidence 56778 99999 999999999999999999887777677777776 677888876 6666665554
Q ss_pred -HHHHHHHhcc---HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHH
Q 009803 274 -RELRRRLNYG---ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA 349 (525)
Q Consensus 274 -~~L~~~l~~g---~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqa 349 (525)
..|..++..| ..|+.+||.+|+|||++||++|.|+|+++.|||||||||||+|+++|||++||+|||||+|||||+
T Consensus 87 e~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrqa 166 (342)
T COG0568 87 EKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQA 166 (342)
T ss_pred HHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHHH
Confidence 5677776666 459999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCC
Q 009803 350 VRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLK 429 (525)
Q Consensus 350 I~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~ 429 (525)
|.++|.+++|+||+|+|+.+.+++++++.+.+.+++|++|+.+|||+.+|+++++|..++.....++|||.+++++++..
T Consensus 167 I~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~ded~~ 246 (342)
T COG0568 167 ITRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSE 246 (342)
T ss_pred HHHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCCCcccH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998889
Q ss_pred CCcccCCCCCCCHHHHHHHHHHHHHHHHHHhc-CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 009803 430 PSEVIADPEAETAEDLLIKKFMKEDLEKVLDT-LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRK 508 (525)
Q Consensus 430 l~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~-L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkK 508 (525)
+.|+++|+...+|++.+....+...+...|.. |+|+|+.||++|||++|++|.|++|||+.+|||++|||||+.+||+|
T Consensus 247 l~d~leD~~~~~p~~~~~~~~~~~~~~~~L~~~Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~isrERvRQIE~kAl~K 326 (342)
T COG0568 247 LGDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAKALRK 326 (342)
T ss_pred HHHHhhcCCcCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCcchHHHHHHHhCCcHHHHHHHHHHHHHH
Confidence 99999999877999999999999999999999 99999999999999999999999999999999999999999999999
Q ss_pred HH-hHHhhchhhhhhc
Q 009803 509 LK-NKKRTKHLMQYAI 523 (525)
Q Consensus 509 LR-~~l~~~~L~~yl~ 523 (525)
|| .......+++|++
T Consensus 327 Lr~~~~~~~~~~~~l~ 342 (342)
T COG0568 327 LRRHPERSALLRSYLD 342 (342)
T ss_pred HHHhhhhhhHHHHhhC
Confidence 99 5555566788864
No 7
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=100.00 E-value=3.8e-60 Score=510.83 Aligned_cols=302 Identities=40% Similarity=0.674 Sum_probs=276.7
Q ss_pred CCCCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHH
Q 009803 208 VDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILC 286 (525)
Q Consensus 208 ~~~~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A 286 (525)
....|+++ ||++| +++|+||++||++|+++|+.+..++.. +. ...+|+.. ....|++.+..|..|
T Consensus 207 ~~~~d~l~~YL~~i-~~~~lLt~eEE~~La~~i~~g~~~~~~---~~-------~~~~~~~~---~~~~l~~~~~~g~~A 272 (509)
T PRK05901 207 TATADPVKAYLKQI-GKVKLLNAEEEVELAKRIEAGLYAEEL---LA-------EGEKLDPE---LRRDLQWIGRDGKRA 272 (509)
T ss_pred cccccHHHHHHHHh-ccCCCCCHHHHHHHHHHHHhCCchhhh---hh-------hcccchhh---hhhhhhhhccchHHH
Confidence 34578999 99999 999999999999999999976433221 11 11224422 456788889999999
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccc
Q 009803 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH 366 (525)
Q Consensus 287 ~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~ 366 (525)
+++||.+|+|||++||++|.++|++++||||||+||||+|+++|||++|++|+|||+||||++|.++|++++|+||+|.|
T Consensus 273 r~~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~~ 352 (509)
T PRK05901 273 KNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVH 352 (509)
T ss_pred HHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHH
Q 009803 367 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLL 446 (525)
Q Consensus 367 ~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~ 446 (525)
+.+.+++++++.+.|.+.+|+.||.+|||+.+|+++++|..++.....++|||.+++++++..+.++++|+....|++.+
T Consensus 353 ~~e~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~~p~~~~ 432 (509)
T PRK05901 353 MVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDAV 432 (509)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCCCCCHHHHH
Confidence 99999999999999999999999999999999999999999999888999999999877777788999988777899999
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhhhhhc
Q 009803 447 IKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 523 (525)
Q Consensus 447 ~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~~yl~ 523 (525)
....++..|..+|..|++|||.||.+|||+++++++|++|||+.||||++|||||+.+||+|||.......|++|++
T Consensus 433 ~~~~l~~~L~~aL~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~~~~~~l~~~l~ 509 (509)
T PRK05901 433 SFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDFLD 509 (509)
T ss_pred HHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 99999999999999999999999999999998899999999999999999999999999999999999999999974
No 8
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=100.00 E-value=3.8e-59 Score=481.98 Aligned_cols=300 Identities=42% Similarity=0.710 Sum_probs=275.4
Q ss_pred CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHH
Q 009803 210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD 288 (525)
Q Consensus 210 ~~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e 288 (525)
.+|++. ||++| +++|+||++||++|+++|+.+..++.. |+..+|.... ....|...++.|..|++
T Consensus 24 ~~~~~~~Yl~~i-~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~ 89 (324)
T PRK07921 24 AADLVRVYLNGI-GKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARR 89 (324)
T ss_pred CCChHHHHHHHh-cccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHH
Confidence 368899 99999 999999999999999999986655432 2233333211 34678889999999999
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchH
Q 009803 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV 368 (525)
Q Consensus 289 ~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~ 368 (525)
+||..|+++|+++|++|.+++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.+++++++++||+|.|+.
T Consensus 90 ~Lv~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~ 169 (324)
T PRK07921 90 HLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLV 169 (324)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHH
Q 009803 369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK 448 (525)
Q Consensus 369 ~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~ 448 (525)
+.+++++++...|.+.+|+.||.+|||+.+|+++++|..++.....++|||.+++++++.++.++++|+...+|++.+..
T Consensus 170 ~~~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~pe~~~~~ 249 (324)
T PRK07921 170 EQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIA 249 (324)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCCCCCHHHHHHH
Confidence 99999999999999999999999999999999999999999888889999999987766678888988766789988888
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhhhhhc
Q 009803 449 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 523 (525)
Q Consensus 449 ~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~~yl~ 523 (525)
..+...|..+|+.|+++|+.||.+|||++|++++|++|||+.||||++|||||+.+|++|||.......|+.|+.
T Consensus 250 ~~~~~~l~~~L~~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~~~~~~l~~~~~ 324 (324)
T PRK07921 250 GLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSYAS 324 (324)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHHHHHHHHhhC
Confidence 899999999999999999999999999998999999999999999999999999999999999998889998863
No 9
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=3.6e-55 Score=460.09 Aligned_cols=273 Identities=45% Similarity=0.767 Sum_probs=260.9
Q ss_pred CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHH
Q 009803 210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD 288 (525)
Q Consensus 210 ~~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e 288 (525)
..|+++ ||++| +++|+||++||.+|+.+++. |+..|++
T Consensus 94 ~~d~~~~yl~~i-~~~~~l~~~ee~~L~~~~~~----------------------------------------Gd~~A~~ 132 (367)
T PRK09210 94 INDPVRMYLKEI-GRVPLLTAEEEIELAKRIEE----------------------------------------GDEEAKQ 132 (367)
T ss_pred cCcHHHHHHHHh-hccCCCCHHHHHHHHHHHHh----------------------------------------hHHHHHH
Confidence 468999 99999 99999999999999988864 4578999
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchH
Q 009803 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV 368 (525)
Q Consensus 289 ~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~ 368 (525)
.||..|+++|+++|++|.+++.+++||+||||+|||+|+++|||.+|++|+|||+||||++|.++|++++|++|+|.|+.
T Consensus 133 ~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~~ 212 (367)
T PRK09210 133 RLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMV 212 (367)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHH
Q 009803 369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK 448 (525)
Q Consensus 369 ~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~ 448 (525)
+.++++.++.+.|.+++||.||.+|||+.+|+++++|..++.....++|||.+++++++..+.++++|+...+|++.+..
T Consensus 213 ~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~~~~p~~~~~~ 292 (367)
T PRK09210 213 ETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAY 292 (367)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCCCCCHHHHHHH
Confidence 99999999999999999999999999999999999999999888889999999987777788899998877789999999
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhhhhhc
Q 009803 449 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 523 (525)
Q Consensus 449 ~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~~yl~ 523 (525)
..++..|..+|..||++||.||.+|||++||+++|++|||+.||||++|||||+.+||+|||++.....|+.|++
T Consensus 293 ~~~~~~l~~~l~~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~~~~~~~l~~~~~ 367 (367)
T PRK09210 293 ELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 367 (367)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhChHHHhHHHHhhC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999974
No 10
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=2.7e-52 Score=464.69 Aligned_cols=270 Identities=40% Similarity=0.667 Sum_probs=251.3
Q ss_pred HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHHHHHH
Q 009803 216 YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNI 295 (525)
Q Consensus 216 yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv~~nl 295 (525)
||.++ ...+.||++++..++++|+. |.. .+..|+++||.+|+
T Consensus 349 ~L~~i-e~~~~Ls~eElk~l~~~i~~---------------g~~----------------------~~~~a~~~Li~~nl 390 (619)
T PRK05658 349 ELEAI-EEETGLTIEELKEINRQISK---------------GEA----------------------KARRAKKEMVEANL 390 (619)
T ss_pred HHHHH-HHHhCCCHHHHHHHHHHHhc---------------cch----------------------hhhHHHHHHHHHHH
Confidence 67777 66777777777777776664 210 12478999999999
Q ss_pred HHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHH
Q 009803 296 RLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVK 375 (525)
Q Consensus 296 rLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ 375 (525)
|||++||++|.++|++++||||||+||||+|+++|||++|++|+|||+||||++|.++|++++|+||+|.|+.+.+++++
T Consensus 391 rlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~irip~~~~~~~~k~~ 470 (619)
T PRK05658 391 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLN 470 (619)
T ss_pred HHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCceecCHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHHHHHHHHH
Q 009803 376 EARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDL 455 (525)
Q Consensus 376 ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~~~~~~L 455 (525)
++.+.+.+++|+.||.+|||+.||+++++|..++.....++|||.+++++++.++.++++|+...+|++.+....++..|
T Consensus 471 ~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~~~~~l~d~i~d~~~~~p~~~~~~~~~~~~l 550 (619)
T PRK05658 471 RISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREAT 550 (619)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCCCCCchhhhcCCCCCCChHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999888999999999888777889999988777899999999999999
Q ss_pred HHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhhhhhc
Q 009803 456 EKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 523 (525)
Q Consensus 456 ~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~~yl~ 523 (525)
..+|..||+||+.||++|||++++.++|++|||+.||||++|||||+.+|++|||++.....|+.|++
T Consensus 551 ~~~l~~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr~~~~~~~l~~~~~ 618 (619)
T PRK05658 551 TDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRSFLD 618 (619)
T ss_pred HHHHHcCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHhchHHHHHHHHHhc
Confidence 99999999999999999999988899999999999999999999999999999999999999999986
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=4.5e-48 Score=383.49 Aligned_cols=238 Identities=45% Similarity=0.777 Sum_probs=226.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceeccc
Q 009803 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF 365 (525)
Q Consensus 286 A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~ 365 (525)
|+++||..|+++|+++|++|.++|.+++||+|||++||++|+++|||++|++|+|||+||||++|.++++++.+.+|+|.
T Consensus 1 a~~~Li~~~~~lv~~ia~~~~~~~~~~eDLiQeG~igL~~A~~~fd~~~g~~FstYA~~~Ir~~I~~~l~~~~~~vrip~ 80 (238)
T TIGR02393 1 AKKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80 (238)
T ss_pred CHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCChHHHhHHHHHHHHHHHHHHcCCcEEeCH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHH
Q 009803 366 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL 445 (525)
Q Consensus 366 ~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~ 445 (525)
++...++++.++.+.+.+++|+.||.+|||+.+|+++++|..++.....++|||.+++++++.++.+.++|+...+|++.
T Consensus 81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~p~~~ 160 (238)
T TIGR02393 81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESPDDY 160 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcccHHHHhcCCCCCChHHH
Confidence 99999999999999999999999999999999999999999999887789999999877666677788888777789988
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhhhhhc
Q 009803 446 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 523 (525)
Q Consensus 446 ~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~~yl~ 523 (525)
+....+...|..+|+.||++||.||.+|||+++++++|++|||+.||||+++|+|++.+|++|||+.+....|+.|++
T Consensus 161 ~~~~~~~~~l~~~l~~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~~~~~~~~~~ 238 (238)
T TIGR02393 161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKSFLD 238 (238)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHHHhHHHHhhC
Confidence 888889999999999999999999999999887788999999999999999999999999999999999999999875
No 12
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=2.8e-45 Score=373.90 Aligned_cols=262 Identities=26% Similarity=0.418 Sum_probs=226.5
Q ss_pred CHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHH
Q 009803 212 DPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKM 290 (525)
Q Consensus 212 d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~L 290 (525)
+..+ ||+++ +++|+||+++|.+|+++++. .|+..|+++|
T Consensus 6 ~~~~~y~~~~-~~~~~l~~~~e~~L~~~~~~---------------------------------------~gd~~A~~~L 45 (289)
T PRK07500 6 SADRSMIRSA-MKAPYLEREEEHALAYRWKD---------------------------------------HRDEDALHRI 45 (289)
T ss_pred hHHHHHHHHH-hcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHH
Confidence 4566 99999 99999999999999987752 1457899999
Q ss_pred HHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHH-
Q 009803 291 ITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVE- 369 (525)
Q Consensus 291 v~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~- 369 (525)
|..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|+|||+||||++|.++++++++++|+|.+...
T Consensus 46 v~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~~~~~~ 125 (289)
T PRK07500 46 ISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQK 125 (289)
T ss_pred HHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCccHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999765
Q ss_pred -HHHHHHHHHHHHHH---HcCCCCCHHHHHHHcCCCHHHHHHHH-hCCCCCCCcccccccccCC--CCCcccCCCCCCCH
Q 009803 370 -ATYRVKEARKQLYS---ENGRHPNNEEVAEATGLSMKRLHAVL-LSPKAPRSLDQKIGINQNL--KPSEVIADPEAETA 442 (525)
Q Consensus 370 -~~~ki~ka~~~L~~---~lgr~Pt~eEIA~~lgis~~~v~~~l-~~~~~~~SLD~~i~~d~~~--~l~d~l~d~~~~~p 442 (525)
...++++.+..+.+ .+|+.||.+|||+.||+++++|..+. .....++|||.+++++++. ++.+.++++.. +|
T Consensus 126 ~~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~i~d~~~-~p 204 (289)
T PRK07500 126 ALFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDSP-LP 204 (289)
T ss_pred HHHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCCCcccHHHhccCCCC-Cc
Confidence 45566666666655 68999999999999999999998875 3455799999998765443 46777877643 56
Q ss_pred HHHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803 443 EDLLIK----KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 516 (525)
Q Consensus 443 ee~~~~----~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~ 516 (525)
++.+.. ......|..+|+.||++||.||.+||+.. +++|++|||+.||||++||+|++++|++|||..+...
T Consensus 205 e~~~~~~~~~~~~~~~l~~al~~L~~rer~vl~lr~~~~--~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~~~ 280 (289)
T PRK07500 205 DEQVESSIDGERRRRWLTQALQTLNERELRIIRERRLRE--DGATLEALGEELGISKERVRQIEARALEKLRRALLSQ 280 (289)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 665443 34567799999999999999999999732 2399999999999999999999999999999988754
No 13
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=4.3e-45 Score=371.60 Aligned_cols=261 Identities=28% Similarity=0.440 Sum_probs=223.8
Q ss_pred CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHH
Q 009803 210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD 288 (525)
Q Consensus 210 ~~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e 288 (525)
+.+++. |++++ +++|+||.++|.+|+.+++. .|+..|++
T Consensus 12 ~~~~~~~y~~~~-~~~~~l~~~~e~~l~~~~~~---------------------------------------~Gd~~a~~ 51 (284)
T PRK06596 12 PEGNLDAYIQAV-NKIPMLTAEEEYMLAKRLRE---------------------------------------HGDLEAAK 51 (284)
T ss_pred CccHHHHHHHHH-hccCCCCHHHHHHHHHHHHH---------------------------------------cCCHHHHH
Confidence 457888 99999 99999999999999887542 25578999
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchH
Q 009803 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV 368 (525)
Q Consensus 289 ~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~ 368 (525)
.||..|+++|+++|++|.+++.+++||+|||++||++|+++|||++|++|+|||+||||++|.+++++++++||+|.+..
T Consensus 52 ~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~p~~~~ 131 (284)
T PRK06596 52 QLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKA 131 (284)
T ss_pred HHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeeeccchHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999988999999864
Q ss_pred --HHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHh-CCCCCCCcccccccccC--CCCCcccCCCCCCCHH
Q 009803 369 --EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL-SPKAPRSLDQKIGINQN--LKPSEVIADPEAETAE 443 (525)
Q Consensus 369 --~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~-~~~~~~SLD~~i~~d~~--~~l~d~l~d~~~~~pe 443 (525)
....++++....+. .+++||.+|||+.||+++++|..++. ....++|||.+++++++ .++.+.++++. .+|+
T Consensus 132 ~~~~~~~~~~~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~~-~~p~ 208 (284)
T PRK06596 132 QRKLFFNLRKAKKRLG--WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDKS-SDPA 208 (284)
T ss_pred HHHHHHHHHHHHHHhc--cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcCCCC-CCch
Confidence 23445555555543 35999999999999999999999875 34578999999865532 34667777763 4677
Q ss_pred HHHHHH----HHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803 444 DLLIKK----FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 515 (525)
Q Consensus 444 e~~~~~----~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~ 515 (525)
+.+... .+...|..+|+.||++||.||.+||+.+ +++|++|||+.||||++||||++.+|++|||..+..
T Consensus 209 ~~~~~~~~~~~~~~~L~~al~~L~~rEr~VL~lry~~~--~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~l~~ 282 (284)
T PRK06596 209 DVLEEDNWEDQRRALLADALEGLDERSRDIIEARWLDD--DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEA 282 (284)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCC--CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 766654 3577899999999999999999999853 459999999999999999999999999999997754
No 14
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=100.00 E-value=2.1e-44 Score=372.88 Aligned_cols=268 Identities=36% Similarity=0.573 Sum_probs=249.2
Q ss_pred CCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHH
Q 009803 211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDK 289 (525)
Q Consensus 211 ~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~ 289 (525)
.|... ||.+| +..|+||+++|..|..+++. |+..|++.
T Consensus 52 ~~~~~~y~~~~-~~~~~l~~~ee~~li~~~~~----------------------------------------Gd~~A~~~ 90 (325)
T PRK05657 52 LDATQLYLNEI-GYSPLLTAEEEVYFARRALR----------------------------------------GDFAARQR 90 (325)
T ss_pred ccHHHHHHHHH-hcCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHH
Confidence 56778 99999 99999999999999887763 56789999
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHH
Q 009803 290 MITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVE 369 (525)
Q Consensus 290 Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~ 369 (525)
||..|.++|+++|++|.+++.+++||+||||+|+|+++++||+.+|++|+||++||||++|.++++++.+.+|+|.++.+
T Consensus 91 Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~~~~~ 170 (325)
T PRK05657 91 MIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVK 170 (325)
T ss_pred HHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHHH
Q 009803 370 ATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKK 449 (525)
Q Consensus 370 ~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~ 449 (525)
.++.+.++.+.+...+|+.|+.+|||+.+|+++++|..++.......|||.++..+...++.+.+.++...+|++.+...
T Consensus 171 ~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~ 250 (325)
T PRK05657 171 ELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDD 250 (325)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCCcchhhhccCCCCCCHHHHHHHH
Confidence 99989999999999999999999999999999999999998888889999998776666777888877666899998888
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhh
Q 009803 450 FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLM 519 (525)
Q Consensus 450 ~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~ 519 (525)
+....|..+|..||+++|.||.+|||+.+.+.+|++|||+.||||+++|++++++|+++||+.+...++.
T Consensus 251 e~~~~L~~aL~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~~~~~~ 320 (325)
T PRK05657 251 DMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQGLS 320 (325)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhCccc
Confidence 8889999999999999999999999876666699999999999999999999999999999999877664
No 15
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=100.00 E-value=1.8e-44 Score=364.38 Aligned_cols=257 Identities=29% Similarity=0.489 Sum_probs=217.0
Q ss_pred HHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHH
Q 009803 213 PLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMI 291 (525)
Q Consensus 213 ~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv 291 (525)
++. ||+++ +++|+|++++|.+|+.++.. .|+..|++.||
T Consensus 2 ~~~~yl~~~-~~~~~l~~~~e~~l~~~~~~---------------------------------------~gd~~a~~~Lv 41 (270)
T TIGR02392 2 SLDAYIRAV-NRIPMLTPEEEYQLAKRLRE---------------------------------------HGDLDAAKKLV 41 (270)
T ss_pred hHHHHHHHH-hcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHH
Confidence 567 99999 99999999999999886532 25678999999
Q ss_pred HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchH--H
Q 009803 292 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV--E 369 (525)
Q Consensus 292 ~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~--~ 369 (525)
..|+++|+++|++|.+++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++++++++++|+|.+.. +
T Consensus 42 ~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir~p~~~~~~~ 121 (270)
T TIGR02392 42 LSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRK 121 (270)
T ss_pred HHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCceecCchHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999988999998764 3
Q ss_pred HHHHHHHHHHHHHHHcCCCC-CHHHHHHHcCCCHHHHHHHHh-CCCCCCCcccccccccCC--CCCcccCCCCCCCHHHH
Q 009803 370 ATYRVKEARKQLYSENGRHP-NNEEVAEATGLSMKRLHAVLL-SPKAPRSLDQKIGINQNL--KPSEVIADPEAETAEDL 445 (525)
Q Consensus 370 ~~~ki~ka~~~L~~~lgr~P-t~eEIA~~lgis~~~v~~~l~-~~~~~~SLD~~i~~d~~~--~l~d~l~d~~~~~pee~ 445 (525)
...++++....+. .++.| +.+|||+.||+++++|..++. ....++|||.+++++++. .+.+.++++. .+|++.
T Consensus 122 ~~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~l~d~~-~~pe~~ 198 (270)
T TIGR02392 122 LFFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKT-SDPEDT 198 (270)
T ss_pred HHHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCCccccHHHHhcCCC-CChHHH
Confidence 4555666555543 22556 699999999999999999865 334589999998765432 4556677654 367776
Q ss_pred HHHH----HHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 446 LIKK----FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 446 ~~~~----~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
+... .+...|..+|..||++||.||.+||+.+ +++|++|||+.||||.++|+|++.+|++|||+.+.
T Consensus 199 ~~~~~~~~~~~~~L~~al~~L~~rer~vl~l~y~~~--~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~l~ 269 (270)
T TIGR02392 199 LEEEQWEELQRQALANALGSLDARSRRIIEARWLDD--DKLTLQELAAEYGVSAERIRQIEKNAMKKLKAALA 269 (270)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhcCC--CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 6543 3567899999999999999999999753 34999999999999999999999999999998663
No 16
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=7.4e-44 Score=359.02 Aligned_cols=221 Identities=25% Similarity=0.372 Sum_probs=200.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 009803 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL 363 (525)
Q Consensus 284 ~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRi 363 (525)
..++++||.+|++||++||++|.++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++++++.++||+
T Consensus 39 ~~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I~~~lr~~~~~ir~ 118 (264)
T PRK07122 39 QRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKV 118 (264)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHcCCcccc
Confidence 45899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhC--CCCCCCcccccccccCC--CCCcccCCCCC
Q 009803 364 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKIGINQNL--KPSEVIADPEA 439 (525)
Q Consensus 364 P~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~--~~~~~SLD~~i~~d~~~--~l~d~l~d~~~ 439 (525)
|.++.+.+++++++...+.+++|+.||.+|||+.||+++++|.+++.. ...++|||.+++++++. .+.+.++
T Consensus 119 Pr~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~d~~~---- 194 (264)
T PRK07122 119 PRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDARAIADTLG---- 194 (264)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCCCCcccchhccC----
Confidence 999999999999999999999999999999999999999999998853 45789999998653322 3333333
Q ss_pred CCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803 440 ETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513 (525)
Q Consensus 440 ~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l 513 (525)
+++..+...+....|..+|+.||+++|.||.++|+.+ +|++|||+.||||.++|++++++|+++||..+
T Consensus 195 -~~~~~~e~~~~~~~l~~~l~~L~~rer~vl~l~y~~~----~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l 263 (264)
T PRK07122 195 -DVDAGLDQIENREALRPLLAALPERERTVLVLRFFES----MTQTQIAERVGISQMHVSRLLAKTLARLRDQL 263 (264)
T ss_pred -CcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhcCC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHc
Confidence 3455566667788899999999999999999999876 99999999999999999999999999999865
No 17
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=3.3e-42 Score=345.44 Aligned_cols=227 Identities=27% Similarity=0.453 Sum_probs=201.7
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCC-CCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccc
Q 009803 282 YGILCKDKMITSNIRLVISIAKNYQGA-GMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT 360 (525)
Q Consensus 282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~-g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~ 360 (525)
++..|+++||..|+++|+++|++|.+. +.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++++++.++
T Consensus 22 gd~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~~ 101 (256)
T PRK07408 22 PSIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPT 101 (256)
T ss_pred CCHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcCCe
Confidence 457899999999999999999999875 6679999999999999999999999999999999999999999999999999
Q ss_pred eecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHh--CCCCCCCcccccccccC--CCCCcccCC
Q 009803 361 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL--SPKAPRSLDQKIGINQN--LKPSEVIAD 436 (525)
Q Consensus 361 iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~--~~~~~~SLD~~i~~d~~--~~l~d~l~d 436 (525)
||+|.++...+++++++...|.+++|++||.+|||+.+|+++++|..++. .....+|||.+++++++ ..+.+.+++
T Consensus 102 vr~pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~~~d 181 (256)
T PRK07408 102 VRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDEDGSTSLGDLLPD 181 (256)
T ss_pred eeeCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCCCccccccccCC
Confidence 99999999999999999999999999999999999999999999999864 34568899998865433 245666666
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803 437 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 515 (525)
Q Consensus 437 ~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~ 515 (525)
+... +.. ...+....|..+|..||+++|.||.++|+.+ +|++|||+.||||.++|++++++|++|||+.+..
T Consensus 182 ~~~~-~~~--~~~~~~~~l~~~l~~L~~~~r~vl~l~y~~~----~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~~ 253 (256)
T PRK07408 182 PRYR-SFQ--LAQEDRIRLQQALAQLEERTREVLEFVFLHD----LTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQP 253 (256)
T ss_pred cccc-hhh--hhHHHHHHHHHHHHcCCHHHHHHHHHHHHCC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhc
Confidence 5432 221 2334557799999999999999999999877 9999999999999999999999999999998764
No 18
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=100.00 E-value=8e-41 Score=340.20 Aligned_cols=271 Identities=37% Similarity=0.561 Sum_probs=245.6
Q ss_pred CCCCCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHH
Q 009803 207 EVDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 285 (525)
Q Consensus 207 ~~~~~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~ 285 (525)
+...+|.++ ||.+| +.+|.||.++|.+|..+++. |+..
T Consensus 8 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~li~~~~~----------------------------------------gd~~ 46 (285)
T TIGR02394 8 ETRVADVTQLYLREI-GFKPLLTAEEEIAYARRALA----------------------------------------GDFE 46 (285)
T ss_pred ccCcchHHHHHHHHH-hccCCCCHHHHHHHHHHHHc----------------------------------------CCHH
Confidence 345678999 99999 99999999999999887663 4578
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceeccc
Q 009803 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF 365 (525)
Q Consensus 286 A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~ 365 (525)
|++.||..|.++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|+||+.|||+.++.+++.++.+.+++|.
T Consensus 47 a~~~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain~~i~~~~~~~~~p~ 126 (285)
T TIGR02394 47 ARKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPV 126 (285)
T ss_pred HHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHHHHHHHcCCceeCcH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHH
Q 009803 366 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL 445 (525)
Q Consensus 366 ~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~ 445 (525)
++...++.+.+..+.+.+.+|+.|+..++|..+|++++++..++......+|+|.++..++...+.+.+.++...+|++.
T Consensus 127 ~~~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~~~~pe~~ 206 (285)
T TIGR02394 127 HVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESL 206 (285)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchhhhhcCCCCCCHHHH
Confidence 99999999999888888899999999999999999999999999888889999988765554455566666655679999
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 009803 446 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHL 518 (525)
Q Consensus 446 ~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L 518 (525)
+...+....|..+|..||+++|.||.|+||+.+.+.+|++|||+.||||.++|++++++|+++||+.+...+.
T Consensus 207 ~~~~e~~~~L~~al~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~~~~~ 279 (285)
T TIGR02394 207 VQNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERDGV 279 (285)
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 9999999999999999999999999999975444459999999999999999999999999999999876443
No 19
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=100.00 E-value=7e-41 Score=335.23 Aligned_cols=242 Identities=28% Similarity=0.425 Sum_probs=215.4
Q ss_pred hcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHH
Q 009803 221 TSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVIS 300 (525)
Q Consensus 221 ~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv~~nlrLV~~ 300 (525)
++++|+||+++|.+|+.+++. ++..|++.||..|+++|++
T Consensus 10 ~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~~~~~v~~ 49 (254)
T TIGR02850 10 TSKLPVLKNQEMRELFIRMQS----------------------------------------GDTTAREKLINGNLRLVLS 49 (254)
T ss_pred ccCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHHH
Confidence 478999999999999877653 4578999999999999999
Q ss_pred HHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHHHHHHH
Q 009803 301 IAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQ 380 (525)
Q Consensus 301 IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~ 380 (525)
+|++|.+++.+++||+||||+|||+++++|||.+|.+|+||++|||++.|.++++++. .+|+|.++...++++.++...
T Consensus 50 ~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~-~ir~p~~~~~~~~~~~~~~~~ 128 (254)
T TIGR02850 50 VIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDK 128 (254)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CccCchHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999975 789999999999999999999
Q ss_pred HHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCC--CCCcccCCCCCCCHHHHHHHHHHHHHHHHH
Q 009803 381 LYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNL--KPSEVIADPEAETAEDLLIKKFMKEDLEKV 458 (525)
Q Consensus 381 L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~--~l~d~l~d~~~~~pee~~~~~~~~~~L~~a 458 (525)
+.+++|+.||.+|||+.+|+++++|..++.....++|||.++.++++. ++.+.+.++.. .++ .......|..+
T Consensus 129 l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~~~d~~~-~~~----~~~~~~~l~~~ 203 (254)
T TIGR02850 129 LISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEKN-KDS----QWLEGIALKEA 203 (254)
T ss_pred HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCCCCcchhhhhcCCccc-cHH----HHHhHHHHHHH
Confidence 999999999999999999999999999998888899999987544332 35566665432 222 12234578999
Q ss_pred HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803 459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512 (525)
Q Consensus 459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~ 512 (525)
++.||+++|.||.+||+.+ +|++|||+.||+|+++|++++.+|++|||+.
T Consensus 204 l~~L~~rer~vi~~~~~~~----~t~~eIA~~lgis~~~V~~~~~ral~kLr~~ 253 (254)
T TIGR02850 204 MKRLNEREKMILNMRFFEG----KTQMEVAEEIGISQAQVSRLEKAALKHMRKY 253 (254)
T ss_pred HHcCCHHHHHHHHHHHcCC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 9999999999999999866 9999999999999999999999999999975
No 20
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=100.00 E-value=2.6e-40 Score=332.02 Aligned_cols=227 Identities=30% Similarity=0.422 Sum_probs=205.0
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcc
Q 009803 282 YGILCKDKMITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS 358 (525)
Q Consensus 282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~---~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~ 358 (525)
++..|+++||..|+++|+++|++|.+ .+++++||+|||++|||+|+++|||++|++|+|||+||||++|.++++++.
T Consensus 20 ~~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~ 99 (257)
T PRK05911 20 QEIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQD 99 (257)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 45789999999999999999999862 456899999999999999999999999999999999999999999999987
Q ss_pred cceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCC--CCCCccccccc--cc--CCCCCc
Q 009803 359 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPK--APRSLDQKIGI--NQ--NLKPSE 432 (525)
Q Consensus 359 r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~--~~~SLD~~i~~--d~--~~~l~d 432 (525)
| +|.++.+.++++.++...|.+.+|+.||.+|||+.+|+++++|..++.... .++|||.++.. ++ +.++.+
T Consensus 100 ~---~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~~~~~~~~~l~~ 176 (257)
T PRK05911 100 W---VPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQSDDEAGLALEE 176 (257)
T ss_pred C---CCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCCCCCccccchhh
Confidence 7 899999999999999999999999999999999999999999999986543 46899987643 11 234677
Q ss_pred ccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803 433 VIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512 (525)
Q Consensus 433 ~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~ 512 (525)
.++|+....|++.+...+....|..+|+.||+++|.||.++|+.+ +|++|||+.||||.++|++++++|+++||+.
T Consensus 177 ~l~d~~~~~~~~~~~~~~~~~~l~~al~~L~~~er~vi~l~y~e~----~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 252 (257)
T PRK05911 177 RIADERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYYYEE----LVLKEIGKILGVSESRVSQIHSKALLKLRAT 252 (257)
T ss_pred hccCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 788776667888888888889999999999999999999999877 9999999999999999999999999999998
Q ss_pred Hhh
Q 009803 513 KRT 515 (525)
Q Consensus 513 l~~ 515 (525)
+..
T Consensus 253 l~~ 255 (257)
T PRK05911 253 LSA 255 (257)
T ss_pred HHh
Confidence 753
No 21
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=100.00 E-value=3.5e-39 Score=323.51 Aligned_cols=242 Identities=28% Similarity=0.444 Sum_probs=214.7
Q ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHH
Q 009803 222 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI 301 (525)
Q Consensus 222 ~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv~~nlrLV~~I 301 (525)
.++|+|+++|+..|+.+++. ++..|+++||..|.++|+++
T Consensus 14 ~~~~~l~~~~~~~l~~~~~~----------------------------------------gd~~a~~~l~~~~~~~v~~~ 53 (258)
T PRK08215 14 SKLPVLKNEEMRELFERMQN----------------------------------------GDKEAREKLINGNLRLVLSV 53 (258)
T ss_pred CCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHHHHHHHHH
Confidence 66899999999998877653 45789999999999999999
Q ss_pred HHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHHHHHHHH
Q 009803 302 AKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQL 381 (525)
Q Consensus 302 A~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L 381 (525)
|++|.+++.+++||+|||++|||+++++|||.+|++|+||+++||+++|.++++++. .+|+|.++.....++.++...+
T Consensus 54 a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~~-~vrip~~~~~~~~~~~~~~~~l 132 (258)
T PRK08215 54 IQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREKL 132 (258)
T ss_pred HHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-ceEecHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999985 7899999999999999999999
Q ss_pred HHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCC--CCCcccCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009803 382 YSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNL--KPSEVIADPEAETAEDLLIKKFMKEDLEKVL 459 (525)
Q Consensus 382 ~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~--~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL 459 (525)
.+++|+.|+.+|||+.+|+++++|..++.....+.|||.++.++++. ++.+.++++.. .++.. .....|..+|
T Consensus 133 ~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~-~~~~~----~~~~~l~~~l 207 (258)
T PRK08215 133 INENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDEKN-KDENW----LEEIALKEAM 207 (258)
T ss_pred HHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchhhhhhccCccc-cHHHH----HhHHHHHHHH
Confidence 99999999999999999999999999988777888999988655432 24555555432 22222 2345788999
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803 460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513 (525)
Q Consensus 460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l 513 (525)
+.||++++.||.++|+.+ +|++|||+.||||.++|++++++|+++||+.+
T Consensus 208 ~~L~~~er~vi~~~~~~~----~t~~eIA~~lgis~~~V~~~~~~al~kLr~~l 257 (258)
T PRK08215 208 KKLNDREKLILNLRFFQG----KTQMEVAEEIGISQAQVSRLEKAALKHMRKYI 257 (258)
T ss_pred HcCCHHHHHHHHHHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999866 99999999999999999999999999999865
No 22
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=100.00 E-value=1.5e-38 Score=315.43 Aligned_cols=222 Identities=31% Similarity=0.477 Sum_probs=202.2
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCC-CHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccc
Q 009803 282 YGILCKDKMITSNIRLVISIAKNYQGAGM-NLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT 360 (525)
Q Consensus 282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~-~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~ 360 (525)
++..++ .||+.|+|||.++|++|.+++. +.+||+|-|++||++|+++|||++|.+|+|||...|+++|.+++|++. .
T Consensus 21 g~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~LR~~~-~ 98 (247)
T COG1191 21 GDEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKND-S 98 (247)
T ss_pred cCHHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHHHHhCC-C
Confidence 457888 9999999999999999998877 999999999999999999999999999999999999999999999999 8
Q ss_pred eecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCC--CCCCCcccccccccCCCCCcccCCCC
Q 009803 361 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSP--KAPRSLDQKIGINQNLKPSEVIADPE 438 (525)
Q Consensus 361 iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~--~~~~SLD~~i~~d~~~~l~d~l~d~~ 438 (525)
+++|.++.+..+++..+...+.+++||+||++|||+.+|++.+++..++... ...+|+|..+..+++.. .++.
T Consensus 99 v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d~~-----~~~~ 173 (247)
T COG1191 99 VKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDD-----VDDQ 173 (247)
T ss_pred ccCcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccccc-----hhhc
Confidence 9999999999999999999999999999999999999999999999998765 36788887765443333 2223
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 439 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 439 ~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
..+|.+.+...+....|.+++..|++|||.||.+||..+ +|++|||++||||..+|+|++.+|++|||+.+.
T Consensus 174 ~~~~~~~~~~~~~~~~l~~ai~~L~EREk~Vl~l~y~ee----lt~kEI~~~LgISes~VSql~kkai~kLr~~l~ 245 (247)
T COG1191 174 IENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRYKEE----LTQKEIAEVLGISESRVSRLHKKAIKKLRKELN 245 (247)
T ss_pred cccchhHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHhc----cCHHHHHHHhCccHHHHHHHHHHHHHHHHHHhc
Confidence 346778888888888899999999999999999999988 999999999999999999999999999999775
No 23
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=100.00 E-value=5.1e-38 Score=316.91 Aligned_cols=249 Identities=24% Similarity=0.355 Sum_probs=222.0
Q ss_pred hcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHH
Q 009803 221 TSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVIS 300 (525)
Q Consensus 221 ~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv~~nlrLV~~ 300 (525)
+|++|+||+++|.+|+.+++. .++..+++.|+..|.++|+.
T Consensus 6 ~~~~~~~~~~~e~~l~~~~~~---------------------------------------~~d~~a~~~l~~~y~~lv~~ 46 (268)
T PRK06288 6 SGKIPKYAQQDETELWREYKK---------------------------------------TGDPKIREYLILKYSPLVKY 46 (268)
T ss_pred cCCCccccchHHHHHHHHHHH---------------------------------------cCCHHHHHHHHHHHHHHHHH
Confidence 588999999999999987663 14578999999999999999
Q ss_pred HHHHhh-C--CCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHHHH
Q 009803 301 IAKNYQ-G--AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEA 377 (525)
Q Consensus 301 IA~~y~-~--~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka 377 (525)
+|++|. + .+.+++||+||||+|||+++++|||.+|++|+||++||||+.|.+++++.. ++|.++....++++++
T Consensus 47 ~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~~---~~p~~~~~~~~~i~~~ 123 (268)
T PRK06288 47 VAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSID---WIPRSVRQKARQIERA 123 (268)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC---ccCHHHHHHHHHHHHH
Confidence 999986 2 567899999999999999999999999999999999999999999999764 4899999999999999
Q ss_pred HHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCC--CCCCCccccccccc---CCCCCcccCCCCCCCHHHHHHHHHHH
Q 009803 378 RKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSP--KAPRSLDQKIGINQ---NLKPSEVIADPEAETAEDLLIKKFMK 452 (525)
Q Consensus 378 ~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~--~~~~SLD~~i~~d~---~~~l~d~l~d~~~~~pee~~~~~~~~ 452 (525)
...|.+++|+.||.+|||+.+|++.+++..++... ...+|||..+..++ ...+.+.++++...+|++.+...+..
T Consensus 124 ~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~l~~~~~~~~~~~pe~~~~~~e~~ 203 (268)
T PRK06288 124 IAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLESPAALNPDEIAEREEIK 203 (268)
T ss_pred HHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccCCCcccchhhhhccCCCCCCHHHHHHHHHHH
Confidence 99999999999999999999999999999988543 46789998764221 23456777777677899988888888
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803 453 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 515 (525)
Q Consensus 453 ~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~ 515 (525)
..|..+|+.||+++|.||.++|+.+ +|++|||+.||+|.++|++++++|+++||.++..
T Consensus 204 ~~l~~~l~~L~~~~r~vl~l~~~~~----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~~ 262 (268)
T PRK06288 204 RVIVEAIKTLPEREKKVLILYYYED----LTLKEIGKVLGVTESRISQLHTKAVLQLRAKLAE 262 (268)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999887 9999999999999999999999999999998864
No 24
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=100.00 E-value=2.8e-37 Score=309.01 Aligned_cols=245 Identities=26% Similarity=0.347 Sum_probs=216.2
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHH
Q 009803 224 SRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAK 303 (525)
Q Consensus 224 ~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~ 303 (525)
.|.||+++|.+|..+++. .++..|+++||..|.++|+.+|+
T Consensus 7 ~~~l~~~~~~~li~~~~~---------------------------------------~gd~~a~~~l~~~y~~~v~~~a~ 47 (255)
T TIGR02941 7 PTNLTKEDVIQWIAEFQQ---------------------------------------NQNGEAQEKLVDHYQNLVYSIAY 47 (255)
T ss_pred CCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHHHHhHHHHHHHHH
Confidence 367999999988877663 13578999999999999999999
Q ss_pred HhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHHHHHHHHHH
Q 009803 304 NYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYS 383 (525)
Q Consensus 304 ~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~ 383 (525)
+|.+++.+++||+||||+|||+++++||+..|.+|.||+++||++.|.++++++.+.+++|.++....++++++...+.+
T Consensus 48 ~~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~iri~~~~~~~~~~~~~~~~~l~~ 127 (255)
T TIGR02941 48 KYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTD 127 (255)
T ss_pred HHhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HcCCCCCHHHHHHHcCCCHHHHHHHHhC--CCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHHHHHHHHHHHHHhc
Q 009803 384 ENGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDT 461 (525)
Q Consensus 384 ~lgr~Pt~eEIA~~lgis~~~v~~~l~~--~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~ 461 (525)
.+|+.|+.+|||+.+|++.+++..++.. .....|||.+++.+++......+ +. ..+|++.+...+....+..+|+.
T Consensus 128 ~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~-~~-~~~~~~~~~~~e~~~~l~~~l~~ 205 (255)
T TIGR02941 128 HLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSDGSTVARL-DS-VGEVEDGYDQTERRMVLEKILPI 205 (255)
T ss_pred HhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCCCcccccc-cc-cCCcchHHHHHHHHHHHHHHHHc
Confidence 9999999999999999999999888754 34678999988765443322221 11 12456666677777889999999
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803 462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513 (525)
Q Consensus 462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l 513 (525)
||+++|.||.++|+.+ +|++|||+.||||.++|++++++|+++||+.+
T Consensus 206 L~~~~r~ii~l~~~~g----~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~ 253 (255)
T TIGR02941 206 LSEREKSIIHCTFEEN----LSQKETGERLGISQMHVSRLQRQAISKLKEAA 253 (255)
T ss_pred CCHHHHHHHHHHHcCC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 9999999999999877 99999999999999999999999999999865
No 25
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=100.00 E-value=3.8e-37 Score=303.38 Aligned_cols=223 Identities=32% Similarity=0.487 Sum_probs=199.1
Q ss_pred hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccc
Q 009803 281 NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT 360 (525)
Q Consensus 281 ~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~ 360 (525)
.++..|+++||..|.++|+++|++|.+++.+++||+|||++|||+++++|||.+|.+|+||++|||++.|.++++++. .
T Consensus 7 ~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~~~-~ 85 (231)
T TIGR02885 7 NGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDG-I 85 (231)
T ss_pred cCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-C
Confidence 466889999999999999999999999999999999999999999999999999999999999999999999999986 7
Q ss_pred eecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCC--CCCcccCCCC
Q 009803 361 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNL--KPSEVIADPE 438 (525)
Q Consensus 361 iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~--~l~d~l~d~~ 438 (525)
+++|.++...+++++++...+..++|+.||.+|||+.+|++++++..++.....+.|||.+++++++. ++.+.+.++.
T Consensus 86 i~~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~~ 165 (231)
T TIGR02885 86 IKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLDQIADKG 165 (231)
T ss_pred eECCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCCCcchhhhhcCCCC
Confidence 99999999999999999999999999999999999999999999999988777889999988655432 3455665543
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803 439 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513 (525)
Q Consensus 439 ~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l 513 (525)
. +++.. .....|..+++.||++++.||.++|+.+ +|++|||+.||||+++|++++++|++|||..+
T Consensus 166 ~--~~~~~---~~~~~l~~~l~~L~~~e~~i~~~~~~~~----~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~l 231 (231)
T TIGR02885 166 S--EDSDW---LEKIALKEAISKLDERERQIIMLRYFKD----KTQTEVANMLGISQVQVSRLEKKVLKKMKEKL 231 (231)
T ss_pred c--cHHhH---HHHHHHHHHHHcCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHhC
Confidence 2 22222 2356788999999999999999999876 99999999999999999999999999999753
No 26
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=100.00 E-value=1.4e-36 Score=298.33 Aligned_cols=221 Identities=29% Similarity=0.445 Sum_probs=198.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 009803 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL 363 (525)
Q Consensus 284 ~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRi 363 (525)
..|++.||..|.++|+++|++|.+++.+.+||+|||++|||+++++||+.+|.+|+||++|||++.|.++++++.|.+++
T Consensus 2 ~~a~~~lv~~y~~~v~~~a~~~~~~~~~~eDl~Qe~~i~l~~a~~~f~~~~~~~F~ty~~~~i~~~~~~~~r~~~~~~ri 81 (227)
T TIGR02980 2 KEAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVRV 81 (227)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCcHHHHHHHHHHHHHHHHHHcCCceec
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCC--CCCcccccccccC--CCCCcccCCCCC
Q 009803 364 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKA--PRSLDQKIGINQN--LKPSEVIADPEA 439 (525)
Q Consensus 364 P~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~--~~SLD~~i~~d~~--~~l~d~l~d~~~ 439 (525)
|.++...+++++++...+.+.+|+.|+.+|+|+.+|++.+++..++..... +.|||.++.++++ ..+.+.+.
T Consensus 82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~~---- 157 (227)
T TIGR02980 82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTLG---- 157 (227)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCcccccccC----
Confidence 999999999999999999999999999999999999999999998876544 8999998763222 12333333
Q ss_pred CCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803 440 ETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513 (525)
Q Consensus 440 ~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l 513 (525)
++++.+........|..+|..||++++.||.++|+.+ +|++|||+.||+|+++|++++++|+++||+.+
T Consensus 158 -~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~y~~~----~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~l 226 (227)
T TIGR02980 158 -DEDDALETVEDRLALKPLLAALPERERRILLLRFFED----KTQSEIAERLGISQMHVSRLLRRALKKLREQL 226 (227)
T ss_pred -CcchHHHhHHHHHHHHHHHHcCCHHHHHHHHHHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 3344445556677899999999999999999999877 99999999999999999999999999999864
No 27
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=5.3e-36 Score=299.41 Aligned_cols=226 Identities=30% Similarity=0.358 Sum_probs=202.8
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcc
Q 009803 282 YGILCKDKMITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS 358 (525)
Q Consensus 282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~---~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~ 358 (525)
++..|++.||..|.++|+++|++|.+ ++.+.+||+||||+|||+++++|||.+|.+|+||+++||++.|.++++++.
T Consensus 19 ~d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~d~lR~~~ 98 (251)
T PRK07670 19 RDPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKED 98 (251)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 45889999999999999999999975 678999999999999999999999999999999999999999999999876
Q ss_pred cceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHh--CCCCCCCcccccccccCC-CCCcccC
Q 009803 359 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL--SPKAPRSLDQKIGINQNL-KPSEVIA 435 (525)
Q Consensus 359 r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~--~~~~~~SLD~~i~~d~~~-~l~d~l~ 435 (525)
++|.++.+.+++++++...+.+.+|+.|+.+|||..+|+++++|..++. ....+.|||.++.++++. .+.+.+.
T Consensus 99 ---~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~ 175 (251)
T PRK07670 99 ---WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDDGENVSVTIR 175 (251)
T ss_pred ---CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccCCCCcchhhhhhc
Confidence 4899999999999999999999999999999999999999999999985 456789999987654432 2233444
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 436 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 436 d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
+....+|++.+...+....|..+|..||+++|.||.++|+.+ +|++|||+.||+|.++|+++++||+++||.++.
T Consensus 176 ~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~ 250 (251)
T PRK07670 176 DDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFYKEE----LTLTEIGQVLNLSTSRISQIHSKALFKLKKLLE 250 (251)
T ss_pred CcCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 555557888888888888999999999999999999999877 999999999999999999999999999998764
No 28
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=100.00 E-value=2.7e-35 Score=295.02 Aligned_cols=248 Identities=25% Similarity=0.329 Sum_probs=215.3
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHH
Q 009803 223 SSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIA 302 (525)
Q Consensus 223 ~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv~~nlrLV~~IA 302 (525)
..|.|++++|.+|..+++. .++..|+++||..|.++|+++|
T Consensus 6 ~~~~l~~~e~~~li~~~~~---------------------------------------~gd~~a~~~l~~~~~~~v~~~a 46 (257)
T PRK08583 6 QPTKLTKEEVNKWIAEYQE---------------------------------------NQDEEAQEKLVKHYKNLVESLA 46 (257)
T ss_pred cCCcCChHHHHHHHHHHHH---------------------------------------cCCHHHHHHHHHHHHHHHHHHH
Confidence 3478999999888776653 1457899999999999999999
Q ss_pred HHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHHHHHHHHH
Q 009803 303 KNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLY 382 (525)
Q Consensus 303 ~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~ 382 (525)
++|.+++.+++||+||||+|||+++++||+.+|.+|+||+++||++.|.++++++.|.+++|.+.....++++++...+.
T Consensus 47 ~~~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~~~i~r~~~~~~~~~~~~~~~~~ 126 (257)
T PRK08583 47 YKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELT 126 (257)
T ss_pred HHHhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHHHHHHhcCCCcCCCHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999989999999999999999999999999999999999999999999999
Q ss_pred HHcCCCCCHHHHHHHcCCCHHHHHHHHhCC--CCCCCcccccccccCCCCCcccCCCCCCCHHHHHHHHHHHHHHHHHHh
Q 009803 383 SENGRHPNNEEVAEATGLSMKRLHAVLLSP--KAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLD 460 (525)
Q Consensus 383 ~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~--~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL~ 460 (525)
..+++.|+.+++|+.+|++.+++..+.... ..+.|+|.+++.+++.....+. + ...+|++.+...+....|..+|.
T Consensus 127 ~~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~-~-~~~~~e~~~~~~~~~~~l~~~l~ 204 (257)
T PRK08583 127 TELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDGSTVTLL-D-IVGQQEDGYELTEQRMILEKILP 204 (257)
T ss_pred HHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCCCCccchHh-h-hcCCcchhHHHHHHHHHHHHHHH
Confidence 999999999999999999999998877543 4678999887654332111111 1 11245566666677788999999
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 515 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~ 515 (525)
.||+++|.||.++|+.+ +|++|||+.||||.++|++++++|+++||+.+..
T Consensus 205 ~L~~~~r~vl~l~~~~g----~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l~~ 255 (257)
T PRK08583 205 VLSDREKSIIQCTFIEN----LSQKETGERLGISQMHVSRLQRQAIKKLREAAFL 255 (257)
T ss_pred hCCHHHHHHHHHHHhCC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 99999999999999887 9999999999999999999999999999998754
No 29
>PRK05572 sporulation sigma factor SigF; Validated
Probab=100.00 E-value=4.4e-35 Score=292.89 Aligned_cols=241 Identities=29% Similarity=0.452 Sum_probs=211.0
Q ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHH
Q 009803 222 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI 301 (525)
Q Consensus 222 ~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv~~nlrLV~~I 301 (525)
.+.|.||.+++.+|..+++. ++..|+++||..|.++|+++
T Consensus 9 ~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~y~~~v~~~ 48 (252)
T PRK05572 9 KKKPQLKDEENKELIKKSQD----------------------------------------GDQEARDTLVEKNLRLVWSV 48 (252)
T ss_pred cCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHHHH
Confidence 56899999999888765542 45789999999999999999
Q ss_pred HHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHHHHHHHH
Q 009803 302 AKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQL 381 (525)
Q Consensus 302 A~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L 381 (525)
|++|.+++.+++||+|||++++|+++++|++.+|.+|.||+++||++.|.+++++.. .+|+|.++....++++++...+
T Consensus 49 a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~~~-~~r~~~~~~~~~~~~~~~~~~l 127 (252)
T PRK05572 49 VQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDKDEL 127 (252)
T ss_pred HHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CCCCCHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999998889999999999999999999885 7899999999999999999999
Q ss_pred HHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCC--CCCcccCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009803 382 YSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNL--KPSEVIADPEAETAEDLLIKKFMKEDLEKVL 459 (525)
Q Consensus 382 ~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~--~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL 459 (525)
..++|+.|+..|+|+.+|++++++..++.....+.||+.++.+++.. +..+.+.++.. +. ......|..+|
T Consensus 128 ~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~~~---~~----~~~~~~l~~~l 200 (252)
T PRK05572 128 SKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITLLDQIADQSE---ED----WFDKIALKEAI 200 (252)
T ss_pred HHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCCCCcchhhhhcCCCch---hh----HHHHHHHHHHH
Confidence 99999999999999999999999999988777889999887654322 22344443221 11 22356789999
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
+.||++++.||.++|+.+ +|++|||+.+|+|.++|++++++|+++||..+.
T Consensus 201 ~~L~~~~~~v~~l~~~~~----~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l~ 251 (252)
T PRK05572 201 RELDERERLIVYLRYFKD----KTQSEVAKRLGISQVQVSRLEKKILKQMKEKLD 251 (252)
T ss_pred HcCCHHHHHHHHHHHhCC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence 999999999999999866 999999999999999999999999999998764
No 30
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=100.00 E-value=2.7e-35 Score=289.09 Aligned_cols=217 Identities=30% Similarity=0.467 Sum_probs=195.5
Q ss_pred HHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccc
Q 009803 290 MITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH 366 (525)
Q Consensus 290 Lv~~nlrLV~~IA~~y~~---~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~ 366 (525)
|+..|.++|+++|++|.+ ++.+++||+|||++|||+++++|||.+|++|+||+++||++.|.+++++.. ++|.+
T Consensus 1 L~~~~~~lv~~~a~~~~~~~~~~~~~eDl~Qe~~~~l~~a~~~fd~~~~~~f~t~~~~~i~~~~~~~lr~~~---~~p~~ 77 (224)
T TIGR02479 1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLD---WVPRS 77 (224)
T ss_pred CHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHHcC---ccCHH
Confidence 588999999999999986 789999999999999999999999999999999999999999999999875 48999
Q ss_pred hHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHh--CCCCCCCcccccccc-cCCCCCcccCCCCCCCHH
Q 009803 367 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL--SPKAPRSLDQKIGIN-QNLKPSEVIADPEAETAE 443 (525)
Q Consensus 367 ~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~--~~~~~~SLD~~i~~d-~~~~l~d~l~d~~~~~pe 443 (525)
+...++++.++...+.+.+|+.|+.+|||+.+|+++++|..++. .....+|+|....++ +..++.+.++++...+|+
T Consensus 78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (224)
T TIGR02479 78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDKSEDPE 157 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhccccccCCHH
Confidence 99999999999999999999999999999999999999999985 345577888766533 233455666655566888
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803 444 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513 (525)
Q Consensus 444 e~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l 513 (525)
+.+...+....|..+|+.||+++|+||.++|+.+ +|++|||+.||+|.++|++++++|+++||+++
T Consensus 158 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~y~~~----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 223 (224)
T TIGR02479 158 EELEREELREALAEAIESLSEREQLVLSLYYYEE----LNLKEIGEVLGLTESRVSQIHSQALKKLRAKL 223 (224)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhCC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHc
Confidence 8888888889999999999999999999999887 99999999999999999999999999999865
No 31
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=100.00 E-value=1.5e-34 Score=286.15 Aligned_cols=210 Identities=20% Similarity=0.364 Sum_probs=182.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhccccee
Q 009803 286 CKDKMITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR 362 (525)
Q Consensus 286 A~e~Lv~~nlrLV~~IA~~y~~---~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iR 362 (525)
-...|+..|+++|.++|++|.+ .+.+.+||+|||++|||+|+++|||.+| +|+||++||||++|.+++++..|
T Consensus 16 ~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~~--- 91 (231)
T PRK12427 16 EEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELDW--- 91 (231)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcCC---
Confidence 4567899999999999999875 4679999999999999999999998666 89999999999999999998776
Q ss_pred cccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhC--CCCCCCcccccccccCCCCCcccCCCCCC
Q 009803 363 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKIGINQNLKPSEVIADPEAE 440 (525)
Q Consensus 363 iP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~--~~~~~SLD~~i~~d~~~~l~d~l~d~~~~ 440 (525)
+|.++...+++++++...+.+++|+.||.+|||+.+|+++++|..++.. .....|||.+++++++. +.+++ .
T Consensus 92 ~~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~---~~~~~---~ 165 (231)
T PRK12427 92 RPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAHN---DILQS---R 165 (231)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCcc---cccCC---C
Confidence 6888888999999999999999999999999999999999999998753 45789999998665432 22222 2
Q ss_pred CHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803 441 TAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512 (525)
Q Consensus 441 ~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~ 512 (525)
.+++.. .....|..++..||+++|.||.++|+.+ +|++|||+.||||.++|+|++.+|++|||.+
T Consensus 166 ~~~~~~---~~~~~l~~~l~~L~~~er~vi~l~~~~~----~t~~EIA~~lgis~~~V~q~~~~~~~kLr~~ 230 (231)
T PRK12427 166 DLEENI---IIEDNLKQALSQLDEREQLILHLYYQHE----MSLKEIALVLDLTEARICQLNKKIAQKIKSF 230 (231)
T ss_pred CHHHHH---HHHHHHHHHHHcCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 344332 2455789999999999999999999876 9999999999999999999999999999964
No 32
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=100.00 E-value=7.4e-34 Score=281.20 Aligned_cols=225 Identities=30% Similarity=0.435 Sum_probs=198.6
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhh---CCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcc
Q 009803 282 YGILCKDKMITSNIRLVISIAKNYQ---GAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS 358 (525)
Q Consensus 282 ~g~~A~e~Lv~~nlrLV~~IA~~y~---~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~ 358 (525)
.|.-++++|+..|.++|+++|++|. +++.+++||+||||+|||+++++|||.+|.+|+||+++||++.|.++++++.
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 4567899999999999999999997 6789999999999999999999999999999999999999999999999987
Q ss_pred cceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhC--CCCCCCcccccccccCCCCCcccCC
Q 009803 359 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKIGINQNLKPSEVIAD 436 (525)
Q Consensus 359 r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~--~~~~~SLD~~i~~d~~~~l~d~l~d 436 (525)
+ +|.++....+++.++...+.+.+|++|+.+|||+.+|++.++|..++.. ...++|++..++++++. +.. ..+
T Consensus 85 ~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~-~~~-~~~ 159 (236)
T PRK06986 85 W---VPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDS-ILV-TED 159 (236)
T ss_pred C---CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCcc-ccc-ccC
Confidence 5 6888888888899999999999999999999999999999999998864 34567888887654443 222 223
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803 437 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 515 (525)
Q Consensus 437 ~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~ 515 (525)
+...+|++.+...+....|..+|+.||+++|.||.++|+.+ +|++|||+.||||.++|+++++||+++||+.+..
T Consensus 160 ~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~~ 234 (236)
T PRK06986 160 HQDEDPLQQLEDEELREALVEAIESLPEREQLVLSLYYQEE----LNLKEIGAVLGVSESRVSQIHSQAIKRLRARLGE 234 (236)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHhccC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 33457888888888889999999999999999999999877 9999999999999999999999999999997753
No 33
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=99.96 E-value=3.3e-28 Score=240.58 Aligned_cols=209 Identities=29% Similarity=0.484 Sum_probs=168.0
Q ss_pred HHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHH
Q 009803 213 PLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMI 291 (525)
Q Consensus 213 ~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv 291 (525)
.+. |+.++ ++.|+||+++|..|...++. ++..|++.|+
T Consensus 17 ~~~~~~~~~-~~~~~~~~~~e~~l~~~~~~----------------------------------------gd~~a~~~l~ 55 (233)
T PRK05803 17 FLVSYVKNN-SFPQPLSEEEERKYLELMKE----------------------------------------GDEEARNILI 55 (233)
T ss_pred HHHHHHHHh-cccCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHH
Confidence 345 99999 99999999999988766542 4578999999
Q ss_pred HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHH
Q 009803 292 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEAT 371 (525)
Q Consensus 292 ~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~ 371 (525)
..|.++|+++|.+|.+++.+++||+|||++++|+++++||+++|.+|.||+++|+|+.+.++++++.+..+
T Consensus 56 ~~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~~~~--------- 126 (233)
T PRK05803 56 ERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTKK--------- 126 (233)
T ss_pred HHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhcccc---------
Confidence 99999999999999999999999999999999999999999889999999999999999999987643100
Q ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCccccccccc---CCCCCcccCCCCCCCHHHHHHH
Q 009803 372 YRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQ---NLKPSEVIADPEAETAEDLLIK 448 (525)
Q Consensus 372 ~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~---~~~l~d~l~d~~~~~pee~~~~ 448 (525)
..+++...+.++ ..++.+..++. .+++++.+..
T Consensus 127 -------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~ 162 (233)
T PRK05803 127 -------------------------------------------EVSLQDPIGVDKEGNEISLIDILGSE-EDDVIEQVEL 162 (233)
T ss_pred -------------------------------------------CCCccccccCCCCcCcccHHHHccCC-CCCHHHHHHH
Confidence 011111111010 11122223322 2357777777
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803 449 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 515 (525)
Q Consensus 449 ~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~ 515 (525)
+.....|..+|+.||+++|+||.++|+.++.+.+|++|||+.||+|.++|+++++||+++||+.+..
T Consensus 163 ~~~~~~l~~~l~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~~ 229 (233)
T PRK05803 163 KMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKELYR 229 (233)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 7778889999999999999999999975433449999999999999999999999999999998765
No 34
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=99.94 E-value=5.7e-25 Score=217.24 Aligned_cols=180 Identities=28% Similarity=0.498 Sum_probs=137.5
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccce
Q 009803 282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 361 (525)
Q Consensus 282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~i 361 (525)
++..|++.|+..|.++|+.+|++|.+++.+++|++||+|+++|+++++|++..+++|.||+++++||.+.++++++.+..
T Consensus 49 gd~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~d~lRk~~~~~ 128 (234)
T PRK08301 49 GDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNNKVK 128 (234)
T ss_pred cCHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 55789999999999999999999999999999999999999999999999988889999999999999999998765410
Q ss_pred ecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCccccccc--ccC-CCCCcccCCCC
Q 009803 362 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGI--NQN-LKPSEVIADPE 438 (525)
Q Consensus 362 RiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~--d~~-~~l~d~l~d~~ 438 (525)
. ..+++.+... ++. ....+...+.
T Consensus 129 ~----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~- 155 (234)
T PRK08301 129 A----------------------------------------------------EVSFDEPLNIDWDGNELLLSDVLGTD- 155 (234)
T ss_pred c----------------------------------------------------ccccccccccccCCCcccHHHhccCc-
Confidence 0 0111111100 000 0011111111
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 439 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 439 ~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
...++..+........|..+|+.||+++|.||.|+|++...+.+|++|||+.||||.++|+++++||+++||+.+.
T Consensus 156 ~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l~ 231 (234)
T PRK08301 156 NDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEIN 231 (234)
T ss_pred ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 1233344444555667999999999999999999995211111999999999999999999999999999999765
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=99.94 E-value=7.5e-25 Score=215.93 Aligned_cols=205 Identities=28% Similarity=0.489 Sum_probs=157.3
Q ss_pred HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHHHHHH
Q 009803 216 YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNI 295 (525)
Q Consensus 216 yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv~~nl 295 (525)
|.-.-.+..+.|++.+|.+|..+++. ++..|++.|+..|.
T Consensus 19 ~~~~~~~~~~~~~~~~~~~li~~~~~----------------------------------------gd~~af~~l~~~y~ 58 (227)
T TIGR02846 19 YVTNNGSFPQPLSEEEEKKYLDRLKE----------------------------------------GDEEARNVLIERNL 58 (227)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhH
Confidence 54333266778999998888776653 45789999999999
Q ss_pred HHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHH
Q 009803 296 RLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVK 375 (525)
Q Consensus 296 rLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ 375 (525)
++|+++|.+|.++..+++||+||+|+++|+++++|+++.+.+|.||+++|+++.|.+++++..+..+
T Consensus 59 ~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~Rk~~r~~~------------- 125 (227)
T TIGR02846 59 RLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHLRALKKTKG------------- 125 (227)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHHHHHhcccc-------------
Confidence 9999999999999999999999999999999999999888899999999999999999987653100
Q ss_pred HHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCccccccccc---CCCCCcccCCCCCCCHHHHHHHHHHH
Q 009803 376 EARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQ---NLKPSEVIADPEAETAEDLLIKKFMK 452 (525)
Q Consensus 376 ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~---~~~l~d~l~d~~~~~pee~~~~~~~~ 452 (525)
..+++...+.+. .....+...+ ...++++........
T Consensus 126 ---------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~ 165 (227)
T TIGR02846 126 ---------------------------------------EVSLQDPIGVDKEGNEISLIDILGS-DGDSVIEQVELNLEI 165 (227)
T ss_pred ---------------------------------------ceeccccccCCcccCcccHHHHhcC-CCCChHHHHHHHHHH
Confidence 011111110000 0011112221 123566666666666
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803 453 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513 (525)
Q Consensus 453 ~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l 513 (525)
..|..+|+.||+++|+||.++|.++..+.+|++|||++||+|.++|++++++|+++||+.+
T Consensus 166 ~~l~~~i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~~ 226 (227)
T TIGR02846 166 KKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYKEL 226 (227)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 7899999999999999999999732112299999999999999999999999999999864
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=99.93 E-value=5.7e-24 Score=210.59 Aligned_cols=180 Identities=30% Similarity=0.517 Sum_probs=139.1
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccce
Q 009803 282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 361 (525)
Q Consensus 282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~i 361 (525)
++..|++.|+..|.+.|+++|++|.+++.+++|++||+++++|+++++|++..+++|.||++.+++|.+.++++++.+..
T Consensus 49 ~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~d~~Rk~~r~~ 128 (234)
T TIGR02835 49 GDESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILMYLRRNNKTR 128 (234)
T ss_pred CCHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhcccc
Confidence 55889999999999999999999999999999999999999999999999988889999999999999999999865410
Q ss_pred ecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCccccccc--ccC-CCCCcccCCCC
Q 009803 362 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGI--NQN-LKPSEVIADPE 438 (525)
Q Consensus 362 RiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~--d~~-~~l~d~l~d~~ 438 (525)
. ..+++..+.. +++ ....+. .++.
T Consensus 129 ~----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~-~~~~ 155 (234)
T TIGR02835 129 S----------------------------------------------------EVSFDEPLNVDWDGNELLLSDV-LGTD 155 (234)
T ss_pred C----------------------------------------------------cccccccccCCCCCCcchHHHh-cCCC
Confidence 0 0111111100 000 000111 1112
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 439 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 439 ~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
...+++.+........|..+|+.||+++|.||.++|++.+++.+|++|||+.||||..+|+++.+||+++||+.+.
T Consensus 156 ~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l~ 231 (234)
T TIGR02835 156 SDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKEIN 231 (234)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhh
Confidence 2234444555556678999999999999999999996322223999999999999999999999999999999775
No 37
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=99.91 E-value=6.4e-23 Score=197.91 Aligned_cols=189 Identities=24% Similarity=0.309 Sum_probs=144.8
Q ss_pred HHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHh
Q 009803 277 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD 356 (525)
Q Consensus 277 ~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~ 356 (525)
.....++..|++.|+..|.++|+.+|++|.++..+++|++||++++||+++.+||+.++.+|.||++.++++.+.+++++
T Consensus 16 ~~~~~~d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n~~~d~~r~ 95 (208)
T PRK08295 16 ELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQIITAIKT 95 (208)
T ss_pred HHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHH
Confidence 33445669999999999999999999999999999999999999999999999999887899999999999999999886
Q ss_pred cccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCccccccc-ccCCCCCcccC
Q 009803 357 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGI-NQNLKPSEVIA 435 (525)
Q Consensus 357 ~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~-d~~~~l~d~l~ 435 (525)
..+..+.|. ....|++..+.+ +.+..+.+.+.
T Consensus 96 ~~r~~~~~~-----------------------------------------------~~~~s~~~~~~~~~~~~~~~~~~~ 128 (208)
T PRK08295 96 ANRQKHIPL-----------------------------------------------NSYVSLDKPIYDEESDRTLLDVIS 128 (208)
T ss_pred hhhhccccc-----------------------------------------------cceeecCCcccCCccchhHHHHhc
Confidence 543211110 011222222211 11112223333
Q ss_pred CCCCCCHHHHHHHHHHHHHH-HHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 436 DPEAETAEDLLIKKFMKEDL-EKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 436 d~~~~~pee~~~~~~~~~~L-~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
++...+|++.+........+ ..+++.||+++|.||.+ |..+ +|++|||+.||+|.++|+.+++||+++||+++.
T Consensus 129 ~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l-~~e~----~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l~ 203 (208)
T PRK08295 129 EAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLEL-YLDG----KSYQEIAEELNRHVKSIDNALQRVKRKLEKYLE 203 (208)
T ss_pred CcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHH-HHcc----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 33334677766555555555 45679999999999999 8776 999999999999999999999999999999886
Q ss_pred hch
Q 009803 515 TKH 517 (525)
Q Consensus 515 ~~~ 517 (525)
...
T Consensus 204 ~~~ 206 (208)
T PRK08295 204 NRE 206 (208)
T ss_pred hhc
Confidence 543
No 38
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=99.90 E-value=3.3e-22 Score=190.21 Aligned_cols=170 Identities=15% Similarity=0.229 Sum_probs=140.5
Q ss_pred HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHH
Q 009803 276 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS 355 (525)
Q Consensus 276 L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir 355 (525)
+.....++..|++.|+..|.++|+.+|++|.+++.+++|++||+|+++|+++.+|++. +.+|.+|++..+++.+.++++
T Consensus 11 ~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n~~~d~~R 89 (186)
T PRK05602 11 LARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLNLCYDRLR 89 (186)
T ss_pred HHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHHHHHHHHH
Confidence 3445556699999999999999999999999999999999999999999999999986 458999999999999999998
Q ss_pred hcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccC
Q 009803 356 DQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIA 435 (525)
Q Consensus 356 ~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~ 435 (525)
++... +.+. ..+ ..
T Consensus 90 ~~~~~--------------------------------------------------------~~~~---------~~~-~~ 103 (186)
T PRK05602 90 RRREV--------------------------------------------------------PVED---------APD-VP 103 (186)
T ss_pred hcCCC--------------------------------------------------------Cccc---------ccc-cC
Confidence 66420 0000 000 01
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803 436 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 515 (525)
Q Consensus 436 d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~ 515 (525)
+. ...+++.+...+....+..+|+.||+++|.||.++|..+ +|++|||+.||+|..+|+++++||+++||+.+..
T Consensus 104 ~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 178 (186)
T PRK05602 104 DP-APGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQG----LSNIEAAAVMDISVDALESLLARGRRALRAQLAD 178 (186)
T ss_pred CC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHhcC----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 11 124566666666677899999999999999999999887 9999999999999999999999999999998876
Q ss_pred ch
Q 009803 516 KH 517 (525)
Q Consensus 516 ~~ 517 (525)
.+
T Consensus 179 ~~ 180 (186)
T PRK05602 179 LP 180 (186)
T ss_pred cc
Confidence 44
No 39
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=99.90 E-value=3.5e-22 Score=191.80 Aligned_cols=174 Identities=14% Similarity=0.169 Sum_probs=138.9
Q ss_pred HHHHH-HHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHH
Q 009803 274 RELRR-RLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRK 352 (525)
Q Consensus 274 ~~L~~-~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~ 352 (525)
..|.. ...++..++++|+..|.++|+++|.+|.++..+++|++||+|+++|+++.+||+.+| .|.+|++..+++.+.+
T Consensus 18 ~~li~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~d 96 (194)
T PRK09646 18 DALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHRRAVD 96 (194)
T ss_pred HHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHHHHHH
Confidence 34444 444569999999999999999999999999999999999999999999999998765 6999999999999999
Q ss_pred HHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCc
Q 009803 353 SLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSE 432 (525)
Q Consensus 353 ~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d 432 (525)
+++++.+..+. +.... .. +
T Consensus 97 ~~r~~~~~~~~-------------------------------------------------------~~~~~---~~---~ 115 (194)
T PRK09646 97 RVRSEQAASQR-------------------------------------------------------EVRYG---AR---N 115 (194)
T ss_pred HHHhhcccccc-------------------------------------------------------ccccc---cc---c
Confidence 99876531110 00000 00 0
Q ss_pred ccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803 433 VIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512 (525)
Q Consensus 433 ~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~ 512 (525)
. +.....+++.+...+....|..+|..||+++|.||.|+|..| +|++|||+.||+|..+|+++++||+++||++
T Consensus 116 ~--~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 116 V--DPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYYGG----LTYREVAERLAVPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred c--cccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCCChHhHHHHHHHHHHHHHHH
Confidence 0 001113444444455567899999999999999999999887 9999999999999999999999999999998
Q ss_pred Hhh
Q 009803 513 KRT 515 (525)
Q Consensus 513 l~~ 515 (525)
+..
T Consensus 190 l~~ 192 (194)
T PRK09646 190 LGV 192 (194)
T ss_pred hcc
Confidence 753
No 40
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=99.89 E-value=4.7e-22 Score=188.36 Aligned_cols=180 Identities=15% Similarity=0.237 Sum_probs=142.3
Q ss_pred HHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHH
Q 009803 273 QRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRK 352 (525)
Q Consensus 273 ~~~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~ 352 (525)
...+.....++..|+.+|+..|.++|+.+|++|.+++.+++|++||+++++|+++.+|++.. .|.+|++..+++.+.+
T Consensus 6 ~~li~~~~~gd~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~~ 83 (187)
T TIGR02948 6 KKRIKEVRKGDENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLTID 83 (187)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHHH
Confidence 34455556677999999999999999999999999999999999999999999999999865 6999999999999999
Q ss_pred HHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCc
Q 009803 353 SLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSE 432 (525)
Q Consensus 353 ~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d 432 (525)
++++..+... ++.....++...+.+
T Consensus 84 ~~rk~~~~~~-------------------------------------------------------~~~~~~~~~~~~~~~ 108 (187)
T TIGR02948 84 RLRKRKPDFY-------------------------------------------------------LDDEVQGTDGLTMES 108 (187)
T ss_pred HHHhhccccc-------------------------------------------------------ccccccCcccccccc
Confidence 9886432100 000000000111111
Q ss_pred ccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803 433 VIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512 (525)
Q Consensus 433 ~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~ 512 (525)
...+ ..+.|++.+...+....+..+|..||+++|.||.++|..| +|++|||+.||+|.++|+++++||+++||..
T Consensus 109 ~~~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 109 QLAA-DEAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYMED----LSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred cccc-CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 1111 1235677777777777899999999999999999999877 9999999999999999999999999999997
Q ss_pred Hh
Q 009803 513 KR 514 (525)
Q Consensus 513 l~ 514 (525)
+.
T Consensus 184 l~ 185 (187)
T TIGR02948 184 LR 185 (187)
T ss_pred hh
Confidence 75
No 41
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=99.89 E-value=3.5e-22 Score=191.28 Aligned_cols=179 Identities=17% Similarity=0.183 Sum_probs=144.6
Q ss_pred HHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHH
Q 009803 273 QRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRK 352 (525)
Q Consensus 273 ~~~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~ 352 (525)
...+.....++..|++.|+..|.+.|+++|+++.++..+++|++||+|+++|+++++|++. ..|.+|++.++++.+.+
T Consensus 14 ~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~--~~f~~wl~~i~~n~~~~ 91 (194)
T PRK12513 14 EALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPR--ARFRTWLYQIARNLLID 91 (194)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CchHHHHHHHHHHHHHH
Confidence 3445555556699999999999999999999999999999999999999999999999974 36999999999999999
Q ss_pred HHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCc
Q 009803 353 SLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSE 432 (525)
Q Consensus 353 ~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d 432 (525)
+++++.+....+ .+. +.. . .
T Consensus 92 ~~R~~~~~~~~~-----------------------------------------------------~~~----~~~--~-~ 111 (194)
T PRK12513 92 HWRRHGARQAPS-----------------------------------------------------LDA----DEQ--L-H 111 (194)
T ss_pred HHHHhccccccc-----------------------------------------------------ccc----chh--h-h
Confidence 998776421110 000 000 0 0
Q ss_pred ccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803 433 VIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512 (525)
Q Consensus 433 ~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~ 512 (525)
...+ ...+|++.+...+....|..+|+.||+++|.||.|+|+.| +|++|||+.||+|.++|+++++||+++||+.
T Consensus 112 ~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 186 (194)
T PRK12513 112 ALAD-DGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGD----LELEEIAELTGVPEETVKSRLRYALQKLREL 186 (194)
T ss_pred hcCC-CCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeehccC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 0111 1235677667777778899999999999999999999887 9999999999999999999999999999998
Q ss_pred Hhhchh
Q 009803 513 KRTKHL 518 (525)
Q Consensus 513 l~~~~L 518 (525)
+...++
T Consensus 187 l~~~~~ 192 (194)
T PRK12513 187 LAEEVA 192 (194)
T ss_pred HHHhhc
Confidence 876543
No 42
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=99.89 E-value=1.2e-21 Score=186.77 Aligned_cols=165 Identities=16% Similarity=0.261 Sum_probs=135.7
Q ss_pred hccHHHHHHHHHHHHHHHHHHHHHhhCC----CCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHh
Q 009803 281 NYGILCKDKMITSNIRLVISIAKNYQGA----GMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD 356 (525)
Q Consensus 281 ~~g~~A~e~Lv~~nlrLV~~IA~~y~~~----g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~ 356 (525)
.++..|+++|+..|.+.|+.+|.++.++ +.+++|++||+|+++|+++.+|++. +..|.||++..+++.+.+++++
T Consensus 20 ~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~n~~~d~~r~ 98 (189)
T PRK09648 20 AGDRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAAHKVADAHRA 98 (189)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHHHHHHHHHHH
Confidence 4558999999999999999999998865 3689999999999999999999864 4589999999999999999987
Q ss_pred cccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCC
Q 009803 357 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD 436 (525)
Q Consensus 357 ~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d 436 (525)
+.+.... ..+ ...+...
T Consensus 99 ~~r~~~~-----------------------------------------------------~~~---------~~~~~~~- 115 (189)
T PRK09648 99 AGRDKAV-----------------------------------------------------PTE---------EVPERPS- 115 (189)
T ss_pred hCCCccc-----------------------------------------------------ccc---------ccccccc-
Confidence 6541100 000 0000111
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 437 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 437 ~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
...+|++.+...+....|..+|..||+++|+||.++|+.| +|++|||+.||+|..+|+++++||+++||+.+.
T Consensus 116 -~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 188 (189)
T PRK09648 116 -DDAGPEERALRSESSNRMRELLDTLPEKQREILILRVVVG----LSAEETAEAVGSTPGAVRVAQHRALARLRAEIE 188 (189)
T ss_pred -cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 1225777777777778899999999999999999999987 999999999999999999999999999998763
No 43
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=99.89 E-value=6.1e-22 Score=189.48 Aligned_cols=189 Identities=21% Similarity=0.262 Sum_probs=139.9
Q ss_pred HHHHHHH-HhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHH
Q 009803 273 QRELRRR-LNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVR 351 (525)
Q Consensus 273 ~~~L~~~-l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~ 351 (525)
+..|... ..++..|++.||..|.+.|+++|+++.++..+++||+||+|+.+|+++.+|++..+..|.||++.+|++.+.
T Consensus 6 ~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~~~~ 85 (198)
T TIGR02859 6 DEEIVELARQGNTHALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTRQII 85 (198)
T ss_pred hHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHHHHH
Confidence 3344444 445589999999999999999999999999999999999999999999999998878999999999999998
Q ss_pred HHHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCccccccc-ccCCCC
Q 009803 352 KSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGI-NQNLKP 430 (525)
Q Consensus 352 ~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~-d~~~~l 430 (525)
++++...+..+.+. ....|++.+... +++.++
T Consensus 86 ~~~r~~~~~~~~~~-----------------------------------------------~~~~~~~~~~~~~~~~~~~ 118 (198)
T TIGR02859 86 TAIKTATRQKHIPL-----------------------------------------------NSYVSLNKPIYDEESDRTL 118 (198)
T ss_pred HHHHHHHHhcccch-----------------------------------------------hhhcCcccccccccccchH
Confidence 88875422111000 011233322111 111112
Q ss_pred CcccCCCCCCCHHHHHHHHHHHHHHHHHHhcC-CHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 009803 431 SEVIADPEAETAEDLLIKKFMKEDLEKVLDTL-NPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKL 509 (525)
Q Consensus 431 ~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~L-~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKL 509 (525)
.+.+.+....+|++.+...+....|.++|+.| ++.++.|+ ++|..+ +|++|||+.||+|.++|+...+||+++|
T Consensus 119 ~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~-~~~~~~----~s~~eIA~~l~~s~~tV~~~l~r~r~~L 193 (198)
T TIGR02859 119 LDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVL-QSYLDG----KSYQEIACDLNRHVKSIDNALQRVKRKL 193 (198)
T ss_pred HHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHH-HHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 22222222346787777777778899999995 55566665 557666 9999999999999999999999999999
Q ss_pred HhHH
Q 009803 510 KNKK 513 (525)
Q Consensus 510 R~~l 513 (525)
|+.+
T Consensus 194 ~~~l 197 (198)
T TIGR02859 194 EKYL 197 (198)
T ss_pred HHhc
Confidence 9865
No 44
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=99.89 E-value=1.3e-21 Score=185.33 Aligned_cols=175 Identities=14% Similarity=0.183 Sum_probs=139.8
Q ss_pred HHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhc
Q 009803 278 RRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ 357 (525)
Q Consensus 278 ~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~ 357 (525)
....++..+++.++..|.++|+++|+++.++..+++|++||++++||+++.+|++.. .|.+|++..+|+.+.++++++
T Consensus 11 ~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~~~d~~R~~ 88 (187)
T PRK09641 11 QVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNLTIDRLRKR 88 (187)
T ss_pred HHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHHHHHHHHhc
Confidence 334456999999999999999999999999999999999999999999999999853 799999999999999999876
Q ss_pred ccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCC
Q 009803 358 SRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADP 437 (525)
Q Consensus 358 ~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~ 437 (525)
.+... ++.....++.....+.+.+.
T Consensus 89 ~~~~~-------------------------------------------------------~~~~~~~~~~~~~~~~~~~~ 113 (187)
T PRK09641 89 KPDYY-------------------------------------------------------LDAEVAGTEGLTMYSQLAAD 113 (187)
T ss_pred Ccccc-------------------------------------------------------ccccccCCcchhhhcccccC
Confidence 43100 00000001111111111221
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 438 EAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 438 ~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
..+|++.+...+....|..+|+.||+++++||.++|..+ +|++|||+.||||.++|++.++||+++||+.+.
T Consensus 114 -~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~~~----~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l~ 185 (187)
T PRK09641 114 -DALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIED----LSLKEISEILDLPVGTVKTRIHRGREALRKQLR 185 (187)
T ss_pred -cCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhhC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 235777777777778899999999999999999999877 999999999999999999999999999999775
No 45
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=99.89 E-value=1.5e-21 Score=182.96 Aligned_cols=174 Identities=18% Similarity=0.180 Sum_probs=139.5
Q ss_pred HHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcc
Q 009803 279 RLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS 358 (525)
Q Consensus 279 ~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~ 358 (525)
...++..|+++|+..|.++|+.++++|.+++.+.+|++||++++||+++++|+ .+.+|.+|++.++++.+.+++++..
T Consensus 4 ~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~r~~~ 81 (182)
T PRK09652 4 VQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYLRKQG 81 (182)
T ss_pred hhcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHHHccc
Confidence 34567899999999999999999999999999999999999999999999999 4568999999999999999998765
Q ss_pred cceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCC
Q 009803 359 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPE 438 (525)
Q Consensus 359 r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~ 438 (525)
+....+ +++ ..+.++....+...+
T Consensus 82 ~~~~~~----------------------------------------------------~~~--~~~~~~~~~~~~~~~-- 105 (182)
T PRK09652 82 RRPPAS----------------------------------------------------DVD--AEEAEDFDLADALRD-- 105 (182)
T ss_pred CCCCcc----------------------------------------------------ccc--ccccccccccccccc--
Confidence 411110 000 000011111111111
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 439 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 439 ~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
..+|++.+........+..+|..||+++++||.++|+.+ +|++|||+.||+|..+|++.++||+++||+.+.
T Consensus 106 ~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 177 (182)
T PRK09652 106 ISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEG----LSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQ 177 (182)
T ss_pred ccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 135777777777788899999999999999999999877 999999999999999999999999999999775
No 46
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=99.88 E-value=1.3e-21 Score=193.36 Aligned_cols=193 Identities=19% Similarity=0.192 Sum_probs=153.5
Q ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHH
Q 009803 222 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI 301 (525)
Q Consensus 222 ~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv~~nlrLV~~I 301 (525)
...|+|++..+..|...++. ++..|++.|+..|.+.|+++
T Consensus 7 ~~~~~~~~~~~~~l~~~~~~----------------------------------------gd~~a~~~l~~~y~~~l~~~ 46 (231)
T PRK11922 7 SRPPPLSAASDRELVARVLA----------------------------------------GDEAAFEALMRRHNRRLYRT 46 (231)
T ss_pred CCCCCcCcccHHHHHHHHHc----------------------------------------CCHHHHHHHHHHHHHHHHHH
Confidence 56788888888777665542 56789999999999999999
Q ss_pred HHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHHHHHHHH
Q 009803 302 AKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQL 381 (525)
Q Consensus 302 A~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L 381 (525)
++++.+++.+++|++||+|+++|+++++|++. ..|.+|++..+++.+.+++++..+..+++..
T Consensus 47 a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~Rk~~r~~~~~~~--------------- 109 (231)
T PRK11922 47 ARAILRNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNEALGRLRRRRRLVNLAEM--------------- 109 (231)
T ss_pred HHHHhCChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHHHHHHHHhhcccccchhc---------------
Confidence 99999999999999999999999999999985 4799999999999999999876542111000
Q ss_pred HHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHHHHHHHHHHHHHhc
Q 009803 382 YSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDT 461 (525)
Q Consensus 382 ~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~ 461 (525)
..+. .. .++ ...... ....+|++.+...+....|..+|+.
T Consensus 110 -----------------------------------~~~~-~~-~~~--~~~~~~-~~~~~~e~~~~~~e~~~~l~~~l~~ 149 (231)
T PRK11922 110 -----------------------------------VMAS-TI-AGG--ERTPLA-DPAEDPERAAARREIRALLERAIDA 149 (231)
T ss_pred -----------------------------------cccc-cc-ccc--cccccC-cccCChHHHHHHHHHHHHHHHHHHh
Confidence 0000 00 000 000011 1223577777777888889999999
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803 462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 515 (525)
Q Consensus 462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~ 515 (525)
||+++|+||.++|..+ +|++|||+.||+|.++|+++++||+++||+.+..
T Consensus 150 L~~~~r~i~~l~~~~g----~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~~ 199 (231)
T PRK11922 150 LPDAFRAVFVLRVVEE----LSVEETAQALGLPEETVKTRLHRARRLLRESLAR 199 (231)
T ss_pred CCHHHhhhheeehhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999887 9999999999999999999999999999998864
No 47
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=99.88 E-value=2.7e-21 Score=180.24 Aligned_cols=165 Identities=19% Similarity=0.309 Sum_probs=136.9
Q ss_pred HhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhccc
Q 009803 280 LNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR 359 (525)
Q Consensus 280 l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r 359 (525)
..++..|++.|+..|.+.+++++.++.++..+++|++||+++.+|+.+++|+...+ .|.+|++.++++.+.++++++.+
T Consensus 6 ~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R~~~~ 84 (170)
T TIGR02952 6 QDREEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFRGSKR 84 (170)
T ss_pred HccCHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHHhcCC
Confidence 34668999999999999999999999998899999999999999999999997555 89999999999999999997754
Q ss_pred ceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCC
Q 009803 360 TIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEA 439 (525)
Q Consensus 360 ~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~ 439 (525)
.... +.+.. .+... ..
T Consensus 85 ~~~~-----------------------------------------------------~~~~~---------~~~~~--~~ 100 (170)
T TIGR02952 85 HPLF-----------------------------------------------------SLDVF---------KELLS--NE 100 (170)
T ss_pred CCCC-----------------------------------------------------cHHHH---------hhcCC--CC
Confidence 1110 00000 00000 11
Q ss_pred CCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803 440 ETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513 (525)
Q Consensus 440 ~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l 513 (525)
.+|++.+...+....+..+|..|||++|+||.++|..| +|++|||+.||||..+|++..+||+++||+.+
T Consensus 101 ~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g----~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~l 170 (170)
T TIGR02952 101 PNPEEAILKEEANEKLLKALKILTPKQQHVIALRFGQN----LPIAEVARILGKTEGAVKILQFRAIKKLARQM 170 (170)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence 25676666677778899999999999999999999987 99999999999999999999999999999753
No 48
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=99.88 E-value=1.2e-21 Score=180.10 Aligned_cols=151 Identities=20% Similarity=0.254 Sum_probs=123.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 009803 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL 363 (525)
Q Consensus 284 ~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRi 363 (525)
..|++.|+..|.++|+.+++++ +...+++|++|||++++|+++++|++..| .|.+|++..+++.+.++++++.+...
T Consensus 3 ~~af~~l~~~y~~~l~~~~~~~-~~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~~~~~- 79 (154)
T PRK06759 3 PATFTEAVVLYEGLIVNQIKKL-GIYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFAVQE- 79 (154)
T ss_pred cccHHHHHHHHHHHHHHHHHHh-CCcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHHhhcc-
Confidence 4689999999999999999986 55679999999999999999999998766 79999999999999999987632000
Q ss_pred ccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHH
Q 009803 364 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAE 443 (525)
Q Consensus 364 P~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pe 443 (525)
.... + + .|+
T Consensus 80 --------------------------------------------------------~~~~-~---------~-----~~~ 88 (154)
T PRK06759 80 --------------------------------------------------------KCVC-V---------G-----EYE 88 (154)
T ss_pred --------------------------------------------------------cccc-c---------C-----CCc
Confidence 0000 0 0 111
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803 444 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512 (525)
Q Consensus 444 e~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~ 512 (525)
+.....+....|..+|..||+++|.||.++|+.| +|++|||+.||+|..+|+++++||+++||+.
T Consensus 89 ~~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~~~~----~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 89 DHFHFEDVEMKVKDFMSVLDEKEKYIIFERFFVG----KTMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred ccccHHHHHHHHHHHHHhCCHHHHHHHHHHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 1122233456799999999999999999999988 9999999999999999999999999999973
No 49
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=99.88 E-value=2.6e-21 Score=185.17 Aligned_cols=170 Identities=16% Similarity=0.197 Sum_probs=135.8
Q ss_pred HHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHh
Q 009803 277 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD 356 (525)
Q Consensus 277 ~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~ 356 (525)
.+...++..|++.|+..|.+.|+.+++++.++..+++|++||+|+++|+. ..|++..+ .|.||++.++++.+.+++++
T Consensus 21 ~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~~d~~Rk 98 (194)
T PRK12519 21 SALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRAIDRLRS 98 (194)
T ss_pred HHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHHHHHHHh
Confidence 33444668999999999999999999999999899999999999999976 67887654 79999999999999999987
Q ss_pred cccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCC
Q 009803 357 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD 436 (525)
Q Consensus 357 ~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d 436 (525)
+.+..+.. +. . ... ...+
T Consensus 99 ~~~~~~~~------------------------------------------------------~~----~-~~~---~~~~ 116 (194)
T PRK12519 99 RRSRQRLL------------------------------------------------------ER----W-QQE---LLGE 116 (194)
T ss_pred cccccchh------------------------------------------------------hh----h-hhh---hccc
Confidence 65411000 00 0 000 0000
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 437 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 437 ~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
.....+++.+...+....|..+|..||+++++||.++|..| +|++|||+.||+|..+|+++++||+++||+.+.
T Consensus 117 ~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 190 (194)
T PRK12519 117 ASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEG----LSQSEIAKRLGIPLGTVKARARQGLLKLRELLQ 190 (194)
T ss_pred ccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhhcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 11124556666666667899999999999999999999887 999999999999999999999999999999765
No 50
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=99.88 E-value=5.3e-21 Score=180.74 Aligned_cols=169 Identities=14% Similarity=0.123 Sum_probs=136.6
Q ss_pred HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHH
Q 009803 276 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS 355 (525)
Q Consensus 276 L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir 355 (525)
+.....++..|+..|+..|.+.|+.+|.+|.++..+++|++||+|+++|+++++|++..+ .|.||++..++|.+.++++
T Consensus 10 i~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~R 88 (179)
T PRK12514 10 IVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGL-SPMTWLITIARNHAIDRLR 88 (179)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCcccc-cHHHHHHHHHHHHHHHHHH
Confidence 333455668999999999999999999999999999999999999999999999987543 6999999999999999998
Q ss_pred hcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccC
Q 009803 356 DQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIA 435 (525)
Q Consensus 356 ~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~ 435 (525)
++.+. .. .++. . .+ ..
T Consensus 89 ~~~~~-~~-----------------------------------------------------~~~~------~---~~-~~ 104 (179)
T PRK12514 89 ARKAV-AV-----------------------------------------------------DIDE------A---HD-LA 104 (179)
T ss_pred hcCCc-cc-----------------------------------------------------cccc------c---hh-cc
Confidence 75431 00 0000 0 00 00
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 436 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 436 d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
+. ..+|++.+...+....|..+|..||+++++||.++|..| +|++|||+.||+|..+|++.++||+++||+++.
T Consensus 105 ~~-~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 178 (179)
T PRK12514 105 DP-SPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEG----LSYKELAERHDVPLNTMRTWLRRSLLKLRECLS 178 (179)
T ss_pred cc-CCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCChHHHHHHHHHHHHHHHHHhc
Confidence 11 124565555555556789999999999999999999877 999999999999999999999999999999764
No 51
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=99.88 E-value=5.7e-21 Score=183.69 Aligned_cols=173 Identities=23% Similarity=0.196 Sum_probs=140.4
Q ss_pred HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHH
Q 009803 275 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSL 354 (525)
Q Consensus 275 ~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~i 354 (525)
.+.+...++..|++.|+..|.+.|+.+|.++.++..+++|++||+++++|+.+.+|++.. ..|.||++..+++.+.+++
T Consensus 16 li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~n~~~d~~ 94 (196)
T PRK12524 16 LLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVCNLCTDRL 94 (196)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHHHHHHHHHH
Confidence 344444556999999999999999999999999999999999999999999999998533 4799999999999999998
Q ss_pred HhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCccc
Q 009803 355 SDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVI 434 (525)
Q Consensus 355 r~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l 434 (525)
+++.+.. ..++.. .+.
T Consensus 95 Rk~~~~~------------------------------------------------------~~~~~~---------~~~- 110 (196)
T PRK12524 95 RRRRRAS------------------------------------------------------VDLDDA---------PEP- 110 (196)
T ss_pred HhhcCCC------------------------------------------------------CCcccc---------ccc-
Confidence 8654300 000000 000
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 435 ADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 435 ~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
.+. ..++++.+...+....|..+|+.||+++|.||.|+|..+ ++++|||+.||||..+|+++++||+++||+++.
T Consensus 111 ~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~~~g----~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 185 (196)
T PRK12524 111 ADA-APGAEEALIEGDRMRALDAALAALPERQRQAVVLRHIEG----LSNPEIAEVMEIGVEAVESLTARGKRALAALLA 185 (196)
T ss_pred ccc-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 111 124566666667778899999999999999999999987 999999999999999999999999999999887
Q ss_pred hch
Q 009803 515 TKH 517 (525)
Q Consensus 515 ~~~ 517 (525)
..+
T Consensus 186 ~~~ 188 (196)
T PRK12524 186 GQR 188 (196)
T ss_pred hcc
Confidence 543
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=99.87 E-value=6.7e-21 Score=180.90 Aligned_cols=177 Identities=15% Similarity=0.156 Sum_probs=138.8
Q ss_pred HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHH
Q 009803 276 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS 355 (525)
Q Consensus 276 L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir 355 (525)
+.....++..+++.|+..|.+.|+.+|+++.++..+++|++||+++++|+++.+|++. ..|.+|++..+++.+.++++
T Consensus 11 ~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~~~~~~r 88 (190)
T TIGR02939 11 VERVQRGEKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNTAKNHLV 88 (190)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHHHHHHHH
Confidence 3334445689999999999999999999999999999999999999999999999975 36999999999999999987
Q ss_pred hcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccC
Q 009803 356 DQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIA 435 (525)
Q Consensus 356 ~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~ 435 (525)
++.+..... ..+.+.. ....+...
T Consensus 89 ~~~r~~~~~--------------------------------------------------~~~~~~~------~~~~~~~~ 112 (190)
T TIGR02939 89 AQGRRPPTS--------------------------------------------------DVEIEDA------EHFEGADR 112 (190)
T ss_pred HhccCCCcc--------------------------------------------------cccccch------hhhccccc
Confidence 654311000 0000000 00000000
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 436 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 436 d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
.....+|++.+...+....|..+|+.||+++|.||.++|..+ +|++|||+.||+|..+|++.++||+++||+++.
T Consensus 113 ~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~----~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l~ 187 (190)
T TIGR02939 113 LREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLRELEG----LSYEDIARIMDCPVGTVRSRIFRAREAIAIRLR 187 (190)
T ss_pred ccccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhhhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 001235676667777778899999999999999999999877 999999999999999999999999999999875
No 53
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=99.87 E-value=7.6e-21 Score=181.81 Aligned_cols=173 Identities=20% Similarity=0.264 Sum_probs=139.1
Q ss_pred CHHHHHH-HHhccHHHHHHHHHHHHHHHHHHHHHhhCCC---CCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHH
Q 009803 272 DQRELRR-RLNYGILCKDKMITSNIRLVISIAKNYQGAG---MNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIK 347 (525)
Q Consensus 272 d~~~L~~-~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g---~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIR 347 (525)
++..|.. ...++..|++.|+..|.+.|+.++.++.+++ .+++|++||+++++|+++++|++..+ .|.||++..++
T Consensus 4 ~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~iar 82 (189)
T PRK06811 4 NEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAISK 82 (189)
T ss_pred cHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHHH
Confidence 3444444 4445589999999999999999999998853 47999999999999999999997655 79999999999
Q ss_pred HHHHHHHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccC
Q 009803 348 QAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQN 427 (525)
Q Consensus 348 qaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~ 427 (525)
+.+.++++++.+.... .+.+. .
T Consensus 83 n~~~d~~rk~~~~~~~----------------------------------------------------~~~~~------~ 104 (189)
T PRK06811 83 YKAIDYKRKLTKNNEI----------------------------------------------------DSIDE------F 104 (189)
T ss_pred HHHHHHHHHhcccccc----------------------------------------------------ccchh------h
Confidence 9999999876541100 00000 0
Q ss_pred CCCCcccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 009803 428 LKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR 507 (525)
Q Consensus 428 ~~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALk 507 (525)
..+ ...+|++.+...+....|..+|..|||++|.||.|+|..| +|++|||+.||+|..+|+++++||++
T Consensus 105 ------~~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~EIAe~lgis~~~V~~~l~Ra~~ 173 (189)
T PRK06811 105 ------ILI-SEESIENEIILKENKEEILKLINDLEKLDREIFIRRYLLG----EKIEEIAKKLGLTRSAIDNRLSRGRK 173 (189)
T ss_pred ------hhc-ccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcc----CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 000 1125666667777778899999999999999999999877 99999999999999999999999999
Q ss_pred HHHhHHh
Q 009803 508 KLKNKKR 514 (525)
Q Consensus 508 KLR~~l~ 514 (525)
+||+...
T Consensus 174 ~Lr~~~~ 180 (189)
T PRK06811 174 KLQKNKL 180 (189)
T ss_pred HHHHccc
Confidence 9998653
No 54
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=99.87 E-value=6e-21 Score=181.23 Aligned_cols=170 Identities=16% Similarity=0.191 Sum_probs=131.5
Q ss_pred HHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHh
Q 009803 277 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD 356 (525)
Q Consensus 277 ~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~ 356 (525)
.....++..|++.|+..|.+.|+.++++|.+++.+++|++||+++++|+++++|++.. ..|.+|++..+++.+.+++++
T Consensus 15 ~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~-~~~~~wl~~ia~n~~~d~~rk 93 (186)
T PRK13919 15 ALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRR-GSARAWLLALAHHAAVDHVRR 93 (186)
T ss_pred HHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCccc-cchHHHHHHHHHHHHHHHHHh
Confidence 3334566999999999999999999999999989999999999999999999998754 369999999999999999987
Q ss_pred cccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCC
Q 009803 357 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD 436 (525)
Q Consensus 357 ~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d 436 (525)
..+..+. .+.+ .......+ .++
T Consensus 94 ~~~~~~~----------------------------------------------------~~~~-----~~~~~~~~-~~~ 115 (186)
T PRK13919 94 RAARPQP----------------------------------------------------LEPD-----EREPEAFD-LPG 115 (186)
T ss_pred hhccccc----------------------------------------------------cccc-----cccccccc-CCC
Confidence 6431000 0000 00000000 001
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 437 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 437 ~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
+. .++ ........|..+|+.||+++|.||.++|..+ +|++|||+.||+|..+|+.+++||+++||..+.
T Consensus 116 ~~--~~~---~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~----~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l~ 184 (186)
T PRK13919 116 PG--LDE---EGHLDRTRLGRALKALSPEERRVIEVLYYQG----YTHREAAQLLGLPLGTLKTRARRALSRLKEVLR 184 (186)
T ss_pred cc--ccH---HHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence 10 111 1222345689999999999999999999887 999999999999999999999999999999764
No 55
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=99.87 E-value=1.1e-20 Score=180.75 Aligned_cols=175 Identities=13% Similarity=0.126 Sum_probs=138.3
Q ss_pred HHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhc
Q 009803 278 RRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ 357 (525)
Q Consensus 278 ~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~ 357 (525)
....|+..+++.|+..|.+.|+.++++|.++..+++|++||+++++|+++.+|++.. .|.+|++..+++.+.++++++
T Consensus 13 ~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~~d~~rk~ 90 (193)
T PRK11923 13 RVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTAKNHLVSR 90 (193)
T ss_pred HHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHHHHHHHHh
Confidence 333456899999999999999999999999989999999999999999999999863 599999999999999999865
Q ss_pred ccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCC
Q 009803 358 SRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADP 437 (525)
Q Consensus 358 ~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~ 437 (525)
.+.... ....++.....++. ..+.
T Consensus 91 ~~~~~~--------------------------------------------------~~~~~~~~~~~~~~----~~~~-- 114 (193)
T PRK11923 91 GRRPPD--------------------------------------------------SDVSSEDAEFYDGD----HALK-- 114 (193)
T ss_pred cCCCcc--------------------------------------------------ccccccchhhhccc----cccc--
Confidence 441100 00000000000000 0011
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 438 EAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 438 ~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
...+|++.+...+....+..+|..||+++|.||.++|..| +|++|||+.||+|..+|+++.+||+++||+++.
T Consensus 115 ~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 187 (193)
T PRK11923 115 DIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREFDG----LSYEDIASVMQCPVGTVRSRIFRAREAIDKALQ 187 (193)
T ss_pred CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 1235676666777778899999999999999999999877 999999999999999999999999999999876
No 56
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=7.9e-21 Score=180.51 Aligned_cols=169 Identities=14% Similarity=0.141 Sum_probs=135.5
Q ss_pred HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHH
Q 009803 275 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSL 354 (525)
Q Consensus 275 ~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~i 354 (525)
.+.....++..|++.|+..|.+.++.+++++.++..+++|++||+|+.+|+.+++|++.. ..|.+|++..+++.+.+++
T Consensus 13 l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~ 91 (182)
T PRK12537 13 CLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPAR-GSARGWIYSVTRHLALNVL 91 (182)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCccc-ccHHHHHHHHHHHHHHHHH
Confidence 344445566999999999999999999999999999999999999999999999998644 3799999999999999999
Q ss_pred HhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCccc
Q 009803 355 SDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVI 434 (525)
Q Consensus 355 r~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l 434 (525)
+++.+...+ +.. . .+..
T Consensus 92 r~~~~~~~~-------------------------------------------------------~~~-----~---~~~~ 108 (182)
T PRK12537 92 RDTRREVVL-------------------------------------------------------DDD-----A---EETA 108 (182)
T ss_pred HhccccCcc-------------------------------------------------------ccc-----h---hhhc
Confidence 876531100 000 0 0000
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803 435 ADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513 (525)
Q Consensus 435 ~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l 513 (525)
.+ ..++++..........|..+|+.||+++|+||.++|..| +|++|||+.||||.++|+.+++||+++||.++
T Consensus 109 ~~--~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 181 (182)
T PRK12537 109 QT--LHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYVDG----CSHAEIAQRLGAPLGTVKAWIKRSLKALRECM 181 (182)
T ss_pred cc--ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCChhhHHHHHHHHHHHHHHHh
Confidence 00 112333444444556789999999999999999999888 99999999999999999999999999999875
No 57
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=7.5e-21 Score=180.91 Aligned_cols=171 Identities=13% Similarity=0.127 Sum_probs=137.2
Q ss_pred HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHH
Q 009803 276 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS 355 (525)
Q Consensus 276 L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir 355 (525)
+.....++..+++.|+..|.++|+++|++|.++..+++|++||+|+++|+++++|++.++ .|.||++..+++.+.++++
T Consensus 16 ~~~~~~~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~~d~~R 94 (187)
T PRK12534 16 LTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKAIDHLR 94 (187)
T ss_pred HHHHHcCCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHHHHH
Confidence 444455668999999999999999999999999999999999999999999999998654 6899999999999999998
Q ss_pred hcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccC
Q 009803 356 DQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIA 435 (525)
Q Consensus 356 ~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~ 435 (525)
++.+..+. .+++.. .+..
T Consensus 95 ~~~~~~~~----------------------------------------------------~~~~~~---------~~~~- 112 (187)
T PRK12534 95 ANAPQRRN----------------------------------------------------VALDDA---------GELR- 112 (187)
T ss_pred hccccccc----------------------------------------------------ccccch---------hhhc-
Confidence 76431000 000000 0000
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 436 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 436 d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
++ ..++++.....+....|..+|..||++++.|+.++|..| +|++|||+.||+|.++|+++++||+++||+.+.
T Consensus 113 ~~-~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l~ 186 (187)
T PRK12534 113 AA-DASPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEG----ITYEELAARTDTPIGTVKSWIRRGLAKLKACLE 186 (187)
T ss_pred cc-cCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCCChhHHHHHHHHHHHHHHHHHc
Confidence 00 113444445556677899999999999999999999877 999999999999999999999999999999764
No 58
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=9.4e-21 Score=187.89 Aligned_cols=165 Identities=17% Similarity=0.214 Sum_probs=135.6
Q ss_pred hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccc
Q 009803 281 NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT 360 (525)
Q Consensus 281 ~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~ 360 (525)
.|+..|++.|+..|.+.|+.+++++.++..+++|++||+|+.+|+.+++|++..+ .|.+|++..+++.++++++++.+.
T Consensus 59 ~gd~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~~id~~Rk~~~~ 137 (233)
T PRK12538 59 TDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNRCIDLRRKPRTE 137 (233)
T ss_pred hCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHHHHHHHHhhccc
Confidence 3568999999999999999999999999899999999999999999999987544 799999999999999998764210
Q ss_pred eecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCC
Q 009803 361 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAE 440 (525)
Q Consensus 361 iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~ 440 (525)
. ++. . . +. .+ ...
T Consensus 138 -~-------------------------------------------------------~~~-~--~------~~-~~-~~~ 150 (233)
T PRK12538 138 -N-------------------------------------------------------VDA-V--P------EV-AD-GKP 150 (233)
T ss_pred -c-------------------------------------------------------ccc-c--c------cc-cc-CCC
Confidence 0 000 0 0 00 00 012
Q ss_pred CHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhch
Q 009803 441 TAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 517 (525)
Q Consensus 441 ~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~ 517 (525)
.+++.+...+....|..+|..||+++|+||.|+|..| +|++|||+.||+|.++|+++++||+++||+.+....
T Consensus 151 ~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~~eg----~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~~~~ 223 (233)
T PRK12538 151 DAVSVIERNELSDLLEAAMQRLPEQQRIAVILSYHEN----MSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLRRHE 223 (233)
T ss_pred CHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3455555566667899999999999999999999988 999999999999999999999999999999887543
No 59
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=3.6e-21 Score=183.11 Aligned_cols=175 Identities=19% Similarity=0.220 Sum_probs=138.8
Q ss_pred hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccc
Q 009803 281 NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT 360 (525)
Q Consensus 281 ~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~ 360 (525)
.++..|+..|+..|.+.++.+|.++.++..+++|++||+|+.+|+++.+|++..+..|.||++..++|.+.++++++.+.
T Consensus 5 ~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~~~ 84 (185)
T PRK12542 5 NNDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNKRH 84 (185)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 35688999999999999999999999998999999999999999999999875445899999999999999999876431
Q ss_pred eecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCC
Q 009803 361 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAE 440 (525)
Q Consensus 361 iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~ 440 (525)
... . +. . .. +.... ..+
T Consensus 85 ~~~------------------~------------------------------------~~-~----~~---~~~~~-~~~ 101 (185)
T PRK12542 85 ETF------------------L------------------------------------EE-Y----ER---ESIEA-VDE 101 (185)
T ss_pred hhh------------------h------------------------------------hh-c----cc---cchhh-hhc
Confidence 000 0 00 0 00 00000 011
Q ss_pred CHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhhh
Q 009803 441 TAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQ 520 (525)
Q Consensus 441 ~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~~ 520 (525)
.+++..........|..+|..||+++|+||.|+|..| +|++|||+.||+|.++|+++++||+++||+.+....-..
T Consensus 102 ~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~~~ 177 (185)
T PRK12542 102 NIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVFYN----LTYQEISSVMGITEANVRKQFERARKRVQNMIGGIQHDE 177 (185)
T ss_pred cHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccchHH
Confidence 3444333444456799999999999999999999988 999999999999999999999999999999987765555
Q ss_pred hh
Q 009803 521 YA 522 (525)
Q Consensus 521 yl 522 (525)
|+
T Consensus 178 ~~ 179 (185)
T PRK12542 178 FK 179 (185)
T ss_pred HH
Confidence 53
No 60
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=99.87 E-value=4.3e-21 Score=183.21 Aligned_cols=172 Identities=20% Similarity=0.286 Sum_probs=134.4
Q ss_pred CCHHHHHHHHh----ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHH
Q 009803 271 VDQRELRRRLN----YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWI 346 (525)
Q Consensus 271 ~d~~~L~~~l~----~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wI 346 (525)
+++..|...++ ++..|++.|+..|.+.|+++|.+|.++..+++|++||+++.+|+++++|++. ..|.||++.++
T Consensus 8 ~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~~--~~~~~wl~~ia 85 (188)
T PRK09640 8 LNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLYSIT 85 (188)
T ss_pred CCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcCC--CcchHHHHHHH
Confidence 44555555554 4699999999999999999999999999999999999999999999999863 47999999999
Q ss_pred HHHHHHHHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCccccccccc
Q 009803 347 KQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQ 426 (525)
Q Consensus 347 RqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~ 426 (525)
++.+.+++++..+.... ..+...
T Consensus 86 ~n~~~d~~R~~~~~~~~-----------------------------------------------------~~~~~~---- 108 (188)
T PRK09640 86 YNECITQYRKERRKRRL-----------------------------------------------------MDALSL---- 108 (188)
T ss_pred HHHHHHHHHHhcccccC-----------------------------------------------------cchhhh----
Confidence 99999999875431100 000000
Q ss_pred CCCCCcccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803 427 NLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF 506 (525)
Q Consensus 427 ~~~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RAL 506 (525)
+...++. ++.....+....|..+|+.||+++|+||.|+|..| +|++|||+.||||..+|+.+++||+
T Consensus 109 -----~~~~~~~----~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Ra~ 175 (188)
T PRK09640 109 -----DPLEEAS----EEKAPKPEERGGLDRWLVHVNPIDREILVLRFVAE----LEFQEIADIMHMGLSATKMRYKRAL 175 (188)
T ss_pred -----ccccccc----ccccccHHHHHHHHHHHHhcChhheeeeeeHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 0000000 00011123345689999999999999999999987 9999999999999999999999999
Q ss_pred HHHHhHHh
Q 009803 507 RKLKNKKR 514 (525)
Q Consensus 507 kKLR~~l~ 514 (525)
++||+.+.
T Consensus 176 ~~Lr~~l~ 183 (188)
T PRK09640 176 DKLREKFA 183 (188)
T ss_pred HHHHHHHH
Confidence 99999774
No 61
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=2.7e-20 Score=174.01 Aligned_cols=170 Identities=19% Similarity=0.167 Sum_probs=141.2
Q ss_pred HHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcc
Q 009803 279 RLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS 358 (525)
Q Consensus 279 ~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~ 358 (525)
...++..|++.|+..|.+.|+++|+++.++..+++|++||+++.||++.++|+ .+..|.+|++..+++.+.+++++..
T Consensus 7 ~~~~~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~~r~~~ 84 (179)
T PRK11924 7 DATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDLLRRRR 84 (179)
T ss_pred HHccCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHHHHhcc
Confidence 34567899999999999999999999999999999999999999999999998 3458999999999999999998765
Q ss_pred cceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCC
Q 009803 359 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPE 438 (525)
Q Consensus 359 r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~ 438 (525)
+.... ..+ +. .+...+..
T Consensus 85 ~~~~~-----------------------------------------------------~~~-----~~----~~~~~~~~ 102 (179)
T PRK11924 85 REKAV-----------------------------------------------------LSD-----DA----LEPEFAET 102 (179)
T ss_pred ccccc-----------------------------------------------------Ccc-----cc----cccccCCc
Confidence 41110 000 00 00000002
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803 439 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 516 (525)
Q Consensus 439 ~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~ 516 (525)
..+|++.+...+....+..+|+.||++++.||.++|..+ +|++|||+.||+|+.+|+++++||+++||+.+...
T Consensus 103 ~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~~----~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~~~ 176 (179)
T PRK11924 103 AETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEG----LSYREIAEILGVPVGTVKSRLRRARQLLRECLEAQ 176 (179)
T ss_pred cCCHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 346888888888889999999999999999999999877 99999999999999999999999999999988653
No 62
>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=99.86 E-value=1.8e-20 Score=177.65 Aligned_cols=179 Identities=15% Similarity=0.152 Sum_probs=137.9
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhC----CCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhc
Q 009803 282 YGILCKDKMITSNIRLVISIAKNYQG----AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ 357 (525)
Q Consensus 282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~----~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~ 357 (525)
++..|++.|+..|.+.|+.+|++|.+ +..+++|++||+++.+|+++.+|++..+.+|.+|++..+++.+.++++++
T Consensus 4 ~~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~~ 83 (189)
T TIGR02984 4 GDQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRRH 83 (189)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHHH
Confidence 56899999999999999999999853 56789999999999999999999976667899999999999999998865
Q ss_pred cc-ceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCccccccccc-CCCCCcccC
Q 009803 358 SR-TIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQ-NLKPSEVIA 435 (525)
Q Consensus 358 ~r-~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~-~~~l~d~l~ 435 (525)
.+ -.+. + ....+++.....++ ...+.+.+.
T Consensus 84 ~~~~~r~-------------------------~-----------------------~~~~~~~~~~~~~~~~~~~~~~~~ 115 (189)
T TIGR02984 84 LGAQKRD-------------------------I-----------------------RREQSLDAGGRLDESSVRLAAQLA 115 (189)
T ss_pred HHHHhhh-------------------------c-----------------------ccccCCCcccccCCcchhHHHHcc
Confidence 21 0000 0 00012221110011 111222222
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803 436 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513 (525)
Q Consensus 436 d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l 513 (525)
+ ...+|++.+...+....|..+|..|||++|.||.++|+.| +|++|||+.||||.++|++.++||+++||+.+
T Consensus 116 ~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~~~g----~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~l 188 (189)
T TIGR02984 116 A-DGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRHLEG----LSFAEVAERMDRSEGAVSMLWVRGLARLRQIL 188 (189)
T ss_pred C-CCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 2 2335777777777778899999999999999999999877 99999999999999999999999999999865
No 63
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=2.3e-20 Score=178.15 Aligned_cols=174 Identities=20% Similarity=0.230 Sum_probs=141.4
Q ss_pred HHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHH
Q 009803 274 RELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS 353 (525)
Q Consensus 274 ~~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ 353 (525)
..+.....++..|++.|+..|.+.++.++.++.++..+++|++||+|+.+|+++++|++. ..|.+|++..+++.+.++
T Consensus 11 ~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~ 88 (189)
T PRK12515 11 MLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARFKALSA 88 (189)
T ss_pred HHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHHHHHHH
Confidence 344445556699999999999999999999999999999999999999999999999964 479999999999999999
Q ss_pred HHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcc
Q 009803 354 LSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEV 433 (525)
Q Consensus 354 ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~ 433 (525)
+++..+. .+ .. + . . ..
T Consensus 89 ~r~~~~~-~~-------------------------------------------------------~~----~-~--~-~~ 104 (189)
T PRK12515 89 LRRRKHE-EI-------------------------------------------------------DD----E-A--A-AA 104 (189)
T ss_pred HHccCCC-CC-------------------------------------------------------cc----c-c--c-cc
Confidence 9865420 00 00 0 0 0 00
Q ss_pred cCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803 434 IADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513 (525)
Q Consensus 434 l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l 513 (525)
..+ ..++|++.....+....+..+|+.||+++|+||.++|..+ +|++|||+.||+|..+|+++++||+++||+.+
T Consensus 105 ~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 105 IED-GADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYYHE----KSVEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred cCC-CCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 111 1235666666666677899999999999999999999987 99999999999999999999999999999988
Q ss_pred hhchh
Q 009803 514 RTKHL 518 (525)
Q Consensus 514 ~~~~L 518 (525)
...+.
T Consensus 180 ~~~~~ 184 (189)
T PRK12515 180 KAAGV 184 (189)
T ss_pred HHhcc
Confidence 76543
No 64
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=2.4e-20 Score=181.12 Aligned_cols=172 Identities=15% Similarity=0.168 Sum_probs=134.3
Q ss_pred HhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhccc
Q 009803 280 LNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR 359 (525)
Q Consensus 280 l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r 359 (525)
.+++..++++|+..|.+.|+.++.++.++..+++|++||+|+.+|+++..|++.++ .|.||++.++|+.+.++++++.+
T Consensus 33 ~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d~~Rk~~~ 111 (206)
T PRK12526 33 ISRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFDMLRKIKA 111 (206)
T ss_pred HcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHHHHHHhcc
Confidence 34668999999999999999999999999889999999999999999999997665 59999999999999999987654
Q ss_pred ceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCC
Q 009803 360 TIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEA 439 (525)
Q Consensus 360 ~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~ 439 (525)
..... ++. + .....+.+.+. .
T Consensus 112 ~~~~~-----------------------------------------------------~~~----~-~~~~~~~~~~~-~ 132 (206)
T PRK12526 112 KKEQN-----------------------------------------------------LGD----D-IWPIEQALAES-Q 132 (206)
T ss_pred ccccc-----------------------------------------------------ccc----c-cchhhhhcccc-c
Confidence 11000 000 0 00000111111 1
Q ss_pred CCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803 440 ETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 516 (525)
Q Consensus 440 ~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~ 516 (525)
..+. ..........|..+|..||+++|.||.++|+.+ +|++|||+.||+|.++|+.+++||+++||+.+...
T Consensus 133 ~~~~-~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~ 204 (206)
T PRK12526 133 SESE-EFSDHLMDKQILSYIEKLPEAQQTVVKGVYFQE----LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQMGEQ 204 (206)
T ss_pred CchH-HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence 1222 222233446789999999999999999999988 99999999999999999999999999999988643
No 65
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=3e-20 Score=176.10 Aligned_cols=165 Identities=16% Similarity=0.241 Sum_probs=134.3
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccce
Q 009803 282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 361 (525)
Q Consensus 282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~i 361 (525)
++..|+..|+..|.+.|+.+++.|.++..+++|++||+|+.+|+++.+|++.. .|.+|++..+++.+.++++...+..
T Consensus 4 ~d~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~~~~~ 81 (179)
T PRK12543 4 GDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKRWRRF 81 (179)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhhcccc
Confidence 56789999999999999999999999999999999999999999999999864 6999999999999999877654210
Q ss_pred ecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCC
Q 009803 362 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET 441 (525)
Q Consensus 362 RiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~ 441 (525)
+. ++.. . + ..+ ......
T Consensus 82 ~~------------------------------------------------------~~~~-~-~----~~~---~~~~~~ 98 (179)
T PRK12543 82 RI------------------------------------------------------FEKA-E-E----QRK---PVSIDF 98 (179)
T ss_pred cc------------------------------------------------------cccc-c-c----ccc---cccccC
Confidence 00 0000 0 0 000 001113
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803 442 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 516 (525)
Q Consensus 442 pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~ 516 (525)
|+. +...+....|..+|..||+++|.||.|+|..| +|++|||+.||||..+|+..++||+++||+.+...
T Consensus 99 ~~~-~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~~e~----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~ 168 (179)
T PRK12543 99 SED-VLSKESNQELIELIHKLPYKLRQVIILRYLHD----YSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIE 168 (179)
T ss_pred hHH-HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcc----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 444 55666778899999999999999999999988 99999999999999999999999999999998754
No 66
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=99.85 E-value=4.9e-20 Score=173.04 Aligned_cols=164 Identities=12% Similarity=0.081 Sum_probs=131.2
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccce
Q 009803 282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 361 (525)
Q Consensus 282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~i 361 (525)
++..+++.|+..|.+.++++|.++.++..+++|++||.|+.+|+..++|++.. ..|.+|++..++|.+.++++++.+..
T Consensus 6 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~Rk~~~~~ 84 (173)
T PRK09645 6 AEAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSARARP 84 (173)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHHHHHHHhhcccc
Confidence 46889999999999999999999999888999999999999999999997533 47999999999999999998764310
Q ss_pred ecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCC
Q 009803 362 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET 441 (525)
Q Consensus 362 RiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~ 441 (525)
.. .. ++. .+ .++. .
T Consensus 85 ~~-----------------------------------------------------~~------~~~---~~-~~~~---~ 98 (173)
T PRK09645 85 VE-----------------------------------------------------GG------DDV---LG-VPEQ---S 98 (173)
T ss_pred cc-----------------------------------------------------cc------ccc---cc-CCCC---C
Confidence 00 00 000 00 0011 1
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803 442 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 516 (525)
Q Consensus 442 pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~ 516 (525)
+++..........|..+|+.||+++|+||.|+|..| +|++|||+.||+|.++|+.+++||+++||+.+...
T Consensus 99 ~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~~~g----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~ 169 (173)
T PRK09645 99 APDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRG----WSTAQIAADLGIPEGTVKSRLHYALRALRLALQER 169 (173)
T ss_pred CchHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhcc
Confidence 122233333445789999999999999999999988 99999999999999999999999999999988653
No 67
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=99.85 E-value=7.9e-20 Score=175.47 Aligned_cols=171 Identities=15% Similarity=0.147 Sum_probs=137.0
Q ss_pred CHHH-HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHH
Q 009803 272 DQRE-LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAV 350 (525)
Q Consensus 272 d~~~-L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI 350 (525)
++.. +.....++..+++.|+..|.+.|++++.++.++..+++|++||+|+.+|+++++|++. ..|.+|++..+++.+
T Consensus 13 ~~~~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~--~~f~~wL~~i~rn~~ 90 (192)
T PRK09643 13 SDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGD--AAVSSWLHRIVVNAC 90 (192)
T ss_pred CHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCC--CccHHHHHHHHHHHH
Confidence 3444 4445556699999999999999999999999999999999999999999999999975 369999999999999
Q ss_pred HHHHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCC
Q 009803 351 RKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKP 430 (525)
Q Consensus 351 ~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l 430 (525)
.+++++..+..+. +++ +..
T Consensus 91 ~d~~Rk~~~~~~~-----------------------------------------------------~~~-----~~~--- 109 (192)
T PRK09643 91 LDRLRRAKARPTV-----------------------------------------------------PLD-----DVY--- 109 (192)
T ss_pred HHHHHccccCCCC-----------------------------------------------------Ccc-----ccc---
Confidence 9999876531000 000 000
Q ss_pred CcccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803 431 SEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510 (525)
Q Consensus 431 ~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR 510 (525)
+. .. .+++.+...+....|..+|+.||+++|+||.|+|..+ +|++|||+.||+|..+|+.+++||+++||
T Consensus 110 -~~-~~----~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~~~g----~s~~EIA~~lg~s~~tV~~rl~rar~~Lr 179 (192)
T PRK09643 110 -PV-AQ----LERDPTARVETALAVQRALMRLPVEQRAALVAVDMQG----YSVADAARMLGVAEGTVKSRCARGRARLA 179 (192)
T ss_pred -cc-cC----CcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 00 00 1222333445566799999999999999999999987 99999999999999999999999999999
Q ss_pred hHHhh
Q 009803 511 NKKRT 515 (525)
Q Consensus 511 ~~l~~ 515 (525)
+.+..
T Consensus 180 ~~l~~ 184 (192)
T PRK09643 180 ELLGY 184 (192)
T ss_pred HHHHH
Confidence 98864
No 68
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=99.85 E-value=7e-20 Score=164.67 Aligned_cols=157 Identities=23% Similarity=0.345 Sum_probs=132.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceeccc
Q 009803 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF 365 (525)
Q Consensus 286 A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~ 365 (525)
|++.++..|.++|+++++++.+++.+.+|++|||++++|++++.|++. .+|.+|+++++++.+.++++++.+ .+.
T Consensus 2 a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~---~~~ 76 (158)
T TIGR02937 2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR---LRR 76 (158)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhcc---CCc
Confidence 789999999999999999999999999999999999999999999998 689999999999999999998765 111
Q ss_pred chHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHH
Q 009803 366 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL 445 (525)
Q Consensus 366 ~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~ 445 (525)
.. ... .. .. .....+++.
T Consensus 77 ~~---------------------------------------------------~~~------~~----~~-~~~~~~~~~ 94 (158)
T TIGR02937 77 EL---------------------------------------------------DLL------EE----LL-DSDPSPEEE 94 (158)
T ss_pred ch---------------------------------------------------hhh------hh----cc-cccCCHHHH
Confidence 00 000 00 00 112246666
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803 446 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513 (525)
Q Consensus 446 ~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l 513 (525)
.........|..+++.||+.++.||.++|+.| +|..|||+.||+|+.+|+++..+++++||+.+
T Consensus 95 ~~~~~~~~~l~~~l~~L~~~~~~ii~~~~~~g----~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~l 158 (158)
T TIGR02937 95 LEQEEEREALREALEKLPEREREVLVLRYLEG----LSYKEIAEILGISVGTVKRRLKRARKKLRELL 158 (158)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHhhHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 66777778899999999999999999998877 99999999999999999999999999999753
No 69
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=99.85 E-value=4.3e-20 Score=173.67 Aligned_cols=166 Identities=15% Similarity=0.137 Sum_probs=130.9
Q ss_pred HHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHh
Q 009803 277 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD 356 (525)
Q Consensus 277 ~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~ 356 (525)
.....++..|++.|+..|.+.|+.+|++|.++..+++|++||+|+++|++++.|++. .+|.+|++..+++.+.+++++
T Consensus 10 ~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~r~ 87 (176)
T PRK09638 10 QKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASRLYKDHLRK 87 (176)
T ss_pred HHHHCCCHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHH
Confidence 344456699999999999999999999999999999999999999999999999874 479999999999999999987
Q ss_pred cccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCC
Q 009803 357 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD 436 (525)
Q Consensus 357 ~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d 436 (525)
..+.... .+ ... + ...+
T Consensus 88 ~~~~~~~----------------------------~~---------------------------~~~-~-------~~~~ 104 (176)
T PRK09638 88 QKREKLR----------------------------LQ---------------------------RAK-E-------ETLR 104 (176)
T ss_pred hccccch----------------------------hh---------------------------hcc-c-------ccCC
Confidence 6431100 00 000 0 0000
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 437 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 437 ~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
. ... +..........|..+|+.||+++|+||.++|..| +|++|||+.||+|..+|++.++||+++||+.+.
T Consensus 105 ~--~~~-~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~l~ 175 (176)
T PRK09638 105 K--EKW-EAAIKGAEWSEMLDALSKLDPEFRAPVILKHYYG----YTYEEIAKMLNIPEGTVKSRVHHGIKQLRKEWG 175 (176)
T ss_pred c--cch-HHHHHhhhHHHHHHHHHcCCHHHhheeeehhhcC----CCHHHHHHHHCCChhHHHHHHHHHHHHHHHHhc
Confidence 0 000 1112223345688999999999999999999877 999999999999999999999999999999763
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=99.85 E-value=3.2e-20 Score=170.31 Aligned_cols=160 Identities=16% Similarity=0.170 Sum_probs=129.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceeccc
Q 009803 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF 365 (525)
Q Consensus 286 A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~ 365 (525)
|+++|+..|.+.|+++++++.++..+.+|++||+++++|+++.+|++. .+|.+|++.++|+.+.+++++..+....
T Consensus 2 a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~--~~~~~wl~~i~r~~~~d~~r~~~~~~~~-- 77 (161)
T TIGR02985 2 AFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEV--ESFKAYLFTIVKNRSLNYLRHKQVEEKY-- 77 (161)
T ss_pred hHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc--ccHHHHHHHHHHHHHHHHHHHHHhHhHH--
Confidence 789999999999999999999998999999999999999999999864 4799999999999999998876531000
Q ss_pred chHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHH
Q 009803 366 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL 445 (525)
Q Consensus 366 ~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~ 445 (525)
...+ .++.. .....+++++.
T Consensus 78 ------------~~~~-----------------------------------------~~~~~-------~~~~~~~~~~~ 97 (161)
T TIGR02985 78 ------------QEEI-----------------------------------------LEIEV-------DELSENDPEEE 97 (161)
T ss_pred ------------HHHH-----------------------------------------Hhhcc-------cccCCCCcHHH
Confidence 0000 00000 00011245566
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803 446 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513 (525)
Q Consensus 446 ~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l 513 (525)
+...+....|..++..||+++++||.++|..+ +|..|||+.||+|+++|+++++||+++||+.+
T Consensus 98 ~~~~e~~~~l~~~l~~L~~~~r~il~l~~~~~----~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~l 161 (161)
T TIGR02985 98 LEAKELQLIIYKAIEKLPEQCRKIFILSRFEG----KSYKEIAEELGISVKTVEYHISKALKELRKEL 161 (161)
T ss_pred HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 66667777899999999999999999999877 99999999999999999999999999999753
No 71
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=6.6e-20 Score=176.03 Aligned_cols=175 Identities=18% Similarity=0.142 Sum_probs=134.0
Q ss_pred HHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHh
Q 009803 277 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD 356 (525)
Q Consensus 277 ~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~ 356 (525)
.+...++..+++.|+..|.+.|+.+|.++.++..+++|++||+++.+|+.+++|++..+ .|.+|++..++|.+.+++++
T Consensus 19 ~~~~~~d~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn~~ld~~Rk 97 (194)
T PRK12531 19 EKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRNLCFDLLRK 97 (194)
T ss_pred HHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHHHHHHHHHH
Confidence 34445668999999999999999999999999889999999999999999999997544 69999999999999999987
Q ss_pred cccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCC
Q 009803 357 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD 436 (525)
Q Consensus 357 ~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d 436 (525)
..+.... ...+.... + + .......+
T Consensus 98 ~~~~~~~----------------------------------------------------~~~~~~~~-~-~-~~~~~~~~ 122 (194)
T PRK12531 98 QKGKDLH----------------------------------------------------IHADDIWP-S-D-YYPPDLVD 122 (194)
T ss_pred hcccccc----------------------------------------------------cchhhccc-c-c-cccccccc
Confidence 6531000 00000000 0 0 00000000
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803 437 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 516 (525)
Q Consensus 437 ~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~ 516 (525)
...++.. .....+..+|..||+++|+||.++|..+ +|++|||+.||||.++|+.+++||+++||+.+...
T Consensus 123 --~~~~e~~----~~~~~l~~~l~~Lp~~~r~v~~l~~~eg----~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~~~ 192 (194)
T PRK12531 123 --HYSPEQD----MLKEQVMKFLDRLPKAQRDVLQAVYLEE----LPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSMDAE 192 (194)
T ss_pred --ccCHHHH----HHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHhhhc
Confidence 1123322 2235688899999999999999999987 99999999999999999999999999999988754
Q ss_pred h
Q 009803 517 H 517 (525)
Q Consensus 517 ~ 517 (525)
.
T Consensus 193 ~ 193 (194)
T PRK12531 193 S 193 (194)
T ss_pred c
Confidence 3
No 72
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=99.84 E-value=1e-19 Score=170.44 Aligned_cols=162 Identities=19% Similarity=0.245 Sum_probs=129.7
Q ss_pred HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHH
Q 009803 276 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS 355 (525)
Q Consensus 276 L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir 355 (525)
+.....++..|++.++..|.+.+++++.++.++..+++|++||+++.+|+.+++|++. .+|.||++..+++.+.++++
T Consensus 7 ~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R 84 (169)
T TIGR02954 7 VKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHP--KYFNTWLTRILINECIDLLK 84 (169)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCc--cccHHHHHHHHHHHHHHHHH
Confidence 3444556699999999999999999999999999999999999999999999999975 36999999999999999998
Q ss_pred hcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccC
Q 009803 356 DQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIA 435 (525)
Q Consensus 356 ~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~ 435 (525)
+..+. .| ++.... ..
T Consensus 85 ~~~~~--~~-----------------------------------------------------~~~~~~----------~~ 99 (169)
T TIGR02954 85 KKKKV--IP-----------------------------------------------------FDPNTS----------IE 99 (169)
T ss_pred hcCCc--Cc-----------------------------------------------------cccccc----------cc
Confidence 76431 00 000000 00
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 436 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 436 d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
+. .++. .. .....+..+|+.||+++|+||.++|+.| +|++|||+.||||..+|+.+.+||+++||+.+.
T Consensus 100 ~~---~~~~--~~-~~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~l~ 168 (169)
T TIGR02954 100 KG---ECET--HA-DSRLDLYKAIDTLNDKYQTAIILRYYHD----LTIKEIAEVMNKPEGTVKTYLHRALKKLKKRLE 168 (169)
T ss_pred cc---hhhh--ch-HHHHHHHHHHHhCCHHHhHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 00 0110 00 1123688999999999999999999987 999999999999999999999999999999763
No 73
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=99.84 E-value=1e-19 Score=172.64 Aligned_cols=165 Identities=16% Similarity=0.138 Sum_probs=135.3
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccce
Q 009803 282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 361 (525)
Q Consensus 282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~i 361 (525)
.+..|+++|+..|.+.|+++++++.++..+++|++||+++.+|+++++|++. ..|.+|++..+++.+.+++++..+-.
T Consensus 13 ~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~--~~~~awl~~ia~n~~~d~~Rk~~~~~ 90 (179)
T PRK09415 13 DKEDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGK--SSLKTWLYRIAINHCKDYLKSWHNKK 90 (179)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--cccHHHHHHHHHHHHHHHHHhhcccc
Confidence 3478999999999999999999999998999999999999999999999864 36999999999999999998754310
Q ss_pred ecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCC
Q 009803 362 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET 441 (525)
Q Consensus 362 RiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~ 441 (525)
.. +.+. ...+... ...+
T Consensus 91 ~~-----------------------------------------------------~~~~--------~~~~~~~--~~~~ 107 (179)
T PRK09415 91 VI-----------------------------------------------------VTED--------IFTYMES--QKES 107 (179)
T ss_pred cc-----------------------------------------------------cccc--------ccccccc--cccC
Confidence 00 0000 0000001 1224
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803 442 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 515 (525)
Q Consensus 442 pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~ 515 (525)
|++.+...+....|..+|+.||+++|+||.|+|..| +|++|||+.||||.++|+++++||+++||+.+..
T Consensus 108 ~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l~~ 177 (179)
T PRK09415 108 VEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEE----LSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEE 177 (179)
T ss_pred cHHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 666666667778899999999999999999999987 9999999999999999999999999999997753
No 74
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=7.7e-20 Score=173.56 Aligned_cols=168 Identities=20% Similarity=0.202 Sum_probs=131.7
Q ss_pred HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhC-CCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHH
Q 009803 275 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQG-AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS 353 (525)
Q Consensus 275 ~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~-~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ 353 (525)
.+....+++..|++.|+..|.+.|+.++.++.+ ...+++|++||+++.+|+.++.|++. ..|.+|++..++|.+.++
T Consensus 11 ~~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~~~d~ 88 (181)
T PRK12536 11 LLLRGLAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYKLMDF 88 (181)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHHHHHH
Confidence 345566677999999999999999999998764 57899999999999999999999974 469999999999999999
Q ss_pred HHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcc
Q 009803 354 LSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEV 433 (525)
Q Consensus 354 ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~ 433 (525)
++++.+.... ..+++. . .+.
T Consensus 89 ~Rk~~~~~~~---------------------------------------------------~~~~~~----~-----~~~ 108 (181)
T PRK12536 89 LRSRARREAL---------------------------------------------------HDPLDD----E-----SEL 108 (181)
T ss_pred HHHHhccccc---------------------------------------------------cCCccc----h-----hhh
Confidence 9876431000 000000 0 000
Q ss_pred cCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803 434 IADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513 (525)
Q Consensus 434 l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l 513 (525)
..+... .+. +....+..+|+.||++++.||.++|..| +|++|||+.||+|.++|+.+++||+++||+.+
T Consensus 109 ~~~~~~-~~~------~~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l 177 (181)
T PRK12536 109 FATSDD-EAA------EARRDLGKLLEQLPDRQRLPIVHVKLEG----LSVAETAQLTGLSESAVKVGIHRGLKALAAKI 177 (181)
T ss_pred cCCCCc-chH------HHHHHHHHHHHHCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 011110 111 2344689999999999999999999887 99999999999999999999999999999987
Q ss_pred hh
Q 009803 514 RT 515 (525)
Q Consensus 514 ~~ 515 (525)
..
T Consensus 178 ~~ 179 (181)
T PRK12536 178 RG 179 (181)
T ss_pred cC
Confidence 64
No 75
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=1.1e-19 Score=170.96 Aligned_cols=167 Identities=11% Similarity=0.159 Sum_probs=131.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecc
Q 009803 285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP 364 (525)
Q Consensus 285 ~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP 364 (525)
..+++|+..|.++|+.+|++|.++..+++|++||+++.+|+++++|++.. +|.+|++..+++.+.++++++.+....+
T Consensus 3 ~~~~~l~~~y~~~i~~~~~~~~~~~~daeDvvQe~~i~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~Rk~~~~~~~~ 80 (173)
T PRK12522 3 EKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE--NYKKWITTICVRTFYDFYRKKKRWKDRI 80 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcCCcc--chHHHHHHHHHHHHHHHHHHhccccccc
Confidence 45899999999999999999999999999999999999999999999753 7999999999999999998765411000
Q ss_pred cchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHH
Q 009803 365 FHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAED 444 (525)
Q Consensus 365 ~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee 444 (525)
.. . .+. + ...+.........++.
T Consensus 81 ~~-------------------------------------------------~-~~~----~---~~~~~~~~~~~~~~~~ 103 (173)
T PRK12522 81 LD-------------------------------------------------L-FHK----E---DGGEIEFADDVNISEE 103 (173)
T ss_pred cc-------------------------------------------------c-cch----h---hhhhhccccCCCChHH
Confidence 00 0 000 0 0000000001112333
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803 445 LLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 515 (525)
Q Consensus 445 ~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~ 515 (525)
....+....|..+|..||+++++||.|+|..| +|++|||+.||+|.++|+.+++||+++||+.+..
T Consensus 104 -~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~ 169 (173)
T PRK12522 104 -FIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQ----YSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEG 169 (173)
T ss_pred -HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 44455677899999999999999999999988 9999999999999999999999999999997754
No 76
>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=99.84 E-value=2.2e-19 Score=179.45 Aligned_cols=183 Identities=13% Similarity=0.152 Sum_probs=141.9
Q ss_pred cCCHHHHHHHHh-ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHH-------hhhhcCCcCCCchhhH
Q 009803 270 GVDQRELRRRLN-YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVR-------GAEKFDASKGFKFSTY 341 (525)
Q Consensus 270 g~d~~~L~~~l~-~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLir-------AiekFDp~kG~rFsTY 341 (525)
+.++..|...++ |+..|+..|+..|.+.|+.++.++.++..+++|++||+|+.+|. .+.+|++. ..|.||
T Consensus 23 ~~~d~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~--~~~~tW 100 (244)
T TIGR03001 23 HAADLYLACACAQGEPAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGR--GPLLSW 100 (244)
T ss_pred cccHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCC--CchHhH
Confidence 345555655544 55899999999999999999999999999999999999999994 78889864 379999
Q ss_pred HHHHHHHHHHHHHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccc
Q 009803 342 AHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQK 421 (525)
Q Consensus 342 A~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~ 421 (525)
++.+++|.+.++++++.+...+ +.
T Consensus 101 L~~Ia~N~~id~lRk~~r~~~~-------------------------------------------------------~~- 124 (244)
T TIGR03001 101 VRIVATRIALELQAQERRHSPV-------------------------------------------------------EE- 124 (244)
T ss_pred HHHHHHHHHHHHHHHhcccCcc-------------------------------------------------------cc-
Confidence 9999999999999865431100 00
Q ss_pred cccccCCCCCcccCCCCCCCHHHHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHH
Q 009803 422 IGINQNLKPSEVIADPEAETAEDLLIK----KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRER 497 (525)
Q Consensus 422 i~~d~~~~l~d~l~d~~~~~pee~~~~----~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~er 497 (525)
+ + ...+. .+. ..+|++.+.. .+....|..+|++||+++|+||.|+|..| +|++|||++||||.++
T Consensus 125 ---~-~-~~~~~-~~~-~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~eg----~S~~EIA~~Lgis~~T 193 (244)
T TIGR03001 125 ---P-T-ELAAL-PAP-GSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHFVDG----LSMDRIGAMYQVHRST 193 (244)
T ss_pred ---c-c-ccccc-cCC-CCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHH
Confidence 0 0 00000 011 1234444432 23556799999999999999999999987 9999999999999999
Q ss_pred HHHHHHHHHHHHHhHHhhchhhhh
Q 009803 498 IRQIESSAFRKLKNKKRTKHLMQY 521 (525)
Q Consensus 498 VRqie~RALkKLR~~l~~~~L~~y 521 (525)
|+.+++||+++||+.+.......|
T Consensus 194 Vk~rl~RAr~~Lr~~l~~~~~~~~ 217 (244)
T TIGR03001 194 VSRWVAQARERLLERTRRRLAERL 217 (244)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhc
Confidence 999999999999999987665544
No 77
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=1.5e-19 Score=172.81 Aligned_cols=181 Identities=15% Similarity=0.163 Sum_probs=137.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceeccc
Q 009803 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF 365 (525)
Q Consensus 286 A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~ 365 (525)
+++.|+..|.+.|+.+|.++.++..+++|++||.|+.+|+.+++|++. .+|.||++..++|.+.++++++.+....+.
T Consensus 3 ~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~--~~~~~WL~~ia~n~~~d~~Rk~~r~~~~~~ 80 (191)
T PRK12520 3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQ--SSLKTYLVGILKHKIIDAIRSGRREVRLSL 80 (191)
T ss_pred chHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--ccHHHHHHHHHHHHHHHHHHhhcCcCcccc
Confidence 689999999999999999999999999999999999999999999854 369999999999999999987754211100
Q ss_pred chHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHH
Q 009803 366 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL 445 (525)
Q Consensus 366 ~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~ 445 (525)
.. .......++ ++.... . + ......++. ..+|++.
T Consensus 81 ~~------------------~~~~~~~~~-----------------------~~~~~~-~-~-~~~~~~~~~-~~~~~~~ 115 (191)
T PRK12520 81 DD------------------ADEQSDDDL-----------------------FDALFA-A-D-GHYREPPSD-WGDPDAA 115 (191)
T ss_pred cc------------------cccchhhhh-----------------------hhhhcc-c-c-cccccCccc-cCCHHHH
Confidence 00 000000000 000000 0 0 000011111 2367777
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhch
Q 009803 446 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 517 (525)
Q Consensus 446 ~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~ 517 (525)
+...+....|..+|..||+++|.||.|+|..+ +|++|||+.||+|.++|+++++||+++||+++....
T Consensus 116 ~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 183 (191)
T PRK12520 116 LSRREFFEVLQACVDRLPPRTGRVFMMREWLE----LETEEICQELQITATNAWVLLYRARMRLRECLDLHW 183 (191)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 77777778899999999999999999999988 999999999999999999999999999999988765
No 78
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=99.83 E-value=2.8e-19 Score=170.00 Aligned_cols=172 Identities=20% Similarity=0.265 Sum_probs=137.6
Q ss_pred HHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHh
Q 009803 277 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD 356 (525)
Q Consensus 277 ~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~ 356 (525)
.....++..++..++..|.+.++.+++++.++..+++||+||+|+.+|+++..| +. +..|.||++.+++|.+++++++
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~~R~ 84 (182)
T COG1595 7 AEALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDRLRK 84 (182)
T ss_pred HHHHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHHHHHH
Confidence 344556789999999999999999999999988899999999999999999999 33 3479999999999999999998
Q ss_pred cccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCC
Q 009803 357 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD 436 (525)
Q Consensus 357 ~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d 436 (525)
..+.... .+ +.+ ..+...+
T Consensus 85 ~~r~~~~------------------------------------------------------~~-----~~~--~~~~~~~ 103 (182)
T COG1595 85 RKRRRAR------------------------------------------------------VE-----EAD--LLPEEAD 103 (182)
T ss_pred hcccccc------------------------------------------------------cc-----ccc--ccccccC
Confidence 7652211 00 000 0000111
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803 437 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 516 (525)
Q Consensus 437 ~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~ 516 (525)
+....+ +.+...+....|..+|..||+++|.+|.|+|+.| +|++|||+.||||.++|+.+++||+++||+.+...
T Consensus 104 ~~~~~~-~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~~g----ls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~~~ 178 (182)
T COG1595 104 PAPDLA-ELLLAEEELERLRRALARLPPRQREAFLLRYLEG----LSYEEIAEILGISVGTVKSRLHRARKKLREQLEEA 178 (182)
T ss_pred cccccc-hHHHHHHHHHHHHHHHHhCCHHHhHHhhhHhhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence 111011 2455566778899999999999999999999988 99999999999999999999999999999988653
No 79
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=99.83 E-value=2.6e-19 Score=170.35 Aligned_cols=165 Identities=13% Similarity=0.107 Sum_probs=129.0
Q ss_pred HHHHhccHHHHHHHHHHHHHHHHHHHHH----hhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHH
Q 009803 277 RRRLNYGILCKDKMITSNIRLVISIAKN----YQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRK 352 (525)
Q Consensus 277 ~~~l~~g~~A~e~Lv~~nlrLV~~IA~~----y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~ 352 (525)
.....++..|++.|+..|.+.|+.++++ |.++..+++|++||+++.+|++++.|++.. .|.+|++..+++.+.+
T Consensus 13 ~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~~n~~~d 90 (184)
T PRK12539 13 LASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIARYKLID 90 (184)
T ss_pred HHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHHHHHHHH
Confidence 3444566899999999999999999874 557788999999999999999999999753 6999999999999999
Q ss_pred HHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCc
Q 009803 353 SLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSE 432 (525)
Q Consensus 353 ~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d 432 (525)
++++..+. ..+ .+.+. . + .
T Consensus 91 ~~R~~~~~-~~~---------------------------------------------------~~~~~----~-~----~ 109 (184)
T PRK12539 91 HLRRTRAS-LAD---------------------------------------------------VPIDD----A-D----E 109 (184)
T ss_pred HHHHHhcc-ccc---------------------------------------------------cChhh----h-c----c
Confidence 99875431 000 00000 0 0 0
Q ss_pred ccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803 433 VIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512 (525)
Q Consensus 433 ~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~ 512 (525)
.... .+ ....+....|..+|..||+++|+||.|+|..| +|++|||+.||+|..+|+++++||+++||+.
T Consensus 110 ~~~~----~~---~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 110 LVAH----DD---HAAVESTLDLGRLLARLPEKMRLAIQAVKLEG----LSVAEAATRSGMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred ccCC----cH---HhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CcHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 0000 11 11223345789999999999999999999877 9999999999999999999999999999998
Q ss_pred Hhh
Q 009803 513 KRT 515 (525)
Q Consensus 513 l~~ 515 (525)
+..
T Consensus 179 l~~ 181 (184)
T PRK12539 179 IGR 181 (184)
T ss_pred Hhh
Confidence 764
No 80
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=99.83 E-value=4.1e-19 Score=174.36 Aligned_cols=171 Identities=14% Similarity=0.134 Sum_probs=137.2
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccce
Q 009803 282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 361 (525)
Q Consensus 282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~i 361 (525)
....++..|+..|.+.++.+++++.++..+.+|++||+|+.+|+.+++|++. .|.+|++.+++|.+.++++++.+..
T Consensus 15 ~~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~~~~~ 91 (216)
T PRK12533 15 ARGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRRANAH 91 (216)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhhcccc
Confidence 3467999999999999999999999999999999999999999999999853 4999999999999999998765310
Q ss_pred ecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCC
Q 009803 362 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET 441 (525)
Q Consensus 362 RiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~ 441 (525)
.. . ....+. + ...... .. +...+
T Consensus 92 ~~----------------------------------------------------~-~~~~~~-~-~~~~~~-~~-~~~~~ 114 (216)
T PRK12533 92 EV----------------------------------------------------A-APDTLD-D-ADSLDD-WQ-PAGED 114 (216)
T ss_pred cc----------------------------------------------------c-cccccc-c-cccccc-cc-cCCCC
Confidence 00 0 000000 0 000000 11 11235
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803 442 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 516 (525)
Q Consensus 442 pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~ 516 (525)
|++.+...+....|..+|+.||+++|+||.|+|..+ +|++|||+.||||.++|+++++||+++||+++...
T Consensus 115 ~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~eg----~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~ 185 (216)
T PRK12533 115 PLALLLRAEDVRLVNAALAKLPVEYREVLVLRELED----MSYREIAAIADVPVGTVMSRLARARRRLAALLGGA 185 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHccc
Confidence 777777777788899999999999999999999987 99999999999999999999999999999998654
No 81
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=99.83 E-value=3.3e-19 Score=168.68 Aligned_cols=166 Identities=22% Similarity=0.208 Sum_probs=123.4
Q ss_pred HHhccHHHHHHHHHHHHHHHHHHHHHhhCCCC-----CHHHHHHHHHHHHHH-hhhhcCCcCCCchhhHHHHHHHHHHHH
Q 009803 279 RLNYGILCKDKMITSNIRLVISIAKNYQGAGM-----NLQDLVQEGCRGLVR-GAEKFDASKGFKFSTYAHWWIKQAVRK 352 (525)
Q Consensus 279 ~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~-----~~eDLIQEG~lGLir-AiekFDp~kG~rFsTYA~~wIRqaI~~ 352 (525)
...++..|++.|+..|.+.++.+|++|.++.. +++|++||+|+.+|+ ...+|++. ..|.+|++.+++|.+.+
T Consensus 11 ~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d 88 (183)
T TIGR02999 11 WQNGDAAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAKAMRRILVD 88 (183)
T ss_pred HHcCCHHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHHHHHHHHHH
Confidence 34456899999999999999999999998877 899999999999998 78889754 36999999999999999
Q ss_pred HHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCc
Q 009803 353 SLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSE 432 (525)
Q Consensus 353 ~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d 432 (525)
+++++.+..+.. ...+.. ..+
T Consensus 89 ~~R~~~~~~~~~---------------------------------------------------~~~~~~--------~~~ 109 (183)
T TIGR02999 89 HARRRRAQKRGG---------------------------------------------------GAVRVP--------LDE 109 (183)
T ss_pred HHHHHHHHhccC---------------------------------------------------Cccccc--------ccc
Confidence 988654210000 000000 000
Q ss_pred ccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803 433 VIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512 (525)
Q Consensus 433 ~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~ 512 (525)
..++... ...+. ......+...|+.||+++|.||.|+|..| +|++|||+.||+|.++|+.+++||+++||+.
T Consensus 110 ~~~~~~~-~~~~~---~~~l~~~~~~l~~Lp~~~r~v~~l~~~~g----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 110 VLPDAEA-DLDEE---LLDLDDALDKLAQVDPRQAEVVELRFFAG----LTVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred ccCCCCc-cHHHH---HHHHHHHHHHhhcCCHHHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 0001000 11111 11122344456779999999999999988 9999999999999999999999999999987
Q ss_pred H
Q 009803 513 K 513 (525)
Q Consensus 513 l 513 (525)
+
T Consensus 182 l 182 (183)
T TIGR02999 182 L 182 (183)
T ss_pred h
Confidence 5
No 82
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=99.83 E-value=2.2e-19 Score=170.21 Aligned_cols=165 Identities=12% Similarity=0.041 Sum_probs=131.2
Q ss_pred hccHHHHHHHHHHHHHHHHHHHHHhhC--CCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcc
Q 009803 281 NYGILCKDKMITSNIRLVISIAKNYQG--AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS 358 (525)
Q Consensus 281 ~~g~~A~e~Lv~~nlrLV~~IA~~y~~--~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~ 358 (525)
.|+..+++.|+..|.+.|+.++..+.+ +..+++|++||+|+.+|+..++|++.....|.||++..++|.+.++++++.
T Consensus 9 ~~d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~Rk~~ 88 (178)
T PRK12529 9 SADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRRRQS 88 (178)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999998766665 457899999999999999999998544457999999999999999887643
Q ss_pred cceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCC
Q 009803 359 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPE 438 (525)
Q Consensus 359 r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~ 438 (525)
+. . .. .+.. .+ .....
T Consensus 89 ~~--~----------------~~------------------------------------~~~~---------~~-~~~~~ 104 (178)
T PRK12529 89 LE--L----------------AW------------------------------------LEAL---------AT-LPEPL 104 (178)
T ss_pred HH--h----------------hh------------------------------------hhHh---------hh-ccCcC
Confidence 20 0 00 0000 00 00111
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803 439 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513 (525)
Q Consensus 439 ~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l 513 (525)
.++|++.+...+....|..+|..||+++|.||.|+|..| +|++|||+.||+|.++|+.+++||+.+|++.+
T Consensus 105 ~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g----~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~~ 175 (178)
T PRK12529 105 HPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATLDG----MKQKDIAQALDIALPTVKKYIHQAYVTCLSLM 175 (178)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence 235666666666667899999999999999999999987 99999999999999999999999999998864
No 83
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=99.83 E-value=1e-19 Score=168.02 Aligned_cols=157 Identities=18% Similarity=0.240 Sum_probs=125.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceeccc
Q 009803 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF 365 (525)
Q Consensus 286 A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~ 365 (525)
|++.++..|.+.|+.+|+++.++..+++|++||+++.+|+++++|++.. .|.+|++..+++.+.++++++.+.-.. .
T Consensus 2 ~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~~-~ 78 (159)
T TIGR02989 2 AFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRLV-F 78 (159)
T ss_pred HHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhcccccc-c
Confidence 7899999999999999999999999999999999999999999999753 699999999999999999987541100 0
Q ss_pred chHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHH
Q 009803 366 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL 445 (525)
Q Consensus 366 ~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~ 445 (525)
. ++.. +.+.+.. +|.+.
T Consensus 79 ~-------------------------~~~~------------------------------------~~~~~~~--~~~~~ 95 (159)
T TIGR02989 79 D-------------------------DELL------------------------------------EALAAEA--EATEA 95 (159)
T ss_pred C-------------------------HHHH------------------------------------HHHHhhc--ccchH
Confidence 0 0000 0000000 11111
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803 446 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512 (525)
Q Consensus 446 ~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~ 512 (525)
.........|..+++.||++++.||.++|..| +|++|||+.||||.++|+...+||+++||++
T Consensus 96 ~~~~~~~~~l~~~i~~L~~~~r~v~~l~~~~g----~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~~ 158 (159)
T TIGR02989 96 DRSEDELQALEGCLEKLPERQRELLQLRYQRG----VSLTALAEQLGRTVNAVYKALSRLRVRLRDC 158 (159)
T ss_pred hhHHHHHHHHHHHHHHCCHHHHHHHHHHHhcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHhc
Confidence 22233446789999999999999999999877 9999999999999999999999999999975
No 84
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=99.83 E-value=2e-19 Score=169.04 Aligned_cols=167 Identities=17% Similarity=0.137 Sum_probs=129.5
Q ss_pred HHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcc
Q 009803 279 RLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS 358 (525)
Q Consensus 279 ~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~ 358 (525)
...++..+++.|+..|.+.|+.+++++.+. .+++|++||+|+.+|+.+++|++. ..|.+|++..+++.+.+++++..
T Consensus 5 ~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~-~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~~ 81 (175)
T PRK12518 5 CQRGDRQSFRQLYRRYQQKVRSTLYQLCGR-ELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARRQFA 81 (175)
T ss_pred HHcCCHHHHHHHHHHHHHHHHHHHHHHcCH-hHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHHHhh
Confidence 345678999999999999999999998754 689999999999999999999974 47999999999999999988653
Q ss_pred cceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCC
Q 009803 359 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPE 438 (525)
Q Consensus 359 r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~ 438 (525)
+.-.. .+.. .... . ....
T Consensus 82 ~~~~~------------------------------------------------------~~~~---~~~~---~-~~~~- 99 (175)
T PRK12518 82 QRPSR------------------------------------------------------IQDD---SLND---Q-PSRP- 99 (175)
T ss_pred ccccc------------------------------------------------------hhcc---cccc---c-ccCC-
Confidence 21000 0000 0000 0 0000
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803 439 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 516 (525)
Q Consensus 439 ~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~ 516 (525)
...++ ....+....+..+|+.||+++|.||.|+|+.| +|++|||+.||+|..+|++..+||+++||+.+...
T Consensus 100 ~~~~~--~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g----~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~~~ 171 (175)
T PRK12518 100 SDTPD--LMQLHYQDLVQQGLQTLSLEHRAVLVLHDLED----LPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQQ 171 (175)
T ss_pred CCcHH--HHHHHHHHHHHHHHHhCCHHHeeeeeehHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 11222 22223345688999999999999999999988 99999999999999999999999999999988764
No 85
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=99.82 E-value=5.6e-19 Score=167.62 Aligned_cols=163 Identities=17% Similarity=0.203 Sum_probs=128.4
Q ss_pred HHHhccHHHHHHHHHHHHHHHHHHHHHhhCC----CCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHH
Q 009803 278 RRLNYGILCKDKMITSNIRLVISIAKNYQGA----GMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS 353 (525)
Q Consensus 278 ~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~----g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ 353 (525)
....++..|++.|+..|.+.|+.+|++++++ ..+++|++||+++.+|...++|++. ..|.+|++..+|+.+.++
T Consensus 15 ~~~~gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn~~~d~ 92 (184)
T PRK12512 15 SANAGDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARNKLIDA 92 (184)
T ss_pred HHHccCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHHHHHHH
Confidence 3345679999999999999999999998862 4689999999999999999999863 479999999999999999
Q ss_pred HHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcc
Q 009803 354 LSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEV 433 (525)
Q Consensus 354 ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~ 433 (525)
++++.+.... +++. ..+.
T Consensus 93 ~Rr~~~~~~~-----------------------------------------------------~~~~---------~~~~ 110 (184)
T PRK12512 93 LRRRGRRVFV-----------------------------------------------------DIDD---------FAET 110 (184)
T ss_pred HHhhcccccC-----------------------------------------------------Cchh---------cccc
Confidence 9876431111 0000 0011
Q ss_pred cCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803 434 IADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513 (525)
Q Consensus 434 l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l 513 (525)
+++.. +.+ ......+..+|+.||+++|+||.++|..| +|++|||+.||+|..+|+...+||+++||..+
T Consensus 111 ~~~~~---~~~----~~~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 111 LPAEP---ATE----TLPAGDVGRHLETLPPRQRDVVQSISVEG----ASIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred ccccc---hhh----HHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 11110 111 11234578899999999999999999887 99999999999999999999999999999988
Q ss_pred hh
Q 009803 514 RT 515 (525)
Q Consensus 514 ~~ 515 (525)
..
T Consensus 180 ~~ 181 (184)
T PRK12512 180 RS 181 (184)
T ss_pred hc
Confidence 65
No 86
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=99.82 E-value=4e-19 Score=169.60 Aligned_cols=167 Identities=14% Similarity=0.081 Sum_probs=128.5
Q ss_pred HHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhc
Q 009803 278 RRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ 357 (525)
Q Consensus 278 ~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~ 357 (525)
+...++..|++.|+..|.+.++.++. +.++..+++|++||+|+.+|+..++|++. ..|.+|++..+++.+.++++++
T Consensus 17 ~~~~gd~~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~~~d~~Rk~ 93 (185)
T PRK09649 17 SAAKGNGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVADHIRHV 93 (185)
T ss_pred HHHccCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHHHHHHHHHh
Confidence 33446689999999999999999995 68888899999999999999999999864 4799999999999999999875
Q ss_pred ccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCC
Q 009803 358 SRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADP 437 (525)
Q Consensus 358 ~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~ 437 (525)
.+..+. +.+. . .+...+.
T Consensus 94 ~~~~~~-----------------------------------------------------~~~~----~-----~~~~~~~ 111 (185)
T PRK09649 94 RSRPRT-----------------------------------------------------TRGA----R-----PEHLIDG 111 (185)
T ss_pred cccccc-----------------------------------------------------cccc----c-----hhhccCh
Confidence 431100 0000 0 0000000
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhch
Q 009803 438 EAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 517 (525)
Q Consensus 438 ~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~ 517 (525)
+......+....|..+|+.||+++|+||.|+|..+ +|++|||+.||+|.++|+++++||+++||+.+....
T Consensus 112 -----~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~~~g----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~~~~~~ 182 (185)
T PRK09649 112 -----DRHARGFEDLVEVTTMIADLTTDQREALLLTQLLG----LSYADAAAVCGCPVGTIRSRVARARDALLADAEPDD 182 (185)
T ss_pred -----hhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCccc
Confidence 00000111224588899999999999999999988 999999999999999999999999999999665544
Q ss_pred h
Q 009803 518 L 518 (525)
Q Consensus 518 L 518 (525)
|
T Consensus 183 ~ 183 (185)
T PRK09649 183 L 183 (185)
T ss_pred c
Confidence 3
No 87
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=99.82 E-value=2.8e-19 Score=165.83 Aligned_cols=156 Identities=17% Similarity=0.123 Sum_probs=126.1
Q ss_pred HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHH
Q 009803 292 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEAT 371 (525)
Q Consensus 292 ~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~ 371 (525)
..|.+.++.+|.++.++..+++|++||+|+.+|+++++|++. .|.+|++..++|.+.++++++.+..+.
T Consensus 2 ~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n~~~d~~Rk~~~~~~~-------- 70 (160)
T PRK09642 2 QTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATNHAIDYKRKKARENEE-------- 70 (160)
T ss_pred chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHHHHHHHHHHhcccccc--------
Confidence 568999999999999999999999999999999999999863 499999999999999999876431000
Q ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHHHHH
Q 009803 372 YRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFM 451 (525)
Q Consensus 372 ~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~~~ 451 (525)
..+.. + . .+... ...+|++.+...+.
T Consensus 71 --------------------------------------------~~~~~----~-~---~~~~~--~~~~~~~~~~~~e~ 96 (160)
T PRK09642 71 --------------------------------------------LSLCK----E-T---EENIK--SSHNIEDLLLTKEQ 96 (160)
T ss_pred --------------------------------------------cccch----h-h---hhhcc--CCCChHHHHHHHHH
Confidence 00000 0 0 00001 11245666666677
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803 452 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 516 (525)
Q Consensus 452 ~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~ 516 (525)
...|..+|+.||+++|.||.|+|..| +|++|||+.||+|.++|+++++||+++||+.+...
T Consensus 97 ~~~l~~~l~~Lp~~~r~v~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 157 (160)
T PRK09642 97 KLLIAQKLRELPENYRDVVLAHYLEE----KSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKEE 157 (160)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHhC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhh
Confidence 78899999999999999999999988 99999999999999999999999999999988654
No 88
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=99.82 E-value=8.7e-19 Score=170.25 Aligned_cols=165 Identities=18% Similarity=0.269 Sum_probs=136.5
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccce
Q 009803 282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 361 (525)
Q Consensus 282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~i 361 (525)
++..++++|+..|.+.++.++.++.++..+.+|++||+++.+|+...+|++ + .|.+|++..+|+.+.+++++..+ .
T Consensus 25 ~d~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~~-~ 100 (203)
T PRK09647 25 ATMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRAR-I 100 (203)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhccc-C
Confidence 458899999999999999999999999999999999999999999999985 3 69999999999999999987643 1
Q ss_pred ecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCC
Q 009803 362 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET 441 (525)
Q Consensus 362 RiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~ 441 (525)
+. ..++ + + . +.... ...+
T Consensus 101 ~~----------------------------------------------------~~~~-----~-~--~-~~~~~-~~~~ 118 (203)
T PRK09647 101 RM----------------------------------------------------EALP-----E-D--Y-DRVPG-DEPN 118 (203)
T ss_pred cc----------------------------------------------------cccc-----c-c--c-cccCC-CCCC
Confidence 10 0000 0 0 0 01111 1235
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803 442 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 516 (525)
Q Consensus 442 pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~ 516 (525)
|+..+........|..+|..||++++.||.|+|+.| ++++|||+.||||..+|++.++||+++||+.+...
T Consensus 119 ~~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~~~g----~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~~ 189 (203)
T PRK09647 119 PEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEG----LSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAAH 189 (203)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 666666777778899999999999999999999888 99999999999999999999999999999988754
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=99.82 E-value=2.7e-19 Score=171.41 Aligned_cols=173 Identities=13% Similarity=0.135 Sum_probs=132.0
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhccccee
Q 009803 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR 362 (525)
Q Consensus 283 g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iR 362 (525)
+..+|+.|+..|.+.|+.+|.++.++..+++|++||+|+.+|+.+.+|++. ..|.+|++..++|.+.++++++.+...
T Consensus 9 ~~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~~~~~~ 86 (193)
T TIGR02947 9 RAQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKAQRRPQ 86 (193)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHhcCCcc
Confidence 378999999999999999999999998999999999999999999999864 469999999999999999987654110
Q ss_pred cccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCH
Q 009803 363 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETA 442 (525)
Q Consensus 363 iP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~p 442 (525)
.. ..+++. . .... + ..+ ........+
T Consensus 87 ~~-------------------------~~~~~~-----------~------------~~~~-~----~~~-~~~~~~~~~ 112 (193)
T TIGR02947 87 QS-------------------------DDDDIE-----------D------------WQLA-K----AAS-HTSNGLRSA 112 (193)
T ss_pred cc-------------------------cchhhh-----------h------------hhhc-c----ccc-cccccccch
Confidence 00 000000 0 0000 0 000 000011123
Q ss_pred HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803 443 EDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 515 (525)
Q Consensus 443 ee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~ 515 (525)
+...........|..+|+.||+++|+||.|+|..| +|++|||+.||||.++|+.+++||+++||+.+..
T Consensus 113 e~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~~~g----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 181 (193)
T TIGR02947 113 ELEALDGLPDQDIKDALQGLPEEFRQAVYLADVEG----FAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVD 181 (193)
T ss_pred hHHHHhhhhHHHHHHHHHhCCHHHhhheeehhhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 33333444456789999999999999999999887 9999999999999999999999999999998864
No 90
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=99.82 E-value=6.9e-19 Score=168.59 Aligned_cols=162 Identities=14% Similarity=0.148 Sum_probs=129.4
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccce
Q 009803 282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 361 (525)
Q Consensus 282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~i 361 (525)
++..++.+|+..|.+.++.+|++++++..+++|++||+|+.+|+..++|++. ..|.+|++..++|.+.++++++.+..
T Consensus 7 ~~~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~awL~~Ia~n~~~d~~R~~~~~~ 84 (187)
T PRK12516 7 EGTPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVG--TNMKAWLFTILRNEFYSQMRKRGREV 84 (187)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCc--ccHHHHHHHHHHHHHHHHHHhhcCCc
Confidence 4578999999999999999999999999999999999999999999999864 36999999999999999998765310
Q ss_pred ecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCC
Q 009803 362 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET 441 (525)
Q Consensus 362 RiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~ 441 (525)
.. .+.. ..+.... .+.
T Consensus 85 ~~------------------------------------------------------~~~~--------~~~~~~~--~~~ 100 (187)
T PRK12516 85 QD------------------------------------------------------TDGM--------FTEQLAV--HPS 100 (187)
T ss_pred cc------------------------------------------------------cccc--------cccccCC--Ccc
Confidence 00 0000 0000000 001
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhch
Q 009803 442 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 517 (525)
Q Consensus 442 pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~ 517 (525)
.. .......|..+|+.||+++|+||.|+|..| +|++|||+.||||.++|+++++||+++||+.+....
T Consensus 101 ~~----~~~~~~~l~~~L~~Lp~~~r~i~~L~~~~g----~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~~~ 168 (187)
T PRK12516 101 QY----GTLDLQDFRAALDQLPDDQREAIILVGASG----FAYEEAAEICGCAVGTIKSRVNRARQRLQEILQIEG 168 (187)
T ss_pred hh----hHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence 11 111235689999999999999999999987 999999999999999999999999999999987654
No 91
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=99.81 E-value=5.6e-19 Score=163.95 Aligned_cols=159 Identities=15% Similarity=0.163 Sum_probs=128.3
Q ss_pred hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccc
Q 009803 281 NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT 360 (525)
Q Consensus 281 ~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~ 360 (525)
+|+..+++.|+..|.+.|+.++..+.++..+++|++||+|+.+|++.++|+. ...|.+|++..+++.+.++++++.+.
T Consensus 2 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~~~d~~rk~~~~ 79 (162)
T TIGR02983 2 SATEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNLARSRWRRRRLL 79 (162)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHHHHHHHHhhccc
Confidence 3568999999999999999999999999999999999999999999999964 34799999999999999998865430
Q ss_pred eecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCC
Q 009803 361 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAE 440 (525)
Q Consensus 361 iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~ 440 (525)
.. . +... .+. +..
T Consensus 80 -~~-----------------------------------------------------~-~~~~--------~~~--~~~-- 92 (162)
T TIGR02983 80 -EL-----------------------------------------------------P-TREL--------PDA--AAP-- 92 (162)
T ss_pred -cc-----------------------------------------------------c-cccc--------Ccc--cCC--
Confidence 00 0 0000 000 000
Q ss_pred CHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803 441 TAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 515 (525)
Q Consensus 441 ~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~ 515 (525)
.+ .........|..+|..||+++|.||.|+|..| +|.+|||+.||+|.++|+++++||+++||+.+..
T Consensus 93 ~~---~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 160 (162)
T TIGR02983 93 DP---APDVALRAALARALRRLPARQRAVVVLRYYED----LSEAQVAEALGISVGTVKSRLSRALARLRELLEE 160 (162)
T ss_pred cc---chhHHHHHHHHHHHHhCCHHHHHHhhhHHHhc----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 01 11233456788999999999999999999877 9999999999999999999999999999997753
No 92
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=99.81 E-value=5.7e-19 Score=166.14 Aligned_cols=163 Identities=13% Similarity=0.095 Sum_probs=129.0
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccce
Q 009803 282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 361 (525)
Q Consensus 282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~i 361 (525)
++..++..|+..|.+.|+.++.++.++..+++|++||+|+.+|+. .+|+.. ..|.+|++.+++|.+.++++++.+-.
T Consensus 7 ~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~~~~ 83 (172)
T PRK12523 7 PHSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAALEQ 83 (172)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 558899999999999999999999999999999999999999987 446543 36999999999999999998764200
Q ss_pred ecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCC
Q 009803 362 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET 441 (525)
Q Consensus 362 RiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~ 441 (525)
.... ++ . . .......+
T Consensus 84 ------------------~~~~---------~~------------------------~-------~------~~~~~~~~ 99 (172)
T PRK12523 84 ------------------AYLA---------EL------------------------A-------L------VPEAEQPS 99 (172)
T ss_pred ------------------HHHH---------HH------------------------h-------h------cccccCCC
Confidence 0000 00 0 0 00001123
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803 442 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 515 (525)
Q Consensus 442 pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~ 515 (525)
|++.....+....|..+|+.||+++|.||.|+|..| +|++|||+.||+|.++|+++++||+++||..+..
T Consensus 100 ~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~~~g----~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l~~ 169 (172)
T PRK12523 100 PEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDG----MGHAEIAERLGVSVSRVRQYLAQGLRQCYIALYG 169 (172)
T ss_pred hHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 555444444456799999999999999999999987 9999999999999999999999999999987754
No 93
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=99.81 E-value=7.3e-19 Score=164.14 Aligned_cols=157 Identities=17% Similarity=0.152 Sum_probs=130.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccc
Q 009803 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH 366 (525)
Q Consensus 287 ~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~ 366 (525)
++.|+..|.+.|+.+|+++.++..+++|++||+++.+|+++++|++. .|.+|++..+++.+.+++++..+....
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~--- 76 (165)
T PRK09644 3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFV--- 76 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhcccc---
Confidence 67899999999999999999999999999999999999999999863 599999999999999999876531100
Q ss_pred hHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHH
Q 009803 367 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLL 446 (525)
Q Consensus 367 ~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~ 446 (525)
+.+++ +.+. ..+|++.+
T Consensus 77 -----------------------~~~~~-------------------------------------~~~~---~~~~~~~~ 93 (165)
T PRK09644 77 -----------------------GTDEI-------------------------------------EAIQ---AESTEEYV 93 (165)
T ss_pred -----------------------chhHH-------------------------------------hhhc---ccChHHHH
Confidence 00000 0000 12455555
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803 447 IKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 516 (525)
Q Consensus 447 ~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~ 516 (525)
...+....|..+|..||+++|+||.++|..| +|++|||+.||+|.++|+++++||+++||+.+...
T Consensus 94 ~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~ 159 (165)
T PRK09644 94 VAKNSYEKLIQIIHTLPVIEAQAILLCDVHE----LTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEE 159 (165)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHhHHHhc----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 5666677899999999999999999999988 99999999999999999999999999999988654
No 94
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=99.81 E-value=1e-18 Score=162.61 Aligned_cols=160 Identities=18% Similarity=0.172 Sum_probs=130.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 009803 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL 363 (525)
Q Consensus 284 ~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRi 363 (525)
..+++.|+..|.+.++.+|+++.++..+++|++||+|+.+|++ .|+. +..|.+|++..+++.+.+++++..+..+.
T Consensus 2 ~~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~~~~~ 77 (166)
T PRK09639 2 DETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKRRRAR 77 (166)
T ss_pred chHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhcccccc
Confidence 3689999999999999999999999999999999999999999 6764 34799999999999999999876531110
Q ss_pred ccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHH
Q 009803 364 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAE 443 (525)
Q Consensus 364 P~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pe 443 (525)
. +.. ....+. + ....|+
T Consensus 78 ~------------------------------------------------------~~~------~~~~~~--~-~~~~~e 94 (166)
T PRK09639 78 I------------------------------------------------------LGE------FQWQEV--D-NEPSPE 94 (166)
T ss_pred c------------------------------------------------------cch------hhhhhc--c-CCCChH
Confidence 0 000 000000 1 123566
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803 444 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 515 (525)
Q Consensus 444 e~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~ 515 (525)
+.....+....|..+|..||+++|.||.++| .| +|++|||+.||+|..+|+..++||+++||+.+..
T Consensus 95 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-~g----~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~~ 161 (166)
T PRK09639 95 EIWIRKEEITKVQEVLAKMTERDRTVLLLRF-SG----YSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQ 161 (166)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 6666667777899999999999999999999 77 9999999999999999999999999999998764
No 95
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=1e-18 Score=162.31 Aligned_cols=158 Identities=14% Similarity=0.123 Sum_probs=125.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 009803 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL 363 (525)
Q Consensus 284 ~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRi 363 (525)
..|+++|+..|.+.|+.++.++.++..+++|++||+|+.+|+..+.|++ ..|.+|++.++++.+.++++++.+.
T Consensus 3 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~---~~~~~wl~~i~~n~~~d~~R~~~~~--- 76 (161)
T PRK12528 3 SATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQI---IEPRAFLTTIAKRVLCNHYRRQDLE--- 76 (161)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhccccccc---cCHHHHHHHHHHHHHHHHHHHHHHH---
Confidence 3689999999999999999999999899999999999999999988864 2699999999999999998865320
Q ss_pred ccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHH
Q 009803 364 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAE 443 (525)
Q Consensus 364 P~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pe 443 (525)
.... .+ ++ + .++.....++
T Consensus 77 ---------------~~~~---------~~------------------------~~------------~-~~~~~~~~~~ 95 (161)
T PRK12528 77 ---------------RAYL---------EA------------------------LA------------Q-LPERVAPSEE 95 (161)
T ss_pred ---------------HhhH---------HH------------------------hh------------c-cccccCCCHH
Confidence 0000 00 00 0 0000111344
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803 444 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512 (525)
Q Consensus 444 e~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~ 512 (525)
......+....|..+|..||+++|.||.|+|..| +|++|||+.||+|.++|+++++||+++||..
T Consensus 96 ~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~~g----~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~ 160 (161)
T PRK12528 96 ERAIILETLVELDQLLDGLPPLVKRAFLLAQVDG----LGYGEIATELGISLATVKRYLNKAAMRCYFA 160 (161)
T ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhc
Confidence 3333344456799999999999999999999988 9999999999999999999999999999964
No 96
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=1.8e-18 Score=160.72 Aligned_cols=158 Identities=13% Similarity=0.146 Sum_probs=125.4
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccce
Q 009803 282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 361 (525)
Q Consensus 282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~i 361 (525)
++..+++.++..|.+.|+.++.++.++..+++|++||+++.+|+..++|++. .|.||++..+++.+.++++++.+..
T Consensus 2 ~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~ 78 (161)
T PRK12541 2 KRKQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEKKYK 78 (161)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhccccc
Confidence 3467999999999999999999999999999999999999999999999863 5999999999999999998775410
Q ss_pred ecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCC
Q 009803 362 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET 441 (525)
Q Consensus 362 RiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~ 441 (525)
.. ..+. .. .......
T Consensus 79 ~~-----------------------------------------------------~~~~-------~~-----~~~~~~~ 93 (161)
T PRK12541 79 TT-----------------------------------------------------TIEE-------FH-----LPNVPST 93 (161)
T ss_pred cc-----------------------------------------------------chhh-------hh-----ccCCCCc
Confidence 00 0000 00 0000111
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803 442 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512 (525)
Q Consensus 442 pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~ 512 (525)
+++.....+. ..+..+|..||+++|.||.|+|..| +|++|||+.||+|.++|++.++||+++||+.
T Consensus 94 ~~~~~~~~~~-~~~~~~l~~L~~~~r~v~~l~~~~~----~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 94 EHEYFIKHEI-ASWLDSLSSLPLERRNVLLLRDYYG----FSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HHHHHHHhHH-HHHHHHHHHCCHHHHHHhhhHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 2233333333 3456789999999999999999988 9999999999999999999999999999974
No 97
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=99.80 E-value=2.2e-18 Score=165.01 Aligned_cols=178 Identities=15% Similarity=0.083 Sum_probs=133.5
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccch
Q 009803 288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHM 367 (525)
Q Consensus 288 e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~ 367 (525)
.+.+..|.+.|+.+|+++.++..+++|++||+|+.+|+...+|++. .+|.+|++..+++.+.++++++.+....+.-
T Consensus 5 ~~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~~~- 81 (188)
T TIGR02943 5 PQELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVSDL- 81 (188)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCcccc-
Confidence 3578889999999999999999999999999999999999999864 4799999999999999999877542111000
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHH
Q 009803 368 VEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLI 447 (525)
Q Consensus 368 ~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~ 447 (525)
...+. .-.++.... ..+.......++ ..++|+..+.
T Consensus 82 ------------------~~~~~------------------------~~~~~~~~~-~~~~~~~~~~~~-~~~~~e~~~~ 117 (188)
T TIGR02943 82 ------------------DDELD------------------------DEAFNALFT-QNGHWAQHGQPQ-HWNTPEKQLE 117 (188)
T ss_pred ------------------ccccc------------------------cchhhhhhc-cccchhcccccc-ccCCHHHHHH
Confidence 00000 000000000 000000011111 1235777777
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803 448 KKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 516 (525)
Q Consensus 448 ~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~ 516 (525)
..+....+..+|..||+++|+||.++|..+ +|++|||+.||+|.++|++++.||+++||+++...
T Consensus 118 ~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~ 182 (188)
T TIGR02943 118 NKEFWEVFEACLYHLPEQTARVFMMREVLG----FESDEICQELEISTSNCHVLLYRARLSLRACLSIN 182 (188)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHhC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 777778899999999999999999999988 99999999999999999999999999999988753
No 98
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=2.2e-18 Score=165.34 Aligned_cols=181 Identities=17% Similarity=0.152 Sum_probs=133.3
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCC-HHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccc
Q 009803 288 DKMITSNIRLVISIAKNYQGAGMN-LQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH 366 (525)
Q Consensus 288 e~Lv~~nlrLV~~IA~~y~~~g~~-~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~ 366 (525)
+..+..|.+.|+.+|+++.++..+ ++|++||+|+.+|+++++|++. .+|.+|++..++|.+.++++++.+.......
T Consensus 8 ~~~~~~~~~~l~~~a~~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~~ 85 (195)
T PRK12532 8 DAELIESRKLLLHFARLQLPDHPDLAEDLVQETLLSAYSAGDSFQGR--ALVNSWLFAILKNKIIDALRQIGRQRKVFTL 85 (195)
T ss_pred hhhHHHHHHHHHHHHHHHcCChhhhHHHHHHHHHHHHHHhccccccc--chHHHHHHHHHHHHHHHHHHHhccccccccc
Confidence 456788999999999999998888 9999999999999999999864 4799999999999999999876542111000
Q ss_pred hHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHH
Q 009803 367 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLL 446 (525)
Q Consensus 367 ~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~ 446 (525)
. ......+.. .+. .. .+.....+..++ ...+|++.+
T Consensus 86 ~-------------------~~~~~~~~~--------------------~~~---~~-~~~~~~~~~~~~-~~~~~e~~~ 121 (195)
T PRK12532 86 L-------------------DDELLDEAF--------------------ESH---FS-QNGHWTPEGQPQ-HWNTPEKSL 121 (195)
T ss_pred c-------------------cccccchhh--------------------hhh---hc-cccccccccCcc-ccCCHHHHH
Confidence 0 000000000 000 00 000000000111 123677777
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 009803 447 IKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHL 518 (525)
Q Consensus 447 ~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L 518 (525)
...+....+..+|..||+++|+||.|+|..| +|++|||+.||+|.++|+++++||+++||+++....+
T Consensus 122 ~~~e~~~~l~~~l~~L~~~~r~i~~L~~~~g----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~ 189 (195)
T PRK12532 122 NNNEFQKILQSCLYNLPENTARVFTLKEILG----FSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKWF 189 (195)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHhhhHHHhC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 7777778899999999999999999999987 9999999999999999999999999999999876543
No 99
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=2.6e-18 Score=164.59 Aligned_cols=176 Identities=17% Similarity=0.121 Sum_probs=131.6
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccch
Q 009803 288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHM 367 (525)
Q Consensus 288 e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~ 367 (525)
+..|..|.+.++.+|.+|.++..+++|++||+|+.+|+.+++|++. .+|.+|++..++|.+.++++++.+..... ..
T Consensus 10 ~~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~-~~ 86 (189)
T PRK12530 10 SLEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQ--SALKTWIFAILKNKIIDLIRYRKRFVNES-EL 86 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCC--ccHHHHHHHHHHHHHHHHHHhhccCCCcc-cc
Confidence 3457788999999999999998999999999999999999999865 36999999999999999998765421110 00
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHH
Q 009803 368 VEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLI 447 (525)
Q Consensus 368 ~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~ 447 (525)
. .+ ..+.... +.......+........+|++.+.
T Consensus 87 ------------------~-----~~-------------------~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~ 120 (189)
T PRK12530 87 ------------------I-----EE-------------------DSPNSFF----DEKGHWKPEYYEPSEWQEVENTVY 120 (189)
T ss_pred ------------------c-----cc-------------------ccchhhh----cccccccccccCCccccCHHHHHH
Confidence 0 00 0000000 000000000111111235667777
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803 448 KKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 516 (525)
Q Consensus 448 ~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~ 516 (525)
..+....|..+|+.||+++|+||.|+|..| +|++|||+.||+|.++|+.+++||+++||+++...
T Consensus 121 ~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~ 185 (189)
T PRK12530 121 KEEFWLIFEACLNHLPAQQARVFMMREYLE----LSSEQICQECDISTSNLHVLLYRARLQLQACLSKN 185 (189)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHhHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 777778899999999999999999999987 99999999999999999999999999999988644
No 100
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=2.4e-18 Score=160.80 Aligned_cols=158 Identities=11% Similarity=0.134 Sum_probs=126.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 009803 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL 363 (525)
Q Consensus 284 ~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRi 363 (525)
...+.+++..|.+.|+.+|+++.++..+++|++||+++.+|+..++|++. ..|.+|++..++|.+.++++++.+....
T Consensus 5 ~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~~~~~~~ 82 (164)
T PRK12547 5 SKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMG--TNLKAWLFTILRNEFYSQMRKRGREVQD 82 (164)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCc--ccHHHHHHHHHHHHHHHHHHhhcccccc
Confidence 46799999999999999999999999999999999999999999999854 3699999999999999999876431000
Q ss_pred ccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHH
Q 009803 364 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAE 443 (525)
Q Consensus 364 P~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pe 443 (525)
.+... . .. .+ ..++
T Consensus 83 ------------------------------------------------------~~~~~--~-----~~--~~---~~~~ 96 (164)
T PRK12547 83 ------------------------------------------------------SDGVF--T-----AR--VA---VHPA 96 (164)
T ss_pred ------------------------------------------------------ccccc--c-----cc--CC---CCch
Confidence 00000 0 00 00 0111
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803 444 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 515 (525)
Q Consensus 444 e~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~ 515 (525)
.. .......|..+|..||+++|+||.|+|..| +|++|||+.||||.++|+++++||+++||..+..
T Consensus 97 ~~--~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 162 (164)
T PRK12547 97 QY--GSLDLQDFKKALNLLSADQREAIILIGASG----FSYEDAAAICGCAVGTIKSRVSRARNRLQELLKV 162 (164)
T ss_pred hh--hHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 11 112235688999999999999999999977 9999999999999999999999999999998764
No 101
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=2.7e-18 Score=166.07 Aligned_cols=180 Identities=16% Similarity=0.147 Sum_probs=131.1
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchH
Q 009803 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV 368 (525)
Q Consensus 289 ~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~ 368 (525)
.++..|.+.++.+|+++.++..+++|++||+|+.+|+.+++|++. ..|.+|++.+++|.+.++++++.+...++..
T Consensus 12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~-- 87 (201)
T PRK12545 12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQ--SAHKTWVFGILRNKLIDTLRARQRTVNLSAL-- 87 (201)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhcccc--chHHHHHHHHHHHHHHHHHHhhccccccccc--
Confidence 348899999999999999999999999999999999999999975 3699999999999999999887542111000
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHH
Q 009803 369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK 448 (525)
Q Consensus 369 ~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~ 448 (525)
..++. ....++............+..++. ..++++....
T Consensus 88 ----------------------~~~~~------------------~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~ 126 (201)
T PRK12545 88 ----------------------DAELD------------------GEALLDRELFKDNGHWAAHAKPRP-WPKPETILQQ 126 (201)
T ss_pred ----------------------ccccc------------------hhhhhhhhhhcccccccccccCcC-CCCHHHHHHH
Confidence 00000 000000000000000000111111 2246666666
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhch
Q 009803 449 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 517 (525)
Q Consensus 449 ~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~ 517 (525)
.+....|..+|..||+++|.||.|+|+.| +|++|||+.||+|.++|+++++||+++||+++...+
T Consensus 127 ~~~~~~l~~~L~~Lp~~~r~v~~L~~~eg----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~ 191 (201)
T PRK12545 127 QQFWTLFETCLDHLPEQIGRVFMMREFLD----FEIDDICTELTLTANHCSVLLYRARTRLRTCLSEKG 191 (201)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 66667889999999999999999999988 999999999999999999999999999999986544
No 102
>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=99.80 E-value=2.4e-18 Score=177.46 Aligned_cols=183 Identities=17% Similarity=0.134 Sum_probs=135.6
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccce
Q 009803 282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 361 (525)
Q Consensus 282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~i 361 (525)
|+..++++|+..|.+.++++|+++.++..+++|++||.|+.+|+.+++|++. ..|.+|++..++|.+.++++++.+..
T Consensus 2 gd~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~~ 79 (324)
T TIGR02960 2 VDGAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQRRP 79 (324)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhccCCc
Confidence 4578999999999999999999999999999999999999999999999864 46999999999999999998765411
Q ss_pred ecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccC------
Q 009803 362 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIA------ 435 (525)
Q Consensus 362 RiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~------ 435 (525)
..... .. . ........ ..+......+.+.
T Consensus 80 ~~~~~------------------~~-~-------------------------~~~~~~~~-~~~~~~~~~~~~~~~~~~~ 114 (324)
T TIGR02960 80 RPVGL------------------GA-P-------------------------SADGTAAA-SEAAEVTWLEPLPDLTLDL 114 (324)
T ss_pred Ccccc------------------CC-C-------------------------CCcccccc-cccccccccCCCCcccccc
Confidence 00000 00 0 00000000 0000000000000
Q ss_pred -CCCCCCHHHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803 436 -DPEAETAEDLLIKKF-MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513 (525)
Q Consensus 436 -d~~~~~pee~~~~~~-~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l 513 (525)
.....+|++.+...+ ....+..+|+.||+++|.||.|+|..+ +|++|||+.||+|.++|+++++||+++||+++
T Consensus 115 ~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~~g----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 190 (324)
T TIGR02960 115 DDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDVLG----WRAAETAELLGTSTASVNSALQRARATLDEVG 190 (324)
T ss_pred ccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHHhC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhc
Confidence 111235666655544 456788999999999999999999988 99999999999999999999999999999988
Q ss_pred hh
Q 009803 514 RT 515 (525)
Q Consensus 514 ~~ 515 (525)
..
T Consensus 191 ~~ 192 (324)
T TIGR02960 191 PS 192 (324)
T ss_pred cc
Confidence 74
No 103
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=3.7e-18 Score=164.84 Aligned_cols=168 Identities=16% Similarity=0.071 Sum_probs=129.7
Q ss_pred HHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHh
Q 009803 277 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD 356 (525)
Q Consensus 277 ~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~ 356 (525)
.....++..+++.|+..|.+.++.+++ +.++..+++|++||.|+.+|+..++|++. ..|.+|++..+|+.+.+++++
T Consensus 17 ~~~~~~d~~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk 93 (196)
T PRK12535 17 LAAGRGDRAALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAAR--SSARTWLLSLARRVWVDNIRH 93 (196)
T ss_pred HHHHcCCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCc--ccHHHHHHHHHHHHHHHHHHh
Confidence 344456689999999999999999975 67888899999999999999999999863 379999999999999999997
Q ss_pred cccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCC
Q 009803 357 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD 436 (525)
Q Consensus 357 ~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d 436 (525)
+.+..+. ..+ ... ...+ .
T Consensus 94 ~~~~~~~-----------------------------------------------------~~~-~~~-----~~~~---~ 111 (196)
T PRK12535 94 DMARPRK-----------------------------------------------------SAT-EYE-----DAAA---T 111 (196)
T ss_pred hccCCCc-----------------------------------------------------ccc-ccc-----cccc---c
Confidence 6531110 000 000 0000 0
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803 437 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 516 (525)
Q Consensus 437 ~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~ 516 (525)
. ..++..... .....|..+|+.||+++|+||.|+|..| +|++|||+.||+|.++|+++++||+++||+++...
T Consensus 112 -~-~~~~~~~~~-~~~~~l~~~l~~Lp~~~r~v~~l~~~~g----~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~ 184 (196)
T PRK12535 112 -T-ASNETTGSW-SEWIDVRTLIDALPPERREALILTQVLG----YTYEEAAKIADVRVGTIRSRVARARADLIAATATG 184 (196)
T ss_pred -c-CCcchhHHH-HHHHHHHHHHHcCCHHHHHHhhhHHHhC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccc
Confidence 0 011111111 1234689999999999999999999988 99999999999999999999999999999988654
No 104
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=99.80 E-value=5.1e-18 Score=176.42 Aligned_cols=186 Identities=19% Similarity=0.188 Sum_probs=136.4
Q ss_pred HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHH
Q 009803 275 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSL 354 (525)
Q Consensus 275 ~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~i 354 (525)
.+.+...++..++++|+..|.+.|+.+|+++.++..+++|++||+|+.+|+.+++|++. ..|.+|++..++|.+.+++
T Consensus 9 l~~~~~~gd~~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~ 86 (339)
T PRK08241 9 LLARAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATNVCLDAL 86 (339)
T ss_pred HHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHHHHHHHH
Confidence 34444556689999999999999999999999998999999999999999999999853 4699999999999999999
Q ss_pred HhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCccc
Q 009803 355 SDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVI 434 (525)
Q Consensus 355 r~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l 434 (525)
+++.+.. .+.. .+. + ..........+....+.+.+
T Consensus 87 Rk~~~~~-~~~~------------------~~~-~-------------------------~~~~~~~~~~~~~~~~~~~~ 121 (339)
T PRK08241 87 EGRARRP-LPTD------------------LGA-P-------------------------AADPVDELVERPEVPWLEPY 121 (339)
T ss_pred Hhhcccc-Cccc------------------cCC-C-------------------------cCcccccccccccccccCCC
Confidence 8765310 0000 000 0 00000000000000011111
Q ss_pred CCC----CCCCHHHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 009803 435 ADP----EAETAEDLLIKKF-MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKL 509 (525)
Q Consensus 435 ~d~----~~~~pee~~~~~~-~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKL 509 (525)
.+. ...+|++.+...+ ....|..+|++||+++|.||.|+|..+ +|++|||++||+|.++|+++++||+++|
T Consensus 122 ~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~~g----~s~~EIA~~lgis~~tVk~~l~RAr~~L 197 (339)
T PRK08241 122 PDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLILRDVLG----WSAAEVAELLDTSVAAVNSALQRARATL 197 (339)
T ss_pred CcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhHHhhC----CCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 111 1235666555544 445689999999999999999999988 9999999999999999999999999999
Q ss_pred Hh
Q 009803 510 KN 511 (525)
Q Consensus 510 R~ 511 (525)
|+
T Consensus 198 r~ 199 (339)
T PRK08241 198 AE 199 (339)
T ss_pred hh
Confidence 98
No 105
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=99.79 E-value=6.6e-18 Score=164.46 Aligned_cols=179 Identities=17% Similarity=0.153 Sum_probs=134.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccc
Q 009803 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH 366 (525)
Q Consensus 287 ~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~ 366 (525)
-..++..|.+.|+.+|+++.++..+++|++||+|+.+|+.+.+|++. .+|.+|++.+++|.+.++++++.+....+..
T Consensus 20 ~~~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfikl~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~~~~~~~~~ 97 (206)
T PRK12544 20 DPVFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGR--AAFKTWVFAILKNKIIDLLRQKKRHVSASSL 97 (206)
T ss_pred hHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhhccccccccc
Confidence 45788999999999999999999999999999999999999999864 4799999999999999999977642111000
Q ss_pred hHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCC-CcccCCCCCCCHHHH
Q 009803 367 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKP-SEVIADPEAETAEDL 445 (525)
Q Consensus 367 ~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l-~d~l~d~~~~~pee~ 445 (525)
. ....+ + ..+..+ . +....+ .....+ ...+|+..
T Consensus 98 ~------------------~~~~~--~---------~~~~~~-------------~--~~~~~~~~~~~~~-~~~~~e~~ 132 (206)
T PRK12544 98 L------------------RDEEE--E---------EDFEEL-------------F--DESGHWQKDERPQ-AWGNPEES 132 (206)
T ss_pred c------------------cccch--h---------hHHHHh-------------h--ccccccccccccc-ccCCHHHH
Confidence 0 00000 0 000000 0 000000 000111 12357777
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803 446 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 516 (525)
Q Consensus 446 ~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~ 516 (525)
+...+....+..+|..||+++|+||.|+|..+ +|++|||+.||+|..+|+++++||+++||+.+...
T Consensus 133 ~~~~e~~~~l~~~L~~L~~~~r~v~~L~~~~g----~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~ 199 (206)
T PRK12544 133 LEQEQFWRIFEACLDGLPAKYARVFMMREFIE----LETNEICHAVDLSVSNLNVLLYRARLRLRECLENK 199 (206)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 77777777899999999999999999999988 99999999999999999999999999999998753
No 106
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=99.79 E-value=7.3e-18 Score=156.60 Aligned_cols=158 Identities=16% Similarity=0.188 Sum_probs=126.1
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchH
Q 009803 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV 368 (525)
Q Consensus 289 ~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~ 368 (525)
.++..|.+.++.+|.++.++..+++|++||+++.+|+....|++. .|.+|++..+|+.+.++++++.+....
T Consensus 2 ~~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn~~~d~~R~~~~~~~~----- 73 (163)
T PRK07037 2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRNLAIDHYRRQALENKY----- 73 (163)
T ss_pred hHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHHHHHHHHHhhcccccc-----
Confidence 367789999999999999999999999999999999999888763 488999999999999999876531100
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHH
Q 009803 369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK 448 (525)
Q Consensus 369 ~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~ 448 (525)
+ ....... +. .+. ..+|+..+..
T Consensus 74 ------------------------------------------------~------~~~~~~~-~~-~~~-~~~~~~~~~~ 96 (163)
T PRK07037 74 ------------------------------------------------H------GDEEDGL-DV-PSP-EASPEAALIN 96 (163)
T ss_pred ------------------------------------------------c------ccccccc-cc-CCC-CCCHHHHHHH
Confidence 0 0000000 00 111 1246666666
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803 449 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 515 (525)
Q Consensus 449 ~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~ 515 (525)
.+....|..+|+.||+++|.||.++|..| +|++|||+.||+|.++|+..+.||+++||+.+..
T Consensus 97 ~~~~~~l~~~l~~L~~~~r~v~~l~~~~~----~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l~~ 159 (163)
T PRK07037 97 RDTLRHVADALSELPARTRYAFEMYRLHG----ETQKDIARELGVSPTLVNFMIRDALVHCRKCLDA 159 (163)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 66677899999999999999999999987 9999999999999999999999999999998764
No 107
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=99.79 E-value=1.3e-18 Score=159.78 Aligned_cols=152 Identities=17% Similarity=0.153 Sum_probs=123.0
Q ss_pred HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHH
Q 009803 292 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEAT 371 (525)
Q Consensus 292 ~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~ 371 (525)
..|.+.|+.++.++.++..+++|++||+++.+|+.+++|++ .+|.||++..+++.+.++++++.+....+
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~~------- 71 (154)
T TIGR02950 2 REYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTID------- 71 (154)
T ss_pred chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhcccc-------
Confidence 57899999999999998889999999999999999999997 47999999999999999998765311000
Q ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHHHHH
Q 009803 372 YRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFM 451 (525)
Q Consensus 372 ~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~~~ 451 (525)
.+ . ..+...+ ....|++.+...+.
T Consensus 72 --------------------~~---------------------------~--------~~~~~~~-~~~~~~~~~~~~~~ 95 (154)
T TIGR02950 72 --------------------DD---------------------------A--------IGDLEQH-PVESPEHHLLIKIE 95 (154)
T ss_pred --------------------Hh---------------------------h--------hhhcccc-ccCChhHHHHHHHH
Confidence 00 0 0000001 11245666666666
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803 452 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513 (525)
Q Consensus 452 ~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l 513 (525)
...|..+|+.||+++++||.++|+.| +|++|||+.||+|..+|++..+||+++||+.+
T Consensus 96 ~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~l 153 (154)
T TIGR02950 96 QEEITHHLSRLPENYRTVLILREFKE----FSYKEIAELLNLSLAKVKSNLFRARKELKKLL 153 (154)
T ss_pred HHHHHHHHHhCCHhheeeeeehhhcc----CcHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 67899999999999999999999877 99999999999999999999999999999865
No 108
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=99.78 E-value=7.1e-18 Score=156.39 Aligned_cols=154 Identities=14% Similarity=0.109 Sum_probs=124.3
Q ss_pred HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHH
Q 009803 292 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEAT 371 (525)
Q Consensus 292 ~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~ 371 (525)
..|.+.++.++.++.++..+++|++||+|+.+|+..+.|++ .+|.||++..+++.+.++++++.+...
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~---~~~~~wL~~ia~n~~~d~~R~~~~~~~--------- 69 (159)
T PRK12527 2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQI---EHPRAFLYRTALNLVVDRHRRHRVRQA--------- 69 (159)
T ss_pred hhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhccccccc---cchHHHHHHHHHHHHHHHHHHHhcccc---------
Confidence 56888999999999998889999999999999999999875 279999999999999999986532000
Q ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHHHHH
Q 009803 372 YRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFM 451 (525)
Q Consensus 372 ~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~~~ 451 (525)
.+++. .. +. .. ...++|++.+..++.
T Consensus 70 --------------------------------------------~~~~~-~~-~~-----~~---~~~~~~~~~~~~~~~ 95 (159)
T PRK12527 70 --------------------------------------------EPLEV-LD-EE-----ER---LHSPSPQTRLDLGQR 95 (159)
T ss_pred --------------------------------------------cchhh-hh-cc-----cc---ccCCCHHHHHHHHHH
Confidence 00000 00 00 00 012256777666677
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803 452 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 515 (525)
Q Consensus 452 ~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~ 515 (525)
...|..+|..||+++++||.|+|+.+ +|++|||+.||+|.++|+..+.||+++||+.+..
T Consensus 96 ~~~l~~~l~~L~~~~r~v~~l~~~~~----~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~~ 155 (159)
T PRK12527 96 LALLQRALAELPPACRDSFLLRKLEG----LSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQ 155 (159)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 77899999999999999999999988 9999999999999999999999999999998764
No 109
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=1.1e-17 Score=160.25 Aligned_cols=161 Identities=14% Similarity=0.111 Sum_probs=127.4
Q ss_pred hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccc
Q 009803 281 NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT 360 (525)
Q Consensus 281 ~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~ 360 (525)
..+..+++.++..|.+.|+.+|+++.++..+++|++||+|+.+|+.++.|++. ..|.+|++..+++.+.+..+++.+.
T Consensus 19 ~~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~~~~~ 96 (188)
T PRK12517 19 LSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFERKQFD 96 (188)
T ss_pred hccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHHhccC
Confidence 45688999999999999999999999999999999999999999999999864 3699999999999876655432210
Q ss_pred eecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCC
Q 009803 361 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAE 440 (525)
Q Consensus 361 iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~ 440 (525)
. ...+ . +...+....
T Consensus 97 --~----------------------------------------------------~~~~-------~----~~~~~~~~~ 111 (188)
T PRK12517 97 --L----------------------------------------------------VDIE-------D----DSIEDDASH 111 (188)
T ss_pred --c----------------------------------------------------cCcc-------c----ccccCcccc
Confidence 0 0000 0 001111111
Q ss_pred CHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803 441 TAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 516 (525)
Q Consensus 441 ~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~ 516 (525)
+++... ....|..+|..||+++|.||.++|..| +|++|||+.||||..+|+.+++||+++||+.+...
T Consensus 112 ~~e~~~----~~~~l~~~l~~Lp~~~r~v~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 179 (188)
T PRK12517 112 SSEEEM----EQEWLRRQIAKLDPEYREPLLLQVIGG----FSGEEIAEILDLNKNTVMTRLFRARNQLKEALEKP 179 (188)
T ss_pred ChhHHH----HHHHHHHHHHhCCHHHHHHHHHHHHhC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 333322 235689999999999999999999988 99999999999999999999999999999998753
No 110
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=8.7e-18 Score=160.32 Aligned_cols=160 Identities=14% Similarity=0.156 Sum_probs=127.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecc
Q 009803 285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP 364 (525)
Q Consensus 285 ~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP 364 (525)
.++..++..|.+.++.+|.++.++..+++|++||+|+.+|+..++|++.. .|.+|++..++|.+.++++++.+....
T Consensus 5 ~~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~~~~~- 81 (182)
T PRK12540 5 DSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGS--NLPAWLFTILRNLFRSDYRKRRREVED- 81 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCc--hHHHHHHHHHHHHHHHHHHhccccccc-
Confidence 57889999999999999999999999999999999999999999998653 699999999999999998876531000
Q ss_pred cchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHH
Q 009803 365 FHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAED 444 (525)
Q Consensus 365 ~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee 444 (525)
.+. ...+... + .++.
T Consensus 82 -----------------------------------------------------~~~--------~~~~~~~-~---~~~~ 96 (182)
T PRK12540 82 -----------------------------------------------------ADG--------SYAKTLK-S---QPGQ 96 (182)
T ss_pred -----------------------------------------------------ccc--------ccccccc-C---CCch
Confidence 000 0000000 0 1111
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 009803 445 LLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHL 518 (525)
Q Consensus 445 ~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L 518 (525)
.. ......|..+|+.||+++|+||.|+|..+ +|++|||+.||+|..+|+++++||+++||+.+.....
T Consensus 97 ~~--~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g----~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~~ 164 (182)
T PRK12540 97 NA--HLEFEEFRAALDKLPQDQREALILVGASG----FSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDGA 164 (182)
T ss_pred HH--HHHHHHHHHHHHhCCHHHHHHhhHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 11 11234689999999999999999999887 9999999999999999999999999999999986553
No 111
>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=99.78 E-value=1e-17 Score=164.58 Aligned_cols=115 Identities=16% Similarity=0.187 Sum_probs=104.2
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCC--CCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcc-
Q 009803 282 YGILCKDKMITSNIRLVISIAKNYQGAG--MNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS- 358 (525)
Q Consensus 282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g--~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~- 358 (525)
|+.. +++||..|.|+|.++|++|.++. .+.+|++|+|++|||+|+++|||++|.+|.|||.+||++.|.+++++..
T Consensus 7 gd~~-~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dylRk~~k 85 (218)
T TIGR02895 7 GNEE-REELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYIRKNQK 85 (218)
T ss_pred CChH-HHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHhccc
Confidence 3455 99999999999999999998764 5899999999999999999999999999999999999999999999887
Q ss_pred --cceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHH
Q 009803 359 --RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEA 397 (525)
Q Consensus 359 --r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~ 397 (525)
+.+++|....+....+..+...+..+.++.|+.+||+..
T Consensus 86 ~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~ 126 (218)
T TIGR02895 86 YQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEY 126 (218)
T ss_pred ccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHH
Confidence 788999877666778888888999999999999999854
No 112
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=99.78 E-value=1.3e-17 Score=158.97 Aligned_cols=154 Identities=14% Similarity=0.110 Sum_probs=126.7
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccc
Q 009803 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH 366 (525)
Q Consensus 287 ~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~ 366 (525)
++.|+..|.+.|+.++.++.++..+++|++||+++.+|+.+..|++. .+|.+|++..+++.+.++++++.+...++
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~~--~~~~~wL~~i~~n~~~d~~Rk~~~~~~~~-- 78 (181)
T PRK09637 3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNTIIDFYRKKNRSEELP-- 78 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhccc--cchHHHHHHHHHHHHHHHHHhccccCCcc--
Confidence 67899999999999999999999999999999999999999999853 47999999999999999998765411000
Q ss_pred hHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHH
Q 009803 367 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLL 446 (525)
Q Consensus 367 ~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~ 446 (525)
.+ +...+ ++++..
T Consensus 79 ---------------------------------------------------------~~------~~~~~----~~~~~~ 91 (181)
T PRK09637 79 ---------------------------------------------------------DD------LLFED----EEREEN 91 (181)
T ss_pred ---------------------------------------------------------hh------hhccC----CChhHH
Confidence 00 00000 111222
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803 447 IKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 515 (525)
Q Consensus 447 ~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~ 515 (525)
...+....+..+|+.||+++|.||.|+|..| ++++|||++||+|..+|+.++.||+++||+.+..
T Consensus 92 ~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g----~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (181)
T PRK09637 92 AKKELAPCLRPFIDALPEKYAEALRLTELEG----LSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156 (181)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHhcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 3344567799999999999999999999988 9999999999999999999999999999998764
No 113
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=99.77 E-value=1.3e-17 Score=157.16 Aligned_cols=162 Identities=13% Similarity=0.096 Sum_probs=126.5
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhccccee
Q 009803 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR 362 (525)
Q Consensus 283 g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iR 362 (525)
+..|+..++..|.+.++.++.++.++..+++|++||.|+.+|+. ..|++.. .|.+|++..+++.+.++++++.+..
T Consensus 8 ~~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~~~~- 83 (172)
T PRK09651 8 ASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNALEK- 83 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHHHHh-
Confidence 46799999999999999999999999999999999999999998 3565432 5899999999999999988653200
Q ss_pred cccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCH
Q 009803 363 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETA 442 (525)
Q Consensus 363 iP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~p 442 (525)
.. . + .+. . +.+....+|
T Consensus 84 -----------------~~----------------------------------~--~-~~~-----~----~~~~~~~~~ 100 (172)
T PRK09651 84 -----------------AY----------------------------------L--E-MLA-----L----MPEGGAPSP 100 (172)
T ss_pred -----------------hh----------------------------------h--h-HHh-----h----ccccCCCCh
Confidence 00 0 0 000 0 000011134
Q ss_pred HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803 443 EDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 515 (525)
Q Consensus 443 ee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~ 515 (525)
+......+....|..+|+.||+++|+||.++|+.| +|++|||+.||+|.++|+..++||+++|+.....
T Consensus 101 ~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~~~~ 169 (172)
T PRK09651 101 EERESQLETLQLLDSMLDGLNGKTREAFLLSQLDG----LTYSEIAHKLGVSVSSVKKYVAKATEHCLLFRLE 169 (172)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHhHHhhhhhccC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 44444445556799999999999999999999988 9999999999999999999999999999986543
No 114
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=99.76 E-value=2.5e-17 Score=158.11 Aligned_cols=157 Identities=12% Similarity=0.146 Sum_probs=122.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 009803 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL 363 (525)
Q Consensus 284 ~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRi 363 (525)
..+++.|+. |.+.|+++|+.+.++..+++|++||+|+.+|+.+..|+.. ..|.+|++..++|.+.++++++.+...
T Consensus 7 ~~~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r~~~- 82 (188)
T PRK12546 7 RDPRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKREVP- 82 (188)
T ss_pred hhHHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhccccc-
Confidence 456777766 7799999999999999999999999999999999999863 469999999999999999887653100
Q ss_pred ccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHH
Q 009803 364 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAE 443 (525)
Q Consensus 364 P~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pe 443 (525)
..+. ...+...+.. ..+
T Consensus 83 -----------------------------------------------------~~~~--------~~~~~~~~~~--~~~ 99 (188)
T PRK12546 83 -----------------------------------------------------DPEG--------VHAASLAVKP--AHD 99 (188)
T ss_pred -----------------------------------------------------Cccc--------ccccccccCC--cch
Confidence 0000 0000000000 111
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803 444 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 515 (525)
Q Consensus 444 e~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~ 515 (525)
. ......+..+|+.||+++|+||.|+|..+ +|.+|||+.||||..+|+++++||+++||+.+..
T Consensus 100 ~----~~~~~~l~~~L~~Lp~~~r~v~~L~~~~g----~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~ 163 (188)
T PRK12546 100 G----RLAMSDFRAAFAQLPDEQREALILVGASG----FSYEEAAEMCGVAVGTVKSRANRARARLAELLQL 163 (188)
T ss_pred h----HHHHHHHHHHHHhCCHHHhHHhhhHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 1 11234688999999999999999999987 9999999999999999999999999999998864
No 115
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=99.76 E-value=2.6e-17 Score=155.01 Aligned_cols=149 Identities=18% Similarity=0.210 Sum_probs=121.3
Q ss_pred HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHH
Q 009803 292 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEAT 371 (525)
Q Consensus 292 ~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~ 371 (525)
..|.+.++.++.++.++..+++|++||+++.+|+++.+|++. .+|.+|++..+++.+.+++++..+...++
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~~--~~f~~wl~~iarn~~~d~~Rk~~~~~~~~------- 72 (170)
T TIGR02959 2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDG--QKIQSWLYQIARNTIIDFYRSKSRSVELP------- 72 (170)
T ss_pred chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhccCccccc-------
Confidence 458899999999999999999999999999999999999863 58999999999999999998875411100
Q ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHHHHH
Q 009803 372 YRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFM 451 (525)
Q Consensus 372 ~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~~~ 451 (525)
+ + .... . ++++.....+.
T Consensus 73 -----------------------------------------------~-----~-------~~~~-~--~~~~~~~~~e~ 90 (170)
T TIGR02959 73 -----------------------------------------------E-----S-------LLAA-D--SAREETFVKEL 90 (170)
T ss_pred -----------------------------------------------h-----h-------hccc-C--CccHHHHHHHH
Confidence 0 0 0000 0 11222333445
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803 452 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 515 (525)
Q Consensus 452 ~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~ 515 (525)
...|..+|+.||+++|.||.++|..+ +|++|||+.||+|..+|++.++||+++||..+..
T Consensus 91 ~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 150 (170)
T TIGR02959 91 SQCIPPMIKELPDEYREAIRLTELEG----LSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLET 150 (170)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 56789999999999999999999988 9999999999999999999999999999998763
No 116
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=99.75 E-value=3.1e-17 Score=156.66 Aligned_cols=156 Identities=14% Similarity=0.138 Sum_probs=122.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccc
Q 009803 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH 366 (525)
Q Consensus 287 ~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~ 366 (525)
.+..+..+++.|+.+|.++.++..+++|++||.|+.+|+....|++. .+|.+|++..+++.+.++++++.+.....
T Consensus 6 ~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~~~~~~-- 81 (182)
T PRK12511 6 KRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRVEARRA-- 81 (182)
T ss_pred hhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhccccccc--
Confidence 44557789999999999999998999999999999999999999864 37999999999999999998765411000
Q ss_pred hHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHH
Q 009803 367 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLL 446 (525)
Q Consensus 367 ~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~ 446 (525)
++ +. +. .+.....+..
T Consensus 82 -------------------------~~------------------------~~------------~~-~~~~~~~~~~-- 97 (182)
T PRK12511 82 -------------------------DE------------------------LA------------VL-ADASLPAAQE-- 97 (182)
T ss_pred -------------------------cc------------------------hh------------hc-cccCCCcchH--
Confidence 00 00 00 0000001111
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803 447 IKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 515 (525)
Q Consensus 447 ~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~ 515 (525)
.......|..+|..||+++|+||.|+|..| +|++|||+.||||.++|+++++||+++||+.+..
T Consensus 98 -~~~~~~~l~~~l~~Lp~~~R~v~~L~~~eg----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~~ 161 (182)
T PRK12511 98 -HAVRLAQIRDAFFDLPEEQRAALHLVAIEG----LSYQEAAAVLGIPIGTLMSRIGRARAALRAFEEG 161 (182)
T ss_pred -HHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 112345688999999999999999999987 9999999999999999999999999999998864
No 117
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=99.75 E-value=6.7e-17 Score=151.65 Aligned_cols=159 Identities=16% Similarity=0.118 Sum_probs=127.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 009803 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL 363 (525)
Q Consensus 284 ~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRi 363 (525)
..++.+++..|.+.++.+|.+|.++..+++|++||+|+.+|+....++. ..|.+|++..++|.+.+++++....
T Consensus 8 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~~--- 81 (168)
T PRK12525 8 NTLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDLE--- 81 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHHH---
Confidence 5689999999999999999999999999999999999999987665542 3699999999999999988754210
Q ss_pred ccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHH
Q 009803 364 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAE 443 (525)
Q Consensus 364 P~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pe 443 (525)
+.... ++ . + .+.+...+|+
T Consensus 82 ---------------~~~~~---------------------------------~~------~------~-~~~~~~~~~~ 100 (168)
T PRK12525 82 ---------------RAYLQ---------------------------------SL------A------E-APEAVQPSPE 100 (168)
T ss_pred ---------------HHHHH---------------------------------HH------h------c-ccccccCChH
Confidence 00000 00 0 0 0001123566
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803 444 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513 (525)
Q Consensus 444 e~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l 513 (525)
+..........|..+|+.||+++|.||.|+|..| +|++|||+.||+|..+|+..+.||+++||..+
T Consensus 101 ~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~eg----~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~~ 166 (168)
T PRK12525 101 EQWMVIETLLAIDRLLDGLSGKARAAFLMSQLEG----LTYVEIGERLGVSLSRIHQYMVEAFKCCYQGF 166 (168)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhh
Confidence 6666666678899999999999999999999988 99999999999999999999999999999865
No 118
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=99.73 E-value=9.5e-17 Score=164.06 Aligned_cols=160 Identities=15% Similarity=0.124 Sum_probs=124.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecc
Q 009803 285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP 364 (525)
Q Consensus 285 ~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP 364 (525)
..+.+++..|.+.++.+|+++.++..+++|++||+|+. |.....|+ ...|.+|++..++|.+.++++++.+....
T Consensus 4 ~~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~---~~~~~~WL~~Ia~n~~~d~lR~~~~~~~~- 78 (293)
T PRK09636 4 ADAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQ---IRDPRAWLTRVVTRLCLDRLRSARHRRET- 78 (293)
T ss_pred cHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhccccc---ccCHHHHHHHHHHHHHHHHHHhhhccccc-
Confidence 34778999999999999999999989999999999999 66667776 34799999999999999999875430000
Q ss_pred cchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHH
Q 009803 365 FHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAED 444 (525)
Q Consensus 365 ~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee 444 (525)
.... .+.+...+.. .+|++
T Consensus 79 ----------------------------------------------------~~~~--------~~~e~~~~~~-~~~~~ 97 (293)
T PRK09636 79 ----------------------------------------------------YVGP--------WLPEPVVEEL-DDPLE 97 (293)
T ss_pred ----------------------------------------------------ccCC--------cCCcCCCCCC-CChHH
Confidence 0000 0000011111 13443
Q ss_pred H-HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 445 L-LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 445 ~-~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
. .........+..+|+.|||++|.||.|+|..+ +|++|||+.||+|..+|+++++||+++||+...
T Consensus 98 ~~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~~~g----~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~ 164 (293)
T PRK09636 98 AVVAAEDLSLALMLALERLSPLERAAFLLHDVFG----VPFDEIASTLGRSPAACRQLASRARKHVRAARP 164 (293)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 3 33445556789999999999999999999988 999999999999999999999999999999754
No 119
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=99.72 E-value=1.1e-16 Score=148.13 Aligned_cols=155 Identities=16% Similarity=0.180 Sum_probs=112.7
Q ss_pred CCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHHHHHHHHHHHcC
Q 009803 307 GAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENG 386 (525)
Q Consensus 307 ~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lg 386 (525)
++..+++|++||+|+.+|+....+ + +..|.+|++..++|.+.++++++.+..+....
T Consensus 2 ~~~~~AeDivQe~fl~~~~~~~~~-~--~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~-------------------- 58 (161)
T PRK09047 2 RDDDAALDIVQDAMIKLAEKYGDR-P--AAEWPPLFQRILQNRIHDWFRRQKVRNTWVSL-------------------- 58 (161)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhhc-c--cCchHHHHHHHHHHHHHHHHHhhccccccccc--------------------
Confidence 344578999999999999998863 3 45799999999999999999876531110000
Q ss_pred CCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCC--CCCHHHHHHHHHHHHHHHHHHhcCCH
Q 009803 387 RHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPE--AETAEDLLIKKFMKEDLEKVLDTLNP 464 (525)
Q Consensus 387 r~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~--~~~pee~~~~~~~~~~L~~aL~~L~~ 464 (525)
..++..... +++....+.+.+.. ..+|++.+...+....|..+|+.||+
T Consensus 59 ----------------------------~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~ 109 (161)
T PRK09047 59 ----------------------------FSSFSDDDD-DDDFDPLETLDSADEGAESPADKLERAQVLQLIEEAIQKLPA 109 (161)
T ss_pred ----------------------------ccccccccc-cccccHHHHhccccccCCCHHHHHHHHHHHHHHHHHHHhCCH
Confidence 000000000 00011111111111 23677777777788889999999999
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhch
Q 009803 465 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 517 (525)
Q Consensus 465 rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~ 517 (525)
++|+||.|+|+.| +|++|||+.||||.++|+.+++||+++||+++...+
T Consensus 110 ~~r~v~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~ 158 (161)
T PRK09047 110 RQREAFLLRYWED----MDVAETAAAMGCSEGSVKTHCSRATHALAKALEAKG 158 (161)
T ss_pred HHHHHHHHHHHhc----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 9999999999988 999999999999999999999999999999887654
No 120
>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=99.69 E-value=7.2e-16 Score=156.92 Aligned_cols=156 Identities=18% Similarity=0.161 Sum_probs=120.0
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchH
Q 009803 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV 368 (525)
Q Consensus 289 ~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~ 368 (525)
+++..|.+.++.+|+++.++..+++|++||+++.+++. .|+. ...|.+|++.+++|.+.+++++..+.-..
T Consensus 1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~--~~~~~awL~~Ia~n~~ld~lR~~~~~~~~----- 71 (281)
T TIGR02957 1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQ--IENPKAYLTKVVTRRCIDVLRSARARREV----- 71 (281)
T ss_pred ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Cccc--ccCHHHHHHHHHHHHHHHHHHHhhhcccc-----
Confidence 47899999999999999999999999999999998775 4543 23699999999999999999865420000
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHH
Q 009803 369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK 448 (525)
Q Consensus 369 ~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~ 448 (525)
... ..+.+...+. ..+|++....
T Consensus 72 ------------------------------------------------~~~--------~~~~e~~~~~-~~~~~~~~~~ 94 (281)
T TIGR02957 72 ------------------------------------------------YVG--------PWLPEPLLTT-SADPAESVEL 94 (281)
T ss_pred ------------------------------------------------cCC--------CCCCcccCCC-CCChHHHHHH
Confidence 000 0000001111 1245554433
Q ss_pred -HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 449 -KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 449 -~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
+.+...+..+|+.|||+||.||.|+|..+ +|++|||+.||+|..+|+++.+||+++||+...
T Consensus 95 ~e~~~~~l~~~l~~L~~~~R~v~~L~~~~g----~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~ 157 (281)
T TIGR02957 95 AESLSMAYLLLLERLSPLERAVFVLREVFD----YPYEEIASIVGKSEANCRQLVSRARRHLDARRP 157 (281)
T ss_pred HHHHHHHHHHHHhhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 34556788999999999999999999988 999999999999999999999999999998653
No 121
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=99.69 E-value=7.6e-16 Score=152.46 Aligned_cols=159 Identities=12% Similarity=0.130 Sum_probs=124.9
Q ss_pred HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHH
Q 009803 275 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSL 354 (525)
Q Consensus 275 ~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~i 354 (525)
.|.+.+.++..+++.++..| +.++.++.++.++..+++||+||+|+.+|+. |+.. ..|.+|++.+++|.+.+++
T Consensus 8 ~~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~--~~~~~WL~~IarN~~id~~ 81 (228)
T PRK06704 8 ILKNHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNK--DICMTLVYKIARNRWLDQI 81 (228)
T ss_pred HHhcccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCcc--ccHHHHHHHHHHHHHHHHH
Confidence 45566667788999888888 7899999999999999999999999999986 5543 2599999999999999998
Q ss_pred HhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCccc
Q 009803 355 SDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVI 434 (525)
Q Consensus 355 r~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l 434 (525)
+++.+.-.+ . + ... .
T Consensus 82 Rk~k~~~~~-------------------------------------------------------~-----~-~~~----~ 96 (228)
T PRK06704 82 KSKSVHEKI-------------------------------------------------------R-----D-QIT----F 96 (228)
T ss_pred hcccccccc-------------------------------------------------------c-----c-ccc----c
Confidence 876431000 0 0 000 0
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 435 ADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 435 ~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
. .+.+.. ......+..+|+.||+++|.||.|+|..+ +|++|||+.||+|.++|+++++||+++||+.+.
T Consensus 97 ~-----~~~~~~--~~~~~~l~~~L~~Lp~~~R~v~lL~~~eg----~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~ 165 (228)
T PRK06704 97 E-----EPHEKI--ADLHEMVGKVLSSLNVQQSAILLLKDVFQ----YSIADIAKVCSVSEGAVKASLFRSRNRLKTVSE 165 (228)
T ss_pred C-----ChHHHH--HHHHHHHHHHHHhCCHHHhhHhhhHHhhC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 0 111111 12335688999999999999999999987 999999999999999999999999999999876
Q ss_pred h
Q 009803 515 T 515 (525)
Q Consensus 515 ~ 515 (525)
.
T Consensus 166 ~ 166 (228)
T PRK06704 166 E 166 (228)
T ss_pred h
Confidence 4
No 122
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=99.69 E-value=1.1e-15 Score=156.42 Aligned_cols=161 Identities=16% Similarity=0.133 Sum_probs=124.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecc
Q 009803 285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP 364 (525)
Q Consensus 285 ~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP 364 (525)
..+..++..|.+.++.+|+++.++..+++|++||.|+.+|++...+ . ..|.+|++...+|.+.+++++..+.-..
T Consensus 5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~-~---~~~~aWL~~Ia~n~~id~lRk~~~rr~~- 79 (290)
T PRK09635 5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD-I---DDERGWLIVVTSRLCLDHIKSASTRRER- 79 (290)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc-c---ccHHHHHHHHHHHHHHHHHhhhhccCcC-
Confidence 4688999999999999999999999999999999999999987653 1 3699999999999999999875320000
Q ss_pred cchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHH
Q 009803 365 FHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAED 444 (525)
Q Consensus 365 ~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee 444 (525)
....+... ..+...+ ..+|++
T Consensus 80 --------------------------------------------------~~~~~~~~-------~~~~~~~--~~~~~~ 100 (290)
T PRK09635 80 --------------------------------------------------PQDIAAWH-------DGDASVS--SVDPAD 100 (290)
T ss_pred --------------------------------------------------cccccccC-------ccccCCC--CCCcHH
Confidence 00000000 0000111 113333
Q ss_pred -HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803 445 -LLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513 (525)
Q Consensus 445 -~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l 513 (525)
.....+....+..+|+.|||++|.||.|+|..+ +|++|||+.||+|..+|+++.+||+++||+..
T Consensus 101 ~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~~~g----~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~ 166 (290)
T PRK09635 101 RVTLDDEVRLALLIMLERLGPAERVVFVLHEIFG----LPYQQIATTIGSQASTCRQLAHRARRKINESR 166 (290)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHHhC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence 344555667899999999999999999999998 99999999999999999999999999999854
No 123
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=99.55 E-value=6.5e-14 Score=127.59 Aligned_cols=136 Identities=12% Similarity=0.187 Sum_probs=100.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhh-----cCCcCCCchhhHHHHHHHHHHHHHHHhcccce
Q 009803 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEK-----FDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 361 (525)
Q Consensus 287 ~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiek-----FDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~i 361 (525)
++.++..|.++++.+|++|... +| +||.++.+|..+.+ |++. ..|.||++..++|.+.++++++.+..
T Consensus 1 f~~~~~~y~~~l~~~~~~~~~~----~~-~qdvf~~~w~~~~~~~~~~~~~~--~~~~~wL~~iarN~~id~~Rk~~~~~ 73 (142)
T TIGR03209 1 FEEIYMNFKNTIDIFTRKYNLY----YD-YNDILYHLWIILKKIDLNKFNTE--NDLEKYISTSLKRYCLDICNKKNRDK 73 (142)
T ss_pred ChHHHHHHHHHHHHHHHHhcch----hh-HHHHHHHHHHHHHHhhhhhcCch--hHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 4679999999999999999662 34 49999999999875 5432 47999999999999999998764310
Q ss_pred ecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCC
Q 009803 362 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET 441 (525)
Q Consensus 362 RiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~ 441 (525)
+. .. +. + ..+.. ..
T Consensus 74 ~~-----------------~~------------------------------------~~----~--------~~~~~-~~ 87 (142)
T TIGR03209 74 KI-----------------IY------------------------------------NS----E--------ITDIK-LS 87 (142)
T ss_pred hh-----------------hh------------------------------------hh----h--------hhccc-cc
Confidence 00 00 00 0 00000 01
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHH
Q 009803 442 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIR 499 (525)
Q Consensus 442 pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVR 499 (525)
+.+.....+....+..+|+.||+++|+||.|+|..| +|++|||++||+|.+||+
T Consensus 88 ~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~~----~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 88 LINVYSSNDLEFEFNDLISILPNKQKKIIYMKFFED----MKEIDIAKKLHISRQSVY 141 (142)
T ss_pred hhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHhhc
Confidence 122233334456788999999999999999999988 999999999999999997
No 124
>PRK09191 two-component response regulator; Provisional
Probab=99.53 E-value=1.1e-13 Score=136.86 Aligned_cols=136 Identities=13% Similarity=0.112 Sum_probs=111.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceeccc
Q 009803 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF 365 (525)
Q Consensus 286 A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~ 365 (525)
++.+|+..|.+.++++|.++.++..+++|++||+|+.+|+...+|++. ..|.+|++.++++.... ..
T Consensus 2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~----~~------- 68 (261)
T PRK09191 2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSS----AG------- 68 (261)
T ss_pred chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhcc----cc-------
Confidence 578999999999999999999999999999999999999999999864 46899999876543210 00
Q ss_pred chHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHH
Q 009803 366 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL 445 (525)
Q Consensus 366 ~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~ 445 (525)
. . .. .. . .+..
T Consensus 69 --------------------------------------------------------~--~-~~------~~-~--~~~~- 79 (261)
T PRK09191 69 --------------------------------------------------------A--N-DP------EP-G--SPFE- 79 (261)
T ss_pred --------------------------------------------------------c--c-CC------CC-C--CCch-
Confidence 0 0 00 00 0 0110
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 446 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 446 ~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
..+..+|+.||+++|+||.|+|..+ +|++|||+.||+|.++|+.+.++|+++||..+.
T Consensus 80 -------~~l~~~l~~L~~~~r~v~~l~~~~~----~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~ 137 (261)
T PRK09191 80 -------ARAERRLAGLTPLPRQAFLLTALEG----FSVEEAAEILGVDPAEAEALLDDARAEIARQVA 137 (261)
T ss_pred -------HHHHHHHHhCCHHHhHHHHHHHHhc----CCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCC
Confidence 1688999999999999999999887 999999999999999999999999999998765
No 125
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=99.39 E-value=1.9e-11 Score=121.95 Aligned_cols=82 Identities=16% Similarity=0.227 Sum_probs=74.7
Q ss_pred HHhccHHHHHHHHHHHHHHHHHHHHHhhCCCC--CHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHh
Q 009803 279 RLNYGILCKDKMITSNIRLVISIAKNYQGAGM--NLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD 356 (525)
Q Consensus 279 ~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~--~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~ 356 (525)
...++..|++.|+..|.++|+++|.+|+++.. +.+|++|||++++|+++++|++.+|..|.+|++.+|++.+.+++++
T Consensus 12 ~~~gD~~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn~~iDylRk 91 (237)
T PRK08311 12 IKNGDEELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKRRLIDYFRK 91 (237)
T ss_pred HHCCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 33456889999999999999999999998765 5899999999999999999999988889999999999999999998
Q ss_pred cccc
Q 009803 357 QSRT 360 (525)
Q Consensus 357 ~~r~ 360 (525)
+.+-
T Consensus 92 ~~~~ 95 (237)
T PRK08311 92 ESKH 95 (237)
T ss_pred hhcc
Confidence 7663
No 126
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=99.39 E-value=2.9e-11 Score=115.91 Aligned_cols=172 Identities=25% Similarity=0.318 Sum_probs=118.8
Q ss_pred HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCC---CCCHHH--HHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHH
Q 009803 276 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGA---GMNLQD--LVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAV 350 (525)
Q Consensus 276 L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~---g~~~eD--LIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI 350 (525)
|.+..+||..|.++|+..|++.++.+|+++.+. +.+.+| |++|.|+.+++.-...++.....|-.|+...+++.+
T Consensus 8 l~~~~~GD~~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~~~~~rr~l 87 (185)
T PF07638_consen 8 LDRWRQGDEAALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALLARIMRRKL 87 (185)
T ss_pred HHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHHHHHHHHHH
Confidence 444555679999999999999999999987643 345555 577888877774333233333468899999999999
Q ss_pred HHHHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCC
Q 009803 351 RKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKP 430 (525)
Q Consensus 351 ~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l 430 (525)
.++.+.+....|- |.. ...+|+...
T Consensus 88 id~~R~~~a~KRg----------------------~~~-------------------------~~~~l~~~~-------- 112 (185)
T PF07638_consen 88 IDHARRRQAQKRG----------------------GDQ-------------------------VRVELDERA-------- 112 (185)
T ss_pred HHHHHHHHHHhcC----------------------CCC-------------------------cccchhhhh--------
Confidence 9988766532111 000 011122111
Q ss_pred CcccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803 431 SEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510 (525)
Q Consensus 431 ~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR 510 (525)
.+...+.|++.+. +.+.+..+.. |+|+++++|.++|..| +|.+|||+.||||..+|+.....|..+|+
T Consensus 113 ----~~~~~~~~~~~~~---l~e~l~~L~~-l~~~~~~~v~l~~~~G----ls~~EIA~~lgiS~~tV~r~l~~aR~~l~ 180 (185)
T PF07638_consen 113 ----DSGDEPSPEELLE---LEEALERLLA-LDPRQRRVVELRFFEG----LSVEEIAERLGISERTVRRRLRRARAWLR 180 (185)
T ss_pred ----ccccCCCHHHHHH---HHHHHHHHHc-cCHHHHHHHHHHHHCC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 1111234555433 3344555445 9999999999999877 99999999999999999999999999999
Q ss_pred hHHh
Q 009803 511 NKKR 514 (525)
Q Consensus 511 ~~l~ 514 (525)
..+.
T Consensus 181 ~~l~ 184 (185)
T PF07638_consen 181 RELR 184 (185)
T ss_pred HHhc
Confidence 8764
No 127
>PF04542 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR007627 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [, ]. The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation [, ].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1OR7_B 1H3L_B 2Z2S_C 2Q1Z_C 2O7G_B 1SMY_F 1IW7_P 2BE5_F 2A6E_F 2CW0_F ....
Probab=99.28 E-value=1.2e-11 Score=98.69 Aligned_cols=70 Identities=23% Similarity=0.377 Sum_probs=67.3
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhccc
Q 009803 290 MITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR 359 (525)
Q Consensus 290 Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r 359 (525)
|++.|.++|++++++|.+++.+.+|++||++++||+++++||++++..|.+|++..+++.+.++++++.|
T Consensus 1 L~~~~~~~l~~~~~~~~~~~~~~eD~~qe~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~r~~~r 70 (71)
T PF04542_consen 1 LYERYYPLLYRYARRYTGDPEDAEDLVQEAFIKLWRAIDSYDPDRGDSFRAWLFRIARNRILDYLRKRRR 70 (71)
T ss_dssp HHHHTHHHHHHHHHTCTTCSSHHHHHHHHHHHHHHHHHHHTSTTSSSHHHHHHHHHHHHHHHHHHHCSSS
T ss_pred CHHHHHHHHHHHHHHHhCCHhhHHHHhhHHHHHHHhhhhcccccccCCHHHHHHHHHHHHHHHHHHHhcC
Confidence 6899999999999999999999999999999999999999999999899999999999999999998765
No 128
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=99.25 E-value=1.7e-11 Score=92.83 Aligned_cols=50 Identities=46% Similarity=0.726 Sum_probs=46.0
Q ss_pred HHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 458 VLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 458 aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
+|+.||++|++||.++|+.+ +|+.|||+.||+|+++|++++.+|++|||+
T Consensus 1 Al~~L~~~er~vi~~~y~~~----~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 1 ALDQLPPREREVIRLRYFEG----LTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp HHCTS-HHHHHHHHHHHTST-----SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred ChhhCCHHHHHHHHHHhcCC----CCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 58899999999999999877 999999999999999999999999999995
No 129
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=99.11 E-value=1e-10 Score=96.33 Aligned_cols=77 Identities=31% Similarity=0.538 Sum_probs=66.2
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHH
Q 009803 369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL 445 (525)
Q Consensus 369 ~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~ 445 (525)
+.+++|.++.+.|.+++||.||.+|||+.||+++++|..++.+...++||+.+++.+++.++.+++.|+...+|++.
T Consensus 1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d~~~~~P~e~ 77 (78)
T PF04539_consen 1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIEDDDAPSPEEE 77 (78)
T ss_dssp HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-SSS--HHHH
T ss_pred ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecCCCCCChhhc
Confidence 46789999999999999999999999999999999999999999999999999998888899999999988888875
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=98.94 E-value=2.5e-09 Score=81.96 Aligned_cols=53 Identities=28% Similarity=0.457 Sum_probs=46.0
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 009803 453 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKL 509 (525)
Q Consensus 453 ~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKL 509 (525)
+.|..+|..||+++|.||.++|..| +|+.|||+.+|+|.++|++.+.||+++|
T Consensus 2 ~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~eIa~~l~~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 2 EALQQALAQLPERQREIFLLRYFQG----MSYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp HHHHHHHHCS-HHHHHHHHHHHTS-------HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHC----cCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 5688999999999999999999988 9999999999999999999999999987
No 131
>PRK06930 positive control sigma-like factor; Validated
Probab=98.69 E-value=9e-08 Score=91.00 Aligned_cols=70 Identities=19% Similarity=0.332 Sum_probs=61.8
Q ss_pred HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803 443 EDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 516 (525)
Q Consensus 443 ee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~ 516 (525)
.+..........|..+++.||+++|.||.++|+.| +|++|||+.||+|.++|++++.||+++|+..+...
T Consensus 96 ~~~~~~~e~~~~l~~al~~L~~rer~V~~L~~~eg----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~ 165 (170)
T PRK06930 96 PESVISEWDKIRIEDALSVLTEREKEVYLMHRGYG----LSYSEIADYLNIKKSTVQSMIERAEKKIARQINES 165 (170)
T ss_pred hhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 33344455667899999999999999999999888 99999999999999999999999999999988754
No 132
>PRK00118 putative DNA-binding protein; Validated
Probab=98.48 E-value=8e-07 Score=77.81 Aligned_cols=61 Identities=18% Similarity=0.163 Sum_probs=54.6
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhch
Q 009803 453 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 517 (525)
Q Consensus 453 ~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~ 517 (525)
..+.-....||+++++|+.++|..+ +|..|||+.+|+|+.+|+.++.||+++||+++..-+
T Consensus 9 ~l~d~~~~~L~ekqRevl~L~y~eg----~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~ 69 (104)
T PRK00118 9 LLFDFYGSLLTEKQRNYMELYYLDD----YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLH 69 (104)
T ss_pred HHHHHHhccCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHC
Confidence 3445567899999999999999987 999999999999999999999999999999987643
No 133
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=98.30 E-value=2.2e-06 Score=63.69 Aligned_cols=54 Identities=44% Similarity=0.701 Sum_probs=49.4
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803 453 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510 (525)
Q Consensus 453 ~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR 510 (525)
..+..++..||+.++.++.++|..+ +|..+||+.+|+|..+|+++.+++..+||
T Consensus 2 ~~~~~~~~~l~~~~~~~~~~~~~~~----~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 2 ERLEEALDKLPEREREVILLRFGEG----LSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 3577889999999999999999866 99999999999999999999999988874
No 134
>PRK04217 hypothetical protein; Provisional
Probab=98.12 E-value=6.3e-06 Score=72.92 Aligned_cols=57 Identities=23% Similarity=0.116 Sum_probs=51.6
Q ss_pred HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhh
Q 009803 459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLM 519 (525)
Q Consensus 459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~ 519 (525)
...|++.++++|.++|..+ +|++|||+.||||+.+|++++.+|+++|++.+......
T Consensus 40 ~~~Lt~eereai~l~~~eG----lS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~~~ 96 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEG----LTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGREL 96 (110)
T ss_pred cccCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhccce
Confidence 3579999999999999877 99999999999999999999999999999998765543
No 135
>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=98.10 E-value=8.7e-06 Score=74.72 Aligned_cols=58 Identities=19% Similarity=0.330 Sum_probs=49.8
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhhhhh
Q 009803 460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYA 522 (525)
Q Consensus 460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~~yl 522 (525)
.-||++|++||.+++ .| +|++|||+.||+|+.+|++++++|+++|+.......+-.++
T Consensus 5 ~~Lte~qr~VL~Lr~-~G----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l~~~~ 62 (137)
T TIGR00721 5 TFLTERQIKVLELRE-KG----LSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDFVKFI 62 (137)
T ss_pred CCCCHHHHHHHHHHH-cC----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHHHHHh
Confidence 359999999999964 44 99999999999999999999999999999876665555444
No 136
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=98.03 E-value=1.5e-05 Score=73.56 Aligned_cols=51 Identities=31% Similarity=0.444 Sum_probs=46.3
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803 460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 515 (525)
Q Consensus 460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~ 515 (525)
..|+++|++||.+++ .+ +|++|||+.||+|+.+|++++++|+++||+....
T Consensus 5 ~~Lt~rqreVL~lr~-~G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t 55 (141)
T PRK03975 5 SFLTERQIEVLRLRE-RG----LTQQEIADILGTSRANVSSIEKRARENIEKARET 55 (141)
T ss_pred cCCCHHHHHHHHHHH-cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 469999999999954 55 9999999999999999999999999999987764
No 137
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPro: IPR009042 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....
Probab=98.03 E-value=2.4e-06 Score=61.01 Aligned_cols=31 Identities=42% Similarity=0.553 Sum_probs=28.0
Q ss_pred CHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHH
Q 009803 212 DPLR-YLRATTSSSRLLTANEEMQLSAGIQDLL 243 (525)
Q Consensus 212 d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~ 243 (525)
|+++ ||++| +++||||++||++|+++|+.+.
T Consensus 2 D~l~~Yl~ei-~~~~LLt~eeE~~LA~~i~~g~ 33 (37)
T PF00140_consen 2 DSLRLYLKEI-GRYPLLTAEEEIELARRIRKGD 33 (37)
T ss_dssp HHHHHHHHHH-HHS-EETTHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHH-cCCCCCCHHHHHHHHHHHHHhH
Confidence 7899 99999 9999999999999999999854
No 138
>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=97.98 E-value=3.4e-05 Score=67.18 Aligned_cols=57 Identities=23% Similarity=0.379 Sum_probs=45.0
Q ss_pred HHHHH-hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803 455 LEKVL-DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 515 (525)
Q Consensus 455 L~~aL-~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~ 515 (525)
|.+.. .-|+++|+.++.++|..| +|+.|||+.+|||+..|...++||.++|...-..
T Consensus 10 L~d~Yg~LLT~kQ~~~l~lyy~eD----lSlsEIAe~~~iSRqaV~d~ikr~~~~L~~yE~k 67 (101)
T PF04297_consen 10 LFDFYGELLTEKQREILELYYEED----LSLSEIAEELGISRQAVYDSIKRAEKKLEEYEEK 67 (101)
T ss_dssp HHHHHGGGS-HHHHHHHHHHCTS-------HHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHCCHHHHHHHHHHHccC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 44444 349999999999999888 9999999999999999999999999999876544
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=97.90 E-value=5e-05 Score=69.46 Aligned_cols=62 Identities=11% Similarity=0.205 Sum_probs=55.2
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803 450 FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513 (525)
Q Consensus 450 ~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l 513 (525)
.....|..+|+.|++.+|.||.++|+.. .++|..+||..||+|+.+|+++..+++.+|+..+
T Consensus 71 ~~~~~I~~~l~~Ld~~er~II~~rY~~~--~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~l 132 (134)
T TIGR01636 71 RNRDAIENCLNEADEQTRVIIQELYMKK--RPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEEL 132 (134)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHccC--CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 4556789999999999999999999754 3379999999999999999999999999998764
No 140
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=97.80 E-value=4.9e-05 Score=57.41 Aligned_cols=47 Identities=36% Similarity=0.525 Sum_probs=41.2
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
..|+++|+.|+.+ +..+ +|..|||+.||+|+.+|+++..++++||+.
T Consensus 2 ~~l~~~e~~i~~~-~~~g----~s~~eia~~l~is~~tv~~~~~~~~~kl~~ 48 (58)
T smart00421 2 ASLTPREREVLRL-LAEG----LTNKEIAERLGISEKTVKTHLSNIMRKLGV 48 (58)
T ss_pred CCCCHHHHHHHHH-HHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence 4689999998877 4444 899999999999999999999999998864
No 141
>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=97.78 E-value=8.8e-05 Score=60.87 Aligned_cols=47 Identities=19% Similarity=0.196 Sum_probs=41.1
Q ss_pred HHHHHHhcCCHHHHHHHHHHH-hcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 454 DLEKVLDTLNPRERQVVRWRF-GLEDGRMKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 454 ~L~~aL~~L~~rER~VL~lRy-gl~~g~~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
.+.+-|+.||++.++++.|.+ ..+ +|++|||+.||+|..+|++++++
T Consensus 8 ~~~~~l~~l~~~~r~af~L~R~~eG----lS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 8 KLAERLTWVDSLAEAAAALAREEAG----KTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred hHHHHHhcCCHHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHhc
Confidence 466778999999999999964 455 99999999999999999998775
No 142
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=97.68 E-value=0.0046 Score=70.16 Aligned_cols=32 Identities=34% Similarity=0.583 Sum_probs=30.3
Q ss_pred CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHH
Q 009803 210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDL 242 (525)
Q Consensus 210 ~~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~ 242 (525)
..||++ ||+++ |++||||+|+|+++|++|..+
T Consensus 102 t~DPVRMYLREM-G~V~LLTREgEIeIAKRIE~G 134 (619)
T PRK05658 102 TDDPVRMYLREM-GTVELLTREGEIEIAKRIEAG 134 (619)
T ss_pred CCChHHHHHHHh-ccCcCCCcHHHHHHHHHHHHH
Confidence 479999 99999 999999999999999999975
No 143
>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=97.66 E-value=0.00026 Score=61.57 Aligned_cols=55 Identities=27% Similarity=0.491 Sum_probs=49.4
Q ss_pred HHHHHHHHHhcCC-HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 009803 451 MKEDLEKVLDTLN-PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKL 509 (525)
Q Consensus 451 ~~~~L~~aL~~L~-~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKL 509 (525)
.+..+..+++.|+ +.+|.||.++|..+ ++..+|++.||+|+.++..+..+|++.|
T Consensus 44 ~k~ei~~~I~~l~d~~~r~iL~~~Yi~~----~~~~~I~~~l~~S~~t~yr~~~~Al~~L 99 (100)
T PF07374_consen 44 EKLEIRRAINKLEDPDERLILRMRYINK----LTWEQIAEELNISRRTYYRIHKKALKEL 99 (100)
T ss_pred HHHHHHHHHHHccChhHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence 3456888888886 78999999999976 9999999999999999999999999876
No 144
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=97.66 E-value=0.00019 Score=55.38 Aligned_cols=48 Identities=31% Similarity=0.465 Sum_probs=42.7
Q ss_pred CCHHHHHHHHHHHhcC---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 009803 462 LNPRERQVVRWRFGLE---DGRMKTLQEIGELMGVSRERIRQIESSAFRKL 509 (525)
Q Consensus 462 L~~rER~VL~lRygl~---~g~~~Tl~EIAe~LgIS~erVRqie~RALkKL 509 (525)
|+++|+++|..-|-.| -.+..|+.|||+.||||+.++..++.+|.+||
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 7899999999988664 23568999999999999999999999999987
No 145
>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=97.57 E-value=0.00019 Score=54.26 Aligned_cols=46 Identities=37% Similarity=0.571 Sum_probs=40.2
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803 462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512 (525)
Q Consensus 462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~ 512 (525)
|+++|+.|+.+. ..+ +|.+|||+.+|+|+.+|+++.++++++|+..
T Consensus 1 l~~~e~~i~~~~-~~~----~s~~eia~~l~~s~~tv~~~~~~~~~~l~~~ 46 (57)
T cd06170 1 LTPREREVLRLL-AEG----KTNKEIADILGISEKTVKTHLRNIMRKLGVK 46 (57)
T ss_pred CCHHHHHHHHHH-HcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 689999998874 344 8999999999999999999999999988763
No 146
>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=97.40 E-value=0.00041 Score=53.95 Aligned_cols=47 Identities=26% Similarity=0.354 Sum_probs=39.5
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
..|+++|.+|+.+.. .| +|.+|||+.+|||..+|+.+..+.++||.-
T Consensus 2 ~~LT~~E~~vl~~l~-~G----~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 2 PSLTERELEVLRLLA-QG----MSNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp GSS-HHHHHHHHHHH-TT----S-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred CccCHHHHHHHHHHH-hc----CCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 479999999998754 44 899999999999999999999999999864
No 147
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=97.16 E-value=0.00074 Score=58.06 Aligned_cols=49 Identities=24% Similarity=0.284 Sum_probs=41.7
Q ss_pred HHHHHHH-hcCCHHHHHHHHHHHhcCC---CCCCCHHHHHHHHCCCHHHHHHH
Q 009803 453 EDLEKVL-DTLNPRERQVVRWRFGLED---GRMKTLQEIGELMGVSRERIRQI 501 (525)
Q Consensus 453 ~~L~~aL-~~L~~rER~VL~lRygl~~---g~~~Tl~EIAe~LgIS~erVRqi 501 (525)
+.+..+| ..|+|+|+.+|.+||++-+ ..++|++|||+.+|||+.+|...
T Consensus 23 ~~l~~~l~~lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~ 75 (94)
T TIGR01321 23 DDMQLLLELILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRG 75 (94)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHH
Confidence 4566777 4599999999999999875 45699999999999999999843
No 148
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=97.10 E-value=0.00094 Score=65.72 Aligned_cols=51 Identities=8% Similarity=0.067 Sum_probs=45.7
Q ss_pred HHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 456 EKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 456 ~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
.++...|+++|++|+.+. ..| +|.+|||+.|++|..||+....+.++||.-
T Consensus 138 ~~~~~~LS~RE~eVL~Li-a~G----~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv 188 (217)
T PRK13719 138 LEAKNKVTKYQNDVFILY-SFG----FSHEYIAQLLNITVGSSKNKISEILKFFGI 188 (217)
T ss_pred hhccCCCCHHHHHHHHHH-HCC----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 556789999999999985 455 999999999999999999999999999964
No 149
>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=97.08 E-value=0.00094 Score=66.40 Aligned_cols=51 Identities=29% Similarity=0.490 Sum_probs=44.8
Q ss_pred HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
...|+++|++||.+. ..| +|..|||++||||..||+.++.++++||+..-+
T Consensus 169 ~~~Lt~re~evl~~~-a~G----~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~~ 219 (232)
T TIGR03541 169 AGVLSEREREVLAWT-ALG----RRQADIAAILGISERTVENHLRSARRKLGVATT 219 (232)
T ss_pred hccCCHHHHHHHHHH-HCC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCH
Confidence 347999999999996 444 999999999999999999999999999985433
No 150
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=97.05 E-value=0.0011 Score=64.81 Aligned_cols=46 Identities=17% Similarity=0.258 Sum_probs=41.9
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
.|++||++||.+. ..| +|.+|||+.||+|..||+.+..+.++||.-
T Consensus 137 ~LT~RE~eVL~ll-a~G----~snkeIA~~L~iS~~TVk~h~~~I~~KL~v 182 (207)
T PRK15411 137 SLSRTESSMLRMW-MAG----QGTIQISDQMNIKAKTVSSHKGNIKRKIKT 182 (207)
T ss_pred cCCHHHHHHHHHH-HcC----CCHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence 5999999999985 344 999999999999999999999999999974
No 151
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=97.05 E-value=0.0013 Score=62.59 Aligned_cols=47 Identities=23% Similarity=0.364 Sum_probs=42.3
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
..|+++|++|+.+. ..| +|.+|||+.|++|..||+....+.++||.-
T Consensus 132 ~~LSpRErEVLrLL-AqG----kTnKEIAe~L~IS~rTVkth~srImkKLgV 178 (198)
T PRK15201 132 RHFSVTERHLLKLI-ASG----YHLSETAALLSLSEEQTKSLRRSIMRKLHV 178 (198)
T ss_pred CCCCHHHHHHHHHH-HCC----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 36999999999985 344 999999999999999999999999999965
No 152
>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=97.04 E-value=0.0011 Score=66.76 Aligned_cols=49 Identities=24% Similarity=0.440 Sum_probs=44.0
Q ss_pred HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803 459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512 (525)
Q Consensus 459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~ 512 (525)
+..|+++|++|+.+.. .| +|.+|||++||||..||+....++++||.-.
T Consensus 188 ~~~LT~RE~evl~l~a-~G----~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~ 236 (247)
T TIGR03020 188 AGLITAREAEILAWVR-DG----KTNEEIAAILGISSLTVKNHLQHIFKKLDVR 236 (247)
T ss_pred ccCCCHHHHHHHHHHH-CC----CCHHHHHHHHCcCHHHHHHHHHHHHHHhCCC
Confidence 4579999999999854 55 9999999999999999999999999999753
No 153
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=97.01 E-value=0.0012 Score=63.69 Aligned_cols=46 Identities=28% Similarity=0.299 Sum_probs=41.7
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803 460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510 (525)
Q Consensus 460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR 510 (525)
..|++||++|+.+.- .| +|.+|||+.|+||..||+.+..+.++||-
T Consensus 149 ~~Lt~rE~evl~~~~-~G----~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~ 194 (216)
T PRK10840 149 KRLSPKESEVLRLFA-EG----FLVTEIAKKLNRSIKTISSQKKSAMMKLG 194 (216)
T ss_pred ccCCHHHHHHHHHHH-CC----CCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 459999999999863 34 99999999999999999999999999995
No 154
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=96.99 E-value=0.0014 Score=64.24 Aligned_cols=47 Identities=23% Similarity=0.341 Sum_probs=42.3
Q ss_pred HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803 459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510 (525)
Q Consensus 459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR 510 (525)
...|++||++||.+.- .| +|.+|||+.|+||..||+.+..+.++||.
T Consensus 132 ~~~LT~RE~eVL~ll~-~G----~snkeIA~~L~iS~~TV~~h~~~I~~KLg 178 (207)
T PRK11475 132 SRMLSPTEREILRFMS-RG----YSMPQIAEQLERNIKTIRAHKFNVMSKLG 178 (207)
T ss_pred cCCCCHHHHHHHHHHH-CC----CCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 3469999999999853 44 99999999999999999999999999995
No 155
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=96.96 E-value=0.0021 Score=56.49 Aligned_cols=53 Identities=26% Similarity=0.225 Sum_probs=48.8
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhch
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 517 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~ 517 (525)
.|+..|-+.|+|-+.++ +|.+|-|+.||||+.|+..++..|.+|+-..+-...
T Consensus 41 ~L~~dElEAiRL~D~eg----l~QeeaA~~MgVSR~T~~ril~~ARkKiA~ALv~Gk 93 (106)
T PF02001_consen 41 VLTVDELEAIRLVDYEG----LSQEEAAERMGVSRPTFQRILESARKKIADALVEGK 93 (106)
T ss_pred EeeHHHHHHHHHHHHcC----CCHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHCCC
Confidence 58888999999999988 999999999999999999999999999999886544
No 156
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=96.94 E-value=0.0015 Score=64.33 Aligned_cols=48 Identities=17% Similarity=0.171 Sum_probs=43.7
Q ss_pred HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
+..|+++|++|+.+.+. | +|.+|||+.|++|..||+.+..++++||.-
T Consensus 153 ~~~Lt~rE~~Vl~l~~~-G----~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v 200 (216)
T PRK10100 153 SALLTHREKEILNKLRI-G----ASNNEIARSLFISENTVKTHLYNLFKKIAV 200 (216)
T ss_pred cCCCCHHHHHHHHHHHc-C----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 34699999999999874 5 999999999999999999999999999975
No 157
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=96.90 E-value=0.0018 Score=64.86 Aligned_cols=47 Identities=19% Similarity=0.439 Sum_probs=42.6
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~ 512 (525)
.|++||++||.+- ..| +|..|||++||||..||+.++.++++||--.
T Consensus 179 ~LT~rE~evl~~~-a~G----~t~~eIa~~l~is~~TV~~h~~~~~~KL~~~ 225 (240)
T PRK10188 179 NFSKREKEILKWT-AEG----KTSAEIAMILSISENTVNFHQKNMQKKFNAP 225 (240)
T ss_pred CCCHHHHHHHHHH-HcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 5999999999987 344 9999999999999999999999999999643
No 158
>PRK13870 transcriptional regulator TraR; Provisional
Probab=96.90 E-value=0.0017 Score=64.81 Aligned_cols=47 Identities=28% Similarity=0.556 Sum_probs=41.8
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~ 512 (525)
.|++||++||.+- ..| +|..|||.+||||..||..++.+|++||--.
T Consensus 173 ~LT~RE~E~L~W~-A~G----KT~~EIa~ILgISe~TV~~Hl~na~~KLga~ 219 (234)
T PRK13870 173 WLDPKEATYLRWI-AVG----KTMEEIADVEGVKYNSVRVKLREAMKRFDVR 219 (234)
T ss_pred CCCHHHHHHHHHH-HcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence 5999999999875 333 9999999999999999999999999999543
No 159
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=96.87 E-value=0.0017 Score=63.67 Aligned_cols=47 Identities=30% Similarity=0.393 Sum_probs=42.3
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
..|++||++|+++- ..| +|.+|||+.|++|..||+.+.++.++||.-
T Consensus 147 ~~LT~RE~eVL~ll-a~G----~snkeIA~~L~iS~~TVk~h~~~i~~KL~v 193 (211)
T COG2197 147 ELLTPRELEVLRLL-AEG----LSNKEIAEELNLSEKTVKTHVSNILRKLGV 193 (211)
T ss_pred CCCCHHHHHHHHHH-HCC----CCHHHHHHHHCCCHhHHHHHHHHHHHHcCC
Confidence 47999999999884 444 999999999999999999999999999964
No 160
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=96.83 E-value=0.0015 Score=48.36 Aligned_cols=41 Identities=22% Similarity=0.337 Sum_probs=23.6
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
..|++.||..|...+-.| +|..+||+.||+|++||...+.|
T Consensus 3 ~~Lt~~eR~~I~~l~~~G----~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG----MSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHHHHCS-------HHHHHHHTT--HHHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC----CCHHHHHHHHCcCcHHHHHHHhc
Confidence 468999999998777555 99999999999999999987765
No 161
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=96.79 E-value=0.0031 Score=61.98 Aligned_cols=53 Identities=23% Similarity=0.351 Sum_probs=46.3
Q ss_pred cCCHHHHHHHHHHHhcC---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803 461 TLNPRERQVVRWRFGLE---DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~---~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l 513 (525)
.|+++|++||+.-|-.| -.+..|++|||+.||||+.++.+++++|.+||=..+
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~~~ 210 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIEAY 210 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 69999999999998765 235589999999999999999999999999996543
No 162
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=96.71 E-value=0.0081 Score=57.97 Aligned_cols=64 Identities=20% Similarity=0.288 Sum_probs=54.0
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhh
Q 009803 451 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLM 519 (525)
Q Consensus 451 ~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~ 519 (525)
....+...+++|++|||+|+..-- .| +..++||..||||.-||..+..+.++|++...-..-++
T Consensus 132 ~~~~~~~~l~tLT~RERqVl~~vV-~G----~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~SlaeLvr 195 (202)
T COG4566 132 RQAAIRARLATLTPRERQVLDLVV-RG----LMNKQIAFDLGISERTVELHRANVMEKMQARSLAELVR 195 (202)
T ss_pred HHHHHHHHHHhcCHHHHHHHHHHH-cC----cccHHHHHHcCCchhhHHHHHHHHHHHHhhccHHHHHH
Confidence 446788899999999999998764 45 89999999999999999999999999998755444443
No 163
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=96.70 E-value=0.0034 Score=54.33 Aligned_cols=49 Identities=20% Similarity=0.239 Sum_probs=44.1
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803 460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512 (525)
Q Consensus 460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~ 512 (525)
.-|+.+|+..+.++|..| +|+.|||+.++||+..|...+.|+-+.|-..
T Consensus 16 sLLT~KQ~~Y~~lyy~dD----lSl~EIAee~~VSRqAIyDnIKr~~~~L~~Y 64 (105)
T COG2739 16 SLLTKKQKNYLELYYLDD----LSLSEIAEEFNVSRQAIYDNIKRTEKILEDY 64 (105)
T ss_pred HHHhHHHHHHHHHHHHhh----ccHHHHHHHhCccHHHHHHHHHHHHHHHHHH
Confidence 458999999999999988 9999999999999999999999987776543
No 164
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=96.70 E-value=0.0037 Score=57.95 Aligned_cols=47 Identities=28% Similarity=0.397 Sum_probs=42.3
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
..|+++|++||.+ +..+ +|.+|||+.+++|..||+.+..++++||.-
T Consensus 148 ~~lt~~e~~vl~l-~~~g----~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~ 194 (211)
T PRK15369 148 PLLTPRERQILKL-ITEG----YTNRDIAEQLSISIKTVETHRLNMMRKLDV 194 (211)
T ss_pred cCCCHHHHHHHHH-HHCC----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 4599999999998 5555 899999999999999999999999999963
No 165
>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family. This model represents a family of phage proteins, including ArpU, called a putative autolysin regulatory protein. ArpU was described as a regulator of cellular muramidase-2 of Enterococcus hirae but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors. We propose that this is a phage transcriptional activator family.
Probab=96.66 E-value=0.012 Score=53.41 Aligned_cols=63 Identities=16% Similarity=0.142 Sum_probs=54.1
Q ss_pred HHHHHHHHHH-hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 450 FMKEDLEKVL-DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 450 ~~~~~L~~aL-~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
.....+..++ +.|++.+|+||.++|...++ ++..+|+..||+|+.+...+..+|+.++-..+.
T Consensus 67 ~~~~~i~~ai~~~l~~~~r~Il~~~Yl~~~~--~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~l~ 130 (132)
T TIGR01637 67 QEARAIVNAIVNQLDEISRQILYDKYLEPDQ--KYDYQIMMELGYSHRQYYRIKKRALLRFATLYG 130 (132)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHcCccc--cchHHHHHHhCCcHHHHHHHHHHHHHHHHHHhC
Confidence 3445677777 99999999999999987333 899999999999999999999999999987654
No 166
>PRK09483 response regulator; Provisional
Probab=96.62 E-value=0.0037 Score=59.31 Aligned_cols=46 Identities=24% Similarity=0.336 Sum_probs=41.3
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803 460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510 (525)
Q Consensus 460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR 510 (525)
..|+++|++||.+. ..| +|.+|||+.|++|..||+.+.++.++||-
T Consensus 147 ~~Lt~rE~~vl~~~-~~G----~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~ 192 (217)
T PRK09483 147 ASLSERELQIMLMI-TKG----QKVNEISEQLNLSPKTVNSYRYRMFSKLN 192 (217)
T ss_pred cccCHHHHHHHHHH-HCC----CCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 46999999999874 344 99999999999999999999999999994
No 167
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=96.60 E-value=0.007 Score=47.11 Aligned_cols=50 Identities=34% Similarity=0.566 Sum_probs=42.7
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
..|+++|.+|+.+.- .+ +|..|||..+|+|..+|+....+.++||.-.-+
T Consensus 3 ~~Lt~rE~~v~~l~~-~G----~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~~r 52 (65)
T COG2771 3 ADLTPREREILRLVA-QG----KSNKEIARILGISEETVKTHLRNIYRKLGVKNR 52 (65)
T ss_pred ccCCHHHHHHHHHHH-CC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCH
Confidence 368999999997753 33 899999999999999999999999999975443
No 168
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=96.46 E-value=0.068 Score=55.82 Aligned_cols=159 Identities=11% Similarity=0.057 Sum_probs=99.0
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccch
Q 009803 288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHM 367 (525)
Q Consensus 288 e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~ 367 (525)
+..+..-.+-++.---+|+++-.-.|+.+||+|+..++.-.+=-|-+. -..|.+..-|+.-++.++++.+.-..|.+.
T Consensus 8 e~~~r~~~~r~~a~L~r~~rd~dlAEEa~~dA~~~Ale~WPr~G~P~~--PaAWL~~v~R~~aiD~~Rr~~~~~~~~~el 85 (415)
T COG4941 8 EAAARIERPRAMAALARYLRDLDLAEEALQDAFAAALERWPRAGPPRN--PAAWLIAVGRNRAIDRVRRRARRDAAPPEL 85 (415)
T ss_pred HHHHHHhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHhCcccCCCCC--hHHHHHHHHhhhHHHHHHHHHHhccCChhh
Confidence 344444444444444556666556899999999877666655444332 467888888999999888776532222110
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHH
Q 009803 368 VEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLI 447 (525)
Q Consensus 368 ~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~ 447 (525)
.++.+ |......+. +++...
T Consensus 86 -----------------------------------------------~~~~e-----~~e~~~a~~--------~~d~~i 105 (415)
T COG4941 86 -----------------------------------------------LLSDE-----DEEMEEAEA--------LDDEHI 105 (415)
T ss_pred -----------------------------------------------ccccc-----chhhhcccc--------cccccc
Confidence 00000 000000000 011111
Q ss_pred HHHHHHHHHHHH-hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803 448 KKFMKEDLEKVL-DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512 (525)
Q Consensus 448 ~~~~~~~L~~aL-~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~ 512 (525)
.++....|--|- -.|++.+|--|.+|...| +|..|||..|=|+..++-|++.||.++++..
T Consensus 106 ~Dd~LRLiFvccHPal~~~~riALtLR~v~G----Ls~~eIArAFLv~e~am~QRivRAK~ri~~a 167 (415)
T COG4941 106 RDDRLRLIFVCCHPALPPEQRIALTLRLVGG----LSTAEIARAFLVPEAAMAQRIVRAKARIREA 167 (415)
T ss_pred chhhHHhhhhhcCCCCChhhHHHHHHHHHcC----CcHHHHHHHHcCCcHHHHHHHHHHHHHHHhc
Confidence 111122222222 469999999999998876 9999999999999999999999999999873
No 169
>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=96.34 E-value=0.0048 Score=42.72 Aligned_cols=27 Identities=30% Similarity=0.559 Sum_probs=21.4
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 481 MKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 481 ~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
|+|.+|||+.+|+|+++|+ |++++|++
T Consensus 2 ~mtr~diA~~lG~t~ETVS----R~l~~l~~ 28 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVS----RILKKLER 28 (32)
T ss_dssp E--HHHHHHHHTS-HHHHH----HHHHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHH----HHHHHHHH
Confidence 4899999999999999999 77888875
No 170
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=96.27 E-value=0.012 Score=54.22 Aligned_cols=56 Identities=18% Similarity=0.243 Sum_probs=47.5
Q ss_pred HHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 454 DLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 454 ~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
.+...+..|+++|++|+.+ +..+ ++.++||+.+|+|..+|+....++++||+..-.
T Consensus 134 ~~~~~~~~l~~~e~~vl~~-~~~~----~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~~~ 189 (202)
T PRK09390 134 DIRARIASLSERERQVMDG-LVAG----LSNKVIARDLDISPRTVEVYRANVMTKMQAGSL 189 (202)
T ss_pred HHHHHHHhhhhhHHHHHHH-HHcc----CchHHHHHHcCCCHHHHHHHHHHHHHHHccccH
Confidence 3556678899999999996 4444 899999999999999999999999999975443
No 171
>PRK10651 transcriptional regulator NarL; Provisional
Probab=96.20 E-value=0.0088 Score=56.11 Aligned_cols=47 Identities=17% Similarity=0.329 Sum_probs=41.8
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
..|+++|++|+.+. ..+ ++.++||+.+++|..||+.+..+.++||.-
T Consensus 154 ~~Lt~rE~~vl~~l-~~g----~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~ 200 (216)
T PRK10651 154 NQLTPRERDILKLI-AQG----LPNKMIARRLDITESTVKVHVKHMLKKMKL 200 (216)
T ss_pred ccCCHHHHHHHHHH-HcC----CCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 45999999999984 344 899999999999999999999999999964
No 172
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=96.09 E-value=0.017 Score=49.63 Aligned_cols=53 Identities=23% Similarity=0.166 Sum_probs=47.5
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhch
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 517 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~ 517 (525)
.|+..|-+.|+|...++ +|.+|-|..||||+.|+-..+..|++|+-.++-...
T Consensus 33 ~lt~eElEAlRLvD~~~----l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~aLveGk 85 (99)
T COG1342 33 ILTIEELEALRLVDYEG----LTQEEAALRMGISRQTFWRLLTSARKKVADALVEGK 85 (99)
T ss_pred eecHHHHHHHHHHhHhh----ccHHHHHHHhcccHHHHHHHHHHHHHHHHHHHhcCC
Confidence 46777888999999988 999999999999999999999999999998886543
No 173
>PRK01381 Trp operon repressor; Provisional
Probab=96.02 E-value=0.0088 Score=51.91 Aligned_cols=48 Identities=23% Similarity=0.285 Sum_probs=39.7
Q ss_pred HHHHHHHHhc-CCHHHHHHHHHHHhcCC---CCCCCHHHHHHHHCCCHHHHH
Q 009803 452 KEDLEKVLDT-LNPRERQVVRWRFGLED---GRMKTLQEIGELMGVSRERIR 499 (525)
Q Consensus 452 ~~~L~~aL~~-L~~rER~VL~lRygl~~---g~~~Tl~EIAe~LgIS~erVR 499 (525)
...+..+|.. |+|+|+..|..||+.-. ...+|+.||++.+|||..+|.
T Consensus 22 ~~~~~~~l~~llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTIT 73 (99)
T PRK01381 22 EDLHLPLLTLLLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATIT 73 (99)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeeh
Confidence 3456667765 99999999999998753 234999999999999999887
No 174
>PRK13558 bacterio-opsin activator; Provisional
Probab=95.46 E-value=0.028 Score=63.67 Aligned_cols=53 Identities=26% Similarity=0.228 Sum_probs=45.7
Q ss_pred HhcCCHHHHHHHHHHHhcC---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 459 LDTLNPRERQVVRWRFGLE---DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 459 L~~L~~rER~VL~lRygl~---~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
...|+++|+++|..-|..| -.+.-|++|||+.||||+.|+.+++++|.+||=.
T Consensus 605 ~~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l~~ 660 (665)
T PRK13558 605 ENDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKLVG 660 (665)
T ss_pred hhhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4689999999999999876 1122399999999999999999999999999854
No 175
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=95.32 E-value=0.017 Score=51.97 Aligned_cols=50 Identities=22% Similarity=0.326 Sum_probs=43.6
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 515 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~ 515 (525)
-|+++|-.||.||- .| .|.+|||++||-|+..|+-++.+|+.++.+.-+.
T Consensus 8 flte~qikvl~lRe-kG----~tQ~eIA~~L~TTraNvSaIEkrA~enIekarnT 57 (143)
T COG1356 8 FLTEQQIKVLVLRE-KG----LTQSEIARILKTTRANVSAIEKRALENIEKARNT 57 (143)
T ss_pred eeehhheeeeehhh-cc----ccHHHHHHHHccchhhHHHHHHHHHHHHHHHHHH
Confidence 38889999999994 23 8999999999999999999999999999876543
No 176
>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=95.12 E-value=0.034 Score=44.71 Aligned_cols=45 Identities=22% Similarity=0.457 Sum_probs=30.0
Q ss_pred HhcCCHHHHHHHHH--HHhcCCCCCCCHHHHHHHHCCC-HHHHHHHHH
Q 009803 459 LDTLNPRERQVVRW--RFGLEDGRMKTLQEIGELMGVS-RERIRQIES 503 (525)
Q Consensus 459 L~~L~~rER~VL~l--Rygl~~g~~~Tl~EIAe~LgIS-~erVRqie~ 503 (525)
|..|+++|++||.. .|....|-|-|+.|||+.||++ ..+|.+.+.
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 46799999999875 3555567778999999999996 999986543
No 177
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=95.11 E-value=0.058 Score=41.33 Aligned_cols=49 Identities=14% Similarity=0.176 Sum_probs=42.1
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~ 512 (525)
+|+..++-++.+.|.-.+ .|++.||..+|||+++|.++.+..+.-|...
T Consensus 2 kLs~~d~lll~L~~LR~~---~~~~~La~~FgIs~stvsri~~~~~~~L~~~ 50 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYLRLN---LTFQDLAYRFGISQSTVSRIFHEWIPLLYQV 50 (53)
T ss_pred CCCHHHHHHHHHHHHHcC---CcHhHHhhheeecHHHHHHHHHHHHHHHHHh
Confidence 588888888888776654 8999999999999999999999888877654
No 178
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=95.05 E-value=0.046 Score=50.92 Aligned_cols=49 Identities=27% Similarity=0.323 Sum_probs=42.5
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803 460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513 (525)
Q Consensus 460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l 513 (525)
..|+++|++|+.+.. .+ +|.++||+.+++|..+|+.+..+.++||.-.-
T Consensus 136 ~~Lt~~E~~il~~l~-~g----~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~~~~ 184 (196)
T PRK10360 136 DPLTKRERQVAEKLA-QG----MAVKEIAAELGLSPKTVHVHRANLMEKLGVSN 184 (196)
T ss_pred cCCCHHHHHHHHHHH-CC----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC
Confidence 469999999999854 34 89999999999999999999999999986433
No 179
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=95.05 E-value=0.048 Score=51.06 Aligned_cols=46 Identities=22% Similarity=0.304 Sum_probs=39.1
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
.|+++|..|+.+ +..+ +|.+|||+.|++|..||+.+..++++||.-
T Consensus 149 ~lt~re~~vl~~-l~~g----~s~~eIa~~l~~s~~tv~~~~~~~~~kl~~ 194 (210)
T PRK09935 149 VLSNREVTILRY-LVSG----LSNKEIADQLLLSNKTVSAHKSNIYGKLGL 194 (210)
T ss_pred cCCHHHHHHHHH-HHcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 488888888764 3344 999999999999999999999999999953
No 180
>PRK10403 transcriptional regulator NarP; Provisional
Probab=94.99 E-value=0.047 Score=50.99 Aligned_cols=49 Identities=18% Similarity=0.271 Sum_probs=42.2
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803 460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513 (525)
Q Consensus 460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l 513 (525)
..|+++|.+|+.+. ..+ +|.++||+.+|+|..||+.+..+.++||.-.-
T Consensus 152 ~~Lt~~e~~vl~~~-~~g----~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~~ 200 (215)
T PRK10403 152 SVLTERELDVLHEL-AQG----LSNKQIASVLNISEQTVKVHIRNLLRKLNVRS 200 (215)
T ss_pred ccCCHHHHHHHHHH-HCC----CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCC
Confidence 35999999999865 344 99999999999999999999999999995433
No 181
>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=94.95 E-value=0.081 Score=39.24 Aligned_cols=40 Identities=20% Similarity=0.343 Sum_probs=28.4
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
|++.++.||..-+-.+ ..|..|||+.+|+|..+|++++.+
T Consensus 1 l~~~~~~Il~~l~~~~---~~t~~ela~~~~is~~tv~~~l~~ 40 (48)
T PF13412_consen 1 LDETQRKILNYLRENP---RITQKELAEKLGISRSTVNRYLKK 40 (48)
T ss_dssp --HHHHHHHHHHHHCT---TS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHcC---CCCHHHHHHHhCCCHHHHHHHHHH
Confidence 5778888887665422 399999999999999999965543
No 182
>PRK15320 transcriptional activator SprB; Provisional
Probab=94.90 E-value=0.053 Score=52.78 Aligned_cols=66 Identities=11% Similarity=0.088 Sum_probs=48.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 440 ETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 440 ~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
++|++.+..-.. -....+--.|+++|.+|+.+-- .| +|.+|||+.|++|..||+....+.+.||.-
T Consensus 144 ~~~~~~~~~~~~-~~~~~~~~~LSdREIEVL~LLA-kG----~SNKEIAekL~LS~KTVSTYKnRLLeKLgA 209 (251)
T PRK15320 144 ETPEEVLFNINQ-YAWWNLPPGVTQAKYALLILLS-SG----HPAIELAKKFGLGTKTVSIYRKKVMYRLGM 209 (251)
T ss_pred CChHHHhhhccc-eeeecCCCCCCHHHHHHHHHHH-cC----CCHHHHHHHhccchhhHHHHHHHHHHHcCC
Confidence 466665433111 1122233578999999988752 33 999999999999999999999999999863
No 183
>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=94.81 E-value=0.16 Score=46.39 Aligned_cols=51 Identities=22% Similarity=0.433 Sum_probs=43.6
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 452 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 452 ~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
+..|..+++.|.+.++.||.+||+...+ +|..+||..|+||..+++.....
T Consensus 72 k~~id~~~~~l~de~k~Ii~lry~~r~~--~TW~~IA~~l~i~erta~r~~~~ 122 (130)
T PF05263_consen 72 KEAIDRWLETLIDEEKRIIKLRYDRRSR--RTWYQIAQKLHISERTARRWRDR 122 (130)
T ss_pred HHHHHHHHHhhCHHHHHHHHHHHccccc--chHHHHHHHhCccHHHHHHHHHH
Confidence 4567778899999999999999986644 99999999999999999865544
No 184
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=94.41 E-value=0.046 Score=40.79 Aligned_cols=32 Identities=22% Similarity=0.276 Sum_probs=21.8
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 009803 469 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSA 505 (525)
Q Consensus 469 VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RA 505 (525)
||.+.. .+ +|..+||+.||||+.+|+++..+-
T Consensus 10 ii~l~~-~G----~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 10 IIRLLR-EG----WSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp HHHHHH-HT------HHHHHHHHTS-HHHHHHHHT--
T ss_pred HHHHHH-CC----CCHHHHHHHHCcCHHHHHHHHHHc
Confidence 555544 34 999999999999999999887653
No 185
>PRK04841 transcriptional regulator MalT; Provisional
Probab=94.32 E-value=0.071 Score=62.42 Aligned_cols=47 Identities=21% Similarity=0.257 Sum_probs=42.3
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
..|+++|++|+.+.. .| +|.+|||+.|+||..||+.++++.++||.-
T Consensus 837 ~~lt~~e~~v~~~~~-~g----~~~~~ia~~l~~s~~tv~~h~~~~~~kl~v 883 (903)
T PRK04841 837 SPLTQREWQVLGLIY-SG----YSNEQIAGELDVAATTIKTHIRNLYQKLGI 883 (903)
T ss_pred CCCCHHHHHHHHHHH-cC----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 359999999999854 44 999999999999999999999999999964
No 186
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=94.31 E-value=0.095 Score=49.08 Aligned_cols=47 Identities=30% Similarity=0.398 Sum_probs=41.2
Q ss_pred HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803 459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510 (525)
Q Consensus 459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR 510 (525)
+..|+++|++|+.+.. .+ .|.++||+.+++|..||+....+.++||.
T Consensus 141 ~~~lt~~E~~vl~~l~-~g----~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~ 187 (204)
T PRK09958 141 LDSLSKQEISVMRYIL-DG----KDNNDIAEKMFISNKTVSTYKSRLMEKLE 187 (204)
T ss_pred cccCCHHHHHHHHHHH-cC----CCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 3569999999998754 33 79999999999999999999999999994
No 187
>PF12645 HTH_16: Helix-turn-helix domain; InterPro: IPR024760 This domain appears to be a helix-turn-helix domain, suggesting a transcriptional regulatory protein. Some proteins with this domain are annotated as conjugative transposon proteins.
Probab=94.22 E-value=0.19 Score=40.39 Aligned_cols=56 Identities=14% Similarity=0.132 Sum_probs=46.0
Q ss_pred HHHHHhccHHHHHHHHHHHHHHHHHHHHHhh----C--CCCCHHHHHHHHHHHHHHhhhhcC
Q 009803 276 LRRRLNYGILCKDKMITSNIRLVISIAKNYQ----G--AGMNLQDLVQEGCRGLVRGAEKFD 331 (525)
Q Consensus 276 L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~----~--~g~~~eDLIQEG~lGLirAiekFD 331 (525)
+.++.+||..|.++++..|.+++.+.+.+-. + ++.-=+|+-|+-...|++++.+|+
T Consensus 4 I~~A~~GD~~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~ 65 (65)
T PF12645_consen 4 IKAAKQGDPEAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE 65 (65)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence 4556678899999999999999999988722 2 233338999999999999999996
No 188
>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 993W gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator. GpQ positively regulates expression of the phage late gene operons. Bacterial host RNA polymerase modified by antitermination proteins transcribes through termination sites that otherwise prevent expression of the regulated genes [, ].; GO: 0003677 DNA binding, 0060567 negative regulation of transcription termination, DNA-dependent
Probab=93.98 E-value=0.32 Score=43.99 Aligned_cols=52 Identities=15% Similarity=0.136 Sum_probs=47.6
Q ss_pred HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
|..-.+.+-.+|.++|..+ +|...||..+++|...||+...+|-..+..++.
T Consensus 60 L~~~~~~~~~ll~~~Yv~g----~s~r~IA~~~~~s~~~ir~~l~~ae~~i~g~l~ 111 (125)
T PF06530_consen 60 LKKRDPEEYDLLILYYVYG----WSKRQIARKLKCSEGKIRKRLQRAEGFIDGCLS 111 (125)
T ss_pred HHccCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHhhhhHhhhhH
Confidence 4557889999999999988 999999999999999999999999999988764
No 189
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=93.91 E-value=0.19 Score=36.90 Aligned_cols=40 Identities=20% Similarity=0.321 Sum_probs=26.9
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
|++-.+.||..--.. ...|+.+||+.+|+|..+|.+++.+
T Consensus 1 lD~~D~~Il~~Lq~d---~r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 1 LDELDRKILRLLQED---GRRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp --HHHHHHHHHHHH----TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHc---CCccHHHHHHHHCcCHHHHHHHHHH
Confidence 355667777765432 2399999999999999999976654
No 190
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=93.87 E-value=0.087 Score=55.12 Aligned_cols=36 Identities=19% Similarity=0.364 Sum_probs=32.0
Q ss_pred HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 009803 468 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR 507 (525)
Q Consensus 468 ~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALk 507 (525)
+|-.|+|..+ +|.+|||++|||||.+|.+++.+|++
T Consensus 20 ~vA~lYY~~g----~tQ~eIA~~lgiSR~~VsRlL~~Ar~ 55 (318)
T PRK15418 20 RIAWFYYHDG----LTQSEIGERLGLTRLKVSRLLEKGRQ 55 (318)
T ss_pred HHHHHHHhcC----CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4667888776 99999999999999999999999876
No 191
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=93.66 E-value=0.14 Score=40.64 Aligned_cols=35 Identities=26% Similarity=0.301 Sum_probs=26.7
Q ss_pred HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 468 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 468 ~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
..+.++.-.+|. +++.+||+.||||..+||....+
T Consensus 11 kA~e~y~~~~g~--i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 11 KAFEIYKESNGK--IKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred HHHHHHHHhCCC--ccHHHHHHHHCCCHHHHHHHhhh
Confidence 455555444433 99999999999999999987554
No 192
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=93.61 E-value=0.17 Score=33.29 Aligned_cols=36 Identities=25% Similarity=0.420 Sum_probs=27.4
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHH
Q 009803 462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQI 501 (525)
Q Consensus 462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqi 501 (525)
+++.++..+...|..+ .|..+|++.+|+|+.+|..+
T Consensus 6 ~~~~~~~~i~~~~~~~----~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 6 LTPEQIEEARRLLAAG----ESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHh
Confidence 4555666565555443 79999999999999999865
No 193
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=93.37 E-value=0.24 Score=44.19 Aligned_cols=49 Identities=20% Similarity=0.337 Sum_probs=41.3
Q ss_pred HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
+..|++.+..-|... ....| +++|+++.||||..|||.++.+.+++|.-
T Consensus 31 ~~~L~~E~~~Fi~~F-i~~rG---nlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 31 FARLSPEQLEFIKLF-IKNRG---NLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred hhcCCHHHHHHHHHH-HHhcC---CHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 678998887776654 44444 99999999999999999999999999975
No 194
>PF13730 HTH_36: Helix-turn-helix domain
Probab=93.33 E-value=0.34 Score=36.78 Aligned_cols=47 Identities=21% Similarity=0.435 Sum_probs=33.5
Q ss_pred cCCHHHHHHHHHHHhc--CCCCC-CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 461 TLNPRERQVVRWRFGL--EDGRM-KTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 461 ~L~~rER~VL~lRygl--~~g~~-~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
.|++.++.|+..-.-. +++.. .|.+.||+.+|+|+.||+ ++++.|.+
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~----~~i~~L~~ 51 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQ----RAIKELEE 51 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 5788888776543322 22223 389999999999999999 67777764
No 195
>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=93.32 E-value=0.18 Score=43.01 Aligned_cols=38 Identities=26% Similarity=0.351 Sum_probs=29.8
Q ss_pred HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803 459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE 502 (525)
Q Consensus 459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie 502 (525)
++.|++| ..|+.+. ..+ +|..+||+.+|||+.||..+.
T Consensus 34 ~~~Ls~R-~~I~~ll-~~G----~S~~eIA~~LgISrsTIyRi~ 71 (88)
T TIGR02531 34 IQSLAQR-LQVAKML-KQG----KTYSDIEAETGASTATISRVK 71 (88)
T ss_pred HHhhhHH-HHHHHHH-HCC----CCHHHHHHHHCcCHHHHHHHH
Confidence 3468888 7777763 222 899999999999999999733
No 196
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=93.10 E-value=0.13 Score=38.06 Aligned_cols=32 Identities=19% Similarity=0.250 Sum_probs=22.0
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803 466 ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE 502 (525)
Q Consensus 466 ER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie 502 (525)
..+|+.|+ -.+ +|..+||+.+|||+.||..++
T Consensus 11 ~~~i~~l~-~~G----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 11 IEEIKELY-AEG----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp HHHHHHHH-HTT------HHHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHHH-HCC----CCHHHHHHHHCcCHHHHHHHH
Confidence 34566654 333 999999999999999999765
No 197
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=93.05 E-value=1 Score=48.10 Aligned_cols=126 Identities=21% Similarity=0.188 Sum_probs=70.6
Q ss_pred HHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHH-HHH
Q 009803 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEG-CRG 322 (525)
Q Consensus 244 ~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG-~lG 322 (525)
++.+...+|...+|+.||..+.|...|++...+...+... .. ..++++.+.++ -..
T Consensus 217 ~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~-------------------~~----~~SLd~~~~~~~~~~ 273 (367)
T PRK09210 217 KLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIA-------------------QE----PVSLETPIGEEDDSH 273 (367)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHh-------------------cC----CCCcCCCCCCCCcch
Confidence 3455667788889999999999999999987665432211 10 11111111100 001
Q ss_pred HHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHHHHHHHHHHHc----CCCCCHHHHHHHc
Q 009803 323 LVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSEN----GRHPNNEEVAEAT 398 (525)
Q Consensus 323 LirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~l----gr~Pt~eEIA~~l 398 (525)
|..-+. |+.............++..+.+++.. +|..-.. -+.... |.+-|.+|||+.+
T Consensus 274 l~d~i~--d~~~~~p~~~~~~~~~~~~l~~~l~~------L~~rEr~----------Vl~lrygl~~~~~~tl~EIa~~l 335 (367)
T PRK09210 274 LGDFIE--DQDATSPADHAAYELLKEQLEDVLDT------LTDREEN----------VLRLRFGLDDGRTRTLEEVGKVF 335 (367)
T ss_pred hhhhcc--CCCCCCHHHHHHHHHHHHHHHHHHHh------CCHHHHH----------HHHHHhccCCCCCccHHHHHHHH
Confidence 111111 11222234445566667777766642 3322111 112222 3677999999999
Q ss_pred CCCHHHHHHHHh
Q 009803 399 GLSMKRLHAVLL 410 (525)
Q Consensus 399 gis~~~v~~~l~ 410 (525)
|+|.++|+++..
T Consensus 336 gvs~erVrQi~~ 347 (367)
T PRK09210 336 GVTRERIRQIEA 347 (367)
T ss_pred CCCHHHHHHHHH
Confidence 999999998853
No 198
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=92.90 E-value=1.4 Score=43.70 Aligned_cols=34 Identities=24% Similarity=0.332 Sum_probs=27.5
Q ss_pred HHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHH
Q 009803 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR 278 (525)
Q Consensus 245 le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~ 278 (525)
+.+....|....|++||..+.|...|++.+.+..
T Consensus 89 ~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~ 122 (238)
T TIGR02393 89 LIKAERQLTQELGREPTDEELAERMGMPAEKVRE 122 (238)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 4455677788899999999999999999876543
No 199
>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=92.84 E-value=0.26 Score=37.41 Aligned_cols=41 Identities=29% Similarity=0.501 Sum_probs=28.9
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 465 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 465 rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
|++.||.+-+-. +.+.|.+|||+.||||+.||+ +-++.|+.
T Consensus 1 R~~~il~~L~~~--~~~it~~eLa~~l~vS~rTi~----~~i~~L~~ 41 (55)
T PF08279_consen 1 RQKQILKLLLES--KEPITAKELAEELGVSRRTIR----RDIKELRE 41 (55)
T ss_dssp HHHHHHHHHHHT--TTSBEHHHHHHHCTS-HHHHH----HHHHHHHH
T ss_pred CHHHHHHHHHHc--CCCcCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 456677664333 334999999999999999999 45555554
No 200
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=92.84 E-value=1.2 Score=49.57 Aligned_cols=126 Identities=16% Similarity=0.219 Sum_probs=69.0
Q ss_pred HHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHH-HHHH
Q 009803 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQE-GCRG 322 (525)
Q Consensus 244 ~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQE-G~lG 322 (525)
++.+.+.+|...+|+.||..+.|...|++.+.+...+.. ....+++++.+.+ +...
T Consensus 359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~-----------------------~~~~~SLD~~i~~d~~~~ 415 (509)
T PRK05901 359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKY-----------------------NREPISLDKTIGKEGDSQ 415 (509)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh-----------------------cCCCcccccccccCCccc
Confidence 455667888888999999999999999987665433211 1111222222211 1111
Q ss_pred HHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHHHHHHHHHHHc----CCCCCHHHHHHHc
Q 009803 323 LVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSEN----GRHPNNEEVAEAT 398 (525)
Q Consensus 323 LirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~l----gr~Pt~eEIA~~l 398 (525)
+...+. |+........+..+..+..+..++.. +|..-. .-+.... +.+-|..|||+.+
T Consensus 416 l~d~l~--D~~~~~p~~~~~~~~l~~~L~~aL~~------L~eREr----------~VI~lRyGL~~~e~~TL~EIa~~l 477 (509)
T PRK05901 416 FGDFIE--DSEAVSPVDAVSFTLLQDQLQEVLET------LSEREA----------GVIRMRFGLTDGQPKTLDEIGQVY 477 (509)
T ss_pred HHHhcc--CCCCCCHHHHHHHHHHHHHHHHHHhh------CCHHHH----------HHHHHHhhccCCCCCCHHHHHHHH
Confidence 111111 11111223334444555555555532 222211 1112223 4567999999999
Q ss_pred CCCHHHHHHHHh
Q 009803 399 GLSMKRLHAVLL 410 (525)
Q Consensus 399 gis~~~v~~~l~ 410 (525)
|+|.++|+++..
T Consensus 478 GVSrERVRQIe~ 489 (509)
T PRK05901 478 GVTRERIRQIES 489 (509)
T ss_pred CCCHHHHHHHHH
Confidence 999999999853
No 201
>PHA00675 hypothetical protein
Probab=92.44 E-value=0.28 Score=40.60 Aligned_cols=40 Identities=18% Similarity=0.085 Sum_probs=32.0
Q ss_pred hcCCHHHHHHHHHHH-hcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803 460 DTLNPRERQVVRWRF-GLEDGRMKTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 460 ~~L~~rER~VL~lRy-gl~~g~~~Tl~EIAe~LgIS~erVRqie~ 503 (525)
..|++.+-+.|+.++ -.+ .|+.+||..||||+++|.+|..
T Consensus 21 AKLt~~qV~~IR~l~~r~G----~s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 21 AKLTDAEVERIRELHEVEG----MSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred cccCHHHHHHHHHHHHhcC----ccHHHHHHHhCCCHHHHHHHHc
Confidence 467777777677666 444 7999999999999999998864
No 202
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=92.02 E-value=2.1 Score=44.96 Aligned_cols=35 Identities=20% Similarity=0.368 Sum_probs=28.7
Q ss_pred HHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHH
Q 009803 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR 278 (525)
Q Consensus 244 ~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~ 278 (525)
++.+.+..|...+|++||..+.|...|++...+..
T Consensus 174 ~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~ 208 (324)
T PRK07921 174 KLARIKRELHQQLGREATDEELAEESGIPEEKIAD 208 (324)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence 45566778888899999999999999999866543
No 203
>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=91.85 E-value=0.31 Score=39.70 Aligned_cols=37 Identities=30% Similarity=0.390 Sum_probs=28.4
Q ss_pred HHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHH
Q 009803 243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRR 279 (525)
Q Consensus 243 ~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~ 279 (525)
.++.+.+.+|...+||.||..+.|..+|++...+...
T Consensus 4 ~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~ 40 (78)
T PF04539_consen 4 RKIERARRELEQELGREPTDEEIAEELGISVEEVREL 40 (78)
T ss_dssp HHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHH
Confidence 3456778899999999999999999999998776544
No 204
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=91.71 E-value=1.4 Score=47.96 Aligned_cols=39 Identities=33% Similarity=0.463 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHH
Q 009803 371 TYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVL 409 (525)
Q Consensus 371 ~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l 409 (525)
+..+.+.+..|..++|+.||..|.|..+|+++..++..+
T Consensus 110 ~~~l~~~~~~l~~~~g~~pt~~ewa~~~~~~~~~l~~~l 148 (415)
T PRK07598 110 YLRLIEVRERLTSELGHRPSLERWAKTADISLADLKPTL 148 (415)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCcHHHHHHhh
Confidence 345667788999999999999999988887776666555
No 205
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=91.65 E-value=0.39 Score=47.25 Aligned_cols=47 Identities=13% Similarity=0.105 Sum_probs=34.9
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR 507 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALk 507 (525)
.|+++|.+++........+..+|.+|||+.||+|..||+....++..
T Consensus 158 ~Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~ 204 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVN 204 (239)
T ss_pred CCCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHh
Confidence 48889887765433211123399999999999999999998887744
No 206
>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=91.13 E-value=0.55 Score=37.05 Aligned_cols=46 Identities=22% Similarity=0.400 Sum_probs=30.0
Q ss_pred CCHHHHHHHHHHHhcC-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 462 LNPRERQVVRWRFGLE-DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 462 L~~rER~VL~lRygl~-~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
|++....-|..-|.+. ++.+.+..+||+.||||+.+|. .+++||.+
T Consensus 2 Lt~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt----~ml~~L~~ 48 (60)
T PF01325_consen 2 LTESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVT----EMLKRLAE 48 (60)
T ss_dssp CSCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHH----HHHHHHHH
T ss_pred CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHH----HHHHHHHH
Confidence 3443333333333332 5667999999999999999999 56666654
No 207
>PF13518 HTH_28: Helix-turn-helix domain
Probab=91.10 E-value=0.43 Score=35.47 Aligned_cols=25 Identities=20% Similarity=0.304 Sum_probs=21.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAF 506 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RAL 506 (525)
.|+.+||..+|||+.+|+++..+-.
T Consensus 13 ~s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 13 ESVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred CCHHHHHHHHCCCHhHHHHHHHHHH
Confidence 6999999999999999998776543
No 208
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=90.89 E-value=0.52 Score=37.04 Aligned_cols=29 Identities=21% Similarity=0.280 Sum_probs=24.7
Q ss_pred HHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 009803 473 RFGLEDGRMKTLQEIGELMGVSRERIRQIESSA 505 (525)
Q Consensus 473 Rygl~~g~~~Tl~EIAe~LgIS~erVRqie~RA 505 (525)
-|..| ++..|||+.||+++.+|.+...+-
T Consensus 9 LY~~G----~~~~eIA~~Lg~~~~TV~~W~~r~ 37 (58)
T PF06056_consen 9 LYLQG----WSIKEIAEELGVPRSTVYSWKDRY 37 (58)
T ss_pred HHHcC----CCHHHHHHHHCCChHHHHHHHHhh
Confidence 34555 999999999999999999987764
No 209
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=90.62 E-value=0.36 Score=37.12 Aligned_cols=40 Identities=23% Similarity=0.309 Sum_probs=26.6
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
.|+..|+.=|.-+|-.| .+..+||..|||+++||+.|...
T Consensus 6 ~LTl~eK~~iI~~~e~g----~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 6 SLTLEEKLEIIKRLEEG----ESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp S--HHHHHHHHHHHHCT----T-HHHHHHHHT--CCHHHHHHHC
T ss_pred cCCHHHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHHh
Confidence 46666666555555444 69999999999999999998765
No 210
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=90.59 E-value=0.71 Score=35.56 Aligned_cols=43 Identities=23% Similarity=0.303 Sum_probs=32.0
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
.|++.+..||..-+..+ +..+|..|||+.+|+++.+|.++..+
T Consensus 2 glt~~q~~vL~~l~~~~-~~~~t~~~la~~l~~~~~~vs~~v~~ 44 (62)
T PF12802_consen 2 GLTPSQFRVLMALARHP-GEELTQSELAERLGISKSTVSRIVKR 44 (62)
T ss_dssp TSTHHHHHHHHHHHHST-TSGEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHHCC-CCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 36788888887766554 33489999999999999999955443
No 211
>smart00351 PAX Paired Box domain.
Probab=90.49 E-value=0.74 Score=41.57 Aligned_cols=41 Identities=20% Similarity=0.094 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803 462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF 506 (525)
Q Consensus 462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RAL 506 (525)
++..+|.=|...|-.+ .|..+||+.||||+.+|..++.+..
T Consensus 18 ~s~~~R~riv~~~~~G----~s~~~iA~~~gvs~~tV~kwi~r~~ 58 (125)
T smart00351 18 LPDEERQRIVELAQNG----VRPCDISRQLCVSHGCVSKILGRYY 58 (125)
T ss_pred CCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 5555555555555443 8999999999999999999988864
No 212
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=89.97 E-value=3.7 Score=41.56 Aligned_cols=144 Identities=18% Similarity=0.189 Sum_probs=78.8
Q ss_pred HHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHHHHH
Q 009803 215 RYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSN 294 (525)
Q Consensus 215 ~yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv~~n 294 (525)
.|||+- . +.--|--=.+++.++ +.+..+|+..+|++||..+.|...|++.+++.. .+...+
T Consensus 91 d~LR~~-~--~v~vpR~~~~~~~~i------~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~----------~~~~~~ 151 (247)
T COG1191 91 DYLRKN-D--SVKVPRSLRELGRRI------EEAIDELEQELGREPTDEEIAEELGIDKEEYIE----------ALLAIN 151 (247)
T ss_pred HHHHhC-C--CccCcHHHHHHHHHH------HHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHH----------HHHHhc
Confidence 377776 4 222233334444444 456778889999999999999999999866543 333333
Q ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHH
Q 009803 295 IRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRV 374 (525)
Q Consensus 295 lrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki 374 (525)
....+++--.....+... -+...+..+..+-.|-..+.+..++.. +|..-..
T Consensus 152 ~~~~~sld~~~~~~~d~~-----------------~~~~~~~~~~~~~~~~~~~~l~~ai~~------L~EREk~----- 203 (247)
T COG1191 152 GSQLLSLDEDVLKDDDDD-----------------VDDQIENPDDGVEKEELLEILKEAIEP------LPEREKL----- 203 (247)
T ss_pred cccccchhhhhccccccc-----------------hhhccccchhHHHHHHHHHHHHHHHHc------cCHHHHH-----
Confidence 222222222221111110 011122344555566666666666541 2221110
Q ss_pred HHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHh
Q 009803 375 KEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL 410 (525)
Q Consensus 375 ~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~ 410 (525)
-+.-....+-|..|||+.||+|..+|..+.+
T Consensus 204 -----Vl~l~y~eelt~kEI~~~LgISes~VSql~k 234 (247)
T COG1191 204 -----VLVLRYKEELTQKEIAEVLGISESRVSRLHK 234 (247)
T ss_pred -----HHHHHHHhccCHHHHHHHhCccHHHHHHHHH
Confidence 1111223456789999999999999988753
No 213
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=89.97 E-value=0.44 Score=50.02 Aligned_cols=36 Identities=22% Similarity=0.267 Sum_probs=30.7
Q ss_pred HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 009803 468 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR 507 (525)
Q Consensus 468 ~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALk 507 (525)
.+-.+||..+ +|..|||++||||+.+|+..+.+|.+
T Consensus 17 ~~A~lYY~~g----ltQ~eIA~~LgiSR~~v~rlL~~Ar~ 52 (321)
T COG2390 17 RAAWLYYVEG----LTQSEIAERLGISRATVSRLLAKARE 52 (321)
T ss_pred HHHHHHHhcC----CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3556777766 99999999999999999988888865
No 214
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=89.82 E-value=1.2 Score=40.45 Aligned_cols=53 Identities=21% Similarity=0.265 Sum_probs=41.6
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 453 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 453 ~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
.++..++=.|++.+-+|+..-.-.+ .|+|..|||+.+|++++||. ||+++|=.
T Consensus 16 ~dvl~c~~GLs~~Dv~v~~~LL~~~--~~~tvdelae~lnr~rStv~----rsl~~L~~ 68 (126)
T COG3355 16 EDVLKCVYGLSELDVEVYKALLEEN--GPLTVDELAEILNRSRSTVY----RSLQNLLE 68 (126)
T ss_pred HHHHHHHhCCcHHHHHHHHHHHhhc--CCcCHHHHHHHHCccHHHHH----HHHHHHHH
Confidence 4566777789999999887654223 35999999999999999998 77777743
No 215
>PHA02591 hypothetical protein; Provisional
Probab=89.33 E-value=0.81 Score=38.06 Aligned_cols=22 Identities=32% Similarity=0.527 Sum_probs=20.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~ 503 (525)
+|.++||+.||+|.++||+..+
T Consensus 60 lSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 60 FTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred CCHHHHHHHhCCCHHHHHHHHh
Confidence 9999999999999999998865
No 216
>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA. It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.
Probab=88.86 E-value=0.93 Score=38.47 Aligned_cols=43 Identities=28% Similarity=0.463 Sum_probs=32.2
Q ss_pred HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHH--CCCHHHHHHHHHH
Q 009803 459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELM--GVSRERIRQIESS 504 (525)
Q Consensus 459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~L--gIS~erVRqie~R 504 (525)
++.||+..+++..+|--.-+ .|+.|+|+.| .||++.|.-+..+
T Consensus 35 ~~~l~~~l~~~a~lRl~~Pd---~SL~EL~~~~~~~iSKSgvnhrlrK 79 (85)
T PF02650_consen 35 LDKLPEKLREFAELRLENPD---ASLKELGELLEPPISKSGVNHRLRK 79 (85)
T ss_dssp GGGS-HHHHHHHHHHHH-TT---S-HHHHHHTT--T--HHHHHHHHHH
T ss_pred cccCCHHHHHHHHHHHHCcc---ccHHHHHHHHcCcCcHHHHHHHHHH
Confidence 57899999999999975543 9999999999 9999999866543
No 217
>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=88.66 E-value=0.67 Score=35.06 Aligned_cols=36 Identities=22% Similarity=0.302 Sum_probs=25.9
Q ss_pred HHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803 467 RQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE 502 (525)
Q Consensus 467 R~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie 502 (525)
|-+-.+.+.-..+.++|+.||++.+|+++.+|..+.
T Consensus 4 ral~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L 39 (52)
T PF09339_consen 4 RALRILEALAESGGPLTLSEIARALGLPKSTVHRLL 39 (52)
T ss_dssp HHHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 333444555555666999999999999999998554
No 218
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=88.62 E-value=1 Score=37.57 Aligned_cols=41 Identities=27% Similarity=0.341 Sum_probs=33.6
Q ss_pred cCCHHHHHHHHHH---HhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803 461 TLNPRERQVVRWR---FGLEDGRMKTLQEIGELMGVSRERIRQIE 502 (525)
Q Consensus 461 ~L~~rER~VL~lR---ygl~~g~~~Tl~EIAe~LgIS~erVRqie 502 (525)
.|++++++||..- |. ..|+|..-++||+.+|+|..|||+..
T Consensus 1 ~Lt~rq~~IL~alV~~Y~-~~~~PVgSk~ia~~l~~s~aTIRN~M 44 (78)
T PF03444_consen 1 MLTERQREILKALVELYI-ETGEPVGSKTIAEELGRSPATIRNEM 44 (78)
T ss_pred CCCHHHHHHHHHHHHHHH-hcCCCcCHHHHHHHHCCChHHHHHHH
Confidence 3889999987654 33 36889999999999999999999654
No 219
>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=88.62 E-value=1.3 Score=37.98 Aligned_cols=49 Identities=29% Similarity=0.342 Sum_probs=36.8
Q ss_pred HhcCCHHHHHHHHHH----HhcC-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 459 LDTLNPRERQVVRWR----FGLE-DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 459 L~~L~~rER~VL~lR----ygl~-~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
...+++++..+|..- ||.+ ...++|..|||+.+|+++++|+ |++++|.+
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 357899999877643 3321 2346999999999999999998 67777754
No 220
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=88.57 E-value=1.2 Score=35.77 Aligned_cols=41 Identities=10% Similarity=0.306 Sum_probs=27.6
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 466 ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 466 ER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
+..||.+-.. .+++.+|..|||+.+||++.+|+ +.|.+|.+
T Consensus 8 ~~~IL~~L~~-~g~~~~ta~eLa~~lgl~~~~v~----r~L~~L~~ 48 (68)
T smart00550 8 EEKILEFLEN-SGDETSTALQLAKNLGLPKKEVN----RVLYSLEK 48 (68)
T ss_pred HHHHHHHHHH-CCCCCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 3445444332 23334999999999999999999 45555544
No 221
>PRK15479 transcriptional regulatory protein TctD; Provisional
Probab=88.24 E-value=0.79 Score=43.10 Aligned_cols=49 Identities=27% Similarity=0.246 Sum_probs=42.6
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHH
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMG-----VSRERIRQIESSAFRKLK 510 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~Lg-----IS~erVRqie~RALkKLR 510 (525)
.|+++|.+|+.+.. .+-|.++|.++|++.+. +|..+|+....+.++||.
T Consensus 148 ~Lt~~E~~il~~l~-~~~~~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl~ 201 (221)
T PRK15479 148 ALTPREQALLTVLM-YRRTRPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKLQ 201 (221)
T ss_pred ecCHHHHHHHHHHH-hCCCCcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhcC
Confidence 59999999998764 44467789999999986 999999999999999985
No 222
>PRK12423 LexA repressor; Provisional
Probab=88.18 E-value=0.94 Score=44.14 Aligned_cols=48 Identities=27% Similarity=0.424 Sum_probs=36.4
Q ss_pred hcCCHHHHHHHHHH--HhcCCCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHHh
Q 009803 460 DTLNPRERQVVRWR--FGLEDGRMKTLQEIGELMG-VSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 460 ~~L~~rER~VL~lR--ygl~~g~~~Tl~EIAe~Lg-IS~erVRqie~RALkKLR~ 511 (525)
..|++++++|+..- |...+|-+.|..|||+.|| +|+.+|+ ++|++|++
T Consensus 2 ~~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~----~~l~~L~~ 52 (202)
T PRK12423 2 DTLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVAR----KHVQALAE 52 (202)
T ss_pred CcCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHH----HHHHHHHH
Confidence 35899999988753 3334555679999999999 5999999 46666665
No 223
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=88.16 E-value=1.8 Score=43.72 Aligned_cols=35 Identities=23% Similarity=0.315 Sum_probs=28.3
Q ss_pred HHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHH
Q 009803 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR 278 (525)
Q Consensus 244 ~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~ 278 (525)
++.+...+|...+|++||..+.|...|++...+..
T Consensus 114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~ 148 (256)
T PRK07408 114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQE 148 (256)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHH
Confidence 34556778888899999999999999999876543
No 224
>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=88.00 E-value=0.6 Score=37.16 Aligned_cols=44 Identities=27% Similarity=0.323 Sum_probs=32.5
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
.|++.|..|+..-.-.+ ++|..|||+.+|+++.+|+ +++++|.+
T Consensus 5 gLs~~E~~vy~~Ll~~~---~~t~~eIa~~l~i~~~~v~----~~L~~L~~ 48 (68)
T PF01978_consen 5 GLSENEAKVYLALLKNG---PATAEEIAEELGISRSTVY----RALKSLEE 48 (68)
T ss_dssp CHHHHHHHHHHHHHHHC---HEEHHHHHHHHTSSHHHHH----HHHHHHHH
T ss_pred CcCHHHHHHHHHHHHcC---CCCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 36777777776543222 3999999999999999999 56666643
No 225
>PHA02547 55 RNA polymerase sigma factor; Provisional
Probab=87.96 E-value=1.8 Score=41.25 Aligned_cols=63 Identities=14% Similarity=0.259 Sum_probs=46.2
Q ss_pred HHHHHHHHHHHhhCCCCC---HHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHh
Q 009803 294 NIRLVISIAKNYQGAGMN---LQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD 356 (525)
Q Consensus 294 nlrLV~~IA~~y~~~g~~---~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~ 356 (525)
-+..+..++++|.-+|.. -+|.|.+|.-.+++.+..|||++...+-.|.+..+-++..+.|..
T Consensus 46 imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~k 111 (179)
T PHA02547 46 IMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKK 111 (179)
T ss_pred HHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHH
Confidence 444555555555444544 589999999999999999999998777777777666666655543
No 226
>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=87.94 E-value=1.8 Score=36.61 Aligned_cols=42 Identities=19% Similarity=0.120 Sum_probs=28.7
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHH
Q 009803 465 RERQVVRWRFGLEDGRMKTLQEIGELMG-VSRERIRQIESSAFRKLK 510 (525)
Q Consensus 465 rER~VL~lRygl~~g~~~Tl~EIAe~Lg-IS~erVRqie~RALkKLR 510 (525)
|+--+...+...+ +|+.+||+.|| .+..+|.....+.-+++.
T Consensus 32 R~ia~yl~~~~~~----~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~ 74 (90)
T cd06571 32 RQIAMYLARELTG----LSLPEIGRAFGGRDHSTVLHAVRKIEELLE 74 (90)
T ss_pred HHHHHHHHHHHhC----CCHHHHHHHhCCCCHhHHHHHHHHHHHHHH
Confidence 3333444444445 99999999999 999999955554444443
No 227
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=87.79 E-value=1.3 Score=33.85 Aligned_cols=40 Identities=25% Similarity=0.422 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
|+..|-.||..-+-.++ .|..+||+.+++++.+|.++..+
T Consensus 1 lt~~q~~iL~~l~~~~~---~~~~~la~~~~~~~~~~t~~i~~ 40 (59)
T PF01047_consen 1 LTPSQFRILRILYENGG---ITQSELAEKLGISRSTVTRIIKR 40 (59)
T ss_dssp STHHHHHHHHHHHHHSS---EEHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHcCC---CCHHHHHHHHCCChhHHHHHHHH
Confidence 56667777777765543 99999999999999999955443
No 228
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=87.69 E-value=0.93 Score=34.18 Aligned_cols=29 Identities=31% Similarity=0.547 Sum_probs=24.1
Q ss_pred CCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 479 GRMK-TLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 479 g~~~-Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
|..+ |..|||+.+|+|+.+|+ +++++|.+
T Consensus 17 ~~~l~s~~~la~~~~vs~~tv~----~~l~~L~~ 46 (60)
T smart00345 17 GDKLPSERELAAQLGVSRTTVR----EALSRLEA 46 (60)
T ss_pred CCcCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 3346 99999999999999999 67777765
No 229
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=87.63 E-value=0.84 Score=43.14 Aligned_cols=50 Identities=16% Similarity=0.129 Sum_probs=43.1
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCC-----HHHHHHHHHHHHHHHHh
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVS-----RERIRQIESSAFRKLKN 511 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS-----~erVRqie~RALkKLR~ 511 (525)
.|+++|.+|+.+-.- +.|..+|.+||++.++.+ ..+|+.+..+.++||..
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 599999999987653 456679999999999986 78999999999999974
No 230
>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=87.59 E-value=1.8 Score=36.92 Aligned_cols=45 Identities=31% Similarity=0.436 Sum_probs=31.3
Q ss_pred cCCHHHHHHHHHHHh-----cCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 009803 461 TLNPRERQVVRWRFG-----LEDGRMKTLQEIGELMGVSRERIRQIESSAFRK 508 (525)
Q Consensus 461 ~L~~rER~VL~lRyg-----l~~g~~~Tl~EIAe~LgIS~erVRqie~RALkK 508 (525)
-++|.|+.-|..|+- +.+| +|+.||++.+|+|..||. +.+|+|+.
T Consensus 26 L~T~~E~~~l~~R~~va~~lL~~g--~syreIa~~tgvS~aTIt-Rvsr~Lk~ 75 (87)
T PF01371_consen 26 LCTPDELEALAQRWQVAKELLDEG--KSYREIAEETGVSIATIT-RVSRCLKY 75 (87)
T ss_dssp HSSHHHHHHHHHHHHHHHHHHHTT--SSHHHHHHHHTSTHHHHH-HHHHHHHH
T ss_pred hCCHHHHHHHHHHHHHHHHHHHCC--CCHHHHHHHhCCCHHHHH-HHHHHHHc
Confidence 467777766655542 2233 999999999999999997 33444443
No 231
>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=87.11 E-value=1.2 Score=34.91 Aligned_cols=43 Identities=23% Similarity=0.338 Sum_probs=26.2
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803 462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510 (525)
Q Consensus 462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR 510 (525)
|+..|..||..-. ..+.++|..+|++.+|+++.+|. +++++|.
T Consensus 1 lt~~q~~vL~~l~--~~~~~~t~~~l~~~~~~~~~~vs----~~i~~L~ 43 (68)
T PF13463_consen 1 LTRPQWQVLRALA--HSDGPMTQSDLAERLGISKSTVS----RIIKKLE 43 (68)
T ss_dssp --HHHHHHHHHHT----TS-BEHHHHHHHTT--HHHHH----HHHHHHH
T ss_pred CCHHHHHHHHHHH--ccCCCcCHHHHHHHHCcCHHHHH----HHHHHHH
Confidence 4556666655443 34456999999999999999999 4555554
No 232
>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]
Probab=87.08 E-value=0.75 Score=53.46 Aligned_cols=48 Identities=19% Similarity=0.184 Sum_probs=42.9
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l 513 (525)
-|+.||++|+.+-| .| +|.+|||+.+.||-.||+.+.++-..||.-.-
T Consensus 831 ~Ls~RE~eVL~Lia-~G----~SN~eIa~~L~isl~TVKtH~rniy~KLgV~~ 878 (894)
T COG2909 831 PLSQRELEVLGLIA-QG----LSNEEIAQELFISLTTVKTHIRNIYQKLGVAN 878 (894)
T ss_pred CccHHHHHHHHHHH-cc----CCHHHHHHHHHHHHHHHHHHHHHHHHHhCcch
Confidence 48999999999998 33 89999999999999999999999999996443
No 233
>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=87.03 E-value=0.96 Score=43.07 Aligned_cols=50 Identities=18% Similarity=0.129 Sum_probs=42.8
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHH--HHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEI--GELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EI--Ae~LgIS~erVRqie~RALkKLR~ 511 (525)
.|+++|.+||.+-. .+.|..+|.++| +..++++..+|+.+..+.++||..
T Consensus 156 ~Lt~~E~~il~~l~-~~~g~v~s~~~i~~~~~~~~~~~tv~~~v~rlr~Kl~~ 207 (227)
T TIGR03787 156 DLTVTEFWMVHALA-KHPGHVKSRQQLMDAAKIVVDDSTITSHIKRIRKKFQA 207 (227)
T ss_pred cCCHHHHHHHHHHH-hCCCccccHHHHHHHhhhcCCccCHHHHHHHHHHHhcc
Confidence 49999999998754 344667899999 888999999999999999999963
No 234
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional
Probab=87.02 E-value=1 Score=43.16 Aligned_cols=50 Identities=20% Similarity=0.226 Sum_probs=44.1
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHHh
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMG-----VSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~Lg-----IS~erVRqie~RALkKLR~ 511 (525)
.|+++|++|+.+... +.|+..|.++|++.+. ++..+|+....+.++||..
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 599999999998765 4566799999999998 9999999999999999963
No 235
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=86.80 E-value=3.8 Score=41.34 Aligned_cols=32 Identities=22% Similarity=0.285 Sum_probs=25.4
Q ss_pred hHHHHHHhhcCCCCchHHhHHhhcCCHHHHHH
Q 009803 247 GLREVLSERCGGSPTFAQWAAAAGVDQRELRR 278 (525)
Q Consensus 247 ~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~ 278 (525)
.....|...+|++|+..+.|+..|++...+..
T Consensus 114 ~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~ 145 (257)
T PRK05911 114 DAMDSLRQSLGKEPTDGELCEYLNISQQELSG 145 (257)
T ss_pred HHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHH
Confidence 34456777889999999999999998876543
No 236
>cd00131 PAX Paired Box domain
Probab=86.80 E-value=1.8 Score=39.26 Aligned_cols=41 Identities=17% Similarity=0.054 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803 462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF 506 (525)
Q Consensus 462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RAL 506 (525)
|+...|.=|...|-.+ +|..+||+.||||+.+|..+.++-.
T Consensus 18 lS~d~R~rIv~~~~~G----~s~~~iA~~~~Vs~~tV~r~i~r~~ 58 (128)
T cd00131 18 LPDSIRQRIVELAQSG----IRPCDISRQLRVSHGCVSKILNRYY 58 (128)
T ss_pred CCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 5554444444445444 9999999999999999998877754
No 237
>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=86.66 E-value=2.2 Score=41.92 Aligned_cols=31 Identities=35% Similarity=0.493 Sum_probs=25.0
Q ss_pred hHHHHHHhhcCCCCchHHhHHhhcCCHHHHH
Q 009803 247 GLREVLSERCGGSPTFAQWAAAAGVDQRELR 277 (525)
Q Consensus 247 ~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~ 277 (525)
+....|...+|+.||..+.|+..|++...+.
T Consensus 101 ~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~ 131 (231)
T TIGR02885 101 YMKEELSKELGREPTINELAEALGVSPEEIV 131 (231)
T ss_pred HHHHHHHHHHCcCCCHHHHHHHHCcCHHHHH
Confidence 3455677778999999999999999876654
No 238
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=86.59 E-value=1 Score=42.29 Aligned_cols=49 Identities=24% Similarity=0.230 Sum_probs=42.5
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHH
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMG-----VSRERIRQIESSAFRKLK 510 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~Lg-----IS~erVRqie~RALkKLR 510 (525)
.|+++|.+|+.+. ..+.|..+|.++|++.+. ++..+|+....+.++||.
T Consensus 149 ~Lt~~E~~il~~l-~~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl~ 202 (219)
T PRK10336 149 TLKPKEFALLELL-MRNAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLG 202 (219)
T ss_pred ecCHHHHHHHHHH-HhCCCccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhcC
Confidence 4999999999865 345567799999999996 999999999999999985
No 239
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=86.57 E-value=7.7 Score=41.65 Aligned_cols=35 Identities=26% Similarity=0.362 Sum_probs=28.0
Q ss_pred HHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHH
Q 009803 243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELR 277 (525)
Q Consensus 243 ~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~ 277 (525)
.++.+....|...+|+.||..+.|...|++...+.
T Consensus 223 ~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~ 257 (373)
T PRK07406 223 SRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLR 257 (373)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence 34455667778888999999999999999976653
No 240
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=86.57 E-value=1.7 Score=37.49 Aligned_cols=39 Identities=15% Similarity=0.245 Sum_probs=29.8
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803 462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~ 503 (525)
|++.++.||..-.- + .+.|+.+||+.+|+|+.+|+.+..
T Consensus 1 ld~~D~~il~~L~~-~--~~~~~~~la~~l~~s~~tv~~~l~ 39 (108)
T smart00344 1 LDEIDRKILEELQK-D--ARISLAELAKKVGLSPSTVHNRVK 39 (108)
T ss_pred CCHHHHHHHHHHHH-h--CCCCHHHHHHHHCcCHHHHHHHHH
Confidence 46677888876543 2 249999999999999999995443
No 241
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=86.50 E-value=1.9 Score=33.03 Aligned_cols=38 Identities=32% Similarity=0.351 Sum_probs=26.9
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE 502 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie 502 (525)
.|++-||.-|....-++ +++.|||..+|-|+..|+..+
T Consensus 4 ~Lt~~Eqaqid~m~qlG----~s~~~isr~i~RSr~~Ir~yl 41 (50)
T PF11427_consen 4 TLTDAEQAQIDVMHQLG----MSLREISRRIGRSRTCIRRYL 41 (50)
T ss_dssp ---HHHHHHHHHHHHTT------HHHHHHHHT--HHHHHHHH
T ss_pred cCCHHHHHHHHHHHHhc----hhHHHHHHHhCccHHHHHHHh
Confidence 47888888888777777 999999999999999999664
No 242
>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=86.50 E-value=2 Score=34.55 Aligned_cols=39 Identities=33% Similarity=0.393 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHcCCC-HHHHHHHHh
Q 009803 372 YRVKEARKQLYSENGRHPNNEEVAEATGLS-MKRLHAVLL 410 (525)
Q Consensus 372 ~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis-~~~v~~~l~ 410 (525)
.++-..-..+..++|..||..|||+.+|++ ...|...+.
T Consensus 9 ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~ 48 (65)
T PF01726_consen 9 KEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLK 48 (65)
T ss_dssp HHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHH
Confidence 344455566778899999999999999997 888887764
No 243
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=86.49 E-value=8.2 Score=39.18 Aligned_cols=34 Identities=35% Similarity=0.479 Sum_probs=27.2
Q ss_pred HHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHH
Q 009803 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR 278 (525)
Q Consensus 245 le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~ 278 (525)
+.+...+|...+|+.||..+.|...|++.+.+..
T Consensus 129 i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~ 162 (264)
T PRK07122 129 LGRATAELSQRLGRAPTASELAAELGMDREEVVE 162 (264)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 3445667777889999999999999999876543
No 244
>PRK05949 RNA polymerase sigma factor; Validated
Probab=86.45 E-value=5.2 Score=42.04 Aligned_cols=34 Identities=24% Similarity=0.330 Sum_probs=26.8
Q ss_pred HHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHH
Q 009803 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR 278 (525)
Q Consensus 245 le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~ 278 (525)
+.+.+..+...+|++||..+.|...|++...+..
T Consensus 180 l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~ 213 (327)
T PRK05949 180 IKKTQRELSQKLGRSATPAEIAKELELEPSQIRE 213 (327)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence 4445566777889999999999999999766543
No 245
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=86.16 E-value=12 Score=38.53 Aligned_cols=98 Identities=19% Similarity=0.200 Sum_probs=52.2
Q ss_pred CCCCCHHHHHHHcC--CCHHHHHHHHhCCCCCCCcccccccccCCCC---CcccCCCCCCCHHH-HHHHHHHHHHHHHHH
Q 009803 386 GRHPNNEEVAEATG--LSMKRLHAVLLSPKAPRSLDQKIGINQNLKP---SEVIADPEAETAED-LLIKKFMKEDLEKVL 459 (525)
Q Consensus 386 gr~Pt~eEIA~~lg--is~~~v~~~l~~~~~~~SLD~~i~~d~~~~l---~d~l~d~~~~~pee-~~~~~~~~~~L~~aL 459 (525)
+..+++++||+.++ ||.++|++.+......-=+.. +++..+ ...+..+....+.. .-.+.++.+.-.++|
T Consensus 135 ~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk----~~~g~y~~t~~~l~~~~~~~~~avr~~h~q~l~lA~~al 210 (271)
T TIGR02147 135 PFADDPEELAKRCFPKISAEQVKESLDLLERLGLIKK----NEDGFYKQTDKAVSTGDEVIPLAVRQYQKQMIDLAKEAL 210 (271)
T ss_pred CCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeE----CCCCcEEeecceeecCCccchHHHHHHHHHHHHHHHHHH
Confidence 34567889999999 999999998864321111110 111111 11122222112221 112233445556778
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHH
Q 009803 460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGEL 490 (525)
Q Consensus 460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~ 490 (525)
+..|+.+|.+=.+-++.+. -++++|.+.
T Consensus 211 ~~~p~~eR~~S~lT~~i~~---~~~~~i~~~ 238 (271)
T TIGR02147 211 DALPPSERDVSTVTFGISE---EAYKEIVKK 238 (271)
T ss_pred HhCCccccccceeeEecCH---HHHHHHHHH
Confidence 8999999997766665542 345555444
No 246
>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=86.08 E-value=1.4 Score=42.45 Aligned_cols=48 Identities=17% Similarity=0.270 Sum_probs=36.7
Q ss_pred hcCCHHHHHHHHHHH--hcCCCCCCCHHHHHHHHCCC-HHHHHHHHHHHHHHHHh
Q 009803 460 DTLNPRERQVVRWRF--GLEDGRMKTLQEIGELMGVS-RERIRQIESSAFRKLKN 511 (525)
Q Consensus 460 ~~L~~rER~VL~lRy--gl~~g~~~Tl~EIAe~LgIS-~erVRqie~RALkKLR~ 511 (525)
..|+++|++||..-. ...++.+.|..|||+.+|++ +.+|+ +.+++|.+
T Consensus 2 ~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~----~~l~~L~~ 52 (199)
T TIGR00498 2 KPLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAE----EHLKALER 52 (199)
T ss_pred CccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHH----HHHHHHHH
Confidence 358999999987764 23356778999999999998 99999 44555543
No 247
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=85.77 E-value=1.8 Score=40.19 Aligned_cols=40 Identities=15% Similarity=0.227 Sum_probs=31.1
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~ 503 (525)
.|++.++.||..--- || ..|+.+||+.+|+|+.+|+.+..
T Consensus 6 ~lD~~D~~Il~~Lq~--d~-R~s~~eiA~~lglS~~tV~~Ri~ 45 (153)
T PRK11179 6 QIDNLDRGILEALME--NA-RTPYAELAKQFGVSPGTIHVRVE 45 (153)
T ss_pred ccCHHHHHHHHHHHH--cC-CCCHHHHHHHHCcCHHHHHHHHH
Confidence 477888888876533 22 38999999999999999995543
No 248
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=85.39 E-value=10 Score=38.00 Aligned_cols=35 Identities=23% Similarity=0.186 Sum_probs=27.4
Q ss_pred HHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHH
Q 009803 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRR 279 (525)
Q Consensus 245 le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~ 279 (525)
+.+...++...+|++||..+.|...|++.+.+...
T Consensus 122 ~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~ 156 (254)
T TIGR02850 122 ALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFA 156 (254)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHH
Confidence 33455677778899999999999999998766543
No 249
>PF12728 HTH_17: Helix-turn-helix domain
Probab=85.36 E-value=0.92 Score=33.91 Aligned_cols=24 Identities=29% Similarity=0.457 Sum_probs=21.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSA 505 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RA 505 (525)
+|.+|+|+.||||+.+|+++..+.
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcC
Confidence 799999999999999999887643
No 250
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=85.33 E-value=14 Score=37.34 Aligned_cols=34 Identities=24% Similarity=0.371 Sum_probs=27.4
Q ss_pred HHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHH
Q 009803 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELR 277 (525)
Q Consensus 244 ~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~ 277 (525)
.+.+....|+..+|+.||..+.|...|++...+.
T Consensus 119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~ 152 (268)
T PRK06288 119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYN 152 (268)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHH
Confidence 4555667788889999999999999999876543
No 251
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=85.24 E-value=2.4 Score=36.07 Aligned_cols=44 Identities=20% Similarity=0.148 Sum_probs=36.8
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803 460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF 506 (525)
Q Consensus 460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RAL 506 (525)
..|++.-|..|..+...+| .++.++|+.||||+.|++.+..|=.
T Consensus 7 A~Lt~~gR~~lv~~vv~~g---~~~a~aA~~~gVS~~Ta~kW~~Ryr 50 (85)
T PF13011_consen 7 ARLTPRGRLRLVRRVVEQG---WPVAHAAAEFGVSRRTAYKWLARYR 50 (85)
T ss_pred CCCCHHHHHHHHHHHHHcC---CcHHHHHHHhCCCHHHHHHHHHHHH
Confidence 3589999998888876543 8999999999999999998877643
No 252
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=85.15 E-value=1.4 Score=40.20 Aligned_cols=42 Identities=24% Similarity=0.317 Sum_probs=33.0
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
..|++.++.||..-- .|++ .|+.|||+.+|+|+.+|+.+..+
T Consensus 4 ~~lD~~D~~IL~~L~--~d~r-~~~~eia~~lglS~~~v~~Ri~~ 45 (154)
T COG1522 4 MKLDDIDRRILRLLQ--EDAR-ISNAELAERVGLSPSTVLRRIKR 45 (154)
T ss_pred ccccHHHHHHHHHHH--HhCC-CCHHHHHHHHCCCHHHHHHHHHH
Confidence 468888889988753 2333 99999999999999999965443
No 253
>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=84.91 E-value=2.6 Score=31.19 Aligned_cols=23 Identities=22% Similarity=0.317 Sum_probs=19.4
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Q 009803 481 MKTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 481 ~~Tl~EIAe~LgIS~erVRqie~ 503 (525)
+++..||++.+|+|+.+|++.+.
T Consensus 15 ~~~~~el~~~l~~s~~~vs~hL~ 37 (47)
T PF01022_consen 15 PLTVSELAEELGLSQSTVSHHLK 37 (47)
T ss_dssp SEEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCchhhHHHhccccchHHHHHHH
Confidence 59999999999999999996543
No 254
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=84.71 E-value=0.96 Score=33.86 Aligned_cols=22 Identities=23% Similarity=0.483 Sum_probs=19.5
Q ss_pred CHHHHHHHHCCCHHHHHHHHHH
Q 009803 483 TLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 483 Tl~EIAe~LgIS~erVRqie~R 504 (525)
|+++||+..|||..||+..++.
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 7899999999999999977653
No 255
>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=84.59 E-value=1.3 Score=35.50 Aligned_cols=28 Identities=36% Similarity=0.611 Sum_probs=23.9
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 480 RMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 480 ~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
-++|.++||..+|+|+++|. +.+++|++
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~----r~l~~l~~ 54 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVS----RILKRLKD 54 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHH----HHHHHHHH
T ss_pred ecCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 35899999999999999998 66777765
No 256
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=84.46 E-value=7.9 Score=34.50 Aligned_cols=27 Identities=37% Similarity=0.522 Sum_probs=22.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAFRKLKNK 512 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RALkKLR~~ 512 (525)
.|+.|||+.||||..+|. ++|++|.-.
T Consensus 72 ~tl~Ela~~l~Vs~~ti~----~~Lkrlg~t 98 (119)
T PF01710_consen 72 ATLRELAERLGVSPSTIW----RALKRLGIT 98 (119)
T ss_pred cCHHHHHHHcCCCHHHHH----HHHHHcCch
Confidence 899999999999999998 666666543
No 257
>PRK00215 LexA repressor; Validated
Probab=84.34 E-value=1.9 Score=41.73 Aligned_cols=43 Identities=19% Similarity=0.322 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHH--HhcCCCCCCCHHHHHHHHCC-CHHHHHHHHHH
Q 009803 462 LNPRERQVVRWR--FGLEDGRMKTLQEIGELMGV-SRERIRQIESS 504 (525)
Q Consensus 462 L~~rER~VL~lR--ygl~~g~~~Tl~EIAe~LgI-S~erVRqie~R 504 (525)
|+++|++||.+- |....+.+.|+.|||+.+|+ |+.+|..++.+
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~ 47 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKA 47 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 788899988644 33345667899999999999 99999955443
No 258
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=84.20 E-value=1.1 Score=43.68 Aligned_cols=39 Identities=21% Similarity=0.232 Sum_probs=27.8
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~ 503 (525)
.|+++ +|+.+-- .|...+|.+|||+.||||+.||+....
T Consensus 161 ~Lt~r--~Vl~~~~--~g~~g~s~~eIa~~l~iS~~Tv~~~~~ 199 (225)
T PRK10046 161 PLTLN--AVRKLFK--EPGVQHTAETVAQALTISRTTARRYLE 199 (225)
T ss_pred HHHHH--HHHHHHH--cCCCCcCHHHHHHHhCccHHHHHHHHH
Confidence 35554 5665432 222238999999999999999998764
No 259
>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=84.15 E-value=1.9 Score=31.25 Aligned_cols=38 Identities=18% Similarity=0.288 Sum_probs=26.2
Q ss_pred CHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803 463 NPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 463 ~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~ 503 (525)
.+-|+.+|.-..-..+ -+..+.|+.||||+.+++..+.
T Consensus 3 ~~~E~~~i~~aL~~~~---gn~~~aA~~Lgisr~tL~~klk 40 (42)
T PF02954_consen 3 EEFEKQLIRQALERCG---GNVSKAARLLGISRRTLYRKLK 40 (42)
T ss_dssp HHHHHHHHHHHHHHTT---T-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhC---CCHHHHHHHHCCCHHHHHHHHH
Confidence 3456677766655544 3889999999999999985543
No 260
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=84.08 E-value=1.7 Score=31.41 Aligned_cols=27 Identities=37% Similarity=0.639 Sum_probs=22.6
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 481 MKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 481 ~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
++|..+||+.+|+|+.+|+ +++++|.+
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 4899999999999999997 56666654
No 261
>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=84.04 E-value=13 Score=38.23 Aligned_cols=34 Identities=24% Similarity=0.437 Sum_probs=26.9
Q ss_pred HHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHH
Q 009803 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR 278 (525)
Q Consensus 245 le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~ 278 (525)
+.+.+..+...+|+.||..+.|...|++...+..
T Consensus 163 ~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~ 196 (298)
T TIGR02997 163 IKKVQRELSQKLGRTPSEAEIAEALELEPEQVRE 196 (298)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 3445566777889999999999999999876543
No 262
>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=83.68 E-value=5.6 Score=40.16 Aligned_cols=55 Identities=27% Similarity=0.417 Sum_probs=41.6
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhcCCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 453 EDLEKVLDTLNPRERQVVRWRFGLEDG--RMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 453 ~~L~~aL~~L~~rER~VL~lRygl~~g--~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
..++-++++|+--|.+.+...+-.=++ --.+..+||+.+|||+..|+ +|+++|-.
T Consensus 168 a~Vq~Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ir----eAlrkLE~ 224 (251)
T TIGR02787 168 AAVQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIV----NALRKLES 224 (251)
T ss_pred HHHHHHHHhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 457778999998887766655433222 34899999999999999999 67777754
No 263
>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=83.56 E-value=1.3 Score=41.62 Aligned_cols=29 Identities=28% Similarity=0.346 Sum_probs=25.6
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803 480 RMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512 (525)
Q Consensus 480 ~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~ 512 (525)
-|+|.+|||..+|+|+++|. |++++|++.
T Consensus 142 ~~~t~~~iA~~lG~tretvs----R~l~~l~~~ 170 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTIT----RLLGDLRKK 170 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHH----HHHHHHHHC
Confidence 46899999999999999999 788888763
No 264
>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=83.52 E-value=5.2 Score=31.09 Aligned_cols=36 Identities=19% Similarity=0.299 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803 464 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE 502 (525)
Q Consensus 464 ~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie 502 (525)
|.-+.||.+-.. +.++|..|||+.+|++..+|+..+
T Consensus 10 p~R~~Il~~L~~---~~~~t~~ela~~l~~~~~t~s~hL 45 (61)
T PF12840_consen 10 PTRLRILRLLAS---NGPMTVSELAEELGISQSTVSYHL 45 (61)
T ss_dssp HHHHHHHHHHHH---CSTBEHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHhc---CCCCCHHHHHHHHCCCHHHHHHHH
Confidence 455556655422 235999999999999999999543
No 265
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=83.49 E-value=1.7 Score=40.83 Aligned_cols=40 Identities=18% Similarity=0.199 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
|++.+++||..- ..|| ..|+.|||+.+|+|+.+|+.+..|
T Consensus 12 lD~~D~~IL~~L--q~d~-R~s~~eiA~~lglS~~tv~~Ri~r 51 (164)
T PRK11169 12 LDRIDRNILNEL--QKDG-RISNVELSKRVGLSPTPCLERVRR 51 (164)
T ss_pred HHHHHHHHHHHh--ccCC-CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 666778888753 2233 399999999999999999955443
No 266
>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=83.36 E-value=2.6 Score=40.04 Aligned_cols=42 Identities=21% Similarity=0.272 Sum_probs=35.0
Q ss_pred CHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 009803 463 NPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR 507 (525)
Q Consensus 463 ~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALk 507 (525)
|+.-|.-++..|..++ +|++.+|..+|||..|+|.+..+|..
T Consensus 4 ~~e~R~~~R~~YV~~~---~sLe~aA~~~gVs~~TarrWK~~Ak~ 45 (165)
T PF08822_consen 4 PQETRDAVRRAYVFDR---LSLEQAAAKCGVSYATARRWKREAKA 45 (165)
T ss_pred cHHHHHHHHHHHHhCC---CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3455677788887654 99999999999999999999998854
No 267
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=83.34 E-value=2.3 Score=39.31 Aligned_cols=34 Identities=21% Similarity=0.104 Sum_probs=27.3
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803 469 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF 506 (525)
Q Consensus 469 VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RAL 506 (525)
++...++.| +|..|||++||||..||.....+--
T Consensus 13 ~~~~~~~~G----~S~re~Ak~~gvs~sTvy~wv~r~~ 46 (138)
T COG3415 13 VVDAVVGEG----LSCREAAKRFGVSISTVYRWVRRYR 46 (138)
T ss_pred HHHHHHHcC----ccHHHHHHHhCccHHHHHHHHHHhc
Confidence 444444555 9999999999999999998887754
No 268
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=83.27 E-value=1.4 Score=31.89 Aligned_cols=24 Identities=25% Similarity=0.479 Sum_probs=21.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSA 505 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RA 505 (525)
+|.+|+|+.||||+.+|+++....
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcC
Confidence 689999999999999999987654
No 269
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=83.22 E-value=14 Score=29.04 Aligned_cols=23 Identities=30% Similarity=0.408 Sum_probs=19.9
Q ss_pred CCCHHHHHHHcCCCHHHHHHHHh
Q 009803 388 HPNNEEVAEATGLSMKRLHAVLL 410 (525)
Q Consensus 388 ~Pt~eEIA~~lgis~~~v~~~l~ 410 (525)
+++.++||+.+|++...+..+..
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~ 23 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFK 23 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Confidence 36889999999999999988764
No 270
>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=82.89 E-value=0.97 Score=42.57 Aligned_cols=50 Identities=14% Similarity=0.212 Sum_probs=42.0
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHH-----HHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEI-----GELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EI-----Ae~LgIS~erVRqie~RALkKLR~ 511 (525)
.|+++|.+|+.+-.. +-|..+|.++| |..+++|..+|+....+.++||..
T Consensus 154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~l~~Kl~~ 208 (226)
T TIGR02154 154 SLGPTEFRLLHFFMT-HPERVYSREQLLDRVWGRDVYVEERTVDVHIRRLRKALNP 208 (226)
T ss_pred EcCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCCCCCCCCccHHHHHHHHHHhhcc
Confidence 599999999987654 34556888888 778999999999999999999963
No 271
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=82.82 E-value=6.6 Score=36.40 Aligned_cols=65 Identities=26% Similarity=0.379 Sum_probs=36.7
Q ss_pred HHHHHhcCCHHHHHHHHHH----HhcCCCCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHhHHhhchhh
Q 009803 455 LEKVLDTLNPRERQVVRWR----FGLEDGRMKTLQEIGELMGVSRERIRQIES--SAFRKLKNKKRTKHLM 519 (525)
Q Consensus 455 L~~aL~~L~~rER~VL~lR----ygl~~g~~~Tl~EIAe~LgIS~erVRqie~--RALkKLR~~l~~~~L~ 519 (525)
+..+=.+|++.|+....+- |...+|..+|+.|||+.+|||+.+.-++.+ +++....+.+....+.
T Consensus 4 ~~~le~~L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~~~~Fiey~n~la~~~~~ 74 (142)
T PF13022_consen 4 LKELEAKLTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQQNKAFIEYKNELADRFLS 74 (142)
T ss_dssp HHHHHTTS-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHHH-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHcCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHhcCHHHHHHHHHHHHHHHH
Confidence 4445578999888833322 222244669999999999999999998874 4444444444433333
No 272
>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=82.76 E-value=1.5 Score=31.45 Aligned_cols=25 Identities=32% Similarity=0.380 Sum_probs=22.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAF 506 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RAL 506 (525)
+|..|+|+.||||+.+|+.+.....
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 5889999999999999999987754
No 273
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=82.73 E-value=2.9 Score=32.39 Aligned_cols=39 Identities=26% Similarity=0.371 Sum_probs=26.7
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 466 ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 466 ER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
+..|+.+-.- ....|.+|+|+.||||..||| |=|..|-+
T Consensus 2 ~~~Il~~l~~---~~~~s~~ela~~~~VS~~TiR----RDl~~L~~ 40 (57)
T PF08220_consen 2 QQQILELLKE---KGKVSVKELAEEFGVSEMTIR----RDLNKLEK 40 (57)
T ss_pred HHHHHHHHHH---cCCEEHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 3455554322 234899999999999999999 44445543
No 274
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=82.52 E-value=14 Score=38.56 Aligned_cols=34 Identities=21% Similarity=0.375 Sum_probs=27.0
Q ss_pred HHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHH
Q 009803 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELR 277 (525)
Q Consensus 244 ~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~ 277 (525)
++.+.+..+...+|+.||..+.|...|++...+.
T Consensus 169 ~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~ 202 (317)
T PRK07405 169 KIKKAQRQLSQQLGRAATIGELAEELELTPKQVR 202 (317)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHH
Confidence 3455667777788999999999999999876543
No 275
>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=82.48 E-value=4.2 Score=31.53 Aligned_cols=28 Identities=29% Similarity=0.515 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 480 RMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 480 ~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
.++|..|||+.+|+|+.+|+ +.+++|++
T Consensus 24 ~~~s~~ela~~~g~s~~tv~----r~l~~L~~ 51 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVS----RTLKELEE 51 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 45999999999999999998 56666655
No 276
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=82.40 E-value=3.6 Score=34.44 Aligned_cols=32 Identities=22% Similarity=0.451 Sum_probs=26.9
Q ss_pred cCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 476 LEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 476 l~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
+.++.+.|-++||+.||+|+.+|- +.+++||+
T Consensus 14 ~~~~~~~SGe~La~~LgiSRtaVw----K~Iq~Lr~ 45 (79)
T COG1654 14 LLTGNFVSGEKLAEELGISRTAVW----KHIQQLRE 45 (79)
T ss_pred HcCCCcccHHHHHHHHCccHHHHH----HHHHHHHH
Confidence 345677999999999999999998 67778875
No 277
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=81.29 E-value=3 Score=34.27 Aligned_cols=50 Identities=20% Similarity=0.373 Sum_probs=33.1
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHhcC-CCCCCCHHHHHHHHCCCHHHHHHH
Q 009803 452 KEDLEKVLDTLNPRERQVVRWRFGLE-DGRMKTLQEIGELMGVSRERIRQI 501 (525)
Q Consensus 452 ~~~L~~aL~~L~~rER~VL~lRygl~-~g~~~Tl~EIAe~LgIS~erVRqi 501 (525)
...|......|++.|+.|...-.-.- .-..+|..|||+..|||..+|-..
T Consensus 4 ~~~i~~~~~~ls~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf 54 (77)
T PF01418_consen 4 LEKIRSQYNSLSPTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRF 54 (77)
T ss_dssp HHHHHHHGGGS-HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHH
T ss_pred HHHHHHHHhhCCHHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHH
Confidence 45677778899999999876432211 113499999999999999999743
No 278
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=81.18 E-value=1.5 Score=41.83 Aligned_cols=30 Identities=30% Similarity=0.552 Sum_probs=25.4
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 478 DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 478 ~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
..+|+|+.||++.+|+|+++|+ -++++|..
T Consensus 38 s~~Pmtl~Ei~E~lg~Sks~vS----~~lkkL~~ 67 (177)
T COG1510 38 SRKPLTLDEIAEALGMSKSNVS----MGLKKLQD 67 (177)
T ss_pred cCCCccHHHHHHHHCCCcchHH----HHHHHHHh
Confidence 3578999999999999999999 56777754
No 279
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=81.01 E-value=18 Score=36.16 Aligned_cols=34 Identities=26% Similarity=0.251 Sum_probs=26.7
Q ss_pred HHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHH
Q 009803 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR 278 (525)
Q Consensus 245 le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~ 278 (525)
+++....+...+|+.|+..++|...|++...+..
T Consensus 111 ~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~ 144 (251)
T PRK07670 111 VEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEA 144 (251)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHH
Confidence 3444566777889999999999999998866544
No 280
>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=80.26 E-value=2.4 Score=33.27 Aligned_cols=30 Identities=37% Similarity=0.572 Sum_probs=22.9
Q ss_pred CCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 478 DGRMK-TLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 478 ~g~~~-Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
.|..+ |..+||+.||||+.+|| +|+..|..
T Consensus 20 ~g~~lps~~~la~~~~vsr~tvr----~al~~L~~ 50 (64)
T PF00392_consen 20 PGDRLPSERELAERYGVSRTTVR----EALRRLEA 50 (64)
T ss_dssp TTSBE--HHHHHHHHTS-HHHHH----HHHHHHHH
T ss_pred CCCEeCCHHHHHHHhccCCcHHH----HHHHHHHH
Confidence 34557 99999999999999999 77777754
No 281
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=80.11 E-value=4.7 Score=30.01 Aligned_cols=24 Identities=21% Similarity=0.452 Sum_probs=21.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSA 505 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RA 505 (525)
.|+++||+.+|||..+|+.+..+.
T Consensus 28 ~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 28 RSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHhh
Confidence 599999999999999999887764
No 282
>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=80.07 E-value=4.3 Score=30.82 Aligned_cols=51 Identities=14% Similarity=0.188 Sum_probs=40.5
Q ss_pred cCCHHHHHHHHHHHhcCCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 461 TLNPRERQVVRWRFGLEDG-RMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g-~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
.+++.+..+|.-.|..+.. ......+||..+||+...|......-..+.|+
T Consensus 6 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 6 RFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 4678888999999887532 12467899999999999999999887777663
No 283
>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=79.98 E-value=3.5 Score=31.57 Aligned_cols=26 Identities=38% Similarity=0.640 Sum_probs=22.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
.|..+||+.+|+|+++|+ +++++|.+
T Consensus 26 ~~~~~la~~~~is~~~v~----~~l~~L~~ 51 (66)
T cd07377 26 PSERELAEELGVSRTTVR----EALRELEA 51 (66)
T ss_pred CCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 469999999999999999 67777765
No 284
>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=79.91 E-value=1.4 Score=32.20 Aligned_cols=25 Identities=32% Similarity=0.457 Sum_probs=22.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAF 506 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RAL 506 (525)
+|..|+|+.+|||..+|+..+.+.+
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999987765
No 285
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=79.74 E-value=4.6 Score=33.39 Aligned_cols=25 Identities=24% Similarity=0.372 Sum_probs=21.4
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 480 RMKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 480 ~~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
.++|..|||+.+|+|+.+|+.++..
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~ 43 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNT 43 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHH
Confidence 4699999999999999999955543
No 286
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=79.51 E-value=2.1 Score=40.62 Aligned_cols=28 Identities=21% Similarity=0.325 Sum_probs=24.8
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 480 RMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 480 ~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
-+.|.++||..+|+|+++|. |.|++|++
T Consensus 148 ~~~t~~~iA~~lG~tretvs----R~l~~l~~ 175 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVT----KVIGELSR 175 (202)
T ss_pred ecCCHHHHHHHhCccHHHHH----HHHHHHHH
Confidence 36899999999999999999 77888875
No 287
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=78.98 E-value=5.2 Score=29.14 Aligned_cols=22 Identities=36% Similarity=0.504 Sum_probs=19.6
Q ss_pred CCCHHHHHHHHCCCHHHHHHHH
Q 009803 481 MKTLQEIGELMGVSRERIRQIE 502 (525)
Q Consensus 481 ~~Tl~EIAe~LgIS~erVRqie 502 (525)
+.|..+|++.||+|+.+|++.+
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~l 35 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRDL 35 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHHH
Confidence 4899999999999999998554
No 288
>CHL00148 orf27 Ycf27; Reviewed
Probab=78.92 E-value=3 Score=39.87 Aligned_cols=50 Identities=14% Similarity=0.086 Sum_probs=42.4
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHH-------CCCHHHHHHHHHHHHHHHHh
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELM-------GVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~L-------gIS~erVRqie~RALkKLR~ 511 (525)
.|+++|.+|+.+.. .+.|+.+|.+||++.+ +++..+|+.+..+.++||..
T Consensus 161 ~Lt~~E~~il~~l~-~~~~~~~s~~~i~~~l~~~~~~~~~~~~tv~~~i~~lr~KL~~ 217 (240)
T CHL00148 161 RLTGMEFSLLELLI-SKSGEIFSRATILKEVWGYTPERHIDTRVVDVHISRLRAKLED 217 (240)
T ss_pred EcCHHHHHHHHHHH-HCCCEEEcHHHHHHHhcCCCcccCCCcccHHHHHHHHHHHhcc
Confidence 49999999998765 3345669999999999 48999999999999999974
No 289
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=78.78 E-value=39 Score=35.21 Aligned_cols=84 Identities=18% Similarity=0.132 Sum_probs=50.8
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchH
Q 009803 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV 368 (525)
Q Consensus 289 ~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~ 368 (525)
+-+...+..+-.++... .+-+-|.|.-..+++.+.....-+|.....++.-.|.-+++. +
T Consensus 120 r~l~~a~~~I~~~~~~L-----~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~----~----------- 179 (310)
T PRK00423 120 RNLAFALSELDRIASQL-----GLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRR----C----------- 179 (310)
T ss_pred HHHHHHHHHHHHHHHHc-----CCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHH----c-----------
Confidence 33344445565565554 333567777777777776666678876666555554444422 2
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHH
Q 009803 369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVL 409 (525)
Q Consensus 369 ~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l 409 (525)
|-+-|..||+..++++..++....
T Consensus 180 -----------------~~prtl~eI~~~~~v~~k~i~~~~ 203 (310)
T PRK00423 180 -----------------KVPRTLDEIAEVSRVSRKEIGRCY 203 (310)
T ss_pred -----------------CCCcCHHHHHHHhCCCHHHHHHHH
Confidence 334466788888888877776543
No 290
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=78.50 E-value=4.1 Score=33.70 Aligned_cols=42 Identities=21% Similarity=0.282 Sum_probs=27.0
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH-----HHHHHHHhHHh
Q 009803 469 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES-----SAFRKLKNKKR 514 (525)
Q Consensus 469 VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~-----RALkKLR~~l~ 514 (525)
|..++--.+ +|..|+|+.+|+|+.+|+++++ -.+.+|.+.+.
T Consensus 23 i~~~~~~~~----ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~ 69 (80)
T PF13744_consen 23 IRELREERG----LTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLE 69 (80)
T ss_dssp HHHHHHCCT------HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHH
T ss_pred HHHHHHHcC----CCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHH
Confidence 444444444 9999999999999999999884 23555555544
No 291
>PRK10072 putative transcriptional regulator; Provisional
Probab=78.37 E-value=3.5 Score=35.75 Aligned_cols=32 Identities=22% Similarity=0.372 Sum_probs=27.8
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 469 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 469 VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
|-.+|...+ +|..++|+.+|||..+|++++..
T Consensus 38 ik~LR~~~g----lTQ~elA~~lGvS~~TVs~WE~G 69 (96)
T PRK10072 38 FEQLRKGTG----LKIDDFARVLGVSVAMVKEWESR 69 (96)
T ss_pred HHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHcC
Confidence 556677777 99999999999999999999863
No 292
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=78.35 E-value=5.6 Score=42.96 Aligned_cols=51 Identities=22% Similarity=0.268 Sum_probs=40.0
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
.+++.||..+.+.+.+-...+.|+.++|+.|+||+.|+.+-+.+.-+.|.+
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 477888887777766666778999999999999999999765555555544
No 293
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=78.26 E-value=19 Score=37.12 Aligned_cols=24 Identities=21% Similarity=0.303 Sum_probs=21.2
Q ss_pred CCCCHHHHHHHcCCCHHHHHHHHh
Q 009803 387 RHPNNEEVAEATGLSMKRLHAVLL 410 (525)
Q Consensus 387 r~Pt~eEIA~~lgis~~~v~~~l~ 410 (525)
..-|..|||+.+|+|..+|+.++.
T Consensus 244 ~~~t~~EIa~~lgvs~~~V~q~~~ 267 (289)
T PRK07500 244 DGATLEALGEELGISKERVRQIEA 267 (289)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 566999999999999999998764
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=78.19 E-value=4.1 Score=31.78 Aligned_cols=40 Identities=18% Similarity=0.361 Sum_probs=28.3
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 465 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 465 rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
|+-.+|.+-+. + ..+|+.|||+.+|+|..+|++. +..|+.
T Consensus 6 rq~~Ll~~L~~-~--~~~~~~ela~~l~~S~rti~~~----i~~L~~ 45 (59)
T PF08280_consen 6 RQLKLLELLLK-N--KWITLKELAKKLNISERTIKND----INELNE 45 (59)
T ss_dssp HHHHHHHHHHH-H--TSBBHHHHHHHCTS-HHHHHHH----HHHHHT
T ss_pred HHHHHHHHHHc-C--CCCcHHHHHHHHCCCHHHHHHH----HHHHHH
Confidence 45566666665 2 3499999999999999999954 445554
No 295
>PHA01976 helix-turn-helix protein
Probab=78.18 E-value=4.2 Score=31.87 Aligned_cols=32 Identities=19% Similarity=0.236 Sum_probs=25.9
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 469 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 469 VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
+-.+|-..+ +|..++|+.+|||+.+|+++++.
T Consensus 7 l~~~R~~~g----lt~~~lA~~~gvs~~~v~~~e~g 38 (67)
T PHA01976 7 LIKARNARA----WSAPELSRRAGVRHSLIYDFEAD 38 (67)
T ss_pred HHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHcC
Confidence 344454455 99999999999999999999864
No 296
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=78.15 E-value=23 Score=34.61 Aligned_cols=35 Identities=37% Similarity=0.468 Sum_probs=27.2
Q ss_pred HHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHH
Q 009803 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR 278 (525)
Q Consensus 244 ~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~ 278 (525)
++.+...+|...+|+.|+..+.|+..|++...+..
T Consensus 84 ~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~ 118 (224)
T TIGR02479 84 KLERAIRELEARLGREPTEEEIAEELGMDLKEYRQ 118 (224)
T ss_pred HHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHH
Confidence 34555667778889999999999999998765443
No 297
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=77.66 E-value=3.8 Score=33.36 Aligned_cols=32 Identities=38% Similarity=0.487 Sum_probs=25.9
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 469 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 469 VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
+-.+|-..+ +|.+|.|+.+|||+.||-.+++-
T Consensus 6 ~k~~R~~~~----ltQ~elA~~vgVsRQTi~~iEkg 37 (68)
T COG1476 6 LKELRAELG----LTQEELAKLVGVSRQTIIAIEKG 37 (68)
T ss_pred HHHHHHHhC----cCHHHHHHHcCcCHHHHHHHHcC
Confidence 444555555 99999999999999999998864
No 298
>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=77.42 E-value=4.5 Score=33.52 Aligned_cols=31 Identities=39% Similarity=0.642 Sum_probs=22.7
Q ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 477 EDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 477 ~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
+++.+.|.+|||+.+|+|+..|+++ +.+|++
T Consensus 21 ~~~~~~s~~eiA~~~~i~~~~l~ki----l~~L~~ 51 (83)
T PF02082_consen 21 PDGKPVSSKEIAERLGISPSYLRKI----LQKLKK 51 (83)
T ss_dssp TTSC-BEHHHHHHHHTS-HHHHHHH----HHHHHH
T ss_pred CCCCCCCHHHHHHHHCcCHHHHHHH----HHHHhh
Confidence 3445699999999999999999955 455554
No 299
>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=76.49 E-value=3.9 Score=32.78 Aligned_cols=25 Identities=12% Similarity=0.208 Sum_probs=22.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAF 506 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RAL 506 (525)
.|+.+||..+||++.+++++.....
T Consensus 24 ~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 24 ESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp CHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CceEeeecccccccccccHHHHHHh
Confidence 8999999999999999999988876
No 300
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=75.94 E-value=1.4 Score=34.72 Aligned_cols=25 Identities=32% Similarity=0.566 Sum_probs=22.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAF 506 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RAL 506 (525)
||..|+|+.+|||..+||..+.+.+
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 5889999999999999999988765
No 301
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=75.82 E-value=3.1 Score=40.68 Aligned_cols=28 Identities=21% Similarity=0.403 Sum_probs=24.1
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 480 RMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 480 ~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
-|+|.++||..+|+|+++|. |.+++|++
T Consensus 183 ~~lt~~~iA~~lG~sr~tvs----R~l~~l~~ 210 (235)
T PRK11161 183 LTMTRGDIGNYLGLTVETIS----RLLGRFQK 210 (235)
T ss_pred ccccHHHHHHHhCCcHHHHH----HHHHHHHH
Confidence 35899999999999999999 66777775
No 302
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=75.74 E-value=14 Score=35.12 Aligned_cols=27 Identities=37% Similarity=0.576 Sum_probs=24.1
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 481 MKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 481 ~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
+.|.++||..+|+|+++|+ |++++|++
T Consensus 168 ~~t~~~lA~~lG~tr~tvs----R~l~~l~~ 194 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVG----RVLKMLED 194 (211)
T ss_pred CCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 6899999999999999999 67777775
No 303
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=75.52 E-value=26 Score=34.81 Aligned_cols=34 Identities=18% Similarity=0.330 Sum_probs=27.1
Q ss_pred HHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHH
Q 009803 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR 278 (525)
Q Consensus 245 le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~ 278 (525)
+.+....|...+|+.||..+.|+..|++.+.+..
T Consensus 103 i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~ 136 (231)
T PRK12427 103 TNDAIREIAKRLGHEPNFEEISAELNLTAEEYQE 136 (231)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHH
Confidence 3445567777889999999999999999876543
No 304
>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=75.49 E-value=4.1 Score=30.50 Aligned_cols=23 Identities=35% Similarity=0.599 Sum_probs=19.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~R 504 (525)
+|..|+|+.+|+|+.+|+.++..
T Consensus 10 ls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 10 LSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHTT
T ss_pred CCHHHHHHHhCCCcchhHHHhcC
Confidence 99999999999999999998875
No 305
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=75.32 E-value=4.3 Score=31.78 Aligned_cols=23 Identities=22% Similarity=0.462 Sum_probs=19.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~R 504 (525)
+|..++|+.+|+|..+|+++++-
T Consensus 15 ls~~~lA~~~g~s~s~v~~iE~G 37 (64)
T PF13560_consen 15 LSQAQLADRLGVSQSTVSRIERG 37 (64)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHTT
T ss_pred CCHHHHHHHHCcCHHHHHHHHCC
Confidence 99999999999999999999864
No 306
>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=75.12 E-value=5.1 Score=33.64 Aligned_cols=23 Identities=22% Similarity=0.407 Sum_probs=20.4
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Q 009803 481 MKTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 481 ~~Tl~EIAe~LgIS~erVRqie~ 503 (525)
..|+.+||+.+|||+.||+..+.
T Consensus 19 ~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 19 KATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred CCCHHHHHHHhCCCHHHHHHHhc
Confidence 47999999999999999997554
No 307
>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=75.09 E-value=5.7 Score=29.57 Aligned_cols=23 Identities=30% Similarity=0.488 Sum_probs=21.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~R 504 (525)
+|..++|+.+|+|+.+|+.+++.
T Consensus 16 ltq~~lA~~~gvs~~~vs~~e~g 38 (58)
T TIGR03070 16 LTQADLADLAGVGLRFIRDVENG 38 (58)
T ss_pred CCHHHHHHHhCCCHHHHHHHHCC
Confidence 99999999999999999999864
No 308
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=75.05 E-value=8.6 Score=31.75 Aligned_cols=44 Identities=20% Similarity=0.354 Sum_probs=33.8
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
.|+..+..||.+-+..+ ++|..+|++.+++|+.+|+ +++++|.+
T Consensus 7 ~l~~~~~~il~~l~~~~---~~~~~~la~~~~~s~~~i~----~~l~~L~~ 50 (101)
T smart00347 7 GLTPTQFLVLRILYEEG---PLSVSELAKRLGVSPSTVT----RVLDRLEK 50 (101)
T ss_pred CCCHHHHHHHHHHHHcC---CcCHHHHHHHHCCCchhHH----HHHHHHHH
Confidence 46777777877766533 3999999999999999988 55666654
No 309
>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=74.93 E-value=7.3 Score=36.52 Aligned_cols=49 Identities=22% Similarity=0.368 Sum_probs=36.5
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH------HHHHHHhHHh
Q 009803 462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS------AFRKLKNKKR 514 (525)
Q Consensus 462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R------ALkKLR~~l~ 514 (525)
.+|..-.|=.+|-..| +|..++|+.+|||+.+|.+++.. .+..|.+...
T Consensus 23 ~~p~~~~Ir~~R~~lG----mTq~eLAerlGVS~~tIs~iE~G~~~~~psl~~L~kIA~ 77 (150)
T TIGR02612 23 QTPKEGWVRAIRKALG----MSGAQLAGRLGVTPQRVEALEKSELSGTVTLKTLRAAAE 77 (150)
T ss_pred ccCcHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHcCCCCCCCCHHHHHHHHH
Confidence 3444445667777777 99999999999999999999985 3445554443
No 310
>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=74.90 E-value=7.9 Score=30.78 Aligned_cols=27 Identities=22% Similarity=0.465 Sum_probs=21.7
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 481 MKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 481 ~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
+.|..+||+.+|+|+.+|++ .+++|++
T Consensus 13 ~~~~~eLa~~l~vS~~tv~~----~l~~L~~ 39 (69)
T TIGR00122 13 PFSGEKLGEALGMSRTAVNK----HIQTLRE 39 (69)
T ss_pred CcCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence 37899999999999999995 4555543
No 311
>PHA00542 putative Cro-like protein
Probab=74.80 E-value=5.4 Score=33.26 Aligned_cols=24 Identities=25% Similarity=0.256 Sum_probs=22.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSA 505 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RA 505 (525)
+|..++|+.+|||+.+|.+++...
T Consensus 32 lTq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 32 WSQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred CCHHHHHHHHCcCHHHHHHHHcCC
Confidence 999999999999999999998654
No 312
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=74.72 E-value=6.7 Score=37.44 Aligned_cols=111 Identities=15% Similarity=0.147 Sum_probs=56.8
Q ss_pred CCCCCHHHHHHHc--CCCHHHHHHHHhCCCCCCCcccccccccCCCC---CcccCCCCCCCHHH-HHHHHHHHHHHHHHH
Q 009803 386 GRHPNNEEVAEAT--GLSMKRLHAVLLSPKAPRSLDQKIGINQNLKP---SEVIADPEAETAED-LLIKKFMKEDLEKVL 459 (525)
Q Consensus 386 gr~Pt~eEIA~~l--gis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l---~d~l~d~~~~~pee-~~~~~~~~~~L~~aL 459 (525)
+-.+++.+||+.+ ++|.+++++.+......-=+.. +++..+ ...+..+....+.. .-....+.+.-.++|
T Consensus 37 ~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k----~~~g~y~~t~~~l~~~~~~~~~avr~~h~q~~~lA~~al 112 (171)
T PF14394_consen 37 PFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKK----DGDGKYVQTDKSLTTSSEIPSEAVRSYHKQMLELAQEAL 112 (171)
T ss_pred CCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEE----CCCCcEEEecceeeCCCCCcHHHHHHHHHHHHHHHHHHH
Confidence 4456899999999 9999999998864321111110 111111 01121111111211 111223334445667
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
+..|+.+|.+=.+-++.+. .++++| +..+...++++.....
T Consensus 113 ~~~p~~~R~~s~~T~~vs~---~~~~ki-----------~~~i~~fRk~i~~i~~ 153 (171)
T PF14394_consen 113 DRVPPEERDFSGLTMSVSR---EDYEKI-----------KKEIREFRKKIIAIAE 153 (171)
T ss_pred HhCCccccceeeeEEEeCH---HHHHHH-----------HHHHHHHHHHHHHHHh
Confidence 7888888887766655542 344443 4444555555555443
No 313
>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=74.33 E-value=24 Score=35.26 Aligned_cols=33 Identities=18% Similarity=0.302 Sum_probs=25.4
Q ss_pred HHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHH
Q 009803 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELR 277 (525)
Q Consensus 245 le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~ 277 (525)
+......+....|+.|+..+.|...|++.+.+.
T Consensus 118 ~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~ 150 (255)
T TIGR02941 118 IKKAIDELTDHLQRSPKIIEIADHLGLSEEEVL 150 (255)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence 334556677778999999999999999876543
No 314
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=74.22 E-value=5.9 Score=38.28 Aligned_cols=32 Identities=19% Similarity=0.291 Sum_probs=25.2
Q ss_pred HHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803 467 RQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 467 R~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~ 503 (525)
+.|..++ ..+ +|+.+||+.||||+.||.++..
T Consensus 163 ~~i~~~~-~~g----~s~~~iak~lgis~~Tv~r~~k 194 (200)
T PRK13413 163 EKIKKLL-DKG----TSKSEIARKLGVSRTTLARFLK 194 (200)
T ss_pred HHHHHHH-HCC----CCHHHHHHHHCCCHHHHHHHHH
Confidence 4555553 333 8999999999999999998775
No 315
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=73.75 E-value=37 Score=37.32 Aligned_cols=46 Identities=15% Similarity=0.263 Sum_probs=32.4
Q ss_pred HHHhcCCHHHHHHHHH---------HHhcCC---CCCCCHHHHHHHHCCCHHHHHHHH
Q 009803 457 KVLDTLNPRERQVVRW---------RFGLED---GRMKTLQEIGELMGVSRERIRQIE 502 (525)
Q Consensus 457 ~aL~~L~~rER~VL~l---------Rygl~~---g~~~Tl~EIAe~LgIS~erVRqie 502 (525)
.++..|.-|++.++.. -|+.+| -+|+++++||+.+|++.+||+...
T Consensus 294 wLiksL~qR~~TLlkV~~~Iv~~Q~~Ff~~g~~~l~PL~LrdvA~~i~~HESTISRai 351 (444)
T COG1508 294 WLIKSLEQREETLLKVAEEIVEYQKAFFEGGEEALKPLVLRDVADEIGMHESTISRAI 351 (444)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCCcccHHHHHHHhCccHHHHHHHH
Confidence 3456777777766542 133322 378999999999999999999543
No 316
>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=73.74 E-value=18 Score=31.74 Aligned_cols=44 Identities=9% Similarity=0.188 Sum_probs=33.3
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803 460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510 (525)
Q Consensus 460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR 510 (525)
..|++.+..||..-+.. + +.|..|||+.+|+++.+|. +.+++|-
T Consensus 24 ~~lt~~q~~iL~~l~~~-~--~~t~~ela~~~~~~~~tvs----~~l~~Le 67 (118)
T TIGR02337 24 HGLTEQQWRILRILAEQ-G--SMEFTQLANQACILRPSLT----GILARLE 67 (118)
T ss_pred cCCCHHHHHHHHHHHHc-C--CcCHHHHHHHhCCCchhHH----HHHHHHH
Confidence 36889998888765432 2 4899999999999999997 4455553
No 317
>PRK06030 hypothetical protein; Provisional
Probab=73.43 E-value=11 Score=34.31 Aligned_cols=37 Identities=14% Similarity=0.143 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 464 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 464 ~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
+|+-.+...|-..+ +|+.+||+.||.+..||..-..+
T Consensus 56 aRqIAMYL~r~~~~----~sl~~IG~~FGRDHSTV~haikk 92 (124)
T PRK06030 56 IRQIAMYVAHVSLG----WPMNEVALAFGRDRTTVGHACHT 92 (124)
T ss_pred HHHHHHHHHHHHcC----CCHHHHHHHHCCChhHHHHHHHH
Confidence 45545555555555 99999999999999999965553
No 318
>PRK09954 putative kinase; Provisional
Probab=73.42 E-value=6.5 Score=41.34 Aligned_cols=43 Identities=21% Similarity=0.380 Sum_probs=33.5
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 009803 462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR 507 (525)
Q Consensus 462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALk 507 (525)
|+++++.||.+.. .+ ...|..|||+.||||+.+|+.++.+-.+
T Consensus 1 ~~~~~~~il~~l~--~~-~~~s~~~la~~l~~s~~~v~~~i~~L~~ 43 (362)
T PRK09954 1 MNNREKEILAILR--RN-PLIQQNEIADILQISRSRVAAHIMDLMR 43 (362)
T ss_pred CChHHHHHHHHHH--HC-CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4667777776654 23 3699999999999999999999886443
No 319
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=72.79 E-value=10 Score=33.81 Aligned_cols=25 Identities=12% Similarity=0.078 Sum_probs=22.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAF 506 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RAL 506 (525)
+|..+||..+|||..++.++.....
T Consensus 30 ~sv~evA~e~gIs~~tl~~W~r~y~ 54 (121)
T PRK09413 30 MTVSLVARQHGVAASQLFLWRKQYQ 54 (121)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHh
Confidence 8999999999999999999987643
No 320
>PF13551 HTH_29: Winged helix-turn helix
Probab=72.67 E-value=5.9 Score=33.78 Aligned_cols=24 Identities=25% Similarity=0.351 Sum_probs=21.4
Q ss_pred C-CHHHHHHHHCCCHHHHHHHHHHH
Q 009803 482 K-TLQEIGELMGVSRERIRQIESSA 505 (525)
Q Consensus 482 ~-Tl~EIAe~LgIS~erVRqie~RA 505 (525)
. |..+||+.+|||+.||+.++++-
T Consensus 12 ~~~~~~ia~~lg~s~~Tv~r~~~~~ 36 (112)
T PF13551_consen 12 VSTIAEIARRLGISRRTVYRWLKRY 36 (112)
T ss_pred CCcHHHHHHHHCcCHHHHHHHHHHH
Confidence 6 69999999999999999887763
No 321
>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=72.58 E-value=12 Score=28.74 Aligned_cols=25 Identities=28% Similarity=0.565 Sum_probs=20.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAFRKLK 510 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RALkKLR 510 (525)
.+..||++.+|+++.+|+. +++.|.
T Consensus 21 ~~~~ei~~~~~i~~~~i~~----~l~~L~ 45 (78)
T cd00090 21 LTVSELAERLGLSQSTVSR----HLKKLE 45 (78)
T ss_pred cCHHHHHHHHCcCHhHHHH----HHHHHH
Confidence 8999999999999999984 455554
No 322
>PRK05572 sporulation sigma factor SigF; Validated
Probab=72.55 E-value=31 Score=34.44 Aligned_cols=32 Identities=28% Similarity=0.422 Sum_probs=24.5
Q ss_pred HHhHHHHHHhhcCCCCchHHhHHhhcCCHHHH
Q 009803 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQREL 276 (525)
Q Consensus 245 le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L 276 (525)
+.+....+....|+.|+..+.|+..|++...+
T Consensus 120 ~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v 151 (252)
T PRK05572 120 IRKDKDELSKELGREPTIEELAEYLGVTPEEV 151 (252)
T ss_pred HHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHH
Confidence 34455666677899999999999999887544
No 323
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=72.40 E-value=7.9 Score=37.84 Aligned_cols=46 Identities=13% Similarity=0.095 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHHHhc-CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 462 LNPRERQVVRWRFGL-EDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 462 L~~rER~VL~lRygl-~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
++.++|-+-.+.... ++..+.|.++||+.+|+|+++|. |.|++|++
T Consensus 149 ~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvs----R~L~~L~~ 195 (226)
T PRK10402 149 FPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLL----YVLAQFIQ 195 (226)
T ss_pred ChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHH----HHHHHHHH
Confidence 356666554443221 22345799999999999999999 78888876
No 324
>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=72.23 E-value=5.9 Score=33.24 Aligned_cols=47 Identities=17% Similarity=0.297 Sum_probs=30.3
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803 465 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513 (525)
Q Consensus 465 rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l 513 (525)
.||-|-.-.|..+.. .|..+.|..||||++||..-...=|.++-..+
T Consensus 5 eeR~i~i~~yIi~~~--aTVR~~Ak~FGvSKSTVHkDvteRL~~in~~L 51 (82)
T PF12116_consen 5 EERVIEIANYIIETK--ATVRQAAKVFGVSKSTVHKDVTERLPKINPEL 51 (82)
T ss_dssp HHHHHHHHHHHHHH-----HHHHHHHHTS-HHHHHHHHTTHHHHH-HHH
T ss_pred HHHHHHHHHHHHHcc--cHHHHHHHHHCCcHHHHHHHHHHHHHhcCHHH
Confidence 345555566666533 89999999999999999987766555554433
No 325
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=72.19 E-value=5.1 Score=38.01 Aligned_cols=36 Identities=17% Similarity=0.191 Sum_probs=28.0
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHC-CCHHHHHHHHHH
Q 009803 465 RERQVVRWRFGLEDGRMKTLQEIGELMG-VSRERIRQIESS 504 (525)
Q Consensus 465 rER~VL~lRygl~~g~~~Tl~EIAe~Lg-IS~erVRqie~R 504 (525)
..-+.|.-.+..| +|..|||..|| ||++.|--..+|
T Consensus 6 e~~~~L~~lw~~G----~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 6 ERVERLRKLWAEG----LSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred HHHHHHHHHHHcC----CCHHHHHHHhCCcchhhhhhhhhc
Confidence 3344555555555 99999999999 999999887776
No 326
>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=72.12 E-value=8.5 Score=33.76 Aligned_cols=41 Identities=22% Similarity=0.295 Sum_probs=26.5
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 465 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 465 rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
+.++|...+- + ++..++|..+|+|..+|++|+.+..++-++
T Consensus 62 R~~~I~~~f~--G----~n~~eLA~kyglS~r~I~~Ii~~~~~~~~~ 102 (108)
T PF08765_consen 62 RNREIRREFN--G----MNVRELARKYGLSERQIYRIIKRVRRRERR 102 (108)
T ss_dssp HHHHHHHH----S----S-HHHHHHHHT--HHHHHHHHHHHHH----
T ss_pred HHHHHHHHhC--C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4556665432 3 899999999999999999999988776654
No 327
>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=72.02 E-value=2.7 Score=30.13 Aligned_cols=23 Identities=35% Similarity=0.583 Sum_probs=19.4
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHH
Q 009803 483 TLQEIGELMGVSRERIRQIESSA 505 (525)
Q Consensus 483 Tl~EIAe~LgIS~erVRqie~RA 505 (525)
|..|+|+.+|||..++|..+...
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~G 23 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYEREG 23 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHTT
T ss_pred CHHHHHHHHCCCHHHHHHHHHCC
Confidence 56899999999999999988765
No 328
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=71.66 E-value=41 Score=33.69 Aligned_cols=33 Identities=24% Similarity=0.211 Sum_probs=26.4
Q ss_pred HhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHH
Q 009803 246 EGLREVLSERCGGSPTFAQWAAAAGVDQRELRR 278 (525)
Q Consensus 246 e~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~ 278 (525)
.+....+....|+.|+..+.|...|++.+.+..
T Consensus 126 ~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~ 158 (258)
T PRK08215 126 LQVREKLINENSKEPTVEEIAKELEVPREEVVF 158 (258)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHH
Confidence 344566777889999999999999999876543
No 329
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=71.65 E-value=4.6 Score=39.74 Aligned_cols=27 Identities=19% Similarity=0.454 Sum_probs=24.1
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 481 MKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 481 ~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
++|.++||..+|+|+++|. |++++|++
T Consensus 179 ~lt~~~IA~~lGisretls----R~L~~L~~ 205 (230)
T PRK09391 179 PMSRRDIADYLGLTIETVS----RALSQLQD 205 (230)
T ss_pred cCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 5899999999999999999 77888876
No 330
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=71.00 E-value=10 Score=34.63 Aligned_cols=30 Identities=33% Similarity=0.657 Sum_probs=25.5
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 478 DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 478 ~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
+|++.|..+||+.+|||+..|| +++.+|++
T Consensus 22 ~g~~~s~~~ia~~~~is~~~vr----k~l~~L~~ 51 (141)
T PRK11014 22 EGRMTSISEVTEVYGVSRNHMV----KIINQLSR 51 (141)
T ss_pred CCCccCHHHHHHHHCcCHHHHH----HHHHHHHh
Confidence 4567899999999999999999 66777765
No 331
>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=70.92 E-value=5.2 Score=31.35 Aligned_cols=23 Identities=30% Similarity=0.466 Sum_probs=20.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~R 504 (525)
+|..|+|+.+|||..++|.+..+
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 58899999999999999998865
No 332
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=70.64 E-value=12 Score=36.28 Aligned_cols=44 Identities=20% Similarity=0.188 Sum_probs=34.0
Q ss_pred HHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 458 VLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 458 aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
.+..|++++..|+.+-.-.+ +.|..|||+.+|+|+.+|++++.+
T Consensus 137 ~~~~ls~~~~~IL~~l~~~g---~~s~~eia~~l~is~stv~r~L~~ 180 (203)
T TIGR01884 137 LLAGLSREELKVLEVLKAEG---EKSVKNIAKKLGKSLSTISRHLRE 180 (203)
T ss_pred hhcCCCHHHHHHHHHHHHcC---CcCHHHHHHHHCcCHHHHHHHHHH
Confidence 35679999988887654322 389999999999999999955444
No 333
>PRK01905 DNA-binding protein Fis; Provisional
Probab=70.59 E-value=20 Score=29.51 Aligned_cols=36 Identities=14% Similarity=0.228 Sum_probs=25.5
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803 465 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 465 rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~ 503 (525)
-|+.+|...+-..+ -+..+.|+.||||+.+++....
T Consensus 37 ~E~~~i~~aL~~~~---gn~s~aAr~LGIsrstL~rklk 72 (77)
T PRK01905 37 VEKPLLEVVMEQAG---GNQSLAAEYLGINRNTLRKKLQ 72 (77)
T ss_pred HHHHHHHHHHHHcC---CCHHHHHHHHCCCHHHHHHHHH
Confidence 35666655554443 3789999999999999875443
No 334
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=70.42 E-value=15 Score=33.21 Aligned_cols=49 Identities=8% Similarity=0.131 Sum_probs=34.3
Q ss_pred HHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803 453 EDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 453 ~~L~~aL~--~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~ 503 (525)
..+...+. .|++.+-.||..-+-.+ .+.|..|||+.+|+++.+|.+...
T Consensus 18 ~~~~~~l~~~glt~~q~~vL~~l~~~~--~~~t~~eLa~~l~~~~~tvt~~v~ 68 (144)
T PRK03573 18 ALIDHRLKPLELTQTHWVTLHNIHQLP--PEQSQIQLAKAIGIEQPSLVRTLD 68 (144)
T ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHcC--CCCCHHHHHHHhCCChhhHHHHHH
Confidence 33444443 58888877776654332 238999999999999999994443
No 335
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=70.04 E-value=9 Score=38.66 Aligned_cols=50 Identities=18% Similarity=0.282 Sum_probs=38.8
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHhcCCC---CCCCHHHHHHHHCCCHHHHHHHHH
Q 009803 452 KEDLEKVLDTLNPRERQVVRWRFGLEDG---RMKTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 452 ~~~L~~aL~~L~~rER~VL~lRygl~~g---~~~Tl~EIAe~LgIS~erVRqie~ 503 (525)
...|...+..|++.|+.|..+- +++. ..+|..|||+..|+|..+|-..-+
T Consensus 4 ~~~i~~~~~~Lt~~e~~Ia~yi--l~n~~~v~~~si~~lA~~~~vS~aTv~Rf~k 56 (284)
T PRK11302 4 LEKIQSRLEHLSKSERKVAEVI--LASPQTAIHSSIATLAKMANVSEPTVNRFCR 56 (284)
T ss_pred HHHHHHHHhhCCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCCHHHHHHHHH
Confidence 3567788899999999998644 4332 238999999999999999975443
No 336
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=70.00 E-value=6.2 Score=39.94 Aligned_cols=33 Identities=21% Similarity=0.321 Sum_probs=26.9
Q ss_pred HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 468 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 468 ~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
.+..--|..+ |.+.+||++||||+.+|+.+..|
T Consensus 10 ~~Akk~yl~g----mk~~dIAeklGvspntiksWKrr 42 (279)
T COG5484 10 IIAKKDYLKG----MKLKDIAEKLGVSPNTIKSWKRR 42 (279)
T ss_pred HHHHHHHHhh----ccHHHHHHHhCCChHHHHHHHHh
Confidence 3444456555 99999999999999999998775
No 337
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=69.69 E-value=23 Score=39.95 Aligned_cols=103 Identities=12% Similarity=0.174 Sum_probs=56.7
Q ss_pred CCCCHHHHHHHcCCCHHHHHHHHhCCCCC---CCcccccccccCCCCCcccCCCCCCCHHHHHHHHHHHHHHHHHHhcCC
Q 009803 387 RHPNNEEVAEATGLSMKRLHAVLLSPKAP---RSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLN 463 (525)
Q Consensus 387 r~Pt~eEIA~~lgis~~~v~~~l~~~~~~---~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~ 463 (525)
...|..+||+.+|+|.+.|+.-+...... ..+. .+.... +-.+... ++. .+...+..-+
T Consensus 16 ~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~-~i~~~~----Gy~l~~~---~~~----------~~~~~~~~~~ 77 (584)
T PRK09863 16 QDRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIG-SISGSA----KYHLEIL---NRR----------SLFQLLQKSD 77 (584)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchh-heecCC----ceEEEeC---CHH----------HHHHHHhcCC
Confidence 35689999999999999997765421110 0000 000000 1111110 111 1111222223
Q ss_pred HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803 464 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510 (525)
Q Consensus 464 ~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR 510 (525)
+ |+..+.++.... .+.++.++|+.|.||+.||.+-+.+.-+.|.
T Consensus 78 ~-e~~~il~~Ll~~--~~~~~~~La~~l~vS~sTi~~dl~~v~~~l~ 121 (584)
T PRK09863 78 N-EDRLLLLRLLLN--TFTPMAQLASALNLSRTWVAERLPRLNQRYE 121 (584)
T ss_pred H-HHHHHHHHHHHc--CCccHHHHHHHhCCCHHHHHHHHHHHHHhhh
Confidence 3 343344444443 4699999999999999999977666666554
No 338
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=69.63 E-value=7.9 Score=28.91 Aligned_cols=24 Identities=17% Similarity=0.311 Sum_probs=20.5
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 481 MKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 481 ~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
+.|..+|++.+|+|+.+|+.++++
T Consensus 10 ~~~~~~i~~~l~is~~~v~~~l~~ 33 (66)
T smart00418 10 ELCVCELAEILGLSQSTVSHHLKK 33 (66)
T ss_pred CccHHHHHHHHCCCHHHHHHHHHH
Confidence 489999999999999999955544
No 339
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=69.35 E-value=17 Score=31.61 Aligned_cols=37 Identities=30% Similarity=0.428 Sum_probs=29.0
Q ss_pred cCCHHHHHHHHHHHhc-----CCCCCCCHHHHHHHHCCCHHHHH
Q 009803 461 TLNPRERQVVRWRFGL-----EDGRMKTLQEIGELMGVSRERIR 499 (525)
Q Consensus 461 ~L~~rER~VL~lRygl-----~~g~~~Tl~EIAe~LgIS~erVR 499 (525)
-|+|.||+-+-.|+-. +|. +|..||++.||+|..+|-
T Consensus 37 lLTpdEReal~~Rv~Iv~eLL~ge--~sQREi~~~LgvsiAtIT 78 (103)
T COG2973 37 LLTPDEREALGTRVRIVEELLRGE--LSQREIAQKLGVSIATIT 78 (103)
T ss_pred HcCHhHHHHHHHHHHHHHHHHhcc--ccHHHHHHHhCcchhhhc
Confidence 4888888877766543 232 999999999999998875
No 340
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=69.32 E-value=13 Score=37.95 Aligned_cols=51 Identities=27% Similarity=0.481 Sum_probs=39.7
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHHhcCCC---CCCCHHHHHHHHCCCHHHHHHHHH
Q 009803 451 MKEDLEKVLDTLNPRERQVVRWRFGLEDG---RMKTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 451 ~~~~L~~aL~~L~~rER~VL~lRygl~~g---~~~Tl~EIAe~LgIS~erVRqie~ 503 (525)
+...|+..+..|++.|+.|...- +++. ..+|..+||+..|||..+|-..-+
T Consensus 15 i~~~i~~~~~~Lt~~e~~Ia~yi--l~~~~~v~~~si~~lA~~~~vS~aTi~Rf~k 68 (292)
T PRK11337 15 LGPYIRMKQEGLTPLESRVVEWL--LKPGDLSEATALKDIAEALAVSEAMIVKVAK 68 (292)
T ss_pred HHHHHHHHHhhcCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCChHHHHHHHH
Confidence 34578888999999999998754 4322 238999999999999999875443
No 341
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=69.24 E-value=7.4 Score=39.71 Aligned_cols=45 Identities=20% Similarity=0.307 Sum_probs=37.1
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803 460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510 (525)
Q Consensus 460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR 510 (525)
..|++.|+.||.+--+.||- .++.||-+.+|.|+.+|. |.+++|-
T Consensus 191 ~~L~~~e~~il~~i~~~GGr--i~Q~eL~r~lglsktTvs----R~L~~LE 235 (258)
T COG2512 191 YDLNEDEKEILDLIRERGGR--ITQAELRRALGLSKTTVS----RILRRLE 235 (258)
T ss_pred CCCCHHHHHHHHHHHHhCCE--EeHHHHHHhhCCChHHHH----HHHHHHH
Confidence 46899999999987766543 899999999999999999 5555553
No 342
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=68.90 E-value=7.1 Score=37.58 Aligned_cols=30 Identities=33% Similarity=0.346 Sum_probs=27.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
+|-.|||+.|++|++|++.+..|+.++...
T Consensus 19 lt~gEIAdELNvSreTa~WL~~r~~~~~~~ 48 (203)
T COG0856 19 LTTGEIADELNVSRETATWLLTRAFKKESV 48 (203)
T ss_pred CcHHHhhhhhhhhHHHHHHHHhhhhhccCC
Confidence 999999999999999999999998877644
No 343
>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=68.66 E-value=4 Score=33.89 Aligned_cols=34 Identities=18% Similarity=0.260 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhch
Q 009803 480 RMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 517 (525)
Q Consensus 480 ~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~ 517 (525)
++.|+.++|+.++||+.++... +++|++.+...+
T Consensus 29 ~~~s~~~la~~~~iS~sti~~~----i~~l~~~l~~~~ 62 (87)
T PF05043_consen 29 EYVSIEDLAEELFISRSTIYRD----IKKLNKYLKKYG 62 (87)
T ss_dssp SEEEHHHHHHHHT--HHHHHHH----HHHHHHHHHCCT
T ss_pred CCcCHHHHHHHHCCCHHHHHHH----HHHHHHHHHHcC
Confidence 3489999999999999999955 455555444433
No 344
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=68.57 E-value=9.9 Score=32.47 Aligned_cols=40 Identities=20% Similarity=0.298 Sum_probs=29.3
Q ss_pred HHHHHHHHHcCCC-CCHHHHHHHcCCCHHHHHHHHhCCCCC
Q 009803 376 EARKQLYSENGRH-PNNEEVAEATGLSMKRLHAVLLSPKAP 415 (525)
Q Consensus 376 ka~~~L~~~lgr~-Pt~eEIA~~lgis~~~v~~~l~~~~~~ 415 (525)
..+.+|.....-. -++++||..||+|+.+++.++...+++
T Consensus 10 ~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil~~tqr~ 50 (97)
T COG4367 10 RTKQELQANFELCPLSDEEIATALNWTEVKLEKILQVTQRP 50 (97)
T ss_pred HHHHHHHHhhhhccccHHHHHHHhCCCHHHHHHHHHHhhcc
Confidence 3445555544443 489999999999999999999765443
No 345
>PRK10870 transcriptional repressor MprA; Provisional
Probab=68.01 E-value=30 Score=32.94 Aligned_cols=50 Identities=16% Similarity=0.123 Sum_probs=35.5
Q ss_pred HHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 454 DLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 454 ~L~~aL~--~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
.+...+. .|++-+-.||..-+.. ++.+.|..|||+.+|+++.+|.++..+
T Consensus 43 ~~~~~l~~~gLt~~q~~iL~~L~~~-~~~~it~~eLa~~l~l~~~tvsr~v~r 94 (176)
T PRK10870 43 NRNKMLKAQGINETLFMALITLESQ-ENHSIQPSELSCALGSSRTNATRIADE 94 (176)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHhcC-CCCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4455554 4788877777666532 334589999999999999999854443
No 346
>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=67.96 E-value=6.7 Score=30.91 Aligned_cols=23 Identities=30% Similarity=0.567 Sum_probs=21.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~R 504 (525)
+|..|+|+.+|||..++|.+..+
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 57899999999999999998776
No 347
>PF13551 HTH_29: Winged helix-turn helix
Probab=67.93 E-value=6.5 Score=33.52 Aligned_cols=23 Identities=22% Similarity=0.186 Sum_probs=20.7
Q ss_pred CHHHHHHHcCCCHHHHHHHHhCC
Q 009803 390 NNEEVAEATGLSMKRLHAVLLSP 412 (525)
Q Consensus 390 t~eEIA~~lgis~~~v~~~l~~~ 412 (525)
|..+||+.+|++...|..+++..
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~ 36 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRY 36 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHH
Confidence 79999999999999999998643
No 348
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=67.85 E-value=13 Score=33.81 Aligned_cols=46 Identities=13% Similarity=0.110 Sum_probs=34.2
Q ss_pred HHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803 455 LEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 455 L~~aL~--~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~ 503 (525)
+...+. .|++.|-.||..-+.. + +.|..|||+.+|+++.+|..++.
T Consensus 29 ~~~~l~~~glt~~q~~vL~~l~~~-~--~~t~~eLa~~l~i~~~tvsr~l~ 76 (144)
T PRK11512 29 LNEYLSPLDITAAQFKVLCSIRCA-A--CITPVELKKVLSVDLGALTRMLD 76 (144)
T ss_pred HHHHhcccCCCHHHHHHHHHHHHc-C--CCCHHHHHHHHCCCHHHHHHHHH
Confidence 444443 5888888888766532 2 39999999999999999994443
No 349
>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=67.33 E-value=18 Score=31.84 Aligned_cols=44 Identities=27% Similarity=0.337 Sum_probs=32.0
Q ss_pred HHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 009803 456 EKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSA 505 (525)
Q Consensus 456 ~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RA 505 (525)
...-..+.+.+-.-++.. .+ +|..++|+.+|+|+.+|+++++..
T Consensus 59 ~~~~~~~~~~~i~~~r~~--~g----ltq~~lA~~lg~~~~tis~~e~g~ 102 (127)
T TIGR03830 59 RKVDGLLTPPEIRRIRKK--LG----LSQREAAELLGGGVNAFSRYERGE 102 (127)
T ss_pred HHccCCcCHHHHHHHHHH--cC----CCHHHHHHHhCCCHHHHHHHHCCC
Confidence 333356777654444444 44 899999999999999999988743
No 350
>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=66.91 E-value=15 Score=35.22 Aligned_cols=39 Identities=18% Similarity=0.302 Sum_probs=30.0
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE 502 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie 502 (525)
.|++.-|.-|.-.+..++ +|+++||..+||+..||.-|+
T Consensus 16 ~lse~~r~~Iy~~~~~~~---~sv~~vS~~ygi~~~RV~AIv 54 (172)
T PF12298_consen 16 VLSEELREQIYEDVMQDG---KSVREVSQKYGIKIQRVEAIV 54 (172)
T ss_pred cCCHHHHHHHHHHHHhCC---CCHHHHHHHhCCCHHHHHHHH
Confidence 366666776666665543 799999999999999998443
No 351
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=66.83 E-value=6.1 Score=38.66 Aligned_cols=27 Identities=19% Similarity=0.337 Sum_probs=23.2
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 481 MKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 481 ~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
++|.++||..+|+++++|. |++++|++
T Consensus 173 ~~t~~~iA~~lG~tretvs----R~l~~L~~ 199 (236)
T PRK09392 173 PYEKRVLASYLGMTPENLS----RAFAALAS 199 (236)
T ss_pred eCCHHHHHHHhCCChhHHH----HHHHHHHh
Confidence 5788999999999999998 67777765
No 352
>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=66.79 E-value=40 Score=32.91 Aligned_cols=30 Identities=40% Similarity=0.546 Sum_probs=24.0
Q ss_pred HHHHHHhhcCCCCchHHhHHhhcCCHHHHH
Q 009803 248 LREVLSERCGGSPTFAQWAAAAGVDQRELR 277 (525)
Q Consensus 248 ~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~ 277 (525)
....+....|+.|+..+.|...|++...+.
T Consensus 95 ~~~~l~~~~~~~p~~~ela~~l~~~~~~v~ 124 (227)
T TIGR02980 95 ATEELTQRLGRSPTIAEIAEELGVSEEEVV 124 (227)
T ss_pred HHHHHHHHHCCCCCHHHHHHHhCCCHHHHH
Confidence 455666778999999999999999876543
No 353
>PF14502 HTH_41: Helix-turn-helix domain
Probab=66.74 E-value=10 Score=28.78 Aligned_cols=29 Identities=38% Similarity=0.584 Sum_probs=25.2
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 479 GRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 479 g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
.+-.|..|.++.|++|+.+|. .||+.|.+
T Consensus 4 dRi~tI~e~~~~~~vs~GtiQ----~Alk~Le~ 32 (48)
T PF14502_consen 4 DRIPTISEYSEKFGVSRGTIQ----NALKFLEE 32 (48)
T ss_pred cccCCHHHHHHHhCcchhHHH----HHHHHHHH
Confidence 355799999999999999998 78888875
No 354
>PF14493 HTH_40: Helix-turn-helix domain
Probab=66.04 E-value=11 Score=31.75 Aligned_cols=27 Identities=15% Similarity=0.261 Sum_probs=25.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAFRK 508 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RALkK 508 (525)
+|+.|||+.-|++.+||..++.++...
T Consensus 14 ~si~eIA~~R~L~~sTI~~HL~~~~~~ 40 (91)
T PF14493_consen 14 LSIEEIAKIRGLKESTIYGHLAELIES 40 (91)
T ss_pred CCHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence 999999999999999999998887765
No 355
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=65.98 E-value=69 Score=31.56 Aligned_cols=31 Identities=26% Similarity=0.292 Sum_probs=24.3
Q ss_pred hHHHHHHhhcCCCCchHHhHHhhcCCHHHHH
Q 009803 247 GLREVLSERCGGSPTFAQWAAAAGVDQRELR 277 (525)
Q Consensus 247 ~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~ 277 (525)
.....+....|++|+..++|+..|++...+.
T Consensus 99 ~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~ 129 (236)
T PRK06986 99 QAIRQLEQELGREPTDTEVAEKLGLSLEEYR 129 (236)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHcCCCHHHHH
Confidence 3445566678999999999999999876544
No 356
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=65.94 E-value=11 Score=37.57 Aligned_cols=24 Identities=21% Similarity=0.297 Sum_probs=21.3
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 481 MKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 481 ~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
|+|..|||++||||..+||+++..
T Consensus 25 ~~sa~elA~~Lgis~~avR~HL~~ 48 (218)
T COG2345 25 PVSADELAEELGISPMAVRRHLDD 48 (218)
T ss_pred CccHHHHHHHhCCCHHHHHHHHHH
Confidence 499999999999999999977653
No 357
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=65.62 E-value=4.8 Score=31.66 Aligned_cols=25 Identities=32% Similarity=0.448 Sum_probs=21.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAF 506 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RAL 506 (525)
+|..|+|+.+|||..++|.++...+
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~~gl 25 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYERIGL 25 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999998876554
No 358
>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=65.54 E-value=10 Score=28.14 Aligned_cols=22 Identities=18% Similarity=0.348 Sum_probs=16.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~ 503 (525)
+|+.+.|+.+||++.|++.+..
T Consensus 17 ~S~r~AA~~ygVp~sTL~~r~~ 38 (45)
T PF05225_consen 17 MSIRKAAKKYGVPRSTLRRRLR 38 (45)
T ss_dssp S-HHHHHHHHT--HHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHc
Confidence 9999999999999999995544
No 359
>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=65.43 E-value=20 Score=26.91 Aligned_cols=51 Identities=14% Similarity=0.221 Sum_probs=39.6
Q ss_pred cCCHHHHHHHHHHHhcCCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 461 TLNPRERQVVRWRFGLEDG-RMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g-~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
.+++.+..+|.-.|..+.. ......+||..+|+|...|+.....-..+.+.
T Consensus 6 ~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 6 RFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 4677788888888877532 22568899999999999999998887776653
No 360
>PRK15482 transcriptional regulator MurR; Provisional
Probab=65.34 E-value=12 Score=38.06 Aligned_cols=49 Identities=8% Similarity=0.255 Sum_probs=38.4
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhcCCC---CCCCHHHHHHHHCCCHHHHHHHHH
Q 009803 453 EDLEKVLDTLNPRERQVVRWRFGLEDG---RMKTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 453 ~~L~~aL~~L~~rER~VL~lRygl~~g---~~~Tl~EIAe~LgIS~erVRqie~ 503 (525)
..|......|++.|+.|..+- +++. .-+|..|||+..|+|..+|-..-+
T Consensus 5 ~~i~~~~~~Lt~~e~~Ia~yI--l~n~~~v~~~si~elA~~~~vS~aTv~Rf~k 56 (285)
T PRK15482 5 TKIRNAESEFTENEQKIADFL--RANVSELKSVSSRKMAKQLGISQSSIVKFAQ 56 (285)
T ss_pred HHHHHHHhhcCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCCHHHHHHHHH
Confidence 467778899999999998644 4432 239999999999999999875443
No 361
>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=65.22 E-value=12 Score=35.89 Aligned_cols=43 Identities=21% Similarity=0.234 Sum_probs=32.0
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
..|++-|+.....+.....| +|.++||+.+|+|+.+|++++.-
T Consensus 101 ~~lt~~e~a~~~~~l~~~~g--~s~~~iA~~lg~s~~~V~r~l~l 143 (187)
T TIGR00180 101 EDLSPIEEAQAYKRLLEKFS--MTQEDLAKKIGKSRAHITNLLRL 143 (187)
T ss_pred cCCCHHHHHHHHHHHHHHhC--CCHHHHHHHHCcCHHHHHHHHHH
Confidence 47888887765555432222 89999999999999999977643
No 362
>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=64.64 E-value=8.2 Score=30.52 Aligned_cols=23 Identities=26% Similarity=0.384 Sum_probs=20.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~R 504 (525)
+|..|+|+.+|||..++|..+..
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 47899999999999999988765
No 363
>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=64.31 E-value=15 Score=29.42 Aligned_cols=23 Identities=22% Similarity=0.497 Sum_probs=21.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~R 504 (525)
+|..++|+.+|+|+.+|++++..
T Consensus 19 ~t~~~lA~~~gis~~tis~~~~g 41 (78)
T TIGR02607 19 LSIRALAKALGVSRSTLSRIVNG 41 (78)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Confidence 89999999999999999998863
No 364
>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=64.19 E-value=12 Score=33.45 Aligned_cols=30 Identities=23% Similarity=0.394 Sum_probs=24.0
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 478 DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 478 ~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
++.+.|..|||+.+|+|+.+|+++ +++|++
T Consensus 22 ~~~~~s~~eia~~l~is~~~v~~~----l~~L~~ 51 (130)
T TIGR02944 22 DSQPYSAAEIAEQTGLNAPTVSKI----LKQLSL 51 (130)
T ss_pred CCCCccHHHHHHHHCcCHHHHHHH----HHHHHH
Confidence 456799999999999999999954 455554
No 365
>PRK11050 manganese transport regulator MntR; Provisional
Probab=63.72 E-value=27 Score=32.47 Aligned_cols=27 Identities=19% Similarity=0.351 Sum_probs=22.1
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 481 MKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 481 ~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
+.+..|||+.||||+.+|+ +++++|.+
T Consensus 51 ~~t~~eLA~~l~is~stVs----r~l~~Le~ 77 (152)
T PRK11050 51 EARQVDIAARLGVSQPTVA----KMLKRLAR 77 (152)
T ss_pred CCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 4899999999999999999 45555544
No 366
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=63.21 E-value=9.3 Score=37.62 Aligned_cols=30 Identities=30% Similarity=0.624 Sum_probs=25.7
Q ss_pred CCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 478 DGRMK-TLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 478 ~g~~~-Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
.|..+ |-.|+|+.||||+.+|| .||..|..
T Consensus 27 pG~~LPsE~eLae~~gVSRt~VR----eAL~~L~~ 57 (239)
T PRK04984 27 PGSILPAERELSELIGVTRTTLR----EVLQRLAR 57 (239)
T ss_pred CCCcCCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 45568 79999999999999999 78888865
No 367
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=62.99 E-value=7.5 Score=31.21 Aligned_cols=23 Identities=22% Similarity=0.538 Sum_probs=19.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~R 504 (525)
.|+.|||+.+|||+.+|+..++.
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~ 23 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNG 23 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCC
Confidence 37899999999999999977643
No 368
>TIGR00647 MG103 conserved hypothetical protein.
Probab=62.76 E-value=17 Score=37.56 Aligned_cols=43 Identities=16% Similarity=0.248 Sum_probs=35.8
Q ss_pred HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC------CCHHHHHHHHHH
Q 009803 459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMG------VSRERIRQIESS 504 (525)
Q Consensus 459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~Lg------IS~erVRqie~R 504 (525)
++.||+..+++..+|--.- ..|++|+|+.|. ||++.|.-+..+
T Consensus 225 l~~Lp~~L~~~a~lRl~~P---d~SL~ELgell~~~~~~~isKSgvnhRlrK 273 (279)
T TIGR00647 225 FEKLPLNFQRICLLKIDHP---DWSLEQIAEFFASKYKVKISRSGIQHRLRK 273 (279)
T ss_pred cccCCHHHHHHHHHHHhCc---ccCHHHHHHHhccCCCCCcCHHHHHHHHHH
Confidence 5799999999999996443 389999999994 999999866544
No 369
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=62.04 E-value=23 Score=31.80 Aligned_cols=49 Identities=12% Similarity=0.173 Sum_probs=33.7
Q ss_pred HHHHhcCCHHHH-HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 456 EKVLDTLNPRER-QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 456 ~~aL~~L~~rER-~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
..++..|.+.-| .||.+-. ++.+++..||++.+|+|+.+|+++ |+.|++
T Consensus 7 ~~~fkaLadptRl~IL~~L~---~~~~~~v~ela~~l~lsqstvS~H----L~~L~~ 56 (117)
T PRK10141 7 LQLFKILSDETRLGIVLLLR---ESGELCVCDLCTALDQSQPKISRH----LALLRE 56 (117)
T ss_pred HHHHHHhCCHHHHHHHHHHH---HcCCcCHHHHHHHHCcCHHHHHHH----HHHHHH
Confidence 456667776555 5555432 122499999999999999999965 445554
No 370
>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=61.67 E-value=9.1 Score=36.90 Aligned_cols=30 Identities=37% Similarity=0.562 Sum_probs=25.8
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 478 DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 478 ~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
.|..++-.++|+.||||+..|| .||..|..
T Consensus 31 pG~~L~e~~La~~lgVSRtpVR----eAL~~L~~ 60 (212)
T TIGR03338 31 PGAKLNESDIAARLGVSRGPVR----EAFRALEE 60 (212)
T ss_pred CCCEecHHHHHHHhCCChHHHH----HHHHHHHH
Confidence 3456899999999999999999 78888864
No 371
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=61.48 E-value=15 Score=36.62 Aligned_cols=38 Identities=18% Similarity=0.155 Sum_probs=27.8
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803 466 ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 466 ER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~ 503 (525)
+|-+-.|.++-..+.++|+.|||+.+|+++.+|..++.
T Consensus 9 ~ral~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~ 46 (248)
T TIGR02431 9 ARGLAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLL 46 (248)
T ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34444444544445679999999999999999996654
No 372
>PRK10161 transcriptional regulator PhoB; Provisional
Probab=61.36 E-value=9.4 Score=36.33 Aligned_cols=50 Identities=10% Similarity=0.127 Sum_probs=39.9
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHH-----HHCCCHHHHHHHHHHHHHHHHh
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGE-----LMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe-----~LgIS~erVRqie~RALkKLR~ 511 (525)
.|+++|.+|+.+-. .+-|+.+|.++|.. .++++..+|+....+.++||..
T Consensus 154 ~Lt~~E~~ll~~l~-~~~~~~~s~~~l~~~~~~~~~~~~~~tv~~~i~rlr~Kl~~ 208 (229)
T PRK10161 154 EMGPTEFKLLHFFM-THPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEP 208 (229)
T ss_pred EcCHHHHHHHHHHH-hCCCceEcHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhcc
Confidence 59999999987654 44566688777654 5678999999999999999963
No 373
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=61.34 E-value=26 Score=27.18 Aligned_cols=33 Identities=9% Similarity=0.051 Sum_probs=24.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 514 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~ 514 (525)
.+..+.|+.|+|.+.||+.++.|.-+.+.-.+.
T Consensus 13 ~n~~~tA~~L~iHrNTl~yRl~ki~~l~g~dl~ 45 (59)
T PF13556_consen 13 GNISKTARALHIHRNTLRYRLKKIEELLGLDLD 45 (59)
T ss_dssp T-HHHHHHHHTS-HHHHHHHHHHHHHHHS--TT
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHCcCCC
Confidence 699999999999999999998888776654433
No 374
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=60.58 E-value=15 Score=33.11 Aligned_cols=22 Identities=23% Similarity=0.366 Sum_probs=21.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~ 503 (525)
+|..+||+.||+|+..|+|.++
T Consensus 23 ~Sq~~iA~LLGltqaAVS~Yls 44 (119)
T COG2522 23 LSQYRIAKLLGLTQAAVSQYLS 44 (119)
T ss_pred CcHHHHHHHhCCCHHHHHHHHc
Confidence 9999999999999999999875
No 375
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=60.40 E-value=10 Score=30.28 Aligned_cols=24 Identities=21% Similarity=0.184 Sum_probs=19.3
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q 009803 480 RMKTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 480 ~~~Tl~EIAe~LgIS~erVRqie~ 503 (525)
.|.|-.|||+.+|+|..+||.++.
T Consensus 14 ~p~~T~eiA~~~gls~~~aR~yL~ 37 (62)
T PF04703_consen 14 GPLKTREIADALGLSIYQARYYLE 37 (62)
T ss_dssp S-EEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Confidence 459999999999999999996653
No 376
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=60.05 E-value=18 Score=31.89 Aligned_cols=40 Identities=25% Similarity=0.415 Sum_probs=33.4
Q ss_pred HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
...|++.|-..|+-.+ + +|..+-|..||+|.++|++++..
T Consensus 41 ~~~ls~~eIk~iRe~~--~----lSQ~vFA~~L~vs~~Tv~~WEqG 80 (104)
T COG2944 41 VKTLSPTEIKAIREKL--G----LSQPVFARYLGVSVSTVRKWEQG 80 (104)
T ss_pred CCCCCHHHHHHHHHHh--C----CCHHHHHHHHCCCHHHHHHHHcC
Confidence 3568988867666554 4 89999999999999999999974
No 377
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=59.91 E-value=21 Score=32.50 Aligned_cols=22 Identities=14% Similarity=0.324 Sum_probs=19.3
Q ss_pred CCCHHHHHHHHCCCHHHHHHHH
Q 009803 481 MKTLQEIGELMGVSRERIRQIE 502 (525)
Q Consensus 481 ~~Tl~EIAe~LgIS~erVRqie 502 (525)
+.+..+||+.||||+.+|+..+
T Consensus 22 ~~~~~ela~~l~vs~~svs~~l 43 (142)
T PRK03902 22 YARVSDIAEALSVHPSSVTKMV 43 (142)
T ss_pred CcCHHHHHHHhCCChhHHHHHH
Confidence 4799999999999999999544
No 378
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=59.73 E-value=10 Score=37.00 Aligned_cols=37 Identities=19% Similarity=0.253 Sum_probs=28.8
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 469 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 469 VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
|+.-.|. .|..++-.+||+.||||+..|| .||+.|..
T Consensus 24 I~~g~l~--pG~~L~e~~La~~lgVSRtpVR----EAL~~L~~ 60 (221)
T PRK11414 24 LSIGALK--PGARLITKNLAEQLGMSITPVR----EALLRLVS 60 (221)
T ss_pred HHhCCCC--CCCccCHHHHHHHHCCCchhHH----HHHHHHHH
Confidence 4444433 4556888999999999999999 78888864
No 379
>PRK09726 antitoxin HipB; Provisional
Probab=59.66 E-value=16 Score=30.61 Aligned_cols=23 Identities=22% Similarity=0.409 Sum_probs=21.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~R 504 (525)
+|..++|+.+|||+.+|+++++.
T Consensus 26 ltq~elA~~~gvs~~tis~~e~g 48 (88)
T PRK09726 26 WTQSELAKKIGIKQATISNFENN 48 (88)
T ss_pred CCHHHHHHHHCcCHHHHHHHHCC
Confidence 99999999999999999999884
No 380
>PRK13239 alkylmercury lyase; Provisional
Probab=59.62 E-value=17 Score=35.83 Aligned_cols=28 Identities=29% Similarity=0.363 Sum_probs=25.5
Q ss_pred cCCCCCHHHHHHHcCCCHHHHHHHHhCC
Q 009803 385 NGRHPNNEEVAEATGLSMKRLHAVLLSP 412 (525)
Q Consensus 385 lgr~Pt~eEIA~~lgis~~~v~~~l~~~ 412 (525)
.|++||..+||+.+|+++++|+.+|...
T Consensus 33 ~G~pvt~~~lA~~~~~~~~~v~~~L~~l 60 (206)
T PRK13239 33 KGRPVSVTTLAAALGWPVEEVEAVLEAM 60 (206)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhC
Confidence 5889999999999999999999998753
No 381
>TIGR01387 cztR_silR_copR heavy metal response regulator. Members of this family contain a response regulator receiver domain (Pfam:PF00072) and an associated transcriptional regulatory region (Pfam:PF00486). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc. Most members encoded by genes adjacent to genes for encoding a member of the heavy metal sensor histidine kinase family (TIGRFAMs:TIGR01386), its partner in the two-component response regulator system.
Probab=59.08 E-value=15 Score=34.19 Aligned_cols=50 Identities=16% Similarity=0.149 Sum_probs=41.8
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHHh
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELM-----GVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~L-----gIS~erVRqie~RALkKLR~ 511 (525)
.|+++|.+|+.+-. .+.|+.+|.++|.+.+ ..+..+|..++.+-++||..
T Consensus 147 ~Lt~~E~~il~~l~-~~~~~~~sr~~i~~~~~~~~~~~~~~~~~~~i~~lr~kl~~ 201 (218)
T TIGR01387 147 TLTRKEFQLLWLLM-RRTGEVLPRTVIASLVWGMNFDSDTNVVDVAIRRLRAKVDD 201 (218)
T ss_pred eCCHHHHHHHHHHH-hCCCeeEcHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhhcC
Confidence 59999999998765 4567889999999999 45678899998888888863
No 382
>smart00862 Trans_reg_C Transcriptional regulatory protein, C terminal. This domain is almost always found associated with the response regulator receiver domain. It may play a role in DNA binding.
Probab=59.03 E-value=33 Score=27.07 Aligned_cols=50 Identities=22% Similarity=0.318 Sum_probs=36.7
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHH------CCCHHHHHHHHHHHHHHHHh
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELM------GVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~L------gIS~erVRqie~RALkKLR~ 511 (525)
.|+++|..+|.+-. ...|...|.++|.+.+ ..+..+|++...+-.++|..
T Consensus 5 ~Lt~~e~~lL~~L~-~~~~~~vs~~~l~~~lw~~~~~~~~~~~l~~~i~~LR~~l~~ 60 (78)
T smart00862 5 KLTPKEFRLLELLL-RNPGRVVSREELLEAVWGDDDDDVDDNTLDVHISRLRKKLED 60 (78)
T ss_pred ecCHHHHHHHHHHH-hCCCCccCHHHHHHHHcCCCCCCCccchHHHHHHHHHHHHhc
Confidence 47899999776543 4456789999999986 35677788777777776654
No 383
>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=58.69 E-value=12 Score=36.67 Aligned_cols=30 Identities=30% Similarity=0.624 Sum_probs=25.9
Q ss_pred CCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 478 DGRMK-TLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 478 ~g~~~-Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
.|..+ |-.++|+.||||+..|| .||.+|..
T Consensus 26 pG~~LpsE~~La~~lgVSRtpVR----EAL~~Le~ 56 (235)
T TIGR02812 26 PGSILPAERELSELIGVTRTTLR----EVLQRLAR 56 (235)
T ss_pred CCCcCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 45568 89999999999999999 78888875
No 384
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=58.64 E-value=20 Score=26.71 Aligned_cols=48 Identities=13% Similarity=0.198 Sum_probs=37.3
Q ss_pred cCCHHHHHHHHHHHhcCCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 009803 461 TLNPRERQVVRWRFGLEDG-RMKTLQEIGELMGVSRERIRQIESSAFRK 508 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g-~~~Tl~EIAe~LgIS~erVRqie~RALkK 508 (525)
.+++.+..+|.-.|..+.. ......+||..+|++...|.........+
T Consensus 6 ~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~ 54 (56)
T smart00389 6 SFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAK 54 (56)
T ss_pred cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhc
Confidence 3778888899888876632 23568899999999999999988766544
No 385
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=58.53 E-value=12 Score=36.60 Aligned_cols=38 Identities=13% Similarity=0.215 Sum_probs=29.4
Q ss_pred HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 468 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 468 ~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
.|+.-.|- .|..++..++|+.||||+..|| .||.+|..
T Consensus 19 ~I~~g~l~--pG~~L~e~eLae~lgVSRtpVR----EAL~~L~~ 56 (224)
T PRK11534 19 DIIRGNFQ--PDEKLRMSLLTSRYALGVGPLR----EALSQLVA 56 (224)
T ss_pred HHHhCCCC--CCCcCCHHHHHHHHCCChHHHH----HHHHHHHH
Confidence 35554443 3456899999999999999999 78888864
No 386
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=58.40 E-value=90 Score=31.99 Aligned_cols=24 Identities=21% Similarity=0.307 Sum_probs=21.2
Q ss_pred CCCCHHHHHHHcCCCHHHHHHHHh
Q 009803 387 RHPNNEEVAEATGLSMKRLHAVLL 410 (525)
Q Consensus 387 r~Pt~eEIA~~lgis~~~v~~~l~ 410 (525)
.+-|..|||+.+|+|..+|+++..
T Consensus 247 ~~~Tl~EIA~~lgvS~~rVrqi~~ 270 (284)
T PRK06596 247 DKSTLQELAAEYGVSAERVRQIEK 270 (284)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHH
Confidence 467899999999999999998864
No 387
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=58.34 E-value=14 Score=37.30 Aligned_cols=47 Identities=17% Similarity=0.288 Sum_probs=36.5
Q ss_pred HHHHHhcCCHHHHHHHHHHHhcCCC---CCCCHHHHHHHHCCCHHHHHHHHH
Q 009803 455 LEKVLDTLNPRERQVVRWRFGLEDG---RMKTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 455 L~~aL~~L~~rER~VL~lRygl~~g---~~~Tl~EIAe~LgIS~erVRqie~ 503 (525)
|......|++.|+.|..+- ++.. ..+|..|+|+..|+|..+|-..-+
T Consensus 3 i~~~~~~Lt~~e~~ia~yi--l~n~~~v~~~si~elA~~~~vS~aTv~Rf~k 52 (278)
T PRK11557 3 IRQRYPGLAQSDRKLADYL--LLQPDTARHLSSQQLANEAGVSQSSVVKFAQ 52 (278)
T ss_pred hhHhhhhCCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCCHHHHHHHHH
Confidence 5566788999999998654 4332 239999999999999999985543
No 388
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=58.31 E-value=13 Score=36.99 Aligned_cols=37 Identities=22% Similarity=0.342 Sum_probs=28.9
Q ss_pred HHHHHHhcCCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 469 VVRWRFGLEDGRMK-TLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 469 VL~lRygl~~g~~~-Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
|+.-.|. .|..+ |-.+||+.||||+..|| .||++|..
T Consensus 20 I~~g~l~--pG~~LPsE~eLa~~~gVSRtpVR----EAL~~L~~ 57 (251)
T PRK09990 20 IVDGVLK--VGQALPSERRLCEKLGFSRSALR----EGLTVLRG 57 (251)
T ss_pred HHcCCCC--CCCcCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 4444443 45568 89999999999999999 78888864
No 389
>PRK03837 transcriptional regulator NanR; Provisional
Probab=57.86 E-value=13 Score=36.42 Aligned_cols=37 Identities=30% Similarity=0.497 Sum_probs=28.4
Q ss_pred HHHHHHhcCCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 469 VVRWRFGLEDGRMK-TLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 469 VL~lRygl~~g~~~-Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
|+.-.|. .|..+ +..+||+.||||+..|| .||..|..
T Consensus 26 I~~g~l~--pG~~Lp~E~~Lae~~gVSRt~VR----EAL~~L~~ 63 (241)
T PRK03837 26 IRSGEFG--PGDQLPSERELMAFFGVGRPAVR----EALQALKR 63 (241)
T ss_pred HHhCCCC--CCCCCCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 4444433 34558 89999999999999999 78888874
No 390
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=57.85 E-value=18 Score=36.53 Aligned_cols=37 Identities=22% Similarity=0.217 Sum_probs=26.7
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803 466 ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE 502 (525)
Q Consensus 466 ER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie 502 (525)
+|-+-.|.+.-+.+.++|+.||++.+|+++.+|..++
T Consensus 11 ~ral~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL 47 (263)
T PRK09834 11 SRGLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLL 47 (263)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 3444445544444456999999999999999999443
No 391
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=57.77 E-value=13 Score=37.12 Aligned_cols=38 Identities=24% Similarity=0.401 Sum_probs=29.1
Q ss_pred HHHHHHHhcCCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 468 QVVRWRFGLEDGRMK-TLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 468 ~VL~lRygl~~g~~~-Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
.|+.-.|. -|..+ |-.++|+.||||+..|| .||+.|..
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 35544443 34558 69999999999999999 78888875
No 392
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=57.73 E-value=13 Score=36.95 Aligned_cols=38 Identities=21% Similarity=0.353 Sum_probs=28.9
Q ss_pred HHHHHHHhcCCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 468 QVVRWRFGLEDGRMK-TLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 468 ~VL~lRygl~~g~~~-Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
.|+.-.|. .|..+ |-.++|+.||||+..|| .||..|..
T Consensus 22 ~I~~g~l~--pG~~LpsE~eLa~~lgVSRtpVR----EAL~~L~~ 60 (254)
T PRK09464 22 LILEGTLR--PGEKLPPERELAKQFDVSRPSLR----EAIQRLEA 60 (254)
T ss_pred HHHcCCCC--CCCcCCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 34444443 34557 89999999999999999 78888865
No 393
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=57.10 E-value=18 Score=31.97 Aligned_cols=52 Identities=17% Similarity=0.181 Sum_probs=44.4
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803 460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 515 (525)
Q Consensus 460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~ 515 (525)
.+|.+-||-...-+|-.= +|-+|||-.+.++..||..+...-..|.|+.-+.
T Consensus 27 ~QLkELErvF~ETHYPDI----YTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~ 78 (125)
T KOG0484|consen 27 AQLKELERVFAETHYPDI----YTREEIALKIDLTEARVQVWFQNRRAKFRKQERA 78 (125)
T ss_pred HHHHHHHHHHHhhcCCcc----hhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHH
Confidence 567778887777777654 9999999999999999999999999999987654
No 394
>PRK11517 transcriptional regulatory protein YedW; Provisional
Probab=57.06 E-value=20 Score=33.62 Aligned_cols=49 Identities=14% Similarity=0.087 Sum_probs=41.0
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHH
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELM-----GVSRERIRQIESSAFRKLK 510 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~L-----gIS~erVRqie~RALkKLR 510 (525)
.|+++|.+|+.+-. .+-|+..|.++|.+.+ ..+..+|+.+..|-++||.
T Consensus 147 ~Lt~~E~~il~~l~-~~~g~~~s~~~i~~~~w~~~~~~~~~tv~~~i~rlr~Kl~ 200 (223)
T PRK11517 147 TLTRKEFQLLWLLA-SRAGEIIPRTVIASEIWGINFDSDTNTVDVAIRRLRAKVD 200 (223)
T ss_pred eCCHHHHHHHHHHH-hCCCccCCHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhhc
Confidence 69999999998754 4567889999999997 4467899999988888885
No 395
>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=56.94 E-value=22 Score=27.17 Aligned_cols=46 Identities=20% Similarity=0.186 Sum_probs=29.2
Q ss_pred cccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHH
Q 009803 363 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAV 408 (525)
Q Consensus 363 iP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~ 408 (525)
||....+.+-...+.-..|..+.-..-+..+||+.+|+++.+|+.=
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 4555555555555555566555445668899999999999999863
No 396
>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=56.56 E-value=10 Score=32.21 Aligned_cols=22 Identities=27% Similarity=0.291 Sum_probs=16.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~ 503 (525)
+|..|||+.+|.|+..|.+++.
T Consensus 4 ~tq~eIA~~lGks~s~Vs~~l~ 25 (93)
T PF08535_consen 4 WTQEEIAKRLGKSRSWVSNHLA 25 (93)
T ss_dssp --HHHHHHHTT--HHHHHHHHG
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 8999999999999999998764
No 397
>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=56.52 E-value=23 Score=31.48 Aligned_cols=25 Identities=32% Similarity=0.441 Sum_probs=21.4
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803 478 DGRMKTLQEIGELMGVSRERIRQIE 502 (525)
Q Consensus 478 ~g~~~Tl~EIAe~LgIS~erVRqie 502 (525)
++.+.|..|||+.+|+|+..|+++.
T Consensus 22 ~~~~~s~~eia~~~~i~~~~v~~il 46 (132)
T TIGR00738 22 DEGPVSVKEIAERQGISRSYLEKIL 46 (132)
T ss_pred CCCcCcHHHHHHHHCcCHHHHHHHH
Confidence 3458999999999999999999554
No 398
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=55.94 E-value=22 Score=35.57 Aligned_cols=41 Identities=22% Similarity=0.261 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 009803 464 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR 507 (525)
Q Consensus 464 ~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALk 507 (525)
+|++.|+.+-... ...+..||++.||||..|||.-+..--.
T Consensus 4 ~R~~~Il~~l~~~---~~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 4 ARQQAIVDLLLNH---TSLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred HHHHHHHHHHHHc---CCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 5666666654322 2599999999999999999988876433
No 399
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=55.73 E-value=15 Score=36.66 Aligned_cols=38 Identities=24% Similarity=0.336 Sum_probs=29.1
Q ss_pred HHHHHHHhcCCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 468 QVVRWRFGLEDGRMK-TLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 468 ~VL~lRygl~~g~~~-Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
.|+.-.|. .|..+ |-.|+|+.||||+..|| .||+.|..
T Consensus 14 ~I~~g~l~--pG~~LpsE~eLae~~gVSRtpVR----EAL~~Le~ 52 (253)
T PRK10421 14 LIEEKNLE--AGMKLPAERQLAMQLGVSRNSLR----EALAKLVS 52 (253)
T ss_pred HHHcCCCC--CCCcCCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 34444443 44568 78999999999999999 78888865
No 400
>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=55.70 E-value=30 Score=31.38 Aligned_cols=44 Identities=18% Similarity=0.240 Sum_probs=33.7
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHH----CCCHHHHHHHHHHHHH
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELM----GVSRERIRQIESSAFR 507 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~L----gIS~erVRqie~RALk 507 (525)
.|++.|.+|+..-+..+ +.|..||.+.| |+++.||+..+.|-.+
T Consensus 1 ~Lt~~E~~VM~vlW~~~---~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~ 48 (130)
T TIGR02698 1 SISDAEWEVMRVVWTLG---ETTSRDIIRILAEKKDWSDSTIKTLLGRLVD 48 (130)
T ss_pred CCCHHHHHHHHHHHcCC---CCCHHHHHHHHhhccCCcHHHHHHHHHHHHH
Confidence 47899999988776433 48999977776 7999999977666544
No 401
>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=55.69 E-value=33 Score=29.83 Aligned_cols=43 Identities=16% Similarity=0.100 Sum_probs=32.5
Q ss_pred cCCHHHHHHHHHHHh-cCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803 461 TLNPRERQVVRWRFG-LEDGRMKTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 461 ~L~~rER~VL~lRyg-l~~g~~~Tl~EIAe~LgIS~erVRqie~ 503 (525)
.|++.|-.||..-+- ...+.+.|..+||+.+++++.+|...+.
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~ 65 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIK 65 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHH
Confidence 689998888866551 1122349999999999999999995544
No 402
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=55.61 E-value=23 Score=33.24 Aligned_cols=26 Identities=15% Similarity=0.265 Sum_probs=21.4
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803 478 DGRMKTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 478 ~g~~~Tl~EIAe~LgIS~erVRqie~ 503 (525)
++.+....+||+.|||++.+|.++++
T Consensus 21 ~~~~~~~~diA~~L~Vsp~sVt~ml~ 46 (154)
T COG1321 21 EKGFARTKDIAERLKVSPPSVTEMLK 46 (154)
T ss_pred ccCcccHHHHHHHhCCCcHHHHHHHH
Confidence 44568999999999999999985443
No 403
>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=55.28 E-value=61 Score=35.48 Aligned_cols=24 Identities=25% Similarity=0.267 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHcCCCHHHHHHHHh
Q 009803 387 RHPNNEEVAEATGLSMKRLHAVLL 410 (525)
Q Consensus 387 r~Pt~eEIA~~lgis~~~v~~~l~ 410 (525)
++-|..+||+.+|+.+.+|..+..
T Consensus 317 kPLtlkdiA~~lglheSTVSRav~ 340 (429)
T TIGR02395 317 KPLTLREVAEELGLHESTISRAIN 340 (429)
T ss_pred cCCcHHHHHHHhCCCccchhhhhc
Confidence 455899999999999999999874
No 404
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=55.22 E-value=12 Score=35.87 Aligned_cols=26 Identities=23% Similarity=0.364 Sum_probs=22.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAFR 507 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RALk 507 (525)
||..|||+.+|.|..|||++..-.-+
T Consensus 62 ~Ti~EIAeelG~TeqTir~hlkgetk 87 (182)
T COG1318 62 MTISEIAEELGRTEQTVRNHLKGETK 87 (182)
T ss_pred CcHHHHHHHhCCCHHHHHHHHhcchh
Confidence 99999999999999999988765433
No 405
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.14 E-value=31 Score=30.57 Aligned_cols=48 Identities=17% Similarity=0.285 Sum_probs=38.4
Q ss_pred HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803 459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510 (525)
Q Consensus 459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR 510 (525)
.+.|++.+-+.+.+++--- =+++||-..+|+|--+||......|++|-
T Consensus 39 F~~Lt~d~LeFv~lf~r~R----GnlKEvEr~lg~sYptvR~kld~vlramg 86 (122)
T COG3877 39 FEYLTSDQLEFVELFLRCR----GNLKEVERELGISYPTVRTKLDEVLRAMG 86 (122)
T ss_pred ccccCHhHhHHHHHHHHHc----cCHHHHHHHHCCccHHHHHHHHHHHHHcC
Confidence 3567777777777766554 28999999999999999998888877763
No 406
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=55.01 E-value=20 Score=32.47 Aligned_cols=23 Identities=22% Similarity=0.234 Sum_probs=21.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~R 504 (525)
+|..++|+.+|||+.+|+++++.
T Consensus 19 ltq~~lA~~~gvs~~~is~~E~g 41 (135)
T PRK09706 19 LSQRSLAKAVKVSHVSISQWERD 41 (135)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Confidence 99999999999999999999865
No 407
>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=54.91 E-value=9 Score=32.78 Aligned_cols=25 Identities=28% Similarity=0.450 Sum_probs=22.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAF 506 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RAL 506 (525)
+|..|+|+.+|||..++|-.+...+
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~~Gl 25 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDIGL 25 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999988754
No 408
>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=54.74 E-value=10 Score=30.36 Aligned_cols=24 Identities=21% Similarity=0.354 Sum_probs=18.9
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 481 MKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 481 ~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
..|+.|||..||+|++.|+.++..
T Consensus 14 ~~S~~eLa~~~~~s~~~ve~mL~~ 37 (69)
T PF09012_consen 14 RVSLAELAREFGISPEAVEAMLEQ 37 (69)
T ss_dssp SEEHHHHHHHTT--HHHHHHHHHH
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHH
Confidence 489999999999999999976543
No 409
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=54.53 E-value=24 Score=35.84 Aligned_cols=26 Identities=8% Similarity=0.134 Sum_probs=21.6
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803 478 DGRMKTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 478 ~g~~~Tl~EIAe~LgIS~erVRqie~ 503 (525)
.+.++|+.|||+.+|+++.+|..+++
T Consensus 37 ~~~~~tl~eIa~~lglpkStv~RlL~ 62 (271)
T PRK10163 37 SGGSSSVSDISLNLDLPLSTTFRLLK 62 (271)
T ss_pred CCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 34569999999999999999985543
No 410
>PRK11569 transcriptional repressor IclR; Provisional
Probab=54.45 E-value=21 Score=36.30 Aligned_cols=33 Identities=12% Similarity=0.192 Sum_probs=24.8
Q ss_pred HHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803 471 RWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 471 ~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~ 503 (525)
.|.++-..+.++|+.|||+.+|+++.+|..++.
T Consensus 33 IL~~l~~~~~~~~lseia~~lglpksTv~RlL~ 65 (274)
T PRK11569 33 LLEWIAESNGSVALTELAQQAGLPNSTTHRLLT 65 (274)
T ss_pred HHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 333333345669999999999999999995543
No 411
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=54.29 E-value=23 Score=40.48 Aligned_cols=51 Identities=22% Similarity=0.305 Sum_probs=39.8
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHHhcCCC---CCCCHHHHHHHHCCCHHHHHHHHH
Q 009803 451 MKEDLEKVLDTLNPRERQVVRWRFGLEDG---RMKTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 451 ~~~~L~~aL~~L~~rER~VL~lRygl~~g---~~~Tl~EIAe~LgIS~erVRqie~ 503 (525)
+...|...+..|++.||.|..+- +++. ..+|..|||+..|+|..+|-..-+
T Consensus 343 l~~~I~~~~~~Lt~~E~~IA~yI--l~n~~~v~~~si~eLA~~~~vS~aTV~Rf~k 396 (638)
T PRK14101 343 VFERIRQMRDALTPAERRVADLA--LNHPRSIINDPIVDIARKADVSQPTVIRFCR 396 (638)
T ss_pred HHHHHHHHHhhcCHHHHHHHHHH--HhCHHHHHhccHHHHHHHhCCCHHHHHHHHH
Confidence 45578888999999999998654 4322 238999999999999999875443
No 412
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=54.17 E-value=28 Score=29.51 Aligned_cols=39 Identities=23% Similarity=0.397 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803 462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~ 503 (525)
|++.+..||...+..++ .+..+||+.+++++.+|.++..
T Consensus 20 lt~~q~~~L~~l~~~~~---~~~~~la~~l~i~~~~vt~~l~ 58 (126)
T COG1846 20 LTPPQYQVLLALYEAGG---ITVKELAERLGLDRSTVTRLLK 58 (126)
T ss_pred CCHHHHHHHHHHHHhCC---CcHHHHHHHHCCCHHHHHHHHH
Confidence 99999999988876653 3339999999999999995543
No 413
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.08 E-value=41 Score=28.86 Aligned_cols=39 Identities=23% Similarity=0.335 Sum_probs=27.6
Q ss_pred CCHHHHHH----HHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803 462 LNPRERQV----VRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 462 L~~rER~V----L~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~ 503 (525)
|++.|+++ |.-.|-+. ++|.++||..||+|...|..++.
T Consensus 3 Ln~eq~~~Tk~elqan~el~---~LS~~~iA~~Ln~t~~~lekil~ 45 (97)
T COG4367 3 LNPEQKQRTKQELQANFELC---PLSDEEIATALNWTEVKLEKILQ 45 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhc---cccHHHHHHHhCCCHHHHHHHHH
Confidence 55555544 33344333 59999999999999999887764
No 414
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=53.79 E-value=22 Score=35.93 Aligned_cols=41 Identities=10% Similarity=0.200 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 009803 464 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRK 508 (525)
Q Consensus 464 ~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkK 508 (525)
+|++.|+.+---. ...+..|+|+.||||+.|||+-+.. |.+
T Consensus 5 eR~~~Il~~L~~~---~~v~v~eLa~~l~VS~~TIRRDL~~-Le~ 45 (256)
T PRK10434 5 QRQAAILEYLQKQ---GKTSVEELAQYFDTTGTTIRKDLVI-LEH 45 (256)
T ss_pred HHHHHHHHHHHHc---CCEEHHHHHHHHCCCHHHHHHHHHH-HHH
Confidence 4566666554322 2489999999999999999988776 443
No 415
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=53.54 E-value=26 Score=27.47 Aligned_cols=25 Identities=20% Similarity=0.408 Sum_probs=22.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAF 506 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RAL 506 (525)
.|+.+||+.+|+|...+.++..+..
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~ 26 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKET 26 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHh
Confidence 7999999999999999998887665
No 416
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=53.51 E-value=28 Score=24.21 Aligned_cols=23 Identities=39% Similarity=0.603 Sum_probs=20.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~R 504 (525)
+|..++|+.+|++..+|++++..
T Consensus 11 ~s~~~la~~~~i~~~~i~~~~~~ 33 (56)
T smart00530 11 LTQEELAEKLGVSRSTLSRIENG 33 (56)
T ss_pred CCHHHHHHHhCCCHHHHHHHHCC
Confidence 89999999999999999987764
No 417
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=52.91 E-value=21 Score=25.39 Aligned_cols=24 Identities=25% Similarity=0.293 Sum_probs=17.1
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 481 MKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 481 ~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
+.|+.+||..+|+|+...+...++
T Consensus 8 ~~~l~~iA~~~g~S~~~f~r~Fk~ 31 (42)
T PF00165_consen 8 KLTLEDIAEQAGFSPSYFSRLFKK 31 (42)
T ss_dssp S--HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Confidence 499999999999999888855443
No 418
>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=52.77 E-value=50 Score=31.39 Aligned_cols=53 Identities=25% Similarity=0.443 Sum_probs=34.5
Q ss_pred HHHHHhcCCHHHHHHHHHHHhc---CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 455 LEKVLDTLNPRERQVVRWRFGL---EDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 455 L~~aL~~L~~rER~VL~lRygl---~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
+...++.+..+.-.|+.+-... ++--.+|+++||+.+|+|+.+|. |+++.|.+
T Consensus 46 i~~~l~l~g~k~~~Vl~~il~~~d~~N~v~~t~~~ia~~l~iS~~Tv~----r~ik~L~e 101 (165)
T PF05732_consen 46 IIKVLDLIGNKAFRVLMYILENMDKDNAVVATQKEIAEKLGISKPTVS----RAIKELEE 101 (165)
T ss_pred HHHHhhhhchhHHHHHHHHHHhcCCCCeEEeeHHHHHHHhCCCHHHHH----HHHHHHHh
Confidence 3334454545444554433221 11234799999999999999988 88888876
No 419
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=52.46 E-value=27 Score=29.02 Aligned_cols=33 Identities=24% Similarity=0.322 Sum_probs=26.9
Q ss_pred HHHHHHHhcCCCCCCCHHHHHHHHC------CCHHHHHHHHHH
Q 009803 468 QVVRWRFGLEDGRMKTLQEIGELMG------VSRERIRQIESS 504 (525)
Q Consensus 468 ~VL~lRygl~~g~~~Tl~EIAe~Lg------IS~erVRqie~R 504 (525)
.+...|--.+ +|..++|+.+| +|..+|.++++-
T Consensus 15 ~lk~~R~~lG----LTQ~dvA~~lg~~~g~i~SQstISR~Es~ 53 (75)
T smart00352 15 TFKQRRIKLG----FTQADVGLALGALYGPDFSQTTICRFEAL 53 (75)
T ss_pred HHHHHHHHcC----CCHHHHHHHhcccccCcCCHHHHHHHHhc
Confidence 3455666666 99999999999 599999998863
No 420
>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=52.37 E-value=26 Score=27.03 Aligned_cols=23 Identities=35% Similarity=0.601 Sum_probs=18.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~R 504 (525)
+|..++|+.+|+++.++.++++.
T Consensus 13 lt~~~~a~~~~i~~~~i~~~e~g 35 (64)
T PF12844_consen 13 LTQKDLAEKLGISRSTISKIENG 35 (64)
T ss_dssp --HHHHHHHHTS-HHHHHHHHTT
T ss_pred CCHHHHHHHHCcCHHHHHHHHCC
Confidence 99999999999999999999865
No 421
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=52.21 E-value=10 Score=32.80 Aligned_cols=26 Identities=27% Similarity=0.333 Sum_probs=23.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAFR 507 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RALk 507 (525)
+|..|+|+.+|||..++|-.+..++-
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~~Gll 27 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESIGLI 27 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 78999999999999999999887654
No 422
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=52.11 E-value=27 Score=31.07 Aligned_cols=22 Identities=27% Similarity=0.437 Sum_probs=20.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~ 503 (525)
.|..++|..||||+.+|..+..
T Consensus 19 ~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 19 KSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred chHHHHHHHhCcHHHHHHHHHH
Confidence 7999999999999999998866
No 423
>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=52.05 E-value=10 Score=33.14 Aligned_cols=25 Identities=28% Similarity=0.531 Sum_probs=22.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAF 506 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RAL 506 (525)
||..|+|+.+|||..++|..+...+
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gl 25 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKEGL 25 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999988765
No 424
>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=52.03 E-value=9.8 Score=28.10 Aligned_cols=20 Identities=20% Similarity=0.356 Sum_probs=17.7
Q ss_pred HHHHHHCCCHHHHHHHHHHH
Q 009803 486 EIGELMGVSRERIRQIESSA 505 (525)
Q Consensus 486 EIAe~LgIS~erVRqie~RA 505 (525)
+||+.+|||+.+|+++++.-
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCC
Confidence 79999999999999988753
No 425
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=51.96 E-value=81 Score=34.84 Aligned_cols=24 Identities=13% Similarity=0.174 Sum_probs=21.0
Q ss_pred CCCCHHHHHHHcCCCHHHHHHHHh
Q 009803 387 RHPNNEEVAEATGLSMKRLHAVLL 410 (525)
Q Consensus 387 r~Pt~eEIA~~lgis~~~v~~~l~ 410 (525)
++-|..+||+.+|+.+.+|..+..
T Consensus 342 kPLtlkdvAe~lglheSTVSRav~ 365 (455)
T PRK05932 342 KPLVLKDIAEELGMHESTISRATT 365 (455)
T ss_pred cCccHHHHHHHhCCCccchhhhhc
Confidence 345899999999999999999874
No 426
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=51.95 E-value=15 Score=34.73 Aligned_cols=23 Identities=13% Similarity=0.216 Sum_probs=0.0
Q ss_pred CCCHHHHHHHcCCCHHHHHHHHh
Q 009803 388 HPNNEEVAEATGLSMKRLHAVLL 410 (525)
Q Consensus 388 ~Pt~eEIA~~lgis~~~v~~~l~ 410 (525)
+-|..+||+.+|+++..|..++.
T Consensus 49 PLt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 49 PLTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp -----------------------
T ss_pred CCCHHHHHHHhCCCHhHHHHHHc
Confidence 44889999999999999998764
No 427
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=51.92 E-value=27 Score=29.90 Aligned_cols=42 Identities=19% Similarity=0.313 Sum_probs=27.6
Q ss_pred cCCHHHHHHHHHHHh-cCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803 461 TLNPRERQVVRWRFG-LEDGRMKTLQEIGELMGVSRERIRQIE 502 (525)
Q Consensus 461 ~L~~rER~VL~lRyg-l~~g~~~Tl~EIAe~LgIS~erVRqie 502 (525)
.|++.++.|+.+.-. ....+.+++.+|++.|+++...||+.+
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al 86 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKAL 86 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHH
Confidence 577777777766544 112234999999999999999999543
No 428
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=51.50 E-value=28 Score=35.03 Aligned_cols=37 Identities=16% Similarity=0.176 Sum_probs=27.2
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 465 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 465 rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
|.+.|+.+ ... ....+..||++.||||..|||.-+..
T Consensus 6 R~~~Il~~--l~~-~~~~~~~ela~~l~vS~~TirRdL~~ 42 (251)
T PRK13509 6 RHQILLEL--LAQ-LGFVTVEKVIERLGISPATARRDINK 42 (251)
T ss_pred HHHHHHHH--HHH-cCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 44444443 332 23489999999999999999988775
No 429
>cd00383 trans_reg_C Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and a response regulator. The former autophosphorylates in a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. The C-terminal effector domain contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunite of RNA polymerase.
Probab=51.49 E-value=37 Score=27.93 Aligned_cols=50 Identities=20% Similarity=0.246 Sum_probs=36.8
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHHh
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMG-----VSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~Lg-----IS~erVRqie~RALkKLR~ 511 (525)
.|+++|..+|.+-. ...|+..|.++|.+.+. .+..++++.+.+-.+||..
T Consensus 23 ~Lt~~e~~lL~~L~-~~~~~~vs~~~l~~~lw~~~~~~~~~~l~~~I~rLRkkl~~ 77 (95)
T cd00383 23 ELTPKEFELLELLA-RNPGRVLSREQLLEAVWGDDYDVDDRTVDVHISRLRKKLED 77 (95)
T ss_pred EeCHHHHHHHHHHH-hCCCCcCCHHHHHHHhcCCCCCCCcccHHHHHHHHHHHhcc
Confidence 48899999988755 44678899999999884 5666677666665555543
No 430
>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family contains mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation []. Homologues of neugrin are found in fungi suggesting they have a alternative role or more than one function.
Probab=51.30 E-value=26 Score=35.10 Aligned_cols=42 Identities=26% Similarity=0.300 Sum_probs=32.9
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~ 503 (525)
.|+..+.+-|++-+-. +...+|...+|+.|+||++.||.|+.
T Consensus 10 ~Ls~~~~~~ir~L~~~-~p~~~t~~~Lae~F~vspe~irrILk 51 (225)
T PF06413_consen 10 KLSREAMEQIRYLHKE-DPEEWTVERLAESFKVSPEAIRRILK 51 (225)
T ss_pred CCCHHHHHHHHHHHHh-CccccCHHHHHhhCCCCHHHHHHHHh
Confidence 5777777777666544 34458999999999999999998875
No 431
>PRK10643 DNA-binding transcriptional regulator BasR; Provisional
Probab=51.29 E-value=22 Score=33.17 Aligned_cols=49 Identities=12% Similarity=0.011 Sum_probs=36.5
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHH-----HCCCHHHHHHHHHHHHHHHH
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGEL-----MGVSRERIRQIESSAFRKLK 510 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~-----LgIS~erVRqie~RALkKLR 510 (525)
.|+++|.+|+.+..- .-|.+.|-++|.+. ++++..+|+.+.++.++||.
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 599999999987543 33434455555543 58899999999999999985
No 432
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=51.25 E-value=26 Score=30.77 Aligned_cols=54 Identities=20% Similarity=0.393 Sum_probs=37.8
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803 453 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF 506 (525)
Q Consensus 453 ~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RAL 506 (525)
..|..+|..++-+--+|..+.+...-+..|-..||+..||||.-+||....--+
T Consensus 8 ~~l~~~L~~~glk~~eI~IY~lLve~~~~mri~ei~rEl~is~rtvr~~v~~l~ 61 (113)
T COG5625 8 RKLGKALEAIGLKKNEIRIYSLLVEKGRGMRIREIQRELGISERTVRAAVAVLL 61 (113)
T ss_pred HHHHHHHHHcCCCcchhhhhhHHHHhcCCchHHHHHHHHhHHHHHHHHHHHHHH
Confidence 456677766555444555555555444449999999999999999997665554
No 433
>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=51.22 E-value=33 Score=24.05 Aligned_cols=23 Identities=43% Similarity=0.621 Sum_probs=20.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~R 504 (525)
+|..++|..+|+|+.+|.+++..
T Consensus 13 ~s~~~~a~~~~~~~~~v~~~~~g 35 (58)
T cd00093 13 LTQEELAEKLGVSRSTISRIENG 35 (58)
T ss_pred CCHHHHHHHHCCCHHHHHHHHcC
Confidence 89999999999999999987664
No 434
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=51.20 E-value=26 Score=30.93 Aligned_cols=35 Identities=29% Similarity=0.420 Sum_probs=27.3
Q ss_pred HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 468 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 468 ~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
+||.-.|...-| +|..+.|+.|||++.+|..+.+-
T Consensus 12 EiL~eeflep~g--lt~~~lA~~lgV~r~~is~ling 46 (104)
T COG3093 12 EILREEFLEPLG--LTQTELAEALGVTRNTISELING 46 (104)
T ss_pred HHHHHHHhcccc--CCHHHHHHHhCCCHHHHHHHHcC
Confidence 466666655312 99999999999999999988753
No 435
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=50.90 E-value=12 Score=32.79 Aligned_cols=26 Identities=19% Similarity=0.244 Sum_probs=23.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAFR 507 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RALk 507 (525)
+|..|+|+.+|||..++|-.+..++=
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~~GLi 26 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKIGLL 26 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCC
Confidence 57899999999999999999987654
No 436
>PHA00738 putative HTH transcription regulator
Probab=50.85 E-value=34 Score=30.41 Aligned_cols=35 Identities=9% Similarity=0.049 Sum_probs=25.4
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803 465 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE 502 (525)
Q Consensus 465 rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie 502 (525)
.-+.||.+-. .+.+++..+|++.+++|+.+|++.+
T Consensus 13 tRr~IL~lL~---~~e~~~V~eLae~l~lSQptVS~HL 47 (108)
T PHA00738 13 LRRKILELIA---ENYILSASLISHTLLLSYTTVLRHL 47 (108)
T ss_pred HHHHHHHHHH---HcCCccHHHHHHhhCCCHHHHHHHH
Confidence 3345555432 2334999999999999999999664
No 437
>COG3711 BglG Transcriptional antiterminator [Transcription]
Probab=50.77 E-value=18 Score=39.73 Aligned_cols=47 Identities=21% Similarity=0.139 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 464 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 464 ~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
..||..+.+-+...+ .+.++.++|..|++|+.+|.+-......++..
T Consensus 84 ~~er~~~~ll~~~~~-~~~~l~~La~~l~vs~~ti~~dl~~v~~~l~~ 130 (491)
T COG3711 84 KDERIIIILLLLLLS-ELLSLHELADELFVSKSTIINDLKDVRLKLLL 130 (491)
T ss_pred hHHHHHHHHHHHHhc-ChhhHHHHHHHHHhHHHHHHHHHHHHHHHHHh
Confidence 677777777766654 67999999999999999999888875555543
No 438
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=50.57 E-value=21 Score=35.64 Aligned_cols=37 Identities=22% Similarity=0.136 Sum_probs=28.1
Q ss_pred HHHHHHhcCCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 469 VVRWRFGLEDGRMK-TLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 469 VL~lRygl~~g~~~-Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
|+.-.|. .|..+ |-.+||+.||||+..|| .||+.|..
T Consensus 21 I~~g~l~--pG~~LpsE~eLae~~gVSRtpVR----EAL~~L~~ 58 (253)
T PRK11523 21 IEQGVYL--VGDKLPAERFIADEKNVSRTVVR----EAIIMLEV 58 (253)
T ss_pred HHcCCCC--CCCCCCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 4444443 34568 58899999999999999 78888864
No 439
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=50.30 E-value=20 Score=36.22 Aligned_cols=37 Identities=24% Similarity=0.325 Sum_probs=28.8
Q ss_pred CHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803 463 NPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE 502 (525)
Q Consensus 463 ~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie 502 (525)
.+|.+.|+.+---.+ ..+.+|+++.||||..|||.=+
T Consensus 4 ~eR~~~Il~~l~~~g---~v~v~eLa~~~~VS~~TIRRDL 40 (253)
T COG1349 4 EERHQKILELLKEKG---KVSVEELAELFGVSEMTIRRDL 40 (253)
T ss_pred HHHHHHHHHHHHHcC---cEEHHHHHHHhCCCHHHHHHhH
Confidence 357777877754333 3899999999999999999744
No 440
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=50.16 E-value=21 Score=39.70 Aligned_cols=45 Identities=16% Similarity=0.230 Sum_probs=32.4
Q ss_pred HHhcCCHHHHHHHHH---------HHhcCCC---CCCCHHHHHHHHCCCHHHHHHHH
Q 009803 458 VLDTLNPRERQVVRW---------RFGLEDG---RMKTLQEIGELMGVSRERIRQIE 502 (525)
Q Consensus 458 aL~~L~~rER~VL~l---------Rygl~~g---~~~Tl~EIAe~LgIS~erVRqie 502 (525)
++..|.-|.+.+++. -|+..|. +|+|+++||+.+|+..+||+...
T Consensus 334 li~si~qR~~TllkV~~~Iv~~Q~~Ff~~G~~~LkPLtlkdVAe~lglHeSTVSRa~ 390 (481)
T PRK12469 334 LIRNAQQRFDTIQRVAECIVARQRDFFRYGEIALKPLVLRDVAEELGLHESTISRAT 390 (481)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCcCCcHHHHHHHhCCCcchhhHHh
Confidence 345666676666542 2444333 89999999999999999999543
No 441
>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=49.98 E-value=12 Score=31.49 Aligned_cols=25 Identities=28% Similarity=0.453 Sum_probs=22.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAF 506 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RAL 506 (525)
+|..|+|+.+|||..++|.++.+.+
T Consensus 2 ~ti~evA~~~gvs~~tLR~ye~~Gl 26 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEEKGL 26 (88)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 7999999999999999999987764
No 442
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=49.91 E-value=12 Score=31.47 Aligned_cols=26 Identities=19% Similarity=0.262 Sum_probs=22.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAFR 507 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RALk 507 (525)
+|..|+|+.+|||..++|.++...+-
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~~Gli 27 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYERLGLL 27 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCCc
Confidence 78999999999999999999876543
No 443
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=49.87 E-value=35 Score=32.10 Aligned_cols=27 Identities=26% Similarity=0.288 Sum_probs=23.1
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 481 MKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 481 ~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
.+|-+|||+.|||+...|| +.+.+|..
T Consensus 28 ~~tdEeLa~~Lgi~~~~VR----k~L~~L~e 54 (158)
T TIGR00373 28 EFTDEEISLELGIKLNEVR----KALYALYD 54 (158)
T ss_pred CCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 4999999999999999999 56666654
No 444
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=49.83 E-value=28 Score=35.62 Aligned_cols=49 Identities=22% Similarity=0.422 Sum_probs=38.7
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHHhcCCC---CCCCHHHHHHHHCCCHHHHHHH
Q 009803 451 MKEDLEKVLDTLNPRERQVVRWRFGLEDG---RMKTLQEIGELMGVSRERIRQI 501 (525)
Q Consensus 451 ~~~~L~~aL~~L~~rER~VL~lRygl~~g---~~~Tl~EIAe~LgIS~erVRqi 501 (525)
+...|....+.|++.||.|-.+- +++. .-+|.+|||+..|||+.||-..
T Consensus 5 l~~~I~~~~~~Lt~~er~iA~yi--l~~~~~~~~~si~elA~~a~VS~aTv~Rf 56 (281)
T COG1737 5 LLERIRERYDSLTKSERKIADYI--LANPDEVALLSIAELAERAGVSPATVVRF 56 (281)
T ss_pred HHHHHHHHHhcCCHHHHHHHHHH--HhCHHHHHHHHHHHHHHHhCCCHHHHHHH
Confidence 45678888999999999987643 4332 2389999999999999998743
No 445
>PRK04158 transcriptional repressor CodY; Validated
Probab=49.62 E-value=29 Score=35.42 Aligned_cols=56 Identities=29% Similarity=0.421 Sum_probs=44.8
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHhcCCCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 452 KEDLEKVLDTLNPRERQVVRWRFGLEDGR--MKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 452 ~~~L~~aL~~L~~rER~VL~lRygl~~g~--~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
+..++.++++|+--|.+-+.+-|..=||. -+.-.-||+..||||+-|= .||+||-.
T Consensus 170 ~~~V~~Ai~tLSySEleAv~hIf~eL~g~EG~lvASkiADrvgITRSVIV----NALRK~ES 227 (256)
T PRK04158 170 KAVVQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIV----NALRKLES 227 (256)
T ss_pred HHHHHHHHHhcCHhHHHHHHHHHHhcCCCcceEEeeecccccCCchhhhh----hhhhhhhc
Confidence 45578889999999999999998775552 2677899999999987665 78888754
No 446
>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=49.46 E-value=19 Score=39.41 Aligned_cols=44 Identities=25% Similarity=0.392 Sum_probs=30.9
Q ss_pred HhcCCHHHHHHHHH---------HHhcCCC---CCCCHHHHHHHHCCCHHHHHHHH
Q 009803 459 LDTLNPRERQVVRW---------RFGLEDG---RMKTLQEIGELMGVSRERIRQIE 502 (525)
Q Consensus 459 L~~L~~rER~VL~l---------Rygl~~g---~~~Tl~EIAe~LgIS~erVRqie 502 (525)
+..|.-|.+.+++. -|+..|. +|+|+++||+.+|++.+||+...
T Consensus 284 i~~i~~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdiA~~lglheSTVSRav 339 (429)
T TIGR02395 284 IKALEQREETLLKVAEAIVEHQKDFFLGGPAALKPLTLREVAEELGLHESTISRAI 339 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccCcCCcHHHHHHHhCCCccchhhhh
Confidence 45566666555432 2444432 89999999999999999999543
No 447
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=49.41 E-value=13 Score=31.96 Aligned_cols=25 Identities=20% Similarity=0.348 Sum_probs=22.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAF 506 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RAL 506 (525)
+|..|+|+.+|||..++|-.+..++
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gl 25 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDKIGL 25 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999988765
No 448
>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=31.00 Aligned_cols=23 Identities=22% Similarity=0.465 Sum_probs=21.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~R 504 (525)
+|..|+|+.+|||..++|.++..
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~~ 23 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 57899999999999999999776
No 449
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=49.17 E-value=41 Score=28.92 Aligned_cols=22 Identities=27% Similarity=0.445 Sum_probs=20.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~ 503 (525)
+|.++||..||+|.+.|.+++.
T Consensus 24 ls~~~ia~dL~~s~~~le~vL~ 45 (89)
T PF10078_consen 24 LSLEQIAADLGTSPEHLEQVLN 45 (89)
T ss_pred CCHHHHHHHhCCCHHHHHHHHc
Confidence 9999999999999999997764
No 450
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=49.14 E-value=19 Score=32.53 Aligned_cols=23 Identities=35% Similarity=0.440 Sum_probs=20.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~R 504 (525)
||-+|+|+.+|+|+.||..+..+
T Consensus 1 MT~eELA~~tG~srQTINrWvRk 23 (122)
T PF07037_consen 1 MTPEELAELTGYSRQTINRWVRK 23 (122)
T ss_pred CCHHHHHHHhCccHHHHHHHHHh
Confidence 68999999999999999987653
No 451
>PRK06424 transcription factor; Provisional
Probab=49.11 E-value=27 Score=32.54 Aligned_cols=32 Identities=19% Similarity=0.135 Sum_probs=26.0
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 469 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 469 VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
|-.+|--.+ +|..|+|+.+|+++.+|+++++.
T Consensus 89 Ir~lRe~~G----LSQ~eLA~~iGvs~stIskiE~G 120 (144)
T PRK06424 89 VKNARERLS----MSQADLAAKIFERKNVIASIERG 120 (144)
T ss_pred HHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHCC
Confidence 334454455 99999999999999999999863
No 452
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=48.96 E-value=39 Score=32.70 Aligned_cols=39 Identities=15% Similarity=0.199 Sum_probs=32.0
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE 502 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie 502 (525)
.|++.|..||..-+..+ +.|..+||+.+++++.+|..+.
T Consensus 42 gLt~~q~~iL~~L~~~~---~itq~eLa~~l~l~~sTvtr~l 80 (185)
T PRK13777 42 DLNINEHHILWIAYHLK---GASISEIAKFGVMHVSTAFNFS 80 (185)
T ss_pred CCCHHHHHHHHHHHhCC---CcCHHHHHHHHCCCHhhHHHHH
Confidence 68999999987766543 3999999999999999988543
No 453
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=48.84 E-value=43 Score=31.71 Aligned_cols=31 Identities=26% Similarity=0.469 Sum_probs=24.6
Q ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 477 EDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 477 ~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
.++.+.|.++||+.+|+|..-+.++ +.+|++
T Consensus 21 ~~~~~vs~~eIA~~~~ip~~~l~kI----l~~L~~ 51 (164)
T PRK10857 21 SEAGPVPLADISERQGISLSYLEQL----FSRLRK 51 (164)
T ss_pred CCCCcCcHHHHHHHHCcCHHHHHHH----HHHHHH
Confidence 3557899999999999999998855 455554
No 454
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=48.76 E-value=58 Score=31.32 Aligned_cols=50 Identities=24% Similarity=0.312 Sum_probs=31.5
Q ss_pred HHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 454 DLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 454 ~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
.+..++. -++.-..||..-.- .| ++|-++||+.|||+...||++ |.+|..
T Consensus 13 ~l~~~~~-~~~~~~~Vl~~L~~--~g-~~tdeeLA~~Lgi~~~~VRk~----L~~L~e 62 (178)
T PRK06266 13 VLFEIME-GDEEGFEVLKALIK--KG-EVTDEEIAEQTGIKLNTVRKI----LYKLYD 62 (178)
T ss_pred HHHHHhc-CCccHhHHHHHHHH--cC-CcCHHHHHHHHCCCHHHHHHH----HHHHHH
Confidence 3444444 24444455554322 22 499999999999999999954 455543
No 455
>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=48.57 E-value=13 Score=31.83 Aligned_cols=25 Identities=12% Similarity=0.252 Sum_probs=22.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAF 506 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RAL 506 (525)
|+..|+|+.+|||..++|-.+...+
T Consensus 1 m~i~eva~~~gvs~~tlR~ye~~Gl 25 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDHIGL 25 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999987664
No 456
>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=48.42 E-value=13 Score=31.95 Aligned_cols=24 Identities=17% Similarity=0.356 Sum_probs=21.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSA 505 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RA 505 (525)
+|+.|+|+.+|||..++|.++...
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye~~G 25 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDRLG 25 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCC
Confidence 799999999999999999987654
No 457
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=47.91 E-value=14 Score=31.87 Aligned_cols=25 Identities=20% Similarity=0.372 Sum_probs=21.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAF 506 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RAL 506 (525)
+|..|+|+.+|||..|+|..+..++
T Consensus 1 y~i~e~A~~~gvs~~tlR~Ye~~Gl 25 (99)
T cd04772 1 YRTVDLARAIGLSPQTVRNYESLGL 25 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 4788999999999999998887654
No 458
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=47.91 E-value=14 Score=32.08 Aligned_cols=26 Identities=27% Similarity=0.355 Sum_probs=22.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAFR 507 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RALk 507 (525)
+|..|+|+.+|||..|+|-.+..++-
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~~Gll 27 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKLGLI 27 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 78999999999999999988876543
No 459
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=47.89 E-value=24 Score=34.64 Aligned_cols=26 Identities=27% Similarity=0.408 Sum_probs=23.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
-|-.|+|+.+|||+.||| +|+..|.+
T Consensus 26 PsE~eLa~~~~VSR~TVR----~Al~~L~~ 51 (230)
T TIGR02018 26 PSEHELVAQYGCSRMTVN----RALRELTD 51 (230)
T ss_pred cCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 399999999999999999 78887765
No 460
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=47.88 E-value=15 Score=36.04 Aligned_cols=38 Identities=29% Similarity=0.504 Sum_probs=30.0
Q ss_pred HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 468 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 468 ~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
.|+..++- -|.+++..+||+.||||+.-|| .||.+|-.
T Consensus 28 ~Il~g~l~--pG~~l~e~~La~~~gvSrtPVR----eAL~rL~~ 65 (230)
T COG1802 28 AILSGELA--PGERLSEEELAEELGVSRTPVR----EALRRLEA 65 (230)
T ss_pred HHHhCCCC--CCCCccHHHHHHHhCCCCccHH----HHHHHHHH
Confidence 35555543 4567999999999999999999 78888764
No 461
>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=47.87 E-value=14 Score=31.45 Aligned_cols=25 Identities=32% Similarity=0.525 Sum_probs=22.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAF 506 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RAL 506 (525)
||..|+|+.+|||+.+|+.++...+
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~~Gl 25 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEEKGL 25 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999987655
No 462
>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=47.73 E-value=14 Score=31.92 Aligned_cols=25 Identities=24% Similarity=0.375 Sum_probs=22.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAF 506 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RAL 506 (525)
+|..|+|+.+|||..++|..+...+
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~~Gl 25 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDEIGL 25 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999887665
No 463
>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=47.71 E-value=56 Score=30.24 Aligned_cols=54 Identities=20% Similarity=0.209 Sum_probs=38.9
Q ss_pred cccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCC
Q 009803 363 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPR 416 (525)
Q Consensus 363 iP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~ 416 (525)
-|.-..+.-....+.+.-|...-++..|..+|++.+|++++.|..+++..+-.+
T Consensus 21 Cp~C~~~~e~~f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGRL~~ 74 (137)
T TIGR03826 21 CPSCYEEEEREFEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGRLQL 74 (137)
T ss_pred CHHHhHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCCeec
Confidence 344444444555566666666667778999999999999999999987655333
No 464
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=47.64 E-value=37 Score=38.39 Aligned_cols=46 Identities=26% Similarity=0.260 Sum_probs=35.2
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
|++|+.+||.+- .+ .+.|..++|+.||||..|||+-+..-=.-|++
T Consensus 2 l~~R~~~iL~~L--~~--~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~ 47 (584)
T PRK09863 2 LNERELKIVDLL--EQ--QDRSGGELAQQLGVSRRTIVRDIAYINFTLNG 47 (584)
T ss_pred hHHHHHHHHHHH--Hc--CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 578888888754 22 35999999999999999999876655444444
No 465
>PF00486 Trans_reg_C: Transcriptional regulatory protein, C terminal; InterPro: IPR001867 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain that is almost always found associated with the response regulator receiver domain (see IPR001789 from INTERPRO). It may play a role in DNA binding [].; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2K4J_A 2JPB_A 1ODD_A 1OPC_A 1KGS_A 2PMU_E 2JZY_A 1GXP_B 1QQI_A 2Z33_A ....
Probab=47.63 E-value=52 Score=25.94 Aligned_cols=51 Identities=24% Similarity=0.301 Sum_probs=40.8
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHHhH
Q 009803 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMG-----VSRERIRQIESSAFRKLKNK 512 (525)
Q Consensus 461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~Lg-----IS~erVRqie~RALkKLR~~ 512 (525)
.|+++|..+|.+-. ...|++.|-++|.+.+- .+..+|.+.+.+-.+||...
T Consensus 5 ~Lt~~e~~lL~~L~-~~~~~~vs~~~l~~~~w~~~~~~~~~~l~~~I~rLR~kL~~~ 60 (77)
T PF00486_consen 5 KLTPKEFRLLELLL-RNPGRVVSREELIEALWGDEEDVSDNSLDVHISRLRKKLEDA 60 (77)
T ss_dssp ESSHHHHHHHHHHH-HTTTSEEEHHHHHHHHTSSSSTTCTHHHHHHHHHHHHHHHSS
T ss_pred ecCHHHHHHHHHHH-hCCCCCCCHHHhCChhhhcccccchhhHHHHHHHHHHHHhhc
Confidence 48999999998654 45678899999999873 67888888888877777763
No 466
>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=47.62 E-value=14 Score=32.58 Aligned_cols=26 Identities=23% Similarity=0.310 Sum_probs=23.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAFR 507 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RALk 507 (525)
|+..|+|+.+|||..++|-.+..++=
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye~~GLl 26 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEEQGLL 26 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCC
Confidence 58899999999999999999887653
No 467
>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=47.62 E-value=41 Score=24.60 Aligned_cols=21 Identities=19% Similarity=0.351 Sum_probs=18.8
Q ss_pred CCCHHHHHHHHCCCHHHHHHH
Q 009803 481 MKTLQEIGELMGVSRERIRQI 501 (525)
Q Consensus 481 ~~Tl~EIAe~LgIS~erVRqi 501 (525)
..|+.+||+..|+|+..+.+.
T Consensus 16 ~~s~~~Ia~~~gvs~~~~y~~ 36 (47)
T PF00440_consen 16 AVSIRDIARRAGVSKGSFYRY 36 (47)
T ss_dssp TSSHHHHHHHHTSCHHHHHHH
T ss_pred hCCHHHHHHHHccchhhHHHH
Confidence 399999999999999998754
No 468
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=47.41 E-value=14 Score=31.70 Aligned_cols=25 Identities=20% Similarity=0.266 Sum_probs=22.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAF 506 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RAL 506 (525)
|+..|+|+.+|||..+||-.+...+
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye~~GL 25 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLREGL 25 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 6789999999999999998887665
No 469
>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=47.20 E-value=44 Score=30.46 Aligned_cols=32 Identities=19% Similarity=0.128 Sum_probs=22.4
Q ss_pred HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 468 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 468 ~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
.||.|.. .+ +.--+||..|+||...|++++.|
T Consensus 25 rIvela~-~G----~rp~~Isr~l~Vs~gcVsKIl~R 56 (125)
T PF00292_consen 25 RIVELAK-EG----VRPCDISRQLRVSHGCVSKILSR 56 (125)
T ss_dssp HHHHHHH-TT------HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHhh-hc----CCHHHHHHHHccchhHHHHHHHH
Confidence 4666664 34 89999999999999999988765
No 470
>PF11662 DUF3263: Protein of unknown function (DUF3263); InterPro: IPR021678 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=47.11 E-value=77 Score=26.51 Aligned_cols=45 Identities=22% Similarity=0.319 Sum_probs=34.3
Q ss_pred cCCHHHHHHHHHH--HhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 009803 461 TLNPRERQVVRWR--FGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR 507 (525)
Q Consensus 461 ~L~~rER~VL~lR--ygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALk 507 (525)
.|+++++.||-+- ..-.+| -+-+.|-+.||+|.-+--|+++.-+.
T Consensus 2 ~Ls~~d~~iL~fE~~ww~~~G--aKe~aIre~fGls~~rYyq~Ln~LiD 48 (77)
T PF11662_consen 2 GLSDRDRAILDFERRWWRHGG--AKEEAIREEFGLSPTRYYQRLNALID 48 (77)
T ss_pred CCCHHHHHHHHHHHHhCcCCC--CcHHHHHHHHCCCHHHHHHHHHHHhC
Confidence 5899999998652 222223 57899999999999999999887653
No 471
>PHA02943 hypothetical protein; Provisional
Probab=47.10 E-value=41 Score=31.80 Aligned_cols=22 Identities=32% Similarity=0.327 Sum_probs=19.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~ 503 (525)
.|..|||+.||+|.+.|+.++.
T Consensus 25 ~TtseIAkaLGlS~~qa~~~Ly 46 (165)
T PHA02943 25 KTTSRIANKLGVSHSMARNALY 46 (165)
T ss_pred ccHHHHHHHHCCCHHHHHHHHH
Confidence 8999999999999999997653
No 472
>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=47.03 E-value=6.4 Score=37.30 Aligned_cols=47 Identities=15% Similarity=0.246 Sum_probs=0.0
Q ss_pred HHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803 454 DLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE 502 (525)
Q Consensus 454 ~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie 502 (525)
.|..+...|=..|+.-|. .|.+.-.|+|+++||+.+|++.+||+...
T Consensus 24 TL~~v~~~iv~~Q~~ff~--~g~~~l~PLt~~~iA~~lgl~~STVSRav 70 (160)
T PF04552_consen 24 TLLRVAQAIVERQKDFFL--GGPGALKPLTMKDIADELGLHESTVSRAV 70 (160)
T ss_dssp -------------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHh--cCcccCcCCCHHHHHHHhCCCHhHHHHHH
Confidence 345555556566655443 23334478999999999999999999543
No 473
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=47.02 E-value=14 Score=31.73 Aligned_cols=25 Identities=12% Similarity=0.402 Sum_probs=22.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAF 506 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RAL 506 (525)
|+..|+|+.+|||..++|.++...+
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye~~Gl 25 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEEIGL 25 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999987654
No 474
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=46.98 E-value=25 Score=34.80 Aligned_cols=28 Identities=32% Similarity=0.405 Sum_probs=23.7
Q ss_pred CCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 480 RMK-TLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 480 ~~~-Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
..+ |-.|+++.||||+.||| +|+..|-+
T Consensus 27 ~~LPsE~eL~~~~~VSR~TvR----~Al~~L~~ 55 (240)
T PRK09764 27 DALPTESALQTEFGVSRVTVR----QALRQLVE 55 (240)
T ss_pred CcCCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 335 88999999999999999 78887764
No 475
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=46.95 E-value=14 Score=32.36 Aligned_cols=26 Identities=27% Similarity=0.445 Sum_probs=23.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAFR 507 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RALk 507 (525)
+|..|+|+.+|||..++|-.+..++-
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye~~gll 26 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEKEGLL 26 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 58899999999999999999887653
No 476
>PRK14999 histidine utilization repressor; Provisional
Probab=46.78 E-value=26 Score=34.73 Aligned_cols=26 Identities=31% Similarity=0.402 Sum_probs=22.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
-|-.|+|+.+|||+.||| +|+..|..
T Consensus 37 PsE~eLa~~~gVSR~TVR----~Al~~L~~ 62 (241)
T PRK14999 37 PSEAELVAQYGFSRMTIN----RALRELTD 62 (241)
T ss_pred CCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 389999999999999999 78877764
No 477
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=46.62 E-value=1.2e+02 Score=26.02 Aligned_cols=88 Identities=20% Similarity=0.275 Sum_probs=49.6
Q ss_pred CHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHH
Q 009803 390 NNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQV 469 (525)
Q Consensus 390 t~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~V 469 (525)
++.|+|+.+|+|...++.+.....-+ +...+++.- .+ ++. +|. +=+.|
T Consensus 2 ~I~e~a~~~gvs~~tLR~ye~~Gll~-----p~r~~~g~R---~Y------~~~----------dv~--------~l~~I 49 (96)
T cd04774 2 KVDEVAKRLGLTKRTLKYYEEIGLVS-----PERSEGRYR---LY------SEE----------DLK--------RLERI 49 (96)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCCC-----CCcCCCCCE---EE------CHH----------HHH--------HHHHH
Confidence 56799999999999999987532111 111011100 00 111 121 22346
Q ss_pred HHHHHhcCCCCCCCHHHHHHHHCCCHHHH---HHHHHHHHHHHHhHH
Q 009803 470 VRWRFGLEDGRMKTLQEIGELMGVSRERI---RQIESSAFRKLKNKK 513 (525)
Q Consensus 470 L~lRygl~~g~~~Tl~EIAe~LgIS~erV---Rqie~RALkKLR~~l 513 (525)
..++-..| +|+++|...++...+.+ -+.....|..++..+
T Consensus 50 ~~L~~~~G----~~l~ei~~~l~~~~~~~~~~~~~~~~~l~~~~~~l 92 (96)
T cd04774 50 LRLREVLG----FSLQEVTHFLERPLEPVDGGHRYSAESLREIHDAL 92 (96)
T ss_pred HHHHHHcC----CCHHHHHHHHhccccccchhHHHHHHHHHHHHHHH
Confidence 67776556 99999999999877543 222334455555444
No 478
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=46.48 E-value=29 Score=36.69 Aligned_cols=43 Identities=23% Similarity=0.424 Sum_probs=33.9
Q ss_pred hcCCHHHHHHHHH---HHhcCCCCCCCHHHHHHH--HCCCHHHHHHHHH
Q 009803 460 DTLNPRERQVVRW---RFGLEDGRMKTLQEIGEL--MGVSRERIRQIES 503 (525)
Q Consensus 460 ~~L~~rER~VL~l---Rygl~~g~~~Tl~EIAe~--LgIS~erVRqie~ 503 (525)
..|++|+++|+.. .| ...++|.+.+++++. +|+|..|||+-..
T Consensus 2 ~~l~~R~~~Il~~IV~~y-i~~~~pv~s~~l~~~~~l~~S~aTIR~dm~ 49 (339)
T PRK00082 2 SMLDERQREILRAIVEDY-IATGEPVGSKTLSKRYGLGVSSATIRNDMA 49 (339)
T ss_pred CccCHHHHHHHHHHHHHH-HhcCCCcCHHHHHHHhCCCCChHHHHHHHH
Confidence 3588999999863 23 335778999999977 9999999996554
No 479
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=46.40 E-value=32 Score=34.64 Aligned_cols=38 Identities=24% Similarity=0.246 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803 464 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 464 ~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R 504 (525)
+|+..|+.+- .. ....+..|+|+.||||..|||.=+..
T Consensus 7 eR~~~I~~~l--~~-~~~v~v~eLa~~~~VS~~TIRRDL~~ 44 (252)
T PRK10681 7 ERIGQLLQAL--KR-SDKLHLKDAAALLGVSEMTIRRDLNA 44 (252)
T ss_pred HHHHHHHHHH--HH-cCCCcHHHHHHHhCCCHHHHHHHHHH
Confidence 3555565543 22 22489999999999999999976664
No 480
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=46.35 E-value=27 Score=34.15 Aligned_cols=26 Identities=27% Similarity=0.427 Sum_probs=23.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
-|-.|+|+.||||+.||| +||..|.+
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 78888865
No 481
>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=46.34 E-value=33 Score=27.30 Aligned_cols=32 Identities=19% Similarity=0.260 Sum_probs=26.5
Q ss_pred HHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHh
Q 009803 379 KQLYSENGRHPNNEEVAEATGLSMKRLHAVLL 410 (525)
Q Consensus 379 ~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~ 410 (525)
.+++.+++..-+..+||+.||++..+|+..-.
T Consensus 13 ~e~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 13 FEIYKESNGKIKLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred HHHHHHhCCCccHHHHHHHHCCCHHHHHHHhh
Confidence 34566777788999999999999999998754
No 482
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=46.10 E-value=1e+02 Score=34.42 Aligned_cols=37 Identities=14% Similarity=0.179 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHcC---CCCCHHHHHHHcCCCHHHHHHHHh
Q 009803 374 VKEARKQLYSENG---RHPNNEEVAEATGLSMKRLHAVLL 410 (525)
Q Consensus 374 i~ka~~~L~~~lg---r~Pt~eEIA~~lgis~~~v~~~l~ 410 (525)
|-+.+..+..... ++-|..+||+.+|+.+..|..+..
T Consensus 352 Iv~~Q~~Ff~~G~~~LkPLtlkdVAe~lglHeSTVSRa~~ 391 (481)
T PRK12469 352 IVARQRDFFRYGEIALKPLVLRDVAEELGLHESTISRATG 391 (481)
T ss_pred HHHHHHHHHhCCcccCcCCcHHHHHHHhCCCcchhhHHhc
Confidence 3334444444322 455899999999999999999874
No 483
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=46.09 E-value=14 Score=33.15 Aligned_cols=26 Identities=27% Similarity=0.344 Sum_probs=23.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAFR 507 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RALk 507 (525)
||..|+|+.+|||..++|-.+...+-
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~~GLl 26 (127)
T cd01108 1 MNIGEAAKLTGLSAKMIRYYEEIGLI 26 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 68899999999999999998887654
No 484
>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=45.75 E-value=49 Score=24.38 Aligned_cols=26 Identities=27% Similarity=0.240 Sum_probs=21.5
Q ss_pred cCCCCCHHHHHHHcCCCHHHHHHHHh
Q 009803 385 NGRHPNNEEVAEATGLSMKRLHAVLL 410 (525)
Q Consensus 385 lgr~Pt~eEIA~~lgis~~~v~~~l~ 410 (525)
....-|..|||+.+|+|...|..+..
T Consensus 17 y~~~~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 17 YFEGLTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp HTST-SHHHHHHHHTSCHHHHHHHHH
T ss_pred hcCCCCHHHHHHHHCCcHHHHHHHHH
Confidence 36677899999999999999988764
No 485
>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=45.49 E-value=24 Score=24.49 Aligned_cols=21 Identities=19% Similarity=0.434 Sum_probs=17.2
Q ss_pred CHHHHHHHcCCCHHHHHHHHh
Q 009803 390 NNEEVAEATGLSMKRLHAVLL 410 (525)
Q Consensus 390 t~eEIA~~lgis~~~v~~~l~ 410 (525)
|.+|||..+|++.+.|..++.
T Consensus 4 tr~diA~~lG~t~ETVSR~l~ 24 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVSRILK 24 (32)
T ss_dssp -HHHHHHHHTS-HHHHHHHHH
T ss_pred CHHHHHHHhCCcHHHHHHHHH
Confidence 568999999999999998874
No 486
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=45.47 E-value=82 Score=31.50 Aligned_cols=54 Identities=28% Similarity=0.406 Sum_probs=43.6
Q ss_pred HHHHHHhcCCHHHHHHHHHHHhcCCCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 454 DLEKVLDTLNPRERQVVRWRFGLEDGR--MKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 454 ~L~~aL~~L~~rER~VL~lRygl~~g~--~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
.+.-+++.|+--|-+.+..-|+.-||. -++-.-||+..||+|+-|- .||+||-.
T Consensus 175 ~V~mAi~tLSYSEleAve~I~eELdG~EG~lvASkiADrvGITRSVIV----NALRKlES 230 (261)
T COG4465 175 VVQMAISTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIV----NALRKLES 230 (261)
T ss_pred HHHHHHhhccHHHHHHHHHHHHhcCCccceeeehhhhhhhCchHHHHH----HHHHHhhh
Confidence 456678999999999999999876553 3788899999999977654 78888864
No 487
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=45.35 E-value=45 Score=30.15 Aligned_cols=30 Identities=33% Similarity=0.492 Sum_probs=24.2
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 478 DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 478 ~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
++++.|..|||+.+++|..-|+++ +.+|++
T Consensus 22 ~~~~~s~~~ia~~~~ip~~~l~ki----l~~L~~ 51 (135)
T TIGR02010 22 ETGPVTLADISERQGISLSYLEQL----FAKLRK 51 (135)
T ss_pred CCCcCcHHHHHHHHCcCHHHHHHH----HHHHHH
Confidence 456899999999999999999955 455554
No 488
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=45.29 E-value=32 Score=32.70 Aligned_cols=23 Identities=26% Similarity=0.404 Sum_probs=21.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESS 504 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~R 504 (525)
+|++++|+.+|||+.+|+++++.
T Consensus 21 lt~~elA~~~gis~~~is~~E~g 43 (185)
T PRK09943 21 LSQRRAAELSGLTHSAISTIEQD 43 (185)
T ss_pred CCHHHHHHHHCCCHHHHHHHHcC
Confidence 99999999999999999999974
No 489
>PRK13705 plasmid-partitioning protein SopA; Provisional
Probab=45.29 E-value=29 Score=37.36 Aligned_cols=55 Identities=22% Similarity=0.313 Sum_probs=39.9
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHhcC---CC---CCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803 452 KEDLEKVLDTLNPRERQVVRWRFGLE---DG---RMKTLQEIGELMGVSRERIRQIESSAF 506 (525)
Q Consensus 452 ~~~L~~aL~~L~~rER~VL~lRygl~---~g---~~~Tl~EIAe~LgIS~erVRqie~RAL 506 (525)
...+..|++.++...+.+...-|+.+ .. ..++..|+|+.+|||..+||..+...+
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~k~~r~~~i~e~A~~~gvs~~tiR~ye~~gl 64 (388)
T PRK13705 4 METLNQCINAGHEMTKAIAIAQFNDDSPEARKITRRWRIGEAADLVGVSSQAIRDAEKAGR 64 (388)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCcCCCccccccCCCCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 34567777777777777777666221 11 347899999999999999998866544
No 490
>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=45.25 E-value=16 Score=32.37 Aligned_cols=27 Identities=22% Similarity=0.305 Sum_probs=23.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAFRK 508 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RALkK 508 (525)
||..|+|+.+|||..++|-.+..++=.
T Consensus 1 ~~ige~a~~~gvs~~tLryYe~~GLi~ 27 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEEKGLLP 27 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 689999999999999999998876543
No 491
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=45.10 E-value=38 Score=35.21 Aligned_cols=39 Identities=23% Similarity=0.284 Sum_probs=29.6
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803 465 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF 506 (525)
Q Consensus 465 rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RAL 506 (525)
|.++|+.+.. ++.+.+..+||+.+|||+.+|++.+.+-.
T Consensus 5 r~~~il~~L~---~~~~~s~~~LA~~lgvsr~tV~~~l~~L~ 43 (319)
T PRK11886 5 VMLQLLSLLA---DGDFHSGEQLGEELGISRAAIWKHIQTLE 43 (319)
T ss_pred HHHHHHHHHH---cCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4556665543 34568999999999999999998887654
No 492
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=45.09 E-value=15 Score=32.96 Aligned_cols=26 Identities=23% Similarity=0.399 Sum_probs=22.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSAFR 507 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RALk 507 (525)
|+..|+|+.+|||..++|-.+...+-
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~~GLl 26 (127)
T TIGR02044 1 MNIGQVAKLTGLSSKMIRYYEEKGLI 26 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 68899999999999999998877654
No 493
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=45.09 E-value=27 Score=26.27 Aligned_cols=24 Identities=33% Similarity=0.576 Sum_probs=19.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 009803 482 KTLQEIGELMGVSRERIRQIESSA 505 (525)
Q Consensus 482 ~Tl~EIAe~LgIS~erVRqie~RA 505 (525)
++.+|+++.+|+|+.++....++.
T Consensus 4 l~~~ev~~~~g~s~~ti~~~~k~g 27 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTIYRLIKDG 27 (51)
T ss_dssp E-HHHHHHHHSS-HHHHHHHHHHH
T ss_pred ccHHHHHHHHCCCHHHHHHHHhcc
Confidence 578999999999999999887743
No 494
>COG4709 Predicted membrane protein [Function unknown]
Probab=45.07 E-value=61 Score=31.62 Aligned_cols=58 Identities=24% Similarity=0.275 Sum_probs=44.1
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHhc---C-CCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803 449 KFMKEDLEKVLDTLNPRERQVVRWRFGL---E-DGRMKTLQEIGELMGVSRERIRQIESSAF 506 (525)
Q Consensus 449 ~~~~~~L~~aL~~L~~rER~VL~lRygl---~-~g~~~Tl~EIAe~LgIS~erVRqie~RAL 506 (525)
.+....|+..|+.||+.+|.=+...|-. + +....|-+||+..||=+.+-.+++..+..
T Consensus 4 ~efL~eL~~yL~~Lp~~~r~e~m~dyeehF~~a~~~GksE~EI~~~LG~P~eiA~ei~s~~~ 65 (195)
T COG4709 4 TEFLNELEQYLEGLPREERREIMYDYEEHFREAQEAGKSEEEIAKDLGDPKEIAAEILSERG 65 (195)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhhhhcCCCHHHHHHHhCCHHHHHHHHHHHcc
Confidence 4556678999999999988866655432 1 12338999999999999999998876654
No 495
>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=44.93 E-value=29 Score=34.02 Aligned_cols=27 Identities=30% Similarity=0.475 Sum_probs=23.6
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803 481 MKTLQEIGELMGVSRERIRQIESSAFRKLKN 511 (525)
Q Consensus 481 ~~Tl~EIAe~LgIS~erVRqie~RALkKLR~ 511 (525)
--|-.|+|+.||||+.||| +|+..|.+
T Consensus 24 LPsE~eLa~~~gVSR~TVR----~Al~~L~~ 50 (233)
T TIGR02404 24 LPSEHELMDQYGASRETVR----KALNLLTE 50 (233)
T ss_pred CcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 3589999999999999999 78888765
No 496
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=44.93 E-value=24 Score=38.91 Aligned_cols=45 Identities=18% Similarity=0.350 Sum_probs=31.5
Q ss_pred HHhcCCHHHHHHHHH---------HHhcCCC---CCCCHHHHHHHHCCCHHHHHHHH
Q 009803 458 VLDTLNPRERQVVRW---------RFGLEDG---RMKTLQEIGELMGVSRERIRQIE 502 (525)
Q Consensus 458 aL~~L~~rER~VL~l---------Rygl~~g---~~~Tl~EIAe~LgIS~erVRqie 502 (525)
++..|.-|.+.+++. -|+..|. +|+|+++||+.+|+..+||+...
T Consensus 308 li~~i~~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdvAe~lglheSTVSRav 364 (455)
T PRK05932 308 LIKSLEQRKETLLKVARCIVEQQRDFFEHGEEALKPLVLKDIAEELGMHESTISRAT 364 (455)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCcCccHHHHHHHhCCCccchhhhh
Confidence 345566666655432 2444333 89999999999999999999543
No 497
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=44.88 E-value=50 Score=26.66 Aligned_cols=34 Identities=21% Similarity=0.170 Sum_probs=22.5
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHC-CCHHHHHHHH
Q 009803 465 RERQVVRWRFGLEDGRMKTLQEIGELMG-VSRERIRQIE 502 (525)
Q Consensus 465 rER~VL~lRygl~~g~~~Tl~EIAe~Lg-IS~erVRqie 502 (525)
|+-.+...+-..+ +|+.+||+.|| ....+|..-.
T Consensus 33 R~va~yL~r~~~~----~sl~~Ig~~fg~rdHstV~~a~ 67 (70)
T PF08299_consen 33 RQVAMYLARELTG----LSLSEIGRYFGGRDHSTVIHAI 67 (70)
T ss_dssp HHHHHHHHHHHS-------HHHHHHHCTSSTHHHHHHHH
T ss_pred HHHHHHHHHHHhC----CCHHHHHHHhCCCCHHHHHHHH
Confidence 4444444554455 99999999999 9999998443
No 498
>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=44.84 E-value=74 Score=23.62 Aligned_cols=27 Identities=22% Similarity=0.159 Sum_probs=18.8
Q ss_pred HcCCCCCHHHHHHHcCCCHHHHHHHHh
Q 009803 384 ENGRHPNNEEVAEATGLSMKRLHAVLL 410 (525)
Q Consensus 384 ~lgr~Pt~eEIA~~lgis~~~v~~~l~ 410 (525)
..-..-+..|||+.+|+|+..|...+.
T Consensus 22 ~~~~g~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 22 RYFQGMSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp HHTS---HHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHCcCHHHHHHHHCcCHHHHHHHHH
Confidence 344566889999999999999987764
No 499
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=44.64 E-value=42 Score=32.31 Aligned_cols=37 Identities=24% Similarity=0.219 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803 464 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 464 ~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~ 503 (525)
+|++.|+.+--- ....+..++++.||||..|||.-+.
T Consensus 7 ~R~~~Il~~l~~---~~~~~~~~La~~~~vS~~TiRRDl~ 43 (185)
T PRK04424 7 ERQKALQELIEE---NPFITDEELAEKFGVSIQTIRLDRM 43 (185)
T ss_pred HHHHHHHHHHHH---CCCEEHHHHHHHHCcCHHHHHHHHH
Confidence 355555544332 2248999999999999999996443
No 500
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=44.50 E-value=40 Score=29.08 Aligned_cols=36 Identities=11% Similarity=0.192 Sum_probs=25.4
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803 465 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 503 (525)
Q Consensus 465 rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~ 503 (525)
-|+.+|...+-..+ -...+.|+.||||+.+++..+.
T Consensus 55 ~Er~~i~~aL~~~~---gn~s~AAr~LGIsRsTL~rKLk 90 (95)
T PRK00430 55 VEAPLLDMVMQYTR---GNQTRAALMLGINRGTLRKKLK 90 (95)
T ss_pred HHHHHHHHHHHHcC---CCHHHHHHHhCCCHHHHHHHHH
Confidence 35666655554433 3789999999999999885443
Done!