Query 009449
Match_columns 534
No_of_seqs 363 out of 1790
Neff 5.9
Searched_HMMs 46136
Date Thu Mar 28 13:15:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009449.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009449hhsearch_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 6.5E-64 1.4E-68 530.2 36.2 312 218-533 59-412 (415)
2 PRK05949 RNA polymerase sigma 100.0 4.4E-60 9.5E-65 491.0 36.5 308 223-533 18-326 (327)
3 PRK07406 RNA polymerase sigma 100.0 3.6E-60 7.7E-65 498.0 35.7 308 224-532 64-372 (373)
4 PRK07405 RNA polymerase sigma 100.0 6.8E-59 1.5E-63 480.5 35.6 306 225-533 10-316 (317)
5 TIGR02997 Sig70-cyanoRpoD RNA 100.0 1.1E-58 2.3E-63 475.0 35.0 293 227-520 5-298 (298)
6 COG0568 RpoD DNA-directed RNA 100.0 2.2E-58 4.7E-63 474.6 30.5 312 222-533 8-342 (342)
7 PRK05901 RNA polymerase sigma 100.0 2.2E-57 4.7E-62 491.0 30.1 298 223-533 211-509 (509)
8 PRK07921 RNA polymerase sigma 100.0 2.9E-56 6.3E-61 461.7 32.6 295 225-532 28-323 (324)
9 PRK09210 RNA polymerase sigma 100.0 4.6E-52 9.9E-57 437.5 30.6 272 222-533 95-367 (367)
10 PRK05658 RNA polymerase sigma 100.0 9.2E-50 2E-54 445.2 31.8 259 275-533 353-618 (619)
11 TIGR02393 RpoD_Cterm RNA polym 100.0 5.6E-48 1.2E-52 383.4 26.9 238 296-533 1-238 (238)
12 PRK07122 RNA polymerase sigma 100.0 4.8E-43 1.1E-47 353.8 26.8 220 295-523 40-263 (264)
13 PRK05657 RNA polymerase sigma 100.0 3.3E-42 7.1E-47 357.3 30.9 269 221-529 51-320 (325)
14 PRK07500 rpoH2 RNA polymerase 100.0 7.2E-42 1.6E-46 349.5 29.8 260 225-526 8-280 (289)
15 PRK06596 RNA polymerase factor 100.0 5.8E-41 1.3E-45 342.0 30.3 259 223-525 14-282 (284)
16 PRK07408 RNA polymerase sigma 100.0 4E-41 8.7E-46 338.2 27.7 229 291-526 20-254 (256)
17 TIGR02392 rpoH_proteo alternat 100.0 5.9E-40 1.3E-44 332.1 29.9 226 294-524 34-269 (270)
18 PRK05911 RNA polymerase sigma 100.0 2E-39 4.3E-44 326.2 29.0 225 294-525 22-255 (257)
19 TIGR02850 spore_sigG RNA polym 100.0 5.2E-39 1.1E-43 322.3 28.0 219 294-522 33-253 (254)
20 TIGR02394 rpoS_proteo RNA poly 100.0 5.3E-38 1.2E-42 320.0 29.2 246 283-528 33-279 (285)
21 COG1191 FliA DNA-directed RNA 100.0 6.2E-38 1.3E-42 312.2 26.0 229 285-524 13-245 (247)
22 PRK08215 sporulation sigma fac 100.0 1.2E-37 2.7E-42 312.8 28.0 220 294-523 36-257 (258)
23 TIGR02885 spore_sigF RNA polym 100.0 4.1E-37 8.9E-42 303.5 26.3 224 290-523 5-231 (231)
24 TIGR02980 SigBFG RNA polymeras 100.0 2.1E-36 4.5E-41 297.5 26.1 221 294-523 2-226 (227)
25 TIGR02941 Sigma_B RNA polymera 100.0 4E-36 8.8E-41 301.0 28.0 234 284-523 16-253 (255)
26 PRK06288 RNA polymerase sigma 100.0 8.8E-36 1.9E-40 301.1 29.6 226 294-526 30-263 (268)
27 PRK07670 RNA polymerase sigma 100.0 1.3E-35 2.9E-40 296.9 28.3 235 283-524 8-250 (251)
28 TIGR02479 FliA_WhiG RNA polyme 100.0 3.3E-35 7.1E-40 288.9 25.7 217 300-523 1-223 (224)
29 PRK12427 flagellar biosynthesi 100.0 3.8E-34 8.3E-39 283.8 25.6 210 296-522 16-230 (231)
30 PRK06986 fliA flagellar biosyn 100.0 6.1E-34 1.3E-38 282.2 26.9 225 292-525 5-234 (236)
31 PRK08583 RNA polymerase sigma 100.0 9.1E-34 2E-38 284.3 27.3 233 284-525 16-255 (257)
32 PRK05572 sporulation sigma fac 100.0 1.1E-33 2.3E-38 283.4 27.1 228 285-524 21-251 (252)
33 PRK05803 sporulation sigma fac 100.0 1.4E-26 2.9E-31 229.4 24.1 185 289-526 42-230 (233)
34 PRK08301 sporulation sigma fac 99.9 1.8E-24 3.8E-29 214.0 22.6 189 283-524 39-231 (234)
35 TIGR02846 spore_sigmaK RNA pol 99.9 4.5E-24 9.7E-29 210.8 22.7 188 283-523 35-226 (227)
36 PRK08295 RNA polymerase factor 99.9 8.7E-24 1.9E-28 204.1 22.5 196 280-527 8-206 (208)
37 TIGR02835 spore_sigmaE RNA pol 99.9 2.2E-23 4.7E-28 206.8 22.7 190 283-525 39-232 (234)
38 TIGR02859 spore_sigH RNA polym 99.9 7.1E-23 1.5E-27 196.0 21.2 191 281-523 4-197 (198)
39 PRK05602 RNA polymerase sigma 99.9 1.1E-22 2.4E-27 193.7 20.6 176 281-528 5-181 (186)
40 PRK09646 RNA polymerase sigma 99.9 1.8E-22 4E-27 194.0 20.6 176 282-525 16-192 (194)
41 PRK12513 RNA polymerase sigma 99.9 2E-22 4.3E-27 193.2 20.0 181 281-528 11-192 (194)
42 PRK09648 RNA polymerase sigma 99.9 4E-22 8.6E-27 190.4 21.2 172 284-524 12-188 (189)
43 TIGR02948 SigW_bacill RNA poly 99.9 3.4E-22 7.4E-27 189.5 20.3 179 284-524 6-185 (187)
44 PRK09641 RNA polymerase sigma 99.9 4.4E-22 9.4E-27 188.7 20.8 181 282-524 4-185 (187)
45 TIGR02952 Sig70_famx2 RNA poly 99.9 1E-21 2.2E-26 183.2 20.3 167 288-523 3-170 (170)
46 PRK06811 RNA polymerase factor 99.9 1.5E-21 3.2E-26 187.0 20.4 175 281-525 3-181 (189)
47 PRK12514 RNA polymerase sigma 99.9 1.5E-21 3.3E-26 184.6 19.9 173 282-524 5-178 (179)
48 PRK12519 RNA polymerase sigma 99.9 1.6E-21 3.5E-26 186.8 20.1 175 282-524 15-190 (194)
49 TIGR02939 RpoE_Sigma70 RNA pol 99.9 3.3E-21 7.2E-26 183.1 21.2 181 282-524 6-187 (190)
50 PRK12537 RNA polymerase sigma 99.9 2.5E-21 5.3E-26 184.2 20.2 173 281-523 8-181 (182)
51 PRK09652 RNA polymerase sigma 99.9 1.8E-21 3.9E-26 182.4 18.9 173 290-524 4-177 (182)
52 PRK13919 putative RNA polymera 99.9 2.4E-21 5.2E-26 184.1 19.7 176 281-524 8-184 (186)
53 PRK11923 algU RNA polymerase s 99.9 5E-21 1.1E-25 183.2 21.8 179 283-524 7-187 (193)
54 PRK12524 RNA polymerase sigma 99.9 4.2E-21 9.1E-26 184.9 21.3 177 281-527 11-188 (196)
55 PRK06759 RNA polymerase factor 99.9 1.5E-21 3.2E-26 179.8 17.2 150 295-522 4-153 (154)
56 PRK12534 RNA polymerase sigma 99.9 3.9E-21 8.4E-26 183.1 19.6 174 283-524 12-186 (187)
57 PRK12538 RNA polymerase sigma 99.9 5.3E-21 1.2E-25 190.1 20.6 174 282-527 49-223 (233)
58 PRK12526 RNA polymerase sigma 99.9 8.3E-21 1.8E-25 184.6 21.0 178 284-526 26-204 (206)
59 PRK11922 RNA polymerase sigma 99.9 9.7E-21 2.1E-25 187.4 20.7 184 281-525 15-199 (231)
60 PRK12515 RNA polymerase sigma 99.9 1.4E-20 3.1E-25 179.8 20.6 178 280-528 6-184 (189)
61 PRK09640 RNA polymerase sigma 99.9 4.4E-21 9.6E-26 183.4 17.0 173 280-524 7-183 (188)
62 PRK11924 RNA polymerase sigma 99.9 1.6E-20 3.6E-25 175.5 20.4 172 287-526 4-176 (179)
63 TIGR02984 Sig-70_plancto1 RNA 99.9 1.4E-20 3.1E-25 178.4 20.3 177 294-523 6-188 (189)
64 PRK12542 RNA polymerase sigma 99.9 4.4E-21 9.6E-26 182.7 16.4 172 294-532 8-179 (185)
65 PRK09643 RNA polymerase sigma 99.9 1.9E-20 4.1E-25 180.1 20.7 172 281-525 12-184 (192)
66 TIGR02954 Sig70_famx3 RNA poly 99.9 2.3E-20 5E-25 175.0 19.4 167 281-524 1-168 (169)
67 PRK09638 RNA polymerase sigma 99.9 1.7E-20 3.7E-25 176.5 18.2 172 281-524 3-175 (176)
68 PRK12531 RNA polymerase sigma 99.9 1.8E-20 3.9E-25 180.2 18.5 180 283-528 14-194 (194)
69 PRK12522 RNA polymerase sigma 99.9 3.2E-20 7E-25 174.8 18.8 166 295-524 3-168 (173)
70 TIGR02985 Sig70_bacteroi1 RNA 99.9 2.5E-20 5.3E-25 171.1 17.3 160 296-523 2-161 (161)
71 PRK12543 RNA polymerase sigma 99.9 3.1E-20 6.6E-25 176.3 18.4 164 294-527 6-169 (179)
72 PRK12520 RNA polymerase sigma 99.9 2.6E-20 5.7E-25 178.3 17.9 181 296-527 3-183 (191)
73 TIGR03001 Sig-70_gmx1 RNA poly 99.8 6.6E-20 1.4E-24 183.6 21.0 184 279-531 22-217 (244)
74 TIGR02937 sigma70-ECF RNA poly 99.8 8E-20 1.7E-24 164.2 18.8 157 296-523 2-158 (158)
75 PRK09415 RNA polymerase factor 99.8 5.2E-20 1.1E-24 174.8 18.4 164 293-525 14-177 (179)
76 PRK09645 RNA polymerase sigma 99.8 5.5E-20 1.2E-24 172.9 18.3 163 294-527 8-170 (173)
77 TIGR02989 Sig-70_gvs1 RNA poly 99.8 4.3E-20 9.2E-25 170.7 16.8 158 296-523 2-159 (159)
78 PRK12539 RNA polymerase sigma 99.8 1.4E-19 3.1E-24 172.4 19.4 169 283-525 8-181 (184)
79 TIGR02999 Sig-70_X6 RNA polyme 99.8 1.5E-19 3.3E-24 171.1 19.3 172 283-523 4-182 (183)
80 PRK09649 RNA polymerase sigma 99.8 1.3E-19 2.8E-24 173.3 18.7 171 284-528 12-183 (185)
81 PRK12512 RNA polymerase sigma 99.8 1.7E-19 3.8E-24 171.3 19.4 167 285-526 11-182 (184)
82 PRK12533 RNA polymerase sigma 99.8 1.9E-19 4.1E-24 177.1 20.1 171 293-527 16-186 (216)
83 PRK12536 RNA polymerase sigma 99.8 1E-19 2.2E-24 172.9 17.5 169 284-525 9-179 (181)
84 COG1595 RpoE DNA-directed RNA 99.8 2.6E-19 5.7E-24 170.4 20.2 170 289-526 9-178 (182)
85 PRK12529 RNA polymerase sigma 99.8 2.4E-19 5.3E-24 170.3 18.9 164 293-524 11-176 (178)
86 PRK12518 RNA polymerase sigma 99.8 1.7E-19 3.7E-24 169.6 17.1 168 289-527 4-172 (175)
87 PRK09642 RNA polymerase sigma 99.8 1.7E-19 3.6E-24 167.5 16.7 156 302-526 2-157 (160)
88 PRK12523 RNA polymerase sigma 99.8 2.1E-19 4.6E-24 169.3 17.4 163 292-525 6-169 (172)
89 TIGR02947 SigH_actino RNA poly 99.8 1.8E-19 3.8E-24 172.9 16.7 172 294-525 10-181 (193)
90 PRK09644 RNA polymerase sigma 99.8 3.1E-19 6.7E-24 166.9 17.5 157 297-526 3-159 (165)
91 PRK12528 RNA polymerase sigma 99.8 6E-19 1.3E-23 164.1 19.2 157 295-522 4-160 (161)
92 PRK12516 RNA polymerase sigma 99.8 3.5E-19 7.5E-24 171.0 17.8 160 294-527 9-168 (187)
93 TIGR02943 Sig70_famx1 RNA poly 99.8 7.3E-19 1.6E-23 168.6 18.6 178 299-527 6-183 (188)
94 PRK12532 RNA polymerase sigma 99.8 8E-19 1.7E-23 168.6 18.4 181 298-528 8-189 (195)
95 TIGR02983 SigE-fam_strep RNA p 99.8 5.5E-19 1.2E-23 164.1 16.7 156 293-524 4-159 (162)
96 PRK12545 RNA polymerase sigma 99.8 9.6E-19 2.1E-23 169.5 18.9 180 299-528 12-192 (201)
97 PRK12547 RNA polymerase sigma 99.8 1E-18 2.2E-23 163.6 17.9 158 294-525 5-162 (164)
98 PRK09639 RNA polymerase sigma 99.8 1.4E-18 3.1E-23 161.8 18.9 160 294-525 2-161 (166)
99 PRK12530 RNA polymerase sigma 99.8 1.2E-18 2.6E-23 167.2 18.6 175 299-526 11-185 (189)
100 PRK12544 RNA polymerase sigma 99.8 1.5E-18 3.4E-23 169.2 19.2 181 297-527 20-200 (206)
101 PRK09647 RNA polymerase sigma 99.8 1.8E-18 4E-23 168.3 19.6 164 294-527 27-190 (203)
102 PRK12541 RNA polymerase sigma 99.8 1.9E-18 4E-23 160.8 18.1 156 294-522 4-159 (161)
103 PRK12535 RNA polymerase sigma 99.8 2.6E-18 5.6E-23 166.2 19.2 171 284-526 13-184 (196)
104 PRK08241 RNA polymerase factor 99.8 3.1E-18 6.6E-23 178.2 20.6 188 284-522 7-200 (339)
105 TIGR02960 SigX5 RNA polymerase 99.8 2.9E-18 6.3E-23 176.9 19.3 181 294-525 4-192 (324)
106 TIGR02950 SigM_subfam RNA poly 99.8 1E-18 2.2E-23 160.6 14.1 153 301-523 1-153 (154)
107 PRK09637 RNA polymerase sigma 99.8 5.6E-18 1.2E-22 161.7 18.4 154 297-525 3-156 (181)
108 PRK12540 RNA polymerase sigma 99.8 3.8E-18 8.3E-23 163.1 17.2 160 295-528 5-164 (182)
109 PRK12527 RNA polymerase sigma 99.8 5.3E-18 1.2E-22 157.4 17.7 155 301-525 1-155 (159)
110 TIGR02895 spore_sigI RNA polym 99.8 5.2E-18 1.1E-22 167.2 18.3 118 289-406 3-125 (218)
111 PRK07037 extracytoplasmic-func 99.8 8E-18 1.7E-22 156.5 18.5 158 299-525 2-159 (163)
112 PRK09651 RNA polymerase sigma 99.8 1.1E-17 2.4E-22 157.9 19.1 161 294-525 9-169 (172)
113 TIGR02959 SigZ RNA polymerase 99.8 9.1E-18 2E-22 158.3 16.9 148 302-524 2-149 (170)
114 PRK12517 RNA polymerase sigma 99.8 1.5E-17 3.3E-22 159.7 18.6 163 290-527 18-180 (188)
115 PRK12525 RNA polymerase sigma 99.8 3.7E-17 8E-22 153.6 19.4 159 294-523 8-166 (168)
116 PRK12546 RNA polymerase sigma 99.8 2.9E-17 6.2E-22 158.1 17.5 157 295-526 8-164 (188)
117 PRK12511 RNA polymerase sigma 99.7 2.9E-17 6.4E-22 157.1 16.1 158 296-526 5-162 (182)
118 PRK09047 RNA polymerase factor 99.7 6.5E-17 1.4E-21 149.7 15.6 155 317-527 2-158 (161)
119 PRK09636 RNA polymerase sigma 99.7 1.3E-16 2.9E-21 163.2 17.7 159 296-524 5-164 (293)
120 TIGR02957 SigX4 RNA polymerase 99.7 8.4E-16 1.8E-20 156.7 17.4 156 299-524 1-157 (281)
121 PRK09635 sigI RNA polymerase s 99.7 1E-15 2.2E-20 157.0 17.8 161 295-523 5-166 (290)
122 PRK06704 RNA polymerase factor 99.7 1E-15 2.2E-20 152.1 17.1 158 286-525 9-166 (228)
123 TIGR03209 P21_Cbot clostridium 99.6 3E-14 6.5E-19 130.0 13.4 136 297-509 1-141 (142)
124 PRK09191 two-component respons 99.6 3.6E-14 7.8E-19 140.4 13.9 137 296-525 2-138 (261)
125 PRK08311 putative RNA polymera 99.5 3.9E-12 8.5E-17 127.2 18.9 89 282-370 4-95 (237)
126 PF07638 Sigma70_ECF: ECF sigm 99.4 7.3E-12 1.6E-16 120.3 19.3 175 283-524 4-184 (185)
127 PF04542 Sigma70_r2: Sigma-70 99.3 1.2E-11 2.5E-16 99.0 7.4 70 300-369 1-70 (71)
128 PF04539 Sigma70_r3: Sigma-70 99.2 2.1E-11 4.5E-16 100.8 6.9 78 379-456 1-78 (78)
129 PF04545 Sigma70_r4: Sigma-70, 99.2 3.7E-11 8.1E-16 91.4 7.0 50 468-521 1-50 (50)
130 PF08281 Sigma70_r4_2: Sigma-7 98.9 2.3E-09 5E-14 82.5 7.1 54 462-519 1-54 (54)
131 PRK06930 positive control sigm 98.7 1.9E-07 4E-12 89.2 13.8 72 451-526 94-165 (170)
132 PRK00118 putative DNA-binding 98.4 9.6E-07 2.1E-11 77.7 8.6 61 464-528 10-70 (104)
133 cd06171 Sigma70_r4 Sigma70, re 98.3 1.9E-06 4.1E-11 64.2 6.7 54 463-520 2-55 (55)
134 TIGR00721 tfx DNA-binding prot 98.2 3.6E-06 7.8E-11 77.6 6.8 57 470-531 5-61 (137)
135 PRK03975 tfx putative transcri 98.1 5.1E-06 1.1E-10 77.0 6.9 51 470-525 5-55 (141)
136 PRK04217 hypothetical protein; 98.1 5.9E-06 1.3E-10 73.5 6.4 56 470-529 41-96 (110)
137 PF04297 UPF0122: Putative hel 98.0 3.1E-05 6.7E-10 67.8 8.6 54 470-527 16-69 (101)
138 TIGR01636 phage_rinA phage tra 97.9 5.9E-05 1.3E-09 69.3 8.7 60 460-523 71-132 (134)
139 smart00421 HTH_LUXR helix_turn 97.8 3.7E-05 7.9E-10 58.2 5.5 47 470-521 2-48 (58)
140 PF00196 GerE: Bacterial regul 97.7 6.8E-05 1.5E-09 58.6 5.7 47 470-521 2-48 (58)
141 cd06170 LuxR_C_like C-terminal 97.6 0.00013 2.9E-09 55.3 5.9 46 472-522 1-46 (57)
142 PF07374 DUF1492: Protein of u 97.6 0.00031 6.7E-09 61.4 8.5 55 461-519 44-99 (100)
143 TIGR03879 near_KaiC_dom probab 97.6 0.00012 2.7E-09 60.4 5.5 47 464-514 8-55 (73)
144 PF04967 HTH_10: HTH DNA bindi 97.5 0.00039 8.3E-09 54.1 6.6 48 472-519 1-51 (53)
145 TIGR01321 TrpR trp operon repr 97.4 0.0002 4.3E-09 62.0 5.0 48 464-511 24-75 (94)
146 PRK15411 rcsA colanic acid cap 97.4 0.00024 5.3E-09 69.5 6.1 46 471-521 137-182 (207)
147 PRK15201 fimbriae regulatory p 97.4 0.00031 6.7E-09 67.3 6.3 48 470-522 132-179 (198)
148 PRK10840 transcriptional regul 97.4 0.0003 6.5E-09 68.1 6.0 47 470-521 149-195 (216)
149 PRK13719 conjugal transfer tra 97.3 0.00033 7.3E-09 69.2 6.0 52 466-522 138-189 (217)
150 PRK11475 DNA-binding transcrip 97.3 0.00037 8.1E-09 68.5 6.2 47 470-521 133-179 (207)
151 PRK13870 transcriptional regul 97.3 0.00037 8.1E-09 69.8 6.0 47 471-522 173-219 (234)
152 TIGR03541 reg_near_HchA LuxR f 97.3 0.0004 8.8E-09 69.2 6.0 51 469-524 169-219 (232)
153 TIGR03020 EpsA transcriptional 97.3 0.00044 9.4E-09 70.0 6.2 50 469-523 188-237 (247)
154 PRK10100 DNA-binding transcrip 97.3 0.00048 1E-08 68.2 6.1 47 470-521 154-200 (216)
155 PRK10188 DNA-binding transcrip 97.3 0.0005 1.1E-08 69.1 6.2 47 471-522 179-225 (240)
156 COG4566 TtrR Response regulato 97.2 0.0011 2.4E-08 64.2 8.2 66 460-530 131-196 (202)
157 COG2197 CitB Response regulato 97.2 0.00047 1E-08 67.9 5.8 48 470-522 147-194 (211)
158 COG2771 CsgD DNA-binding HTH d 97.1 0.0014 3E-08 51.4 6.4 50 470-524 3-52 (65)
159 PF13936 HTH_38: Helix-turn-he 97.1 0.00063 1.4E-08 50.6 4.0 41 470-514 3-43 (44)
160 PF02001 DUF134: Protein of un 97.1 0.0011 2.4E-08 58.7 6.0 52 472-527 42-93 (106)
161 PRK09483 response regulator; P 97.0 0.0013 2.8E-08 62.6 5.9 46 470-520 147-192 (217)
162 COG3413 Predicted DNA binding 96.9 0.0019 4.2E-08 63.6 6.8 52 471-522 155-209 (215)
163 COG4941 Predicted RNA polymera 96.9 0.023 4.9E-07 59.6 14.0 158 299-522 9-167 (415)
164 PRK15369 two component system 96.8 0.0025 5.5E-08 59.0 5.9 47 470-521 148-194 (211)
165 TIGR01637 phage_arpU phage tra 96.6 0.012 2.7E-07 53.5 9.3 61 460-524 67-130 (132)
166 PRK10651 transcriptional regul 96.6 0.0036 7.9E-08 58.7 5.7 47 470-521 154-200 (216)
167 PRK01381 Trp operon repressor; 96.6 0.0023 5.1E-08 55.8 3.7 48 462-509 22-73 (99)
168 COG1356 tfx Transcriptional re 96.5 0.0022 4.7E-08 58.0 3.4 48 472-524 9-56 (143)
169 COG2739 Uncharacterized protei 96.5 0.0098 2.1E-07 51.9 7.1 49 470-522 16-64 (105)
170 PRK09390 fixJ response regulat 96.5 0.0078 1.7E-07 55.5 7.0 55 464-523 134-188 (202)
171 PF00140 Sigma70_r1_2: Sigma-7 96.3 0.0031 6.6E-08 45.4 2.5 32 224-255 3-35 (37)
172 PRK15320 transcriptional activ 96.3 0.0077 1.7E-07 58.8 5.7 66 450-521 144-209 (251)
173 COG1342 Predicted DNA-binding 96.2 0.0099 2.1E-07 51.4 5.7 52 472-527 34-85 (99)
174 PRK10403 transcriptional regul 96.0 0.012 2.5E-07 55.1 5.7 48 470-522 152-199 (215)
175 PRK10360 DNA-binding transcrip 95.8 0.017 3.7E-07 53.9 5.6 50 470-524 136-185 (196)
176 PRK09935 transcriptional regul 95.7 0.022 4.8E-07 53.4 5.9 46 471-521 149-194 (210)
177 PRK13558 bacterio-opsin activa 95.7 0.02 4.2E-07 65.1 6.6 50 469-522 605-661 (665)
178 PRK09958 DNA-binding transcrip 95.6 0.022 4.8E-07 53.4 5.9 47 469-520 141-187 (204)
179 PRK04841 transcriptional regul 95.6 0.018 4E-07 67.4 6.3 48 470-522 837-884 (903)
180 PRK05658 RNA polymerase sigma 95.6 2.9 6.2E-05 47.9 23.7 34 217-253 102-135 (619)
181 TIGR02531 yecD_yerC TrpR-relat 94.9 0.054 1.2E-06 46.5 5.4 40 469-515 34-73 (88)
182 PF13384 HTH_23: Homeodomain-l 94.9 0.024 5.3E-07 42.5 2.8 33 478-515 9-41 (50)
183 PF13613 HTH_Tnp_4: Helix-turn 94.6 0.085 1.8E-06 40.6 5.3 50 471-523 2-51 (53)
184 PRK15418 transcriptional regul 94.5 0.049 1.1E-06 57.2 4.9 37 477-517 19-55 (318)
185 PF05263 DUF722: Protein of un 94.5 0.13 2.8E-06 47.3 7.1 57 461-519 71-127 (130)
186 PF00325 Crp: Bacterial regula 94.4 0.05 1.1E-06 38.0 3.3 27 491-521 2-28 (32)
187 PF13412 HTH_24: Winged helix- 94.4 0.095 2.1E-06 39.1 5.0 41 472-515 1-41 (48)
188 PF12645 HTH_16: Helix-turn-he 94.1 0.21 4.5E-06 40.5 6.8 55 287-341 4-65 (65)
189 PF02796 HTH_7: Helix-turn-hel 94.0 0.049 1.1E-06 40.6 2.8 33 476-513 11-43 (45)
190 cd00569 HTH_Hin_like Helix-tur 93.9 0.1 2.2E-06 34.6 4.1 36 472-511 6-41 (42)
191 PF06530 Phage_antitermQ: Phag 93.5 0.43 9.3E-06 43.4 8.5 55 468-526 59-113 (125)
192 PRK07598 RNA polymerase sigma 93.3 0.91 2E-05 49.5 12.0 38 381-418 110-147 (415)
193 PRK09210 RNA polymerase sigma 92.6 1.6 3.6E-05 46.6 12.8 130 254-420 217-347 (367)
194 PF09862 DUF2089: Protein of u 92.5 0.28 6.1E-06 44.0 5.7 50 468-521 30-79 (113)
195 TIGR02393 RpoD_Cterm RNA polym 92.3 2.2 4.9E-05 42.4 12.6 35 254-288 88-122 (238)
196 PRK05901 RNA polymerase sigma 92.3 3.5 7.6E-05 46.2 15.2 36 254-289 359-394 (509)
197 COG2909 MalT ATP-dependent tra 92.0 0.17 3.6E-06 58.9 4.5 47 471-522 831-877 (894)
198 PF06056 Terminase_5: Putative 91.8 0.27 5.9E-06 38.9 4.3 27 489-515 11-37 (58)
199 PF13518 HTH_28: Helix-turn-he 91.8 0.25 5.4E-06 37.0 3.9 27 490-516 11-37 (52)
200 smart00351 PAX Paired Box doma 91.7 0.39 8.4E-06 43.6 5.8 42 472-517 18-59 (125)
201 PRK10430 DNA-binding transcrip 91.7 0.28 6.2E-06 48.3 5.3 46 471-517 158-204 (239)
202 COG2390 DeoR Transcriptional r 91.6 0.22 4.8E-06 52.4 4.7 36 478-517 17-52 (321)
203 PF01726 LexA_DNA_bind: LexA D 91.5 0.26 5.6E-06 39.9 3.9 45 469-513 1-48 (65)
204 PF04539 Sigma70_r3: Sigma-70 91.5 0.49 1.1E-05 38.7 5.7 38 253-290 4-41 (78)
205 PF04218 CENP-B_N: CENP-B N-te 91.3 0.2 4.2E-06 38.8 2.9 40 471-514 6-45 (53)
206 PF10668 Phage_terminase: Phag 91.2 0.32 7E-06 38.8 4.1 35 478-514 11-45 (60)
207 PF13730 HTH_36: Helix-turn-he 90.9 0.69 1.5E-05 35.3 5.6 47 471-521 2-51 (55)
208 PHA00675 hypothetical protein 90.9 0.43 9.3E-06 39.9 4.6 41 470-513 21-61 (78)
209 PF13404 HTH_AsnC-type: AsnC-t 90.8 0.63 1.4E-05 34.4 5.0 39 473-514 2-40 (42)
210 PRK07921 RNA polymerase sigma 90.3 4 8.7E-05 43.0 12.6 36 253-288 173-208 (324)
211 PF02650 HTH_WhiA: WhiA C-term 89.8 0.55 1.2E-05 40.1 4.6 44 469-515 35-80 (85)
212 PHA02591 hypothetical protein; 89.5 0.56 1.2E-05 39.3 4.2 25 489-513 57-81 (83)
213 PF01022 HTH_5: Bacterial regu 89.2 0.75 1.6E-05 34.3 4.5 37 474-514 2-38 (47)
214 cd00131 PAX Paired Box domain 89.2 0.88 1.9E-05 41.5 5.8 42 472-517 18-59 (128)
215 TIGR02395 rpoN_sigma RNA polym 88.8 21 0.00045 39.3 17.0 29 484-512 311-339 (429)
216 TIGR02147 Fsuc_second hypothet 88.5 9.7 0.00021 39.3 13.5 98 397-501 136-239 (271)
217 PF08279 HTH_11: HTH domain; 88.5 0.77 1.7E-05 35.0 4.2 38 475-514 1-38 (55)
218 PF12840 HTH_20: Helix-turn-he 88.4 1.5 3.2E-05 34.4 5.9 43 465-513 3-46 (61)
219 PRK07406 RNA polymerase sigma 88.0 8.7 0.00019 41.4 13.3 126 383-513 95-261 (373)
220 COG1191 FliA DNA-directed RNA 87.7 11 0.00023 38.6 12.9 124 254-421 111-235 (247)
221 PF12802 MarR_2: MarR family; 87.6 1.1 2.3E-05 34.7 4.6 43 471-514 2-44 (62)
222 COG3355 Predicted transcriptio 87.5 1.8 4E-05 39.6 6.7 53 463-521 16-68 (126)
223 PF01726 LexA_DNA_bind: LexA D 86.6 2.2 4.7E-05 34.5 5.9 42 382-423 9-51 (65)
224 PRK11083 DNA-binding response 86.3 0.96 2.1E-05 42.8 4.5 50 471-521 154-208 (228)
225 PF03444 HrcA_DNA-bdg: Winged 86.0 1.4 3.1E-05 37.0 4.7 42 472-513 2-45 (78)
226 PHA02547 55 RNA polymerase sig 86.0 2.5 5.5E-05 40.5 6.9 65 303-367 45-112 (179)
227 PF01325 Fe_dep_repress: Iron 86.0 0.96 2.1E-05 35.9 3.5 46 472-521 2-48 (60)
228 PRK10710 DNA-binding transcrip 85.9 1.1 2.3E-05 43.0 4.6 50 471-521 160-214 (240)
229 PRK10046 dpiA two-component re 85.9 0.75 1.6E-05 44.9 3.5 39 471-513 161-199 (225)
230 PRK05932 RNA polymerase factor 85.7 35 0.00077 37.8 16.8 46 467-512 307-364 (455)
231 smart00550 Zalpha Z-DNA-bindin 85.6 2 4.3E-05 34.8 5.3 37 476-513 8-44 (68)
232 PRK05911 RNA polymerase sigma 85.3 9.5 0.0002 38.6 11.3 34 255-288 112-145 (257)
233 PRK07408 RNA polymerase sigma 85.3 3.4 7.5E-05 41.8 8.1 35 254-288 114-148 (256)
234 PRK06288 RNA polymerase sigma 85.0 27 0.00059 35.4 14.5 35 254-288 119-153 (268)
235 PF13542 HTH_Tnp_ISL3: Helix-t 84.9 2.1 4.5E-05 32.2 4.8 33 478-515 19-51 (52)
236 PRK10336 DNA-binding transcrip 84.9 1.1 2.5E-05 42.1 4.2 49 471-520 149-202 (219)
237 smart00342 HTH_ARAC helix_turn 84.4 17 0.00038 28.6 10.5 73 398-514 1-74 (84)
238 TIGR02997 Sig70-cyanoRpoD RNA 84.1 15 0.00032 38.0 12.4 34 383-416 33-66 (298)
239 COG3415 Transposase and inacti 84.0 1.8 3.8E-05 40.3 4.8 28 489-516 19-46 (138)
240 TIGR02885 spore_sigF RNA polym 84.0 6.1 0.00013 39.0 9.1 34 255-288 99-132 (231)
241 PRK12469 RNA polymerase factor 84.0 36 0.00079 38.0 15.9 47 467-513 333-391 (481)
242 PRK07122 RNA polymerase sigma 83.9 15 0.00033 37.4 12.1 36 254-289 128-163 (264)
243 PF12728 HTH_17: Helix-turn-he 83.8 1.2 2.5E-05 33.5 3.0 24 492-515 2-25 (51)
244 PRK05949 RNA polymerase sigma 83.7 13 0.00029 39.2 11.9 35 254-288 179-213 (327)
245 PF13463 HTH_27: Winged helix 83.6 2.1 4.5E-05 33.7 4.5 41 472-514 1-41 (68)
246 PF00356 LacI: Bacterial regul 83.4 1.2 2.5E-05 33.7 2.8 22 493-514 1-22 (46)
247 PF01710 HTH_Tnp_IS630: Transp 83.3 10 0.00022 33.9 9.5 24 489-512 69-92 (119)
248 PF01418 HTH_6: Helix-turn-hel 83.1 2 4.4E-05 35.5 4.4 53 461-513 3-56 (77)
249 smart00344 HTH_ASNC helix_turn 83.0 2.5 5.3E-05 36.6 5.2 40 472-514 1-40 (108)
250 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 83.0 2.3 5.1E-05 32.8 4.3 39 471-513 4-42 (50)
251 PRK00423 tfb transcription ini 82.9 65 0.0014 33.7 18.6 178 299-519 120-304 (310)
252 PRK15479 transcriptional regul 82.8 1.9 4.1E-05 40.5 4.8 50 471-521 148-202 (221)
253 PRK12423 LexA repressor; Provi 82.8 1.7 3.7E-05 42.5 4.5 47 471-521 3-52 (202)
254 TIGR02850 spore_sigG RNA polym 82.5 15 0.00032 37.0 11.3 37 254-290 121-157 (254)
255 PF13744 HTH_37: Helix-turn-he 82.5 2.7 5.8E-05 35.0 5.0 44 479-526 23-71 (80)
256 TIGR02154 PhoB phosphate regul 82.3 1.1 2.3E-05 42.3 2.8 50 471-521 154-208 (226)
257 smart00345 HTH_GNTR helix_turn 82.1 2.4 5.1E-05 32.0 4.2 29 489-521 17-46 (60)
258 PF01371 Trp_repressor: Trp re 81.7 1.8 3.9E-05 37.1 3.7 45 472-517 27-74 (87)
259 cd04762 HTH_MerR-trunc Helix-T 81.6 1.4 3.1E-05 31.7 2.7 25 492-516 1-25 (49)
260 PRK13413 mpi multiple promoter 81.4 2.5 5.3E-05 41.1 5.1 34 476-514 162-195 (200)
261 TIGR01764 excise DNA binding d 81.3 1.8 3.8E-05 31.4 3.1 24 492-515 2-25 (49)
262 TIGR01610 phage_O_Nterm phage 81.3 3.3 7.2E-05 35.7 5.3 49 469-521 20-73 (95)
263 COG2973 TrpR Trp operon repres 81.3 3.5 7.7E-05 36.1 5.3 45 472-520 38-85 (103)
264 PRK07670 RNA polymerase sigma 80.9 26 0.00056 35.2 12.4 37 254-290 110-146 (251)
265 TIGR03787 marine_sort_RR prote 80.6 2.3 5.1E-05 40.4 4.5 50 471-521 156-207 (227)
266 PF01047 MarR: MarR family; I 80.4 2.4 5.3E-05 32.5 3.7 40 472-514 1-40 (59)
267 PF13551 HTH_29: Winged helix- 80.2 3.1 6.7E-05 35.7 4.8 33 478-515 3-36 (112)
268 PF01978 TrmB: Sugar-specific 79.8 1.2 2.7E-05 35.5 2.0 44 471-521 5-48 (68)
269 PRK07405 RNA polymerase sigma 79.7 23 0.0005 37.2 11.9 36 253-288 168-203 (317)
270 PF13011 LZ_Tnp_IS481: leucine 79.4 3.6 7.8E-05 35.2 4.7 43 471-516 8-50 (85)
271 PHA01976 helix-turn-helix prot 78.9 3.1 6.7E-05 32.8 4.0 26 489-514 13-38 (67)
272 PF01381 HTH_3: Helix-turn-hel 78.4 2.2 4.7E-05 32.2 2.9 26 489-514 7-32 (55)
273 PRK11179 DNA-binding transcrip 78.3 4.1 8.9E-05 37.9 5.3 41 471-514 6-46 (153)
274 PF14394 DUF4423: Domain of un 78.1 6.6 0.00014 37.7 6.7 88 396-487 37-130 (171)
275 TIGR02479 FliA_WhiG RNA polyme 78.0 43 0.00092 32.8 12.7 36 253-288 83-118 (224)
276 PF13022 HTH_Tnp_1_2: Helix-tu 77.7 6.4 0.00014 36.8 6.1 61 465-526 4-71 (142)
277 cd04761 HTH_MerR-SF Helix-Turn 77.4 1.8 4E-05 31.7 2.1 25 492-516 1-25 (49)
278 CHL00148 orf27 Ycf27; Reviewed 77.0 3.2 6.9E-05 39.7 4.3 50 471-521 161-217 (240)
279 PF07750 GcrA: GcrA cell cycle 76.7 2.8 6E-05 40.0 3.7 37 474-514 5-42 (162)
280 PF13560 HTH_31: Helix-turn-he 76.7 3.1 6.7E-05 32.8 3.4 26 489-514 12-37 (64)
281 TIGR02787 codY_Gpos GTP-sensin 76.6 11 0.00023 38.4 7.9 56 462-521 167-224 (251)
282 COG1508 RpoN DNA-directed RNA 76.4 51 0.0011 36.4 13.6 49 465-513 292-352 (444)
283 PRK11511 DNA-binding transcrip 76.1 45 0.00097 30.0 11.3 39 382-420 9-47 (127)
284 PHA00542 putative Cro-like pro 76.1 3.4 7.3E-05 34.7 3.6 27 489-515 29-55 (82)
285 PRK11169 leucine-responsive tr 76.0 4.4 9.5E-05 38.2 4.8 40 472-514 12-51 (164)
286 PF08822 DUF1804: Protein of u 76.0 5.4 0.00012 38.2 5.3 42 473-517 4-45 (165)
287 TIGR03830 CxxCG_CxxCG_HTH puta 75.6 8.9 0.00019 34.0 6.5 46 464-515 57-102 (127)
288 COG1476 Predicted transcriptio 75.6 3.8 8.2E-05 33.7 3.6 26 489-514 12-37 (68)
289 COG0856 Orotate phosphoribosyl 75.3 3.5 7.6E-05 39.9 3.9 41 477-522 9-49 (203)
290 TIGR00498 lexA SOS regulatory 75.3 4.2 9E-05 39.3 4.6 43 470-512 2-47 (199)
291 PRK10072 putative transcriptio 75.1 3.8 8.2E-05 35.8 3.8 31 479-513 38-68 (96)
292 cd06571 Bac_DnaA_C C-terminal 74.7 8.5 0.00018 32.7 5.8 33 489-521 42-75 (90)
293 TIGR00122 birA_repr_reg BirA b 74.5 6.5 0.00014 31.4 4.8 25 490-514 12-36 (69)
294 COG2522 Predicted transcriptio 74.4 5.1 0.00011 36.4 4.5 24 490-513 21-44 (119)
295 COG1522 Lrp Transcriptional re 74.3 6.1 0.00013 36.1 5.2 42 470-514 4-45 (154)
296 PF02954 HTH_8: Bacterial regu 73.7 4 8.8E-05 29.8 3.1 37 474-513 4-40 (42)
297 smart00419 HTH_CRP helix_turn_ 73.5 4.8 0.0001 29.1 3.5 28 490-521 7-34 (48)
298 smart00420 HTH_DEOR helix_turn 73.5 6.8 0.00015 28.6 4.4 25 490-514 13-37 (53)
299 PF13551 HTH_29: Winged helix- 73.4 13 0.00029 31.6 6.9 24 400-423 14-37 (112)
300 PF08220 HTH_DeoR: DeoR-like h 73.3 4.8 0.0001 31.4 3.6 25 489-513 12-36 (57)
301 TIGR03070 couple_hipB transcri 73.1 5.2 0.00011 29.9 3.7 26 489-514 13-38 (58)
302 smart00418 HTH_ARSR helix_turn 72.7 6 0.00013 29.7 4.0 26 489-514 8-33 (66)
303 PRK09413 IS2 repressor TnpA; R 72.4 7.9 0.00017 34.7 5.3 35 478-516 20-54 (121)
304 cd00092 HTH_CRP helix_turn_hel 72.4 5.9 0.00013 30.8 4.0 29 489-521 23-51 (67)
305 TIGR02844 spore_III_D sporulat 72.4 6.9 0.00015 33.1 4.6 36 474-513 6-41 (80)
306 PRK05572 sporulation sigma fac 72.4 54 0.0012 32.8 12.0 34 254-287 119-152 (252)
307 COG1405 SUA7 Transcription ini 72.3 92 0.002 32.5 13.8 171 322-514 93-274 (285)
308 PRK07500 rpoH2 RNA polymerase 72.3 31 0.00067 35.7 10.4 26 397-422 244-269 (289)
309 TIGR02612 mob_myst_A mobile my 72.2 7.2 0.00016 36.8 5.2 38 473-514 24-61 (150)
310 PF00046 Homeobox: Homeobox do 72.2 5.8 0.00012 30.3 3.8 50 471-520 6-56 (57)
311 PF08535 KorB: KorB domain; I 71.8 3.4 7.3E-05 35.3 2.7 24 490-513 2-25 (93)
312 cd00090 HTH_ARSR Arsenical Res 71.8 8.9 0.00019 29.6 5.0 37 474-514 7-43 (78)
313 PF13411 MerR_1: MerR HTH fami 71.1 2.1 4.5E-05 33.9 1.2 25 492-516 1-25 (69)
314 PF08280 HTH_Mga: M protein tr 71.0 6.1 0.00013 31.0 3.8 36 475-513 6-41 (59)
315 PRK09954 putative kinase; Prov 71.0 7 0.00015 41.2 5.4 43 472-517 1-43 (362)
316 PF01527 HTH_Tnp_1: Transposas 70.9 3.6 7.8E-05 33.1 2.5 35 478-516 14-48 (76)
317 TIGR03697 NtcA_cyano global ni 70.6 5.2 0.00011 37.6 3.9 29 490-522 142-170 (193)
318 PF13545 HTH_Crp_2: Crp-like h 70.5 4.8 0.0001 32.3 3.2 29 490-522 27-55 (76)
319 TIGR02337 HpaR homoprotocatech 70.5 19 0.0004 31.7 7.2 41 470-513 24-64 (118)
320 PF14493 HTH_40: Helix-turn-he 70.2 9.8 0.00021 32.3 5.2 30 489-518 11-40 (91)
321 PRK00215 LexA repressor; Valid 70.2 7.3 0.00016 37.8 5.0 43 472-514 2-47 (205)
322 PF09339 HTH_IclR: IclR helix- 70.1 6.1 0.00013 29.9 3.5 25 489-513 16-40 (52)
323 cd07377 WHTH_GntR Winged helix 70.1 8.6 0.00019 29.5 4.5 26 492-521 26-51 (66)
324 TIGR01884 cas_HTH CRISPR locus 69.9 11 0.00024 36.7 6.1 44 468-514 137-180 (203)
325 TIGR00647 MG103 conserved hypo 69.8 8.9 0.00019 39.8 5.6 45 469-516 225-275 (279)
326 PF08765 Mor: Mor transcriptio 69.4 9.5 0.00021 33.6 5.1 42 475-522 62-103 (108)
327 COG2944 Predicted transcriptio 69.3 13 0.00029 33.0 5.9 39 470-514 42-80 (104)
328 COG5484 Uncharacterized conser 68.2 5.7 0.00012 40.4 3.8 26 489-514 17-42 (279)
329 COG1654 BirA Biotin operon rep 68.1 10 0.00022 32.0 4.7 31 488-522 16-46 (79)
330 cd01104 HTH_MlrA-CarA Helix-Tu 68.1 6.4 0.00014 31.0 3.4 23 492-514 1-23 (68)
331 KOG0484 Transcription factor P 67.6 8.1 0.00017 34.3 4.1 51 470-524 27-77 (125)
332 PRK08215 sporulation sigma fac 67.1 71 0.0015 32.1 11.5 34 255-288 125-158 (258)
333 PRK11564 stationary phase indu 67.1 13 0.00028 40.3 6.6 51 471-521 10-60 (426)
334 TIGR02607 antidote_HigA addict 67.0 10 0.00023 30.6 4.5 25 489-513 16-40 (78)
335 PF00376 MerR: MerR family reg 66.8 3.6 7.7E-05 29.7 1.5 24 493-516 1-24 (38)
336 PRK09863 putative frv operon r 66.6 52 0.0011 37.3 11.5 103 397-520 16-121 (584)
337 TIGR02941 Sigma_B RNA polymera 66.5 69 0.0015 32.1 11.3 34 255-288 118-151 (255)
338 PRK10219 DNA-binding transcrip 66.2 72 0.0016 27.3 10.0 38 384-421 7-44 (107)
339 PF00392 GntR: Bacterial regul 65.3 7.4 0.00016 30.7 3.2 29 489-521 21-50 (64)
340 COG0568 RpoD DNA-directed RNA 64.8 81 0.0018 33.8 11.7 42 247-288 183-224 (342)
341 cd04764 HTH_MlrA-like_sg1 Heli 64.8 8.2 0.00018 30.5 3.4 23 492-514 1-23 (67)
342 PRK15340 transcriptional regul 64.4 1.5E+02 0.0032 29.7 12.9 33 389-421 116-148 (216)
343 TIGR02980 SigBFG RNA polymeras 64.1 75 0.0016 31.0 10.8 32 257-288 94-125 (227)
344 PRK11512 DNA-binding transcrip 63.6 35 0.00076 31.1 7.9 40 471-513 37-76 (144)
345 PF06971 Put_DNA-bind_N: Putat 63.1 15 0.00033 28.3 4.4 45 373-417 3-47 (50)
346 COG1318 Predicted transcriptio 62.6 7.6 0.00016 37.4 3.2 27 490-516 60-86 (182)
347 smart00347 HTH_MARR helix_turn 62.5 17 0.00036 30.1 5.1 44 471-521 7-50 (101)
348 PRK10141 DNA-binding transcrip 62.1 19 0.00041 32.6 5.6 44 467-513 8-52 (117)
349 PF13556 HTH_30: PucR C-termin 61.6 18 0.00039 28.3 4.7 36 489-524 10-45 (59)
350 smart00422 HTH_MERR helix_turn 61.5 6.2 0.00013 31.1 2.2 25 492-516 1-25 (70)
351 PF01710 HTH_Tnp_IS630: Transp 61.3 9.6 0.00021 34.1 3.6 25 489-513 16-40 (119)
352 PRK06986 fliA flagellar biosyn 61.1 1.5E+02 0.0032 29.3 12.3 34 255-288 97-130 (236)
353 PRK11302 DNA-binding transcrip 60.7 22 0.00047 36.0 6.5 52 462-513 4-56 (284)
354 COG2345 Predicted transcriptio 60.3 16 0.00034 36.7 5.2 26 489-514 23-48 (218)
355 cd04763 HTH_MlrA-like Helix-Tu 60.3 11 0.00023 30.0 3.4 23 492-514 1-23 (68)
356 PRK10870 transcriptional repre 60.2 44 0.00096 31.9 8.1 50 464-514 43-94 (176)
357 smart00354 HTH_LACI helix_turn 60.2 8.9 0.00019 31.0 2.9 23 492-514 1-23 (70)
358 TIGR02394 rpoS_proteo RNA poly 60.0 2.1E+02 0.0045 29.3 15.8 31 222-252 12-43 (285)
359 PRK01905 DNA-binding protein F 59.9 32 0.00069 28.5 6.2 36 476-514 38-73 (77)
360 PRK11337 DNA-binding transcrip 59.5 24 0.00053 36.0 6.6 53 461-513 15-68 (292)
361 PRK11557 putative DNA-binding 59.2 18 0.0004 36.6 5.7 49 465-513 3-52 (278)
362 PRK10955 DNA-binding transcrip 59.2 7 0.00015 37.1 2.5 46 471-521 156-210 (232)
363 PF08784 RPA_C: Replication pr 58.9 15 0.00032 31.7 4.2 43 471-513 44-87 (102)
364 smart00346 HTH_ICLR helix_turn 58.9 19 0.0004 29.8 4.7 26 490-515 19-44 (91)
365 PRK13239 alkylmercury lyase; P 58.8 19 0.00041 35.8 5.4 29 395-423 33-61 (206)
366 PRK11161 fumarate/nitrate redu 58.4 11 0.00025 36.7 3.8 29 490-522 183-211 (235)
367 PRK10572 DNA-binding transcrip 58.3 2.1E+02 0.0046 28.8 15.4 38 384-421 185-222 (290)
368 PF11662 DUF3263: Protein of u 58.0 33 0.00072 28.9 5.9 46 471-516 2-47 (77)
369 PRK09726 antitoxin HipB; Provi 58.0 14 0.0003 31.2 3.8 26 489-514 23-48 (88)
370 COG1846 MarR Transcriptional r 57.9 18 0.0004 30.8 4.7 39 472-514 20-59 (126)
371 PRK03573 transcriptional regul 57.7 48 0.001 30.1 7.6 42 471-514 28-69 (144)
372 PRK13503 transcriptional activ 57.6 1.1E+02 0.0023 30.6 10.8 38 384-421 173-210 (278)
373 PRK11753 DNA-binding transcrip 57.2 13 0.00028 35.5 4.0 28 491-522 168-195 (211)
374 cd00086 homeodomain Homeodomai 55.6 27 0.00059 26.2 4.8 51 471-521 6-57 (59)
375 PRK13918 CRP/FNR family transc 55.5 12 0.00026 35.5 3.4 28 490-521 148-175 (202)
376 PF02082 Rrf2: Transcriptional 55.4 20 0.00044 29.7 4.3 24 490-513 24-47 (83)
377 PF12085 DUF3562: Protein of u 55.3 16 0.00035 29.8 3.5 38 493-533 9-46 (66)
378 PRK15482 transcriptional regul 55.3 30 0.00065 35.3 6.5 51 463-513 5-56 (285)
379 PRK09863 putative frv operon r 55.3 23 0.0005 40.1 6.1 46 472-521 2-47 (584)
380 PRK10161 transcriptional regul 55.1 13 0.00029 35.3 3.6 50 471-521 154-208 (229)
381 PF07037 DUF1323: Putative tra 54.6 13 0.00029 33.7 3.3 23 492-514 1-23 (122)
382 TIGR01889 Staph_reg_Sar staphy 54.4 31 0.00067 30.1 5.6 44 471-514 22-66 (109)
383 COG3877 Uncharacterized protei 53.9 24 0.00052 31.5 4.6 48 469-520 39-86 (122)
384 PF05043 Mga: Mga helix-turn-h 53.7 7.6 0.00016 32.4 1.5 33 489-521 28-60 (87)
385 smart00352 POU Found in Pit-Oc 53.4 21 0.00045 29.9 4.0 31 479-513 16-52 (75)
386 PF04963 Sigma54_CBD: Sigma-54 52.9 3.1 6.8E-05 40.5 -1.1 95 398-519 52-146 (194)
387 PF12844 HTH_19: Helix-turn-he 52.7 18 0.00039 28.1 3.4 26 489-514 10-35 (64)
388 PRK09706 transcriptional repre 52.6 18 0.00038 32.9 3.8 26 489-514 16-41 (135)
389 PRK09391 fixK transcriptional 52.6 17 0.00036 35.9 3.9 29 490-522 178-206 (230)
390 TIGR02698 CopY_TcrY copper tra 52.4 35 0.00075 31.1 5.7 44 471-517 1-48 (130)
391 smart00530 HTH_XRE Helix-turn- 52.4 19 0.00042 25.2 3.4 25 490-514 9-33 (56)
392 cd01392 HTH_LacI Helix-turn-he 51.8 9.7 0.00021 28.3 1.7 21 495-515 1-21 (52)
393 COG4367 Uncharacterized protei 51.8 35 0.00076 29.5 5.1 40 385-424 9-49 (97)
394 PF00165 HTH_AraC: Bacterial r 51.7 22 0.00048 25.5 3.5 27 489-515 6-32 (42)
395 PF05225 HTH_psq: helix-turn-h 51.3 45 0.00097 24.8 5.2 22 492-513 17-38 (45)
396 TIGR00180 parB_part ParB-like 51.2 26 0.00056 33.8 4.9 43 470-514 101-143 (187)
397 PF13443 HTH_26: Cro/C1-type H 51.0 15 0.00032 28.4 2.7 26 490-515 9-34 (63)
398 COG1737 RpiR Transcriptional r 50.7 32 0.00069 35.4 5.8 54 460-513 4-58 (281)
399 COG3093 VapI Plasmid maintenan 50.6 23 0.00049 31.5 4.0 35 478-514 12-46 (104)
400 COG1510 Predicted transcriptio 50.4 15 0.00032 35.5 3.0 29 489-521 39-67 (177)
401 COG2512 Predicted membrane-ass 50.2 21 0.00046 36.6 4.3 45 470-520 191-235 (258)
402 PRK15121 right oriC-binding tr 50.1 1.6E+02 0.0035 30.0 10.9 41 381-421 4-44 (289)
403 PF00440 TetR_N: Bacterial reg 49.8 19 0.00041 26.6 3.0 23 489-511 14-36 (47)
404 PRK10411 DNA-binding transcrip 49.8 28 0.00061 35.0 5.1 41 474-517 4-44 (240)
405 smart00389 HOX Homeodomain. DN 49.6 32 0.00069 25.8 4.3 47 472-518 7-54 (56)
406 cd04768 HTH_BmrR-like Helix-Tu 49.6 12 0.00026 32.1 2.1 25 492-516 1-25 (96)
407 cd00093 HTH_XRE Helix-turn-hel 49.1 27 0.00059 24.5 3.8 25 490-514 11-35 (58)
408 PF04703 FaeA: FaeA-like prote 48.8 17 0.00037 29.2 2.7 24 490-513 14-37 (62)
409 PF00325 Crp: Bacterial regula 48.7 25 0.00055 24.6 3.2 24 400-423 4-27 (32)
410 PF00292 PAX: 'Paired box' dom 48.6 30 0.00066 31.7 4.6 33 478-515 25-57 (125)
411 PF06413 Neugrin: Neugrin; In 48.4 27 0.00059 35.1 4.7 42 471-513 10-51 (225)
412 PRK06424 transcription factor; 48.3 22 0.00048 33.3 3.8 25 489-513 95-119 (144)
413 TIGR02812 fadR_gamma fatty aci 48.3 26 0.00056 34.5 4.5 31 487-521 25-56 (235)
414 PF04814 HNF-1_N: Hepatocyte n 48.2 31 0.00067 33.5 4.8 51 463-516 106-156 (180)
415 PF02787 CPSase_L_D3: Carbamoy 47.8 1.7E+02 0.0037 26.6 9.4 24 490-513 71-94 (123)
416 PRK06030 hypothetical protein; 47.8 42 0.0009 30.7 5.4 40 474-517 56-95 (124)
417 cd04775 HTH_Cfa-like Helix-Tur 47.5 13 0.00029 32.3 2.1 26 492-517 2-27 (102)
418 PF12324 HTH_15: Helix-turn-he 47.2 40 0.00087 28.4 4.7 28 396-423 36-63 (77)
419 smart00862 Trans_reg_C Transcr 47.1 59 0.0013 25.7 5.8 50 471-521 5-60 (78)
420 PHA00738 putative HTH transcri 47.1 37 0.0008 30.4 4.7 38 473-513 11-48 (108)
421 cd01105 HTH_GlnR-like Helix-Tu 47.0 15 0.00032 31.1 2.2 25 492-516 2-26 (88)
422 TIGR02944 suf_reg_Xantho FeS a 46.9 29 0.00063 31.1 4.3 25 489-513 23-47 (130)
423 PRK09392 ftrB transcriptional 46.5 21 0.00046 34.9 3.6 28 491-522 173-200 (236)
424 PRK10643 DNA-binding transcrip 46.5 26 0.00057 32.7 4.1 47 471-520 149-202 (222)
425 PRK06596 RNA polymerase factor 46.2 2.6E+02 0.0057 28.7 11.8 25 397-421 247-271 (284)
426 PRK13890 conjugal transfer pro 46.2 26 0.00056 31.6 3.8 26 489-514 16-41 (120)
427 PRK11517 transcriptional regul 46.1 34 0.00074 32.1 4.9 49 471-520 147-200 (223)
428 PRK14101 bifunctional glucokin 45.6 41 0.0009 38.6 6.3 54 460-513 342-396 (638)
429 PRK14082 hypothetical protein; 45.6 67 0.0014 26.2 5.5 56 294-351 8-63 (65)
430 PRK03902 manganese transport t 45.4 35 0.00077 31.2 4.7 25 489-513 20-44 (142)
431 COG1481 Uncharacterized protei 45.4 40 0.00087 35.5 5.5 43 469-514 251-295 (308)
432 cd01107 HTH_BmrR Helix-Turn-He 45.4 16 0.00034 32.1 2.2 26 492-517 1-26 (108)
433 TIGR01387 cztR_silR_copR heavy 45.3 29 0.00064 32.3 4.3 50 471-521 147-201 (218)
434 PRK11014 transcriptional repre 45.2 28 0.00061 31.8 4.0 30 488-521 22-51 (141)
435 PF08279 HTH_11: HTH domain; 45.2 52 0.0011 24.7 4.9 26 399-424 16-41 (55)
436 PF13309 HTH_22: HTH domain 45.2 17 0.00037 29.2 2.2 20 493-512 44-63 (64)
437 cd04773 HTH_TioE_rpt2 Second H 45.2 15 0.00033 32.3 2.1 25 492-516 1-25 (108)
438 PRK09943 DNA-binding transcrip 45.0 27 0.00059 33.3 4.0 26 489-514 18-43 (185)
439 PF05331 DUF742: Protein of un 44.9 34 0.00073 30.9 4.3 40 470-514 39-78 (114)
440 PRK10402 DNA-binding transcrip 44.9 24 0.00051 34.6 3.6 45 473-522 150-196 (226)
441 PRK10434 srlR DNA-bindng trans 44.6 29 0.00062 35.2 4.3 38 474-514 5-42 (256)
442 PRK13777 transcriptional regul 44.4 1E+02 0.0022 30.0 7.9 40 471-513 42-81 (185)
443 cd04765 HTH_MlrA-like_sg2 Heli 44.3 26 0.00056 30.4 3.4 23 492-514 1-23 (99)
444 PRK13509 transcriptional repre 44.2 34 0.00074 34.6 4.7 38 474-514 5-42 (251)
445 PRK04984 fatty acid metabolism 44.1 29 0.00062 34.3 4.1 31 487-521 26-57 (239)
446 PRK06266 transcription initiat 43.7 74 0.0016 30.8 6.8 38 473-513 21-58 (178)
447 cd04782 HTH_BltR Helix-Turn-He 43.6 17 0.00037 31.3 2.2 25 492-516 1-25 (97)
448 cd04766 HTH_HspR Helix-Turn-He 43.5 17 0.00036 30.8 2.1 26 492-517 2-27 (91)
449 PRK00082 hrcA heat-inducible t 43.4 37 0.0008 36.1 5.1 45 470-519 2-54 (339)
450 cd04772 HTH_TioE_rpt1 First He 43.3 18 0.00039 31.4 2.2 26 492-517 1-26 (99)
451 COG2963 Transposase and inacti 43.2 46 0.00099 29.2 4.9 43 471-517 7-51 (116)
452 cd00592 HTH_MerR-like Helix-Tu 43.1 18 0.00039 30.9 2.2 25 492-516 1-25 (100)
453 cd01106 HTH_TipAL-Mta Helix-Tu 43.1 18 0.00038 31.4 2.2 25 492-516 1-25 (103)
454 PRK11050 manganese transport r 43.1 72 0.0016 29.8 6.4 25 490-514 50-74 (152)
455 TIGR00270 conserved hypothetic 43.1 31 0.00067 32.7 3.9 25 489-513 80-104 (154)
456 cd04789 HTH_Cfa Helix-Turn-Hel 43.0 18 0.00038 31.5 2.2 26 492-517 2-27 (102)
457 PRK15044 transcriptional regul 42.8 4E+02 0.0087 28.0 12.3 39 382-420 192-230 (295)
458 PF05930 Phage_AlpA: Prophage 42.8 28 0.00061 26.3 3.0 24 492-515 4-27 (51)
459 PRK00430 fis global DNA-bindin 42.6 1.1E+02 0.0024 26.5 7.1 37 475-514 55-91 (95)
460 PRK08359 transcription factor; 42.6 30 0.00066 33.5 3.9 25 489-513 96-120 (176)
461 PF04645 DUF603: Protein of un 42.2 31 0.00068 33.2 3.8 26 489-514 16-42 (181)
462 cd00383 trans_reg_C Effector d 42.2 56 0.0012 26.9 5.1 50 471-521 23-77 (95)
463 PF12116 SpoIIID: Stage III sp 42.2 31 0.00068 29.3 3.4 32 490-521 18-49 (82)
464 cd04774 HTH_YfmP Helix-Turn-He 42.1 18 0.0004 31.2 2.1 26 492-517 1-26 (96)
465 PRK09744 DNA-binding transcrip 41.8 33 0.00072 28.7 3.4 19 493-511 12-30 (75)
466 cd01109 HTH_YyaN Helix-Turn-He 41.6 19 0.00042 31.7 2.2 26 492-517 1-26 (113)
467 cd04788 HTH_NolA-AlbR Helix-Tu 41.5 19 0.00041 30.9 2.1 26 492-517 1-26 (96)
468 PF08006 DUF1700: Protein of u 41.5 64 0.0014 30.8 6.0 57 458-514 3-63 (181)
469 PF02042 RWP-RK: RWP-RK domain 41.3 58 0.0013 25.4 4.5 28 479-512 9-36 (52)
470 PF06322 Phage_NinH: Phage Nin 41.2 38 0.00082 27.3 3.5 27 479-512 11-37 (64)
471 TIGR03826 YvyF flagellar opero 41.0 74 0.0016 29.6 6.0 53 374-426 22-74 (137)
472 PRK10906 DNA-binding transcrip 40.5 37 0.0008 34.4 4.4 38 474-514 5-42 (252)
473 cd01282 HTH_MerR-like_sg3 Heli 40.2 21 0.00045 31.6 2.2 26 492-517 1-26 (112)
474 PRK05657 RNA polymerase sigma 40.1 3.6E+02 0.0079 28.3 11.9 34 256-289 176-209 (325)
475 cd04780 HTH_MerR-like_sg5 Heli 40.1 21 0.00045 30.8 2.2 25 492-516 1-25 (95)
476 cd01279 HTH_HspR-like Helix-Tu 40.1 20 0.00043 31.0 2.0 25 492-516 2-26 (98)
477 PRK11886 bifunctional biotin-- 40.0 46 0.001 34.7 5.1 39 475-516 5-43 (319)
478 COG1321 TroR Mn-dependent tran 40.0 43 0.00092 31.6 4.4 25 489-513 22-46 (154)
479 PRK11414 colanic acid/biofilm 40.0 31 0.00067 33.7 3.6 31 487-521 30-60 (221)
480 PF04552 Sigma54_DBD: Sigma-54 39.9 9.6 0.00021 36.3 0.0 48 464-513 24-71 (160)
481 PF04545 Sigma70_r4: Sigma-70, 39.8 84 0.0018 23.2 5.2 26 396-421 18-43 (50)
482 cd04768 HTH_BmrR-like Helix-Tu 39.7 2.4E+02 0.0052 24.1 8.9 35 490-524 56-90 (96)
483 PF12298 Bot1p: Eukaryotic mit 39.7 55 0.0012 31.6 5.1 38 472-512 17-54 (172)
484 COG3711 BglG Transcriptional a 39.5 55 0.0012 35.9 5.9 113 396-521 17-130 (491)
485 PF14502 HTH_41: Helix-turn-he 39.5 53 0.0012 25.2 3.9 30 488-521 3-32 (48)
486 TIGR03338 phnR_burk phosphonat 39.2 33 0.00072 33.1 3.6 30 488-521 31-60 (212)
487 cd04769 HTH_MerR2 Helix-Turn-H 39.0 22 0.00048 31.6 2.2 27 492-518 1-27 (116)
488 cd01108 HTH_CueR Helix-Turn-He 38.9 22 0.00047 32.2 2.1 26 492-517 1-26 (127)
489 TIGR02044 CueR Cu(I)-responsiv 38.4 22 0.00048 32.1 2.1 26 492-517 1-26 (127)
490 PRK03837 transcriptional regul 38.3 41 0.0009 33.0 4.3 30 488-521 33-63 (241)
491 TIGR02325 C_P_lyase_phnF phosp 38.3 36 0.00078 33.4 3.8 28 490-521 31-58 (238)
492 smart00342 HTH_ARAC helix_turn 38.2 48 0.001 26.0 3.9 26 491-516 1-26 (84)
493 cd04783 HTH_MerR1 Helix-Turn-H 38.1 23 0.00049 31.9 2.1 27 492-518 1-27 (126)
494 PF09012 FeoC: FeoC like trans 38.0 17 0.00038 29.1 1.3 26 489-514 12-37 (69)
495 cd01111 HTH_MerD Helix-Turn-He 38.0 24 0.00051 31.2 2.2 26 492-517 1-26 (107)
496 TIGR02684 dnstrm_HI1420 probab 38.0 86 0.0019 26.9 5.6 24 489-514 43-66 (89)
497 PRK11534 DNA-binding transcrip 38.0 41 0.00088 32.9 4.1 37 479-521 20-56 (224)
498 PF13730 HTH_36: Helix-turn-he 37.9 43 0.00094 25.2 3.4 28 396-423 23-50 (55)
499 PRK09393 ftrA transcriptional 37.8 2.1E+02 0.0046 29.5 9.6 39 383-421 219-257 (322)
500 COG4709 Predicted membrane pro 37.7 61 0.0013 31.9 5.0 59 458-516 3-65 (195)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=6.5e-64 Score=530.18 Aligned_cols=312 Identities=29% Similarity=0.521 Sum_probs=292.0
Q ss_pred CCchhHHHHHHhhccCCCCCCchHHHHHHhhchHHHH--------------------HHHHHHHHHHHhCCCCchHHHHH
Q 009449 218 KQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVAN--------------------LERIKTTLEKESGKAASLNCWAQ 277 (534)
Q Consensus 218 ~~~~~~~~~~~~~~~~~~lLt~~eE~~L~~~iq~~~~--------------------le~~~~~l~~~~g~~ps~~ewa~ 277 (534)
.||.+.|+ ..+.+.||||++||++|+++||.++. |++++..|.+++|++||..+||.
T Consensus 59 ~d~v~~yl---~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~ 135 (415)
T PRK07598 59 TDLVRLYL---QEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAK 135 (415)
T ss_pred CChHHHHH---HhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHH
Confidence 36655555 35555799999999999999999999 89999999999999999999995
Q ss_pred HcC----------------------CCHHHHHHHHHhcHHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 009449 278 AAG----------------------VSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQ 335 (534)
Q Consensus 278 a~g----------------------~d~~~L~~~l~~G~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~r 335 (534)
++| ++.++|++.++.|..|+++||.+|+++|+++|++|.++|++++||+|||++|||+
T Consensus 136 ~~~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~r 215 (415)
T PRK07598 136 TADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLER 215 (415)
T ss_pred HhCCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHH
Confidence 554 5566666777889899999999999999999999999999999999999999999
Q ss_pred hhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHH
Q 009449 336 GAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEI 415 (534)
Q Consensus 336 A~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv 415 (534)
|+++|||++|++|+|||+||||++|.+++++++++||+|.|+.+.+++++++.+.+.+++||.|+.+|||+.+||++++|
T Consensus 216 avekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~v 295 (415)
T PRK07598 216 AVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQV 295 (415)
T ss_pred HHHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHH
Q 009449 416 RSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLE 495 (534)
Q Consensus 416 ~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~ 495 (534)
+.++...+.++|||.+++++++..+.+.+.++. .+|++.+....+...|..+|..|||+||+||.|+|||+|++++|++
T Consensus 296 r~~l~~~~~~~SLd~~vg~~~d~~l~d~l~~~~-~~pee~~~~~~l~~~L~~~L~~L~~reR~VI~LRygl~d~~~~Tl~ 374 (415)
T PRK07598 296 REVLLRVPRSVSLETKVGKDKDTELGDLLETDD-ISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLA 374 (415)
T ss_pred HHHHHHccCCcccccccCCCccccHHHhccCCC-CCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCCCHH
Confidence 999999999999999999988888888887554 6899999999999999999999999999999999999999999999
Q ss_pred HHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchhhhc
Q 009449 496 EIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFLV 533 (534)
Q Consensus 496 EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~yl~ 533 (534)
|||+.||||+++|++++++|++|||++-....|++|+.
T Consensus 375 EIA~~LGvS~erVRqie~rAl~KLR~~~~~~~l~~y~~ 412 (415)
T PRK07598 375 EIGRALDLSRERVRQIESKALQKLRQPKRRNRIRDYLE 412 (415)
T ss_pred HHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHHH
Confidence 99999999999999999999999999999999999985
No 2
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00 E-value=4.4e-60 Score=491.04 Aligned_cols=308 Identities=33% Similarity=0.557 Sum_probs=291.5
Q ss_pred HHHHHHhhccC-CCCCCchHHHHHHhhchHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhcHHHHHHHH
Q 009449 223 FSAERALNSRG-RRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELI 301 (534)
Q Consensus 223 ~~~~~~~~~~~-~~lLt~~eE~~L~~~iq~~~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l~~G~~A~e~LI 301 (534)
+.+..|++..+ .||||++||++|++.|+.++.+++.+..|.+++|+.|+..+||.++++++.+|+..++.|..|++.||
T Consensus 18 d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~~Li 97 (327)
T PRK05949 18 DMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQKMI 97 (327)
T ss_pred CHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHHHHH
Confidence 33445565555 69999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHHH
Q 009449 302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREI 381 (534)
Q Consensus 302 ~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i 381 (534)
..|+++|+++|++|.+++.+++||+|||++|||+++++|||++|++|+|||+||||++|.+++.+++++||+|.|+.+.+
T Consensus 98 ~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~~~~~ 177 (327)
T PRK05949 98 EANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEKL 177 (327)
T ss_pred HHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHHHH
Q 009449 382 SKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHM 461 (534)
Q Consensus 382 ~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~el 461 (534)
++++++.+.+.+++||.||.+|||+.+|+++++|..++.....++|||.+++++++.++.+.+++.. .+|++.+....+
T Consensus 178 ~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~~-~~pe~~~~~~~~ 256 (327)
T PRK05949 178 NKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEG-PSPDQYITQELL 256 (327)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCCC-CCHHHHHHHHHH
Confidence 9999999999999999999999999999999999999998899999999998887778888888765 689999999999
Q ss_pred HHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchhhhc
Q 009449 462 KKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFLV 533 (534)
Q Consensus 462 ~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~yl~ 533 (534)
...|..+|+.|||+||+||.+||||+|++++|++|||+.||||+++|+|++.+|++|||+. ...|+.|+.
T Consensus 257 ~~~L~~~L~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~~--~~~l~~~~~ 326 (327)
T PRK05949 257 RQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRRR--RANVKEYLA 326 (327)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence 9999999999999999999999999999999999999999999999999999999999994 467788874
No 3
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=3.6e-60 Score=498.05 Aligned_cols=308 Identities=33% Similarity=0.618 Sum_probs=294.1
Q ss_pred HHHHHhhccC-CCCCCchHHHHHHhhchHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhcHHHHHHHHH
Q 009449 224 SAERALNSRG-RRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIK 302 (534)
Q Consensus 224 ~~~~~~~~~~-~~lLt~~eE~~L~~~iq~~~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l~~G~~A~e~LI~ 302 (534)
.+..|++..+ .||||++||++|+++|+.++.+++.+..|+++.|++|+..+||.++|++..+|.+++..|..|++.||.
T Consensus 64 ~l~~Yl~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Li~ 143 (373)
T PRK07406 64 SIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMVQ 143 (373)
T ss_pred HHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHHHHH
Confidence 3455666555 699999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHHHH
Q 009449 303 STRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREIS 382 (534)
Q Consensus 303 ~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i~ 382 (534)
+|+++|+++|++|.++|.+++||+|||++|||+++++|||.+|++|+|||+||||++|.++|++++++||+|.|+.+.++
T Consensus 144 ~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~~~~~ 223 (373)
T PRK07406 144 SNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETIS 223 (373)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHHHHH
Q 009449 383 KIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMK 462 (534)
Q Consensus 383 ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~el~ 462 (534)
+++++...|.+++||.||.+|||+.+|+++++|..++.....++|||.+++++++..+.+++++.. .+|++.+....+.
T Consensus 224 ~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d~l~d~~-~~pee~~~~~~~~ 302 (373)
T PRK07406 224 RIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADG-ETPEDDVAKNLLR 302 (373)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHHhcCCCC-CCHHHHHHHHHHH
Confidence 999999999999999999999999999999999999888888999999998877778889888764 5899999999999
Q ss_pred HHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchhhh
Q 009449 463 KDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFL 532 (534)
Q Consensus 463 e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~yl 532 (534)
..|..+|..||++||.||.+||||+|++++|++|||+.||||++||||++.+|++|||++.....|..|+
T Consensus 303 ~~L~~aL~~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~~~~~~~l~~~~ 372 (373)
T PRK07406 303 EDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 372 (373)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHh
Confidence 9999999999999999999999999889999999999999999999999999999999999999999986
No 4
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=6.8e-59 Score=480.50 Aligned_cols=306 Identities=30% Similarity=0.548 Sum_probs=290.1
Q ss_pred HHHHhhccC-CCCCCchHHHHHHhhchHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhcHHHHHHHHHH
Q 009449 225 AERALNSRG-RRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKS 303 (534)
Q Consensus 225 ~~~~~~~~~-~~lLt~~eE~~L~~~iq~~~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l~~G~~A~e~LI~~ 303 (534)
+..|++..+ .||||++||++|+++|+.++.+++++..|++++|+.|+..+||.++++++.+|+..++.|..|++.||..
T Consensus 10 ~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~L~~~ 89 (317)
T PRK07405 10 VRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRKMVEA 89 (317)
T ss_pred HHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHHHHHH
Confidence 445565555 6999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHHHHH
Q 009449 304 TRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISK 383 (534)
Q Consensus 304 nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i~k 383 (534)
|+++|+++|++|.+++.+++||+|||++|||+++++|||++|++|+|||+||||++|.+++.+++++||+|.|+...+++
T Consensus 90 ~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~~~~~~ 169 (317)
T PRK07405 90 NLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNK 169 (317)
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHHHHHH
Q 009449 384 IQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKK 463 (534)
Q Consensus 384 i~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~el~e 463 (534)
++++.+.+.+.+|+.||.+|||+.+|++++++..+......+.|||.+++++.+..+.+.++++. .+|++.+....+..
T Consensus 170 l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~~-~~pe~~~~~~~~~~ 248 (317)
T PRK07405 170 IKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTG-ASPEDFATQSSLQL 248 (317)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCCC-CCHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999988888999999998877778888888765 68999999999999
Q ss_pred HHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchhhhc
Q 009449 464 DVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFLV 533 (534)
Q Consensus 464 ~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~yl~ 533 (534)
.|..+|+.|||+||+||.+||||+|++++|++|||+.||||++||||++.+|++|||+. ...|..|+.
T Consensus 249 ~l~~al~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~--~~~l~~~~~ 316 (317)
T PRK07405 249 DLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKR--KANIQEYLA 316 (317)
T ss_pred HHHHHHHcCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999985 467777764
No 5
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=100.00 E-value=1.1e-58 Score=475.04 Aligned_cols=293 Identities=36% Similarity=0.604 Sum_probs=279.3
Q ss_pred HHhh-ccCCCCCCchHHHHHHhhchHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhcHHHHHHHHHHhH
Q 009449 227 RALN-SRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTR 305 (534)
Q Consensus 227 ~~~~-~~~~~lLt~~eE~~L~~~iq~~~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l~~G~~A~e~LI~~nl 305 (534)
.|++ ....||||++||++|++.++.+..+++.+..|+++.|++|+..+||+++|++..+|...++.|..|++.||.+|+
T Consensus 5 ~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv~~~l 84 (298)
T TIGR02997 5 LYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMIKANL 84 (298)
T ss_pred HHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHHHHhH
Confidence 3444 445799999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHHHHHHH
Q 009449 306 PLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQ 385 (534)
Q Consensus 306 rLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i~ki~ 385 (534)
++|+++|++|.++|.+++||+|||++|||+|+++|||.+|++|+|||+||||++|.+++.+++++||+|.++...+++++
T Consensus 85 rlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~~~~~~~~~~r 164 (298)
T TIGR02997 85 RLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLNKIK 164 (298)
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHHHHHHHH
Q 009449 386 KARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDV 465 (534)
Q Consensus 386 ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~el~e~L 465 (534)
++.+.+.+.+|+.||.+|||+.+|+++++|..++.....++|||.+++++++..+.+.+++. .++|++.+...++...|
T Consensus 165 k~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~-~~~pe~~~~~~~~~~~L 243 (298)
T TIGR02997 165 KVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDD-GESPEEQVERESLRQDL 243 (298)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccCC-CCCHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999888999999999877666777777774 46899999999999999
Q ss_pred HHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449 466 FRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520 (534)
Q Consensus 466 ~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR 520 (534)
..+|+.|||+||+||.+||||+|++++|++|||+.||||++||+|++++|++|||
T Consensus 244 ~~~L~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr 298 (298)
T TIGR02997 244 ESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298 (298)
T ss_pred HHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 9999999999999999999999999999999999999999999999999999996
No 6
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=100.00 E-value=2.2e-58 Score=474.61 Aligned_cols=312 Identities=33% Similarity=0.546 Sum_probs=285.0
Q ss_pred hHHHHHHhhccC-CCCCCchHHHHHHhhchHHHHHHHHHHHHHH-HhCCCCchH---------------HHHHHcCCCH-
Q 009449 222 IFSAERALNSRG-RRLTIARNEAEMSKGVQVVANLERIKTTLEK-ESGKAASLN---------------CWAQAAGVSE- 283 (534)
Q Consensus 222 ~~~~~~~~~~~~-~~lLt~~eE~~L~~~iq~~~~le~~~~~l~~-~~g~~ps~~---------------ewa~a~g~d~- 283 (534)
.+.+..|++..+ .++++.++|+++.++++....+......+.. .++..|+.. +|+.....++
T Consensus 8 ~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Ee 87 (342)
T COG0568 8 ADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEEE 87 (342)
T ss_pred hhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHHH
Confidence 455566666665 4899999999999999988877666777766 567888876 5555444444
Q ss_pred HHHHHHHHhcHH---HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHH
Q 009449 284 RVLKQHLAFGWY---CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (534)
Q Consensus 284 ~~L~~~l~~G~~---A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI 360 (534)
..|..++..|.. |+.+||.+|++||++||++|.++|+++.||||||+|||++|+++|||++||+|||||+||||++|
T Consensus 88 ~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrqaI 167 (342)
T COG0568 88 KALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAI 167 (342)
T ss_pred HHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHHHH
Confidence 667888888854 99999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhh
Q 009449 361 SKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKY 440 (534)
Q Consensus 361 ~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l 440 (534)
.++|.++.|+||+|+|+++.+++++++.+.+.+++|++|+.+|||+.+|+++++|..++.....++|||.|+|++++..+
T Consensus 168 ~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~ded~~l 247 (342)
T COG0568 168 TRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSEL 247 (342)
T ss_pred HHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCCCcccHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhccCCCCCCChHHHHHHHHHHHHHHHHHhh-CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449 441 LEFAPDRSVKSPKEIVMRQHMKKDVFRILES-LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL 519 (534)
Q Consensus 441 ~e~i~d~~~~spee~v~~~el~e~L~~~L~~-L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL 519 (534)
+|+++|....+|++.+....+.+++...|.. |+|+|+.||++|||++|+++.|++|||+.+|||++|||||+.+|++||
T Consensus 248 ~d~leD~~~~~p~~~~~~~~~~~~~~~~L~~~Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~isrERvRQIE~kAl~KL 327 (342)
T COG0568 248 GDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAKALRKL 327 (342)
T ss_pred HHHhhcCCcCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCcchHHHHHHHhCCcHHHHHHHHHHHHHHH
Confidence 9999999888999999999999999999999 999999999999999999999999999999999999999999999999
Q ss_pred H-hHhhhhcchhhhc
Q 009449 520 R-DSETCRDLSHFLV 533 (534)
Q Consensus 520 R-~~l~~~~L~~yl~ 533 (534)
| .+.....+++|++
T Consensus 328 r~~~~~~~~~~~~l~ 342 (342)
T COG0568 328 RRHPERSALLRSYLD 342 (342)
T ss_pred HHhhhhhhHHHHhhC
Confidence 9 5555666788874
No 7
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=100.00 E-value=2.2e-57 Score=491.00 Aligned_cols=298 Identities=32% Similarity=0.521 Sum_probs=271.9
Q ss_pred HHHHHHhhccC-CCCCCchHHHHHHhhchHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhcHHHHHHHH
Q 009449 223 FSAERALNSRG-RRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELI 301 (534)
Q Consensus 223 ~~~~~~~~~~~-~~lLt~~eE~~L~~~iq~~~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l~~G~~A~e~LI 301 (534)
+.++.|++..+ .||||++||++|+++|+.+..++... . ...+|+.. ...+|++.+..|..|+++||
T Consensus 211 d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~~---~-------~~~~~~~~---~~~~l~~~~~~g~~Ar~~LI 277 (509)
T PRK05901 211 DPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEELL---A-------EGEKLDPE---LRRDLQWIGRDGKRAKNHLL 277 (509)
T ss_pred cHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhhh---h-------hcccchhh---hhhhhhhhccchHHHHHHHH
Confidence 33455666555 59999999999999999875544321 1 11224322 45778888999999999999
Q ss_pred HHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHHH
Q 009449 302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREI 381 (534)
Q Consensus 302 ~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i 381 (534)
.+|+|||++||++|.++|++++||||||+|||++|+++|||++|++|+|||+||||++|.+++.++.|+||+|.|+++.+
T Consensus 278 ~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~~~~e~i 357 (509)
T PRK05901 278 EANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVETI 357 (509)
T ss_pred HHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHHHH
Q 009449 382 SKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHM 461 (534)
Q Consensus 382 ~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~el 461 (534)
+++.++.++|.+.+||.||.+|||+.+|+++++|..++.....++|||.+++++++..+.++++|+...+|++.+....+
T Consensus 358 ~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~~p~~~~~~~~l 437 (509)
T PRK05901 358 NKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSFTLL 437 (509)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCCCCCHHHHHHHHHH
Confidence 99999999999999999999999999999999999999888899999999988877889999999887899999999999
Q ss_pred HHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchhhhc
Q 009449 462 KKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFLV 533 (534)
Q Consensus 462 ~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~yl~ 533 (534)
...|..+|..|+++|+.||.+||||++++++|++|||+.||||++|||||+.+|+.|||+......|++|++
T Consensus 438 ~~~L~~aL~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~~~~~~l~~~l~ 509 (509)
T PRK05901 438 QDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDFLD 509 (509)
T ss_pred HHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999974
No 8
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=100.00 E-value=2.9e-56 Score=461.70 Aligned_cols=295 Identities=33% Similarity=0.559 Sum_probs=269.3
Q ss_pred HHHHhhccC-CCCCCchHHHHHHhhchHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhcHHHHHHHHHH
Q 009449 225 AERALNSRG-RRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKS 303 (534)
Q Consensus 225 ~~~~~~~~~-~~lLt~~eE~~L~~~iq~~~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l~~G~~A~e~LI~~ 303 (534)
+..|++..+ .||||++||++|+++|+.+..++.. |+..+|+... ...+|...++.|..|++.||..
T Consensus 28 ~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~~Lv~~ 94 (324)
T PRK07921 28 VRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARRHLLEA 94 (324)
T ss_pred HHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHHHHHHH
Confidence 345555555 6999999999999999988766553 2223332111 3467888999999999999999
Q ss_pred hHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHHHHH
Q 009449 304 TRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISK 383 (534)
Q Consensus 304 nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i~k 383 (534)
|+++|+++|++|.+++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.+++++++++||+|.|+.+.+++
T Consensus 95 ~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~~~~~~ 174 (324)
T PRK07921 95 NLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNK 174 (324)
T ss_pred HHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHHHHHH
Q 009449 384 IQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKK 463 (534)
Q Consensus 384 i~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~el~e 463 (534)
++++.+.|.+++|+.||.+|||+.+|+++++|..++.....++|||.+++++++.++.++++|+...+|++.+....+..
T Consensus 175 l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~~~~~ 254 (324)
T PRK07921 175 LARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGLLHT 254 (324)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCCCCCHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999888888999999998877778899999877778999999999999
Q ss_pred HHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchhhh
Q 009449 464 DVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFL 532 (534)
Q Consensus 464 ~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~yl 532 (534)
.|..+|..|+++|+.||.+||||+|++++|++|||+.||||+++|||++.+|++|||.......|..|+
T Consensus 255 ~l~~~L~~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~~~~~~l~~~~ 323 (324)
T PRK07921 255 DIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSYA 323 (324)
T ss_pred HHHHHHHhCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHHHHHHHHhh
Confidence 999999999999999999999999889999999999999999999999999999999999888899886
No 9
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=4.6e-52 Score=437.50 Aligned_cols=272 Identities=32% Similarity=0.559 Sum_probs=255.0
Q ss_pred hHHHHHHhhccC-CCCCCchHHHHHHhhchHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhcHHHHHHH
Q 009449 222 IFSAERALNSRG-RRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREEL 300 (534)
Q Consensus 222 ~~~~~~~~~~~~-~~lLt~~eE~~L~~~iq~~~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l~~G~~A~e~L 300 (534)
.++++.|++..+ .|+||++||.+|++.++.+ +..|++.|
T Consensus 95 ~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~G----------------------------------------d~~A~~~L 134 (367)
T PRK09210 95 NDPVRMYLKEIGRVPLLTAEEEIELAKRIEEG----------------------------------------DEEAKQRL 134 (367)
T ss_pred CcHHHHHHHHhhccCCCCHHHHHHHHHHHHhh----------------------------------------HHHHHHHH
Confidence 345566676555 5999999999999866532 13589999
Q ss_pred HHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHH
Q 009449 301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNRE 380 (534)
Q Consensus 301 I~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~ 380 (534)
|..|+++|+++|++|.+++.+++||+|||++|||+|+++|||.+|++|+|||+||||++|.++++++.|++|+|.|+++.
T Consensus 135 i~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~~~~ 214 (367)
T PRK09210 135 AEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 214 (367)
T ss_pred HHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHHH
Q 009449 381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQH 460 (534)
Q Consensus 381 i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~e 460 (534)
++++.++.+.|.+++||.||.+|||+.+|+++++|+.++.....++|||.+++++++..+.++++|+...+|++.+....
T Consensus 215 ~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~~~~p~~~~~~~~ 294 (367)
T PRK09210 215 INKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYEL 294 (367)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCCCCCHHHHHHHHH
Confidence 99999999999999999999999999999999999999988888999999999887788999999988789999999999
Q ss_pred HHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchhhhc
Q 009449 461 MKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFLV 533 (534)
Q Consensus 461 l~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~yl~ 533 (534)
++..|..+|..||++||.||.+||||+|++++|++|||+.||||++||||++.+|++|||++.....|+.|++
T Consensus 295 ~~~~l~~~l~~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~~~~~~~l~~~~~ 367 (367)
T PRK09210 295 LKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 367 (367)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhChHHHhHHHHhhC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999974
No 10
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=9.2e-50 Score=445.18 Aligned_cols=259 Identities=30% Similarity=0.594 Sum_probs=243.6
Q ss_pred HHHHcCCCHHH---HHHHHHhcH----HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCc
Q 009449 275 WAQAAGVSERV---LKQHLAFGW----YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYK 347 (534)
Q Consensus 275 wa~a~g~d~~~---L~~~l~~G~----~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~r 347 (534)
.....+++.++ +.++++.|. .|+++||.+|+|||++||++|.++|++++||||||++||++|+++|||++|++
T Consensus 353 ie~~~~Ls~eElk~l~~~i~~g~~~~~~a~~~Li~~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~ 432 (619)
T PRK05658 353 IEEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 432 (619)
T ss_pred HHHHhCCCHHHHHHHHHHHhccchhhhHHHHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCc
Confidence 34445565544 445566773 58999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHHHHHHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcc
Q 009449 348 FSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGS 427 (534)
Q Consensus 348 FSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~S 427 (534)
|+|||+||||++|.++++++.++||+|.|+.+.++++.++.+.+.+++||.||.+|||+.+|+++++|..++.....++|
T Consensus 433 FstYA~~wIr~aI~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~S 512 (619)
T PRK05658 433 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPIS 512 (619)
T ss_pred hHHHhHHHHHHHHHHHHHHcCCceecCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999998889999
Q ss_pred cccccccchhhhhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHH
Q 009449 428 IDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEW 507 (534)
Q Consensus 428 LD~~i~~~~~~~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrer 507 (534)
||.|++++++..+.++++|....+|++.+....++..|..+|..||++|+.||++||||+++.++|++|||+.||||+++
T Consensus 513 ld~~i~~~~~~~l~d~i~d~~~~~p~~~~~~~~~~~~l~~~l~~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eR 592 (619)
T PRK05658 513 LETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRER 592 (619)
T ss_pred CCCCCCCCCCCchhhhcCCCCCCChHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHH
Confidence 99999988888899999998888999999999999999999999999999999999999988999999999999999999
Q ss_pred HHHHHHHHHHHHHhHhhhhcchhhhc
Q 009449 508 IRKLEKKAMTKLRDSETCRDLSHFLV 533 (534)
Q Consensus 508 VRqi~~RAL~KLR~~l~~~~L~~yl~ 533 (534)
|||++.+|++|||++.....|+.|++
T Consensus 593 VrQie~~al~kLr~~~~~~~l~~~~~ 618 (619)
T PRK05658 593 IRQIEAKALRKLRHPSRSRKLRSFLD 618 (619)
T ss_pred HHHHHHHHHHHHhchHHHHHHHHHhc
Confidence 99999999999999999999999986
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=5.6e-48 Score=383.41 Aligned_cols=238 Identities=37% Similarity=0.685 Sum_probs=228.3
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccccc
Q 009449 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC 375 (534)
Q Consensus 296 A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~ 375 (534)
|+++||..|+++|+++|++|.+++.+++||+|||++||++|+++|||++|++|+|||+||||++|.++++++.+.+++|.
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 chHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHH
Q 009449 376 KLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEI 455 (534)
Q Consensus 376 ~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~ 455 (534)
++.+.++++.++.+.+.+++|+.||.+|||+.+|++++++..++.....++|||.+++++++.++.+.++|+...+|++.
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 99999999999999999999999999999999999999999998887788999999987766678888998877889999
Q ss_pred HHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchhhhc
Q 009449 456 VMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFLV 533 (534)
Q Consensus 456 v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~yl~ 533 (534)
+...++...|..+|+.||++|+.||.++|||++++++|++|||+.||||+++|+|++.+|++|||+.+....|+.|++
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 999999999999999999999999999999999999999999999999999999999999999999999999999975
No 12
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=4.8e-43 Score=353.85 Aligned_cols=220 Identities=23% Similarity=0.346 Sum_probs=201.0
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccc
Q 009449 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (534)
Q Consensus 295 ~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP 374 (534)
.++++||.+|++||+++|++|.++|++++||+|||+|||++|+++|||++|++|+|||+||||++|.++++++.++||+|
T Consensus 40 ~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I~~~lr~~~~~ir~P 119 (264)
T PRK07122 40 RQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVP 119 (264)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHcCCccccC
Confidence 48899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHH--hhhhcccccccccchhh--hhhhccCCCCCC
Q 009449 375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC--LRIVGSIDQKIGDCLNA--KYLEFAPDRSVK 450 (534)
Q Consensus 375 ~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~--~~~~~SLD~~i~~~~~~--~l~e~i~d~~~~ 450 (534)
.++.+.+++++++...+.+++|+.||.+|||+.+|+++++|..++.. ...+.|||.+++++++. .+.+.+ +
T Consensus 120 r~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~d~~-----~ 194 (264)
T PRK07122 120 RRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDARAIADTL-----G 194 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCCCCcccchhcc-----C
Confidence 99999999999999999999999999999999999999999998764 34688999998654332 233333 3
Q ss_pred ChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449 451 SPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE 523 (534)
Q Consensus 451 spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l 523 (534)
+++..+...+....|..+|+.||++++.||.++| ++++|++|||+.||||+++|++++++|+++||..+
T Consensus 195 ~~~~~~e~~~~~~~l~~~l~~L~~rer~vl~l~y----~~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l 263 (264)
T PRK07122 195 DVDAGLDQIENREALRPLLAALPERERTVLVLRF----FESMTQTQIAERVGISQMHVSRLLAKTLARLRDQL 263 (264)
T ss_pred CcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHh----cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHc
Confidence 4556667777888899999999999999999999 88999999999999999999999999999999875
No 13
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=100.00 E-value=3.3e-42 Score=357.34 Aligned_cols=269 Identities=25% Similarity=0.477 Sum_probs=246.4
Q ss_pred hhHHHHHHhhccC-CCCCCchHHHHHHhhchHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhcHHHHHH
Q 009449 221 TIFSAERALNSRG-RRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREE 299 (534)
Q Consensus 221 ~~~~~~~~~~~~~-~~lLt~~eE~~L~~~iq~~~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l~~G~~A~e~ 299 (534)
..+.+..|++-.+ .|+||+++|.+|...++. ++..|++.
T Consensus 51 ~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~----------------------------------------Gd~~A~~~ 90 (325)
T PRK05657 51 VLDATQLYLNEIGYSPLLTAEEEVYFARRALR----------------------------------------GDFAARQR 90 (325)
T ss_pred cccHHHHHHHHHhcCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHH
Confidence 3456677786666 599999999888764321 12569999
Q ss_pred HHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHH
Q 009449 300 LIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNR 379 (534)
Q Consensus 300 LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~ 379 (534)
||..|.++|+++|++|.+++.+++||+|||++|+|+++++||+.+|++|+||++||||++|.+++.++.+++++|.++..
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 HHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHH
Q 009449 380 EISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQ 459 (534)
Q Consensus 380 ~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~ 459 (534)
.++++.++.+.+.+.+|+.|+.+|||+.+|+++++|..++.....+.|||.++..+...++.+.++++...+|++.+...
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 99999999999999999999999999999999999999998777888999998877777788888887767899999999
Q ss_pred HHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcch
Q 009449 460 HMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLS 529 (534)
Q Consensus 460 el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~ 529 (534)
+....|..+|..||+++|.||.++|||.+++++|++|||+.||||++||++++++|+++||+.+...++.
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 9999999999999999999999999999999999999999999999999999999999999999887765
No 14
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=7.2e-42 Score=349.53 Aligned_cols=260 Identities=24% Similarity=0.344 Sum_probs=219.2
Q ss_pred HHHHhhccC-CCCCCchHHHHHHhhchHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhcHHHHHHHHHH
Q 009449 225 AERALNSRG-RRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKS 303 (534)
Q Consensus 225 ~~~~~~~~~-~~lLt~~eE~~L~~~iq~~~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l~~G~~A~e~LI~~ 303 (534)
+..|++..+ .|+||+++|.+|.++++. .++..|+++||..
T Consensus 8 ~~~y~~~~~~~~~l~~~~e~~L~~~~~~---------------------------------------~gd~~A~~~Lv~~ 48 (289)
T PRK07500 8 DRSMIRSAMKAPYLEREEEHALAYRWKD---------------------------------------HRDEDALHRIISA 48 (289)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHHHH
Confidence 344555444 699999999999885421 0235699999999
Q ss_pred hHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHH--HH
Q 009449 304 TRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNR--EI 381 (534)
Q Consensus 304 nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~--~i 381 (534)
|.++|+++|++|.+++.+++||+|||++|||+++++|||.+|.+|+|||+||||++|.++++++.+.+|+|.+... ..
T Consensus 49 ~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~~~~~~~~~ 128 (289)
T PRK07500 49 HMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALF 128 (289)
T ss_pred hHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCccHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999998765 44
Q ss_pred HHHHHHHHHHHH---hcCCCCCHHHHHHHcCCCHHHHHHHHH-Hhhhhcccccccccchhh--hhhhccCCCCCCChHHH
Q 009449 382 SKIQKARKALTN---SHGKYPEDIEIAKYTGLSLAEIRSASE-CLRIVGSIDQKIGDCLNA--KYLEFAPDRSVKSPKEI 455 (534)
Q Consensus 382 ~ki~ka~~~L~~---elGr~Pt~eEIA~~lgis~~kv~~~l~-~~~~~~SLD~~i~~~~~~--~l~e~i~d~~~~spee~ 455 (534)
.++++.+..+.+ .+|+.||.+|||+.+|++++++..+.. ....++|||.+++++++. ++.+.++++. .+|++.
T Consensus 129 ~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~i~d~~-~~pe~~ 207 (289)
T PRK07500 129 FNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDS-PLPDEQ 207 (289)
T ss_pred HHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCCCcccHHHhccCCC-CCchHH
Confidence 556666666555 689999999999999999999987753 344689999998765443 5788888765 467766
Q ss_pred HHH----HHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhh
Q 009449 456 VMR----QHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCR 526 (534)
Q Consensus 456 v~~----~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~ 526 (534)
+.. ......|..+|+.||++|++||.++|+. .+++|++|||+.||||+++|+|++++|++|||..+...
T Consensus 208 ~~~~~~~~~~~~~l~~al~~L~~rer~vl~lr~~~--~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~~~ 280 (289)
T PRK07500 208 VESSIDGERRRRWLTQALQTLNERELRIIRERRLR--EDGATLEALGEELGISKERVRQIEARALEKLRRALLSQ 280 (289)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 543 3456779999999999999999999942 37999999999999999999999999999999988644
No 15
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=5.8e-41 Score=342.03 Aligned_cols=259 Identities=26% Similarity=0.396 Sum_probs=213.5
Q ss_pred HHHHHHhhc-cCCCCCCchHHHHHHhhchHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhcHHHHHHHH
Q 009449 223 FSAERALNS-RGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELI 301 (534)
Q Consensus 223 ~~~~~~~~~-~~~~lLt~~eE~~L~~~iq~~~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l~~G~~A~e~LI 301 (534)
+++..|.+. .+.|+||+++|.+|+.+.+ ..++..|++.||
T Consensus 14 ~~~~~y~~~~~~~~~l~~~~e~~l~~~~~---------------------------------------~~Gd~~a~~~Lv 54 (284)
T PRK06596 14 GNLDAYIQAVNKIPMLTAEEEYMLAKRLR---------------------------------------EHGDLEAAKQLV 54 (284)
T ss_pred cHHHHHHHHHhccCCCCHHHHHHHHHHHH---------------------------------------HcCCHHHHHHHH
Confidence 344556654 4468899999988877421 012256999999
Q ss_pred HHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchH--H
Q 009449 302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN--R 379 (534)
Q Consensus 302 ~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~--~ 379 (534)
..|+++|+++|++|.+.+.+++||+|||++||++|+++|||++|++|+|||+||||++|.++++++.++|++|.+.. .
T Consensus 55 ~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~p~~~~~~~ 134 (284)
T PRK06596 55 LSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQRK 134 (284)
T ss_pred HHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeeeccchHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999888899998753 2
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHh-hhhcccccccccch--hhhhhhccCCCCCCChHHHH
Q 009449 380 EISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL-RIVGSIDQKIGDCL--NAKYLEFAPDRSVKSPKEIV 456 (534)
Q Consensus 380 ~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~-~~~~SLD~~i~~~~--~~~l~e~i~d~~~~spee~v 456 (534)
...++.+....+. .++.||.+|||+.+|+++++|..++... ..++|||.++++++ +.++.+.++|+. .+|++.+
T Consensus 135 ~~~~~~~~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~~-~~p~~~~ 211 (284)
T PRK06596 135 LFFNLRKAKKRLG--WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDKS-SDPADVL 211 (284)
T ss_pred HHHHHHHHHHHhc--cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcCCCC-CCchHHH
Confidence 3334444444443 3499999999999999999999986533 36889999986552 245778888774 5787776
Q ss_pred HHH----HHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449 457 MRQ----HMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC 525 (534)
Q Consensus 457 ~~~----el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~ 525 (534)
+.. ++...|..+|+.||++|+.||.+|||. + +++|++|||+.||||+++|+|++.+|++|||..+..
T Consensus 212 ~~~~~~~~~~~~L~~al~~L~~rEr~VL~lry~~-~-~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~l~~ 282 (284)
T PRK06596 212 EEDNWEDQRRALLADALEGLDERSRDIIEARWLD-D-DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEA 282 (284)
T ss_pred HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC-C-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 654 357789999999999999999999953 2 699999999999999999999999999999998754
No 16
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=4e-41 Score=338.24 Aligned_cols=229 Identities=23% Similarity=0.338 Sum_probs=202.8
Q ss_pred Hhc-HHHHHHHHHHhHHHHHHHHHHhhCC-CCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhc
Q 009449 291 AFG-WYCREELIKSTRPLVLFLARNYRGL-GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA 368 (534)
Q Consensus 291 ~~G-~~A~e~LI~~nlrLV~sIArrY~~~-g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~s 368 (534)
..| ..|+++||..|+++|+++|++|.+. +.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++++++.
T Consensus 20 ~~gd~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~ 99 (256)
T PRK07408 20 QNPSIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKS 99 (256)
T ss_pred HCCCHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcC
Confidence 355 6799999999999999999999876 66799999999999999999999999999999999999999999999999
Q ss_pred cccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHH--hhhhcccccccccchh--hhhhhcc
Q 009449 369 RGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC--LRIVGSIDQKIGDCLN--AKYLEFA 444 (534)
Q Consensus 369 r~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~--~~~~~SLD~~i~~~~~--~~l~e~i 444 (534)
++||+|.++.+.+++++++...|.+++|++||.+|||+.+|++++++..+... ...+.|||.+++++++ ..+.+.+
T Consensus 100 ~~vr~pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~~ 179 (256)
T PRK07408 100 PTVRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDEDGSTSLGDLL 179 (256)
T ss_pred CeeeeCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCCCcccccccc
Confidence 99999999999999999999999999999999999999999999999998653 3467899999865433 2456666
Q ss_pred CCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449 445 PDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET 524 (534)
Q Consensus 445 ~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~ 524 (534)
+++... +.. ...+....|..+|..||+++|.||.++| ++++|++|||+.||+|.++|++++++|+++||..+.
T Consensus 180 ~d~~~~-~~~--~~~~~~~~l~~~l~~L~~~~r~vl~l~y----~~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~ 252 (256)
T PRK07408 180 PDPRYR-SFQ--LAQEDRIRLQQALAQLEERTREVLEFVF----LHDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQ 252 (256)
T ss_pred CCcccc-hhh--hhHHHHHHHHHHHHcCCHHHHHHHHHHH----HCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 665432 211 2345567899999999999999999999 789999999999999999999999999999999876
Q ss_pred hh
Q 009449 525 CR 526 (534)
Q Consensus 525 ~~ 526 (534)
..
T Consensus 253 ~~ 254 (256)
T PRK07408 253 PE 254 (256)
T ss_pred cc
Confidence 53
No 17
>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=5.9e-40 Score=332.09 Aligned_cols=226 Identities=28% Similarity=0.459 Sum_probs=191.6
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI 373 (534)
Q Consensus 294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl 373 (534)
..|++.||..|+++|+++|++|.+++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++++++.+++|+
T Consensus 34 ~~a~~~Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir~ 113 (270)
T TIGR02392 34 LDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKV 113 (270)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCceec
Confidence 56999999999999999999999999999999999999999999999999999999999999999999999998778999
Q ss_pred ccchH--HHHHHHHHHHHHHHHhcCCCC-CHHHHHHHcCCCHHHHHHHHHHhh-hhcccccccccchh--hhhhhccCCC
Q 009449 374 PCKLN--REISKIQKARKALTNSHGKYP-EDIEIAKYTGLSLAEIRSASECLR-IVGSIDQKIGDCLN--AKYLEFAPDR 447 (534)
Q Consensus 374 P~~~~--~~i~ki~ka~~~L~~elGr~P-t~eEIA~~lgis~~kv~~~l~~~~-~~~SLD~~i~~~~~--~~l~e~i~d~ 447 (534)
|.+.. +...++.++...+. .++.| +.+|||+.+|+++++|..+..... .+.|||.+++++++ ..+.+.++|.
T Consensus 114 p~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~l~d~ 191 (270)
T TIGR02392 114 ATTKAQRKLFFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDK 191 (270)
T ss_pred CchHHHHHHHHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCCccccHHHHhcCC
Confidence 98753 34445555554443 22556 699999999999999999865433 47899999876543 2466777776
Q ss_pred CCCChHHHHHHH----HHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449 448 SVKSPKEIVMRQ----HMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE 523 (534)
Q Consensus 448 ~~~spee~v~~~----el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l 523 (534)
. .+|++.+... .+...|..+|..||++||.||.++||. .+++|++|||+.||||+++|+|++.+|++|||..+
T Consensus 192 ~-~~pe~~~~~~~~~~~~~~~L~~al~~L~~rer~vl~l~y~~--~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~l 268 (270)
T TIGR02392 192 T-SDPEDTLEEEQWEELQRQALANALGSLDARSRRIIEARWLD--DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAAL 268 (270)
T ss_pred C-CChHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhcC--CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 5 4787766643 356789999999999999999999953 35899999999999999999999999999999876
Q ss_pred h
Q 009449 524 T 524 (534)
Q Consensus 524 ~ 524 (534)
.
T Consensus 269 ~ 269 (270)
T TIGR02392 269 A 269 (270)
T ss_pred c
Confidence 4
No 18
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=100.00 E-value=2e-39 Score=326.24 Aligned_cols=225 Identities=24% Similarity=0.373 Sum_probs=204.4
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccc
Q 009449 294 WYCREELIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG 370 (534)
Q Consensus 294 ~~A~e~LI~~nlrLV~sIArrY~~---~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~ 370 (534)
..|+++||..|+++|+++|++|.+ .+.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++++++.
T Consensus 22 ~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~-- 99 (257)
T PRK05911 22 IEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQD-- 99 (257)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcC--
Confidence 679999999999999999999862 356899999999999999999999999999999999999999999999875
Q ss_pred cccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhh--hhccccccccc--c--hhhhhhhcc
Q 009449 371 IKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGD--C--LNAKYLEFA 444 (534)
Q Consensus 371 iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~--~~~SLD~~i~~--~--~~~~l~e~i 444 (534)
++|.++.+.++++.++.+.+.+.+|+.|+.+|||+.+|++++++..++.... .++|||.++.. + .+.++.+.+
T Consensus 100 -~~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~~~~~~~~~l~~~l 178 (257)
T PRK05911 100 -WVPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQSDDEAGLALEERI 178 (257)
T ss_pred -CCCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCCCCCccccchhhhc
Confidence 4899999999999999999999999999999999999999999999887654 36899987643 1 233567788
Q ss_pred CCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449 445 PDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET 524 (534)
Q Consensus 445 ~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~ 524 (534)
+|.....|++.+...++...|..+|+.|||+||+||.++| ++++|++|||+.||+|+++|++++++|+++||+.+.
T Consensus 179 ~d~~~~~~~~~~~~~~~~~~l~~al~~L~~~er~vi~l~y----~e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l~ 254 (257)
T PRK05911 179 ADERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYY----YEELVLKEIGKILGVSESRVSQIHSKALLKLRATLS 254 (257)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 8877678889898889999999999999999999999999 899999999999999999999999999999999875
Q ss_pred h
Q 009449 525 C 525 (534)
Q Consensus 525 ~ 525 (534)
.
T Consensus 255 ~ 255 (257)
T PRK05911 255 A 255 (257)
T ss_pred h
Confidence 3
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=5.2e-39 Score=322.25 Aligned_cols=219 Identities=23% Similarity=0.300 Sum_probs=197.4
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI 373 (534)
Q Consensus 294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl 373 (534)
..|++.||..|.++|+++|++|.+++.+++||+|||++|||+++++|||.+|.+|+||++|||+|.|.+++++.. .+|+
T Consensus 33 ~~a~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~-~ir~ 111 (254)
T TIGR02850 33 TTAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRV 111 (254)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CccC
Confidence 469999999999999999999999999999999999999999999999999999999999999999999999974 8899
Q ss_pred ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchh--hhhhhccCCCCCCC
Q 009449 374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLN--AKYLEFAPDRSVKS 451 (534)
Q Consensus 374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~--~~l~e~i~d~~~~s 451 (534)
|.++.+.++++.++...+.+++|+.||.+|||+.+|++++++..++.....+.|||.++.++++ ..+.+.+.++..
T Consensus 112 p~~~~~~~~~~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~~~d~~~-- 189 (254)
T TIGR02850 112 SRSLRDIAYKALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEKN-- 189 (254)
T ss_pred chHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCCCCcchhhhhcCCccc--
Confidence 9999999999999999999999999999999999999999999999888888999998854433 245666766532
Q ss_pred hHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 452 PKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 452 pee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
+.+ .......+..++..|++++++||.++| ++++|++|||+.||+|+++|++++.+|++|||+.
T Consensus 190 ~~~---~~~~~~~l~~~l~~L~~rer~vi~~~~----~~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~~ 253 (254)
T TIGR02850 190 KDS---QWLEGIALKEAMKRLNEREKMILNMRF----FEGKTQMEVAEEIGISQAQVSRLEKAALKHMRKY 253 (254)
T ss_pred cHH---HHHhHHHHHHHHHcCCHHHHHHHHHHH----cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 222 223445789999999999999999999 7899999999999999999999999999999975
No 20
>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=5.3e-38 Score=320.02 Aligned_cols=246 Identities=28% Similarity=0.510 Sum_probs=227.2
Q ss_pred HHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHH
Q 009449 283 ERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (534)
Q Consensus 283 ~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~ 361 (534)
+..|+..++.| ..|++.||..|.++|+++|++|.+++.+++||+|||++|||+++++|||..|++|+||++|||+.++.
T Consensus 33 ~~~li~~~~~gd~~a~~~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain 112 (285)
T TIGR02394 33 EIAYARRALAGDFEARKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIE 112 (285)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHH
Confidence 35567777777 77999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhh
Q 009449 362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYL 441 (534)
Q Consensus 362 ~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~ 441 (534)
+++.++.+.+++|.++.+.++.+.+..+.+.+.+|+.|+.+++|+.+|++++++..++.......|+|.++.++....+.
T Consensus 113 ~~i~~~~~~~~~p~~~~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~ 192 (285)
T TIGR02394 113 RAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLL 192 (285)
T ss_pred HHHHHcCCceeCcHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchh
Confidence 99999999999999999999999999888899999999999999999999999999988877888999888766555666
Q ss_pred hccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 442 EFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 442 e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
+.+.++...+|++.+...+....|..+|..||+++|.||.|+|||.+++++|++|||+.||||.++|++++++|+++||.
T Consensus 193 ~~~~~~~~~~pe~~~~~~e~~~~L~~al~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~ 272 (285)
T TIGR02394 193 DTIADEQSIDPESLVQNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRR 272 (285)
T ss_pred hhhcCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 67776666789999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Hhhhhcc
Q 009449 522 SETCRDL 528 (534)
Q Consensus 522 ~l~~~~L 528 (534)
.+...++
T Consensus 273 ~l~~~~~ 279 (285)
T TIGR02394 273 ILERDGV 279 (285)
T ss_pred HHHHhhh
Confidence 9876543
No 21
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=100.00 E-value=6.2e-38 Score=312.16 Aligned_cols=229 Identities=30% Similarity=0.446 Sum_probs=207.9
Q ss_pred HHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCC-CHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHH
Q 009449 285 VLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGI-PFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK 362 (534)
Q Consensus 285 ~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~-~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~ 362 (534)
.+....+.| ..++ .||+.|+|||.++|++|.+++. +.+||+|-|++||++|+++|||++|.+|+|||...|+++|.+
T Consensus 13 ~~~~~~~~g~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d 91 (247)
T COG1191 13 KLLEYYAEGDEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILD 91 (247)
T ss_pred HHHHHHHhcCHHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHH
Confidence 344555566 6788 9999999999999999998877 999999999999999999999999999999999999999999
Q ss_pred HHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhh--hhcccccccccchhhhh
Q 009449 363 MVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGDCLNAKY 440 (534)
Q Consensus 363 ~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~--~~~SLD~~i~~~~~~~l 440 (534)
++|+.. .+++|..+.+..+++..+...+.+++||+||++|||+.+|++.+++..++.... ...|+|..+..+++..
T Consensus 92 ~LR~~~-~v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d~~- 169 (247)
T COG1191 92 YLRKND-SVKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDD- 169 (247)
T ss_pred HHHhCC-CccCcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccccc-
Confidence 999998 999999999999999999999999999999999999999999999999988775 6778887765444433
Q ss_pred hhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449 441 LEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520 (534)
Q Consensus 441 ~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR 520 (534)
.++...+|.+.+...+..+.|.+++..|+++||.|+.+|| ++++|++|||+.||||..+|+|++.+|++|||
T Consensus 170 ----~~~~~~~~~~~~~~~~~~~~l~~ai~~L~EREk~Vl~l~y----~eelt~kEI~~~LgISes~VSql~kkai~kLr 241 (247)
T COG1191 170 ----VDDQIENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRY----KEELTQKEIAEVLGISESRVSRLHKKAIKKLR 241 (247)
T ss_pred ----hhhccccchhHHHHHHHHHHHHHHHHccCHHHHHHHHHHH----HhccCHHHHHHHhCccHHHHHHHHHHHHHHHH
Confidence 2333457888888889989999999999999999999999 99999999999999999999999999999999
Q ss_pred hHhh
Q 009449 521 DSET 524 (534)
Q Consensus 521 ~~l~ 524 (534)
..+.
T Consensus 242 ~~l~ 245 (247)
T COG1191 242 KELN 245 (247)
T ss_pred HHhc
Confidence 8875
No 22
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=100.00 E-value=1.2e-37 Score=312.82 Aligned_cols=220 Identities=24% Similarity=0.305 Sum_probs=197.4
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI 373 (534)
Q Consensus 294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl 373 (534)
..|+++||..|.++|+++|++|.+++.+++||+|||++|+|+++++|||.+|.+|+||+++||+++|.+++++.. .+++
T Consensus 36 ~~a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~~-~vri 114 (258)
T PRK08215 36 KEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRV 114 (258)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-ceEe
Confidence 568999999999999999999999999999999999999999999999999999999999999999999999984 8899
Q ss_pred ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhh--hhhhccCCCCCCC
Q 009449 374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNA--KYLEFAPDRSVKS 451 (534)
Q Consensus 374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~--~l~e~i~d~~~~s 451 (534)
|.++.....++.++...+.+++|+.|+.+|||+.+|++++++..++.....+.|||.++.++++. ++.+.++++.. .
T Consensus 115 p~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~-~ 193 (258)
T PRK08215 115 SRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDEKN-K 193 (258)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchhhhhhccCccc-c
Confidence 99999999999999999999999999999999999999999999988877888999988655432 34566655431 2
Q ss_pred hHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449 452 PKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE 523 (534)
Q Consensus 452 pee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l 523 (534)
++. ......+..+++.||+++++||.++| ++++|++|||+.||+|.++|++++++|+++||+.+
T Consensus 194 ~~~----~~~~~~l~~~l~~L~~~er~vi~~~~----~~~~t~~eIA~~lgis~~~V~~~~~~al~kLr~~l 257 (258)
T PRK08215 194 DEN----WLEEIALKEAMKKLNDREKLILNLRF----FQGKTQMEVAEEIGISQAQVSRLEKAALKHMRKYI 257 (258)
T ss_pred HHH----HHhHHHHHHHHHcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 222 23345788999999999999999999 78999999999999999999999999999999875
No 23
>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=4.1e-37 Score=303.53 Aligned_cols=224 Identities=26% Similarity=0.366 Sum_probs=200.0
Q ss_pred HHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhc
Q 009449 290 LAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA 368 (534)
Q Consensus 290 l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~s 368 (534)
++.| ..|++.||..|.++|+++|++|.+++.+++||+|||++|||+++++|||..|.+|+||++|||++.|.++++++.
T Consensus 5 ~~~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~~~ 84 (231)
T TIGR02885 5 AQNGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDG 84 (231)
T ss_pred HHcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC
Confidence 3445 679999999999999999999999999999999999999999999999999999999999999999999999985
Q ss_pred cccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchh--hhhhhccCC
Q 009449 369 RGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLN--AKYLEFAPD 446 (534)
Q Consensus 369 r~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~--~~l~e~i~d 446 (534)
.+++|.++.....++.++...+..++|+.||.+|||+.+|++++++..++.....+.|||.+++++++ .++.+.+++
T Consensus 85 -~i~~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~ 163 (231)
T TIGR02885 85 -IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLDQIAD 163 (231)
T ss_pred -CeECCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCCCcchhhhhcCC
Confidence 78999999999999999999999999999999999999999999999998888888999998865533 235566666
Q ss_pred CCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449 447 RSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE 523 (534)
Q Consensus 447 ~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l 523 (534)
+.. +++.. .....+..+++.||+++++||.++| ++++|++|||+.||+|+++|++++++|+++||..+
T Consensus 164 ~~~--~~~~~---~~~~~l~~~l~~L~~~e~~i~~~~~----~~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~l 231 (231)
T TIGR02885 164 KGS--EDSDW---LEKIALKEAISKLDERERQIIMLRY----FKDKTQTEVANMLGISQVQVSRLEKKVLKKMKEKL 231 (231)
T ss_pred CCc--cHHhH---HHHHHHHHHHHcCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHhC
Confidence 532 22222 2355788999999999999999999 78999999999999999999999999999999753
No 24
>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=2.1e-36 Score=297.51 Aligned_cols=221 Identities=30% Similarity=0.429 Sum_probs=199.3
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI 373 (534)
Q Consensus 294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl 373 (534)
..|++.||..|.++|+++|++|.+++.+++||+|||++|+|+|+++||+++|.+|+||++|||++.|.++++++.+.+++
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 ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhh--hcccccccccchh--hhhhhccCCCCC
Q 009449 374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRI--VGSIDQKIGDCLN--AKYLEFAPDRSV 449 (534)
Q Consensus 374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~--~~SLD~~i~~~~~--~~l~e~i~d~~~ 449 (534)
|.++.+.+++++++...+.+++|+.|+.+|+|+.+|++.+++..++..... +.|||.++.++++ ..+.+.+
T Consensus 82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~----- 156 (227)
T TIGR02980 82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTL----- 156 (227)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCccccccc-----
Confidence 999999999999999999999999999999999999999999998877665 8899998863222 1222222
Q ss_pred CChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449 450 KSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE 523 (534)
Q Consensus 450 ~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l 523 (534)
.+|++.+........|..+|..||+++++||.++| ++++|++|||+.||+|+++|++++++|+++||+.+
T Consensus 157 ~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~y----~~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~l 226 (227)
T TIGR02980 157 GDEDDALETVEDRLALKPLLAALPERERRILLLRF----FEDKTQSEIAERLGISQMHVSRLLRRALKKLREQL 226 (227)
T ss_pred CCcchHHHhHHHHHHHHHHHHcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 24455556667778899999999999999999999 78999999999999999999999999999999764
No 25
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=100.00 E-value=4e-36 Score=301.01 Aligned_cols=234 Identities=24% Similarity=0.296 Sum_probs=207.9
Q ss_pred HHHHHHHHh-c-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHH
Q 009449 284 RVLKQHLAF-G-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (534)
Q Consensus 284 ~~L~~~l~~-G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~ 361 (534)
..|...++. | ..|+++||..|.++|+.+|++|.+++.+++||+|||+++||+++++||++.|.+|+||+++||++.|.
T Consensus 16 ~~li~~~~~~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~~ 95 (255)
T TIGR02941 16 IQWIAEFQQNQNGEAQEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIK 95 (255)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHHH
Confidence 445565655 4 77999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhh--hhcccccccccchhhh
Q 009449 362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGDCLNAK 439 (534)
Q Consensus 362 ~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~--~~~SLD~~i~~~~~~~ 439 (534)
++++++.+.+++|.++.+..++++++...+.+.+|+.|+.+|||+.+|++.+++..++.... .+.|||.+++.+++..
T Consensus 96 ~~lr~~~~~iri~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~ 175 (255)
T TIGR02941 96 RYLRDKTWSVHVPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSDGS 175 (255)
T ss_pred HHHHHcCCCcCCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCCCc
Confidence 99999999999999999999999999999999999999999999999999999998876543 5789999887654433
Q ss_pred hhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449 440 YLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL 519 (534)
Q Consensus 440 l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL 519 (534)
....+ + ...+|++.+...+....+..+|+.|||++|.||.++| ++++|++|||+.||+|.++|++++++|+++|
T Consensus 176 ~~~~~-~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~ii~l~~----~~g~s~~eIA~~lgis~~~V~~~~~ra~~~L 249 (255)
T TIGR02941 176 TVARL-D-SVGEVEDGYDQTERRMVLEKILPILSEREKSIIHCTF----EENLSQKETGERLGISQMHVSRLQRQAISKL 249 (255)
T ss_pred ccccc-c-ccCCcchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH----cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 22221 1 1235677777778888899999999999999999999 8999999999999999999999999999999
Q ss_pred HhHh
Q 009449 520 RDSE 523 (534)
Q Consensus 520 R~~l 523 (534)
|..+
T Consensus 250 r~~~ 253 (255)
T TIGR02941 250 KEAA 253 (255)
T ss_pred HHHh
Confidence 9864
No 26
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=100.00 E-value=8.8e-36 Score=301.09 Aligned_cols=226 Identities=30% Similarity=0.404 Sum_probs=203.6
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhh-C--CCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccc
Q 009449 294 WYCREELIKSTRPLVLFLARNYR-G--LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG 370 (534)
Q Consensus 294 ~~A~e~LI~~nlrLV~sIArrY~-~--~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~ 370 (534)
..|++.++..|.++|+.+|++|. + .+.+++||+|||++|||+++++|||.+|++|+||++||||+.|.+++++.
T Consensus 30 ~~a~~~l~~~y~~lv~~~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~--- 106 (268)
T PRK06288 30 PKIREYLILKYSPLVKYVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSI--- 106 (268)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhc---
Confidence 56899999999999999999986 2 56789999999999999999999999999999999999999999999865
Q ss_pred cccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHh--hhhcccccccccc---hhhhhhhccC
Q 009449 371 IKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL--RIVGSIDQKIGDC---LNAKYLEFAP 445 (534)
Q Consensus 371 iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~--~~~~SLD~~i~~~---~~~~l~e~i~ 445 (534)
+++|.++....++++++...|.+++|+.||.+|||+.+|++.+++..+.... ..+.|||.++..+ ....+.+.++
T Consensus 107 ~~~p~~~~~~~~~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~l~~~~~ 186 (268)
T PRK06288 107 DWIPRSVRQKARQIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLE 186 (268)
T ss_pred CccCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccCCCcccchhhhhcc
Confidence 4689999999999999999999999999999999999999999999988655 3568999876422 2234667777
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449 446 DRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC 525 (534)
Q Consensus 446 d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~ 525 (534)
++..++|++.+...+....|..+|+.|||++|+||.++| ++++|++|||+.||+|.++|++++++|+++||..+..
T Consensus 187 ~~~~~~pe~~~~~~e~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~~ 262 (268)
T PRK06288 187 SPAALNPDEIAEREEIKRVIVEAIKTLPEREKKVLILYY----YEDLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLAE 262 (268)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 777778999999999999999999999999999999999 8999999999999999999999999999999998764
Q ss_pred h
Q 009449 526 R 526 (534)
Q Consensus 526 ~ 526 (534)
.
T Consensus 263 ~ 263 (268)
T PRK06288 263 I 263 (268)
T ss_pred H
Confidence 3
No 27
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=1.3e-35 Score=296.95 Aligned_cols=235 Identities=23% Similarity=0.335 Sum_probs=208.2
Q ss_pred HHHHHHHHH-hc-HHHHHHHHHHhHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHH
Q 009449 283 ERVLKQHLA-FG-WYCREELIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIR 357 (534)
Q Consensus 283 ~~~L~~~l~-~G-~~A~e~LI~~nlrLV~sIArrY~~---~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR 357 (534)
+..|.++++ .| ..|++.||..|.++|+++|++|.+ ++.+++||+|||++|||+++++|||.+|.+|+||+++||+
T Consensus 8 e~~l~~~~~~~~d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~ir 87 (251)
T PRK07670 8 EQKLWDRWKEERDPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIR 87 (251)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHH
Confidence 455666644 34 679999999999999999999975 6889999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHH--hhhhcccccccccc
Q 009449 358 KSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC--LRIVGSIDQKIGDC 435 (534)
Q Consensus 358 ~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~--~~~~~SLD~~i~~~ 435 (534)
|.|.++++++. ++|.++.+.+++++++.+.+.+.+|+.|+.+|||+.+|+++++|..++.. ...+.|||.++.++
T Consensus 88 n~~~d~lR~~~---~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~ 164 (251)
T PRK07670 88 GAIIDGLRKED---WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQ 164 (251)
T ss_pred HHHHHHHHhcC---CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccCC
Confidence 99999999865 69999999999999999999999999999999999999999999998763 44678999998654
Q ss_pred hhh-hhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 436 LNA-KYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 436 ~~~-~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
++. .+.+.+.+....+|++.+...+....|..+|..||+++|+||.++| ++++|++|||+.||+|.++|++++++
T Consensus 165 ~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~EIA~~lgis~~tV~~~~~r 240 (251)
T PRK07670 165 DDGENVSVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFY----KEELTLTEIGQVLNLSTSRISQIHSK 240 (251)
T ss_pred CCcchhhhhhcCcCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 433 2333445555568888888888889999999999999999999999 89999999999999999999999999
Q ss_pred HHHHHHhHhh
Q 009449 515 AMTKLRDSET 524 (534)
Q Consensus 515 AL~KLR~~l~ 524 (534)
|+++||..+.
T Consensus 241 a~~~Lr~~l~ 250 (251)
T PRK07670 241 ALFKLKKLLE 250 (251)
T ss_pred HHHHHHHHhh
Confidence 9999998764
No 28
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=100.00 E-value=3.3e-35 Score=288.90 Aligned_cols=217 Identities=29% Similarity=0.453 Sum_probs=196.9
Q ss_pred HHHHhHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccc
Q 009449 300 LIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCK 376 (534)
Q Consensus 300 LI~~nlrLV~sIArrY~~---~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~ 376 (534)
|+..|.++|+++|++|.+ ++.+++||+|||++|||+++++|||++|++|+||+++||++.+.+++++.. ++|.+
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 789999999999999999999999999999999999999999999998764 68999
Q ss_pred hHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhh--hhcccccccccc-hhhhhhhccCCCCCCChH
Q 009449 377 LNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGDC-LNAKYLEFAPDRSVKSPK 453 (534)
Q Consensus 377 ~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~--~~~SLD~~i~~~-~~~~l~e~i~d~~~~spe 453 (534)
+...++++.++..++.+++|+.|+.+|||+.+|+++++|..++.... ...|+|.+..++ +...+.+.++++...+|+
T Consensus 78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (224)
T TIGR02479 78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDKSEDPE 157 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhccccccCCHH
Confidence 99999999999999999999999999999999999999999986544 567888766543 334566667766667899
Q ss_pred HHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449 454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE 523 (534)
Q Consensus 454 e~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l 523 (534)
+.+...+....|..+|+.||+++|+||.++| ++++|++|||+.||+|.++|++++++|+++||..+
T Consensus 158 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~y----~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 223 (224)
T TIGR02479 158 EELEREELREALAEAIESLSEREQLVLSLYY----YEELNLKEIGEVLGLTESRVSQIHSQALKKLRAKL 223 (224)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----hCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHc
Confidence 9999999999999999999999999999999 89999999999999999999999999999999865
No 29
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=100.00 E-value=3.8e-34 Score=283.77 Aligned_cols=210 Identities=22% Similarity=0.284 Sum_probs=182.1
Q ss_pred HHHHHHHHhHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccc
Q 009449 296 CREELIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK 372 (534)
Q Consensus 296 A~e~LI~~nlrLV~sIArrY~~---~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iR 372 (534)
....|+..|+++|.++|++|.. .+.+.+||+|||++|||+|+++|||.+| +|+||++||||++|.+++++.. +
T Consensus 16 ~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~---~ 91 (231)
T PRK12427 16 EEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELD---W 91 (231)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcC---C
Confidence 3468899999999999999975 4679999999999999999999998666 8999999999999999999764 4
Q ss_pred cccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHH--hhhhcccccccccchhhhhhhccCCCCCC
Q 009449 373 IPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC--LRIVGSIDQKIGDCLNAKYLEFAPDRSVK 450 (534)
Q Consensus 373 lP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~--~~~~~SLD~~i~~~~~~~l~e~i~d~~~~ 450 (534)
.|.++....++++++.+.+.+++|+.||.+|||+.+|++++++..++.. ...+.|||.+++++++.. .+++ .
T Consensus 92 ~~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~---~~~~---~ 165 (231)
T PRK12427 92 RPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAHND---ILQS---R 165 (231)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCccc---ccCC---C
Confidence 7888999999999999999999999999999999999999999998764 346789999987654322 2221 2
Q ss_pred ChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 451 SPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 451 spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
.+++.. .....|..++..||+++|.||.++| ++++|++|||+.||||+++|+|++.+|++|||..
T Consensus 166 ~~~~~~---~~~~~l~~~l~~L~~~er~vi~l~~----~~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr~~ 230 (231)
T PRK12427 166 DLEENI---IIEDNLKQALSQLDEREQLILHLYY----QHEMSLKEIALVLDLTEARICQLNKKIAQKIKSF 230 (231)
T ss_pred CHHHHH---HHHHHHHHHHHcCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 344333 2455789999999999999999999 8999999999999999999999999999999964
No 30
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=100.00 E-value=6.1e-34 Score=282.17 Aligned_cols=225 Identities=28% Similarity=0.423 Sum_probs=199.8
Q ss_pred hcHHHHHHHHHHhHHHHHHHHHHhh---CCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhc
Q 009449 292 FGWYCREELIKSTRPLVLFLARNYR---GLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA 368 (534)
Q Consensus 292 ~G~~A~e~LI~~nlrLV~sIArrY~---~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~s 368 (534)
.|.-++++|+..|.++|+++|++|. +++.+++||+|||++|||+++++|||.+|.+|+||+++||+|.|.++++++.
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 4667899999999999999999997 6789999999999999999999999999999999999999999999999875
Q ss_pred cccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhh--hhcccccccccchhhhhhhccCC
Q 009449 369 RGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGDCLNAKYLEFAPD 446 (534)
Q Consensus 369 r~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~--~~~SLD~~i~~~~~~~l~e~i~d 446 (534)
+ +|.++....+++.++...+.+.+|++|+.+|||+.+|++.++|..++.... .+.|+|.+++++++. +.. ..+
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 3 688888888889999999999999999999999999999999999887543 466888887655443 222 223
Q ss_pred CCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449 447 RSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC 525 (534)
Q Consensus 447 ~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~ 525 (534)
+..++|++.+...+....|..+|+.|||++|+||.++| .+++|++|||+.||||.++|++++++|+++||+.+..
T Consensus 160 ~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~~ 234 (236)
T PRK06986 160 HQDEDPLQQLEDEELREALVEAIESLPEREQLVLSLYY----QEELNLKEIGAVLGVSESRVSQIHSQAIKRLRARLGE 234 (236)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHh----ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 34467888888888899999999999999999999999 8999999999999999999999999999999998753
No 31
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=100.00 E-value=9.1e-34 Score=284.32 Aligned_cols=233 Identities=24% Similarity=0.290 Sum_probs=205.8
Q ss_pred HHHHHHHH-hc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHH
Q 009449 284 RVLKQHLA-FG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (534)
Q Consensus 284 ~~L~~~l~-~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~ 361 (534)
..|...++ .| ..|++.||..|.++|+++|++|.+++.+++||+||||++||+++++||+..|.+|+||+++||+|.|.
T Consensus 16 ~~li~~~~~~gd~~a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~~ 95 (257)
T PRK08583 16 NKWIAEYQENQDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIK 95 (257)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHH
Confidence 44555554 34 77999999999999999999999999999999999999999999999999988999999999999999
Q ss_pred HHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhh--hhcccccccccchhhh
Q 009449 362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGDCLNAK 439 (534)
Q Consensus 362 ~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~--~~~SLD~~i~~~~~~~ 439 (534)
++++++.+.+++|.++.+..+++.++...+...+++.|+.+|+|+.+|++.+.+..+..... .+.|+|.+++.+++..
T Consensus 96 ~~lr~~~~~~~i~r~~~~~~~~~~~~~~~~~~~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~ 175 (257)
T PRK08583 96 RYLRDKTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDGS 175 (257)
T ss_pred HHHHhcCCCcCCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCCCCc
Confidence 99999999999999999999999999999999999999999999999999999988766542 5678998876543321
Q ss_pred ---hhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 440 ---YLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 440 ---l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
+.+.+ .+|++.+...+....+..+|..|||++|+||.++| ++++|++|||+.||||+++|++++++|+
T Consensus 176 ~~~~~~~~-----~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~eIA~~l~is~~tV~~~~~ra~ 246 (257)
T PRK08583 176 TVTLLDIV-----GQQEDGYELTEQRMILEKILPVLSDREKSIIQCTF----IENLSQKETGERLGISQMHVSRLQRQAI 246 (257)
T ss_pred cchHhhhc-----CCcchhHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----hCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 22222 35666677777788899999999999999999999 8999999999999999999999999999
Q ss_pred HHHHhHhhh
Q 009449 517 TKLRDSETC 525 (534)
Q Consensus 517 ~KLR~~l~~ 525 (534)
++||..+..
T Consensus 247 ~kLr~~l~~ 255 (257)
T PRK08583 247 KKLREAAFL 255 (257)
T ss_pred HHHHHHhcc
Confidence 999988753
No 32
>PRK05572 sporulation sigma factor SigF; Validated
Probab=100.00 E-value=1.1e-33 Score=283.36 Aligned_cols=228 Identities=26% Similarity=0.398 Sum_probs=200.3
Q ss_pred HHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHH
Q 009449 285 VLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKM 363 (534)
Q Consensus 285 ~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~ 363 (534)
.+...+..| ..|++.||..|.++|+++|++|.+++.+++||+|||++++|+++++||+.+|.+|.||+++||++.|.++
T Consensus 21 ~li~~~~~gd~~a~~~L~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~ 100 (252)
T PRK05572 21 ELIKKSQDGDQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRF 100 (252)
T ss_pred HHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHH
Confidence 344555555 6799999999999999999999999999999999999999999999999988899999999999999999
Q ss_pred HHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhh--hhh
Q 009449 364 VARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNA--KYL 441 (534)
Q Consensus 364 lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~--~l~ 441 (534)
+++.. .+++|.++....++++++...+..++|+.|+.+|||+.+|++++.+..+......+.||+.++.+++.. ++.
T Consensus 101 lr~~~-~~r~~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~ 179 (252)
T PRK05572 101 LRDDG-TVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITLL 179 (252)
T ss_pred HHhCC-CCCCCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCCCCcchhh
Confidence 99884 789999999999999999999999999999999999999999999999888888889999887654322 233
Q ss_pred hccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 442 EFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 442 e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
+.++++.. +. ......|..++..||+++++||.++| ++++|++|||+.+|+|+++|++++++|+++||.
T Consensus 180 d~~~~~~~---~~----~~~~~~l~~~l~~L~~~~~~v~~l~~----~~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~ 248 (252)
T PRK05572 180 DQIADQSE---ED----WFDKIALKEAIRELDERERLIVYLRY----FKDKTQSEVAKRLGISQVQVSRLEKKILKQMKE 248 (252)
T ss_pred hhcCCCch---hh----HHHHHHHHHHHHcCCHHHHHHHHHHH----hCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 44444321 11 23456789999999999999999999 789999999999999999999999999999998
Q ss_pred Hhh
Q 009449 522 SET 524 (534)
Q Consensus 522 ~l~ 524 (534)
.+.
T Consensus 249 ~l~ 251 (252)
T PRK05572 249 KLD 251 (252)
T ss_pred Hhc
Confidence 764
No 33
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=99.95 E-value=1.4e-26 Score=229.39 Aligned_cols=185 Identities=24% Similarity=0.391 Sum_probs=149.7
Q ss_pred HHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHh
Q 009449 289 HLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH 367 (534)
Q Consensus 289 ~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~ 367 (534)
.+..| ..|++.|+..|.++|+++|.+|.+++.+++|++|||++++|+++++||+++|.+|.||+++|+||.+.+++++.
T Consensus 42 ~~~~gd~~a~~~l~~~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~ 121 (233)
T PRK05803 42 LMKEGDEEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNL 121 (233)
T ss_pred HHHcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHH
Confidence 33344 67999999999999999999999999999999999999999999999998888999999999999999999876
Q ss_pred ccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccc---hhhhhhhcc
Q 009449 368 ARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDC---LNAKYLEFA 444 (534)
Q Consensus 368 sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~---~~~~l~e~i 444 (534)
.+..+ ..+++.+.+.+ ....+.+..
T Consensus 122 ~~~~~----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~ 149 (233)
T PRK05803 122 KKTKK----------------------------------------------------EVSLQDPIGVDKEGNEISLIDIL 149 (233)
T ss_pred hcccc----------------------------------------------------CCCccccccCCCCcCcccHHHHc
Confidence 42110 01111111100 111222333
Q ss_pred CCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449 445 PDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET 524 (534)
Q Consensus 445 ~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~ 524 (534)
++. .++|++.+..+...+.|..+|..|||++|+||.++|++.+++++|++|||+.||+|+++|++++++|+++||..+.
T Consensus 150 ~~~-~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~ 228 (233)
T PRK05803 150 GSE-EDDVIEQVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKELY 228 (233)
T ss_pred cCC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 332 2357777787788889999999999999999999998887799999999999999999999999999999999876
Q ss_pred hh
Q 009449 525 CR 526 (534)
Q Consensus 525 ~~ 526 (534)
..
T Consensus 229 ~~ 230 (233)
T PRK05803 229 RA 230 (233)
T ss_pred Hh
Confidence 43
No 34
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=99.93 E-value=1.8e-24 Score=213.98 Aligned_cols=189 Identities=24% Similarity=0.385 Sum_probs=148.6
Q ss_pred HHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHH
Q 009449 283 ERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (534)
Q Consensus 283 ~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~ 361 (534)
+..|...++.| ..|++.++..|.++|+.+|++|.+++.+++|++||+|+++|+++++|++..+++|.||++++++|.+.
T Consensus 39 ~~~L~~~~~~gd~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~ 118 (234)
T PRK08301 39 EEYLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEIL 118 (234)
T ss_pred HHHHHHHHHccCHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHH
Confidence 56677777777 77999999999999999999999999999999999999999999999998888999999999999999
Q ss_pred HHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccc--hh-h
Q 009449 362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDC--LN-A 438 (534)
Q Consensus 362 ~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~--~~-~ 438 (534)
++++++.+... ..+++.+...+ .. .
T Consensus 119 d~lRk~~~~~~----------------------------------------------------~~~~~~~~~~~~~~~~~ 146 (234)
T PRK08301 119 MYLRRNNKVKA----------------------------------------------------EVSFDEPLNIDWDGNEL 146 (234)
T ss_pred HHHHHHhcccc----------------------------------------------------ccccccccccccCCCcc
Confidence 99987643100 01112111100 00 0
Q ss_pred hhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009449 439 KYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTK 518 (534)
Q Consensus 439 ~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~K 518 (534)
...+..++. ...++..+......+.|..+|+.|||++|+||.|+|||...+++|++|||+.||||.+||++++++|+++
T Consensus 147 ~~~~~~~~~-~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~ 225 (234)
T PRK08301 147 LLSDVLGTD-NDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKR 225 (234)
T ss_pred cHHHhccCc-ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 011111111 1233444455556678999999999999999999998776789999999999999999999999999999
Q ss_pred HHhHhh
Q 009449 519 LRDSET 524 (534)
Q Consensus 519 LR~~l~ 524 (534)
||+.+.
T Consensus 226 Lr~~l~ 231 (234)
T PRK08301 226 LKKEIN 231 (234)
T ss_pred HHHHHH
Confidence 998765
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=99.93 E-value=4.5e-24 Score=210.77 Aligned_cols=188 Identities=27% Similarity=0.412 Sum_probs=149.0
Q ss_pred HHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHH
Q 009449 283 ERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (534)
Q Consensus 283 ~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~ 361 (534)
+..|...++.| ..|++.|+..|.++|+++|.+|.++..+++||+||+|+++|+++++|+++.+.+|.||+++|++|.+.
T Consensus 35 ~~~li~~~~~gd~~af~~l~~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~ 114 (227)
T TIGR02846 35 EKKYLDRLKEGDEEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEIL 114 (227)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHH
Confidence 45667777777 78999999999999999999999999999999999999999999999998888999999999999999
Q ss_pred HHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccc---hhh
Q 009449 362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDC---LNA 438 (534)
Q Consensus 362 ~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~---~~~ 438 (534)
+++++..+..+. .+++...+.+ ...
T Consensus 115 d~~Rk~~r~~~~----------------------------------------------------~~~~~~~~~~~~~~~~ 142 (227)
T TIGR02846 115 MHLRALKKTKGE----------------------------------------------------VSLQDPIGVDKEGNEI 142 (227)
T ss_pred HHHHHHhccccc----------------------------------------------------eeccccccCCcccCcc
Confidence 999876531100 0111111000 001
Q ss_pred hhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009449 439 KYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTK 518 (534)
Q Consensus 439 ~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~K 518 (534)
.+.+...+. ..+|++.+...+..+.|.++|+.|||++|+||.++|.+..++++|++|||+.||+|+++|++++++|+++
T Consensus 143 ~~~~~~~~~-~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~ 221 (227)
T TIGR02846 143 SLIDILGSD-GDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMK 221 (227)
T ss_pred cHHHHhcCC-CCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 111222221 2356777777777788999999999999999999995444489999999999999999999999999999
Q ss_pred HHhHh
Q 009449 519 LRDSE 523 (534)
Q Consensus 519 LR~~l 523 (534)
||+.+
T Consensus 222 Lr~~~ 226 (227)
T TIGR02846 222 LYKEL 226 (227)
T ss_pred HHHHh
Confidence 99864
No 36
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=99.92 E-value=8.7e-24 Score=204.11 Aligned_cols=196 Identities=23% Similarity=0.321 Sum_probs=154.5
Q ss_pred CCCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHH
Q 009449 280 GVSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358 (534)
Q Consensus 280 g~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~ 358 (534)
.++...|...++.| ..|++.|+..|.++|+.+|++|.++..+++|++||+++++|+++++||+.++.+|.||++.++++
T Consensus 8 ~~~~~~l~~~~~~~d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n 87 (208)
T PRK08295 8 ELEDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITR 87 (208)
T ss_pred CCChHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHH
Confidence 34566777777777 78999999999999999999999999999999999999999999999998877999999999999
Q ss_pred HHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhccccccccc-chh
Q 009449 359 SISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGD-CLN 437 (534)
Q Consensus 359 aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~-~~~ 437 (534)
.+.+++++..+..+.+.. ...|.+.++.+ +.+
T Consensus 88 ~~~d~~r~~~r~~~~~~~-----------------------------------------------~~~s~~~~~~~~~~~ 120 (208)
T PRK08295 88 QIITAIKTANRQKHIPLN-----------------------------------------------SYVSLDKPIYDEESD 120 (208)
T ss_pred HHHHHHHHhhhhcccccc-----------------------------------------------ceeecCCcccCCccc
Confidence 999999865432221110 01233333211 222
Q ss_pred hhhhhccCCCCCCChHHHHHHHHHHHHHH-HHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 438 AKYLEFAPDRSVKSPKEIVMRQHMKKDVF-RILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 438 ~~l~e~i~d~~~~spee~v~~~el~e~L~-~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
..+.+.++++...+|++.+...+....+. .++..||+.+++||.+ | .+++|++|||+.||+|.++|+..++||+
T Consensus 121 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l-~----~e~~s~~EIA~~lgis~~tV~~~l~rar 195 (208)
T PRK08295 121 RTLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLEL-Y----LDGKSYQEIAEELNRHVKSIDNALQRVK 195 (208)
T ss_pred hhHHHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHH-H----HccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 23344444444457887776666666664 5679999999999999 7 7999999999999999999999999999
Q ss_pred HHHHhHhhhhc
Q 009449 517 TKLRDSETCRD 527 (534)
Q Consensus 517 ~KLR~~l~~~~ 527 (534)
++||+++....
T Consensus 196 ~~Lr~~l~~~~ 206 (208)
T PRK08295 196 RKLEKYLENRE 206 (208)
T ss_pred HHHHHHHHhhc
Confidence 99999887654
No 37
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=99.92 E-value=2.2e-23 Score=206.76 Aligned_cols=190 Identities=23% Similarity=0.402 Sum_probs=148.3
Q ss_pred HHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHH
Q 009449 283 ERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (534)
Q Consensus 283 ~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~ 361 (534)
+..|...+..| ..|++.++..|.+.|+++|++|.+++.+++|++||+++++|+++++|++..+++|+||++.+++|.+.
T Consensus 39 ~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~ 118 (234)
T TIGR02835 39 EEALLQKLTQGDESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEIL 118 (234)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHH
Confidence 45566777776 78999999999999999999999999999999999999999999999998888999999999999999
Q ss_pred HHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccc---cchhh
Q 009449 362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIG---DCLNA 438 (534)
Q Consensus 362 ~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~---~~~~~ 438 (534)
+++++..+... ..+++.++. ++...
T Consensus 119 d~~Rk~~r~~~----------------------------------------------------~~~~~~~~~~~~~~~~~ 146 (234)
T TIGR02835 119 MYLRRNNKTRS----------------------------------------------------EVSFDEPLNVDWDGNEL 146 (234)
T ss_pred HHHHHhccccC----------------------------------------------------cccccccccCCCCCCcc
Confidence 99997653110 001111110 00000
Q ss_pred hhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009449 439 KYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTK 518 (534)
Q Consensus 439 ~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~K 518 (534)
...+. .++....+++.+......+.|..+|+.||+++|+|+.|+|.+.+++++|++|||+.||+|.++|++++++|+++
T Consensus 147 ~~~~~-~~~~~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~ 225 (234)
T TIGR02835 147 LLSDV-LGTDSDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKR 225 (234)
T ss_pred hHHHh-cCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 01111 11122234444555566678999999999999999999996655689999999999999999999999999999
Q ss_pred HHhHhhh
Q 009449 519 LRDSETC 525 (534)
Q Consensus 519 LR~~l~~ 525 (534)
||+.+..
T Consensus 226 LR~~l~~ 232 (234)
T TIGR02835 226 LKKEINR 232 (234)
T ss_pred HHHHhhc
Confidence 9998753
No 38
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=99.91 E-value=7.1e-23 Score=196.04 Aligned_cols=191 Identities=21% Similarity=0.270 Sum_probs=148.4
Q ss_pred CCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHH
Q 009449 281 VSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (534)
Q Consensus 281 ~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~a 359 (534)
|++..|...++.| ..|++.|+..|.+.|+++|+++.++..+++||+||+++.+|+++.+|++..+..|+||++.+|++.
T Consensus 4 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~~ 83 (198)
T TIGR02859 4 LEDEEIVELARQGNTHALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTRQ 83 (198)
T ss_pred cchHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHHH
Confidence 5567778888888 779999999999999999999999999999999999999999999999987779999999999999
Q ss_pred HHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhccccccccc-chhh
Q 009449 360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGD-CLNA 438 (534)
Q Consensus 360 I~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~-~~~~ 438 (534)
+.++++...+..+.+. ....|++.+... +.+.
T Consensus 84 ~~~~~r~~~~~~~~~~-----------------------------------------------~~~~~~~~~~~~~~~~~ 116 (198)
T TIGR02859 84 IITAIKTATRQKHIPL-----------------------------------------------NSYVSLNKPIYDEESDR 116 (198)
T ss_pred HHHHHHHHHHhcccch-----------------------------------------------hhhcCcccccccccccc
Confidence 9988875432111110 011233333211 1112
Q ss_pred hhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhC-CHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449 439 KYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESL-DSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMT 517 (534)
Q Consensus 439 ~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L-~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~ 517 (534)
++.+.+++....+|++.+...+..+.|.++|+.| ++.++.|+. +| .+++|++|||+.||+|.++|++.++||++
T Consensus 117 ~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~-~~----~~~~s~~eIA~~l~~s~~tV~~~l~r~r~ 191 (198)
T TIGR02859 117 TLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQ-SY----LDGKSYQEIACDLNRHVKSIDNALQRVKR 191 (198)
T ss_pred hHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHH-HH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 2333333333357888888888888899999985 566666664 57 68999999999999999999999999999
Q ss_pred HHHhHh
Q 009449 518 KLRDSE 523 (534)
Q Consensus 518 KLR~~l 523 (534)
+||..+
T Consensus 192 ~L~~~l 197 (198)
T TIGR02859 192 KLEKYL 197 (198)
T ss_pred HHHHhc
Confidence 999875
No 39
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=99.90 E-value=1.1e-22 Score=193.75 Aligned_cols=176 Identities=19% Similarity=0.202 Sum_probs=147.2
Q ss_pred CCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHH
Q 009449 281 VSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (534)
Q Consensus 281 ~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~a 359 (534)
++++.|...+..| ..|++.|+..|.++|+.+|++|.+++.+++|++||+|+++|+++.+||+. +..|.+|++..+++.
T Consensus 5 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n~ 83 (186)
T PRK05602 5 DPDEELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLNL 83 (186)
T ss_pred ccHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHHH
Confidence 4567788888877 78999999999999999999999999999999999999999999999986 458999999999999
Q ss_pred HHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhh
Q 009449 360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAK 439 (534)
Q Consensus 360 I~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~ 439 (534)
+.++++++... +.. .++
T Consensus 84 ~~d~~R~~~~~---~~~--------------------------------------------------~~~---------- 100 (186)
T PRK05602 84 CYDRLRRRREV---PVE--------------------------------------------------DAP---------- 100 (186)
T ss_pred HHHHHHhcCCC---Ccc--------------------------------------------------ccc----------
Confidence 99999865311 000 000
Q ss_pred hhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449 440 YLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL 519 (534)
Q Consensus 440 l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL 519 (534)
+ ..+. ...|++.+...+....+..+|..||+++|+||.|+| ++++|++|||+.||+|+.+|+++++||+++|
T Consensus 101 --~-~~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~L 172 (186)
T PRK05602 101 --D-VPDP-APGPDAGLEARQRARRVEQALAALPERQREAIVLQY----YQGLSNIEAAAVMDISVDALESLLARGRRAL 172 (186)
T ss_pred --c-cCCC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHH----hcCCCHHHHHHHhCcCHHHHHHHHHHHHHHH
Confidence 0 0111 124566666667777899999999999999999999 8999999999999999999999999999999
Q ss_pred HhHhhhhcc
Q 009449 520 RDSETCRDL 528 (534)
Q Consensus 520 R~~l~~~~L 528 (534)
|+.+...+.
T Consensus 173 r~~l~~~~~ 181 (186)
T PRK05602 173 RAQLADLPG 181 (186)
T ss_pred HHHHHhccc
Confidence 999876554
No 40
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=99.90 E-value=1.8e-22 Score=194.03 Aligned_cols=176 Identities=19% Similarity=0.161 Sum_probs=143.6
Q ss_pred CHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHH
Q 009449 282 SERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (534)
Q Consensus 282 d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI 360 (534)
+...|...+..| ..|+++|+..|.++|+++|.+|.++..+++|++||+|+++|+++.+||+.+| .|.+|++..++|.+
T Consensus 16 ~~~~li~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n~~ 94 (194)
T PRK09646 16 DLDALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHRRA 94 (194)
T ss_pred cHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHHHH
Confidence 356677777777 7899999999999999999999999999999999999999999999998765 79999999999999
Q ss_pred HHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhh
Q 009449 361 SKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKY 440 (534)
Q Consensus 361 ~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l 440 (534)
+++++++.+..+.-. .. ...
T Consensus 95 ~d~~r~~~~~~~~~~---------------------------------------------------~~----~~~----- 114 (194)
T PRK09646 95 VDRVRSEQAASQREV---------------------------------------------------RY----GAR----- 114 (194)
T ss_pred HHHHHhhcccccccc---------------------------------------------------cc----ccc-----
Confidence 999987642110000 00 000
Q ss_pred hhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449 441 LEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520 (534)
Q Consensus 441 ~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR 520 (534)
+ .+.....+++.+...+..+.+..+|..||+++|+||.|+| .+++|++|||+.||+|..+|+++++||+++||
T Consensus 115 -~--~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr 187 (194)
T PRK09646 115 -N--VDPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAY----YGGLTYREVAERLAVPLGTVKTRMRDGLIRLR 187 (194)
T ss_pred -c--ccccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCChHhHHHHHHHHHHHHH
Confidence 0 0011123445555556667899999999999999999999 89999999999999999999999999999999
Q ss_pred hHhhh
Q 009449 521 DSETC 525 (534)
Q Consensus 521 ~~l~~ 525 (534)
..+..
T Consensus 188 ~~l~~ 192 (194)
T PRK09646 188 DCLGV 192 (194)
T ss_pred HHhcc
Confidence 98764
No 41
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=99.90 E-value=2e-22 Score=193.23 Aligned_cols=181 Identities=20% Similarity=0.211 Sum_probs=149.4
Q ss_pred CCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHH
Q 009449 281 VSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (534)
Q Consensus 281 ~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~a 359 (534)
.++..|...+..| ..|++.|+..|.+.|+++|+++.++..+++|++||+|+++|++..+|++.. .|.+|++.++++.
T Consensus 11 ~~~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~~--~f~~wl~~i~~n~ 88 (194)
T PRK12513 11 ASDEALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRA--RFRTWLYQIARNL 88 (194)
T ss_pred CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCCC--chHHHHHHHHHHH
Confidence 3466777777877 789999999999999999999999999999999999999999999999753 6999999999999
Q ss_pred HHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhh
Q 009449 360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAK 439 (534)
Q Consensus 360 I~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~ 439 (534)
+++++++..+....+.. .+. .
T Consensus 89 ~~~~~R~~~~~~~~~~~---------------------------------------------------~~~--------~ 109 (194)
T PRK12513 89 LIDHWRRHGARQAPSLD---------------------------------------------------ADE--------Q 109 (194)
T ss_pred HHHHHHHhccccccccc---------------------------------------------------cch--------h
Confidence 99999877542211100 000 0
Q ss_pred hhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449 440 YLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL 519 (534)
Q Consensus 440 l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL 519 (534)
. ....+ ...+|++.+...+....+..+|+.||+++|+||.|+| .+++|++|||+.||+|+++|+++++||+++|
T Consensus 110 ~-~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~ra~~~L 183 (194)
T PRK12513 110 L-HALAD-DGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLRE----HGDLELEEIAELTGVPEETVKSRLRYALQKL 183 (194)
T ss_pred h-hhcCC-CCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeeh----ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 0 00111 1236777777777888999999999999999999999 8999999999999999999999999999999
Q ss_pred HhHhhhhcc
Q 009449 520 RDSETCRDL 528 (534)
Q Consensus 520 R~~l~~~~L 528 (534)
|..+...++
T Consensus 184 r~~l~~~~~ 192 (194)
T PRK12513 184 RELLAEEVA 192 (194)
T ss_pred HHHHHHhhc
Confidence 999887654
No 42
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=99.90 E-value=4e-22 Score=190.39 Aligned_cols=172 Identities=21% Similarity=0.308 Sum_probs=141.9
Q ss_pred HHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCC----CCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHH
Q 009449 284 RVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGL----GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358 (534)
Q Consensus 284 ~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~----g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~ 358 (534)
..|...+..| ..|+++|+..|.+.|+.+|.++.++ ..+++|++||+++++|+++.+|++. +..|.||++..++|
T Consensus 12 ~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~n 90 (189)
T PRK09648 12 DALVAEAVAGDRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAAH 90 (189)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHHH
Confidence 4567777777 7899999999999999999999765 4689999999999999999999864 45899999999999
Q ss_pred HHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhh
Q 009449 359 SISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNA 438 (534)
Q Consensus 359 aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~ 438 (534)
.+.++++++.+....+. +.
T Consensus 91 ~~~d~~r~~~r~~~~~~-----------------------------------------------------~~-------- 109 (189)
T PRK09648 91 KVADAHRAAGRDKAVPT-----------------------------------------------------EE-------- 109 (189)
T ss_pred HHHHHHHHhCCCccccc-----------------------------------------------------cc--------
Confidence 99999987653211100 00
Q ss_pred hhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009449 439 KYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTK 518 (534)
Q Consensus 439 ~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~K 518 (534)
..+.. + ...+|++.+...+..+.|..+|..|||++|+||.++| ++++|++|||+.||+|..+|++.++||+++
T Consensus 110 -~~~~~-~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~ 182 (189)
T PRK09648 110 -VPERP-S-DDAGPEERALRSESSNRMRELLDTLPEKQREILILRV----VVGLSAEETAEAVGSTPGAVRVAQHRALAR 182 (189)
T ss_pred -ccccc-c-cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 00000 1 1136777777778888899999999999999999999 899999999999999999999999999999
Q ss_pred HHhHhh
Q 009449 519 LRDSET 524 (534)
Q Consensus 519 LR~~l~ 524 (534)
||+.+.
T Consensus 183 Lr~~l~ 188 (189)
T PRK09648 183 LRAEIE 188 (189)
T ss_pred HHHHhc
Confidence 998764
No 43
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=99.90 E-value=3.4e-22 Score=189.45 Aligned_cols=179 Identities=15% Similarity=0.205 Sum_probs=143.2
Q ss_pred HHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHH
Q 009449 284 RVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK 362 (534)
Q Consensus 284 ~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~ 362 (534)
+.|+..+..| ..|+++|+..|.+.|+++|.+|.++..+++|++||+++++|++..+||+.. .|.||++..++|.+.+
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 4456667777 779999999999999999999999999999999999999999999999865 6999999999999999
Q ss_pred HHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhh
Q 009449 363 MVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLE 442 (534)
Q Consensus 363 ~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e 442 (534)
++++..+... ++......+...+.+
T Consensus 84 ~~rk~~~~~~-------------------------------------------------------~~~~~~~~~~~~~~~ 108 (187)
T TIGR02948 84 RLRKRKPDFY-------------------------------------------------------LDDEVQGTDGLTMES 108 (187)
T ss_pred HHHhhccccc-------------------------------------------------------ccccccCcccccccc
Confidence 9986532100 000000000001111
Q ss_pred ccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 443 FAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 443 ~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
..++. .++|++.+...+..+.+..+|..|||++|+||.++| .+++|++|||+.||+|.++|++.++||+++||..
T Consensus 109 ~~~~~-~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 109 QLAAD-EAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKY----MEDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred ccccC-cCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 11111 236777777777778899999999999999999999 8999999999999999999999999999999988
Q ss_pred hh
Q 009449 523 ET 524 (534)
Q Consensus 523 l~ 524 (534)
+.
T Consensus 184 l~ 185 (187)
T TIGR02948 184 LR 185 (187)
T ss_pred hh
Confidence 65
No 44
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=99.90 E-value=4.4e-22 Score=188.71 Aligned_cols=181 Identities=17% Similarity=0.199 Sum_probs=145.8
Q ss_pred CHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHH
Q 009449 282 SERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (534)
Q Consensus 282 d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI 360 (534)
+.+.|...++.| ..|++.++..|.++|+++|+++.++..+++|++||+++++|++..+|++.. .|.+|++..++|.+
T Consensus 4 ~~~~li~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~~ 81 (187)
T PRK09641 4 LIKRLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNLT 81 (187)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHHH
Confidence 345667777777 779999999999999999999999999999999999999999999999853 79999999999999
Q ss_pred HHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhh
Q 009449 361 SKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKY 440 (534)
Q Consensus 361 ~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l 440 (534)
.+++++..+.. +++.....++....
T Consensus 82 ~d~~R~~~~~~-------------------------------------------------------~~~~~~~~~~~~~~ 106 (187)
T PRK09641 82 IDRLRKRKPDY-------------------------------------------------------YLDAEVAGTEGLTM 106 (187)
T ss_pred HHHHHhcCccc-------------------------------------------------------cccccccCCcchhh
Confidence 99998754210 01100000111111
Q ss_pred hhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449 441 LEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520 (534)
Q Consensus 441 ~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR 520 (534)
.+.+.+ ...+|++.+...+....+..+|+.||+++++||.++| ..++|++|||+.||||.++|++.++||+++||
T Consensus 107 ~~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~----~~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr 181 (187)
T PRK09641 107 YSQLAA-DDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKY----IEDLSLKEISEILDLPVGTVKTRIHRGREALR 181 (187)
T ss_pred hccccc-CcCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHH----hhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 111122 1235777777778888899999999999999999999 89999999999999999999999999999999
Q ss_pred hHhh
Q 009449 521 DSET 524 (534)
Q Consensus 521 ~~l~ 524 (534)
..+.
T Consensus 182 ~~l~ 185 (187)
T PRK09641 182 KQLR 185 (187)
T ss_pred HHHh
Confidence 8875
No 45
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=99.89 E-value=1e-21 Score=183.17 Aligned_cols=167 Identities=15% Similarity=0.241 Sum_probs=138.2
Q ss_pred HHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHH
Q 009449 288 QHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVAR 366 (534)
Q Consensus 288 ~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~ 366 (534)
..+..| ..|++.|+..|.+.+++++.++.++..+++|++||+++.+|++.++|+...+ .|.+|++.+++|.+.+++++
T Consensus 3 ~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R~ 81 (170)
T TIGR02952 3 ERAQDREEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFRG 81 (170)
T ss_pred HHHHccCHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHHh
Confidence 344555 7899999999999999999999998899999999999999999999987555 89999999999999999987
Q ss_pred hccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCC
Q 009449 367 HARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPD 446 (534)
Q Consensus 367 ~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d 446 (534)
+.+.... +.+. ..+...
T Consensus 82 ~~~~~~~-----------------------------------------------------~~~~---------~~~~~~- 98 (170)
T TIGR02952 82 SKRHPLF-----------------------------------------------------SLDV---------FKELLS- 98 (170)
T ss_pred cCCCCCC-----------------------------------------------------cHHH---------HhhcCC-
Confidence 6431110 0000 000001
Q ss_pred CCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449 447 RSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE 523 (534)
Q Consensus 447 ~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l 523 (534)
...+|++.+...+..+.+..+|..|||++|+||.++| .+|+|++|||+.||+|.++|++.++||+++||+.+
T Consensus 99 -~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~l 170 (170)
T TIGR02952 99 -NEPNPEEAILKEEANEKLLKALKILTPKQQHVIALRF----GQNLPIAEVARILGKTEGAVKILQFRAIKKLARQM 170 (170)
T ss_pred -CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence 1135777777777788899999999999999999999 89999999999999999999999999999999763
No 46
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=99.88 E-value=1.5e-21 Score=187.00 Aligned_cols=175 Identities=16% Similarity=0.246 Sum_probs=145.1
Q ss_pred CCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCC---CCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHH
Q 009449 281 VSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLG---IPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356 (534)
Q Consensus 281 ~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g---~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wI 356 (534)
++++.|+..+..| ..|++.|+..|.+.|+.++.++.++. .+++|++||+++++|+++++|++..+ .|.||++..+
T Consensus 3 ~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~ia 81 (189)
T PRK06811 3 INEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAIS 81 (189)
T ss_pred CcHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHH
Confidence 5677888888888 67999999999999999999998853 57999999999999999999997654 8999999999
Q ss_pred HHHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccch
Q 009449 357 RKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCL 436 (534)
Q Consensus 357 R~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~ 436 (534)
+|.+.++++++.+..... +.+..
T Consensus 82 rn~~~d~~rk~~~~~~~~----------------------------------------------------~~~~~----- 104 (189)
T PRK06811 82 KYKAIDYKRKLTKNNEID----------------------------------------------------SIDEF----- 104 (189)
T ss_pred HHHHHHHHHHhccccccc----------------------------------------------------cchhh-----
Confidence 999999998765311000 00000
Q ss_pred hhhhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 437 NAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 437 ~~~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
. . ...++|++.+...+....|..+|..|||++++||.|+| .+++|++|||+.||+|..+|++.++||+
T Consensus 105 ---~---~--~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIAe~lgis~~~V~~~l~Ra~ 172 (189)
T PRK06811 105 ---I---L--ISEESIENEIILKENKEEILKLINDLEKLDREIFIRRY----LLGEKIEEIAKKLGLTRSAIDNRLSRGR 172 (189)
T ss_pred ---h---h--cccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 0 0 01135677777777888899999999999999999999 8999999999999999999999999999
Q ss_pred HHHHhHhhh
Q 009449 517 TKLRDSETC 525 (534)
Q Consensus 517 ~KLR~~l~~ 525 (534)
++||.....
T Consensus 173 ~~Lr~~~~~ 181 (189)
T PRK06811 173 KKLQKNKLN 181 (189)
T ss_pred HHHHHcccC
Confidence 999986543
No 47
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=99.88 E-value=1.5e-21 Score=184.64 Aligned_cols=173 Identities=16% Similarity=0.150 Sum_probs=141.5
Q ss_pred CHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHH
Q 009449 282 SERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (534)
Q Consensus 282 d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI 360 (534)
+...|...+..| ..|+..|+..|.+.|+.+|.+|.++..+++|++||+|+++|+++++|++.. ..|.||++..++|.+
T Consensus 5 ~~~~li~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~-~~~~~wl~~ia~n~~ 83 (179)
T PRK12514 5 DIEKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSG-LSPMTWLITIARNHA 83 (179)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHH
Confidence 455667777777 779999999999999999999999999999999999999999999998754 369999999999999
Q ss_pred HHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhh
Q 009449 361 SKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKY 440 (534)
Q Consensus 361 ~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l 440 (534)
.+++++..+. ..+ ++. .
T Consensus 84 ~d~~R~~~~~-~~~-----------------------------------------------------~~~---------~ 100 (179)
T PRK12514 84 IDRLRARKAV-AVD-----------------------------------------------------IDE---------A 100 (179)
T ss_pred HHHHHhcCCc-ccc-----------------------------------------------------ccc---------c
Confidence 9999875421 000 000 0
Q ss_pred hhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449 441 LEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520 (534)
Q Consensus 441 ~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR 520 (534)
.+ ..+. ..+|++.+...+....|..+|..||+++++||.++| ++|+|++|||+.||+|..+|++.++||+++||
T Consensus 101 ~~-~~~~-~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 174 (179)
T PRK12514 101 HD-LADP-SPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAY----LEGLSYKELAERHDVPLNTMRTWLRRSLLKLR 174 (179)
T ss_pred hh-cccc-CCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCChHHHHHHHHHHHHHHH
Confidence 00 0111 135666666556666799999999999999999999 89999999999999999999999999999999
Q ss_pred hHhh
Q 009449 521 DSET 524 (534)
Q Consensus 521 ~~l~ 524 (534)
+++.
T Consensus 175 ~~l~ 178 (179)
T PRK12514 175 ECLS 178 (179)
T ss_pred HHhc
Confidence 9864
No 48
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=99.88 E-value=1.6e-21 Score=186.78 Aligned_cols=175 Identities=22% Similarity=0.207 Sum_probs=141.4
Q ss_pred CHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHH
Q 009449 282 SERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (534)
Q Consensus 282 d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI 360 (534)
+...|...+..| ..|++.|+..|.+.|+++++++.++..+++|++||+|+++|+. ..|++..+ .|.||++.++++.+
T Consensus 15 ~~~~l~~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~ 92 (194)
T PRK12519 15 SDAELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRA 92 (194)
T ss_pred cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHH
Confidence 456677777777 7899999999999999999999999999999999999999976 67887654 79999999999999
Q ss_pred HHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhh
Q 009449 361 SKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKY 440 (534)
Q Consensus 361 ~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l 440 (534)
+++++++.+..... + ..+. ..
T Consensus 93 ~d~~Rk~~~~~~~~-~--------------------------------------------------~~~~--------~~ 113 (194)
T PRK12519 93 IDRLRSRRSRQRLL-E--------------------------------------------------RWQQ--------EL 113 (194)
T ss_pred HHHHHhcccccchh-h--------------------------------------------------hhhh--------hh
Confidence 99998764311000 0 0000 00
Q ss_pred hhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449 441 LEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520 (534)
Q Consensus 441 ~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR 520 (534)
..+....+|++.+...+....|..+|..||+++++||.|+| .+++|++|||+.||+|.++|+++++||+++||
T Consensus 114 ---~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 186 (194)
T PRK12519 114 ---LGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAY----YEGLSQSEIAKRLGIPLGTVKARARQGLLKLR 186 (194)
T ss_pred ---cccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhh----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 00011134666666667777899999999999999999999 89999999999999999999999999999999
Q ss_pred hHhh
Q 009449 521 DSET 524 (534)
Q Consensus 521 ~~l~ 524 (534)
+.+.
T Consensus 187 ~~l~ 190 (194)
T PRK12519 187 ELLQ 190 (194)
T ss_pred HHHH
Confidence 8764
No 49
>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=99.88 E-value=3.3e-21 Score=183.10 Aligned_cols=181 Identities=15% Similarity=0.182 Sum_probs=144.5
Q ss_pred CHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHH
Q 009449 282 SERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (534)
Q Consensus 282 d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI 360 (534)
++..|...+..| ..|++.|+..|.+.|+.+|+++.++..+++|++||+++++|+++.+|++. ..|.+|++..+++.+
T Consensus 6 ~d~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~~ 83 (190)
T TIGR02939 6 LDLELVERVQRGEKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNTA 83 (190)
T ss_pred cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHHH
Confidence 456677777777 67999999999999999999999999999999999999999999999975 369999999999999
Q ss_pred HHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhh
Q 009449 361 SKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKY 440 (534)
Q Consensus 361 ~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l 440 (534)
.+++++..+...... .+.+.. ..+
T Consensus 84 ~~~~r~~~r~~~~~~--------------------------------------------------~~~~~~------~~~ 107 (190)
T TIGR02939 84 KNHLVAQGRRPPTSD--------------------------------------------------VEIEDA------EHF 107 (190)
T ss_pred HHHHHHhccCCCccc--------------------------------------------------ccccch------hhh
Confidence 999986543211000 000000 000
Q ss_pred hhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449 441 LEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520 (534)
Q Consensus 441 ~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR 520 (534)
.+........+|++.+...+....+..+|..||+++++||.++| .+++|++|||+.||+|..+|++.++||+++||
T Consensus 108 ~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr 183 (190)
T TIGR02939 108 EGADRLREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLRE----LEGLSYEDIARIMDCPVGTVRSRIFRAREAIA 183 (190)
T ss_pred cccccccccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhh----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 00000011235777777777888899999999999999999999 89999999999999999999999999999999
Q ss_pred hHhh
Q 009449 521 DSET 524 (534)
Q Consensus 521 ~~l~ 524 (534)
+++.
T Consensus 184 ~~l~ 187 (190)
T TIGR02939 184 IRLR 187 (190)
T ss_pred HHhh
Confidence 9875
No 50
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=99.88 E-value=2.5e-21 Score=184.22 Aligned_cols=173 Identities=17% Similarity=0.179 Sum_probs=140.4
Q ss_pred CCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHH
Q 009449 281 VSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (534)
Q Consensus 281 ~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~a 359 (534)
++...|...+..| ..|++.|+..|.+.|+.++.++.++..+++|++||+|+.+|+..++|++..+ .|.+|++..++|.
T Consensus 8 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wL~~iarn~ 86 (182)
T PRK12537 8 FDYEACLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARG-SARGWIYSVTRHL 86 (182)
T ss_pred hhHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHH
Confidence 3456677777777 7899999999999999999999999999999999999999999999986443 7999999999999
Q ss_pred HHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhh
Q 009449 360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAK 439 (534)
Q Consensus 360 I~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~ 439 (534)
+.+++++..+.... +.. . .
T Consensus 87 ~~d~~r~~~~~~~~-------------------------------------------------------~~~---~--~- 105 (182)
T PRK12537 87 ALNVLRDTRREVVL-------------------------------------------------------DDD---A--E- 105 (182)
T ss_pred HHHHHHhccccCcc-------------------------------------------------------ccc---h--h-
Confidence 99999876421100 000 0 0
Q ss_pred hhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449 440 YLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL 519 (534)
Q Consensus 440 l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL 519 (534)
+...+ ..++++.....+....|..+|+.|||++|+||.++| .+++|++|||+.||||.++|++.++||+++|
T Consensus 106 --~~~~~--~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~~~s~~eIA~~lgis~~tV~~~l~ra~~~L 177 (182)
T PRK12537 106 --ETAQT--LHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAY----VDGCSHAEIAQRLGAPLGTVKAWIKRSLKAL 177 (182)
T ss_pred --hhccc--ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCChhhHHHHHHHHHHHH
Confidence 00000 113334444445566899999999999999999999 8999999999999999999999999999999
Q ss_pred HhHh
Q 009449 520 RDSE 523 (534)
Q Consensus 520 R~~l 523 (534)
|.++
T Consensus 178 r~~l 181 (182)
T PRK12537 178 RECM 181 (182)
T ss_pred HHHh
Confidence 9875
No 51
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=99.88 E-value=1.8e-21 Score=182.43 Aligned_cols=173 Identities=18% Similarity=0.190 Sum_probs=139.1
Q ss_pred HHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhc
Q 009449 290 LAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA 368 (534)
Q Consensus 290 l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~s 368 (534)
++.| ..|+++|+..|.++|+.++++|.+++.+.+|++||+++++|+++.+|+ .+.+|.||++.++++.+.+.+++..
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 4555 679999999999999999999999999999999999999999999999 3458999999999999999998764
Q ss_pred cccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCC
Q 009449 369 RGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRS 448 (534)
Q Consensus 369 r~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~ 448 (534)
+....+. .+.+ +.++....+...+
T Consensus 82 ~~~~~~~--------------------------------------------------~~~~----~~~~~~~~~~~~~-- 105 (182)
T PRK09652 82 RRPPASD--------------------------------------------------VDAE----EAEDFDLADALRD-- 105 (182)
T ss_pred CCCCccc--------------------------------------------------cccc----ccccccccccccc--
Confidence 3211100 0000 0000001111111
Q ss_pred CCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449 449 VKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET 524 (534)
Q Consensus 449 ~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~ 524 (534)
..+|++.+...+....+..+|..|||++++||.++| ..++|++|||+.||+|+.+|++.+++|+++||+.+.
T Consensus 106 ~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 177 (182)
T PRK09652 106 ISTPENELLSAELEQRVRAAIESLPEELRTAITLRE----IEGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQ 177 (182)
T ss_pred ccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 135777777777888999999999999999999999 899999999999999999999999999999998765
No 52
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=99.88 E-value=2.4e-21 Score=184.13 Aligned_cols=176 Identities=20% Similarity=0.246 Sum_probs=137.1
Q ss_pred CCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHH
Q 009449 281 VSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (534)
Q Consensus 281 ~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~a 359 (534)
+++..|...+..| ..|++.++..|.+.|+.+|++|.+++.+++|++||+++.+|++.++|++..+ .|.+|++..++|.
T Consensus 8 ~~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~~-~~~~wl~~ia~n~ 86 (186)
T PRK13919 8 LSDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRG-SARAWLLALAHHA 86 (186)
T ss_pred cCHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCcccc-chHHHHHHHHHHH
Confidence 3566777777777 7899999999999999999999999999999999999999999999987643 6999999999999
Q ss_pred HHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhh
Q 009449 360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAK 439 (534)
Q Consensus 360 I~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~ 439 (534)
+.+++++..+... +. +.+. . +..
T Consensus 87 ~~d~~rk~~~~~~-~~---------------------------------------------------~~~~----~-~~~ 109 (186)
T PRK13919 87 AVDHVRRRAARPQ-PL---------------------------------------------------EPDE----R-EPE 109 (186)
T ss_pred HHHHHHhhhcccc-cc---------------------------------------------------cccc----c-ccc
Confidence 9999987642100 00 0000 0 000
Q ss_pred hhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449 440 YLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL 519 (534)
Q Consensus 440 l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL 519 (534)
..+ .++ +..........+.|..++..||+++++||.++| .+++|++|||+.||+|..+|+..++||+++|
T Consensus 110 ~~~-~~~-----~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~eIA~~lgis~~~V~~~l~ra~~~L 179 (186)
T PRK13919 110 AFD-LPG-----PGLDEEGHLDRTRLGRALKALSPEERRVIEVLY----YQGYTHREAAQLLGLPLGTLKTRARRALSRL 179 (186)
T ss_pred ccc-CCC-----ccccHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 000 011 111112223345789999999999999999999 8999999999999999999999999999999
Q ss_pred HhHhh
Q 009449 520 RDSET 524 (534)
Q Consensus 520 R~~l~ 524 (534)
|..+.
T Consensus 180 r~~l~ 184 (186)
T PRK13919 180 KEVLR 184 (186)
T ss_pred HHHhc
Confidence 98764
No 53
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=99.88 E-value=5e-21 Score=183.18 Aligned_cols=179 Identities=16% Similarity=0.158 Sum_probs=144.2
Q ss_pred HHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHH
Q 009449 283 ERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (534)
Q Consensus 283 ~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~ 361 (534)
.+.|...++.| ..|++.|+..|.+.|+.++++|.++..+++|++||+++++|+++.+|++.. .|.+|++..+++.+.
T Consensus 7 ~~~ll~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~~ 84 (193)
T PRK11923 7 DQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTAK 84 (193)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHHH
Confidence 45667777777 779999999999999999999999999999999999999999999999874 599999999999999
Q ss_pred HHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccc-cccchhhhh
Q 009449 362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQK-IGDCLNAKY 440 (534)
Q Consensus 362 ~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~-i~~~~~~~l 440 (534)
++++++.+...... ..++.. ...+ .
T Consensus 85 d~~rk~~~~~~~~~--------------------------------------------------~~~~~~~~~~~-~--- 110 (193)
T PRK11923 85 NHLVSRGRRPPDSD--------------------------------------------------VSSEDAEFYDG-D--- 110 (193)
T ss_pred HHHHHhcCCCcccc--------------------------------------------------ccccchhhhcc-c---
Confidence 99987643211000 000000 0000 0
Q ss_pred hhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449 441 LEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520 (534)
Q Consensus 441 ~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR 520 (534)
..+. ...+|++.+...+..+.+..+|..||+++|+||.++| .+|+|++|||+.||+|..+|++.+.||+++||
T Consensus 111 -~~~~--~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr 183 (193)
T PRK11923 111 -HALK--DIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLRE----FDGLSYEDIASVMQCPVGTVRSRIFRAREAID 183 (193)
T ss_pred -cccc--CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 0011 1236777777778888999999999999999999999 89999999999999999999999999999999
Q ss_pred hHhh
Q 009449 521 DSET 524 (534)
Q Consensus 521 ~~l~ 524 (534)
.++.
T Consensus 184 ~~l~ 187 (193)
T PRK11923 184 KALQ 187 (193)
T ss_pred HHHH
Confidence 9875
No 54
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=99.88 E-value=4.2e-21 Score=184.87 Aligned_cols=177 Identities=20% Similarity=0.202 Sum_probs=146.3
Q ss_pred CCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHH
Q 009449 281 VSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (534)
Q Consensus 281 ~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~a 359 (534)
+++..|+..+..| ..|++.|+..|.+.|+.+|.++.++..+++|++||+++.+|+...+|++.. ..|.||++..+++.
T Consensus 11 ~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~n~ 89 (196)
T PRK12524 11 VSDEALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVCNL 89 (196)
T ss_pred cCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHHHHH
Confidence 4567788888877 789999999999999999999999999999999999999999999998533 37999999999999
Q ss_pred HHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhh
Q 009449 360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAK 439 (534)
Q Consensus 360 I~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~ 439 (534)
+.+.++++.+.. . .++.. .
T Consensus 90 ~~d~~Rk~~~~~-~-----------------------------------------------------~~~~~-~------ 108 (196)
T PRK12524 90 CTDRLRRRRRAS-V-----------------------------------------------------DLDDA-P------ 108 (196)
T ss_pred HHHHHHhhcCCC-C-----------------------------------------------------Ccccc-c------
Confidence 999998753210 0 00000 0
Q ss_pred hhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449 440 YLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL 519 (534)
Q Consensus 440 l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL 519 (534)
+ ..+. ..+|++.+...+....|..+|+.||+++|+||.|+| .++++++|||+.||||..+|+++++||+++|
T Consensus 109 --~-~~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~----~~g~s~~eIA~~lgis~~tV~~~l~Ra~~~L 180 (196)
T PRK12524 109 --E-PADA-APGAEEALIEGDRMRALDAALAALPERQRQAVVLRH----IEGLSNPEIAEVMEIGVEAVESLTARGKRAL 180 (196)
T ss_pred --c-cccc-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 0 0011 124666677777778899999999999999999999 8999999999999999999999999999999
Q ss_pred HhHhhhhc
Q 009449 520 RDSETCRD 527 (534)
Q Consensus 520 R~~l~~~~ 527 (534)
|..+...+
T Consensus 181 r~~l~~~~ 188 (196)
T PRK12524 181 AALLAGQR 188 (196)
T ss_pred HHHHHhcc
Confidence 99886533
No 55
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=99.88 E-value=1.5e-21 Score=179.75 Aligned_cols=150 Identities=18% Similarity=0.269 Sum_probs=124.2
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccc
Q 009449 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (534)
Q Consensus 295 ~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP 374 (534)
.|++.|++.|.++|+.+++++ ++..+++|++||+++++|+++++|++..| .|.+|++..+++.+.++++++.+..
T Consensus 4 ~af~~l~~~y~~~l~~~~~~~-~~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~~~~--- 78 (154)
T PRK06759 4 ATFTEAVVLYEGLIVNQIKKL-GIYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFAVQ--- 78 (154)
T ss_pred ccHHHHHHHHHHHHHHHHHHh-CCcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHHhhc---
Confidence 589999999999999999986 56689999999999999999999998766 7999999999999999998763100
Q ss_pred cchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHH
Q 009449 375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKE 454 (534)
Q Consensus 375 ~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee 454 (534)
. . . . + + ++|++
T Consensus 79 -~-----------------~------------------------------~-~-~----------------~---~~~~~ 89 (154)
T PRK06759 79 -E-----------------K------------------------------C-V-C----------------V---GEYED 89 (154)
T ss_pred -c-----------------c------------------------------c-c-c----------------c---CCCcc
Confidence 0 0 0 0 0 0 01122
Q ss_pred HHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 455 IVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 455 ~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
.+...+....|..++..|||++|+||.++| ++++|++|||+.||+|.++|+++++||+++||+.
T Consensus 90 ~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~----~~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 90 HFHFEDVEMKVKDFMSVLDEKEKYIIFERF----FVGKTMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred cccHHHHHHHHHHHHHhCCHHHHHHHHHHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 222334456799999999999999999999 8999999999999999999999999999999964
No 56
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=3.9e-21 Score=183.07 Aligned_cols=174 Identities=16% Similarity=0.149 Sum_probs=139.7
Q ss_pred HHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHH
Q 009449 283 ERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (534)
Q Consensus 283 ~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~ 361 (534)
...+...+..| ..+++.++..|.++|+.+|++|.++..+++|++||+|+.+|++.++|++.++ .|.||++..++|.+.
T Consensus 12 ~~~l~~~~~~~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~~ 90 (187)
T PRK12534 12 TGRLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKAI 90 (187)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHH
Confidence 34455555556 7899999999999999999999999999999999999999999999998654 688999999999999
Q ss_pred HHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhh
Q 009449 362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYL 441 (534)
Q Consensus 362 ~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~ 441 (534)
+++++..+.... .++|.. .
T Consensus 91 d~~R~~~~~~~~----------------------------------------------------~~~~~~---------~ 109 (187)
T PRK12534 91 DHLRANAPQRRN----------------------------------------------------VALDDA---------G 109 (187)
T ss_pred HHHHhccccccc----------------------------------------------------ccccch---------h
Confidence 999876421000 001100 0
Q ss_pred hccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 442 EFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 442 e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
+. .++ ..+|++.....+....+..+|..||+++++|+.++| .+++|++|||+.||+|.++|+++++||+++||.
T Consensus 110 ~~-~~~-~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 110 EL-RAA-DASPLERTERASTRRRIDHCLAELEPPRSELIRTAF----FEGITYEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred hh-ccc-cCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 00 001 123445555566778899999999999999999999 899999999999999999999999999999998
Q ss_pred Hhh
Q 009449 522 SET 524 (534)
Q Consensus 522 ~l~ 524 (534)
.+.
T Consensus 184 ~l~ 186 (187)
T PRK12534 184 CLE 186 (187)
T ss_pred HHc
Confidence 764
No 57
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=5.3e-21 Score=190.10 Aligned_cols=174 Identities=18% Similarity=0.234 Sum_probs=142.7
Q ss_pred CHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHH
Q 009449 282 SERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (534)
Q Consensus 282 d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI 360 (534)
++..|...+..| ..|++.|+..|.+.|+++++++.++..+++|++||+|+.+|++.++|++..+ .|.+|++..++|.+
T Consensus 49 ~d~~Li~~~~~gd~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~~ 127 (233)
T PRK12538 49 EDEELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNRC 127 (233)
T ss_pred cHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHHH
Confidence 455666777777 7799999999999999999999999999999999999999999999987544 79999999999999
Q ss_pred HHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhh
Q 009449 361 SKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKY 440 (534)
Q Consensus 361 ~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l 440 (534)
+++++++.+. .+ . .++.
T Consensus 128 id~~Rk~~~~-~~--~--------------------------------------------------~~~~---------- 144 (233)
T PRK12538 128 IDLRRKPRTE-NV--D--------------------------------------------------AVPE---------- 144 (233)
T ss_pred HHHHHhhccc-cc--c--------------------------------------------------cccc----------
Confidence 9998764210 00 0 0000
Q ss_pred hhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449 441 LEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520 (534)
Q Consensus 441 ~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR 520 (534)
. .+ ...++++.+...+..+.|..+|..||+++|+||.|+| .+++|++|||+.||+|.++|+++++||+++||
T Consensus 145 --~-~~-~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~----~eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr 216 (233)
T PRK12538 145 --V-AD-GKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSY----HENMSNGEIAEVMDTTVAAVESLLKRGRQQLR 216 (233)
T ss_pred --c-cc-CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 0 00 1124455566667777899999999999999999999 89999999999999999999999999999999
Q ss_pred hHhhhhc
Q 009449 521 DSETCRD 527 (534)
Q Consensus 521 ~~l~~~~ 527 (534)
+.+....
T Consensus 217 ~~l~~~~ 223 (233)
T PRK12538 217 DLLRRHE 223 (233)
T ss_pred HHHHHhh
Confidence 9886544
No 58
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=8.3e-21 Score=184.63 Aligned_cols=178 Identities=15% Similarity=0.118 Sum_probs=137.5
Q ss_pred HHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHH
Q 009449 284 RVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK 362 (534)
Q Consensus 284 ~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~ 362 (534)
..|...+..| ..|+++|+..|.+.|+.++.++.++..+++|++||+|+.+|+++..|++.++ .|.||++.++||.+++
T Consensus 26 ~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d 104 (206)
T PRK12526 26 QWLILVAISRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFD 104 (206)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHH
Confidence 3345555555 7899999999999999999999999899999999999999999999998765 6999999999999999
Q ss_pred HHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhh
Q 009449 363 MVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLE 442 (534)
Q Consensus 363 ~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e 442 (534)
++++..+...... .+++ .+ ..+
T Consensus 105 ~~Rk~~~~~~~~~-------------------------~~~~---------------------~~------------~~~ 126 (206)
T PRK12526 105 MLRKIKAKKEQNL-------------------------GDDI---------------------WP------------IEQ 126 (206)
T ss_pred HHHHhcccccccc-------------------------cccc---------------------ch------------hhh
Confidence 9987643110000 0000 00 000
Q ss_pred ccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 443 FAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 443 ~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
.+.+.. ..+. ..........|..+|..||+++++||.++| ++++|++|||+.||+|..+|+..++||+++||..
T Consensus 127 ~~~~~~-~~~~-~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 200 (206)
T PRK12526 127 ALAESQ-SESE-EFSDHLMDKQILSYIEKLPEAQQTVVKGVY----FQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQ 200 (206)
T ss_pred hccccc-CchH-HHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 011111 1222 232333446799999999999999999999 8999999999999999999999999999999998
Q ss_pred hhhh
Q 009449 523 ETCR 526 (534)
Q Consensus 523 l~~~ 526 (534)
+...
T Consensus 201 l~~~ 204 (206)
T PRK12526 201 MGEQ 204 (206)
T ss_pred Hhhc
Confidence 8643
No 59
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=9.7e-21 Score=187.38 Aligned_cols=184 Identities=18% Similarity=0.189 Sum_probs=147.8
Q ss_pred CCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHH
Q 009449 281 VSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (534)
Q Consensus 281 ~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~a 359 (534)
+++..|...+..| ..|++.++..|.+.|+++|+++.++..+++|++||+|+++|+++++|++. ..|.+|++..+++.
T Consensus 15 ~~~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~ 92 (231)
T PRK11922 15 ASDRELVARVLAGDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNE 92 (231)
T ss_pred ccHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHH
Confidence 4456677777777 78999999999999999999999999999999999999999999999986 37999999999999
Q ss_pred HHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhh
Q 009449 360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAK 439 (534)
Q Consensus 360 I~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~ 439 (534)
+.+++++..+....+.. ..+.... + +
T Consensus 93 ~~d~~Rk~~r~~~~~~~--------------------------------------------------~~~~~~~-~-~-- 118 (231)
T PRK11922 93 ALGRLRRRRRLVNLAEM--------------------------------------------------VMASTIA-G-G-- 118 (231)
T ss_pred HHHHHHhhcccccchhc--------------------------------------------------ccccccc-c-c--
Confidence 99999876532211100 0000000 0 0
Q ss_pred hhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449 440 YLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL 519 (534)
Q Consensus 440 l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL 519 (534)
...... ....+|++.+...+..+.|..+|+.||+++++||.++| .+++|++|||+.||+|.++|++.++||+++|
T Consensus 119 ~~~~~~-~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIAe~lgis~~tVk~~l~Rar~kL 193 (231)
T PRK11922 119 ERTPLA-DPAEDPERAAARREIRALLERAIDALPDAFRAVFVLRV----VEELSVEETAQALGLPEETVKTRLHRARRLL 193 (231)
T ss_pred cccccC-cccCChHHHHHHHHHHHHHHHHHHhCCHHHhhhheeeh----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 000111 12246778888888888999999999999999999999 8999999999999999999999999999999
Q ss_pred HhHhhh
Q 009449 520 RDSETC 525 (534)
Q Consensus 520 R~~l~~ 525 (534)
|+.+..
T Consensus 194 r~~l~~ 199 (231)
T PRK11922 194 RESLAR 199 (231)
T ss_pred HHHHHH
Confidence 998864
No 60
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=1.4e-20 Score=179.80 Aligned_cols=178 Identities=17% Similarity=0.184 Sum_probs=147.4
Q ss_pred CCCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHH
Q 009449 280 GVSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358 (534)
Q Consensus 280 g~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~ 358 (534)
.+++..|...+..| ..|++.|+..|.+.|+.++.++.++..+++|++||+|+.+|++.++|++. ..|.+|++..+++
T Consensus 6 ~~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n 83 (189)
T PRK12515 6 ATTDEMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARF 83 (189)
T ss_pred ccCHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHH
Confidence 35677788877777 77999999999999999999999999999999999999999999999974 3799999999999
Q ss_pred HHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhh
Q 009449 359 SISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNA 438 (534)
Q Consensus 359 aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~ 438 (534)
.+.+++++..+. .+. . +
T Consensus 84 ~~~d~~r~~~~~-~~~-------------------------------------------------------~----~--- 100 (189)
T PRK12515 84 KALSALRRRKHE-EID-------------------------------------------------------D----E--- 100 (189)
T ss_pred HHHHHHHccCCC-CCc-------------------------------------------------------c----c---
Confidence 999999865310 000 0 0
Q ss_pred hhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009449 439 KYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTK 518 (534)
Q Consensus 439 ~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~K 518 (534)
......+ ..++|++.+...+....+..+|+.||+++|+||.|+| .+++|++|||+.||+|..+|++.+.||+++
T Consensus 101 -~~~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~eIA~~lgis~~tV~~~l~Rar~~ 174 (189)
T PRK12515 101 -AAAAIED-GADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVY----YHEKSVEEVGEIVGIPESTVKTRMFYARKK 174 (189)
T ss_pred -cccccCC-CCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 0000111 1235666666667778899999999999999999999 899999999999999999999999999999
Q ss_pred HHhHhhhhcc
Q 009449 519 LRDSETCRDL 528 (534)
Q Consensus 519 LR~~l~~~~L 528 (534)
||..+...++
T Consensus 175 Lr~~l~~~~~ 184 (189)
T PRK12515 175 LAELLKAAGV 184 (189)
T ss_pred HHHHHHHhcc
Confidence 9999877654
No 61
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=99.87 E-value=4.4e-21 Score=183.39 Aligned_cols=173 Identities=20% Similarity=0.251 Sum_probs=137.2
Q ss_pred CCCHHHHHHHHHh----cHHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHH
Q 009449 280 GVSERVLKQHLAF----GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYW 355 (534)
Q Consensus 280 g~d~~~L~~~l~~----G~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~w 355 (534)
.++++.|+..++. +..|++.|+..|.+.|+++|.+|.++..+++|++||+++.+|+++++|++. ..|.||++.+
T Consensus 7 ~~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~~--~~~~~wl~~i 84 (188)
T PRK09640 7 ELNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLYSI 84 (188)
T ss_pred CCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcCC--CcchHHHHHH
Confidence 4567777777774 378999999999999999999999999999999999999999999999863 4799999999
Q ss_pred HHHHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccc
Q 009449 356 IRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDC 435 (534)
Q Consensus 356 IR~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~ 435 (534)
++|.+.+++++..+..... . ++ ..
T Consensus 85 a~n~~~d~~R~~~~~~~~~-~-------------------------~~-----------------------~~------- 108 (188)
T PRK09640 85 TYNECITQYRKERRKRRLM-D-------------------------AL-----------------------SL------- 108 (188)
T ss_pred HHHHHHHHHHHhcccccCc-c-------------------------hh-----------------------hh-------
Confidence 9999999998754211000 0 00 00
Q ss_pred hhhhhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009449 436 LNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKA 515 (534)
Q Consensus 436 ~~~~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RA 515 (534)
+..+++. ++.....+....|..+|+.||+++|+||.|+| .+++|++|||+.||||..+|+..+.||
T Consensus 109 ------~~~~~~~----~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra 174 (188)
T PRK09640 109 ------DPLEEAS----EEKAPKPEERGGLDRWLVHVNPIDREILVLRF----VAELEFQEIADIMHMGLSATKMRYKRA 174 (188)
T ss_pred ------ccccccc----ccccccHHHHHHHHHHHHhcChhheeeeeeHH----hcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 0000110 01111223445789999999999999999999 899999999999999999999999999
Q ss_pred HHHHHhHhh
Q 009449 516 MTKLRDSET 524 (534)
Q Consensus 516 L~KLR~~l~ 524 (534)
+++||..+.
T Consensus 175 ~~~Lr~~l~ 183 (188)
T PRK09640 175 LDKLREKFA 183 (188)
T ss_pred HHHHHHHHH
Confidence 999999764
No 62
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=1.6e-20 Score=175.47 Aligned_cols=172 Identities=20% Similarity=0.213 Sum_probs=142.3
Q ss_pred HHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHH
Q 009449 287 KQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVA 365 (534)
Q Consensus 287 ~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr 365 (534)
...+..| ..|++.+++.|.+.|+++|+++.++..+++|++||+++.+|++.++|+ .+..|.+|++..+++.+.++++
T Consensus 4 ~~~~~~~~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~~r 81 (179)
T PRK11924 4 MPVDATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDLLR 81 (179)
T ss_pred HHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHHHH
Confidence 3445555 789999999999999999999999999999999999999999999998 3458999999999999999998
Q ss_pred HhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccC
Q 009449 366 RHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAP 445 (534)
Q Consensus 366 ~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~ 445 (534)
+..+..... .+ ... +...
T Consensus 82 ~~~~~~~~~-----------------------------------------------------~~-~~~--------~~~~ 99 (179)
T PRK11924 82 RRRREKAVL-----------------------------------------------------SD-DAL--------EPEF 99 (179)
T ss_pred hcccccccC-----------------------------------------------------cc-ccc--------cccc
Confidence 764311100 00 000 0000
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449 446 DRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC 525 (534)
Q Consensus 446 d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~ 525 (534)
+....+|++.+...+....+..+|..|||++++||.++| .+++|.+|||+.||+|+.+|++++++|+++||+.+..
T Consensus 100 ~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~~ 175 (179)
T PRK11924 100 AETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRY----VEGLSYREIAEILGVPVGTVKSRLRRARQLLRECLEA 175 (179)
T ss_pred CCccCCHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 002357888888889999999999999999999999999 7899999999999999999999999999999998765
Q ss_pred h
Q 009449 526 R 526 (534)
Q Consensus 526 ~ 526 (534)
.
T Consensus 176 ~ 176 (179)
T PRK11924 176 Q 176 (179)
T ss_pred H
Confidence 4
No 63
>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=1.4e-20 Score=178.38 Aligned_cols=177 Identities=18% Similarity=0.170 Sum_probs=138.5
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhh----CCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcc
Q 009449 294 WYCREELIKSTRPLVLFLARNYR----GLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (534)
Q Consensus 294 ~~A~e~LI~~nlrLV~sIArrY~----~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr 369 (534)
..|++.|+..|.+.|+.+|++|. ++..+++|++||+++.+|+++..|++..+..|.+|++..+++.+.+++++..+
T Consensus 6 ~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~~~~ 85 (189)
T TIGR02984 6 QEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRRHLG 85 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHHHHH
Confidence 67999999999999999999985 35679999999999999999999998666689999999999999999986520
Q ss_pred -ccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccc-cchhhhhhhccCCC
Q 009449 370 -GIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIG-DCLNAKYLEFAPDR 447 (534)
Q Consensus 370 -~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~-~~~~~~l~e~i~d~ 447 (534)
..+.+. ...+++.+.. ++....+.+.+.+
T Consensus 86 ~~~r~~~------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~- 116 (189)
T TIGR02984 86 AQKRDIR------------------------------------------------REQSLDAGGRLDESSVRLAAQLAA- 116 (189)
T ss_pred HHhhhcc------------------------------------------------cccCCCcccccCCcchhHHHHccC-
Confidence 000000 0012222111 1111122233333
Q ss_pred CCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449 448 SVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE 523 (534)
Q Consensus 448 ~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l 523 (534)
..++|++.+...+....|..+|..|||++|+||.++| ++++|++|||+.||||.++|++.++||+++||+.+
T Consensus 117 ~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~----~~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~l 188 (189)
T TIGR02984 117 DGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRH----LEGLSFAEVAERMDRSEGAVSMLWVRGLARLRQIL 188 (189)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 2346777777777778899999999999999999999 89999999999999999999999999999999875
No 64
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=4.4e-21 Score=182.75 Aligned_cols=172 Identities=14% Similarity=0.148 Sum_probs=137.2
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI 373 (534)
Q Consensus 294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl 373 (534)
..|++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|++..+|++..+..|.||++..++|.+.++++++.+....
T Consensus 8 ~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~~~~~~ 87 (185)
T PRK12542 8 YEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNKRHETF 87 (185)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhhhhhhh
Confidence 67999999999999999999999999999999999999999999999875445899999999999999999876421000
Q ss_pred ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChH
Q 009449 374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPK 453 (534)
Q Consensus 374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spe 453 (534)
. . ..+. +.... ..++++
T Consensus 88 ~------------------~---------------------------------~~~~-----------~~~~~-~~~~~~ 104 (185)
T PRK12542 88 L------------------E---------------------------------EYER-----------ESIEA-VDENIE 104 (185)
T ss_pred h------------------h---------------------------------hccc-----------cchhh-hhccHH
Confidence 0 0 0000 00000 011344
Q ss_pred HHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchhhh
Q 009449 454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFL 532 (534)
Q Consensus 454 e~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~yl 532 (534)
+.....+....|..+|..|||++|+||.|+| .+++|++|||+.||+|.++|++.++||+++||..+....-..|+
T Consensus 105 ~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~~~~~ 179 (185)
T PRK12542 105 EWEKRKMSEVQIDTLLKELNESNRQVFKYKV----FYNLTYQEISSVMGITEANVRKQFERARKRVQNMIGGIQHDEFK 179 (185)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccchHHHH
Confidence 4444444556799999999999999999999 89999999999999999999999999999999998766655553
No 65
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=99.86 E-value=1.9e-20 Score=180.08 Aligned_cols=172 Identities=16% Similarity=0.173 Sum_probs=141.2
Q ss_pred CCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHH
Q 009449 281 VSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (534)
Q Consensus 281 ~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~a 359 (534)
+++..+...+..| ..+++.+++.|.+.|++++.++.++..+++|++||+|+.+|++.++|++.. .|.+|++..++|.
T Consensus 12 ~~~~~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~~--~f~~wL~~i~rn~ 89 (192)
T PRK09643 12 RSDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDA--AVSSWLHRIVVNA 89 (192)
T ss_pred cCHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCCC--ccHHHHHHHHHHH
Confidence 4567777777777 789999999999999999999999999999999999999999999999753 6999999999999
Q ss_pred HHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhh
Q 009449 360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAK 439 (534)
Q Consensus 360 I~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~ 439 (534)
+.+++++..+.... +++. ..
T Consensus 90 ~~d~~Rk~~~~~~~-----------------------------------------------------~~~~----~~--- 109 (192)
T PRK09643 90 CLDRLRRAKARPTV-----------------------------------------------------PLDD----VY--- 109 (192)
T ss_pred HHHHHHccccCCCC-----------------------------------------------------Cccc----cc---
Confidence 99999876421110 0000 00
Q ss_pred hhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449 440 YLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL 519 (534)
Q Consensus 440 l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL 519 (534)
+ .. ..+++.+...+....|..+|+.||+++|+||.|+| .+++|++|||+.||+|..+|++.++||+++|
T Consensus 110 --~-~~----~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~----~~g~s~~EIA~~lg~s~~tV~~rl~rar~~L 178 (192)
T PRK09643 110 --P-VA----QLERDPTARVETALAVQRALMRLPVEQRAALVAVD----MQGYSVADAARMLGVAEGTVKSRCARGRARL 178 (192)
T ss_pred --c-cc----CCcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 0 00 01223344455667899999999999999999999 8999999999999999999999999999999
Q ss_pred HhHhhh
Q 009449 520 RDSETC 525 (534)
Q Consensus 520 R~~l~~ 525 (534)
|..+..
T Consensus 179 r~~l~~ 184 (192)
T PRK09643 179 AELLGY 184 (192)
T ss_pred HHHHHH
Confidence 998764
No 66
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=99.86 E-value=2.3e-20 Score=174.96 Aligned_cols=167 Identities=16% Similarity=0.252 Sum_probs=134.5
Q ss_pred CCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHH
Q 009449 281 VSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (534)
Q Consensus 281 ~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~a 359 (534)
|+++.+...+..| ..|++.++..|.+.|+++|.++.++..+++|++||+++.+|++.++|++.. .|.||++..+++.
T Consensus 1 ~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~~--~~~~wl~~i~~n~ 78 (169)
T TIGR02954 1 MNDEELVKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPK--YFNTWLTRILINE 78 (169)
T ss_pred CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCcc--ccHHHHHHHHHHH
Confidence 3556677777777 789999999999999999999999999999999999999999999999753 6999999999999
Q ss_pred HHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhh
Q 009449 360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAK 439 (534)
Q Consensus 360 I~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~ 439 (534)
+++++++..+.. |. +.....+
T Consensus 79 ~~d~~R~~~~~~--~~-----------------------------------------------------~~~~~~~---- 99 (169)
T TIGR02954 79 CIDLLKKKKKVI--PF-----------------------------------------------------DPNTSIE---- 99 (169)
T ss_pred HHHHHHhcCCcC--cc-----------------------------------------------------ccccccc----
Confidence 999998764211 10 0000000
Q ss_pred hhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449 440 YLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL 519 (534)
Q Consensus 440 l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL 519 (534)
+. .++... .....+..+|..||+++++||.++| .+|+|++|||+.||||..+|+..++||+++|
T Consensus 100 ------~~---~~~~~~---~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eiA~~lgis~~tv~~~l~Ra~~~L 163 (169)
T TIGR02954 100 ------KG---ECETHA---DSRLDLYKAIDTLNDKYQTAIILRY----YHDLTIKEIAEVMNKPEGTVKTYLHRALKKL 163 (169)
T ss_pred ------cc---hhhhch---HHHHHHHHHHHhCCHHHhHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 00 000000 1123688899999999999999999 8999999999999999999999999999999
Q ss_pred HhHhh
Q 009449 520 RDSET 524 (534)
Q Consensus 520 R~~l~ 524 (534)
|..+.
T Consensus 164 r~~l~ 168 (169)
T TIGR02954 164 KKRLE 168 (169)
T ss_pred HHHhc
Confidence 98764
No 67
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=99.86 E-value=1.7e-20 Score=176.54 Aligned_cols=172 Identities=15% Similarity=0.145 Sum_probs=136.8
Q ss_pred CCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHH
Q 009449 281 VSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (534)
Q Consensus 281 ~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~a 359 (534)
+++..+...+..| ..|++.|+..|.+.|+.+|++|.++..+++|++||+++++|++++.|++. .+|.+|++..+++.
T Consensus 3 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n~ 80 (176)
T PRK09638 3 MDEKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASRL 80 (176)
T ss_pred ccHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHH
Confidence 4566677777777 78999999999999999999999999999999999999999999999874 47999999999999
Q ss_pred HHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhh
Q 009449 360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAK 439 (534)
Q Consensus 360 I~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~ 439 (534)
+.+++++..+...... . ..+.
T Consensus 81 ~~d~~r~~~~~~~~~~---------------------------~-----------------------~~~~--------- 101 (176)
T PRK09638 81 YKDHLRKQKREKLRLQ---------------------------R-----------------------AKEE--------- 101 (176)
T ss_pred HHHHHHHhccccchhh---------------------------h-----------------------cccc---------
Confidence 9999997643110000 0 0000
Q ss_pred hhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449 440 YLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL 519 (534)
Q Consensus 440 l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL 519 (534)
..+. ... +..........|..+|..||+++++||.++| ..|+|++|||+.||+|..+|++.+.||+.+|
T Consensus 102 ----~~~~--~~~-~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l 170 (176)
T PRK09638 102 ----TLRK--EKW-EAAIKGAEWSEMLDALSKLDPEFRAPVILKH----YYGYTYEEIAKMLNIPEGTVKSRVHHGIKQL 170 (176)
T ss_pred ----cCCc--cch-HHHHHhhhHHHHHHHHHcCCHHHhheeeehh----hcCCCHHHHHHHHCCChhHHHHHHHHHHHHH
Confidence 0000 000 1122233445688999999999999999999 8999999999999999999999999999999
Q ss_pred HhHhh
Q 009449 520 RDSET 524 (534)
Q Consensus 520 R~~l~ 524 (534)
|+.+.
T Consensus 171 ~~~l~ 175 (176)
T PRK09638 171 RKEWG 175 (176)
T ss_pred HHHhc
Confidence 98763
No 68
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=1.8e-20 Score=180.18 Aligned_cols=180 Identities=18% Similarity=0.145 Sum_probs=138.5
Q ss_pred HHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHH
Q 009449 283 ERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (534)
Q Consensus 283 ~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~ 361 (534)
...|+..+..| ..|++.|+..|.+.|+.+|.++.++..+++|++||+++.+|+...+|++..+ .|.+|++..++|.++
T Consensus 14 ~~~li~~~~~~d~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn~~l 92 (194)
T PRK12531 14 WLECMEKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRNLCF 92 (194)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHHHHH
Confidence 34566677777 7799999999999999999999999899999999999999999999997554 799999999999999
Q ss_pred HHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhh
Q 009449 362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYL 441 (534)
Q Consensus 362 ~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~ 441 (534)
+++++..+..... . .+....++ ...
T Consensus 93 d~~Rk~~~~~~~~-~---------------------------------------------------~~~~~~~~---~~~ 117 (194)
T PRK12531 93 DLLRKQKGKDLHI-H---------------------------------------------------ADDIWPSD---YYP 117 (194)
T ss_pred HHHHHhccccccc-c---------------------------------------------------hhhccccc---ccc
Confidence 9999764211000 0 00000000 000
Q ss_pred hccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 442 EFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 442 e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
..+. ....++.. ...+.+..++..||+++++||.|+| .+++|++|||+.||||.++|+..+++|+++||.
T Consensus 118 ~~~~--~~~~~e~~----~~~~~l~~~l~~Lp~~~r~v~~l~~----~eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~ 187 (194)
T PRK12531 118 PDLV--DHYSPEQD----MLKEQVMKFLDRLPKAQRDVLQAVY----LEELPHQQVAEMFDIPLGTVKSRLRLAVEKLRH 187 (194)
T ss_pred cccc--cccCHHHH----HHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 0000 01123322 2335688899999999999999999 899999999999999999999999999999999
Q ss_pred Hhhhhcc
Q 009449 522 SETCRDL 528 (534)
Q Consensus 522 ~l~~~~L 528 (534)
.+....|
T Consensus 188 ~l~~~~~ 194 (194)
T PRK12531 188 SMDAESL 194 (194)
T ss_pred HhhhccC
Confidence 9876543
No 69
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=3.2e-20 Score=174.80 Aligned_cols=166 Identities=13% Similarity=0.160 Sum_probs=132.0
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccc
Q 009449 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (534)
Q Consensus 295 ~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP 374 (534)
..+++|+..|.++|+.+|++|.++..+++|++||+++.+|++.++|++.. +|.+|++..++|.+.++++++.+....+
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 46899999999999999999999999999999999999999999999854 7999999999999999998775321110
Q ss_pred cchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHH
Q 009449 375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKE 454 (534)
Q Consensus 375 ~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee 454 (534)
... .+. +..... ..++.. ..++.
T Consensus 81 ~~~--------------------------------------------------~~~----~~~~~~--~~~~~~-~~~~~ 103 (173)
T PRK12522 81 LDL--------------------------------------------------FHK----EDGGEI--EFADDV-NISEE 103 (173)
T ss_pred ccc--------------------------------------------------cch----hhhhhh--ccccCC-CChHH
Confidence 000 000 000000 001111 13333
Q ss_pred HHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449 455 IVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET 524 (534)
Q Consensus 455 ~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~ 524 (534)
+...+..+.+..+|..||+++++|+.|+| .+++|++|||+.||+|.++|+..++||+++||+.+.
T Consensus 104 -~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 168 (173)
T PRK12522 104 -FIQKVEAEMIREVIQLLNEKYKTVLVLYY----YEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLE 168 (173)
T ss_pred -HHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 55566778899999999999999999999 899999999999999999999999999999998865
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=2.5e-20 Score=171.12 Aligned_cols=160 Identities=19% Similarity=0.235 Sum_probs=131.3
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccccc
Q 009449 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC 375 (534)
Q Consensus 296 A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~ 375 (534)
|+++|+..|.+.|+++++++.++..+++|++||+++++|+++.+|++.. +|.+|++.++|+.+.+++++..+....
T Consensus 2 a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~~--~~~~wl~~i~r~~~~d~~r~~~~~~~~-- 77 (161)
T TIGR02985 2 AFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEVE--SFKAYLFTIVKNRSLNYLRHKQVEEKY-- 77 (161)
T ss_pred hHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhccccc--cHHHHHHHHHHHHHHHHHHHHHhHhHH--
Confidence 7899999999999999999999999999999999999999999998743 799999999999999999876421000
Q ss_pred chHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHH
Q 009449 376 KLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEI 455 (534)
Q Consensus 376 ~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~ 455 (534)
. .. +. +.. ......++|++.
T Consensus 78 ------------~-------------~~------------------------~~----~~~-------~~~~~~~~~~~~ 97 (161)
T TIGR02985 78 ------------Q-------------EE------------------------IL----EIE-------VDELSENDPEEE 97 (161)
T ss_pred ------------H-------------HH------------------------HH----hhc-------ccccCCCCcHHH
Confidence 0 00 00 000 000111356666
Q ss_pred HHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449 456 VMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE 523 (534)
Q Consensus 456 v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l 523 (534)
+...+....|..++..||+++++||.++| .+++|.+|||+.||+|+++|++++++|+++||+.+
T Consensus 98 ~~~~e~~~~l~~~l~~L~~~~r~il~l~~----~~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~l 161 (161)
T TIGR02985 98 LEAKELQLIIYKAIEKLPEQCRKIFILSR----FEGKSYKEIAEELGISVKTVEYHISKALKELRKEL 161 (161)
T ss_pred HHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 77777788899999999999999999999 79999999999999999999999999999999753
No 71
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=3.1e-20 Score=176.26 Aligned_cols=164 Identities=18% Similarity=0.244 Sum_probs=134.1
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI 373 (534)
Q Consensus 294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl 373 (534)
..|++.++..|.+.|+.++++|.++..+++|++||+|+.+|+++.+|++.. .|.+|++..+++.+.+++++..+..+.
T Consensus 6 ~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~~~~~~~ 83 (179)
T PRK12543 6 QEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKRWRRFRI 83 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhhcccccc
Confidence 579999999999999999999999999999999999999999999999864 699999999999999988754321000
Q ss_pred ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChH
Q 009449 374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPK 453 (534)
Q Consensus 374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spe 453 (534)
++... + .........|+
T Consensus 84 ------------------------------------------------------~~~~~--~-------~~~~~~~~~~~ 100 (179)
T PRK12543 84 ------------------------------------------------------FEKAE--E-------QRKPVSIDFSE 100 (179)
T ss_pred ------------------------------------------------------ccccc--c-------ccccccccChH
Confidence 00000 0 00000112345
Q ss_pred HHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449 454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD 527 (534)
Q Consensus 454 e~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~ 527 (534)
. +...+..+.|..+|..|||++|+||.|+| .+++|++|||+.||||..+|+..++||+++||+.+....
T Consensus 101 ~-~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~----~e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~ 169 (179)
T PRK12543 101 D-VLSKESNQELIELIHKLPYKLRQVIILRY----LHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIEE 169 (179)
T ss_pred H-HHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5 66667778899999999999999999999 899999999999999999999999999999999887543
No 72
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=2.6e-20 Score=178.30 Aligned_cols=181 Identities=17% Similarity=0.187 Sum_probs=138.7
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccccc
Q 009449 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC 375 (534)
Q Consensus 296 A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~ 375 (534)
+++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|+.+++|++.. +|.||++..++|.++++++++.+....+.
T Consensus 3 ~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~~--~~~~WL~~ia~n~~~d~~Rk~~r~~~~~~ 80 (191)
T PRK12520 3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQS--SLKTYLVGILKHKIIDAIRSGRREVRLSL 80 (191)
T ss_pred chHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhcccc--cHHHHHHHHHHHHHHHHHHhhcCcCcccc
Confidence 7899999999999999999999999999999999999999999998643 69999999999999999998754221111
Q ss_pred chHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHH
Q 009449 376 KLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEI 455 (534)
Q Consensus 376 ~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~ 455 (534)
.. ......+++ ++..... .......++. ..+|++.
T Consensus 81 ~~------------------~~~~~~~~~-----------------------~~~~~~~---~~~~~~~~~~-~~~~~~~ 115 (191)
T PRK12520 81 DD------------------ADEQSDDDL-----------------------FDALFAA---DGHYREPPSD-WGDPDAA 115 (191)
T ss_pred cc------------------cccchhhhh-----------------------hhhhccc---ccccccCccc-cCCHHHH
Confidence 00 000000000 0000000 0000011111 2467777
Q ss_pred HHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449 456 VMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD 527 (534)
Q Consensus 456 v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~ 527 (534)
+...+....|..+|..|||++|+||.|+| .+++|++|||+.||+|.++|++.++||+++||+++....
T Consensus 116 ~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 183 (191)
T PRK12520 116 LSRREFFEVLQACVDRLPPRTGRVFMMRE----WLELETEEICQELQITATNAWVLLYRARMRLRECLDLHW 183 (191)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 77777788899999999999999999999 899999999999999999999999999999999988765
No 73
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=99.85 E-value=6.6e-20 Score=183.60 Aligned_cols=184 Identities=16% Similarity=0.177 Sum_probs=145.8
Q ss_pred cCCCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHH-------hhhccCCcCCCchhh
Q 009449 279 AGVSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQ-------GAERFDHTRGYKFST 350 (534)
Q Consensus 279 ~g~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~r-------A~ekFDp~kG~rFST 350 (534)
.+.++..|...++.| ..|++.|+..|.+.|+.++.++.++..+++|++||+|+.+|. .+.+|++. ..|.|
T Consensus 22 ~~~~d~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~--~~~~t 99 (244)
T TIGR03001 22 LHAADLYLACACAQGEPAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGR--GPLLS 99 (244)
T ss_pred ccccHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCC--CchHh
Confidence 445677888888888 679999999999999999999999999999999999999994 78889864 37999
Q ss_pred HHHHHHHHHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhccccc
Q 009449 351 YVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQ 430 (534)
Q Consensus 351 YA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~ 430 (534)
|++.+++|.++++++++.+...+. .
T Consensus 100 WL~~Ia~N~~id~lRk~~r~~~~~-------------------------------------------------------~ 124 (244)
T TIGR03001 100 WVRIVATRIALELQAQERRHSPVE-------------------------------------------------------E 124 (244)
T ss_pred HHHHHHHHHHHHHHHHhcccCccc-------------------------------------------------------c
Confidence 999999999999998754211000 0
Q ss_pred ccccchhhhhhhccCCCCCCChHHHHHH----HHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHH
Q 009449 431 KIGDCLNAKYLEFAPDRSVKSPKEIVMR----QHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKE 506 (534)
Q Consensus 431 ~i~~~~~~~l~e~i~d~~~~spee~v~~----~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISre 506 (534)
+. ...+ ..+. ..+|++.+.. .+..+.|..+|+.||+++|+||.|+| .+++|++|||++||||.+
T Consensus 125 ----~~--~~~~-~~~~-~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~----~eg~S~~EIA~~Lgis~~ 192 (244)
T TIGR03001 125 ----PT--ELAA-LPAP-GSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHF----VDGLSMDRIGAMYQVHRS 192 (244)
T ss_pred ----cc--cccc-ccCC-CCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHH
Confidence 00 0000 0011 1244544433 23567799999999999999999999 999999999999999999
Q ss_pred HHHHHHHHHHHHHHhHhhhhcchhh
Q 009449 507 WIRKLEKKAMTKLRDSETCRDLSHF 531 (534)
Q Consensus 507 rVRqi~~RAL~KLR~~l~~~~L~~y 531 (534)
+|+..++||+++||+.+.......|
T Consensus 193 TVk~rl~RAr~~Lr~~l~~~~~~~~ 217 (244)
T TIGR03001 193 TVSRWVAQARERLLERTRRRLAERL 217 (244)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999887665443
No 74
>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=8e-20 Score=164.16 Aligned_cols=157 Identities=31% Similarity=0.382 Sum_probs=133.2
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccccc
Q 009449 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC 375 (534)
Q Consensus 296 A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~ 375 (534)
|++.++..|.++|+++++++.+++.+.+|++|||++++|++++.|++. ..|.+|+++++++.+.++++++.+ .+.
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 589999999999999999998764 111
Q ss_pred chHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHH
Q 009449 376 KLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEI 455 (534)
Q Consensus 376 ~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~ 455 (534)
.. ... ... ....+.|++.
T Consensus 77 ~~---------------------------------------------------~~~----------~~~-~~~~~~~~~~ 94 (158)
T TIGR02937 77 EL---------------------------------------------------DLL----------EEL-LDSDPSPEEE 94 (158)
T ss_pred ch---------------------------------------------------hhh----------hhc-ccccCCHHHH
Confidence 00 000 000 0112356677
Q ss_pred HHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449 456 VMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE 523 (534)
Q Consensus 456 v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l 523 (534)
.........|..+++.||+.++.||.++| ..|+|..|||+.+|+|+.+|+++..+|+++||+.+
T Consensus 95 ~~~~~~~~~l~~~l~~L~~~~~~ii~~~~----~~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~l 158 (158)
T TIGR02937 95 LEQEEEREALREALEKLPEREREVLVLRY----LEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158 (158)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 77777888899999999999999999998 78999999999999999999999999999999753
No 75
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=99.85 E-value=5.2e-20 Score=174.84 Aligned_cols=164 Identities=17% Similarity=0.120 Sum_probs=135.8
Q ss_pred cHHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccc
Q 009449 293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK 372 (534)
Q Consensus 293 G~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iR 372 (534)
...|+++++..|.+.|+.+|.++.++..+++|++||+++.+|++..+|++. ..|.+|++..+++.+.+++++..+...
T Consensus 14 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~--~~~~awl~~ia~n~~~d~~Rk~~~~~~ 91 (179)
T PRK09415 14 KEDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGK--SSLKTWLYRIAINHCKDYLKSWHNKKV 91 (179)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--cccHHHHHHHHHHHHHHHHHhhccccc
Confidence 367999999999999999999999999999999999999999999999874 369999999999999999987532110
Q ss_pred cccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCCh
Q 009449 373 IPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSP 452 (534)
Q Consensus 373 lP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~sp 452 (534)
.+ .+. .+... . ...++|
T Consensus 92 ~~-----------------------------------------------------~~~--------~~~~~-~-~~~~~~ 108 (179)
T PRK09415 92 IV-----------------------------------------------------TED--------IFTYM-E-SQKESV 108 (179)
T ss_pred cc-----------------------------------------------------ccc--------ccccc-c-ccccCc
Confidence 00 000 00000 0 111356
Q ss_pred HHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449 453 KEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC 525 (534)
Q Consensus 453 ee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~ 525 (534)
++.+...+....+..+|..||+++|+||.|+| ++|+|++|||+.||||.++|++++.||+++||..+..
T Consensus 109 e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l~~ 177 (179)
T PRK09415 109 EEEVIQNAEDERLASAVMSLPIKYREVIYLFY----YEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEE 177 (179)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 67777777788899999999999999999999 8999999999999999999999999999999987753
No 76
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=99.85 E-value=5.5e-20 Score=172.87 Aligned_cols=163 Identities=18% Similarity=0.086 Sum_probs=130.9
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI 373 (534)
Q Consensus 294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl 373 (534)
..|++.|+..|.+.|+++|.++.++..+++|++||.|+.+|+..++|++.. ..|.+|++..++|.+.++++++.+....
T Consensus 8 ~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~Rk~~~~~~~ 86 (173)
T PRK09645 8 AALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSARARPVE 86 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHHHHHHHhhcccccc
Confidence 579999999999999999999999989999999999999999999997532 3799999999999999999876421100
Q ss_pred ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChH
Q 009449 374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPK 453 (534)
Q Consensus 374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spe 453 (534)
..+.. .+ .++. .++
T Consensus 87 -----------------------------------------------------~~~~~---------~~-~~~~---~~~ 100 (173)
T PRK09645 87 -----------------------------------------------------GGDDV---------LG-VPEQ---SAP 100 (173)
T ss_pred -----------------------------------------------------ccccc---------cc-CCCC---CCc
Confidence 00000 00 0011 122
Q ss_pred HHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449 454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD 527 (534)
Q Consensus 454 e~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~ 527 (534)
+.+........|..+|+.|||++|+||.|+| ++++|++|||+.||+|.++|+..++||+++||+.+...+
T Consensus 101 ~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~----~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~ 170 (173)
T PRK09645 101 DEVDRALDRLLVADALAQLSPEHRAVLVRSY----YRGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQERG 170 (173)
T ss_pred hHHHHHhHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhccc
Confidence 2333334455789999999999999999999 899999999999999999999999999999999887544
No 77
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=99.84 E-value=4.3e-20 Score=170.67 Aligned_cols=158 Identities=20% Similarity=0.197 Sum_probs=126.6
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccccc
Q 009449 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC 375 (534)
Q Consensus 296 A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~ 375 (534)
|++.++..|.+.|+.+|+++.++..++||++||+++.+|++.++||+.. .|.+|++..++|.++++++++.+... +.
T Consensus 2 ~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~-~~ 78 (159)
T TIGR02989 2 AFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRL-VF 78 (159)
T ss_pred HHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhccccc-cc
Confidence 7899999999999999999999999999999999999999999999764 69999999999999999998753210 00
Q ss_pred chHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHH
Q 009449 376 KLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEI 455 (534)
Q Consensus 376 ~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~ 455 (534)
. ++. .+.+.+. .+|.+.
T Consensus 79 ~-------------------------~~~------------------------------------~~~~~~~--~~~~~~ 95 (159)
T TIGR02989 79 D-------------------------DEL------------------------------------LEALAAE--AEATEA 95 (159)
T ss_pred C-------------------------HHH------------------------------------HHHHHhh--cccchH
Confidence 0 000 0000000 011122
Q ss_pred HHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449 456 VMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE 523 (534)
Q Consensus 456 v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l 523 (534)
.........+..+++.||+++++||.++| .+|+|.+|||+.||||.++|+..++||+++||+++
T Consensus 96 ~~~~~~~~~l~~~i~~L~~~~r~v~~l~~----~~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~~~ 159 (159)
T TIGR02989 96 DRSEDELQALEGCLEKLPERQRELLQLRY----QRGVSLTALAEQLGRTVNAVYKALSRLRVRLRDCV 159 (159)
T ss_pred hhHHHHHHHHHHHHHHCCHHHHHHHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcC
Confidence 22334456789999999999999999999 89999999999999999999999999999999753
No 78
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=1.4e-19 Score=172.43 Aligned_cols=169 Identities=13% Similarity=0.075 Sum_probs=133.3
Q ss_pred HHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHH----HhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHH
Q 009449 283 ERVLKQHLAFG-WYCREELIKSTRPLVLFLAR----NYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIR 357 (534)
Q Consensus 283 ~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIAr----rY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR 357 (534)
...|...+..| ..|++.|+..|.+.|+.+|+ +|.++..+++|++||+++.+|++...|++.. .|.+|++..++
T Consensus 8 ~~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~~ 85 (184)
T PRK12539 8 LKALMLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIAR 85 (184)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHHH
Confidence 45666777777 78999999999999999987 4557889999999999999999999999754 69999999999
Q ss_pred HHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchh
Q 009449 358 KSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLN 437 (534)
Q Consensus 358 ~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~ 437 (534)
|.+.+++++..+.. .+. +.+. .
T Consensus 86 n~~~d~~R~~~~~~-~~~---------------------------------------------------~~~~----~-- 107 (184)
T PRK12539 86 YKLIDHLRRTRASL-ADV---------------------------------------------------PIDD----A-- 107 (184)
T ss_pred HHHHHHHHHHhccc-ccc---------------------------------------------------Chhh----h--
Confidence 99999998754210 000 0000 0
Q ss_pred hhhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449 438 AKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMT 517 (534)
Q Consensus 438 ~~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~ 517 (534)
. . .. +.+.....+..+.+..++..||+++|+|+.|+| .+|+|++|||+.||+|..+|++.++||++
T Consensus 108 ~---~-~~------~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~ra~~ 173 (184)
T PRK12539 108 D---E-LV------AHDDHAAVESTLDLGRLLARLPEKMRLAIQAVK----LEGLSVAEAATRSGMSESAVKVSVHRGLK 173 (184)
T ss_pred c---c-cc------CCcHHhhHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 0 0 00 001111223445789999999999999999999 89999999999999999999999999999
Q ss_pred HHHhHhhh
Q 009449 518 KLRDSETC 525 (534)
Q Consensus 518 KLR~~l~~ 525 (534)
+||+.+..
T Consensus 174 ~Lr~~l~~ 181 (184)
T PRK12539 174 ALAALIGR 181 (184)
T ss_pred HHHHHHhh
Confidence 99998754
No 79
>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=99.84 E-value=1.5e-19 Score=171.13 Aligned_cols=172 Identities=19% Similarity=0.164 Sum_probs=128.5
Q ss_pred HHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCC-----CHHHHHHHHHHHHHH-hhhccCCcCCCchhhHHHHH
Q 009449 283 ERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGI-----PFSDLLQAGNVGVLQ-GAERFDHTRGYKFSTYVQYW 355 (534)
Q Consensus 283 ~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~-----~~eDLiQEG~lgL~r-A~ekFDp~kG~rFSTYA~~w 355 (534)
...|...+..| ..|++.|+..|.+.|+.+|++|.++.. +++|++||+|+.+|+ ...+|++. ..|.+|++.+
T Consensus 4 ~~~li~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~i 81 (183)
T TIGR02999 4 VTELLQQWQNGDAAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAKA 81 (183)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHHH
Confidence 34566777777 679999999999999999999999877 899999999999998 78889764 3699999999
Q ss_pred HHHHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccc
Q 009449 356 IRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDC 435 (534)
Q Consensus 356 IR~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~ 435 (534)
++|.+.++++++.+..+.... ....++
T Consensus 82 ~~n~~~d~~R~~~~~~~~~~~-----------------------------------------------~~~~~~------ 108 (183)
T TIGR02999 82 MRRILVDHARRRRAQKRGGGA-----------------------------------------------VRVPLD------ 108 (183)
T ss_pred HHHHHHHHHHHHHHHhccCCc-----------------------------------------------cccccc------
Confidence 999999999875321000000 000000
Q ss_pred hhhhhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009449 436 LNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKA 515 (534)
Q Consensus 436 ~~~~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RA 515 (534)
+..++. .++.. ......+.+...|+.|||++|+||.|+| ++|+|++|||+.||+|.++|+..++||
T Consensus 109 ------~~~~~~---~~~~~-~~~~~l~~~~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tVk~~l~Ra 174 (183)
T TIGR02999 109 ------EVLPDA---EADLD-EELLDLDDALDKLAQVDPRQAEVVELRF----FAGLTVEEIAELLGVSVRTVERDWRFA 174 (183)
T ss_pred ------cccCCC---CccHH-HHHHHHHHHHHHhhcCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 000011 11111 1111123344556779999999999999 899999999999999999999999999
Q ss_pred HHHHHhHh
Q 009449 516 MTKLRDSE 523 (534)
Q Consensus 516 L~KLR~~l 523 (534)
+++||+.+
T Consensus 175 r~~Lr~~l 182 (183)
T TIGR02999 175 RAWLADEL 182 (183)
T ss_pred HHHHHHHh
Confidence 99999875
No 80
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=99.84 E-value=1.3e-19 Score=173.29 Aligned_cols=171 Identities=18% Similarity=0.098 Sum_probs=132.5
Q ss_pred HHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHH
Q 009449 284 RVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK 362 (534)
Q Consensus 284 ~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~ 362 (534)
..|...+..| ..|++.|+..|.+.|+.+++ +.++..+++|++||+|+.+|+..++|++. ..|.+|++.+++|.+.+
T Consensus 12 ~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~~~d 88 (185)
T PRK09649 12 TALALSAAKGNGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVAD 88 (185)
T ss_pred HHHHHHHHccCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHHHHH
Confidence 4566667777 77999999999999999995 68888999999999999999999999864 37999999999999999
Q ss_pred HHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhh
Q 009449 363 MVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLE 442 (534)
Q Consensus 363 ~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e 442 (534)
++++..+..+... +. .. +
T Consensus 89 ~~Rk~~~~~~~~~-----------------------------------------------------~~----~~-----~ 106 (185)
T PRK09649 89 HIRHVRSRPRTTR-----------------------------------------------------GA----RP-----E 106 (185)
T ss_pred HHHHhcccccccc-----------------------------------------------------cc----ch-----h
Confidence 9987542110000 00 00 0
Q ss_pred ccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 443 FAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 443 ~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
...+. +......+....|..+|..|||++|+||.|+| ++++|++|||+.||+|.++|++.++||+++||+.
T Consensus 107 ~~~~~-----~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 177 (185)
T PRK09649 107 HLIDG-----DRHARGFEDLVEVTTMIADLTTDQREALLLTQ----LLGLSYADAAAVCGCPVGTIRSRVARARDALLAD 177 (185)
T ss_pred hccCh-----hhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 00000 00011112234588899999999999999999 9999999999999999999999999999999997
Q ss_pred hhhhcc
Q 009449 523 ETCRDL 528 (534)
Q Consensus 523 l~~~~L 528 (534)
+....|
T Consensus 178 ~~~~~~ 183 (185)
T PRK09649 178 AEPDDL 183 (185)
T ss_pred CCcccc
Confidence 665544
No 81
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=1.7e-19 Score=171.30 Aligned_cols=167 Identities=20% Similarity=0.210 Sum_probs=131.0
Q ss_pred HHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCC----CCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHH
Q 009449 285 VLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGL----GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (534)
Q Consensus 285 ~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~----g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~a 359 (534)
.+...+..| ..|++.|+..|.+.|+.+|+++.++ ..+++|++||+++.+|+..++|++. ..|.+|++..+|+.
T Consensus 11 ~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn~ 88 (184)
T PRK12512 11 DLMRSANAGDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARNK 88 (184)
T ss_pred HHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHHH
Confidence 345555655 7899999999999999999998753 4699999999999999999999874 37999999999999
Q ss_pred HHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhh
Q 009449 360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAK 439 (534)
Q Consensus 360 I~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~ 439 (534)
+.++++++.+....+ ++.
T Consensus 89 ~~d~~Rr~~~~~~~~-----------------------------------------------------~~~--------- 106 (184)
T PRK12512 89 LIDALRRRGRRVFVD-----------------------------------------------------IDD--------- 106 (184)
T ss_pred HHHHHHhhcccccCC-----------------------------------------------------chh---------
Confidence 999998764311110 000
Q ss_pred hhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449 440 YLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL 519 (534)
Q Consensus 440 l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL 519 (534)
+.+.+++.. +.+ ....+.+..+|+.||+++++||.++| .+++|++|||+.||+|..+|+..++||+++|
T Consensus 107 ~~~~~~~~~---~~~----~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~l~is~~tV~~~l~ra~~~L 175 (184)
T PRK12512 107 FAETLPAEP---ATE----TLPAGDVGRHLETLPPRQRDVVQSIS----VEGASIKETAAKLSMSEGAVRVALHRGLAAL 175 (184)
T ss_pred ccccccccc---hhh----HHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 000011110 011 12234678899999999999999999 8999999999999999999999999999999
Q ss_pred HhHhhhh
Q 009449 520 RDSETCR 526 (534)
Q Consensus 520 R~~l~~~ 526 (534)
|..+...
T Consensus 176 r~~l~~~ 182 (184)
T PRK12512 176 AAKFRSE 182 (184)
T ss_pred HHHhhcC
Confidence 9988754
No 82
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=1.9e-19 Score=177.12 Aligned_cols=171 Identities=18% Similarity=0.126 Sum_probs=137.9
Q ss_pred cHHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccc
Q 009449 293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK 372 (534)
Q Consensus 293 G~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iR 372 (534)
...++..|+..|.+.++.++.++.++..+++|++||+|+.+|+..++|++. .|.+|++.+++|.++++++++.+...
T Consensus 16 ~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~~~~~~ 92 (216)
T PRK12533 16 RGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRRANAHE 92 (216)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhhccccc
Confidence 356999999999999999999999999999999999999999999999853 49999999999999999987643110
Q ss_pred cccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCCh
Q 009449 373 IPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSP 452 (534)
Q Consensus 373 lP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~sp 452 (534)
.... + .++ .+ ... +.. ++...+|
T Consensus 93 ~~~~-------------------------~------------------------~~~----~~--~~~-~~~-~~~~~~~ 115 (216)
T PRK12533 93 VAAP-------------------------D------------------------TLD----DA--DSL-DDW-QPAGEDP 115 (216)
T ss_pred cccc-------------------------c------------------------ccc----cc--ccc-ccc-ccCCCCH
Confidence 0000 0 000 00 000 000 1112467
Q ss_pred HHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449 453 KEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD 527 (534)
Q Consensus 453 ee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~ 527 (534)
++.+...+....|..+|..||+++|+||.|+| .+++|++|||+.||||.++|+++++||+++||+.+....
T Consensus 116 e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y----~eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~~ 186 (216)
T PRK12533 116 LALLLRAEDVRLVNAALAKLPVEYREVLVLRE----LEDMSYREIAAIADVPVGTVMSRLARARRRLAALLGGAS 186 (216)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccc
Confidence 78888888888999999999999999999999 899999999999999999999999999999999886543
No 83
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=99.83 E-value=1e-19 Score=172.95 Aligned_cols=169 Identities=16% Similarity=0.151 Sum_probs=131.7
Q ss_pred HHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhC-CCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHH
Q 009449 284 RVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRG-LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (534)
Q Consensus 284 ~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~-~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~ 361 (534)
..++.....| ..|++.++..|.+.|+.++.++.+ ...+++|++||+++.+|+..+.|++. ..|.+|++..++|.++
T Consensus 9 ~~~~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~~~ 86 (181)
T PRK12536 9 RALLLRGLAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYKLM 86 (181)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHHHH
Confidence 3455555555 789999999999999999998764 57899999999999999999999975 3699999999999999
Q ss_pred HHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhh
Q 009449 362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYL 441 (534)
Q Consensus 362 ~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~ 441 (534)
+++++..+.... + .+++. . .
T Consensus 87 d~~Rk~~~~~~~--~-------------------------------------------------~~~~~----~-----~ 106 (181)
T PRK12536 87 DFLRSRARREAL--H-------------------------------------------------DPLDD----E-----S 106 (181)
T ss_pred HHHHHHhccccc--c-------------------------------------------------CCccc----h-----h
Confidence 999986431100 0 00000 0 0
Q ss_pred hccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 442 EFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 442 e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
+...+.. ..+ .+....+..+|..||++++.||.++| .+++|++|||+.||+|+++|+..+++|+++||+
T Consensus 107 ~~~~~~~-~~~------~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 107 ELFATSD-DEA------AEARRDLGKLLEQLPDRQRLPIVHVK----LEGLSVAETAQLTGLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred hhcCCCC-cch------HHHHHHHHHHHHHCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 0001111 111 13345689999999999999999999 899999999999999999999999999999999
Q ss_pred Hhhh
Q 009449 522 SETC 525 (534)
Q Consensus 522 ~l~~ 525 (534)
.+..
T Consensus 176 ~l~~ 179 (181)
T PRK12536 176 KIRG 179 (181)
T ss_pred HhcC
Confidence 8764
No 84
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=99.83 E-value=2.6e-19 Score=170.44 Aligned_cols=170 Identities=22% Similarity=0.247 Sum_probs=136.7
Q ss_pred HHHhcHHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhc
Q 009449 289 HLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA 368 (534)
Q Consensus 289 ~l~~G~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~s 368 (534)
.......++..++..+.+.++.+|+++.++..+++||+||+|+.+|+++..| +. +..|.||++.+++|.+++.+++..
T Consensus 9 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~~R~~~ 86 (182)
T COG1595 9 ALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDRLRKRK 86 (182)
T ss_pred HHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHHHHHHhc
Confidence 3444578999999999999999999999998899999999999999999999 33 348999999999999999999876
Q ss_pred cccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCC
Q 009449 369 RGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRS 448 (534)
Q Consensus 369 r~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~ 448 (534)
+....... .+ ......++.
T Consensus 87 r~~~~~~~---------------------------------------------------~~----------~~~~~~~~~ 105 (182)
T COG1595 87 RRRARVEE---------------------------------------------------AD----------LLPEEADPA 105 (182)
T ss_pred cccccccc---------------------------------------------------cc----------ccccccCcc
Confidence 43221000 00 000001111
Q ss_pred CCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhh
Q 009449 449 VKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCR 526 (534)
Q Consensus 449 ~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~ 526 (534)
.+.+ +.+...+....|..+|..||+++|+||.|+| .+|+|++|||+.||||.+||+..+++|+.+||..+...
T Consensus 106 ~~~~-~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~----~~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~~~ 178 (182)
T COG1595 106 PDLA-ELLLAEEELERLRRALARLPPRQREAFLLRY----LEGLSYEEIAEILGISVGTVKSRLHRARKKLREQLEEA 178 (182)
T ss_pred cccc-hHHHHHHHHHHHHHHHHhCCHHHhHHhhhHh----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence 0111 2456667778899999999999999999999 99999999999999999999999999999999987654
No 85
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=99.83 E-value=2.4e-19 Score=170.26 Aligned_cols=164 Identities=10% Similarity=0.034 Sum_probs=131.2
Q ss_pred cHHHHHHHHHHhHHHHHHHHHHhhC--CCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccc
Q 009449 293 GWYCREELIKSTRPLVLFLARNYRG--LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG 370 (534)
Q Consensus 293 G~~A~e~LI~~nlrLV~sIArrY~~--~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~ 370 (534)
+..|++.|+..|.+.|+.++.++.+ +..+++|++||+|+.+|+..++|++.....|.||++..++|.+.++++++.+.
T Consensus 11 d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~Rk~~~~ 90 (178)
T PRK12529 11 DRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRRRQSLE 90 (178)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3679999999999999998766665 46789999999999999999999854445799999999999999998765310
Q ss_pred cccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCC
Q 009449 371 IKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVK 450 (534)
Q Consensus 371 iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~ 450 (534)
+. ..+. ..+ ..+...+
T Consensus 91 ---~~---------------------------------------------------~~~~---------~~~-~~~~~~~ 106 (178)
T PRK12529 91 ---LA---------------------------------------------------WLEA---------LAT-LPEPLHP 106 (178)
T ss_pred ---hh---------------------------------------------------hhhH---------hhh-ccCcCCC
Confidence 00 0000 000 0111123
Q ss_pred ChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449 451 SPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET 524 (534)
Q Consensus 451 spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~ 524 (534)
+|++.+...+....|..+|..|||++|+||.|+| .+|+|++|||+.||+|.++|+..+++|+.++++.+.
T Consensus 107 ~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~~~ 176 (178)
T PRK12529 107 SPEQQSVILETLHEIDALLDTLRPRVKQAFLMAT----LDGMKQKDIAQALDIALPTVKKYIHQAYVTCLSLMP 176 (178)
T ss_pred CHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhCC
Confidence 6677666667777899999999999999999999 899999999999999999999999999999998743
No 86
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=99.83 E-value=1.7e-19 Score=169.63 Aligned_cols=168 Identities=20% Similarity=0.197 Sum_probs=130.0
Q ss_pred HHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHh
Q 009449 289 HLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH 367 (534)
Q Consensus 289 ~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~ 367 (534)
.++.| ..|++.++..|.+.|+.+++++.+ ..+++|++||+|+.+|+..++|++. ..|.+|++..+++.+.+++++.
T Consensus 4 ~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~ 80 (175)
T PRK12518 4 RCQRGDRQSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARRQF 80 (175)
T ss_pred HHHcCCHHHHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHHHh
Confidence 34455 779999999999999999999875 4789999999999999999999974 4799999999999999999865
Q ss_pred ccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCC
Q 009449 368 ARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDR 447 (534)
Q Consensus 368 sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~ 447 (534)
.+. +.. .+... .. +. +..
T Consensus 81 ~~~---~~~---------------------------------------------------~~~~~-~~------~~-~~~ 98 (175)
T PRK12518 81 AQR---PSR---------------------------------------------------IQDDS-LN------DQ-PSR 98 (175)
T ss_pred hcc---ccc---------------------------------------------------hhccc-cc------cc-ccC
Confidence 321 000 00000 00 00 000
Q ss_pred CCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449 448 SVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD 527 (534)
Q Consensus 448 ~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~ 527 (534)
....| .....+....+..+|+.||+++|+||.|+| ++|+|++|||+.||+|..+|++.++||+++||..+...+
T Consensus 99 ~~~~~--~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~~~~ 172 (175)
T PRK12518 99 PSDTP--DLMQLHYQDLVQQGLQTLSLEHRAVLVLHD----LEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQQG 172 (175)
T ss_pred CCCcH--HHHHHHHHHHHHHHHHhCCHHHeeeeeehH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 00122 222233445688999999999999999999 899999999999999999999999999999999987644
No 87
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=99.83 E-value=1.7e-19 Score=167.48 Aligned_cols=156 Identities=13% Similarity=0.078 Sum_probs=127.2
Q ss_pred HHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHHH
Q 009449 302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREI 381 (534)
Q Consensus 302 ~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i 381 (534)
+.|.+.|+.+|.++.++..+++|++||+|+.+|++.++|++. .|.+|++..++|.+.++++++.+.....
T Consensus 2 ~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n~~~d~~Rk~~~~~~~~------- 71 (160)
T PRK09642 2 QTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATNHAIDYKRKKARENEEL------- 71 (160)
T ss_pred chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHHHHHHHHHHhccccccc-------
Confidence 578999999999999999999999999999999999999863 4999999999999999998764211000
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHHHH
Q 009449 382 SKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHM 461 (534)
Q Consensus 382 ~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~el 461 (534)
.+. .+. .+... ..++|++.+...+.
T Consensus 72 ---------------------------------------------~~~----~~~----~~~~~--~~~~~~~~~~~~e~ 96 (160)
T PRK09642 72 ---------------------------------------------SLC----KET----EENIK--SSHNIEDLLLTKEQ 96 (160)
T ss_pred ---------------------------------------------ccc----hhh----hhhcc--CCCChHHHHHHHHH
Confidence 000 000 00000 11256666777777
Q ss_pred HHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhh
Q 009449 462 KKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCR 526 (534)
Q Consensus 462 ~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~ 526 (534)
...|..+|+.|||++|+||.|+| .+|+|++|||+.||+|.++|+++++||+++||+.+...
T Consensus 97 ~~~l~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 157 (160)
T PRK09642 97 KLLIAQKLRELPENYRDVVLAHY----LEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKEE 157 (160)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhh
Confidence 78899999999999999999999 89999999999999999999999999999999988654
No 88
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=99.83 E-value=2.1e-19 Score=169.26 Aligned_cols=163 Identities=17% Similarity=0.097 Sum_probs=129.8
Q ss_pred hc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccc
Q 009449 292 FG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG 370 (534)
Q Consensus 292 ~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~ 370 (534)
.| ..|+..++..|.+.|+.+|.++.++..+++|++||+|+.+|+. ..|+.. ..|.+|++.+++|.+.++++++.+.
T Consensus 6 ~~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~~~ 82 (172)
T PRK12523 6 SPHSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAALE 82 (172)
T ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45 6799999999999999999999999999999999999999987 446543 3699999999999999999876420
Q ss_pred cccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCC
Q 009449 371 IKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVK 450 (534)
Q Consensus 371 iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~ 450 (534)
. ... +++ + . .......
T Consensus 83 ~------------------~~~---------~~~------------------------~------------~-~~~~~~~ 98 (172)
T PRK12523 83 Q------------------AYL---------AEL------------------------A------------L-VPEAEQP 98 (172)
T ss_pred H------------------HHH---------HHH------------------------h------------h-cccccCC
Confidence 0 000 000 0 0 0001112
Q ss_pred ChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449 451 SPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC 525 (534)
Q Consensus 451 spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~ 525 (534)
+|++.....+....+..+|..||+++|+||.|+| .+|+|++|||+.||+|.++|++.+++|+++||..+..
T Consensus 99 ~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~----~~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l~~ 169 (172)
T PRK12523 99 SPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNR----LDGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIALYG 169 (172)
T ss_pred ChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 4555555555556899999999999999999999 8999999999999999999999999999999987653
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=1.8e-19 Score=172.87 Aligned_cols=172 Identities=12% Similarity=0.042 Sum_probs=132.6
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI 373 (534)
Q Consensus 294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl 373 (534)
..+|+.|+..|.+.|+.+|.++.++..+++|++||+|+.+|++..+|++. ..|.+|++..++|.+.++++++.+....
T Consensus 10 ~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~~~~~~~ 87 (193)
T TIGR02947 10 AQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKAQRRPQQ 87 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHhcCCccc
Confidence 56999999999999999999999999999999999999999999999864 3699999999999999999876431100
Q ss_pred ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChH
Q 009449 374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPK 453 (534)
Q Consensus 374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spe 453 (534)
.. .+++.. . .+.. . .....+....++
T Consensus 88 ~~-------------------------~~~~~~-----------~--------~~~~----~------~~~~~~~~~~~e 113 (193)
T TIGR02947 88 SD-------------------------DDDIED-----------W--------QLAK----A------ASHTSNGLRSAE 113 (193)
T ss_pred cc-------------------------chhhhh-----------h--------hhcc----c------cccccccccchh
Confidence 00 000000 0 0000 0 000001112344
Q ss_pred HHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449 454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC 525 (534)
Q Consensus 454 e~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~ 525 (534)
......+....|..+|..||+++|+||.|+| .+++|++|||+.||+|.++|+.+++||+++||+.+..
T Consensus 114 ~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 181 (193)
T TIGR02947 114 LEALDGLPDQDIKDALQGLPEEFRQAVYLAD----VEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVD 181 (193)
T ss_pred HHHHhhhhHHHHHHHHHhCCHHHhhheeehh----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4444445566899999999999999999999 8999999999999999999999999999999998864
No 90
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=99.82 E-value=3.1e-19 Score=166.89 Aligned_cols=157 Identities=17% Similarity=0.110 Sum_probs=131.6
Q ss_pred HHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccc
Q 009449 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCK 376 (534)
Q Consensus 297 ~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~ 376 (534)
++.|+..|.+.|+.+|+++.++..+++|++||+++.+|+++++|++. .|.+|++..++|.+.+++++..+.....
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~~-- 77 (165)
T PRK09644 3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFVG-- 77 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhccccc--
Confidence 67899999999999999999999999999999999999999999863 5999999999999999998764311000
Q ss_pred hHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHH
Q 009449 377 LNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIV 456 (534)
Q Consensus 377 ~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v 456 (534)
.+++ +.+. ..+|++.+
T Consensus 78 ------------------------~~~~-------------------------------------~~~~---~~~~~~~~ 93 (165)
T PRK09644 78 ------------------------TDEI-------------------------------------EAIQ---AESTEEYV 93 (165)
T ss_pred ------------------------hhHH-------------------------------------hhhc---ccChHHHH
Confidence 0000 0000 12456666
Q ss_pred HHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhh
Q 009449 457 MRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCR 526 (534)
Q Consensus 457 ~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~ 526 (534)
...+....+..+|..||+++|+||.|+| .+++|++|||+.||+|.++|++.++||+++||+.+...
T Consensus 94 ~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~ 159 (165)
T PRK09644 94 VAKNSYEKLIQIIHTLPVIEAQAILLCD----VHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEE 159 (165)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHhHH----HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 6667778899999999999999999999 89999999999999999999999999999999988654
No 91
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=99.82 E-value=6e-19 Score=164.11 Aligned_cols=157 Identities=15% Similarity=0.108 Sum_probs=126.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccc
Q 009449 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (534)
Q Consensus 295 ~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP 374 (534)
.|+++|+..|.+.|+.+|.++.++..+++|++||+|+.+|+..+.|++. .|.+|++.+++|.+.+++++..+..
T Consensus 4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~--- 77 (161)
T PRK12528 4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQII---EPRAFLTTIAKRVLCNHYRRQDLER--- 77 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhcccccccc---CHHHHHHHHHHHHHHHHHHHHHHHH---
Confidence 5899999999999999999999999999999999999999998888652 6999999999999999998753100
Q ss_pred cchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHH
Q 009449 375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKE 454 (534)
Q Consensus 375 ~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee 454 (534)
. . .++ ++ + .++...+.+++
T Consensus 78 -~--------------~---------~~~------------------------~~------------~-~~~~~~~~~~~ 96 (161)
T PRK12528 78 -A--------------Y---------LEA------------------------LA------------Q-LPERVAPSEEE 96 (161)
T ss_pred -h--------------h---------HHH------------------------hh------------c-cccccCCCHHH
Confidence 0 0 000 00 0 00111123444
Q ss_pred HHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 455 IVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 455 ~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
.....+....|..+|..||+++|+||.|+| .+|+|++|||+.||+|.++|++.+++|+++||..
T Consensus 97 ~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~----~~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~ 160 (161)
T PRK12528 97 RAIILETLVELDQLLDGLPPLVKRAFLLAQ----VDGLGYGEIATELGISLATVKRYLNKAAMRCYFA 160 (161)
T ss_pred HHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhc
Confidence 444445556899999999999999999999 8999999999999999999999999999999964
No 92
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=99.82 E-value=3.5e-19 Score=171.01 Aligned_cols=160 Identities=14% Similarity=0.113 Sum_probs=128.6
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI 373 (534)
Q Consensus 294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl 373 (534)
..++..++..|.+.|+.+|.++.++..+++|++||+|+.+|+..++|++.. .|.+|++..++|.+.++++++.+..
T Consensus 9 ~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~~--~~~awL~~Ia~n~~~d~~R~~~~~~-- 84 (187)
T PRK12516 9 TPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGT--NMKAWLFTILRNEFYSQMRKRGREV-- 84 (187)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCcc--cHHHHHHHHHHHHHHHHHHhhcCCc--
Confidence 579999999999999999999999999999999999999999999998643 6999999999999999998764311
Q ss_pred ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChH
Q 009449 374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPK 453 (534)
Q Consensus 374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spe 453 (534)
.. .+.. +.+..... +...
T Consensus 85 -~~---------------------------------------------------~~~~--------~~~~~~~~--~~~~ 102 (187)
T PRK12516 85 -QD---------------------------------------------------TDGM--------FTEQLAVH--PSQY 102 (187)
T ss_pred -cc---------------------------------------------------cccc--------cccccCCC--cchh
Confidence 00 0000 00000000 0111
Q ss_pred HHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449 454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD 527 (534)
Q Consensus 454 e~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~ 527 (534)
.......|..+|..||+++|+||.|+| .+++|++|||+.||+|.++|+++++||+++||+.+....
T Consensus 103 ----~~~~~~~l~~~L~~Lp~~~r~i~~L~~----~~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~~~ 168 (187)
T PRK12516 103 ----GTLDLQDFRAALDQLPDDQREAIILVG----ASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQIEG 168 (187)
T ss_pred ----hHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence 112235689999999999999999999 899999999999999999999999999999999987654
No 93
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=99.81 E-value=7.3e-19 Score=168.65 Aligned_cols=178 Identities=14% Similarity=0.111 Sum_probs=135.0
Q ss_pred HHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchH
Q 009449 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN 378 (534)
Q Consensus 299 ~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~ 378 (534)
+.+..|.+.|+.+|+++.++..+++|++||+|+.+|+...+|++. .+|.+|++..++|.++++++++.+....+.-
T Consensus 6 ~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~~~-- 81 (188)
T TIGR02943 6 QELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVSDL-- 81 (188)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCcccc--
Confidence 568889999999999999999999999999999999999999875 3799999999999999999876542211100
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHH
Q 009449 379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMR 458 (534)
Q Consensus 379 ~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~ 458 (534)
...+.. ..++...... ..+.........++|++.+..
T Consensus 82 -----------------~~~~~~------------------------~~~~~~~~~~--~~~~~~~~~~~~~~~e~~~~~ 118 (188)
T TIGR02943 82 -----------------DDELDD------------------------EAFNALFTQN--GHWAQHGQPQHWNTPEKQLEN 118 (188)
T ss_pred -----------------cccccc------------------------chhhhhhccc--cchhccccccccCCHHHHHHH
Confidence 000000 0000000000 000000111122467777888
Q ss_pred HHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449 459 QHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD 527 (534)
Q Consensus 459 ~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~ 527 (534)
++....+..+|..||+++|+||.|+| .+++|++|||+.||+|.++|++++.||+++||+.+....
T Consensus 119 ~e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~~ 183 (188)
T TIGR02943 119 KEFWEVFEACLYHLPEQTARVFMMRE----VLGFESDEICQELEISTSNCHVLLYRARLSLRACLSINW 183 (188)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHH----HhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 88888899999999999999999999 899999999999999999999999999999999987554
No 94
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=8e-19 Score=168.59 Aligned_cols=181 Identities=17% Similarity=0.112 Sum_probs=134.6
Q ss_pred HHHHHHhHHHHHHHHHHhhCCCCC-HHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccc
Q 009449 298 EELIKSTRPLVLFLARNYRGLGIP-FSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCK 376 (534)
Q Consensus 298 e~LI~~nlrLV~sIArrY~~~g~~-~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~ 376 (534)
++.+..|.+.|+.+|+++.++..+ ++|++||+|+.+|++.++|++. ..|.+|++..++|.++++++++.+.......
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 356788999999999999999888 9999999999999999999864 3799999999999999999976532111000
Q ss_pred hHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHH
Q 009449 377 LNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIV 456 (534)
Q Consensus 377 ~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v 456 (534)
. .....++.. .+.. ..+ .....+..+ ....+|++.+
T Consensus 86 ~-------------------~~~~~~~~~--------------------~~~~---~~~-~~~~~~~~~-~~~~~~e~~~ 121 (195)
T PRK12532 86 L-------------------DDELLDEAF--------------------ESHF---SQN-GHWTPEGQP-QHWNTPEKSL 121 (195)
T ss_pred c-------------------cccccchhh--------------------hhhh---ccc-cccccccCc-cccCCHHHHH
Confidence 0 000000000 0000 000 000000001 1124678888
Q ss_pred HHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcc
Q 009449 457 MRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDL 528 (534)
Q Consensus 457 ~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L 528 (534)
...+....+..+|..||+++|+||.|+| .+++|++|||+.||+|..+|+++++||+++||+++....+
T Consensus 122 ~~~e~~~~l~~~l~~L~~~~r~i~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~ 189 (195)
T PRK12532 122 NNNEFQKILQSCLYNLPENTARVFTLKE----ILGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKWF 189 (195)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHhhhHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 7788888899999999999999999999 8999999999999999999999999999999999876654
No 95
>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=5.5e-19 Score=164.13 Aligned_cols=156 Identities=19% Similarity=0.203 Sum_probs=127.4
Q ss_pred cHHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccc
Q 009449 293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK 372 (534)
Q Consensus 293 G~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iR 372 (534)
+..|++.++..|.+.|+++|.++.++..+++|++||+|+.+|++.++|+. ...|.+|++..+++.+.+++++..+. .
T Consensus 4 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~~~d~~rk~~~~-~ 80 (162)
T TIGR02983 4 TEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNLARSRWRRRRLL-E 80 (162)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHHHHHHHHhhccc-c
Confidence 36799999999999999999999999999999999999999999999964 34899999999999999999866420 0
Q ss_pred cccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCCh
Q 009449 373 IPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSP 452 (534)
Q Consensus 373 lP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~sp 452 (534)
.+ +... ++.. +
T Consensus 81 ~~------------------------------------------------------~~~~------------~~~~---~ 91 (162)
T TIGR02983 81 LP------------------------------------------------------TREL------------PDAA---A 91 (162)
T ss_pred cc------------------------------------------------------cccc------------Cccc---C
Confidence 00 0000 0000 0
Q ss_pred HHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449 453 KEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET 524 (534)
Q Consensus 453 ee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~ 524 (534)
.+........+.|..++..||+++++||.|+| .+++|.+|||+.||+|.++|++++.||+++||+.+.
T Consensus 92 ~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 159 (162)
T TIGR02983 92 PDPAPDVALRAALARALRRLPARQRAVVVLRY----YEDLSEAQVAEALGISVGTVKSRLSRALARLRELLE 159 (162)
T ss_pred CccchhHHHHHHHHHHHHhCCHHHHHHhhhHH----HhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 01112334456789999999999999999999 899999999999999999999999999999998865
No 96
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=9.6e-19 Score=169.54 Aligned_cols=180 Identities=18% Similarity=0.195 Sum_probs=133.0
Q ss_pred HHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchH
Q 009449 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN 378 (534)
Q Consensus 299 ~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~ 378 (534)
.++..|.+.|+.+|++++++..+++|++||+|+.+|+..++|++.. .|.||++.+++|.+.++++++.+...++..
T Consensus 12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~-- 87 (201)
T PRK12545 12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQS--AHKTWVFGILRNKLIDTLRARQRTVNLSAL-- 87 (201)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhccccc--hHHHHHHHHHHHHHHHHHHhhccccccccc--
Confidence 4488999999999999999999999999999999999999999753 699999999999999999987532111100
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhh-hhccCCCCCCChHHHHH
Q 009449 379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKY-LEFAPDRSVKSPKEIVM 457 (534)
Q Consensus 379 ~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l-~e~i~d~~~~spee~v~ 457 (534)
.+++.. ...++...... ...+ .+..++ ...+|++...
T Consensus 88 ----------------------~~~~~~------------------~~~~~~~~~~~-~~~~~~~~~~~-~~~~~~~~~~ 125 (201)
T PRK12545 88 ----------------------DAELDG------------------EALLDRELFKD-NGHWAAHAKPR-PWPKPETILQ 125 (201)
T ss_pred ----------------------ccccch------------------hhhhhhhhhcc-cccccccccCc-CCCCHHHHHH
Confidence 000000 00000000000 0000 000111 1235666666
Q ss_pred HHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcc
Q 009449 458 RQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDL 528 (534)
Q Consensus 458 ~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L 528 (534)
..+....+..+|..|||++|+||.|+| ++++|++|||+.||+|.++|++.++||+++||+.+...++
T Consensus 126 ~~~~~~~l~~~L~~Lp~~~r~v~~L~~----~eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~~ 192 (201)
T PRK12545 126 QQQFWTLFETCLDHLPEQIGRVFMMRE----FLDFEIDDICTELTLTANHCSVLLYRARTRLRTCLSEKGL 192 (201)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 666667899999999999999999999 8999999999999999999999999999999999876554
No 97
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=1e-18 Score=163.63 Aligned_cols=158 Identities=13% Similarity=0.107 Sum_probs=126.3
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI 373 (534)
Q Consensus 294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl 373 (534)
...+.+++..|.+.|+.+|+++.++..+++|++||+++.+|+..++|++.. .|.+|++..++|.+.+.+++..+..
T Consensus 5 ~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~~-- 80 (164)
T PRK12547 5 SKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGT--NLKAWLFTILRNEFYSQMRKRGREV-- 80 (164)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhcccc--
Confidence 357899999999999999999999999999999999999999999998643 6999999999999999998764210
Q ss_pred ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChH
Q 009449 374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPK 453 (534)
Q Consensus 374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spe 453 (534)
.. .+...... .+ .+++
T Consensus 81 -~~---------------------------------------------------~~~~~~~~---------~~---~~~~ 96 (164)
T PRK12547 81 -QD---------------------------------------------------SDGVFTAR---------VA---VHPA 96 (164)
T ss_pred -cc---------------------------------------------------cccccccc---------CC---CCch
Confidence 00 00000000 00 0111
Q ss_pred HHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449 454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC 525 (534)
Q Consensus 454 e~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~ 525 (534)
.. .....+.+..+|..|||++|+||.|+| .+|+|++|||+.||+|.++|++.++||+++||..+.-
T Consensus 97 ~~--~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 162 (164)
T PRK12547 97 QY--GSLDLQDFKKALNLLSADQREAIILIG----ASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLKV 162 (164)
T ss_pred hh--hHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 11 112245788999999999999999999 8999999999999999999999999999999998754
No 98
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=99.81 E-value=1.4e-18 Score=161.78 Aligned_cols=160 Identities=19% Similarity=0.138 Sum_probs=131.2
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI 373 (534)
Q Consensus 294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl 373 (534)
..|++.++..|.+.|+.+|+++.++..+++|++||+|+.+|++ .|+. +..|.+|++..+++.+.+++++..+..+.
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 3589999999999999999999999999999999999999999 6764 34799999999999999999876432111
Q ss_pred ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChH
Q 009449 374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPK 453 (534)
Q Consensus 374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spe 453 (534)
... . ....+. ....+|+
T Consensus 78 ~~~----------------------------------------------------------~--~~~~~~---~~~~~~e 94 (166)
T PRK09639 78 ILG----------------------------------------------------------E--FQWQEV---DNEPSPE 94 (166)
T ss_pred ccc----------------------------------------------------------h--hhhhhc---cCCCChH
Confidence 000 0 000000 1123677
Q ss_pred HHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449 454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC 525 (534)
Q Consensus 454 e~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~ 525 (534)
+.+...+....+..+|..||++++.||.++| +|+|++|||+.||+|..+|+..++||+++||..+..
T Consensus 95 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-----~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~~ 161 (166)
T PRK09639 95 EIWIRKEEITKVQEVLAKMTERDRTVLLLRF-----SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQ 161 (166)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 7777777778899999999999999999998 689999999999999999999999999999998764
No 99
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=1.2e-18 Score=167.20 Aligned_cols=175 Identities=17% Similarity=0.090 Sum_probs=132.2
Q ss_pred HHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchH
Q 009449 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN 378 (534)
Q Consensus 299 ~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~ 378 (534)
..|..|.+.|+.+|.+|.++..+++|++||+|+.+|+...+|++.. +|.+|++..++|.+.++++++.+..... ..
T Consensus 11 ~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~~--~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~-~~- 86 (189)
T PRK12530 11 LEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQS--ALKTWIFAILKNKIIDLIRYRKRFVNES-EL- 86 (189)
T ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCCc--cHHHHHHHHHHHHHHHHHHhhccCCCcc-cc-
Confidence 4578889999999999999999999999999999999999998753 6999999999999999999765321110 00
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHH
Q 009449 379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMR 458 (534)
Q Consensus 379 ~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~ 458 (534)
.++. .+.... +.......+........+|++.+..
T Consensus 87 ----------------------~~~~-------------------~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~ 121 (189)
T PRK12530 87 ----------------------IEED-------------------SPNSFF----DEKGHWKPEYYEPSEWQEVENTVYK 121 (189)
T ss_pred ----------------------cccc-------------------cchhhh----cccccccccccCCccccCHHHHHHH
Confidence 0000 000000 0000000000001112467777777
Q ss_pred HHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhh
Q 009449 459 QHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCR 526 (534)
Q Consensus 459 ~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~ 526 (534)
.+....+..+|+.||+++|+||.|+| .+++|++|||+.||+|.++|+++++||+++||+++...
T Consensus 122 ~~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~ 185 (189)
T PRK12530 122 EEFWLIFEACLNHLPAQQARVFMMRE----YLELSSEQICQECDISTSNLHVLLYRARLQLQACLSKN 185 (189)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHhHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 78888899999999999999999999 89999999999999999999999999999999988643
No 100
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=1.5e-18 Score=169.23 Aligned_cols=181 Identities=16% Similarity=0.182 Sum_probs=135.9
Q ss_pred HHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccc
Q 009449 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCK 376 (534)
Q Consensus 297 ~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~ 376 (534)
-..++..|.+.|+.+|+++.++..+++|++||+|+.+|+.+.+|++. .+|++|++.+++|.+++++++..+....+..
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 36789999999999999999999999999999999999999999864 3799999999999999999977542211100
Q ss_pred hHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHH
Q 009449 377 LNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIV 456 (534)
Q Consensus 377 ~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v 456 (534)
. ........+ +... +. ...+..........+|++.+
T Consensus 98 ~------------------~~~~~~~~~------------------------~~~~-~~-~~~~~~~~~~~~~~~~e~~~ 133 (206)
T PRK12544 98 L------------------RDEEEEEDF------------------------EELF-DE-SGHWQKDERPQAWGNPEESL 133 (206)
T ss_pred c------------------cccchhhHH------------------------HHhh-cc-cccccccccccccCCHHHHH
Confidence 0 000000000 0000 00 00000000011124677777
Q ss_pred HHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449 457 MRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD 527 (534)
Q Consensus 457 ~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~ 527 (534)
...+....+..+|..|||++|+||.|+| ++++|++|||+.||+|..+|++.++||+++||+.+....
T Consensus 134 ~~~e~~~~l~~~L~~L~~~~r~v~~L~~----~~g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~~ 200 (206)
T PRK12544 134 EQEQFWRIFEACLDGLPAKYARVFMMRE----FIELETNEICHAVDLSVSNLNVLLYRARLRLRECLENKW 200 (206)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 7777778899999999999999999999 899999999999999999999999999999999987543
No 101
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=99.81 E-value=1.8e-18 Score=168.34 Aligned_cols=164 Identities=23% Similarity=0.294 Sum_probs=136.5
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI 373 (534)
Q Consensus 294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl 373 (534)
..++++|+..|.+.++.++.+|.++..+++|++||+|+.+|++..+|++ + .|.+|++..+|+.+.+++++..+ .+.
T Consensus 27 ~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~~-~~~ 102 (203)
T PRK09647 27 MPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRAR-IRM 102 (203)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhccc-Ccc
Confidence 5799999999999999999999999999999999999999999999985 3 69999999999999999987642 110
Q ss_pred ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChH
Q 009449 374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPK 453 (534)
Q Consensus 374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spe 453 (534)
. .++. + + +... ...++|+
T Consensus 103 --~--------------------------------------------------~~~~----~----~-~~~~-~~~~~~~ 120 (203)
T PRK09647 103 --E--------------------------------------------------ALPE----D----Y-DRVP-GDEPNPE 120 (203)
T ss_pred --c--------------------------------------------------cccc----c----c-cccC-CCCCCHH
Confidence 0 0000 0 0 0011 1123566
Q ss_pred HHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449 454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD 527 (534)
Q Consensus 454 e~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~ 527 (534)
..+...++.+.|..+|..||+++++||.|+| .++++++|||+.||+|..+|++.++||+++||+.+...+
T Consensus 121 ~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~----~~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~~~ 190 (203)
T PRK09647 121 QIYHDARLDPDLQAALDSLPPEFRAAVVLCD----IEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAAHA 190 (203)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 6677777788899999999999999999999 899999999999999999999999999999999887543
No 102
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=1.9e-18 Score=160.83 Aligned_cols=156 Identities=13% Similarity=0.117 Sum_probs=124.6
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI 373 (534)
Q Consensus 294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl 373 (534)
..|+++++..|.+.|+.+|.++.++..+++|++||+++.+|+..++|++. .|.||++..++|.+.+++++..+....
T Consensus 4 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~~~ 80 (161)
T PRK12541 4 KQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEKKYKTT 80 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhccccccc
Confidence 46999999999999999999999999999999999999999999999863 599999999999999999876431100
Q ss_pred ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChH
Q 009449 374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPK 453 (534)
Q Consensus 374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spe 453 (534)
..+. + . .......++
T Consensus 81 -----------------------------------------------------~~~~---------~-~--~~~~~~~~~ 95 (161)
T PRK12541 81 -----------------------------------------------------TIEE---------F-H--LPNVPSTEH 95 (161)
T ss_pred -----------------------------------------------------chhh---------h-h--ccCCCCcHH
Confidence 0000 0 0 000001122
Q ss_pred HHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 454 e~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
+.....+. ..+..+|..||+++|.||.|+| .+++|++|||+.||+|..+|++.++||+++||+.
T Consensus 96 ~~~~~~~~-~~~~~~l~~L~~~~r~v~~l~~----~~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 96 EYFIKHEI-ASWLDSLSSLPLERRNVLLLRD----YYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HHHHHhHH-HHHHHHHHHCCHHHHHHhhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 32333333 4556789999999999999999 8999999999999999999999999999999975
No 103
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=2.6e-18 Score=166.22 Aligned_cols=171 Identities=18% Similarity=0.097 Sum_probs=132.2
Q ss_pred HHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHH
Q 009449 284 RVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK 362 (534)
Q Consensus 284 ~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~ 362 (534)
.+|...+..| ..|++.++..|.+.++.+++ +.++..+++|++||.|+.+|+..++|++. ..|.+|++..++|.+++
T Consensus 13 ~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~Iarn~~id 89 (196)
T PRK12535 13 TDLALAAGRGDRAALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAAR--SSARTWLLSLARRVWVD 89 (196)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCc--ccHHHHHHHHHHHHHHH
Confidence 4455666666 77999999999999999975 67888999999999999999999999864 37999999999999999
Q ss_pred HHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhh
Q 009449 363 MVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLE 442 (534)
Q Consensus 363 ~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e 442 (534)
++++..+..+. + .+ ... . .
T Consensus 90 ~~Rk~~~~~~~--~---------------------------------------------------~~-~~~-~----~-- 108 (196)
T PRK12535 90 NIRHDMARPRK--S---------------------------------------------------AT-EYE-D----A-- 108 (196)
T ss_pred HHHhhccCCCc--c---------------------------------------------------cc-ccc-c----c--
Confidence 99976431110 0 00 000 0 0
Q ss_pred ccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 443 FAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 443 ~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
.+.. ..|+.... ......|..+|+.|||++++||.|+| ++++|++|||+.||+|.++|++.++||+++||+.
T Consensus 109 --~~~~-~~~~~~~~-~~~~~~l~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~ 180 (196)
T PRK12535 109 --AATT-ASNETTGS-WSEWIDVRTLIDALPPERREALILTQ----VLGYTYEEAAKIADVRVGTIRSRVARARADLIAA 180 (196)
T ss_pred --cccc-CCcchhHH-HHHHHHHHHHHHcCCHHHHHHhhhHH----HhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 0000 11221111 12234789999999999999999999 9999999999999999999999999999999998
Q ss_pred hhhh
Q 009449 523 ETCR 526 (534)
Q Consensus 523 l~~~ 526 (534)
+...
T Consensus 181 l~~~ 184 (196)
T PRK12535 181 TATG 184 (196)
T ss_pred hccc
Confidence 7644
No 104
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=99.80 E-value=3.1e-18 Score=178.25 Aligned_cols=188 Identities=20% Similarity=0.235 Sum_probs=140.0
Q ss_pred HHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHH
Q 009449 284 RVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK 362 (534)
Q Consensus 284 ~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~ 362 (534)
.+|+..+..| ..|+++|+..|.+.|+.+|.++.++..+++|++||+|+.+|+.+++|++. ..|.+|++..++|.+++
T Consensus 7 ~~l~~~~~~gd~~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d 84 (339)
T PRK08241 7 AALLARAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATNVCLD 84 (339)
T ss_pred HHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHHHHHH
Confidence 4577777777 77999999999999999999999999999999999999999999999853 37999999999999999
Q ss_pred HHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhh
Q 009449 363 MVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLE 442 (534)
Q Consensus 363 ~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e 442 (534)
+++++.+.. .+.. .+. +.. ........+.+..+.+
T Consensus 85 ~~Rk~~~~~-~~~~------------------~~~-~~~-------------------------~~~~~~~~~~~~~~~~ 119 (339)
T PRK08241 85 ALEGRARRP-LPTD------------------LGA-PAA-------------------------DPVDELVERPEVPWLE 119 (339)
T ss_pred HHHhhcccc-Cccc------------------cCC-CcC-------------------------cccccccccccccccC
Confidence 998764311 0000 000 000 0000000000000111
Q ss_pred ccCCC----CCCChHHHHHHHH-HHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449 443 FAPDR----SVKSPKEIVMRQH-MKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMT 517 (534)
Q Consensus 443 ~i~d~----~~~spee~v~~~e-l~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~ 517 (534)
.+++. ...+|++.+...+ ....|..+|..||+++|+||.|+| .+++|++|||+.||+|..+|+++++||++
T Consensus 120 ~~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~RAr~ 195 (339)
T PRK08241 120 PYPDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLILRD----VLGWSAAEVAELLDTSVAAVNSALQRARA 195 (339)
T ss_pred CCCcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhHH----hhCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 11111 1246777666554 345689999999999999999999 89999999999999999999999999999
Q ss_pred HHHhH
Q 009449 518 KLRDS 522 (534)
Q Consensus 518 KLR~~ 522 (534)
+||+.
T Consensus 196 ~Lr~~ 200 (339)
T PRK08241 196 TLAER 200 (339)
T ss_pred HHhhc
Confidence 99983
No 105
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=99.79 E-value=2.9e-18 Score=176.91 Aligned_cols=181 Identities=16% Similarity=0.146 Sum_probs=135.0
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI 373 (534)
Q Consensus 294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl 373 (534)
..|++.|+..|.+.|+++|.++.++..+++|++||+|+.+|+..++|++. ..|.+|++..++|.++++++++.+....
T Consensus 4 ~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~~~~ 81 (324)
T TIGR02960 4 GAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQRRPRP 81 (324)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhccCCcCc
Confidence 57999999999999999999999999999999999999999999999864 3699999999999999999876431100
Q ss_pred ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccC-------C
Q 009449 374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAP-------D 446 (534)
Q Consensus 374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~-------d 446 (534)
... .. .... ..+. ...+....+.+.++ .
T Consensus 82 ~~~------------------~~-~~~~-------------------------~~~~-~~~~~~~~~~~~~~~~~~~~~~ 116 (324)
T TIGR02960 82 VGL------------------GA-PSAD-------------------------GTAA-ASEAAEVTWLEPLPDLTLDLDD 116 (324)
T ss_pred ccc------------------CC-CCCc-------------------------cccc-ccccccccccCCCCcccccccc
Confidence 000 00 0000 0000 00000000000000 1
Q ss_pred CCCCChHHHHHHHH-HHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449 447 RSVKSPKEIVMRQH-MKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC 525 (534)
Q Consensus 447 ~~~~spee~v~~~e-l~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~ 525 (534)
....+|++.+...+ +...+..+|..|||++|+||.|+| .+++|++|||+.||+|.++|+++++||+++||+.+..
T Consensus 117 ~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 192 (324)
T TIGR02960 117 PAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRD----VLGWRAAETAELLGTSTASVNSALQRARATLDEVGPS 192 (324)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccc
Confidence 11235776665554 456788999999999999999999 8999999999999999999999999999999998774
No 106
>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=1e-18 Score=160.63 Aligned_cols=153 Identities=16% Similarity=0.142 Sum_probs=124.9
Q ss_pred HHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHH
Q 009449 301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNRE 380 (534)
Q Consensus 301 I~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~ 380 (534)
+..|.+.|+.++.++.++..+++|++||+++.+|+++++|++ .+|.||++..+++.+.++++++.+....+
T Consensus 1 y~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~~------ 71 (154)
T TIGR02950 1 YREYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTID------ 71 (154)
T ss_pred CchHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhcccc------
Confidence 357899999999999999899999999999999999999997 37999999999999999998764211000
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHHH
Q 009449 381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQH 460 (534)
Q Consensus 381 i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~e 460 (534)
.+ .+.+... +....|++.+...+
T Consensus 72 ---------------------~~-----------------------------------~~~~~~~-~~~~~~~~~~~~~~ 94 (154)
T TIGR02950 72 ---------------------DD-----------------------------------AIGDLEQ-HPVESPEHHLLIKI 94 (154)
T ss_pred ---------------------Hh-----------------------------------hhhhccc-cccCChhHHHHHHH
Confidence 00 0000000 11125666666667
Q ss_pred HHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449 461 MKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE 523 (534)
Q Consensus 461 l~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l 523 (534)
....|..+|..||+++++||.++| .+|+|++|||+.||+|..+|++.++||+++||+.+
T Consensus 95 ~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~l 153 (154)
T TIGR02950 95 EQEEITHHLSRLPENYRTVLILRE----FKEFSYKEIAELLNLSLAKVKSNLFRARKELKKLL 153 (154)
T ss_pred HHHHHHHHHHhCCHhheeeeeehh----hccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 777899999999999999999999 89999999999999999999999999999999865
No 107
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=99.79 E-value=5.6e-18 Score=161.72 Aligned_cols=154 Identities=12% Similarity=0.106 Sum_probs=127.2
Q ss_pred HHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccc
Q 009449 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCK 376 (534)
Q Consensus 297 ~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~ 376 (534)
++.+++.|.+.|+.+|.++.++..+++|++||+++.+|+.+..|++. ..|.+|++..+++.+.+++++..+...++.
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~~--~~~~~wL~~i~~n~~~d~~Rk~~~~~~~~~- 79 (181)
T PRK09637 3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNTIIDFYRKKNRSEELPD- 79 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhccc--cchHHHHHHHHHHHHHHHHHhccccCCcch-
Confidence 67899999999999999999999999999999999999999999853 379999999999999999987643111000
Q ss_pred hHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHH
Q 009449 377 LNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIV 456 (534)
Q Consensus 377 ~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v 456 (534)
+ +...+ .+++..
T Consensus 80 ----------------------------------------------------------~------~~~~~----~~~~~~ 91 (181)
T PRK09637 80 ----------------------------------------------------------D------LLFED----EEREEN 91 (181)
T ss_pred ----------------------------------------------------------h------hhccC----CChhHH
Confidence 0 00000 112223
Q ss_pred HHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449 457 MRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC 525 (534)
Q Consensus 457 ~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~ 525 (534)
...+....+..+|+.||+++|+||.|+| .+|++++|||+.||+|..+|+..+.||+++||+.+..
T Consensus 92 ~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (181)
T PRK09637 92 AKKELAPCLRPFIDALPEKYAEALRLTE----LEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156 (181)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 3445667899999999999999999999 8999999999999999999999999999999998753
No 108
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=99.79 E-value=3.8e-18 Score=163.12 Aligned_cols=160 Identities=16% Similarity=0.156 Sum_probs=128.0
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccc
Q 009449 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (534)
Q Consensus 295 ~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP 374 (534)
.++..++..+.+.|+.+|.++.++..+++|++||+|+.+|+..++|++.. .|.+|++..++|.+.+.++++.+....
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 47789999999999999999999999999999999999999999998753 699999999999999999876431000
Q ss_pred cchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHH
Q 009449 375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKE 454 (534)
Q Consensus 375 ~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee 454 (534)
.+. .+.+.. ++ .++.
T Consensus 82 -----------------------------------------------------~~~--------~~~~~~-~~---~~~~ 96 (182)
T PRK12540 82 -----------------------------------------------------ADG--------SYAKTL-KS---QPGQ 96 (182)
T ss_pred -----------------------------------------------------ccc--------cccccc-cC---CCch
Confidence 000 000000 00 1111
Q ss_pred HHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcc
Q 009449 455 IVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDL 528 (534)
Q Consensus 455 ~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L 528 (534)
.. ......|..+|+.|||++|+||.|+| .+++|++|||+.||+|..+|++.++||+++||+.+.....
T Consensus 97 ~~--~~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~~ 164 (182)
T PRK12540 97 NA--HLEFEEFRAALDKLPQDQREALILVG----ASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDGA 164 (182)
T ss_pred HH--HHHHHHHHHHHHhCCHHHHHHhhHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 11 11234689999999999999999999 8999999999999999999999999999999999886654
No 109
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=99.79 E-value=5.3e-18 Score=157.44 Aligned_cols=155 Identities=14% Similarity=0.064 Sum_probs=125.8
Q ss_pred HHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHH
Q 009449 301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNRE 380 (534)
Q Consensus 301 I~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~ 380 (534)
+..|.+.++.++.++.++..+++|++||+|+.+|+..+.|++. +|.||++..++|.+.++++++.+....
T Consensus 1 ~~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~~---~~~~wL~~ia~n~~~d~~R~~~~~~~~------- 70 (159)
T PRK12527 1 MENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIE---HPRAFLYRTALNLVVDRHRRHRVRQAE------- 70 (159)
T ss_pred ChhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhcccccccc---chHHHHHHHHHHHHHHHHHHHhccccc-------
Confidence 3578889999999999998999999999999999999998752 799999999999999999865321000
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHHH
Q 009449 381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQH 460 (534)
Q Consensus 381 i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~e 460 (534)
+++. .. +. .....++|++.+..++
T Consensus 71 ----------------------------------------------~~~~-~~-~~--------~~~~~~~~~~~~~~~~ 94 (159)
T PRK12527 71 ----------------------------------------------PLEV-LD-EE--------ERLHSPSPQTRLDLGQ 94 (159)
T ss_pred ----------------------------------------------chhh-hh-cc--------ccccCCCHHHHHHHHH
Confidence 0000 00 00 0011235677777777
Q ss_pred HHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449 461 MKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC 525 (534)
Q Consensus 461 l~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~ 525 (534)
....+..+|..|||++++||.|+| ++++|++|||+.||+|.++|+..+.||+++||+.+..
T Consensus 95 ~~~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~~ 155 (159)
T PRK12527 95 RLALLQRALAELPPACRDSFLLRK----LEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQ 155 (159)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 778899999999999999999999 8999999999999999999999999999999998764
No 110
>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=5.2e-18 Score=167.19 Aligned_cols=118 Identities=17% Similarity=0.267 Sum_probs=106.0
Q ss_pred HHHhcHHHHHHHHHHhHHHHHHHHHHhhCCC--CCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHH
Q 009449 289 HLAFGWYCREELIKSTRPLVLFLARNYRGLG--IPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVAR 366 (534)
Q Consensus 289 ~l~~G~~A~e~LI~~nlrLV~sIArrY~~~g--~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~ 366 (534)
.++.|...+++||..|.|+|.++|.+|.++. .+.+|++|+|++|||+|+++|||++|.+|.|||.+||++.|.+++++
T Consensus 3 ~~~~gd~~~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dylRk 82 (218)
T TIGR02895 3 PIQPGNEEREELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYIRK 82 (218)
T ss_pred hhhcCChHHHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence 3566755599999999999999999998764 58999999999999999999999999999999999999999999998
Q ss_pred hc---cccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHH
Q 009449 367 HA---RGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAK 406 (534)
Q Consensus 367 ~s---r~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~ 406 (534)
.. +.+++|....+....+..+..++..++++.|+.+||+.
T Consensus 83 ~~k~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~ 125 (218)
T TIGR02895 83 NQKYQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILE 125 (218)
T ss_pred cccccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHH
Confidence 87 56788876666677888888899999999999999976
No 111
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=99.78 E-value=8e-18 Score=156.49 Aligned_cols=158 Identities=15% Similarity=0.184 Sum_probs=126.8
Q ss_pred HHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchH
Q 009449 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN 378 (534)
Q Consensus 299 ~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~ 378 (534)
.++..+.+.++.+|.++.++..+++|++||+++.+|+....|++. .|.+|++..+++.+.++++++.+.....
T Consensus 2 ~~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn~~~d~~R~~~~~~~~~---- 74 (163)
T PRK07037 2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRNLAIDHYRRQALENKYH---- 74 (163)
T ss_pred hHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHHHHHHHHHhhccccccc----
Confidence 357888999999999999999999999999999999998888763 4889999999999999998765211000
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHH
Q 009449 379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMR 458 (534)
Q Consensus 379 ~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~ 458 (534)
..+ +. .. + .++. ..+|++.+..
T Consensus 75 ------------------------------------------------~~~-----~~--~~-~-~~~~-~~~~~~~~~~ 96 (163)
T PRK07037 75 ------------------------------------------------GDE-----ED--GL-D-VPSP-EASPEAALIN 96 (163)
T ss_pred ------------------------------------------------ccc-----cc--cc-c-cCCC-CCCHHHHHHH
Confidence 000 00 00 0 0111 1356666666
Q ss_pred HHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449 459 QHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC 525 (534)
Q Consensus 459 ~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~ 525 (534)
.+..+.+..+|+.|||++|+||.++| .+++|++|||+.||+|.++|++.+.||+++||..+..
T Consensus 97 ~~~~~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l~~ 159 (163)
T PRK07037 97 RDTLRHVADALSELPARTRYAFEMYR----LHGETQKDIARELGVSPTLVNFMIRDALVHCRKCLDA 159 (163)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 67778899999999999999999999 8999999999999999999999999999999998754
No 112
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=99.78 E-value=1.1e-17 Score=157.90 Aligned_cols=161 Identities=15% Similarity=0.099 Sum_probs=126.9
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI 373 (534)
Q Consensus 294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl 373 (534)
..|++.++..|.+.++.++.++.++..+++|++||.|+.+|+. ..|++-. .|.+|++..++|.+.+++++..+..
T Consensus 9 ~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~~~~-- 83 (172)
T PRK09651 9 SLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNALEK-- 83 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHHHHh--
Confidence 4699999999999999999999999999999999999999998 3554432 5899999999999999998653100
Q ss_pred ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChH
Q 009449 374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPK 453 (534)
Q Consensus 374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spe 453 (534)
.. .+. ++ + +++...++|+
T Consensus 84 -~~------------------------~~~------------------------~~------------~-~~~~~~~~~~ 101 (172)
T PRK09651 84 -AY------------------------LEM------------------------LA------------L-MPEGGAPSPE 101 (172)
T ss_pred -hh------------------------hhH------------------------Hh------------h-ccccCCCChH
Confidence 00 000 00 0 0011112444
Q ss_pred HHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449 454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC 525 (534)
Q Consensus 454 e~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~ 525 (534)
......+....|..+|..|||++|+||.|+| ++++|++|||+.||+|.++|+..++||+++|+.....
T Consensus 102 ~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~~~~ 169 (172)
T PRK09651 102 ERESQLETLQLLDSMLDGLNGKTREAFLLSQ----LDGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLFRLE 169 (172)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHhHHhhhhh----ccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4454555567799999999999999999999 8999999999999999999999999999999976543
No 113
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=99.77 E-value=9.1e-18 Score=158.33 Aligned_cols=148 Identities=14% Similarity=0.175 Sum_probs=121.9
Q ss_pred HHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHHH
Q 009449 302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREI 381 (534)
Q Consensus 302 ~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i 381 (534)
..|.+.|+.++.++.++..+++|++||+++.+|+++.+|++. .+|.+|++..+++.+.+++++..+...++.
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~~--~~f~~wl~~iarn~~~d~~Rk~~~~~~~~~------ 73 (170)
T TIGR02959 2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDG--QKIQSWLYQIARNTIIDFYRSKSRSVELPE------ 73 (170)
T ss_pred chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhccCccccch------
Confidence 468899999999999999999999999999999999999864 489999999999999999988753111100
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHHHH
Q 009449 382 SKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHM 461 (534)
Q Consensus 382 ~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~el 461 (534)
. .... .++++.....+.
T Consensus 74 ------------------------------------------------~------------~~~~---~~~~~~~~~~e~ 90 (170)
T TIGR02959 74 ------------------------------------------------S------------LLAA---DSAREETFVKEL 90 (170)
T ss_pred ------------------------------------------------h------------hccc---CCccHHHHHHHH
Confidence 0 0000 012223334455
Q ss_pred HHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449 462 KKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET 524 (534)
Q Consensus 462 ~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~ 524 (534)
...+..+|..||+++|+||.|+| .+++|++|||+.||+|..+|++.++||+++||..+.
T Consensus 91 ~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 91 SQCIPPMIKELPDEYREAIRLTE----LEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 66799999999999999999999 899999999999999999999999999999999875
No 114
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=99.77 E-value=1.5e-17 Score=159.67 Aligned_cols=163 Identities=17% Similarity=0.132 Sum_probs=128.2
Q ss_pred HHhcHHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcc
Q 009449 290 LAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (534)
Q Consensus 290 l~~G~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr 369 (534)
+.....+++.++..|.+.|+.+|+++.++..+++|++||+|+.+|+....|++. ..|.+|++..++|.+.+..++..+
T Consensus 18 ~~~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~~~~ 95 (188)
T PRK12517 18 MLSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFERKQF 95 (188)
T ss_pred hhccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHHhcc
Confidence 344578999999999999999999999999999999999999999999999865 369999999999987766543221
Q ss_pred ccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCC
Q 009449 370 GIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSV 449 (534)
Q Consensus 370 ~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~ 449 (534)
. .. ..+. +...+...
T Consensus 96 ~--~~----------------------------------------------------~~~~-----------~~~~~~~~ 110 (188)
T PRK12517 96 D--LV----------------------------------------------------DIED-----------DSIEDDAS 110 (188)
T ss_pred C--cc----------------------------------------------------Cccc-----------ccccCccc
Confidence 0 00 0000 00011111
Q ss_pred CChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449 450 KSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD 527 (534)
Q Consensus 450 ~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~ 527 (534)
.+|+... ..+.|..+|..||+++|.||.++| .+++|++|||+.||||..+|+.+++||+++||..+....
T Consensus 111 ~~~e~~~----~~~~l~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 180 (188)
T PRK12517 111 HSSEEEM----EQEWLRRQIAKLDPEYREPLLLQV----IGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALEKPD 180 (188)
T ss_pred cChhHHH----HHHHHHHHHHhCCHHHHHHHHHHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 2333322 235689999999999999999999 899999999999999999999999999999999987543
No 115
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=99.76 E-value=3.7e-17 Score=153.62 Aligned_cols=159 Identities=16% Similarity=0.108 Sum_probs=128.3
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI 373 (534)
Q Consensus 294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl 373 (534)
..++.+++..|.+.++.+|.+|.++..+++|++||+|+.+|+..+.++. ..|.+|++..++|.+.+++++....
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 3588999999999999999999999999999999999999987665543 2699999999999999998764210
Q ss_pred ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChH
Q 009449 374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPK 453 (534)
Q Consensus 374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spe 453 (534)
+ .... +.+ + .+.+..++|+
T Consensus 82 ------------~---~~~~---------------------------------~~~------------~-~~~~~~~~~~ 100 (168)
T PRK12525 82 ------------R---AYLQ---------------------------------SLA------------E-APEAVQPSPE 100 (168)
T ss_pred ------------H---HHHH---------------------------------HHh------------c-ccccccCChH
Confidence 0 0000 000 0 0011123666
Q ss_pred HHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449 454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE 523 (534)
Q Consensus 454 e~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l 523 (534)
+.....+..+.|..+|..|||++|+||.|+| .+++|++|||+.||+|..+|+..+.+|+++||..+
T Consensus 101 ~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~----~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~~ 166 (168)
T PRK12525 101 EQWMVIETLLAIDRLLDGLSGKARAAFLMSQ----LEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQGF 166 (168)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhh
Confidence 6666667778899999999999999999999 89999999999999999999999999999999765
No 116
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=99.75 E-value=2.9e-17 Score=158.06 Aligned_cols=157 Identities=15% Similarity=0.143 Sum_probs=122.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccc
Q 009449 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (534)
Q Consensus 295 ~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP 374 (534)
.+++.|+. |.+.|+++|.++.++..+++|++||+|+.+|+.+..|+.. ..|.+|++..++|.+.+++++..+..
T Consensus 8 ~~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r~~--- 81 (188)
T PRK12546 8 DPRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKREV--- 81 (188)
T ss_pred hHHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhcccc---
Confidence 35566655 7799999999999999999999999999999999999864 37999999999999999998764210
Q ss_pred cchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHH
Q 009449 375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKE 454 (534)
Q Consensus 375 ~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee 454 (534)
.. .+. ...+...+.. ..+.
T Consensus 82 ~~---------------------------------------------------~~~--------~~~~~~~~~~--~~~~ 100 (188)
T PRK12546 82 PD---------------------------------------------------PEG--------VHAASLAVKP--AHDG 100 (188)
T ss_pred cC---------------------------------------------------ccc--------ccccccccCC--cchh
Confidence 00 000 0000000000 1111
Q ss_pred HHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhh
Q 009449 455 IVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCR 526 (534)
Q Consensus 455 ~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~ 526 (534)
......+..+|..|||++++||.|+| .+++|.+|||+.||||..+|++++.||+++||+.+...
T Consensus 101 ----~~~~~~l~~~L~~Lp~~~r~v~~L~~----~~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~~ 164 (188)
T PRK12546 101 ----RLAMSDFRAAFAQLPDEQREALILVG----ASGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQLE 164 (188)
T ss_pred ----HHHHHHHHHHHHhCCHHHhHHhhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence 12234688999999999999999999 89999999999999999999999999999999988653
No 117
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=99.75 E-value=2.9e-17 Score=157.10 Aligned_cols=158 Identities=15% Similarity=0.094 Sum_probs=123.4
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccccc
Q 009449 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC 375 (534)
Q Consensus 296 A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~ 375 (534)
..+..+..+.+.|+.+|.++.++..+++|++||+|+.+|+....|++. ..|.+|++..+++.++++++++.+.....
T Consensus 5 ~~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~~~~~~- 81 (182)
T PRK12511 5 SKRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRVEARRA- 81 (182)
T ss_pred chhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhccccccc-
Confidence 345557889999999999999999999999999999999999999864 37999999999999999998764311000
Q ss_pred chHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHH
Q 009449 376 KLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEI 455 (534)
Q Consensus 376 ~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~ 455 (534)
+++ + +. .+...+.+.+
T Consensus 82 --------------------------~~~------------------------~------------~~-~~~~~~~~~~- 97 (182)
T PRK12511 82 --------------------------DEL------------------------A------------VL-ADASLPAAQE- 97 (182)
T ss_pred --------------------------cch------------------------h------------hc-cccCCCcchH-
Confidence 000 0 00 0000011111
Q ss_pred HHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhh
Q 009449 456 VMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCR 526 (534)
Q Consensus 456 v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~ 526 (534)
.......|..+|..||+++|+||.|+| .+++|++|||+.||||.++|++.++||+++||..+...
T Consensus 98 --~~~~~~~l~~~l~~Lp~~~R~v~~L~~----~eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~~~ 162 (182)
T PRK12511 98 --HAVRLAQIRDAFFDLPEEQRAALHLVA----IEGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEEGT 162 (182)
T ss_pred --HHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhc
Confidence 122345788999999999999999999 89999999999999999999999999999999987643
No 118
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=99.73 E-value=6.5e-17 Score=149.71 Aligned_cols=155 Identities=14% Similarity=0.137 Sum_probs=114.2
Q ss_pred CCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcC
Q 009449 317 GLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHG 396 (534)
Q Consensus 317 ~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elG 396 (534)
++..+++|++||+|+.+|+.... ++ +..|.+|++..++|.++++++++.+.......
T Consensus 2 ~~~~~AeDivQe~fl~~~~~~~~-~~--~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~-------------------- 58 (161)
T PRK09047 2 RDDDAALDIVQDAMIKLAEKYGD-RP--AAEWPPLFQRILQNRIHDWFRRQKVRNTWVSL-------------------- 58 (161)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhh-cc--cCchHHHHHHHHHHHHHHHHHhhccccccccc--------------------
Confidence 34567999999999999999886 33 34799999999999999999876431111000
Q ss_pred CCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCC--CCChHHHHHHHHHHHHHHHHHhhCCH
Q 009449 397 KYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRS--VKSPKEIVMRQHMKKDVFRILESLDS 474 (534)
Q Consensus 397 r~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~--~~spee~v~~~el~e~L~~~L~~L~~ 474 (534)
..++..... +++....+.+.+.. .++|++.+...+....|..+|..||+
T Consensus 59 ----------------------------~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~ 109 (161)
T PRK09047 59 ----------------------------FSSFSDDDD-DDDFDPLETLDSADEGAESPADKLERAQVLQLIEEAIQKLPA 109 (161)
T ss_pred ----------------------------ccccccccc-cccccHHHHhccccccCCCHHHHHHHHHHHHHHHHHHHhCCH
Confidence 000000000 00011111122211 24678888888888899999999999
Q ss_pred HHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449 475 RERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD 527 (534)
Q Consensus 475 rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~ 527 (534)
++|+||.|+| ++++|++|||+.||+|..+|+++++||+++||+.+...+
T Consensus 110 ~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~ 158 (161)
T PRK09047 110 RQREAFLLRY----WEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEAKG 158 (161)
T ss_pred HHHHHHHHHH----HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 9999999999 899999999999999999999999999999999987654
No 119
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=99.72 E-value=1.3e-16 Score=163.24 Aligned_cols=159 Identities=16% Similarity=0.164 Sum_probs=124.1
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccccc
Q 009449 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC 375 (534)
Q Consensus 296 A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~ 375 (534)
.+.++++.|.+.++.+|+++.++..++||++||+|+. |.....|++ ..|.+|++..++|.+++++++..+.. ..
T Consensus 5 ~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~~---~~~~~WL~~Ia~n~~~d~lR~~~~~~--~~ 78 (293)
T PRK09636 5 DAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQI---RDPRAWLTRVVTRLCLDRLRSARHRR--ET 78 (293)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhcccccc---cCHHHHHHHHHHHHHHHHHHhhhccc--cc
Confidence 4678999999999999999999999999999999999 666777763 47999999999999999998754210 00
Q ss_pred chHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHH
Q 009449 376 KLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEI 455 (534)
Q Consensus 376 ~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~ 455 (534)
.. + ..+..+ ..+.. .+|++.
T Consensus 79 ~~------------------~-----------------------------~~~~e~------------~~~~~-~~~~~~ 98 (293)
T PRK09636 79 YV------------------G-----------------------------PWLPEP------------VVEEL-DDPLEA 98 (293)
T ss_pred cc------------------C-----------------------------CcCCcC------------CCCCC-CChHHH
Confidence 00 0 000000 01111 134443
Q ss_pred H-HHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449 456 V-MRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET 524 (534)
Q Consensus 456 v-~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~ 524 (534)
. ....+...+..+|+.|||++|+||.|+| .+++|++|||+.||+|..+|+++++||+++||+...
T Consensus 99 ~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~----~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~ 164 (293)
T PRK09636 99 VVAAEDLSLALMLALERLSPLERAAFLLHD----VFGVPFDEIASTLGRSPAACRQLASRARKHVRAARP 164 (293)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 3 3445556789999999999999999999 899999999999999999999999999999999764
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=99.68 E-value=8.4e-16 Score=156.72 Aligned_cols=156 Identities=20% Similarity=0.192 Sum_probs=120.3
Q ss_pred HHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchH
Q 009449 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN 378 (534)
Q Consensus 299 ~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~ 378 (534)
+++..|.+.++.+|+++.++..++||++||+|+.+++. .|+.. ..|.+|++.+++|.+++++++..+.......
T Consensus 1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~~--~~~~awL~~Ia~n~~ld~lR~~~~~~~~~~~-- 74 (281)
T TIGR02957 1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQI--ENPKAYLTKVVTRRCIDVLRSARARREVYVG-- 74 (281)
T ss_pred ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Ccccc--cCHHHHHHHHHHHHHHHHHHHhhhcccccCC--
Confidence 36899999999999999999999999999999997775 45432 3699999999999999999875321000000
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHH
Q 009449 379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMR 458 (534)
Q Consensus 379 ~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~ 458 (534)
+ -+..+ ..+. ..+|++.+..
T Consensus 75 --------------------~---------------------------~~~e~------------~~~~-~~~~~~~~~~ 94 (281)
T TIGR02957 75 --------------------P---------------------------WLPEP------------LLTT-SADPAESVEL 94 (281)
T ss_pred --------------------C---------------------------CCCcc------------cCCC-CCChHHHHHH
Confidence 0 00000 0011 1345555443
Q ss_pred H-HHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449 459 Q-HMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET 524 (534)
Q Consensus 459 ~-el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~ 524 (534)
. .+...+..+|+.|||+||.||.|+| ..++|++|||+.||+|..+|+++++||+++||+...
T Consensus 95 ~e~~~~~l~~~l~~L~~~~R~v~~L~~----~~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~ 157 (281)
T TIGR02957 95 AESLSMAYLLLLERLSPLERAVFVLRE----VFDYPYEEIASIVGKSEANCRQLVSRARRHLDARRP 157 (281)
T ss_pred HHHHHHHHHHHHhhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 3 4556788899999999999999999 899999999999999999999999999999998654
No 121
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=99.68 E-value=1e-15 Score=157.04 Aligned_cols=161 Identities=16% Similarity=0.095 Sum_probs=124.9
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccc
Q 009449 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (534)
Q Consensus 295 ~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP 374 (534)
..+..+++.|.+.++.+|+++.++..++||++||+|+.+|++...+ . ..|.+|++...+|.+++++++..+.-..+
T Consensus 5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~-~---~~~~aWL~~Ia~n~~id~lRk~~~rr~~~ 80 (290)
T PRK09635 5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD-I---DDERGWLIVVTSRLCLDHIKSASTRRERP 80 (290)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc-c---ccHHHHHHHHHHHHHHHHHhhhhccCcCc
Confidence 4688999999999999999999999999999999999999987543 1 26999999999999999998753210000
Q ss_pred cchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHH
Q 009449 375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKE 454 (534)
Q Consensus 375 ~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee 454 (534)
. ..+... . .+..+ ...+|++
T Consensus 81 ~---------------------------------------------------~~~~~~--~-----~~~~~--~~~~~~~ 100 (290)
T PRK09635 81 Q---------------------------------------------------DIAAWH--D-----GDASV--SSVDPAD 100 (290)
T ss_pred c---------------------------------------------------cccccC--c-----cccCC--CCCCcHH
Confidence 0 000000 0 00001 1123443
Q ss_pred -HHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449 455 -IVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE 523 (534)
Q Consensus 455 -~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l 523 (534)
.....+....+..+|..|||++|.||.|+| ..++|++|||+.||+|..+|+++++||+++||...
T Consensus 101 ~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~----~~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~ 166 (290)
T PRK09635 101 RVTLDDEVRLALLIMLERLGPAERVVFVLHE----IFGLPYQQIATTIGSQASTCRQLAHRARRKINESR 166 (290)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHhhHHH----HhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence 344556667899999999999999999999 89999999999999999999999999999999854
No 122
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=99.68 E-value=1e-15 Score=152.08 Aligned_cols=158 Identities=20% Similarity=0.167 Sum_probs=121.6
Q ss_pred HHHHHHhcHHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHH
Q 009449 286 LKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVA 365 (534)
Q Consensus 286 L~~~l~~G~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr 365 (534)
|.+.+.....+++.+++.| +.++.+|.++.++..+++|++||+|+.+|+. |+... .|.+|++.+++|.+++.++
T Consensus 9 ~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~~--~~~~WL~~IarN~~id~~R 82 (228)
T PRK06704 9 LKNHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNKD--ICMTLVYKIARNRWLDQIK 82 (228)
T ss_pred HhcccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCccc--cHHHHHHHHHHHHHHHHHh
Confidence 3344444456888777777 7899999999999999999999999999986 55432 5999999999999999998
Q ss_pred HhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccC
Q 009449 366 RHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAP 445 (534)
Q Consensus 366 ~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~ 445 (534)
++.+...+ .+ + ..
T Consensus 83 k~k~~~~~------------------------------------------------------~~-----~--------~~ 95 (228)
T PRK06704 83 SKSVHEKI------------------------------------------------------RD-----Q--------IT 95 (228)
T ss_pred cccccccc------------------------------------------------------cc-----c--------cc
Confidence 76421000 00 0 00
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449 446 DRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC 525 (534)
Q Consensus 446 d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~ 525 (534)
..++.+.. .+..+.+..+|+.||+++|+|+.|+| .+++|++|||+.||+|.++|++.++||+++||+.+..
T Consensus 96 ---~~~~~~~~--~~~~~~l~~~L~~Lp~~~R~v~lL~~----~eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~ 166 (228)
T PRK06704 96 ---FEEPHEKI--ADLHEMVGKVLSSLNVQQSAILLLKD----VFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEE 166 (228)
T ss_pred ---cCChHHHH--HHHHHHHHHHHHhCCHHHhhHhhhHH----hhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 00111111 12345688999999999999999999 8999999999999999999999999999999998754
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=99.57 E-value=3e-14 Score=130.03 Aligned_cols=136 Identities=14% Similarity=0.233 Sum_probs=100.8
Q ss_pred HHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhc-----cCCcCCCchhhHHHHHHHHHHHHHHHHhcccc
Q 009449 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAER-----FDHTRGYKFSTYVQYWIRKSISKMVARHARGI 371 (534)
Q Consensus 297 ~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ek-----FDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~i 371 (534)
++.++..|.++++++|++|... +| +||.++.+|....+ |++. ..|.||++..++|.++++++++.+..
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 4689999999999999999652 34 49999999999865 5543 47999999999999999998764210
Q ss_pred ccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCC
Q 009449 372 KIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKS 451 (534)
Q Consensus 372 RlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~s 451 (534)
... . ..+ .+ +.. ..
T Consensus 74 ~~~-----------------~--------~~~------------------------~~----------------~~~-~~ 87 (142)
T TIGR03209 74 KII-----------------Y--------NSE------------------------IT----------------DIK-LS 87 (142)
T ss_pred hhh-----------------h--------hhh------------------------hh----------------ccc-cc
Confidence 000 0 000 00 000 01
Q ss_pred hHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHH
Q 009449 452 PKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIR 509 (534)
Q Consensus 452 pee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVR 509 (534)
+.+.+...+....+..+|+.|||.+|+||.|+| .+++|++|||+.||+|.+||+
T Consensus 88 ~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~----~~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 88 LINVYSSNDLEFEFNDLISILPNKQKKIIYMKF----FEDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred hhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHhhc
Confidence 122333444556788999999999999999999 899999999999999999997
No 124
>PRK09191 two-component response regulator; Provisional
Probab=99.56 E-value=3.6e-14 Score=140.44 Aligned_cols=137 Identities=18% Similarity=0.124 Sum_probs=112.4
Q ss_pred HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccccc
Q 009449 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC 375 (534)
Q Consensus 296 A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~ 375 (534)
|+..++..|.+.|+++|.++.++..+++|++||+++.+|+...+|++. ..|.+|++.++++...... .
T Consensus 2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~~~----------~ 69 (261)
T PRK09191 2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSSAG----------A 69 (261)
T ss_pred chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhcccc----------c
Confidence 578999999999999999999999999999999999999999999874 3689999987765321000 0
Q ss_pred chHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHH
Q 009449 376 KLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEI 455 (534)
Q Consensus 376 ~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~ 455 (534)
+ . ... ..+..
T Consensus 70 -----------------------------------------------------~-----~---------~~~--~~~~~- 79 (261)
T PRK09191 70 -----------------------------------------------------N-----D---------PEP--GSPFE- 79 (261)
T ss_pred -----------------------------------------------------c-----C---------CCC--CCCch-
Confidence 0 0 000 01111
Q ss_pred HHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449 456 VMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC 525 (534)
Q Consensus 456 v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~ 525 (534)
..+..+|+.||+++|+|+.|+| .+++|++|||+.||+|.++|+.+.++|+++||..+..
T Consensus 80 -------~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~~ 138 (261)
T PRK09191 80 -------ARAERRLAGLTPLPRQAFLLTA----LEGFSVEEAAEILGVDPAEAEALLDDARAEIARQVAT 138 (261)
T ss_pred -------HHHHHHHHhCCHHHhHHHHHHH----HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCCC
Confidence 1688899999999999999999 8999999999999999999999999999999987653
No 125
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=99.45 E-value=3.9e-12 Score=127.18 Aligned_cols=89 Identities=19% Similarity=0.321 Sum_probs=80.2
Q ss_pred CHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCC--CHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHH
Q 009449 282 SERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGI--PFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358 (534)
Q Consensus 282 d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~--~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~ 358 (534)
+.+.|+..++.| ..|++.|+..|.++|+++|.+|.++.. +.+|++|||++++|+++++||+.+|..|.+|++++|++
T Consensus 4 ~~~~Li~~~~~gD~~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn 83 (237)
T PRK08311 4 SLEDILEKIKNGDEELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKR 83 (237)
T ss_pred cHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHH
Confidence 455677777777 679999999999999999999998865 59999999999999999999999888999999999999
Q ss_pred HHHHHHHHhccc
Q 009449 359 SISKMVARHARG 370 (534)
Q Consensus 359 aI~~~lr~~sr~ 370 (534)
.+.+++++..+.
T Consensus 84 ~~iDylRk~~~~ 95 (237)
T PRK08311 84 RLIDYFRKESKH 95 (237)
T ss_pred HHHHHHHHhhcc
Confidence 999999987653
No 126
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=99.44 E-value=7.3e-12 Score=120.30 Aligned_cols=175 Identities=19% Similarity=0.253 Sum_probs=124.1
Q ss_pred HHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCC---CCCHHHH--HHHHHHHHHHhhhccCCcCCCchhhHHHHHH
Q 009449 283 ERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGL---GIPFSDL--LQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356 (534)
Q Consensus 283 ~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~---g~~~eDL--iQEG~lgL~rA~ekFDp~kG~rFSTYA~~wI 356 (534)
...|+..++.| ..|.+.|+..|++.++.+|+++... +.+.+|. ++|+|+.+++.-...+++....|-.|+...+
T Consensus 4 it~ll~~~~~GD~~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~~~~~ 83 (185)
T PF07638_consen 4 ITELLDRWRQGDEAALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALLARIM 83 (185)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHHHHHH
Confidence 35677888888 6799999999999999999987633 3455554 6777887776433323333346888999999
Q ss_pred HHHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccch
Q 009449 357 RKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCL 436 (534)
Q Consensus 357 R~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~ 436 (534)
++.+.+.++.+.+..|-... ...+||....
T Consensus 84 rr~lid~~R~~~a~KRg~~~-----------------------------------------------~~~~l~~~~~--- 113 (185)
T PF07638_consen 84 RRKLIDHARRRQAQKRGGDQ-----------------------------------------------VRVELDERAD--- 113 (185)
T ss_pred HHHHHHHHHHHHHHhcCCCC-----------------------------------------------cccchhhhhc---
Confidence 99999999876532221110 0012221110
Q ss_pred hhhhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 437 NAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 437 ~~~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
+...++|++.+ ++.+.+..+.. |+|++++||.++| +.|+|.+|||+.||||+.||+.....|.
T Consensus 114 ---------~~~~~~~~~~~---~l~e~l~~L~~-l~~~~~~~v~l~~----~~Gls~~EIA~~lgiS~~tV~r~l~~aR 176 (185)
T PF07638_consen 114 ---------SGDEPSPEELL---ELEEALERLLA-LDPRQRRVVELRF----FEGLSVEEIAERLGISERTVRRRLRRAR 176 (185)
T ss_pred ---------cccCCCHHHHH---HHHHHHHHHHc-cCHHHHHHHHHHH----HCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 01113555544 34445555555 9999999999999 8999999999999999999999999999
Q ss_pred HHHHhHhh
Q 009449 517 TKLRDSET 524 (534)
Q Consensus 517 ~KLR~~l~ 524 (534)
.+|+..+.
T Consensus 177 ~~l~~~l~ 184 (185)
T PF07638_consen 177 AWLRRELR 184 (185)
T ss_pred HHHHHHhc
Confidence 99998764
No 127
>PF04542 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR007627 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [, ]. The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation [, ].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1OR7_B 1H3L_B 2Z2S_C 2Q1Z_C 2O7G_B 1SMY_F 1IW7_P 2BE5_F 2A6E_F 2CW0_F ....
Probab=99.27 E-value=1.2e-11 Score=99.00 Aligned_cols=70 Identities=24% Similarity=0.375 Sum_probs=67.0
Q ss_pred HHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcc
Q 009449 300 LIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (534)
Q Consensus 300 LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr 369 (534)
|++.|.++|+.+|++|.+++.+++|++||+++++|+++++||++++..|.+|++..+++.+.+.++++.|
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 6899999999999999999999999999999999999999999999899999999999999999997754
No 128
>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=99.23 E-value=2.1e-11 Score=100.83 Aligned_cols=78 Identities=33% Similarity=0.483 Sum_probs=67.2
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHH
Q 009449 379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIV 456 (534)
Q Consensus 379 ~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v 456 (534)
+.+++|.+++++|.+++||.||.+|||+.|||++++|..++.+.+.+.|||.+++.+++..+.++++|+..++|++.+
T Consensus 1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d~~~~~P~e~~ 78 (78)
T PF04539_consen 1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIEDDDAPSPEEEV 78 (78)
T ss_dssp HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-SSS--HHHH-
T ss_pred ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecCCCCCChhhcc
Confidence 468999999999999999999999999999999999999999999999999999988889999999999888998754
No 129
>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=99.21 E-value=3.7e-11 Score=91.39 Aligned_cols=50 Identities=40% Similarity=0.650 Sum_probs=46.4
Q ss_pred HHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 468 ILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 468 ~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
+|+.|||+|++||.++| ++++|++|||+.||+|+++|++++.+|++|||+
T Consensus 1 Al~~L~~~er~vi~~~y----~~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 1 ALDQLPPREREVIRLRY----FEGLTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp HHCTS-HHHHHHHHHHH----TST-SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred ChhhCCHHHHHHHHHHh----cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 58899999999999999 899999999999999999999999999999995
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=98.95 E-value=2.3e-09 Score=82.52 Aligned_cols=54 Identities=26% Similarity=0.500 Sum_probs=46.5
Q ss_pred HHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449 462 KKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL 519 (534)
Q Consensus 462 ~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL 519 (534)
++.|..++..|||++|+||.++| .+++|++|||+.+|+|.++|++.+.+|+++|
T Consensus 1 r~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIa~~l~~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 1 REALQQALAQLPERQREIFLLRY----FQGMSYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp HHHHHHHHHCS-HHHHHHHHHHH----TS---HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHHHH----HHCcCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 35789999999999999999999 9999999999999999999999999999987
No 131
>PRK06930 positive control sigma-like factor; Validated
Probab=98.74 E-value=1.9e-07 Score=89.20 Aligned_cols=72 Identities=19% Similarity=0.232 Sum_probs=64.1
Q ss_pred ChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhh
Q 009449 451 SPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCR 526 (534)
Q Consensus 451 spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~ 526 (534)
.|.+.....+....|..++..|||++++||.|+| .+++|++|||+.||+|.++|++++.||+++|+..+...
T Consensus 94 ~~~~~~~~~e~~~~l~~al~~L~~rer~V~~L~~----~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~ 165 (170)
T PRK06930 94 EEPESVISEWDKIRIEDALSVLTEREKEVYLMHR----GYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQINES 165 (170)
T ss_pred CChhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 3445555666778899999999999999999999 89999999999999999999999999999999987644
No 132
>PRK00118 putative DNA-binding protein; Validated
Probab=98.43 E-value=9.6e-07 Score=77.74 Aligned_cols=61 Identities=26% Similarity=0.195 Sum_probs=55.2
Q ss_pred HHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcc
Q 009449 464 DVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDL 528 (534)
Q Consensus 464 ~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L 528 (534)
.+.-....||+++++|+.++| .+++|.+|||+.+|+|++||+.++.+|+++||+++..-++
T Consensus 10 l~d~~~~~L~ekqRevl~L~y----~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~ 70 (104)
T PRK00118 10 LFDFYGSLLTEKQRNYMELYY----LDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHL 70 (104)
T ss_pred HHHHHhccCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence 444466789999999999999 8999999999999999999999999999999998876654
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=98.31 E-value=1.9e-06 Score=64.17 Aligned_cols=54 Identities=33% Similarity=0.547 Sum_probs=50.0
Q ss_pred HHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449 463 KDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520 (534)
Q Consensus 463 e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR 520 (534)
+.+..++..|++.++.++.++| .+++|..+||+.+|+|..+|+++..++..+|+
T Consensus 2 ~~~~~~~~~l~~~~~~~~~~~~----~~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 2 ERLEEALDKLPEREREVILLRF----GEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred HHHHHHHHhCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 3577889999999999999999 78999999999999999999999999998874
No 134
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=98.18 E-value=3.6e-06 Score=77.64 Aligned_cols=57 Identities=28% Similarity=0.406 Sum_probs=49.5
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchhh
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHF 531 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~y 531 (534)
..|+++|++|+.|++ +|+|++|||+.||+|+++|++++++|+++|+.....-.+-.+
T Consensus 5 ~~Lte~qr~VL~Lr~-----~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l~~~ 61 (137)
T TIGR00721 5 TFLTERQIKVLELRE-----KGLSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDFVKF 61 (137)
T ss_pred CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHHHHH
Confidence 359999999999975 899999999999999999999999999999986555544433
No 135
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=98.14 E-value=5.1e-06 Score=76.96 Aligned_cols=51 Identities=25% Similarity=0.367 Sum_probs=47.0
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC 525 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~ 525 (534)
..|+|+|++||.+++ +++|++|||+.||+|+.+|++++++|+++||+....
T Consensus 5 ~~Lt~rqreVL~lr~-----~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t 55 (141)
T PRK03975 5 SFLTERQIEVLRLRE-----RGLTQQEIADILGTSRANVSSIEKRARENIEKARET 55 (141)
T ss_pred cCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 469999999999965 899999999999999999999999999999987654
No 136
>PRK04217 hypothetical protein; Provisional
Probab=98.11 E-value=5.9e-06 Score=73.49 Aligned_cols=56 Identities=20% Similarity=0.032 Sum_probs=51.5
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcch
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLS 529 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~ 529 (534)
..|++.|++|+.++| .+++|++|||+.+|||+.||++++.+|+++|++.+......
T Consensus 41 ~~Lt~eereai~l~~----~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~~~ 96 (110)
T PRK04217 41 IFMTYEEFEALRLVD----YEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGREL 96 (110)
T ss_pred ccCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhccce
Confidence 569999999999999 89999999999999999999999999999999998765543
No 137
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=98.00 E-value=3.1e-05 Score=67.84 Aligned_cols=54 Identities=30% Similarity=0.370 Sum_probs=43.5
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD 527 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~ 527 (534)
.-|+++|++++.++| .+++|+.|||+.+|||+.+|...+.||.++|...-..-+
T Consensus 16 ~LLT~kQ~~~l~lyy----~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~yE~kL~ 69 (101)
T PF04297_consen 16 ELLTEKQREILELYY----EEDLSLSEIAEELGISRQAVYDSIKRAEKKLEEYEEKLG 69 (101)
T ss_dssp GGS-HHHHHHHHHHC----TS---HHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHHH-
T ss_pred HHCCHHHHHHHHHHH----ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 449999999999999 899999999999999999999999999999987654443
No 138
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.
Probab=97.88 E-value=5.9e-05 Score=69.29 Aligned_cols=60 Identities=13% Similarity=0.227 Sum_probs=54.1
Q ss_pred HHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCC--CCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449 460 HMKKDVFRILESLDSRERQVLVLRYGLNDHRP--KSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE 523 (534)
Q Consensus 460 el~e~L~~~L~~L~~rEReVL~LryGL~d~e~--~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l 523 (534)
...+.|..+|+.|++.+++||.++| +.+ +|..+||..||+|+.+|+++..+|+.+|+..+
T Consensus 71 ~~~~~I~~~l~~Ld~~er~II~~rY----~~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~l 132 (134)
T TIGR01636 71 RNRDAIENCLNEADEQTRVIIQELY----MKKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEEL 132 (134)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHH----ccCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 4566789999999999999999999 443 59999999999999999999999999999765
No 139
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=97.83 E-value=3.7e-05 Score=58.25 Aligned_cols=47 Identities=30% Similarity=0.309 Sum_probs=42.3
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
..|+++|+.|+.+.+ .++|.+|||+.+|+|+.+|+++..+++.+|..
T Consensus 2 ~~l~~~e~~i~~~~~-----~g~s~~eia~~l~is~~tv~~~~~~~~~kl~~ 48 (58)
T smart00421 2 ASLTPREREVLRLLA-----EGLTNKEIAERLGISEKTVKTHLSNIMRKLGV 48 (58)
T ss_pred CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence 468999999987744 78999999999999999999999999999874
No 140
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=97.73 E-value=6.8e-05 Score=58.65 Aligned_cols=47 Identities=30% Similarity=0.325 Sum_probs=41.7
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
..|+++|.+|+.+.. .|+|.+|||+.+|||..||+.+..++++||.-
T Consensus 2 ~~LT~~E~~vl~~l~-----~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 2 PSLTERELEVLRLLA-----QGMSNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp GSS-HHHHHHHHHHH-----TTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred CccCHHHHHHHHHHH-----hcCCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 469999999999987 89999999999999999999999999999874
No 141
>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=97.63 E-value=0.00013 Score=55.34 Aligned_cols=46 Identities=30% Similarity=0.388 Sum_probs=41.7
Q ss_pred CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
|+++|++|+.+.+ .++|.+|||+.+|+|+.+|+.+..+++++|+..
T Consensus 1 l~~~e~~i~~~~~-----~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~~ 46 (57)
T cd06170 1 LTPREREVLRLLA-----EGKTNKEIADILGISEKTVKTHLRNIMRKLGVK 46 (57)
T ss_pred CCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 6899999998854 789999999999999999999999999998864
No 142
>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This entry is represented by Streptococcus phage 7201, Orf19. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several hypothetical, highly conserved Streptococcal and related phage proteins. The function of this family is unknown.
Probab=97.60 E-value=0.00031 Score=61.38 Aligned_cols=55 Identities=27% Similarity=0.462 Sum_probs=49.9
Q ss_pred HHHHHHHHHhhCC-HHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449 461 MKKDVFRILESLD-SRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL 519 (534)
Q Consensus 461 l~e~L~~~L~~L~-~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL 519 (534)
.+..+..+++.|+ +.+|.||.++| ..+++..+||+.||+|+.+|..+..+|++.|
T Consensus 44 ~k~ei~~~I~~l~d~~~r~iL~~~Y----i~~~~~~~I~~~l~~S~~t~yr~~~~Al~~L 99 (100)
T PF07374_consen 44 EKLEIRRAINKLEDPDERLILRMRY----INKLTWEQIAEELNISRRTYYRIHKKALKEL 99 (100)
T ss_pred HHHHHHHHHHHccChhHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence 4456888888885 79999999999 8899999999999999999999999999876
No 143
>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=97.60 E-value=0.00012 Score=60.42 Aligned_cols=47 Identities=19% Similarity=0.136 Sum_probs=41.9
Q ss_pred HHHHHHhhCCHHHHHHHhhH-hcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 464 DVFRILESLDSRERQVLVLR-YGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 464 ~L~~~L~~L~~rEReVL~Lr-yGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
.+.+-|+.||++.++++.|. | .+++|++|||+.||+|..+|++++++
T Consensus 8 ~~~~~l~~l~~~~r~af~L~R~----~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 8 KLAERLTWVDSLAEAAAALARE----EAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred hHHHHHhcCCHHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 45667899999999999995 4 58999999999999999999998875
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=97.48 E-value=0.00039 Score=54.08 Aligned_cols=48 Identities=33% Similarity=0.480 Sum_probs=42.1
Q ss_pred CCHHHHHHHhhHh--cCCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449 472 LDSRERQVLVLRY--GLNDH-RPKSLEEIGKLFHVSKEWIRKLEKKAMTKL 519 (534)
Q Consensus 472 L~~rEReVL~Lry--GL~d~-e~~Sl~EIA~~LgISrerVRqi~~RAL~KL 519 (534)
|+++|++||..-| |..|. .+.|+.|||+.||||+++|..++++|.+||
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 7899999998766 44443 578999999999999999999999999987
No 145
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=97.44 E-value=0.0002 Score=61.96 Aligned_cols=48 Identities=27% Similarity=0.173 Sum_probs=41.7
Q ss_pred HHHHHH-hhCCHHHHHHHhhHhcCCC---CCCCCHHHHHHHhCCCHHHHHHH
Q 009449 464 DVFRIL-ESLDSRERQVLVLRYGLND---HRPKSLEEIGKLFHVSKEWIRKL 511 (534)
Q Consensus 464 ~L~~~L-~~L~~rEReVL~LryGL~d---~e~~Sl~EIA~~LgISrerVRqi 511 (534)
.+...| ..|+|+|+.+|.+||||.+ ..++|++|||+.+|||+.+|...
T Consensus 24 ~l~~~l~~lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~ 75 (94)
T TIGR01321 24 DMQLLLELILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRG 75 (94)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHH
Confidence 455566 4599999999999999987 57899999999999999999754
No 146
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=97.42 E-value=0.00024 Score=69.54 Aligned_cols=46 Identities=13% Similarity=0.196 Sum_probs=43.8
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
.|+|+|++|+.+.- +|+|.+|||+.||+|..||+.+..+.++||.-
T Consensus 137 ~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v 182 (207)
T PRK15411 137 SLSRTESSMLRMWM-----AGQGTIQISDQMNIKAKTVSSHKGNIKRKIKT 182 (207)
T ss_pred cCCHHHHHHHHHHH-----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence 49999999999996 89999999999999999999999999999984
No 147
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=97.40 E-value=0.00031 Score=67.26 Aligned_cols=48 Identities=27% Similarity=0.330 Sum_probs=44.6
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
..|+|+|++|+.+.- +|+|.+|||+.|++|..||+....++++||.-.
T Consensus 132 ~~LSpRErEVLrLLA-----qGkTnKEIAe~L~IS~rTVkth~srImkKLgV~ 179 (198)
T PRK15201 132 RHFSVTERHLLKLIA-----SGYHLSETAALLSLSEEQTKSLRRSIMRKLHVK 179 (198)
T ss_pred CCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 459999999999996 899999999999999999999999999999753
No 148
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=97.37 E-value=0.0003 Score=68.09 Aligned_cols=47 Identities=32% Similarity=0.265 Sum_probs=43.9
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
..|++||++|+.+.- +|+|.+|||+.|+||..||+.+..+.++||--
T Consensus 149 ~~Lt~rE~evl~~~~-----~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~v 195 (216)
T PRK10840 149 KRLSPKESEVLRLFA-----EGFLVTEIAKKLNRSIKTISSQKKSAMMKLGV 195 (216)
T ss_pred ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 359999999999986 89999999999999999999999999999953
No 149
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=97.34 E-value=0.00033 Score=69.18 Aligned_cols=52 Identities=13% Similarity=0.091 Sum_probs=47.6
Q ss_pred HHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 466 FRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 466 ~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
.++...|+|+|++|+.+.- +|+|.+|||+.|++|..||+.+..+.++||.-.
T Consensus 138 ~~~~~~LS~RE~eVL~Lia-----~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv~ 189 (217)
T PRK13719 138 LEAKNKVTKYQNDVFILYS-----FGFSHEYIAQLLNITVGSSKNKISEILKFFGIS 189 (217)
T ss_pred hhccCCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 4566889999999999986 899999999999999999999999999999743
No 150
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=97.33 E-value=0.00037 Score=68.49 Aligned_cols=47 Identities=26% Similarity=0.283 Sum_probs=44.1
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
..|++||++|+.+.. +|+|.+|||+.|+||..||+.+..+.++||--
T Consensus 133 ~~LT~RE~eVL~ll~-----~G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv 179 (207)
T PRK11475 133 RMLSPTEREILRFMS-----RGYSMPQIAEQLERNIKTIRAHKFNVMSKLGV 179 (207)
T ss_pred CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 469999999999986 89999999999999999999999999999963
No 151
>PRK13870 transcriptional regulator TraR; Provisional
Probab=97.31 E-value=0.00037 Score=69.76 Aligned_cols=47 Identities=26% Similarity=0.228 Sum_probs=43.9
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
.|++||++||.+-- +|+|..|||.+||||..||..++..|++||--.
T Consensus 173 ~LT~RE~E~L~W~A-----~GKT~~EIa~ILgISe~TV~~Hl~na~~KLga~ 219 (234)
T PRK13870 173 WLDPKEATYLRWIA-----VGKTMEEIADVEGVKYNSVRVKLREAMKRFDVR 219 (234)
T ss_pred CCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence 59999999999986 999999999999999999999999999999643
No 152
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=97.29 E-value=0.0004 Score=69.22 Aligned_cols=51 Identities=24% Similarity=0.271 Sum_probs=46.0
Q ss_pred HhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449 469 LESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET 524 (534)
Q Consensus 469 L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~ 524 (534)
...|+++|++||.+.. +|+|.+|||++||||..||+.++.+|++||+..-.
T Consensus 169 ~~~Lt~re~evl~~~a-----~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~~ 219 (232)
T TIGR03541 169 AGVLSEREREVLAWTA-----LGRRQADIAAILGISERTVENHLRSARRKLGVATT 219 (232)
T ss_pred hccCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCH
Confidence 3479999999999965 89999999999999999999999999999985433
No 153
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=97.28 E-value=0.00044 Score=69.99 Aligned_cols=50 Identities=20% Similarity=0.236 Sum_probs=45.7
Q ss_pred HhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449 469 LESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE 523 (534)
Q Consensus 469 L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l 523 (534)
+..|+++|++|+.+.. +|+|.+|||+.||||..||+.++.++++||.-.-
T Consensus 188 ~~~LT~RE~evl~l~a-----~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~n 237 (247)
T TIGR03020 188 AGLITAREAEILAWVR-----DGKTNEEIAAILGISSLTVKNHLQHIFKKLDVRN 237 (247)
T ss_pred ccCCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCCCC
Confidence 4579999999999975 8999999999999999999999999999998543
No 154
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=97.26 E-value=0.00048 Score=68.15 Aligned_cols=47 Identities=19% Similarity=0.188 Sum_probs=44.5
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
..|+++|++|+.+.+ +|+|.+|||+.|++|..||+.+..++++||.-
T Consensus 154 ~~Lt~rE~~Vl~l~~-----~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v 200 (216)
T PRK10100 154 ALLTHREKEILNKLR-----IGASNNEIARSLFISENTVKTHLYNLFKKIAV 200 (216)
T ss_pred CCCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 469999999999998 69999999999999999999999999999975
No 155
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=97.25 E-value=0.0005 Score=69.07 Aligned_cols=47 Identities=19% Similarity=0.306 Sum_probs=44.2
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
.|+++|++||.+.. +|+|..|||++||||..||+.++.++++||--.
T Consensus 179 ~LT~rE~evl~~~a-----~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~~~ 225 (240)
T PRK10188 179 NFSKREKEILKWTA-----EGKTSAEIAMILSISENTVNFHQKNMQKKFNAP 225 (240)
T ss_pred CCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 59999999999997 899999999999999999999999999999743
No 156
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=97.25 E-value=0.0011 Score=64.19 Aligned_cols=66 Identities=21% Similarity=0.183 Sum_probs=56.6
Q ss_pred HHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchh
Q 009449 460 HMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSH 530 (534)
Q Consensus 460 el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~ 530 (534)
.....+...+.+|+||||+|+...- .|+..++||..||||.-||..+..+.++|++......-++-
T Consensus 131 ~~~~~~~~~l~tLT~RERqVl~~vV-----~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~SlaeLvr~ 196 (202)
T COG4566 131 DRQAAIRARLATLTPRERQVLDLVV-----RGLMNKQIAFDLGISERTVELHRANVMEKMQARSLAELVRM 196 (202)
T ss_pred HHHHHHHHHHHhcCHHHHHHHHHHH-----cCcccHHHHHHcCCchhhHHHHHHHHHHHHhhccHHHHHHH
Confidence 3456788899999999999999886 89999999999999999999999999999987654444443
No 157
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=97.24 E-value=0.00047 Score=67.86 Aligned_cols=48 Identities=27% Similarity=0.254 Sum_probs=44.6
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
..|++||++|+++.- +|+|.+|||+.|++|..||+.+.++.++||.-.
T Consensus 147 ~~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~v~ 194 (211)
T COG2197 147 ELLTPRELEVLRLLA-----EGLSNKEIAEELNLSEKTVKTHVSNILRKLGVR 194 (211)
T ss_pred CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHhHHHHHHHHHHHHcCCC
Confidence 469999999999985 899999999999999999999999999999743
No 158
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=97.13 E-value=0.0014 Score=51.36 Aligned_cols=50 Identities=28% Similarity=0.377 Sum_probs=44.7
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET 524 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~ 524 (534)
..|+++|.+|+.+.- .|+|..|||..+|+|..||+....++.+||.-.-+
T Consensus 3 ~~Lt~rE~~v~~l~~-----~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~~r 52 (65)
T COG2771 3 ADLTPREREILRLVA-----QGKSNKEIARILGISEETVKTHLRNIYRKLGVKNR 52 (65)
T ss_pred ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCH
Confidence 359999999998886 78999999999999999999999999999975443
No 159
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=97.11 E-value=0.00063 Score=50.64 Aligned_cols=41 Identities=22% Similarity=0.248 Sum_probs=25.0
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
..|++.||..|...+ .+|+|..+||+.||++++||...+.|
T Consensus 3 ~~Lt~~eR~~I~~l~----~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEALL----EQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHHHH----CS---HHHHHHHTT--HHHHHHHHHH
T ss_pred cchhhhHHHHHHHHH----HcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 468999999999988 79999999999999999999988776
No 160
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=97.10 E-value=0.0011 Score=58.68 Aligned_cols=52 Identities=21% Similarity=0.153 Sum_probs=48.4
Q ss_pred CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449 472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD 527 (534)
Q Consensus 472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~ 527 (534)
|+..|-+.|+|.+ .+++|++|-|+.||||+.|+..++..|.+|+-..+....
T Consensus 42 L~~dElEAiRL~D----~egl~QeeaA~~MgVSR~T~~ril~~ARkKiA~ALv~Gk 93 (106)
T PF02001_consen 42 LTVDELEAIRLVD----YEGLSQEEAAERMGVSRPTFQRILESARKKIADALVEGK 93 (106)
T ss_pred eeHHHHHHHHHHH----HcCCCHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHCCC
Confidence 8889999999999 899999999999999999999999999999998876544
No 161
>PRK09483 response regulator; Provisional
Probab=96.98 E-value=0.0013 Score=62.55 Aligned_cols=46 Identities=22% Similarity=0.390 Sum_probs=42.8
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR 520 (534)
..|+++|++|+.+.. +|+|.+|||+.|++|..||+.+.++.++||-
T Consensus 147 ~~Lt~rE~~vl~~~~-----~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~ 192 (217)
T PRK09483 147 ASLSERELQIMLMIT-----KGQKVNEISEQLNLSPKTVNSYRYRMFSKLN 192 (217)
T ss_pred cccCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 469999999998865 8999999999999999999999999999995
No 162
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=96.93 E-value=0.0019 Score=63.64 Aligned_cols=52 Identities=33% Similarity=0.440 Sum_probs=45.5
Q ss_pred hCCHHHHHHHhhHh--cCCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 471 SLDSRERQVLVLRY--GLNDH-RPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 471 ~L~~rEReVL~Lry--GL~d~-e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
.|+|+|++||+.-| |..|. ...+++|||+.||||++++.+++++|.+||=..
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~~ 209 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIEA 209 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 59999999999876 44444 678999999999999999999999999998654
No 163
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=96.86 E-value=0.023 Score=59.61 Aligned_cols=158 Identities=20% Similarity=0.143 Sum_probs=101.0
Q ss_pred HHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchH
Q 009449 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN 378 (534)
Q Consensus 299 ~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~ 378 (534)
..+..-.+.++.---+|+++-...||.+||+|+...+.-.+=-|-+ .-..|++..-|+.-++.+++..+.-..|.+.
T Consensus 9 ~~~r~~~~r~~a~L~r~~rd~dlAEEa~~dA~~~Ale~WPr~G~P~--~PaAWL~~v~R~~aiD~~Rr~~~~~~~~~el- 85 (415)
T COG4941 9 AAARIERPRAMAALARYLRDLDLAEEALQDAFAAALERWPRAGPPR--NPAAWLIAVGRNRAIDRVRRRARRDAAPPEL- 85 (415)
T ss_pred HHHHHhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHhCcccCCCC--ChHHHHHHHHhhhHHHHHHHHHHhccCChhh-
Confidence 3344444555555556777767899999999986544433322222 3578999999999999999887544444321
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHH
Q 009449 379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMR 458 (534)
Q Consensus 379 ~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~ 458 (534)
.++.+ +...+ ..+ .+++....
T Consensus 86 ----------------------------------------------~~~~e-----~~e~~---~a~-----~~~d~~i~ 106 (415)
T COG4941 86 ----------------------------------------------LLSDE-----DEEME---EAE-----ALDDEHIR 106 (415)
T ss_pred ----------------------------------------------ccccc-----chhhh---ccc-----cccccccc
Confidence 00110 00000 000 01111111
Q ss_pred HHHHHHHHHHH-hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 459 QHMKKDVFRIL-ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 459 ~el~e~L~~~L-~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
.+....|.-|. -.|++.+|-.+.||. .-|+|..|||..|=|+..++-|.+.||+++++..
T Consensus 107 Dd~LRLiFvccHPal~~~~riALtLR~----v~GLs~~eIArAFLv~e~am~QRivRAK~ri~~a 167 (415)
T COG4941 107 DDRLRLIFVCCHPALPPEQRIALTLRL----VGGLSTAEIARAFLVPEAAMAQRIVRAKARIREA 167 (415)
T ss_pred hhhHHhhhhhcCCCCChhhHHHHHHHH----HcCCcHHHHHHHHcCCcHHHHHHHHHHHHHHHhc
Confidence 11112222222 469999999999999 8899999999999999999999999999999964
No 164
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=96.77 E-value=0.0025 Score=59.04 Aligned_cols=47 Identities=26% Similarity=0.268 Sum_probs=43.1
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
..|+++|++|+.+. .++++.+|||+.+++|..||+.+..++++||.-
T Consensus 148 ~~lt~~e~~vl~l~-----~~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~ 194 (211)
T PRK15369 148 PLLTPRERQILKLI-----TEGYTNRDIAEQLSISIKTVETHRLNMMRKLDV 194 (211)
T ss_pred cCCCHHHHHHHHHH-----HCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 45999999999984 489999999999999999999999999999963
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=96.64 E-value=0.012 Score=53.45 Aligned_cols=61 Identities=18% Similarity=0.207 Sum_probs=53.6
Q ss_pred HHHHHHHHHH-hhCCHHHHHHHhhHhcCCCCC--CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449 460 HMKKDVFRIL-ESLDSRERQVLVLRYGLNDHR--PKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET 524 (534)
Q Consensus 460 el~e~L~~~L-~~L~~rEReVL~LryGL~d~e--~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~ 524 (534)
.....+..++ +.|++.+|+||..+| .. +++..+|+..+|+|+.+...+..+|+.++-..+.
T Consensus 67 ~~~~~i~~ai~~~l~~~~r~Il~~~Y----l~~~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~l~ 130 (132)
T TIGR01637 67 QEARAIVNAIVNQLDEISRQILYDKY----LEPDQKYDYQIMMELGYSHRQYYRIKKRALLRFATLYG 130 (132)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHH----cCccccchHHHHHHhCCcHHHHHHHHHHHHHHHHHHhC
Confidence 3445677777 999999999999999 55 8899999999999999999999999999887654
No 166
>PRK10651 transcriptional regulator NarL; Provisional
Probab=96.59 E-value=0.0036 Score=58.73 Aligned_cols=47 Identities=19% Similarity=0.282 Sum_probs=43.4
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
..|+++|++|+.+.. ++++.++||+.+++|..||+.+..+.++||.-
T Consensus 154 ~~Lt~rE~~vl~~l~-----~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~ 200 (216)
T PRK10651 154 NQLTPRERDILKLIA-----QGLPNKMIARRLDITESTVKVHVKHMLKKMKL 200 (216)
T ss_pred ccCCHHHHHHHHHHH-----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 459999999999875 88999999999999999999999999999964
No 167
>PRK01381 Trp operon repressor; Provisional
Probab=96.56 E-value=0.0023 Score=55.80 Aligned_cols=48 Identities=23% Similarity=0.187 Sum_probs=40.0
Q ss_pred HHHHHHHHhh-CCHHHHHHHhhHhcCCC---CCCCCHHHHHHHhCCCHHHHH
Q 009449 462 KKDVFRILES-LDSRERQVLVLRYGLND---HRPKSLEEIGKLFHVSKEWIR 509 (534)
Q Consensus 462 ~e~L~~~L~~-L~~rEReVL~LryGL~d---~e~~Sl~EIA~~LgISrerVR 509 (534)
.+.+...|.. |+|+|+.+|..||++.. ..++|+.|||+.+|||..||.
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 3455556654 99999999999999975 346999999999999999885
No 168
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=96.51 E-value=0.0022 Score=57.99 Aligned_cols=48 Identities=23% Similarity=0.457 Sum_probs=44.8
Q ss_pred CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449 472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET 524 (534)
Q Consensus 472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~ 524 (534)
|+++|-+||.||- +|.|++|||++||-|+..|+-++.+|+.++.+...
T Consensus 9 lte~qikvl~lRe-----kG~tQ~eIA~~L~TTraNvSaIEkrA~enIekarn 56 (143)
T COG1356 9 LTEQQIKVLVLRE-----KGLTQSEIARILKTTRANVSAIEKRALENIEKARN 56 (143)
T ss_pred eehhheeeeehhh-----ccccHHHHHHHHccchhhHHHHHHHHHHHHHHHHH
Confidence 8999999999996 99999999999999999999999999999987644
No 169
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=96.50 E-value=0.0098 Score=51.90 Aligned_cols=49 Identities=31% Similarity=0.343 Sum_probs=44.7
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
.-|+.+|+..+.++| ..++|+.|||+.++||+++|...+.|+-..|-..
T Consensus 16 sLLT~KQ~~Y~~lyy----~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~Y 64 (105)
T COG2739 16 SLLTKKQKNYLELYY----LDDLSLSEIAEEFNVSRQAIYDNIKRTEKILEDY 64 (105)
T ss_pred HHHhHHHHHHHHHHH----HhhccHHHHHHHhCccHHHHHHHHHHHHHHHHHH
Confidence 448999999999999 8899999999999999999999999998877654
No 170
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=96.47 E-value=0.0078 Score=55.46 Aligned_cols=55 Identities=25% Similarity=0.252 Sum_probs=48.0
Q ss_pred HHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449 464 DVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE 523 (534)
Q Consensus 464 ~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l 523 (534)
.+...+..|+++|++|+.+.+ .+++.++||+.+|+|..+|+.+..++++||+..-
T Consensus 134 ~~~~~~~~l~~~e~~vl~~~~-----~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~~ 188 (202)
T PRK09390 134 DIRARIASLSERERQVMDGLV-----AGLSNKVIARDLDISPRTVEVYRANVMTKMQAGS 188 (202)
T ss_pred HHHHHHHhhhhhHHHHHHHHH-----ccCchHHHHHHcCCCHHHHHHHHHHHHHHHcccc
Confidence 455667889999999999754 6899999999999999999999999999997543
No 171
>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=96.31 E-value=0.0031 Score=45.38 Aligned_cols=32 Identities=22% Similarity=0.213 Sum_probs=24.1
Q ss_pred HHHHHhhccC-CCCCCchHHHHHHhhchHHHHH
Q 009449 224 SAERALNSRG-RRLTIARNEAEMSKGVQVVANL 255 (534)
Q Consensus 224 ~~~~~~~~~~-~~lLt~~eE~~L~~~iq~~~~l 255 (534)
.++-|++..+ .||||++||++|+++|+.+...
T Consensus 3 ~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~~~ 35 (37)
T PF00140_consen 3 SLRLYLKEIGRYPLLTAEEEIELARRIRKGDEA 35 (37)
T ss_dssp HHHHHHHHHHHS-EETTHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHHh
Confidence 3455555444 6999999999999999988654
No 172
>PRK15320 transcriptional activator SprB; Provisional
Probab=96.25 E-value=0.0077 Score=58.82 Aligned_cols=66 Identities=17% Similarity=0.270 Sum_probs=51.8
Q ss_pred CChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 450 KSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 450 ~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
++||+.+..-. .-....+--.|+++|.+|+.+-- +|+|.+|||+.|++|..||+....+.+.||.-
T Consensus 144 ~~~~~~~~~~~-~~~~~~~~~~LSdREIEVL~LLA-----kG~SNKEIAekL~LS~KTVSTYKnRLLeKLgA 209 (251)
T PRK15320 144 ETPEEVLFNIN-QYAWWNLPPGVTQAKYALLILLS-----SGHPAIELAKKFGLGTKTVSIYRKKVMYRLGM 209 (251)
T ss_pred CChHHHhhhcc-ceeeecCCCCCCHHHHHHHHHHH-----cCCCHHHHHHHhccchhhHHHHHHHHHHHcCC
Confidence 46776554321 11223333679999999999986 89999999999999999999999999999873
No 173
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=96.24 E-value=0.0099 Score=51.38 Aligned_cols=52 Identities=21% Similarity=0.121 Sum_probs=47.4
Q ss_pred CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449 472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD 527 (534)
Q Consensus 472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~ 527 (534)
|+..|-+.|+|.. +++++++|-|.+||||+.|+...+..|++|+-.++....
T Consensus 34 lt~eElEAlRLvD----~~~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~aLveGk 85 (99)
T COG1342 34 LTIEELEALRLVD----YEGLTQEEAALRMGISRQTFWRLLTSARKKVADALVEGK 85 (99)
T ss_pred ecHHHHHHHHHHh----HhhccHHHHHHHhcccHHHHHHHHHHHHHHHHHHHhcCC
Confidence 7788888999998 999999999999999999999999999999998876543
No 174
>PRK10403 transcriptional regulator NarP; Provisional
Probab=96.03 E-value=0.012 Score=55.15 Aligned_cols=48 Identities=21% Similarity=0.221 Sum_probs=43.5
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
..|+++|.+|+.+.. +++|.+|||+.+|+|..||+.+..+.++||.-.
T Consensus 152 ~~Lt~~e~~vl~~~~-----~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~ 199 (215)
T PRK10403 152 SVLTERELDVLHELA-----QGLSNKQIASVLNISEQTVKVHIRNLLRKLNVR 199 (215)
T ss_pred ccCCHHHHHHHHHHH-----CCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 359999999999875 789999999999999999999999999999643
No 175
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=95.77 E-value=0.017 Score=53.89 Aligned_cols=50 Identities=26% Similarity=0.243 Sum_probs=44.5
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET 524 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~ 524 (534)
..|+++|.+|+.+.. +++|.++||+.+++|..||+.+..+.++||.-.-+
T Consensus 136 ~~Lt~~E~~il~~l~-----~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~~~~~ 185 (196)
T PRK10360 136 DPLTKRERQVAEKLA-----QGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSND 185 (196)
T ss_pred cCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCH
Confidence 369999999999976 68999999999999999999999999999974433
No 176
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=95.65 E-value=0.022 Score=53.36 Aligned_cols=46 Identities=22% Similarity=0.157 Sum_probs=41.5
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
.|+++|.+|+.+.. +++|.+|||+.+++|..||+.+..++++||.-
T Consensus 149 ~lt~re~~vl~~l~-----~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~~ 194 (210)
T PRK09935 149 VLSNREVTILRYLV-----SGLSNKEIADQLLLSNKTVSAHKSNIYGKLGL 194 (210)
T ss_pred cCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 48999999988654 78999999999999999999999999999963
No 177
>PRK13558 bacterio-opsin activator; Provisional
Probab=95.65 E-value=0.02 Score=65.05 Aligned_cols=50 Identities=20% Similarity=0.180 Sum_probs=45.1
Q ss_pred HhhCCHHHHHHHhhHhcCCCCCCC-------CHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 469 LESLDSRERQVLVLRYGLNDHRPK-------SLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 469 L~~L~~rEReVL~LryGL~d~e~~-------Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
...|+++|+++|..-| ..|| |.+|||+.||||+.|+.+++++|.+||=..
T Consensus 605 ~~~lt~~q~e~l~~a~----~~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l~~~ 661 (665)
T PRK13558 605 ENDLTDRQLTALQKAY----VSGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKLVGA 661 (665)
T ss_pred hhhCCHHHHHHHHHHH----HcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4679999999999998 5566 999999999999999999999999998644
No 178
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=95.64 E-value=0.022 Score=53.44 Aligned_cols=47 Identities=23% Similarity=0.335 Sum_probs=43.2
Q ss_pred HhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449 469 LESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520 (534)
Q Consensus 469 L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR 520 (534)
+..|+++|.+|+.+.. .+.|.+|||+.+++|..||+.+..+.++||.
T Consensus 141 ~~~lt~~E~~vl~~l~-----~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~ 187 (204)
T PRK09958 141 LDSLSKQEISVMRYIL-----DGKDNNDIAEKMFISNKTVSTYKSRLMEKLE 187 (204)
T ss_pred cccCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 3569999999999887 7889999999999999999999999999994
No 179
>PRK04841 transcriptional regulator MalT; Provisional
Probab=95.61 E-value=0.018 Score=67.35 Aligned_cols=48 Identities=31% Similarity=0.277 Sum_probs=44.4
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
..|+++|.+|+.+.. +|+|.+|||..|+||..||+.++++...||.-.
T Consensus 837 ~~lt~~e~~v~~~~~-----~g~~~~~ia~~l~~s~~tv~~h~~~~~~kl~v~ 884 (903)
T PRK04841 837 SPLTQREWQVLGLIY-----SGYSNEQIAGELDVAATTIKTHIRNLYQKLGIA 884 (903)
T ss_pred CCCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 349999999999986 899999999999999999999999999999743
No 180
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=95.60 E-value=2.9 Score=47.90 Aligned_cols=34 Identities=15% Similarity=0.135 Sum_probs=28.7
Q ss_pred CCCchhHHHHHHhhccCCCCCCchHHHHHHhhchHHH
Q 009449 217 LKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVA 253 (534)
Q Consensus 217 ~~~~~~~~~~~~~~~~~~~lLt~~eE~~L~~~iq~~~ 253 (534)
..||.+-|+ ..+...+|||.++||++|++|..+.
T Consensus 102 t~DPVRMYL---REMG~V~LLTREgEIeIAKRIE~G~ 135 (619)
T PRK05658 102 TDDPVRMYL---REMGTVELLTREGEIEIAKRIEAGE 135 (619)
T ss_pred CCChHHHHH---HHhccCcCCCcHHHHHHHHHHHHHH
Confidence 368888877 4677889999999999999998764
No 181
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=94.90 E-value=0.054 Score=46.51 Aligned_cols=40 Identities=25% Similarity=0.271 Sum_probs=32.8
Q ss_pred HhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009449 469 LESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKA 515 (534)
Q Consensus 469 L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RA 515 (534)
+..|++| .+|+.+.- .++|..|||+.+|||+.||..+ .++
T Consensus 34 ~~~Ls~R-~~I~~ll~-----~G~S~~eIA~~LgISrsTIyRi-~R~ 73 (88)
T TIGR02531 34 IQSLAQR-LQVAKMLK-----QGKTYSDIEAETGASTATISRV-KRC 73 (88)
T ss_pred HHhhhHH-HHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHH-HHh
Confidence 3458999 78887764 7899999999999999999984 444
No 182
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=94.86 E-value=0.024 Score=42.54 Aligned_cols=33 Identities=27% Similarity=0.267 Sum_probs=23.3
Q ss_pred HHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009449 478 QVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKA 515 (534)
Q Consensus 478 eVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RA 515 (534)
+||.++. +++|..+||+.||||+.||+++..+-
T Consensus 9 ~ii~l~~-----~G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 9 QIIRLLR-----EGWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp -HHHHHH-----HT--HHHHHHHHTS-HHHHHHHHT--
T ss_pred HHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 3566665 59999999999999999999987663
No 183
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=94.57 E-value=0.085 Score=40.64 Aligned_cols=50 Identities=16% Similarity=0.264 Sum_probs=42.2
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE 523 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l 523 (534)
+|+..++-++.|.| | -.+.+++.+|..+|||+++|.++.+....-|-..+
T Consensus 2 kLs~~d~lll~L~~-L--R~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l 51 (53)
T PF13613_consen 2 KLSLEDQLLLTLMY-L--RLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVL 51 (53)
T ss_pred CCCHHHHHHHHHHH-H--HcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhc
Confidence 57888888888777 2 37899999999999999999999999888776543
No 184
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=94.47 E-value=0.049 Score=57.17 Aligned_cols=37 Identities=19% Similarity=0.306 Sum_probs=33.9
Q ss_pred HHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449 477 RQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMT 517 (534)
Q Consensus 477 ReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~ 517 (534)
-.|-.||| .+++|++|||+.|||||.+|.+++.+|++
T Consensus 19 ~~vA~lYY----~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~ 55 (318)
T PRK15418 19 ARIAWFYY----HDGLTQSEIGERLGLTRLKVSRLLEKGRQ 55 (318)
T ss_pred HHHHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34778999 89999999999999999999999999976
No 185
>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=94.47 E-value=0.13 Score=47.30 Aligned_cols=57 Identities=23% Similarity=0.399 Sum_probs=46.2
Q ss_pred HHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449 461 MKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL 519 (534)
Q Consensus 461 l~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL 519 (534)
.++.|...++.|.+.++.||.+||+= ..++|..+||..|+++..+++.....-...+
T Consensus 71 ~k~~id~~~~~l~de~k~Ii~lry~~--r~~~TW~~IA~~l~i~erta~r~~~~fK~~i 127 (130)
T PF05263_consen 71 QKEAIDRWLETLIDEEKRIIKLRYDR--RSRRTWYQIAQKLHISERTARRWRDRFKNDI 127 (130)
T ss_pred HHHHHHHHHHhhCHHHHHHHHHHHcc--cccchHHHHHHHhCccHHHHHHHHHHHHHHh
Confidence 34567788899999999999999932 2359999999999999999988766554433
No 186
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=94.44 E-value=0.05 Score=38.04 Aligned_cols=27 Identities=19% Similarity=0.453 Sum_probs=20.2
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 491 PKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 491 ~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
++|.+|||+.+|+|+++|+ |++++|++
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 4789999999999999996 66677764
No 187
>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=94.35 E-value=0.095 Score=39.10 Aligned_cols=41 Identities=20% Similarity=0.314 Sum_probs=30.1
Q ss_pred CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009449 472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKA 515 (534)
Q Consensus 472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RA 515 (534)
|++.++.||..-+ ...+.|..|||+.+|+|..+|++++.+-
T Consensus 1 l~~~~~~Il~~l~---~~~~~t~~ela~~~~is~~tv~~~l~~L 41 (48)
T PF13412_consen 1 LDETQRKILNYLR---ENPRITQKELAEKLGISRSTVNRYLKKL 41 (48)
T ss_dssp --HHHHHHHHHHH---HCTTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCHHHHHHHHHHH---HcCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 5678888887766 2467999999999999999998766543
No 188
>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=94.14 E-value=0.21 Score=40.47 Aligned_cols=55 Identities=22% Similarity=0.259 Sum_probs=44.7
Q ss_pred HHHHHhc-HHHHHHHHHHhHHHHHHHHHHh----hC--CCCCHHHHHHHHHHHHHHhhhccC
Q 009449 287 KQHLAFG-WYCREELIKSTRPLVLFLARNY----RG--LGIPFSDLLQAGNVGVLQGAERFD 341 (534)
Q Consensus 287 ~~~l~~G-~~A~e~LI~~nlrLV~sIArrY----~~--~g~~~eDLiQEG~lgL~rA~ekFD 341 (534)
+.....| ..|.+++++.|.+++.+.+.+- .+ .+.--+|+-|+--..|++++.+|+
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 4445555 7899999999999999988762 22 245569999999999999999996
No 189
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=94.02 E-value=0.049 Score=40.59 Aligned_cols=33 Identities=24% Similarity=0.236 Sum_probs=24.2
Q ss_pred HHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 476 ERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 476 EReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
..+|+.|+- +|+|..+||+.+|||+.||..++.
T Consensus 11 ~~~i~~l~~-----~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 11 IEEIKELYA-----EGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHHH-----TT--HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHh
Confidence 455666664 789999999999999999988753
No 190
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=93.94 E-value=0.1 Score=34.55 Aligned_cols=36 Identities=17% Similarity=0.154 Sum_probs=28.4
Q ss_pred CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHH
Q 009449 472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKL 511 (534)
Q Consensus 472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi 511 (534)
+++.++..+...| ..+.|..+||+.+|+++.+|..+
T Consensus 6 ~~~~~~~~i~~~~----~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 6 LTPEQIEEARRLL----AAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHh
Confidence 4555666665566 46789999999999999999875
No 191
>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 993W gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator. GpQ positively regulates expression of the phage late gene operons. Bacterial host RNA polymerase modified by antitermination proteins transcribes through termination sites that otherwise prevent expression of the regulated genes [, ].; GO: 0003677 DNA binding, 0060567 negative regulation of transcription termination, DNA-dependent
Probab=93.49 E-value=0.43 Score=43.38 Aligned_cols=55 Identities=24% Similarity=0.204 Sum_probs=49.2
Q ss_pred HHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhh
Q 009449 468 ILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCR 526 (534)
Q Consensus 468 ~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~ 526 (534)
.|..-.|.+-++|.++| ..+.|...||..+++|...|++.+.+|-..+..++...
T Consensus 59 ~L~~~~~~~~~ll~~~Y----v~g~s~r~IA~~~~~s~~~ir~~l~~ae~~i~g~l~~~ 113 (125)
T PF06530_consen 59 RLKKRDPEEYDLLILYY----VYGWSKRQIARKLKCSEGKIRKRLQRAEGFIDGCLSML 113 (125)
T ss_pred HHHccCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHhhhhHhhhhHHh
Confidence 34557999999999999 89999999999999999999999999999999876543
No 192
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=93.28 E-value=0.91 Score=49.50 Aligned_cols=38 Identities=26% Similarity=0.380 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHH
Q 009449 381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSA 418 (534)
Q Consensus 381 i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~ 418 (534)
...+.+.+..|..++|++||.+|.|..+|+++..++..
T Consensus 110 ~~~l~~~~~~l~~~~g~~pt~~ewa~~~~~~~~~l~~~ 147 (415)
T PRK07598 110 YLRLIEVRERLTSELGHRPSLERWAKTADISLADLKPT 147 (415)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCcHHHHHHh
Confidence 34566778889999999999999998888776655544
No 193
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=92.65 E-value=1.6 Score=46.64 Aligned_cols=130 Identities=12% Similarity=0.165 Sum_probs=71.2
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhcHHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHH-HHH
Q 009449 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAG-NVG 332 (534)
Q Consensus 254 ~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l~~G~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG-~lg 332 (534)
++.+....|..++|+.||..+.|+..|++.+.+...+... .. ..++++.+.++ -..
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 3455667788889999999999999999998876543211 00 01111111100 001
Q ss_pred HHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCH
Q 009449 333 VLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSL 412 (534)
Q Consensus 333 L~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~ 412 (534)
+...+. |+.............++..+.+++. .+|..-...+ . ..+.-..|..-|.+|||+.+|+|.
T Consensus 274 l~d~i~--d~~~~~p~~~~~~~~~~~~l~~~l~------~L~~rEr~Vl----~--lrygl~~~~~~tl~EIa~~lgvs~ 339 (367)
T PRK09210 274 LGDFIE--DQDATSPADHAAYELLKEQLEDVLD------TLTDREENVL----R--LRFGLDDGRTRTLEEVGKVFGVTR 339 (367)
T ss_pred hhhhcc--CCCCCCHHHHHHHHHHHHHHHHHHH------hCCHHHHHHH----H--HHhccCCCCCccHHHHHHHHCCCH
Confidence 111111 1111223444556666777776664 2443211111 1 011111236789999999999999
Q ss_pred HHHHHHHH
Q 009449 413 AEIRSASE 420 (534)
Q Consensus 413 ~kv~~~l~ 420 (534)
++|+++..
T Consensus 340 erVrQi~~ 347 (367)
T PRK09210 340 ERIRQIEA 347 (367)
T ss_pred HHHHHHHH
Confidence 99998754
No 194
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=92.52 E-value=0.28 Score=44.03 Aligned_cols=50 Identities=20% Similarity=0.206 Sum_probs=44.0
Q ss_pred HHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 468 ILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 468 ~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
.+..|++.+.+-|.... ...=+++|+++.||||..|||..+.+.+.+|--
T Consensus 30 ~~~~L~~E~~~Fi~~Fi----~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 30 WFARLSPEQLEFIKLFI----KNRGNLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred hhhcCCHHHHHHHHHHH----HhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 36789999998888777 455599999999999999999999999999975
No 195
>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=92.35 E-value=2.2 Score=42.45 Aligned_cols=35 Identities=17% Similarity=0.311 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 009449 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (534)
Q Consensus 254 ~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~ 288 (534)
++.+....+....|++||.++-|+..|++.+.+..
T Consensus 88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~ 122 (238)
T TIGR02393 88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVRE 122 (238)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 44456677888899999999999999999988654
No 196
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=92.33 E-value=3.5 Score=46.17 Aligned_cols=36 Identities=22% Similarity=0.348 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHH
Q 009449 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH 289 (534)
Q Consensus 254 ~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~ 289 (534)
++.+....|...+|+.||..+.|+..|++.+.+...
T Consensus 359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~ 394 (509)
T PRK05901 359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVREI 394 (509)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 455567788888999999999999999999876553
No 197
>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]
Probab=92.02 E-value=0.17 Score=58.90 Aligned_cols=47 Identities=28% Similarity=0.239 Sum_probs=43.9
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
.|+.||.+|+.+.| +|+|.+|||+.+.||-.||+.+++....||.-.
T Consensus 831 ~Ls~RE~eVL~Lia-----~G~SN~eIa~~L~isl~TVKtH~rniy~KLgV~ 877 (894)
T COG2909 831 PLSQRELEVLGLIA-----QGLSNEEIAQELFISLTTVKTHIRNIYQKLGVA 877 (894)
T ss_pred CccHHHHHHHHHHH-----ccCCHHHHHHHHHHHHHHHHHHHHHHHHHhCcc
Confidence 38999999999999 899999999999999999999999999998643
No 198
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=91.82 E-value=0.27 Score=38.90 Aligned_cols=27 Identities=15% Similarity=0.174 Sum_probs=24.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEKKA 515 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~RA 515 (534)
.+|++..|||+.||+++.||.+...+-
T Consensus 11 ~~G~~~~eIA~~Lg~~~~TV~~W~~r~ 37 (58)
T PF06056_consen 11 LQGWSIKEIAEELGVPRSTVYSWKDRY 37 (58)
T ss_pred HcCCCHHHHHHHHCCChHHHHHHHHhh
Confidence 489999999999999999999988764
No 199
>PF13518 HTH_28: Helix-turn-helix domain
Probab=91.77 E-value=0.25 Score=36.96 Aligned_cols=27 Identities=22% Similarity=0.314 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 490 RPKSLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 490 e~~Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
++.|+.+||..+|||+.+|+.+..+-.
T Consensus 11 ~g~s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 11 EGESVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred cCCCHHHHHHHHCCCHhHHHHHHHHHH
Confidence 567999999999999999998876654
No 200
>smart00351 PAX Paired Box domain.
Probab=91.73 E-value=0.39 Score=43.57 Aligned_cols=42 Identities=21% Similarity=0.188 Sum_probs=34.2
Q ss_pred CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449 472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMT 517 (534)
Q Consensus 472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~ 517 (534)
++..+|.-|...| .++.|..+||+.||||+.+|..++.+...
T Consensus 18 ~s~~~R~riv~~~----~~G~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 18 LPDEERQRIVELA----QNGVRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred CCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 5565666666666 57899999999999999999999988753
No 201
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=91.71 E-value=0.28 Score=48.29 Aligned_cols=46 Identities=15% Similarity=0.099 Sum_probs=36.2
Q ss_pred hCCHHHHHHHhhHh-cCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449 471 SLDSRERQVLVLRY-GLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMT 517 (534)
Q Consensus 471 ~L~~rEReVL~Lry-GL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~ 517 (534)
.|+++|.+++.... +. ..+|+|.+|||+.||+|..||+.+..++..
T Consensus 158 ~Lt~re~~~l~~~i~~~-~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~ 204 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAH-QDYEFSTDELANAVNISRVSCRKYLIWLVN 204 (239)
T ss_pred CCCHHHHHHHHHHHHhC-CCCCcCHHHHHHHhCchHHHHHHHHHHHHh
Confidence 48899977764433 22 148999999999999999999999887744
No 202
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=91.64 E-value=0.22 Score=52.43 Aligned_cols=36 Identities=22% Similarity=0.233 Sum_probs=32.5
Q ss_pred HHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449 478 QVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMT 517 (534)
Q Consensus 478 eVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~ 517 (534)
.+-.+|| .+++|+.|||++||||+.+|+..+.+|++
T Consensus 17 ~~A~lYY----~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~ 52 (321)
T COG2390 17 RAAWLYY----VEGLTQSEIAERLGISRATVSRLLAKARE 52 (321)
T ss_pred HHHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3557899 89999999999999999999999998875
No 203
>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=91.49 E-value=0.26 Score=39.87 Aligned_cols=45 Identities=18% Similarity=0.318 Sum_probs=27.8
Q ss_pred HhhCCHHHHHHHhhHhc--CCCCCCCCHHHHHHHhCCC-HHHHHHHHH
Q 009449 469 LESLDSRERQVLVLRYG--LNDHRPKSLEEIGKLFHVS-KEWIRKLEK 513 (534)
Q Consensus 469 L~~L~~rEReVL~LryG--L~d~e~~Sl~EIA~~LgIS-rerVRqi~~ 513 (534)
+..|+++|++||...-- -..+-+-|..|||+.||++ .++|.+++.
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 35799999999876321 1124567999999999996 999977653
No 204
>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=91.48 E-value=0.49 Score=38.67 Aligned_cols=38 Identities=26% Similarity=0.408 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHH
Q 009449 253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (534)
Q Consensus 253 ~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l 290 (534)
.++.+++..|..++||.||..+.|+..|++.+.+...+
T Consensus 4 ~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l 41 (78)
T PF04539_consen 4 RKIERARRELEQELGREPTDEEIAEELGISVEEVRELL 41 (78)
T ss_dssp HHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHH
Confidence 46778889999999999999999999999998876644
No 205
>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=91.32 E-value=0.2 Score=38.83 Aligned_cols=40 Identities=25% Similarity=0.346 Sum_probs=28.1
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
.|+..|+.=|.-+| ..|.+..+||..|||+++||+.++..
T Consensus 6 ~LTl~eK~~iI~~~----e~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 6 SLTLEEKLEIIKRL----EEGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp S--HHHHHHHHHHH----HCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred cCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 46666666555566 57889999999999999999998865
No 206
>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=91.25 E-value=0.32 Score=38.85 Aligned_cols=35 Identities=20% Similarity=0.250 Sum_probs=26.6
Q ss_pred HHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 478 QVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 478 eVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
..+.++... ...+++.|||+.||||..+|+....+
T Consensus 11 kA~e~y~~~--~g~i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 11 KAFEIYKES--NGKIKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred HHHHHHHHh--CCCccHHHHHHHHCCCHHHHHHHhhh
Confidence 344444422 45899999999999999999987654
No 207
>PF13730 HTH_36: Helix-turn-helix domain
Probab=90.87 E-value=0.69 Score=35.27 Aligned_cols=47 Identities=19% Similarity=0.292 Sum_probs=34.4
Q ss_pred hCCHHHHHHHhhHhcCCCCCCC---CHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 471 SLDSRERQVLVLRYGLNDHRPK---SLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~---Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
.|++.++.|+....-..+..+. |.+.||+.+|+|+.||+ ++++.|.+
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 5888888887665544322333 89999999999999996 56666654
No 208
>PHA00675 hypothetical protein
Probab=90.86 E-value=0.43 Score=39.87 Aligned_cols=41 Identities=20% Similarity=0.101 Sum_probs=31.1
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
..|++.+-+.|+..+- ..+.|+.+||+.||||+++|.+|..
T Consensus 21 AKLt~~qV~~IR~l~~---r~G~s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 21 AKLTDAEVERIRELHE---VEGMSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred cccCHHHHHHHHHHHH---hcCccHHHHHHHhCCCHHHHHHHHc
Confidence 3466666665555541 2678999999999999999999865
No 209
>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=90.78 E-value=0.63 Score=34.37 Aligned_cols=39 Identities=21% Similarity=0.328 Sum_probs=26.6
Q ss_pred CHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 473 DSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 473 ~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
++-.+.||...-. ....|+.+||+.+|+|..+|...+.+
T Consensus 2 D~~D~~Il~~Lq~---d~r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 2 DELDRKILRLLQE---DGRRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp -HHHHHHHHHHHH----TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CHHHHHHHHHHHH---cCCccHHHHHHHHCcCHHHHHHHHHH
Confidence 4455566655541 35789999999999999999887654
No 210
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=90.33 E-value=4 Score=43.04 Aligned_cols=36 Identities=28% Similarity=0.454 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 009449 253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (534)
Q Consensus 253 ~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~ 288 (534)
.++.++...|...+|+.||..+.|+..|++.+.+..
T Consensus 173 ~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~ 208 (324)
T PRK07921 173 NKLARIKRELHQQLGREATDEELAEESGIPEEKIAD 208 (324)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence 345567778888899999999999999999987654
No 211
>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA. It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.
Probab=89.82 E-value=0.55 Score=40.09 Aligned_cols=44 Identities=30% Similarity=0.449 Sum_probs=34.3
Q ss_pred HhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHh--CCCHHHHHHHHHHH
Q 009449 469 LESLDSRERQVLVLRYGLNDHRPKSLEEIGKLF--HVSKEWIRKLEKKA 515 (534)
Q Consensus 469 L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~L--gISrerVRqi~~RA 515 (534)
++.||+..+++..+|. ...+.|+.|+|+.| .||++.|..+..+-
T Consensus 35 ~~~l~~~l~~~a~lRl---~~Pd~SL~EL~~~~~~~iSKSgvnhrlrKl 80 (85)
T PF02650_consen 35 LDKLPEKLREFAELRL---ENPDASLKELGELLEPPISKSGVNHRLRKL 80 (85)
T ss_dssp GGGS-HHHHHHHHHHH---H-TTS-HHHHHHTT--T--HHHHHHHHHHH
T ss_pred cccCCHHHHHHHHHHH---HCccccHHHHHHHHcCcCcHHHHHHHHHHH
Confidence 5789999999999998 35899999999999 99999998877654
No 212
>PHA02591 hypothetical protein; Provisional
Probab=89.52 E-value=0.56 Score=39.29 Aligned_cols=25 Identities=24% Similarity=0.340 Sum_probs=22.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
..|+|.++||+.||++.++|++...
T Consensus 57 eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 57 RKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 4789999999999999999999865
No 213
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=89.24 E-value=0.75 Score=34.31 Aligned_cols=37 Identities=19% Similarity=0.244 Sum_probs=28.7
Q ss_pred HHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 474 SRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 474 ~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
|.-.+|+.+-. ..+++..||++.+|+|+++|++.+..
T Consensus 2 ~~R~~Il~~L~----~~~~~~~el~~~l~~s~~~vs~hL~~ 38 (47)
T PF01022_consen 2 PTRLRILKLLS----EGPLTVSELAEELGLSQSTVSHHLKK 38 (47)
T ss_dssp HHHHHHHHHHT----TSSEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHH----hCCCchhhHHHhccccchHHHHHHHH
Confidence 44556776666 57899999999999999999977643
No 214
>cd00131 PAX Paired Box domain
Probab=89.16 E-value=0.88 Score=41.54 Aligned_cols=42 Identities=19% Similarity=0.156 Sum_probs=33.3
Q ss_pred CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449 472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMT 517 (534)
Q Consensus 472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~ 517 (534)
|+...|.-|...| .+|+|..+||+.||||+.+|..+..+-..
T Consensus 18 lS~d~R~rIv~~~----~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e 59 (128)
T cd00131 18 LPDSIRQRIVELA----QSGIRPCDISRQLRVSHGCVSKILNRYYE 59 (128)
T ss_pred CCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 5555555555666 57999999999999999999999887553
No 215
>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=88.78 E-value=21 Score=39.26 Aligned_cols=29 Identities=17% Similarity=0.234 Sum_probs=24.3
Q ss_pred hcCCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 009449 484 YGLNDHRPKSLEEIGKLFHVSKEWIRKLE 512 (534)
Q Consensus 484 yGL~d~e~~Sl~EIA~~LgISrerVRqi~ 512 (534)
+|-....++|+++||+.+|++.+||+...
T Consensus 311 ~G~~~LkPLtlkdiA~~lglheSTVSRav 339 (429)
T TIGR02395 311 GGPAALKPLTLREVAEELGLHESTISRAI 339 (429)
T ss_pred cCcccCcCCcHHHHHHHhCCCccchhhhh
Confidence 45444689999999999999999998654
No 216
>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=88.51 E-value=9.7 Score=39.29 Aligned_cols=98 Identities=19% Similarity=0.225 Sum_probs=55.6
Q ss_pred CCCCHHHHHHHcC--CCHHHHHHHHHHhhhhcccccccccchhhhhh---hccCCCCCCChH-HHHHHHHHHHHHHHHHh
Q 009449 397 KYPEDIEIAKYTG--LSLAEIRSASECLRIVGSIDQKIGDCLNAKYL---EFAPDRSVKSPK-EIVMRQHMKKDVFRILE 470 (534)
Q Consensus 397 r~Pt~eEIA~~lg--is~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~---e~i~d~~~~spe-e~v~~~el~e~L~~~L~ 470 (534)
-.++.++||+.++ ||+++++..+......--+.. .+ ++.+. ..+..+....|. -.-.+..+.+.-.++|+
T Consensus 136 ~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk-~~---~g~y~~t~~~l~~~~~~~~~avr~~h~q~l~lA~~al~ 211 (271)
T TIGR02147 136 FADDPEELAKRCFPKISAEQVKESLDLLERLGLIKK-NE---DGFYKQTDKAVSTGDEVIPLAVRQYQKQMIDLAKEALD 211 (271)
T ss_pred CCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeE-CC---CCcEEeecceeecCCccchHHHHHHHHHHHHHHHHHHH
Confidence 4567889999999 999999998887654322221 11 11111 111111111111 11223334445567888
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHh
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLF 501 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~L 501 (534)
..|+.+|.+=.+-+|++ ..++++|.+.+
T Consensus 212 ~~p~~eR~~S~lT~~i~---~~~~~~i~~~i 239 (271)
T TIGR02147 212 ALPPSERDVSTVTFGIS---EEAYKEIVKKI 239 (271)
T ss_pred hCCccccccceeeEecC---HHHHHHHHHHH
Confidence 99999999888877654 24555555443
No 217
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=88.50 E-value=0.77 Score=34.98 Aligned_cols=38 Identities=29% Similarity=0.427 Sum_probs=26.7
Q ss_pred HHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 475 RERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 475 rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
|+.+|+.+.+ ....+.|.+|||+.||||+.||+..+..
T Consensus 1 R~~~il~~L~--~~~~~it~~eLa~~l~vS~rTi~~~i~~ 38 (55)
T PF08279_consen 1 RQKQILKLLL--ESKEPITAKELAEELGVSRRTIRRDIKE 38 (55)
T ss_dssp HHHHHHHHHH--HTTTSBEHHHHHHHCTS-HHHHHHHHHH
T ss_pred CHHHHHHHHH--HcCCCcCHHHHHHHhCCCHHHHHHHHHH
Confidence 4556666653 1134599999999999999999865544
No 218
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=88.42 E-value=1.5 Score=34.40 Aligned_cols=43 Identities=21% Similarity=0.346 Sum_probs=31.9
Q ss_pred HHHHHhhCCHHHHHHHhhH-hcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 465 VFRILESLDSRERQVLVLR-YGLNDHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 465 L~~~L~~L~~rEReVL~Lr-yGL~d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
+.++|. +|.-..|+.+- - ..++|..|||+.+|++.++|+.++.
T Consensus 3 i~~aL~--~p~R~~Il~~L~~----~~~~t~~ela~~l~~~~~t~s~hL~ 46 (61)
T PF12840_consen 3 IFKALS--DPTRLRILRLLAS----NGPMTVSELAEELGISQSTVSYHLK 46 (61)
T ss_dssp HHHHHT--SHHHHHHHHHHHH----CSTBEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHhC--CHHHHHHHHHHhc----CCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 444553 46667777766 4 6899999999999999999986543
No 219
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=88.05 E-value=8.7 Score=41.42 Aligned_cols=126 Identities=21% Similarity=0.261 Sum_probs=70.8
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHH------------hhhhccc-----------ccccccchhhh
Q 009449 383 KIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC------------LRIVGSI-----------DQKIGDCLNAK 439 (534)
Q Consensus 383 ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~------------~~~~~SL-----------D~~i~~~~~~~ 439 (534)
.+.+.+..|..++|+.|+..+.|...|++...+...+.. .+.+.++ +..+. ++...
T Consensus 95 ~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Li~~~l~lV~~iA~ry~~~~~~~eDLiQ-EG~ig 173 (373)
T PRK07406 95 ELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQ-EGSLG 173 (373)
T ss_pred HHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHH-HHHHH
Confidence 345567788888999999999999999998766654321 1111111 11111 11111
Q ss_pred hhhccC--CCCCCChHHHHHHHHHHHHHHHHHhh------CCHHHHH----------HHhhHhcCCCCCCCCHHHHHHHh
Q 009449 440 YLEFAP--DRSVKSPKEIVMRQHMKKDVFRILES------LDSRERQ----------VLVLRYGLNDHRPKSLEEIGKLF 501 (534)
Q Consensus 440 l~e~i~--d~~~~spee~v~~~el~e~L~~~L~~------L~~rERe----------VL~LryGL~d~e~~Sl~EIA~~L 501 (534)
+...+. |+.-..+.......-+++.|.++|.. ||-.-.. -+...+ +..-|.+|||+.+
T Consensus 174 L~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~~~~~~i~~a~~~l~~~l----gr~Pt~~EIA~~l 249 (373)
T PRK07406 174 LIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEF----GRKPTEEEIAESM 249 (373)
T ss_pred HHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHHHHHHHHHHHHHHHHHHh----CCCCCHHHHHHHh
Confidence 111111 22222344455444555556555532 5543322 223344 4566899999999
Q ss_pred CCCHHHHHHHHH
Q 009449 502 HVSKEWIRKLEK 513 (534)
Q Consensus 502 gISrerVRqi~~ 513 (534)
|++.+.|+.+..
T Consensus 250 g~~~e~v~~~~~ 261 (373)
T PRK07406 250 EMTIEKLRFIAK 261 (373)
T ss_pred CCCHHHHHHHHH
Confidence 999999987643
No 220
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=87.66 E-value=11 Score=38.56 Aligned_cols=124 Identities=15% Similarity=0.095 Sum_probs=71.0
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhcHHHHHHHHHHhHHHHHHHHHHhhCCCCC-HHHHHHHHHHH
Q 009449 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIP-FSDLLQAGNVG 332 (534)
Q Consensus 254 ~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l~~G~~A~e~LI~~nlrLV~sIArrY~~~g~~-~eDLiQEG~lg 332 (534)
+++.+...|+.++|++||..+-|+..|++.+++...+. ..+...+.++--.....+.+ ..|
T Consensus 111 ~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~----------~~~~~~~~sld~~~~~~~d~~~~~-------- 172 (247)
T COG1191 111 RIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALL----------AINGSQLLSLDEDVLKDDDDDVDD-------- 172 (247)
T ss_pred HHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHH----------Hhccccccchhhhhccccccchhh--------
Confidence 34567778899999999999999999999988665332 22222222222221111111 111
Q ss_pred HHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCH
Q 009449 333 VLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSL 412 (534)
Q Consensus 333 L~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~ 412 (534)
..+..+..+-.|-..+.+..++. .+|..-.. -+.-....+-|--|||+.+||+.
T Consensus 173 ----------~~~~~~~~~~~~~~~~~l~~ai~------~L~EREk~----------Vl~l~y~eelt~kEI~~~LgISe 226 (247)
T COG1191 173 ----------QIENPDDGVEKEELLEILKEAIE------PLPEREKL----------VLVLRYKEELTQKEIAEVLGISE 226 (247)
T ss_pred ----------ccccchhHHHHHHHHHHHHHHHH------ccCHHHHH----------HHHHHHHhccCHHHHHHHhCccH
Confidence 12224455566666677766664 12322100 01111123457789999999999
Q ss_pred HHHHHHHHH
Q 009449 413 AEIRSASEC 421 (534)
Q Consensus 413 ~kv~~~l~~ 421 (534)
.+|.++...
T Consensus 227 s~VSql~kk 235 (247)
T COG1191 227 SRVSRLHKK 235 (247)
T ss_pred HHHHHHHHH
Confidence 999877543
No 221
>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=87.59 E-value=1.1 Score=34.70 Aligned_cols=43 Identities=16% Similarity=0.206 Sum_probs=31.9
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
.|++.|..||...+.-++ .+.|..|||+.+++++.+|..++.+
T Consensus 2 glt~~q~~vL~~l~~~~~-~~~t~~~la~~l~~~~~~vs~~v~~ 44 (62)
T PF12802_consen 2 GLTPSQFRVLMALARHPG-EELTQSELAERLGISKSTVSRIVKR 44 (62)
T ss_dssp TSTHHHHHHHHHHHHSTT-SGEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHHCCC-CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 478888888877764322 2389999999999999999765544
No 222
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=87.55 E-value=1.8 Score=39.61 Aligned_cols=53 Identities=15% Similarity=0.354 Sum_probs=42.1
Q ss_pred HHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 463 KDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 463 e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
+++..++-.|++.+.+|+....- ...+.|..|||+.+|++++||. ||+++|=.
T Consensus 16 ~dvl~c~~GLs~~Dv~v~~~LL~--~~~~~tvdelae~lnr~rStv~----rsl~~L~~ 68 (126)
T COG3355 16 EDVLKCVYGLSELDVEVYKALLE--ENGPLTVDELAEILNRSRSTVY----RSLQNLLE 68 (126)
T ss_pred HHHHHHHhCCcHHHHHHHHHHHh--hcCCcCHHHHHHHHCccHHHHH----HHHHHHHH
Confidence 35667888899999998876542 2469999999999999999995 66766643
No 223
>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=86.57 E-value=2.2 Score=34.51 Aligned_cols=42 Identities=19% Similarity=0.264 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHcCCC-HHHHHHHHHHhh
Q 009449 382 SKIQKARKALTNSHGKYPEDIEIAKYTGLS-LAEIRSASECLR 423 (534)
Q Consensus 382 ~ki~ka~~~L~~elGr~Pt~eEIA~~lgis-~~kv~~~l~~~~ 423 (534)
.+|-.....+..+.|..||..|||+.+|+. ...|...+....
T Consensus 9 ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le 51 (65)
T PF01726_consen 9 KEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALE 51 (65)
T ss_dssp HHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 455566677788999999999999999997 888988877664
No 224
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=86.28 E-value=0.96 Score=42.78 Aligned_cols=50 Identities=18% Similarity=0.063 Sum_probs=42.7
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCC-----HHHHHHHHHHHHHHHHh
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVS-----KEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgIS-----rerVRqi~~RAL~KLR~ 521 (534)
.|+++|.+|+.+..- +.++++|.+||++.++.+ ..||+.+..+.++||..
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 499999999988772 223569999999999986 78999999999999974
No 225
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=86.00 E-value=1.4 Score=37.03 Aligned_cols=42 Identities=24% Similarity=0.241 Sum_probs=33.5
Q ss_pred CCHHHHHHHhhHhcC--CCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 472 LDSRERQVLVLRYGL--NDHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 472 L~~rEReVL~LryGL--~d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
|+++|++||...--+ ..+++-.-++||+.+++|..|||+.+.
T Consensus 2 Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~ 45 (78)
T PF03444_consen 2 LTERQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMA 45 (78)
T ss_pred CCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHH
Confidence 789999987654322 346888999999999999999998653
No 226
>PHA02547 55 RNA polymerase sigma factor; Provisional
Probab=85.99 E-value=2.5 Score=40.51 Aligned_cols=65 Identities=15% Similarity=0.186 Sum_probs=50.6
Q ss_pred HhHHHHHHHHHHhhCCCCC---HHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHh
Q 009449 303 STRPLVLFLARNYRGLGIP---FSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH 367 (534)
Q Consensus 303 ~nlrLV~sIArrY~~~g~~---~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~ 367 (534)
+-+..+..++++|.-++.. -+|.|.+|.-..++.+..|||++...+-+|++..+-++..+-|...
T Consensus 45 ~imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~kE 112 (179)
T PHA02547 45 AIMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKKE 112 (179)
T ss_pred HHHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHHH
Confidence 3445555666666555555 6899999999999999999999988888888888888877777644
No 227
>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=85.98 E-value=0.96 Score=35.88 Aligned_cols=46 Identities=22% Similarity=0.343 Sum_probs=30.7
Q ss_pred CCHHHHHHHhhHhcCC-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 472 LDSRERQVLVLRYGLN-DHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 472 L~~rEReVL~LryGL~-d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
|++....-|...|-|. ++...+..+||+.||||+.+|.. ++++|.+
T Consensus 2 Lt~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~----ml~~L~~ 48 (60)
T PF01325_consen 2 LTESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTE----MLKRLAE 48 (60)
T ss_dssp CSCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHH----HHHHHHH
T ss_pred CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHH----HHHHHHH
Confidence 3444444444444443 45789999999999999999964 5556653
No 228
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional
Probab=85.93 E-value=1.1 Score=43.02 Aligned_cols=50 Identities=20% Similarity=0.088 Sum_probs=44.0
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHh
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFH-----VSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~Lg-----ISrerVRqi~~RAL~KLR~ 521 (534)
.|+++|.+|+.+... +.+++.|.++|++.+. ++..||..+..+.++||..
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 499999999998873 3456899999999998 9999999999999999974
No 229
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=85.89 E-value=0.75 Score=44.94 Aligned_cols=39 Identities=15% Similarity=0.144 Sum_probs=29.5
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
.|+++ +|+.+.- .+..++|.+|||+.||||+.||+.+..
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 35665 6766554 122379999999999999999998875
No 230
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=85.75 E-value=35 Score=37.79 Aligned_cols=46 Identities=20% Similarity=0.366 Sum_probs=33.1
Q ss_pred HHHhhCCHHHHHHHhh------------HhcCCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 009449 467 RILESLDSRERQVLVL------------RYGLNDHRPKSLEEIGKLFHVSKEWIRKLE 512 (534)
Q Consensus 467 ~~L~~L~~rEReVL~L------------ryGL~d~e~~Sl~EIA~~LgISrerVRqi~ 512 (534)
.++..|.-|.+.+++. .+|-....++|+++||+.+|+..+||+...
T Consensus 307 ~li~~i~~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdvAe~lglheSTVSRav 364 (455)
T PRK05932 307 WLIKSLEQRKETLLKVARCIVEQQRDFFEHGEEALKPLVLKDIAEELGMHESTISRAT 364 (455)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCcCccHHHHHHHhCCCccchhhhh
Confidence 3445566666555432 346545689999999999999999998654
No 231
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=85.60 E-value=2 Score=34.80 Aligned_cols=37 Identities=11% Similarity=0.171 Sum_probs=25.3
Q ss_pred HHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 476 ERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 476 EReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
+..|+.+... .+.++.|..|||+.+|+++.+|++++.
T Consensus 8 ~~~IL~~L~~-~g~~~~ta~eLa~~lgl~~~~v~r~L~ 44 (68)
T smart00550 8 EEKILEFLEN-SGDETSTALQLAKNLGLPKKEVNRVLY 44 (68)
T ss_pred HHHHHHHHHH-CCCCCcCHHHHHHHHCCCHHHHHHHHH
Confidence 3445444442 122359999999999999999975543
No 232
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=85.28 E-value=9.5 Score=38.64 Aligned_cols=34 Identities=18% Similarity=0.200 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 009449 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (534)
Q Consensus 255 le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~ 288 (534)
+......+...+|++|+..+-|+..|++.+.+..
T Consensus 112 l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~ 145 (257)
T PRK05911 112 LADAMDSLRQSLGKEPTDGELCEYLNISQQELSG 145 (257)
T ss_pred HHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHH
Confidence 3344556777889999999999999999887644
No 233
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=85.27 E-value=3.4 Score=41.76 Aligned_cols=35 Identities=20% Similarity=0.280 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 009449 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (534)
Q Consensus 254 ~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~ 288 (534)
++.+.+..|...+|++|+..+.|+..|++.+.+..
T Consensus 114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~ 148 (256)
T PRK07408 114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQE 148 (256)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHH
Confidence 45566778888999999999999999999987654
No 234
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=84.96 E-value=27 Score=35.38 Aligned_cols=35 Identities=26% Similarity=0.284 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 009449 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (534)
Q Consensus 254 ~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~ 288 (534)
++.+.+..|+..+|++||..+-|...|++.+.+..
T Consensus 119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~ 153 (268)
T PRK06288 119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYNS 153 (268)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHH
Confidence 45566778888899999999999999999877654
No 235
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=84.92 E-value=2.1 Score=32.18 Aligned_cols=33 Identities=18% Similarity=0.290 Sum_probs=26.4
Q ss_pred HHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009449 478 QVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKA 515 (534)
Q Consensus 478 eVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RA 515 (534)
.|+.+.. +..|.++||+.+|||..+|+.+..+.
T Consensus 19 ~i~~~~~-----~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 19 YILKLLR-----ESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHHHHHh-----hcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 4555554 34699999999999999999988764
No 236
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=84.92 E-value=1.1 Score=42.09 Aligned_cols=49 Identities=20% Similarity=0.130 Sum_probs=41.2
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHH
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFH-----VSKEWIRKLEKKAMTKLR 520 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~Lg-----ISrerVRqi~~RAL~KLR 520 (534)
.|+++|.+|+.+.. -+.+..+|.++|++.+. ++..+|+.+..+.++||.
T Consensus 149 ~Lt~~E~~il~~l~-~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl~ 202 (219)
T PRK10336 149 TLKPKEFALLELLM-RNAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLG 202 (219)
T ss_pred ecCHHHHHHHHHHH-hCCCccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhcC
Confidence 49999999998765 22234599999999996 999999999999999985
No 237
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=84.41 E-value=17 Score=28.63 Aligned_cols=73 Identities=16% Similarity=0.109 Sum_probs=46.1
Q ss_pred CCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHH
Q 009449 398 YPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRER 477 (534)
Q Consensus 398 ~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rER 477 (534)
+++.++||+.+|++...+..+...... .+|.+.+.. . .+ .
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~~-------------------------~s~~~~~~~-~---r~-----------~ 40 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKETG-------------------------TTPKQYLRD-R---RL-----------E 40 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHhC-------------------------cCHHHHHHH-H---HH-----------H
Confidence 368899999999999998877653310 122222111 0 11 1
Q ss_pred HHHhhHhcCCCCCCCCHHHHHHHhCC-CHHHHHHHHHH
Q 009449 478 QVLVLRYGLNDHRPKSLEEIGKLFHV-SKEWIRKLEKK 514 (534)
Q Consensus 478 eVL~LryGL~d~e~~Sl~EIA~~LgI-SrerVRqi~~R 514 (534)
.++.+.. ..+.++.|||..+|+ +.....+...+
T Consensus 41 ~a~~~l~----~~~~~~~~ia~~~g~~s~~~f~r~Fk~ 74 (84)
T smart00342 41 RARRLLR----DTDLSVTEIALRVGFSSQSYFSRAFKK 74 (84)
T ss_pred HHHHHHH----cCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 2333333 237899999999999 99888766544
No 238
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=84.12 E-value=15 Score=38.00 Aligned_cols=34 Identities=35% Similarity=0.488 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHH
Q 009449 383 KIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIR 416 (534)
Q Consensus 383 ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~ 416 (534)
.+......|...+|++||..+.|+..|++...+.
T Consensus 33 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 66 (298)
T TIGR02997 33 VLEELREELEEQLGREPSKEEWAAAAGLSEAELR 66 (298)
T ss_pred HHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHH
Confidence 3445667788889999999999999998865443
No 239
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=84.04 E-value=1.8 Score=40.34 Aligned_cols=28 Identities=21% Similarity=0.114 Sum_probs=25.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
.+|+|..|||++||||.+||..+..+..
T Consensus 19 ~~G~S~re~Ak~~gvs~sTvy~wv~r~~ 46 (138)
T COG3415 19 GEGLSCREAAKRFGVSISTVYRWVRRYR 46 (138)
T ss_pred HcCccHHHHHHHhCccHHHHHHHHHHhc
Confidence 4899999999999999999999888754
No 240
>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=84.03 E-value=6.1 Score=38.97 Aligned_cols=34 Identities=32% Similarity=0.446 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 009449 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (534)
Q Consensus 255 le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~ 288 (534)
+.+....+...+|+.||..+.|+..|++.+.+..
T Consensus 99 ~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~ 132 (231)
T TIGR02885 99 IRYMKEELSKELGREPTINELAEALGVSPEEIVM 132 (231)
T ss_pred HHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHH
Confidence 3445567777889999999999999999887654
No 241
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=84.03 E-value=36 Score=38.00 Aligned_cols=47 Identities=15% Similarity=0.278 Sum_probs=34.3
Q ss_pred HHHhhCCHHHHHHHh------------hHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 467 RILESLDSRERQVLV------------LRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 467 ~~L~~L~~rEReVL~------------LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
.++..|.-|.+.+++ +.+|.....++|+++||+.+|+..+||+...+
T Consensus 333 wli~si~qR~~TllkV~~~Iv~~Q~~Ff~~G~~~LkPLtlkdVAe~lglHeSTVSRa~~ 391 (481)
T PRK12469 333 WLIRNAQQRFDTIQRVAECIVARQRDFFRYGEIALKPLVLRDVAEELGLHESTISRATG 391 (481)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCcCCcHHHHHHHhCCCcchhhHHhc
Confidence 344566666665554 23565556899999999999999999986543
No 242
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=83.86 E-value=15 Score=37.37 Aligned_cols=36 Identities=19% Similarity=0.284 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHH
Q 009449 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH 289 (534)
Q Consensus 254 ~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~ 289 (534)
++.+....+...+|+.||..+.|+..|++.+++...
T Consensus 128 ~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~ 163 (264)
T PRK07122 128 RLGRATAELSQRLGRAPTASELAAELGMDREEVVEG 163 (264)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 344556677788899999999999999999887553
No 243
>PF12728 HTH_17: Helix-turn-helix domain
Probab=83.81 E-value=1.2 Score=33.53 Aligned_cols=24 Identities=13% Similarity=0.300 Sum_probs=21.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKA 515 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RA 515 (534)
+|.+|+|+.||||+.+|+++..+.
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcC
Confidence 589999999999999999987653
No 244
>PRK05949 RNA polymerase sigma factor; Validated
Probab=83.70 E-value=13 Score=39.20 Aligned_cols=35 Identities=11% Similarity=0.275 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 009449 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (534)
Q Consensus 254 ~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~ 288 (534)
++.+....+..++|++|+..+.|+..|++.+.+..
T Consensus 179 ~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~ 213 (327)
T PRK05949 179 KIKKTQRELSQKLGRSATPAEIAKELELEPSQIRE 213 (327)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence 34455667777889999999999999999887655
No 245
>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=83.56 E-value=2.1 Score=33.66 Aligned_cols=41 Identities=22% Similarity=0.293 Sum_probs=26.2
Q ss_pred CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
|++.|..||..-. ....+++..+||+.+++++.+|...+.+
T Consensus 1 lt~~q~~vL~~l~--~~~~~~t~~~l~~~~~~~~~~vs~~i~~ 41 (68)
T PF13463_consen 1 LTRPQWQVLRALA--HSDGPMTQSDLAERLGISKSTVSRIIKK 41 (68)
T ss_dssp --HHHHHHHHHHT----TS-BEHHHHHHHTT--HHHHHHHHHH
T ss_pred CCHHHHHHHHHHH--ccCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 4666777765554 2457999999999999999999754443
No 246
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=83.40 E-value=1.2 Score=33.68 Aligned_cols=22 Identities=18% Similarity=0.285 Sum_probs=19.7
Q ss_pred CHHHHHHHhCCCHHHHHHHHHH
Q 009449 493 SLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 493 Sl~EIA~~LgISrerVRqi~~R 514 (534)
|++|||+..|||..||+..++.
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 7899999999999999987763
No 247
>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=83.35 E-value=10 Score=33.91 Aligned_cols=24 Identities=21% Similarity=0.202 Sum_probs=20.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLE 512 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~ 512 (534)
..+.|+.|||+.||||.++|...+
T Consensus 69 ~pd~tl~Ela~~l~Vs~~ti~~~L 92 (119)
T PF01710_consen 69 NPDATLRELAERLGVSPSTIWRAL 92 (119)
T ss_pred CCCcCHHHHHHHcCCCHHHHHHHH
Confidence 378999999999999999997443
No 248
>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=83.13 E-value=2 Score=35.47 Aligned_cols=53 Identities=17% Similarity=0.142 Sum_probs=36.3
Q ss_pred HHHHHHHHHhhCCHHHHHHHhhHhc-CCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 461 MKKDVFRILESLDSRERQVLVLRYG-LNDHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 461 l~e~L~~~L~~L~~rEReVL~LryG-L~d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
+.+.|......|++.|+.|.....- .++...+|..|||+..|||+.+|....+
T Consensus 3 l~~~i~~~~~~ls~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~k 56 (77)
T PF01418_consen 3 LLEKIRSQYNSLSPTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCK 56 (77)
T ss_dssp HHHHHHHHGGGS-HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHhhCCHHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHH
Confidence 3456777789999999998765441 1134579999999999999999975443
No 249
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=82.99 E-value=2.5 Score=36.58 Aligned_cols=40 Identities=25% Similarity=0.243 Sum_probs=31.1
Q ss_pred CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
|++.++.|+....- ....|..|||+.+|+|+.+|+..+.+
T Consensus 1 ld~~D~~il~~L~~---~~~~~~~~la~~l~~s~~tv~~~l~~ 40 (108)
T smart00344 1 LDEIDRKILEELQK---DARISLAELAKKVGLSPSTVHNRVKR 40 (108)
T ss_pred CCHHHHHHHHHHHH---hCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 46677888776651 24689999999999999999865544
No 250
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=82.99 E-value=2.3 Score=32.76 Aligned_cols=39 Identities=26% Similarity=0.266 Sum_probs=26.3
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
.|++.|+--|.... ..++++.|||..+|-|+..|+..+.
T Consensus 4 ~Lt~~Eqaqid~m~----qlG~s~~~isr~i~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 4 TLTDAEQAQIDVMH----QLGMSLREISRRIGRSRTCIRRYLK 42 (50)
T ss_dssp ---HHHHHHHHHHH----HTT--HHHHHHHHT--HHHHHHHHH
T ss_pred cCCHHHHHHHHHHH----HhchhHHHHHHHhCccHHHHHHHhc
Confidence 47777777776666 6799999999999999999987653
No 251
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=82.89 E-value=65 Score=33.71 Aligned_cols=178 Identities=14% Similarity=0.045 Sum_probs=87.6
Q ss_pred HHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchH
Q 009449 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN 378 (534)
Q Consensus 299 ~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~ 378 (534)
+-+......|-.++.+. .+.+-+.|....+++.+..-..-+|.....++.-.|.-++. .
T Consensus 120 r~l~~a~~~I~~~~~~L-----~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR----~------------ 178 (310)
T PRK00423 120 RNLAFALSELDRIASQL-----GLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACR----R------------ 178 (310)
T ss_pred HHHHHHHHHHHHHHHHc-----CCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHH----H------------
Confidence 33344456677777665 22356667777777777655666776655544444443332 1
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHH
Q 009449 379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMR 458 (534)
Q Consensus 379 ~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~ 458 (534)
.|-+-|..||+..++++..++..........+.++.+..+ ...+..-+.+.- .-|.+..
T Consensus 179 ----------------~~~prtl~eI~~~~~v~~k~i~~~~~~l~k~L~~~~~~~~--p~~~i~r~~~~L-~L~~~v~-- 237 (310)
T PRK00423 179 ----------------CKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPTD--PIDYVPRFASEL-GLSGEVQ-- 237 (310)
T ss_pred ----------------cCCCcCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCCC--HHHHHHHHHHHc-CCCHHHH--
Confidence 1222356677777777777776654444433333332211 111111111000 0111111
Q ss_pred HHHHHHHHHHHh-hC----CHHH--HHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449 459 QHMKKDVFRILE-SL----DSRE--RQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL 519 (534)
Q Consensus 459 ~el~e~L~~~L~-~L----~~rE--ReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL 519 (534)
+.....+..+.+ .| +|.- .-+|.+-.=+. +.+.|++|||...||+..+|++....-.+.|
T Consensus 238 ~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~-g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l 304 (310)
T PRK00423 238 KKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLL-GERRTQREVAEVAGVTEVTVRNRYKELAEKL 304 (310)
T ss_pred HHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHh-CCCCCHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 111111222211 11 2211 11222211112 4679999999999999999998776666554
No 252
>PRK15479 transcriptional regulatory protein TctD; Provisional
Probab=82.84 E-value=1.9 Score=40.53 Aligned_cols=50 Identities=26% Similarity=0.304 Sum_probs=41.3
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHh
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFH-----VSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~Lg-----ISrerVRqi~~RAL~KLR~ 521 (534)
.|+++|.+|+.+.. -..+...|.++|++.+. +|..+|..+..+.++||..
T Consensus 148 ~Lt~~E~~il~~l~-~~~~~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl~~ 202 (221)
T PRK15479 148 ALTPREQALLTVLM-YRRTRPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKLQG 202 (221)
T ss_pred ecCHHHHHHHHHHH-hCCCCcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhcCC
Confidence 49999999998775 11134579999999986 9999999999999999963
No 253
>PRK12423 LexA repressor; Provisional
Probab=82.77 E-value=1.7 Score=42.46 Aligned_cols=47 Identities=26% Similarity=0.378 Sum_probs=34.1
Q ss_pred hCCHHHHHHHhhHhcC-C-CCCCCCHHHHHHHhC-CCHHHHHHHHHHHHHHHHh
Q 009449 471 SLDSRERQVLVLRYGL-N-DHRPKSLEEIGKLFH-VSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 471 ~L~~rEReVL~LryGL-~-d~e~~Sl~EIA~~Lg-ISrerVRqi~~RAL~KLR~ 521 (534)
.|++++++|+..---. . .+-..|..|||+.|| +|+.+|+. ++++|++
T Consensus 3 ~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~----~l~~L~~ 52 (202)
T PRK12423 3 TLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARK----HVQALAE 52 (202)
T ss_pred cCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHH----HHHHHHH
Confidence 4899999998755421 1 122469999999999 59999984 6666665
No 254
>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=82.54 E-value=15 Score=37.01 Aligned_cols=37 Identities=16% Similarity=0.179 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHH
Q 009449 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (534)
Q Consensus 254 ~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l 290 (534)
++.+....+..++|++|+..+.|+..|++.+.+...+
T Consensus 121 ~~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~ 157 (254)
T TIGR02850 121 KALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFAL 157 (254)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 3445566777888999999999999999998876543
No 255
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=82.48 E-value=2.7 Score=34.99 Aligned_cols=44 Identities=18% Similarity=0.208 Sum_probs=29.4
Q ss_pred HHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH-----HHHHHHHhHhhhh
Q 009449 479 VLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK-----KAMTKLRDSETCR 526 (534)
Q Consensus 479 VL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~-----RAL~KLR~~l~~~ 526 (534)
|..++- ..++|+.|+|+.+|+++++|+.+++ -.+.+|...+..-
T Consensus 23 i~~~~~----~~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aL 71 (80)
T PF13744_consen 23 IRELRE----ERGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEAL 71 (80)
T ss_dssp HHHHHH----CCT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHT
T ss_pred HHHHHH----HcCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHc
Confidence 445555 6899999999999999999999884 2355555554443
No 256
>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=82.29 E-value=1.1 Score=42.35 Aligned_cols=50 Identities=20% Similarity=0.180 Sum_probs=42.0
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHH-----HHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEI-----GKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EI-----A~~LgISrerVRqi~~RAL~KLR~ 521 (534)
.|+++|.+|+.+... +.+++.|.++| |..++++..||+.+..+.++||..
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 499999999988872 22347788888 888999999999999999999963
No 257
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=82.15 E-value=2.4 Score=32.04 Aligned_cols=29 Identities=24% Similarity=0.324 Sum_probs=23.3
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 489 HRPK-SLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 489 ~e~~-Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
+... |..|||+.+|+|+.+|+ +++++|.+
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 4456 89999999999999997 56666664
No 258
>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=81.74 E-value=1.8 Score=37.14 Aligned_cols=45 Identities=22% Similarity=0.245 Sum_probs=31.1
Q ss_pred CCHHHHHHHhhHhcCCC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449 472 LDSRERQVLVLRYGLND---HRPKSLEEIGKLFHVSKEWIRKLEKKAMT 517 (534)
Q Consensus 472 L~~rEReVL~LryGL~d---~e~~Sl~EIA~~LgISrerVRqi~~RAL~ 517 (534)
++|.|++-|..|+-+-. .+++|+.||++.+|+|..||.. .+|+++
T Consensus 27 ~T~~E~~~l~~R~~va~~lL~~g~syreIa~~tgvS~aTItR-vsr~Lk 74 (87)
T PF01371_consen 27 CTPDELEALAQRWQVAKELLDEGKSYREIAEETGVSIATITR-VSRCLK 74 (87)
T ss_dssp SSHHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHH-HHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHH-HHHHHH
Confidence 67777665555443221 2689999999999999999964 344444
No 259
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=81.63 E-value=1.4 Score=31.68 Aligned_cols=25 Identities=24% Similarity=0.284 Sum_probs=22.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
+|..|+|+.+|||+.+|+.+...+.
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 5889999999999999999988764
No 260
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=81.44 E-value=2.5 Score=41.05 Aligned_cols=34 Identities=24% Similarity=0.295 Sum_probs=27.6
Q ss_pred HHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 476 ERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 476 EReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
++.|..++ ..++|..+||+.||||+.||.++...
T Consensus 162 ~~~i~~~~-----~~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 162 EEKIKKLL-----DKGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred HHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 34566664 36899999999999999999988763
No 261
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=81.33 E-value=1.8 Score=31.45 Aligned_cols=24 Identities=25% Similarity=0.356 Sum_probs=21.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKA 515 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RA 515 (534)
+|.+|+|+.||||+.+|+++....
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcC
Confidence 589999999999999999988654
No 262
>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=81.32 E-value=3.3 Score=35.69 Aligned_cols=49 Identities=27% Similarity=0.350 Sum_probs=37.0
Q ss_pred HhhCCHHHHHHHhhH----hcCC-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 469 LESLDSRERQVLVLR----YGLN-DHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 469 L~~L~~rEReVL~Lr----yGL~-d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
...+++++..||... ||.. ...+.|..|||+.+|+++++|+ |++++|.+
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 467899999877633 3422 2468999999999999999996 56666654
No 263
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=81.29 E-value=3.5 Score=36.06 Aligned_cols=45 Identities=27% Similarity=0.289 Sum_probs=34.6
Q ss_pred CCHHHHHHHhhHhcCCC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449 472 LDSRERQVLVLRYGLND---HRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520 (534)
Q Consensus 472 L~~rEReVL~LryGL~d---~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR 520 (534)
|+|.||+-+-.|+-+-. ...+|..||+..||+|..+| .|+-+-|+
T Consensus 38 LTpdEReal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtI----TRGSN~LK 85 (103)
T COG2973 38 LTPDEREALGTRVRIVEELLRGELSQREIAQKLGVSIATI----TRGSNSLK 85 (103)
T ss_pred cCHhHHHHHHHHHHHHHHHHhccccHHHHHHHhCcchhhh----ccchhhhc
Confidence 89999988887775431 15899999999999999998 35555544
No 264
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=80.94 E-value=26 Score=35.16 Aligned_cols=37 Identities=16% Similarity=0.198 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHH
Q 009449 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (534)
Q Consensus 254 ~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l 290 (534)
.+.+....+...+|+.|+..++|+..|++.+.+...+
T Consensus 110 ~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~ 146 (251)
T PRK07670 110 KVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATM 146 (251)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 3445556677788999999999999999998876543
No 265
>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=80.57 E-value=2.3 Score=40.44 Aligned_cols=50 Identities=16% Similarity=0.064 Sum_probs=41.5
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHH--HHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEI--GKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EI--A~~LgISrerVRqi~~RAL~KLR~ 521 (534)
.|+++|.+||.+.. -+.+.-.|.++| |..++++..||+.+..+.++||..
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 39999999998887 111233599999 888999999999999999999974
No 266
>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=80.35 E-value=2.4 Score=32.50 Aligned_cols=40 Identities=15% Similarity=0.334 Sum_probs=29.2
Q ss_pred CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
|++.|-.||..-+ ...+.|..|||+.+++++.+|.++..+
T Consensus 1 lt~~q~~iL~~l~---~~~~~~~~~la~~~~~~~~~~t~~i~~ 40 (59)
T PF01047_consen 1 LTPSQFRILRILY---ENGGITQSELAEKLGISRSTVTRIIKR 40 (59)
T ss_dssp STHHHHHHHHHHH---HHSSEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHH---HcCCCCHHHHHHHHCCChhHHHHHHHH
Confidence 4556666666655 246799999999999999999766554
No 267
>PF13551 HTH_29: Winged helix-turn helix
Probab=80.20 E-value=3.1 Score=35.70 Aligned_cols=33 Identities=21% Similarity=0.314 Sum_probs=26.6
Q ss_pred HHHhhHhcCCCCCCC-CHHHHHHHhCCCHHHHHHHHHHH
Q 009449 478 QVLVLRYGLNDHRPK-SLEEIGKLFHVSKEWIRKLEKKA 515 (534)
Q Consensus 478 eVL~LryGL~d~e~~-Sl~EIA~~LgISrerVRqi~~RA 515 (534)
.||.+.. ++. |..+||+.+|+|+.||+.++.+-
T Consensus 3 ~~l~l~~-----~g~~~~~~ia~~lg~s~~Tv~r~~~~~ 36 (112)
T PF13551_consen 3 QILLLLA-----EGVSTIAEIARRLGISRRTVYRWLKRY 36 (112)
T ss_pred HHHHHHH-----cCCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence 3455544 677 59999999999999999988773
No 268
>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=79.80 E-value=1.2 Score=35.49 Aligned_cols=44 Identities=23% Similarity=0.394 Sum_probs=33.0
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
.|++.|.+|+..-. ...+.|..|||+.+|+++.+|+. ++++|.+
T Consensus 5 gLs~~E~~vy~~Ll---~~~~~t~~eIa~~l~i~~~~v~~----~L~~L~~ 48 (68)
T PF01978_consen 5 GLSENEAKVYLALL---KNGPATAEEIAEELGISRSTVYR----ALKSLEE 48 (68)
T ss_dssp CHHHHHHHHHHHHH---HHCHEEHHHHHHHHTSSHHHHHH----HHHHHHH
T ss_pred CcCHHHHHHHHHHH---HcCCCCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence 46778888775543 14689999999999999999975 5555543
No 269
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=79.74 E-value=23 Score=37.16 Aligned_cols=36 Identities=14% Similarity=0.375 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 009449 253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (534)
Q Consensus 253 ~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~ 288 (534)
.++.+....+...+|+.|+..+.|++.|++.+.+..
T Consensus 168 ~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~ 203 (317)
T PRK07405 168 NKIKKAQRQLSQQLGRAATIGELAEELELTPKQVRE 203 (317)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence 345566677778889999999999999998877654
No 270
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=79.43 E-value=3.6 Score=35.20 Aligned_cols=43 Identities=23% Similarity=0.173 Sum_probs=35.9
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
.|+|.-|..|..+. + .++.+..++|+.||||+.|++++..|=.
T Consensus 8 ~Lt~~gR~~lv~~v-v--~~g~~~a~aA~~~gVS~~Ta~kW~~Ryr 50 (85)
T PF13011_consen 8 RLTPRGRLRLVRRV-V--EQGWPVAHAAAEFGVSRRTAYKWLARYR 50 (85)
T ss_pred CCCHHHHHHHHHHH-H--HcCCcHHHHHHHhCCCHHHHHHHHHHHH
Confidence 58888888887766 1 2589999999999999999999987754
No 271
>PHA01976 helix-turn-helix protein
Probab=78.93 E-value=3.1 Score=32.80 Aligned_cols=26 Identities=23% Similarity=0.213 Sum_probs=23.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
..++|.+|+|+.+|||+.+|+++++.
T Consensus 13 ~~glt~~~lA~~~gvs~~~v~~~e~g 38 (67)
T PHA01976 13 ARAWSAPELSRRAGVRHSLIYDFEAD 38 (67)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 57899999999999999999999864
No 272
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=78.45 E-value=2.2 Score=32.22 Aligned_cols=26 Identities=19% Similarity=0.323 Sum_probs=21.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
..++|++|+|+.+|+|+.+|+.++..
T Consensus 7 ~~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 7 EKGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HTTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred HcCCCHHHHHHHhCCCcchhHHHhcC
Confidence 46899999999999999999998865
No 273
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=78.31 E-value=4.1 Score=37.94 Aligned_cols=41 Identities=24% Similarity=0.289 Sum_probs=32.3
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
.|++..+.||..-- .....|+.|||+.+|+|+.+|+.+..+
T Consensus 6 ~lD~~D~~Il~~Lq---~d~R~s~~eiA~~lglS~~tV~~Ri~r 46 (153)
T PRK11179 6 QIDNLDRGILEALM---ENARTPYAELAKQFGVSPGTIHVRVEK 46 (153)
T ss_pred ccCHHHHHHHHHHH---HcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 37778888877664 135789999999999999999866543
No 274
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=78.12 E-value=6.6 Score=37.68 Aligned_cols=88 Identities=22% Similarity=0.213 Sum_probs=50.1
Q ss_pred CCCCCHHHHHHHc--CCCHHHHHHHHHHhhhhcccccccccchhhhhh---hccC-CCCCCChHHHHHHHHHHHHHHHHH
Q 009449 396 GKYPEDIEIAKYT--GLSLAEIRSASECLRIVGSIDQKIGDCLNAKYL---EFAP-DRSVKSPKEIVMRQHMKKDVFRIL 469 (534)
Q Consensus 396 Gr~Pt~eEIA~~l--gis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~---e~i~-d~~~~spee~v~~~el~e~L~~~L 469 (534)
+-.|+.++||+.+ +||+++++..+......--+.. ++++.+. ..+. .....+..-.-.+..+.+.-.++|
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 3456899999999 9999999999887654322221 1111111 1111 111111111222233344455677
Q ss_pred hhCCHHHHHHHhhHhcCC
Q 009449 470 ESLDSRERQVLVLRYGLN 487 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~ 487 (534)
+..|+.+|.+=-+-+|++
T Consensus 113 ~~~p~~~R~~s~~T~~vs 130 (171)
T PF14394_consen 113 DRVPPEERDFSGLTMSVS 130 (171)
T ss_pred HhCCccccceeeeEEEeC
Confidence 888899998887777654
No 275
>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=77.96 E-value=43 Score=32.82 Aligned_cols=36 Identities=25% Similarity=0.318 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 009449 253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (534)
Q Consensus 253 ~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~ 288 (534)
.++.+....+...+|+.|+.++.|+..|++.+.+..
T Consensus 83 ~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~ 118 (224)
T TIGR02479 83 RKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQ 118 (224)
T ss_pred HHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHH
Confidence 345566777888899999999999999999877654
No 276
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=77.73 E-value=6.4 Score=36.76 Aligned_cols=61 Identities=16% Similarity=0.201 Sum_probs=35.4
Q ss_pred HHHHHhhCCHHHHHHHhhH-----hcCCCCCCCCHHHHHHHhCCCHHHHHHHHH--HHHHHHHhHhhhh
Q 009449 465 VFRILESLDSRERQVLVLR-----YGLNDHRPKSLEEIGKLFHVSKEWIRKLEK--KAMTKLRDSETCR 526 (534)
Q Consensus 465 L~~~L~~L~~rEReVL~Lr-----yGL~d~e~~Sl~EIA~~LgISrerVRqi~~--RAL~KLR~~l~~~ 526 (534)
+..+=..|++.|+....+. .+.+ +..+|+.|||+.+||++.+..++.+ +++....+.+...
T Consensus 4 ~~~le~~L~~~Q~kAa~ll~~ne~~~~~-~~r~T~~eiAee~Gis~~tLYrWr~~~~~Fiey~n~la~~ 71 (142)
T PF13022_consen 4 LKELEAKLTLQQRKAAQLLVENELMPEN-GERRTQAEIAEEVGISRSTLYRWRQQNKAFIEYKNELADR 71 (142)
T ss_dssp HHHHHTTS-HHHHHHHHHHHHHHHS-------S-HHHHHHHHTS-HHHHHHHHHH-HHHHHHHHHHHHH
T ss_pred HHHHHHHcCHHHHHHHHHHHHHHHhhhc-cccchHHHHHHHhCCCHHHHHHHHhcCHHHHHHHHHHHHH
Confidence 4445578899888843332 2222 3779999999999999999999985 3344444444333
No 277
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=77.38 E-value=1.8 Score=31.74 Aligned_cols=25 Identities=28% Similarity=0.355 Sum_probs=22.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
+|..|+|+.+||++.+|+.++.+.+
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999987775
No 278
>CHL00148 orf27 Ycf27; Reviewed
Probab=76.96 E-value=3.2 Score=39.71 Aligned_cols=50 Identities=22% Similarity=0.117 Sum_probs=42.3
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHh-------CCCHHHHHHHHHHHHHHHHh
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLF-------HVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~L-------gISrerVRqi~~RAL~KLR~ 521 (534)
.|+++|.+|+.+.. -+.+++.|.+||++.+ +++..+|..+..+.++||..
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 49999999998776 1223679999999999 48999999999999999974
No 279
>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=76.68 E-value=2.8 Score=39.98 Aligned_cols=37 Identities=14% Similarity=0.112 Sum_probs=29.7
Q ss_pred HHHHHHHhhHhcCCCCCCCCHHHHHHHhC-CCHHHHHHHHHH
Q 009449 474 SRERQVLVLRYGLNDHRPKSLEEIGKLFH-VSKEWIRKLEKK 514 (534)
Q Consensus 474 ~rEReVL~LryGL~d~e~~Sl~EIA~~Lg-ISrerVRqi~~R 514 (534)
+..-+.|.-.+ .+|+|..|||+.|| ||++.|--..+|
T Consensus 5 de~~~~L~~lw----~~G~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 5 DERVERLRKLW----AEGLSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred HHHHHHHHHHH----HcCCCHHHHHHHhCCcchhhhhhhhhc
Confidence 44445555556 68999999999999 999999887776
No 280
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=76.66 E-value=3.1 Score=32.77 Aligned_cols=26 Identities=15% Similarity=0.235 Sum_probs=21.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
..++|..++|+.+|+|.++|+++++-
T Consensus 12 ~~gls~~~lA~~~g~s~s~v~~iE~G 37 (64)
T PF13560_consen 12 RAGLSQAQLADRLGVSQSTVSRIERG 37 (64)
T ss_dssp CHTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 46899999999999999999999863
No 281
>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=76.58 E-value=11 Score=38.42 Aligned_cols=56 Identities=18% Similarity=0.151 Sum_probs=44.0
Q ss_pred HHHHHHHHhhCCHHHHHHHhhHhcCCCC--CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 462 KKDVFRILESLDSRERQVLVLRYGLNDH--RPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 462 ~e~L~~~L~~L~~rEReVL~LryGL~d~--e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
+..++-+++.|+--|.+.+...+-.-+. .-.+..+||+.+|||+..|+ +|+++|..
T Consensus 167 ka~Vq~Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ir----eAlrkLE~ 224 (251)
T TIGR02787 167 KAAVQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIV----NALRKLES 224 (251)
T ss_pred HHHHHHHHHhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 3456778999999988888777655433 46899999999999999986 56777764
No 282
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=76.44 E-value=51 Score=36.43 Aligned_cols=49 Identities=18% Similarity=0.286 Sum_probs=35.7
Q ss_pred HHHHHhhCCHHHHHHHhh------------HhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 465 VFRILESLDSRERQVLVL------------RYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 465 L~~~L~~L~~rEReVL~L------------ryGL~d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
...++..|.-|++.++.. .+|-.--.++++++||+.+|+..+||+....
T Consensus 292 A~wLiksL~qR~~TLlkV~~~Iv~~Q~~Ff~~g~~~l~PL~LrdvA~~i~~HESTISRai~ 352 (444)
T COG1508 292 AKWLIKSLEQREETLLKVAEEIVEYQKAFFEGGEEALKPLVLRDVADEIGMHESTISRAIT 352 (444)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCCcccHHHHHHHhCccHHHHHHHHh
Confidence 344557777777766542 4444445779999999999999999986554
No 283
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=76.15 E-value=45 Score=29.99 Aligned_cols=39 Identities=8% Similarity=0.006 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHH
Q 009449 382 SKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASE 420 (534)
Q Consensus 382 ~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~ 420 (534)
..+.++..-+.+.....++.++||+.+|+++..+.....
T Consensus 9 ~~i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk 47 (127)
T PRK11511 9 ITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFK 47 (127)
T ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 445566666777777889999999999999999987754
No 284
>PHA00542 putative Cro-like protein
Probab=76.14 E-value=3.4 Score=34.73 Aligned_cols=27 Identities=22% Similarity=0.112 Sum_probs=24.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEKKA 515 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~RA 515 (534)
..++|..|+|+.+|||+.+|.+++...
T Consensus 29 ~~glTq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 29 RAGWSQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHHcCC
Confidence 468999999999999999999998643
No 285
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=75.97 E-value=4.4 Score=38.25 Aligned_cols=40 Identities=20% Similarity=0.091 Sum_probs=31.3
Q ss_pred CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
|++.+++||..-- .....|+.|||+.+|+|+.+|+.++.+
T Consensus 12 lD~~D~~IL~~Lq---~d~R~s~~eiA~~lglS~~tv~~Ri~r 51 (164)
T PRK11169 12 LDRIDRNILNELQ---KDGRISNVELSKRVGLSPTPCLERVRR 51 (164)
T ss_pred HHHHHHHHHHHhc---cCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 5667777876543 246899999999999999999876544
No 286
>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=75.96 E-value=5.4 Score=38.21 Aligned_cols=42 Identities=21% Similarity=0.182 Sum_probs=34.0
Q ss_pred CHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449 473 DSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMT 517 (534)
Q Consensus 473 ~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~ 517 (534)
|+.-|.-++..|- ++++|++.+|...|||..|+|.+..+|..
T Consensus 4 ~~e~R~~~R~~YV---~~~~sLe~aA~~~gVs~~TarrWK~~Ak~ 45 (165)
T PF08822_consen 4 PQETRDAVRRAYV---FDRLSLEQAAAKCGVSYATARRWKREAKA 45 (165)
T ss_pred cHHHHHHHHHHHH---hCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3444566676771 37899999999999999999999999864
No 287
>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=75.64 E-value=8.9 Score=34.01 Aligned_cols=46 Identities=13% Similarity=0.028 Sum_probs=35.1
Q ss_pred HHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009449 464 DVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKA 515 (534)
Q Consensus 464 ~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RA 515 (534)
.....-..+.+.+-.-++..+ ++|..++|+.+|+++.+|+++++..
T Consensus 57 ~~~~~~~~~~~~~i~~~r~~~------gltq~~lA~~lg~~~~tis~~e~g~ 102 (127)
T TIGR03830 57 FYRKVDGLLTPPEIRRIRKKL------GLSQREAAELLGGGVNAFSRYERGE 102 (127)
T ss_pred HHHHccCCcCHHHHHHHHHHc------CCCHHHHHHHhCCCHHHHHHHHCCC
Confidence 334444667887766666665 7899999999999999999988643
No 288
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=75.60 E-value=3.8 Score=33.66 Aligned_cols=26 Identities=35% Similarity=0.348 Sum_probs=23.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
..++|++|.|+.+|||+.||-.+++-
T Consensus 12 ~~~ltQ~elA~~vgVsRQTi~~iEkg 37 (68)
T COG1476 12 ELGLTQEELAKLVGVSRQTIIAIEKG 37 (68)
T ss_pred HhCcCHHHHHHHcCcCHHHHHHHHcC
Confidence 45899999999999999999998763
No 289
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=75.27 E-value=3.5 Score=39.89 Aligned_cols=41 Identities=22% Similarity=0.182 Sum_probs=34.1
Q ss_pred HHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 477 RQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 477 ReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
+..+.|.- .|+|..|||+.||+|++|++-+..|+..+...+
T Consensus 9 ~kA~eLk~-----~Glt~gEIAdELNvSreTa~WL~~r~~~~~~~~ 49 (203)
T COG0856 9 KKARELKS-----KGLTTGEIADELNVSRETATWLLTRAFKKESVP 49 (203)
T ss_pred HHHHHHHH-----CCCcHHHhhhhhhhhHHHHHHHHhhhhhccCCC
Confidence 34556664 899999999999999999999999998776543
No 290
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=75.26 E-value=4.2 Score=39.32 Aligned_cols=43 Identities=21% Similarity=0.237 Sum_probs=32.8
Q ss_pred hhCCHHHHHHHhhHhc--CCCCCCCCHHHHHHHhCCC-HHHHHHHH
Q 009449 470 ESLDSRERQVLVLRYG--LNDHRPKSLEEIGKLFHVS-KEWIRKLE 512 (534)
Q Consensus 470 ~~L~~rEReVL~LryG--L~d~e~~Sl~EIA~~LgIS-rerVRqi~ 512 (534)
..|+++|++||....- ..++.+.|..|||+.+|++ +++|..++
T Consensus 2 ~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l 47 (199)
T TIGR00498 2 KPLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHL 47 (199)
T ss_pred CccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHH
Confidence 3589999999887651 1124568999999999998 99997544
No 291
>PRK10072 putative transcriptional regulator; Provisional
Probab=75.06 E-value=3.8 Score=35.78 Aligned_cols=31 Identities=16% Similarity=0.269 Sum_probs=26.7
Q ss_pred HHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 479 VLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 479 VL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
|-.+|. ..++|..|+|+.+|||..+|++++.
T Consensus 38 ik~LR~----~~glTQ~elA~~lGvS~~TVs~WE~ 68 (96)
T PRK10072 38 FEQLRK----GTGLKIDDFARVLGVSVAMVKEWES 68 (96)
T ss_pred HHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 445566 5789999999999999999999986
No 292
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=74.71 E-value=8.5 Score=32.72 Aligned_cols=33 Identities=24% Similarity=0.238 Sum_probs=27.3
Q ss_pred CCCCCHHHHHHHhC-CCHHHHHHHHHHHHHHHHh
Q 009449 489 HRPKSLEEIGKLFH-VSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 489 ~e~~Sl~EIA~~Lg-ISrerVRqi~~RAL~KLR~ 521 (534)
.-++|+.|||+.|| .+.++|.....+.-+++..
T Consensus 42 ~~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~ 75 (90)
T cd06571 42 LTGLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE 75 (90)
T ss_pred HhCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh
Confidence 35899999999999 9999998777766666654
No 293
>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=74.53 E-value=6.5 Score=31.45 Aligned_cols=25 Identities=24% Similarity=0.316 Sum_probs=21.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 490 RPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 490 e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
...|..|||+.+|+|+.+|++.+.+
T Consensus 12 ~~~~~~eLa~~l~vS~~tv~~~l~~ 36 (69)
T TIGR00122 12 NPFSGEKLGEALGMSRTAVNKHIQT 36 (69)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4678999999999999999865544
No 294
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=74.37 E-value=5.1 Score=36.39 Aligned_cols=24 Identities=17% Similarity=0.144 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 490 RPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 490 e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
+|+|+.+||+.||+|+..|+|.++
T Consensus 21 eG~Sq~~iA~LLGltqaAVS~Yls 44 (119)
T COG2522 21 EGLSQYRIAKLLGLTQAAVSQYLS 44 (119)
T ss_pred cCCcHHHHHHHhCCCHHHHHHHHc
Confidence 599999999999999999999875
No 295
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=74.29 E-value=6.1 Score=36.13 Aligned_cols=42 Identities=21% Similarity=0.202 Sum_probs=33.0
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
..|++.+++||...- . .-..|+.|||+.+|+|+.+|+.+..+
T Consensus 4 ~~lD~~D~~IL~~L~--~-d~r~~~~eia~~lglS~~~v~~Ri~~ 45 (154)
T COG1522 4 MKLDDIDRRILRLLQ--E-DARISNAELAERVGLSPSTVLRRIKR 45 (154)
T ss_pred ccccHHHHHHHHHHH--H-hCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 357788888887654 1 34599999999999999999876554
No 296
>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=73.74 E-value=4 Score=29.78 Aligned_cols=37 Identities=14% Similarity=0.176 Sum_probs=24.5
Q ss_pred HHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 474 SRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 474 ~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
+-|+.+|.-..- ..+-+..+.|+.||||+.+++..+.
T Consensus 4 ~~E~~~i~~aL~---~~~gn~~~aA~~Lgisr~tL~~klk 40 (42)
T PF02954_consen 4 EFEKQLIRQALE---RCGGNVSKAARLLGISRRTLYRKLK 40 (42)
T ss_dssp HHHHHHHHHHHH---HTTT-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHH---HhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 445555554441 2355889999999999999987654
No 297
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=73.54 E-value=4.8 Score=29.14 Aligned_cols=28 Identities=21% Similarity=0.489 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 490 RPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 490 e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
-+.|..|||+.+|+|+.+|+ +++++|.+
T Consensus 7 ~~~s~~~la~~l~~s~~tv~----~~l~~L~~ 34 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVS----RTLKRLEK 34 (48)
T ss_pred eccCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 36899999999999999995 55555654
No 298
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=73.50 E-value=6.8 Score=28.64 Aligned_cols=25 Identities=36% Similarity=0.360 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 490 RPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 490 e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
.+.|..+|++.+|+++.+|++.+..
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~ 37 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNK 37 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4689999999999999999766543
No 299
>PF13551 HTH_29: Winged helix-turn helix
Probab=73.36 E-value=13 Score=31.64 Aligned_cols=24 Identities=25% Similarity=0.178 Sum_probs=22.0
Q ss_pred CHHHHHHHcCCCHHHHHHHHHHhh
Q 009449 400 EDIEIAKYTGLSLAEIRSASECLR 423 (534)
Q Consensus 400 t~eEIA~~lgis~~kv~~~l~~~~ 423 (534)
+..+||+.+|++...|..++....
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~ 37 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYR 37 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHH
Confidence 799999999999999999988765
No 300
>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=73.28 E-value=4.8 Score=31.39 Aligned_cols=25 Identities=28% Similarity=0.270 Sum_probs=21.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
....|.+|+|+.||||..|||.-+.
T Consensus 12 ~~~~s~~ela~~~~VS~~TiRRDl~ 36 (57)
T PF08220_consen 12 KGKVSVKELAEEFGVSEMTIRRDLN 36 (57)
T ss_pred cCCEEHHHHHHHHCcCHHHHHHHHH
Confidence 4678999999999999999986543
No 301
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=73.09 E-value=5.2 Score=29.94 Aligned_cols=26 Identities=19% Similarity=0.258 Sum_probs=23.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
..++|+.++|+.+|+|+++|+.++..
T Consensus 13 ~~gltq~~lA~~~gvs~~~vs~~e~g 38 (58)
T TIGR03070 13 ALGLTQADLADLAGVGLRFIRDVENG 38 (58)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 35889999999999999999999853
No 302
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=72.68 E-value=6 Score=29.71 Aligned_cols=26 Identities=15% Similarity=0.189 Sum_probs=22.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
..+.|..+|++.+|+|+.+|+.++.+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~ 33 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKK 33 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHH
Confidence 35789999999999999999876654
No 303
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=72.39 E-value=7.9 Score=34.75 Aligned_cols=35 Identities=6% Similarity=0.071 Sum_probs=28.9
Q ss_pred HHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 478 QVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 478 eVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
+++...+ ..+.|..+||..+|||..+|+++..+..
T Consensus 20 ~aV~~~~----~~g~sv~evA~e~gIs~~tl~~W~r~y~ 54 (121)
T PRK09413 20 AIVQQSF----EPGMTVSLVARQHGVAASQLFLWRKQYQ 54 (121)
T ss_pred HHHHHHH----cCCCCHHHHHHHHCcCHHHHHHHHHHHh
Confidence 3555555 5789999999999999999999988753
No 304
>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=72.38 E-value=5.9 Score=30.77 Aligned_cols=29 Identities=17% Similarity=0.440 Sum_probs=23.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
..+.|..|||+.+|+|+.+|+ +++++|++
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~----r~l~~L~~ 51 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVS----RTLKELEE 51 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 357899999999999999996 55555554
No 305
>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=72.37 E-value=6.9 Score=33.07 Aligned_cols=36 Identities=22% Similarity=0.205 Sum_probs=27.3
Q ss_pred HHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 474 SRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 474 ~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
+|..+|+.+.- . ...|+++||+.+|||+.||+..+.
T Consensus 6 ~R~~~I~e~l~---~-~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 6 ERVLEIGKYIV---E-TKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred HHHHHHHHHHH---H-CCCCHHHHHHHhCCCHHHHHHHhc
Confidence 35555555544 2 577999999999999999998664
No 306
>PRK05572 sporulation sigma factor SigF; Validated
Probab=72.36 E-value=54 Score=32.84 Aligned_cols=34 Identities=24% Similarity=0.357 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHH
Q 009449 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLK 287 (534)
Q Consensus 254 ~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~ 287 (534)
++.+....+..+.|+.|+..+-|++.|++.+.+.
T Consensus 119 ~~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~ 152 (252)
T PRK05572 119 KIRKDKDELSKELGREPTIEELAEYLGVTPEEVV 152 (252)
T ss_pred HHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHH
Confidence 4445566677778999999999999998887653
No 307
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=72.32 E-value=92 Score=32.46 Aligned_cols=171 Identities=19% Similarity=0.075 Sum_probs=81.6
Q ss_pred HHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCH
Q 009449 322 FSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPED 401 (534)
Q Consensus 322 ~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~ 401 (534)
.+.=++-++-.+-+-.....-.+. -.-=|..|.|.++..-+.+- ..+ -..+-.+..-.....|-.-|.
T Consensus 93 ~ernl~~a~~~l~~~~~~l~LP~~--v~e~A~~iyr~a~~~~l~rG-------Rsi---e~v~AA~iY~acR~~~~prtl 160 (285)
T COG1405 93 KERNLITALEELERIASALGLPES--VRETAARIYRKAVDKGLLRG-------RSI---ESVAAACIYAACRINGVPRTL 160 (285)
T ss_pred hhhHHHHHHHHHHHHHHHhCCCch--HHHHHHHHHHHHhhcCCCcC-------CcH---HHHHHHHHHHHHHHcCCCccH
Confidence 444555555555555555543332 22233445555544333221 111 111222223334456677799
Q ss_pred HHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhh-hccCCCCCCChHHHHHHHHHHHHHHHHHh-hC----CHH
Q 009449 402 IEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYL-EFAPDRSVKSPKEIVMRQHMKKDVFRILE-SL----DSR 475 (534)
Q Consensus 402 eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~-e~i~d~~~~spee~v~~~el~e~L~~~L~-~L----~~r 475 (534)
.|||..++++...+............+..+.-+ ...+. -+..+-.. +++-.- ...+.+..+.. .+ .|-
T Consensus 161 ~eIa~a~~V~~kei~rtyr~~~~~L~l~~~~~~--p~~yi~rf~s~L~l-~~~v~~---~a~ei~~~~~~~g~~~Gk~P~ 234 (285)
T COG1405 161 DEIAKALGVSKKEIGRTYRLLVRELKLKIPPVD--PSDYIPRFASKLGL-SDEVRR---KAIEIVKKAKRAGLTAGKSPA 234 (285)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHhcCCCCCCCC--HHHHHHHHHHHcCC-CHHHHH---HHHHHHHHHHHhCcccCCCch
Confidence 999999999998888776644433333322211 11111 11111111 111111 11112222211 01 111
Q ss_pred -----HHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 476 -----ERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 476 -----EReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
--.+--+.+ +...|++|||+..|||..|||+....
T Consensus 235 glAaaaiy~as~l~----~~~~tq~eva~v~~vtevTIrnryke 274 (285)
T COG1405 235 GLAAAAIYLASLLL----GERRTQKEVAKVAGVTEVTIRNRYKE 274 (285)
T ss_pred hHHHHHHHHHHHHh----CCchHHHHHHHHhCCeeeHHHHHHHH
Confidence 111122223 47899999999999999999998843
No 308
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=72.29 E-value=31 Score=35.66 Aligned_cols=26 Identities=12% Similarity=0.059 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHcCCCHHHHHHHHHHh
Q 009449 397 KYPEDIEIAKYTGLSLAEIRSASECL 422 (534)
Q Consensus 397 r~Pt~eEIA~~lgis~~kv~~~l~~~ 422 (534)
..-|..|||+.+|+|..+|+++...+
T Consensus 244 ~~~t~~EIa~~lgvs~~~V~q~~~~A 269 (289)
T PRK07500 244 DGATLEALGEELGISKERVRQIEARA 269 (289)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 45699999999999999999876543
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=72.20 E-value=7.2 Score=36.76 Aligned_cols=38 Identities=21% Similarity=0.197 Sum_probs=31.0
Q ss_pred CHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 473 DSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 473 ~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
+|..-.|=.+|- ..|+|..|+|+.+|||+.+|.+++..
T Consensus 24 ~p~~~~Ir~~R~----~lGmTq~eLAerlGVS~~tIs~iE~G 61 (150)
T TIGR02612 24 TPKEGWVRAIRK----ALGMSGAQLAGRLGVTPQRVEALEKS 61 (150)
T ss_pred cCcHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 444444656666 67999999999999999999999984
No 310
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=72.16 E-value=5.8 Score=30.26 Aligned_cols=50 Identities=14% Similarity=0.158 Sum_probs=38.5
Q ss_pred hCCHHHHHHHhhHhcCCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449 471 SLDSRERQVLVLRYGLNDH-RPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~-e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR 520 (534)
.+++.+..+|.-.|..+.. .....++||..+||+...|..+...-..+.|
T Consensus 6 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k 56 (57)
T PF00046_consen 6 RFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEK 56 (57)
T ss_dssp SSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhC
Confidence 4678888888888854322 2234578999999999999999988777766
No 311
>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=71.82 E-value=3.4 Score=35.31 Aligned_cols=24 Identities=25% Similarity=0.295 Sum_probs=17.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 490 RPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 490 e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
.|+|..|||+.+|.|+..|.+++.
T Consensus 2 ~G~tq~eIA~~lGks~s~Vs~~l~ 25 (93)
T PF08535_consen 2 FGWTQEEIAKRLGKSRSWVSNHLA 25 (93)
T ss_dssp TT--HHHHHHHTT--HHHHHHHHG
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 478999999999999999998764
No 312
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=71.78 E-value=8.9 Score=29.55 Aligned_cols=37 Identities=19% Similarity=0.283 Sum_probs=26.4
Q ss_pred HHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 474 SRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 474 ~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
+.+..|+...+ ..+.+..||++.+|+++.+|+..+.+
T Consensus 7 ~~~~~il~~l~----~~~~~~~ei~~~~~i~~~~i~~~l~~ 43 (78)
T cd00090 7 PTRLRILRLLL----EGPLTVSELAERLGLSQSTVSRHLKK 43 (78)
T ss_pred hHHHHHHHHHH----HCCcCHHHHHHHHCcCHhHHHHHHHH
Confidence 44555665444 23399999999999999999755443
No 313
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=71.14 E-value=2.1 Score=33.94 Aligned_cols=25 Identities=28% Similarity=0.485 Sum_probs=22.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
+|..|+|+.+|||+.+||.++.+.+
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 4789999999999999999988776
No 314
>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=71.00 E-value=6.1 Score=30.97 Aligned_cols=36 Identities=22% Similarity=0.279 Sum_probs=27.8
Q ss_pred HHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 475 RERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 475 rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
|+-+++.+-+. ....|+.|+|+.+|+|..+|++.+.
T Consensus 6 rq~~Ll~~L~~---~~~~~~~ela~~l~~S~rti~~~i~ 41 (59)
T PF08280_consen 6 RQLKLLELLLK---NKWITLKELAKKLNISERTIKNDIN 41 (59)
T ss_dssp HHHHHHHHHHH---HTSBBHHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHc---CCCCcHHHHHHHHCCCHHHHHHHHH
Confidence 55667777764 4689999999999999999986554
No 315
>PRK09954 putative kinase; Provisional
Probab=70.97 E-value=7 Score=41.23 Aligned_cols=43 Identities=16% Similarity=0.315 Sum_probs=34.5
Q ss_pred CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449 472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMT 517 (534)
Q Consensus 472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~ 517 (534)
|++++++||.+.. .....|..|||+.||||+.+|+.++.+=.+
T Consensus 1 ~~~~~~~il~~l~---~~~~~s~~~la~~l~~s~~~v~~~i~~L~~ 43 (362)
T PRK09954 1 MNNREKEILAILR---RNPLIQQNEIADILQISRSRVAAHIMDLMR 43 (362)
T ss_pred CChHHHHHHHHHH---HCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4677778887765 235799999999999999999999986443
No 316
>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=70.88 E-value=3.6 Score=33.15 Aligned_cols=35 Identities=14% Similarity=0.159 Sum_probs=28.0
Q ss_pred HHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 478 QVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 478 eVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
.||.... ..+.|..+||..+||++.+++++.....
T Consensus 14 ~~v~~~~----~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 14 QAVREYL----ESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp HHHHHHH----HHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHH----HCCCceEeeecccccccccccHHHHHHh
Confidence 3444443 4689999999999999999999998886
No 317
>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=70.60 E-value=5.2 Score=37.60 Aligned_cols=29 Identities=17% Similarity=0.180 Sum_probs=24.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 490 RPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 490 e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
-+.|.+|||..+|+|+++|. |++++|++.
T Consensus 142 ~~~t~~~iA~~lG~tretvs----R~l~~l~~~ 170 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTIT----RLLGDLRKK 170 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHH----HHHHHHHHC
Confidence 36899999999999999995 777788764
No 318
>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=70.54 E-value=4.8 Score=32.33 Aligned_cols=29 Identities=31% Similarity=0.566 Sum_probs=23.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 490 RPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 490 e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
-++|.++||..+|+|+++|. +.+++|++.
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~----r~l~~l~~~ 55 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVS----RILKRLKDE 55 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHH----HHHHHHHHT
T ss_pred ecCCHHHHHHHHCCCHHHHH----HHHHHHHHC
Confidence 36899999999999999996 566666653
No 319
>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=70.53 E-value=19 Score=31.72 Aligned_cols=41 Identities=5% Similarity=0.142 Sum_probs=32.6
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
..|++.+..||...+ ...+.|..|||+.+|+++.+|.+++.
T Consensus 24 ~~lt~~q~~iL~~l~---~~~~~t~~ela~~~~~~~~tvs~~l~ 64 (118)
T TIGR02337 24 HGLTEQQWRILRILA---EQGSMEFTQLANQACILRPSLTGILA 64 (118)
T ss_pred cCCCHHHHHHHHHHH---HcCCcCHHHHHHHhCCCchhHHHHHH
Confidence 468999988887655 24689999999999999999964443
No 320
>PF14493 HTH_40: Helix-turn-helix domain
Probab=70.18 E-value=9.8 Score=32.31 Aligned_cols=30 Identities=20% Similarity=0.186 Sum_probs=27.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEKKAMTK 518 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~RAL~K 518 (534)
.+|+|++|||+.-|++.+||..++.++...
T Consensus 11 ~~G~si~eIA~~R~L~~sTI~~HL~~~~~~ 40 (91)
T PF14493_consen 11 QKGLSIEEIAKIRGLKESTIYGHLAELIES 40 (91)
T ss_pred HcCCCHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence 479999999999999999999999888765
No 321
>PRK00215 LexA repressor; Validated
Probab=70.17 E-value=7.3 Score=37.81 Aligned_cols=43 Identities=21% Similarity=0.227 Sum_probs=32.1
Q ss_pred CCHHHHHHHhhHhc--CCCCCCCCHHHHHHHhCC-CHHHHHHHHHH
Q 009449 472 LDSRERQVLVLRYG--LNDHRPKSLEEIGKLFHV-SKEWIRKLEKK 514 (534)
Q Consensus 472 L~~rEReVL~LryG--L~d~e~~Sl~EIA~~LgI-SrerVRqi~~R 514 (534)
|+++|.+||.+-.= ...+.+.|+.|||+.+|+ ++++|..++.+
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~ 47 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKA 47 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 68888888864431 112456799999999999 99999766544
No 322
>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=70.12 E-value=6.1 Score=29.95 Aligned_cols=25 Identities=24% Similarity=0.404 Sum_probs=20.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
..++|+.|||+.+|+++++|..++.
T Consensus 16 ~~~~t~~eia~~~gl~~stv~r~L~ 40 (52)
T PF09339_consen 16 GGPLTLSEIARALGLPKSTVHRLLQ 40 (52)
T ss_dssp BSCEEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 4568999999999999999976543
No 323
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=70.07 E-value=8.6 Score=29.46 Aligned_cols=26 Identities=27% Similarity=0.374 Sum_probs=21.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
.|..+||+.+|+|+++|+ +++++|.+
T Consensus 26 ~~~~~la~~~~is~~~v~----~~l~~L~~ 51 (66)
T cd07377 26 PSERELAEELGVSRTTVR----EALRELEA 51 (66)
T ss_pred CCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 359999999999999997 56666664
No 324
>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=69.88 E-value=11 Score=36.73 Aligned_cols=44 Identities=25% Similarity=0.249 Sum_probs=35.2
Q ss_pred HHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 468 ILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 468 ~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
....|++++..|+.+.. ...+.+..|||+.+|+|+.+|++++.+
T Consensus 137 ~~~~ls~~~~~IL~~l~---~~g~~s~~eia~~l~is~stv~r~L~~ 180 (203)
T TIGR01884 137 LLAGLSREELKVLEVLK---AEGEKSVKNIAKKLGKSLSTISRHLRE 180 (203)
T ss_pred hhcCCCHHHHHHHHHHH---HcCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 35679999999987776 124679999999999999999866554
No 325
>TIGR00647 MG103 conserved hypothetical protein.
Probab=69.77 E-value=8.9 Score=39.78 Aligned_cols=45 Identities=29% Similarity=0.411 Sum_probs=38.7
Q ss_pred HhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhC------CCHHHHHHHHHHHH
Q 009449 469 LESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFH------VSKEWIRKLEKKAM 516 (534)
Q Consensus 469 L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~Lg------ISrerVRqi~~RAL 516 (534)
++.||+.-+++..+|. ...+.|++|+|+.|. ||++.|..+++|-.
T Consensus 225 l~~Lp~~L~~~a~lRl---~~Pd~SL~ELgell~~~~~~~isKSgvnhRlrKl~ 275 (279)
T TIGR00647 225 FEKLPLNFQRICLLKI---DHPDWSLEQIAEFFASKYKVKISRSGIQHRLRKLK 275 (279)
T ss_pred cccCCHHHHHHHHHHH---hCcccCHHHHHHHhccCCCCCcCHHHHHHHHHHHH
Confidence 5789999999999998 368899999999994 99999988776543
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=69.37 E-value=9.5 Score=33.63 Aligned_cols=42 Identities=17% Similarity=0.351 Sum_probs=26.9
Q ss_pred HHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 475 RERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 475 rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
+.++|.. .| .|.+..|+|..+|+|..+|++|+.+..++-++.
T Consensus 62 R~~~I~~-~f-----~G~n~~eLA~kyglS~r~I~~Ii~~~~~~~~~~ 103 (108)
T PF08765_consen 62 RNREIRR-EF-----NGMNVRELARKYGLSERQIYRIIKRVRRRERRR 103 (108)
T ss_dssp HHHHHHH-H-------SS-HHHHHHHHT--HHHHHHHHHHHHH-----
T ss_pred HHHHHHH-Hh-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHh
Confidence 4455554 33 488999999999999999999999988776643
No 327
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=69.33 E-value=13 Score=32.96 Aligned_cols=39 Identities=21% Similarity=0.216 Sum_probs=35.4
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
..|++.|-..|+-.+ ++|+.+-|..||+|.++|+.++..
T Consensus 42 ~~ls~~eIk~iRe~~------~lSQ~vFA~~L~vs~~Tv~~WEqG 80 (104)
T COG2944 42 KTLSPTEIKAIREKL------GLSQPVFARYLGVSVSTVRKWEQG 80 (104)
T ss_pred CCCCHHHHHHHHHHh------CCCHHHHHHHHCCCHHHHHHHHcC
Confidence 669999988888887 789999999999999999999974
No 328
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=68.22 E-value=5.7 Score=40.45 Aligned_cols=26 Identities=19% Similarity=0.323 Sum_probs=24.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
.++|.+.+||+.||||+.+|+.+..|
T Consensus 17 l~gmk~~dIAeklGvspntiksWKrr 42 (279)
T COG5484 17 LKGMKLKDIAEKLGVSPNTIKSWKRR 42 (279)
T ss_pred HhhccHHHHHHHhCCChHHHHHHHHh
Confidence 58899999999999999999998876
No 329
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=68.14 E-value=10 Score=32.04 Aligned_cols=31 Identities=19% Similarity=0.239 Sum_probs=25.5
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 488 DHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 488 d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
++...|-++||+.||+|+.+|. +.+++||+.
T Consensus 16 ~~~~~SGe~La~~LgiSRtaVw----K~Iq~Lr~~ 46 (79)
T COG1654 16 TGNFVSGEKLAEELGISRTAVW----KHIQQLREE 46 (79)
T ss_pred CCCcccHHHHHHHHCccHHHHH----HHHHHHHHh
Confidence 3578999999999999999996 566677753
No 330
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=68.06 E-value=6.4 Score=30.98 Aligned_cols=23 Identities=22% Similarity=0.403 Sum_probs=20.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~R 514 (534)
+|..|+|+.+|||..+++.+..+
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 47899999999999999998865
No 331
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=67.65 E-value=8.1 Score=34.32 Aligned_cols=51 Identities=20% Similarity=0.208 Sum_probs=45.7
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET 524 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~ 524 (534)
.+|.+-||-...-+| -+-+|-+|||-.+.++..+|..+...-..|.|++-+
T Consensus 27 ~QLkELErvF~ETHY----PDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 27 AQLKELERVFAETHY----PDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred HHHHHHHHHHHhhcC----CcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence 568888999999999 789999999999999999999999998889887654
No 332
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=67.14 E-value=71 Score=32.11 Aligned_cols=34 Identities=15% Similarity=0.152 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 009449 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (534)
Q Consensus 255 le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~ 288 (534)
+.+....+..+.|+.|+..+-|...|++.+.+..
T Consensus 125 ~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~ 158 (258)
T PRK08215 125 ALQVREKLINENSKEPTVEEIAKELEVPREEVVF 158 (258)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHH
Confidence 3445667777889999999999999999988654
No 333
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=67.12 E-value=13 Score=40.27 Aligned_cols=51 Identities=16% Similarity=0.157 Sum_probs=41.1
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
.+++.||..+.+.+=|...++.|+.++|+.|+||++||.+-+.+..+.|..
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 377888877766665555688999999999999999999877777666655
No 334
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=67.03 E-value=10 Score=30.55 Aligned_cols=25 Identities=16% Similarity=0.219 Sum_probs=23.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
..++|..++|+.+|+|+.+|++++.
T Consensus 16 ~~~~t~~~lA~~~gis~~tis~~~~ 40 (78)
T TIGR02607 16 PLGLSIRALAKALGVSRSTLSRIVN 40 (78)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 4788999999999999999999886
No 335
>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=66.76 E-value=3.6 Score=29.71 Aligned_cols=24 Identities=29% Similarity=0.509 Sum_probs=19.7
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 493 SLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 493 Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
|..|+|+.+|||..++|..+...+
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~Gl 24 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYEREGL 24 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHTTS
T ss_pred CHHHHHHHHCCCHHHHHHHHHCCC
Confidence 467999999999999999887653
No 336
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=66.60 E-value=52 Score=37.28 Aligned_cols=103 Identities=17% Similarity=0.266 Sum_probs=58.7
Q ss_pred CCCCHHHHHHHcCCCHHHHHHHHHHhhhhc---ccccccccchhhhhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCC
Q 009449 397 KYPEDIEIAKYTGLSLAEIRSASECLRIVG---SIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLD 473 (534)
Q Consensus 397 r~Pt~eEIA~~lgis~~kv~~~l~~~~~~~---SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~ 473 (534)
...|..+||+.+|+|..+|+.-........ .+. .+....+ -.+.. .++. .+...+..-+
T Consensus 16 ~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~-~i~~~~G----y~l~~---~~~~----------~~~~~~~~~~ 77 (584)
T PRK09863 16 QDRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIG-SISGSAK----YHLEI---LNRR----------SLFQLLQKSD 77 (584)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchh-heecCCc----eEEEe---CCHH----------HHHHHHhcCC
Confidence 457999999999999999987665443211 110 0000000 00100 1111 1111122223
Q ss_pred HHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449 474 SRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520 (534)
Q Consensus 474 ~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR 520 (534)
+ |+..+.++.-+ .++.++.++|+.|.||++||.+-+.+..+.|.
T Consensus 78 ~-e~~~il~~Ll~--~~~~~~~~La~~l~vS~sTi~~dl~~v~~~l~ 121 (584)
T PRK09863 78 N-EDRLLLLRLLL--NTFTPMAQLASALNLSRTWVAERLPRLNQRYE 121 (584)
T ss_pred H-HHHHHHHHHHH--cCCccHHHHHHHhCCCHHHHHHHHHHHHHhhh
Confidence 3 33333333322 36899999999999999999988888877766
No 337
>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=66.50 E-value=69 Score=32.07 Aligned_cols=34 Identities=15% Similarity=0.200 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 009449 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (534)
Q Consensus 255 le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~ 288 (534)
+......+....|+.|+..+-|...|++.+.+..
T Consensus 118 ~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~ 151 (255)
T TIGR02941 118 IKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLE 151 (255)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 3445566777789999999999999999877644
No 338
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=66.22 E-value=72 Score=27.34 Aligned_cols=38 Identities=16% Similarity=-0.023 Sum_probs=29.6
Q ss_pred HHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHH
Q 009449 384 IQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC 421 (534)
Q Consensus 384 i~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~ 421 (534)
+.++..-+...+...++.++||+.+|++...+......
T Consensus 7 ~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~ 44 (107)
T PRK10219 7 IQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRT 44 (107)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 44455556666778899999999999999998877543
No 339
>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=65.32 E-value=7.4 Score=30.66 Aligned_cols=29 Identities=24% Similarity=0.349 Sum_probs=21.6
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 489 HRPK-SLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 489 ~e~~-Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
++.+ |..+||+.+|||+.+|+ +|+..|..
T Consensus 21 g~~lps~~~la~~~~vsr~tvr----~al~~L~~ 50 (64)
T PF00392_consen 21 GDRLPSERELAERYGVSRTTVR----EALRRLEA 50 (64)
T ss_dssp TSBE--HHHHHHHHTS-HHHHH----HHHHHHHH
T ss_pred CCEeCCHHHHHHHhccCCcHHH----HHHHHHHH
Confidence 4677 99999999999999997 56666553
No 340
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=64.82 E-value=81 Score=33.77 Aligned_cols=42 Identities=26% Similarity=0.423 Sum_probs=32.9
Q ss_pred hhchHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 009449 247 KGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (534)
Q Consensus 247 ~~iq~~~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~ 288 (534)
.+++..-++-+++..|..++|++|+..+-|+..|++...+..
T Consensus 183 h~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~ 224 (342)
T COG0568 183 HQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVRE 224 (342)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHH
Confidence 344445567778888888899999999999999998875443
No 341
>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=64.77 E-value=8.2 Score=30.54 Aligned_cols=23 Identities=22% Similarity=0.397 Sum_probs=21.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~R 514 (534)
+|..|+|+.+|||..++|.+..+
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 47899999999999999999876
No 342
>PRK15340 transcriptional regulator InvF; Provisional
Probab=64.35 E-value=1.5e+02 Score=29.71 Aligned_cols=33 Identities=12% Similarity=-0.002 Sum_probs=25.9
Q ss_pred HHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHH
Q 009449 389 KALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC 421 (534)
Q Consensus 389 ~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~ 421 (534)
+.|..+.....+.++||+.+|+++..+..+...
T Consensus 116 ~~Ll~~~~~~~sleeLA~~~gvS~r~f~RlFk~ 148 (216)
T PRK15340 116 GYLLAQSTSGNTMRMLGEDYGVSYTHFRRLCSR 148 (216)
T ss_pred HHHHhCccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 334555567789999999999999999887543
No 343
>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=64.13 E-value=75 Score=31.03 Aligned_cols=32 Identities=22% Similarity=0.360 Sum_probs=25.6
Q ss_pred HHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 009449 257 RIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (534)
Q Consensus 257 ~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~ 288 (534)
+....+....|+.|+..+.|+..|++.+.+..
T Consensus 94 ~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~ 125 (227)
T TIGR02980 94 KATEELTQRLGRSPTIAEIAEELGVSEEEVVE 125 (227)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHH
Confidence 34556677779999999999999999887643
No 344
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=63.63 E-value=35 Score=31.12 Aligned_cols=40 Identities=13% Similarity=0.066 Sum_probs=32.8
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
.|++.|-.||...+ ...+.|..|||+.+|+++.+|..++.
T Consensus 37 glt~~q~~vL~~l~---~~~~~t~~eLa~~l~i~~~tvsr~l~ 76 (144)
T PRK11512 37 DITAAQFKVLCSIR---CAACITPVELKKVLSVDLGALTRMLD 76 (144)
T ss_pred CCCHHHHHHHHHHH---HcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 58999988887665 14579999999999999999975544
No 345
>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=63.05 E-value=15 Score=28.27 Aligned_cols=45 Identities=20% Similarity=0.235 Sum_probs=31.0
Q ss_pred cccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHH
Q 009449 373 IPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRS 417 (534)
Q Consensus 373 lP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~ 417 (534)
+|.-+.+.+-...++-..|..+.-..-+-.+||+.+|+++.+|+.
T Consensus 3 Ip~~ti~RL~~Y~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 3 IPKATIRRLPLYLRYLEQLKEEGVERVSSQELAEALGITPAQVRK 47 (50)
T ss_dssp -SHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHcCCeeECHHHHHHHHCCCHHHhcc
Confidence 455556666666666667766555667889999999999999985
No 346
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=62.55 E-value=7.6 Score=37.44 Aligned_cols=27 Identities=15% Similarity=0.154 Sum_probs=23.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 490 RPKSLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 490 e~~Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
-++|..|||+.+|.|+.|||+++.-.-
T Consensus 60 ag~Ti~EIAeelG~TeqTir~hlkget 86 (182)
T COG1318 60 AGMTISEIAEELGRTEQTVRNHLKGET 86 (182)
T ss_pred ccCcHHHHHHHhCCCHHHHHHHHhcch
Confidence 589999999999999999999876443
No 347
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=62.53 E-value=17 Score=30.07 Aligned_cols=44 Identities=25% Similarity=0.379 Sum_probs=33.8
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
.|+..+..||.+-+. ..+.|..+||+.+++++.+|+ +++++|.+
T Consensus 7 ~l~~~~~~il~~l~~---~~~~~~~~la~~~~~s~~~i~----~~l~~L~~ 50 (101)
T smart00347 7 GLTPTQFLVLRILYE---EGPLSVSELAKRLGVSPSTVT----RVLDRLEK 50 (101)
T ss_pred CCCHHHHHHHHHHHH---cCCcCHHHHHHHHCCCchhHH----HHHHHHHH
Confidence 477788888877773 246899999999999999987 45555554
No 348
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=62.08 E-value=19 Score=32.55 Aligned_cols=44 Identities=9% Similarity=0.132 Sum_probs=31.0
Q ss_pred HHHhhCCHH-HHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 467 RILESLDSR-ERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 467 ~~L~~L~~r-EReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
+.+..|.+. -+.||.+-. +..+++..||++.+|+|+.+|++++.
T Consensus 8 ~~fkaLadptRl~IL~~L~---~~~~~~v~ela~~l~lsqstvS~HL~ 52 (117)
T PRK10141 8 QLFKILSDETRLGIVLLLR---ESGELCVCDLCTALDQSQPKISRHLA 52 (117)
T ss_pred HHHHHhCCHHHHHHHHHHH---HcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 445555444 446666553 13579999999999999999987653
No 349
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=61.56 E-value=18 Score=28.27 Aligned_cols=36 Identities=14% Similarity=0.138 Sum_probs=27.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET 524 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~ 524 (534)
..+.+..+.|+.|+|.++||+.++.|+-..+.-.+.
T Consensus 10 ~~~~n~~~tA~~L~iHrNTl~yRl~ki~~l~g~dl~ 45 (59)
T PF13556_consen 10 ENNGNISKTARALHIHRNTLRYRLKKIEELLGLDLD 45 (59)
T ss_dssp HTTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--TT
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCcCCC
Confidence 467899999999999999999999998877654443
No 350
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=61.51 E-value=6.2 Score=31.13 Aligned_cols=25 Identities=28% Similarity=0.345 Sum_probs=21.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
+|..|+|+.+|||+.+|+.++...+
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~~gl 25 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYERIGL 25 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999877554
No 351
>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=61.28 E-value=9.6 Score=34.12 Aligned_cols=25 Identities=32% Similarity=0.393 Sum_probs=23.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
..|.|..|+|..|+||+.||..+..
T Consensus 16 ~~g~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 16 EKGKSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred HccchHHHHHHHhCcHHHHHHHHHH
Confidence 5788999999999999999998876
No 352
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=61.05 E-value=1.5e+02 Score=29.33 Aligned_cols=34 Identities=21% Similarity=0.257 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 009449 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (534)
Q Consensus 255 le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~ 288 (534)
+......+....|++|+..+.|+..|++.+.+..
T Consensus 97 ~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~ 130 (236)
T PRK06986 97 VAQAIRQLEQELGREPTDTEVAEKLGLSLEEYRE 130 (236)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHH
Confidence 3344556667789999999999999999877554
No 353
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=60.71 E-value=22 Score=35.97 Aligned_cols=52 Identities=19% Similarity=0.231 Sum_probs=40.0
Q ss_pred HHHHHHHHhhCCHHHHHHHhhHhcCC-CCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 462 KKDVFRILESLDSRERQVLVLRYGLN-DHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 462 ~e~L~~~L~~L~~rEReVL~LryGL~-d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
.+.|...+..|+|.|+.|......=. +...+|..|||+..|+|..||-..-+
T Consensus 4 ~~~i~~~~~~Lt~~e~~Ia~yil~n~~~v~~~si~~lA~~~~vS~aTv~Rf~k 56 (284)
T PRK11302 4 LEKIQSRLEHLSKSERKVAEVILASPQTAIHSSIATLAKMANVSEPTVNRFCR 56 (284)
T ss_pred HHHHHHHHhhCCHHHHHHHHHHHhCHHHHHhcCHHHHHHHhCCCHHHHHHHHH
Confidence 35677888999999999987654111 12458999999999999999976554
No 354
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=60.31 E-value=16 Score=36.65 Aligned_cols=26 Identities=19% Similarity=0.261 Sum_probs=23.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
..+.|..|||++||||..+||+++..
T Consensus 23 ~g~~sa~elA~~Lgis~~avR~HL~~ 48 (218)
T COG2345 23 SGPVSADELAEELGISPMAVRRHLDD 48 (218)
T ss_pred cCCccHHHHHHHhCCCHHHHHHHHHH
Confidence 46999999999999999999987654
No 355
>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=60.31 E-value=11 Score=30.00 Aligned_cols=23 Identities=17% Similarity=0.309 Sum_probs=20.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~R 514 (534)
++..|+|+.+|||..++|.++..
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 47899999999999999998765
No 356
>PRK10870 transcriptional repressor MprA; Provisional
Probab=60.18 E-value=44 Score=31.92 Aligned_cols=50 Identities=8% Similarity=0.127 Sum_probs=36.2
Q ss_pred HHHHHHh--hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 464 DVFRILE--SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 464 ~L~~~L~--~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
.+...+. .|++.+-.||...+. .+..+.|..|||+.+++++.+|.++..+
T Consensus 43 ~~~~~l~~~gLt~~q~~iL~~L~~-~~~~~it~~eLa~~l~l~~~tvsr~v~r 94 (176)
T PRK10870 43 NRNKMLKAQGINETLFMALITLES-QENHSIQPSELSCALGSSRTNATRIADE 94 (176)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHhc-CCCCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4455554 488888888877762 1235689999999999999999755543
No 357
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=60.16 E-value=8.9 Score=30.96 Aligned_cols=23 Identities=17% Similarity=0.349 Sum_probs=19.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~R 514 (534)
.|..|||+..|||+.||+.+++.
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~ 23 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNG 23 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCC
Confidence 37899999999999999987653
No 358
>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=60.02 E-value=2.1e+02 Score=29.29 Aligned_cols=31 Identities=16% Similarity=0.095 Sum_probs=24.0
Q ss_pred hHHHHHHhhccC-CCCCCchHHHHHHhhchHH
Q 009449 222 IFSAERALNSRG-RRLTIARNEAEMSKGVQVV 252 (534)
Q Consensus 222 ~~~~~~~~~~~~-~~lLt~~eE~~L~~~iq~~ 252 (534)
.+|+.-|+...+ .|.||.++|.+|...++.+
T Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~g 43 (285)
T TIGR02394 12 ADVTQLYLREIGFKPLLTAEEEIAYARRALAG 43 (285)
T ss_pred chHHHHHHHHHhccCCCCHHHHHHHHHHHHcC
Confidence 466666775555 6899999999999988754
No 359
>PRK01905 DNA-binding protein Fis; Provisional
Probab=59.87 E-value=32 Score=28.47 Aligned_cols=36 Identities=11% Similarity=0.183 Sum_probs=24.8
Q ss_pred HHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 476 ERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 476 EReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
|+.+|...+ . ..+-+..+.|+.+|||+.+++..+.+
T Consensus 38 E~~~i~~aL--~-~~~gn~s~aAr~LGIsrstL~rklkk 73 (77)
T PRK01905 38 EKPLLEVVM--E-QAGGNQSLAAEYLGINRNTLRKKLQQ 73 (77)
T ss_pred HHHHHHHHH--H-HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 455544433 1 23457999999999999998766554
No 360
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=59.45 E-value=24 Score=35.97 Aligned_cols=53 Identities=21% Similarity=0.182 Sum_probs=40.8
Q ss_pred HHHHHHHHHhhCCHHHHHHHhhHhcCC-CCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 461 MKKDVFRILESLDSRERQVLVLRYGLN-DHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 461 l~e~L~~~L~~L~~rEReVL~LryGL~-d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
+...|...+..|++.|+.|.....-=. ....+|..|||+..|||..||-..-+
T Consensus 15 i~~~i~~~~~~Lt~~e~~Ia~yil~~~~~v~~~si~~lA~~~~vS~aTi~Rf~k 68 (292)
T PRK11337 15 LGPYIRMKQEGLTPLESRVVEWLLKPGDLSEATALKDIAEALAVSEAMIVKVAK 68 (292)
T ss_pred HHHHHHHHHhhcCHHHHHHHHHHHhCHHHHHhcCHHHHHHHhCCChHHHHHHHH
Confidence 344788889999999999987654110 12458999999999999999976544
No 361
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=59.24 E-value=18 Score=36.55 Aligned_cols=49 Identities=14% Similarity=0.095 Sum_probs=37.5
Q ss_pred HHHHHhhCCHHHHHHHhhHhcCC-CCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 465 VFRILESLDSRERQVLVLRYGLN-DHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 465 L~~~L~~L~~rEReVL~LryGL~-d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
|......|++.|+.|......=. ....+|..|+|+..|+|..||-..-+
T Consensus 3 i~~~~~~Lt~~e~~ia~yil~n~~~v~~~si~elA~~~~vS~aTv~Rf~k 52 (278)
T PRK11557 3 IRQRYPGLAQSDRKLADYLLLQPDTARHLSSQQLANEAGVSQSSVVKFAQ 52 (278)
T ss_pred hhHhhhhCCHHHHHHHHHHHhCHHHHHhcCHHHHHHHhCCCHHHHHHHHH
Confidence 55667889999999987665111 12349999999999999999976554
No 362
>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional
Probab=59.15 E-value=7 Score=37.11 Aligned_cols=46 Identities=24% Similarity=0.141 Sum_probs=39.3
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCC---------HHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKS---------LEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~S---------l~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
.|+++|.+|+.+.. ++.+ ..++|..++++..+|+.+..+.++||..
T Consensus 156 ~Lt~~E~~~l~~l~-----~~~~~v~sr~~l~~~~~~~~~~~~~~tv~~~i~~lr~Kl~~ 210 (232)
T PRK10955 156 ELTGTEFTLLYLLA-----QHLGQVVSREHLSQEVLGKRLTPFDRAIDMHISNLRRKLPD 210 (232)
T ss_pred cCCHHHHHHHHHHH-----hCCCceEcHHHHHHHHhCCCCCCCCcCHHHHHHHHHHhccc
Confidence 49999999998887 4444 4778888999999999999999999963
No 363
>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=58.95 E-value=15 Score=31.75 Aligned_cols=43 Identities=21% Similarity=0.228 Sum_probs=31.2
Q ss_pred hCCHHHHHHHhhHhc-CCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 471 SLDSRERQVLVLRYG-LNDHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 471 ~L~~rEReVL~LryG-L~d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
.|++.+++|+.+.-. -...+|.+..+|++.|+++...|++.+.
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~ 87 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALD 87 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHH
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHH
Confidence 688888888887765 4456899999999999999999986543
No 364
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=58.93 E-value=19 Score=29.83 Aligned_cols=26 Identities=19% Similarity=0.189 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009449 490 RPKSLEEIGKLFHVSKEWIRKLEKKA 515 (534)
Q Consensus 490 e~~Sl~EIA~~LgISrerVRqi~~RA 515 (534)
.+.|..|||+.+|+++.+|+.++..-
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L 44 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTL 44 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 47999999999999999998766543
No 365
>PRK13239 alkylmercury lyase; Provisional
Probab=58.78 E-value=19 Score=35.77 Aligned_cols=29 Identities=17% Similarity=0.268 Sum_probs=26.7
Q ss_pred cCCCCCHHHHHHHcCCCHHHHHHHHHHhh
Q 009449 395 HGKYPEDIEIAKYTGLSLAEIRSASECLR 423 (534)
Q Consensus 395 lGr~Pt~eEIA~~lgis~~kv~~~l~~~~ 423 (534)
.|+.|+.++||+.+|+++++++.++....
T Consensus 33 ~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 33 KGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 58999999999999999999999988765
No 366
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=58.38 E-value=11 Score=36.74 Aligned_cols=29 Identities=17% Similarity=0.315 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 490 RPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 490 e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
-+.|.++||..+|+|+++|. |.+++|++.
T Consensus 183 ~~lt~~~iA~~lG~sr~tvs----R~l~~l~~~ 211 (235)
T PRK11161 183 LTMTRGDIGNYLGLTVETIS----RLLGRFQKS 211 (235)
T ss_pred ccccHHHHHHHhCCcHHHHH----HHHHHHHHC
Confidence 35899999999999999996 556677653
No 367
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=58.28 E-value=2.1e+02 Score=28.83 Aligned_cols=38 Identities=11% Similarity=0.041 Sum_probs=29.0
Q ss_pred HHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHH
Q 009449 384 IQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC 421 (534)
Q Consensus 384 i~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~ 421 (534)
+.++..-+.+......+.+++|+.+|+|+..+..+.+.
T Consensus 185 i~~~~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk~ 222 (290)
T PRK10572 185 VREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQ 222 (290)
T ss_pred HHHHHHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 44455555566677889999999999999988877543
No 368
>PF11662 DUF3263: Protein of unknown function (DUF3263); InterPro: IPR021678 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=57.97 E-value=33 Score=28.89 Aligned_cols=46 Identities=20% Similarity=0.182 Sum_probs=36.9
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
.|+++++.||.+---.....|-+-+.|-+.||+|.-+..|.++.-+
T Consensus 2 ~Ls~~d~~iL~fE~~ww~~~GaKe~aIre~fGls~~rYyq~Ln~Li 47 (77)
T PF11662_consen 2 GLSDRDRAILDFERRWWRHGGAKEEAIREEFGLSPTRYYQRLNALI 47 (77)
T ss_pred CCCHHHHHHHHHHHHhCcCCCCcHHHHHHHHCCCHHHHHHHHHHHh
Confidence 5899999998764433334577889999999999999999988764
No 369
>PRK09726 antitoxin HipB; Provisional
Probab=57.95 E-value=14 Score=31.20 Aligned_cols=26 Identities=15% Similarity=0.221 Sum_probs=23.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
..++|.+|+|+.+|||+.+|+++++.
T Consensus 23 ~~gltq~elA~~~gvs~~tis~~e~g 48 (88)
T PRK09726 23 QNGWTQSELAKKIGIKQATISNFENN 48 (88)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 35789999999999999999999874
No 370
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=57.95 E-value=18 Score=30.81 Aligned_cols=39 Identities=21% Similarity=0.307 Sum_probs=31.4
Q ss_pred CCHHHHHHHhhHhcCCCCCCCCH-HHHHHHhCCCHHHHHHHHHH
Q 009449 472 LDSRERQVLVLRYGLNDHRPKSL-EEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 472 L~~rEReVL~LryGL~d~e~~Sl-~EIA~~LgISrerVRqi~~R 514 (534)
|++.|..|+...+ ..+-.. .+||+.+++++++|..++.+
T Consensus 20 lt~~q~~~L~~l~----~~~~~~~~~la~~l~i~~~~vt~~l~~ 59 (126)
T COG1846 20 LTPPQYQVLLALY----EAGGITVKELAERLGLDRSTVTRLLKR 59 (126)
T ss_pred CCHHHHHHHHHHH----HhCCCcHHHHHHHHCCCHHHHHHHHHH
Confidence 9999999998887 333334 99999999999999765543
No 371
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=57.71 E-value=48 Score=30.09 Aligned_cols=42 Identities=12% Similarity=0.040 Sum_probs=32.0
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
.|++.|-.||..-+-. ..+.|..|||+.+|+++++|.....+
T Consensus 28 glt~~q~~vL~~l~~~--~~~~t~~eLa~~l~~~~~tvt~~v~~ 69 (144)
T PRK03573 28 ELTQTHWVTLHNIHQL--PPEQSQIQLAKAIGIEQPSLVRTLDQ 69 (144)
T ss_pred CCCHHHHHHHHHHHHc--CCCCCHHHHHHHhCCChhhHHHHHHH
Confidence 5889888887665511 24689999999999999999755443
No 372
>PRK13503 transcriptional activator RhaS; Provisional
Probab=57.56 E-value=1.1e+02 Score=30.59 Aligned_cols=38 Identities=13% Similarity=0.046 Sum_probs=27.7
Q ss_pred HHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHH
Q 009449 384 IQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC 421 (534)
Q Consensus 384 i~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~ 421 (534)
+.++..-+.+......|.+++|+.+|+++..+..+.+.
T Consensus 173 i~~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk~ 210 (278)
T PRK13503 173 LNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQ 210 (278)
T ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 33444444455566789999999999999998877553
No 373
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=57.20 E-value=13 Score=35.48 Aligned_cols=28 Identities=25% Similarity=0.476 Sum_probs=23.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 491 PKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 491 ~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
..|.+|||..+|+|+++|+ |++++|++.
T Consensus 168 ~~t~~~lA~~lG~tr~tvs----R~l~~l~~~ 195 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVG----RVLKMLEDQ 195 (211)
T ss_pred CCCHHHHHHHhCCCHHHHH----HHHHHHHHC
Confidence 6899999999999999996 566677653
No 374
>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=55.62 E-value=27 Score=26.25 Aligned_cols=51 Identities=14% Similarity=0.175 Sum_probs=38.3
Q ss_pred hCCHHHHHHHhhHhcCCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 471 SLDSRERQVLVLRYGLNDH-RPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~-e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
.+++.+..+|.-.|..+.. ......+||..+|++...|..+......+.+.
T Consensus 6 ~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 6 RFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 3667777788888755433 23447889999999999999998887776653
No 375
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=55.53 E-value=12 Score=35.47 Aligned_cols=28 Identities=14% Similarity=0.163 Sum_probs=23.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 490 RPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 490 e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
-+.|.++||..+|+|+++|. |++++|++
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 35799999999999999996 67777775
No 376
>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=55.44 E-value=20 Score=29.74 Aligned_cols=24 Identities=29% Similarity=0.540 Sum_probs=19.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 490 RPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 490 e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
...|.+|||+.+|+++..|+++..
T Consensus 24 ~~~s~~eiA~~~~i~~~~l~kil~ 47 (83)
T PF02082_consen 24 KPVSSKEIAERLGISPSYLRKILQ 47 (83)
T ss_dssp C-BEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHH
Confidence 348999999999999999986654
No 377
>PF12085 DUF3562: Protein of unknown function (DUF3562); InterPro: IPR021945 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 62 to 84 amino acids in length. This protein has two completely conserved residues (A and Y) that may be functionally important.
Probab=55.32 E-value=16 Score=29.80 Aligned_cols=38 Identities=16% Similarity=0.292 Sum_probs=31.7
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchhhhc
Q 009449 493 SLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFLV 533 (534)
Q Consensus 493 Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~yl~ 533 (534)
.+++||+..+++.+.|++.....+..|+.-.+ ..+||.
T Consensus 9 ~i~~iA~~t~~P~e~V~~my~dt~~~l~~~AR---V~DYl~ 46 (66)
T PF12085_consen 9 VIRSIAEETGTPAETVRRMYDDTMRELSSGAR---VHDYLP 46 (66)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHHHcCCc---hhhhHH
Confidence 57899999999999999999999999986544 455553
No 378
>PRK15482 transcriptional regulator MurR; Provisional
Probab=55.32 E-value=30 Score=35.30 Aligned_cols=51 Identities=12% Similarity=0.136 Sum_probs=39.3
Q ss_pred HHHHHHHhhCCHHHHHHHhhHhcCC-CCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 463 KDVFRILESLDSRERQVLVLRYGLN-DHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 463 e~L~~~L~~L~~rEReVL~LryGL~-d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
..|......|++.|+.|.....-=. ....+|..|||+..|+|..||-..-+
T Consensus 5 ~~i~~~~~~Lt~~e~~Ia~yIl~n~~~v~~~si~elA~~~~vS~aTv~Rf~k 56 (285)
T PRK15482 5 TKIRNAESEFTENEQKIADFLRANVSELKSVSSRKMAKQLGISQSSIVKFAQ 56 (285)
T ss_pred HHHHHHHhhcCHHHHHHHHHHHhCHHHHHhcCHHHHHHHhCCCHHHHHHHHH
Confidence 4677888999999999987654100 12458999999999999999976544
No 379
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=55.31 E-value=23 Score=40.13 Aligned_cols=46 Identities=22% Similarity=0.177 Sum_probs=37.5
Q ss_pred CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
|++|+.++|.+-- ..+.|..++|+.||||.-||++-+...-..|++
T Consensus 2 l~~R~~~iL~~L~----~~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~ 47 (584)
T PRK09863 2 LNERELKIVDLLE----QQDRSGGELAQQLGVSRRTIVRDIAYINFTLNG 47 (584)
T ss_pred hHHHHHHHHHHHH----cCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 5788999987653 357999999999999999999887766555555
No 380
>PRK10161 transcriptional regulator PhoB; Provisional
Probab=55.12 E-value=13 Score=35.35 Aligned_cols=50 Identities=16% Similarity=0.143 Sum_probs=39.7
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHH-----HHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEI-----GKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EI-----A~~LgISrerVRqi~~RAL~KLR~ 521 (534)
.|+++|.+|+.+.. -..++..|.++| |..++++..+|+.+..+.++||..
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 49999999997766 223467887776 446688999999999999999974
No 381
>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=54.62 E-value=13 Score=33.69 Aligned_cols=23 Identities=26% Similarity=0.323 Sum_probs=20.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~R 514 (534)
||.+|+|+.+|+++.||..+.++
T Consensus 1 MT~eELA~~tG~srQTINrWvRk 23 (122)
T PF07037_consen 1 MTPEELAELTGYSRQTINRWVRK 23 (122)
T ss_pred CCHHHHHHHhCccHHHHHHHHHh
Confidence 68999999999999999998764
No 382
>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=54.44 E-value=31 Score=30.11 Aligned_cols=44 Identities=27% Similarity=0.229 Sum_probs=33.3
Q ss_pred hCCHHHHHHHhhHhcC-CCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 471 SLDSRERQVLVLRYGL-NDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 471 ~L~~rEReVL~LryGL-~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
.|++.|-.||..-+=+ ....+.|..|||+.+++++++|...+.+
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~ 66 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKK 66 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHH
Confidence 6899998888654411 1236799999999999999999765543
No 383
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.92 E-value=24 Score=31.50 Aligned_cols=48 Identities=17% Similarity=0.189 Sum_probs=39.6
Q ss_pred HhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449 469 LESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520 (534)
Q Consensus 469 L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR 520 (534)
.+.|++.|-+.+.+++- -.=+++||-+.+|+|.-+||..+...++++-
T Consensus 39 F~~Lt~d~LeFv~lf~r----~RGnlKEvEr~lg~sYptvR~kld~vlramg 86 (122)
T COG3877 39 FEYLTSDQLEFVELFLR----CRGNLKEVERELGISYPTVRTKLDEVLRAMG 86 (122)
T ss_pred ccccCHhHhHHHHHHHH----HccCHHHHHHHHCCccHHHHHHHHHHHHHcC
Confidence 35688888888888883 3349999999999999999999888887764
No 384
>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=53.69 E-value=7.6 Score=32.37 Aligned_cols=33 Identities=21% Similarity=0.232 Sum_probs=25.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
.+..|+.++|+.++||+++|.+.+.+..+.|+.
T Consensus 28 ~~~~s~~~la~~~~iS~sti~~~i~~l~~~l~~ 60 (87)
T PF05043_consen 28 NEYVSIEDLAEELFISRSTIYRDIKKLNKYLKK 60 (87)
T ss_dssp -SEEEHHHHHHHHT--HHHHHHHHHHHHHHHHC
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 578999999999999999999877777766664
No 385
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=53.44 E-value=21 Score=29.92 Aligned_cols=31 Identities=16% Similarity=0.124 Sum_probs=25.4
Q ss_pred HHhhHhcCCCCCCCCHHHHHHHhC------CCHHHHHHHHH
Q 009449 479 VLVLRYGLNDHRPKSLEEIGKLFH------VSKEWIRKLEK 513 (534)
Q Consensus 479 VL~LryGL~d~e~~Sl~EIA~~Lg------ISrerVRqi~~ 513 (534)
+...|- ..++|..++|+.+| +|..+|.++++
T Consensus 16 lk~~R~----~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es 52 (75)
T smart00352 16 FKQRRI----KLGFTQADVGLALGALYGPDFSQTTICRFEA 52 (75)
T ss_pred HHHHHH----HcCCCHHHHHHHhcccccCcCCHHHHHHHHh
Confidence 344555 56899999999999 59999999886
No 386
>PF04963 Sigma54_CBD: Sigma-54 factor, core binding domain; InterPro: IPR007046 This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme []. The centre of this domain contains a very weak similarity to a helix-turn-helix motif, which may represent a DNA binding domain.; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent; PDB: 2K9L_A 2K9M_A.
Probab=52.86 E-value=3.1 Score=40.54 Aligned_cols=95 Identities=21% Similarity=0.193 Sum_probs=31.5
Q ss_pred CCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHH
Q 009449 398 YPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRER 477 (534)
Q Consensus 398 ~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rER 477 (534)
..+.++||+.+|++.+++..++...+ ++| |.|= .+.+..+.+.- ++...- . ++.-.
T Consensus 52 ~~~~~eia~~l~~~~~~v~~~l~~lQ---~le-P~Gi-------------gAr~l~EcLll-----Ql~~~~-~-~~~~~ 107 (194)
T PF04963_consen 52 TESLEEIAEELGVSEEEVEKALELLQ---SLE-PAGI-------------GARDLQECLLL-----QLERKG-P-PDLAY 107 (194)
T ss_dssp SS-HHHHHHHCTS-HHHHHHHHHHHH---TTS-S--T-------------TTS-TTHHHHH-----HHHHS--S---TTH
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHH---cCC-CCcc-------------CcCCHHHHHHH-----HHhccC-C-cHHHH
Confidence 45889999999999999999988776 333 2221 01122222211 111111 1 22233
Q ss_pred HHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449 478 QVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL 519 (534)
Q Consensus 478 eVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL 519 (534)
.+|.-++ ++.....++.||+.+|+|.+.|...... +++|
T Consensus 108 ~il~~~l--~~l~~~~~~~ia~~l~~s~~~v~~~~~~-Ir~L 146 (194)
T PF04963_consen 108 RILENHL--ELLANKDYKKIAKKLGISEEEVQEAIEL-IRTL 146 (194)
T ss_dssp HHHHHHH--HHHHH----------------------------
T ss_pred HHHHHHH--HHHHHhhhcccccccccccccccccccc-cccc
Confidence 3444333 3334567889999999999999866543 3344
No 387
>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=52.70 E-value=18 Score=28.07 Aligned_cols=26 Identities=15% Similarity=0.309 Sum_probs=20.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
..++|+.++|+.+|+++.++.++++-
T Consensus 10 ~~~lt~~~~a~~~~i~~~~i~~~e~g 35 (64)
T PF12844_consen 10 EKGLTQKDLAEKLGISRSTISKIENG 35 (64)
T ss_dssp HCT--HHHHHHHHTS-HHHHHHHHTT
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 46899999999999999999999854
No 388
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=52.61 E-value=18 Score=32.90 Aligned_cols=26 Identities=23% Similarity=0.206 Sum_probs=23.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
..++|..++|+.+|||+++|+++++.
T Consensus 16 ~~gltq~~lA~~~gvs~~~is~~E~g 41 (135)
T PRK09706 16 QLKLSQRSLAKAVKVSHVSISQWERD 41 (135)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 46899999999999999999998865
No 389
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=52.56 E-value=17 Score=35.89 Aligned_cols=29 Identities=24% Similarity=0.436 Sum_probs=24.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 490 RPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 490 e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
-..|.++||..+|+++++|. |++++|++.
T Consensus 178 i~lt~~~IA~~lGisretls----R~L~~L~~~ 206 (230)
T PRK09391 178 LPMSRRDIADYLGLTIETVS----RALSQLQDR 206 (230)
T ss_pred ecCCHHHHHHHHCCCHHHHH----HHHHHHHHC
Confidence 35799999999999999996 667777754
No 390
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=52.44 E-value=35 Score=31.14 Aligned_cols=44 Identities=16% Similarity=0.225 Sum_probs=34.5
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHh----CCCHHHHHHHHHHHHH
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLF----HVSKEWIRKLEKKAMT 517 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~L----gISrerVRqi~~RAL~ 517 (534)
.|++.|.+|+...+- ..+.|..||.+.| ++++.||...+.|-.+
T Consensus 1 ~Lt~~E~~VM~vlW~---~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~ 48 (130)
T TIGR02698 1 SISDAEWEVMRVVWT---LGETTSRDIIRILAEKKDWSDSTIKTLLGRLVD 48 (130)
T ss_pred CCCHHHHHHHHHHHc---CCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHH
Confidence 378999999977762 3578999977776 7999999888776554
No 391
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=52.44 E-value=19 Score=25.15 Aligned_cols=25 Identities=20% Similarity=0.341 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 490 RPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 490 e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
.++|..++|+.+|++..+|.+++..
T Consensus 9 ~~~s~~~la~~~~i~~~~i~~~~~~ 33 (56)
T smart00530 9 KGLTQEELAEKLGVSRSTLSRIENG 33 (56)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 5789999999999999999987754
No 392
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=51.82 E-value=9.7 Score=28.28 Aligned_cols=21 Identities=14% Similarity=0.169 Sum_probs=18.1
Q ss_pred HHHHHHhCCCHHHHHHHHHHH
Q 009449 495 EEIGKLFHVSKEWIRKLEKKA 515 (534)
Q Consensus 495 ~EIA~~LgISrerVRqi~~RA 515 (534)
+|||+.+|||+.+|+++++.-
T Consensus 1 ~~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 1 KDIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred CcHHHHHCcCHHHHHHHHcCC
Confidence 379999999999999987653
No 393
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=51.81 E-value=35 Score=29.50 Aligned_cols=40 Identities=15% Similarity=0.125 Sum_probs=29.6
Q ss_pred HHHHHHHHHhcCC-CCCHHHHHHHcCCCHHHHHHHHHHhhh
Q 009449 385 QKARKALTNSHGK-YPEDIEIAKYTGLSLAEIRSASECLRI 424 (534)
Q Consensus 385 ~ka~~~L~~elGr-~Pt~eEIA~~lgis~~kv~~~l~~~~~ 424 (534)
+..+.+|.....- .-+++|||+.+|++..+++.++...+.
T Consensus 9 ~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil~~tqr 49 (97)
T COG4367 9 QRTKQELQANFELCPLSDEEIATALNWTEVKLEKILQVTQR 49 (97)
T ss_pred HHHHHHHHHhhhhccccHHHHHHHhCCCHHHHHHHHHHhhc
Confidence 3445555555543 458999999999999999999876543
No 394
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=51.67 E-value=22 Score=25.50 Aligned_cols=27 Identities=26% Similarity=0.349 Sum_probs=19.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEKKA 515 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~RA 515 (534)
.++.|+.+||..+|+|+...++..++.
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 467999999999999999887765543
No 395
>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=51.35 E-value=45 Score=24.85 Aligned_cols=22 Identities=18% Similarity=0.317 Sum_probs=16.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~ 513 (534)
+|+.+.|+.+||++.|++....
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 9999999999999999986554
No 396
>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=51.20 E-value=26 Score=33.77 Aligned_cols=43 Identities=23% Similarity=0.230 Sum_probs=31.8
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
..|++-|+.....+. +. ..++|.++||+.+|+|+.+|++.+.-
T Consensus 101 ~~lt~~e~a~~~~~l-~~-~~g~s~~~iA~~lg~s~~~V~r~l~l 143 (187)
T TIGR00180 101 EDLSPIEEAQAYKRL-LE-KFSMTQEDLAKKIGKSRAHITNLLRL 143 (187)
T ss_pred cCCCHHHHHHHHHHH-HH-HhCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 468888766654442 11 14789999999999999999987654
No 397
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=51.04 E-value=15 Score=28.45 Aligned_cols=26 Identities=8% Similarity=0.187 Sum_probs=19.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009449 490 RPKSLEEIGKLFHVSKEWIRKLEKKA 515 (534)
Q Consensus 490 e~~Sl~EIA~~LgISrerVRqi~~RA 515 (534)
.++|..++|+..||++.+|+.+.+.-
T Consensus 9 ~~it~~~La~~~gis~~tl~~~~~~~ 34 (63)
T PF13443_consen 9 RGITQKDLARKTGISRSTLSRILNGK 34 (63)
T ss_dssp TT--HHHHHHHHT--HHHHHHHHTTT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcc
Confidence 57899999999999999999988855
No 398
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=50.69 E-value=32 Score=35.36 Aligned_cols=54 Identities=15% Similarity=0.159 Sum_probs=40.4
Q ss_pred HHHHHHHHHHhhCCHHHHHHHhhHhcCC-CCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 460 HMKKDVFRILESLDSRERQVLVLRYGLN-DHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 460 el~e~L~~~L~~L~~rEReVL~LryGL~-d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
.+...|......|++.||.|-....-=. ....+|.+|||+..|||+.||-..-+
T Consensus 4 ~l~~~I~~~~~~Lt~~er~iA~yil~~~~~~~~~si~elA~~a~VS~aTv~Rf~~ 58 (281)
T COG1737 4 NLLERIRERYDSLTKSERKIADYILANPDEVALLSIAELAERAGVSPATVVRFAR 58 (281)
T ss_pred hHHHHHHHHHhcCCHHHHHHHHHHHhCHHHHHHHHHHHHHHHhCCCHHHHHHHHH
Confidence 3456788889999999999877554100 12347999999999999999965443
No 399
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=50.56 E-value=23 Score=31.52 Aligned_cols=35 Identities=14% Similarity=0.197 Sum_probs=26.6
Q ss_pred HHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 478 QVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 478 eVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
+||.-.| .+.-++|..+.|+.|||++.+|..+.+-
T Consensus 12 EiL~eef--lep~glt~~~lA~~lgV~r~~is~ling 46 (104)
T COG3093 12 EILREEF--LEPLGLTQTELAEALGVTRNTISELING 46 (104)
T ss_pred HHHHHHH--hccccCCHHHHHHHhCCCHHHHHHHHcC
Confidence 3556566 1113799999999999999999988753
No 400
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=50.39 E-value=15 Score=35.50 Aligned_cols=29 Identities=31% Similarity=0.548 Sum_probs=24.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
.+++|+.||++.+|+|+++|++ ++++|..
T Consensus 39 ~~Pmtl~Ei~E~lg~Sks~vS~----~lkkL~~ 67 (177)
T COG1510 39 RKPLTLDEIAEALGMSKSNVSM----GLKKLQD 67 (177)
T ss_pred CCCccHHHHHHHHCCCcchHHH----HHHHHHh
Confidence 4899999999999999999975 6666654
No 401
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=50.18 E-value=21 Score=36.58 Aligned_cols=45 Identities=18% Similarity=0.246 Sum_probs=35.3
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR 520 (534)
..|++.|++||.+--+= +-..+++||-+.+|+|+.||+. ++++|-
T Consensus 191 ~~L~~~e~~il~~i~~~--GGri~Q~eL~r~lglsktTvsR----~L~~LE 235 (258)
T COG2512 191 YDLNEDEKEILDLIRER--GGRITQAELRRALGLSKTTVSR----ILRRLE 235 (258)
T ss_pred CCCCHHHHHHHHHHHHh--CCEEeHHHHHHhhCCChHHHHH----HHHHHH
Confidence 45899999999887642 2358999999999999999974 455554
No 402
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=50.07 E-value=1.6e+02 Score=29.98 Aligned_cols=41 Identities=12% Similarity=-0.064 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHH
Q 009449 381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC 421 (534)
Q Consensus 381 i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~ 421 (534)
...+.++..-+...+...++.++||+.+|++...+..+...
T Consensus 4 ~~~i~~~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F~~ 44 (289)
T PRK15121 4 AGIIRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKD 44 (289)
T ss_pred HHHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34566677777777888899999999999999998877553
No 403
>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=49.79 E-value=19 Score=26.58 Aligned_cols=23 Identities=22% Similarity=0.187 Sum_probs=20.9
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKL 511 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi 511 (534)
+.+.|..+||+..|+|+.++.+.
T Consensus 14 ~~~~s~~~Ia~~~gvs~~~~y~~ 36 (47)
T PF00440_consen 14 YEAVSIRDIARRAGVSKGSFYRY 36 (47)
T ss_dssp TTTSSHHHHHHHHTSCHHHHHHH
T ss_pred HHhCCHHHHHHHHccchhhHHHH
Confidence 57899999999999999999764
No 404
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=49.78 E-value=28 Score=35.02 Aligned_cols=41 Identities=27% Similarity=0.364 Sum_probs=32.0
Q ss_pred HHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449 474 SRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMT 517 (534)
Q Consensus 474 ~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~ 517 (534)
+|++.|+.+-. .....+.+|||+.||||..|||.-+..--.
T Consensus 4 ~R~~~Il~~l~---~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 4 ARQQAIVDLLL---NHTSLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred HHHHHHHHHHH---HcCCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 56666666654 246899999999999999999998876533
No 405
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=49.62 E-value=32 Score=25.75 Aligned_cols=47 Identities=13% Similarity=0.132 Sum_probs=35.5
Q ss_pred CCHHHHHHHhhHhcCCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009449 472 LDSRERQVLVLRYGLNDH-RPKSLEEIGKLFHVSKEWIRKLEKKAMTK 518 (534)
Q Consensus 472 L~~rEReVL~LryGL~d~-e~~Sl~EIA~~LgISrerVRqi~~RAL~K 518 (534)
+++.+..+|.-.|..+.. ......+||..+|++...|..+......+
T Consensus 7 ~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~ 54 (56)
T smart00389 7 FTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAK 54 (56)
T ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhc
Confidence 677888888888854432 23347889999999999999988776554
No 406
>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=49.55 E-value=12 Score=32.14 Aligned_cols=25 Identities=24% Similarity=0.307 Sum_probs=22.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
+|..|+|+.+|||..|+|-.+..++
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~~Gl 25 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDIGL 25 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 4889999999999999999998754
No 407
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=49.12 E-value=27 Score=24.54 Aligned_cols=25 Identities=24% Similarity=0.357 Sum_probs=22.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 490 RPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 490 e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
.++|..++|..+|+++.+|.+++..
T Consensus 11 ~~~s~~~~a~~~~~~~~~v~~~~~g 35 (58)
T cd00093 11 KGLTQEELAEKLGVSRSTISRIENG 35 (58)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 5789999999999999999987664
No 408
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=48.84 E-value=17 Score=29.21 Aligned_cols=24 Identities=21% Similarity=0.119 Sum_probs=19.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 490 RPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 490 e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
.+.|-.|||+.+|+|+.+||.++.
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 589999999999999999997764
No 409
>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=48.68 E-value=25 Score=24.62 Aligned_cols=24 Identities=25% Similarity=0.365 Sum_probs=19.2
Q ss_pred CHHHHHHHcCCCHHHHHHHHHHhh
Q 009449 400 EDIEIAKYTGLSLAEIRSASECLR 423 (534)
Q Consensus 400 t~eEIA~~lgis~~kv~~~l~~~~ 423 (534)
|.+|||..+|++.+.|..++...+
T Consensus 4 tr~diA~~lG~t~ETVSR~l~~l~ 27 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVSRILKKLE 27 (32)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CHHHHHHHhCCcHHHHHHHHHHHH
Confidence 568999999999999999887654
No 410
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=48.60 E-value=30 Score=31.73 Aligned_cols=33 Identities=15% Similarity=0.197 Sum_probs=24.2
Q ss_pred HHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009449 478 QVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKA 515 (534)
Q Consensus 478 eVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RA 515 (534)
.||.|.. .+.+..+||.+|.||...|++++.|=
T Consensus 25 rIvela~-----~G~rp~~Isr~l~Vs~gcVsKIl~Ry 57 (125)
T PF00292_consen 25 RIVELAK-----EGVRPCDISRQLRVSHGCVSKILSRY 57 (125)
T ss_dssp HHHHHHH-----TT--HHHHHHHHT--HHHHHHHHHHH
T ss_pred HHHHHhh-----hcCCHHHHHHHHccchhHHHHHHHHH
Confidence 4666766 79999999999999999999988763
No 411
>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=48.44 E-value=27 Score=35.13 Aligned_cols=42 Identities=21% Similarity=0.241 Sum_probs=33.1
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
.|+..+.+-|++.+-.+ -+.+|...+|+.|+||++.||.|+.
T Consensus 10 ~Ls~~~~~~ir~L~~~~-p~~~t~~~Lae~F~vspe~irrILk 51 (225)
T PF06413_consen 10 KLSREAMEQIRYLHKED-PEEWTVERLAESFKVSPEAIRRILK 51 (225)
T ss_pred CCCHHHHHHHHHHHHhC-ccccCHHHHHhhCCCCHHHHHHHHh
Confidence 47777777777666333 2568999999999999999999875
No 412
>PRK06424 transcription factor; Provisional
Probab=48.33 E-value=22 Score=33.32 Aligned_cols=25 Identities=16% Similarity=0.194 Sum_probs=23.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
..++|++|+|+.+|+++++|+++++
T Consensus 95 ~~GLSQ~eLA~~iGvs~stIskiE~ 119 (144)
T PRK06424 95 RLSMSQADLAAKIFERKNVIASIER 119 (144)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 5789999999999999999999986
No 413
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=48.30 E-value=26 Score=34.55 Aligned_cols=31 Identities=16% Similarity=0.258 Sum_probs=25.8
Q ss_pred CCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 487 NDHRPK-SLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 487 ~d~e~~-Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
..|+.+ |-.++|+.||||+..|| .|+.+|..
T Consensus 25 ~pG~~LpsE~~La~~lgVSRtpVR----EAL~~Le~ 56 (235)
T TIGR02812 25 PPGSILPAERELSELIGVTRTTLR----EVLQRLAR 56 (235)
T ss_pred CCCCcCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 446778 79999999999999997 67777764
No 414
>PF04814 HNF-1_N: Hepatocyte nuclear factor 1 (HNF-1), N terminus; InterPro: IPR006899 This domain consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerisation sequence [] and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3) [].; GO: 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2GYP_B 1IC8_B 2H8R_B 1G2Y_D 1F93_H 1G39_D 1G2Z_B 1JB6_B.
Probab=48.22 E-value=31 Score=33.55 Aligned_cols=51 Identities=14% Similarity=0.098 Sum_probs=35.5
Q ss_pred HHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 463 KDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 463 e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
..|+.+|..=+-.=++.|..+.+ ....+..+|++..|||.+.|+|++.++.
T Consensus 106 ~~Ve~llr~D~~~VkeeIK~fl~---~h~IsQ~~V~q~TGisQS~lSq~L~kGt 156 (180)
T PF04814_consen 106 AEVEELLRRDPWRVKEEIKAFLQ---QHNISQREVVQVTGISQSHLSQHLNKGT 156 (180)
T ss_dssp HHHHHCTTS-HHHHHHHHHHHHH---HCT--CHHHHHHHT--HHHHHHHHCTB-
T ss_pred HHHHHHHhhCHHHHHHHHHHHHH---HcCCcHHHHHHHhhhhHHHHHHHHHcCC
Confidence 56666666656666777777774 5789999999999999999999976543
No 415
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=47.80 E-value=1.7e+02 Score=26.57 Aligned_cols=24 Identities=38% Similarity=0.408 Sum_probs=18.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 490 RPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 490 e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
.|.|-..||...|++...|++...
T Consensus 71 ~GFsD~~IA~l~~~~e~~vr~~R~ 94 (123)
T PF02787_consen 71 LGFSDRQIARLWGVSEEEVRELRK 94 (123)
T ss_dssp TT--HHHHHHHHTS-HHHHHHHHH
T ss_pred cCCCHHHHHhccCCCHHHHHHHHH
Confidence 578999999999999999987544
No 416
>PRK06030 hypothetical protein; Provisional
Probab=47.78 E-value=42 Score=30.74 Aligned_cols=40 Identities=10% Similarity=0.055 Sum_probs=28.9
Q ss_pred HHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449 474 SRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMT 517 (534)
Q Consensus 474 ~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~ 517 (534)
+|+--+...+- .-+.|+.+||+.||-+.+||..-..+.-+
T Consensus 56 aRqIAMYL~r~----~~~~sl~~IG~~FGRDHSTV~haikkIe~ 95 (124)
T PRK06030 56 IRQIAMYVAHV----SLGWPMNEVALAFGRDRTTVGHACHTVED 95 (124)
T ss_pred HHHHHHHHHHH----HcCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 44444444444 56889999999999999999877664444
No 417
>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=47.53 E-value=13 Score=32.28 Aligned_cols=26 Identities=15% Similarity=0.258 Sum_probs=23.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKAMT 517 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RAL~ 517 (534)
+|..|+|+.+|||+.|+|-.+..++-
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~~Gll 27 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESIGLI 27 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 68999999999999999999988654
No 418
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=47.20 E-value=40 Score=28.40 Aligned_cols=28 Identities=21% Similarity=0.285 Sum_probs=21.0
Q ss_pred CCCCCHHHHHHHcCCCHHHHHHHHHHhh
Q 009449 396 GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (534)
Q Consensus 396 Gr~Pt~eEIA~~lgis~~kv~~~l~~~~ 423 (534)
|+.-|.++||..+|+++++|..++....
T Consensus 36 G~PVt~~~LA~a~g~~~e~v~~~L~~~p 63 (77)
T PF12324_consen 36 GQPVTVEQLAAALGWPVEEVRAALAAMP 63 (77)
T ss_dssp TS-B-HHHHHHHHT--HHHHHHHHHH-T
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHhCC
Confidence 7888999999999999999999987664
No 419
>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=47.14 E-value=59 Score=25.71 Aligned_cols=50 Identities=26% Similarity=0.215 Sum_probs=37.0
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHh------CCCHHHHHHHHHHHHHHHHh
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLF------HVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~L------gISrerVRqi~~RAL~KLR~ 521 (534)
.|+++|..+|.+.. ...++..|.++|.+.+ ..+..+|++...+-+++|..
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 37889999877665 2334578999999875 35677888888777777765
No 420
>PHA00738 putative HTH transcription regulator
Probab=47.06 E-value=37 Score=30.42 Aligned_cols=38 Identities=18% Similarity=0.070 Sum_probs=28.1
Q ss_pred CHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 473 DSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 473 ~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
+|.=+.||.+.. ++++++..||++.+++|+.+|++++.
T Consensus 11 dptRr~IL~lL~---~~e~~~V~eLae~l~lSQptVS~HLK 48 (108)
T PHA00738 11 KILRRKILELIA---ENYILSASLISHTLLLSYTTVLRHLK 48 (108)
T ss_pred CHHHHHHHHHHH---HcCCccHHHHHHhhCCCHHHHHHHHH
Confidence 344455665544 14579999999999999999998753
No 421
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=46.95 E-value=15 Score=31.12 Aligned_cols=25 Identities=32% Similarity=0.397 Sum_probs=22.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
+|..|+|+.+|||..++|.++.+.+
T Consensus 2 ~ti~evA~~~gvs~~tLR~ye~~Gl 26 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEEKGL 26 (88)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 6899999999999999999988764
No 422
>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=46.93 E-value=29 Score=31.10 Aligned_cols=25 Identities=24% Similarity=0.262 Sum_probs=21.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
....|..|||+.+|+|+.+|++++.
T Consensus 23 ~~~~s~~eia~~l~is~~~v~~~l~ 47 (130)
T TIGR02944 23 SQPYSAAEIAEQTGLNAPTVSKILK 47 (130)
T ss_pred CCCccHHHHHHHHCcCHHHHHHHHH
Confidence 4678999999999999999976543
No 423
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=46.54 E-value=21 Score=34.88 Aligned_cols=28 Identities=14% Similarity=0.261 Sum_probs=22.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 491 PKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 491 ~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
+.|.++||..+|+++++|. |++++|++.
T Consensus 173 ~~t~~~iA~~lG~tretvs----R~l~~L~~~ 200 (236)
T PRK09392 173 PYEKRVLASYLGMTPENLS----RAFAALASH 200 (236)
T ss_pred eCCHHHHHHHhCCChhHHH----HHHHHHHhC
Confidence 5678999999999999996 566666653
No 424
>PRK10643 DNA-binding transcriptional regulator BasR; Provisional
Probab=46.47 E-value=26 Score=32.72 Aligned_cols=47 Identities=17% Similarity=0.010 Sum_probs=35.4
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCH-HHHHH------HhCCCHHHHHHHHHHHHHHHH
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSL-EEIGK------LFHVSKEWIRKLEKKAMTKLR 520 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl-~EIA~------~LgISrerVRqi~~RAL~KLR 520 (534)
.|+++|.+|+.+.. . ..+++. +||+. .++++..||+.+.++.++||.
T Consensus 149 ~Lt~~E~~il~~l~-~--~~g~~~~~~~~~~~~~~~~~~~~~~tv~~~i~~lr~Kl~ 202 (222)
T PRK10643 149 ILTPKEFALLSRLM-L--KAGSPVHREILYQDIYNWDDEPSSNTLEVHIHNLRDKVG 202 (222)
T ss_pred ecCHHHHHHHHHHH-h--CCCceEcHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhCC
Confidence 49999999998754 1 245553 55543 368899999999999999985
No 425
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=46.25 E-value=2.6e+02 Score=28.67 Aligned_cols=25 Identities=20% Similarity=0.178 Sum_probs=21.7
Q ss_pred CCCCHHHHHHHcCCCHHHHHHHHHH
Q 009449 397 KYPEDIEIAKYTGLSLAEIRSASEC 421 (534)
Q Consensus 397 r~Pt~eEIA~~lgis~~kv~~~l~~ 421 (534)
..-|..|||+.+|+|.++|+++...
T Consensus 247 ~~~Tl~EIA~~lgvS~~rVrqi~~~ 271 (284)
T PRK06596 247 DKSTLQELAAEYGVSAERVRQIEKN 271 (284)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4678999999999999999987653
No 426
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=46.19 E-value=26 Score=31.62 Aligned_cols=26 Identities=19% Similarity=0.234 Sum_probs=23.3
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
..++|.+|+|+..|||+++|.++++.
T Consensus 16 ~~Glsq~eLA~~~Gis~~~is~iE~g 41 (120)
T PRK13890 16 ERHMTKKELSERSGVSISFLSDLTTG 41 (120)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 46899999999999999999998863
No 427
>PRK11517 transcriptional regulatory protein YedW; Provisional
Probab=46.06 E-value=34 Score=32.12 Aligned_cols=49 Identities=14% Similarity=0.053 Sum_probs=39.9
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHH
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLF-----HVSKEWIRKLEKKAMTKLR 520 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~L-----gISrerVRqi~~RAL~KLR 520 (534)
.|+++|.+|+.+.. -+.++-.|.++|...+ ..+..+|..+..|-++||.
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 59999999998876 2334567999999986 4477899999999999996
No 428
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=45.57 E-value=41 Score=38.61 Aligned_cols=54 Identities=15% Similarity=0.179 Sum_probs=41.4
Q ss_pred HHHHHHHHHHhhCCHHHHHHHhhHhcCC-CCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 460 HMKKDVFRILESLDSRERQVLVLRYGLN-DHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 460 el~e~L~~~L~~L~~rEReVL~LryGL~-d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
.+.+.|......|++.||.|.....-=. ....+|..|||+..++|..||-..-+
T Consensus 342 ~l~~~I~~~~~~Lt~~E~~IA~yIl~n~~~v~~~si~eLA~~~~vS~aTV~Rf~k 396 (638)
T PRK14101 342 AVFERIRQMRDALTPAERRVADLALNHPRSIINDPIVDIARKADVSQPTVIRFCR 396 (638)
T ss_pred HHHHHHHHHHhhcCHHHHHHHHHHHhCHHHHHhccHHHHHHHhCCCHHHHHHHHH
Confidence 3455788889999999999987654100 12457999999999999999976544
No 429
>PRK14082 hypothetical protein; Provisional
Probab=45.56 E-value=67 Score=26.18 Aligned_cols=56 Identities=18% Similarity=0.068 Sum_probs=41.4
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhH
Q 009449 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTY 351 (534)
Q Consensus 294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTY 351 (534)
....+.+|..+.+.+..-..+ -.-..-+||.||--+.+++.+..++...+.-|--|
T Consensus 8 ~~e~e~ii~~FepkIkKsL~~--T~yqeREDLeQElk~Ki~eK~~~~~~~e~PGF~ef 63 (65)
T PRK14082 8 TEEIEHLIENFSPMIKKKLSN--TSYQEREDLEQELKIKIIEKADMLLCQEVPGFWEF 63 (65)
T ss_pred HHHHHHHHHHccHHHHHHHhc--CChhhHHHHHHHHHHHHHHHHHHhhcccCCcHHHh
Confidence 345678899988887754432 22357899999999999999999987766555443
No 430
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=45.44 E-value=35 Score=31.15 Aligned_cols=25 Identities=12% Similarity=0.200 Sum_probs=20.9
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
....+..+||+.||||+.+|+..+.
T Consensus 20 ~~~~~~~ela~~l~vs~~svs~~l~ 44 (142)
T PRK03902 20 KGYARVSDIAEALSVHPSSVTKMVQ 44 (142)
T ss_pred CCCcCHHHHHHHhCCChhHHHHHHH
Confidence 3567999999999999999986553
No 431
>COG1481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.40 E-value=40 Score=35.46 Aligned_cols=43 Identities=37% Similarity=0.533 Sum_probs=36.9
Q ss_pred HhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCC--CHHHHHHHHHH
Q 009449 469 LESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHV--SKEWIRKLEKK 514 (534)
Q Consensus 469 L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgI--SrerVRqi~~R 514 (534)
++.||+..+++-.+|. +.++.|++|+|+.+.. |++.|..+..|
T Consensus 251 l~~lpe~l~e~a~LRl---~hpd~SLeeLg~~l~~~iSKSGvnHrlrk 295 (308)
T COG1481 251 LEKLPEKLREAALLRL---EHPDASLEELGELLEPPISKSGVNHRLRK 295 (308)
T ss_pred hhhCCHHHHHHHHHhh---cChhhhHHHHHHHhcCcccHHHHHHHHHH
Confidence 4789999999999997 4689999999999988 88888876554
No 432
>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=45.39 E-value=16 Score=32.12 Aligned_cols=26 Identities=23% Similarity=0.278 Sum_probs=23.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKAMT 517 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RAL~ 517 (534)
++..|+|+.+|||..|+|-.+..++-
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~~GLi 26 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKIGLL 26 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCC
Confidence 47899999999999999999988654
No 433
>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=45.32 E-value=29 Score=32.27 Aligned_cols=50 Identities=18% Similarity=0.157 Sum_probs=40.8
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHHh
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLF-----HVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~L-----gISrerVRqi~~RAL~KLR~ 521 (534)
.|+++|.+|+.+... +.++-.|.++|+..+ ..+..+|..++.+-++||..
T Consensus 147 ~Lt~~E~~il~~l~~-~~~~~~sr~~i~~~~~~~~~~~~~~~~~~~i~~lr~kl~~ 201 (218)
T TIGR01387 147 TLTRKEFQLLWLLMR-RTGEVLPRTVIASLVWGMNFDSDTNVVDVAIRRLRAKVDD 201 (218)
T ss_pred eCCHHHHHHHHHHHh-CCCeeEcHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhhcC
Confidence 499999999988872 223558999999998 56778999999999999963
No 434
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=45.24 E-value=28 Score=31.84 Aligned_cols=30 Identities=23% Similarity=0.451 Sum_probs=24.0
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 488 DHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 488 d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
+++..|..|||+.+|||+..|++ ++.+|++
T Consensus 22 ~g~~~s~~~ia~~~~is~~~vrk----~l~~L~~ 51 (141)
T PRK11014 22 EGRMTSISEVTEVYGVSRNHMVK----IINQLSR 51 (141)
T ss_pred CCCccCHHHHHHHHCcCHHHHHH----HHHHHHh
Confidence 34567999999999999999974 5666664
No 435
>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=45.23 E-value=52 Score=24.71 Aligned_cols=26 Identities=31% Similarity=0.248 Sum_probs=21.9
Q ss_pred CCHHHHHHHcCCCHHHHHHHHHHhhh
Q 009449 399 PEDIEIAKYTGLSLAEIRSASECLRI 424 (534)
Q Consensus 399 Pt~eEIA~~lgis~~kv~~~l~~~~~ 424 (534)
-|.+|||+.+|+|...|...+.....
T Consensus 16 it~~eLa~~l~vS~rTi~~~i~~L~~ 41 (55)
T PF08279_consen 16 ITAKELAEELGVSRRTIRRDIKELRE 41 (55)
T ss_dssp BEHHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred cCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 78999999999999999988876653
No 436
>PF13309 HTH_22: HTH domain
Probab=45.18 E-value=17 Score=29.15 Aligned_cols=20 Identities=10% Similarity=0.215 Sum_probs=18.1
Q ss_pred CHHHHHHHhCCCHHHHHHHH
Q 009449 493 SLEEIGKLFHVSKEWIRKLE 512 (534)
Q Consensus 493 Sl~EIA~~LgISrerVRqi~ 512 (534)
+...+|+.||||+.||...+
T Consensus 44 av~~vA~~L~iS~~TVY~YL 63 (64)
T PF13309_consen 44 AVEYVAEKLGISRATVYRYL 63 (64)
T ss_pred HHHHHHHHHCCCHHHHHHHc
Confidence 88999999999999998754
No 437
>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=45.16 E-value=15 Score=32.26 Aligned_cols=25 Identities=24% Similarity=0.438 Sum_probs=22.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
+|..|+|+.+|||+.|+|..+..++
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gl 25 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKEGL 25 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999988765
No 438
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=44.96 E-value=27 Score=33.34 Aligned_cols=26 Identities=15% Similarity=0.180 Sum_probs=23.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
..++|++|+|+.+|||+.+|+++++.
T Consensus 18 ~~glt~~elA~~~gis~~~is~~E~g 43 (185)
T PRK09943 18 QQGLSQRRAAELSGLTHSAISTIEQD 43 (185)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 46899999999999999999999964
No 439
>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=44.90 E-value=34 Score=30.91 Aligned_cols=40 Identities=28% Similarity=0.345 Sum_probs=35.3
Q ss_pred hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
..|.+.++.|+.+.- ...|..|||..++++..-||-+..-
T Consensus 39 ~~l~pE~~~Il~lC~-----~~~SVAEiAA~L~lPlgVvrVLvsD 78 (114)
T PF05331_consen 39 AGLGPEHRAILELCR-----RPLSVAEIAARLGLPLGVVRVLVSD 78 (114)
T ss_pred CCCCHHHHHHHHHHC-----CCccHHHHHHhhCCCchhhhhhHHH
Confidence 569999999999987 5999999999999999999877643
No 440
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=44.85 E-value=24 Score=34.60 Aligned_cols=45 Identities=9% Similarity=0.081 Sum_probs=30.4
Q ss_pred CHHHHHHHhhHhcCC--CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449 473 DSRERQVLVLRYGLN--DHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522 (534)
Q Consensus 473 ~~rEReVL~LryGL~--d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~ 522 (534)
+.++|-+-.|.. +. +.-+.|.+|||..+|+|+++|. |++++|++.
T Consensus 150 ~~~~Rla~~L~~-~~~~~~~~~t~~~lA~~lG~sretvs----R~L~~L~~~ 196 (226)
T PRK10402 150 PLENRLAAFILL-TQEGDLYHEKHTQAAEYLGVSYRHLL----YVLAQFIQD 196 (226)
T ss_pred hHHHHHHHHHHh-cccCCcccchHHHHHHHHCCcHHHHH----HHHHHHHHC
Confidence 555555444432 11 1234689999999999999996 677777764
No 441
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=44.61 E-value=29 Score=35.24 Aligned_cols=38 Identities=24% Similarity=0.254 Sum_probs=29.8
Q ss_pred HHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 474 SRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 474 ~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
+|+..|+.+-- .....+..|+|+.||||+.|||+-+..
T Consensus 5 eR~~~Il~~L~---~~~~v~v~eLa~~l~VS~~TIRRDL~~ 42 (256)
T PRK10434 5 QRQAAILEYLQ---KQGKTSVEELAQYFDTTGTTIRKDLVI 42 (256)
T ss_pred HHHHHHHHHHH---HcCCEEHHHHHHHHCCCHHHHHHHHHH
Confidence 56666666554 134689999999999999999998776
No 442
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=44.43 E-value=1e+02 Score=29.97 Aligned_cols=40 Identities=23% Similarity=0.272 Sum_probs=33.2
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
.|++.|-.||...+. ..+.|..|||+.+++++++|..++.
T Consensus 42 gLt~~q~~iL~~L~~---~~~itq~eLa~~l~l~~sTvtr~l~ 81 (185)
T PRK13777 42 DLNINEHHILWIAYH---LKGASISEIAKFGVMHVSTAFNFSK 81 (185)
T ss_pred CCCHHHHHHHHHHHh---CCCcCHHHHHHHHCCCHhhHHHHHH
Confidence 699999999877763 4689999999999999999875443
No 443
>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=44.29 E-value=26 Score=30.45 Aligned_cols=23 Identities=17% Similarity=0.316 Sum_probs=21.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~R 514 (534)
+|..|+|+.+|||..|+|.++..
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~~ 23 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 47899999999999999999776
No 444
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=44.19 E-value=34 Score=34.60 Aligned_cols=38 Identities=18% Similarity=0.110 Sum_probs=28.8
Q ss_pred HHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 474 SRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 474 ~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
+|+..|+.+-- .....+.+|+|+.||||+.|||.-+..
T Consensus 5 ~R~~~Il~~l~---~~~~~~~~ela~~l~vS~~TirRdL~~ 42 (251)
T PRK13509 5 QRHQILLELLA---QLGFVTVEKVIERLGISPATARRDINK 42 (251)
T ss_pred HHHHHHHHHHH---HcCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 34555554433 246789999999999999999998776
No 445
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=44.13 E-value=29 Score=34.27 Aligned_cols=31 Identities=16% Similarity=0.258 Sum_probs=25.3
Q ss_pred CCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 487 NDHRPK-SLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 487 ~d~e~~-Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
..|+.+ |-.|+|+.||||+.+|| .|+..|..
T Consensus 26 ~pG~~LPsE~eLae~~gVSRt~VR----eAL~~L~~ 57 (239)
T PRK04984 26 PPGSILPAERELSELIGVTRTTLR----EVLQRLAR 57 (239)
T ss_pred CCCCcCCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 345677 79999999999999997 57777764
No 446
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=43.73 E-value=74 Score=30.75 Aligned_cols=38 Identities=21% Similarity=0.137 Sum_probs=27.6
Q ss_pred CHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 473 DSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 473 ~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
++.-..||..-. . ....|-+|||..|||+...||+++.
T Consensus 21 ~~~~~~Vl~~L~--~-~g~~tdeeLA~~Lgi~~~~VRk~L~ 58 (178)
T PRK06266 21 DEEGFEVLKALI--K-KGEVTDEEIAEQTGIKLNTVRKILY 58 (178)
T ss_pred CccHhHHHHHHH--H-cCCcCHHHHHHHHCCCHHHHHHHHH
Confidence 444555655433 1 3479999999999999999986654
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=43.63 E-value=17 Score=31.27 Aligned_cols=25 Identities=24% Similarity=0.271 Sum_probs=22.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
+|..|+|+.+|||..++|..+..++
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gl 25 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDKIGL 25 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 4789999999999999999988765
No 448
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=43.48 E-value=17 Score=30.82 Aligned_cols=26 Identities=12% Similarity=0.121 Sum_probs=22.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKAMT 517 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RAL~ 517 (534)
+|..|+|+.+|||+.+|+.++...+-
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~~Gli 27 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYERLGLL 27 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCCc
Confidence 58899999999999999999876543
No 449
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=43.43 E-value=37 Score=36.10 Aligned_cols=45 Identities=27% Similarity=0.356 Sum_probs=35.8
Q ss_pred hhCCHHHHHHHh------hHhcCCCCCCCCHHHHHHH--hCCCHHHHHHHHHHHHHHH
Q 009449 470 ESLDSRERQVLV------LRYGLNDHRPKSLEEIGKL--FHVSKEWIRKLEKKAMTKL 519 (534)
Q Consensus 470 ~~L~~rEReVL~------LryGL~d~e~~Sl~EIA~~--LgISrerVRqi~~RAL~KL 519 (534)
..|++|+++|+. +.. +++.+.+++|+. +|+|..|||+-+. .|.++
T Consensus 2 ~~l~~R~~~Il~~IV~~yi~~----~~pv~s~~l~~~~~l~~S~aTIR~dm~-~Le~~ 54 (339)
T PRK00082 2 SMLDERQREILRAIVEDYIAT----GEPVGSKTLSKRYGLGVSSATIRNDMA-DLEEL 54 (339)
T ss_pred CccCHHHHHHHHHHHHHHHhc----CCCcCHHHHHHHhCCCCChHHHHHHHH-HHHhC
Confidence 358899999996 444 789999999977 9999999998765 34443
No 450
>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=43.33 E-value=18 Score=31.37 Aligned_cols=26 Identities=12% Similarity=0.208 Sum_probs=22.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKAMT 517 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RAL~ 517 (534)
++..|+|+.+|||..|+|..+..++-
T Consensus 1 y~i~e~A~~~gvs~~tlR~Ye~~Gll 26 (99)
T cd04772 1 YRTVDLARAIGLSPQTVRNYESLGLI 26 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCC
Confidence 47899999999999999998876653
No 451
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=43.18 E-value=46 Score=29.22 Aligned_cols=43 Identities=12% Similarity=0.189 Sum_probs=32.4
Q ss_pred hCCHHHH-HHHhhHhcCCCCCCCCHHHHHHHhCC-CHHHHHHHHHHHHH
Q 009449 471 SLDSRER-QVLVLRYGLNDHRPKSLEEIGKLFHV-SKEWIRKLEKKAMT 517 (534)
Q Consensus 471 ~L~~rER-eVL~LryGL~d~e~~Sl~EIA~~LgI-SrerVRqi~~RAL~ 517 (534)
..|+..+ +|+.++. ..+.|..+||..+|| +.+.++++......
T Consensus 7 ~~s~EfK~~iv~~~~----~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~ 51 (116)
T COG2963 7 KYSPEFKLEAVALYL----RGGDTVSEVAREFGIVSATQLYKWRIQLQK 51 (116)
T ss_pred cCCHHHHHHHHHHHH----hcCccHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 3455544 5677776 568899999999996 99998877766554
No 452
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=43.14 E-value=18 Score=30.90 Aligned_cols=25 Identities=32% Similarity=0.453 Sum_probs=22.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
+|..|+|+.+||++.+|+.+....+
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~~Gl 25 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEEKGL 25 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999987665
No 453
>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=43.09 E-value=18 Score=31.39 Aligned_cols=25 Identities=20% Similarity=0.247 Sum_probs=22.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
+|..|+|+.+|||..++|..+...+
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~~Gl 25 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDEIGL 25 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 4789999999999999999988765
No 454
>PRK11050 manganese transport regulator MntR; Provisional
Probab=43.06 E-value=72 Score=29.75 Aligned_cols=25 Identities=20% Similarity=0.193 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 490 RPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 490 e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
.+.+..|||+.++|++.+|+..+.+
T Consensus 50 ~~~t~~eLA~~l~is~stVsr~l~~ 74 (152)
T PRK11050 50 GEARQVDIAARLGVSQPTVAKMLKR 74 (152)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 5789999999999999999755443
No 455
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=43.06 E-value=31 Score=32.66 Aligned_cols=25 Identities=28% Similarity=0.384 Sum_probs=23.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
..++|++++|+.+|+++++|+++++
T Consensus 80 ~~glSqeeLA~~lgvs~s~IsriE~ 104 (154)
T TIGR00270 80 KRGWSQEQLAKKIQEKESLIKKIEN 104 (154)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 5789999999999999999999986
No 456
>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=43.03 E-value=18 Score=31.53 Aligned_cols=26 Identities=15% Similarity=0.198 Sum_probs=23.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKAMT 517 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RAL~ 517 (534)
++..|+|+.+|||+.|+|..+..++-
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~~Gll 27 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKLGLI 27 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 68999999999999999998887554
No 457
>PRK15044 transcriptional regulator SirC; Provisional
Probab=42.83 E-value=4e+02 Score=28.04 Aligned_cols=39 Identities=10% Similarity=0.083 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHH
Q 009449 382 SKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASE 420 (534)
Q Consensus 382 ~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~ 420 (534)
....++..-+.+...+.++.++||+.+|++...+.+...
T Consensus 192 s~~~kV~~~I~~nl~~~~SLeeLA~~lgmS~~tL~R~Fk 230 (295)
T PRK15044 192 TTKEKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLA 230 (295)
T ss_pred hHHHHHHHHHHhCcccCCCHHHHHHHhCCCHHHHHHHHH
Confidence 345566677777888999999999999999999987654
No 458
>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=42.82 E-value=28 Score=26.33 Aligned_cols=24 Identities=29% Similarity=0.419 Sum_probs=19.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKA 515 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RA 515 (534)
.+.+|+++.+|+|+.|+....+..
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 468999999999999999887744
No 459
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=42.64 E-value=1.1e+02 Score=26.46 Aligned_cols=37 Identities=16% Similarity=0.129 Sum_probs=25.9
Q ss_pred HHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 475 RERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 475 rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
-|+.+|...+- ..+-...+.|+.||||+.+++..+.+
T Consensus 55 ~Er~~i~~aL~---~~~gn~s~AAr~LGIsRsTL~rKLkr 91 (95)
T PRK00430 55 VEAPLLDMVMQ---YTRGNQTRAALMLGINRGTLRKKLKK 91 (95)
T ss_pred HHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 45555554441 13557999999999999998766554
No 460
>PRK08359 transcription factor; Validated
Probab=42.61 E-value=30 Score=33.53 Aligned_cols=25 Identities=20% Similarity=0.234 Sum_probs=23.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
..++|++|+|+.+|+++.+|+.++.
T Consensus 96 ~kglSQeeLA~~lgvs~stI~~iE~ 120 (176)
T PRK08359 96 KSGLSYEELSHEVGLSVNDLRRIAH 120 (176)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 5789999999999999999999875
No 461
>PF04645 DUF603: Protein of unknown function, DUF603; InterPro: IPR006739 This family includes several uncharacterised proteins from Borrelia species.
Probab=42.24 E-value=31 Score=33.24 Aligned_cols=26 Identities=31% Similarity=0.258 Sum_probs=21.5
Q ss_pred CCC-CCHHHHHHHhCCCHHHHHHHHHH
Q 009449 489 HRP-KSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 489 ~e~-~Sl~EIA~~LgISrerVRqi~~R 514 (534)
.+| ++..|||+.||||+..|..+.++
T Consensus 16 ~eg~L~d~~Ia~~lgvs~~nV~kmR~K 42 (181)
T PF04645_consen 16 KEGRLSDAEIAKELGVSRVNVWKMRQK 42 (181)
T ss_pred hcCCccHHHHHHHHCchHHHHHHHHHH
Confidence 455 89999999999999999766543
No 462
>cd00383 trans_reg_C Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and a response regulator. The former autophosphorylates in a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. The C-terminal effector domain contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunite of RNA polymerase.
Probab=42.20 E-value=56 Score=26.93 Aligned_cols=50 Identities=24% Similarity=0.177 Sum_probs=37.1
Q ss_pred hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHh
Q 009449 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFH-----VSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~Lg-----ISrerVRqi~~RAL~KLR~ 521 (534)
.|+++|..+|.+.+ ...++..|.++|.+.+- .+..++.+.+.+-++||..
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 38899999888766 34457899999999884 5667777777766666654
No 463
>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=42.16 E-value=31 Score=29.27 Aligned_cols=32 Identities=22% Similarity=0.316 Sum_probs=21.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 490 RPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 490 e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
...|..+.|..||||++||..-...=|.++-.
T Consensus 18 ~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in~ 49 (82)
T PF12116_consen 18 TKATVRQAAKVFGVSKSTVHKDVTERLPKINP 49 (82)
T ss_dssp H---HHHHHHHHTS-HHHHHHHHTTHHHHH-H
T ss_pred cccHHHHHHHHHCCcHHHHHHHHHHHHHhcCH
Confidence 47799999999999999998877655555443
No 464
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=42.06 E-value=18 Score=31.18 Aligned_cols=26 Identities=15% Similarity=0.310 Sum_probs=22.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKAMT 517 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RAL~ 517 (534)
++..|+|+.+|||..++|.++..++-
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye~~Gll 26 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEEIGLV 26 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999876543
No 465
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=41.77 E-value=33 Score=28.67 Aligned_cols=19 Identities=11% Similarity=-0.005 Sum_probs=18.3
Q ss_pred CHHHHHHHhCCCHHHHHHH
Q 009449 493 SLEEIGKLFHVSKEWIRKL 511 (534)
Q Consensus 493 Sl~EIA~~LgISrerVRqi 511 (534)
+...+|+.||||+++|+|+
T Consensus 12 s~~kvA~aLGIs~~AVsQW 30 (75)
T PRK09744 12 SKTKLANAAGVRLASVAAW 30 (75)
T ss_pred cHHHHHHHHCCCHHHHHHH
Confidence 8899999999999999998
No 466
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=41.57 E-value=19 Score=31.71 Aligned_cols=26 Identities=19% Similarity=0.313 Sum_probs=23.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKAMT 517 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RAL~ 517 (534)
+|..|+|+.+|||+.|+|-.+..++-
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye~~gll 26 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEKEGLL 26 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999887764
No 467
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=41.53 E-value=19 Score=30.95 Aligned_cols=26 Identities=8% Similarity=0.115 Sum_probs=22.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKAMT 517 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RAL~ 517 (534)
++..|+|+.+|||..|+|..+..++-
T Consensus 1 m~i~eva~~~gvs~~tlR~ye~~Gll 26 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDHIGLL 26 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999886643
No 468
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=41.45 E-value=64 Score=30.76 Aligned_cols=57 Identities=23% Similarity=0.254 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHHhhCCHHHHHHHhhHhcCC----CCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 458 RQHMKKDVFRILESLDSRERQVLVLRYGLN----DHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 458 ~~el~e~L~~~L~~L~~rEReVL~LryGL~----d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
+++.-++|+..|..||+.|++=+.-+|-=. +.+|+|-+||.+.||=+++-++++...
T Consensus 3 k~efL~~L~~~L~~lp~~e~~e~l~~Y~e~f~d~~~~G~sEeeii~~LG~P~~iA~~i~~~ 63 (181)
T PF08006_consen 3 KNEFLNELEKYLKKLPEEEREEILEYYEEYFDDAGEEGKSEEEIIAELGSPKEIAREILAE 63 (181)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHcCCHHHHHHHHHHh
Confidence 345556888899999999887766655211 135789999999999999999988754
No 469
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=41.31 E-value=58 Score=25.39 Aligned_cols=28 Identities=18% Similarity=0.128 Sum_probs=21.7
Q ss_pred HHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 009449 479 VLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLE 512 (534)
Q Consensus 479 VL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~ 512 (534)
-|.-+| .++++|.|+.|||+...++.+-
T Consensus 9 ~L~~~f------hlp~~eAA~~Lgv~~T~LKr~C 36 (52)
T PF02042_consen 9 DLSQYF------HLPIKEAAKELGVSVTTLKRRC 36 (52)
T ss_pred HHHHHh------CCCHHHHHHHhCCCHHHHHHHH
Confidence 345566 7899999999999988776553
No 470
>PF06322 Phage_NinH: Phage NinH protein; InterPro: IPR010454 This entry is represented by Bacteriophage 933W, NinH. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=41.21 E-value=38 Score=27.35 Aligned_cols=27 Identities=22% Similarity=0.484 Sum_probs=22.0
Q ss_pred HHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 009449 479 VLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLE 512 (534)
Q Consensus 479 VL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~ 512 (534)
+|.-.|| ...|+|..|++++.||++..
T Consensus 11 lLi~~~G-------nqtEvaR~l~c~R~TVrKY~ 37 (64)
T PF06322_consen 11 LLIETYG-------NQTEVARRLGCNRATVRKYS 37 (64)
T ss_pred HHHHHhC-------cHHHHHHHhcccHHHHHHHh
Confidence 4455664 78999999999999999764
No 471
>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=41.03 E-value=74 Score=29.63 Aligned_cols=53 Identities=23% Similarity=0.132 Sum_probs=38.6
Q ss_pred ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhc
Q 009449 374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVG 426 (534)
Q Consensus 374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~ 426 (534)
|.-..+.-....+++.-|...-++..|..||++.+|++++.|..+....+-.+
T Consensus 22 p~C~~~~e~~f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGRL~~ 74 (137)
T TIGR03826 22 PSCYEEEEREFEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGRLQL 74 (137)
T ss_pred HHHhHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCCeec
Confidence 33333444555566666666667889999999999999999999987766433
No 472
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=40.51 E-value=37 Score=34.41 Aligned_cols=38 Identities=26% Similarity=0.246 Sum_probs=28.3
Q ss_pred HHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 474 SRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 474 ~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
+|..+|+.+.- .....+..|+|+.|+||..|||+-+..
T Consensus 5 ~R~~~Il~~l~---~~~~~~~~ela~~l~vS~~TiRRdL~~ 42 (252)
T PRK10906 5 QRHDAIIELVK---QQGYVSTEELVEHFSVSPQTIRRDLND 42 (252)
T ss_pred HHHHHHHHHHH---HcCCEeHHHHHHHhCCCHHHHHHHHHH
Confidence 45666665553 234689999999999999999985543
No 473
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=40.18 E-value=21 Score=31.60 Aligned_cols=26 Identities=19% Similarity=0.204 Sum_probs=23.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKAMT 517 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RAL~ 517 (534)
++..|+|+.+|||..|+|..+..++-
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye~~GLl 26 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEEQGLL 26 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCC
Confidence 57899999999999999999987654
No 474
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=40.13 E-value=3.6e+02 Score=28.34 Aligned_cols=34 Identities=15% Similarity=0.035 Sum_probs=26.9
Q ss_pred HHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHH
Q 009449 256 ERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH 289 (534)
Q Consensus 256 e~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~ 289 (534)
.+....|+..+|+.|+..+-|...|++.+.+...
T Consensus 176 ~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~ 209 (325)
T PRK05657 176 LRAARELEHKLDHEPSAEEIAELLDKPVDDVSRM 209 (325)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 3445567777899999999999999998876554
No 475
>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=40.11 E-value=21 Score=30.80 Aligned_cols=25 Identities=20% Similarity=0.194 Sum_probs=22.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
++..|+|+.+|||..+||-.+...+
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye~~GL 25 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLREGL 25 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999888765
No 476
>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=40.08 E-value=20 Score=31.00 Aligned_cols=25 Identities=8% Similarity=0.239 Sum_probs=22.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
+|..|+|+.+|||..++|.++...+
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye~~Gl 26 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDRLGL 26 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5899999999999999999877553
No 477
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=40.03 E-value=46 Score=34.68 Aligned_cols=39 Identities=26% Similarity=0.139 Sum_probs=29.9
Q ss_pred HHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 475 RERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 475 rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
+.++|+.+.. +....+..|||+.+|||+.+|++.+.+-.
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 4555665554 24678999999999999999999876654
No 478
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=40.03 E-value=43 Score=31.64 Aligned_cols=25 Identities=16% Similarity=0.167 Sum_probs=21.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
.......+||+.|||++.+|.+.++
T Consensus 22 ~~~~~~~diA~~L~Vsp~sVt~ml~ 46 (154)
T COG1321 22 KGFARTKDIAERLKVSPPSVTEMLK 46 (154)
T ss_pred cCcccHHHHHHHhCCCcHHHHHHHH
Confidence 4568999999999999999976543
No 479
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=40.00 E-value=31 Score=33.67 Aligned_cols=31 Identities=13% Similarity=0.134 Sum_probs=25.9
Q ss_pred CCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 487 NDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 487 ~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
..|+.++..++|+.||||+..|| .|++.|..
T Consensus 30 ~pG~~L~e~~La~~lgVSRtpVR----EAL~~L~~ 60 (221)
T PRK11414 30 KPGARLITKNLAEQLGMSITPVR----EALLRLVS 60 (221)
T ss_pred CCCCccCHHHHHHHHCCCchhHH----HHHHHHHH
Confidence 44678899999999999999997 67777764
No 480
>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=39.87 E-value=9.6 Score=36.30 Aligned_cols=48 Identities=13% Similarity=0.349 Sum_probs=0.0
Q ss_pred HHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449 464 DVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK 513 (534)
Q Consensus 464 ~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~ 513 (534)
.|..+...|=..|..-|. .|-....++|+++||+.+|++.+||+....
T Consensus 24 TL~~v~~~iv~~Q~~ff~--~g~~~l~PLt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 24 TLLRVAQAIVERQKDFFL--GGPGALKPLTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp --------------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHh--cCcccCcCCCHHHHHHHhCCCHhHHHHHHc
Confidence 455555667777777554 243346899999999999999999986544
No 481
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=39.78 E-value=84 Score=23.23 Aligned_cols=26 Identities=23% Similarity=0.068 Sum_probs=21.6
Q ss_pred CCCCCHHHHHHHcCCCHHHHHHHHHH
Q 009449 396 GKYPEDIEIAKYTGLSLAEIRSASEC 421 (534)
Q Consensus 396 Gr~Pt~eEIA~~lgis~~kv~~~l~~ 421 (534)
...-|..|||+.+|+|...|......
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 56678999999999999999987654
No 482
>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=39.75 E-value=2.4e+02 Score=24.07 Aligned_cols=35 Identities=17% Similarity=0.126 Sum_probs=27.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449 490 RPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET 524 (534)
Q Consensus 490 e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~ 524 (534)
-|+|+++|.+.+......+...+..-+..|++.+.
T Consensus 56 ~G~~l~~I~~~l~~~~~~~~~~l~~~~~~l~~~i~ 90 (96)
T cd04768 56 LGFSLAEIKELLDTEMEELTAMLLEKKQAIQQKID 90 (96)
T ss_pred cCCCHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHH
Confidence 68999999999998766777777777777766543
No 483
>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=39.69 E-value=55 Score=31.61 Aligned_cols=38 Identities=13% Similarity=0.208 Sum_probs=27.7
Q ss_pred CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 009449 472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLE 512 (534)
Q Consensus 472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~ 512 (534)
|++.-|+-|.-.+- ..++|+++||..+||...||.-|+
T Consensus 17 lse~~r~~Iy~~~~---~~~~sv~~vS~~ygi~~~RV~AIv 54 (172)
T PF12298_consen 17 LSEELREQIYEDVM---QDGKSVREVSQKYGIKIQRVEAIV 54 (172)
T ss_pred CCHHHHHHHHHHHH---hCCCCHHHHHHHhCCCHHHHHHHH
Confidence 55555555544441 467799999999999999996544
No 484
>COG3711 BglG Transcriptional antiterminator [Transcription]
Probab=39.51 E-value=55 Score=35.93 Aligned_cols=113 Identities=22% Similarity=0.122 Sum_probs=62.7
Q ss_pred CCCCCHHHHHHHcCCCHHHHHHHHHHhhhhccccc-ccccchhhhhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCH
Q 009449 396 GKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQ-KIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDS 474 (534)
Q Consensus 396 Gr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~-~i~~~~~~~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~ 474 (534)
...-+..++|+.+|+|..+++.-.........-+. ++-...+ +-.+.++. +...... . .........
T Consensus 17 ~~~~~~~~la~~l~vS~Rti~~~i~~In~~l~~~~~~~~~~~~---~~~~~~~~-----~~~~~~~---~-~~~~~~~~~ 84 (491)
T COG3711 17 NPLLTIKELAEQLGVSRRTIRYDIKKINESLEEGGIPIIKRKG---GGYILEED-----ERALELE---E-LQELTSYDK 84 (491)
T ss_pred CCCCCHHHHHHHhCccHHHHHHHHHHHHHHHHhCCceEEecCC---CcEEecCc-----HHHHHHH---h-cccccccCh
Confidence 34557889999999999999866554432211110 0000000 00111110 0000000 0 001111226
Q ss_pred HHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 475 RERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 475 rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
.||..+.+.+=+.+ +..++.++|..+++|+.||.+-......+++.
T Consensus 85 ~er~~~~ll~~~~~-~~~~l~~La~~l~vs~~ti~~dl~~v~~~l~~ 130 (491)
T COG3711 85 DERIIIILLLLLLS-ELLSLHELADELFVSKSTIINDLKDVRLKLLL 130 (491)
T ss_pred HHHHHHHHHHHHhc-ChhhHHHHHHHHHhHHHHHHHHHHHHHHHHHh
Confidence 67777777664443 68999999999999999999998876666554
No 485
>PF14502 HTH_41: Helix-turn-helix domain
Probab=39.49 E-value=53 Score=25.23 Aligned_cols=30 Identities=27% Similarity=0.378 Sum_probs=0.0
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 488 DHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 488 d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
+..-.|..|.++.|++|+.+| ..|++.|.+
T Consensus 3 GdRi~tI~e~~~~~~vs~Gti----Q~Alk~Le~ 32 (48)
T PF14502_consen 3 GDRIPTISEYSEKFGVSRGTI----QNALKFLEE 32 (48)
T ss_pred CcccCCHHHHHHHhCcchhHH----HHHHHHHHH
No 486
>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=39.18 E-value=33 Score=33.09 Aligned_cols=30 Identities=20% Similarity=0.225 Sum_probs=25.2
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 488 DHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 488 d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
.|+.++..++|+.||||+..|| .|+..|..
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 3678899999999999999997 57777764
No 487
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=39.02 E-value=22 Score=31.57 Aligned_cols=27 Identities=22% Similarity=0.228 Sum_probs=23.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKAMTK 518 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RAL~K 518 (534)
+|..|+|+.+|||+.|+|-.+..++-.
T Consensus 1 ~~ige~a~~~gvs~~tLryYe~~GLi~ 27 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEEKGLLP 27 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 588999999999999999999877643
No 488
>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=38.90 E-value=22 Score=32.19 Aligned_cols=26 Identities=27% Similarity=0.312 Sum_probs=22.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKAMT 517 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RAL~ 517 (534)
+|..|+|+.+|||..|+|-.+...+-
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~~GLl 26 (127)
T cd01108 1 MNIGEAAKLTGLSAKMIRYYEEIGLI 26 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999998877654
No 489
>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=38.44 E-value=22 Score=32.07 Aligned_cols=26 Identities=27% Similarity=0.411 Sum_probs=22.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKAMT 517 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RAL~ 517 (534)
|+..|+|+.+|||..|+|-.+..++-
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~~GLl 26 (127)
T TIGR02044 1 MNIGQVAKLTGLSSKMIRYYEEKGLI 26 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999998876653
No 490
>PRK03837 transcriptional regulator NanR; Provisional
Probab=38.32 E-value=41 Score=33.04 Aligned_cols=30 Identities=23% Similarity=0.310 Sum_probs=24.9
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 488 DHRPK-SLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 488 d~e~~-Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
.|+.+ +..++|+.||||+.+|| .|+..|..
T Consensus 33 pG~~Lp~E~~Lae~~gVSRt~VR----EAL~~L~~ 63 (241)
T PRK03837 33 PGDQLPSERELMAFFGVGRPAVR----EALQALKR 63 (241)
T ss_pred CCCCCCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 35677 89999999999999997 57777764
No 491
>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=38.28 E-value=36 Score=33.41 Aligned_cols=28 Identities=18% Similarity=0.304 Sum_probs=23.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 490 RPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 490 e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
.=-|-.|+|+.+|||+.||| +|+..|..
T Consensus 31 ~LPsE~eLa~~~~VSR~TvR----~Al~~L~~ 58 (238)
T TIGR02325 31 YLPAEMQLAERFGVNRHTVR----RAIAALVE 58 (238)
T ss_pred cCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 34589999999999999997 67777765
No 492
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=38.24 E-value=48 Score=26.01 Aligned_cols=26 Identities=27% Similarity=0.474 Sum_probs=22.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 491 PKSLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 491 ~~Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
+.|+++||+.+|+|...+.++..+..
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~ 26 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKET 26 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHh
Confidence 36899999999999999988887654
No 493
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=38.08 E-value=23 Score=31.94 Aligned_cols=27 Identities=22% Similarity=0.303 Sum_probs=23.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKAMTK 518 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RAL~K 518 (534)
++..|+|+.+|||..|||..+..++-.
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~~GLl~ 27 (126)
T cd04783 1 LTIGELAKAAGVNVETIRYYQRRGLLP 27 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 578999999999999999998876654
No 494
>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=38.01 E-value=17 Score=29.15 Aligned_cols=26 Identities=23% Similarity=0.336 Sum_probs=19.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
....|+.|||..||+++++|+..+..
T Consensus 12 ~~~~S~~eLa~~~~~s~~~ve~mL~~ 37 (69)
T PF09012_consen 12 RGRVSLAELAREFGISPEAVEAMLEQ 37 (69)
T ss_dssp S-SEEHHHHHHHTT--HHHHHHHHHH
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 46789999999999999999876653
No 495
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=37.98 E-value=24 Score=31.16 Aligned_cols=26 Identities=15% Similarity=0.116 Sum_probs=23.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449 492 KSLEEIGKLFHVSKEWIRKLEKKAMT 517 (534)
Q Consensus 492 ~Sl~EIA~~LgISrerVRqi~~RAL~ 517 (534)
+|..|+|+.+|||..|||..+..++-
T Consensus 1 y~Ige~A~~~gvs~~tlR~ye~~GLl 26 (107)
T cd01111 1 YSISQLALDAGVSVHIVRDYLLRGLL 26 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 47899999999999999999987654
No 496
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=37.98 E-value=86 Score=26.89 Aligned_cols=24 Identities=17% Similarity=0.149 Sum_probs=20.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449 489 HRPKSLEEIGKLFHVSKEWIRKLEKK 514 (534)
Q Consensus 489 ~e~~Sl~EIA~~LgISrerVRqi~~R 514 (534)
..++| ++|+..|||+.+|.+++..
T Consensus 43 ~~glS--qLAe~~GIs~stLs~iE~g 66 (89)
T TIGR02684 43 ARGMT--QLARKTGLSRESLYKALSG 66 (89)
T ss_pred HCChH--HHHHHHCCCHHHHHHHHcC
Confidence 34555 6999999999999999864
No 497
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=37.97 E-value=41 Score=32.87 Aligned_cols=37 Identities=8% Similarity=0.184 Sum_probs=28.2
Q ss_pred HHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449 479 VLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521 (534)
Q Consensus 479 VL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~ 521 (534)
|+.-.| ..|+.++..++|+.||||+..|| .|+.+|..
T Consensus 20 I~~g~l--~pG~~L~e~eLae~lgVSRtpVR----EAL~~L~~ 56 (224)
T PRK11534 20 IIRGNF--QPDEKLRMSLLTSRYALGVGPLR----EALSQLVA 56 (224)
T ss_pred HHhCCC--CCCCcCCHHHHHHHHCCChHHHH----HHHHHHHH
Confidence 444444 34678899999999999999997 57777764
No 498
>PF13730 HTH_36: Helix-turn-helix domain
Probab=37.89 E-value=43 Score=25.16 Aligned_cols=28 Identities=29% Similarity=0.411 Sum_probs=23.8
Q ss_pred CCCCCHHHHHHHcCCCHHHHHHHHHHhh
Q 009449 396 GKYPEDIEIAKYTGLSLAEIRSASECLR 423 (534)
Q Consensus 396 Gr~Pt~eEIA~~lgis~~kv~~~l~~~~ 423 (534)
+-.|+.+.||+.+|++..+|..++....
T Consensus 23 ~~~pS~~~la~~~g~s~~Tv~~~i~~L~ 50 (55)
T PF13730_consen 23 GCFPSQETLAKDLGVSRRTVQRAIKELE 50 (55)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4568999999999999999998876543
No 499
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=37.82 E-value=2.1e+02 Score=29.53 Aligned_cols=39 Identities=8% Similarity=-0.026 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHH
Q 009449 383 KIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC 421 (534)
Q Consensus 383 ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~ 421 (534)
.+.++..-+...+....+.+++|+.+|++...+....+.
T Consensus 219 ~~~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~ 257 (322)
T PRK09393 219 RLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEA 257 (322)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 455556666666778899999999999999998877543
No 500
>COG4709 Predicted membrane protein [Function unknown]
Probab=37.70 E-value=61 Score=31.86 Aligned_cols=59 Identities=24% Similarity=0.255 Sum_probs=45.3
Q ss_pred HHHHHHHHHHHHhhCCHHHHHHHhhHhc----CCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449 458 RQHMKKDVFRILESLDSRERQVLVLRYG----LNDHRPKSLEEIGKLFHVSKEWIRKLEKKAM 516 (534)
Q Consensus 458 ~~el~e~L~~~L~~L~~rEReVL~LryG----L~d~e~~Sl~EIA~~LgISrerVRqi~~RAL 516 (534)
+.+.-.+|+..|+.||+.+|.=+...|- -.+..++|-+||++.||=+.+-.+++..+..
T Consensus 3 k~efL~eL~~yL~~Lp~~~r~e~m~dyeehF~~a~~~GksE~EI~~~LG~P~eiA~ei~s~~~ 65 (195)
T COG4709 3 KTEFLNELEQYLEGLPREERREIMYDYEEHFREAQEAGKSEEEIAKDLGDPKEIAAEILSERG 65 (195)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhhhhcCCCHHHHHHHhCCHHHHHHHHHHHcc
Confidence 3455568899999999999876665541 1234689999999999999999888776654
Done!