Query 017044
Match_columns 378
No_of_seqs 164 out of 1363
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 05:07:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017044.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017044hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK07598 RNA polymerase sigma 100.0 1.2E-30 2.7E-35 263.3 13.1 126 253-378 58-232 (415)
2 TIGR02997 Sig70-cyanoRpoD RNA 100.0 2.2E-28 4.7E-33 234.5 12.5 124 255-378 1-131 (298)
3 PRK07406 RNA polymerase sigma 99.9 1.3E-26 2.9E-31 231.2 13.0 125 253-377 61-192 (373)
4 PRK05949 RNA polymerase sigma 99.9 4.3E-26 9.3E-31 223.2 13.8 126 253-378 16-148 (327)
5 PRK07405 RNA polymerase sigma 99.9 2.5E-25 5.4E-30 216.5 12.8 126 253-378 6-138 (317)
6 PRK05901 RNA polymerase sigma 99.9 7.3E-24 1.6E-28 218.9 8.9 114 252-378 208-328 (509)
7 COG0568 RpoD DNA-directed RNA 99.9 5.3E-23 1.1E-27 203.7 8.2 126 253-378 7-159 (342)
8 PRK07921 RNA polymerase sigma 99.8 8.7E-21 1.9E-25 186.0 8.8 113 253-378 24-143 (324)
9 PRK09210 RNA polymerase sigma 99.7 1E-16 2.2E-21 159.2 8.6 89 250-378 91-186 (367)
10 PRK05658 RNA polymerase sigma 99.7 7.4E-17 1.6E-21 169.5 6.4 52 327-378 379-437 (619)
11 TIGR02392 rpoH_proteo alternat 99.6 3E-15 6.6E-20 141.9 8.0 84 256-378 2-92 (270)
12 PRK06596 RNA polymerase factor 99.6 3.8E-15 8.1E-20 143.0 8.5 88 252-378 11-105 (284)
13 PRK07122 RNA polymerase sigma 99.5 1.4E-14 3E-19 137.8 4.3 52 327-378 39-97 (264)
14 PRK07500 rpoH2 RNA polymerase 99.5 1.6E-13 3.5E-18 132.2 8.4 86 254-378 5-97 (289)
15 PRK05657 RNA polymerase sigma 99.3 2.9E-12 6.3E-17 125.8 8.1 85 253-377 51-142 (325)
16 TIGR02394 rpoS_proteo RNA poly 99.3 1.1E-11 2.5E-16 118.3 8.8 90 249-378 7-103 (285)
17 PRK07408 RNA polymerase sigma 99.2 2E-11 4.3E-16 115.3 6.3 53 326-378 23-83 (256)
18 COG1191 FliA DNA-directed RNA 99.1 7.1E-11 1.5E-15 113.3 6.3 52 326-378 22-81 (247)
19 TIGR02850 spore_sigG RNA polym 99.1 1.6E-10 3.6E-15 108.5 7.6 76 263-378 9-91 (254)
20 PRK08215 sporulation sigma fac 99.1 2.7E-10 5.9E-15 107.1 7.7 76 263-378 12-94 (258)
21 PRK05911 RNA polymerase sigma 99.0 2.7E-10 5.9E-15 107.9 4.5 53 326-378 21-83 (257)
22 PRK06288 RNA polymerase sigma 98.9 2.2E-09 4.8E-14 101.7 6.5 76 264-378 6-91 (268)
23 PRK05803 sporulation sigma fac 98.8 1.3E-08 2.9E-13 94.3 8.0 82 256-377 17-105 (233)
24 TIGR02941 Sigma_B RNA polymera 98.7 3.3E-08 7.3E-13 92.6 7.3 72 268-378 8-86 (255)
25 PRK08583 RNA polymerase sigma 98.6 9.3E-08 2E-12 89.7 7.3 71 268-377 8-85 (257)
26 TIGR02885 spore_sigF RNA polym 98.5 1.7E-07 3.7E-12 86.3 5.1 53 326-378 9-68 (231)
27 PRK05572 sporulation sigma fac 98.4 5.6E-07 1.2E-11 84.6 7.8 78 261-378 5-89 (252)
28 PRK07670 RNA polymerase sigma 98.3 7.2E-07 1.6E-11 83.8 6.2 53 326-378 20-82 (251)
29 PRK12427 flagellar biosynthesi 98.3 4.3E-07 9.4E-12 85.1 4.4 51 327-378 14-74 (231)
30 PF00140 Sigma70_r1_2: Sigma-7 98.1 9.2E-07 2E-11 62.2 0.8 35 254-288 1-35 (37)
31 TIGR02846 spore_sigmaK RNA pol 98.0 2.4E-05 5.1E-10 72.6 8.1 82 256-377 15-104 (227)
32 PRK08301 sporulation sigma fac 97.8 5.6E-05 1.2E-09 69.9 7.5 52 326-377 50-108 (234)
33 TIGR02835 spore_sigmaE RNA pol 97.5 0.00027 5.8E-09 65.9 7.7 52 326-377 50-108 (234)
34 PF04542 Sigma70_r2: Sigma-70 97.5 8.8E-05 1.9E-09 55.2 2.8 45 333-377 1-52 (71)
35 PRK05658 RNA polymerase sigma 97.2 0.00033 7.2E-09 74.7 4.3 35 253-287 102-136 (619)
36 PRK08295 RNA polymerase factor 97.0 0.00093 2E-08 59.9 4.9 53 325-377 21-80 (208)
37 TIGR02859 spore_sigH RNA polym 96.8 0.0015 3.1E-08 58.1 4.4 52 326-377 17-75 (198)
38 PRK08311 putative RNA polymera 96.8 0.0017 3.6E-08 62.1 5.0 52 326-377 16-76 (237)
39 PF04539 Sigma70_r3: Sigma-70 96.6 0.0031 6.6E-08 49.2 4.3 40 285-324 3-42 (78)
40 PRK09652 RNA polymerase sigma 96.2 0.0044 9.5E-08 53.5 3.5 50 326-377 8-64 (182)
41 PRK05602 RNA polymerase sigma 96.1 0.0051 1.1E-07 54.6 3.4 52 325-377 17-75 (186)
42 PRK11922 RNA polymerase sigma 95.9 0.013 2.8E-07 54.5 5.4 61 265-365 7-67 (231)
43 TIGR02895 spore_sigI RNA polym 95.9 0.0045 9.8E-08 58.7 2.4 26 353-378 36-68 (218)
44 TIGR02948 SigW_bacill RNA poly 95.8 0.0077 1.7E-07 52.8 3.3 51 325-377 15-72 (187)
45 PRK09641 RNA polymerase sigma 95.5 0.013 2.8E-07 51.4 3.6 50 326-377 16-72 (187)
46 PRK09648 RNA polymerase sigma 95.4 0.033 7.2E-07 49.5 5.8 51 326-377 22-83 (189)
47 PRK12519 RNA polymerase sigma 95.3 0.023 5.1E-07 50.6 4.4 51 326-377 27-83 (194)
48 PRK09646 RNA polymerase sigma 95.3 0.026 5.7E-07 50.7 4.7 46 326-371 28-80 (194)
49 PRK06759 RNA polymerase factor 94.8 0.033 7.2E-07 47.5 3.8 48 328-377 4-58 (154)
50 PRK06986 fliA flagellar biosyn 94.7 0.017 3.6E-07 53.9 1.8 31 348-378 31-68 (236)
51 PRK11923 algU RNA polymerase s 94.6 0.073 1.6E-06 47.4 5.7 40 326-365 18-57 (193)
52 PRK12513 RNA polymerase sigma 94.6 0.034 7.3E-07 49.7 3.6 41 325-365 23-63 (194)
53 PRK09640 RNA polymerase sigma 94.2 0.062 1.3E-06 48.0 4.4 61 315-377 9-80 (188)
54 PRK11924 RNA polymerase sigma 94.0 0.064 1.4E-06 46.1 3.9 50 326-377 11-67 (179)
55 PRK13919 putative RNA polymera 93.5 0.079 1.7E-06 46.8 3.6 41 325-365 20-60 (186)
56 PRK06811 RNA polymerase factor 93.2 0.12 2.7E-06 46.2 4.4 51 326-377 16-76 (189)
57 TIGR02939 RpoE_Sigma70 RNA pol 92.6 0.16 3.5E-06 44.6 4.3 40 326-365 18-57 (190)
58 PRK12534 RNA polymerase sigma 92.2 0.17 3.6E-06 44.9 3.8 47 325-371 22-75 (187)
59 PRK12531 RNA polymerase sigma 92.2 0.21 4.5E-06 45.0 4.5 51 326-377 25-82 (194)
60 TIGR02952 Sig70_famx2 RNA poly 92.0 0.21 4.6E-06 43.0 4.2 51 326-377 9-66 (170)
61 PRK12514 RNA polymerase sigma 91.8 0.16 3.4E-06 44.8 3.2 40 326-365 17-56 (179)
62 PRK09638 RNA polymerase sigma 91.7 0.2 4.4E-06 43.7 3.8 40 326-365 16-55 (176)
63 PRK12526 RNA polymerase sigma 90.5 0.32 7E-06 44.4 4.1 52 325-377 35-93 (206)
64 PRK12524 RNA polymerase sigma 90.2 0.3 6.4E-06 44.0 3.4 40 326-365 24-63 (196)
65 PRK12538 RNA polymerase sigma 89.5 0.34 7.4E-06 45.7 3.5 51 326-377 61-118 (233)
66 PRK12512 RNA polymerase sigma 87.8 0.7 1.5E-05 40.8 4.1 41 325-365 19-63 (184)
67 TIGR02954 Sig70_famx3 RNA poly 86.9 0.74 1.6E-05 40.1 3.7 41 325-365 13-53 (169)
68 PRK12536 RNA polymerase sigma 85.6 1.1 2.4E-05 39.7 4.2 43 323-365 16-59 (181)
69 PRK12537 RNA polymerase sigma 85.6 0.98 2.1E-05 40.1 3.8 41 325-365 20-60 (182)
70 COG1191 FliA DNA-directed RNA 84.9 1.2 2.7E-05 43.4 4.4 63 256-326 88-150 (247)
71 PRK12515 RNA polymerase sigma 83.7 0.89 1.9E-05 40.5 2.7 41 325-365 19-59 (189)
72 PRK12518 RNA polymerase sigma 83.1 1.4 3.1E-05 38.3 3.7 39 326-365 9-47 (175)
73 PRK07408 RNA polymerase sigma 82.1 2.5 5.4E-05 40.3 5.2 36 287-322 114-149 (256)
74 PRK09643 RNA polymerase sigma 81.9 2.3 5E-05 38.3 4.6 42 324-365 23-64 (192)
75 PRK12539 RNA polymerase sigma 80.2 3.6 7.8E-05 36.6 5.2 50 326-377 19-79 (184)
76 TIGR02850 spore_sigG RNA polym 79.7 3.3 7.2E-05 39.2 5.1 37 287-323 121-157 (254)
77 PRK07122 RNA polymerase sigma 79.5 3.4 7.5E-05 39.8 5.2 37 287-323 128-164 (264)
78 TIGR02393 RpoD_Cterm RNA polym 79.4 3.6 7.8E-05 38.6 5.2 36 287-322 88-123 (238)
79 PRK07921 RNA polymerase sigma 78.8 3.5 7.6E-05 41.3 5.2 38 285-322 172-209 (324)
80 PRK09415 RNA polymerase factor 77.9 2.4 5.1E-05 37.6 3.3 41 325-365 13-53 (179)
81 COG1595 RpoE DNA-directed RNA 76.9 3.3 7.2E-05 36.8 4.0 42 324-365 11-52 (182)
82 PRK12427 flagellar biosynthesi 76.3 4.2 9.2E-05 38.3 4.7 37 287-323 102-138 (231)
83 PRK05911 RNA polymerase sigma 76.1 4.2 9.2E-05 38.9 4.7 36 288-323 112-147 (257)
84 TIGR02983 SigE-fam_strep RNA p 74.8 3.9 8.5E-05 35.1 3.8 40 326-365 4-43 (162)
85 PRK09210 RNA polymerase sigma 74.8 5.2 0.00011 40.6 5.2 37 287-323 217-253 (367)
86 PRK12541 RNA polymerase sigma 71.9 3.3 7.2E-05 35.7 2.7 39 327-365 4-42 (161)
87 PRK07406 RNA polymerase sigma 71.7 6.7 0.00015 40.3 5.2 38 285-322 222-259 (373)
88 PRK05901 RNA polymerase sigma 69.0 8 0.00017 41.5 5.2 38 286-323 358-395 (509)
89 PRK12528 RNA polymerase sigma 68.5 7.3 0.00016 33.6 4.0 38 328-365 4-41 (161)
90 TIGR02885 spore_sigF RNA polym 68.2 10 0.00022 35.2 5.1 36 288-323 99-134 (231)
91 TIGR02479 FliA_WhiG RNA polyme 67.5 8.9 0.00019 35.4 4.6 38 286-323 83-120 (224)
92 PRK07670 RNA polymerase sigma 65.8 9.2 0.0002 36.1 4.5 37 287-323 110-146 (251)
93 PRK05949 RNA polymerase sigma 65.2 12 0.00026 37.6 5.3 36 287-322 179-214 (327)
94 PRK09647 RNA polymerase sigma 64.8 7.6 0.00017 35.7 3.6 40 326-365 26-65 (203)
95 PF01726 LexA_DNA_bind: LexA D 62.4 16 0.00035 28.6 4.5 27 297-323 20-47 (65)
96 PRK07598 RNA polymerase sigma 62.4 11 0.00025 39.4 4.7 39 286-324 262-300 (415)
97 PRK08215 sporulation sigma fac 62.1 15 0.00033 34.8 5.2 34 288-321 125-158 (258)
98 PRK15044 transcriptional regul 61.6 29 0.00063 35.0 7.3 91 257-360 172-264 (295)
99 PRK06288 RNA polymerase sigma 60.6 14 0.0003 35.4 4.7 37 287-323 119-155 (268)
100 PRK07405 RNA polymerase sigma 60.2 17 0.00036 36.2 5.3 38 286-323 168-205 (317)
101 PRK12547 RNA polymerase sigma 58.2 14 0.0003 32.2 3.9 40 326-365 4-43 (164)
102 PRK11511 DNA-binding transcrip 58.1 46 0.00099 28.5 7.0 38 288-325 11-48 (127)
103 smart00342 HTH_ARAC helix_turn 57.4 36 0.00079 25.1 5.6 59 302-364 1-62 (84)
104 TIGR02997 Sig70-cyanoRpoD RNA 56.8 21 0.00046 34.8 5.3 38 286-323 161-198 (298)
105 TIGR02999 Sig-70_X6 RNA polyme 55.0 22 0.00048 31.1 4.7 40 326-365 15-59 (183)
106 PRK10219 DNA-binding transcrip 55.0 52 0.0011 26.8 6.6 38 288-325 7-44 (107)
107 COG0568 RpoD DNA-directed RNA 53.7 22 0.00048 36.5 5.0 41 281-321 184-224 (342)
108 TIGR02980 SigBFG RNA polymeras 51.8 20 0.00042 33.1 4.0 33 289-321 93-125 (227)
109 PRK07500 rpoH2 RNA polymerase 51.3 46 0.001 32.6 6.7 63 256-321 104-167 (289)
110 PRK08241 RNA polymerase factor 51.1 23 0.0005 34.6 4.5 40 326-365 17-56 (339)
111 PRK12523 RNA polymerase sigma 50.9 21 0.00045 31.3 3.8 40 326-365 8-47 (172)
112 PRK09651 RNA polymerase sigma 50.7 20 0.00044 31.5 3.8 40 326-365 8-47 (172)
113 TIGR01446 DnaD_dom DnaD and ph 50.1 23 0.00049 27.3 3.5 58 297-358 7-71 (73)
114 PRK12533 RNA polymerase sigma 48.6 18 0.0004 33.8 3.3 40 326-365 16-55 (216)
115 TIGR03001 Sig-70_gmx1 RNA poly 47.8 24 0.00052 33.7 4.0 51 315-365 25-76 (244)
116 PRK09649 RNA polymerase sigma 47.0 45 0.00097 29.8 5.4 39 326-365 22-60 (185)
117 PF04967 HTH_10: HTH DNA bindi 46.8 40 0.00088 25.7 4.3 48 270-327 1-48 (53)
118 TIGR02947 SigH_actino RNA poly 46.0 18 0.00039 32.3 2.8 40 326-365 9-48 (193)
119 TIGR02984 Sig-70_plancto1 RNA 43.7 19 0.00042 31.4 2.5 28 350-377 33-67 (189)
120 PRK05572 sporulation sigma fac 43.1 46 0.001 31.4 5.1 34 287-320 119-152 (252)
121 PRK12516 RNA polymerase sigma 42.2 34 0.00073 30.9 3.9 40 326-365 8-47 (187)
122 COG1476 Predicted transcriptio 41.8 62 0.0014 26.2 4.9 50 303-362 15-64 (68)
123 PRK12517 RNA polymerase sigma 41.2 29 0.00064 31.2 3.4 42 324-365 19-60 (188)
124 PRK09685 DNA-binding transcrip 41.2 2.8E+02 0.0061 26.3 10.1 37 288-324 199-236 (302)
125 PRK09645 RNA polymerase sigma 40.2 33 0.00072 29.8 3.4 40 326-365 7-46 (173)
126 PHA01976 helix-turn-helix prot 39.6 86 0.0019 23.3 5.2 47 303-359 16-62 (67)
127 PRK06986 fliA flagellar biosyn 39.6 38 0.00083 31.5 3.9 34 288-321 97-130 (236)
128 PRK15186 AraC family transcrip 38.4 79 0.0017 31.4 6.1 67 291-361 186-254 (291)
129 TIGR02941 Sigma_B RNA polymera 38.2 40 0.00087 31.8 3.9 35 288-322 118-152 (255)
130 PF12324 HTH_15: Helix-turn-he 37.5 35 0.00075 28.3 2.9 26 300-325 36-61 (77)
131 TIGR03764 ICE_PFGI_1_parB inte 37.3 2.1E+02 0.0046 28.6 8.7 22 346-367 200-222 (258)
132 PRK05657 RNA polymerase sigma 37.0 64 0.0014 32.3 5.3 36 288-323 175-210 (325)
133 TIGR03826 YvyF flagellar opero 35.5 59 0.0013 29.4 4.3 33 295-327 39-71 (137)
134 PRK15121 right oriC-binding tr 34.8 1.8E+02 0.004 27.9 7.8 38 288-325 7-44 (289)
135 PRK13503 transcriptional activ 34.3 78 0.0017 29.5 5.1 35 290-324 175-209 (278)
136 COG4977 Transcriptional regula 33.7 64 0.0014 33.0 4.7 51 291-341 225-289 (328)
137 KOG0197 Tyrosine kinases [Sign 33.0 19 0.00041 38.5 0.8 69 246-345 277-345 (468)
138 PRK13239 alkylmercury lyase; P 32.5 53 0.0011 31.6 3.7 27 299-325 33-59 (206)
139 COG4367 Uncharacterized protei 32.0 1.3E+02 0.0029 25.9 5.5 45 291-335 11-62 (97)
140 PRK12529 RNA polymerase sigma 31.8 55 0.0012 29.0 3.5 42 324-365 9-52 (178)
141 PF13404 HTH_AsnC-type: AsnC-t 31.1 77 0.0017 22.8 3.5 24 302-325 17-40 (42)
142 PRK15185 transcriptional regul 30.4 1.4E+02 0.003 30.5 6.4 68 289-360 209-278 (309)
143 PRK12525 RNA polymerase sigma 29.8 99 0.0021 27.0 4.7 38 328-365 9-46 (168)
144 PRK06596 RNA polymerase factor 28.7 1.6E+02 0.0035 28.7 6.4 24 300-323 149-172 (284)
145 COG3413 Predicted DNA binding 26.1 1.8E+02 0.0039 27.0 6.0 57 269-338 155-211 (215)
146 PRK12544 RNA polymerase sigma 23.5 77 0.0017 29.2 3.0 35 331-365 21-55 (206)
147 TIGR02844 spore_III_D sporulat 23.5 2.6E+02 0.0056 23.1 5.7 37 287-326 7-43 (80)
148 PRK06704 RNA polymerase factor 23.2 94 0.002 29.8 3.6 47 318-365 8-54 (228)
149 PRK12519 RNA polymerase sigma 23.2 3.3E+02 0.0071 24.1 6.9 29 301-329 156-184 (194)
150 PF02796 HTH_7: Helix-turn-hel 22.8 99 0.0021 22.1 2.8 22 303-324 22-43 (45)
151 PRK04217 hypothetical protein; 22.8 2.5E+02 0.0054 24.5 5.8 25 302-326 58-82 (110)
152 PRK12523 RNA polymerase sigma 21.8 3.8E+02 0.0083 23.3 7.0 31 302-332 135-166 (172)
153 PRK12527 RNA polymerase sigma 21.1 5.1E+02 0.011 22.1 7.5 30 300-329 119-148 (159)
154 PRK10371 DNA-binding transcrip 21.0 2.2E+02 0.0047 27.8 5.7 37 289-325 194-230 (302)
155 PF01381 HTH_3: Helix-turn-hel 20.9 1.5E+02 0.0033 21.0 3.5 39 303-348 10-48 (55)
156 TIGR02394 rpoS_proteo RNA poly 20.1 2E+02 0.0043 27.9 5.2 33 290-322 137-169 (285)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=99.97 E-value=1.2e-30 Score=263.29 Aligned_cols=126 Identities=38% Similarity=0.572 Sum_probs=118.6
Q ss_pred CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHH--------------------HHHHHHHHHhhcCCCcchHHHHHHh
Q 017044 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR--------------------LEKEKSKLQSQFGREPTLIEWAKAI 312 (378)
Q Consensus 253 ~~D~l~~YLkei~~~~LLTaeEE~eL~~~IQ~l~~--------------------LEkik~~Le~~lGrePT~~EWA~Aa 312 (378)
.+|+++.||++||+.+|||++||++|+++||.+++ |++++.+|++++|++||..|||.++
T Consensus 58 ~~d~v~~yl~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~~~ 137 (415)
T PRK07598 58 STDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTA 137 (415)
T ss_pred CCChHHHHHHhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHHHh
Confidence 57999999999999999999999999999999999 9999999999999999999999887
Q ss_pred ccchhhhhhhc----------------------cccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-----
Q 017044 313 GLSCRDLKSEL----------------------HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT----- 365 (378)
Q Consensus 313 G~s~~eLr~~L----------------------~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG----- 365 (378)
|+++.+|+.+| ..|+.|+++||++|+|||++||++|.|+|+.++||||||+||
T Consensus 138 ~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~rav 217 (415)
T PRK07598 138 DISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAV 217 (415)
T ss_pred CCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHH
Confidence 77766666665 578899999999999999999999999999999999999999
Q ss_pred --cccCCCccccccC
Q 017044 366 --FNFGKWLLLFQYH 378 (378)
Q Consensus 366 --FDpsRG~rFstY~ 378 (378)
|||+||++|+||.
T Consensus 218 ekFDp~rG~rFSTYa 232 (415)
T PRK07598 218 EKFDPTKGYRFSTYA 232 (415)
T ss_pred HHcCcccCCCHHHHH
Confidence 9999999999994
No 2
>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=99.95 E-value=2.2e-28 Score=234.49 Aligned_cols=124 Identities=44% Similarity=0.658 Sum_probs=121.0
Q ss_pred cHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccccHHHHHHHH
Q 017044 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI 334 (378)
Q Consensus 255 D~l~~YLkei~~~~LLTaeEE~eL~~~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI 334 (378)
|++..||++++++|+||++||++|+++|+.++.+++++.+|++.+|++||..+||+++|++..+|..++..|..|+++||
T Consensus 1 ~~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv 80 (298)
T TIGR02997 1 DLVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMI 80 (298)
T ss_pred CcHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHH
Confidence 46788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCccccccC
Q 017044 335 NANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQYH 378 (378)
Q Consensus 335 ~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY~ 378 (378)
.+|+|+|++||++|.|+|++++||||||++| |||++|++|+||.
T Consensus 81 ~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya 131 (298)
T TIGR02997 81 KANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYA 131 (298)
T ss_pred HHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHH
Confidence 9999999999999999999999999999999 9999999999993
No 3
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=99.94 E-value=1.3e-26 Score=231.20 Aligned_cols=125 Identities=36% Similarity=0.635 Sum_probs=122.9
Q ss_pred CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccccHHHHHH
Q 017044 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332 (378)
Q Consensus 253 ~~D~l~~YLkei~~~~LLTaeEE~eL~~~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G~~ARek 332 (378)
..|++..||++++++++||++||++|+++|+.++.|++++.+|++.+|++|+..+||+++|++..+|++++..|..|+++
T Consensus 61 ~~d~l~~Yl~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~ 140 (373)
T PRK07406 61 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEK 140 (373)
T ss_pred CCCHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHH
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 333 LINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 333 LI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
||.+|+++|++||++|.++|++++||||||+|| |||++|++|+||
T Consensus 141 Li~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTY 192 (373)
T PRK07406 141 MVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTY 192 (373)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHH
Confidence 999999999999999999999999999999999 999999999999
No 4
>PRK05949 RNA polymerase sigma factor; Validated
Probab=99.93 E-value=4.3e-26 Score=223.22 Aligned_cols=126 Identities=37% Similarity=0.560 Sum_probs=123.3
Q ss_pred CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccccHHHHHH
Q 017044 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332 (378)
Q Consensus 253 ~~D~l~~YLkei~~~~LLTaeEE~eL~~~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G~~ARek 332 (378)
..|++..||++++++|+||++||++|+++||.++.+++.+..|+..+|++|+..+||.++|++..+|...+..|..|+++
T Consensus 16 ~~d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~~ 95 (327)
T PRK05949 16 SADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQK 95 (327)
T ss_pred CCCHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHHH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCccccccC
Q 017044 333 LINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQYH 378 (378)
Q Consensus 333 LI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY~ 378 (378)
||++|+++|++||++|.+.|++++||||||+|| |||++|++|+||.
T Consensus 96 Li~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa 148 (327)
T PRK05949 96 MIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYA 148 (327)
T ss_pred HHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhh
Confidence 999999999999999999999999999999999 9999999999994
No 5
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=99.92 E-value=2.5e-25 Score=216.46 Aligned_cols=126 Identities=38% Similarity=0.547 Sum_probs=122.9
Q ss_pred CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccccHHHHHH
Q 017044 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332 (378)
Q Consensus 253 ~~D~l~~YLkei~~~~LLTaeEE~eL~~~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G~~ARek 332 (378)
.+|++..||++++++|+||++||++|+++|+.++.+++++..|++++|++|+..+||+++|++..+|..++..|..|+++
T Consensus 6 ~~~~~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~ 85 (317)
T PRK07405 6 STDLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRK 85 (317)
T ss_pred CCcHHHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHH
Confidence 36789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCccccccC
Q 017044 333 LINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQYH 378 (378)
Q Consensus 333 LI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY~ 378 (378)
||..|+++|+++|++|.+.|.+++||||||++| |||++|++|+||.
T Consensus 86 L~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa 138 (317)
T PRK07405 86 MVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYA 138 (317)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHH
Confidence 999999999999999999999999999999999 9999999999993
No 6
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=99.89 E-value=7.3e-24 Score=218.88 Aligned_cols=114 Identities=33% Similarity=0.439 Sum_probs=98.3
Q ss_pred CCCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccccHHHHH
Q 017044 252 DRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSRE 331 (378)
Q Consensus 252 ~~~D~l~~YLkei~~~~LLTaeEE~eL~~~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G~~ARe 331 (378)
...|+++.||++++++++||++||++|+++|+.+..++.. +.+ ..+|+ .....+|+.+++.|..||+
T Consensus 208 ~~~d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~---~~~-------~~~~~---~~~~~~l~~~~~~g~~Ar~ 274 (509)
T PRK05901 208 ATADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEEL---LAE-------GEKLD---PELRRDLQWIGRDGKRAKN 274 (509)
T ss_pred ccccHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhh---hhh-------cccch---hhhhhhhhhhccchHHHHH
Confidence 3678999999999999999999999999999987443331 211 12243 2256889999999999999
Q ss_pred HHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCccccccC
Q 017044 332 KLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQYH 378 (378)
Q Consensus 332 kLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY~ 378 (378)
+||.+|||||++||++|.|+|++|+||||||||| |||+||++|+||.
T Consensus 275 ~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA 328 (509)
T PRK05901 275 HLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYA 328 (509)
T ss_pred HHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhh
Confidence 9999999999999999999999999999999999 9999999999994
No 7
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=99.88 E-value=5.3e-23 Score=203.68 Aligned_cols=126 Identities=33% Similarity=0.463 Sum_probs=111.8
Q ss_pred CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHh-hcCCCcchH---------------HHHHHhccch
Q 017044 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS-QFGREPTLI---------------EWAKAIGLSC 316 (378)
Q Consensus 253 ~~D~l~~YLkei~~~~LLTaeEE~eL~~~IQ~l~~LEkik~~Le~-~lGrePT~~---------------EWA~AaG~s~ 316 (378)
..|.+..|+.+++..+++++++|.++...++....+......|.. .+|+.|+.. +|+.....++
T Consensus 7 ~~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~E 86 (342)
T COG0568 7 SADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEE 86 (342)
T ss_pred chhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHH
Confidence 467899999999999999999999999999998888777888877 667888876 5655555544
Q ss_pred -hhhhhhccccHH---HHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCccccccC
Q 017044 317 -RDLKSELHSGNS---SREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQYH 378 (378)
Q Consensus 317 -~eLr~~L~~G~~---ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY~ 378 (378)
..|..++..|.. |+.+||.+|||||++|||+|.|+|++|.||||||||| |||+|||+|+||.
T Consensus 87 e~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA 159 (342)
T COG0568 87 EKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYA 159 (342)
T ss_pred HHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHH
Confidence 778888888865 9999999999999999999999999999999999999 9999999999993
No 8
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=99.83 E-value=8.7e-21 Score=186.03 Aligned_cols=113 Identities=35% Similarity=0.498 Sum_probs=97.8
Q ss_pred CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccccHHHHHH
Q 017044 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332 (378)
Q Consensus 253 ~~D~l~~YLkei~~~~LLTaeEE~eL~~~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G~~ARek 332 (378)
..|++..||++++++++||++||++|+++|+.+..++.. |+..+|+... ...+|+.+++.|..|+++
T Consensus 24 ~~~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~~ 90 (324)
T PRK07921 24 AADLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARRH 90 (324)
T ss_pred CCChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHHH
Confidence 357899999999999999999999999999988765544 1222332111 456889999999999999
Q ss_pred HHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCccccccC
Q 017044 333 LINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQYH 378 (378)
Q Consensus 333 LI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY~ 378 (378)
||.+|+++|+++|++|.|+|++++||||||+|| |||++|++|+||.
T Consensus 91 Lv~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA 143 (324)
T PRK07921 91 LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYA 143 (324)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHH
Confidence 999999999999999999999999999999999 9999999999993
No 9
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=99.67 E-value=1e-16 Score=159.17 Aligned_cols=89 Identities=40% Similarity=0.673 Sum_probs=82.5
Q ss_pred CCCCCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccccHHH
Q 017044 250 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSS 329 (378)
Q Consensus 250 ~~~~~D~l~~YLkei~~~~LLTaeEE~eL~~~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G~~A 329 (378)
+...+|+++.||++++++|+||++||.+|+++++. | +..|
T Consensus 91 ~~~~~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~---------------G-------------------------d~~A 130 (367)
T PRK09210 91 GVKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEE---------------G-------------------------DEEA 130 (367)
T ss_pred ccccCcHHHHHHHHhhccCCCCHHHHHHHHHHHHh---------------h-------------------------HHHH
Confidence 34467899999999999999999999999998886 3 3679
Q ss_pred HHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCccccccC
Q 017044 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQYH 378 (378)
Q Consensus 330 RekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY~ 378 (378)
+++||..|+++|++||++|.++|+.++||||||+|| |||++|++|+||.
T Consensus 131 ~~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA 186 (367)
T PRK09210 131 KQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYA 186 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHH
Confidence 999999999999999999999999999999999999 9999999999993
No 10
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=99.66 E-value=7.4e-17 Score=169.52 Aligned_cols=52 Identities=31% Similarity=0.625 Sum_probs=50.2
Q ss_pred HHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCccccccC
Q 017044 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQYH 378 (378)
Q Consensus 327 ~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY~ 378 (378)
..|+++||.+|||||++||++|.++|++|+||||||||| |||+||++|+||.
T Consensus 379 ~~a~~~Li~~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA 437 (619)
T PRK05658 379 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 437 (619)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHh
Confidence 478999999999999999999999999999999999999 9999999999994
No 11
>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=99.58 E-value=3e-15 Score=141.95 Aligned_cols=84 Identities=26% Similarity=0.510 Sum_probs=77.0
Q ss_pred HHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccccHHHHHHHHH
Q 017044 256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 335 (378)
Q Consensus 256 ~l~~YLkei~~~~LLTaeEE~eL~~~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~ 335 (378)
++..||++++++++|+.++|.+|+.++.. .| +..|+++||.
T Consensus 2 ~~~~yl~~~~~~~~l~~~~e~~l~~~~~~--------------~g-------------------------d~~a~~~Lv~ 42 (270)
T TIGR02392 2 SLDAYIRAVNRIPMLTPEEEYQLAKRLRE--------------HG-------------------------DLDAAKKLVL 42 (270)
T ss_pred hHHHHHHHHhcCCCCCHHHHHHHHHHHHH--------------CC-------------------------CHHHHHHHHH
Confidence 67889999999999999999999987532 13 5789999999
Q ss_pred HhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCccccccC
Q 017044 336 ANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQYH 378 (378)
Q Consensus 336 sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY~ 378 (378)
.|+++|.++|++|.++|.+++||||||++| |||++|++|+||.
T Consensus 43 ~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA 92 (270)
T TIGR02392 43 SHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFA 92 (270)
T ss_pred HhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhh
Confidence 999999999999999999999999999999 9999999999994
No 12
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=99.58 E-value=3.8e-15 Score=142.97 Aligned_cols=88 Identities=26% Similarity=0.472 Sum_probs=80.2
Q ss_pred CCCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccccHHHHH
Q 017044 252 DRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSRE 331 (378)
Q Consensus 252 ~~~D~l~~YLkei~~~~LLTaeEE~eL~~~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G~~ARe 331 (378)
.+.+++..|++++++.++|+.++|.+|+.+++. .| +..|++
T Consensus 11 ~~~~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~--------------~G-------------------------d~~a~~ 51 (284)
T PRK06596 11 SPEGNLDAYIQAVNKIPMLTAEEEYMLAKRLRE--------------HG-------------------------DLEAAK 51 (284)
T ss_pred CCccHHHHHHHHHhccCCCCHHHHHHHHHHHHH--------------cC-------------------------CHHHHH
Confidence 356899999999999999999999999987542 14 578999
Q ss_pred HHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCccccccC
Q 017044 332 KLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQYH 378 (378)
Q Consensus 332 kLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY~ 378 (378)
.||..|+++|.+||++|.+.|++++||||||++| |||++|++|+||.
T Consensus 52 ~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA 105 (284)
T PRK06596 52 QLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFA 105 (284)
T ss_pred HHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHH
Confidence 9999999999999999999999999999999999 9999999999993
No 13
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=99.49 E-value=1.4e-14 Score=137.76 Aligned_cols=52 Identities=25% Similarity=0.491 Sum_probs=50.1
Q ss_pred HHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCccccccC
Q 017044 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQYH 378 (378)
Q Consensus 327 ~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY~ 378 (378)
..+|++||.+|+|||++||++|.++|++++||||||+|| |||++|++|+||.
T Consensus 39 ~~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA 97 (264)
T PRK07122 39 QRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFA 97 (264)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHH
Confidence 569999999999999999999999999999999999999 9999999999993
No 14
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=99.45 E-value=1.6e-13 Score=132.19 Aligned_cols=86 Identities=21% Similarity=0.343 Sum_probs=78.7
Q ss_pred CcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccccHHHHHHH
Q 017044 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL 333 (378)
Q Consensus 254 ~D~l~~YLkei~~~~LLTaeEE~eL~~~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G~~ARekL 333 (378)
.+.++.||+++.++++||.++|.+|+++++.. | +..|+++|
T Consensus 5 ~~~~~~y~~~~~~~~~l~~~~e~~L~~~~~~~--------------g-------------------------d~~A~~~L 45 (289)
T PRK07500 5 ASADRSMIRSAMKAPYLEREEEHALAYRWKDH--------------R-------------------------DEDALHRI 45 (289)
T ss_pred hhHHHHHHHHHhcCCCCCHHHHHHHHHHHHHC--------------C-------------------------CHHHHHHH
Confidence 35678899999999999999999999887531 3 57899999
Q ss_pred HHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCccccccC
Q 017044 334 INANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQYH 378 (378)
Q Consensus 334 I~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY~ 378 (378)
|..|+++|.++|++|.+.|.+++||+|||++| |||++|.+|.||.
T Consensus 46 v~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya 97 (289)
T PRK07500 46 ISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYA 97 (289)
T ss_pred HHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHH
Confidence 99999999999999999999999999999998 9999999999994
No 15
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=99.32 E-value=2.9e-12 Score=125.80 Aligned_cols=85 Identities=33% Similarity=0.488 Sum_probs=79.9
Q ss_pred CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccccHHHHHH
Q 017044 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332 (378)
Q Consensus 253 ~~D~l~~YLkei~~~~LLTaeEE~eL~~~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G~~ARek 332 (378)
..|.++.|+.+|+..|+||+++|..|+.+++. | +..|++.
T Consensus 51 ~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~---------------G-------------------------d~~A~~~ 90 (325)
T PRK05657 51 VLDATQLYLNEIGYSPLLTAEEEVYFARRALR---------------G-------------------------DFAARQR 90 (325)
T ss_pred cccHHHHHHHHHhcCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHH
Confidence 46789999999999999999999999988876 4 5689999
Q ss_pred HHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 333 LINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 333 LI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
||..|+++|.++|++|.+.+.+.+||+|||+|| ||+++|++|+||
T Consensus 91 Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fsty 142 (325)
T PRK05657 91 MIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTY 142 (325)
T ss_pred HHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHH
Confidence 999999999999999999999999999999999 999999999998
No 16
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=99.27 E-value=1.1e-11 Score=118.30 Aligned_cols=90 Identities=31% Similarity=0.443 Sum_probs=82.5
Q ss_pred CCCCCCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccccHH
Q 017044 249 EGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNS 328 (378)
Q Consensus 249 ~~~~~~D~l~~YLkei~~~~LLTaeEE~eL~~~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G~~ 328 (378)
.+.-..|++.+||.+|+..+.|+.++|.+|+..++. | +..
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~---------------g-------------------------d~~ 46 (285)
T TIGR02394 7 TETRVADVTQLYLREIGFKPLLTAEEEIAYARRALA---------------G-------------------------DFE 46 (285)
T ss_pred cccCcchHHHHHHHHHhccCCCCHHHHHHHHHHHHc---------------C-------------------------CHH
Confidence 344468899999999999999999999999988876 4 478
Q ss_pred HHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCccccccC
Q 017044 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQYH 378 (378)
Q Consensus 329 ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY~ 378 (378)
|.+.||..+.++|..+|++|.+.+...+||+|||+|| |||++|++|.||.
T Consensus 47 a~~~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya 103 (285)
T TIGR02394 47 ARKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYA 103 (285)
T ss_pred HHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhh
Confidence 9999999999999999999999999999999999999 9999999999873
No 17
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=99.20 E-value=2e-11 Score=115.34 Aligned_cols=53 Identities=25% Similarity=0.323 Sum_probs=49.4
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCC-CCChhhHHHHhhcc-------cccCCCccccccC
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGR-GISLHDLLQVNQAT-------FNFGKWLLLFQYH 378 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~gr-Gls~eDLIQEG~iG-------FDpsRG~rFstY~ 378 (378)
+..|+++||..|++||++||++|.++ +.+++||||||+|| |||++|++|+||.
T Consensus 23 d~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya 83 (256)
T PRK07408 23 SIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFA 83 (256)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHH
Confidence 46899999999999999999999876 77899999999999 9999999999993
No 18
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=99.13 E-value=7.1e-11 Score=113.26 Aligned_cols=52 Identities=27% Similarity=0.463 Sum_probs=49.3
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCC-ChhhHHHHhhcc-------cccCCCccccccC
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGI-SLHDLLQVNQAT-------FNFGKWLLLFQYH 378 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGl-s~eDLIQEG~iG-------FDpsRG~rFstY~ 378 (378)
...++ +||+.|++||.+||++|.++|. .++||||.|||| |||++|.+|+||.
T Consensus 22 ~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA 81 (247)
T COG1191 22 DEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYA 81 (247)
T ss_pred CHHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHH
Confidence 46788 9999999999999999999998 999999999999 9999999999993
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=99.10 E-value=1.6e-10 Score=108.54 Aligned_cols=76 Identities=34% Similarity=0.536 Sum_probs=69.2
Q ss_pred ccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHH
Q 017044 263 GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVV 342 (378)
Q Consensus 263 ei~~~~LLTaeEE~eL~~~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVv 342 (378)
+.+++|+||+++|.+|+..++. | +..|+++|+..|+++|.
T Consensus 9 ~~~~~~~l~~~~~~~li~~~~~---------------g-------------------------d~~a~~~L~~~~~~~v~ 48 (254)
T TIGR02850 9 NTSKLPVLKNQEMRELFIRMQS---------------G-------------------------DTTAREKLINGNLRLVL 48 (254)
T ss_pred cccCCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHHHhHHHHH
Confidence 4578999999999999877764 3 46799999999999999
Q ss_pred HHHHhccCCCCChhhHHHHhhcc-------cccCCCccccccC
Q 017044 343 HVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQYH 378 (378)
Q Consensus 343 sIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY~ 378 (378)
++|++|.+.+.+.+||+|||++| |||++|.+|.||.
T Consensus 49 ~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl 91 (254)
T TIGR02850 49 SVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYA 91 (254)
T ss_pred HHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHH
Confidence 99999999999999999999998 9999999999983
No 20
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=99.07 E-value=2.7e-10 Score=107.12 Aligned_cols=76 Identities=34% Similarity=0.562 Sum_probs=68.3
Q ss_pred ccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHH
Q 017044 263 GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVV 342 (378)
Q Consensus 263 ei~~~~LLTaeEE~eL~~~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVv 342 (378)
+..++|+|+++|+..|+..++. | +..++++||..|+++|.
T Consensus 12 ~~~~~~~l~~~~~~~l~~~~~~---------------g-------------------------d~~a~~~l~~~~~~~v~ 51 (258)
T PRK08215 12 NTSKLPVLKNEEMRELFERMQN---------------G-------------------------DKEAREKLINGNLRLVL 51 (258)
T ss_pred cCCCCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHHHHHHHHH
Confidence 3466779999999999877764 3 56899999999999999
Q ss_pred HHHHhccCCCCChhhHHHHhhcc-------cccCCCccccccC
Q 017044 343 HVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQYH 378 (378)
Q Consensus 343 sIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY~ 378 (378)
.+|++|.+.+.+.+||+|||++| |||++|++|.||.
T Consensus 52 ~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l 94 (258)
T PRK08215 52 SVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYA 94 (258)
T ss_pred HHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHH
Confidence 99999999999999999999998 9999999999983
No 21
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=99.00 E-value=2.7e-10 Score=107.88 Aligned_cols=53 Identities=25% Similarity=0.204 Sum_probs=48.2
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccC---CCCChhhHHHHhhcc-------cccCCCccccccC
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQG---RGISLHDLLQVNQAT-------FNFGKWLLLFQYH 378 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~g---rGls~eDLIQEG~iG-------FDpsRG~rFstY~ 378 (378)
+..||++||..|++||.+||++|.+ .+++++||+|+|+|| |||++|++|.||.
T Consensus 21 ~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya 83 (257)
T PRK05911 21 EIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYA 83 (257)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHH
Confidence 5679999999999999999999862 356899999999999 9999999999993
No 22
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=98.90 E-value=2.2e-09 Score=101.72 Aligned_cols=76 Identities=22% Similarity=0.243 Sum_probs=67.1
Q ss_pred cCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHH
Q 017044 264 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH 343 (378)
Q Consensus 264 i~~~~LLTaeEE~eL~~~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvs 343 (378)
.|++++||.++|.+|+++++.. | +..+.+.|+..|++||..
T Consensus 6 ~~~~~~~~~~~e~~l~~~~~~~--------------~-------------------------d~~a~~~l~~~y~~lv~~ 46 (268)
T PRK06288 6 SGKIPKYAQQDETELWREYKKT--------------G-------------------------DPKIREYLILKYSPLVKY 46 (268)
T ss_pred cCCCccccchHHHHHHHHHHHc--------------C-------------------------CHHHHHHHHHHHHHHHHH
Confidence 4789999999999999887751 2 578999999999999999
Q ss_pred HHHhcc-C--CCCChhhHHHHhhcc-------cccCCCccccccC
Q 017044 344 VAKQYQ-G--RGISLHDLLQVNQAT-------FNFGKWLLLFQYH 378 (378)
Q Consensus 344 IAKkY~-g--rGls~eDLIQEG~iG-------FDpsRG~rFstY~ 378 (378)
+|++|. | .+.+.+||+|||.+| |||.+|++|.||.
T Consensus 47 ~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~ 91 (268)
T PRK06288 47 VAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYA 91 (268)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHH
Confidence 999986 3 567899999999999 9999999999983
No 23
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=98.80 E-value=1.3e-08 Score=94.26 Aligned_cols=82 Identities=28% Similarity=0.476 Sum_probs=75.1
Q ss_pred HHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccccHHHHHHHHH
Q 017044 256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 335 (378)
Q Consensus 256 ~l~~YLkei~~~~LLTaeEE~eL~~~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~ 335 (378)
++..|+.+++..++||+++|.+|...++. | +..|.+.|+.
T Consensus 17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~---------------g-------------------------d~~a~~~l~~ 56 (233)
T PRK05803 17 FLVSYVKNNSFPQPLSEEEERKYLELMKE---------------G-------------------------DEEARNILIE 56 (233)
T ss_pred HHHHHHHHhcccCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHH
Confidence 78889999999999999999988877664 3 4688999999
Q ss_pred HhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 336 ANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 336 sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
.+.++|..+|.+|.|.+.+.+||+|||.|| |++++|..|.||
T Consensus 57 ~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~w 105 (233)
T PRK05803 57 RNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATY 105 (233)
T ss_pred HhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHH
Confidence 999999999999999999999999999998 899999999988
No 24
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=98.70 E-value=3.3e-08 Score=92.62 Aligned_cols=72 Identities=24% Similarity=0.326 Sum_probs=64.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHh
Q 017044 268 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQ 347 (378)
Q Consensus 268 ~LLTaeEE~eL~~~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKk 347 (378)
+.||.++|.+|..+++.+ | +..|.++|+..|.++|+.+|++
T Consensus 8 ~~l~~~~~~~li~~~~~~--------------g-------------------------d~~a~~~l~~~y~~~v~~~a~~ 48 (255)
T TIGR02941 8 TNLTKEDVIQWIAEFQQN--------------Q-------------------------NGEAQEKLVDHYQNLVYSIAYK 48 (255)
T ss_pred CCCCHHHHHHHHHHHHHC--------------C-------------------------CHHHHHHHHHHhHHHHHHHHHH
Confidence 568999999888777751 2 4679999999999999999999
Q ss_pred ccCCCCChhhHHHHhhcc-------cccCCCccccccC
Q 017044 348 YQGRGISLHDLLQVNQAT-------FNFGKWLLLFQYH 378 (378)
Q Consensus 348 Y~grGls~eDLIQEG~iG-------FDpsRG~rFstY~ 378 (378)
|.+.+...+||+|||++| ||+++|..|.||.
T Consensus 49 ~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl 86 (255)
T TIGR02941 49 YSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFA 86 (255)
T ss_pred HhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHH
Confidence 999999999999999998 9999999999983
No 25
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=98.60 E-value=9.3e-08 Score=89.73 Aligned_cols=71 Identities=24% Similarity=0.236 Sum_probs=63.9
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHh
Q 017044 268 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQ 347 (378)
Q Consensus 268 ~LLTaeEE~eL~~~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKk 347 (378)
+.|++++|.+|..+++.. | +..|.+.|+..|.++|..+|++
T Consensus 8 ~~l~~~e~~~li~~~~~~--------------g-------------------------d~~a~~~l~~~~~~~v~~~a~~ 48 (257)
T PRK08583 8 TKLTKEEVNKWIAEYQEN--------------Q-------------------------DEEAQEKLVKHYKNLVESLAYK 48 (257)
T ss_pred CcCChHHHHHHHHHHHHc--------------C-------------------------CHHHHHHHHHHHHHHHHHHHHH
Confidence 779999999888777641 2 4679999999999999999999
Q ss_pred ccCCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 348 YQGRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 348 Y~grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
|.+.+.+.+||+|||++| ||+++|..|.||
T Consensus 49 ~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~ty 85 (257)
T PRK08583 49 YSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAF 85 (257)
T ss_pred HhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHH
Confidence 999999999999999998 999999999988
No 26
>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=98.47 E-value=1.7e-07 Score=86.35 Aligned_cols=53 Identities=32% Similarity=0.522 Sum_probs=50.5
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCccccccC
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQYH 378 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY~ 378 (378)
+..|.++|+..|.++|.++|++|.+.+.+.+||+|||.+| |||.+|.+|.||.
T Consensus 9 d~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl 68 (231)
T TIGR02885 9 DKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYA 68 (231)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHH
Confidence 5789999999999999999999999999999999999998 9999999999983
No 27
>PRK05572 sporulation sigma factor SigF; Validated
Probab=98.44 E-value=5.6e-07 Score=84.58 Aligned_cols=78 Identities=29% Similarity=0.466 Sum_probs=68.5
Q ss_pred HhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHH
Q 017044 261 LWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRL 340 (378)
Q Consensus 261 Lkei~~~~LLTaeEE~eL~~~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRL 340 (378)
+++-...|.||.+++.+|...++. | +..|.+.|+..+.++
T Consensus 5 ~~~~~~~~~l~~~~~~~li~~~~~---------------g-------------------------d~~a~~~L~~~y~~~ 44 (252)
T PRK05572 5 VKNKKKKPQLKDEENKELIKKSQD---------------G-------------------------DQEARDTLVEKNLRL 44 (252)
T ss_pred hccCcCCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHHHhHHH
Confidence 355677899999999888766553 3 467899999999999
Q ss_pred HHHHHHhccCCCCChhhHHHHhhcc-------cccCCCccccccC
Q 017044 341 VVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQYH 378 (378)
Q Consensus 341 VvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY~ 378 (378)
|..+|++|.+.+.+.+||+|||.+| |++.+|..|.||.
T Consensus 45 v~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl 89 (252)
T PRK05572 45 VWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYA 89 (252)
T ss_pred HHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHH
Confidence 9999999999999999999999998 9999999999983
No 28
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=98.35 E-value=7.2e-07 Score=83.78 Aligned_cols=53 Identities=19% Similarity=0.221 Sum_probs=48.9
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccC---CCCChhhHHHHhhcc-------cccCCCccccccC
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQG---RGISLHDLLQVNQAT-------FNFGKWLLLFQYH 378 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~g---rGls~eDLIQEG~iG-------FDpsRG~rFstY~ 378 (378)
+..|.++|+..|.++|..+|++|.+ .+...+||+|||++| |||++|.+|.||.
T Consensus 20 d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl 82 (251)
T PRK07670 20 DPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYA 82 (251)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHH
Confidence 5789999999999999999999965 688999999999998 9999999999983
No 29
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=98.34 E-value=4.3e-07 Score=85.08 Aligned_cols=51 Identities=24% Similarity=0.233 Sum_probs=44.7
Q ss_pred HHHHHHHHHHhHHHHHHHHHhccCC---CCChhhHHHHhhcc-------cccCCCccccccC
Q 017044 327 NSSREKLINANLRLVVHVAKQYQGR---GISLHDLLQVNQAT-------FNFGKWLLLFQYH 378 (378)
Q Consensus 327 ~~ARekLI~sNLRLVvsIAKkY~gr---Gls~eDLIQEG~iG-------FDpsRG~rFstY~ 378 (378)
..-++.||..|++||.+||++|.++ +++.+||||||+|| |||.+| .|.||.
T Consensus 14 ~~~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa 74 (231)
T PRK12427 14 PQEEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYA 74 (231)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHH
Confidence 3567789999999999999999854 57999999999999 998777 899993
No 30
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPro: IPR009042 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....
Probab=98.10 E-value=9.2e-07 Score=62.20 Aligned_cols=35 Identities=40% Similarity=0.439 Sum_probs=31.0
Q ss_pred CcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHH
Q 017044 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRL 288 (378)
Q Consensus 254 ~D~l~~YLkei~~~~LLTaeEE~eL~~~IQ~l~~L 288 (378)
+|+++.||++|++++|||++||++|+++|+.+-..
T Consensus 1 ~D~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~~~ 35 (37)
T PF00140_consen 1 SDSLRLYLKEIGRYPLLTAEEEIELARRIRKGDEA 35 (37)
T ss_dssp HHHHHHHHHHHHHS-EETTHHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHHh
Confidence 37999999999999999999999999999987543
No 31
>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=97.98 E-value=2.4e-05 Score=72.59 Aligned_cols=82 Identities=27% Similarity=0.439 Sum_probs=69.2
Q ss_pred HHHHHHh-ccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccccHHHHHHHH
Q 017044 256 PLRLFLW-GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI 334 (378)
Q Consensus 256 ~l~~YLk-ei~~~~LLTaeEE~eL~~~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI 334 (378)
++-.|+. .-+..+.|++.+|..|...++. | +..|.+.|+
T Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~li~~~~~---------------g-------------------------d~~af~~l~ 54 (227)
T TIGR02846 15 FLVGYVTNNGSFPQPLSEEEEKKYLDRLKE---------------G-------------------------DEEARNVLI 54 (227)
T ss_pred HHHHHHHHHHhCCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHH
Confidence 3444664 4466778999999999877775 4 467889999
Q ss_pred HHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 335 NANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 335 ~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
..+.++|..+|.+|.+...+.+||+||+.++ |++++|..|.||
T Consensus 55 ~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~tw 104 (227)
T TIGR02846 55 ERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATY 104 (227)
T ss_pred HHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHH
Confidence 9999999999999999899999999999997 899999888887
No 32
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=97.82 E-value=5.6e-05 Score=69.92 Aligned_cols=52 Identities=37% Similarity=0.604 Sum_probs=48.1
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
+..|.+.|+..+.++|..+|++|.+.+.+.+||+||+.++ |++.++++|.||
T Consensus 50 d~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~tw 108 (234)
T PRK08301 50 DEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATY 108 (234)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHH
Confidence 4678999999999999999999999999999999999997 899888888887
No 33
>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=97.54 E-value=0.00027 Score=65.90 Aligned_cols=52 Identities=37% Similarity=0.623 Sum_probs=48.3
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
+..|.+.|+..+.++|..++++|.+.+.+-+||+||+.++ |++.+|+.|.||
T Consensus 50 d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~w 108 (234)
T TIGR02835 50 DESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATY 108 (234)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHH
Confidence 5688999999999999999999999999999999999997 898888888887
No 34
>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=97.47 E-value=8.8e-05 Score=55.21 Aligned_cols=45 Identities=18% Similarity=0.211 Sum_probs=42.0
Q ss_pred HHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 333 LINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 333 LI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
|++.+.++|..+|.+|.+.+.+.+|++||+.++ ||+++|..|.+|
T Consensus 1 L~~~~~~~l~~~~~~~~~~~~~~eD~~qe~~~~l~~~~~~~~~~~~~~~~~~ 52 (71)
T PF04542_consen 1 LYERYYPLLYRYARRYTGDPEDAEDLVQEAFIKLWRAIDSYDPDRGDSFRAW 52 (71)
T ss_dssp HHHHTHHHHHHHHHTCTTCSSHHHHHHHHHHHHHHHHHHHTSTTSSSHHHHH
T ss_pred CHHHHHHHHHHHHHHHhCCHhhHHHHhhHHHHHHHhhhhcccccccCCHHHH
Confidence 688999999999999999999999999999998 899999888776
No 35
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=97.18 E-value=0.00033 Score=74.71 Aligned_cols=35 Identities=31% Similarity=0.482 Sum_probs=33.2
Q ss_pred CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHH
Q 017044 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR 287 (378)
Q Consensus 253 ~~D~l~~YLkei~~~~LLTaeEE~eL~~~IQ~l~~ 287 (378)
.+|||++||++||..+|||+++|++++++|..|.+
T Consensus 102 t~DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~ 136 (619)
T PRK05658 102 TDDPVRMYLREMGTVELLTREGEIEIAKRIEAGEN 136 (619)
T ss_pred CCChHHHHHHHhccCcCCCcHHHHHHHHHHHHHHH
Confidence 58999999999999999999999999999998875
No 36
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=97.01 E-value=0.00093 Score=59.88 Aligned_cols=53 Identities=19% Similarity=0.192 Sum_probs=49.0
Q ss_pred ccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 325 ~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
.+..+-+.|+..+.++|..+|.+|.+.+.+.+||+||+.++ |++.+|..|.||
T Consensus 21 ~d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~tw 80 (208)
T PRK08295 21 GDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSF 80 (208)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHH
Confidence 35779999999999999999999999999999999999997 899988889887
No 37
>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=96.81 E-value=0.0015 Score=58.06 Aligned_cols=52 Identities=23% Similarity=0.211 Sum_probs=48.2
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
...|-+.|++.+.+.|..+|.+|.+...+.+||+||+.++ |++++|..|.||
T Consensus 17 d~~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~w 75 (198)
T TIGR02859 17 NTHALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAF 75 (198)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHH
Confidence 4679999999999999999999999999999999999996 899888889887
No 38
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=96.80 E-value=0.0017 Score=62.11 Aligned_cols=52 Identities=21% Similarity=0.276 Sum_probs=47.2
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCC--ChhhHHHHhhcc-------cccCCCcccccc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGI--SLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGl--s~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
+..|.+.|+..+.++|..+|.+|.++.. ..+|++|+|.++ |++++|..|.+|
T Consensus 16 D~~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~aw 76 (237)
T PRK08311 16 DEELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSF 76 (237)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHH
Confidence 4679999999999999999999988776 489999999997 999999888887
No 39
>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=96.60 E-value=0.0031 Score=49.16 Aligned_cols=40 Identities=33% Similarity=0.625 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhcc
Q 017044 285 LIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELH 324 (378)
Q Consensus 285 l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~ 324 (378)
+.++.+++.+|+..+||+||.+|.|+..|++.++++..+.
T Consensus 3 l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~ 42 (78)
T PF04539_consen 3 LRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQ 42 (78)
T ss_dssp HHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHH
Confidence 3456778999999999999999999999999988865543
No 40
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=96.22 E-value=0.0044 Score=53.46 Aligned_cols=50 Identities=12% Similarity=0.122 Sum_probs=44.1
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
+..|.++|+..+.++|..++++|.+.+.+.+|++||+.++ |+ .+..|.+|
T Consensus 8 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~ 64 (182)
T PRK09652 8 DRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTW 64 (182)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHH
Confidence 5679999999999999999999999999999999999998 45 45567666
No 41
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=96.10 E-value=0.0051 Score=54.59 Aligned_cols=52 Identities=13% Similarity=0.121 Sum_probs=45.5
Q ss_pred ccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 325 ~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
.+..|-+.|+..+.++|..+|.+|.+.+.+.+||+||+.++ |+++ +..|.+|
T Consensus 17 ~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~w 75 (186)
T PRK05602 17 GDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTW 75 (186)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHH
Confidence 46789999999999999999999999999999999999997 6765 4566665
No 42
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=95.93 E-value=0.013 Score=54.47 Aligned_cols=61 Identities=20% Similarity=0.240 Sum_probs=53.1
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHH
Q 017044 265 ETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHV 344 (378)
Q Consensus 265 ~~~~LLTaeEE~eL~~~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsI 344 (378)
...|+|+...+..|...++. | +..+-+.|+..+.++|..+
T Consensus 7 ~~~~~~~~~~~~~l~~~~~~---------------g-------------------------d~~a~~~l~~~y~~~l~~~ 46 (231)
T PRK11922 7 SRPPPLSAASDRELVARVLA---------------G-------------------------DEAAFEALMRRHNRRLYRT 46 (231)
T ss_pred CCCCCcCcccHHHHHHHHHc---------------C-------------------------CHHHHHHHHHHHHHHHHHH
Confidence 45688888888888777664 3 5678899999999999999
Q ss_pred HHhccCCCCChhhHHHHhhcc
Q 017044 345 AKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 345 AKkY~grGls~eDLIQEG~iG 365 (378)
|++|.+.+-.-+||+||+.++
T Consensus 47 a~~~~~~~~~AEDlvQE~fi~ 67 (231)
T PRK11922 47 ARAILRNDAEAEDVVQEAYLR 67 (231)
T ss_pred HHHHhCChhhHHHHHHHHHHH
Confidence 999999999999999999998
No 43
>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=95.93 E-value=0.0045 Score=58.68 Aligned_cols=26 Identities=12% Similarity=0.181 Sum_probs=24.1
Q ss_pred CChhhHHHHhhcc-------cccCCCccccccC
Q 017044 353 ISLHDLLQVNQAT-------FNFGKWLLLFQYH 378 (378)
Q Consensus 353 ls~eDLIQEG~iG-------FDpsRG~rFstY~ 378 (378)
.+.+||+|+|+|| |||++|..|.||.
T Consensus 36 ~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya 68 (218)
T TIGR02895 36 TKSDDELSIGLIAFNEAIESYDSNKGKSFLSFA 68 (218)
T ss_pred CChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHH
Confidence 5899999999999 9999999999983
No 44
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=95.84 E-value=0.0077 Score=52.85 Aligned_cols=51 Identities=8% Similarity=0.134 Sum_probs=44.3
Q ss_pred ccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 325 ~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
....+-+.|+..+.++|..+|.+|.+.+.+.+||+||+.++ |++.. .|.+|
T Consensus 15 gd~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~w 72 (187)
T TIGR02948 15 GDENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTW 72 (187)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHH
Confidence 35778999999999999999999999999999999999997 77765 45554
No 45
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=95.54 E-value=0.013 Score=51.44 Aligned_cols=50 Identities=8% Similarity=0.142 Sum_probs=43.5
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
...+-++|+..+.++|..+|.+|.|.+.+.+|++||+.++ |++.. .|.+|
T Consensus 16 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~w 72 (187)
T PRK09641 16 DQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTW 72 (187)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHH
Confidence 5678899999999999999999999999999999999998 66643 56665
No 46
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=95.41 E-value=0.033 Score=49.54 Aligned_cols=51 Identities=16% Similarity=0.195 Sum_probs=41.3
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCC----CCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGR----GISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~gr----Gls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
...|.++|+..+.++|..+|.+|-+. +.+.+||+||+.++ |+. .|..|.+|
T Consensus 22 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~-~~~~~~~w 83 (189)
T PRK09648 22 DRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRD-QGRPFLAF 83 (189)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhc-cCCcHHHH
Confidence 47899999999999999999998543 46899999999998 443 34567666
No 47
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=95.28 E-value=0.023 Score=50.57 Aligned_cols=51 Identities=20% Similarity=0.156 Sum_probs=42.9
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc------cccCCCcccccc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT------FNFGKWLLLFQY 377 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG------FDpsRG~rFstY 377 (378)
+..+-+.|+..+.++|..++++|.+....-+||+||+.++ |++.++ .|.||
T Consensus 27 d~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~~-~f~~w 83 (194)
T PRK12519 27 QSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRKSSYDPKRG-SLSSY 83 (194)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcccc-cHHHH
Confidence 5678999999999999999999999888999999999997 444433 56655
No 48
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=95.26 E-value=0.026 Score=50.72 Aligned_cols=46 Identities=9% Similarity=-0.034 Sum_probs=42.1
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCC
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKW 371 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG 371 (378)
+..+-++|+..+.++|..+|.+|.+..-+-+|++||+.++ |++.+|
T Consensus 28 ~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~ 80 (194)
T PRK09646 28 DQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG 80 (194)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc
Confidence 5689999999999999999999999999999999999997 777665
No 49
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=94.80 E-value=0.033 Score=47.48 Aligned_cols=48 Identities=13% Similarity=0.036 Sum_probs=39.8
Q ss_pred HHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 328 ~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
.+-+.|+..+.++|..+++++.+ ..+.+|++|||.++ |+++.| .|.+|
T Consensus 4 ~af~~l~~~y~~~l~~~~~~~~~-~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~w 58 (154)
T PRK06759 4 ATFTEAVVLYEGLIVNQIKKLGI-YQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAY 58 (154)
T ss_pred ccHHHHHHHHHHHHHHHHHHhCC-cccHHHHHHHHHHHHHHHHHHhCccCC-chHHH
Confidence 45678999999999999999854 56889999999997 787777 57666
No 50
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=94.67 E-value=0.017 Score=53.87 Aligned_cols=31 Identities=16% Similarity=0.165 Sum_probs=27.6
Q ss_pred ccCCCCChhhHHHHhhcc-------cccCCCccccccC
Q 017044 348 YQGRGISLHDLLQVNQAT-------FNFGKWLLLFQYH 378 (378)
Q Consensus 348 Y~grGls~eDLIQEG~iG-------FDpsRG~rFstY~ 378 (378)
|.+.+...+||+|||++| |||++|.+|.||.
T Consensus 31 ~~~~~~~aeDlvQe~~i~l~~~~~~f~~~~~~~f~tyl 68 (236)
T PRK06986 31 RLPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYA 68 (236)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHH
Confidence 346789999999999998 9999999999983
No 51
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=94.62 E-value=0.073 Score=47.39 Aligned_cols=40 Identities=8% Similarity=0.047 Sum_probs=37.1
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
...+-++|+..|.+.|..++++|.+..-+.+||+||+.++
T Consensus 18 d~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~ 57 (193)
T PRK11923 18 DKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIK 57 (193)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHH
Confidence 4678999999999999999999998888999999999997
No 52
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=94.61 E-value=0.034 Score=49.68 Aligned_cols=41 Identities=10% Similarity=-0.003 Sum_probs=38.5
Q ss_pred ccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 325 ~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
.+..+.+.|+..+.++|..+|.+|.|...+.+||+||+.++
T Consensus 23 gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~ 63 (194)
T PRK12513 23 GDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLR 63 (194)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 45789999999999999999999999988999999999998
No 53
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=94.23 E-value=0.062 Score=47.97 Aligned_cols=61 Identities=18% Similarity=0.204 Sum_probs=48.4
Q ss_pred chhhhhhhccc----cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 315 SCRDLKSELHS----GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 315 s~~eLr~~L~~----G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
+.++|-..+.. +..|-+.|+..+.+.|..+|.+|-+.....+||+||+.+. |++ ...|.+|
T Consensus 9 ~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~--~~~~~~w 80 (188)
T PRK09640 9 NDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEG--KSKFKTW 80 (188)
T ss_pred CHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcC--CCcchHH
Confidence 34444445543 5889999999999999999999999999999999999997 553 3356665
No 54
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=94.00 E-value=0.064 Score=46.14 Aligned_cols=50 Identities=14% Similarity=0.071 Sum_probs=43.4
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
+..|-+.|+..+.+.|+.+|+++.+.+.+.+||+||+.+. |+ .+..|.+|
T Consensus 11 ~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~ 67 (179)
T PRK11924 11 DKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTW 67 (179)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHH
Confidence 5789999999999999999999999999999999999998 33 34566665
No 55
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=93.48 E-value=0.079 Score=46.80 Aligned_cols=41 Identities=12% Similarity=0.104 Sum_probs=38.2
Q ss_pred ccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 325 ~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
.+..+-+.|+..+.++|..++++|.+.+.+-+||+||+.++
T Consensus 20 ~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~ 60 (186)
T PRK13919 20 GEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIR 60 (186)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence 35779999999999999999999998999999999999998
No 56
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=93.15 E-value=0.12 Score=46.19 Aligned_cols=51 Identities=12% Similarity=0.111 Sum_probs=41.7
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCC---CChhhHHHHhhcc-------cccCCCcccccc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRG---ISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grG---ls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
+..+-+.|+..+.++|..++.+|.+.+ .+.+|++||+.++ |+++.| .|.+|
T Consensus 16 d~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~w 76 (189)
T PRK06811 16 NEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKW 76 (189)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHH
Confidence 567999999999999999999998754 4689999999997 666544 56555
No 57
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=92.58 E-value=0.16 Score=44.62 Aligned_cols=40 Identities=15% Similarity=0.160 Sum_probs=37.6
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
+..+-+.|+..+.+.|..+|.++.+.....+||+||+.++
T Consensus 18 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~ 57 (190)
T TIGR02939 18 EKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVK 57 (190)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHH
Confidence 5678999999999999999999999889999999999997
No 58
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=92.18 E-value=0.17 Score=44.88 Aligned_cols=47 Identities=13% Similarity=0.055 Sum_probs=41.6
Q ss_pred ccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCC
Q 017044 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKW 371 (378)
Q Consensus 325 ~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG 371 (378)
.+..+-+.|+..+.++|..+|.+|.+...+-+|++||..++ |++.+|
T Consensus 22 ~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~ 75 (187)
T PRK12534 22 GDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA 75 (187)
T ss_pred CCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc
Confidence 35678999999999999999999999989999999999997 666554
No 59
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=92.17 E-value=0.21 Score=44.95 Aligned_cols=51 Identities=14% Similarity=0.080 Sum_probs=42.6
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
+..+-+.|++.+.+.|..+|.+|.|....-+||+||..+. |++.+| .|.+|
T Consensus 25 d~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~w 82 (194)
T PRK12531 25 DKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTW 82 (194)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHH
Confidence 5678999999999999999999998888899999999997 554333 46555
No 60
>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=91.99 E-value=0.21 Score=42.99 Aligned_cols=51 Identities=12% Similarity=-0.003 Sum_probs=42.9
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
+..|-+.|+..+.+.+..++.++.|.....+|++||+.+. |+...+ .|.+|
T Consensus 9 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~w 66 (170)
T TIGR02952 9 EEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAW 66 (170)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHH
Confidence 5788999999999999999988888888999999999997 554444 66665
No 61
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=91.80 E-value=0.16 Score=44.76 Aligned_cols=40 Identities=10% Similarity=0.005 Sum_probs=37.6
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
+..+-++|+..+.+.|..+|.+|.+...+-+|++||+.++
T Consensus 17 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~ 56 (179)
T PRK12514 17 DRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVK 56 (179)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHH
Confidence 5678999999999999999999999989999999999997
No 62
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=91.74 E-value=0.2 Score=43.67 Aligned_cols=40 Identities=10% Similarity=0.051 Sum_probs=37.9
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
+..+.+.|+..+.+.|..+|.+|.+...+-+|++||+.++
T Consensus 16 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~ 55 (176)
T PRK09638 16 DDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLK 55 (176)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHH
Confidence 5789999999999999999999999888999999999997
No 63
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=90.53 E-value=0.32 Score=44.37 Aligned_cols=52 Identities=12% Similarity=0.082 Sum_probs=43.3
Q ss_pred ccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 325 ~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
.+..+-++|+..+.++|..++.+|.+....-+|++||+.+. |++.+|. |.||
T Consensus 35 ~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~~-~~~w 93 (206)
T PRK12526 35 RDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKGA-ATTW 93 (206)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCcccc-hhHH
Confidence 35778899999999999999999988878899999999997 6665552 5555
No 64
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=90.17 E-value=0.3 Score=44.02 Aligned_cols=40 Identities=15% Similarity=0.055 Sum_probs=38.0
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
+..|-+.|+..+.++|..+|.+|.+.....+|++||+.++
T Consensus 24 d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~ 63 (196)
T PRK12524 24 DPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLR 63 (196)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 5789999999999999999999999999999999999997
No 65
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=89.51 E-value=0.34 Score=45.70 Aligned_cols=51 Identities=12% Similarity=0.201 Sum_probs=42.6
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
+..+-+.|+..+.+.|..++.+|.|..-.-+|++||..+. |++.+| .|.+|
T Consensus 61 d~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~W 118 (233)
T PRK12538 61 DEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTW 118 (233)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHH
Confidence 4678899999999999999999998888899999999997 554433 45554
No 66
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=87.78 E-value=0.7 Score=40.81 Aligned_cols=41 Identities=17% Similarity=0.195 Sum_probs=35.6
Q ss_pred ccHHHHHHHHHHhHHHHHHHHHhccCC-C---CChhhHHHHhhcc
Q 017044 325 SGNSSREKLINANLRLVVHVAKQYQGR-G---ISLHDLLQVNQAT 365 (378)
Q Consensus 325 ~G~~ARekLI~sNLRLVvsIAKkY~gr-G---ls~eDLIQEG~iG 365 (378)
.+..|.+.|++.+.++|..+|.+|.++ | .+.+||+||+.+.
T Consensus 19 gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~ 63 (184)
T PRK12512 19 GDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLA 63 (184)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHH
Confidence 367899999999999999999998642 3 4899999999997
No 67
>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=86.92 E-value=0.74 Score=40.09 Aligned_cols=41 Identities=17% Similarity=0.122 Sum_probs=37.9
Q ss_pred ccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 325 ~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
.+..+-+.|+..+.+.|..++.+|-+..-+.+|++||..+.
T Consensus 13 gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~ 53 (169)
T TIGR02954 13 GNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYK 53 (169)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 35789999999999999999999999999999999999885
No 68
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=85.61 E-value=1.1 Score=39.68 Aligned_cols=43 Identities=9% Similarity=0.020 Sum_probs=36.8
Q ss_pred ccccHHHHHHHHHHhHHHHHHHHHhccC-CCCChhhHHHHhhcc
Q 017044 323 LHSGNSSREKLINANLRLVVHVAKQYQG-RGISLHDLLQVNQAT 365 (378)
Q Consensus 323 L~~G~~ARekLI~sNLRLVvsIAKkY~g-rGls~eDLIQEG~iG 365 (378)
...+..+-+.|+..+.+.|..++.++.+ .+-+.+||+||+.+.
T Consensus 16 ~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~ 59 (181)
T PRK12536 16 LAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLA 59 (181)
T ss_pred HcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHH
Confidence 3446778899999999999999988654 578999999999997
No 69
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=85.59 E-value=0.98 Score=40.10 Aligned_cols=41 Identities=10% Similarity=0.072 Sum_probs=38.2
Q ss_pred ccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 325 ~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
.+..+-+.|+..+.+.|..++.++.|....-+|++||..+.
T Consensus 20 ~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~ 60 (182)
T PRK12537 20 GDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIK 60 (182)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHH
Confidence 35789999999999999999999999889999999999997
No 70
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=84.87 E-value=1.2 Score=43.36 Aligned_cols=63 Identities=24% Similarity=0.287 Sum_probs=43.7
Q ss_pred HHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhcccc
Q 017044 256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSG 326 (378)
Q Consensus 256 ~l~~YLkei~~~~LLTaeEE~eL~~~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G 326 (378)
-+..||++-. ..--+---.+++ .+++++..+|+.++||+||..|.|+..|++.++....+..+
T Consensus 88 ei~d~LR~~~--~v~vpR~~~~~~------~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~ 150 (247)
T COG1191 88 EILDYLRKND--SVKVPRSLRELG------RRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAI 150 (247)
T ss_pred HHHHHHHhCC--CccCcHHHHHHH------HHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHh
Confidence 4556787766 222222223333 34556788899999999999999999999998876665543
No 71
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=83.75 E-value=0.89 Score=40.53 Aligned_cols=41 Identities=10% Similarity=0.024 Sum_probs=38.0
Q ss_pred ccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 325 ~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
.+..+-+.|+..+.+.|..++.+|.+...+-+|++||+.+.
T Consensus 19 gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~ 59 (189)
T PRK12515 19 GDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLD 59 (189)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 45679999999999999999999998889999999999997
No 72
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=83.15 E-value=1.4 Score=38.34 Aligned_cols=39 Identities=26% Similarity=0.131 Sum_probs=34.7
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
+..+-+.|+..+.+.|..++.+|.|. .+.+|++||..+.
T Consensus 9 d~~a~~~l~~~~~~~l~~~~~~~~~~-~~aeDivQe~~l~ 47 (175)
T PRK12518 9 DRQSFRQLYRRYQQKVRSTLYQLCGR-ELLDDLVQEVFLR 47 (175)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCH-hHHHHHHHHHHHH
Confidence 56788999999999999999998764 5789999999997
No 73
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=82.11 E-value=2.5 Score=40.35 Aligned_cols=36 Identities=28% Similarity=0.458 Sum_probs=30.7
Q ss_pred HHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhh
Q 017044 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322 (378)
Q Consensus 287 ~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~ 322 (378)
++.++..+|...+|++||..|.|+..|++.++++..
T Consensus 114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~ 149 (256)
T PRK07408 114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEI 149 (256)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHH
Confidence 456678889999999999999999999998877654
No 74
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=81.95 E-value=2.3 Score=38.35 Aligned_cols=42 Identities=19% Similarity=0.138 Sum_probs=38.6
Q ss_pred cccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 324 ~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
..+..+-+.|+..+.+.|..++.++.+....-+||+||..+.
T Consensus 23 ~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~ 64 (192)
T PRK09643 23 AGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLS 64 (192)
T ss_pred CcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHH
Confidence 446789999999999999999999999989999999999995
No 75
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=80.18 E-value=3.6 Score=36.57 Aligned_cols=50 Identities=12% Similarity=0.086 Sum_probs=39.9
Q ss_pred cHHHHHHHHHHhHHHHHHHHH----hccCCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 326 GNSSREKLINANLRLVVHVAK----QYQGRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAK----kY~grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
+..+-+.|+..+.+.|..+|+ +|.+...+-+|++||..+. |++.. .|.+|
T Consensus 19 d~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~w 79 (184)
T PRK12539 19 DAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPW 79 (184)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHH
Confidence 467899999999999999886 5557778999999999996 66644 35444
No 76
>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=79.71 E-value=3.3 Score=39.24 Aligned_cols=37 Identities=27% Similarity=0.341 Sum_probs=29.3
Q ss_pred HHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhc
Q 017044 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL 323 (378)
Q Consensus 287 ~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L 323 (378)
++.++..++...+|++||.+|.|+..|++.+.+...+
T Consensus 121 ~~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~ 157 (254)
T TIGR02850 121 KALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFAL 157 (254)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 3444667788888999999999999999887765543
No 77
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=79.55 E-value=3.4 Score=39.78 Aligned_cols=37 Identities=30% Similarity=0.553 Sum_probs=30.5
Q ss_pred HHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhc
Q 017044 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL 323 (378)
Q Consensus 287 ~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L 323 (378)
++.+...+|...+|++||..|.|+..|++.+++...+
T Consensus 128 ~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~ 164 (264)
T PRK07122 128 RLGRATAELSQRLGRAPTASELAAELGMDREEVVEGL 164 (264)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 3455677888889999999999999999988876544
No 78
>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=79.38 E-value=3.6 Score=38.57 Aligned_cols=36 Identities=31% Similarity=0.533 Sum_probs=30.6
Q ss_pred HHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhh
Q 017044 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322 (378)
Q Consensus 287 ~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~ 322 (378)
++.++..+|...+|++||.+|.|+..|++.++++..
T Consensus 88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~ 123 (238)
T TIGR02393 88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVREI 123 (238)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 455677888889999999999999999998887654
No 79
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=78.80 E-value=3.5 Score=41.32 Aligned_cols=38 Identities=29% Similarity=0.383 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhh
Q 017044 285 LIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322 (378)
Q Consensus 285 l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~ 322 (378)
..++.+++.+|...+|++||..|.|+..|++.+.++..
T Consensus 172 ~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~ 209 (324)
T PRK07921 172 VNKLARIKRELHQQLGREATDEELAEESGIPEEKIADL 209 (324)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 33466778889999999999999999999988777654
No 80
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=77.89 E-value=2.4 Score=37.65 Aligned_cols=41 Identities=15% Similarity=0.096 Sum_probs=37.5
Q ss_pred ccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 325 ~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
....|-+.|+..+.+.|..++.+|.+..-+-+|++|++.+.
T Consensus 13 ~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~ 53 (179)
T PRK09415 13 DKEDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVK 53 (179)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHH
Confidence 35688999999999999999999998888899999999996
No 81
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=76.88 E-value=3.3 Score=36.81 Aligned_cols=42 Identities=17% Similarity=0.186 Sum_probs=37.3
Q ss_pred cccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 324 ~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
.....+-+.++..+.+-+...|.++.|..-+-+||+||.++.
T Consensus 11 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr 52 (182)
T COG1595 11 RGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLR 52 (182)
T ss_pred hcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 345678888999999999999999998877999999999996
No 82
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=76.25 E-value=4.2 Score=38.35 Aligned_cols=37 Identities=16% Similarity=0.397 Sum_probs=30.2
Q ss_pred HHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhc
Q 017044 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL 323 (378)
Q Consensus 287 ~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L 323 (378)
++.+...+|...+|++||..|.|+..|++.+++...+
T Consensus 102 ~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~ 138 (231)
T PRK12427 102 KTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYL 138 (231)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 3455667888889999999999999999988875543
No 83
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=76.14 E-value=4.2 Score=38.88 Aligned_cols=36 Identities=25% Similarity=0.378 Sum_probs=29.0
Q ss_pred HHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhc
Q 017044 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL 323 (378)
Q Consensus 288 LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L 323 (378)
+.+....|...+|++||..|.|+..|++.+++...+
T Consensus 112 l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~ 147 (257)
T PRK05911 112 LADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWF 147 (257)
T ss_pred HHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHH
Confidence 444566788888999999999999999988776543
No 84
>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=74.82 E-value=3.9 Score=35.14 Aligned_cols=40 Identities=15% Similarity=0.127 Sum_probs=37.0
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
+..+-+.|+..+.+.|..+|.+|.|...+-+|++||..+-
T Consensus 4 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~ 43 (162)
T TIGR02983 4 TEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVR 43 (162)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 5678899999999999999999999889999999999885
No 85
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=74.80 E-value=5.2 Score=40.57 Aligned_cols=37 Identities=27% Similarity=0.442 Sum_probs=31.1
Q ss_pred HHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhc
Q 017044 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL 323 (378)
Q Consensus 287 ~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L 323 (378)
++.++..+|...+||+||..|.|+..|++.+.++..+
T Consensus 217 ~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~ 253 (367)
T PRK09210 217 KLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREIL 253 (367)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 4556778888999999999999999999988877543
No 86
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=71.86 E-value=3.3 Score=35.73 Aligned_cols=39 Identities=15% Similarity=0.150 Sum_probs=35.6
Q ss_pred HHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 327 ~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
..+-++++..+.+.|..++.++.|..-+-+|++||+.+.
T Consensus 4 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~ 42 (161)
T PRK12541 4 KQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYR 42 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence 457788999999999999999999989999999999885
No 87
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=71.72 E-value=6.7 Score=40.31 Aligned_cols=38 Identities=29% Similarity=0.483 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhh
Q 017044 285 LIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322 (378)
Q Consensus 285 l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~ 322 (378)
..++.+....|...+|++||..|.|+..|++.+.++..
T Consensus 222 ~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~ 259 (373)
T PRK07406 222 ISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFI 259 (373)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 34456677888889999999999999999998877543
No 88
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=69.05 E-value=8 Score=41.52 Aligned_cols=38 Identities=29% Similarity=0.448 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhc
Q 017044 286 IRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL 323 (378)
Q Consensus 286 ~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L 323 (378)
.+|.+++.+|...+|++||.+|.|+..|++.+.++..+
T Consensus 358 ~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~ 395 (509)
T PRK05901 358 NKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQ 395 (509)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 34666788899999999999999999999887776543
No 89
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=68.46 E-value=7.3 Score=33.62 Aligned_cols=38 Identities=21% Similarity=0.114 Sum_probs=34.9
Q ss_pred HHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 328 ~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
.+-+.|+..+.+.|..++.+|.|....-+|++||..+.
T Consensus 4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk 41 (161)
T PRK12528 4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVK 41 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHH
Confidence 46678999999999999999999888999999999996
No 90
>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=68.18 E-value=10 Score=35.16 Aligned_cols=36 Identities=36% Similarity=0.581 Sum_probs=28.9
Q ss_pred HHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhc
Q 017044 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL 323 (378)
Q Consensus 288 LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L 323 (378)
+.+....|...+|++||..|.|+..|++.+++...+
T Consensus 99 ~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~ 134 (231)
T TIGR02885 99 IRYMKEELSKELGREPTINELAEALGVSPEEIVMAL 134 (231)
T ss_pred HHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHH
Confidence 344566788888999999999999999987766543
No 91
>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=67.46 E-value=8.9 Score=35.38 Aligned_cols=38 Identities=32% Similarity=0.599 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhc
Q 017044 286 IRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL 323 (378)
Q Consensus 286 ~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L 323 (378)
.++.++..+|...+|++|+.+|.|+..|++.+.++..+
T Consensus 83 ~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~ 120 (224)
T TIGR02479 83 RKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQAL 120 (224)
T ss_pred HHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHH
Confidence 34566777888899999999999999999887776554
No 92
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=65.82 E-value=9.2 Score=36.14 Aligned_cols=37 Identities=22% Similarity=0.393 Sum_probs=30.1
Q ss_pred HHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhc
Q 017044 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL 323 (378)
Q Consensus 287 ~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L 323 (378)
++.++...+...+|++|+..|+|+..|++.++++..+
T Consensus 110 ~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~ 146 (251)
T PRK07670 110 KVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATM 146 (251)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 3455667788888999999999999999987776654
No 93
>PRK05949 RNA polymerase sigma factor; Validated
Probab=65.19 E-value=12 Score=37.57 Aligned_cols=36 Identities=25% Similarity=0.423 Sum_probs=30.0
Q ss_pred HHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhh
Q 017044 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322 (378)
Q Consensus 287 ~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~ 322 (378)
++.+.+.++...+|++||..|.|+..|++.+.+...
T Consensus 179 ~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~ 214 (327)
T PRK05949 179 KIKKTQRELSQKLGRSATPAEIAKELELEPSQIREY 214 (327)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 455667778888999999999999999988877655
No 94
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=64.78 E-value=7.6 Score=35.72 Aligned_cols=40 Identities=23% Similarity=0.189 Sum_probs=37.1
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
+..+-++|+..+.+.+..++.+|.+....-+||+||..+.
T Consensus 26 d~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflk 65 (203)
T PRK09647 26 TMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIR 65 (203)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHH
Confidence 4678899999999999999999999888999999999996
No 95
>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=62.42 E-value=16 Score=28.63 Aligned_cols=27 Identities=33% Similarity=0.503 Sum_probs=17.5
Q ss_pred hhcCCCcchHHHHHHhccc-hhhhhhhc
Q 017044 297 SQFGREPTLIEWAKAIGLS-CRDLKSEL 323 (378)
Q Consensus 297 ~~lGrePT~~EWA~AaG~s-~~eLr~~L 323 (378)
+..|.+||..|+|+++|+. ...++..|
T Consensus 20 ~~~G~~Pt~rEIa~~~g~~S~~tv~~~L 47 (65)
T PF01726_consen 20 EENGYPPTVREIAEALGLKSTSTVQRHL 47 (65)
T ss_dssp HHHSS---HHHHHHHHTSSSHHHHHHHH
T ss_pred HHcCCCCCHHHHHHHhCCCChHHHHHHH
Confidence 3469999999999999995 55554333
No 96
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=62.37 E-value=11 Score=39.39 Aligned_cols=39 Identities=21% Similarity=0.413 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhcc
Q 017044 286 IRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELH 324 (378)
Q Consensus 286 ~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~ 324 (378)
-++.+.+..|...+||.||..|.|++.|++.+.++..+.
T Consensus 262 ~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l~ 300 (415)
T PRK07598 262 NKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLL 300 (415)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 356778888889999999999999999999988877643
No 97
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=62.06 E-value=15 Score=34.84 Aligned_cols=34 Identities=24% Similarity=0.286 Sum_probs=27.8
Q ss_pred HHHHHHHHHhhcCCCcchHHHHHHhccchhhhhh
Q 017044 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (378)
Q Consensus 288 LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~ 321 (378)
+.+...++...+|++|+..|.|+..|++.+++..
T Consensus 125 ~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~ 158 (258)
T PRK08215 125 ALQVREKLINENSKEPTVEEIAKELEVPREEVVF 158 (258)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHH
Confidence 4456667888889999999999999998777654
No 98
>PRK15044 transcriptional regulator SirC; Provisional
Probab=61.57 E-value=29 Score=35.03 Aligned_cols=91 Identities=18% Similarity=0.137 Sum_probs=58.3
Q ss_pred HHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccc-cHHHHHHHHH
Q 017044 257 LRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS-GNSSREKLIN 335 (378)
Q Consensus 257 l~~YLkei~~~~LLTaeEE~eL~~~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~-G~~ARekLI~ 335 (378)
+..|++..+....|........ ++++..-+....+++++.++||+.+|++...|.+++.. |....+ ++.
T Consensus 172 Ls~~l~~~~~~~~L~~~~~is~---------~~kV~~~I~~nl~~~~SLeeLA~~lgmS~~tL~R~Fk~eg~T~~~-y~~ 241 (295)
T PRK15044 172 ISAFVRKPGGFDFLERAIKITT---------KEKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAAEEVSFSK-IYL 241 (295)
T ss_pred HHHHHhcccchhhHHHHhhhhH---------HHHHHHHHHhCcccCCCHHHHHHHhCCCHHHHHHHHHHcCCCHHH-HHH
Confidence 5567777777666665544332 34455566677889999999999999999999887764 222222 222
Q ss_pred HhHHHHHHHHHhcc-CCCCChhhHHH
Q 017044 336 ANLRLVVHVAKQYQ-GRGISLHDLLQ 360 (378)
Q Consensus 336 sNLRLVvsIAKkY~-grGls~eDLIQ 360 (378)
.+|| ..|++.- ..++++.++-.
T Consensus 242 -~~RL--~~A~~LL~~t~~sIseIA~ 264 (295)
T PRK15044 242 -DARM--NQAIKLLRMGAGNISQVAT 264 (295)
T ss_pred -HHHH--HHHHHHHHcCCCCHHHHHH
Confidence 3444 5555553 34466666644
No 99
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=60.56 E-value=14 Score=35.37 Aligned_cols=37 Identities=30% Similarity=0.514 Sum_probs=30.7
Q ss_pred HHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhc
Q 017044 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL 323 (378)
Q Consensus 287 ~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L 323 (378)
++.+.+..|+..+|++||..|.|+..|++.+.+...+
T Consensus 119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~ 155 (268)
T PRK06288 119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLL 155 (268)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHH
Confidence 5566778888899999999999999999887765543
No 100
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=60.21 E-value=17 Score=36.24 Aligned_cols=38 Identities=26% Similarity=0.456 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhc
Q 017044 286 IRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL 323 (378)
Q Consensus 286 ~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L 323 (378)
-++.+.+.++...+|++||..|.|++.|++.+.+...+
T Consensus 168 ~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~ 205 (317)
T PRK07405 168 NKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYL 205 (317)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 34566778888889999999999999999877666543
No 101
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=58.19 E-value=14 Score=32.19 Aligned_cols=40 Identities=13% Similarity=0.026 Sum_probs=36.2
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
....-..|+..+.+.|..+|.+|-+....-+|++||..+.
T Consensus 4 ~~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~ 43 (164)
T PRK12547 4 CSKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMK 43 (164)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHH
Confidence 3456678999999999999999999999999999999986
No 102
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=58.13 E-value=46 Score=28.52 Aligned_cols=38 Identities=11% Similarity=0.103 Sum_probs=30.4
Q ss_pred HHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccc
Q 017044 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325 (378)
Q Consensus 288 LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~ 325 (378)
++++..-+...+..+++..++|+.+|++...|.+....
T Consensus 11 i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 11 IHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34455566677788899999999999999999877764
No 103
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=57.40 E-value=36 Score=25.07 Aligned_cols=59 Identities=22% Similarity=0.313 Sum_probs=36.7
Q ss_pred CcchHHHHHHhccchhhhhhhccc--cHHHHHHHHHHhHHHHHHHHHhcc-CCCCChhhHHHHhhc
Q 017044 302 EPTLIEWAKAIGLSCRDLKSELHS--GNSSREKLINANLRLVVHVAKQYQ-GRGISLHDLLQVNQA 364 (378)
Q Consensus 302 ePT~~EWA~AaG~s~~eLr~~L~~--G~~ARekLI~sNLRLVvsIAKkY~-grGls~eDLIQEG~i 364 (378)
+++..++|+.+|++...|.+.+.. |...++-+-. .| +.-|..|- ...+++.||.++-.+
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~~~s~~~~~~~--~r--~~~a~~~l~~~~~~~~~ia~~~g~ 62 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKETGTTPKQYLRD--RR--LERARRLLRDTDLSVTEIALRVGF 62 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHhCcCHHHHHHH--HH--HHHHHHHHHcCCCCHHHHHHHhCC
Confidence 468899999999999999887763 3333333222 22 22233332 236899999866433
No 104
>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=56.77 E-value=21 Score=34.80 Aligned_cols=38 Identities=26% Similarity=0.443 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhc
Q 017044 286 IRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL 323 (378)
Q Consensus 286 ~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L 323 (378)
-++.+.+.++...+|++||..|.|+..|++.+.+...+
T Consensus 161 ~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~ 198 (298)
T TIGR02997 161 NKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELL 198 (298)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 34556677788889999999999999999887765443
No 105
>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=54.98 E-value=22 Score=31.15 Aligned_cols=40 Identities=13% Similarity=0.150 Sum_probs=35.6
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCC-----ChhhHHHHhhcc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGI-----SLHDLLQVNQAT 365 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGl-----s~eDLIQEG~iG 365 (378)
+..+-+.|+..+...|..+|.+|-+... .-+|++||..+.
T Consensus 15 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~ 59 (183)
T TIGR02999 15 DAAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLR 59 (183)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHH
Confidence 4678899999999999999999987665 789999999887
No 106
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=54.98 E-value=52 Score=26.83 Aligned_cols=38 Identities=13% Similarity=0.087 Sum_probs=30.1
Q ss_pred HHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccc
Q 017044 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325 (378)
Q Consensus 288 LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~ 325 (378)
++++..-+...+..+++.+++|+.+|++...|.+....
T Consensus 7 ~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~ 44 (107)
T PRK10219 7 IQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRT 44 (107)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 34455556667788899999999999999998877764
No 107
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=53.74 E-value=22 Score=36.55 Aligned_cols=41 Identities=32% Similarity=0.509 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhh
Q 017044 281 QIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (378)
Q Consensus 281 ~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~ 321 (378)
.+...-+|.+++.+|...+|++|+.+|.|+..|++..+++.
T Consensus 184 ~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~ 224 (342)
T COG0568 184 QVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVRE 224 (342)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHH
Confidence 33444456778888988899999999999999998765543
No 108
>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=51.85 E-value=20 Score=33.06 Aligned_cols=33 Identities=30% Similarity=0.567 Sum_probs=27.0
Q ss_pred HHHHHHHHhhcCCCcchHHHHHHhccchhhhhh
Q 017044 289 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (378)
Q Consensus 289 Ekik~~Le~~lGrePT~~EWA~AaG~s~~eLr~ 321 (378)
.+....+...+|++|+..|.|+..|++++++..
T Consensus 93 ~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~ 125 (227)
T TIGR02980 93 NKATEELTQRLGRSPTIAEIAEELGVSEEEVVE 125 (227)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHH
Confidence 345567777889999999999999998887754
No 109
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=51.34 E-value=46 Score=32.60 Aligned_cols=63 Identities=14% Similarity=0.191 Sum_probs=35.6
Q ss_pred HHHHHHhccCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhh
Q 017044 256 PLRLFLWGPETR-KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (378)
Q Consensus 256 ~l~~YLkei~~~-~LLTaeEE~eL~~~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~ 321 (378)
.+..|+++-... +.-+...+..+...++. ++.....+...+|++||.+|.|+..|++.+++..
T Consensus 104 ~I~~~lr~~~~~iR~p~~~~~~~~~~~~~~---~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~ 167 (289)
T PRK07500 104 SIQDYILRNWSIVRGGTSSAQKALFFNLRR---LRARLAQADEELTKQEIHREIATALGVSLSDVEM 167 (289)
T ss_pred HHHHHHHHCCCceecCccHHHHHHHHHHHH---HHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHH
Confidence 344455543322 22233344444444443 2222222333689999999999999999877753
No 110
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=51.09 E-value=23 Score=34.65 Aligned_cols=40 Identities=13% Similarity=0.091 Sum_probs=36.8
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
+..+-+.|+..+.+.|..+|.+|.|....-+|++||..+-
T Consensus 17 d~~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~ 56 (339)
T PRK08241 17 DRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLR 56 (339)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHH
Confidence 5678899999999999999999999888899999999885
No 111
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=50.92 E-value=21 Score=31.32 Aligned_cols=40 Identities=10% Similarity=-0.048 Sum_probs=36.9
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
...+-..|+..+.+.|..++.+|.+....-+|++||..+.
T Consensus 8 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk 47 (172)
T PRK12523 8 HSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVR 47 (172)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHH
Confidence 3578899999999999999999998889999999999997
No 112
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=50.72 E-value=20 Score=31.50 Aligned_cols=40 Identities=10% Similarity=0.001 Sum_probs=36.4
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
...+-+.++..+.+.+..++.+|.+....-+||+||-.+-
T Consensus 8 ~~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flk 47 (172)
T PRK09651 8 ASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLR 47 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHH
Confidence 4578889999999999999999998888999999999885
No 113
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.
Probab=50.14 E-value=23 Score=27.28 Aligned_cols=58 Identities=26% Similarity=0.451 Sum_probs=38.1
Q ss_pred hhcCCCcc------hHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhccCCCC-ChhhH
Q 017044 297 SQFGREPT------LIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGI-SLHDL 358 (378)
Q Consensus 297 ~~lGrePT------~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY~grGl-s~eDL 358 (378)
+.+||.+| +.+|....|++.+.+...+..+.. + -+.|++-|-.|++++...|+ +++|+
T Consensus 7 ~~~gr~ls~~e~~~i~~~~~~~~~~~evI~~ai~~a~~---~-~~~~~~Yi~~Il~~W~~~gi~T~e~~ 71 (73)
T TIGR01446 7 ENFGRMLSPFEMEDLKYWLDEFGNSPELIKEALKEAVS---N-NKANYKYIDAILNNWKNNGIKTVEDV 71 (73)
T ss_pred HHhCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHH---c-CCCCHHHHHHHHHHHHHcCCCCHHHH
Confidence 34566665 335777777777666655554322 1 24678999999999999986 44443
No 114
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=48.56 E-value=18 Score=33.81 Aligned_cols=40 Identities=15% Similarity=0.160 Sum_probs=36.3
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
...+-+.|+..+.+.+..++.+|.+..-.-+||+||..+-
T Consensus 16 ~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflk 55 (216)
T PRK12533 16 RGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMR 55 (216)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHH
Confidence 3567889999999999999999999888999999999985
No 115
>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=47.78 E-value=24 Score=33.74 Aligned_cols=51 Identities=14% Similarity=0.003 Sum_probs=41.7
Q ss_pred chhhhhhhcccc-HHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 315 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 315 s~~eLr~~L~~G-~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
+...|-.++..| ..|-+.|+..+.+.|..++.++.+...+-+|++||..+-
T Consensus 25 ~d~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlk 76 (244)
T TIGR03001 25 ADLYLACACAQGEPAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQR 76 (244)
T ss_pred cHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 444555555554 579999999999999999999988889999999997663
No 116
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=47.04 E-value=45 Score=29.84 Aligned_cols=39 Identities=23% Similarity=0.123 Sum_probs=33.7
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
+..+-+.|+..+.+.+..+++ |.+....-+|++||..+.
T Consensus 22 d~~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flk 60 (185)
T PRK09649 22 NGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLR 60 (185)
T ss_pred CHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHH
Confidence 467889999999999999995 666667899999999996
No 117
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=46.83 E-value=40 Score=25.75 Aligned_cols=48 Identities=25% Similarity=0.183 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccccH
Q 017044 270 LTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGN 327 (378)
Q Consensus 270 LTaeEE~eL~~~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G~ 327 (378)
||..|...|...+..|.. ..-|+.+..|.|+..|++...+-.+|+.+.
T Consensus 1 LT~~Q~e~L~~A~~~GYf----------d~PR~~tl~elA~~lgis~st~~~~LRrae 48 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYF----------DVPRRITLEELAEELGISKSTVSEHLRRAE 48 (53)
T ss_pred CCHHHHHHHHHHHHcCCC----------CCCCcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 455555555555554211 113778999999999999988887776543
No 118
>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=46.05 E-value=18 Score=32.27 Aligned_cols=40 Identities=18% Similarity=0.037 Sum_probs=35.8
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
...+-+.|+..+...|..+|.++.+....-+||+||..+.
T Consensus 9 ~~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~ 48 (193)
T TIGR02947 9 RAQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAK 48 (193)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 3567889999999999999999998888899999999986
No 119
>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=43.65 E-value=19 Score=31.40 Aligned_cols=28 Identities=18% Similarity=0.063 Sum_probs=20.4
Q ss_pred CCCCChhhHHHHhhcc-------cccCCCcccccc
Q 017044 350 GRGISLHDLLQVNQAT-------FNFGKWLLLFQY 377 (378)
Q Consensus 350 grGls~eDLIQEG~iG-------FDpsRG~rFstY 377 (378)
+...+.+|++||+.+. |+...+..|.+|
T Consensus 33 ~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~w 67 (189)
T TIGR02984 33 RRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGW 67 (189)
T ss_pred CCccCHHHHHHHHHHHHHHHHHhccCcccchHHHH
Confidence 3567899999999997 555445566665
No 120
>PRK05572 sporulation sigma factor SigF; Validated
Probab=43.11 E-value=46 Score=31.45 Aligned_cols=34 Identities=32% Similarity=0.656 Sum_probs=26.9
Q ss_pred HHHHHHHHHHhhcCCCcchHHHHHHhccchhhhh
Q 017044 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (378)
Q Consensus 287 ~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr 320 (378)
++.+....+...+|++|+..|.|++.|++...+.
T Consensus 119 ~~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~ 152 (252)
T PRK05572 119 KIRKDKDELSKELGREPTIEELAEYLGVTPEEVV 152 (252)
T ss_pred HHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHH
Confidence 3455666777788999999999999998876654
No 121
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=42.16 E-value=34 Score=30.89 Aligned_cols=40 Identities=23% Similarity=0.170 Sum_probs=36.5
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
+..+-+.|+..|.+.+..+|.++.|..-.-+||+||..+.
T Consensus 8 ~~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~ 47 (187)
T PRK12516 8 GTPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMK 47 (187)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHH
Confidence 5678889999999999999999999888999999999885
No 122
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=41.77 E-value=62 Score=26.18 Aligned_cols=50 Identities=26% Similarity=0.456 Sum_probs=37.6
Q ss_pred cchHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHh
Q 017044 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVN 362 (378)
Q Consensus 303 PT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG 362 (378)
.|-++.|..+|++...+- .|..| =-...|.|...||+-|. .+++|+++.+
T Consensus 15 ltQ~elA~~vgVsRQTi~-~iEkg------ky~Psl~La~kia~~f~---~~iedIF~~~ 64 (68)
T COG1476 15 LTQEELAKLVGVSRQTII-AIEKG------KYNPSLELALKIARVFG---KTIEDIFQLE 64 (68)
T ss_pred cCHHHHHHHcCcCHHHHH-HHHcC------CCCchHHHHHHHHHHhC---CCHHHHHhhh
Confidence 677889999999876663 22233 13467889999999996 9999999854
No 123
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=41.24 E-value=29 Score=31.24 Aligned_cols=42 Identities=19% Similarity=-0.006 Sum_probs=38.1
Q ss_pred cccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 324 ~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
.....+-+.++..+.+.|..+|.++.+..-+-+|++|+..+.
T Consensus 19 ~~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflk 60 (188)
T PRK12517 19 LSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLR 60 (188)
T ss_pred hccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 346788999999999999999999999888999999999885
No 124
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=41.18 E-value=2.8e+02 Score=26.27 Aligned_cols=37 Identities=19% Similarity=0.162 Sum_probs=28.8
Q ss_pred HHHHHHHHHhhcCCC-cchHHHHHHhccchhhhhhhcc
Q 017044 288 LEKEKSKLQSQFGRE-PTLIEWAKAIGLSCRDLKSELH 324 (378)
Q Consensus 288 LEkik~~Le~~lGre-PT~~EWA~AaG~s~~eLr~~L~ 324 (378)
+.+++.-+.+.+..+ .|.+++|+++|+|..-|.+...
T Consensus 199 l~~~~~~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk 236 (302)
T PRK09685 199 FQKVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFA 236 (302)
T ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 445666677777776 7999999999999988776654
No 125
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=40.25 E-value=33 Score=29.82 Aligned_cols=40 Identities=13% Similarity=0.081 Sum_probs=36.5
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
+..+-+.|+..+.+.|..+|.++.|....-+|++||-.+.
T Consensus 7 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~ 46 (173)
T PRK09645 7 EAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLR 46 (173)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 5678899999999999999999988878899999999986
No 126
>PHA01976 helix-turn-helix protein
Probab=39.58 E-value=86 Score=23.30 Aligned_cols=47 Identities=17% Similarity=0.140 Sum_probs=32.5
Q ss_pred cchHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHH
Q 017044 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLL 359 (378)
Q Consensus 303 PT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLI 359 (378)
.|..++|+.+|++...+.+..... ...+...+..||+-| |+++++|+
T Consensus 16 lt~~~lA~~~gvs~~~v~~~e~g~-------~~p~~~~l~~ia~~l---~v~~~~l~ 62 (67)
T PHA01976 16 WSAPELSRRAGVRHSLIYDFEADK-------RLPNLKTLLRLADAL---GVTLDWLC 62 (67)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCC-------CCCCHHHHHHHHHHH---CcCHHHHh
Confidence 678899999999887776533322 234667778888877 57777764
No 127
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=39.56 E-value=38 Score=31.55 Aligned_cols=34 Identities=32% Similarity=0.558 Sum_probs=27.3
Q ss_pred HHHHHHHHHhhcCCCcchHHHHHHhccchhhhhh
Q 017044 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (378)
Q Consensus 288 LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~ 321 (378)
+.+....+...+|++|+..|+|+..|++.+.+..
T Consensus 97 ~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~ 130 (236)
T PRK06986 97 VAQAIRQLEQELGREPTDTEVAEKLGLSLEEYRE 130 (236)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHH
Confidence 3445666777889999999999999998877543
No 128
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=38.39 E-value=79 Score=31.36 Aligned_cols=67 Identities=19% Similarity=0.261 Sum_probs=44.9
Q ss_pred HHHHHHhhcCCCcchHHHHHHhccchhhhhhhccc-cHHHHHHHHHHhHHHHHHHHHhccC-CCCChhhHHHH
Q 017044 291 EKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS-GNSSREKLINANLRLVVHVAKQYQG-RGISLHDLLQV 361 (378)
Q Consensus 291 ik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~-G~~ARekLI~sNLRLVvsIAKkY~g-rGls~eDLIQE 361 (378)
+...+.....++.+.++||+.+||+...|.+.+.. |..-.+-+. .+|| ..|++.-. .+.++.|+-.+
T Consensus 186 i~~~I~~~~~~~~sl~~lA~~~gmS~stl~R~Fk~~g~s~~~~~~--~~Rl--~~A~~lL~~~~~sI~~IA~~ 254 (291)
T PRK15186 186 IYNIIISDISRKWALKDISDSLYMSCSTLKRKLKQENTSFSEVYL--NARM--NKATKLLRNSEYNITRVAYM 254 (291)
T ss_pred HHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHH--HHHH--HHHHHHHHcCCCCHHHHHHH
Confidence 33446667788999999999999999999988875 444444333 3454 44555543 34677666543
No 129
>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=38.22 E-value=40 Score=31.80 Aligned_cols=35 Identities=29% Similarity=0.474 Sum_probs=28.2
Q ss_pred HHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhh
Q 017044 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322 (378)
Q Consensus 288 LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~ 322 (378)
+.+....+...+|++|+..|.|...|++.+++...
T Consensus 118 ~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~ 152 (255)
T TIGR02941 118 IKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEI 152 (255)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 44566777888899999999999999988776543
No 130
>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=37.48 E-value=35 Score=28.31 Aligned_cols=26 Identities=23% Similarity=0.449 Sum_probs=19.6
Q ss_pred CCCcchHHHHHHhccchhhhhhhccc
Q 017044 300 GREPTLIEWAKAIGLSCRDLKSELHS 325 (378)
Q Consensus 300 GrePT~~EWA~AaG~s~~eLr~~L~~ 325 (378)
|+++|..+.|.+.|.+.++++..|..
T Consensus 36 G~PVt~~~LA~a~g~~~e~v~~~L~~ 61 (77)
T PF12324_consen 36 GQPVTVEQLAAALGWPVEEVRAALAA 61 (77)
T ss_dssp TS-B-HHHHHHHHT--HHHHHHHHHH
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHh
Confidence 99999999999999999998877753
No 131
>TIGR03764 ICE_PFGI_1_parB integrating conjugative element, PFGI_1 class, ParB family protein. Members of this protein family carry the ParB-type nuclease domain and are found in integrating conjugative elements (ICE) in the same class as PFGI-1 of Pseudomonas fluorescens Pf-5.
Probab=37.28 E-value=2.1e+02 Score=28.57 Aligned_cols=22 Identities=23% Similarity=0.531 Sum_probs=17.9
Q ss_pred Hhcc-CCCCChhhHHHHhhcccc
Q 017044 346 KQYQ-GRGISLHDLLQVNQATFN 367 (378)
Q Consensus 346 KkY~-grGls~eDLIQEG~iGFD 367 (378)
.+|. +..++|++|+|+-|-.||
T Consensus 200 ~~~~~~~~~~f~~~f~~~~~~~d 222 (258)
T TIGR03764 200 NRYSSGVEVDFEEVFQEVLARFD 222 (258)
T ss_pred HHHccccCCCHHHHHHHHHHhcC
Confidence 3444 456899999999999999
No 132
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=36.99 E-value=64 Score=32.31 Aligned_cols=36 Identities=19% Similarity=0.303 Sum_probs=28.7
Q ss_pred HHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhc
Q 017044 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL 323 (378)
Q Consensus 288 LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L 323 (378)
+.+....|+..+|++|+..+.|+..|++.++++..+
T Consensus 175 ~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l 210 (325)
T PRK05657 175 YLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRML 210 (325)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 345566777888999999999999999887776544
No 133
>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=35.52 E-value=59 Score=29.39 Aligned_cols=33 Identities=21% Similarity=0.292 Sum_probs=27.4
Q ss_pred HHhhcCCCcchHHHHHHhccchhhhhhhccccH
Q 017044 295 LQSQFGREPTLIEWAKAIGLSCRDLKSELHSGN 327 (378)
Q Consensus 295 Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G~ 327 (378)
|.+.-|+..|..|.+++.|++++.|.+-|++|+
T Consensus 39 Lr~~p~~~ati~eV~e~tgVs~~~I~~~IreGR 71 (137)
T TIGR03826 39 LRKHENRQATVSEIVEETGVSEKLILKFIREGR 71 (137)
T ss_pred HHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 445557778999999999999999999888773
No 134
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=34.81 E-value=1.8e+02 Score=27.92 Aligned_cols=38 Identities=16% Similarity=0.122 Sum_probs=30.6
Q ss_pred HHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccc
Q 017044 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325 (378)
Q Consensus 288 LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~ 325 (378)
++++..-+++.+..+++..++|+.+|+|...|.+....
T Consensus 7 i~~~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F~~ 44 (289)
T PRK15121 7 IRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKD 44 (289)
T ss_pred HHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 44455566777888899999999999999888887764
No 135
>PRK13503 transcriptional activator RhaS; Provisional
Probab=34.27 E-value=78 Score=29.49 Aligned_cols=35 Identities=26% Similarity=0.305 Sum_probs=27.4
Q ss_pred HHHHHHHhhcCCCcchHHHHHHhccchhhhhhhcc
Q 017044 290 KEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELH 324 (378)
Q Consensus 290 kik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~ 324 (378)
++..-+.+....+.|.++||+.+|++...|.+...
T Consensus 175 ~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk 209 (278)
T PRK13503 175 QLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLK 209 (278)
T ss_pred HHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34445566677889999999999999888876665
No 136
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=33.75 E-value=64 Score=32.99 Aligned_cols=51 Identities=22% Similarity=0.289 Sum_probs=37.3
Q ss_pred HHHHHHhhcCCCcchHHHHHHhccchhhhhhhcccc--------------HHHHHHHHHHhHHHH
Q 017044 291 EKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSG--------------NSSREKLINANLRLV 341 (378)
Q Consensus 291 ik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G--------------~~ARekLI~sNLRLV 341 (378)
+..-++..++++.+.++.|..+|||...|.++-... ..||+-|...|+.+.
T Consensus 225 ~i~~me~nle~plsl~~LA~~~~~S~R~leRlF~~~lG~sP~~yy~~lRL~~Ar~LL~~t~~si~ 289 (328)
T COG4977 225 AIELMEANLEEPLSLEELADRAGLSRRQLERLFRAELGVSPARYYLRLRLERARRLLEQTRLSIA 289 (328)
T ss_pred HHHHHHHhhcCCcCHHHHHHHhCCCHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhCCCcHH
Confidence 333455667888999999999999998888766532 357777777776654
No 137
>KOG0197 consensus Tyrosine kinases [Signal transduction mechanisms]
Probab=32.97 E-value=19 Score=38.55 Aligned_cols=69 Identities=20% Similarity=0.293 Sum_probs=54.2
Q ss_pred hccCCCCCCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccc
Q 017044 246 KLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325 (378)
Q Consensus 246 k~~~~~~~~D~l~~YLkei~~~~LLTaeEE~eL~~~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~ 325 (378)
.|..++-+...|..||+. .....|...+...++.+|=.||...+ =+.-||+
T Consensus 277 yIVtE~m~~GsLl~yLr~-~~~~~l~~~~Ll~~a~qIaeGM~YLe----------------------------s~~~IHR 327 (468)
T KOG0197|consen 277 YIVTEYMPKGSLLDYLRT-REGGLLNLPQLLDFAAQIAEGMAYLE----------------------------SKNYIHR 327 (468)
T ss_pred EEEEEecccCcHHHHhhh-cCCCccchHHHHHHHHHHHHHHHHHH----------------------------hCCccch
Confidence 456677778899999998 77789999999999999988775321 1345788
Q ss_pred cHHHHHHHHHHhHHHHHHHH
Q 017044 326 GNSSREKLINANLRLVVHVA 345 (378)
Q Consensus 326 G~~ARekLI~sNLRLVvsIA 345 (378)
+-+|||-||..|+ |++||
T Consensus 328 DLAARNiLV~~~~--~vKIs 345 (468)
T KOG0197|consen 328 DLAARNILVDEDL--VVKIS 345 (468)
T ss_pred hhhhhheeeccCc--eEEEc
Confidence 8999999999987 65554
No 138
>PRK13239 alkylmercury lyase; Provisional
Probab=32.47 E-value=53 Score=31.61 Aligned_cols=27 Identities=22% Similarity=0.395 Sum_probs=24.5
Q ss_pred cCCCcchHHHHHHhccchhhhhhhccc
Q 017044 299 FGREPTLIEWAKAIGLSCRDLKSELHS 325 (378)
Q Consensus 299 lGrePT~~EWA~AaG~s~~eLr~~L~~ 325 (378)
.|++||..+.|++.|.+.++++++|+.
T Consensus 33 ~G~pvt~~~lA~~~~~~~~~v~~~L~~ 59 (206)
T PRK13239 33 KGRPVSVTTLAAALGWPVEEVEAVLEA 59 (206)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 499999999999999999999877765
No 139
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.02 E-value=1.3e+02 Score=25.90 Aligned_cols=45 Identities=24% Similarity=0.169 Sum_probs=31.1
Q ss_pred HHHHHHhhc-CCCcchHHHHHHhccchhhhhhhcc------ccHHHHHHHHH
Q 017044 291 EKSKLQSQF-GREPTLIEWAKAIGLSCRDLKSELH------SGNSSREKLIN 335 (378)
Q Consensus 291 ik~~Le~~l-GrePT~~EWA~AaG~s~~eLr~~L~------~G~~ARekLI~ 335 (378)
.+.+|++.+ -...+.++.|.+.|.+...|++.|. .++..|+-|++
T Consensus 11 Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil~~tqr~~dvW~lRd~l~~ 62 (97)
T COG4367 11 TKQELQANFELCPLSDEEIATALNWTEVKLEKILQVTQRPADVWRLRDFLVQ 62 (97)
T ss_pred HHHHHHHhhhhccccHHHHHHHhCCCHHHHHHHHHHhhccchhHHHHHHHHH
Confidence 344454433 3568999999999999988888773 45566665543
No 140
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=31.82 E-value=55 Score=29.01 Aligned_cols=42 Identities=10% Similarity=-0.111 Sum_probs=32.5
Q ss_pred cccHHHHHHHHHHhHHHHHHHHHhccC--CCCChhhHHHHhhcc
Q 017044 324 HSGNSSREKLINANLRLVVHVAKQYQG--RGISLHDLLQVNQAT 365 (378)
Q Consensus 324 ~~G~~ARekLI~sNLRLVvsIAKkY~g--rGls~eDLIQEG~iG 365 (378)
..+..+-+.|++.+...|..++.++.+ ..-.-+|++||--+-
T Consensus 9 ~~d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~ 52 (178)
T PRK12529 9 SADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLR 52 (178)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHH
Confidence 446778899999999999996544444 245789999999874
No 141
>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=31.07 E-value=77 Score=22.78 Aligned_cols=24 Identities=21% Similarity=0.376 Sum_probs=18.6
Q ss_pred CcchHHHHHHhccchhhhhhhccc
Q 017044 302 EPTLIEWAKAIGLSCRDLKSELHS 325 (378)
Q Consensus 302 ePT~~EWA~AaG~s~~eLr~~L~~ 325 (378)
..+..+.|+.+|++..++.+|+..
T Consensus 17 r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 17 RRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp TS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CccHHHHHHHHCcCHHHHHHHHHH
Confidence 467899999999999998887753
No 142
>PRK15185 transcriptional regulator HilD; Provisional
Probab=30.40 E-value=1.4e+02 Score=30.45 Aligned_cols=68 Identities=21% Similarity=0.190 Sum_probs=43.2
Q ss_pred HHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccc-cHHHHHHHHHHhHHHHHHHHHhc-cCCCCChhhHHH
Q 017044 289 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS-GNSSREKLINANLRLVVHVAKQY-QGRGISLHDLLQ 360 (378)
Q Consensus 289 Ekik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~-G~~ARekLI~sNLRLVvsIAKkY-~grGls~eDLIQ 360 (378)
+++..-+....+++.+.++||+.+|++...|.+++.. |....+-+.. +|+-. |+++ ....+++.|+-.
T Consensus 209 erV~~~I~~n~~~~~SledLA~~lgmS~~tL~R~FK~~G~S~~~yl~~--~Ri~~--A~~LL~~t~~sIseIA~ 278 (309)
T PRK15185 209 ERVYNIISSSPSRQWKLTDVADHIFMSTSTLKRKLAEEGTSFSDIYLS--ARMNQ--AAKLLRIGNHNVNAVAL 278 (309)
T ss_pred HHHHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHH--HHHHH--HHHHHHcCCCCHHHHHH
Confidence 3455556677888999999999999999999888653 5555554443 33322 2222 233456666544
No 143
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=29.81 E-value=99 Score=26.99 Aligned_cols=38 Identities=8% Similarity=0.040 Sum_probs=33.9
Q ss_pred HHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 328 ~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
.+-.++...+.+.+...+.+|.+...+-+||+|+-.+-
T Consensus 9 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~ 46 (168)
T PRK12525 9 TLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQ 46 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHH
Confidence 45567899999999999999999888999999999986
No 144
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=28.71 E-value=1.6e+02 Score=28.75 Aligned_cols=24 Identities=13% Similarity=0.090 Sum_probs=20.5
Q ss_pred CCCcchHHHHHHhccchhhhhhhc
Q 017044 300 GREPTLIEWAKAIGLSCRDLKSEL 323 (378)
Q Consensus 300 GrePT~~EWA~AaG~s~~eLr~~L 323 (378)
+++||..|.|+..|++.++++..+
T Consensus 149 ~~~~t~~eiA~~l~~~~~~v~~~~ 172 (284)
T PRK06596 149 LNPEEVEMVAEELGVSEEEVREME 172 (284)
T ss_pred CCCCCHHHHHHHhCcCHHHHHHHH
Confidence 689999999999999988876553
No 145
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=26.10 E-value=1.8e+02 Score=27.01 Aligned_cols=57 Identities=26% Similarity=0.241 Sum_probs=42.8
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccccHHHHHHHHHHhH
Q 017044 269 LLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANL 338 (378)
Q Consensus 269 LLTaeEE~eL~~~IQ~l~~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNL 338 (378)
.||..|..-|-.++..|.. ..-|..+..+.|+..|++...+...|+ +|-.|||....
T Consensus 155 ~LTdrQ~~vL~~A~~~GYF----------d~PR~~~l~dLA~~lGISkst~~ehLR---rAe~Kl~~~~~ 211 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYF----------DYPRRVSLKDLAKELGISKSTLSEHLR---RAERKLIEAYF 211 (215)
T ss_pred cCCHHHHHHHHHHHHcCCC----------CCCccCCHHHHHHHhCCCHHHHHHHHH---HHHHHHHHHhh
Confidence 7999998888877776322 123778999999999999988876664 56677776543
No 146
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=23.48 E-value=77 Score=29.23 Aligned_cols=35 Identities=9% Similarity=-0.045 Sum_probs=32.1
Q ss_pred HHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 331 EKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 331 ekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
..+++.+-+.+..+|.+|-+....-+|++||..+.
T Consensus 21 ~~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfik 55 (206)
T PRK12544 21 PVFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIG 55 (206)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHH
Confidence 45788899999999999999989999999999996
No 147
>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=23.46 E-value=2.6e+02 Score=23.07 Aligned_cols=37 Identities=19% Similarity=0.211 Sum_probs=28.8
Q ss_pred HHHHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhcccc
Q 017044 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSG 326 (378)
Q Consensus 287 ~LEkik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~G 326 (378)
+++.+.+-|.. | .+|..+.|+.+|++...+.+.|..+
T Consensus 7 R~~~I~e~l~~--~-~~ti~dvA~~~gvS~~TVsr~L~~~ 43 (80)
T TIGR02844 7 RVLEIGKYIVE--T-KATVRETAKVFGVSKSTVHKDVTER 43 (80)
T ss_pred HHHHHHHHHHH--C-CCCHHHHHHHhCCCHHHHHHHhcCC
Confidence 34455555555 4 5799999999999999999999764
No 148
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=23.22 E-value=94 Score=29.75 Aligned_cols=47 Identities=17% Similarity=0.061 Sum_probs=37.0
Q ss_pred hhhhhccccHHHHHHHHHHhHHHHHHHHHhccCCCCChhhHHHHhhcc
Q 017044 318 DLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQVNQAT 365 (378)
Q Consensus 318 eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY~grGls~eDLIQEG~iG 365 (378)
.|++.+.-...+.+.+++.+ +.+...+.++-+..-+-+||+||..+.
T Consensus 8 ~~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk 54 (228)
T PRK06704 8 ILKNHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCK 54 (228)
T ss_pred HHhcccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 45555555666777777776 788999999988888999999999986
No 149
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=23.19 E-value=3.3e+02 Score=24.10 Aligned_cols=29 Identities=21% Similarity=0.232 Sum_probs=24.2
Q ss_pred CCcchHHHHHHhccchhhhhhhccccHHH
Q 017044 301 REPTLIEWAKAIGLSCRDLKSELHSGNSS 329 (378)
Q Consensus 301 rePT~~EWA~AaG~s~~eLr~~L~~G~~A 329 (378)
..-+..|.|+..|++...++.++..+...
T Consensus 156 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~~ 184 (194)
T PRK12519 156 EGLSQSEIAKRLGIPLGTVKARARQGLLK 184 (194)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 35789999999999999999999775543
No 150
>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=22.82 E-value=99 Score=22.07 Aligned_cols=22 Identities=27% Similarity=0.297 Sum_probs=16.3
Q ss_pred cchHHHHHHhccchhhhhhhcc
Q 017044 303 PTLIEWAKAIGLSCRDLKSELH 324 (378)
Q Consensus 303 PT~~EWA~AaG~s~~eLr~~L~ 324 (378)
-+..+.|...|++...+.+.+.
T Consensus 22 ~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 22 MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp --HHHHHHHTTS-HHHHHHHHC
T ss_pred CCHHHHHHHHCcCHHHHHHHHh
Confidence 6788999999999998877664
No 151
>PRK04217 hypothetical protein; Provisional
Probab=22.76 E-value=2.5e+02 Score=24.46 Aligned_cols=25 Identities=28% Similarity=0.170 Sum_probs=21.6
Q ss_pred CcchHHHHHHhccchhhhhhhcccc
Q 017044 302 EPTLIEWAKAIGLSCRDLKSELHSG 326 (378)
Q Consensus 302 ePT~~EWA~AaG~s~~eLr~~L~~G 326 (378)
+-+..|+|+..|++...+..+|...
T Consensus 58 GlS~~EIAk~LGIS~sTV~r~L~RA 82 (110)
T PRK04217 58 GLTQEEAGKRMGVSRGTVWRALTSA 82 (110)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3589999999999999999888764
No 152
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=21.77 E-value=3.8e+02 Score=23.30 Aligned_cols=31 Identities=19% Similarity=0.160 Sum_probs=24.7
Q ss_pred CcchHHHHHHhccchhhhhhhccccHH-HHHH
Q 017044 302 EPTLIEWAKAIGLSCRDLKSELHSGNS-SREK 332 (378)
Q Consensus 302 ePT~~EWA~AaG~s~~eLr~~L~~G~~-ARek 332 (378)
.-+..|.|+..|++...++.+|..+.. |++.
T Consensus 135 g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~ 166 (172)
T PRK12523 135 GMGHAEIAERLGVSVSRVRQYLAQGLRQCYIA 166 (172)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 478999999999999999999877543 4433
No 153
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=21.14 E-value=5.1e+02 Score=22.12 Aligned_cols=30 Identities=10% Similarity=0.055 Sum_probs=25.0
Q ss_pred CCCcchHHHHHHhccchhhhhhhccccHHH
Q 017044 300 GREPTLIEWAKAIGLSCRDLKSELHSGNSS 329 (378)
Q Consensus 300 GrePT~~EWA~AaG~s~~eLr~~L~~G~~A 329 (378)
...-+..|.|+..|+++..++.+|..+...
T Consensus 119 ~~~~s~~eIA~~lgis~~tv~~~l~ra~~~ 148 (159)
T PRK12527 119 LEGLSHQQIAEHLGISRSLVEKHIVNAMKH 148 (159)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 345789999999999999999999876553
No 154
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=20.99 E-value=2.2e+02 Score=27.82 Aligned_cols=37 Identities=8% Similarity=0.101 Sum_probs=28.2
Q ss_pred HHHHHHHHhhcCCCcchHHHHHHhccchhhhhhhccc
Q 017044 289 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325 (378)
Q Consensus 289 Ekik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~L~~ 325 (378)
+++..-+.+.....++..+||+.+|++...|.+....
T Consensus 194 ~~~~~~i~~~~~~~~tl~~lA~~~~~S~~~l~r~Fk~ 230 (302)
T PRK10371 194 SQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQR 230 (302)
T ss_pred HHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3444455566677899999999999999988777664
No 155
>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=20.93 E-value=1.5e+02 Score=20.98 Aligned_cols=39 Identities=21% Similarity=0.220 Sum_probs=24.4
Q ss_pred cchHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhc
Q 017044 303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQY 348 (378)
Q Consensus 303 PT~~EWA~AaG~s~~eLr~~L~~G~~ARekLI~sNLRLVvsIAKkY 348 (378)
-|..|+|+.+|++...+.+.+... ..-++..+..||+-|
T Consensus 10 ls~~~la~~~gis~~~i~~~~~g~-------~~~~~~~~~~ia~~l 48 (55)
T PF01381_consen 10 LSQKELAEKLGISRSTISRIENGK-------RNPSLDTLKKIAKAL 48 (55)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHTTS-------STSBHHHHHHHHHHH
T ss_pred CCHHHHHHHhCCCcchhHHHhcCC-------CCCCHHHHHHHHHHH
Confidence 577888889998887776555542 234555666666655
No 156
>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=20.11 E-value=2e+02 Score=27.85 Aligned_cols=33 Identities=24% Similarity=0.469 Sum_probs=25.2
Q ss_pred HHHHHHHhhcCCCcchHHHHHHhccchhhhhhh
Q 017044 290 KEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322 (378)
Q Consensus 290 kik~~Le~~lGrePT~~EWA~AaG~s~~eLr~~ 322 (378)
+....+...+|++|+..++|...|++..+++..
T Consensus 137 r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~ 169 (285)
T TIGR02394 137 RAARQLEKKLGREPSVEEIAELLDKPVEDVSRV 169 (285)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 334445667799999999999999987776654
Done!