Query 016880
Match_columns 381
No_of_seqs 262 out of 1516
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 03:38:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016880.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016880hhsearch_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 4.6E-38 9.9E-43 318.8 17.5 161 220-380 57-260 (415)
2 TIGR02997 Sig70-cyanoRpoD RNA 100.0 2E-35 4.3E-40 285.9 16.9 155 225-379 3-158 (298)
3 PRK07406 RNA polymerase sigma 100.0 5.8E-35 1.3E-39 292.9 17.0 158 223-380 63-221 (373)
4 PRK05949 RNA polymerase sigma 100.0 2.3E-34 5E-39 283.6 18.0 158 223-380 18-176 (327)
5 PRK07405 RNA polymerase sigma 100.0 1.4E-33 3.1E-38 276.5 17.6 158 223-380 8-166 (317)
6 COG0568 RpoD DNA-directed RNA 100.0 3.7E-32 8E-37 269.6 11.5 160 222-381 8-188 (342)
7 PRK05901 RNA polymerase sigma 100.0 3.9E-32 8.5E-37 281.5 11.4 146 222-380 210-356 (509)
8 PRK07921 RNA polymerase sigma 100.0 8.2E-30 1.8E-34 251.3 13.5 145 223-380 26-171 (324)
9 PRK05658 RNA polymerase sigma 99.9 6.9E-26 1.5E-30 239.4 13.0 105 276-380 354-465 (619)
10 PRK09210 RNA polymerase sigma 99.9 7.5E-25 1.6E-29 218.8 11.7 119 222-380 95-214 (367)
11 PRK07122 RNA polymerase sigma 99.9 4.6E-25 1E-29 211.0 8.7 86 295-380 40-125 (264)
12 TIGR02393 RpoD_Cterm RNA polym 99.9 7.2E-23 1.6E-27 191.8 7.7 84 296-379 1-84 (238)
13 PRK06596 RNA polymerase factor 99.9 3.6E-22 7.7E-27 193.0 11.9 84 295-378 48-131 (284)
14 PRK07500 rpoH2 RNA polymerase 99.9 5.5E-22 1.2E-26 192.3 12.8 117 222-378 5-123 (289)
15 TIGR02392 rpoH_proteo alternat 99.9 1E-21 2.2E-26 187.9 13.0 95 283-377 21-117 (270)
16 PRK07408 RNA polymerase sigma 99.9 9.4E-22 2E-26 187.0 9.6 89 291-379 20-110 (256)
17 COG1191 FliA DNA-directed RNA 99.8 2.2E-20 4.8E-25 178.9 9.2 95 284-380 12-108 (247)
18 PRK05911 RNA polymerase sigma 99.8 1.1E-19 2.4E-24 173.0 9.5 91 286-379 12-107 (257)
19 PRK05657 RNA polymerase sigma 99.8 1.7E-19 3.7E-24 178.0 11.0 117 221-378 51-169 (325)
20 TIGR02850 spore_sigG RNA polym 99.8 1.6E-18 3.5E-23 164.1 11.0 84 295-379 34-117 (254)
21 PRK08215 sporulation sigma fac 99.7 9.9E-18 2.1E-22 158.9 10.0 94 285-379 26-120 (258)
22 TIGR02980 SigBFG RNA polymeras 99.7 8E-18 1.7E-22 155.6 8.7 85 295-379 3-87 (227)
23 TIGR02885 spore_sigF RNA polym 99.7 1.8E-17 3.9E-22 153.9 8.6 90 289-379 4-94 (231)
24 TIGR02394 rpoS_proteo RNA poly 99.7 6.6E-17 1.4E-21 155.7 11.4 96 283-378 33-129 (285)
25 TIGR02941 Sigma_B RNA polymera 99.7 6.3E-17 1.4E-21 152.8 10.1 97 283-379 15-113 (255)
26 TIGR02895 spore_sigI RNA polym 99.7 7.5E-17 1.6E-21 152.0 9.0 89 289-377 3-96 (218)
27 PRK06288 RNA polymerase sigma 99.6 6.6E-16 1.4E-20 147.4 10.8 81 295-378 31-114 (268)
28 PRK08583 RNA polymerase sigma 99.6 8.7E-16 1.9E-20 145.2 10.0 96 283-378 15-112 (257)
29 PRK12427 flagellar biosynthesi 99.6 2.7E-15 5.9E-20 141.1 8.1 73 296-369 16-91 (231)
30 PRK07670 RNA polymerase sigma 99.6 3.7E-15 8E-20 140.9 8.9 92 283-377 8-104 (251)
31 PRK05572 sporulation sigma fac 99.6 1E-14 2.2E-19 137.9 9.9 95 284-379 20-115 (252)
32 TIGR02479 FliA_WhiG RNA polyme 99.5 8.8E-15 1.9E-19 135.6 6.9 75 300-377 1-78 (224)
33 PRK05803 sporulation sigma fac 99.5 2E-13 4.4E-18 127.5 14.3 115 245-369 8-123 (233)
34 PRK06986 fliA flagellar biosyn 99.5 4.2E-14 9.1E-19 132.2 8.2 78 292-369 5-85 (236)
35 TIGR02846 spore_sigmaK RNA pol 99.3 3.7E-11 8E-16 112.1 14.3 113 248-369 9-122 (227)
36 PRK08311 putative RNA polymera 99.3 1.4E-11 3.1E-16 117.5 11.0 91 282-372 4-97 (237)
37 PF04542 Sigma70_r2: Sigma-70 99.3 1.4E-11 3.1E-16 93.0 7.7 70 300-369 1-70 (71)
38 PRK08295 RNA polymerase factor 99.3 3.2E-11 7E-16 109.1 10.6 91 280-370 8-99 (208)
39 PRK08301 sporulation sigma fac 99.2 3.7E-11 8E-16 111.9 10.7 87 283-369 39-126 (234)
40 TIGR02859 spore_sigH RNA polym 99.2 1.2E-10 2.5E-15 104.5 10.2 87 281-367 4-91 (198)
41 TIGR02835 spore_sigmaE RNA pol 99.2 1.5E-10 3.3E-15 108.5 10.8 87 283-369 39-126 (234)
42 TIGR02937 sigma70-ECF RNA poly 99.0 1E-09 2.2E-14 91.2 8.2 72 296-369 2-73 (158)
43 PRK09652 RNA polymerase sigma 99.0 1.1E-09 2.5E-14 95.6 8.2 81 289-371 3-84 (182)
44 PRK05602 RNA polymerase sigma 99.0 1.7E-09 3.6E-14 96.9 9.5 88 281-369 5-93 (186)
45 PRK12513 RNA polymerase sigma 99.0 3.1E-09 6.7E-14 95.7 9.9 91 281-373 11-102 (194)
46 PRK09646 RNA polymerase sigma 98.9 3.7E-09 8.1E-14 95.7 9.4 87 282-369 16-103 (194)
47 TIGR02948 SigW_bacill RNA poly 98.9 4.2E-09 9.1E-14 93.4 9.1 85 283-369 5-90 (187)
48 PRK09641 RNA polymerase sigma 98.9 4.7E-09 1E-13 93.1 9.1 86 282-369 4-90 (187)
49 PRK13919 putative RNA polymera 98.9 5.3E-09 1.1E-13 93.3 9.3 87 282-369 9-96 (186)
50 PRK06811 RNA polymerase factor 98.9 7.9E-09 1.7E-13 93.2 10.3 89 281-370 3-95 (189)
51 PRK09648 RNA polymerase sigma 98.9 9.8E-09 2.1E-13 92.1 10.3 88 283-371 11-103 (189)
52 PRK09640 RNA polymerase sigma 98.9 1.7E-08 3.7E-13 90.8 10.5 88 280-369 7-98 (188)
53 PRK09638 RNA polymerase sigma 98.8 2E-08 4.3E-13 88.7 9.5 88 281-370 3-91 (176)
54 PRK06759 RNA polymerase factor 98.8 2E-08 4.3E-13 86.7 8.8 72 295-368 4-75 (154)
55 TIGR02952 Sig70_famx2 RNA poly 98.8 2.3E-08 5.1E-13 87.2 9.3 84 287-371 2-86 (170)
56 PRK11922 RNA polymerase sigma 98.8 3.5E-08 7.5E-13 92.3 10.3 90 281-372 15-105 (231)
57 PRK12519 RNA polymerase sigma 98.8 2.4E-08 5.3E-13 89.8 8.9 86 282-369 15-101 (194)
58 PRK11923 algU RNA polymerase s 98.8 3.6E-08 7.7E-13 88.6 9.9 87 282-370 6-93 (193)
59 PRK12524 RNA polymerase sigma 98.8 3E-08 6.6E-13 89.9 9.1 88 280-368 10-98 (196)
60 TIGR02954 Sig70_famx3 RNA poly 98.8 5.2E-08 1.1E-12 85.8 10.0 88 281-370 1-89 (169)
61 TIGR02939 RpoE_Sigma70 RNA pol 98.7 6.7E-08 1.5E-12 85.9 10.4 86 282-369 6-92 (190)
62 PRK12514 RNA polymerase sigma 98.7 4.3E-08 9.4E-13 87.1 9.0 87 282-369 5-92 (179)
63 PRK12526 RNA polymerase sigma 98.7 5.5E-08 1.2E-12 89.3 9.7 86 284-370 26-112 (206)
64 PRK11924 RNA polymerase sigma 98.7 8.1E-08 1.8E-12 83.7 9.7 84 286-371 3-87 (179)
65 PRK12534 RNA polymerase sigma 98.7 7.6E-08 1.6E-12 86.1 8.1 85 283-368 12-97 (187)
66 PRK09643 RNA polymerase sigma 98.6 2E-07 4.4E-12 84.6 10.7 88 281-370 12-100 (192)
67 PRK12531 RNA polymerase sigma 98.6 1.1E-07 2.4E-12 86.2 8.4 85 284-369 15-100 (194)
68 PRK12537 RNA polymerase sigma 98.6 1.7E-07 3.7E-12 84.0 9.3 89 281-370 8-97 (182)
69 PRK12538 RNA polymerase sigma 98.6 1.6E-07 3.4E-12 88.8 9.3 85 282-367 49-134 (233)
70 PRK12536 RNA polymerase sigma 98.6 3E-07 6.5E-12 82.3 10.1 85 283-369 8-94 (181)
71 PRK12515 RNA polymerase sigma 98.6 2.2E-07 4.7E-12 83.6 9.1 87 280-368 6-93 (189)
72 TIGR02984 Sig-70_plancto1 RNA 98.5 3E-07 6.4E-12 81.6 8.2 75 293-367 4-83 (189)
73 PRK12512 RNA polymerase sigma 98.5 7.2E-07 1.6E-11 79.6 10.2 86 284-371 10-100 (184)
74 TIGR02989 Sig-70_gvs1 RNA poly 98.5 4.7E-07 1E-11 78.3 8.7 73 296-370 2-74 (159)
75 PRK12539 RNA polymerase sigma 98.5 7.2E-07 1.6E-11 80.1 10.1 85 283-369 8-97 (184)
76 TIGR02985 Sig70_bacteroi1 RNA 98.5 3.4E-07 7.3E-12 78.3 7.1 72 296-369 2-73 (161)
77 PRK12522 RNA polymerase sigma 98.4 1E-06 2.3E-11 78.0 8.7 73 296-370 4-76 (173)
78 PRK12518 RNA polymerase sigma 98.4 1.1E-06 2.4E-11 77.6 8.0 78 288-368 3-81 (175)
79 PRK12543 RNA polymerase sigma 98.3 1.8E-06 4E-11 77.1 8.0 75 292-368 3-78 (179)
80 PRK12542 RNA polymerase sigma 98.3 1.3E-06 2.8E-11 78.4 6.4 78 292-369 5-83 (185)
81 TIGR02999 Sig-70_X6 RNA polyme 98.3 2.8E-06 6E-11 75.5 8.2 84 283-368 4-94 (183)
82 COG1595 RpoE DNA-directed RNA 98.2 8.1E-06 1.8E-10 73.3 10.1 80 291-372 11-90 (182)
83 PRK09415 RNA polymerase factor 98.2 5.2E-06 1.1E-10 74.4 8.5 73 294-368 15-87 (179)
84 TIGR03001 Sig-70_gmx1 RNA poly 98.2 8.3E-06 1.8E-10 78.0 10.2 89 280-370 23-119 (244)
85 TIGR02983 SigE-fam_strep RNA p 98.2 7E-06 1.5E-10 71.5 7.8 74 294-369 5-78 (162)
86 PRK08241 RNA polymerase factor 98.2 8.9E-06 1.9E-10 79.8 9.4 85 283-369 6-91 (339)
87 PRK09649 RNA polymerase sigma 98.1 8.8E-06 1.9E-10 73.5 8.4 84 283-369 11-95 (185)
88 PRK09639 RNA polymerase sigma 98.1 1.3E-05 2.8E-10 70.0 7.8 72 295-370 3-74 (166)
89 PRK12541 RNA polymerase sigma 98.1 1.7E-05 3.6E-10 69.4 8.2 72 295-369 5-76 (161)
90 PRK12547 RNA polymerase sigma 98.1 1.8E-05 4E-10 69.7 8.4 73 295-369 6-78 (164)
91 PRK09644 RNA polymerase sigma 98.0 2E-05 4.2E-10 69.4 7.9 71 297-370 3-73 (165)
92 TIGR02947 SigH_actino RNA poly 98.0 2.1E-05 4.5E-10 71.1 8.0 73 295-369 11-83 (193)
93 PRK12520 RNA polymerase sigma 98.0 2E-05 4.4E-10 71.0 7.8 74 296-371 3-76 (191)
94 PRK12535 RNA polymerase sigma 98.0 3.6E-05 7.8E-10 70.6 9.3 83 284-369 13-96 (196)
95 PRK09645 RNA polymerase sigma 98.0 2.8E-05 6E-10 68.6 8.2 75 294-369 8-82 (173)
96 PRK12528 RNA polymerase sigma 97.9 4.6E-05 9.9E-10 66.6 7.9 71 295-368 4-74 (161)
97 TIGR02960 SigX5 RNA polymerase 97.9 4.5E-05 9.9E-10 74.0 8.5 73 295-369 5-77 (324)
98 PRK09647 RNA polymerase sigma 97.9 4.7E-05 1E-09 70.4 8.2 72 295-369 28-99 (203)
99 TIGR02943 Sig70_famx1 RNA poly 97.9 4E-05 8.6E-10 69.5 7.5 71 298-370 5-75 (188)
100 PRK12516 RNA polymerase sigma 97.9 6.6E-05 1.4E-09 68.3 8.6 74 294-369 9-82 (187)
101 TIGR02950 SigM_subfam RNA poly 97.9 3E-05 6.5E-10 66.8 6.0 65 302-369 2-66 (154)
102 PRK09637 RNA polymerase sigma 97.8 8.2E-05 1.8E-09 67.2 8.9 75 297-373 3-77 (181)
103 PRK12532 RNA polymerase sigma 97.8 4.8E-05 1E-09 68.8 7.3 70 298-369 8-78 (195)
104 PRK12533 RNA polymerase sigma 97.8 9.7E-05 2.1E-09 69.3 9.2 74 293-369 16-89 (216)
105 PRK12523 RNA polymerase sigma 97.7 6.3E-05 1.4E-09 66.7 6.4 75 291-368 5-80 (172)
106 TIGR02959 SigZ RNA polymerase 97.7 9.4E-05 2E-09 65.9 7.3 71 302-374 2-72 (170)
107 PRK09642 RNA polymerase sigma 97.7 5.4E-05 1.2E-09 66.0 5.3 66 301-369 1-66 (160)
108 PRK12544 RNA polymerase sigma 97.6 0.00019 4.1E-09 66.5 8.0 72 297-370 20-91 (206)
109 PRK12545 RNA polymerase sigma 97.6 0.00019 4.1E-09 65.8 7.6 70 299-370 12-81 (201)
110 PRK12517 RNA polymerase sigma 97.6 0.0003 6.5E-09 63.9 8.5 76 290-367 18-93 (188)
111 PRK12540 RNA polymerase sigma 97.6 0.00028 6.1E-09 63.9 8.2 72 296-369 6-77 (182)
112 PRK12529 RNA polymerase sigma 97.6 0.0002 4.3E-09 64.3 7.1 74 295-368 13-88 (178)
113 PRK12546 RNA polymerase sigma 97.5 0.0004 8.6E-09 63.4 8.7 71 296-369 9-79 (188)
114 PRK12530 RNA polymerase sigma 97.5 0.00039 8.4E-09 63.1 7.4 71 298-370 10-80 (189)
115 PRK07037 extracytoplasmic-func 97.4 0.00038 8.3E-09 60.7 6.7 68 299-369 2-69 (163)
116 PRK09651 RNA polymerase sigma 97.4 0.00073 1.6E-08 60.1 8.0 71 295-368 10-80 (172)
117 PRK12511 RNA polymerase sigma 97.2 0.001 2.2E-08 60.4 7.4 71 297-369 6-76 (182)
118 PRK12527 RNA polymerase sigma 97.0 0.0015 3.2E-08 57.0 6.0 64 302-368 2-65 (159)
119 PRK12525 RNA polymerase sigma 97.0 0.0033 7E-08 55.7 8.0 70 295-367 9-78 (168)
120 PRK09636 RNA polymerase sigma 96.9 0.0019 4E-08 62.7 6.7 69 296-368 5-73 (293)
121 TIGR02957 SigX4 RNA polymerase 96.8 0.0026 5.5E-08 61.6 6.1 66 299-368 1-66 (281)
122 PF00140 Sigma70_r1_2: Sigma-7 96.6 0.0012 2.6E-08 46.3 1.6 34 223-256 2-36 (37)
123 PRK09191 two-component respons 96.5 0.0077 1.7E-07 55.6 7.0 63 296-360 2-64 (261)
124 PRK06704 RNA polymerase factor 96.4 0.0095 2E-07 56.9 7.3 73 291-369 13-86 (228)
125 PRK09635 sigI RNA polymerase s 96.3 0.0088 1.9E-07 58.7 6.4 68 296-367 6-73 (290)
126 PF12645 HTH_16: Helix-turn-he 96.2 0.019 4.1E-07 45.1 6.5 56 286-341 3-65 (65)
127 PF07638 Sigma70_ECF: ECF sigm 96.0 0.022 4.7E-07 52.0 7.1 90 283-372 4-99 (185)
128 TIGR03209 P21_Cbot clostridium 95.9 0.023 4.9E-07 48.8 6.4 65 298-369 2-71 (142)
129 PRK09047 RNA polymerase factor 94.9 0.051 1.1E-06 47.0 5.4 47 320-369 5-51 (161)
130 PF04539 Sigma70_r3: Sigma-70 94.5 0.11 2.3E-06 40.7 5.7 40 252-291 3-42 (78)
131 PHA02547 55 RNA polymerase sig 88.6 1.6 3.5E-05 40.9 7.0 64 304-367 46-112 (179)
132 PRK05658 RNA polymerase sigma 71.9 3.7 8E-05 44.6 3.6 32 223-254 104-136 (619)
133 COG1191 FliA DNA-directed RNA 69.9 10 0.00022 37.2 5.8 41 253-293 110-150 (247)
134 TIGR02850 spore_sigG RNA polym 57.1 29 0.00064 33.1 6.3 38 254-291 121-158 (254)
135 TIGR02393 RpoD_Cterm RNA polym 55.6 34 0.00075 32.2 6.4 37 254-290 88-124 (238)
136 PRK07408 RNA polymerase sigma 55.4 34 0.00074 32.8 6.4 37 253-289 113-149 (256)
137 PRK07122 RNA polymerase sigma 55.0 35 0.00075 33.1 6.5 38 254-291 128-165 (264)
138 PRK14082 hypothetical protein; 53.7 49 0.0011 26.5 5.9 54 296-351 10-63 (65)
139 PRK07921 RNA polymerase sigma 51.6 38 0.00083 34.1 6.3 39 252-290 172-210 (324)
140 PRK05911 RNA polymerase sigma 51.2 37 0.0008 32.7 5.9 37 254-290 111-147 (257)
141 PRK12427 flagellar biosynthesi 50.9 40 0.00086 32.0 6.0 37 254-290 102-138 (231)
142 PRK09210 RNA polymerase sigma 47.2 44 0.00095 34.1 6.0 39 253-291 216-254 (367)
143 PRK07670 RNA polymerase sigma 41.5 66 0.0014 30.6 6.0 38 254-291 110-147 (251)
144 TIGR02885 spore_sigF RNA polym 40.3 71 0.0015 29.7 5.9 37 255-291 99-135 (231)
145 PRK05901 RNA polymerase sigma 39.5 71 0.0015 34.6 6.4 39 253-291 358-396 (509)
146 TIGR02479 FliA_WhiG RNA polyme 39.3 79 0.0017 29.3 6.0 38 253-290 83-120 (224)
147 PRK07406 RNA polymerase sigma 38.8 78 0.0017 32.8 6.4 39 252-290 222-260 (373)
148 TIGR01446 DnaD_dom DnaD and ph 37.3 92 0.002 23.9 5.2 58 263-324 6-70 (73)
149 PRK05949 RNA polymerase sigma 37.3 78 0.0017 31.9 6.0 38 253-290 178-215 (327)
150 KOG0917 Uncharacterized conser 36.1 32 0.00069 34.8 2.9 84 45-144 10-94 (338)
151 TIGR03826 YvyF flagellar opero 34.8 95 0.0021 28.0 5.5 41 254-294 31-71 (137)
152 PRK07598 RNA polymerase sigma 34.5 90 0.002 32.9 6.1 40 252-291 261-300 (415)
153 PRK06288 RNA polymerase sigma 34.2 1E+02 0.0022 29.6 6.0 37 254-290 119-155 (268)
154 PRK08215 sporulation sigma fac 33.8 1.1E+02 0.0024 29.1 6.2 36 255-290 125-160 (258)
155 PRK11511 DNA-binding transcrip 31.8 73 0.0016 27.3 4.2 40 253-292 9-48 (127)
156 PRK07405 RNA polymerase sigma 30.6 1.2E+02 0.0026 30.4 6.0 40 252-291 167-206 (317)
157 TIGR02997 Sig70-cyanoRpoD RNA 27.2 1.5E+02 0.0033 29.1 6.0 39 253-291 161-199 (298)
158 PF01726 LexA_DNA_bind: LexA D 24.8 2.4E+02 0.0052 22.0 5.5 23 264-286 20-43 (65)
159 TIGR02980 SigBFG RNA polymeras 23.5 1.7E+02 0.0037 27.1 5.3 35 256-290 93-127 (227)
160 PRK10219 DNA-binding transcrip 22.8 2E+02 0.0043 23.5 5.1 38 255-292 7-44 (107)
161 COG0568 RpoD DNA-directed RNA 22.4 2.1E+02 0.0046 29.6 6.2 41 250-290 186-226 (342)
162 PF15545 Toxin_67: Putative to 21.0 95 0.0021 25.2 2.6 30 348-377 7-36 (70)
163 PRK05572 sporulation sigma fac 20.5 2.5E+02 0.0054 26.7 5.9 36 254-289 119-154 (252)
164 TIGR03761 ICE_PFL4669 integrat 20.5 2.2E+02 0.0047 27.6 5.5 36 305-341 158-193 (216)
165 smart00342 HTH_ARAC helix_turn 20.2 2.7E+02 0.0058 20.4 5.0 23 270-292 2-24 (84)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=4.6e-38 Score=318.83 Aligned_cols=161 Identities=32% Similarity=0.535 Sum_probs=148.4
Q ss_pred chhhHHHHHhhcCCC-CCCCcHHHHHHHHHhHHHHH--------------------HHHHHHHHHHHhCCcCchhHHHHH
Q 016880 220 PTIFSAERALNSRGR-RLTIARNEAEMSKGVQVVAN--------------------LERIKTTLEKESGKAASLNCWAQA 278 (381)
Q Consensus 220 p~~~~v~~~~~~~~~-~lLtaeEE~eL~~~iq~~~~--------------------Le~~r~~L~~~~gr~ps~~ewA~a 278 (381)
++.+.|+-|++.+|+ ||||++||++|+++||.++. |++++..|.+++|++||..+||.+
T Consensus 57 ~~~d~v~~yl~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~~ 136 (415)
T PRK07598 57 RSTDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKT 136 (415)
T ss_pred CCCChHHHHHHhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHHH
Confidence 345667778788886 89999999999999999999 899999999999999999999954
Q ss_pred c----------------------CCCHHHHHHHHHhcHHHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHH
Q 016880 279 A----------------------GVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQG 336 (381)
Q Consensus 279 a----------------------gl~~eeL~~~l~~G~~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikA 336 (381)
+ |+++++|.+.++.|..|+++||++|+++|+++|++|.++|++++||+|||++|||+|
T Consensus 137 ~~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~ra 216 (415)
T PRK07598 137 ADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERA 216 (415)
T ss_pred hCCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHH
Confidence 4 556667777778898899999999999999999999999999999999999999999
Q ss_pred HhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCCccCCCccccc
Q 016880 337 AERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPVPLFLI 380 (381)
Q Consensus 337 vekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~IRlP~~~~Ek 380 (381)
+++|||++|++|+|||+||||++|.+++++++++||+|.|+.++
T Consensus 217 vekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~ 260 (415)
T PRK07598 217 VEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEK 260 (415)
T ss_pred HHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHH
Confidence 99999999999999999999999999999999999999999775
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=2e-35 Score=285.93 Aligned_cols=155 Identities=37% Similarity=0.644 Sum_probs=148.0
Q ss_pred HHHHhhcCC-CCCCCcHHHHHHHHHhHHHHHHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHHhcHHHHHHHHHH
Q 016880 225 AERALNSRG-RRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKS 303 (381)
Q Consensus 225 v~~~~~~~~-~~lLtaeEE~eL~~~iq~~~~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~~G~~Are~LIe~ 303 (381)
+..|++..+ .|+||++||++|++.++.+..+++.+.+|+++.|++|+..+||+++|++..+|+..++.|..|+++||+.
T Consensus 3 ~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv~~ 82 (298)
T TIGR02997 3 VRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMIKA 82 (298)
T ss_pred HHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHHHH
Confidence 345666666 4899999999999999999999999999999999999999999999999999999999998899999999
Q ss_pred hhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCCccCCCcccc
Q 016880 304 TRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPVPLFL 379 (381)
Q Consensus 304 nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~IRlP~~~~E 379 (381)
|+++|+++|++|.++|.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++|.++.++||+|.++.+
T Consensus 83 ~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~~~~~ 158 (298)
T TIGR02997 83 NLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITE 158 (298)
T ss_pred hHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999998754
No 3
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=5.8e-35 Score=292.91 Aligned_cols=158 Identities=34% Similarity=0.653 Sum_probs=151.7
Q ss_pred hHHHHHhhcCCC-CCCCcHHHHHHHHHhHHHHHHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHHhcHHHHHHHH
Q 016880 223 FSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELI 301 (381)
Q Consensus 223 ~~v~~~~~~~~~-~lLtaeEE~eL~~~iq~~~~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~~G~~Are~LI 301 (381)
+.+..|++..++ ||||++||++|++.|+.+..+++.+.+|+++.|+.|+..+||+++|++..+|.+++..|..|+++||
T Consensus 63 d~l~~Yl~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Li 142 (373)
T PRK07406 63 DSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMV 142 (373)
T ss_pred CHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHHHH
Confidence 446778888885 8999999999999999999999999999999999999999999999999999999999988999999
Q ss_pred HHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCCccCCCccccc
Q 016880 302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPVPLFLI 380 (381)
Q Consensus 302 e~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~IRlP~~~~Ek 380 (381)
..|+|+|+++|++|.++|++++||+|||+||||+|+++|||++|++|+|||+||||++|.++|++++++||+|.|+.++
T Consensus 143 ~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~~~ 221 (373)
T PRK07406 143 QSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYET 221 (373)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999998753
No 4
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00 E-value=2.3e-34 Score=283.58 Aligned_cols=158 Identities=37% Similarity=0.598 Sum_probs=151.1
Q ss_pred hHHHHHhhcCCC-CCCCcHHHHHHHHHhHHHHHHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHHhcHHHHHHHH
Q 016880 223 FSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELI 301 (381)
Q Consensus 223 ~~v~~~~~~~~~-~lLtaeEE~eL~~~iq~~~~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~~G~~Are~LI 301 (381)
+.+.-|++..++ |+||++||++|++.|+.+..+++.+..|+++.|+.|+..+||+++++++.+|+..++.|+.|++.||
T Consensus 18 d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~~Li 97 (327)
T PRK05949 18 DMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQKMI 97 (327)
T ss_pred CHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHHHHH
Confidence 445667777775 8999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCCccCCCccccc
Q 016880 302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPVPLFLI 380 (381)
Q Consensus 302 e~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~IRlP~~~~Ek 380 (381)
..|+++|+++|++|.+.+.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++|++++++||+|.|+.+.
T Consensus 98 ~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~~~~ 176 (327)
T PRK05949 98 EANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK 176 (327)
T ss_pred HHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999998753
No 5
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=1.4e-33 Score=276.47 Aligned_cols=158 Identities=32% Similarity=0.554 Sum_probs=151.1
Q ss_pred hHHHHHhhcCCC-CCCCcHHHHHHHHHhHHHHHHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHHhcHHHHHHHH
Q 016880 223 FSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELI 301 (381)
Q Consensus 223 ~~v~~~~~~~~~-~lLtaeEE~eL~~~iq~~~~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~~G~~Are~LI 301 (381)
+.+..|++..++ |+||++||++|++.|+.++.+++++.+|.+++|+.|+..+||+++++++.+|+..++.|+.|+++||
T Consensus 8 ~~~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~L~ 87 (317)
T PRK07405 8 DLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRKMV 87 (317)
T ss_pred cHHHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHHHH
Confidence 446678887775 8999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCCccCCCccccc
Q 016880 302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPVPLFLI 380 (381)
Q Consensus 302 e~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~IRlP~~~~Ek 380 (381)
..|+++|+++|++|.+.+.+.+||+|||++|||+|+++|||++|++|+|||+||||++|.++|.+++++||+|.|+.+.
T Consensus 88 ~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~~~ 166 (317)
T PRK07405 88 EANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK 166 (317)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999998653
No 6
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=99.97 E-value=3.7e-32 Score=269.56 Aligned_cols=160 Identities=33% Similarity=0.556 Sum_probs=140.3
Q ss_pred hhHHHHHhhcCCC-CCCCcHHHHHHHHHhHHHHHHHHHHHHHHH-HhCCcCchh---------------HHHHHcCCCH-
Q 016880 222 IFSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEK-ESGKAASLN---------------CWAQAAGVSE- 283 (381)
Q Consensus 222 ~~~v~~~~~~~~~-~lLtaeEE~eL~~~iq~~~~Le~~r~~L~~-~~gr~ps~~---------------ewA~aagl~~- 283 (381)
.+.+..|+...+. ++++.++|.++...++....+......|.. ..+..|+.. +|+.....++
T Consensus 8 ~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Ee 87 (342)
T COG0568 8 ADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEEE 87 (342)
T ss_pred hhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHHH
Confidence 4556777777665 899999999999999988877777777776 667888876 5554444443
Q ss_pred HHHHHHHHhcHH---HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHH
Q 016880 284 RVLKQHLAFGWY---CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (381)
Q Consensus 284 eeL~~~l~~G~~---Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI 360 (381)
.+|..+++.|.. |+.+||++|++||++||++|.++|+++.||||||+||||+||++|||++||+|||||+||||++|
T Consensus 88 ~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrqaI 167 (342)
T COG0568 88 KALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAI 167 (342)
T ss_pred HHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHHHH
Confidence 778899999953 99999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHcCCCccCCCcccccC
Q 016880 361 SKMVARHARGIKIPVPLFLIW 381 (381)
Q Consensus 361 ~~~Ir~qsr~IRlP~~~~Ek~ 381 (381)
.++|.++.++||+|+|+++++
T Consensus 168 ~raI~~q~rtIRipvh~~e~~ 188 (342)
T COG0568 168 TRAIADQARTIRIPVHQVELI 188 (342)
T ss_pred HHHHHHhcchhhHhHHHHHHH
Confidence 999999999999999998764
No 7
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=99.97 E-value=3.9e-32 Score=281.53 Aligned_cols=146 Identities=32% Similarity=0.517 Sum_probs=127.3
Q ss_pred hhHHHHHhhcCCC-CCCCcHHHHHHHHHhHHHHHHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHHhcHHHHHHH
Q 016880 222 IFSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREEL 300 (381)
Q Consensus 222 ~~~v~~~~~~~~~-~lLtaeEE~eL~~~iq~~~~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~~G~~Are~L 300 (381)
.+.++.|++..++ |+||++||++|+++++.+..+++.. . ....|+.. ...+|.+.+..|..|+++|
T Consensus 210 ~d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~~---~-------~~~~~~~~---~~~~l~~~~~~g~~Ar~~L 276 (509)
T PRK05901 210 ADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEELL---A-------EGEKLDPE---LRRDLQWIGRDGKRAKNHL 276 (509)
T ss_pred ccHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhhh---h-------hcccchhh---hhhhhhhhccchHHHHHHH
Confidence 4557788888875 8999999999999999876555422 1 11234322 4577888999999999999
Q ss_pred HHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCCccCCCccccc
Q 016880 301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPVPLFLI 380 (381)
Q Consensus 301 Ie~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~IRlP~~~~Ek 380 (381)
|..|+|||++||++|.++|++++||||||+||||+||++|||++|++|+|||+||||++|.++|+++.++||+|.|+.+.
T Consensus 277 I~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~~~~e~ 356 (509)
T PRK05901 277 LEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVET 356 (509)
T ss_pred HHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999764
No 8
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=99.96 E-value=8.2e-30 Score=251.34 Aligned_cols=145 Identities=34% Similarity=0.549 Sum_probs=126.1
Q ss_pred hHHHHHhhcCCC-CCCCcHHHHHHHHHhHHHHHHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHHhcHHHHHHHH
Q 016880 223 FSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELI 301 (381)
Q Consensus 223 ~~v~~~~~~~~~-~lLtaeEE~eL~~~iq~~~~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~~G~~Are~LI 301 (381)
+.+..|++..++ |+||++||++|++.++.+..++.. |+..+|+... ...+|...++.|..|+++||
T Consensus 26 ~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~~Lv 92 (324)
T PRK07921 26 DLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARRHLL 92 (324)
T ss_pred ChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHHHHH
Confidence 345667777775 899999999999999988776653 2223332111 45688999999999999999
Q ss_pred HHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCCccCCCccccc
Q 016880 302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPVPLFLI 380 (381)
Q Consensus 302 e~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~IRlP~~~~Ek 380 (381)
..|+++|+++|++|.+.|++++||+|||+||||+|+++|||++|++|+|||+||||++|.++|++++++||+|.|+.++
T Consensus 93 ~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~~~ 171 (324)
T PRK07921 93 EANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ 171 (324)
T ss_pred HHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999998754
No 9
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=99.93 E-value=6.9e-26 Score=239.43 Aligned_cols=105 Identities=33% Similarity=0.739 Sum_probs=94.3
Q ss_pred HHHcCCCH---HHHHHHHHhcH----HHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCcc
Q 016880 276 AQAAGVSE---RVLKQHLAFGW----YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKF 348 (381)
Q Consensus 276 A~aagl~~---eeL~~~l~~G~----~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rF 348 (381)
....+++. ..+.++++.|+ .|+++||.+|+|||++||++|.++|++++||||||+||||+||++|||++|++|
T Consensus 354 e~~~~Ls~eElk~l~~~i~~g~~~~~~a~~~Li~~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~F 433 (619)
T PRK05658 354 EEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 433 (619)
T ss_pred HHHhCCCHHHHHHHHHHHhccchhhhHHHHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCch
Confidence 33445554 44556677785 489999999999999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHHHHHHHHHHcCCCccCCCccccc
Q 016880 349 STYVQYWIRKSISKMVARHARGIKIPVPLFLI 380 (381)
Q Consensus 349 STYA~~wIr~aI~~~Ir~qsr~IRlP~~~~Ek 380 (381)
+|||+||||++|.++|+++.++||+|+|+.++
T Consensus 434 stYA~~wIr~aI~~~i~~~~r~irip~~~~~~ 465 (619)
T PRK05658 434 STYATWWIRQAITRSIADQARTIRIPVHMIET 465 (619)
T ss_pred HHHhHHHHHHHHHHHHHHcCCceecCHHHHHH
Confidence 99999999999999999999999999999764
No 10
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=99.92 E-value=7.5e-25 Score=218.82 Aligned_cols=119 Identities=35% Similarity=0.618 Sum_probs=107.2
Q ss_pred hhHHHHHhhcCCC-CCCCcHHHHHHHHHhHHHHHHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHHhcHHHHHHH
Q 016880 222 IFSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREEL 300 (381)
Q Consensus 222 ~~~v~~~~~~~~~-~lLtaeEE~eL~~~iq~~~~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~~G~~Are~L 300 (381)
.++++.|++..++ |+||++||.+|++.++.+ +..|+++|
T Consensus 95 ~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~G----------------------------------------d~~A~~~L 134 (367)
T PRK09210 95 NDPVRMYLKEIGRVPLLTAEEEIELAKRIEEG----------------------------------------DEEAKQRL 134 (367)
T ss_pred CcHHHHHHHHhhccCCCCHHHHHHHHHHHHhh----------------------------------------HHHHHHHH
Confidence 4567788887775 899999999998755422 12489999
Q ss_pred HHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCCccCCCccccc
Q 016880 301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPVPLFLI 380 (381)
Q Consensus 301 Ie~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~IRlP~~~~Ek 380 (381)
|..|+++|+++|++|.++|.+++||+|||+||||+|+++|||++|++|+|||+||||++|.++|+++.++||+|.|++++
T Consensus 135 i~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~~~~ 214 (367)
T PRK09210 135 AEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 214 (367)
T ss_pred HHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999764
No 11
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=99.91 E-value=4.6e-25 Score=211.02 Aligned_cols=86 Identities=26% Similarity=0.455 Sum_probs=83.1
Q ss_pred HHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCCccCC
Q 016880 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (381)
Q Consensus 295 ~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~IRlP 374 (381)
.++++||..|+|||++||++|.++|++++||||+|+|||++|+++|||++|++|+|||+|||+++|.++|+++.++||+|
T Consensus 40 ~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I~~~lr~~~~~ir~P 119 (264)
T PRK07122 40 RQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVP 119 (264)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHcCCccccC
Confidence 38999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Cccccc
Q 016880 375 VPLFLI 380 (381)
Q Consensus 375 ~~~~Ek 380 (381)
.++.++
T Consensus 120 r~~~~~ 125 (264)
T PRK07122 120 RRLKEL 125 (264)
T ss_pred HHHHHH
Confidence 998654
No 12
>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=99.87 E-value=7.2e-23 Score=191.76 Aligned_cols=84 Identities=42% Similarity=0.858 Sum_probs=81.4
Q ss_pred HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCCccCCC
Q 016880 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPV 375 (381)
Q Consensus 296 Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~IRlP~ 375 (381)
|+++||..|+|+|.++|++|.+.|++++||+|||++||++|+++|||++|++|+|||.||||++|.++++++.+.+|+|.
T Consensus 1 a~~~Li~~~~~lv~~ia~~~~~~~~~~eDLiQeG~igL~~A~~~fd~~~g~~FstYA~~~Ir~~I~~~l~~~~~~vrip~ 80 (238)
T TIGR02393 1 AKKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80 (238)
T ss_pred CHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCChHHHhHHHHHHHHHHHHHHcCCcEEeCH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccc
Q 016880 376 PLFL 379 (381)
Q Consensus 376 ~~~E 379 (381)
++.+
T Consensus 81 ~~~~ 84 (238)
T TIGR02393 81 HMVE 84 (238)
T ss_pred HHHH
Confidence 8754
No 13
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=99.87 E-value=3.6e-22 Score=193.00 Aligned_cols=84 Identities=31% Similarity=0.631 Sum_probs=80.6
Q ss_pred HHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCCccCC
Q 016880 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (381)
Q Consensus 295 ~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~IRlP 374 (381)
.|+++||..|+|+|.++|++|.+.+++.+||+|||++||++|+++|||++|++|+|||+|||+++|.++|+++.++||+|
T Consensus 48 ~a~~~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~p 127 (284)
T PRK06596 48 EAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVA 127 (284)
T ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeeecc
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999987789999
Q ss_pred Cccc
Q 016880 375 VPLF 378 (381)
Q Consensus 375 ~~~~ 378 (381)
.+..
T Consensus 128 ~~~~ 131 (284)
T PRK06596 128 TTKA 131 (284)
T ss_pred chHH
Confidence 9863
No 14
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=99.87 E-value=5.5e-22 Score=192.27 Aligned_cols=117 Identities=26% Similarity=0.411 Sum_probs=103.4
Q ss_pred hhHHHHHhhcCCC-CCCCcHHHHHHHHHhHHHHHHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHHhc-HHHHHH
Q 016880 222 IFSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFG-WYCREE 299 (381)
Q Consensus 222 ~~~v~~~~~~~~~-~lLtaeEE~eL~~~iq~~~~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~~G-~~Are~ 299 (381)
++.+..|++...+ |+||+++|.+|.+.++ ..| ..|+++
T Consensus 5 ~~~~~~y~~~~~~~~~l~~~~e~~L~~~~~----------------------------------------~~gd~~A~~~ 44 (289)
T PRK07500 5 ASADRSMIRSAMKAPYLEREEEHALAYRWK----------------------------------------DHRDEDALHR 44 (289)
T ss_pred hhHHHHHHHHHhcCCCCCHHHHHHHHHHHH----------------------------------------HCCCHHHHHH
Confidence 4556778887775 8999999998866432 113 348999
Q ss_pred HHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCCccCCCccc
Q 016880 300 LIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPVPLF 378 (381)
Q Consensus 300 LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~IRlP~~~~ 378 (381)
||..|+|+|.++|++|.+.+.+.+||+|||++|||+|+++|||++|.+|+|||+||||++|.++|+++.+++|+|.+..
T Consensus 45 Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~~~~ 123 (289)
T PRK07500 45 IISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSA 123 (289)
T ss_pred HHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCccHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999998854
No 15
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=99.87 E-value=1e-21 Score=187.87 Aligned_cols=95 Identities=32% Similarity=0.594 Sum_probs=86.4
Q ss_pred HHHHHHH-HHhcH-HHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHH
Q 016880 283 ERVLKQH-LAFGW-YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (381)
Q Consensus 283 ~eeL~~~-l~~G~-~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI 360 (381)
+.+|..+ .+.|+ .|+++||..|+|+|+++|++|.+.+.+.+||+|+|++||++|+++|||++|++|+|||.|||+++|
T Consensus 21 e~~l~~~~~~~gd~~a~~~Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i 100 (270)
T TIGR02392 21 EYQLAKRLREHGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEI 100 (270)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHH
Confidence 3455555 44665 499999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHcCCCccCCCcc
Q 016880 361 SKMVARHARGIKIPVPL 377 (381)
Q Consensus 361 ~~~Ir~qsr~IRlP~~~ 377 (381)
.++|+++.+++|+|.+.
T Consensus 101 ~~~l~~~~~~ir~p~~~ 117 (270)
T TIGR02392 101 HEYILRNWRLVKVATTK 117 (270)
T ss_pred HHHHHHcCCceecCchH
Confidence 99999987789999875
No 16
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=99.86 E-value=9.4e-22 Score=186.96 Aligned_cols=89 Identities=26% Similarity=0.422 Sum_probs=83.2
Q ss_pred HhcH-HHHHHHHHHhhHHHHHHHHHccCC-CCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcC
Q 016880 291 AFGW-YCREELIKSTRPLVLFLARNYRGL-GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA 368 (381)
Q Consensus 291 ~~G~-~Are~LIe~nlrLV~~IAkry~~r-g~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qs 368 (381)
+.|+ .|+++||..|+|+|.++|++|.++ +.+++||+|+|+||||+|+++|||++|++|+|||+|||+++|.++++++.
T Consensus 20 ~~gd~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~ 99 (256)
T PRK07408 20 QNPSIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKS 99 (256)
T ss_pred HCCCHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcC
Confidence 3555 499999999999999999999876 67799999999999999999999999999999999999999999999999
Q ss_pred CCccCCCcccc
Q 016880 369 RGIKIPVPLFL 379 (381)
Q Consensus 369 r~IRlP~~~~E 379 (381)
++||+|.++.+
T Consensus 100 ~~vr~pr~~~~ 110 (256)
T PRK07408 100 PTVRIPRRWQE 110 (256)
T ss_pred CeeeeCHHHHH
Confidence 99999998764
No 17
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=99.82 E-value=2.2e-20 Score=178.92 Aligned_cols=95 Identities=34% Similarity=0.527 Sum_probs=86.7
Q ss_pred HHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCC-CHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHH
Q 016880 284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGI-PFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (381)
Q Consensus 284 eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~-d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~ 361 (381)
+.+....+.|+. ++ +||+.|+|||.+||++|.+++. ++|||+|.|||||++|+++|||++|.+|+|||..+|+++|.
T Consensus 12 ~~~~~~~~~g~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~ 90 (247)
T COG1191 12 EKLLEYYAEGDEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEIL 90 (247)
T ss_pred HHHHHHHHhcCHHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHH
Confidence 345555666765 88 9999999999999999999987 99999999999999999999999999999999999999999
Q ss_pred HHHHHcCCCccCCCccccc
Q 016880 362 KMVARHARGIKIPVPLFLI 380 (381)
Q Consensus 362 ~~Ir~qsr~IRlP~~~~Ek 380 (381)
+++|+.+ .+++|+.+.++
T Consensus 91 d~LR~~~-~v~vpR~~~~~ 108 (247)
T COG1191 91 DYLRKND-SVKVPRSLREL 108 (247)
T ss_pred HHHHhCC-CccCcHHHHHH
Confidence 9999998 99999987664
No 18
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=99.80 E-value=1.1e-19 Score=173.04 Aligned_cols=91 Identities=23% Similarity=0.322 Sum_probs=79.1
Q ss_pred HHHHH-HhcH-HHHHHHHHHhhHHHHHHHHHccC---CCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHH
Q 016880 286 LKQHL-AFGW-YCREELIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (381)
Q Consensus 286 L~~~l-~~G~-~Are~LIe~nlrLV~~IAkry~~---rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI 360 (381)
++... +.|+ .|+++||..|+|+|+++|++|.+ .+++++||+|+|+||||+|+++|||++|++|+|||.||||++|
T Consensus 12 ~~~~~~~~~~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i 91 (257)
T PRK05911 12 TWQLYWSTQEIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAI 91 (257)
T ss_pred HHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHH
Confidence 44444 2344 49999999999999999999862 3578999999999999999999999999999999999999999
Q ss_pred HHHHHHcCCCccCCCcccc
Q 016880 361 SKMVARHARGIKIPVPLFL 379 (381)
Q Consensus 361 ~~~Ir~qsr~IRlP~~~~E 379 (381)
.++++++.+ +|.++.+
T Consensus 92 ~~~lr~~~~---~pr~~~~ 107 (257)
T PRK05911 92 IDDLRKQDW---VPRSVHQ 107 (257)
T ss_pred HHHHHhcCC---CCHHHHH
Confidence 999999865 7887754
No 19
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=99.80 E-value=1.7e-19 Score=177.96 Aligned_cols=117 Identities=32% Similarity=0.618 Sum_probs=102.4
Q ss_pred hhhHHHHHhhcCC-CCCCCcHHHHHHHHHhHHHHHHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHHhcH-HHHH
Q 016880 221 TIFSAERALNSRG-RRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGW-YCRE 298 (381)
Q Consensus 221 ~~~~v~~~~~~~~-~~lLtaeEE~eL~~~iq~~~~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~~G~-~Are 298 (381)
..+.+..|++..+ .|+||+++|.+|...+ +.|+ .|++
T Consensus 51 ~~~~~~~y~~~~~~~~~l~~~ee~~li~~~-----------------------------------------~~Gd~~A~~ 89 (325)
T PRK05657 51 VLDATQLYLNEIGYSPLLTAEEEVYFARRA-----------------------------------------LRGDFAARQ 89 (325)
T ss_pred cccHHHHHHHHHhcCCCCCHHHHHHHHHHH-----------------------------------------HcCCHHHHH
Confidence 3455677777766 4888888887765422 2333 4899
Q ss_pred HHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCCccCCCccc
Q 016880 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPVPLF 378 (381)
Q Consensus 299 ~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~IRlP~~~~ 378 (381)
+||..|.++|+++|.+|.+.+.+.+||+|||++|||+++++||+++|++|+|||+||||++|.++++++.+.||+|.|++
T Consensus 90 ~Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~~~~ 169 (325)
T PRK05657 90 RMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVV 169 (325)
T ss_pred HHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999865
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=99.77 E-value=1.6e-18 Score=164.13 Aligned_cols=84 Identities=29% Similarity=0.439 Sum_probs=79.9
Q ss_pred HHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCCccCC
Q 016880 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (381)
Q Consensus 295 ~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~IRlP 374 (381)
.|+++|+..|.|+|.++|++|.+.+.+.+||+|||++|||+|+++|||.+|.+|+||+++||++.|.++++++ ..+|+|
T Consensus 34 ~a~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~-~~ir~p 112 (254)
T TIGR02850 34 TAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDN-NPIRVS 112 (254)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhC-CCccCc
Confidence 4899999999999999999999999999999999999999999999999999999999999999999999996 488999
Q ss_pred Ccccc
Q 016880 375 VPLFL 379 (381)
Q Consensus 375 ~~~~E 379 (381)
.++.+
T Consensus 113 ~~~~~ 117 (254)
T TIGR02850 113 RSLRD 117 (254)
T ss_pred hHHHH
Confidence 98754
No 21
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=99.73 E-value=9.9e-18 Score=158.88 Aligned_cols=94 Identities=28% Similarity=0.407 Sum_probs=85.0
Q ss_pred HHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHH
Q 016880 285 VLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKM 363 (381)
Q Consensus 285 eL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~ 363 (381)
.|...++.|+. ++++|+..|.|+|.++|++|.+.+.+.+||+|||++|||+|+++|||++|++|+||+++||+++|.++
T Consensus 26 ~l~~~~~~gd~~a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~ 105 (258)
T PRK08215 26 ELFERMQNGDKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRY 105 (258)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHH
Confidence 34455555554 99999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHcCCCccCCCcccc
Q 016880 364 VARHARGIKIPVPLFL 379 (381)
Q Consensus 364 Ir~qsr~IRlP~~~~E 379 (381)
++++ +.+|+|.++.+
T Consensus 106 lr~~-~~vrip~~~~~ 120 (258)
T PRK08215 106 LRDN-NPIRVSRSLRD 120 (258)
T ss_pred HHhC-CceEecHHHHH
Confidence 9997 58899988754
No 22
>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=99.73 E-value=8e-18 Score=155.60 Aligned_cols=85 Identities=33% Similarity=0.558 Sum_probs=81.5
Q ss_pred HHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCCccCC
Q 016880 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (381)
Q Consensus 295 ~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~IRlP 374 (381)
.|+++||..|.|+|..+|++|.+.+.+.+||+|||++||++|+++||+++|.+|+||+++||++.|.++++++.+.+++|
T Consensus 3 ~a~~~lv~~y~~~v~~~a~~~~~~~~~~eDl~Qe~~i~l~~a~~~f~~~~~~~F~ty~~~~i~~~~~~~~r~~~~~~ri~ 82 (227)
T TIGR02980 3 EAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVRVP 82 (227)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCcHHHHHHHHHHHHHHHHHHcCCceecC
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Ccccc
Q 016880 375 VPLFL 379 (381)
Q Consensus 375 ~~~~E 379 (381)
.++.+
T Consensus 83 ~~~~~ 87 (227)
T TIGR02980 83 RRLKE 87 (227)
T ss_pred HHHHH
Confidence 87643
No 23
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=99.71 E-value=1.8e-17 Score=153.91 Aligned_cols=90 Identities=27% Similarity=0.366 Sum_probs=82.9
Q ss_pred HHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHc
Q 016880 289 HLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH 367 (381)
Q Consensus 289 ~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~q 367 (381)
.++.|+. |+++|+..|.|+|.++|++|.+.+.+.+||+|+|++|||+|+++|||.+|.+|.||+++||++.|.++++++
T Consensus 4 ~~~~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~~ 83 (231)
T TIGR02885 4 LAQNGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDD 83 (231)
T ss_pred HHHcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhC
Confidence 3445554 999999999999999999999999999999999999999999999999999999999999999999999997
Q ss_pred CCCccCCCcccc
Q 016880 368 ARGIKIPVPLFL 379 (381)
Q Consensus 368 sr~IRlP~~~~E 379 (381)
. .+++|.++.+
T Consensus 84 ~-~i~~p~~~~~ 94 (231)
T TIGR02885 84 G-IIKVSRSLKE 94 (231)
T ss_pred C-CeECCHHHHH
Confidence 5 8899998654
No 24
>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=99.70 E-value=6.6e-17 Score=155.69 Aligned_cols=96 Identities=35% Similarity=0.748 Sum_probs=90.6
Q ss_pred HHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHH
Q 016880 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (381)
Q Consensus 283 ~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~ 361 (381)
+.+|+..++.|+. |++.|+..|.++|..+|.+|.+.+.+.+||+|||++|||+|+++||+.+|++|+||+.|||+.+|.
T Consensus 33 ~~~li~~~~~gd~~a~~~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain 112 (285)
T TIGR02394 33 EIAYARRALAGDFEARKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIE 112 (285)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHH
Confidence 4677888888876 999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHcCCCccCCCccc
Q 016880 362 KMVARHARGIKIPVPLF 378 (381)
Q Consensus 362 ~~Ir~qsr~IRlP~~~~ 378 (381)
++++++.+.+++|.++.
T Consensus 113 ~~i~~~~~~~~~p~~~~ 129 (285)
T TIGR02394 113 RAIMNQARTIRLPVHVI 129 (285)
T ss_pred HHHHHcCCceeCcHHHH
Confidence 99999999999998764
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=99.69 E-value=6.3e-17 Score=152.75 Aligned_cols=97 Identities=21% Similarity=0.265 Sum_probs=88.8
Q ss_pred HHHHHHHHHh-cH-HHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHH
Q 016880 283 ERVLKQHLAF-GW-YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (381)
Q Consensus 283 ~eeL~~~l~~-G~-~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI 360 (381)
+.+|+..++. |+ .|+++|+..|.|+|+.+|++|.+.+.+.+||+|+|++|||+|+++||++.|.+|.||+++||++.|
T Consensus 15 ~~~li~~~~~~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~ 94 (255)
T TIGR02941 15 VIQWIAEFQQNQNGEAQEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEI 94 (255)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHH
Confidence 3456676766 54 599999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHcCCCccCCCcccc
Q 016880 361 SKMVARHARGIKIPVPLFL 379 (381)
Q Consensus 361 ~~~Ir~qsr~IRlP~~~~E 379 (381)
.++++++.+.+++|.++.+
T Consensus 95 ~~~lr~~~~~iri~~~~~~ 113 (255)
T TIGR02941 95 KRYLRDKTWSVHVPRRIKE 113 (255)
T ss_pred HHHHHHcCCCcCCCHHHHH
Confidence 9999999999999987644
No 26
>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=99.68 E-value=7.5e-17 Score=151.95 Aligned_cols=89 Identities=18% Similarity=0.301 Sum_probs=81.3
Q ss_pred HHHhcHHHHHHHHHHhhHHHHHHHHHccCCC--CCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHH
Q 016880 289 HLAFGWYCREELIKSTRPLVLFLARNYRGLG--IPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVAR 366 (381)
Q Consensus 289 ~l~~G~~Are~LIe~nlrLV~~IAkry~~rg--~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~ 366 (381)
.++.|+..+++||..|.|+|.++|++|.++. .+.||++|+|++|||+|+++|||++|.+|.|||.+||+++|.+++|+
T Consensus 3 ~~~~gd~~~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dylRk 82 (218)
T TIGR02895 3 PIQPGNEEREELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYIRK 82 (218)
T ss_pred hhhcCChHHHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence 4677887899999999999999999998774 58999999999999999999999999999999999999999999999
Q ss_pred cC---CCccCCCcc
Q 016880 367 HA---RGIKIPVPL 377 (381)
Q Consensus 367 qs---r~IRlP~~~ 377 (381)
.. +.+++|...
T Consensus 83 ~~k~~~~v~~~~~~ 96 (218)
T TIGR02895 83 NQKYQNLLYLDEDY 96 (218)
T ss_pred cccccCeeeCCchH
Confidence 87 567888644
No 27
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=99.65 E-value=6.6e-16 Score=147.38 Aligned_cols=81 Identities=32% Similarity=0.432 Sum_probs=72.9
Q ss_pred HHHHHHHHHhhHHHHHHHHHccC---CCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCCc
Q 016880 295 YCREELIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI 371 (381)
Q Consensus 295 ~Are~LIe~nlrLV~~IAkry~~---rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~I 371 (381)
.+++.++..|.|+|..+|++|.. .+.+.+||+|+|++|||+|+++||+.+|++|+||+.+||++.|.+++|+..
T Consensus 31 ~a~~~l~~~y~~lv~~~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~~--- 107 (268)
T PRK06288 31 KIREYLILKYSPLVKYVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSID--- 107 (268)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC---
Confidence 48899999999999999999862 468899999999999999999999999999999999999999999999753
Q ss_pred cCCCccc
Q 016880 372 KIPVPLF 378 (381)
Q Consensus 372 RlP~~~~ 378 (381)
++|.++.
T Consensus 108 ~~p~~~~ 114 (268)
T PRK06288 108 WIPRSVR 114 (268)
T ss_pred ccCHHHH
Confidence 4677654
No 28
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=99.63 E-value=8.7e-16 Score=145.18 Aligned_cols=96 Identities=23% Similarity=0.268 Sum_probs=87.5
Q ss_pred HHHHHHHHHh-cH-HHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHH
Q 016880 283 ERVLKQHLAF-GW-YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (381)
Q Consensus 283 ~eeL~~~l~~-G~-~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI 360 (381)
+.+|+..++. |+ .|+++|+..|.|+|..+|++|.+.+.+.+||+|+|++|||+++++||+..|.+|.||+++||++.|
T Consensus 15 ~~~li~~~~~~gd~~a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~ 94 (257)
T PRK08583 15 VNKWIAEYQENQDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEI 94 (257)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHH
Confidence 3456666653 55 499999999999999999999999999999999999999999999999999899999999999999
Q ss_pred HHHHHHcCCCccCCCccc
Q 016880 361 SKMVARHARGIKIPVPLF 378 (381)
Q Consensus 361 ~~~Ir~qsr~IRlP~~~~ 378 (381)
.++++++.++++||.++.
T Consensus 95 ~~~lr~~~~~~~i~r~~~ 112 (257)
T PRK08583 95 KRYLRDKTWSVHVPRRIK 112 (257)
T ss_pred HHHHHhcCCCcCCCHHHH
Confidence 999999999999999854
No 29
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=99.59 E-value=2.7e-15 Score=141.15 Aligned_cols=73 Identities=22% Similarity=0.271 Sum_probs=66.7
Q ss_pred HHHHHHHHhhHHHHHHHHHccCC---CCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCC
Q 016880 296 CREELIKSTRPLVLFLARNYRGL---GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (381)
Q Consensus 296 Are~LIe~nlrLV~~IAkry~~r---g~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr 369 (381)
....|+..|+|+|.++|++|..+ +++.+||+|+|++|||+|+++|||..| +|+|||+|||+++|.++|++..+
T Consensus 16 ~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~~ 91 (231)
T PRK12427 16 EEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELDW 91 (231)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcCC
Confidence 56689999999999999999754 679999999999999999999998666 89999999999999999998765
No 30
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=99.58 E-value=3.7e-15 Score=140.86 Aligned_cols=92 Identities=26% Similarity=0.384 Sum_probs=80.5
Q ss_pred HHHHHHHHHh-cHH-HHHHHHHHhhHHHHHHHHHccC---CCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHH
Q 016880 283 ERVLKQHLAF-GWY-CREELIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIR 357 (381)
Q Consensus 283 ~eeL~~~l~~-G~~-Are~LIe~nlrLV~~IAkry~~---rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr 357 (381)
+.+|+++++. |+. |+++|+..|.|+|..+|.+|.+ .+.+.+|++|||++|||+++++||+.+|.+|.||+++||+
T Consensus 8 e~~l~~~~~~~~d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~ir 87 (251)
T PRK07670 8 EQKLWDRWKEERDPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIR 87 (251)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHH
Confidence 5666776444 454 9999999999999999999965 5789999999999999999999999999999999999999
Q ss_pred HHHHHHHHHcCCCccCCCcc
Q 016880 358 KSISKMVARHARGIKIPVPL 377 (381)
Q Consensus 358 ~aI~~~Ir~qsr~IRlP~~~ 377 (381)
+.|.++++++. ++|.++
T Consensus 88 n~~~d~lR~~~---~~p~~~ 104 (251)
T PRK07670 88 GAIIDGLRKED---WLPRSM 104 (251)
T ss_pred HHHHHHHHhcC---CCCHHH
Confidence 99999999865 466654
No 31
>PRK05572 sporulation sigma factor SigF; Validated
Probab=99.56 E-value=1e-14 Score=137.87 Aligned_cols=95 Identities=25% Similarity=0.362 Sum_probs=85.4
Q ss_pred HHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHH
Q 016880 284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK 362 (381)
Q Consensus 284 eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~ 362 (381)
.+|...++.|+. |+++|+..|.++|..+|.+|.+.+.+.+|++|||++++|+++++||+.+|.+|.||+++||++.|.+
T Consensus 20 ~~li~~~~~gd~~a~~~L~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~ 99 (252)
T PRK05572 20 KELIKKSQDGDQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQR 99 (252)
T ss_pred HHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHH
Confidence 445555666664 9999999999999999999999999999999999999999999999998889999999999999999
Q ss_pred HHHHcCCCccCCCcccc
Q 016880 363 MVARHARGIKIPVPLFL 379 (381)
Q Consensus 363 ~Ir~qsr~IRlP~~~~E 379 (381)
++++. ..+|+|.++.+
T Consensus 100 ~lr~~-~~~r~~~~~~~ 115 (252)
T PRK05572 100 FLRDD-GTVKVSRSLKE 115 (252)
T ss_pred HHHhC-CCCCCCHHHHH
Confidence 99987 57899987643
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=99.54 E-value=8.8e-15 Score=135.56 Aligned_cols=75 Identities=36% Similarity=0.530 Sum_probs=68.6
Q ss_pred HHHHhhHHHHHHHHHccC---CCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCCccCCCc
Q 016880 300 LIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPVP 376 (381)
Q Consensus 300 LIe~nlrLV~~IAkry~~---rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~IRlP~~ 376 (381)
|+..|.|+|+++|++|.+ .+.+.+||+|||++|||+|+++|||++|++|+||+.+||++.|.+++|+.. ++|.+
T Consensus 1 L~~~~~~lv~~~a~~~~~~~~~~~~~eDl~Qe~~~~l~~a~~~fd~~~~~~f~t~~~~~i~~~~~~~lr~~~---~~p~~ 77 (224)
T TIGR02479 1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLD---WVPRS 77 (224)
T ss_pred CHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHHcC---ccCHH
Confidence 578999999999999985 689999999999999999999999999999999999999999999999864 46654
Q ss_pred c
Q 016880 377 L 377 (381)
Q Consensus 377 ~ 377 (381)
+
T Consensus 78 ~ 78 (224)
T TIGR02479 78 L 78 (224)
T ss_pred H
Confidence 3
No 33
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=99.52 E-value=2e-13 Score=127.51 Aligned_cols=115 Identities=22% Similarity=0.277 Sum_probs=97.6
Q ss_pred HHHHhHHHHHHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHH
Q 016880 245 MSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFS 323 (381)
Q Consensus 245 L~~~iq~~~~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~E 323 (381)
|..-+++...|..+..++ ++.|....- ++..|+..+..|+. |.+.|+..|.|+|.++|.+|.+.+.+.+
T Consensus 8 ~~~~~~~~~~~~~~~~~~----~~~~~~~~~------~e~~l~~~~~~gd~~a~~~l~~~y~~~l~~~a~~~~~~~~dae 77 (233)
T PRK05803 8 LLYIVKEILFLVSYVKNN----SFPQPLSEE------EERKYLELMKEGDEEARNILIERNLRLVAHIVKKFENTGEDVD 77 (233)
T ss_pred HHHHHHHHHHHHHHHHHh----cccCCCCHH------HHHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHH
Confidence 445677777888777665 555554431 14567788888876 9999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCC
Q 016880 324 DLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (381)
Q Consensus 324 DLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr 369 (381)
|++|||+++||+++++||+++|.+|.||+++||++.+.+++|+..+
T Consensus 78 DlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~ 123 (233)
T PRK05803 78 DLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKK 123 (233)
T ss_pred HHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999989999999999999999999997654
No 34
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=99.50 E-value=4.2e-14 Score=132.19 Aligned_cols=78 Identities=29% Similarity=0.456 Sum_probs=73.2
Q ss_pred hcHHHHHHHHHHhhHHHHHHHHHcc---CCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcC
Q 016880 292 FGWYCREELIKSTRPLVLFLARNYR---GLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA 368 (381)
Q Consensus 292 ~G~~Are~LIe~nlrLV~~IAkry~---~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qs 368 (381)
.|+-++++|+..|.|+|..+|.+|. +.+.+.+||+|+|++|||+++++|||++|.+|.||+.+||++.|.++++++.
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 4666999999999999999999997 5689999999999999999999999999999999999999999999999975
Q ss_pred C
Q 016880 369 R 369 (381)
Q Consensus 369 r 369 (381)
+
T Consensus 85 ~ 85 (236)
T PRK06986 85 W 85 (236)
T ss_pred C
Confidence 4
No 35
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=99.31 E-value=3.7e-11 Score=112.13 Aligned_cols=113 Identities=21% Similarity=0.301 Sum_probs=91.5
Q ss_pred HhHHHHHHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHH
Q 016880 248 GVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLL 326 (381)
Q Consensus 248 ~iq~~~~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLi 326 (381)
-++.+..|-.+-+. .-|+++....- .+..|+.+++.|+. |.+.|++.|.|.|.++|.+|.+...+.+|++
T Consensus 9 ~~~~~~~~~~~~~~---~~~~~~~~~~~------~~~~li~~~~~gd~~af~~l~~~y~~~v~~~~~~~~~~~~dAEDlv 79 (227)
T TIGR02846 9 IVKSLLFLVGYVTN---NGSFPQPLSEE------EEKKYLDRLKEGDEEARNVLIERNLRLVAHIVKKFSNTGEDVDDLI 79 (227)
T ss_pred HHHHHHHHHHHHHH---HHhCCCCCCHH------HHHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHH
Confidence 34455555444332 23455553322 25677788888876 9999999999999999999998889999999
Q ss_pred HHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCC
Q 016880 327 QAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (381)
Q Consensus 327 QEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr 369 (381)
||+++++|+++++||++.+.+|.||+++++++.+.+++|+..+
T Consensus 80 Qevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~Rk~~r 122 (227)
T TIGR02846 80 SIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHLRALKK 122 (227)
T ss_pred HHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999988899999999999999999998654
No 36
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=99.30 E-value=1.4e-11 Score=117.46 Aligned_cols=91 Identities=19% Similarity=0.293 Sum_probs=81.5
Q ss_pred CHHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCC--CHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHH
Q 016880 282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGI--PFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358 (381)
Q Consensus 282 ~~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~--d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~ 358 (381)
+.+.|+..++.|+. |+++|+..|.|+|.++|.++.++.. +.+|++|+|++++|+|+++||+++|..|.+|+..+|++
T Consensus 4 ~~~~Li~~~~~gD~~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn 83 (237)
T PRK08311 4 SLEDILEKIKNGDEELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKR 83 (237)
T ss_pred cHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHH
Confidence 35667888888876 9999999999999999999987765 58999999999999999999999988999999999999
Q ss_pred HHHHHHHHcCCCcc
Q 016880 359 SISKMVARHARGIK 372 (381)
Q Consensus 359 aI~~~Ir~qsr~IR 372 (381)
.+.+++|++.+...
T Consensus 84 ~~iDylRk~~~~~~ 97 (237)
T PRK08311 84 RLIDYFRKESKHNL 97 (237)
T ss_pred HHHHHHHHhhcccc
Confidence 99999998766433
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=99.27 E-value=1.4e-11 Score=92.96 Aligned_cols=70 Identities=24% Similarity=0.375 Sum_probs=66.9
Q ss_pred HHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCC
Q 016880 300 LIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (381)
Q Consensus 300 LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr 369 (381)
|++.|.|+|..++.+|.+.+.+.+|++||++++|++++++||++++..|.+|+...+++.+.+.++++.+
T Consensus 1 L~~~~~~~l~~~~~~~~~~~~~~eD~~qe~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~r~~~r 70 (71)
T PF04542_consen 1 LYERYYPLLYRYARRYTGDPEDAEDLVQEAFIKLWRAIDSYDPDRGDSFRAWLFRIARNRILDYLRKRRR 70 (71)
T ss_dssp HHHHTHHHHHHHHHTCTTCSSHHHHHHHHHHHHHHHHHHHTSTTSSSHHHHHHHHHHHHHHHHHHHCSSS
T ss_pred CHHHHHHHHHHHHHHHhCCHhhHHHHhhHHHHHHHhhhhcccccccCCHHHHHHHHHHHHHHHHHHHhcC
Confidence 6899999999999999999999999999999999999999999999899999999999999999998754
No 38
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=99.26 E-value=3.2e-11 Score=109.10 Aligned_cols=91 Identities=21% Similarity=0.307 Sum_probs=82.3
Q ss_pred CCCHHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHH
Q 016880 280 GVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358 (381)
Q Consensus 280 gl~~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~ 358 (381)
.++.+.|...++.|+. +.+.|+..|.|+|..+|.+|.+...+.+|++||++++||+++.+||+.++.+|.||++.+|++
T Consensus 8 ~~~~~~l~~~~~~~d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n 87 (208)
T PRK08295 8 ELEDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITR 87 (208)
T ss_pred CCChHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHH
Confidence 3456778888888876 999999999999999999999999999999999999999999999998878999999999999
Q ss_pred HHHHHHHHcCCC
Q 016880 359 SISKMVARHARG 370 (381)
Q Consensus 359 aI~~~Ir~qsr~ 370 (381)
.+.+++++..+.
T Consensus 88 ~~~d~~r~~~r~ 99 (208)
T PRK08295 88 QIITAIKTANRQ 99 (208)
T ss_pred HHHHHHHHhhhh
Confidence 999999865443
No 39
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=99.25 E-value=3.7e-11 Score=111.94 Aligned_cols=87 Identities=28% Similarity=0.492 Sum_probs=81.1
Q ss_pred HHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHH
Q 016880 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (381)
Q Consensus 283 ~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~ 361 (381)
+..|...++.|+. |++.++..|.++|..+|.+|.+.+.+.+|++||+++++|+++++||+..+++|.||++.++++.+.
T Consensus 39 ~~~L~~~~~~gd~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~ 118 (234)
T PRK08301 39 EEYLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEIL 118 (234)
T ss_pred HHHHHHHHHccCHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHH
Confidence 5778888888876 999999999999999999999888999999999999999999999998888999999999999999
Q ss_pred HHHHHcCC
Q 016880 362 KMVARHAR 369 (381)
Q Consensus 362 ~~Ir~qsr 369 (381)
+++|++.+
T Consensus 119 d~lRk~~~ 126 (234)
T PRK08301 119 MYLRRNNK 126 (234)
T ss_pred HHHHHHhc
Confidence 99998654
No 40
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=99.19 E-value=1.2e-10 Score=104.51 Aligned_cols=87 Identities=18% Similarity=0.291 Sum_probs=79.8
Q ss_pred CCHHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHH
Q 016880 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (381)
Q Consensus 281 l~~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~a 359 (381)
+++.+|+..++.|+. |.++|+..|.|.|..+|.++.+...+.+|++||+++.+|+++.+||+..+..|.||++.+|++.
T Consensus 4 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~~ 83 (198)
T TIGR02859 4 LEDEEIVELARQGNTHALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTRQ 83 (198)
T ss_pred cchHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHHH
Confidence 457788888888886 9999999999999999999998889999999999999999999999988779999999999999
Q ss_pred HHHHHHHc
Q 016880 360 ISKMVARH 367 (381)
Q Consensus 360 I~~~Ir~q 367 (381)
+.++++..
T Consensus 84 ~~~~~r~~ 91 (198)
T TIGR02859 84 IITAIKTA 91 (198)
T ss_pred HHHHHHHH
Confidence 98888753
No 41
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=99.17 E-value=1.5e-10 Score=108.51 Aligned_cols=87 Identities=28% Similarity=0.512 Sum_probs=80.6
Q ss_pred HHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHH
Q 016880 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (381)
Q Consensus 283 ~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~ 361 (381)
++.|+..++.|+. |++.++..|.+.|..++.+|.+.+.+.+|++||+++++|+++++|++..+++|.||++.++++.+.
T Consensus 39 ~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~ 118 (234)
T TIGR02835 39 EEALLQKLTQGDESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEIL 118 (234)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHH
Confidence 5667777888776 999999999999999999999999999999999999999999999998888899999999999999
Q ss_pred HHHHHcCC
Q 016880 362 KMVARHAR 369 (381)
Q Consensus 362 ~~Ir~qsr 369 (381)
++++++.+
T Consensus 119 d~~Rk~~r 126 (234)
T TIGR02835 119 MYLRRNNK 126 (234)
T ss_pred HHHHHhcc
Confidence 99998654
No 42
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=99.02 E-value=1e-09 Score=91.19 Aligned_cols=72 Identities=29% Similarity=0.380 Sum_probs=68.4
Q ss_pred HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCC
Q 016880 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (381)
Q Consensus 296 Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr 369 (381)
|.+.++..|.++|.++++++.+.+.+.+|++|+|+++|+++++.||+. ..|.+|+..+|++.+.++++++.+
T Consensus 2 a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~ 73 (158)
T TIGR02937 2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR 73 (158)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhcc
Confidence 678999999999999999999888999999999999999999999998 689999999999999999998765
No 43
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=99.00 E-value=1.1e-09 Score=95.60 Aligned_cols=81 Identities=17% Similarity=0.163 Sum_probs=72.7
Q ss_pred HHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHc
Q 016880 289 HLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH 367 (381)
Q Consensus 289 ~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~q 367 (381)
+++.|+. |.++|+..|.++|..++++|.+.+.+.+|++||++++||+++++|| .+.+|.+|++..+++.+.+.+++.
T Consensus 3 ~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~r~~ 80 (182)
T PRK09652 3 RVQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYLRKQ 80 (182)
T ss_pred hhhcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHHHcc
Confidence 4556665 9999999999999999999998889999999999999999999999 445899999999999999999986
Q ss_pred CCCc
Q 016880 368 ARGI 371 (381)
Q Consensus 368 sr~I 371 (381)
.+..
T Consensus 81 ~~~~ 84 (182)
T PRK09652 81 GRRP 84 (182)
T ss_pred cCCC
Confidence 5543
No 44
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=99.00 E-value=1.7e-09 Score=96.89 Aligned_cols=88 Identities=17% Similarity=0.140 Sum_probs=80.4
Q ss_pred CCHHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHH
Q 016880 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (381)
Q Consensus 281 l~~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~a 359 (381)
++++.|+..++.|+. |.+.|+..|.++|..+|.+|.+.+.+.+|++||++++||+++.+||+. +.+|.+|++..+++.
T Consensus 5 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n~ 83 (186)
T PRK05602 5 DPDEELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLNL 83 (186)
T ss_pred ccHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHHH
Confidence 456788888888886 999999999999999999999988999999999999999999999986 458999999999999
Q ss_pred HHHHHHHcCC
Q 016880 360 ISKMVARHAR 369 (381)
Q Consensus 360 I~~~Ir~qsr 369 (381)
+.+.++++..
T Consensus 84 ~~d~~R~~~~ 93 (186)
T PRK05602 84 CYDRLRRRRE 93 (186)
T ss_pred HHHHHHhcCC
Confidence 9999997653
No 45
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=98.97 E-value=3.1e-09 Score=95.75 Aligned_cols=91 Identities=15% Similarity=0.111 Sum_probs=81.1
Q ss_pred CCHHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHH
Q 016880 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (381)
Q Consensus 281 l~~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~a 359 (381)
.+++.|+..+..|+. |.+.|+..|.+.|.++|.++.+...+.+|++|++++++|++..+|++. ..|.+|++..+++.
T Consensus 11 ~~~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~--~~f~~wl~~i~~n~ 88 (194)
T PRK12513 11 ASDEALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPR--ARFRTWLYQIARNL 88 (194)
T ss_pred CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CchHHHHHHHHHHH
Confidence 456778888888876 999999999999999999999988899999999999999999999974 36999999999999
Q ss_pred HHHHHHHcCCCccC
Q 016880 360 ISKMVARHARGIKI 373 (381)
Q Consensus 360 I~~~Ir~qsr~IRl 373 (381)
+.+.+|++.+..+.
T Consensus 89 ~~~~~R~~~~~~~~ 102 (194)
T PRK12513 89 LIDHWRRHGARQAP 102 (194)
T ss_pred HHHHHHHhcccccc
Confidence 99999987655433
No 46
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=98.94 E-value=3.7e-09 Score=95.73 Aligned_cols=87 Identities=21% Similarity=0.101 Sum_probs=79.5
Q ss_pred CHHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHH
Q 016880 282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (381)
Q Consensus 282 ~~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI 360 (381)
+.+.|+..+..|+. +.++|+..|.++|..+|.+|.+...+.+|++||+++++|+.+++||+.+| .|.+|++..+++.+
T Consensus 16 ~~~~li~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n~~ 94 (194)
T PRK09646 16 DLDALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHRRA 94 (194)
T ss_pred cHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHHHH
Confidence 35677888888875 99999999999999999999999999999999999999999999998766 79999999999999
Q ss_pred HHHHHHcCC
Q 016880 361 SKMVARHAR 369 (381)
Q Consensus 361 ~~~Ir~qsr 369 (381)
.+.++++.+
T Consensus 95 ~d~~r~~~~ 103 (194)
T PRK09646 95 VDRVRSEQA 103 (194)
T ss_pred HHHHHhhcc
Confidence 999998654
No 47
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=98.93 E-value=4.2e-09 Score=93.44 Aligned_cols=85 Identities=14% Similarity=0.110 Sum_probs=76.9
Q ss_pred HHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHH
Q 016880 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (381)
Q Consensus 283 ~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~ 361 (381)
++.|+..++.|+. +.++|+..|.|+|..+|.+|.+.+.+.+|++|++++++|+++..||+.. .|.+|+...+++.+.
T Consensus 5 ~~~li~~~~~gd~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~ 82 (187)
T TIGR02948 5 IKKRIKEVRKGDENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLTI 82 (187)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHH
Confidence 3557777888876 9999999999999999999998889999999999999999999999865 599999999999999
Q ss_pred HHHHHcCC
Q 016880 362 KMVARHAR 369 (381)
Q Consensus 362 ~~Ir~qsr 369 (381)
+.+++..+
T Consensus 83 ~~~rk~~~ 90 (187)
T TIGR02948 83 DRLRKRKP 90 (187)
T ss_pred HHHHhhcc
Confidence 99998643
No 48
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=98.92 E-value=4.7e-09 Score=93.12 Aligned_cols=86 Identities=16% Similarity=0.128 Sum_probs=78.1
Q ss_pred CHHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHH
Q 016880 282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (381)
Q Consensus 282 ~~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI 360 (381)
+.+.|+..++.|+. +.++++..|.|+|.++|.++.+...+.+|++||++++|++++.+|++.. .|.+|+...+++.+
T Consensus 4 ~~~~li~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~~ 81 (187)
T PRK09641 4 LIKRLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNLT 81 (187)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHHH
Confidence 35677888888876 9999999999999999999999889999999999999999999999853 69999999999999
Q ss_pred HHHHHHcCC
Q 016880 361 SKMVARHAR 369 (381)
Q Consensus 361 ~~~Ir~qsr 369 (381)
.+++|++.+
T Consensus 82 ~d~~R~~~~ 90 (187)
T PRK09641 82 IDRLRKRKP 90 (187)
T ss_pred HHHHHhcCc
Confidence 999998654
No 49
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=98.92 E-value=5.3e-09 Score=93.30 Aligned_cols=87 Identities=24% Similarity=0.225 Sum_probs=78.7
Q ss_pred CHHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHH
Q 016880 282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (381)
Q Consensus 282 ~~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI 360 (381)
++..|...++.|+. +.+.|+..|.|.|..++++|.+.+.+.+|++||+++.+|+++++|++..+ .|.+|++..+++.+
T Consensus 9 ~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~~-~~~~wl~~ia~n~~ 87 (186)
T PRK13919 9 SDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRG-SARAWLLALAHHAA 87 (186)
T ss_pred CHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCcccc-chHHHHHHHHHHHH
Confidence 56778888888876 99999999999999999999888899999999999999999999997654 69999999999999
Q ss_pred HHHHHHcCC
Q 016880 361 SKMVARHAR 369 (381)
Q Consensus 361 ~~~Ir~qsr 369 (381)
.+.++++.+
T Consensus 88 ~d~~rk~~~ 96 (186)
T PRK13919 88 VDHVRRRAA 96 (186)
T ss_pred HHHHHhhhc
Confidence 999998643
No 50
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=98.91 E-value=7.9e-09 Score=93.23 Aligned_cols=89 Identities=11% Similarity=0.153 Sum_probs=79.4
Q ss_pred CCHHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCC---CCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHH
Q 016880 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLG---IPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356 (381)
Q Consensus 281 l~~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg---~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wI 356 (381)
++++.|+..+..|+. |+++|+..|.|.|..++.++.+.+ .+.+|++||++++||+++++|+++.+ .|.+|++..+
T Consensus 3 ~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~ia 81 (189)
T PRK06811 3 INEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAIS 81 (189)
T ss_pred CcHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHH
Confidence 567888999999886 999999999999999999997753 47899999999999999999997655 7999999999
Q ss_pred HHHHHHHHHHcCCC
Q 016880 357 RKSISKMVARHARG 370 (381)
Q Consensus 357 r~aI~~~Ir~qsr~ 370 (381)
++.+.++++++.+.
T Consensus 82 rn~~~d~~rk~~~~ 95 (189)
T PRK06811 82 KYKAIDYKRKLTKN 95 (189)
T ss_pred HHHHHHHHHHhccc
Confidence 99999999987654
No 51
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=98.90 E-value=9.8e-09 Score=92.15 Aligned_cols=88 Identities=20% Similarity=0.244 Sum_probs=76.7
Q ss_pred HHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCC----CCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHH
Q 016880 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGL----GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIR 357 (381)
Q Consensus 283 ~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~r----g~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr 357 (381)
...|+..+..|+. |+++|+..|.+.|..+|.++.+. ..+.+|++||++++||+++.+|++. +..|.+|++..++
T Consensus 11 ~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~ 89 (189)
T PRK09648 11 LDALVAEAVAGDRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAA 89 (189)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHH
Confidence 3567888888876 99999999999999999988653 3689999999999999999999864 4589999999999
Q ss_pred HHHHHHHHHcCCCc
Q 016880 358 KSISKMVARHARGI 371 (381)
Q Consensus 358 ~aI~~~Ir~qsr~I 371 (381)
+.+.++++++.+..
T Consensus 90 n~~~d~~r~~~r~~ 103 (189)
T PRK09648 90 HKVADAHRAAGRDK 103 (189)
T ss_pred HHHHHHHHHhCCCc
Confidence 99999999876543
No 52
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=98.86 E-value=1.7e-08 Score=90.81 Aligned_cols=88 Identities=18% Similarity=0.214 Sum_probs=78.0
Q ss_pred CCCHHHHHHHHHh---cH-HHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHH
Q 016880 280 GVSERVLKQHLAF---GW-YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYW 355 (381)
Q Consensus 280 gl~~eeL~~~l~~---G~-~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~w 355 (381)
.++++.|+..++. |+ .|.++|+..|.|.|..+|.+|.+...+.+|++||+++.+|+++++|++. ..|.+|++.+
T Consensus 7 ~~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~~--~~~~~wl~~i 84 (188)
T PRK09640 7 ELNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLYSI 84 (188)
T ss_pred CCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcCC--CcchHHHHHH
Confidence 3567788888875 34 4999999999999999999999988999999999999999999999963 4799999999
Q ss_pred HHHHHHHHHHHcCC
Q 016880 356 IRKSISKMVARHAR 369 (381)
Q Consensus 356 Ir~aI~~~Ir~qsr 369 (381)
+++.+.+.+++..+
T Consensus 85 a~n~~~d~~R~~~~ 98 (188)
T PRK09640 85 TYNECITQYRKERR 98 (188)
T ss_pred HHHHHHHHHHHhcc
Confidence 99999999997543
No 53
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=98.82 E-value=2e-08 Score=88.68 Aligned_cols=88 Identities=16% Similarity=0.111 Sum_probs=78.7
Q ss_pred CCHHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHH
Q 016880 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (381)
Q Consensus 281 l~~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~a 359 (381)
+++..++..+..|+. +.+.|+..|.|.|..++.++.+...+.+|++||+++.+|++++.|++. .+|.+|++..+++.
T Consensus 3 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n~ 80 (176)
T PRK09638 3 MDEKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASRL 80 (176)
T ss_pred ccHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHH
Confidence 346677888888876 999999999999999999999888899999999999999999999974 47999999999999
Q ss_pred HHHHHHHcCCC
Q 016880 360 ISKMVARHARG 370 (381)
Q Consensus 360 I~~~Ir~qsr~ 370 (381)
+.+++++..+.
T Consensus 81 ~~d~~r~~~~~ 91 (176)
T PRK09638 81 YKDHLRKQKRE 91 (176)
T ss_pred HHHHHHHhccc
Confidence 99999986543
No 54
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=98.81 E-value=2e-08 Score=86.65 Aligned_cols=72 Identities=18% Similarity=0.307 Sum_probs=65.8
Q ss_pred HHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcC
Q 016880 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA 368 (381)
Q Consensus 295 ~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qs 368 (381)
.+.++|+..|.|+|..+++++. ...+.||++||+++++|+++++||+..| .|.+|++..+++.+.++++++.
T Consensus 4 ~af~~l~~~y~~~l~~~~~~~~-~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~ 75 (154)
T PRK06759 4 ATFTEAVVLYEGLIVNQIKKLG-IYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEF 75 (154)
T ss_pred ccHHHHHHHHHHHHHHHHHHhC-CcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHH
Confidence 3789999999999999999874 4578999999999999999999998777 7999999999999999999874
No 55
>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=98.80 E-value=2.3e-08 Score=87.21 Aligned_cols=84 Identities=12% Similarity=0.044 Sum_probs=73.8
Q ss_pred HHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHH
Q 016880 287 KQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVA 365 (381)
Q Consensus 287 ~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir 365 (381)
+..++.|+. |.+.|+..|.+.+.+++.++.+...+.+|++||+++.+++.+++|+...+ .|.+|++..+++.+.+.+|
T Consensus 2 i~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R 80 (170)
T TIGR02952 2 LERAQDREEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFR 80 (170)
T ss_pred hHHHHccCHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHH
Confidence 345566665 99999999999999999988877789999999999999999999997555 8999999999999999999
Q ss_pred HcCCCc
Q 016880 366 RHARGI 371 (381)
Q Consensus 366 ~qsr~I 371 (381)
++.+..
T Consensus 81 ~~~~~~ 86 (170)
T TIGR02952 81 GSKRHP 86 (170)
T ss_pred hcCCCC
Confidence 875543
No 56
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=98.78 E-value=3.5e-08 Score=92.30 Aligned_cols=90 Identities=17% Similarity=0.149 Sum_probs=80.1
Q ss_pred CCHHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHH
Q 016880 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (381)
Q Consensus 281 l~~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~a 359 (381)
++++.|+..+..|+. +.+.|+..|.+.|.++|.++.+.+.+.+|++||++++||+.+++|++. ..|.+|++..+++.
T Consensus 15 ~~~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~ 92 (231)
T PRK11922 15 ASDRELVARVLAGDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNE 92 (231)
T ss_pred ccHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHH
Confidence 456778888887776 999999999999999999999888999999999999999999999985 37999999999999
Q ss_pred HHHHHHHcCCCcc
Q 016880 360 ISKMVARHARGIK 372 (381)
Q Consensus 360 I~~~Ir~qsr~IR 372 (381)
+.+.+|+..+..+
T Consensus 93 ~~d~~Rk~~r~~~ 105 (231)
T PRK11922 93 ALGRLRRRRRLVN 105 (231)
T ss_pred HHHHHHhhccccc
Confidence 9999998765444
No 57
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=98.78 E-value=2.4e-08 Score=89.78 Aligned_cols=86 Identities=22% Similarity=0.176 Sum_probs=76.8
Q ss_pred CHHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHH
Q 016880 282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (381)
Q Consensus 282 ~~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI 360 (381)
+..+|+..+..|+. +.+.|+..|.+.|..+++++.+...+.+|++|++++.+|+. ..|++..+ .|.||++..+++.+
T Consensus 15 ~~~~l~~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~ 92 (194)
T PRK12519 15 SDAELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRA 92 (194)
T ss_pred cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHH
Confidence 46778888888876 99999999999999999999988889999999999999975 67887665 79999999999999
Q ss_pred HHHHHHcCC
Q 016880 361 SKMVARHAR 369 (381)
Q Consensus 361 ~~~Ir~qsr 369 (381)
.+.++++.+
T Consensus 93 ~d~~Rk~~~ 101 (194)
T PRK12519 93 IDRLRSRRS 101 (194)
T ss_pred HHHHHhccc
Confidence 999998654
No 58
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=98.78 E-value=3.6e-08 Score=88.63 Aligned_cols=87 Identities=13% Similarity=0.100 Sum_probs=77.5
Q ss_pred CHHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHH
Q 016880 282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (381)
Q Consensus 282 ~~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI 360 (381)
+.+.|+..++.|+. +.++|+..|.|.|..++.++.+...+.+|++||+++.+|+++.+|++.. .|.+|++.-.++.+
T Consensus 6 ~~~~ll~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~ 83 (193)
T PRK11923 6 EDQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTA 83 (193)
T ss_pred cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHH
Confidence 35677788888876 9999999999999999999998888999999999999999999999864 48999999999999
Q ss_pred HHHHHHcCCC
Q 016880 361 SKMVARHARG 370 (381)
Q Consensus 361 ~~~Ir~qsr~ 370 (381)
.+.++++.+.
T Consensus 84 ~d~~rk~~~~ 93 (193)
T PRK11923 84 KNHLVSRGRR 93 (193)
T ss_pred HHHHHHhcCC
Confidence 9999976543
No 59
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=98.77 E-value=3e-08 Score=89.95 Aligned_cols=88 Identities=18% Similarity=0.120 Sum_probs=79.3
Q ss_pred CCCHHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHH
Q 016880 280 GVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358 (381)
Q Consensus 280 gl~~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~ 358 (381)
.+++..|+.++..|+. |.++|+..|.|.|..+|.++.+...+.+|++||+++.+|+...+|++.. ..|.+|+..-+++
T Consensus 10 ~~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~n 88 (196)
T PRK12524 10 DVSDEALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVCN 88 (196)
T ss_pred CcCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHHHH
Confidence 3467888888988876 9999999999999999999998889999999999999999999998643 4799999999999
Q ss_pred HHHHHHHHcC
Q 016880 359 SISKMVARHA 368 (381)
Q Consensus 359 aI~~~Ir~qs 368 (381)
.+.+.++++.
T Consensus 89 ~~~d~~Rk~~ 98 (196)
T PRK12524 89 LCTDRLRRRR 98 (196)
T ss_pred HHHHHHHhhc
Confidence 9999999753
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=98.76 E-value=5.2e-08 Score=85.83 Aligned_cols=88 Identities=15% Similarity=0.157 Sum_probs=79.0
Q ss_pred CCHHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHH
Q 016880 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (381)
Q Consensus 281 l~~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~a 359 (381)
|++++|+..+..|+. |.+.++..|.+.|++++.++.+...+.+|++||.++.+++...+|++.. +|.+|++..+++.
T Consensus 1 ~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~~--~~~~wl~~i~~n~ 78 (169)
T TIGR02954 1 MNDEELVKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPK--YFNTWLTRILINE 78 (169)
T ss_pred CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCcc--ccHHHHHHHHHHH
Confidence 356677888888876 9999999999999999999999989999999999999999999999753 6999999999999
Q ss_pred HHHHHHHcCCC
Q 016880 360 ISKMVARHARG 370 (381)
Q Consensus 360 I~~~Ir~qsr~ 370 (381)
+.+.++++.+.
T Consensus 79 ~~d~~R~~~~~ 89 (169)
T TIGR02954 79 CIDLLKKKKKV 89 (169)
T ss_pred HHHHHHhcCCc
Confidence 99999987644
No 61
>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=98.74 E-value=6.7e-08 Score=85.95 Aligned_cols=86 Identities=15% Similarity=0.136 Sum_probs=77.5
Q ss_pred CHHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHH
Q 016880 282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (381)
Q Consensus 282 ~~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI 360 (381)
+++.|+..+..|+. +.+.|+..|.+.|..+|.++.+...+.+|++||++++||+.+.+|++. ..|.+|++...++.+
T Consensus 6 ~d~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~~ 83 (190)
T TIGR02939 6 LDLELVERVQRGEKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNTA 83 (190)
T ss_pred cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHHH
Confidence 45678888888876 999999999999999999999888999999999999999999999975 369999999999999
Q ss_pred HHHHHHcCC
Q 016880 361 SKMVARHAR 369 (381)
Q Consensus 361 ~~~Ir~qsr 369 (381)
.+.++++.+
T Consensus 84 ~~~~r~~~r 92 (190)
T TIGR02939 84 KNHLVAQGR 92 (190)
T ss_pred HHHHHHhcc
Confidence 999987654
No 62
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=98.74 E-value=4.3e-08 Score=87.08 Aligned_cols=87 Identities=14% Similarity=0.030 Sum_probs=77.6
Q ss_pred CHHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHH
Q 016880 282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (381)
Q Consensus 282 ~~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI 360 (381)
+...|+..+..|+. +..+|+..|.+.|..+|.++.+...+.+|++||+++.+|+++++|++..+ .|.||.+.-.++.+
T Consensus 5 ~~~~li~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~~-~~~~wl~~ia~n~~ 83 (179)
T PRK12514 5 DIEKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGL-SPMTWLITIARNHA 83 (179)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCcccc-cHHHHHHHHHHHHH
Confidence 35667777777776 99999999999999999999988899999999999999999999997544 69999999999999
Q ss_pred HHHHHHcCC
Q 016880 361 SKMVARHAR 369 (381)
Q Consensus 361 ~~~Ir~qsr 369 (381)
.+.++++.+
T Consensus 84 ~d~~R~~~~ 92 (179)
T PRK12514 84 IDRLRARKA 92 (179)
T ss_pred HHHHHhcCC
Confidence 999998653
No 63
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=98.73 E-value=5.5e-08 Score=89.34 Aligned_cols=86 Identities=15% Similarity=0.088 Sum_probs=75.5
Q ss_pred HHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHH
Q 016880 284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK 362 (381)
Q Consensus 284 eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~ 362 (381)
..|...+..|+. +.++|+..|.+.|..++.++.+...+.+|++|++++.+|+++..|++.++ .|.||++..+++.+.+
T Consensus 26 ~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d 104 (206)
T PRK12526 26 QWLILVAISRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFD 104 (206)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHH
Confidence 445555666665 99999999999999999999888789999999999999999999998766 5999999999999999
Q ss_pred HHHHcCCC
Q 016880 363 MVARHARG 370 (381)
Q Consensus 363 ~Ir~qsr~ 370 (381)
+++++.+.
T Consensus 105 ~~Rk~~~~ 112 (206)
T PRK12526 105 MLRKIKAK 112 (206)
T ss_pred HHHHhccc
Confidence 99986543
No 64
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=98.71 E-value=8.1e-08 Score=83.71 Aligned_cols=84 Identities=21% Similarity=0.140 Sum_probs=74.2
Q ss_pred HHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHH
Q 016880 286 LKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMV 364 (381)
Q Consensus 286 L~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~I 364 (381)
|...+..|+. |.+.++..|.+.|..+|+++.+...+.+|++|++++.|+++.+.|+ .+..|.+|++..+++.+.+.+
T Consensus 3 ~~~~~~~~~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~~ 80 (179)
T PRK11924 3 LMPVDATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDLL 80 (179)
T ss_pred HHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHHH
Confidence 4455666665 9999999999999999999999899999999999999999999999 345899999999999999999
Q ss_pred HHcCCCc
Q 016880 365 ARHARGI 371 (381)
Q Consensus 365 r~qsr~I 371 (381)
++..+..
T Consensus 81 r~~~~~~ 87 (179)
T PRK11924 81 RRRRREK 87 (179)
T ss_pred Hhccccc
Confidence 9765543
No 65
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=98.66 E-value=7.6e-08 Score=86.10 Aligned_cols=85 Identities=19% Similarity=0.110 Sum_probs=75.8
Q ss_pred HHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHH
Q 016880 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (381)
Q Consensus 283 ~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~ 361 (381)
...+...+..|+. +.++|+..|.++|+.+|.++.+...+.||++||.++.+|+..++|++.++ .|.+|.+.-+++.+.
T Consensus 12 ~~~l~~~~~~~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~~ 90 (187)
T PRK12534 12 TGRLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKAI 90 (187)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHH
Confidence 4556666667765 99999999999999999999988899999999999999999999998655 688999999999999
Q ss_pred HHHHHcC
Q 016880 362 KMVARHA 368 (381)
Q Consensus 362 ~~Ir~qs 368 (381)
++++++.
T Consensus 91 d~~R~~~ 97 (187)
T PRK12534 91 DHLRANA 97 (187)
T ss_pred HHHHhcc
Confidence 9999864
No 66
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=98.65 E-value=2e-07 Score=84.58 Aligned_cols=88 Identities=17% Similarity=0.119 Sum_probs=79.4
Q ss_pred CCHHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHH
Q 016880 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (381)
Q Consensus 281 l~~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~a 359 (381)
++++.++..+..|+. +.+.|+..|.+.|..++.++.+...+.||++||.++.+|+.+++|++. ..|.+|++.-+++.
T Consensus 12 ~~~~~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~--~~f~~wL~~i~rn~ 89 (192)
T PRK09643 12 RSDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGD--AAVSSWLHRIVVNA 89 (192)
T ss_pred cCHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCC--CccHHHHHHHHHHH
Confidence 357788888888886 999999999999999999999888999999999999999999999975 35999999999999
Q ss_pred HHHHHHHcCCC
Q 016880 360 ISKMVARHARG 370 (381)
Q Consensus 360 I~~~Ir~qsr~ 370 (381)
+.+.+|+..+.
T Consensus 90 ~~d~~Rk~~~~ 100 (192)
T PRK09643 90 CLDRLRRAKAR 100 (192)
T ss_pred HHHHHHccccC
Confidence 99999986543
No 67
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=98.63 E-value=1.1e-07 Score=86.19 Aligned_cols=85 Identities=15% Similarity=0.071 Sum_probs=76.3
Q ss_pred HHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHH
Q 016880 284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK 362 (381)
Q Consensus 284 eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~ 362 (381)
..|+..+..|+. +.+.|++.|.|.|..+|.++.+...+.+|++||.++.+|+...+|++..+ .|.+|++.-+++.+.+
T Consensus 15 ~~li~~~~~~d~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn~~ld 93 (194)
T PRK12531 15 LECMEKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRNLCFD 93 (194)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHHHHHH
Confidence 456777887876 99999999999999999999988788999999999999999999997555 7999999999999999
Q ss_pred HHHHcCC
Q 016880 363 MVARHAR 369 (381)
Q Consensus 363 ~Ir~qsr 369 (381)
+++++.+
T Consensus 94 ~~Rk~~~ 100 (194)
T PRK12531 94 LLRKQKG 100 (194)
T ss_pred HHHHhcc
Confidence 9998643
No 68
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=98.62 E-value=1.7e-07 Score=83.97 Aligned_cols=89 Identities=17% Similarity=0.134 Sum_probs=79.6
Q ss_pred CCHHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHH
Q 016880 281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359 (381)
Q Consensus 281 l~~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~a 359 (381)
++.++|...+..|+. +.+.|+..|.+.|..++.++.+...+.+|++||.++.+|+..++|++..+ .|.+|++.-+++.
T Consensus 8 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wL~~iarn~ 86 (182)
T PRK12537 8 FDYEACLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARG-SARGWIYSVTRHL 86 (182)
T ss_pred hhHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHH
Confidence 345678888888876 99999999999999999999988899999999999999999999987544 7999999999999
Q ss_pred HHHHHHHcCCC
Q 016880 360 ISKMVARHARG 370 (381)
Q Consensus 360 I~~~Ir~qsr~ 370 (381)
+.+.++++.+.
T Consensus 87 ~~d~~r~~~~~ 97 (182)
T PRK12537 87 ALNVLRDTRRE 97 (182)
T ss_pred HHHHHHhcccc
Confidence 99999987643
No 69
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=98.62 E-value=1.6e-07 Score=88.83 Aligned_cols=85 Identities=19% Similarity=0.162 Sum_probs=77.3
Q ss_pred CHHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHH
Q 016880 282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (381)
Q Consensus 282 ~~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI 360 (381)
++++|+..++.|+. +.++|+..|.+.|..++.++.+...+.||++||.++.+|+..++|++..+ .|.+|++...++.+
T Consensus 49 ~d~~Li~~~~~gd~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~~ 127 (233)
T PRK12538 49 EDEELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNRC 127 (233)
T ss_pred cHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHHH
Confidence 46677888888876 99999999999999999999988889999999999999999999997555 79999999999999
Q ss_pred HHHHHHc
Q 016880 361 SKMVARH 367 (381)
Q Consensus 361 ~~~Ir~q 367 (381)
.+.+|++
T Consensus 128 id~~Rk~ 134 (233)
T PRK12538 128 IDLRRKP 134 (233)
T ss_pred HHHHHhh
Confidence 9999975
No 70
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=98.60 E-value=3e-07 Score=82.32 Aligned_cols=85 Identities=15% Similarity=0.098 Sum_probs=73.5
Q ss_pred HHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccC-CCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHH
Q 016880 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRG-LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (381)
Q Consensus 283 ~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~-rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI 360 (381)
...++..+..|+. |.++++..|.+.|..++.++.+ ...+.+|++||+++.||+.++.||+. .+|.+|++..+++.+
T Consensus 8 ~~~~~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~~ 85 (181)
T PRK12536 8 LRALLLRGLAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYKL 85 (181)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHHH
Confidence 3456666777765 9999999999999999988664 47899999999999999999999974 369999999999999
Q ss_pred HHHHHHcCC
Q 016880 361 SKMVARHAR 369 (381)
Q Consensus 361 ~~~Ir~qsr 369 (381)
.+++|++.+
T Consensus 86 ~d~~Rk~~~ 94 (181)
T PRK12536 86 MDFLRSRAR 94 (181)
T ss_pred HHHHHHHhc
Confidence 999998644
No 71
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=98.59 E-value=2.2e-07 Score=83.64 Aligned_cols=87 Identities=16% Similarity=0.109 Sum_probs=78.8
Q ss_pred CCCHHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHH
Q 016880 280 GVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358 (381)
Q Consensus 280 gl~~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~ 358 (381)
.++++.|+..+..|+. +.+.|+..|.+.|..++.++.+...+.+|++||+++.+|+...+|++. ..|.+|++.-+++
T Consensus 6 ~~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n 83 (189)
T PRK12515 6 ATTDEMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARF 83 (189)
T ss_pred ccCHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHH
Confidence 3567888888888876 999999999999999999998888999999999999999999999963 3799999999999
Q ss_pred HHHHHHHHcC
Q 016880 359 SISKMVARHA 368 (381)
Q Consensus 359 aI~~~Ir~qs 368 (381)
.+.+.++++.
T Consensus 84 ~~~d~~r~~~ 93 (189)
T PRK12515 84 KALSALRRRK 93 (189)
T ss_pred HHHHHHHccC
Confidence 9999999754
No 72
>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=98.53 E-value=3e-07 Score=81.58 Aligned_cols=75 Identities=20% Similarity=0.233 Sum_probs=66.8
Q ss_pred cH-HHHHHHHHHhhHHHHHHHHHccC----CCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHc
Q 016880 293 GW-YCREELIKSTRPLVLFLARNYRG----LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH 367 (381)
Q Consensus 293 G~-~Are~LIe~nlrLV~~IAkry~~----rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~q 367 (381)
|+ .|.++|+..|.+.|..+|.+|.+ ...+.+|++|++++.+|+++..|++..+.+|.+|++..+++.+.+.++++
T Consensus 4 ~~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~~ 83 (189)
T TIGR02984 4 GDQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRRH 83 (189)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHHH
Confidence 44 49999999999999999998743 45789999999999999999999986666899999999999999999864
No 73
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=98.51 E-value=7.2e-07 Score=79.62 Aligned_cols=86 Identities=17% Similarity=0.162 Sum_probs=73.0
Q ss_pred HHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCC----CCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHH
Q 016880 284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGL----GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358 (381)
Q Consensus 284 eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~r----g~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~ 358 (381)
..|+..+..|+. |.++|++.|.+.|..+|.++.+. ..+.+|++||+++.+|+..+.|++. ..|.+|++.-+++
T Consensus 10 ~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn 87 (184)
T PRK12512 10 TDLMRSANAGDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARN 87 (184)
T ss_pred HHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHH
Confidence 345666666665 99999999999999999988753 3589999999999999999999873 3699999999999
Q ss_pred HHHHHHHHcCCCc
Q 016880 359 SISKMVARHARGI 371 (381)
Q Consensus 359 aI~~~Ir~qsr~I 371 (381)
.+.++++++.+..
T Consensus 88 ~~~d~~Rr~~~~~ 100 (184)
T PRK12512 88 KLIDALRRRGRRV 100 (184)
T ss_pred HHHHHHHhhcccc
Confidence 9999999875543
No 74
>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=98.51 E-value=4.7e-07 Score=78.32 Aligned_cols=73 Identities=15% Similarity=0.149 Sum_probs=67.5
Q ss_pred HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCC
Q 016880 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG 370 (381)
Q Consensus 296 Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~ 370 (381)
+.+.++..|.|.|..+|+++.+...+.||++|++++.+++.+++||+.. .|.+|++..+++.+.+.++++.+.
T Consensus 2 ~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~ 74 (159)
T TIGR02989 2 AFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRD 74 (159)
T ss_pred HHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhccc
Confidence 6789999999999999999999999999999999999999999999753 599999999999999999987543
No 75
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=98.51 E-value=7.2e-07 Score=80.07 Aligned_cols=85 Identities=12% Similarity=0.065 Sum_probs=73.9
Q ss_pred HHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHH----HccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHH
Q 016880 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLAR----NYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIR 357 (381)
Q Consensus 283 ~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAk----ry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr 357 (381)
..+|+..++.|+. |+++|+..|.+.|..+|+ ++.+...+.+|++||.++.+|+....|++.. .|.+|++.-++
T Consensus 8 ~~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~~ 85 (184)
T PRK12539 8 LKALMLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIAR 85 (184)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHHH
Confidence 5667777777875 999999999999999986 4556678999999999999999999999753 59999999999
Q ss_pred HHHHHHHHHcCC
Q 016880 358 KSISKMVARHAR 369 (381)
Q Consensus 358 ~aI~~~Ir~qsr 369 (381)
+.+.+++++..+
T Consensus 86 n~~~d~~R~~~~ 97 (184)
T PRK12539 86 YKLIDHLRRTRA 97 (184)
T ss_pred HHHHHHHHHHhc
Confidence 999999998643
No 76
>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=98.49 E-value=3.4e-07 Score=78.30 Aligned_cols=72 Identities=15% Similarity=0.169 Sum_probs=66.2
Q ss_pred HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCC
Q 016880 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (381)
Q Consensus 296 Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr 369 (381)
|.++|+..|.|.|..+++++.+...+.+|++||+++++++.+.+|++. .+|.+|++..+++.+.+.++++.+
T Consensus 2 a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~--~~~~~wl~~i~r~~~~d~~r~~~~ 73 (161)
T TIGR02985 2 AFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEV--ESFKAYLFTIVKNRSLNYLRHKQV 73 (161)
T ss_pred hHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc--ccHHHHHHHHHHHHHHHHHHHHHh
Confidence 678999999999999999999888899999999999999999999863 369999999999999999997654
No 77
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=98.42 E-value=1e-06 Score=78.00 Aligned_cols=73 Identities=12% Similarity=0.155 Sum_probs=67.4
Q ss_pred HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCC
Q 016880 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG 370 (381)
Q Consensus 296 Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~ 370 (381)
..++|+..|.++|..+|.+|.+...+.+|++||.++.||+.+++|++.. +|.+|++.-+++.+.+++|++.+.
T Consensus 4 ~~~~l~~~y~~~i~~~~~~~~~~~~daeDvvQe~~i~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~Rk~~~~ 76 (173)
T PRK12522 4 KVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE--NYKKWITTICVRTFYDFYRKKKRW 76 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcCCcc--chHHHHHHHHHHHHHHHHHHhccc
Confidence 5789999999999999999999899999999999999999999999854 699999999999999999986553
No 78
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=98.39 E-value=1.1e-06 Score=77.55 Aligned_cols=78 Identities=17% Similarity=0.088 Sum_probs=68.4
Q ss_pred HHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHH
Q 016880 288 QHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVAR 366 (381)
Q Consensus 288 ~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~ 366 (381)
..++.|+. +.++++..|.+.|..++.++.+. .+.+|++||.++.+|+.++.|++. ..|.+|++.-+++.+.+.+|+
T Consensus 3 ~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~-~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~ 79 (175)
T PRK12518 3 LRCQRGDRQSFRQLYRRYQQKVRSTLYQLCGR-ELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARRQ 79 (175)
T ss_pred hHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCH-hHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHHH
Confidence 44556665 99999999999999999998753 688999999999999999999974 469999999999999999997
Q ss_pred cC
Q 016880 367 HA 368 (381)
Q Consensus 367 qs 368 (381)
+.
T Consensus 80 ~~ 81 (175)
T PRK12518 80 FA 81 (175)
T ss_pred hh
Confidence 53
No 79
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=98.32 E-value=1.8e-06 Score=77.13 Aligned_cols=75 Identities=13% Similarity=0.068 Sum_probs=67.7
Q ss_pred hcH-HHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcC
Q 016880 292 FGW-YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA 368 (381)
Q Consensus 292 ~G~-~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qs 368 (381)
.|+ .+.++|+..|.|.|..++..|.+...+.+|++|++++.+|+++.+|++.. .|.+|+...+++.+.+++++..
T Consensus 3 ~~d~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~~ 78 (179)
T PRK12543 3 SGDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKRW 78 (179)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhhc
Confidence 344 49999999999999999999998889999999999999999999999864 6999999999999999988653
No 80
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=98.30 E-value=1.3e-06 Score=78.39 Aligned_cols=78 Identities=13% Similarity=0.067 Sum_probs=70.3
Q ss_pred hcH-HHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCC
Q 016880 292 FGW-YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (381)
Q Consensus 292 ~G~-~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr 369 (381)
.|+ .+.++|+..|.+.|..+|.++.+...+.+|++||.++.+|+...+|++..+..|.||++.-+++.+.+.++++.+
T Consensus 5 ~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~~ 83 (185)
T PRK12542 5 NNDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNKR 83 (185)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 344 499999999999999999999988889999999999999999999997555589999999999999999998754
No 81
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=98.28 E-value=2.8e-06 Score=75.48 Aligned_cols=84 Identities=14% Similarity=0.129 Sum_probs=73.3
Q ss_pred HHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCC-----CHHHHHHHHHHHHHH-HHhhcCCCCCCccchHHHHH
Q 016880 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGI-----PFSDLLQAGNVGVLQ-GAERFDHTRGYKFSTYVQYW 355 (381)
Q Consensus 283 ~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~-----d~EDLiQEG~IGLik-AvekFDpsrG~rFSTYA~~w 355 (381)
...|+..+..|+. |.++|+..|.+.|..+|.+|.+... +.+|++||.++.+|+ ...+|++. + .|.+|+..+
T Consensus 4 ~~~li~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~-~-~~~~wl~~i 81 (183)
T TIGR02999 4 VTELLQQWQNGDAAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR-A-HFFAAAAKA 81 (183)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch-H-HHHHHHHHH
Confidence 4567788888876 9999999999999999999987655 899999999999998 78888754 3 699999999
Q ss_pred HHHHHHHHHHHcC
Q 016880 356 IRKSISKMVARHA 368 (381)
Q Consensus 356 Ir~aI~~~Ir~qs 368 (381)
+++.+.+.++++.
T Consensus 82 ~~n~~~d~~R~~~ 94 (183)
T TIGR02999 82 MRRILVDHARRRR 94 (183)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999999753
No 82
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=98.23 E-value=8.1e-06 Score=73.29 Aligned_cols=80 Identities=21% Similarity=0.218 Sum_probs=70.2
Q ss_pred HhcHHHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCC
Q 016880 291 AFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG 370 (381)
Q Consensus 291 ~~G~~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~ 370 (381)
.....+.++++..|.+.+...+.++.+...+.|||+||.++.+++++..| +..+ .|.||.+.-+++.+.+.+|++.+.
T Consensus 11 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~~~-~~~~wl~~Ia~n~~iD~~R~~~r~ 88 (182)
T COG1595 11 RGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RGRS-SFKAWLYRIARNLAIDRLRKRKRR 88 (182)
T ss_pred hcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CCCC-chHHHHHHHHHHHHHHHHHHhccc
Confidence 34445899999999999999999999887799999999999999999999 4444 799999999999999999987654
Q ss_pred cc
Q 016880 371 IK 372 (381)
Q Consensus 371 IR 372 (381)
..
T Consensus 89 ~~ 90 (182)
T COG1595 89 RA 90 (182)
T ss_pred cc
Confidence 43
No 83
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=98.22 E-value=5.2e-06 Score=74.37 Aligned_cols=73 Identities=14% Similarity=0.036 Sum_probs=67.1
Q ss_pred HHHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcC
Q 016880 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA 368 (381)
Q Consensus 294 ~~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qs 368 (381)
..|.++|+..|.|.|.+++.++.+..-+.+|++|++++.||++..+|++. ..|.+|++..+++.+.+++|+..
T Consensus 15 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~--~~~~awl~~ia~n~~~d~~Rk~~ 87 (179)
T PRK09415 15 EDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGK--SSLKTWLYRIAINHCKDYLKSWH 87 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--cccHHHHHHHHHHHHHHHHHhhc
Confidence 34899999999999999999999888899999999999999999999974 36999999999999999999853
No 84
>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=98.21 E-value=8.3e-06 Score=77.97 Aligned_cols=89 Identities=13% Similarity=0.030 Sum_probs=78.5
Q ss_pred CCCHHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHH-------HHHhhcCCCCCCccchH
Q 016880 280 GVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVL-------QGAERFDHTRGYKFSTY 351 (381)
Q Consensus 280 gl~~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLi-------kAvekFDpsrG~rFSTY 351 (381)
+.++..|+..++.|+. |..+|+..|.+.|..++.++.+...+.||++||.++-+| +.+.+|++. ..|.||
T Consensus 23 ~~~d~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~--~~~~tW 100 (244)
T TIGR03001 23 HAADLYLACACAQGEPAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGR--GPLLSW 100 (244)
T ss_pred cccHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCC--CchHhH
Confidence 3467889999999986 999999999999999999998888999999999999999 478889964 369999
Q ss_pred HHHHHHHHHHHHHHHcCCC
Q 016880 352 VQYWIRKSISKMVARHARG 370 (381)
Q Consensus 352 A~~wIr~aI~~~Ir~qsr~ 370 (381)
.+.-.++.+.++++++.+.
T Consensus 101 L~~Ia~N~~id~lRk~~r~ 119 (244)
T TIGR03001 101 VRIVATRIALELQAQERRH 119 (244)
T ss_pred HHHHHHHHHHHHHHHhccc
Confidence 9999999999999976543
No 85
>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=98.16 E-value=7e-06 Score=71.52 Aligned_cols=74 Identities=16% Similarity=0.021 Sum_probs=67.4
Q ss_pred HHHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCC
Q 016880 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (381)
Q Consensus 294 ~~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr 369 (381)
..+.+.++..|.+.|..++.++.+...+.+|++||+++.+|+..++|+. . ..|.+|++..+++.+.+.++++.+
T Consensus 5 ~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~-~-~~~~~wl~~i~~n~~~d~~rk~~~ 78 (162)
T TIGR02983 5 EEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD-P-DAPDAYVRRVLVNLARSRWRRRRL 78 (162)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC-c-ccHHHHHHHHHHHHHHHHHHhhcc
Confidence 3599999999999999999999988899999999999999999999964 3 479999999999999999997654
No 86
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=98.15 E-value=8.9e-06 Score=79.79 Aligned_cols=85 Identities=18% Similarity=0.135 Sum_probs=76.4
Q ss_pred HHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHH
Q 016880 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (381)
Q Consensus 283 ~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~ 361 (381)
..+|+..++.|+. +.++|+..|.+.|..++.++.+...+.+|++||.++.+|+.+++|++. ..|.+|.+...++.+.
T Consensus 6 ~~~l~~~~~~gd~~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~ 83 (339)
T PRK08241 6 AAALLARAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATNVCL 83 (339)
T ss_pred HHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHHHHH
Confidence 3578888888876 999999999999999999999888899999999999999999999853 3699999999999999
Q ss_pred HHHHHcCC
Q 016880 362 KMVARHAR 369 (381)
Q Consensus 362 ~~Ir~qsr 369 (381)
+++|++.+
T Consensus 84 d~~Rk~~~ 91 (339)
T PRK08241 84 DALEGRAR 91 (339)
T ss_pred HHHHhhcc
Confidence 99998643
No 87
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=98.14 E-value=8.8e-06 Score=73.52 Aligned_cols=84 Identities=19% Similarity=0.110 Sum_probs=73.0
Q ss_pred HHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHH
Q 016880 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361 (381)
Q Consensus 283 ~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~ 361 (381)
...|+.++..|+. +.++|+..|.+.+..++. +.+...+.+|++||.++.+|+..++|++. ..|.+|.+.-.++.+.
T Consensus 11 ~~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~~~ 87 (185)
T PRK09649 11 VTALALSAAKGNGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVA 87 (185)
T ss_pred HHHHHHHHHccCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHHHH
Confidence 4567777788876 999999999999999995 56666899999999999999999999964 3699999999999999
Q ss_pred HHHHHcCC
Q 016880 362 KMVARHAR 369 (381)
Q Consensus 362 ~~Ir~qsr 369 (381)
+.+|++.+
T Consensus 88 d~~Rk~~~ 95 (185)
T PRK09649 88 DHIRHVRS 95 (185)
T ss_pred HHHHHhcc
Confidence 99997543
No 88
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=98.07 E-value=1.3e-05 Score=69.95 Aligned_cols=72 Identities=14% Similarity=-0.008 Sum_probs=64.6
Q ss_pred HHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCC
Q 016880 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG 370 (381)
Q Consensus 295 ~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~ 370 (381)
.+.++|+..|.+.|..+|.++.+...+.+|++||+++.+|+. .|+. +..|.+|++..+++.+.+.+++..+.
T Consensus 3 ~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~~ 74 (166)
T PRK09639 3 ETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKRR 74 (166)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhccc
Confidence 478999999999999999999988899999999999999999 6764 34799999999999999999986543
No 89
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=98.06 E-value=1.7e-05 Score=69.38 Aligned_cols=72 Identities=10% Similarity=0.051 Sum_probs=66.4
Q ss_pred HHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCC
Q 016880 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (381)
Q Consensus 295 ~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr 369 (381)
.+.++++..|.+.|..++.++.+...+.+|++||+++.+++..++|++. .|.||++.-+++.+.++++++.+
T Consensus 5 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~ 76 (161)
T PRK12541 5 QSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEKK 76 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhccc
Confidence 4899999999999999999999888899999999999999999999863 59999999999999999998654
No 90
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=98.05 E-value=1.8e-05 Score=69.72 Aligned_cols=73 Identities=11% Similarity=0.109 Sum_probs=66.7
Q ss_pred HHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCC
Q 016880 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (381)
Q Consensus 295 ~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr 369 (381)
..+.+++..|.+.|..+|.++.+...+.||++||.++.+|+...+|++.. .|.+|++.-+++.+.+.++++.+
T Consensus 6 ~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~ 78 (164)
T PRK12547 6 KNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGT--NLKAWLFTILRNEFYSQMRKRGR 78 (164)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhcc
Confidence 46889999999999999999999989999999999999999999998643 59999999999999999997644
No 91
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=98.02 E-value=2e-05 Score=69.36 Aligned_cols=71 Identities=17% Similarity=0.057 Sum_probs=64.9
Q ss_pred HHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCC
Q 016880 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG 370 (381)
Q Consensus 297 re~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~ 370 (381)
.+.|++.|.|.|..++.++.+...+.+|++|+.++.+|++++.|++. .|.+|.+...++.+.+++++..+.
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~ 73 (165)
T PRK09644 3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKV 73 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhc
Confidence 46899999999999999999888999999999999999999999963 599999999999999999986543
No 92
>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=98.00 E-value=2.1e-05 Score=71.06 Aligned_cols=73 Identities=10% Similarity=-0.008 Sum_probs=67.0
Q ss_pred HHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCC
Q 016880 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (381)
Q Consensus 295 ~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr 369 (381)
.++++|+..|.+.|..++.++.+...+.+|++||.++.+|+...+|++. ..|.+|++..+++.+.+.++++.+
T Consensus 11 ~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~~~ 83 (193)
T TIGR02947 11 QRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKAQR 83 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHhcC
Confidence 4899999999999999999999887899999999999999999999864 369999999999999999998654
No 93
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=98.00 E-value=2e-05 Score=71.01 Aligned_cols=74 Identities=20% Similarity=0.224 Sum_probs=67.2
Q ss_pred HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCCc
Q 016880 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI 371 (381)
Q Consensus 296 Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~I 371 (381)
++++|+..|.+.|..+|.++.+...+.+|++||.++.+|+.+++|+.. .+|.+|++.-+++.+.+.++++.+..
T Consensus 3 ~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~--~~~~~WL~~ia~n~~~d~~Rk~~r~~ 76 (191)
T PRK12520 3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQ--SSLKTYLVGILKHKIIDAIRSGRREV 76 (191)
T ss_pred chHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--ccHHHHHHHHHHHHHHHHHHhhcCcC
Confidence 578999999999999999999888899999999999999999999854 36999999999999999999876543
No 94
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=97.99 E-value=3.6e-05 Score=70.61 Aligned_cols=83 Identities=19% Similarity=0.086 Sum_probs=71.5
Q ss_pred HHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHH
Q 016880 284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK 362 (381)
Q Consensus 284 eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~ 362 (381)
.+|...+..|+. +.++++..|.+.+..++. +.+...+.+|++||.++.+|+..++|++. ..|.+|++..+++.+.+
T Consensus 13 ~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~Iarn~~id 89 (196)
T PRK12535 13 TDLALAAGRGDRAALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAAR--SSARTWLLSLARRVWVD 89 (196)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCc--ccHHHHHHHHHHHHHHH
Confidence 456666777775 899999999999999976 45667899999999999999999999963 36999999999999999
Q ss_pred HHHHcCC
Q 016880 363 MVARHAR 369 (381)
Q Consensus 363 ~Ir~qsr 369 (381)
.+|++.+
T Consensus 90 ~~Rk~~~ 96 (196)
T PRK12535 90 NIRHDMA 96 (196)
T ss_pred HHHhhcc
Confidence 9998643
No 95
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=97.98 E-value=2.8e-05 Score=68.63 Aligned_cols=75 Identities=12% Similarity=-0.019 Sum_probs=67.2
Q ss_pred HHHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCC
Q 016880 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (381)
Q Consensus 294 ~~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr 369 (381)
..+.+.|+..|.+.|..+|.++.+...+.||++||.++.+|+..++|++.. ..|.+|++.-+++.+.+.++++.+
T Consensus 8 ~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~Rk~~~ 82 (173)
T PRK09645 8 AALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSARA 82 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHHHHHHHhhcc
Confidence 358999999999999999999988778999999999999999999998533 379999999999999999997543
No 96
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=97.89 E-value=4.6e-05 Score=66.62 Aligned_cols=71 Identities=17% Similarity=0.097 Sum_probs=64.4
Q ss_pred HHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcC
Q 016880 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA 368 (381)
Q Consensus 295 ~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qs 368 (381)
.+.++|++.|.+.|..++.++.+...+.+|++||.++.+|+....|++ ..|.+|.+.++++.+.+.+|++.
T Consensus 4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~---~~~~~wl~~i~~n~~~d~~R~~~ 74 (161)
T PRK12528 4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQI---IEPRAFLTTIAKRVLCNHYRRQD 74 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhccccccc---cCHHHHHHHHHHHHHHHHHHHHH
Confidence 378999999999999999999988889999999999999999888775 26899999999999999999753
No 97
>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=97.88 E-value=4.5e-05 Score=74.01 Aligned_cols=73 Identities=15% Similarity=0.117 Sum_probs=67.1
Q ss_pred HHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCC
Q 016880 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (381)
Q Consensus 295 ~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr 369 (381)
.+.++|+..|.+.|..+|.++.+...+.||++||.++.+|+...+|++. ..|.+|++...++.+.+.+|++.+
T Consensus 5 ~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~ 77 (324)
T TIGR02960 5 AAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQR 77 (324)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhccC
Confidence 4899999999999999999999888899999999999999999999964 369999999999999999997643
No 98
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=97.88 E-value=4.7e-05 Score=70.37 Aligned_cols=72 Identities=25% Similarity=0.304 Sum_probs=66.7
Q ss_pred HHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCC
Q 016880 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (381)
Q Consensus 295 ~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr 369 (381)
.+.++|+..|.+.+..++.++.+...+.+|++||.++.+|+...+|++ + .|.+|++.-+++.+.+++|+..+
T Consensus 28 ~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~~ 99 (203)
T PRK09647 28 PSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRAR 99 (203)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhccc
Confidence 489999999999999999999988889999999999999999999985 3 69999999999999999998643
No 99
>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=97.88 E-value=4e-05 Score=69.54 Aligned_cols=71 Identities=15% Similarity=0.112 Sum_probs=64.3
Q ss_pred HHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCC
Q 016880 298 EELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG 370 (381)
Q Consensus 298 e~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~ 370 (381)
.+.|..|.+.|..++.++.+...+.+|++|+.++.+|+...+|++. .+|.+|++..+++.+.++++++.+.
T Consensus 5 ~~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~ 75 (188)
T TIGR02943 5 PQELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGRE 75 (188)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhccc
Confidence 3677889999999999999888899999999999999999999964 4799999999999999999987554
No 100
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=97.86 E-value=6.6e-05 Score=68.26 Aligned_cols=74 Identities=12% Similarity=0.103 Sum_probs=67.4
Q ss_pred HHHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCC
Q 016880 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (381)
Q Consensus 294 ~~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr 369 (381)
..++++|+..|.+.+..+|.++.+...+.+|++||.++.+|+..++|+... .|.+|++.-.++.+.+.++++.+
T Consensus 9 ~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~~--~~~awL~~Ia~n~~~d~~R~~~~ 82 (187)
T PRK12516 9 TPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGT--NMKAWLFTILRNEFYSQMRKRGR 82 (187)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCcc--cHHHHHHHHHHHHHHHHHHhhcC
Confidence 348999999999999999999998888999999999999999999998643 59999999999999999998654
No 101
>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=97.85 E-value=3e-05 Score=66.75 Aligned_cols=65 Identities=11% Similarity=0.021 Sum_probs=59.2
Q ss_pred HHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCC
Q 016880 302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (381)
Q Consensus 302 e~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr 369 (381)
..|.|.|..++.++.+.-.+.+|++||.++.+++.+++|++ .+|.+|++..+++.+.+.++++.+
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~ 66 (154)
T TIGR02950 2 REYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKK 66 (154)
T ss_pred chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhh
Confidence 46889999999999887789999999999999999999997 379999999999999999997654
No 102
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=97.84 E-value=8.2e-05 Score=67.21 Aligned_cols=75 Identities=9% Similarity=0.091 Sum_probs=66.9
Q ss_pred HHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCCccC
Q 016880 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI 373 (381)
Q Consensus 297 re~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~IRl 373 (381)
.++|++.|.+.|..+|.++.+...+.+|++||.++.+|+.+..|++. ..|.+|++.-+++.+.+.++++.+...+
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~~--~~~~~wL~~i~~n~~~d~~Rk~~~~~~~ 77 (181)
T PRK09637 3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNTIIDFYRKKNRSEEL 77 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhccc--cchHHHHHHHHHHHHHHHHHhccccCCc
Confidence 46899999999999999999888999999999999999999999953 4799999999999999999987654433
No 103
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=97.84 E-value=4.8e-05 Score=68.78 Aligned_cols=70 Identities=16% Similarity=0.200 Sum_probs=62.1
Q ss_pred HHHHHHhhHHHHHHHHHccCCCCC-HHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCC
Q 016880 298 EELIKSTRPLVLFLARNYRGLGIP-FSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (381)
Q Consensus 298 e~LIe~nlrLV~~IAkry~~rg~d-~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr 369 (381)
++.+..|.+.|..+|.++.+...+ .+|++||.++.+|++..+|++. + .|.+|++.-+++.+.+++|++.+
T Consensus 8 ~~~~~~~~~~l~~~a~~~~~~~~~~AEDivQevfl~~~~~~~~~~~~-~-~~~~wL~~Ia~n~~~d~~Rk~~~ 78 (195)
T PRK12532 8 DAELIESRKLLLHFARLQLPDHPDLAEDLVQETLLSAYSAGDSFQGR-A-LVNSWLFAILKNKIIDALRQIGR 78 (195)
T ss_pred hhhHHHHHHHHHHHHHHHcCChhhhHHHHHHHHHHHHHHhccccccc-c-hHHHHHHHHHHHHHHHHHHHhcc
Confidence 456677899999999999887777 9999999999999999999964 3 79999999999999999998754
No 104
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=97.81 E-value=9.7e-05 Score=69.31 Aligned_cols=74 Identities=16% Similarity=0.075 Sum_probs=67.1
Q ss_pred cHHHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCC
Q 016880 293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (381)
Q Consensus 293 G~~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr 369 (381)
...++++|+..|.+.++.++.++.+...+.+|++||.++-+|+.+.+|++. .|.+|++.-+++.+.+.++++.+
T Consensus 16 ~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~~~ 89 (216)
T PRK12533 16 RGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRRAN 89 (216)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhhcc
Confidence 345899999999999999999999888899999999999999999999863 48999999999999999998643
No 105
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=97.74 E-value=6.3e-05 Score=66.71 Aligned_cols=75 Identities=15% Similarity=0.032 Sum_probs=65.0
Q ss_pred HhcHH-HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcC
Q 016880 291 AFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA 368 (381)
Q Consensus 291 ~~G~~-Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qs 368 (381)
+.|+. ++.+|+..|.+.|..++.++.+...+.+|++||.++.+|+. ..|+.. ..|.+|.+...++.+.+++|++.
T Consensus 5 ~~~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~ 80 (172)
T PRK12523 5 QSPHSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAA 80 (172)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHH
Confidence 34554 89999999999999999999988899999999999999986 446543 36999999999999999999864
No 106
>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=97.73 E-value=9.4e-05 Score=65.86 Aligned_cols=71 Identities=14% Similarity=0.203 Sum_probs=62.0
Q ss_pred HHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCCccCC
Q 016880 302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374 (381)
Q Consensus 302 e~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~IRlP 374 (381)
..|.+.++.++.++.+...+.+|++|+.++.+|+++.+|++. .+|.+|+...+++.+.++++++.+...++
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~~--~~f~~wl~~iarn~~~d~~Rk~~~~~~~~ 72 (170)
T TIGR02959 2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDG--QKIQSWLYQIARNTIIDFYRSKSRSVELP 72 (170)
T ss_pred chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhccCccccc
Confidence 357888899999998888999999999999999999999963 47999999999999999999976554443
No 107
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=97.70 E-value=5.4e-05 Score=65.96 Aligned_cols=66 Identities=11% Similarity=0.086 Sum_probs=59.6
Q ss_pred HHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCC
Q 016880 301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (381)
Q Consensus 301 Ie~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr 369 (381)
++.|.+.|..+|.++.+...+.+|++||.++.+|+..++|++. .|.+|++.-+++.+.++++++.+
T Consensus 1 ~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n~~~d~~Rk~~~ 66 (160)
T PRK09642 1 MQTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATNHAIDYKRKKAR 66 (160)
T ss_pred CchHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHHHHHHHHHHhcc
Confidence 3578999999999999888899999999999999999999963 49999999999999999998654
No 108
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=97.63 E-value=0.00019 Score=66.52 Aligned_cols=72 Identities=18% Similarity=0.215 Sum_probs=65.0
Q ss_pred HHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCC
Q 016880 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG 370 (381)
Q Consensus 297 re~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~ 370 (381)
-..+++.|.+.|..++.++.+...+.+|++||.++.+|+.+.+|+.. .+|.+|.+..+++.+.++++++.+.
T Consensus 20 ~~~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfikl~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~~~ 91 (206)
T PRK12544 20 DPVFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGR--AAFKTWVFAILKNKIIDLLRQKKRH 91 (206)
T ss_pred hHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhhccc
Confidence 45788889999999999999888899999999999999999999964 3699999999999999999986553
No 109
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=97.61 E-value=0.00019 Score=65.82 Aligned_cols=70 Identities=19% Similarity=0.122 Sum_probs=62.8
Q ss_pred HHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCC
Q 016880 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG 370 (381)
Q Consensus 299 ~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~ 370 (381)
.++..|.+-|..+|.++.+...+.+|++||.++.+|+..++|++. ..|.+|++.-+++.+.++++++.+.
T Consensus 12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~r~ 81 (201)
T PRK12545 12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQ--SAHKTWVFGILRNKLIDTLRARQRT 81 (201)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhcccc--chHHHHHHHHHHHHHHHHHHhhccc
Confidence 347889999999999999888899999999999999999999975 3599999999999999999987654
No 110
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=97.58 E-value=0.0003 Score=63.95 Aligned_cols=76 Identities=12% Similarity=0.037 Sum_probs=66.9
Q ss_pred HHhcHHHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHc
Q 016880 290 LAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH 367 (381)
Q Consensus 290 l~~G~~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~q 367 (381)
+.....+.++++..|.+.|..+|.++.+...+.+|++|+.++.+|+.+..|++. ..|.+|++..+++.+.+..+++
T Consensus 18 ~~~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~~ 93 (188)
T PRK12517 18 MLSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFERK 93 (188)
T ss_pred hhccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHHh
Confidence 334556999999999999999999999888899999999999999999999964 3689999999999987777654
No 111
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=97.58 E-value=0.00028 Score=63.92 Aligned_cols=72 Identities=17% Similarity=0.198 Sum_probs=65.5
Q ss_pred HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCC
Q 016880 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (381)
Q Consensus 296 Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr 369 (381)
+...++..|.+.|..+|.++.+...+.+|++|+.++.+|+..++|++.. .|.+|++.-+++.+.+.++++.+
T Consensus 6 ~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~ 77 (182)
T PRK12540 6 SLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGS--NLPAWLFTILRNLFRSDYRKRRR 77 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCc--hHHHHHHHHHHHHHHHHHHhccc
Confidence 5678899999999999999998888999999999999999999998753 58899999999999999998654
No 112
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=97.58 E-value=0.0002 Score=64.25 Aligned_cols=74 Identities=8% Similarity=-0.098 Sum_probs=63.0
Q ss_pred HHHHHHHHHhhHHHHHHHHHccC--CCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcC
Q 016880 295 YCREELIKSTRPLVLFLARNYRG--LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA 368 (381)
Q Consensus 295 ~Are~LIe~nlrLV~~IAkry~~--rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qs 368 (381)
.+++.|+..|.+.|..++..+.+ ...+.+|++||.++-+|+...+|++.....|.||.+...++.+.++++++.
T Consensus 13 ~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~Rk~~ 88 (178)
T PRK12529 13 DKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRRRQS 88 (178)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHHHHH
Confidence 48999999999999997554444 246899999999999999999998544457999999999999999999753
No 113
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=97.54 E-value=0.0004 Score=63.44 Aligned_cols=71 Identities=18% Similarity=0.223 Sum_probs=62.7
Q ss_pred HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCC
Q 016880 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (381)
Q Consensus 296 Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr 369 (381)
.++.|.. |.+.|..+|..+.+...+.+|++||.++.+|+.+..|+.. ..|.+|++.-+++.+.+.++++.+
T Consensus 9 ~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r 79 (188)
T PRK12546 9 PRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKR 79 (188)
T ss_pred HHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhcc
Confidence 4555555 7799999999999989999999999999999999999963 369999999999999999998654
No 114
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=97.45 E-value=0.00039 Score=63.06 Aligned_cols=71 Identities=17% Similarity=0.139 Sum_probs=62.6
Q ss_pred HHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCCC
Q 016880 298 EELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG 370 (381)
Q Consensus 298 e~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr~ 370 (381)
++.|..|.+.+..+|.++.+...+.+|++||.++.+|+....|++.. +|.+|++.-.++.+.+++|++.+.
T Consensus 10 ~~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~~--~~~~wL~~Ia~n~~~d~~Rk~~~~ 80 (189)
T PRK12530 10 SLEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQS--ALKTWIFAILKNKIIDLIRYRKRF 80 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCCc--cHHHHHHHHHHHHHHHHHHhhccC
Confidence 45577788999999999998888999999999999999999998653 699999999999999999986543
No 115
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=97.42 E-value=0.00038 Score=60.67 Aligned_cols=68 Identities=15% Similarity=0.173 Sum_probs=59.5
Q ss_pred HHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCC
Q 016880 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (381)
Q Consensus 299 ~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr 369 (381)
.++..|.+.++.+|.++.+...+.+|++||.++.+++....|++. .|.+|+..-+++.+.++++++.+
T Consensus 2 ~~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn~~~d~~R~~~~ 69 (163)
T PRK07037 2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRNLAIDHYRRQAL 69 (163)
T ss_pred hHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHHHHHHHHHhhcc
Confidence 357788999999999999888899999999999999988877763 47899999999999999997653
No 116
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=97.37 E-value=0.00073 Score=60.14 Aligned_cols=71 Identities=13% Similarity=0.113 Sum_probs=62.5
Q ss_pred HHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcC
Q 016880 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA 368 (381)
Q Consensus 295 ~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qs 368 (381)
.+.+.++..|.+.+..++.++.+...+.+|++||.++.+|+. ..|++-. .|.+|++..+++.+.+.++++.
T Consensus 10 ~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~ 80 (172)
T PRK09651 10 LTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNA 80 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHH
Confidence 489999999999999999999988899999999999999987 4565432 5889999999999999999754
No 117
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=97.23 E-value=0.001 Score=60.42 Aligned_cols=71 Identities=13% Similarity=0.080 Sum_probs=63.1
Q ss_pred HHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCC
Q 016880 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (381)
Q Consensus 297 re~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr 369 (381)
++..+..+.+.|..++.++.+...+.+|++||.++.+|+....|++. ..|.+|.+.-+++.+.++++++.+
T Consensus 6 ~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~ 76 (182)
T PRK12511 6 KRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRV 76 (182)
T ss_pred hhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhcc
Confidence 45557788999999999999888899999999999999999999863 369999999999999999998654
No 118
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=97.01 E-value=0.0015 Score=57.03 Aligned_cols=64 Identities=9% Similarity=0.015 Sum_probs=55.1
Q ss_pred HHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcC
Q 016880 302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA 368 (381)
Q Consensus 302 e~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qs 368 (381)
+.|.+.+...+.++.+...+.+|++||.++.+|+..+.|++ + +|.||...-+++.+.++++++.
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~--~-~~~~wL~~ia~n~~~d~~R~~~ 65 (159)
T PRK12527 2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQI--E-HPRAFLYRTALNLVVDRHRRHR 65 (159)
T ss_pred hhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhccccccc--c-chHHHHHHHHHHHHHHHHHHHh
Confidence 45677777888888777788999999999999999999875 2 7899999999999999999753
No 119
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=96.98 E-value=0.0033 Score=55.68 Aligned_cols=70 Identities=9% Similarity=-0.043 Sum_probs=61.0
Q ss_pred HHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHc
Q 016880 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH 367 (381)
Q Consensus 295 ~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~q 367 (381)
.+..+++..|.+.+..++.++.+...+.+|++|+.++.+|+-.+.++. ..|.+|.+.-.++.+.+.+++.
T Consensus 9 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~ 78 (168)
T PRK12525 9 TLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQ 78 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHH
Confidence 478899999999999999999988889999999999999985554442 3699999999999999999864
No 120
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=96.94 E-value=0.0019 Score=62.69 Aligned_cols=69 Identities=13% Similarity=0.077 Sum_probs=60.1
Q ss_pred HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcC
Q 016880 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA 368 (381)
Q Consensus 296 Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qs 368 (381)
...++++.|.+.+..+|.++.+...+.||++||.++. |.....|+ ...|.+|.+.-+++.+.+.+|++.
T Consensus 5 ~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~---~~~~~~WL~~Ia~n~~~d~lR~~~ 73 (293)
T PRK09636 5 DAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQ---IRDPRAWLTRVVTRLCLDRLRSAR 73 (293)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhccccc---ccCHHHHHHHHHHHHHHHHHHhhh
Confidence 4568899999999999999998888999999999999 55556775 347999999999999999999754
No 121
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=96.77 E-value=0.0026 Score=61.65 Aligned_cols=66 Identities=15% Similarity=0.122 Sum_probs=56.9
Q ss_pred HHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcC
Q 016880 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA 368 (381)
Q Consensus 299 ~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qs 368 (381)
+++..|.+.+..+|.++.+...+.||++||.++.+++. .|+. ...|.+|.+..+++.+.+.++++.
T Consensus 1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~--~~~~~awL~~Ia~n~~ld~lR~~~ 66 (281)
T TIGR02957 1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQ--IENPKAYLTKVVTRRCIDVLRSAR 66 (281)
T ss_pred ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Cccc--ccCHHHHHHHHHHHHHHHHHHHhh
Confidence 36889999999999999998889999999999997765 4543 336999999999999999999753
No 122
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPro: IPR009042 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....
Probab=96.57 E-value=0.0012 Score=46.33 Aligned_cols=34 Identities=21% Similarity=0.157 Sum_probs=26.8
Q ss_pred hHHHHHhhcCC-CCCCCcHHHHHHHHHhHHHHHHH
Q 016880 223 FSAERALNSRG-RRLTIARNEAEMSKGVQVVANLE 256 (381)
Q Consensus 223 ~~v~~~~~~~~-~~lLtaeEE~eL~~~iq~~~~Le 256 (381)
+.++.|++..+ .||||++||++|++.|+.+...+
T Consensus 2 D~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~~~a 36 (37)
T PF00140_consen 2 DSLRLYLKEIGRYPLLTAEEEIELARRIRKGDEAA 36 (37)
T ss_dssp HHHHHHHHHHHHS-EETTHHHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHHhc
Confidence 45677777777 49999999999999999876543
No 123
>PRK09191 two-component response regulator; Provisional
Probab=96.49 E-value=0.0077 Score=55.60 Aligned_cols=63 Identities=13% Similarity=0.027 Sum_probs=55.9
Q ss_pred HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHH
Q 016880 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI 360 (381)
Q Consensus 296 Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI 360 (381)
+..+++..|.+.|...|.++.+...+.+|++|+.++-+|+....|++. ..|.+|.+.++++-.
T Consensus 2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~ 64 (261)
T PRK09191 2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLW 64 (261)
T ss_pred chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHh
Confidence 467899999999999999999888899999999999999999999974 358899998887654
No 124
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=96.42 E-value=0.0095 Score=56.93 Aligned_cols=73 Identities=15% Similarity=-0.077 Sum_probs=58.8
Q ss_pred HhcH-HHHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCC
Q 016880 291 AFGW-YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (381)
Q Consensus 291 ~~G~-~Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr 369 (381)
..|+ .+.+.+++.| +.+...+.++.+...+.||++||.++.+|+. |+.. + .|.+|++.-.++.+.+.++++.+
T Consensus 13 ~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~-~-~~~~WL~~IarN~~id~~Rk~k~ 86 (228)
T PRK06704 13 IDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNK-D-ICMTLVYKIARNRWLDQIKSKSV 86 (228)
T ss_pred cCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCcc-c-cHHHHHHHHHHHHHHHHHhcccc
Confidence 3344 3677777777 7899999999888899999999999988875 6643 2 58999999999999999997653
No 125
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=96.28 E-value=0.0088 Score=58.72 Aligned_cols=68 Identities=10% Similarity=-0.073 Sum_probs=60.0
Q ss_pred HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHc
Q 016880 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH 367 (381)
Q Consensus 296 Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~q 367 (381)
...++++.|.+.+..+|.++.+...+.||++||.++.+|++...+ -..|.+|.+.-.++.+.+.++++
T Consensus 6 ~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~----~~~~~aWL~~Ia~n~~id~lRk~ 73 (290)
T PRK09635 6 PVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD----IDDERGWLIVVTSRLCLDHIKSA 73 (290)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc----cccHHHHHHHHHHHHHHHHHhhh
Confidence 577899999999999999999988999999999999999876442 13689999999999999999974
No 126
>PF12645 HTH_16: Helix-turn-helix domain; InterPro: IPR024760 This domain appears to be a helix-turn-helix domain, suggesting a transcriptional regulatory protein. Some proteins with this domain are annotated as conjugative transposon proteins.
Probab=96.17 E-value=0.019 Score=45.12 Aligned_cols=56 Identities=21% Similarity=0.261 Sum_probs=45.9
Q ss_pred HHHHHHhcHH-HHHHHHHHhhHHHHHHHHHc----cC--CCCCHHHHHHHHHHHHHHHHhhcC
Q 016880 286 LKQHLAFGWY-CREELIKSTRPLVLFLARNY----RG--LGIPFSDLLQAGNVGVLQGAERFD 341 (381)
Q Consensus 286 L~~~l~~G~~-Are~LIe~nlrLV~~IAkry----~~--rg~d~EDLiQEG~IGLikAvekFD 341 (381)
++.+++.|+. |.+++++.|.|+|.+.+.+- .+ .+.--+|+-|+=...|++||.+|+
T Consensus 3 vI~~A~~GD~~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~ 65 (65)
T PF12645_consen 3 VIKAAKQGDPEAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE 65 (65)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence 4556677775 99999999999999988762 22 145569999999999999999996
No 127
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=96.00 E-value=0.022 Score=51.96 Aligned_cols=90 Identities=13% Similarity=0.110 Sum_probs=66.5
Q ss_pred HHHHHHHHHhcHH-HHHHHHHHhhHHHHHHHHHccCC---CCCHHHH--HHHHHHHHHHHHhhcCCCCCCccchHHHHHH
Q 016880 283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGL---GIPFSDL--LQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356 (381)
Q Consensus 283 ~eeL~~~l~~G~~-Are~LIe~nlrLV~~IAkry~~r---g~d~EDL--iQEG~IGLikAvekFDpsrG~rFSTYA~~wI 356 (381)
..+|+..++.|+. |.++|+..|.+-++.+|+++... +.+.+|. ++++++-++..-...+.+.-..|-.|+..-+
T Consensus 4 it~ll~~~~~GD~~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~~~~~ 83 (185)
T PF07638_consen 4 ITELLDRWRQGDEAALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALLARIM 83 (185)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHHHHHH
Confidence 3567888999997 99999999999999999977533 4566665 4555555544222224444457999999999
Q ss_pred HHHHHHHHHHcCCCcc
Q 016880 357 RKSISKMVARHARGIK 372 (381)
Q Consensus 357 r~aI~~~Ir~qsr~IR 372 (381)
++.+.+.+|.+...+|
T Consensus 84 rr~lid~~R~~~a~KR 99 (185)
T PF07638_consen 84 RRKLIDHARRRQAQKR 99 (185)
T ss_pred HHHHHHHHHHHHHHhc
Confidence 9999999998766655
No 128
>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=95.89 E-value=0.023 Score=48.76 Aligned_cols=65 Identities=12% Similarity=0.229 Sum_probs=53.6
Q ss_pred HHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhh-----cCCCCCCccchHHHHHHHHHHHHHHHHcCC
Q 016880 298 EELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAER-----FDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (381)
Q Consensus 298 e~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvek-----FDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr 369 (381)
++++..|.+++..++++|.. -+| +|+-.+.+|+...+ |++. ..|.||.+.-.++.+.+.+|++.+
T Consensus 2 ~~~~~~y~~~l~~~~~~~~~----~~~-~qdvf~~~w~~~~~~~~~~~~~~--~~~~~wL~~iarN~~id~~Rk~~~ 71 (142)
T TIGR03209 2 EEIYMNFKNTIDIFTRKYNL----YYD-YNDILYHLWIILKKIDLNKFNTE--NDLEKYISTSLKRYCLDICNKKNR 71 (142)
T ss_pred hHHHHHHHHHHHHHHHHhcc----hhh-HHHHHHHHHHHHHHhhhhhcCch--hHHHHHHHHHHHHHHHHHHHHHhh
Confidence 57899999999999999954 224 49999999999865 5542 469999999999999999997643
No 129
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=94.92 E-value=0.051 Score=47.04 Aligned_cols=47 Identities=11% Similarity=0.106 Sum_probs=40.0
Q ss_pred CCHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHcCC
Q 016880 320 IPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369 (381)
Q Consensus 320 ~d~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~qsr 369 (381)
.+.+|++||.++.+|+.... ++ +..|.+|.+..+++.+.+++|++.+
T Consensus 5 ~~AeDivQe~fl~~~~~~~~-~~--~~~~~~wl~~ia~n~~~d~~Rk~~~ 51 (161)
T PRK09047 5 DAALDIVQDAMIKLAEKYGD-RP--AAEWPPLFQRILQNRIHDWFRRQKV 51 (161)
T ss_pred HHHHHHHHHHHHHHHHHHhh-cc--cCchHHHHHHHHHHHHHHHHHhhcc
Confidence 46899999999999998876 33 4579999999999999999998653
No 130
>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=94.47 E-value=0.11 Score=40.66 Aligned_cols=40 Identities=25% Similarity=0.401 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHH
Q 016880 252 VANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLA 291 (381)
Q Consensus 252 ~~~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~ 291 (381)
+.++.+++.+|..++||.||.++.|+..|++.+++...+.
T Consensus 3 l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~ 42 (78)
T PF04539_consen 3 LRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQ 42 (78)
T ss_dssp HHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHH
Confidence 4467788999999999999999999999999998876543
No 131
>PHA02547 55 RNA polymerase sigma factor; Provisional
Probab=88.55 E-value=1.6 Score=40.85 Aligned_cols=64 Identities=16% Similarity=0.184 Sum_probs=51.3
Q ss_pred hhHHHHHHHHHccCCCCC---HHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHHHHHc
Q 016880 304 TRPLVLFLARNYRGLGIP---FSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH 367 (381)
Q Consensus 304 nlrLV~~IAkry~~rg~d---~EDLiQEG~IGLikAvekFDpsrG~rFSTYA~~wIr~aI~~~Ir~q 367 (381)
-+.++..++++|.-+|.. .+|+|.+|.-..++.+..|||++..-+-.|.+..+-++..+-|...
T Consensus 46 imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~kE 112 (179)
T PHA02547 46 IMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKKE 112 (179)
T ss_pred HHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHHH
Confidence 355566666666655665 7999999999999999999999988888888888888877777643
No 132
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=71.93 E-value=3.7 Score=44.64 Aligned_cols=32 Identities=22% Similarity=0.212 Sum_probs=24.2
Q ss_pred hHHHHHhhcCC-CCCCCcHHHHHHHHHhHHHHH
Q 016880 223 FSAERALNSRG-RRLTIARNEAEMSKGVQVVAN 254 (381)
Q Consensus 223 ~~v~~~~~~~~-~~lLtaeEE~eL~~~iq~~~~ 254 (381)
++|+=|++.-| -||||.|+|++++++|+.+..
T Consensus 104 DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~ 136 (619)
T PRK05658 104 DPVRMYLREMGTVELLTREGEIEIAKRIEAGEN 136 (619)
T ss_pred ChHHHHHHHhccCcCCCcHHHHHHHHHHHHHHH
Confidence 33455665555 589999999999999997543
No 133
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=69.86 E-value=10 Score=37.18 Aligned_cols=41 Identities=20% Similarity=0.204 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHHhc
Q 016880 253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFG 293 (381)
Q Consensus 253 ~~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~~G 293 (381)
..++.+.++|..++|++||..+.|+..|++.+++...+..+
T Consensus 110 ~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~ 150 (247)
T COG1191 110 RRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAI 150 (247)
T ss_pred HHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHh
Confidence 35667788899999999999999999999999887665544
No 134
>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=57.07 E-value=29 Score=33.05 Aligned_cols=38 Identities=16% Similarity=0.172 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHH
Q 016880 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLA 291 (381)
Q Consensus 254 ~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~ 291 (381)
.+.+.+.++..++|+.|+.++.|+..|++.+.+...+.
T Consensus 121 ~~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~~ 158 (254)
T TIGR02850 121 KALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFALD 158 (254)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34455667778889999999999999999988766544
No 135
>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=55.61 E-value=34 Score=32.21 Aligned_cols=37 Identities=16% Similarity=0.256 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHH
Q 016880 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (381)
Q Consensus 254 ~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l 290 (381)
.+.+...+|..++|+.||.++.|+..|++.+.+....
T Consensus 88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~ 124 (238)
T TIGR02393 88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVREIK 124 (238)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 4555677788889999999999999999998876643
No 136
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=55.37 E-value=34 Score=32.81 Aligned_cols=37 Identities=19% Similarity=0.240 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHH
Q 016880 253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH 289 (381)
Q Consensus 253 ~~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~ 289 (381)
.++.+.+.+|..++|++|+..+.|+..|++.+++...
T Consensus 113 ~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~ 149 (256)
T PRK07408 113 RQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEI 149 (256)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHH
Confidence 3466677888889999999999999999999887654
No 137
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=54.98 E-value=35 Score=33.09 Aligned_cols=38 Identities=21% Similarity=0.305 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHH
Q 016880 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLA 291 (381)
Q Consensus 254 ~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~ 291 (381)
.+.+...+|...+|+.||..+.|+..|++.+++...+.
T Consensus 128 ~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~ 165 (264)
T PRK07122 128 RLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLV 165 (264)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 45556677878889999999999999999988876554
No 138
>PRK14082 hypothetical protein; Provisional
Probab=53.71 E-value=49 Score=26.52 Aligned_cols=54 Identities=19% Similarity=0.104 Sum_probs=43.7
Q ss_pred HHHHHHHHhhHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchH
Q 016880 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTY 351 (381)
Q Consensus 296 Are~LIe~nlrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFDpsrG~rFSTY 351 (381)
..+.+|..+.|.|.+--.+- .--+.+||.||=-|-+++-++.++-..+--|-.|
T Consensus 10 e~e~ii~~FepkIkKsL~~T--~yqeREDLeQElk~Ki~eK~~~~~~~e~PGF~ef 63 (65)
T PRK14082 10 EIEHLIENFSPMIKKKLSNT--SYQEREDLEQELKIKIIEKADMLLCQEVPGFWEF 63 (65)
T ss_pred HHHHHHHHccHHHHHHHhcC--ChhhHHHHHHHHHHHHHHHHHHhhcccCCcHHHh
Confidence 56789999999988766543 2367899999999999999999998777666655
No 139
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=51.59 E-value=38 Score=34.15 Aligned_cols=39 Identities=31% Similarity=0.466 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHH
Q 016880 252 VANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (381)
Q Consensus 252 ~~~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l 290 (381)
...+.+++.+|...+|+.||..+.|+..|++.+.+...+
T Consensus 172 ~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~ 210 (324)
T PRK07921 172 VNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLL 210 (324)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 345667778888889999999999999999988876643
No 140
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=51.19 E-value=37 Score=32.67 Aligned_cols=37 Identities=16% Similarity=0.202 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHH
Q 016880 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (381)
Q Consensus 254 ~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l 290 (381)
++.+....|...+|++|+.++.|+..|++.+++...+
T Consensus 111 ~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~ 147 (257)
T PRK05911 111 KLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWF 147 (257)
T ss_pred HHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHH
Confidence 3445566677788999999999999999998876544
No 141
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=50.89 E-value=40 Score=31.97 Aligned_cols=37 Identities=8% Similarity=0.134 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHH
Q 016880 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (381)
Q Consensus 254 ~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l 290 (381)
++.+....|..++|+.|+..+.|+..|++.+++...+
T Consensus 102 ~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~ 138 (231)
T PRK12427 102 KTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYL 138 (231)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 3455667777888999999999999999988876554
No 142
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=47.18 E-value=44 Score=34.12 Aligned_cols=39 Identities=18% Similarity=0.269 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHH
Q 016880 253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLA 291 (381)
Q Consensus 253 ~~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~ 291 (381)
..+.++..+|..++|+.||..+.|+..|++.+.+...+.
T Consensus 216 ~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~ 254 (367)
T PRK09210 216 NKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILK 254 (367)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 345667778888899999999999999999988776543
No 143
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=41.55 E-value=66 Score=30.57 Aligned_cols=38 Identities=16% Similarity=0.190 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHH
Q 016880 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLA 291 (381)
Q Consensus 254 ~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~ 291 (381)
.+.+....+...+|+.|+..++|+..|++.+++...+.
T Consensus 110 ~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~ 147 (251)
T PRK07670 110 KVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMN 147 (251)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 34555666777889999999999999999988877654
No 144
>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=40.26 E-value=71 Score=29.72 Aligned_cols=37 Identities=32% Similarity=0.439 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHH
Q 016880 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLA 291 (381)
Q Consensus 255 Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~ 291 (381)
+.+....|..++|+.|+..+.|+..|++.+++...+.
T Consensus 99 ~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~ 135 (231)
T TIGR02885 99 IRYMKEELSKELGREPTINELAEALGVSPEEIVMALE 135 (231)
T ss_pred HHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 4455667777889999999999999999888765543
No 145
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=39.50 E-value=71 Score=34.58 Aligned_cols=39 Identities=21% Similarity=0.302 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHH
Q 016880 253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLA 291 (381)
Q Consensus 253 ~~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~ 291 (381)
..+.+++.+|...+|+.|+.++.|+..|++.+.+....+
T Consensus 358 ~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~ 396 (509)
T PRK05901 358 NKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQK 396 (509)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 356667788888999999999999999999988776543
No 146
>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=39.27 E-value=79 Score=29.32 Aligned_cols=38 Identities=26% Similarity=0.330 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHH
Q 016880 253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (381)
Q Consensus 253 ~~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l 290 (381)
..+.+.+.+|...+|+.|+.++.|+..|++.+.+...+
T Consensus 83 ~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~ 120 (224)
T TIGR02479 83 RKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQAL 120 (224)
T ss_pred HHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHH
Confidence 34556677788888999999999999999988876655
No 147
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=38.84 E-value=78 Score=32.77 Aligned_cols=39 Identities=13% Similarity=0.214 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHH
Q 016880 252 VANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (381)
Q Consensus 252 ~~~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l 290 (381)
...+.+....|...+|+.||..+.|+..|++.+.+....
T Consensus 222 ~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~ 260 (373)
T PRK07406 222 ISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIA 260 (373)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 345666677888889999999999999999998876543
No 148
>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=37.32 E-value=92 Score=23.89 Aligned_cols=58 Identities=24% Similarity=0.374 Sum_probs=38.4
Q ss_pred HHHhCCcCc------hhHHHHHcCCCHHHHHHHHHhcHHHHHHHHHHhhHHHHHHHHHccCCCC-CHHH
Q 016880 263 EKESGKAAS------LNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGI-PFSD 324 (381)
Q Consensus 263 ~~~~gr~ps------~~ewA~aagl~~eeL~~~l~~G~~Are~LIe~nlrLV~~IAkry~~rg~-d~ED 324 (381)
+...||.|| +..|....|++.+.+..++.. |... -..+.++|.+|++++...|+ +.+|
T Consensus 6 e~~~gr~ls~~e~~~i~~~~~~~~~~~evI~~ai~~---a~~~-~~~~~~Yi~~Il~~W~~~gi~T~e~ 70 (73)
T TIGR01446 6 EENFGRMLSPFEMEDLKYWLDEFGNSPELIKEALKE---AVSN-NKANYKYIDAILNNWKNNGIKTVED 70 (73)
T ss_pred HHHhCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHH---HHHc-CCCCHHHHHHHHHHHHHcCCCCHHH
Confidence 344576666 457777778877777666553 2221 23467899999999988875 4444
No 149
>PRK05949 RNA polymerase sigma factor; Validated
Probab=37.28 E-value=78 Score=31.92 Aligned_cols=38 Identities=13% Similarity=0.267 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHH
Q 016880 253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (381)
Q Consensus 253 ~~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l 290 (381)
-++.+.+.++..++|+.|+..+.|+..|++.+.+...+
T Consensus 178 ~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~ 215 (327)
T PRK05949 178 NKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYL 215 (327)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 34556666777888999999999999999988876654
No 150
>KOG0917 consensus Uncharacterized conserved protein [Function unknown]
Probab=36.06 E-value=32 Score=34.81 Aligned_cols=84 Identities=30% Similarity=0.364 Sum_probs=57.8
Q ss_pred HHhHHhhhccccccCCcccccccccccchhhccccchhHHhhhhhcccccccccccchH-HHHHhhHHHHHhcccchhhh
Q 016880 45 SFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEIRQKSTSCIGQDASSRSDF-RLLMENLDVLESTFADSDAL 123 (381)
Q Consensus 45 ~~~~~~~~~~~~~~~~~~~~~~~ss~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~-~ll~~nl~~le~~~~~~d~l 123 (381)
|.++.|..--+-..+||+-++-|-=-++|+- +|+-+...| .-+| .-||.-|+.|+..++|.|++
T Consensus 10 si~~~l~~a~e~~k~dpvvayycrlyamq~g-----------mKid~qT~e----~rk~lsgLm~~lealkkqlaDneai 74 (338)
T KOG0917|consen 10 SIQHHLRTAQEHDKRDPVVAYYCRLYAMQTG-----------MKIDSQTPE----CRKFLSGLMDQLEALKKQLADNEAI 74 (338)
T ss_pred HHHHHHHHHHhhcccccHHHHHHHHHHHHhc-----------ccCCccCHH----HHHHHHHHHHHHHHHHHHhcchhhh
Confidence 5566665555555559998888865555542 222222222 2233 46999999999999999999
Q ss_pred HHHHHHHHHhhhhhhhhhhhh
Q 016880 124 RLEREILQQLGKLGALKLFNS 144 (381)
Q Consensus 124 rLer~IL~~~~~lgal~~fn~ 144 (381)
.+|-+-=-|+|.. |+++|+-
T Consensus 75 tne~~aqaHiE~f-AlklF~~ 94 (338)
T KOG0917|consen 75 TNEIVAQAHIENF-ALKLFLY 94 (338)
T ss_pred hhchHHHHHHHHH-HHHHHHh
Confidence 9988877788765 9999764
No 151
>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=34.80 E-value=95 Score=28.02 Aligned_cols=41 Identities=22% Similarity=0.400 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHHhcH
Q 016880 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGW 294 (381)
Q Consensus 254 ~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~~G~ 294 (381)
..++++.-|.+..++..|..+.+++.|++.+.+.+-++.|.
T Consensus 31 ~f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGR 71 (137)
T TIGR03826 31 EFEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGR 71 (137)
T ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 34567777777778889999999999999999999988885
No 152
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=34.53 E-value=90 Score=32.93 Aligned_cols=40 Identities=13% Similarity=0.328 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHH
Q 016880 252 VANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLA 291 (381)
Q Consensus 252 ~~~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~ 291 (381)
.-++.+.+.+|...+|+.|+..+.|+..|++.+.+...+.
T Consensus 261 l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l~ 300 (415)
T PRK07598 261 LNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLL 300 (415)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4456677888888999999999999999999998877654
No 153
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=34.16 E-value=1e+02 Score=29.62 Aligned_cols=37 Identities=27% Similarity=0.287 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHH
Q 016880 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (381)
Q Consensus 254 ~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l 290 (381)
.+.+.+..|+..+|+.||..+.|+..|++.+.+....
T Consensus 119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~ 155 (268)
T PRK06288 119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLL 155 (268)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHH
Confidence 4566677888889999999999999999988776654
No 154
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=33.79 E-value=1.1e+02 Score=29.10 Aligned_cols=36 Identities=17% Similarity=0.173 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHH
Q 016880 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (381)
Q Consensus 255 Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l 290 (381)
+.+...++..+.|+.|+..+.|+..|++.+++...+
T Consensus 125 ~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~~ 160 (258)
T PRK08215 125 ALQVREKLINENSKEPTVEEIAKELEVPREEVVFAL 160 (258)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 444566777788999999999999999998876644
No 155
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=31.79 E-value=73 Score=27.33 Aligned_cols=40 Identities=18% Similarity=0.165 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHHh
Q 016880 253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAF 292 (381)
Q Consensus 253 ~~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~~ 292 (381)
..+.++..-+.......++.+++|+.+|++...|.+..+.
T Consensus 9 ~~i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 9 ITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3445566667777788899999999999999988877764
No 156
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=30.61 E-value=1.2e+02 Score=30.38 Aligned_cols=40 Identities=15% Similarity=0.368 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHH
Q 016880 252 VANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLA 291 (381)
Q Consensus 252 ~~~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~ 291 (381)
...+.+.+.++...+|+.|+..+.|+..|++.+.+.....
T Consensus 167 ~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~ 206 (317)
T PRK07405 167 LNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLE 206 (317)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 3446666777888889999999999999999888766543
No 157
>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=27.21 E-value=1.5e+02 Score=29.07 Aligned_cols=39 Identities=15% Similarity=0.291 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHH
Q 016880 253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLA 291 (381)
Q Consensus 253 ~~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~ 291 (381)
.++.+.+.++...+|+.|+..+.|+..|++.+.+.....
T Consensus 161 ~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~ 199 (298)
T TIGR02997 161 NKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQ 199 (298)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 345555667777889999999999999999888766543
No 158
>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=24.75 E-value=2.4e+02 Score=21.99 Aligned_cols=23 Identities=22% Similarity=0.362 Sum_probs=15.4
Q ss_pred HHhCCcCchhHHHHHcCCC-HHHH
Q 016880 264 KESGKAASLNCWAQAAGVS-ERVL 286 (381)
Q Consensus 264 ~~~gr~ps~~ewA~aagl~-~eeL 286 (381)
.+.|.+||..|.|+..|+. ....
T Consensus 20 ~~~G~~Pt~rEIa~~~g~~S~~tv 43 (65)
T PF01726_consen 20 EENGYPPTVREIAEALGLKSTSTV 43 (65)
T ss_dssp HHHSS---HHHHHHHHTSSSHHHH
T ss_pred HHcCCCCCHHHHHHHhCCCChHHH
Confidence 3469999999999999995 4433
No 159
>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=23.49 E-value=1.7e+02 Score=27.06 Aligned_cols=35 Identities=23% Similarity=0.368 Sum_probs=27.4
Q ss_pred HHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHH
Q 016880 256 ERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (381)
Q Consensus 256 e~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l 290 (381)
.+....+....|+.|+..+.|+..|++.+++....
T Consensus 93 ~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~ 127 (227)
T TIGR02980 93 NKATEELTQRLGRSPTIAEIAEELGVSEEEVVEAL 127 (227)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 33455666777999999999999999988876543
No 160
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=22.82 E-value=2e+02 Score=23.46 Aligned_cols=38 Identities=11% Similarity=0.239 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHHHh
Q 016880 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAF 292 (381)
Q Consensus 255 Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l~~ 292 (381)
++++..-+...+...++.++.|..+|++...|.+.++.
T Consensus 7 ~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~ 44 (107)
T PRK10219 7 IQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRT 44 (107)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 45556667777788899999999999999988777665
No 161
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=22.38 E-value=2.1e+02 Score=29.56 Aligned_cols=41 Identities=27% Similarity=0.430 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHHH
Q 016880 250 QVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (381)
Q Consensus 250 q~~~~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~l 290 (381)
+..-+|-+++.+|..++|++|+.++.|+..|++.+++....
T Consensus 186 e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~ 226 (342)
T COG0568 186 ELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREML 226 (342)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHH
Confidence 33445667888888889999999999999999876654433
No 162
>PF15545 Toxin_67: Putative toxin 67
Probab=21.02 E-value=95 Score=25.17 Aligned_cols=30 Identities=20% Similarity=0.544 Sum_probs=24.7
Q ss_pred cchHHHHHHHHHHHHHHHHcCCCccCCCcc
Q 016880 348 FSTYVQYWIRKSISKMVARHARGIKIPVPL 377 (381)
Q Consensus 348 FSTYA~~wIr~aI~~~Ir~qsr~IRlP~~~ 377 (381)
-+.+..-||++.|.+.-+.....||+|-.+
T Consensus 7 q~~~vRGwiknEi~~i~~~~r~~iRlPpG~ 36 (70)
T PF15545_consen 7 QPSWVRGWIKNEINRIKTGRRKSIRLPPGK 36 (70)
T ss_pred chHHHHHHHHHHHHHHHhCccceecCCCch
Confidence 457888899999999888878899999643
No 163
>PRK05572 sporulation sigma factor SigF; Validated
Probab=20.51 E-value=2.5e+02 Score=26.66 Aligned_cols=36 Identities=22% Similarity=0.315 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHhCCcCchhHHHHHcCCCHHHHHHH
Q 016880 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH 289 (381)
Q Consensus 254 ~Le~~r~~L~~~~gr~ps~~ewA~aagl~~eeL~~~ 289 (381)
++.+....+..+.|+.|+..+.|+..|++.+.+...
T Consensus 119 ~~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~~~ 154 (252)
T PRK05572 119 KIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLA 154 (252)
T ss_pred HHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHH
Confidence 455556677777899999999999999988776543
No 164
>TIGR03761 ICE_PFL4669 integrating conjugative element protein, PFL_4669 family. Members of this protein family, such as PFL4669, are found in integrating conjugative elements (ICE) of the PFGI-1 class as in Pseudomonas fluorescens.
Probab=20.50 E-value=2.2e+02 Score=27.63 Aligned_cols=36 Identities=31% Similarity=0.400 Sum_probs=29.2
Q ss_pred hHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHhhcC
Q 016880 305 RPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFD 341 (381)
Q Consensus 305 lrLV~~IAkry~~rg~d~EDLiQEG~IGLikAvekFD 341 (381)
++-|..++.+|...|++.+|+. +++-.--+|+++|-
T Consensus 158 vR~vf~~~~~yr~~gvtR~D~~-~~n~~a~~Aie~~G 193 (216)
T TIGR03761 158 IRRLFGLAQRYRHSGVTRDDFA-ANNARARKAIERFG 193 (216)
T ss_pred HHHHHHHHHhhhcCCCCHHHHH-hCCHHHHHHHHHcC
Confidence 4556778889999999999997 66777778999884
No 165
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=20.24 E-value=2.7e+02 Score=20.42 Aligned_cols=23 Identities=30% Similarity=0.329 Sum_probs=19.1
Q ss_pred CchhHHHHHcCCCHHHHHHHHHh
Q 016880 270 ASLNCWAQAAGVSERVLKQHLAF 292 (381)
Q Consensus 270 ps~~ewA~aagl~~eeL~~~l~~ 292 (381)
++..++|+..|++...|.+.+..
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~ 24 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKK 24 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Confidence 67889999999998888777764
Done!