Query 017761
Match_columns 366
No_of_seqs 213 out of 1551
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 03:11:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017761.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017761hhsearch_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 1.8E-38 3.9E-43 319.9 16.6 155 208-365 56-258 (415)
2 TIGR02997 Sig70-cyanoRpoD RNA 100.0 6.2E-35 1.3E-39 280.6 16.2 150 212-364 1-156 (298)
3 PRK07406 RNA polymerase sigma 100.0 1.5E-34 3.2E-39 288.2 16.8 152 210-364 61-218 (373)
4 PRK05949 RNA polymerase sigma 100.0 2.1E-33 4.6E-38 275.0 17.7 153 209-364 15-173 (327)
5 PRK07405 RNA polymerase sigma 100.0 3.5E-32 7.5E-37 265.0 17.0 152 210-364 6-163 (317)
6 PRK05901 RNA polymerase sigma 100.0 6.8E-33 1.5E-37 285.5 12.0 151 198-364 197-353 (509)
7 COG0568 RpoD DNA-directed RNA 100.0 5.4E-33 1.2E-37 274.0 10.5 153 210-365 7-185 (342)
8 PRK07921 RNA polymerase sigma 100.0 3E-28 6.4E-33 238.8 13.3 139 210-364 24-168 (324)
9 PRK05658 RNA polymerase sigma 99.9 6.2E-25 1.3E-29 230.7 10.1 79 284-364 379-462 (619)
10 PRK09210 RNA polymerase sigma 99.9 3.1E-24 6.7E-29 213.0 12.0 114 208-364 92-211 (367)
11 TIGR02392 rpoH_proteo alternat 99.9 1.5E-21 3.2E-26 185.5 11.9 109 213-363 2-116 (270)
12 PRK06596 RNA polymerase factor 99.9 1.7E-21 3.7E-26 187.1 12.1 113 209-363 11-129 (284)
13 PRK07122 RNA polymerase sigma 99.9 6.8E-22 1.5E-26 188.0 7.4 80 283-364 38-122 (264)
14 PRK07500 rpoH2 RNA polymerase 99.8 3.5E-20 7.6E-25 178.5 12.2 111 211-363 5-121 (289)
15 TIGR02393 RpoD_Cterm RNA polym 99.8 1.9E-19 4.2E-24 167.5 6.3 77 286-364 1-82 (238)
16 PRK05657 RNA polymerase sigma 99.7 6.8E-18 1.5E-22 165.6 11.5 112 210-364 51-168 (325)
17 PRK07408 RNA polymerase sigma 99.7 2.2E-17 4.8E-22 156.0 9.7 80 283-364 23-108 (256)
18 TIGR02394 rpoS_proteo RNA poly 99.7 3.9E-16 8.6E-21 149.3 12.0 112 208-362 9-126 (285)
19 COG1191 FliA DNA-directed RNA 99.6 9.7E-16 2.1E-20 146.3 9.9 70 283-353 22-97 (247)
20 TIGR02850 spore_sigG RNA polym 99.6 3.6E-15 7.8E-20 140.4 10.8 101 221-364 10-115 (254)
21 PRK05911 RNA polymerase sigma 99.6 2.2E-15 4.7E-20 142.8 7.1 74 283-357 21-102 (257)
22 PRK08215 sporulation sigma fac 99.6 1E-14 2.2E-19 137.5 10.2 99 222-363 14-117 (258)
23 PRK06288 RNA polymerase sigma 99.4 2E-13 4.4E-18 129.5 8.7 99 220-358 5-111 (268)
24 TIGR02980 SigBFG RNA polymeras 99.4 2.7E-13 5.8E-18 124.6 7.5 78 284-363 2-84 (227)
25 TIGR02941 Sigma_B RNA polymera 99.4 1.2E-12 2.5E-17 123.0 10.9 99 224-363 7-110 (255)
26 PRK08583 RNA polymerase sigma 99.4 3.1E-12 6.7E-17 120.2 10.7 100 223-363 6-110 (257)
27 TIGR02885 spore_sigF RNA polym 99.3 5.7E-12 1.2E-16 116.3 8.2 78 283-363 9-91 (231)
28 PRK12427 flagellar biosynthesi 99.2 1.1E-11 2.3E-16 116.1 7.2 70 285-354 15-91 (231)
29 PRK05803 sporulation sigma fac 99.2 1E-10 2.2E-15 108.6 11.2 101 213-354 17-123 (233)
30 TIGR02895 spore_sigI RNA polym 99.2 4E-11 8.6E-16 112.7 7.2 74 280-353 4-84 (218)
31 PRK05572 sporulation sigma fac 99.2 1.9E-10 4.1E-15 108.2 10.6 92 222-353 9-105 (252)
32 TIGR02479 FliA_WhiG RNA polyme 99.1 6.9E-11 1.5E-15 108.8 5.5 68 290-358 1-76 (224)
33 PRK06986 fliA flagellar biosyn 99.1 2E-10 4.3E-15 106.8 7.4 73 282-354 5-85 (236)
34 PRK07670 RNA polymerase sigma 99.1 4.7E-10 1E-14 105.5 9.6 72 283-354 20-99 (251)
35 PRK08301 sporulation sigma fac 98.6 1.9E-07 4.1E-12 86.5 10.2 72 283-354 50-126 (234)
36 TIGR02846 spore_sigmaK RNA pol 98.6 2.9E-07 6.4E-12 85.4 11.5 99 216-354 19-122 (227)
37 PF04542 Sigma70_r2: Sigma-70 98.5 1.7E-07 3.8E-12 70.1 5.4 66 290-355 1-71 (71)
38 TIGR02835 spore_sigmaE RNA pol 98.5 1E-06 2.2E-11 82.2 10.1 72 283-354 50-126 (234)
39 TIGR02937 sigma70-ECF RNA poly 98.2 2.6E-06 5.7E-11 70.1 6.3 69 286-354 2-73 (158)
40 PRK08311 putative RNA polymera 98.2 7.8E-06 1.7E-10 77.8 8.9 80 275-354 7-94 (237)
41 PF00140 Sigma70_r1_2: Sigma-7 98.1 8.2E-07 1.8E-11 62.0 1.2 33 211-244 1-34 (37)
42 PRK08295 RNA polymerase factor 98.1 1.7E-05 3.7E-10 71.4 8.4 70 282-351 21-95 (208)
43 PRK09652 RNA polymerase sigma 98.0 1.3E-05 2.9E-10 69.4 6.4 72 283-354 8-82 (182)
44 PRK11922 RNA polymerase sigma 98.0 2.6E-05 5.7E-10 72.5 8.1 91 222-352 7-100 (231)
45 TIGR02859 spore_sigH RNA polym 97.9 4.1E-05 9E-10 68.2 8.5 78 273-350 6-89 (198)
46 PRK05602 RNA polymerase sigma 97.9 4.8E-05 1E-09 67.7 7.7 74 279-352 14-91 (186)
47 PRK12513 RNA polymerase sigma 97.9 4.7E-05 1E-09 68.2 7.5 79 276-354 17-98 (194)
48 PRK09641 RNA polymerase sigma 97.8 7.2E-05 1.5E-09 65.9 7.6 70 283-352 16-88 (187)
49 PRK09648 RNA polymerase sigma 97.8 0.00013 2.7E-09 65.2 8.5 72 283-354 22-101 (189)
50 TIGR02948 SigW_bacill RNA poly 97.7 9.8E-05 2.1E-09 65.1 7.0 74 278-351 11-87 (187)
51 PRK09640 RNA polymerase sigma 97.7 0.00017 3.6E-09 64.6 8.3 84 271-354 8-98 (188)
52 PRK13919 putative RNA polymera 97.5 0.00031 6.7E-09 62.3 7.9 79 274-352 11-94 (186)
53 PRK09638 RNA polymerase sigma 97.5 0.00038 8.2E-09 61.0 7.9 72 281-352 14-88 (176)
54 PRK12519 RNA polymerase sigma 97.5 0.00032 6.9E-09 62.7 7.4 71 283-353 27-100 (194)
55 PRK11923 algU RNA polymerase s 97.5 0.00067 1.5E-08 60.6 8.8 70 283-352 18-90 (193)
56 PRK06811 RNA polymerase factor 97.4 0.00057 1.2E-08 61.3 8.4 82 273-354 5-94 (189)
57 TIGR02939 RpoE_Sigma70 RNA pol 97.4 0.00066 1.4E-08 59.9 8.4 71 283-353 18-91 (190)
58 PRK09646 RNA polymerase sigma 97.4 0.00074 1.6E-08 60.8 8.0 80 274-353 18-102 (194)
59 PRK06759 RNA polymerase factor 97.4 0.00049 1.1E-08 58.9 6.6 68 285-353 4-75 (154)
60 TIGR02954 Sig70_famx3 RNA poly 97.3 0.0011 2.3E-08 58.0 8.3 75 281-355 12-89 (169)
61 PRK11924 RNA polymerase sigma 97.3 0.001 2.2E-08 57.5 7.5 69 283-351 11-82 (179)
62 PRK12514 RNA polymerase sigma 97.3 0.00073 1.6E-08 59.6 6.7 69 283-351 17-89 (179)
63 PRK05658 RNA polymerase sigma 97.2 0.00083 1.8E-08 71.8 7.8 34 209-243 101-135 (619)
64 TIGR02989 Sig-70_gvs1 RNA poly 97.2 0.00081 1.8E-08 57.7 6.3 69 286-354 2-73 (159)
65 TIGR02985 Sig70_bacteroi1 RNA 97.1 0.00067 1.5E-08 57.5 5.0 68 286-353 2-72 (161)
66 PRK12512 RNA polymerase sigma 97.1 0.0038 8.3E-08 55.3 9.2 73 282-354 19-98 (184)
67 PRK12534 RNA polymerase sigma 97.0 0.0018 4E-08 57.5 7.0 73 280-352 20-96 (187)
68 TIGR02952 Sig70_famx2 RNA poly 97.0 0.0032 6.9E-08 54.5 7.9 71 283-353 9-83 (170)
69 PRK12536 RNA polymerase sigma 96.9 0.0041 9E-08 55.3 8.2 77 277-353 13-93 (181)
70 PRK09643 RNA polymerase sigma 96.9 0.0031 6.8E-08 56.9 7.3 77 277-353 19-98 (192)
71 PRK12524 RNA polymerase sigma 96.9 0.0033 7.1E-08 56.7 7.1 78 274-351 14-96 (196)
72 PRK12522 RNA polymerase sigma 96.8 0.0029 6.3E-08 55.6 6.3 69 286-354 4-75 (173)
73 PRK12531 RNA polymerase sigma 96.8 0.0043 9.3E-08 55.9 7.3 71 283-353 25-99 (194)
74 PRK12539 RNA polymerase sigma 96.8 0.0075 1.6E-07 53.8 8.7 71 283-353 19-96 (184)
75 PRK12526 RNA polymerase sigma 96.8 0.0052 1.1E-07 56.2 7.8 72 283-354 36-111 (206)
76 PRK12537 RNA polymerase sigma 96.7 0.0079 1.7E-07 53.5 8.3 74 281-354 19-96 (182)
77 TIGR02984 Sig-70_plancto1 RNA 96.7 0.0057 1.2E-07 53.8 6.9 69 283-351 5-82 (189)
78 PRK12515 RNA polymerase sigma 96.6 0.006 1.3E-07 54.5 7.0 79 273-351 9-91 (189)
79 PRK12538 RNA polymerase sigma 96.5 0.0082 1.8E-07 56.6 7.4 69 283-351 61-133 (233)
80 PRK12518 RNA polymerase sigma 96.4 0.0092 2E-07 52.2 6.9 68 283-351 9-79 (175)
81 PRK09639 RNA polymerase sigma 96.3 0.0088 1.9E-07 51.8 6.1 67 285-351 3-70 (166)
82 PRK12543 RNA polymerase sigma 96.1 0.015 3.2E-07 51.7 6.4 69 283-351 5-76 (179)
83 PF04539 Sigma70_r3: Sigma-70 96.0 0.015 3.2E-07 45.3 5.2 40 243-282 4-43 (78)
84 PRK09415 RNA polymerase factor 96.0 0.018 3.9E-07 51.2 6.4 69 283-351 14-85 (179)
85 COG1595 RpoE DNA-directed RNA 95.9 0.037 8.1E-07 49.3 8.0 78 279-356 9-89 (182)
86 TIGR02983 SigE-fam_strep RNA p 95.7 0.029 6.3E-07 48.5 6.4 69 283-351 4-75 (162)
87 PRK09647 RNA polymerase sigma 95.3 0.069 1.5E-06 49.1 7.5 69 283-352 26-97 (203)
88 PRK12547 RNA polymerase sigma 95.0 0.074 1.6E-06 46.6 6.7 69 284-352 5-76 (164)
89 PRK12541 RNA polymerase sigma 94.8 0.084 1.8E-06 45.7 6.3 69 284-353 4-75 (161)
90 PRK12532 RNA polymerase sigma 94.7 0.075 1.6E-06 47.7 6.2 65 289-353 9-77 (195)
91 TIGR02999 Sig-70_X6 RNA polyme 94.7 0.14 3E-06 45.2 7.7 69 283-351 15-92 (183)
92 TIGR03001 Sig-70_gmx1 RNA poly 94.7 0.16 3.5E-06 48.4 8.6 82 272-353 25-117 (244)
93 TIGR02947 SigH_actino RNA poly 94.7 0.091 2E-06 47.1 6.5 70 283-352 9-81 (193)
94 PRK08241 RNA polymerase factor 94.6 0.14 3E-06 50.1 8.1 70 283-352 17-89 (339)
95 TIGR02943 Sig70_famx1 RNA poly 94.6 0.069 1.5E-06 48.1 5.5 67 288-354 5-74 (188)
96 PRK12520 RNA polymerase sigma 94.5 0.083 1.8E-06 47.3 5.9 69 286-354 3-74 (191)
97 PRK09644 RNA polymerase sigma 94.2 0.081 1.7E-06 46.2 5.0 63 288-351 4-69 (165)
98 PRK12542 RNA polymerase sigma 94.2 0.056 1.2E-06 48.1 4.0 71 283-353 7-82 (185)
99 PRK12516 RNA polymerase sigma 94.1 0.17 3.7E-06 45.7 7.1 71 283-353 8-81 (187)
100 PRK09637 RNA polymerase sigma 94.1 0.13 2.7E-06 46.3 6.2 65 288-352 4-71 (181)
101 PRK09649 RNA polymerase sigma 94.1 0.29 6.4E-06 43.9 8.4 69 283-352 22-93 (185)
102 PRK12544 RNA polymerase sigma 93.9 0.18 3.9E-06 46.5 7.0 82 268-354 6-90 (206)
103 PRK12528 RNA polymerase sigma 93.9 0.21 4.6E-06 43.2 7.0 66 285-351 4-72 (161)
104 PRK09645 RNA polymerase sigma 93.8 0.19 4E-06 44.0 6.5 70 283-352 7-80 (173)
105 TIGR02959 SigZ RNA polymerase 93.7 0.15 3.2E-06 45.1 5.7 62 293-354 3-67 (170)
106 TIGR02960 SigX5 RNA polymerase 93.6 0.24 5.2E-06 47.9 7.4 70 283-352 3-75 (324)
107 PRK12533 RNA polymerase sigma 93.5 0.27 5.9E-06 45.9 7.3 69 283-352 16-87 (216)
108 PRK12523 RNA polymerase sigma 93.5 0.19 4.1E-06 44.2 6.0 69 283-351 8-78 (172)
109 PRK12546 RNA polymerase sigma 93.1 0.32 7E-06 44.1 7.1 69 285-354 8-79 (188)
110 TIGR02950 SigM_subfam RNA poly 92.9 0.13 2.9E-06 43.7 4.1 59 293-352 3-64 (154)
111 PRK07037 extracytoplasmic-func 92.8 0.23 5E-06 42.9 5.4 62 290-352 3-67 (163)
112 PRK12530 RNA polymerase sigma 92.4 0.3 6.4E-06 44.0 5.8 67 288-354 10-79 (189)
113 PRK09651 RNA polymerase sigma 92.2 0.38 8.3E-06 42.5 6.2 55 283-337 8-63 (172)
114 PRK12540 RNA polymerase sigma 92.0 0.47 1E-05 42.7 6.5 67 286-352 6-75 (182)
115 PRK09642 RNA polymerase sigma 91.9 0.25 5.5E-06 42.6 4.6 61 292-353 2-65 (160)
116 PRK12517 RNA polymerase sigma 91.9 0.52 1.1E-05 42.5 6.8 59 281-339 19-79 (188)
117 PRK12535 RNA polymerase sigma 91.4 0.89 1.9E-05 41.5 7.8 69 283-352 23-94 (196)
118 PRK12545 RNA polymerase sigma 91.1 0.46 1E-05 43.2 5.6 65 290-354 13-80 (201)
119 PRK12525 RNA polymerase sigma 87.2 2.3 5E-05 37.3 6.9 41 285-325 9-49 (168)
120 PRK12511 RNA polymerase sigma 86.7 1.3 2.7E-05 40.0 5.1 68 286-353 5-75 (182)
121 PRK12527 RNA polymerase sigma 86.7 1.1 2.3E-05 38.7 4.5 57 293-350 3-62 (159)
122 TIGR02957 SigX4 RNA polymerase 86.6 1 2.2E-05 43.4 4.8 62 290-351 2-64 (281)
123 PRK09636 RNA polymerase sigma 86.1 1.7 3.7E-05 41.9 6.1 64 287-351 6-71 (293)
124 PRK12529 RNA polymerase sigma 84.1 2.8 6.1E-05 37.3 6.1 69 282-350 10-85 (178)
125 PRK06704 RNA polymerase factor 84.0 2.7 5.8E-05 40.1 6.2 75 275-351 8-83 (228)
126 COG0568 RpoD DNA-directed RNA 82.5 4.8 0.0001 41.0 7.6 33 209-242 64-97 (342)
127 PRK09635 sigI RNA polymerase s 79.7 3.9 8.4E-05 40.0 5.7 42 286-327 6-47 (290)
128 COG1191 FliA DNA-directed RNA 78.2 4.3 9.3E-05 39.5 5.5 40 244-283 111-150 (247)
129 PRK09191 two-component respons 76.4 4.7 0.0001 36.8 5.0 53 287-339 3-57 (261)
130 PRK07408 RNA polymerase sigma 72.9 8.4 0.00018 36.7 5.9 37 244-280 114-150 (256)
131 TIGR02850 spore_sigG RNA polym 70.8 10 0.00022 35.9 6.0 39 244-282 121-159 (254)
132 KOG3099 Bisphosphate 3'-nucleo 69.9 3.9 8.6E-05 41.2 3.0 64 295-360 9-73 (340)
133 PRK07122 RNA polymerase sigma 69.7 11 0.00025 36.2 6.1 38 244-281 128-165 (264)
134 TIGR02393 RpoD_Cterm RNA polym 69.1 12 0.00027 35.0 6.0 38 244-281 88-125 (238)
135 PRK07921 RNA polymerase sigma 68.4 12 0.00026 37.5 6.0 38 243-280 173-210 (324)
136 PRK12427 flagellar biosynthesi 67.7 9.2 0.0002 36.0 4.9 38 244-281 102-139 (231)
137 PRK05911 RNA polymerase sigma 66.8 13 0.00028 35.5 5.8 37 245-281 112-148 (257)
138 TIGR03209 P21_Cbot clostridium 64.1 13 0.00028 31.5 4.7 59 288-351 2-68 (142)
139 PRK09210 RNA polymerase sigma 64.1 14 0.00031 37.4 5.7 39 244-282 217-255 (367)
140 PRK11511 DNA-binding transcrip 62.5 29 0.00063 29.6 6.6 38 245-282 11-48 (127)
141 PF07638 Sigma70_ECF: ECF sigm 60.7 36 0.00078 30.7 7.2 53 276-328 7-66 (185)
142 PRK05901 RNA polymerase sigma 59.0 21 0.00045 38.3 6.1 38 244-281 359-396 (509)
143 PRK07406 RNA polymerase sigma 58.0 23 0.0005 36.4 6.0 37 243-279 223-259 (373)
144 PF01726 LexA_DNA_bind: LexA D 56.3 33 0.00072 26.7 5.3 26 255-280 21-47 (65)
145 PRK07670 RNA polymerase sigma 55.2 26 0.00057 33.1 5.5 39 244-282 110-148 (251)
146 TIGR02885 spore_sigF RNA polym 54.8 21 0.00047 33.0 4.8 37 245-281 99-135 (231)
147 PRK07598 RNA polymerase sigma 52.1 23 0.0005 37.0 5.0 39 244-282 263-301 (415)
148 smart00342 HTH_ARAC helix_turn 51.9 67 0.0015 23.6 6.3 56 259-318 1-59 (84)
149 PRK05949 RNA polymerase sigma 51.5 37 0.0008 34.0 6.2 38 244-281 179-216 (327)
150 PRK08215 sporulation sigma fac 50.7 40 0.00086 32.0 6.0 37 244-280 124-160 (258)
151 TIGR02479 FliA_WhiG RNA polyme 48.8 38 0.00081 31.3 5.4 38 244-281 84-121 (224)
152 PRK09047 RNA polymerase factor 48.0 23 0.00049 30.3 3.6 43 311-353 6-50 (161)
153 PRK07405 RNA polymerase sigma 45.4 52 0.0011 32.7 6.1 38 244-281 169-206 (317)
154 PRK06288 RNA polymerase sigma 45.2 35 0.00077 32.6 4.8 37 244-280 119-155 (268)
155 TIGR01446 DnaD_dom DnaD and ph 45.2 46 0.00099 25.5 4.5 56 255-314 8-70 (73)
156 TIGR02997 Sig70-cyanoRpoD RNA 43.7 61 0.0013 31.6 6.2 38 244-281 162-199 (298)
157 PRK15044 transcriptional regul 41.6 1E+02 0.0022 31.0 7.5 38 245-282 194-231 (295)
158 PRK07500 rpoH2 RNA polymerase 38.4 54 0.0012 32.0 4.9 25 254-278 143-167 (289)
159 PRK10219 DNA-binding transcrip 37.5 73 0.0016 25.9 4.9 37 246-282 8-44 (107)
160 TIGR02980 SigBFG RNA polymeras 35.9 66 0.0014 29.6 4.9 33 247-279 94-126 (227)
161 PRK06986 fliA flagellar biosyn 31.7 83 0.0018 29.3 4.8 37 245-281 97-133 (236)
162 COG4977 Transcriptional regula 30.1 1.2E+02 0.0026 30.9 6.0 37 246-282 223-259 (328)
163 PRK15121 right oriC-binding tr 30.0 2.8E+02 0.0061 26.6 8.3 74 245-319 7-107 (289)
164 PRK15186 AraC family transcrip 29.7 2E+02 0.0043 28.5 7.3 66 245-314 183-250 (291)
165 PF04967 HTH_10: HTH DNA bindi 29.0 2.1E+02 0.0045 21.7 5.7 28 257-284 21-48 (53)
166 TIGR03826 YvyF flagellar opero 28.9 94 0.002 27.9 4.5 33 252-284 39-71 (137)
167 PRK13239 alkylmercury lyase; P 28.8 95 0.002 29.7 4.7 27 256-282 33-59 (206)
168 PF14711 Nitr_red_bet_C: Respi 28.3 1.3E+02 0.0029 24.8 4.9 52 213-273 31-82 (83)
169 TIGR02297 HpaA 4-hydroxyphenyl 28.2 1.2E+02 0.0025 28.5 5.3 35 248-282 191-225 (287)
170 TIGR02941 Sigma_B RNA polymera 26.4 1.2E+02 0.0026 28.6 5.0 36 245-280 118-153 (255)
171 PRK09685 DNA-binding transcrip 26.2 4.3E+02 0.0093 25.0 8.8 37 245-281 199-236 (302)
172 PRK05572 sporulation sigma fac 24.9 1.5E+02 0.0033 27.9 5.4 34 244-277 119-152 (252)
173 COG4367 Uncharacterized protei 23.1 3E+02 0.0065 23.5 6.1 34 258-291 22-61 (97)
174 PRK05657 RNA polymerase sigma 22.6 1.8E+02 0.004 29.0 5.7 37 245-281 175-211 (325)
175 PF00439 Bromodomain: Bromodom 21.8 82 0.0018 24.2 2.5 46 271-316 37-82 (84)
176 PRK15185 transcriptional regul 21.2 2.5E+02 0.0054 28.5 6.3 36 245-280 208-243 (309)
177 PRK04217 hypothetical protein; 21.2 4.6E+02 0.0099 22.6 7.1 26 260-285 59-84 (110)
178 PF01381 HTH_3: Helix-turn-hel 20.8 1.3E+02 0.0029 21.2 3.2 39 260-305 10-48 (55)
179 PRK10371 DNA-binding transcrip 20.7 2.9E+02 0.0063 26.9 6.5 38 245-282 193-230 (302)
180 cd05499 Bromo_BDF1_2_II Bromod 20.3 1.2E+02 0.0025 25.0 3.2 43 271-313 46-88 (102)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=1.8e-38 Score=319.92 Aligned_cols=155 Identities=33% Similarity=0.476 Sum_probs=143.3
Q ss_pred CCCCChhH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHH--------------------HHHHHHHHHhhcCCCCchHHHH
Q 017761 208 VDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLK--------------------LEGLREVLSERCGGSPTFAQWA 266 (366)
Q Consensus 208 ~~~~D~l~-YLkei~~~~~LLt~eEE~eLa~~Iq~l~~--------------------le~~r~~L~~~~GrePT~~eWA 266 (366)
..+.||++ ||++| |+++|||++||++|+++||++++ |++++.+|++++|++||..|||
T Consensus 56 ~~~~d~v~~yl~~i-gr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa 134 (415)
T PRK07598 56 RRSTDLVRLYLQEI-GRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWA 134 (415)
T ss_pred CCCCChHHHHHHhc-ccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence 34589999 99999 99999999999999999999999 8999999999999999999999
Q ss_pred HHhcCCHHHHHHh----------------------hhhhHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHH
Q 017761 267 AAAGVDQRELRRR----------------------LNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLE 324 (366)
Q Consensus 267 ~aag~~~~~L~~~----------------------L~~G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi 324 (366)
.++|+++.+|+.+ ++.|+.|+++||++|+|||++||++|.++|++++||||||+|||+
T Consensus 135 ~~~~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~ 214 (415)
T PRK07598 135 KTADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLE 214 (415)
T ss_pred HHhCCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHH
Confidence 7777666666555 567889999999999999999999999999999999999999999
Q ss_pred h--ccCCC--CCCccccHH-HHHHHHHHHHHhcCCCCCCCcCcccc
Q 017761 325 V--QKSST--PPKVSSSQP-MLIGGSNRQFASHFPTNPEQLDYHFT 365 (366)
Q Consensus 325 ~--ekFD~--G~rFSTYA~-wIr~~I~R~i~d~~~~V~~~l~~~~~ 365 (366)
+ ++||| |++||||+. |||++|.|+|++++|+|+ ||.|++
T Consensus 215 ravekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIr--lP~~i~ 258 (415)
T PRK07598 215 RAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIR--LPVHIT 258 (415)
T ss_pred HHHHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCcee--hhHHHH
Confidence 5 89999 999999987 599999999999999999 999974
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=100.00 E-value=6.2e-35 Score=280.60 Aligned_cols=150 Identities=41% Similarity=0.580 Sum_probs=144.6
Q ss_pred ChhH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhhhHHHHHHH
Q 017761 212 DPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKM 290 (366)
Q Consensus 212 D~l~-YLkei~~~~~LLt~eEE~eLa~~Iq~l~~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~G~~AR~kL 290 (366)
|++. ||+++ +++|+||++||.+|+++++.++.+++++.+|+++.|++||..+||+++|++..+|...+..|..|+++|
T Consensus 1 ~~~~~yl~~~-~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~L 79 (298)
T TIGR02997 1 DLVRLYLQEI-GRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKM 79 (298)
T ss_pred CcHHHHHHHc-cccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHH
Confidence 5788 99999 999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHH-HHHHHHHHHHHhcCCCCCCCcCccc
Q 017761 291 ITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQP-MLIGGSNRQFASHFPTNPEQLDYHF 364 (366)
Q Consensus 291 I~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~-wIr~~I~R~i~d~~~~V~~~l~~~~ 364 (366)
|.+|+|+|++||++|.|+|++++||||||++|||. ++||| |++|+||+. ||++.|.|+|.+++++|+ +|.|.
T Consensus 80 v~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr--~p~~~ 156 (298)
T TIGR02997 80 IKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIR--LPIHI 156 (298)
T ss_pred HHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCee--CcHHH
Confidence 99999999999999999999999999999999994 89999 899999986 599999999999999999 88874
No 3
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=1.5e-34 Score=288.24 Aligned_cols=152 Identities=36% Similarity=0.512 Sum_probs=147.3
Q ss_pred CCChhH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhhhHHHHH
Q 017761 210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD 288 (366)
Q Consensus 210 ~~D~l~-YLkei~~~~~LLt~eEE~eLa~~Iq~l~~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~G~~AR~ 288 (366)
+.|++. ||++| +++||||++||++|+++|+.++.+++++.+|+.++|++|+..+||.++|++..+|+++++.|..|++
T Consensus 61 ~~d~l~~Yl~~i-~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~ 139 (373)
T PRK07406 61 TEDSIRVYLQEI-GRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKE 139 (373)
T ss_pred CCCHHHHHHHHh-cccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHH
Confidence 478999 99999 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHH-HHHHHHHHHHHhcCCCCCCCcCcc
Q 017761 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQP-MLIGGSNRQFASHFPTNPEQLDYH 363 (366)
Q Consensus 289 kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~-wIr~~I~R~i~d~~~~V~~~l~~~ 363 (366)
+||.+|+++|++||++|.++|++++||||||+||||. ++||+ |++|+|||. ||+++|.++|++++++|+ ||.|
T Consensus 140 ~Li~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IR--lP~~ 217 (373)
T PRK07406 140 KMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIR--LPVH 217 (373)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCcee--CCHH
Confidence 9999999999999999999999999999999999994 89999 999999986 599999999999999998 9988
Q ss_pred c
Q 017761 364 F 364 (366)
Q Consensus 364 ~ 364 (366)
.
T Consensus 218 ~ 218 (373)
T PRK07406 218 L 218 (373)
T ss_pred H
Confidence 5
No 4
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00 E-value=2.1e-33 Score=275.04 Aligned_cols=153 Identities=31% Similarity=0.448 Sum_probs=147.7
Q ss_pred CCCChhH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhhhHHHH
Q 017761 209 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCK 287 (366)
Q Consensus 209 ~~~D~l~-YLkei~~~~~LLt~eEE~eLa~~Iq~l~~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~G~~AR 287 (366)
...|++. ||++| +++||||++||++|+++|+.++.+++.+..|+.++|++|+..+||.+++++..+|...++.|..|+
T Consensus 15 ~~~d~~~~yl~~i-~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~ 93 (327)
T PRK05949 15 FSADMVRTYLHEI-GRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAK 93 (327)
T ss_pred CCCCHHHHHHHHc-CCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHH
Confidence 3579999 99999 999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHH-HHHHHHHHHHHhcCCCCCCCcCc
Q 017761 288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQP-MLIGGSNRQFASHFPTNPEQLDY 362 (366)
Q Consensus 288 ~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~-wIr~~I~R~i~d~~~~V~~~l~~ 362 (366)
++||.+|+++|+++|++|.+.|.+++||||||++||+. ++||+ |++|+|||. ||+++|.|+|.+++++|+ ||.
T Consensus 94 ~~Li~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iR--lP~ 171 (327)
T PRK05949 94 QKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIR--LPI 171 (327)
T ss_pred HHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCcee--CCH
Confidence 99999999999999999999999999999999999994 89999 999999986 599999999999999999 999
Q ss_pred cc
Q 017761 363 HF 364 (366)
Q Consensus 363 ~~ 364 (366)
|.
T Consensus 172 ~~ 173 (327)
T PRK05949 172 HI 173 (327)
T ss_pred HH
Confidence 85
No 5
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=3.5e-32 Score=265.01 Aligned_cols=152 Identities=34% Similarity=0.457 Sum_probs=146.7
Q ss_pred CCChhH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhhhHHHHH
Q 017761 210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD 288 (366)
Q Consensus 210 ~~D~l~-YLkei~~~~~LLt~eEE~eLa~~Iq~l~~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~G~~AR~ 288 (366)
++|++. ||++| +++|+||++||++|+++|++++.+++++..|++++|++|+..+||.+++++..+|...+..|..|++
T Consensus 6 ~~~~~~~yl~~i-~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~ 84 (317)
T PRK07405 6 STDLVRTYLREI-GRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKR 84 (317)
T ss_pred CCcHHHHHHHHc-cccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHH
Confidence 368999 99999 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHH-HHHHHHHHHHHhcCCCCCCCcCcc
Q 017761 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQP-MLIGGSNRQFASHFPTNPEQLDYH 363 (366)
Q Consensus 289 kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~-wIr~~I~R~i~d~~~~V~~~l~~~ 363 (366)
+||.+|+++|+++|++|.+.|.+++||||||++||+. ++||+ |++|+||+. ||+++|.++|.+++++|+ ||.|
T Consensus 85 ~L~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir--~p~~ 162 (317)
T PRK07405 85 KMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIR--LPIH 162 (317)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCcc--CChH
Confidence 9999999999999999999999999999999999994 89998 899999986 599999999999999999 9988
Q ss_pred c
Q 017761 364 F 364 (366)
Q Consensus 364 ~ 364 (366)
.
T Consensus 163 ~ 163 (317)
T PRK07405 163 I 163 (317)
T ss_pred H
Confidence 5
No 6
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=99.98 E-value=6.8e-33 Score=285.52 Aligned_cols=151 Identities=27% Similarity=0.352 Sum_probs=129.9
Q ss_pred ccCCCCCcccCCCCChhH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHH
Q 017761 198 SRRKRPSVQEVDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQREL 276 (366)
Q Consensus 198 ~~~~~~~~~~~~~~D~l~-YLkei~~~~~LLt~eEE~eLa~~Iq~l~~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L 276 (366)
.++.+.....+.+.|+++ ||++| +++++||++||++|+++|+.+..++... .+ ..+|+.. ...+|
T Consensus 197 ~~~~~~~~~~~~~~d~l~~YL~~i-~~~~lLt~eEE~~La~~i~~g~~~~~~~---~~-------~~~~~~~---~~~~l 262 (509)
T PRK05901 197 LRQARKDAKLTATADPVKAYLKQI-GKVKLLNAEEEVELAKRIEAGLYAEELL---AE-------GEKLDPE---LRRDL 262 (509)
T ss_pred hhhhhhhhhccccccHHHHHHHHh-ccCCCCCHHHHHHHHHHHHhCCchhhhh---hh-------cccchhh---hhhhh
Confidence 455566666677899999 99999 9999999999999999999875444321 11 1224322 56889
Q ss_pred HHhhhhhHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHH-HHHHHHHHHHHh
Q 017761 277 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQP-MLIGGSNRQFAS 351 (366)
Q Consensus 277 ~~~L~~G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~-wIr~~I~R~i~d 351 (366)
+++++.|..|+++||.+|||||++||++|.|+|++++|||||||||||+ ++||| |++|||||+ |||++|.|+|++
T Consensus 263 ~~~~~~g~~Ar~~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d 342 (509)
T PRK05901 263 QWIGRDGKRAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMAD 342 (509)
T ss_pred hhhccchHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999994 89999 999999986 599999999999
Q ss_pred cCCCCCCCcCccc
Q 017761 352 HFPTNPEQLDYHF 364 (366)
Q Consensus 352 ~~~~V~~~l~~~~ 364 (366)
++|+|+ +|.|.
T Consensus 343 ~~r~IR--vP~~~ 353 (509)
T PRK05901 343 QARTIR--IPVHM 353 (509)
T ss_pred cCCcee--cCHHH
Confidence 999997 99985
No 7
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=99.98 E-value=5.4e-33 Score=274.02 Aligned_cols=153 Identities=31% Similarity=0.399 Sum_probs=137.8
Q ss_pred CCChhH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHh-hcCCCCchH---------------HHHHHhcCC
Q 017761 210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSE-RCGGSPTFA---------------QWAAAAGVD 272 (366)
Q Consensus 210 ~~D~l~-YLkei~~~~~LLt~eEE~eLa~~Iq~l~~le~~r~~L~~-~~GrePT~~---------------eWA~aag~~ 272 (366)
..|.++ |+.++ +..++++.++|.++...++....+..+...|.. ..+..|+.. +|+.....+
T Consensus 7 ~~d~~~~~l~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 85 (342)
T COG0568 7 SADAVRAYLDEI-GRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPE 85 (342)
T ss_pred chhHHHHHHHHh-cchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChH
Confidence 467888 99999 999999999999999999988877777788877 678889887 676666655
Q ss_pred H-HHHHHhhhhhHH---HHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHH--hccCCC--CCCccccHHH-HHH
Q 017761 273 Q-RELRRRLNYGIL---CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLE--VQKSST--PPKVSSSQPM-LIG 343 (366)
Q Consensus 273 ~-~~L~~~L~~G~~---AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi--~ekFD~--G~rFSTYA~w-Ir~ 343 (366)
+ ..|..++..|.. |+.+||.+|||||+||||+|.|+|++|.||||||||||| +++||| ||||||||+| |++
T Consensus 86 Ee~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrq 165 (342)
T COG0568 86 EEKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQ 165 (342)
T ss_pred HHHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHH
Confidence 5 778889988865 999999999999999999999999999999999999999 489999 9999999975 999
Q ss_pred HHHHHHHhcCCCCCCCcCcccc
Q 017761 344 GSNRQFASHFPTNPEQLDYHFT 365 (366)
Q Consensus 344 ~I~R~i~d~~~~V~~~l~~~~~ 365 (366)
+|.|+|.+++|+|+ +|+|.+
T Consensus 166 aI~raI~~q~rtIR--ipvh~~ 185 (342)
T COG0568 166 AITRAIADQARTIR--IPVHQV 185 (342)
T ss_pred HHHHHHHHhcchhh--HhHHHH
Confidence 99999999999999 999953
No 8
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=99.95 E-value=3e-28 Score=238.82 Aligned_cols=139 Identities=30% Similarity=0.369 Sum_probs=122.2
Q ss_pred CCChhH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhhhHHHHH
Q 017761 210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD 288 (366)
Q Consensus 210 ~~D~l~-YLkei~~~~~LLt~eEE~eLa~~Iq~l~~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~G~~AR~ 288 (366)
..|++. ||+++ +++|+||++||++|+++|+.+..++.. |+..+|.... ...+|+..++.|..|++
T Consensus 24 ~~~~~~~Yl~~i-~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~ 89 (324)
T PRK07921 24 AADLVRVYLNGI-GKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARR 89 (324)
T ss_pred CCChHHHHHHHh-cccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHH
Confidence 468999 99999 999999999999999999987666543 2223332111 45789999999999999
Q ss_pred HHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHH-HHHHHHHHHHHhcCCCCCCCcCcc
Q 017761 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQP-MLIGGSNRQFASHFPTNPEQLDYH 363 (366)
Q Consensus 289 kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~-wIr~~I~R~i~d~~~~V~~~l~~~ 363 (366)
+||.+|+++|+++|++|.++|++++||||||+|||+. ++||| |+||+|||. ||+++|.++|++++++|+ +|.|
T Consensus 90 ~Lv~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vr--lP~~ 167 (324)
T PRK07921 90 HLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIR--LPVH 167 (324)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCcc--CCHH
Confidence 9999999999999999999999999999999999994 89999 999999986 599999999999999998 9988
Q ss_pred c
Q 017761 364 F 364 (366)
Q Consensus 364 ~ 364 (366)
.
T Consensus 168 ~ 168 (324)
T PRK07921 168 L 168 (324)
T ss_pred H
Confidence 5
No 9
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=99.91 E-value=6.2e-25 Score=230.72 Aligned_cols=79 Identities=30% Similarity=0.357 Sum_probs=75.3
Q ss_pred HHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHHH-HHHHHHHHHHhcCCCCCC
Q 017761 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQPM-LIGGSNRQFASHFPTNPE 358 (366)
Q Consensus 284 ~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~w-Ir~~I~R~i~d~~~~V~~ 358 (366)
..|+++||.+|||||++||++|.++|++|+|||||||||||+ ++||| |++|||||+| |+++|.|+|++++|+|+
T Consensus 379 ~~a~~~Li~~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~ir- 457 (619)
T PRK05658 379 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR- 457 (619)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCcee-
Confidence 479999999999999999999999999999999999999994 89999 9999999865 99999999999999998
Q ss_pred CcCccc
Q 017761 359 QLDYHF 364 (366)
Q Consensus 359 ~l~~~~ 364 (366)
+|+|.
T Consensus 458 -ip~~~ 462 (619)
T PRK05658 458 -IPVHM 462 (619)
T ss_pred -cCHHH
Confidence 99985
No 10
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=99.91 E-value=3.1e-24 Score=213.03 Aligned_cols=114 Identities=34% Similarity=0.469 Sum_probs=105.9
Q ss_pred CCCCChhH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhhhHHH
Q 017761 208 VDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILC 286 (366)
Q Consensus 208 ~~~~D~l~-YLkei~~~~~LLt~eEE~eLa~~Iq~l~~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~G~~A 286 (366)
....|+++ ||++| ++.|+||++||.+|+++++. | +..|
T Consensus 92 ~~~~d~~~~yl~~i-~~~~~l~~~ee~~L~~~~~~---------------G-------------------------d~~A 130 (367)
T PRK09210 92 VKINDPVRMYLKEI-GRVPLLTAEEEIELAKRIEE---------------G-------------------------DEEA 130 (367)
T ss_pred cccCcHHHHHHHHh-hccCCCCHHHHHHHHHHHHh---------------h-------------------------HHHH
Confidence 34578999 99999 99999999999999998886 4 4689
Q ss_pred HHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHHH-HHHHHHHHHHhcCCCCCCCcC
Q 017761 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQPM-LIGGSNRQFASHFPTNPEQLD 361 (366)
Q Consensus 287 R~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~w-Ir~~I~R~i~d~~~~V~~~l~ 361 (366)
+++||.+|+++|+++|++|.++|++++||||||+|||+. ++||| |++|+|||+| |+++|.++|++++|+|+ +|
T Consensus 131 ~~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~ir--ip 208 (367)
T PRK09210 131 KQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIR--IP 208 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCcee--cc
Confidence 999999999999999999999999999999999999994 89998 9999999865 99999999999999997 99
Q ss_pred ccc
Q 017761 362 YHF 364 (366)
Q Consensus 362 ~~~ 364 (366)
.|.
T Consensus 209 ~~~ 211 (367)
T PRK09210 209 VHM 211 (367)
T ss_pred HHH
Confidence 986
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=99.86 E-value=1.5e-21 Score=185.47 Aligned_cols=109 Identities=23% Similarity=0.363 Sum_probs=97.0
Q ss_pred hhH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhhhHHHHHHHH
Q 017761 213 PLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMI 291 (366)
Q Consensus 213 ~l~-YLkei~~~~~LLt~eEE~eLa~~Iq~l~~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~G~~AR~kLI 291 (366)
++. ||+++ ++.|+|+.++|.+|+.++.. .| +..|+++||
T Consensus 2 ~~~~yl~~~-~~~~~l~~~~e~~l~~~~~~--------------~g-------------------------d~~a~~~Lv 41 (270)
T TIGR02392 2 SLDAYIRAV-NRIPMLTPEEEYQLAKRLRE--------------HG-------------------------DLDAAKKLV 41 (270)
T ss_pred hHHHHHHHH-hcCCCCCHHHHHHHHHHHHH--------------CC-------------------------CHHHHHHHH
Confidence 677 99999 99999999999999987532 13 578999999
Q ss_pred HHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHH-HHHHHHHHHHHhcCCCCCCCcCcc
Q 017761 292 TSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQP-MLIGGSNRQFASHFPTNPEQLDYH 363 (366)
Q Consensus 292 ~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~-wIr~~I~R~i~d~~~~V~~~l~~~ 363 (366)
..|+++|.++|++|.+.|.+++||||||++||+. ++||+ |++|+|||. ||+++|.++|++++++|+ +|.|
T Consensus 42 ~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir--~p~~ 116 (270)
T TIGR02392 42 LSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVK--VATT 116 (270)
T ss_pred HHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCcee--cCch
Confidence 9999999999999999999999999999999994 89999 999999986 599999999999877666 5543
No 12
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=99.86 E-value=1.7e-21 Score=187.08 Aligned_cols=113 Identities=20% Similarity=0.326 Sum_probs=101.0
Q ss_pred CCCChhH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhhhHHHH
Q 017761 209 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCK 287 (366)
Q Consensus 209 ~~~D~l~-YLkei~~~~~LLt~eEE~eLa~~Iq~l~~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~G~~AR 287 (366)
.+.+++. |++++ ++.|+|+.++|.+|+.+++. .| +..|+
T Consensus 11 ~~~~~~~~y~~~~-~~~~~l~~~~e~~l~~~~~~--------------~G-------------------------d~~a~ 50 (284)
T PRK06596 11 SPEGNLDAYIQAV-NKIPMLTAEEEYMLAKRLRE--------------HG-------------------------DLEAA 50 (284)
T ss_pred CCccHHHHHHHHH-hccCCCCHHHHHHHHHHHHH--------------cC-------------------------CHHHH
Confidence 4568999 99999 99999999999999987542 14 57899
Q ss_pred HHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHH-HHHHHHHHHHHhcCCCCCCCcCc
Q 017761 288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQP-MLIGGSNRQFASHFPTNPEQLDY 362 (366)
Q Consensus 288 ~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~-wIr~~I~R~i~d~~~~V~~~l~~ 362 (366)
+.||..|+++|.++|++|.+.|++++||||||++||+. ++||+ |++|+|||. ||+++|.++|++++++|| +|.
T Consensus 51 ~~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr--~p~ 128 (284)
T PRK06596 51 KQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVK--VAT 128 (284)
T ss_pred HHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeee--ccc
Confidence 99999999999999999999999999999999999994 89999 999999986 599999999999988887 555
Q ss_pred c
Q 017761 363 H 363 (366)
Q Consensus 363 ~ 363 (366)
|
T Consensus 129 ~ 129 (284)
T PRK06596 129 T 129 (284)
T ss_pred h
Confidence 4
No 13
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=99.85 E-value=6.8e-22 Score=188.04 Aligned_cols=80 Identities=20% Similarity=0.218 Sum_probs=74.4
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHH-HHHHHHHHHHHhcCCCCC
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQP-MLIGGSNRQFASHFPTNP 357 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~-wIr~~I~R~i~d~~~~V~ 357 (366)
...++++||.+|+|||++||++|.++|++++||||||+||||. ++||| |++|+|||. ||+++|.++|++++|+|+
T Consensus 38 ~~~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I~~~lr~~~~~ir 117 (264)
T PRK07122 38 FQRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVK 117 (264)
T ss_pred HHHHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHcCCccc
Confidence 3569999999999999999999999999999999999999995 89999 999999985 599999999999999987
Q ss_pred CCcCccc
Q 017761 358 EQLDYHF 364 (366)
Q Consensus 358 ~~l~~~~ 364 (366)
+|.|.
T Consensus 118 --~Pr~~ 122 (264)
T PRK07122 118 --VPRRL 122 (264)
T ss_pred --cCHHH
Confidence 88764
No 14
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=99.83 E-value=3.5e-20 Score=178.54 Aligned_cols=111 Identities=18% Similarity=0.212 Sum_probs=100.0
Q ss_pred CChhH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhhhHHHHHH
Q 017761 211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDK 289 (366)
Q Consensus 211 ~D~l~-YLkei~~~~~LLt~eEE~eLa~~Iq~l~~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~G~~AR~k 289 (366)
.+.++ ||+++ .+.++||+++|.+|+++++.. | +..|+++
T Consensus 5 ~~~~~~y~~~~-~~~~~l~~~~e~~L~~~~~~~--------------g-------------------------d~~A~~~ 44 (289)
T PRK07500 5 ASADRSMIRSA-MKAPYLEREEEHALAYRWKDH--------------R-------------------------DEDALHR 44 (289)
T ss_pred hhHHHHHHHHH-hcCCCCCHHHHHHHHHHHHHC--------------C-------------------------CHHHHHH
Confidence 35667 99999 999999999999999987531 3 5789999
Q ss_pred HHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHH-HHHHHHHHHHHhcCCCCCCCcCcc
Q 017761 290 MITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQP-MLIGGSNRQFASHFPTNPEQLDYH 363 (366)
Q Consensus 290 LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~-wIr~~I~R~i~d~~~~V~~~l~~~ 363 (366)
||..|+++|.++|++|.+.|.+++||+|||++||+. ++||+ |.+|+|||. ||+++|.++|+++++.|+ +|.|
T Consensus 45 Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR--~p~~ 121 (289)
T PRK07500 45 IISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVR--GGTS 121 (289)
T ss_pred HHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCcee--cCcc
Confidence 999999999999999999999999999999999994 89999 889999986 599999999999999887 6655
No 15
>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=99.78 E-value=1.9e-19 Score=167.53 Aligned_cols=77 Identities=30% Similarity=0.385 Sum_probs=72.1
Q ss_pred HHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHHH-HHHHHHHHHHhcCCCCCCCc
Q 017761 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQPM-LIGGSNRQFASHFPTNPEQL 360 (366)
Q Consensus 286 AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~w-Ir~~I~R~i~d~~~~V~~~l 360 (366)
||++||.+|++||.++|++|.++|++++||||||++|||. ++||| |++|+|||.| |+++|.++|.++++.|+ +
T Consensus 1 a~~~Li~~~~~lv~~ia~~~~~~~~~~eDLiQeG~igL~~A~~~fd~~~g~~FstYA~~~Ir~~I~~~l~~~~~~vr--i 78 (238)
T TIGR02393 1 AKKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIR--I 78 (238)
T ss_pred CHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCChHHHhHHHHHHHHHHHHHHcCCcEE--e
Confidence 6899999999999999999999999999999999999994 89999 9999999865 99999999999999986 8
Q ss_pred Cccc
Q 017761 361 DYHF 364 (366)
Q Consensus 361 ~~~~ 364 (366)
|.|.
T Consensus 79 p~~~ 82 (238)
T TIGR02393 79 PVHM 82 (238)
T ss_pred CHHH
Confidence 8764
No 16
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=99.74 E-value=6.8e-18 Score=165.56 Aligned_cols=112 Identities=29% Similarity=0.366 Sum_probs=103.0
Q ss_pred CCChhH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhhhHHHHH
Q 017761 210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD 288 (366)
Q Consensus 210 ~~D~l~-YLkei~~~~~LLt~eEE~eLa~~Iq~l~~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~G~~AR~ 288 (366)
..|.++ ||.+| +..|+||+++|..|..+++. | +..|++
T Consensus 51 ~~~~~~~y~~~~-~~~~~l~~~ee~~li~~~~~---------------G-------------------------d~~A~~ 89 (325)
T PRK05657 51 VLDATQLYLNEI-GYSPLLTAEEEVYFARRALR---------------G-------------------------DFAARQ 89 (325)
T ss_pred cccHHHHHHHHH-hcCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHH
Confidence 367888 99999 99999999999999998876 4 568999
Q ss_pred HHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHHH-HHHHHHHHHHhcCCCCCCCcCcc
Q 017761 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQPM-LIGGSNRQFASHFPTNPEQLDYH 363 (366)
Q Consensus 289 kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~w-Ir~~I~R~i~d~~~~V~~~l~~~ 363 (366)
.||..|.++|.++|++|.+.+.+.+||+|||++||+. .+||+ |++|+||++| |++.|.++|.++.++|+ +|.|
T Consensus 90 ~Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir--~p~~ 167 (325)
T PRK05657 90 RMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIR--LPVH 167 (325)
T ss_pred HHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccc--cCHH
Confidence 9999999999999999999999999999999999994 89998 8999999887 99999999999999986 8877
Q ss_pred c
Q 017761 364 F 364 (366)
Q Consensus 364 ~ 364 (366)
.
T Consensus 168 ~ 168 (325)
T PRK05657 168 V 168 (325)
T ss_pred H
Confidence 3
No 17
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=99.71 E-value=2.2e-17 Score=156.03 Aligned_cols=80 Identities=19% Similarity=0.178 Sum_probs=73.2
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccC-CCChhhHHHHhHHHHHh--ccCCC--CCCccccHH-HHHHHHHHHHHhcCCCC
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGA-GMNLQDLVQDVEALLEV--QKSST--PPKVSSSQP-MLIGGSNRQFASHFPTN 356 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~-Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~-wIr~~I~R~i~d~~~~V 356 (366)
+..|+++||.+|++||++||++|.++ +.+++||||||+|||+. ++||| |++|+||+. ||+++|.++++++.++|
T Consensus 23 d~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~~v 102 (256)
T PRK07408 23 SIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTV 102 (256)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcCCee
Confidence 46899999999999999999999876 77799999999999994 89999 999999986 59999999999999999
Q ss_pred CCCcCccc
Q 017761 357 PEQLDYHF 364 (366)
Q Consensus 357 ~~~l~~~~ 364 (366)
+ +|.|.
T Consensus 103 r--~pr~~ 108 (256)
T PRK07408 103 R--IPRRW 108 (256)
T ss_pred e--eCHHH
Confidence 8 88763
No 18
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=99.67 E-value=3.9e-16 Score=149.30 Aligned_cols=112 Identities=29% Similarity=0.346 Sum_probs=101.4
Q ss_pred CCCCChhH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhhhHHH
Q 017761 208 VDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILC 286 (366)
Q Consensus 208 ~~~~D~l~-YLkei~~~~~LLt~eEE~eLa~~Iq~l~~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~G~~A 286 (366)
.-..|.++ ||.+| +..+.|+.++|.+|...++. | ...|
T Consensus 9 ~~~~~~~~~~~~~~-~~~~~~~~~~~~~li~~~~~---------------g-------------------------d~~a 47 (285)
T TIGR02394 9 TRVADVTQLYLREI-GFKPLLTAEEEIAYARRALA---------------G-------------------------DFEA 47 (285)
T ss_pred cCcchHHHHHHHHH-hccCCCCHHHHHHHHHHHHc---------------C-------------------------CHHH
Confidence 34578999 99999 99999999999999988876 4 4789
Q ss_pred HHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHHH-HHHHHHHHHHhcCCCCCCCcC
Q 017761 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQPM-LIGGSNRQFASHFPTNPEQLD 361 (366)
Q Consensus 287 R~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~w-Ir~~I~R~i~d~~~~V~~~l~ 361 (366)
++.|+..|.++|.++|.+|.+.+.+.+||+|||+|||+. ++||+ |++|+||++| |+++|++++.+++++|+ +|
T Consensus 48 ~~~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain~~i~~~~~~~~--~p 125 (285)
T TIGR02394 48 RKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIR--LP 125 (285)
T ss_pred HHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHHHHHHHcCCcee--Cc
Confidence 999999999999999999999999999999999999994 89999 8999999987 88999999999888776 55
Q ss_pred c
Q 017761 362 Y 362 (366)
Q Consensus 362 ~ 362 (366)
-
T Consensus 126 ~ 126 (285)
T TIGR02394 126 V 126 (285)
T ss_pred H
Confidence 3
No 19
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=99.63 E-value=9.7e-16 Score=146.29 Aligned_cols=70 Identities=20% Similarity=0.205 Sum_probs=65.7
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCC-ChhhHHHHhHHHHH--hccCCC--CCCccccHH-HHHHHHHHHHHhcC
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGM-NLQDLVQDVEALLE--VQKSST--PPKVSSSQP-MLIGGSNRQFASHF 353 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl-~~~DLIQEG~iGLi--~ekFD~--G~rFSTYA~-wIr~~I~R~i~d~~ 353 (366)
...++ +||+.|+|||.+||++|.++|. .++||||.|||||| +++||+ |.+|+|||. .|+|+|.++++++.
T Consensus 22 ~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~LR~~~ 97 (247)
T COG1191 22 DEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKND 97 (247)
T ss_pred CHHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHHHHhCC
Confidence 46788 9999999999999999999998 99999999999999 489999 999999975 69999999999987
No 20
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=99.60 E-value=3.6e-15 Score=140.36 Aligned_cols=101 Identities=25% Similarity=0.294 Sum_probs=89.2
Q ss_pred hcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhhhHHHHHHHHHHcHHHHHH
Q 017761 221 TSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVIS 300 (366)
Q Consensus 221 ~~~~~LLt~eEE~eLa~~Iq~l~~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~G~~AR~kLI~sNLRLVvs 300 (366)
|++.|+|++++|.+|+.+++. | +..|+++|+..|+++|.+
T Consensus 10 ~~~~~~l~~~~~~~li~~~~~---------------g-------------------------d~~a~~~L~~~~~~~v~~ 49 (254)
T TIGR02850 10 TSKLPVLKNQEMRELFIRMQS---------------G-------------------------DTTAREKLINGNLRLVLS 49 (254)
T ss_pred ccCCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHHHhHHHHHH
Confidence 478999999999999887775 3 467899999999999999
Q ss_pred HHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHH-HHHHHHHHHHHhcCCCCCCCcCccc
Q 017761 301 IAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQP-MLIGGSNRQFASHFPTNPEQLDYHF 364 (366)
Q Consensus 301 IAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~-wIr~~I~R~i~d~~~~V~~~l~~~~ 364 (366)
+|++|.+.+.+.+||+|||++||+. ++||+ |.+|+||+. ||++.|.++++++. +|+ +|.|.
T Consensus 50 ~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~-~ir--~p~~~ 115 (254)
T TIGR02850 50 VIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIR--VSRSL 115 (254)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCC-Ccc--CchHH
Confidence 9999999999999999999999995 89998 789999976 59999999999965 554 77663
No 21
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=99.58 E-value=2.2e-15 Score=142.76 Aligned_cols=74 Identities=15% Similarity=0.125 Sum_probs=66.3
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHccc---CCCChhhHHHHhHHHHH--hccCCC--CCCccccHH-HHHHHHHHHHHhcCC
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQG---AGMNLQDLVQDVEALLE--VQKSST--PPKVSSSQP-MLIGGSNRQFASHFP 354 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g---~Gl~~~DLIQEG~iGLi--~ekFD~--G~rFSTYA~-wIr~~I~R~i~d~~~ 354 (366)
+..||++||..|++||+++|++|.+ .+++++||+|+|+|||+ +++||| |++|+|||. ||+++|.++|+++.|
T Consensus 21 ~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~ 100 (257)
T PRK05911 21 EIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQDW 100 (257)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCC
Confidence 5779999999999999999999862 35689999999999999 489999 999999986 599999999999876
Q ss_pred CCC
Q 017761 355 TNP 357 (366)
Q Consensus 355 ~V~ 357 (366)
+|
T Consensus 101 -~p 102 (257)
T PRK05911 101 -VP 102 (257)
T ss_pred -CC
Confidence 45
No 22
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=99.57 E-value=1e-14 Score=137.48 Aligned_cols=99 Identities=25% Similarity=0.302 Sum_probs=87.3
Q ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhhhHHHHHHHHHHcHHHHHHH
Q 017761 222 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI 301 (366)
Q Consensus 222 ~~~~LLt~eEE~eLa~~Iq~l~~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~G~~AR~kLI~sNLRLVvsI 301 (366)
.+.|+|+++|+..|..+++. | +..|+++|+..|+++|.++
T Consensus 14 ~~~~~l~~~~~~~l~~~~~~---------------g-------------------------d~~a~~~l~~~~~~~v~~~ 53 (258)
T PRK08215 14 SKLPVLKNEEMRELFERMQN---------------G-------------------------DKEAREKLINGNLRLVLSV 53 (258)
T ss_pred CCCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHHHHHHHHHHH
Confidence 56789999999999887775 3 5688999999999999999
Q ss_pred HHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHH-HHHHHHHHHHHhcCCCCCCCcCcc
Q 017761 302 AKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQP-MLIGGSNRQFASHFPTNPEQLDYH 363 (366)
Q Consensus 302 AkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~-wIr~~I~R~i~d~~~~V~~~l~~~ 363 (366)
|++|.+.+.+.+||+|||++||+. ++||+ |.+|+||+. ||+++|.++++++. +|+ +|.|
T Consensus 54 a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~~-~vr--ip~~ 117 (258)
T PRK08215 54 IQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIR--VSRS 117 (258)
T ss_pred HHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-ceE--ecHH
Confidence 999999999999999999999995 89998 789999975 59999999999975 554 6544
No 23
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=99.45 E-value=2e-13 Score=129.46 Aligned_cols=99 Identities=17% Similarity=0.088 Sum_probs=84.4
Q ss_pred hhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhhhHHHHHHHHHHcHHHHH
Q 017761 220 TTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVI 299 (366)
Q Consensus 220 i~~~~~LLt~eEE~eLa~~Iq~l~~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~G~~AR~kLI~sNLRLVv 299 (366)
+.|+.|+||.++|.+|+..++.. | +..+.+.|+..|++||.
T Consensus 5 ~~~~~~~~~~~~e~~l~~~~~~~--------------~-------------------------d~~a~~~l~~~y~~lv~ 45 (268)
T PRK06288 5 MSGKIPKYAQQDETELWREYKKT--------------G-------------------------DPKIREYLILKYSPLVK 45 (268)
T ss_pred ccCCCccccchHHHHHHHHHHHc--------------C-------------------------CHHHHHHHHHHHHHHHH
Confidence 35889999999999999987741 2 56789999999999999
Q ss_pred HHHHHcc-c--CCCChhhHHHHhHHHHHh--ccCCC--CCCccccHH-HHHHHHHHHHHhcCCCCCC
Q 017761 300 SIAKNYQ-G--AGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQP-MLIGGSNRQFASHFPTNPE 358 (366)
Q Consensus 300 sIAkrY~-g--~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~-wIr~~I~R~i~d~~~~V~~ 358 (366)
.+|++|. | .+.+.+||+|||++||+. ++||+ |.+|+||+. ||++.|.+++++..| +|.
T Consensus 46 ~~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~~~-~p~ 111 (268)
T PRK06288 46 YVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSIDW-IPR 111 (268)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcCc-cCH
Confidence 9999986 2 577899999999999994 89998 789999976 599999999987643 443
No 24
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=99.42 E-value=2.7e-13 Score=124.63 Aligned_cols=78 Identities=23% Similarity=0.229 Sum_probs=72.2
Q ss_pred HHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHH-HHHHHHHHHHHhcCCCCCC
Q 017761 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQP-MLIGGSNRQFASHFPTNPE 358 (366)
Q Consensus 284 ~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~-wIr~~I~R~i~d~~~~V~~ 358 (366)
..|++.||..|.++|.++|++|.++|.+.+||+|||++||+. ++||+ |.+|+||+. ||++.|.++++++.|.|+
T Consensus 2 ~~a~~~lv~~y~~~v~~~a~~~~~~~~~~eDl~Qe~~i~l~~a~~~f~~~~~~~F~ty~~~~i~~~~~~~~r~~~~~~r- 80 (227)
T TIGR02980 2 KEAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVR- 80 (227)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCcHHHHHHHHHHHHHHHHHHcCCcee-
Confidence 468999999999999999999999999999999999999995 89999 899999986 599999999999998887
Q ss_pred CcCcc
Q 017761 359 QLDYH 363 (366)
Q Consensus 359 ~l~~~ 363 (366)
+|.|
T Consensus 81 -i~~~ 84 (227)
T TIGR02980 81 -VPRR 84 (227)
T ss_pred -cCHH
Confidence 7755
No 25
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=99.41 E-value=1.2e-12 Score=122.98 Aligned_cols=99 Identities=21% Similarity=0.124 Sum_probs=86.3
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhhhHHHHHHHHHHcHHHHHHHHH
Q 017761 224 SRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAK 303 (366)
Q Consensus 224 ~~LLt~eEE~eLa~~Iq~l~~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~G~~AR~kLI~sNLRLVvsIAk 303 (366)
.+.|++++|.+|..+++.. | +..|.++|+..|.++|+.+|+
T Consensus 7 ~~~l~~~~~~~li~~~~~~--------------g-------------------------d~~a~~~l~~~y~~~v~~~a~ 47 (255)
T TIGR02941 7 PTNLTKEDVIQWIAEFQQN--------------Q-------------------------NGEAQEKLVDHYQNLVYSIAY 47 (255)
T ss_pred CCCCCHHHHHHHHHHHHHC--------------C-------------------------CHHHHHHHHHHhHHHHHHHHH
Confidence 3668999998888777751 2 468999999999999999999
Q ss_pred HcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHH-HHHHHHHHHHHhcCCCCCCCcCcc
Q 017761 304 NYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQP-MLIGGSNRQFASHFPTNPEQLDYH 363 (366)
Q Consensus 304 rY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~-wIr~~I~R~i~d~~~~V~~~l~~~ 363 (366)
+|.+.+.+.+||+|||++||+. ++||+ |.+|+||+. ||++.|.++++++.|.|+ +|.|
T Consensus 48 ~~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~ir--i~~~ 110 (255)
T TIGR02941 48 KYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKTWSVH--VPRR 110 (255)
T ss_pred HHhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHHHHHHHHcCCCcC--CCHH
Confidence 9999999999999999999996 89998 889999976 599999999999988775 5543
No 26
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=99.36 E-value=3.1e-12 Score=120.20 Aligned_cols=100 Identities=19% Similarity=0.111 Sum_probs=86.6
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhhhHHHHHHHHHHcHHHHHHHH
Q 017761 223 SSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIA 302 (366)
Q Consensus 223 ~~~LLt~eEE~eLa~~Iq~l~~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~G~~AR~kLI~sNLRLVvsIA 302 (366)
..+.|++++|.+|..+++.. | +..|.+.|+..|.++|.++|
T Consensus 6 ~~~~l~~~e~~~li~~~~~~--------------g-------------------------d~~a~~~l~~~~~~~v~~~a 46 (257)
T PRK08583 6 QPTKLTKEEVNKWIAEYQEN--------------Q-------------------------DEEAQEKLVKHYKNLVESLA 46 (257)
T ss_pred cCCcCChHHHHHHHHHHHHc--------------C-------------------------CHHHHHHHHHHHHHHHHHHH
Confidence 34789999999888776641 2 46899999999999999999
Q ss_pred HHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHH-HHHHHHHHHHHhcCCCCCCCcCcc
Q 017761 303 KNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQP-MLIGGSNRQFASHFPTNPEQLDYH 363 (366)
Q Consensus 303 krY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~-wIr~~I~R~i~d~~~~V~~~l~~~ 363 (366)
++|.+.+.+.+||+|||++||+. ++||+ |.+|.||+. ||++++.++++.+.|.++ +|.|
T Consensus 47 ~~~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~~~--i~r~ 110 (257)
T PRK08583 47 YKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVH--VPRR 110 (257)
T ss_pred HHHhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHHHHHHhcCCCcC--CCHH
Confidence 99999999999999999999994 79998 779999975 599999999999988766 6655
No 27
>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=99.30 E-value=5.7e-12 Score=116.35 Aligned_cols=78 Identities=27% Similarity=0.247 Sum_probs=69.8
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHH-HHHHHHHHHHHhcCCCCC
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQP-MLIGGSNRQFASHFPTNP 357 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~-wIr~~I~R~i~d~~~~V~ 357 (366)
+..|.++|+..|.++|.++|++|.+.+.+.+||+|||++||+. .+||+ |.+|+||+. ||+++|.++++++. .|+
T Consensus 9 d~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~~~-~i~ 87 (231)
T TIGR02885 9 DKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDG-IIK 87 (231)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-CeE
Confidence 5789999999999999999999999999999999999999995 89998 789999975 59999999999976 544
Q ss_pred CCcCcc
Q 017761 358 EQLDYH 363 (366)
Q Consensus 358 ~~l~~~ 363 (366)
+|.|
T Consensus 88 --~p~~ 91 (231)
T TIGR02885 88 --VSRS 91 (231)
T ss_pred --CCHH
Confidence 5544
No 28
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=99.25 E-value=1.1e-11 Score=116.09 Aligned_cols=70 Identities=10% Similarity=0.010 Sum_probs=61.1
Q ss_pred HHHHHHHHHcHHHHHHHHHHcccC---CCChhhHHHHhHHHHHh--ccCCC-CCCccccHH-HHHHHHHHHHHhcCC
Q 017761 285 LCKDKMITSNIRLVISIAKNYQGA---GMNLQDLVQDVEALLEV--QKSST-PPKVSSSQP-MLIGGSNRQFASHFP 354 (366)
Q Consensus 285 ~AR~kLI~sNLRLVvsIAkrY~g~---Gl~~~DLIQEG~iGLi~--ekFD~-G~rFSTYA~-wIr~~I~R~i~d~~~ 354 (366)
.-+..||..|++||.++|++|.++ +.+.+||||||+|||+. ++||+ +.+|+||+. ||++.|.+++++..|
T Consensus 15 ~~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~F~tYa~~~Ir~~il~~lr~~~~ 91 (231)
T PRK12427 15 QEEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDEQFAAYAVHRIRGAILDELRELDW 91 (231)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHHHHHhcCC
Confidence 346689999999999999999854 57999999999999994 89996 559999975 599999999998655
No 29
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=99.20 E-value=1e-10 Score=108.62 Aligned_cols=101 Identities=19% Similarity=0.233 Sum_probs=88.0
Q ss_pred hhH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhhhHHHHHHHH
Q 017761 213 PLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMI 291 (366)
Q Consensus 213 ~l~-YLkei~~~~~LLt~eEE~eLa~~Iq~l~~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~G~~AR~kLI 291 (366)
.+. |+.++ ++.++||+++|..|...++. | +..|.+.|+
T Consensus 17 ~~~~~~~~~-~~~~~~~~~~e~~l~~~~~~---------------g-------------------------d~~a~~~l~ 55 (233)
T PRK05803 17 FLVSYVKNN-SFPQPLSEEEERKYLELMKE---------------G-------------------------DEEARNILI 55 (233)
T ss_pred HHHHHHHHh-cccCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHH
Confidence 456 99999 99999999999988877664 3 468899999
Q ss_pred HHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHHH-HHHHHHHHHHhcCC
Q 017761 292 TSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQPM-LIGGSNRQFASHFP 354 (366)
Q Consensus 292 ~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~w-Ir~~I~R~i~d~~~ 354 (366)
..+.++|.++|.+|.+.+.+.+||+|||.|||+. ++||+ |.+|.||+.+ ++..+.++++.+.+
T Consensus 56 ~~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~ 123 (233)
T PRK05803 56 ERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKK 123 (233)
T ss_pred HHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999999999999999994 89998 6789999765 78888888876543
No 30
>TIGR02895 spore_sigI RNA polymerase sigma-I factor. Members of this sigma factor protein family are strictly limited to endospore-forming species in the Firmicutes lineage of bacteria, but are not universally present among such species. Sigma-I was shown to be induced by heat shock (PubMed:11157964) in Bacillus subtilis and is suggested by its phylogenetic profile to be connected to the program of sporulation (PubMed:16311624).
Probab=99.18 E-value=4e-11 Score=112.67 Aligned_cols=74 Identities=8% Similarity=0.012 Sum_probs=65.7
Q ss_pred hhhhHHHHHHHHHHcHHHHHHHHHHcccCC--CChhhHHHHhHHHHH--hccCCC--CCCccccHH-HHHHHHHHHHHhc
Q 017761 280 LNYGILCKDKMITSNIRLVISIAKNYQGAG--MNLQDLVQDVEALLE--VQKSST--PPKVSSSQP-MLIGGSNRQFASH 352 (366)
Q Consensus 280 L~~G~~AR~kLI~sNLRLVvsIAkrY~g~G--l~~~DLIQEG~iGLi--~ekFD~--G~rFSTYA~-wIr~~I~R~i~d~ 352 (366)
++.|...++.||..|.++|.++|++|.+++ .+.+||+|+|++||+ +++||+ |..|.|||. +|++.|.+++++.
T Consensus 4 ~~~gd~~~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dylRk~ 83 (218)
T TIGR02895 4 IQPGNEEREELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYIRKN 83 (218)
T ss_pred hhcCChHHHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHhc
Confidence 344555599999999999999999998875 589999999999999 489999 889999975 5999999999987
Q ss_pred C
Q 017761 353 F 353 (366)
Q Consensus 353 ~ 353 (366)
.
T Consensus 84 ~ 84 (218)
T TIGR02895 84 Q 84 (218)
T ss_pred c
Confidence 7
No 31
>PRK05572 sporulation sigma factor SigF; Validated
Probab=99.15 E-value=1.9e-10 Score=108.17 Aligned_cols=92 Identities=26% Similarity=0.272 Sum_probs=81.3
Q ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhhhHHHHHHHHHHcHHHHHHH
Q 017761 222 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI 301 (366)
Q Consensus 222 ~~~~LLt~eEE~eLa~~Iq~l~~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~G~~AR~kLI~sNLRLVvsI 301 (366)
.+.|.||.+++.+|...++. | ...|.++|+..|.++|.++
T Consensus 9 ~~~~~l~~~~~~~li~~~~~---------------g-------------------------d~~a~~~L~~~y~~~v~~~ 48 (252)
T PRK05572 9 KKKPQLKDEENKELIKKSQD---------------G-------------------------DQEARDTLVEKNLRLVWSV 48 (252)
T ss_pred cCCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHHHhHHHHHHH
Confidence 45789999999888766554 3 4678999999999999999
Q ss_pred HHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHH-HHHHHHHHHHHhcC
Q 017761 302 AKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQP-MLIGGSNRQFASHF 353 (366)
Q Consensus 302 AkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~-wIr~~I~R~i~d~~ 353 (366)
|++|.+.+.+.+||+|||.++|+. ++||+ |.+|.||+. ||+++|.+++++..
T Consensus 49 a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~~~ 105 (252)
T PRK05572 49 VQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG 105 (252)
T ss_pred HHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHhCC
Confidence 999999999999999999999995 89998 789999976 59999999999864
No 32
>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=99.11 E-value=6.9e-11 Score=108.84 Aligned_cols=68 Identities=19% Similarity=0.126 Sum_probs=60.2
Q ss_pred HHHHcHHHHHHHHHHccc---CCCChhhHHHHhHHHHHh--ccCCC--CCCccccHH-HHHHHHHHHHHhcCCCCCC
Q 017761 290 MITSNIRLVISIAKNYQG---AGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQP-MLIGGSNRQFASHFPTNPE 358 (366)
Q Consensus 290 LI~sNLRLVvsIAkrY~g---~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~-wIr~~I~R~i~d~~~~V~~ 358 (366)
|+..|+++|.++|++|.+ .+.+.+||+|||++||+. ++||+ |++|+||+. ||++.+.++++.+.+ +|.
T Consensus 1 L~~~~~~lv~~~a~~~~~~~~~~~~~eDl~Qe~~~~l~~a~~~fd~~~~~~f~t~~~~~i~~~~~~~lr~~~~-~p~ 76 (224)
T TIGR02479 1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLDW-VPR 76 (224)
T ss_pred CHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHHcCc-cCH
Confidence 688999999999999986 789999999999999994 89999 789999975 599999999998654 443
No 33
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=99.09 E-value=2e-10 Score=106.80 Aligned_cols=73 Identities=19% Similarity=0.136 Sum_probs=66.9
Q ss_pred hhHHHHHHHHHHcHHHHHHHHHHcc---cCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHH-HHHHHHHHHHHhcC
Q 017761 282 YGILCKDKMITSNIRLVISIAKNYQ---GAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQP-MLIGGSNRQFASHF 353 (366)
Q Consensus 282 ~G~~AR~kLI~sNLRLVvsIAkrY~---g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~-wIr~~I~R~i~d~~ 353 (366)
+|..++++|+..|.++|.++|++|. +.+.+.+||+|||++||+. ++||+ |.+|+||+. ||++.+.++++.+.
T Consensus 5 ~~~~~~~~L~~~~~~~v~~~a~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~~~lR~~~ 84 (236)
T PRK06986 5 EGKMDQDELVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLD 84 (236)
T ss_pred cccccHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHcC
Confidence 4889999999999999999999997 6789999999999999994 89998 799999975 59999999999876
Q ss_pred C
Q 017761 354 P 354 (366)
Q Consensus 354 ~ 354 (366)
+
T Consensus 85 ~ 85 (236)
T PRK06986 85 W 85 (236)
T ss_pred C
Confidence 5
No 34
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=99.08 E-value=4.7e-10 Score=105.51 Aligned_cols=72 Identities=14% Similarity=-0.030 Sum_probs=65.2
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHccc---CCCChhhHHHHhHHHHHh--ccCCC--CCCccccHH-HHHHHHHHHHHhcCC
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQG---AGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQP-MLIGGSNRQFASHFP 354 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g---~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~-wIr~~I~R~i~d~~~ 354 (366)
...|.++|+..|.++|.++|.+|.+ .+.+.+||+|||++||+. ++||+ |.+|+||+. ||++.|.++++++.+
T Consensus 20 d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~d~lR~~~~ 99 (251)
T PRK07670 20 DPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKEDW 99 (251)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcCC
Confidence 4789999999999999999999975 688999999999999994 89999 799999985 599999999998764
No 35
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=98.63 E-value=1.9e-07 Score=86.55 Aligned_cols=72 Identities=18% Similarity=0.225 Sum_probs=63.4
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHHH-HHHHHHHHHHhcCC
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQPM-LIGGSNRQFASHFP 354 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~w-Ir~~I~R~i~d~~~ 354 (366)
+..|.+.|+..+.++|..+|.+|.+.+.+.+||+||+.++|+. .+||+ +.+|.||+.. +++.+.++++.+.+
T Consensus 50 d~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~d~lRk~~~ 126 (234)
T PRK08301 50 DEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNNK 126 (234)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 4678999999999999999999999999999999999999994 79998 5688999754 88888888886654
No 36
>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=98.63 E-value=2.9e-07 Score=85.42 Aligned_cols=99 Identities=17% Similarity=0.234 Sum_probs=82.0
Q ss_pred HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhhhHHHHHHHHHHcH
Q 017761 216 YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNI 295 (366)
Q Consensus 216 YLkei~~~~~LLt~eEE~eLa~~Iq~l~~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~G~~AR~kLI~sNL 295 (366)
|.-.--+..+.|++.+|..|...++. | +..|.+.|+..|.
T Consensus 19 ~~~~~~~~~~~~~~~~~~~li~~~~~---------------g-------------------------d~~af~~l~~~y~ 58 (227)
T TIGR02846 19 YVTNNGSFPQPLSEEEEKKYLDRLKE---------------G-------------------------DEEARNVLIERNL 58 (227)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHHHhH
Confidence 55444356778999999988877765 3 4678999999999
Q ss_pred HHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHHH-HHHHHHHHHHhcCC
Q 017761 296 RLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQPM-LIGGSNRQFASHFP 354 (366)
Q Consensus 296 RLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~w-Ir~~I~R~i~d~~~ 354 (366)
++|.++|.+|.+.+.+.+||+||+.++|+. ++|++ +..|.||+.+ ++..+.++++...+
T Consensus 59 ~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~Rk~~r 122 (227)
T TIGR02846 59 RLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHLRALKK 122 (227)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHHHHHhc
Confidence 999999999999999999999999999994 79997 5789999765 77888888876543
No 37
>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=98.52 E-value=1.7e-07 Score=70.07 Aligned_cols=66 Identities=14% Similarity=0.028 Sum_probs=58.2
Q ss_pred HHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHHH-HHHHHHHHHHhcCCC
Q 017761 290 MITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQPM-LIGGSNRQFASHFPT 355 (366)
Q Consensus 290 LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~w-Ir~~I~R~i~d~~~~ 355 (366)
|++.|.++|..++.+|.+.+.+.+|++||+.++|+. +.||+ |..|.+|... ++..+.+.++.+.|+
T Consensus 1 L~~~~~~~l~~~~~~~~~~~~~~eD~~qe~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~r~~~rr 71 (71)
T PF04542_consen 1 LYERYYPLLYRYARRYTGDPEDAEDLVQEAFIKLWRAIDSYDPDRGDSFRAWLFRIARNRILDYLRKRRRR 71 (71)
T ss_dssp HHHHTHHHHHHHHHTCTTCSSHHHHHHHHHHHHHHHHHHHTSTTSSSHHHHHHHHHHHHHHHHHHHCSSSS
T ss_pred CHHHHHHHHHHHHHHHhCCHhhHHHHhhHHHHHHHhhhhcccccccCCHHHHHHHHHHHHHHHHHHHhcCC
Confidence 688999999999999999999999999999999994 89997 6579999765 888888888877653
No 38
>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=98.46 E-value=1e-06 Score=82.24 Aligned_cols=72 Identities=19% Similarity=0.221 Sum_probs=62.4
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHHH-HHHHHHHHHHhcCC
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQPM-LIGGSNRQFASHFP 354 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~w-Ir~~I~R~i~d~~~ 354 (366)
+..|.+.|+..+.++|.+++.+|.+.+.+-+||+||+.++++. ++|++ +.+|.||+.. ++..+.++++.+.+
T Consensus 50 d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~d~~Rk~~r 126 (234)
T TIGR02835 50 DESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILMYLRRNNK 126 (234)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence 5789999999999999999999999999999999999999994 79997 4578888754 77788888876554
No 39
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=98.23 E-value=2.6e-06 Score=70.11 Aligned_cols=69 Identities=13% Similarity=0.055 Sum_probs=60.5
Q ss_pred HHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhcCC
Q 017761 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASHFP 354 (366)
Q Consensus 286 AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~~~ 354 (366)
|.+.++..|.++|.+++++|.+.+.+.+|++|||.++|+. ..||+...|.+|+.+ ++..+.++++.+.+
T Consensus 2 a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rk~~~ 73 (158)
T TIGR02937 2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRR 73 (158)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCcchHHHHHHHHHHHHHHHHHHHhcc
Confidence 5688999999999999999999999999999999999994 788887788888765 77888888877665
No 40
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=98.16 E-value=7.8e-06 Score=77.83 Aligned_cols=80 Identities=8% Similarity=0.069 Sum_probs=66.5
Q ss_pred HHHHhhhhh-HHHHHHHHHHcHHHHHHHHHHcccCCC--ChhhHHHHhHHHHH--hccCCC--CCCccccHHH-HHHHHH
Q 017761 275 ELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGM--NLQDLVQDVEALLE--VQKSST--PPKVSSSQPM-LIGGSN 346 (366)
Q Consensus 275 ~L~~~L~~G-~~AR~kLI~sNLRLVvsIAkrY~g~Gl--~~~DLIQEG~iGLi--~ekFD~--G~rFSTYA~w-Ir~~I~ 346 (366)
.|...+..| ..|.+.|+..+.++|..+|.+|.++.. ..+|++|+|.++++ .++||+ |..|.+|+.. |+..+.
T Consensus 7 ~Li~~~~~gD~~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn~~i 86 (237)
T PRK08311 7 DILEKIKNGDEELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKRRLI 86 (237)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHH
Confidence 334444444 779999999999999999999998876 48999999999999 489998 5589999764 889999
Q ss_pred HHHHhcCC
Q 017761 347 RQFASHFP 354 (366)
Q Consensus 347 R~i~d~~~ 354 (366)
++++.+.+
T Consensus 87 DylRk~~~ 94 (237)
T PRK08311 87 DYFRKESK 94 (237)
T ss_pred HHHHHhhc
Confidence 99887665
No 41
>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=98.13 E-value=8.2e-07 Score=62.04 Aligned_cols=33 Identities=42% Similarity=0.554 Sum_probs=29.2
Q ss_pred CChhH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHH
Q 017761 211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLK 244 (366)
Q Consensus 211 ~D~l~-YLkei~~~~~LLt~eEE~eLa~~Iq~l~~ 244 (366)
+||++ ||++| +++||||++||++|+++|+.+..
T Consensus 1 ~D~l~~Yl~ei-~~~~LLt~eeE~~LA~~i~~g~~ 34 (37)
T PF00140_consen 1 SDSLRLYLKEI-GRYPLLTAEEEIELARRIRKGDE 34 (37)
T ss_dssp HHHHHHHHHHH-HHS-EETTHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHH-cCCCCCCHHHHHHHHHHHHHhHH
Confidence 37999 99999 99999999999999999998644
No 42
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=98.06 E-value=1.7e-05 Score=71.35 Aligned_cols=70 Identities=14% Similarity=0.045 Sum_probs=59.6
Q ss_pred hhHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHH-HHHHHHHHHHHh
Q 017761 282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQP-MLIGGSNRQFAS 351 (366)
Q Consensus 282 ~G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~-wIr~~I~R~i~d 351 (366)
....+.+.|+..+.++|..+|.+|.+.+.+.+||+||+.++|+. ..||+ |..|.||+. +++..+.++++.
T Consensus 21 ~d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n~~~d~~r~ 95 (208)
T PRK08295 21 GDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQIITAIKT 95 (208)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHH
Confidence 34789999999999999999999999999999999999999994 89987 368888865 466666666654
No 43
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=98.00 E-value=1.3e-05 Score=69.44 Aligned_cols=72 Identities=7% Similarity=-0.126 Sum_probs=61.4
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhcCC
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASHFP 354 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~~~ 354 (366)
...|.++|+..+.++|..++++|.+.+.+.+|++||+.++|+. ..||.+.+|.+|+.. ++..+.+.++...+
T Consensus 8 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~r~~~~ 82 (182)
T PRK09652 8 DRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKQGR 82 (182)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHHHHHHcccC
Confidence 4679999999999999999999999999999999999999994 788877789988765 77777777765443
No 44
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=97.96 E-value=2.6e-05 Score=72.52 Aligned_cols=91 Identities=13% Similarity=0.099 Sum_probs=69.2
Q ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhhhHHHHHHHHHHcHHHHHHH
Q 017761 222 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI 301 (366)
Q Consensus 222 ~~~~LLt~eEE~eLa~~Iq~l~~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~G~~AR~kLI~sNLRLVvsI 301 (366)
...|+|+...+..|...++. | +..|-+.|+..|.++|..+
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 45778888888777776654 3 5678899999999999999
Q ss_pred HHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhc
Q 017761 302 AKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASH 352 (366)
Q Consensus 302 AkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~ 352 (366)
|.+|.+.+-+.+||+||+.++|+. +.|++...|.||... ++..+.++++.+
T Consensus 47 a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~~~~~~wL~~iarn~~~d~~Rk~ 100 (231)
T PRK11922 47 ARAILRNDAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLNEALGRLRRR 100 (231)
T ss_pred HHHHhCChhhHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHHhh
Confidence 999999999999999999999995 688875445555432 444444444443
No 45
>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=97.93 E-value=4.1e-05 Score=68.17 Aligned_cols=78 Identities=13% Similarity=0.081 Sum_probs=62.0
Q ss_pred HHHHHHhhhhh-HHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHH-HHHHHHH
Q 017761 273 QRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQP-MLIGGSN 346 (366)
Q Consensus 273 ~~~L~~~L~~G-~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~-wIr~~I~ 346 (366)
..+|-..+..| ..|-+.|+..+.+.|..+|.+|.+...+.+||+||+.+.+.. .+||+ +..|.||.. +|+..+.
T Consensus 6 ~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~~~~ 85 (198)
T TIGR02859 6 DEEIVELARQGNTHALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTRQII 85 (198)
T ss_pred hHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHHHHH
Confidence 33444444444 789999999999999999999999999999999999999994 78987 578999874 3555554
Q ss_pred HHHH
Q 017761 347 RQFA 350 (366)
Q Consensus 347 R~i~ 350 (366)
++++
T Consensus 86 ~~~r 89 (198)
T TIGR02859 86 TAIK 89 (198)
T ss_pred HHHH
Confidence 4554
No 46
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=97.87 E-value=4.8e-05 Score=67.70 Aligned_cols=74 Identities=5% Similarity=0.016 Sum_probs=59.3
Q ss_pred hhhhhHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC-CCCccccHHH-HHHHHHHHHHhc
Q 017761 279 RLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST-PPKVSSSQPM-LIGGSNRQFASH 352 (366)
Q Consensus 279 ~L~~G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~-G~rFSTYA~w-Ir~~I~R~i~d~ 352 (366)
....+..|.+.|+..|.++|..+|.+|.+.+.+.+||+||+.++|+. ..||+ +..|.+|..- ++..+.++++.+
T Consensus 14 ~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~~~~f~~wl~~ia~n~~~d~~R~~ 91 (186)
T PRK05602 14 VAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPGEARFDTWLHRVVLNLCYDRLRRR 91 (186)
T ss_pred HHCcCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCCCCcHHHHHHHHHHHHHHHHHHhc
Confidence 33445889999999999999999999999999999999999999994 78987 4667776543 555555555544
No 47
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=97.86 E-value=4.7e-05 Score=68.16 Aligned_cols=79 Identities=5% Similarity=-0.109 Sum_probs=61.3
Q ss_pred HHHhhhhhHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhc
Q 017761 276 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASH 352 (366)
Q Consensus 276 L~~~L~~G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~ 352 (366)
++........|.+.|+..|.+.|.++|.+|.+...+.+|++||+.++|+. ..|+.+..|.+|... ++..+.++++.+
T Consensus 17 ~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~~~f~~wl~~i~~n~~~~~~R~~ 96 (194)
T PRK12513 17 MLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIARNLLIDHWRRH 96 (194)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHHHh
Confidence 33333344889999999999999999999999999999999999999995 678775556666543 556666666654
Q ss_pred CC
Q 017761 353 FP 354 (366)
Q Consensus 353 ~~ 354 (366)
.+
T Consensus 97 ~~ 98 (194)
T PRK12513 97 GA 98 (194)
T ss_pred cc
Confidence 44
No 48
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=97.80 E-value=7.2e-05 Score=65.92 Aligned_cols=70 Identities=9% Similarity=-0.039 Sum_probs=56.2
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhc
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASH 352 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~ 352 (366)
...+.++++..|.++|..+|.+|.|.+.+.+|++||+.++|+. .+|++..+|.+|..- ++..+.++++.+
T Consensus 16 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~~~~~wl~~iarn~~~d~~R~~ 88 (187)
T PRK09641 16 DQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDRLRKR 88 (187)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCcchhHHHHHHHHHHHHHHHHhc
Confidence 4788999999999999999999999999999999999999994 789874466666543 445555555543
No 49
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=97.75 E-value=0.00013 Score=65.17 Aligned_cols=72 Identities=10% Similarity=-0.001 Sum_probs=58.4
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccC----CCChhhHHHHhHHHHHh--ccCCC-CCCccccHHH-HHHHHHHHHHhcCC
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGA----GMNLQDLVQDVEALLEV--QKSST-PPKVSSSQPM-LIGGSNRQFASHFP 354 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~----Gl~~~DLIQEG~iGLi~--ekFD~-G~rFSTYA~w-Ir~~I~R~i~d~~~ 354 (366)
...|.++|+..+.+.|..+|.+|.+. +.+.+|++||+.++|+. ..|+. +..|.||..- ++..+.++++.+.+
T Consensus 22 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~~~r 101 (189)
T PRK09648 22 DRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQGRPFLAFVYGIAAHKVADAHRAAGR 101 (189)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHHHHHHHHHHHHHHhCC
Confidence 37899999999999999999998653 46899999999999994 78876 6778888654 66667777776554
No 50
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=97.71 E-value=9.8e-05 Score=65.06 Aligned_cols=74 Identities=7% Similarity=-0.086 Sum_probs=57.5
Q ss_pred HhhhhhHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHh
Q 017761 278 RRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFAS 351 (366)
Q Consensus 278 ~~L~~G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d 351 (366)
........+..+|+..|.++|.++|.+|.+.+.+.+|++||+.++|+. ..||+...|.||... ++..+.++++.
T Consensus 11 ~~~~gd~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~~wl~~i~~n~~~~~~rk 87 (187)
T TIGR02948 11 EVRKGDENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQRKFSTWLYRIATNLTIDRLRK 87 (187)
T ss_pred HHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCCchHHHHHHHHHHHHHHHHHh
Confidence 333445789999999999999999999999999999999999999994 788874456666443 44444444443
No 51
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=97.69 E-value=0.00017 Score=64.60 Aligned_cols=84 Identities=13% Similarity=0.154 Sum_probs=68.2
Q ss_pred CCHHHHHHhhhh----hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHH
Q 017761 271 VDQRELRRRLNY----GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIG 343 (366)
Q Consensus 271 ~~~~~L~~~L~~----G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~ 343 (366)
++.+.|...+.. +..|.+.|+..|.+.|..+|.+|.+...+.+|++||+.+.|+. ..|+....|.||... ++.
T Consensus 8 ~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~~~~~~~wl~~ia~n 87 (188)
T PRK09640 8 LNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYN 87 (188)
T ss_pred CCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcCCCcchHHHHHHHHH
Confidence 344555556653 5889999999999999999999999999999999999999994 688876678888754 677
Q ss_pred HHHHHHHhcCC
Q 017761 344 GSNRQFASHFP 354 (366)
Q Consensus 344 ~I~R~i~d~~~ 354 (366)
.+.++++.+.+
T Consensus 88 ~~~d~~R~~~~ 98 (188)
T PRK09640 88 ECITQYRKERR 98 (188)
T ss_pred HHHHHHHHhcc
Confidence 77777775443
No 52
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=97.55 E-value=0.00031 Score=62.25 Aligned_cols=79 Identities=9% Similarity=-0.021 Sum_probs=60.9
Q ss_pred HHHHHhh-hhhHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC-CCCccccHHH-HHHHHHHH
Q 017761 274 RELRRRL-NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST-PPKVSSSQPM-LIGGSNRQ 348 (366)
Q Consensus 274 ~~L~~~L-~~G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~-G~rFSTYA~w-Ir~~I~R~ 348 (366)
.+|-..+ .....|.+.++..|.+.|..++++|.+.+.+.+||+||+.+.|+. .+|++ ...|.+|... ++..+.++
T Consensus 11 ~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~~~~~~wl~~ia~n~~~d~ 90 (186)
T PRK13919 11 EALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRGSARAWLLALAHHAAVDH 90 (186)
T ss_pred HHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCccccchHHHHHHHHHHHHHHH
Confidence 3343333 334789999999999999999999999999999999999999994 78876 3467776544 55666666
Q ss_pred HHhc
Q 017761 349 FASH 352 (366)
Q Consensus 349 i~d~ 352 (366)
++.+
T Consensus 91 ~rk~ 94 (186)
T PRK13919 91 VRRR 94 (186)
T ss_pred HHhh
Confidence 6543
No 53
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=97.51 E-value=0.00038 Score=61.02 Aligned_cols=72 Identities=8% Similarity=-0.101 Sum_probs=57.5
Q ss_pred hhhHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhc
Q 017761 281 NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASH 352 (366)
Q Consensus 281 ~~G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~ 352 (366)
..+..|.+.|+..+.+.|..+|.+|.+...+-+|++||+.+.|+. +.|+.+.+|.+|..- ++..+.++++..
T Consensus 14 ~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~~ 88 (176)
T PRK09638 14 KGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRLYKDHLRKQ 88 (176)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHh
Confidence 335789999999999999999999999999999999999999994 778765566666543 555555555543
No 54
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=97.50 E-value=0.00032 Score=62.71 Aligned_cols=71 Identities=15% Similarity=0.050 Sum_probs=57.1
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh-ccCCC-CCCccccHHH-HHHHHHHHHHhcC
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV-QKSST-PPKVSSSQPM-LIGGSNRQFASHF 353 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~-ekFD~-G~rFSTYA~w-Ir~~I~R~i~d~~ 353 (366)
+..|.+.|+..+.++|..++++|.+...+-+|++||+.++|+. ..|++ ...|.||... ++..+.++++.+.
T Consensus 27 d~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~~~f~~wl~~iarn~~~d~~Rk~~ 100 (194)
T PRK12519 27 QSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRKSSYDPKRGSLSSYLLTLTRSRAIDRLRSRR 100 (194)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcccccHHHHHHHHHHHHHHHHHHhcc
Confidence 5789999999999999999999999988999999999999994 45665 3467777544 6666666666543
No 55
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=97.45 E-value=0.00067 Score=60.56 Aligned_cols=70 Identities=9% Similarity=0.001 Sum_probs=54.1
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhc
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASH 352 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~ 352 (366)
...+-++|+..|.+.|..++++|.+..-+.+|++||+.+.++. ..|++...|.+|... .+..+.++++.+
T Consensus 18 d~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~~~~~wl~~ia~n~~~d~~rk~ 90 (193)
T PRK11923 18 DKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAINTAKNHLVSR 90 (193)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCCccHhHHHHHHHHHHHHHHHHh
Confidence 4678999999999999999999999888999999999999994 678774345555432 344455555443
No 56
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=97.45 E-value=0.00057 Score=61.29 Aligned_cols=82 Identities=10% Similarity=-0.043 Sum_probs=61.8
Q ss_pred HHHHHHhhhhh-HHHHHHHHHHcHHHHHHHHHHcccCC---CChhhHHHHhHHHHHh--ccCCC-CCCccccHHH-HHHH
Q 017761 273 QRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAG---MNLQDLVQDVEALLEV--QKSST-PPKVSSSQPM-LIGG 344 (366)
Q Consensus 273 ~~~L~~~L~~G-~~AR~kLI~sNLRLVvsIAkrY~g~G---l~~~DLIQEG~iGLi~--ekFD~-G~rFSTYA~w-Ir~~ 344 (366)
.+.|-..+..| ..|.+.|+..|.++|..++.+|.+.+ .+.+|++||+.++|+. ..|++ ...|.||..- ++..
T Consensus 5 ~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~~~~~wl~~iarn~ 84 (189)
T PRK06811 5 EDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKGSFKKWIAAISKYK 84 (189)
T ss_pred HHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccccHHHHHHHHHHHH
Confidence 34444444444 77999999999999999999998754 4689999999999995 78886 3467777644 5666
Q ss_pred HHHHHHhcCC
Q 017761 345 SNRQFASHFP 354 (366)
Q Consensus 345 I~R~i~d~~~ 354 (366)
+.++++.+.+
T Consensus 85 ~~d~~rk~~~ 94 (189)
T PRK06811 85 AIDYKRKLTK 94 (189)
T ss_pred HHHHHHHhcc
Confidence 6666665443
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=97.43 E-value=0.00066 Score=59.94 Aligned_cols=71 Identities=7% Similarity=0.021 Sum_probs=56.3
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhcC
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASHF 353 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~~ 353 (366)
+..+.+.|+..+.+.|..+|.++.+...+.+||+||+.++|.. .+|++...|.+|... .+..+.+.++.+.
T Consensus 18 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~~~~~~wl~~iarn~~~~~~r~~~ 91 (190)
T TIGR02939 18 EKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGDSAFYTWLYRIAVNTAKNHLVAQG 91 (190)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCCCccHhHHHHHHHHHHHHHHHHhc
Confidence 4779999999999999999999999999999999999999994 678875557776543 4444555554433
No 58
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=97.36 E-value=0.00074 Score=60.84 Aligned_cols=80 Identities=9% Similarity=-0.072 Sum_probs=61.7
Q ss_pred HHHHHhhhh-hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC-CCCccccHHH-HHHHHHHH
Q 017761 274 RELRRRLNY-GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST-PPKVSSSQPM-LIGGSNRQ 348 (366)
Q Consensus 274 ~~L~~~L~~-G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~-G~rFSTYA~w-Ir~~I~R~ 348 (366)
..|-..+.. ...+.++|+..|-++|..++.+|.+..-+-+|++||+.+.|+. .+||+ ...|.+|..- ++..+.++
T Consensus 18 ~~li~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~~~~~wl~~ia~n~~~d~ 97 (194)
T PRK09646 18 DALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARGSALAWLLTLAHRRAVDR 97 (194)
T ss_pred HHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccccHHHHHHHHHHHHHHHH
Confidence 334344433 4789999999999999999999999999999999999999994 78987 3467777543 55555566
Q ss_pred HHhcC
Q 017761 349 FASHF 353 (366)
Q Consensus 349 i~d~~ 353 (366)
++.+.
T Consensus 98 ~r~~~ 102 (194)
T PRK09646 98 VRSEQ 102 (194)
T ss_pred HHhhc
Confidence 65543
No 59
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=97.36 E-value=0.00049 Score=58.89 Aligned_cols=68 Identities=9% Similarity=-0.014 Sum_probs=54.6
Q ss_pred HHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC-CCCccccHHH-HHHHHHHHHHhcC
Q 017761 285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST-PPKVSSSQPM-LIGGSNRQFASHF 353 (366)
Q Consensus 285 ~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~-G~rFSTYA~w-Ir~~I~R~i~d~~ 353 (366)
.|-+.|+..+-++|..+++++. ...+.+|++|||.++|+. ..||+ ...|.+|+.. ++..+.++++.+.
T Consensus 4 ~af~~l~~~y~~~l~~~~~~~~-~~~~aeDi~Qe~~l~l~~~~~~~~~~~~~f~~wl~~i~~n~~ld~~rk~~ 75 (154)
T PRK06759 4 ATFTEAVVLYEGLIVNQIKKLG-IYQDYEEYYQCGLIGLWHAYERYDEKKGSFPAYAVVTVRGYILERLKKEF 75 (154)
T ss_pred ccHHHHHHHHHHHHHHHHHHhC-CcccHHHHHHHHHHHHHHHHHHhCccCCchHHHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999999974 456899999999999995 79986 4468888654 6677777776653
No 60
>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=97.32 E-value=0.0011 Score=58.04 Aligned_cols=75 Identities=12% Similarity=0.032 Sum_probs=59.5
Q ss_pred hhhHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhcCCC
Q 017761 281 NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASHFPT 355 (366)
Q Consensus 281 ~~G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~~~~ 355 (366)
..+..|-+.++..|.+.+..++.+|.+...+.+|++||..+-+.. +.|+++..|.||..- ++..+.++++.+.+.
T Consensus 12 ~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~R~~~~~ 89 (169)
T TIGR02954 12 RGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPKYFNTWLTRILINECIDLLKKKKKV 89 (169)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCccccHHHHHHHHHHHHHHHHHhcCCc
Confidence 335789999999999999999999999999999999999999994 788875567766543 555555666654443
No 61
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=97.27 E-value=0.001 Score=57.53 Aligned_cols=69 Identities=7% Similarity=-0.104 Sum_probs=54.8
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHh
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFAS 351 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d 351 (366)
...|.+.++..+.+.|+++|+++.+.+.+.+||+||+.+.|+. ..|+.+..|.+|..- ++..+..+++.
T Consensus 11 ~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~~~~~~~~~l~~i~~~~~~d~~r~ 82 (179)
T PRK11924 11 DKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRR 82 (179)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHHHh
Confidence 5789999999999999999999999999999999999999994 677755566666543 44444444443
No 62
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=97.26 E-value=0.00073 Score=59.62 Aligned_cols=69 Identities=6% Similarity=-0.069 Sum_probs=53.0
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC-CCCccccHHH-HHHHHHHHHHh
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST-PPKVSSSQPM-LIGGSNRQFAS 351 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~-G~rFSTYA~w-Ir~~I~R~i~d 351 (366)
+..|-.+|+..+.+.|..+|.+|.+...+-+|++||+.+.++. ++|++ +..|.||..- ++..+.+.++.
T Consensus 17 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~~~~~~wl~~ia~n~~~d~~R~ 89 (179)
T PRK12514 17 DRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGLSPMTWLITIARNHAIDRLRA 89 (179)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCcccccHHHHHHHHHHHHHHHHHHh
Confidence 4789999999999999999999999999999999999999994 78876 3334444322 34444444443
No 63
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=97.22 E-value=0.00083 Score=71.80 Aligned_cols=34 Identities=32% Similarity=0.518 Sum_probs=31.7
Q ss_pred CCCChhH-HHHHhhcCCCCCCHHHHHHHHHHHHHHH
Q 017761 209 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLL 243 (366)
Q Consensus 209 ~~~D~l~-YLkei~~~~~LLt~eEE~eLa~~Iq~l~ 243 (366)
.++|||+ ||++| |+++|||+|+|++++++|..+.
T Consensus 101 rt~DPVRMYLREM-G~V~LLTREgEIeIAKRIE~G~ 135 (619)
T PRK05658 101 RTDDPVRMYLREM-GTVELLTREGEIEIAKRIEAGE 135 (619)
T ss_pred CCCChHHHHHHHh-ccCcCCCcHHHHHHHHHHHHHH
Confidence 4689999 99999 9999999999999999999863
No 64
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=97.22 E-value=0.00081 Score=57.73 Aligned_cols=69 Identities=4% Similarity=-0.100 Sum_probs=55.5
Q ss_pred HHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhcCC
Q 017761 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASHFP 354 (366)
Q Consensus 286 AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~~~ 354 (366)
|-+.++..+-++|..+|++|.+...+.+|++||+.+.+.. +.||+...|.+|... ++..+.++++.+.+
T Consensus 2 ~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~~~~ 73 (159)
T TIGR02989 2 AFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGTDFGAWARGIARNKVLNHRRKLGR 73 (159)
T ss_pred HHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHHHHHHhcc
Confidence 4578999999999999999999999999999999999994 789874457777543 55666666665443
No 65
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=97.14 E-value=0.00067 Score=57.50 Aligned_cols=68 Identities=13% Similarity=0.045 Sum_probs=57.1
Q ss_pred HHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHH-HHHHHHHHHHHhcC
Q 017761 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQP-MLIGGSNRQFASHF 353 (366)
Q Consensus 286 AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~-wIr~~I~R~i~d~~ 353 (366)
|-++|+..|.+.|..+++++.+...+.+|++||..++++. .+|+++.+|.+|.. .++..+.+.++.+.
T Consensus 2 a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~~~~~~wl~~i~r~~~~d~~r~~~ 72 (161)
T TIGR02985 2 AFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEVESFKAYLFTIVKNRSLNYLRHKQ 72 (161)
T ss_pred hHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhccccccHHHHHHHHHHHHHHHHHHHHH
Confidence 5578999999999999999998888999999999999994 78888778888864 47777777666544
No 66
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=97.06 E-value=0.0038 Score=55.31 Aligned_cols=73 Identities=7% Similarity=-0.011 Sum_probs=57.3
Q ss_pred hhHHHHHHHHHHcHHHHHHHHHHcccC-C---CChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhcCC
Q 017761 282 YGILCKDKMITSNIRLVISIAKNYQGA-G---MNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASHFP 354 (366)
Q Consensus 282 ~G~~AR~kLI~sNLRLVvsIAkrY~g~-G---l~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~~~ 354 (366)
.+..|.+.|++.+-+.|..+|.+|.+. | -+.+|++||+.+.+.. +.|+.+..|.+|..- ++..+.++++.+.+
T Consensus 19 gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~~~~~~wl~~i~rn~~~d~~Rr~~~ 98 (184)
T PRK12512 19 GDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPGAPFAPWLFAIARNKLIDALRRRGR 98 (184)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCccccHHHHHHHHHHHHHHHHHHhhcc
Confidence 358899999999999999999998753 3 4799999999999984 788776677777654 66666666665443
No 67
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=97.04 E-value=0.0018 Score=57.47 Aligned_cols=73 Identities=7% Similarity=-0.006 Sum_probs=56.6
Q ss_pred hhhhHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC-CCCccccHHH-HHHHHHHHHHhc
Q 017761 280 LNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST-PPKVSSSQPM-LIGGSNRQFASH 352 (366)
Q Consensus 280 L~~G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~-G~rFSTYA~w-Ir~~I~R~i~d~ 352 (366)
...+..+-+.|+..+.++|..+|.+|.+...+-+|++||..+.++. .+|++ ...|.||..- ++..+.++++.+
T Consensus 20 ~~~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~~~wl~~I~~n~~~d~~R~~ 96 (187)
T PRK12534 20 AGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRARGLTWLAMIARNKAIDHLRAN 96 (187)
T ss_pred HcCCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccccHHHHHHHHHHHHHHHHHHhc
Confidence 3345789999999999999999999999999999999999999995 78887 3446566443 444445555543
No 68
>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=96.99 E-value=0.0032 Score=54.50 Aligned_cols=71 Identities=10% Similarity=-0.077 Sum_probs=56.8
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC-CCCccccHHH-HHHHHHHHHHhcC
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST-PPKVSSSQPM-LIGGSNRQFASHF 353 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~-G~rFSTYA~w-Ir~~I~R~i~d~~ 353 (366)
...|-+.|+..+.+.+..++.++.|...+.+|++||+.+.|+. ++|+. +..|.+|..- ++..+.++++.+.
T Consensus 9 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~R~~~ 83 (170)
T TIGR02952 9 EEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKNSFEAWLFTIARNVVNDYFRGSK 83 (170)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccccHHHHHHHHHHHHHHHHHHhcC
Confidence 5789999999999999999998888888999999999999995 78876 3467666543 5666666666543
No 69
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=96.92 E-value=0.0041 Score=55.28 Aligned_cols=77 Identities=9% Similarity=-0.028 Sum_probs=59.0
Q ss_pred HHhhhhhHHHHHHHHHHcHHHHHHHHHHcc-cCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhc
Q 017761 277 RRRLNYGILCKDKMITSNIRLVISIAKNYQ-GAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASH 352 (366)
Q Consensus 277 ~~~L~~G~~AR~kLI~sNLRLVvsIAkrY~-g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~ 352 (366)
......+..|-++++..+-+.|..++.++. +.+.+.+||+||+.+.|+. +.||+...|.+|..- ++..+.++++.+
T Consensus 13 ~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~~~~~~wl~~iarN~~~d~~Rk~ 92 (181)
T PRK12536 13 LRGLAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRADQPLTAWVHAIARYKLMDFLRSR 92 (181)
T ss_pred HHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCCCchHHHHHHHHHHHHHHHHHHH
Confidence 333444678999999999999999998765 4578999999999999994 788875567777543 556666666654
Q ss_pred C
Q 017761 353 F 353 (366)
Q Consensus 353 ~ 353 (366)
.
T Consensus 93 ~ 93 (181)
T PRK12536 93 A 93 (181)
T ss_pred h
Confidence 3
No 70
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=96.89 E-value=0.0031 Score=56.91 Aligned_cols=77 Identities=12% Similarity=0.050 Sum_probs=60.1
Q ss_pred HHhhhhhHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhcC
Q 017761 277 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASHF 353 (366)
Q Consensus 277 ~~~L~~G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~~ 353 (366)
.........+-+.++..+.+.|.+++.++.+...+-+||+||..+-++. +.|+....|.+|..- ++..+.++++.+.
T Consensus 19 ~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~~~f~~wL~~i~rn~~~d~~Rk~~ 98 (192)
T PRK09643 19 AAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDAAVSSWLHRIVVNACLDRLRRAK 98 (192)
T ss_pred HHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHHHHHHHHHccc
Confidence 3333445889999999999999999999999999999999999999994 788875456666543 5555666666543
No 71
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=96.86 E-value=0.0033 Score=56.73 Aligned_cols=78 Identities=10% Similarity=0.001 Sum_probs=59.0
Q ss_pred HHHHHhhhh-hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC-CCCccccHHH-HHHHHHHH
Q 017761 274 RELRRRLNY-GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST-PPKVSSSQPM-LIGGSNRQ 348 (366)
Q Consensus 274 ~~L~~~L~~-G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~-G~rFSTYA~w-Ir~~I~R~ 348 (366)
..|-..+.. +..|-+.|+..|.++|..+|.+|.+...+.+|++||+.+.|+. ..|+. ...|.||..- ++..+.+.
T Consensus 14 ~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~~~~~~wl~~ia~n~~~d~ 93 (196)
T PRK12524 14 EALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGEARVSTWLYRVVCNLCTDR 93 (196)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhccccccchHHHHHHHHHHHHHHHH
Confidence 344444444 4889999999999999999999999999999999999999994 68875 4456666433 44555555
Q ss_pred HHh
Q 017761 349 FAS 351 (366)
Q Consensus 349 i~d 351 (366)
++.
T Consensus 94 ~Rk 96 (196)
T PRK12524 94 LRR 96 (196)
T ss_pred HHh
Confidence 553
No 72
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=96.82 E-value=0.0029 Score=55.64 Aligned_cols=69 Identities=7% Similarity=-0.021 Sum_probs=55.6
Q ss_pred HHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhcCC
Q 017761 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASHFP 354 (366)
Q Consensus 286 AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~~~ 354 (366)
.-+.|+..+-++|..+|.+|.+...+.+|++||..+.|+. +.|+++.+|.+|..- ++..+.++++.+.+
T Consensus 4 ~~~~l~~~y~~~i~~~~~~~~~~~~daeDvvQe~~i~l~~~~~~~~~~~~~~~wl~~i~~n~~~d~~Rk~~~ 75 (173)
T PRK12522 4 KVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTICVRTFYDFYRKKKR 75 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcCCccchHHHHHHHHHHHHHHHHHHhcc
Confidence 3578999999999999999999999999999999999995 788875567776543 56666666665443
No 73
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=96.78 E-value=0.0043 Score=55.88 Aligned_cols=71 Identities=7% Similarity=-0.100 Sum_probs=56.7
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC-CCCccccHHH-HHHHHHHHHHhcC
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST-PPKVSSSQPM-LIGGSNRQFASHF 353 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~-G~rFSTYA~w-Ir~~I~R~i~d~~ 353 (366)
...|-+.|+..|.+.|..+|.+|.+....-+|++||..+.++. ..|+. ...|.+|..- ++..+.++++...
T Consensus 25 d~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~~~~~wL~~iarn~~ld~~Rk~~ 99 (194)
T PRK12531 25 DKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKSALSTWIYTIIRNLCFDLLRKQK 99 (194)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccchHHHHHHHHHHHHHHHHHHHhc
Confidence 4788999999999999999999999888899999999999995 67775 3456666543 5566666666543
No 74
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=96.78 E-value=0.0075 Score=53.79 Aligned_cols=71 Identities=7% Similarity=-0.045 Sum_probs=56.2
Q ss_pred hHHHHHHHHHHcHHHHHHHHH----HcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhcC
Q 017761 283 GILCKDKMITSNIRLVISIAK----NYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASHF 353 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAk----rY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~~ 353 (366)
+..|.+.|+..+.+.|...|+ +|.+...+-+|++||..+.|+. ..|+++..|.+|..- ++..+.++++.+.
T Consensus 19 d~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~~f~~wl~~i~~n~~~d~~R~~~ 96 (184)
T PRK12539 19 DAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQPLTPWVYAIARYKLIDHLRRTR 96 (184)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCCChHHHHHHHHHHHHHHHHHHHh
Confidence 478999999999999999886 5667788999999999999994 688875567777544 5566666666543
No 75
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=96.77 E-value=0.0052 Score=56.19 Aligned_cols=72 Identities=6% Similarity=-0.083 Sum_probs=59.0
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC-CCCccccHHH-HHHHHHHHHHhcCC
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST-PPKVSSSQPM-LIGGSNRQFASHFP 354 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~-G~rFSTYA~w-Ir~~I~R~i~d~~~ 354 (366)
...+-++|+..+.++|..++.+|.+...+-+|++||+.+.++. ..|++ ...|.||... ++..+.++++.+.+
T Consensus 36 d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~~~~~wl~~I~rn~~~d~~Rk~~~ 111 (206)
T PRK12526 36 DKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKGAATTWVYTVMRNAAFDMLRKIKA 111 (206)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCcccchhHHHHHHHHHHHHHHHHHhcc
Confidence 5788899999999999999999998888999999999999994 67876 3457787654 66777777765544
No 76
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=96.71 E-value=0.0079 Score=53.53 Aligned_cols=74 Identities=5% Similarity=-0.112 Sum_probs=60.0
Q ss_pred hhhHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC-CCCccccHHH-HHHHHHHHHHhcCC
Q 017761 281 NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST-PPKVSSSQPM-LIGGSNRQFASHFP 354 (366)
Q Consensus 281 ~~G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~-G~rFSTYA~w-Ir~~I~R~i~d~~~ 354 (366)
..+..|-+.|+..+-+.+..++.++.+...+-+|++||..+.++. ++|+. ...|.+|..- ++..+.++++.+.+
T Consensus 19 ~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~~~~~wL~~iarn~~~d~~r~~~~ 96 (182)
T PRK12537 19 RGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARGSARGWIYSVTRHLALNVLRDTRR 96 (182)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCcccccHHHHHHHHHHHHHHHHHHhccc
Confidence 345789999999999999999999999999999999999999994 78876 4567777543 56666667766543
No 77
>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=96.65 E-value=0.0057 Score=53.84 Aligned_cols=69 Identities=9% Similarity=-0.041 Sum_probs=53.3
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcc----cCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHHH-HHHHHHHHHHh
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQ----GAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQPM-LIGGSNRQFAS 351 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~----g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~w-Ir~~I~R~i~d 351 (366)
...|.+.|+..+.+.|..+|++|. +...+.+|++||+.+.|+. ..|+. +..|.+|... ++..+.++++.
T Consensus 5 ~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~ 82 (189)
T TIGR02984 5 DQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRR 82 (189)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHH
Confidence 468899999999999999999974 3467899999999999994 67765 4567777543 45555555543
No 78
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=96.62 E-value=0.006 Score=54.49 Aligned_cols=79 Identities=11% Similarity=-0.063 Sum_probs=59.7
Q ss_pred HHHHHHhhh-hhHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHH
Q 017761 273 QRELRRRLN-YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQ 348 (366)
Q Consensus 273 ~~~L~~~L~-~G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~ 348 (366)
...|...+. .+..|-+.|+..|.+.+..++.+|.+...+-+|++||+.+.|+. ..|+....|.+|... ++..+.+.
T Consensus 9 ~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~~~~~~wl~~i~~n~~~d~ 88 (189)
T PRK12515 9 DEMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIARFKALSA 88 (189)
T ss_pred HHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHH
Confidence 344444444 44779999999999999999999999889999999999999994 677765466666433 55555555
Q ss_pred HHh
Q 017761 349 FAS 351 (366)
Q Consensus 349 i~d 351 (366)
++.
T Consensus 89 ~r~ 91 (189)
T PRK12515 89 LRR 91 (189)
T ss_pred HHc
Confidence 554
No 79
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=96.50 E-value=0.0082 Score=56.57 Aligned_cols=69 Identities=14% Similarity=0.024 Sum_probs=54.2
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCC-CCccccHHH-HHHHHHHHHHh
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTP-PKVSSSQPM-LIGGSNRQFAS 351 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G-~rFSTYA~w-Ir~~I~R~i~d 351 (366)
+..+-+.|+..+.+.|..++.+|.|..-+-+|++||..+.++. +.|+++ ..|.+|..- ++..+.++++.
T Consensus 61 d~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~~f~~WL~~IarN~~id~~Rk 133 (233)
T PRK12538 61 DEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRAKFSTWLYRVVSNRCIDLRRK 133 (233)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHh
Confidence 4779999999999999999999999888999999999999994 788763 456666433 44444444443
No 80
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=96.45 E-value=0.0092 Score=52.22 Aligned_cols=68 Identities=18% Similarity=-0.010 Sum_probs=53.4
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHh
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFAS 351 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d 351 (366)
...+-+.|+..+.+.|..++.+|.|. -+.+|++||..+.|+. +.|+.+..|.+|..- ++..+.++++.
T Consensus 9 d~~a~~~l~~~~~~~l~~~~~~~~~~-~~aeDivQe~~l~l~~~~~~~~~~~~~~~wl~~ia~n~~~d~~R~ 79 (175)
T PRK12518 9 DRQSFRQLYRRYQQKVRSTLYQLCGR-ELLDDLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNVATDARRQ 79 (175)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCH-hHHHHHHHHHHHHHHHhHHhhCCcccHHHHHHHHHHHHHHHHHHH
Confidence 47889999999999999999998764 5789999999999994 778876567777543 44555555554
No 81
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=96.33 E-value=0.0088 Score=51.78 Aligned_cols=67 Identities=10% Similarity=-0.106 Sum_probs=52.6
Q ss_pred HHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHhccCCCCCCccccHHH-HHHHHHHHHHh
Q 017761 285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEVQKSSTPPKVSSSQPM-LIGGSNRQFAS 351 (366)
Q Consensus 285 ~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~ekFD~G~rFSTYA~w-Ir~~I~R~i~d 351 (366)
.+-++|+..|.+.+..+|.++.+...+-+|++||+.+.++...|+.+..|.||..- ++..+.++++.
T Consensus 3 ~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~~~~~~~~~~~wl~~i~rn~~~d~~rk 70 (166)
T PRK09639 3 ETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRSDFKGIENEKGWLIKSARNVAYNYLRS 70 (166)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHHH
Confidence 46678999999999999999999999999999999999996556555456666543 55555555544
No 82
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=96.11 E-value=0.015 Score=51.65 Aligned_cols=69 Identities=10% Similarity=-0.034 Sum_probs=54.7
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHh
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFAS 351 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d 351 (366)
...|-..|+..|.+.|..++.+|.+..-+-+|++||..+.|+. ..|++...|.+|..- ++..+.++++.
T Consensus 5 d~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~~f~~wl~~iarn~~~~~~r~ 76 (179)
T PRK12543 5 DQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRPFRFWLIGLVIKQIHSWRRK 76 (179)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCCChHHHHHHHHHHHHHHHHHh
Confidence 4678899999999999999999999999999999999999994 788874456666433 44445555543
No 83
>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=96.00 E-value=0.015 Score=45.26 Aligned_cols=40 Identities=30% Similarity=0.381 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhh
Q 017761 243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY 282 (366)
Q Consensus 243 ~~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~ 282 (366)
.++.+.+.+|+.++||+||..|.|..+|++.++++..+..
T Consensus 4 ~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~ 43 (78)
T PF04539_consen 4 RKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQA 43 (78)
T ss_dssp HHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHh
Confidence 4567788999999999999999999999999888876653
No 84
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=95.99 E-value=0.018 Score=51.20 Aligned_cols=69 Identities=12% Similarity=0.017 Sum_probs=54.3
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHh
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFAS 351 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d 351 (366)
...|-++|+..+-+.|..++.+|.+..-+-+|++||+.+.|+. ..|+.+..|.+|... ++..+.++++.
T Consensus 14 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~~~~~awl~~ia~n~~~d~~Rk 85 (179)
T PRK09415 14 KEDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYLKS 85 (179)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHHHHh
Confidence 4788899999999999999999999888999999999999995 678764456666433 44444455543
No 85
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=95.90 E-value=0.037 Score=49.33 Aligned_cols=78 Identities=9% Similarity=-0.049 Sum_probs=59.3
Q ss_pred hhhhhHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhcCCC
Q 017761 279 RLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASHFPT 355 (366)
Q Consensus 279 ~L~~G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~~~~ 355 (366)
.......+-+.++..+.+-+...+.++.|...+-+||+||.++.++. ..|+.+..|.||..- ++.....+++...+.
T Consensus 9 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~~~~~~~~~wl~~Ia~n~~iD~~R~~~r~ 88 (182)
T COG1595 9 ALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSFRGRSSFKAWLYRIARNLAIDRLRKRKRR 88 (182)
T ss_pred HHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHHHHHHHHHHHHHhccc
Confidence 33445778889999999999999999999888999999999999995 677446677777654 455555555544443
Q ss_pred C
Q 017761 356 N 356 (366)
Q Consensus 356 V 356 (366)
.
T Consensus 89 ~ 89 (182)
T COG1595 89 R 89 (182)
T ss_pred c
Confidence 3
No 86
>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=95.72 E-value=0.029 Score=48.47 Aligned_cols=69 Identities=13% Similarity=0.090 Sum_probs=54.1
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHh
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFAS 351 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d 351 (366)
+..+-+.++..+.+.|..++.+|.+...+-+|++||..+-+.. ..|+.+..|.+|..- ++..+.++++.
T Consensus 4 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~rk 75 (162)
T TIGR02983 4 TEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRDPDAPDAYVRRVLVNLARSRWRR 75 (162)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCCcccHHHHHHHHHHHHHHHHHHh
Confidence 5678899999999999999999999999999999999999994 667655566666433 44444555543
No 87
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=95.25 E-value=0.069 Score=49.12 Aligned_cols=69 Identities=10% Similarity=0.001 Sum_probs=55.0
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhc
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASH 352 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~ 352 (366)
...+-++|+..|.+.+..++.+|.+....-+||+||..+.++. ..|+++ .|.+|... ++..+.++++.+
T Consensus 26 d~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~~-~~~~wL~~iarn~~~d~~Rk~ 97 (203)
T PRK09647 26 TMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQPG-TFEGWLHRITTNLFLDMVRRR 97 (203)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc-ccHHHHHHHHHHHHHHHHHhc
Confidence 3678899999999999999999999999999999999999994 677643 46666433 556666666544
No 88
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=95.01 E-value=0.074 Score=46.56 Aligned_cols=69 Identities=12% Similarity=-0.038 Sum_probs=53.4
Q ss_pred HHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhc
Q 017761 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASH 352 (366)
Q Consensus 284 ~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~ 352 (366)
......++..+.+.|..+|.++.+...+-+|++||..+.|+. +.|+.+..|.+|..- ++..+.+.++.+
T Consensus 5 ~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~~~~wl~~i~~n~~~d~~R~~ 76 (164)
T PRK12547 5 SKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRNEFYSQMRKR 76 (164)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCcccHHHHHHHHHHHHHHHHHHhh
Confidence 355678999999999999999999999999999999999995 677764456666433 455555555543
No 89
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=94.76 E-value=0.084 Score=45.75 Aligned_cols=69 Identities=7% Similarity=-0.004 Sum_probs=53.1
Q ss_pred HHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhcC
Q 017761 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASHF 353 (366)
Q Consensus 284 ~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~~ 353 (366)
..+-++++..+.+.|..++.++.|..-+-+|++||..+-++. +.|+.+ .|.||... ++..+.++++.+.
T Consensus 4 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R~~~ 75 (161)
T PRK12541 4 KQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE-EIRPWLFTIAYNAFIDWYRKEK 75 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC-ChHHHHHHHHHHHHHHHHHhcc
Confidence 457788999999999999999999999999999999999884 677653 56666543 4455555555433
No 90
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=94.75 E-value=0.075 Score=47.71 Aligned_cols=65 Identities=14% Similarity=-0.024 Sum_probs=48.5
Q ss_pred HHHHHcHHHHHHHHHHcccCCCC-hhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhcC
Q 017761 289 KMITSNIRLVISIAKNYQGAGMN-LQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASHF 353 (366)
Q Consensus 289 kLI~sNLRLVvsIAkrY~g~Gl~-~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~~ 353 (366)
..+..+-+.|..+|.++.+..-+ -+|++||..+.++. ..|+....|.+|..- ++..+.++++.+.
T Consensus 9 ~~~~~~~~~l~~~a~~~~~~~~~~AEDivQevfl~~~~~~~~~~~~~~~~~wL~~Ia~n~~~d~~Rk~~ 77 (195)
T PRK12532 9 AELIESRKLLLHFARLQLPDHPDLAEDLVQETLLSAYSAGDSFQGRALVNSWLFAILKNKIIDALRQIG 77 (195)
T ss_pred hhHHHHHHHHHHHHHHHcCChhhhHHHHHHHHHHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHhc
Confidence 45777889999999999988777 99999999999995 677754456666443 4555555665543
No 91
>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=94.74 E-value=0.14 Score=45.17 Aligned_cols=69 Identities=12% Similarity=0.017 Sum_probs=51.7
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCC-----ChhhHHHHhHHHHHh---ccCCCCCCccccH-HHHHHHHHHHHHh
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGM-----NLQDLVQDVEALLEV---QKSSTPPKVSSSQ-PMLIGGSNRQFAS 351 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl-----~~~DLIQEG~iGLi~---ekFD~G~rFSTYA-~wIr~~I~R~i~d 351 (366)
+..|-+.|+..+.+.+..+|.+|.+... +-+|++||..+.++. ..|+....|.+|. .+++..+.+.++.
T Consensus 15 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~R~ 92 (183)
T TIGR02999 15 DAAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDRAHFFAAAAKAMRRILVDHARR 92 (183)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHHHHHHH
Confidence 4679999999999999999999987766 899999999999985 2354433455553 2345555555554
No 92
>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=94.72 E-value=0.16 Score=48.42 Aligned_cols=82 Identities=11% Similarity=-0.065 Sum_probs=61.1
Q ss_pred CHHHHHHhhhhh-HHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh---------ccCCCCCCccccHHH-
Q 017761 272 DQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV---------QKSSTPPKVSSSQPM- 340 (366)
Q Consensus 272 ~~~~L~~~L~~G-~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~---------ekFD~G~rFSTYA~w- 340 (366)
+...|...+..| ..|-..|+..+.+.|..++.++.+...+-+|++||..+-++. ..|+....|.||...
T Consensus 25 ~d~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~~~~~tWL~~I 104 (244)
T TIGR03001 25 ADLYLACACAQGEPAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGRGPLLSWVRIV 104 (244)
T ss_pred cHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCCCchHhHHHHH
Confidence 445566666665 679999999999999999999989999999999999999983 345544456666433
Q ss_pred HHHHHHHHHHhcC
Q 017761 341 LIGGSNRQFASHF 353 (366)
Q Consensus 341 Ir~~I~R~i~d~~ 353 (366)
++..+.+.++.+.
T Consensus 105 a~N~~id~lRk~~ 117 (244)
T TIGR03001 105 ATRIALELQAQER 117 (244)
T ss_pred HHHHHHHHHHHhc
Confidence 4555566665443
No 93
>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=94.68 E-value=0.091 Score=47.10 Aligned_cols=70 Identities=10% Similarity=-0.019 Sum_probs=54.2
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhc
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASH 352 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~ 352 (366)
...+-+.|+..+.+.|...+.++.+...+-+|++||-.+-+.. ..|+++..|.+|... ++..+.+.++.+
T Consensus 9 ~~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~~~~~~wL~~iarN~~~d~~Rk~ 81 (193)
T TIGR02947 9 RAQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPGTNLKAWLYRILTNTYINSYRKA 81 (193)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCCCcchHHHHHHHHHHHHHHHHHh
Confidence 3567889999999999999999999888899999999999995 677765456665433 445555555543
No 94
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=94.62 E-value=0.14 Score=50.13 Aligned_cols=70 Identities=7% Similarity=-0.046 Sum_probs=55.7
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhc
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASH 352 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~ 352 (366)
...+-+.|+..|.+.|..+|.+|.+...+-+|++||-.+-++. ..|+....|.+|..- .+..+.++++.+
T Consensus 17 d~~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~~~~~~wL~~Ia~n~~~d~~Rk~ 89 (339)
T PRK08241 17 DRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGRSSLRTWLYRIATNVCLDALEGR 89 (339)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccccchHHHHHHHHHHHHHHHHHhh
Confidence 4788999999999999999999999888999999999999995 677765556666443 455555555543
No 95
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=94.56 E-value=0.069 Score=48.15 Aligned_cols=67 Identities=9% Similarity=-0.097 Sum_probs=53.5
Q ss_pred HHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhcCC
Q 017761 288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASHFP 354 (366)
Q Consensus 288 ~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~~~ 354 (366)
.+.|..+.+.|..++.++.+.-.+-+|++||..+.++. +.|+....|.+|..- ++..+.++++.+.+
T Consensus 5 ~~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~~~~~~wL~~iarn~~~d~~R~~~r 74 (188)
T TIGR02943 5 PQELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGRSALKTWLFAILKNKIIDALRAKGR 74 (188)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccccHHHHHHHHHHHHHHHHHHHhhcc
Confidence 35688899999999999999999999999999999995 677765567777543 56777777776544
No 96
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=94.53 E-value=0.083 Score=47.28 Aligned_cols=69 Identities=7% Similarity=-0.095 Sum_probs=53.0
Q ss_pred HHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhcCC
Q 017761 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASHFP 354 (366)
Q Consensus 286 AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~~~ 354 (366)
+-+.|+..+.+.|...|.++.+...+-+|++||-.+.++. +.|+....|.||..- ++..+.+.++.+.+
T Consensus 3 ~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~~~~~~WL~~ia~n~~~d~~Rk~~r 74 (191)
T PRK12520 3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQSSLKTYLVGILKHKIIDAIRSGRR 74 (191)
T ss_pred chHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhcccccHHHHHHHHHHHHHHHHHHhhcC
Confidence 4568999999999999999999888999999999999995 677654455555433 55666666665444
No 97
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=94.22 E-value=0.081 Score=46.15 Aligned_cols=63 Identities=11% Similarity=-0.047 Sum_probs=46.9
Q ss_pred HHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHh
Q 017761 288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFAS 351 (366)
Q Consensus 288 ~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d 351 (366)
+.|+..|-+.|..++.+|.+...+-+||+||..+.++. +.|++ .+|.+|..- ++..+.++++.
T Consensus 4 ~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~-~~~~~wL~~i~~n~~~d~~R~ 69 (165)
T PRK09644 4 EEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDN-QKVKPWLFKVAYHTFIDFVRK 69 (165)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhccc-cchHHHHHHHHHHHHHHHHHh
Confidence 46899999999999999999999999999999999984 67875 345554322 33334444443
No 98
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=94.18 E-value=0.056 Score=48.14 Aligned_cols=71 Identities=10% Similarity=-0.036 Sum_probs=54.5
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCccccHHH-HHHHHHHHHHhcC
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQPM-LIGGSNRQFASHF 353 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~w-Ir~~I~R~i~d~~ 353 (366)
...+-..|+..+-+.+..+|.+|.+...+-+|++||..+.++. +.|+. +..|.||... ++..+.++++.+.
T Consensus 7 d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~ 82 (185)
T PRK12542 7 DYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNK 82 (185)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4678899999999999999999999888999999999999995 67874 2345555433 4455555555443
No 99
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=94.15 E-value=0.17 Score=45.72 Aligned_cols=71 Identities=14% Similarity=0.001 Sum_probs=55.9
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhcC
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASHF 353 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~~ 353 (366)
+..+-..|+..|.+.+...|.++.+..-+-+|++||-.+-++. ..|+....|.+|... ++..+.++++.+.
T Consensus 8 ~~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~~~~~awL~~Ia~n~~~d~~R~~~ 81 (187)
T PRK12516 8 GTPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYSQMRKRG 81 (187)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCcccHHHHHHHHHHHHHHHHHHhhc
Confidence 4678889999999999999999999888999999999999984 677764456666443 4555556665543
No 100
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=94.14 E-value=0.13 Score=46.25 Aligned_cols=65 Identities=8% Similarity=0.008 Sum_probs=51.2
Q ss_pred HHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhc
Q 017761 288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASH 352 (366)
Q Consensus 288 ~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~ 352 (366)
+.|...+-+.|..+|.++.|...+.+|++||-.+.++. ..|+.+..|.+|..- ++..+.++++.+
T Consensus 4 ~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~~~~~~~wL~~i~~n~~~d~~Rk~ 71 (181)
T PRK09637 4 ESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRKK 71 (181)
T ss_pred HHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhccccchHHHHHHHHHHHHHHHHHhc
Confidence 57899999999999999999999999999999999995 677765566666543 555555555543
No 101
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=94.07 E-value=0.29 Score=43.87 Aligned_cols=69 Identities=10% Similarity=-0.074 Sum_probs=52.4
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhc
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASH 352 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~ 352 (366)
...|-+.|+..+-+.+..+++ |.+...+-+|++||..+.++. ..|+....|.+|..- ++..+.+.++.+
T Consensus 22 d~~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~~~~~~Wl~~Iarn~~~d~~Rk~ 93 (185)
T PRK09649 22 NGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSARSSARTWLLAIARHVVADHIRHV 93 (185)
T ss_pred CHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCccchHHHHHHHHHHHHHHHHHHHh
Confidence 467899999999999999995 677778899999999999995 678764456666432 555555555543
No 102
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=93.93 E-value=0.18 Score=46.48 Aligned_cols=82 Identities=12% Similarity=-0.042 Sum_probs=61.7
Q ss_pred HhcCCHHHHHHhhhhhHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHH
Q 017761 268 AAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGG 344 (366)
Q Consensus 268 aag~~~~~L~~~L~~G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~ 344 (366)
++.|+...|-..|+. ..++..|-+.+..+|.+|.+....-+|++||..+.++. ..|+...+|.+|..- ++..
T Consensus 6 ~~~~~~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfikl~~~~~~~~~~~~~~~WL~~IarN~ 80 (206)
T PRK12544 6 AVAMDSSDLGNLLQD-----PVFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGRAAFKTWVFAILKNK 80 (206)
T ss_pred hhhcchhhHHHHhhh-----HHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHH
Confidence 345666666655554 46888899999999999999999999999999999984 667654457777543 6677
Q ss_pred HHHHHHhcCC
Q 017761 345 SNRQFASHFP 354 (366)
Q Consensus 345 I~R~i~d~~~ 354 (366)
+.++++.+.+
T Consensus 81 ~~d~~Rk~~~ 90 (206)
T PRK12544 81 IIDLLRQKKR 90 (206)
T ss_pred HHHHHHhhcc
Confidence 7777775444
No 103
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=93.91 E-value=0.21 Score=43.24 Aligned_cols=66 Identities=9% Similarity=0.050 Sum_probs=51.0
Q ss_pred HHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHH-HHHHHHHHHHHh
Q 017761 285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQP-MLIGGSNRQFAS 351 (366)
Q Consensus 285 ~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~-wIr~~I~R~i~d 351 (366)
.|-++|+..+-+.|..++.+|.|...+-+|++||..+-++. ..|++ ..|.+|.. +++..+.++++.
T Consensus 4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~-~~~~~wl~~i~~n~~~d~~R~ 72 (161)
T PRK12528 4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQI-IEPRAFLTTIAKRVLCNHYRR 72 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhccccccc-cCHHHHHHHHHHHHHHHHHHH
Confidence 46678999999999999999999988999999999999995 35543 35666643 355555555554
No 104
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=93.79 E-value=0.19 Score=44.00 Aligned_cols=70 Identities=9% Similarity=-0.109 Sum_probs=55.5
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC-CCCccccHHH-HHHHHHHHHHhc
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST-PPKVSSSQPM-LIGGSNRQFASH 352 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~-G~rFSTYA~w-Ir~~I~R~i~d~ 352 (366)
+..+-+.|+..+.+.+..+|.++.+...+-+|++||-.+-++. +.|+. ...|.+|... ++..+.++++.+
T Consensus 7 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~~~~~~wL~~iarn~~~d~~Rk~ 80 (173)
T PRK09645 7 EAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTGRSARAWLFTVARNLVIDERRSA 80 (173)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccccHHHHHHHHHHHHHHHHHHhh
Confidence 4678899999999999999999998888899999999999995 67764 5567666543 555555566543
No 105
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=93.65 E-value=0.15 Score=45.08 Aligned_cols=62 Identities=13% Similarity=0.001 Sum_probs=48.1
Q ss_pred HcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhcCC
Q 017761 293 SNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASHFP 354 (366)
Q Consensus 293 sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~~~ 354 (366)
.+.+.+..++.++.+...+-+|++||..+.|+. ..|+.+..|.+|..- ++..+.++++.+.+
T Consensus 3 ~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~~~~f~~wl~~iarn~~~d~~Rk~~~ 67 (170)
T TIGR02959 3 EFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDGQKIQSWLYQIARNTIIDFYRSKSR 67 (170)
T ss_pred hHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHHHhccC
Confidence 356678888899999889999999999999994 788876677777543 66667777766543
No 106
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=93.59 E-value=0.24 Score=47.86 Aligned_cols=70 Identities=10% Similarity=-0.018 Sum_probs=54.4
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhc
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASH 352 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~ 352 (366)
...+-+.|+..|-+.+..+|.+|.|...+-+|++||-.+-++. ..|+....|.+|... ++..+.++++.+
T Consensus 3 d~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~~~~~~WL~~Ia~n~~~d~~Rk~ 75 (324)
T TIGR02960 3 DGAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGRSSVRTWLYRIATNACLDALEAR 75 (324)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcccchHHHHHHHHHHHHHHHHHhc
Confidence 3578889999999999999999999888999999999999985 667754456666443 455555555543
No 107
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=93.46 E-value=0.27 Score=45.93 Aligned_cols=69 Identities=7% Similarity=-0.024 Sum_probs=53.8
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhc
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASH 352 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~ 352 (366)
...+-+.|+..+.+.+..++.+|.+..-+-+|++||..+-++. .+|+.+ .|.+|... ++..+.+.++.+
T Consensus 16 ~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~-~~~aWL~~IarN~~~d~~Rk~ 87 (216)
T PRK12533 16 RGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD-NARPWLLAIVRHTWYSEWRRR 87 (216)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc-chHhHHHHHHHHHHHHHHHhh
Confidence 4668889999999999999999999989999999999999994 678754 36666543 444455555543
No 108
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=93.46 E-value=0.19 Score=44.24 Aligned_cols=69 Identities=13% Similarity=0.027 Sum_probs=51.2
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh-ccCCCCCCccccHHH-HHHHHHHHHHh
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV-QKSSTPPKVSSSQPM-LIGGSNRQFAS 351 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~-ekFD~G~rFSTYA~w-Ir~~I~R~i~d 351 (366)
...+..+|+..+-+.|..++.++.+...+-+|++||..+.++. ..|+.+..|.+|..- ++..+.++++.
T Consensus 8 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk 78 (172)
T PRK12523 8 HSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGRPELPTPREPRAFLAAVAKGLMFDHFRR 78 (172)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcccccCcchhHHHHHHHHHHHHHHHHHHH
Confidence 3678899999999999999999999889999999999999994 234333345555322 44445555544
No 109
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=93.13 E-value=0.32 Score=44.10 Aligned_cols=69 Identities=14% Similarity=0.017 Sum_probs=51.7
Q ss_pred HHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhcCC
Q 017761 285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASHFP 354 (366)
Q Consensus 285 ~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~~~ 354 (366)
.+.+.|.. +.+.|...|.++.+...+-+|++||-.+.++. ..|+.+..|.+|..- ++..+.+.++.+.+
T Consensus 8 ~~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~~~~~awL~~ia~n~~~d~~Rk~~r 79 (188)
T PRK12546 8 DPRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNTFYSDRRKHKR 79 (188)
T ss_pred hHHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCCcchHHHHHHHHHHHHHHHHHHhcc
Confidence 44555655 77999999999999999999999999999994 678765456666433 55566666665544
No 110
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=92.89 E-value=0.13 Score=43.74 Aligned_cols=59 Identities=7% Similarity=-0.076 Sum_probs=44.1
Q ss_pred HcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhc
Q 017761 293 SNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASH 352 (366)
Q Consensus 293 sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~ 352 (366)
.+-+.|..++.++.+.--+-+|++||..+.|+. ..|+. .+|.||..- ++..+.++++.+
T Consensus 3 ~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~-~~f~~wl~~i~~~~~~d~~r~~ 64 (154)
T TIGR02950 3 EYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD-SSIKPWLFRIARNAFIDWYRKD 64 (154)
T ss_pred hHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC-CchHHHHHHHHHHHHHHHHHHh
Confidence 567888999999988888899999999999994 68886 566666543 445555555543
No 111
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=92.76 E-value=0.23 Score=42.91 Aligned_cols=62 Identities=15% Similarity=0.150 Sum_probs=43.6
Q ss_pred HHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhc
Q 017761 290 MITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASH 352 (366)
Q Consensus 290 LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~ 352 (366)
++..+.+.++.+|.++.+...+-+|++||..+.++. ..|+++ .|.+|... ++..+.++++.+
T Consensus 3 ~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~-~~~~wl~~iarn~~~d~~R~~ 67 (163)
T PRK07037 3 VFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVK-QPVAYLFRIVRNLAIDHYRRQ 67 (163)
T ss_pred HHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCcc-cHHHHHHHHHHHHHHHHHHhh
Confidence 567788899999999999888999999999999984 344432 34444322 445555555543
No 112
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=92.40 E-value=0.3 Score=43.98 Aligned_cols=67 Identities=9% Similarity=-0.136 Sum_probs=51.8
Q ss_pred HHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhcCC
Q 017761 288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASHFP 354 (366)
Q Consensus 288 ~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~~~ 354 (366)
+..|..+.+-+..+|.+|.|...+-+|++||..+-++. ..|+....|.+|... ++..+.++++.+.+
T Consensus 10 ~~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~~~~~~wL~~Ia~n~~~d~~Rk~~~ 79 (189)
T PRK12530 10 SLEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQSALKTWIFAILKNKIIDLIRYRKR 79 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCCccHHHHHHHHHHHHHHHHHHhhcc
Confidence 45678888899999999999888999999999999995 677764457777544 55666666665443
No 113
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=92.22 E-value=0.38 Score=42.47 Aligned_cols=55 Identities=16% Similarity=0.068 Sum_probs=44.8
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh-ccCCCCCCcccc
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV-QKSSTPPKVSSS 337 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~-ekFD~G~rFSTY 337 (366)
...+-.+++..+-+.+..++.+|.+....-+||+||-.+-++. ..|+.-..|.+|
T Consensus 8 ~~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~~~~~~~~~~~~w 63 (172)
T PRK09651 8 ASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVSETLSTIRDPRSF 63 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhhcccccccCHHHH
Confidence 4678889999999999999999999989999999999999995 335432234444
No 114
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=91.99 E-value=0.47 Score=42.71 Aligned_cols=67 Identities=13% Similarity=0.063 Sum_probs=49.6
Q ss_pred HHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhc
Q 017761 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASH 352 (366)
Q Consensus 286 AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~ 352 (366)
+-..++..+.+.|..+|.++.+...+-+|++||..+.++. ..|++...|-+|..- ++..+.++++.+
T Consensus 6 ~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~~~~~~~~~~WL~~Ia~n~~~d~~Rk~ 75 (182)
T PRK12540 6 SLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGSNLPAWLFTILRNLFRSDYRKR 75 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCchHHHHHHHHHHHHHHHHHHhc
Confidence 4457888999999999999999999999999999999995 678764445555332 444444445443
No 115
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=91.91 E-value=0.25 Score=42.60 Aligned_cols=61 Identities=5% Similarity=-0.045 Sum_probs=45.8
Q ss_pred HHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhcC
Q 017761 292 TSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASHF 353 (366)
Q Consensus 292 ~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~~ 353 (366)
+.|-+.+..+|.++.+..-+-+|++||..+.+.. +.|++ ..|.+|... ++..+.++++.+.
T Consensus 2 ~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~-~~~~~wl~~ia~n~~~d~~Rk~~ 65 (160)
T PRK09642 2 QTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQF-RGLKTWMARIATNHAIDYKRKKA 65 (160)
T ss_pred chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccccccc-chhHHHHHHHHHHHHHHHHHHhc
Confidence 4567889999999999888999999999999995 67775 346666443 5566666665543
No 116
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=91.89 E-value=0.52 Score=42.54 Aligned_cols=59 Identities=8% Similarity=-0.173 Sum_probs=49.9
Q ss_pred hhhHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHH
Q 017761 281 NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQP 339 (366)
Q Consensus 281 ~~G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~ 339 (366)
.....+-+.++..+-+.|..+|.++.+..-+-+|++||..+-++. ..|+++..|.+|..
T Consensus 19 ~~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~~~~~~wL~ 79 (188)
T PRK12517 19 LSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEKAAKAWLI 79 (188)
T ss_pred hccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCccchHHHHH
Confidence 336788999999999999999999999989999999999999994 67876555666543
No 117
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=91.39 E-value=0.89 Score=41.46 Aligned_cols=69 Identities=9% Similarity=-0.081 Sum_probs=50.2
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhc
Q 017761 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASH 352 (366)
Q Consensus 283 G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~ 352 (366)
...+-+.++..+...+..+++ |.+...+-+|++||-.+.|+. +.|++...|-+|..- ++..+..+++.+
T Consensus 23 d~~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~~~~~~WL~~Iarn~~id~~Rk~ 94 (196)
T PRK12535 23 DRAALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAARSSARTWLLSLARRVWVDNIRHD 94 (196)
T ss_pred CHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCcccHHHHHHHHHHHHHHHHHHhh
Confidence 467888999999999999976 567778899999999999994 678764445544332 445555555543
No 118
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=91.08 E-value=0.46 Score=43.23 Aligned_cols=65 Identities=9% Similarity=-0.095 Sum_probs=49.6
Q ss_pred HHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhcCC
Q 017761 290 MITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASHFP 354 (366)
Q Consensus 290 LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~~~ 354 (366)
++..+.+-+..+|.+|.+..-+-+|++||..+.++. +.|+....|.||..- ++..+.++++.+.+
T Consensus 13 ~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~~~~~~WL~~IarN~~~d~~Rk~~r 80 (201)
T PRK12545 13 YLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQSAHKTWVFGILRNKLIDTLRARQR 80 (201)
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhccccchHHHHHHHHHHHHHHHHHHhhcc
Confidence 477888889999999999888999999999999995 678765456666433 55666666665443
No 119
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=87.16 E-value=2.3 Score=37.29 Aligned_cols=41 Identities=7% Similarity=0.049 Sum_probs=37.1
Q ss_pred HHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh
Q 017761 285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV 325 (366)
Q Consensus 285 ~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~ 325 (366)
.+-.++...+-+.+...+.+|.+...+-+|++||-.+-++.
T Consensus 9 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~ 49 (168)
T PRK12525 9 TLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLA 49 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHh
Confidence 45667899999999999999999888999999999999995
No 120
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=86.67 E-value=1.3 Score=39.99 Aligned_cols=68 Identities=10% Similarity=-0.011 Sum_probs=51.2
Q ss_pred HHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHHhcC
Q 017761 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFASHF 353 (366)
Q Consensus 286 AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~d~~ 353 (366)
.++..+....+-|...+.++.+..-+-+|++||-.+-++. ..|+....|.+|..- ++..+.++++.+.
T Consensus 5 ~~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~~~~~~WL~~Iarn~~id~~Rk~~ 75 (182)
T PRK12511 5 SKRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRRRR 75 (182)
T ss_pred chhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCccchHHHHHHHHHHHHHHHHHhhc
Confidence 3455677888889999999999888999999999999994 677764456666443 5566666666543
No 121
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=86.67 E-value=1.1 Score=38.74 Aligned_cols=57 Identities=7% Similarity=-0.023 Sum_probs=36.9
Q ss_pred HcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHHH-HHHHHHHHHH
Q 017761 293 SNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQPM-LIGGSNRQFA 350 (366)
Q Consensus 293 sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~w-Ir~~I~R~i~ 350 (366)
.+..-+...+.++.|..-+-+|++||-.+.|+. ..|++ .+|.||..- ++..+.++++
T Consensus 3 ~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~-~~~~~wL~~ia~n~~~d~~R 62 (159)
T PRK12527 3 NYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQI-EHPRAFLYRTALNLVVDRHR 62 (159)
T ss_pred hHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhccccccc-cchHHHHHHHHHHHHHHHHH
Confidence 455667777777788777889999999999995 44543 345444322 3344444444
No 122
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=86.63 E-value=1 Score=43.40 Aligned_cols=62 Identities=13% Similarity=0.059 Sum_probs=43.9
Q ss_pred HHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHhccCCCCCCccccHHH-HHHHHHHHHHh
Q 017761 290 MITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEVQKSSTPPKVSSSQPM-LIGGSNRQFAS 351 (366)
Q Consensus 290 LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~ekFD~G~rFSTYA~w-Ir~~I~R~i~d 351 (366)
++..|.+.+..+|.++.|...+-+|++||..+-+....|+....|.+|... ++..+.++++.
T Consensus 2 l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~~~~~~~~~~awL~~Ia~n~~ld~lR~ 64 (281)
T TIGR02957 2 EFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEADRAQIENPKAYLTKVVTRRCIDVLRS 64 (281)
T ss_pred hHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhCCcccccCHHHHHHHHHHHHHHHHHHH
Confidence 678899999999999999999999999999999765444322334444322 44444444443
No 123
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=86.11 E-value=1.7 Score=41.90 Aligned_cols=64 Identities=11% Similarity=0.023 Sum_probs=46.1
Q ss_pred HHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh-ccCCCCCCccccHHH-HHHHHHHHHHh
Q 017761 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV-QKSSTPPKVSSSQPM-LIGGSNRQFAS 351 (366)
Q Consensus 287 R~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~-ekFD~G~rFSTYA~w-Ir~~I~R~i~d 351 (366)
...++..|.+.+..+|.+|.|...+-+|++||-.+.+.. ..|+ ...|.+|... ++..+.++++.
T Consensus 6 ~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~~~~~~~~~-~~~~~~WL~~Ia~n~~~d~lR~ 71 (293)
T PRK09636 6 AAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLRWNNADRAQ-IRDPRAWLTRVVTRLCLDRLRS 71 (293)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhccccc-ccCHHHHHHHHHHHHHHHHHHh
Confidence 457899999999999999999989999999999999553 4443 3344444332 44555555554
No 124
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=84.15 E-value=2.8 Score=37.26 Aligned_cols=69 Identities=6% Similarity=-0.207 Sum_probs=46.8
Q ss_pred hhHHHHHHHHHHcHHHHHHHHHHccc--CCCChhhHHHHhHHHHHh--ccCCC--CCCccccHHH-HHHHHHHHHH
Q 017761 282 YGILCKDKMITSNIRLVISIAKNYQG--AGMNLQDLVQDVEALLEV--QKSST--PPKVSSSQPM-LIGGSNRQFA 350 (366)
Q Consensus 282 ~G~~AR~kLI~sNLRLVvsIAkrY~g--~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFSTYA~w-Ir~~I~R~i~ 350 (366)
.+..+-..|+..|.+.|..++.++.+ ..-+-+|++||-.+-++. ..|+. ...|.||... ++..+.++++
T Consensus 10 ~d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~R 85 (178)
T PRK12529 10 ADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRR 85 (178)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHH
Confidence 35678899999999999996544444 346789999999999995 56653 3455555332 3344444444
No 125
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=84.01 E-value=2.7 Score=40.07 Aligned_cols=75 Identities=12% Similarity=-0.040 Sum_probs=49.9
Q ss_pred HHHHhhhhhHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHhccCCCCCCccccHHH-HHHHHHHHHHh
Q 017761 275 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEVQKSSTPPKVSSSQPM-LIGGSNRQFAS 351 (366)
Q Consensus 275 ~L~~~L~~G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~ekFD~G~rFSTYA~w-Ir~~I~R~i~d 351 (366)
.|++.+.-...+.+.+++.+ +.+...+.++.+..-+-+||+||-.+-++. +|+....|.+|..- ++..+.+.++.
T Consensus 8 ~~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~-~~~~~~~~~~WL~~IarN~~id~~Rk 83 (228)
T PRK06704 8 ILKNHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQ-KYSNKDICMTLVYKIARNRWLDQIKS 83 (228)
T ss_pred HHhcccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHH-HcCccccHHHHHHHHHHHHHHHHHhc
Confidence 34444444555666667666 788999999999889999999999999885 46653335444322 34444444443
No 126
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=82.50 E-value=4.8 Score=41.05 Aligned_cols=33 Identities=30% Similarity=0.402 Sum_probs=27.9
Q ss_pred CCCChhH-HHHHhhcCCCCCCHHHHHHHHHHHHHH
Q 017761 209 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDL 242 (366)
Q Consensus 209 ~~~D~l~-YLkei~~~~~LLt~eEE~eLa~~Iq~l 242 (366)
...+.+. |+..+ ...++|+++||..|+..++.+
T Consensus 64 ~~~~~~~~~~~~~-~~~~~l~~~Ee~~la~~~~~g 97 (342)
T COG0568 64 RPAGRLSFYIRAI-EAAPLLTPEEEKALARRLKRG 97 (342)
T ss_pred hhhhhHHHHHHHH-hhhcccChHHHHHHHHHHHcC
Confidence 3455667 99999 889999999999999988765
No 127
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=79.75 E-value=3.9 Score=40.05 Aligned_cols=42 Identities=14% Similarity=0.036 Sum_probs=37.1
Q ss_pred HHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHhcc
Q 017761 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEVQK 327 (366)
Q Consensus 286 AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~ek 327 (366)
.-..++..|.+.+..+|.++.|...+-+|++||-.+-++...
T Consensus 6 ~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~ 47 (290)
T PRK09635 6 PVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAP 47 (290)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcC
Confidence 345788999999999999999999999999999999998643
No 128
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=78.21 E-value=4.3 Score=39.53 Aligned_cols=40 Identities=25% Similarity=0.288 Sum_probs=33.5
Q ss_pred HHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhhh
Q 017761 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYG 283 (366)
Q Consensus 244 ~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~G 283 (366)
+++.+..+|+.++||+||..|.|+..|++.+++...+..+
T Consensus 111 ~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~ 150 (247)
T COG1191 111 RIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAI 150 (247)
T ss_pred HHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHh
Confidence 4556778889999999999999999999998877666554
No 129
>PRK09191 two-component response regulator; Provisional
Probab=76.42 E-value=4.7 Score=36.84 Aligned_cols=53 Identities=9% Similarity=0.011 Sum_probs=44.7
Q ss_pred HHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCCCCCccccHH
Q 017761 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSSTPPKVSSSQP 339 (366)
Q Consensus 287 R~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~G~rFSTYA~ 339 (366)
-..|+..+.+.|...|.++.+..-.-+|++||..+=++. ..|++...|.+|..
T Consensus 3 ~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~~~~~~wl~ 57 (261)
T PRK09191 3 LSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEASSPRVGLY 57 (261)
T ss_pred hHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCCcchhhHHH
Confidence 467899999999999999999888999999999999995 67876556666643
No 130
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=72.85 E-value=8.4 Score=36.74 Aligned_cols=37 Identities=22% Similarity=0.258 Sum_probs=31.3
Q ss_pred HHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhh
Q 017761 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 280 (366)
Q Consensus 244 ~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L 280 (366)
++.+.+.+|...+|++||..|.|+..|+++++++...
T Consensus 114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~ 150 (256)
T PRK07408 114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIK 150 (256)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHH
Confidence 4556677888899999999999999999998877643
No 131
>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=70.84 E-value=10 Score=35.92 Aligned_cols=39 Identities=26% Similarity=0.228 Sum_probs=31.4
Q ss_pred HHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhh
Q 017761 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY 282 (366)
Q Consensus 244 ~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~ 282 (366)
++.+...++..++|++||..|.|+..|++++.+...+..
T Consensus 121 ~~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~ 159 (254)
T TIGR02850 121 KALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFALDA 159 (254)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHh
Confidence 344556777888899999999999999999888766543
No 132
>KOG3099 consensus Bisphosphate 3'-nucleotidase BPNT1/Inositol polyphosphate 1-phosphatase [Nucleotide transport and metabolism]
Probab=69.92 E-value=3.9 Score=41.18 Aligned_cols=64 Identities=19% Similarity=0.151 Sum_probs=52.3
Q ss_pred HHHHHHHHHHcccCCCChhhHHHHhHHHHHhccCCCCCCccccHHH-HHHHHHHHHHhcCCCCCCCc
Q 017761 295 IRLVISIAKNYQGAGMNLQDLVQDVEALLEVQKSSTPPKVSSSQPM-LIGGSNRQFASHFPTNPEQL 360 (366)
Q Consensus 295 LRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~ekFD~G~rFSTYA~w-Ir~~I~R~i~d~~~~V~~~l 360 (366)
.|+|.++++-.+..|.-|++|||||..|..-.+| ++.|=|-|-- |..+|+..+..++.-..++|
T Consensus 9 a~~vAss~r~c~q~~~L~qlllqek~~~~~nksf--~~D~kTlAD~l~Qe~Ikq~l~~kFPgl~~~I 73 (340)
T KOG3099|consen 9 ARKVASSARICQQAGGLFQLLLQEKDLGIVNKSF--AKDLKTLADRLAQECIKQSLGKKFPGLKDNI 73 (340)
T ss_pred HHHHhHHHHHHHHhhHHHHHHHhccccccccccc--ccChHHHHHHHHHHHHHHHHHhhCCCcccce
Confidence 5889999999999999999999999999987777 4467788865 77888888888887555443
No 133
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=69.68 E-value=11 Score=36.17 Aligned_cols=38 Identities=34% Similarity=0.460 Sum_probs=31.3
Q ss_pred HHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhh
Q 017761 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 281 (366)
Q Consensus 244 ~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~ 281 (366)
++.+...+|...+|++||..|.|+..|++++++...+.
T Consensus 128 ~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~ 165 (264)
T PRK07122 128 RLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLV 165 (264)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 44556777888889999999999999999988876554
No 134
>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=69.13 E-value=12 Score=34.99 Aligned_cols=38 Identities=24% Similarity=0.293 Sum_probs=31.2
Q ss_pred HHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhh
Q 017761 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 281 (366)
Q Consensus 244 ~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~ 281 (366)
++.+...+|...+|++||.+|.|...|++.+.+...+.
T Consensus 88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~ 125 (238)
T TIGR02393 88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKK 125 (238)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 34556677888899999999999999999988876543
No 135
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=68.39 E-value=12 Score=37.55 Aligned_cols=38 Identities=21% Similarity=0.329 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhh
Q 017761 243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 280 (366)
Q Consensus 243 ~~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L 280 (366)
.++.+.+.+|...+|++||..|.|+..|++.+.+...+
T Consensus 173 ~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~ 210 (324)
T PRK07921 173 NKLARIKRELHQQLGREATDEELAEESGIPEEKIADLL 210 (324)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 34566778888899999999999999999998887654
No 136
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=67.74 E-value=9.2 Score=36.04 Aligned_cols=38 Identities=21% Similarity=0.316 Sum_probs=30.8
Q ss_pred HHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhh
Q 017761 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 281 (366)
Q Consensus 244 ~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~ 281 (366)
++.+...++..++|++||..|.|+..|++.+++...+.
T Consensus 102 ~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~ 139 (231)
T PRK12427 102 KTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLL 139 (231)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 34455677888889999999999999999988866543
No 137
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=66.81 E-value=13 Score=35.55 Aligned_cols=37 Identities=22% Similarity=0.294 Sum_probs=29.6
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhh
Q 017761 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 281 (366)
Q Consensus 245 le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~ 281 (366)
+.+....|...+|++||..|.|+..|++.+++...+.
T Consensus 112 l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~ 148 (257)
T PRK05911 112 LADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFS 148 (257)
T ss_pred HHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHH
Confidence 3445556777889999999999999999988876554
No 138
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=64.12 E-value=13 Score=31.47 Aligned_cols=59 Identities=10% Similarity=-0.028 Sum_probs=37.5
Q ss_pred HHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--c-----cCCCCCCccccHHH-HHHHHHHHHHh
Q 017761 288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--Q-----KSSTPPKVSSSQPM-LIGGSNRQFAS 351 (366)
Q Consensus 288 ~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--e-----kFD~G~rFSTYA~w-Ir~~I~R~i~d 351 (366)
+.++..+-+++..++++|.+ +|.+||-.+.+.. . .|+.+..|.||..- .+..+.+.++.
T Consensus 2 ~~~~~~y~~~l~~~~~~~~~-----~~~~qdvf~~~w~~~~~~~~~~~~~~~~~~~wL~~iarN~~id~~Rk 68 (142)
T TIGR03209 2 EEIYMNFKNTIDIFTRKYNL-----YYDYNDILYHLWIILKKIDLNKFNTENDLEKYISTSLKRYCLDICNK 68 (142)
T ss_pred hHHHHHHHHHHHHHHHHhcc-----hhhHHHHHHHHHHHHHHhhhhhcCchhHHHHHHHHHHHHHHHHHHHH
Confidence 46889999999999999976 3344777777774 2 34443445555332 44444444543
No 139
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=64.08 E-value=14 Score=37.41 Aligned_cols=39 Identities=23% Similarity=0.283 Sum_probs=32.5
Q ss_pred HHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhh
Q 017761 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY 282 (366)
Q Consensus 244 ~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~ 282 (366)
++.+...+|...+|++||..|.|+..|++.+.++..+..
T Consensus 217 ~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~ 255 (367)
T PRK09210 217 KLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKI 255 (367)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHH
Confidence 355667788889999999999999999999888876543
No 140
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=62.48 E-value=29 Score=29.64 Aligned_cols=38 Identities=8% Similarity=0.230 Sum_probs=29.2
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhh
Q 017761 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY 282 (366)
Q Consensus 245 le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~ 282 (366)
+.++..-+......+++.+++|+.+|+++..|.+....
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 34445556666778899999999999999888876654
No 141
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=60.66 E-value=36 Score=30.74 Aligned_cols=53 Identities=23% Similarity=0.224 Sum_probs=37.0
Q ss_pred HHHhhhhh-HHHHHHHHHHcHHHHHHHHHHccc---CCCChhh--HHHHhHHHHHh-ccC
Q 017761 276 LRRRLNYG-ILCKDKMITSNIRLVISIAKNYQG---AGMNLQD--LVQDVEALLEV-QKS 328 (366)
Q Consensus 276 L~~~L~~G-~~AR~kLI~sNLRLVvsIAkrY~g---~Gl~~~D--LIQEG~iGLi~-ekF 328 (366)
|-..++.| ..|.+.|+..+..-.+.+|+++.+ ++.+.+| |++|..+=+.. ..|
T Consensus 7 ll~~~~~GD~~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~ 66 (185)
T PF07638_consen 7 LLDRWRQGDEAALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRF 66 (185)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccc
Confidence 33444455 789999999999999999987752 2445555 57777777764 444
No 142
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=59.00 E-value=21 Score=38.33 Aligned_cols=38 Identities=24% Similarity=0.316 Sum_probs=32.3
Q ss_pred HHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhh
Q 017761 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 281 (366)
Q Consensus 244 ~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~ 281 (366)
++.+.+.+|...+|++||..|.|+..|++.+.+...++
T Consensus 359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~ 396 (509)
T PRK05901 359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQK 396 (509)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 45667888889999999999999999999988876643
No 143
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=58.01 E-value=23 Score=36.35 Aligned_cols=37 Identities=24% Similarity=0.293 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHh
Q 017761 243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRR 279 (366)
Q Consensus 243 ~~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~ 279 (366)
.++.+....|...+|++||..|.|+..|++.+.++..
T Consensus 223 ~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~ 259 (373)
T PRK07406 223 SRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFI 259 (373)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 3455667788888999999999999999999888654
No 144
>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=56.31 E-value=33 Score=26.67 Aligned_cols=26 Identities=31% Similarity=0.461 Sum_probs=17.2
Q ss_pred hcCCCCchHHHHHHhcCC-HHHHHHhh
Q 017761 255 RCGGSPTFAQWAAAAGVD-QRELRRRL 280 (366)
Q Consensus 255 ~~GrePT~~eWA~aag~~-~~~L~~~L 280 (366)
..|.+||..|.|+++|+. .......|
T Consensus 21 ~~G~~Pt~rEIa~~~g~~S~~tv~~~L 47 (65)
T PF01726_consen 21 ENGYPPTVREIAEALGLKSTSTVQRHL 47 (65)
T ss_dssp HHSS---HHHHHHHHTSSSHHHHHHHH
T ss_pred HcCCCCCHHHHHHHhCCCChHHHHHHH
Confidence 459999999999999985 55544433
No 145
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=55.16 E-value=26 Score=33.06 Aligned_cols=39 Identities=28% Similarity=0.278 Sum_probs=31.7
Q ss_pred HHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhh
Q 017761 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY 282 (366)
Q Consensus 244 ~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~ 282 (366)
++.+....+...+|++|+..++|+..|++.+.++..+..
T Consensus 110 ~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~ 148 (251)
T PRK07670 110 KVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNE 148 (251)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHH
Confidence 345556677788899999999999999999888876653
No 146
>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=54.82 E-value=21 Score=32.96 Aligned_cols=37 Identities=32% Similarity=0.466 Sum_probs=29.3
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhh
Q 017761 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 281 (366)
Q Consensus 245 le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~ 281 (366)
+.+....|...+|++||..|.|+..|++.+++...+.
T Consensus 99 ~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~ 135 (231)
T TIGR02885 99 IRYMKEELSKELGREPTINELAEALGVSPEEIVMALE 135 (231)
T ss_pred HHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3445667777889999999999999999887765443
No 147
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=52.15 E-value=23 Score=37.03 Aligned_cols=39 Identities=21% Similarity=0.291 Sum_probs=33.4
Q ss_pred HHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhh
Q 017761 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY 282 (366)
Q Consensus 244 ~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~ 282 (366)
++.+.+.+|...+|+.||..|.|+..|++.+.++..+..
T Consensus 263 ~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l~~ 301 (415)
T PRK07598 263 KIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLR 301 (415)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 456677788889999999999999999999999877553
No 148
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=51.92 E-value=67 Score=23.59 Aligned_cols=56 Identities=18% Similarity=0.240 Sum_probs=33.8
Q ss_pred CCchHHHHHHhcCCHHHHHHhhhhh--HHHHHHHHHHcHHHHHHHHHHcccC-CCChhhHHHH
Q 017761 259 SPTFAQWAAAAGVDQRELRRRLNYG--ILCKDKMITSNIRLVISIAKNYQGA-GMNLQDLVQD 318 (366)
Q Consensus 259 ePT~~eWA~aag~~~~~L~~~L~~G--~~AR~kLI~sNLRLVvsIAkrY~g~-Gl~~~DLIQE 318 (366)
++|..++|..+|++...|.+.+..- ..-++.+-. .| +.-|..|-.. .+++.|+.++
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~~~s~~~~~~~--~r--~~~a~~~l~~~~~~~~~ia~~ 59 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKETGTTPKQYLRD--RR--LERARRLLRDTDLSVTEIALR 59 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHhCcCHHHHHHH--HH--HHHHHHHHHcCCCCHHHHHHH
Confidence 4688999999999999998877643 222222221 12 2233333322 5778887654
No 149
>PRK05949 RNA polymerase sigma factor; Validated
Probab=51.46 E-value=37 Score=34.03 Aligned_cols=38 Identities=26% Similarity=0.351 Sum_probs=30.7
Q ss_pred HHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhh
Q 017761 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 281 (366)
Q Consensus 244 ~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~ 281 (366)
++.+.+.++..++|++||..|.|+..|++.+.+...+.
T Consensus 179 ~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~ 216 (327)
T PRK05949 179 KIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLS 216 (327)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 34455667777889999999999999999988877653
No 150
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=50.70 E-value=40 Score=31.97 Aligned_cols=37 Identities=27% Similarity=0.237 Sum_probs=30.1
Q ss_pred HHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhh
Q 017761 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 280 (366)
Q Consensus 244 ~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L 280 (366)
++.+...++..++|++|+..|.|...|++++++...+
T Consensus 124 ~~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~~ 160 (258)
T PRK08215 124 KALQVREKLINENSKEPTVEEIAKELEVPREEVVFAL 160 (258)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 3445566777888999999999999999998877654
No 151
>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=48.83 E-value=38 Score=31.26 Aligned_cols=38 Identities=39% Similarity=0.494 Sum_probs=31.3
Q ss_pred HHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhh
Q 017761 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 281 (366)
Q Consensus 244 ~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~ 281 (366)
++.+...+|...+|++|+.+|.|+..|++...++..+.
T Consensus 84 ~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~ 121 (224)
T TIGR02479 84 KLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALN 121 (224)
T ss_pred HHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 45566777888889999999999999999988776553
No 152
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=47.95 E-value=23 Score=30.26 Aligned_cols=43 Identities=16% Similarity=0.095 Sum_probs=26.7
Q ss_pred ChhhHHHHhHHHHHhcc-CCCCCCccccHH-HHHHHHHHHHHhcC
Q 017761 311 NLQDLVQDVEALLEVQK-SSTPPKVSSSQP-MLIGGSNRQFASHF 353 (366)
Q Consensus 311 ~~~DLIQEG~iGLi~ek-FD~G~rFSTYA~-wIr~~I~R~i~d~~ 353 (366)
+-+|++||..+.++... .+++..|.+|.. -++..+.++++.+.
T Consensus 6 ~AeDivQe~fl~~~~~~~~~~~~~~~~wl~~ia~n~~~d~~Rk~~ 50 (161)
T PRK09047 6 AALDIVQDAMIKLAEKYGDRPAAEWPPLFQRILQNRIHDWFRRQK 50 (161)
T ss_pred HHHHHHHHHHHHHHHHHhhcccCchHHHHHHHHHHHHHHHHHhhc
Confidence 46899999999998521 123445665542 25566666665543
No 153
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=45.39 E-value=52 Score=32.68 Aligned_cols=38 Identities=21% Similarity=0.366 Sum_probs=31.2
Q ss_pred HHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhh
Q 017761 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 281 (366)
Q Consensus 244 ~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~ 281 (366)
++.+.+.++...+|++||..|.|+..|++.+.+...+.
T Consensus 169 ~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~ 206 (317)
T PRK07405 169 KIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLE 206 (317)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 45566777778889999999999999999888776643
No 154
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=45.23 E-value=35 Score=32.57 Aligned_cols=37 Identities=24% Similarity=0.355 Sum_probs=31.1
Q ss_pred HHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhh
Q 017761 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 280 (366)
Q Consensus 244 ~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L 280 (366)
++.+.+..|+..+|++||..+.|...|++.+.+...+
T Consensus 119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~ 155 (268)
T PRK06288 119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLL 155 (268)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHH
Confidence 5566677888889999999999999999987776654
No 155
>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=45.20 E-value=46 Score=25.47 Aligned_cols=56 Identities=16% Similarity=0.364 Sum_probs=38.0
Q ss_pred hcCCCCc------hHHHHHHhcCCHHHHHHhhhhhHHHHHHHHHHcHHHHHHHHHHcccCCCC-hhh
Q 017761 255 RCGGSPT------FAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMN-LQD 314 (366)
Q Consensus 255 ~~GrePT------~~eWA~aag~~~~~L~~~L~~G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~-~~D 314 (366)
..||+|| +.+|....|++.+.+...++.... + -..|++-|-.|++++...|+. ++|
T Consensus 8 ~~gr~ls~~e~~~i~~~~~~~~~~~evI~~ai~~a~~---~-~~~~~~Yi~~Il~~W~~~gi~T~e~ 70 (73)
T TIGR01446 8 NFGRMLSPFEMEDLKYWLDEFGNSPELIKEALKEAVS---N-NKANYKYIDAILNNWKNNGIKTVED 70 (73)
T ss_pred HhCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHH---c-CCCCHHHHHHHHHHHHHcCCCCHHH
Confidence 3455555 456777777777777666665322 2 235789999999999999874 444
No 156
>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=43.73 E-value=61 Score=31.64 Aligned_cols=38 Identities=26% Similarity=0.441 Sum_probs=30.7
Q ss_pred HHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhh
Q 017761 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 281 (366)
Q Consensus 244 ~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~ 281 (366)
++.+.+.++...+|++||..+.|...|++.+.+...+.
T Consensus 162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~ 199 (298)
T TIGR02997 162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQ 199 (298)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 34455667777889999999999999999988876654
No 157
>PRK15044 transcriptional regulator SirC; Provisional
Probab=41.63 E-value=1e+02 Score=31.03 Aligned_cols=38 Identities=16% Similarity=0.086 Sum_probs=32.0
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhh
Q 017761 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY 282 (366)
Q Consensus 245 le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~ 282 (366)
.+++..-+.+..+++++.++||..+|++...|.+.+..
T Consensus 194 ~~kV~~~I~~nl~~~~SLeeLA~~lgmS~~tL~R~Fk~ 231 (295)
T PRK15044 194 KEKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAA 231 (295)
T ss_pred HHHHHHHHHhCcccCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 45566677778899999999999999999999987754
No 158
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=38.36 E-value=54 Score=32.03 Aligned_cols=25 Identities=20% Similarity=0.198 Sum_probs=21.8
Q ss_pred hhcCCCCchHHHHHHhcCCHHHHHH
Q 017761 254 ERCGGSPTFAQWAAAAGVDQRELRR 278 (366)
Q Consensus 254 ~~~GrePT~~eWA~aag~~~~~L~~ 278 (366)
..+|++||.+|.|+..|++.+++..
T Consensus 143 ~~l~~~pt~~eiA~~l~~~~~~v~~ 167 (289)
T PRK07500 143 EELTKQEIHREIATALGVSLSDVEM 167 (289)
T ss_pred cccCCCCCHHHHHHHhCcCHHHHHH
Confidence 3679999999999999999987754
No 159
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=37.55 E-value=73 Score=25.86 Aligned_cols=37 Identities=16% Similarity=0.138 Sum_probs=28.8
Q ss_pred HHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhh
Q 017761 246 EGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY 282 (366)
Q Consensus 246 e~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~ 282 (366)
+++..-+...+..+++.++.|..+|++...|.+....
T Consensus 8 ~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~ 44 (107)
T PRK10219 8 QTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRT 44 (107)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3445556666788899999999999999888876654
No 160
>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=35.86 E-value=66 Score=29.57 Aligned_cols=33 Identities=36% Similarity=0.484 Sum_probs=26.5
Q ss_pred HHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHh
Q 017761 247 GLREVLSERCGGSPTFAQWAAAAGVDQRELRRR 279 (366)
Q Consensus 247 ~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~ 279 (366)
+....+....|++||..|.|+..|+++..+...
T Consensus 94 ~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~ 126 (227)
T TIGR02980 94 KATEELTQRLGRSPTIAEIAEELGVSEEEVVEA 126 (227)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHH
Confidence 345566677799999999999999998877643
No 161
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=31.71 E-value=83 Score=29.30 Aligned_cols=37 Identities=24% Similarity=0.258 Sum_probs=28.7
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhh
Q 017761 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 281 (366)
Q Consensus 245 le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~ 281 (366)
+.+....+...+|++||..++|+..|++...+...+.
T Consensus 97 ~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~ 133 (236)
T PRK06986 97 VAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLL 133 (236)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHH
Confidence 3345566667789999999999999999887765443
No 162
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=30.12 E-value=1.2e+02 Score=30.93 Aligned_cols=37 Identities=19% Similarity=0.258 Sum_probs=28.4
Q ss_pred HHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhh
Q 017761 246 EGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY 282 (366)
Q Consensus 246 e~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~ 282 (366)
.++..-|+..++.+-+.++.|..+||+...|.+..+.
T Consensus 223 ~~~i~~me~nle~plsl~~LA~~~~~S~R~leRlF~~ 259 (328)
T COG4977 223 LRAIELMEANLEEPLSLEELADRAGLSRRQLERLFRA 259 (328)
T ss_pred HHHHHHHHHhhcCCcCHHHHHHHhCCCHHHHHHHHHH
Confidence 3344455666678889999999999999999887654
No 163
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=30.00 E-value=2.8e+02 Score=26.59 Aligned_cols=74 Identities=15% Similarity=0.089 Sum_probs=48.7
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhhh--------------HHHHHHHHHHcHHHHHHHHHHcc----
Q 017761 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYG--------------ILCKDKMITSNIRLVISIAKNYQ---- 306 (366)
Q Consensus 245 le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~G--------------~~AR~kLI~sNLRLVvsIAkrY~---- 306 (366)
+.++..-++..+..+++.+++|..+|++...|.+....- ..|+..|...++. |..||..+.
T Consensus 7 i~~~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F~~~~g~s~~~yi~~~Rl~~A~~~L~~~~~~-i~~iA~~~Gf~s~ 85 (289)
T PRK15121 7 IRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGAYIRARRLSKAAVALRLTSRP-ILDIALQYRFDSQ 85 (289)
T ss_pred HHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcCCCC-HHHHHHHHCCCCH
Confidence 344455566677888999999999999999888876542 3344445444443 455665542
Q ss_pred ---------cCCCChhhHHHHh
Q 017761 307 ---------GAGMNLQDLVQDV 319 (366)
Q Consensus 307 ---------g~Gl~~~DLIQEG 319 (366)
-.|++-.+.-+.+
T Consensus 86 ~~f~r~Fk~~~g~sP~~~r~~~ 107 (289)
T PRK15121 86 QTFTRAFKKQFAQTPALYRRSP 107 (289)
T ss_pred HHHHHHHHHHHCcCHHHHHhcc
Confidence 1377777777665
No 164
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=29.70 E-value=2e+02 Score=28.49 Aligned_cols=66 Identities=12% Similarity=0.165 Sum_probs=42.1
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhh-hHHHHHHHHHHcHHHHHHHHHHcccC-CCChhh
Q 017761 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY-GILCKDKMITSNIRLVISIAKNYQGA-GMNLQD 314 (366)
Q Consensus 245 le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~-G~~AR~kLI~sNLRLVvsIAkrY~g~-Gl~~~D 314 (366)
.+++...+......+.|.++||..+||+...|.+.+.. |..-.+.+. .+|| ..|+++-.. +.++.+
T Consensus 183 ~~~i~~~I~~~~~~~~sl~~lA~~~gmS~stl~R~Fk~~g~s~~~~~~--~~Rl--~~A~~lL~~~~~sI~~ 250 (291)
T PRK15186 183 AENIYNIIISDISRKWALKDISDSLYMSCSTLKRKLKQENTSFSEVYL--NARM--NKATKLLRNSEYNITR 250 (291)
T ss_pred HHHHHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHH--HHHH--HHHHHHHHcCCCCHHH
Confidence 34455566677788999999999999999999988865 333333332 2444 445554322 344443
No 165
>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=29.01 E-value=2.1e+02 Score=21.67 Aligned_cols=28 Identities=14% Similarity=0.188 Sum_probs=24.0
Q ss_pred CCCCchHHHHHHhcCCHHHHHHhhhhhH
Q 017761 257 GGSPTFAQWAAAAGVDQRELRRRLNYGI 284 (366)
Q Consensus 257 GrePT~~eWA~aag~~~~~L~~~L~~G~ 284 (366)
-|..|..+.|+..|++...+-..|+.+.
T Consensus 21 PR~~tl~elA~~lgis~st~~~~LRrae 48 (53)
T PF04967_consen 21 PRRITLEELAEELGISKSTVSEHLRRAE 48 (53)
T ss_pred CCcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 4667899999999999999998887764
No 166
>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=28.88 E-value=94 Score=27.89 Aligned_cols=33 Identities=15% Similarity=0.240 Sum_probs=27.7
Q ss_pred HHhhcCCCCchHHHHHHhcCCHHHHHHhhhhhH
Q 017761 252 LSERCGGSPTFAQWAAAAGVDQRELRRRLNYGI 284 (366)
Q Consensus 252 L~~~~GrePT~~eWA~aag~~~~~L~~~L~~G~ 284 (366)
|.+.-++..|..+.+++.|++.+.+.+.+++|+
T Consensus 39 Lr~~p~~~ati~eV~e~tgVs~~~I~~~IreGR 71 (137)
T TIGR03826 39 LRKHENRQATVSEIVEETGVSEKLILKFIREGR 71 (137)
T ss_pred HHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 334446667999999999999999999999984
No 167
>PRK13239 alkylmercury lyase; Provisional
Probab=28.79 E-value=95 Score=29.73 Aligned_cols=27 Identities=26% Similarity=0.212 Sum_probs=24.6
Q ss_pred cCCCCchHHHHHHhcCCHHHHHHhhhh
Q 017761 256 CGGSPTFAQWAAAAGVDQRELRRRLNY 282 (366)
Q Consensus 256 ~GrePT~~eWA~aag~~~~~L~~~L~~ 282 (366)
.|++||..+.|++.|.+.+++++.|+.
T Consensus 33 ~G~pvt~~~lA~~~~~~~~~v~~~L~~ 59 (206)
T PRK13239 33 KGRPVSVTTLAAALGWPVEEVEAVLEA 59 (206)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 499999999999999999999887776
No 168
>PF14711 Nitr_red_bet_C: Respiratory nitrate reductase beta C-terminal; PDB: 3IR7_B 1Y5N_B 1R27_D 3EGW_B 1Y5I_B 1Q16_B 1Y4Z_B 1Y5L_B 3IR6_B 3IR5_B ....
Probab=28.34 E-value=1.3e+02 Score=24.85 Aligned_cols=52 Identities=25% Similarity=0.466 Sum_probs=30.4
Q ss_pred hhHHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCCH
Q 017761 213 PLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQ 273 (366)
Q Consensus 213 ~l~YLkei~~~~~LLt~eEE~eLa~~Iq~l~~le~~r~~L~~~~GrePT~~eWA~aag~~~ 273 (366)
|++||-++ ||+-.|.-.-..++.++.+....... ..|.+| ..++.+++|++.
T Consensus 31 Pi~YLAnL------ftAGd~~~V~~~L~rL~AmR~ymR~~--~v~~~~-~~~~l~~~glt~ 82 (83)
T PF14711_consen 31 PIEYLANL------FTAGDEEPVRRALKRLLAMRSYMRAK--NVGGEP-DEEVLEAVGLTE 82 (83)
T ss_dssp -HHHHHHH------HSTT-HHHHHHHHHHHHHHHHHHHHH--HTT-S----HHHHHTT--H
T ss_pred cHHHHHHH------HccCChHHHHHHHHHHHHHHHHHHHH--HhCCCC-cHHHHHHcCCCC
Confidence 78899998 88888887777777665554443322 345444 577888888774
No 169
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=28.25 E-value=1.2e+02 Score=28.53 Aligned_cols=35 Identities=11% Similarity=0.201 Sum_probs=25.6
Q ss_pred HHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhh
Q 017761 248 LREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY 282 (366)
Q Consensus 248 ~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~ 282 (366)
+..-+.+....+.|.++||+.+|++..-|.+..+.
T Consensus 191 ~~~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~ 225 (287)
T TIGR02297 191 FNFLIEENYKQHLRLPEYADRLGISESRLNDICRR 225 (287)
T ss_pred HHHHHHHhhccCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 33344556677889999999999998777765544
No 170
>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=26.36 E-value=1.2e+02 Score=28.58 Aligned_cols=36 Identities=17% Similarity=0.284 Sum_probs=28.3
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhh
Q 017761 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 280 (366)
Q Consensus 245 le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L 280 (366)
+......+...+|++||..+-|...|++.+.+...+
T Consensus 118 ~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~~ 153 (255)
T TIGR02941 118 IKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIM 153 (255)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 344566677778999999999999999988776543
No 171
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=26.20 E-value=4.3e+02 Score=24.98 Aligned_cols=37 Identities=14% Similarity=0.157 Sum_probs=27.7
Q ss_pred HHHHHHHHHhhcCCC-CchHHHHHHhcCCHHHHHHhhh
Q 017761 245 LEGLREVLSERCGGS-PTFAQWAAAAGVDQRELRRRLN 281 (366)
Q Consensus 245 le~~r~~L~~~~Gre-PT~~eWA~aag~~~~~L~~~L~ 281 (366)
+.+++.-+.+.+..+ .|..++|.++|++...|.+...
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 345566666677766 6999999999999877776553
No 172
>PRK05572 sporulation sigma factor SigF; Validated
Probab=24.94 E-value=1.5e+02 Score=27.89 Aligned_cols=34 Identities=29% Similarity=0.409 Sum_probs=26.9
Q ss_pred HHHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHH
Q 017761 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELR 277 (366)
Q Consensus 244 ~le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~ 277 (366)
++.+....+..++|++|+..+-|+..|++.+.+.
T Consensus 119 ~~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~ 152 (252)
T PRK05572 119 KIRKDKDELSKELGREPTIEELAEYLGVTPEEVV 152 (252)
T ss_pred HHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHH
Confidence 4445566777778999999999999999887664
No 173
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.09 E-value=3e+02 Score=23.51 Aligned_cols=34 Identities=15% Similarity=0.029 Sum_probs=25.7
Q ss_pred CCCchHHHHHHhcCCHHHHHHhh------hhhHHHHHHHH
Q 017761 258 GSPTFAQWAAAAGVDQRELRRRL------NYGILCKDKMI 291 (366)
Q Consensus 258 rePT~~eWA~aag~~~~~L~~~L------~~G~~AR~kLI 291 (366)
.+-|.++.|++.+.+...|++.| +.++.-|+-|+
T Consensus 22 ~~LS~~~iA~~Ln~t~~~lekil~~tqr~~dvW~lRd~l~ 61 (97)
T COG4367 22 CPLSDEEIATALNWTEVKLEKILQVTQRPADVWRLRDFLV 61 (97)
T ss_pred ccccHHHHHHHhCCCHHHHHHHHHHhhccchhHHHHHHHH
Confidence 45689999999999999999888 34455555443
No 174
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=22.56 E-value=1.8e+02 Score=28.99 Aligned_cols=37 Identities=14% Similarity=0.103 Sum_probs=29.6
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhh
Q 017761 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 281 (366)
Q Consensus 245 le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~ 281 (366)
+.+....|+..+|++||..+.|...|++.++++..+.
T Consensus 175 ~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~ 211 (325)
T PRK05657 175 YLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLA 211 (325)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 3345566777889999999999999999888876653
No 175
>PF00439 Bromodomain: Bromodomain; InterPro: IPR001487 Bromodomains are found in a variety of mammalian, invertebrate and yeast DNA-binding proteins []. Bromodomains can interact with acetylated lysine []. In some proteins, the classical bromodomain has diverged to such an extent that parts of the region are either missing or contain an insertion (e.g., mammalian protein HRX, Caenorhabditis elegans hypothetical protein ZK783.4, yeast protein YTA7). The bromodomain may occur as a single copy, or in duplicate. The precise function of the domain is unclear, but it may be involved in protein-protein interactions and may play a role in assembly or activity of multi-component complexes involved in transcriptional activation [].; GO: 0005515 protein binding; PDB: 3P1C_A 4A9K_B 3SVH_A 3P1E_B 3P1F_A 1JSP_B 2L85_A 3P1D_B 3DWY_B 2D82_A ....
Probab=21.81 E-value=82 Score=24.21 Aligned_cols=46 Identities=17% Similarity=0.338 Sum_probs=34.0
Q ss_pred CCHHHHHHhhhhhHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHH
Q 017761 271 VDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLV 316 (366)
Q Consensus 271 ~~~~~L~~~L~~G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLI 316 (366)
|+...++.+|..|.+.--.-+...+++++.-|..|.+.|-.+--..
T Consensus 37 ~dL~~I~~kl~~~~Y~s~~~f~~Dv~~i~~Na~~yn~~~s~~~~~A 82 (84)
T PF00439_consen 37 MDLSTIRKKLENGKYKSIEEFEADVRLIFQNARRYNPPDSPIYKAA 82 (84)
T ss_dssp --HHHHHHHHHTTSSSSHHHHHHHHHHHHHHHHHHSCTTSHHHHHH
T ss_pred cchhhhhHHhhccchhhHHHHHHHHHHHHHHHHHHCCCcCHHHHHh
Confidence 5667777777777666666788899999999999999886554433
No 176
>PRK15185 transcriptional regulator HilD; Provisional
Probab=21.20 E-value=2.5e+02 Score=28.49 Aligned_cols=36 Identities=17% Similarity=0.161 Sum_probs=28.7
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhh
Q 017761 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 280 (366)
Q Consensus 245 le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L 280 (366)
.++++.-+....+...|.++||+.+|+++..|.+.+
T Consensus 208 ~erV~~~I~~n~~~~~SledLA~~lgmS~~tL~R~F 243 (309)
T PRK15185 208 KERVYNIISSSPSRQWKLTDVADHIFMSTSTLKRKL 243 (309)
T ss_pred HHHHHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHH
Confidence 445666677778889999999999999987776654
No 177
>PRK04217 hypothetical protein; Provisional
Probab=21.18 E-value=4.6e+02 Score=22.64 Aligned_cols=26 Identities=19% Similarity=0.109 Sum_probs=22.4
Q ss_pred CchHHHHHHhcCCHHHHHHhhhhhHH
Q 017761 260 PTFAQWAAAAGVDQRELRRRLNYGIL 285 (366)
Q Consensus 260 PT~~eWA~aag~~~~~L~~~L~~G~~ 285 (366)
-|..|+|+..|++...+...++.+..
T Consensus 59 lS~~EIAk~LGIS~sTV~r~L~RArk 84 (110)
T PRK04217 59 LTQEEAGKRMGVSRGTVWRALTSARK 84 (110)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 38899999999999999999987543
No 178
>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=20.82 E-value=1.3e+02 Score=21.17 Aligned_cols=39 Identities=18% Similarity=0.172 Sum_probs=24.8
Q ss_pred CchHHHHHHhcCCHHHHHHhhhhhHHHHHHHHHHcHHHHHHHHHHc
Q 017761 260 PTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNY 305 (366)
Q Consensus 260 PT~~eWA~aag~~~~~L~~~L~~G~~AR~kLI~sNLRLVvsIAkrY 305 (366)
-|..++|..+|++...+.+.+.... .=+...+..||+-|
T Consensus 10 ls~~~la~~~gis~~~i~~~~~g~~-------~~~~~~~~~ia~~l 48 (55)
T PF01381_consen 10 LSQKELAEKLGISRSTISRIENGKR-------NPSLDTLKKIAKAL 48 (55)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHTTSS-------TSBHHHHHHHHHHH
T ss_pred CCHHHHHHHhCCCcchhHHHhcCCC-------CCCHHHHHHHHHHH
Confidence 3678888888888888877776632 23455566666655
No 179
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=20.71 E-value=2.9e+02 Score=26.88 Aligned_cols=38 Identities=8% Similarity=0.039 Sum_probs=28.7
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCCHHHHHHhhhh
Q 017761 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY 282 (366)
Q Consensus 245 le~~r~~L~~~~GrePT~~eWA~aag~~~~~L~~~L~~ 282 (366)
++++..-+.......+|..++|..+|++...|.+..+.
T Consensus 193 i~~~~~~i~~~~~~~~tl~~lA~~~~~S~~~l~r~Fk~ 230 (302)
T PRK10371 193 VSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQR 230 (302)
T ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 44455555666677899999999999999877766654
No 180
>cd05499 Bromo_BDF1_2_II Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=20.28 E-value=1.2e+02 Score=25.01 Aligned_cols=43 Identities=16% Similarity=0.356 Sum_probs=35.7
Q ss_pred CCHHHHHHhhhhhHHHHHHHHHHcHHHHHHHHHHcccCCCChh
Q 017761 271 VDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQ 313 (366)
Q Consensus 271 ~~~~~L~~~L~~G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~ 313 (366)
||...+++.|..|.+.--.-+...++||.+-|+.|.+.|-.+-
T Consensus 46 ~dL~~I~~kl~~~~Y~s~~ef~~D~~li~~N~~~yn~~~s~~~ 88 (102)
T cd05499 46 MDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVY 88 (102)
T ss_pred CCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHH
Confidence 5778888888888777777788999999999999999886443
Done!