Query 020126
Match_columns 330
No_of_seqs 202 out of 1856
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 07:13:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020126.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020126hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK07598 RNA polymerase sigma 100.0 6.9E-34 1.5E-38 282.1 14.9 140 191-330 60-241 (415)
2 TIGR02997 Sig70-cyanoRpoD RNA 100.0 6.1E-33 1.3E-37 261.3 15.3 138 192-329 2-139 (298)
3 PRK07406 RNA polymerase sigma 100.0 5.5E-32 1.2E-36 265.2 15.2 139 191-329 63-201 (373)
4 PRK05949 RNA polymerase sigma 100.0 7.3E-31 1.6E-35 252.3 15.4 140 191-330 18-157 (327)
5 PRK07405 RNA polymerase sigma 100.0 4.2E-30 9.1E-35 245.5 15.0 139 191-329 8-146 (317)
6 PRK05901 RNA polymerase sigma 100.0 7.6E-30 1.6E-34 258.7 12.1 127 191-330 211-337 (509)
7 COG0568 RpoD DNA-directed RNA 99.9 7.4E-28 1.6E-32 234.2 10.5 140 191-330 9-168 (342)
8 PRK07921 RNA polymerase sigma 99.9 3.8E-27 8.3E-32 226.8 12.4 126 191-329 26-151 (324)
9 PRK05658 RNA polymerase sigma 99.9 3.8E-24 8.2E-29 220.3 10.3 102 192-330 345-446 (619)
10 PRK09210 RNA polymerase sigma 99.9 1.5E-23 3.2E-28 204.1 11.0 100 190-329 95-194 (367)
11 TIGR02392 rpoH_proteo alternat 99.9 2.9E-23 6.4E-28 193.0 11.3 98 192-329 2-100 (270)
12 PRK06596 RNA polymerase factor 99.9 4.2E-23 9.1E-28 194.2 11.7 103 184-329 10-113 (284)
13 PRK07500 rpoH2 RNA polymerase 99.9 3.3E-21 7.2E-26 182.0 11.8 99 191-329 6-105 (289)
14 PRK07122 RNA polymerase sigma 99.8 2E-21 4.3E-26 181.2 8.1 66 264-329 40-105 (264)
15 PRK05657 RNA polymerase sigma 99.8 1.9E-19 4E-24 173.1 11.4 101 189-329 51-151 (325)
16 TIGR02393 RpoD_Cterm RNA polym 99.8 1.5E-19 3.2E-24 164.7 7.0 65 265-329 1-65 (238)
17 TIGR02394 rpoS_proteo RNA poly 99.8 2.7E-18 6E-23 160.7 11.4 102 188-329 10-111 (285)
18 COG1191 FliA DNA-directed RNA 99.8 1.5E-18 3.2E-23 162.9 9.2 85 204-329 4-89 (247)
19 PRK07408 RNA polymerase sigma 99.7 1.3E-17 2.9E-22 154.4 10.4 66 264-329 25-91 (256)
20 PRK08215 sporulation sigma fac 99.7 1E-16 2.2E-21 147.8 10.7 93 197-329 8-102 (258)
21 TIGR02850 spore_sigG RNA polym 99.7 1.1E-16 2.3E-21 147.5 10.7 89 201-329 11-99 (254)
22 PRK05911 RNA polymerase sigma 99.7 5.7E-17 1.2E-21 150.4 7.9 68 262-329 21-91 (257)
23 PRK06288 RNA polymerase sigma 99.6 2.4E-15 5.2E-20 139.6 10.0 90 200-329 6-99 (268)
24 TIGR02941 Sigma_B RNA polymera 99.6 1.1E-14 2.5E-19 133.5 10.2 86 204-329 8-94 (255)
25 PRK05803 sporulation sigma fac 99.5 4.6E-14 1E-18 128.2 11.6 98 192-329 17-114 (233)
26 TIGR02980 SigBFG RNA polymeras 99.5 2.5E-14 5.4E-19 128.6 7.7 67 263-329 2-68 (227)
27 PRK08583 RNA polymerase sigma 99.5 9.7E-14 2.1E-18 127.6 10.1 86 204-329 8-94 (257)
28 TIGR02895 spore_sigI RNA polym 99.5 4.8E-14 1E-18 130.0 7.3 70 260-329 5-76 (218)
29 PRK05572 sporulation sigma fac 99.5 2.3E-13 5E-18 125.2 10.7 93 197-329 5-97 (252)
30 PRK12427 flagellar biosynthesi 99.5 5.7E-14 1.2E-18 128.8 6.6 65 264-329 15-82 (231)
31 TIGR02885 spore_sigF RNA polym 99.5 1.3E-13 2.9E-18 124.4 8.2 68 262-329 9-76 (231)
32 PRK07670 RNA polymerase sigma 99.4 1E-12 2.3E-17 120.8 9.5 66 264-329 22-90 (251)
33 TIGR02479 FliA_WhiG RNA polyme 99.4 8E-13 1.7E-17 119.0 6.2 61 269-329 1-64 (224)
34 PRK06986 fliA flagellar biosyn 99.3 5.3E-12 1.2E-16 114.8 7.1 69 261-329 5-76 (236)
35 TIGR02846 spore_sigmaK RNA pol 99.2 1.2E-10 2.6E-15 105.7 11.4 98 192-329 15-113 (227)
36 PRK08301 sporulation sigma fac 99.1 3.3E-10 7.1E-15 102.6 10.7 94 196-329 23-117 (234)
37 PF04542 Sigma70_r2: Sigma-70 99.0 7E-10 1.5E-14 81.4 6.0 61 269-329 1-61 (71)
38 TIGR02835 spore_sigmaE RNA pol 99.0 2.5E-09 5.5E-14 97.5 10.5 94 196-329 23-117 (234)
39 PRK08311 putative RNA polymera 98.9 3.6E-09 7.8E-14 98.7 8.9 67 263-329 17-85 (237)
40 PRK08295 RNA polymerase factor 98.8 1.3E-08 2.7E-13 89.5 9.0 66 263-328 23-88 (208)
41 TIGR02859 spore_sigH RNA polym 98.8 3.9E-08 8.4E-13 85.6 9.1 65 263-327 18-82 (198)
42 TIGR02937 sigma70-ECF RNA poly 98.8 1.4E-08 3.1E-13 81.5 5.9 63 265-329 2-64 (158)
43 PRK09652 RNA polymerase sigma 98.6 8.9E-08 1.9E-12 81.1 6.2 65 262-328 8-72 (182)
44 PRK09648 RNA polymerase sigma 98.6 2.7E-07 5.9E-12 80.4 9.0 64 264-328 24-91 (189)
45 PRK11922 RNA polymerase sigma 98.5 3.6E-07 7.9E-12 83.1 8.6 86 201-328 7-92 (231)
46 PRK05602 RNA polymerase sigma 98.5 4.1E-07 8.8E-12 79.2 7.7 64 263-327 19-82 (186)
47 PRK09646 RNA polymerase sigma 98.5 4E-07 8.6E-12 80.2 7.7 64 263-327 29-92 (194)
48 TIGR02948 SigW_bacill RNA poly 98.4 6E-07 1.3E-11 77.3 7.5 64 263-328 17-80 (187)
49 PRK09641 RNA polymerase sigma 98.4 7.3E-07 1.6E-11 76.7 7.7 64 263-328 17-80 (187)
50 PRK12513 RNA polymerase sigma 98.4 1.2E-06 2.5E-11 76.8 7.8 64 263-328 25-88 (194)
51 PRK06759 RNA polymerase factor 98.4 8.8E-07 1.9E-11 74.2 6.6 63 264-328 4-66 (154)
52 PRK11923 algU RNA polymerase s 98.3 2.2E-06 4.7E-11 74.9 8.1 61 264-326 20-80 (193)
53 PRK09640 RNA polymerase sigma 98.3 2.4E-06 5.2E-11 74.8 8.3 77 250-328 8-88 (188)
54 PRK13919 putative RNA polymera 98.3 1.9E-06 4.1E-11 74.7 7.0 65 263-328 22-86 (186)
55 PRK12519 RNA polymerase sigma 98.3 2.3E-06 5E-11 74.8 7.2 64 263-328 28-91 (194)
56 PRK06811 RNA polymerase factor 98.2 4.1E-06 8.9E-11 73.5 8.3 65 263-328 17-84 (189)
57 PRK09638 RNA polymerase sigma 98.2 5.4E-06 1.2E-10 71.0 7.8 64 263-328 17-80 (176)
58 PRK12524 RNA polymerase sigma 98.2 5.1E-06 1.1E-10 73.3 6.9 65 263-328 25-89 (196)
59 TIGR02952 Sig70_famx2 RNA poly 98.1 7.9E-06 1.7E-10 69.2 7.5 66 262-328 9-74 (170)
60 PRK12526 RNA polymerase sigma 98.1 1.1E-05 2.4E-10 72.2 8.6 64 264-328 38-101 (206)
61 PRK11924 RNA polymerase sigma 98.1 8.1E-06 1.8E-10 69.0 7.3 65 262-328 11-75 (179)
62 PRK12514 RNA polymerase sigma 98.1 9.3E-06 2E-10 70.1 7.6 64 263-327 18-81 (179)
63 TIGR02939 RpoE_Sigma70 RNA pol 98.1 1.2E-05 2.6E-10 69.4 8.2 63 263-327 19-81 (190)
64 PRK12534 RNA polymerase sigma 98.1 8.7E-06 1.9E-10 70.8 7.4 64 263-327 24-87 (187)
65 PRK12531 RNA polymerase sigma 98.0 1.6E-05 3.4E-10 70.1 7.7 64 263-327 26-89 (194)
66 TIGR02985 Sig70_bacteroi1 RNA 98.0 1.1E-05 2.4E-10 66.8 5.7 62 265-328 2-63 (161)
67 TIGR02984 Sig-70_plancto1 RNA 98.0 2.1E-05 4.6E-10 67.7 7.6 67 262-328 5-75 (189)
68 TIGR02954 Sig70_famx3 RNA poly 98.0 3E-05 6.6E-10 66.3 7.7 64 263-328 15-78 (169)
69 PRK12536 RNA polymerase sigma 97.9 5.3E-05 1.1E-09 66.0 9.0 65 262-328 19-84 (181)
70 TIGR02989 Sig-70_gvs1 RNA poly 97.9 2.2E-05 4.7E-10 66.0 6.3 62 265-328 2-63 (159)
71 PRK12538 RNA polymerase sigma 97.9 3.3E-05 7.1E-10 71.3 7.4 63 264-327 63-125 (233)
72 PF00140 Sigma70_r1_2: Sigma-7 97.9 3.5E-06 7.5E-11 58.2 0.5 33 191-223 2-34 (37)
73 PRK12512 RNA polymerase sigma 97.8 9.6E-05 2.1E-09 64.1 8.8 64 262-327 20-87 (184)
74 PRK12515 RNA polymerase sigma 97.8 8.5E-05 1.8E-09 65.0 7.8 64 262-327 20-83 (189)
75 PRK12522 RNA polymerase sigma 97.8 6.1E-05 1.3E-09 64.9 6.2 63 264-328 3-65 (173)
76 PRK09643 RNA polymerase sigma 97.7 0.00016 3.5E-09 63.9 8.4 64 262-327 25-88 (192)
77 PRK12543 RNA polymerase sigma 97.7 9.8E-05 2.1E-09 64.2 6.1 63 262-326 5-67 (179)
78 PRK12539 RNA polymerase sigma 97.6 0.00033 7.1E-09 61.2 9.2 63 263-327 20-86 (184)
79 PRK12537 RNA polymerase sigma 97.6 0.00017 3.6E-09 62.9 7.1 73 254-327 12-85 (182)
80 PRK12518 RNA polymerase sigma 97.5 0.00024 5.3E-09 60.8 7.0 63 262-327 9-71 (175)
81 PRK09415 RNA polymerase factor 97.5 0.00023 4.9E-09 62.0 6.3 64 262-327 14-77 (179)
82 TIGR02999 Sig-70_X6 RNA polyme 97.4 0.00043 9.4E-09 59.7 6.6 64 263-328 16-85 (183)
83 PRK12542 RNA polymerase sigma 97.4 0.00023 5E-09 62.0 4.6 66 262-327 7-72 (185)
84 PRK09649 RNA polymerase sigma 97.4 0.00067 1.5E-08 59.6 7.5 61 264-327 24-84 (185)
85 PRK09639 RNA polymerase sigma 97.3 0.00045 9.8E-09 58.5 5.4 61 264-328 3-63 (166)
86 TIGR02983 SigE-fam_strep RNA p 97.2 0.00087 1.9E-08 56.7 6.3 65 262-328 4-68 (162)
87 COG1595 RpoE DNA-directed RNA 97.2 0.0016 3.5E-08 56.9 8.0 70 256-327 7-76 (182)
88 PRK12547 RNA polymerase sigma 97.1 0.0012 2.6E-08 56.6 6.3 65 262-328 4-68 (164)
89 PRK08241 RNA polymerase factor 97.0 0.0024 5.2E-08 61.0 7.8 63 263-327 18-80 (339)
90 PRK09644 RNA polymerase sigma 97.0 0.0016 3.4E-08 55.7 5.8 59 266-327 3-61 (165)
91 PRK12541 RNA polymerase sigma 97.0 0.002 4.4E-08 54.7 6.2 62 263-327 4-65 (161)
92 PRK09645 RNA polymerase sigma 96.9 0.0028 6.1E-08 54.3 6.3 64 263-327 8-71 (173)
93 PRK09647 RNA polymerase sigma 96.8 0.0034 7.3E-08 56.6 6.6 63 263-328 27-89 (203)
94 PRK12528 RNA polymerase sigma 96.8 0.0036 7.8E-08 53.1 6.3 62 264-328 4-65 (161)
95 TIGR03001 Sig-70_gmx1 RNA poly 96.7 0.0051 1.1E-07 57.5 7.7 63 263-327 38-107 (244)
96 TIGR02950 SigM_subfam RNA poly 96.7 0.0018 3.9E-08 54.1 3.9 55 271-328 2-56 (154)
97 TIGR02947 SigH_actino RNA poly 96.7 0.0035 7.6E-08 55.0 5.8 63 263-327 10-72 (193)
98 PRK12520 RNA polymerase sigma 96.5 0.0044 9.6E-08 54.3 5.5 61 265-327 3-63 (191)
99 PF04539 Sigma70_r3: Sigma-70 96.5 0.0044 9.5E-08 47.4 4.7 38 224-261 6-43 (78)
100 PRK12535 RNA polymerase sigma 96.5 0.011 2.5E-07 52.8 8.0 63 263-328 24-86 (196)
101 PRK09637 RNA polymerase sigma 96.5 0.0073 1.6E-07 53.1 6.6 61 266-328 3-63 (181)
102 TIGR02943 Sig70_famx1 RNA poly 96.5 0.0048 1E-07 54.5 5.2 59 267-327 5-63 (188)
103 PRK12533 RNA polymerase sigma 96.4 0.011 2.4E-07 54.2 7.6 63 262-327 16-78 (216)
104 PRK12532 RNA polymerase sigma 96.4 0.0056 1.2E-07 53.8 5.4 59 267-327 8-67 (195)
105 PRK12517 RNA polymerase sigma 96.3 0.0097 2.1E-07 52.7 6.4 66 261-328 20-85 (188)
106 PRK12516 RNA polymerase sigma 96.3 0.011 2.4E-07 52.4 6.6 63 263-327 9-71 (187)
107 TIGR02960 SigX5 RNA polymerase 96.2 0.011 2.5E-07 55.7 6.7 63 263-327 4-66 (324)
108 TIGR02959 SigZ RNA polymerase 96.1 0.0089 1.9E-07 51.8 4.9 56 271-328 2-57 (170)
109 PF12645 HTH_16: Helix-turn-he 96.1 0.026 5.7E-07 43.5 6.9 48 263-310 12-65 (65)
110 PRK09642 RNA polymerase sigma 96.0 0.0063 1.4E-07 51.5 3.2 54 271-327 2-55 (160)
111 PRK12540 RNA polymerase sigma 95.9 0.022 4.7E-07 50.3 6.4 62 264-327 5-66 (182)
112 PRK05658 RNA polymerase sigma 95.9 0.013 2.9E-07 61.5 5.8 33 191-223 104-136 (619)
113 PRK12529 RNA polymerase sigma 95.7 0.022 4.9E-07 49.6 5.6 66 262-327 11-78 (178)
114 PRK12546 RNA polymerase sigma 95.6 0.034 7.4E-07 49.5 6.7 61 264-327 8-68 (188)
115 PRK12523 RNA polymerase sigma 95.6 0.023 4.9E-07 49.0 5.2 63 263-328 9-71 (172)
116 PRK12544 RNA polymerase sigma 95.5 0.029 6.4E-07 50.7 5.8 59 267-327 21-79 (206)
117 PRK09651 RNA polymerase sigma 95.4 0.046 9.9E-07 47.3 6.3 62 263-327 9-70 (172)
118 PRK07037 extracytoplasmic-func 95.3 0.027 5.9E-07 47.6 4.8 57 268-327 2-58 (163)
119 PRK12545 RNA polymerase sigma 95.0 0.046 1E-06 48.8 5.5 58 268-327 12-69 (201)
120 PRK09191 two-component respons 94.9 0.074 1.6E-06 47.6 6.6 61 265-327 2-62 (261)
121 PRK12530 RNA polymerase sigma 94.3 0.076 1.6E-06 46.9 5.1 58 268-327 11-68 (189)
122 PRK12511 RNA polymerase sigma 94.3 0.077 1.7E-06 46.9 5.0 61 265-327 5-65 (182)
123 PRK12525 RNA polymerase sigma 93.5 0.21 4.5E-06 43.0 6.2 61 264-327 9-69 (168)
124 COG0568 RpoD DNA-directed RNA 93.2 0.33 7.1E-06 48.6 7.9 32 191-222 67-98 (342)
125 PRK09636 RNA polymerase sigma 93.1 0.14 3E-06 48.5 4.8 59 265-327 5-63 (293)
126 PRK12527 RNA polymerase sigma 93.1 0.13 2.8E-06 43.6 4.1 54 271-327 2-55 (159)
127 COG1191 FliA DNA-directed RNA 92.2 0.6 1.3E-05 44.7 7.8 66 189-262 85-150 (247)
128 PRK06704 RNA polymerase factor 90.2 0.62 1.3E-05 43.6 5.7 67 255-327 9-75 (228)
129 PRK09635 sigI RNA polymerase s 88.4 0.68 1.5E-05 44.5 4.7 59 264-326 5-63 (290)
130 PF07638 Sigma70_ECF: ECF sigm 88.3 2 4.4E-05 38.1 7.3 63 264-327 17-85 (185)
131 PHA02547 55 RNA polymerase sig 88.1 0.97 2.1E-05 41.7 5.2 60 269-328 42-104 (179)
132 PRK07122 RNA polymerase sigma 87.4 3.1 6.8E-05 39.3 8.4 66 188-260 100-165 (264)
133 PRK05911 RNA polymerase sigma 87.3 1.8 3.9E-05 40.6 6.7 64 188-261 86-149 (257)
134 TIGR02850 spore_sigG RNA polym 86.4 3.5 7.5E-05 38.4 8.0 65 189-261 95-159 (254)
135 PRK12427 flagellar biosynthesi 86.1 2.3 4.9E-05 39.4 6.6 62 189-260 78-139 (231)
136 PRK07408 RNA polymerase sigma 85.8 3.1 6.7E-05 39.0 7.4 65 188-259 86-150 (256)
137 TIGR03209 P21_Cbot clostridium 84.2 2.5 5.3E-05 35.2 5.4 56 267-327 2-60 (142)
138 PRK07921 RNA polymerase sigma 83.9 4.4 9.6E-05 39.9 7.8 35 226-260 177-211 (324)
139 PRK07500 rpoH2 RNA polymerase 82.5 4.8 0.0001 38.6 7.3 69 187-258 99-168 (289)
140 PRK09210 RNA polymerase sigma 82.4 5.3 0.00012 39.7 7.8 37 225-261 219-255 (367)
141 TIGR02393 RpoD_Cterm RNA polym 81.4 2.4 5.3E-05 38.9 4.7 35 226-260 91-125 (238)
142 TIGR02957 SigX4 RNA polymerase 80.3 1.5 3.2E-05 41.5 3.0 41 268-310 1-41 (281)
143 PRK05901 RNA polymerase sigma 79.7 6.6 0.00014 41.4 7.7 36 225-260 361-396 (509)
144 PRK07406 RNA polymerase sigma 77.8 8.9 0.00019 38.7 7.7 35 226-260 227-261 (373)
145 TIGR02885 spore_sigF RNA polym 71.0 6.9 0.00015 35.5 4.6 62 191-260 74-135 (231)
146 COG3413 Predicted DNA binding 71.0 17 0.00038 33.1 7.2 59 204-275 154-212 (215)
147 PRK14082 hypothetical protein; 69.5 18 0.00039 28.6 5.9 56 264-321 9-64 (65)
148 TIGR02479 FliA_WhiG RNA polyme 69.4 7.9 0.00017 35.0 4.6 35 226-260 87-121 (224)
149 PRK05949 RNA polymerase sigma 68.7 7.6 0.00017 38.2 4.7 37 224-260 180-216 (327)
150 PF04967 HTH_10: HTH DNA bindi 68.1 24 0.00053 26.4 6.2 48 206-263 1-48 (53)
151 PRK07598 RNA polymerase sigma 67.8 8 0.00017 39.8 4.8 39 223-261 263-301 (415)
152 PRK06288 RNA polymerase sigma 66.5 9.4 0.0002 35.8 4.6 36 225-260 121-156 (268)
153 PRK07670 RNA polymerase sigma 64.9 11 0.00025 34.8 4.8 35 226-260 113-147 (251)
154 PRK08215 sporulation sigma fac 62.4 13 0.00028 34.6 4.7 34 227-260 128-161 (258)
155 PRK07405 RNA polymerase sigma 62.0 12 0.00027 36.4 4.7 37 224-260 170-206 (317)
156 PRK06596 RNA polymerase factor 62.0 37 0.00081 32.5 7.8 65 188-260 108-173 (284)
157 TIGR02980 SigBFG RNA polymeras 58.8 17 0.00036 32.8 4.7 34 227-260 95-128 (227)
158 TIGR02997 Sig70-cyanoRpoD RNA 55.9 19 0.0004 34.6 4.7 36 225-260 164-199 (298)
159 KOG0037 Ca2+-binding protein, 51.2 2.2E+02 0.0047 27.5 10.8 110 182-314 89-204 (221)
160 PRK06986 fliA flagellar biosyn 50.7 26 0.00057 32.0 4.6 34 227-260 100-133 (236)
161 smart00342 HTH_ARAC helix_turn 50.6 49 0.0011 23.9 5.2 60 238-300 1-62 (84)
162 TIGR02941 Sigma_B RNA polymera 49.2 30 0.00066 32.0 4.8 34 227-260 121-154 (255)
163 PF02796 HTH_7: Helix-turn-hel 45.1 39 0.00085 23.7 3.8 43 202-261 2-44 (45)
164 PRK13239 alkylmercury lyase; P 41.7 41 0.00088 31.8 4.4 27 235-261 33-59 (206)
165 PRK05572 sporulation sigma fac 40.9 46 0.00099 30.9 4.6 62 189-258 93-154 (252)
166 PF13936 HTH_38: Helix-turn-he 38.6 49 0.0011 23.2 3.5 41 203-260 2-42 (44)
167 PF13309 HTH_22: HTH domain 38.4 1.4E+02 0.0029 22.8 6.1 60 188-259 2-63 (64)
168 TIGR03826 YvyF flagellar opero 37.9 67 0.0015 28.5 5.0 47 210-265 27-73 (137)
169 PRK04217 hypothetical protein; 36.1 1.7E+02 0.0036 25.0 6.9 48 203-268 40-88 (110)
170 KOG1161 Protein involved in va 34.9 3.3E+02 0.0072 27.4 9.7 32 296-327 117-148 (310)
171 KOG0030 Myosin essential light 34.8 2E+02 0.0043 26.3 7.4 73 232-323 37-110 (152)
172 COG0122 AlkA 3-methyladenine D 34.6 1.7E+02 0.0037 28.6 7.6 119 191-310 77-240 (285)
173 PRK05657 RNA polymerase sigma 33.9 61 0.0013 31.8 4.5 34 227-260 178-211 (325)
174 PF02885 Glycos_trans_3N: Glyc 33.6 1.5E+02 0.0034 22.2 5.7 31 193-223 2-32 (66)
175 PF01726 LexA_DNA_bind: LexA D 33.3 96 0.0021 23.8 4.6 26 232-257 19-45 (65)
176 PRK10219 DNA-binding transcrip 32.9 94 0.002 24.8 4.7 35 227-261 10-44 (107)
177 COG1916 Uncharacterized homolo 32.7 1.4E+02 0.0031 30.8 6.9 102 211-312 61-181 (388)
178 PRK08583 RNA polymerase sigma 32.6 2.6E+02 0.0057 25.8 8.3 32 228-259 122-153 (257)
179 PF09824 ArsR: ArsR transcript 32.5 17 0.00036 33.3 0.3 20 107-126 44-64 (160)
180 PF04218 CENP-B_N: CENP-B N-te 31.3 63 0.0014 23.7 3.2 41 204-261 5-45 (53)
181 PF12324 HTH_15: Helix-turn-he 31.1 64 0.0014 26.2 3.4 26 236-261 36-61 (77)
182 PRK13558 bacterio-opsin activa 28.8 1.8E+02 0.004 30.3 7.2 56 205-273 607-662 (665)
183 PRK11511 DNA-binding transcrip 28.8 1.1E+02 0.0024 25.6 4.7 35 227-261 14-48 (127)
184 COG1476 Predicted transcriptio 28.5 1.1E+02 0.0024 24.3 4.2 49 240-298 16-64 (68)
185 TIGR03764 ICE_PFGI_1_parB inte 27.6 4.2E+02 0.0092 26.0 8.9 99 202-317 109-229 (258)
186 TIGR03761 ICE_PFL4669 integrat 27.2 1.4E+02 0.003 28.4 5.5 51 251-310 143-193 (216)
187 PRK05449 aspartate alpha-decar 27.0 4.9 0.00011 35.3 -3.9 36 291-326 29-64 (126)
188 PF13730 HTH_36: Helix-turn-he 26.9 2.3E+02 0.0049 19.9 5.6 26 235-260 22-47 (55)
189 cd06919 Asp_decarbox Aspartate 26.9 4.9 0.00011 34.7 -3.8 35 291-325 28-62 (111)
190 PRK15369 two component system 26.1 3.6E+02 0.0079 22.0 7.5 56 206-282 150-205 (211)
191 PF13022 HTH_Tnp_1_2: Helix-tu 25.8 2.5E+02 0.0054 25.4 6.5 28 236-263 32-59 (142)
192 TIGR01446 DnaD_dom DnaD and ph 23.6 2.7E+02 0.0058 20.8 5.6 59 232-294 6-71 (73)
193 PRK13159 cytochrome c-type bio 23.3 82 0.0018 28.6 3.0 33 49-89 118-151 (155)
194 COG0853 PanD Aspartate 1-decar 23.3 7.8 0.00017 34.1 -3.3 33 291-323 28-60 (126)
195 PF08281 Sigma70_r4_2: Sigma-7 23.3 2.7E+02 0.0058 19.4 5.5 24 240-263 28-51 (54)
196 COG4367 Uncharacterized protei 23.2 3.8E+02 0.0081 22.8 6.6 27 236-262 21-47 (97)
197 TIGR02325 C_P_lyase_phnF phosp 23.2 1.4E+02 0.0031 26.8 4.6 40 212-261 15-55 (238)
198 PF02261 Asp_decarbox: Asparta 23.2 5.2 0.00011 34.7 -4.4 33 291-323 29-61 (116)
199 PF13404 HTH_AsnC-type: AsnC-t 23.2 2.1E+02 0.0045 20.1 4.5 23 238-260 17-39 (42)
200 PRK09652 RNA polymerase sigma 22.9 4.1E+02 0.0088 22.2 7.1 29 240-268 146-174 (182)
201 cd04762 HTH_MerR-trunc Helix-T 22.4 1E+02 0.0022 20.2 2.7 23 240-262 2-24 (49)
202 PF00427 PBS_linker_poly: Phyc 22.1 5.5E+02 0.012 22.7 9.6 96 184-306 5-111 (131)
203 PF04545 Sigma70_r4: Sigma-70, 22.0 2.8E+02 0.0061 19.2 5.9 26 237-262 19-44 (50)
204 PRK11924 RNA polymerase sigma 21.9 4E+02 0.0087 22.1 6.8 34 239-272 142-175 (179)
205 TIGR03001 Sig-70_gmx1 RNA poly 21.8 5E+02 0.011 24.3 8.1 57 238-305 177-233 (244)
206 PRK13150 cytochrome c-type bio 21.5 67 0.0014 29.3 2.1 24 49-80 125-148 (159)
207 PRK09639 RNA polymerase sigma 21.5 4.3E+02 0.0092 22.1 6.9 35 237-271 126-160 (166)
208 TIGR01764 excise DNA binding d 20.9 1.1E+02 0.0024 20.2 2.7 23 240-262 3-25 (49)
209 PF08101 DUF1708: Domain of un 20.7 9.8E+02 0.021 25.0 10.6 152 173-328 26-189 (420)
210 COG0140 HisI Phosphoribosyl-AT 20.5 5.2E+02 0.011 21.7 7.4 36 262-297 48-83 (92)
211 COG2188 PhnF Transcriptional r 20.4 1.8E+02 0.0039 27.0 4.8 41 211-261 13-54 (236)
212 PRK15044 transcriptional regul 20.3 2.1E+02 0.0046 28.5 5.5 60 193-261 172-231 (295)
213 TIGR00223 panD L-aspartate-alp 20.3 8.1 0.00018 34.0 -3.8 36 291-326 29-64 (126)
214 TIGR02404 trehalos_R_Bsub treh 20.2 1.7E+02 0.0038 26.5 4.6 24 238-261 24-47 (233)
215 PF10078 DUF2316: Uncharacteri 20.1 1.8E+02 0.0039 24.2 4.2 45 206-262 3-47 (89)
216 TIGR02392 rpoH_proteo alternat 20.1 5.4E+02 0.012 24.2 8.0 65 185-259 92-160 (270)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=6.9e-34 Score=282.09 Aligned_cols=140 Identities=39% Similarity=0.678 Sum_probs=130.5
Q ss_pred hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCcc--------------------chhHHHHHHHhhCCCCchHHHHHHhcC
Q 020126 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS--------------------LDDHKLRLKERLGCEPSMEQLAASLRI 250 (330)
Q Consensus 191 ~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~--------------------Le~~~~~l~~~lg~ePt~~e~A~a~~~ 250 (330)
|.++.||++|++.|+||++||++|+++|+.+.. |++.+.+|++.+|++||.++||.++|+
T Consensus 60 d~v~~yl~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~~~~~ 139 (415)
T PRK07598 60 DLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTADI 139 (415)
T ss_pred ChHHHHHHhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHHHhCC
Confidence 589999999999999999999999999999999 888999999999999999999966554
Q ss_pred ----------------------ChHHHHHHHhhhHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhh
Q 020126 251 ----------------------SRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEK 308 (330)
Q Consensus 251 ----------------------s~~eL~~~l~~g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIek 308 (330)
+.++|...+..|..|+++||..|+++|+++|++|.++|++++||||||+|||++|+++
T Consensus 140 ~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~ravek 219 (415)
T PRK07598 140 SLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEK 219 (415)
T ss_pred cHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHH
Confidence 5555556667888999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCcchhHHHHHhhcccC
Q 020126 309 FDSSKGFKISTYVYWWIRQSIS 330 (330)
Q Consensus 309 FDpsrG~rFsTYA~~wIR~aIS 330 (330)
|||++|++|+|||+||||++|+
T Consensus 220 FDp~rG~rFSTYa~wwIRqaI~ 241 (415)
T PRK07598 220 FDPTKGYRFSTYAYWWIRQGIT 241 (415)
T ss_pred cCcccCCCHHHHHHHHHHHHHH
Confidence 9999999999999999999984
No 2
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=100.00 E-value=6.1e-33 Score=261.28 Aligned_cols=138 Identities=41% Similarity=0.728 Sum_probs=134.8
Q ss_pred hHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHH
Q 020126 192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM 271 (330)
Q Consensus 192 ~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~ 271 (330)
.+..||++|.++|+||++||.+|+++++.|..+++.+..|++.+|++|+..+||+++|++..+|...+..|..|+++||.
T Consensus 2 ~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv~ 81 (298)
T TIGR02997 2 LVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMIK 81 (298)
T ss_pred cHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHHH
Confidence 46679999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 272 ~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
.|+++|+++|++|.++|.+.+||||||++||++|+++|||++|++|+|||+||||++|
T Consensus 82 ~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I 139 (298)
T TIGR02997 82 ANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGI 139 (298)
T ss_pred HhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999876
No 3
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=99.98 E-value=5.5e-32 Score=265.16 Aligned_cols=139 Identities=40% Similarity=0.677 Sum_probs=136.5
Q ss_pred hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHH
Q 020126 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (330)
Q Consensus 191 ~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI 270 (330)
+.+..||++|+++|+||++||++|++++++|..+++.+..+.+.+|++|+.++||.++|++..+|+..+..|..|+++||
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 57888999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 271 ~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
..|+|+|+++|++|.++|++++||+|||+|||++|+++|||++|++|+|||+||||++|
T Consensus 143 ~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI 201 (373)
T PRK07406 143 QSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 201 (373)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999998
No 4
>PRK05949 RNA polymerase sigma factor; Validated
Probab=99.97 E-value=7.3e-31 Score=252.34 Aligned_cols=140 Identities=38% Similarity=0.714 Sum_probs=136.6
Q ss_pred hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHH
Q 020126 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (330)
Q Consensus 191 ~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI 270 (330)
+.+..||++|+++|+||++||++|+++++.|..+++.+..|+..+|++|+..+||.+++++..+|...+..|..|++.||
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 57888999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcccC
Q 020126 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS 330 (330)
Q Consensus 271 ~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aIS 330 (330)
..|+++|+++|++|.+.+.+.+||+|||+|||++|+++|||++|++|+|||+||||++|.
T Consensus 98 ~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~ 157 (327)
T PRK05949 98 EANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAIT 157 (327)
T ss_pred HHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999883
No 5
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=99.97 E-value=4.2e-30 Score=245.53 Aligned_cols=139 Identities=40% Similarity=0.716 Sum_probs=136.0
Q ss_pred hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHH
Q 020126 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (330)
Q Consensus 191 ~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI 270 (330)
+.+..||++|+++|+||++||++|++++++|..++..+..|++.+|++|+..+||.+++++..+|...+..|..|+++|+
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 57788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 271 ~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
..|+++|.++|++|.+.+.+.+||+|||++||++|+++|||++|++|+|||+||||++|
T Consensus 88 ~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I 146 (317)
T PRK07405 88 EANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAI 146 (317)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999987
No 6
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=99.96 E-value=7.6e-30 Score=258.69 Aligned_cols=127 Identities=41% Similarity=0.678 Sum_probs=112.8
Q ss_pred hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHH
Q 020126 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (330)
Q Consensus 191 ~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI 270 (330)
+.++.||++|+++|+||++||++|+++++.|+.+++.. . ...+|+. ....+|+.+++.|..|+++||
T Consensus 211 d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~~---~-------~~~~~~~---~~~~~l~~~~~~g~~Ar~~LI 277 (509)
T PRK05901 211 DPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEELL---A-------EGEKLDP---ELRRDLQWIGRDGKRAKNHLL 277 (509)
T ss_pred cHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhhh---h-------hcccchh---hhhhhhhhhccchHHHHHHHH
Confidence 68899999999999999999999999999998754422 1 1123332 246788999999999999999
Q ss_pred HHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcccC
Q 020126 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS 330 (330)
Q Consensus 271 ~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aIS 330 (330)
..|+|||++||++|.++|++++||||||+||||+||++|||++|++|+|||+||||++|.
T Consensus 278 ~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~ 337 (509)
T PRK05901 278 EANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAIT 337 (509)
T ss_pred HHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999983
No 7
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=99.95 E-value=7.4e-28 Score=234.17 Aligned_cols=140 Identities=39% Similarity=0.618 Sum_probs=122.1
Q ss_pred hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHH-hhCCCCchH---------------HHHHHhcCCh-H
Q 020126 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKE-RLGCEPSME---------------QLAASLRISR-P 253 (330)
Q Consensus 191 ~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~-~lg~ePt~~---------------e~A~a~~~s~-~ 253 (330)
+.+..|+.+++..++++.++|..+.+.++....+......+.. .++..|+.. +|+..+..+. .
T Consensus 9 d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Ee~ 88 (342)
T COG0568 9 DAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEEEK 88 (342)
T ss_pred hHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHHHH
Confidence 4888999999999999999999999999988777667777777 677888875 4444444433 5
Q ss_pred HHHHHHhhhH---HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcccC
Q 020126 254 ELQSILMECS---LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS 330 (330)
Q Consensus 254 eL~~~l~~g~---~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aIS 330 (330)
+|...+..|. .|+.+||.+|++||++||++|.++|+.+.||||||+||||+||++|||++|++|+|||+||||++|+
T Consensus 89 ~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrqaI~ 168 (342)
T COG0568 89 ALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAIT 168 (342)
T ss_pred HHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHHHHH
Confidence 6777777775 4999999999999999999999999999999999999999999999999999999999999999985
No 8
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=99.94 E-value=3.8e-27 Score=226.76 Aligned_cols=126 Identities=40% Similarity=0.722 Sum_probs=110.7
Q ss_pred hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHH
Q 020126 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (330)
Q Consensus 191 ~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI 270 (330)
+.+..||++|+++|+||++||.+|+++++.|..++.. +|..++++.. ...++...++.|..|+++||
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 5788899999999999999999999999998765443 1111111111 45688999999999999999
Q ss_pred HHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 271 ~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
..|+|+|+++|++|.+.|++.+||+|||+|||++|+++|||++|++|+|||+||||++|
T Consensus 93 ~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI 151 (324)
T PRK07921 93 EANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAI 151 (324)
T ss_pred HHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999997
No 9
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=99.90 E-value=3.8e-24 Score=220.31 Aligned_cols=102 Identities=38% Similarity=0.738 Sum_probs=94.3
Q ss_pred hHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHH
Q 020126 192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM 271 (330)
Q Consensus 192 ~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~ 271 (330)
.++.||+++...+.|+++++.+++++++.|+. ....|+++||.
T Consensus 345 ~lq~~L~~ie~~~~Ls~eElk~l~~~i~~g~~-------------------------------------~~~~a~~~Li~ 387 (619)
T PRK05658 345 KLQQELEAIEEETGLTIEELKEINRQISKGEA-------------------------------------KARRAKKEMVE 387 (619)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHHhccch-------------------------------------hhhHHHHHHHH
Confidence 56788999999999999999999999998864 12378999999
Q ss_pred HhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcccC
Q 020126 272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS 330 (330)
Q Consensus 272 ~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aIS 330 (330)
.|+|||++||++|.++|++++||||||+||||+||++|||++|++|+|||+||||++|+
T Consensus 388 ~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~ 446 (619)
T PRK05658 388 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 446 (619)
T ss_pred HHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999984
No 10
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=99.90 E-value=1.5e-23 Score=204.10 Aligned_cols=100 Identities=45% Similarity=0.761 Sum_probs=96.6
Q ss_pred hhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHH
Q 020126 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL 269 (330)
Q Consensus 190 q~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekL 269 (330)
.+.++.||++|++.|+||++||.+|+++++.|+. .|+++|
T Consensus 95 ~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~Gd~----------------------------------------~A~~~L 134 (367)
T PRK09210 95 NDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGDE----------------------------------------EAKQRL 134 (367)
T ss_pred CcHHHHHHHHhhccCCCCHHHHHHHHHHHHhhHH----------------------------------------HHHHHH
Confidence 4789999999999999999999999999999865 799999
Q ss_pred HHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 270 I~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
|..|+|+|+++|++|.++|.+++||+|||+|||++|+++|||++|++|+|||+||||++|
T Consensus 135 i~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI 194 (367)
T PRK09210 135 AEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAI 194 (367)
T ss_pred HHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999987
No 11
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=99.89 E-value=2.9e-23 Score=193.01 Aligned_cols=98 Identities=35% Similarity=0.639 Sum_probs=92.8
Q ss_pred hHHHHHHhcCCCCCCCHHHHHHHHHH-HHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHH
Q 020126 192 RLKGYVKGVVSEELLTHAEVVRLSKK-IKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (330)
Q Consensus 192 ~l~~YL~~i~~~~lLT~eEE~eL~rk-Ik~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI 270 (330)
.+..||++|+++|+|++++|.+|+++ .+.|+. .|++.||
T Consensus 2 ~~~~yl~~~~~~~~l~~~~e~~l~~~~~~~gd~----------------------------------------~a~~~Lv 41 (270)
T TIGR02392 2 SLDAYIRAVNRIPMLTPEEEYQLAKRLREHGDL----------------------------------------DAAKKLV 41 (270)
T ss_pred hHHHHHHHHhcCCCCCHHHHHHHHHHHHHCCCH----------------------------------------HHHHHHH
Confidence 46789999999999999999999998 457765 7899999
Q ss_pred HHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 271 ~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
..|+|+|.++|++|.+.+.+.+||+|+|+|||++|+++|||++|++|+|||.||||++|
T Consensus 42 ~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i 100 (270)
T TIGR02392 42 LSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEI 100 (270)
T ss_pred HHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999987
No 12
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=99.89 E-value=4.2e-23 Score=194.19 Aligned_cols=103 Identities=35% Similarity=0.651 Sum_probs=97.5
Q ss_pred CChhhhhhhHHHHHHhcCCCCCCCHHHHHHHHHHH-HcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhh
Q 020126 184 ISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKI-KTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMEC 262 (330)
Q Consensus 184 ~~pEl~q~~l~~YL~~i~~~~lLT~eEE~eL~rkI-k~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g 262 (330)
++|+ +.+..|++++.+.|+|+.++|.+|+.++ +.|+.
T Consensus 10 ~~~~---~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~~Gd~--------------------------------------- 47 (284)
T PRK06596 10 LSPE---GNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDL--------------------------------------- 47 (284)
T ss_pred CCCc---cHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCCH---------------------------------------
Confidence 6787 7889999999999999999999999985 57765
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
.++++||..|+|+|.++|++|.+.+++.+||+|+|++||++|+++|||++|++|+|||+||||++|
T Consensus 48 -~a~~~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i 113 (284)
T PRK06596 48 -EAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEI 113 (284)
T ss_pred -HHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHH
Confidence 789999999999999999999999999999999999999999999999999999999999999987
No 13
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=99.85 E-value=3.3e-21 Score=181.97 Aligned_cols=99 Identities=29% Similarity=0.572 Sum_probs=93.2
Q ss_pred hhHHHHHHhcCCCCCCCHHHHHHHHHHHH-cCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHH
Q 020126 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIK-TGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL 269 (330)
Q Consensus 191 ~~l~~YL~~i~~~~lLT~eEE~eL~rkIk-~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekL 269 (330)
+.+..||++|.++|+||+++|.+|+++++ .|+. .|+++|
T Consensus 6 ~~~~~y~~~~~~~~~l~~~~e~~L~~~~~~~gd~----------------------------------------~A~~~L 45 (289)
T PRK07500 6 SADRSMIRSAMKAPYLEREEEHALAYRWKDHRDE----------------------------------------DALHRI 45 (289)
T ss_pred hHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCCCH----------------------------------------HHHHHH
Confidence 35567999999999999999999999975 6765 889999
Q ss_pred HHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 270 I~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
|..|+|+|.++|.+|.+.+.+.+||+|+|++||++|+++|||.+|.+|+|||+||||++|
T Consensus 46 v~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I 105 (289)
T PRK07500 46 ISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASI 105 (289)
T ss_pred HHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999987
No 14
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=99.84 E-value=2e-21 Score=181.22 Aligned_cols=66 Identities=27% Similarity=0.445 Sum_probs=64.8
Q ss_pred HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
.++++||..|+|||+++|++|.++|++++||||+|+||||+|+++|||++|++|+|||+||||++|
T Consensus 40 ~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I 105 (264)
T PRK07122 40 RQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEV 105 (264)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHH
Confidence 589999999999999999999999999999999999999999999999999999999999999987
No 15
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=99.80 E-value=1.9e-19 Score=173.15 Aligned_cols=101 Identities=41% Similarity=0.730 Sum_probs=96.5
Q ss_pred hhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHH
Q 020126 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREK 268 (330)
Q Consensus 189 ~q~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~Arek 268 (330)
+-+.++.||++|+..|+||+++|..|+++++.|+. .|++.
T Consensus 51 ~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~Gd~----------------------------------------~A~~~ 90 (325)
T PRK05657 51 VLDATQLYLNEIGYSPLLTAEEEVYFARRALRGDF----------------------------------------AARQR 90 (325)
T ss_pred cccHHHHHHHHHhcCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHH
Confidence 33688899999999999999999999999999986 89999
Q ss_pred HHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 269 LVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 269 LI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
||..|.|+|.++|.+|.+.+.+.+||+|+|+|||++++++||+++|++|+|||+||||++|
T Consensus 91 Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai 151 (325)
T PRK05657 91 MIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTI 151 (325)
T ss_pred HHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999876
No 16
>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=99.79 E-value=1.5e-19 Score=164.73 Aligned_cols=65 Identities=57% Similarity=1.003 Sum_probs=63.4
Q ss_pred HHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 265 ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
|+++||..|+|+|.++|++|.+.|++++||+|+|+|||++|+++|||++|++|+|||+||||++|
T Consensus 1 a~~~Li~~~~~lv~~ia~~~~~~~~~~eDLiQeG~igL~~A~~~fd~~~g~~FstYA~~~Ir~~I 65 (238)
T TIGR02393 1 AKKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAI 65 (238)
T ss_pred CHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCChHHHhHHHHHHHH
Confidence 57899999999999999999999999999999999999999999999999999999999999987
No 17
>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=99.76 E-value=2.7e-18 Score=160.69 Aligned_cols=102 Identities=38% Similarity=0.683 Sum_probs=97.3
Q ss_pred hhhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHH
Q 020126 188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLARE 267 (330)
Q Consensus 188 l~q~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~Are 267 (330)
...++++.||++|..+|.|+.++|.+|+++++.|+. .|++
T Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~gd~----------------------------------------~a~~ 49 (285)
T TIGR02394 10 RVADVTQLYLREIGFKPLLTAEEEIAYARRALAGDF----------------------------------------EARK 49 (285)
T ss_pred CcchHHHHHHHHHhccCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHH
Confidence 455799999999999999999999999999999976 8999
Q ss_pred HHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 268 kLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
.|+..|.++|..+|.+|.+.+.+.+||+|+|+|||++|+++||+.+|++|+|||.|||+.+|
T Consensus 50 ~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ai 111 (285)
T TIGR02394 50 VMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTI 111 (285)
T ss_pred HHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999775
No 18
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=99.76 E-value=1.5e-18 Score=162.95 Aligned_cols=85 Identities=40% Similarity=0.606 Sum_probs=77.3
Q ss_pred CCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHHHhHHHHHHHHHH
Q 020126 204 ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQR 283 (330)
Q Consensus 204 ~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~nLpLV~sIAkr 283 (330)
+.++.++...+....++|+. .++ .||+.|+|||.++|++
T Consensus 4 ~~~~~~e~~~~~~~~~~g~~----------------------------------------~~~-~Li~~ylpLV~~ia~k 42 (247)
T COG1191 4 QPLSKEEEEKLLEYYAEGDE----------------------------------------EAR-RLIERYLPLVKSIARK 42 (247)
T ss_pred cccchHHHHHHHHHHHhcCH----------------------------------------HHH-HHHHHHHHHHHHHHHH
Confidence 45667777777777777654 788 9999999999999999
Q ss_pred cccCCC-ChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 284 YDNMGA-DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 284 Y~~~Gv-d~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
|.+++. ++|||+|.|+|||++||++|||++|.+|+|||.++|+|+|
T Consensus 43 ~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei 89 (247)
T COG1191 43 FENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEI 89 (247)
T ss_pred HHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHH
Confidence 999988 9999999999999999999999999999999999999987
No 19
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=99.73 E-value=1.3e-17 Score=154.38 Aligned_cols=66 Identities=42% Similarity=0.619 Sum_probs=63.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHcccC-CCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 264 LAREKLVMSNVRLVMSIAQRYDNM-GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 264 ~ArekLI~~nLpLV~sIAkrY~~~-Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
.|+++||..|+|+|.++|++|.++ +.+.+||+|+|+|||++|+++|||++|++|+|||++|||++|
T Consensus 25 ~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i 91 (256)
T PRK07408 25 ALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEI 91 (256)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHH
Confidence 799999999999999999999875 677999999999999999999999999999999999999987
No 20
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=99.69 E-value=1e-16 Score=147.77 Aligned_cols=93 Identities=40% Similarity=0.595 Sum_probs=85.8
Q ss_pred HHhcC--CCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHHHhH
Q 020126 197 VKGVV--SEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNV 274 (330)
Q Consensus 197 L~~i~--~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~nL 274 (330)
+++++ ++|+|+++|+..|+.+++.|+. .++++|+..|.
T Consensus 8 ~~~~~~~~~~~l~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~~~ 47 (258)
T PRK08215 8 ICGVNTSKLPVLKNEEMRELFERMQNGDK----------------------------------------EAREKLINGNL 47 (258)
T ss_pred eecccCCCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHH
Confidence 34444 4579999999999999998875 78999999999
Q ss_pred HHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 275 RLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 275 pLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
|+|..+|++|.+.+.+.+||+|+|++||++|+++|||++|.+|.||+++||+++|
T Consensus 48 ~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i 102 (258)
T PRK08215 48 RLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEI 102 (258)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999986
No 21
>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=99.69 E-value=1.1e-16 Score=147.51 Aligned_cols=89 Identities=39% Similarity=0.570 Sum_probs=84.7
Q ss_pred CCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHHHhHHHHHHH
Q 020126 201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI 280 (330)
Q Consensus 201 ~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~nLpLV~sI 280 (330)
.++|+||++||.+|+.+++.|+. .++++|+..|.|+|.++
T Consensus 11 ~~~~~l~~~~~~~li~~~~~gd~----------------------------------------~a~~~L~~~~~~~v~~~ 50 (254)
T TIGR02850 11 SKLPVLKNQEMRELFIRMQSGDT----------------------------------------TAREKLINGNLRLVLSV 50 (254)
T ss_pred cCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHHHHHH
Confidence 46799999999999999998875 78999999999999999
Q ss_pred HHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 281 AQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 281 AkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
|.+|.+.+.+.+||+|+|++||++|+++|||.+|.+|+||+++||+++|
T Consensus 51 a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~ 99 (254)
T TIGR02850 51 IQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEI 99 (254)
T ss_pred HHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999876
No 22
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=99.68 E-value=5.7e-17 Score=150.45 Aligned_cols=68 Identities=28% Similarity=0.436 Sum_probs=63.3
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHccc---CCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 262 CSLAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 262 g~~ArekLI~~nLpLV~sIAkrY~~---~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
+..|+++||..|+|+|.++|++|.. .+++++||+|+|+|||++|+++|||++|++|+|||.||||++|
T Consensus 21 ~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i 91 (257)
T PRK05911 21 EIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAI 91 (257)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHH
Confidence 3479999999999999999999863 3578999999999999999999999999999999999999987
No 23
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=99.61 E-value=2.4e-15 Score=139.58 Aligned_cols=90 Identities=30% Similarity=0.393 Sum_probs=81.5
Q ss_pred cCCCCCCCHHHHHHHHHHHHc-CccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHHHhHHHHH
Q 020126 200 VVSEELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVM 278 (330)
Q Consensus 200 i~~~~lLT~eEE~eL~rkIk~-G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~nLpLV~ 278 (330)
-+.+|+||.++|.+|+++++. |+. .+.+.|+..|.|+|.
T Consensus 6 ~~~~~~~~~~~e~~l~~~~~~~~d~----------------------------------------~a~~~l~~~y~~lv~ 45 (268)
T PRK06288 6 SGKIPKYAQQDETELWREYKKTGDP----------------------------------------KIREYLILKYSPLVK 45 (268)
T ss_pred cCCCccccchHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHH
Confidence 467899999999999999774 443 788999999999999
Q ss_pred HHHHHccc---CCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 279 SIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 279 sIAkrY~~---~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
.+|++|.. .+.+.+||+|+|++||++|+++||+.+|.+|.||+.+|||+.|
T Consensus 46 ~~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i 99 (268)
T PRK06288 46 YVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAI 99 (268)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHH
Confidence 99999863 5678999999999999999999999999999999999999876
No 24
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=99.57 E-value=1.1e-14 Score=133.54 Aligned_cols=86 Identities=34% Similarity=0.406 Sum_probs=80.9
Q ss_pred CCCCHHHHHHHHHHHHc-CccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHHHhHHHHHHHHH
Q 020126 204 ELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ 282 (330)
Q Consensus 204 ~lLT~eEE~eL~rkIk~-G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~nLpLV~sIAk 282 (330)
|.||+++|.+|+.+++. |+. .|.++|+..|.|+|..+|.
T Consensus 8 ~~l~~~~~~~li~~~~~~gd~----------------------------------------~a~~~l~~~y~~~v~~~a~ 47 (255)
T TIGR02941 8 TNLTKEDVIQWIAEFQQNQNG----------------------------------------EAQEKLVDHYQNLVYSIAY 47 (255)
T ss_pred CCCCHHHHHHHHHHHHHCCCH----------------------------------------HHHHHHHHHhHHHHHHHHH
Confidence 67999999999999987 454 7899999999999999999
Q ss_pred HcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 283 RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 283 rY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
+|.+.+.+.+||+|+|++||++|+++||+++|.+|.||+.+||++.|
T Consensus 48 ~~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~ 94 (255)
T TIGR02941 48 KYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEI 94 (255)
T ss_pred HHhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999875
No 25
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=99.54 E-value=4.6e-14 Score=128.18 Aligned_cols=98 Identities=37% Similarity=0.550 Sum_probs=92.7
Q ss_pred hHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHH
Q 020126 192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM 271 (330)
Q Consensus 192 ~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~ 271 (330)
++..|+.++...|+||+++|..|+..++.|+. .+.+.|+.
T Consensus 17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~gd~----------------------------------------~a~~~l~~ 56 (233)
T PRK05803 17 FLVSYVKNNSFPQPLSEEEERKYLELMKEGDE----------------------------------------EARNILIE 56 (233)
T ss_pred HHHHHHHHhcccCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHH
Confidence 67899999999999999999999999998865 78999999
Q ss_pred HhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 272 ~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
.|.|+|..++.+|.+.+.+.+|++|+|+|+|++++++||+++|.+|.+|+.+|||+.+
T Consensus 57 ~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~ 114 (233)
T PRK05803 57 RNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEI 114 (233)
T ss_pred HhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999998754
No 26
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=99.52 E-value=2.5e-14 Score=128.58 Aligned_cols=67 Identities=49% Similarity=0.627 Sum_probs=64.6
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
..|+++|+..|.|+|.++|.+|.+.+.+.+||+|+|++||++|+++||+++|.+|+||+++||+++|
T Consensus 2 ~~a~~~lv~~y~~~v~~~a~~~~~~~~~~eDl~Qe~~i~l~~a~~~f~~~~~~~F~ty~~~~i~~~~ 68 (227)
T TIGR02980 2 KEAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEI 68 (227)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCcHHHHHHHHHHHH
Confidence 4789999999999999999999999999999999999999999999999999999999999999876
No 27
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=99.50 E-value=9.7e-14 Score=127.56 Aligned_cols=86 Identities=33% Similarity=0.374 Sum_probs=80.8
Q ss_pred CCCCHHHHHHHHHHHHc-CccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHHHhHHHHHHHHH
Q 020126 204 ELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ 282 (330)
Q Consensus 204 ~lLT~eEE~eL~rkIk~-G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~nLpLV~sIAk 282 (330)
|.|+++||.+|+.+++. |+. .|.+.|+..|.|+|..+|.
T Consensus 8 ~~l~~~e~~~li~~~~~~gd~----------------------------------------~a~~~l~~~~~~~v~~~a~ 47 (257)
T PRK08583 8 TKLTKEEVNKWIAEYQENQDE----------------------------------------EAQEKLVKHYKNLVESLAY 47 (257)
T ss_pred CcCChHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHHHH
Confidence 77999999999999885 665 7999999999999999999
Q ss_pred HcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 283 RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 283 rY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
+|.+.+.+.+||+|+|+++|++++++||+++|.+|.||+.+||++.|
T Consensus 48 ~~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~ 94 (257)
T PRK08583 48 KYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEI 94 (257)
T ss_pred HHhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999875
No 28
>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=99.49 E-value=4.8e-14 Score=130.03 Aligned_cols=70 Identities=21% Similarity=0.275 Sum_probs=64.1
Q ss_pred hhhHHHHHHHHHHhHHHHHHHHHHcccCC--CChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 260 MECSLAREKLVMSNVRLVMSIAQRYDNMG--ADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 260 ~~g~~ArekLI~~nLpLV~sIAkrY~~~G--vd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
..|...+++||..|.|+|.++|.+|.+++ .+.|||+|+|+|||++||++|||++|.+|.+||.+|||++|
T Consensus 5 ~~gd~~~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i 76 (218)
T TIGR02895 5 QPGNEEREELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRL 76 (218)
T ss_pred hcCChHHHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHH
Confidence 44545599999999999999999998775 58999999999999999999999999999999999999876
No 29
>PRK05572 sporulation sigma factor SigF; Validated
Probab=99.47 E-value=2.3e-13 Score=125.16 Aligned_cols=93 Identities=42% Similarity=0.487 Sum_probs=86.4
Q ss_pred HHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHHHhHHH
Q 020126 197 VKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRL 276 (330)
Q Consensus 197 L~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~nLpL 276 (330)
++.-...|.||++++.+|+.+++.|+. .+.++|+..|.|+
T Consensus 5 ~~~~~~~~~l~~~~~~~li~~~~~gd~----------------------------------------~a~~~L~~~y~~~ 44 (252)
T PRK05572 5 VKNKKKKPQLKDEENKELIKKSQDGDQ----------------------------------------EARDTLVEKNLRL 44 (252)
T ss_pred hccCcCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHH
Confidence 445567899999999999999888865 7899999999999
Q ss_pred HHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 277 VMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 277 V~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
|..+|.+|.+.+.+.+||+|+|+++|++++++||+.+|.+|.||+++||+++|
T Consensus 45 v~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i 97 (252)
T PRK05572 45 VWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEI 97 (252)
T ss_pred HHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999876
No 30
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=99.47 E-value=5.7e-14 Score=128.81 Aligned_cols=65 Identities=22% Similarity=0.345 Sum_probs=59.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHcccC---CCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 264 LAREKLVMSNVRLVMSIAQRYDNM---GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 264 ~ArekLI~~nLpLV~sIAkrY~~~---Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
..+..|+..|+|+|.++|++|..+ +++.+||+|+|+|||++|+++|||..| +|+|||.+|||++|
T Consensus 15 ~~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~i 82 (231)
T PRK12427 15 QEEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAI 82 (231)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHH
Confidence 567789999999999999999753 679999999999999999999998666 89999999999986
No 31
>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=99.46 E-value=1.3e-13 Score=124.39 Aligned_cols=68 Identities=46% Similarity=0.570 Sum_probs=65.2
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 262 g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
+..++++|+..|.|+|.++|.+|.+.+.+.+||+|+|++||++|+++|||.+|.+|.||+++||+++|
T Consensus 9 d~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i 76 (231)
T TIGR02885 9 DKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEI 76 (231)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHH
Confidence 45899999999999999999999999999999999999999999999999999999999999999976
No 32
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=99.40 E-value=1e-12 Score=120.77 Aligned_cols=66 Identities=33% Similarity=0.474 Sum_probs=62.5
Q ss_pred HHHHHHHHHhHHHHHHHHHHccc---CCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 264 LAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 264 ~ArekLI~~nLpLV~sIAkrY~~---~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
.|.+.|+..|.|+|..+|.+|.. .+.+.+||+|+|++||++++++|||++|.+|.||+++|||+.|
T Consensus 22 ~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~ 90 (251)
T PRK07670 22 DAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAI 90 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHH
Confidence 89999999999999999999965 5789999999999999999999999999999999999999875
No 33
>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=99.36 E-value=8e-13 Score=119.05 Aligned_cols=61 Identities=38% Similarity=0.622 Sum_probs=57.8
Q ss_pred HHHHhHHHHHHHHHHccc---CCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 269 LVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 269 LI~~nLpLV~sIAkrY~~---~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
|+..|.|+|..+|++|.+ .+.+.+||+|+|++||++|+++|||++|.+|+||+.+|||+.|
T Consensus 1 L~~~~~~lv~~~a~~~~~~~~~~~~~eDl~Qe~~~~l~~a~~~fd~~~~~~f~t~~~~~i~~~~ 64 (224)
T TIGR02479 1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAM 64 (224)
T ss_pred CHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHH
Confidence 578999999999999986 6899999999999999999999999999999999999999875
No 34
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=99.29 E-value=5.3e-12 Score=114.76 Aligned_cols=69 Identities=33% Similarity=0.542 Sum_probs=64.7
Q ss_pred hhHHHHHHHHHHhHHHHHHHHHHcc---cCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 261 ECSLAREKLVMSNVRLVMSIAQRYD---NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 261 ~g~~ArekLI~~nLpLV~sIAkrY~---~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
+|.-++++|+..|.|+|..+|.+|. +.+.+.+||+|+|++||++++++|||++|.+|.||+.+|||+.|
T Consensus 5 ~~~~~~~~L~~~~~~~v~~~a~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~ 76 (236)
T PRK06986 5 EGKMDQDELVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAM 76 (236)
T ss_pred cccccHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHH
Confidence 5678999999999999999999997 56889999999999999999999999999999999999999875
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=99.20 E-value=1.2e-10 Score=105.73 Aligned_cols=98 Identities=35% Similarity=0.556 Sum_probs=87.1
Q ss_pred hHHHHHHhcC-CCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHH
Q 020126 192 RLKGYVKGVV-SEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (330)
Q Consensus 192 ~l~~YL~~i~-~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI 270 (330)
++-+|+..-+ ..+.|++.+|.+|+.+++.|+. .+.+.|+
T Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~li~~~~~gd~----------------------------------------~af~~l~ 54 (227)
T TIGR02846 15 FLVGYVTNNGSFPQPLSEEEEKKYLDRLKEGDE----------------------------------------EARNVLI 54 (227)
T ss_pred HHHHHHHHHHhCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHH
Confidence 4456665444 4577999999999999999876 8899999
Q ss_pred HHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 271 ~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
..|.|+|.+++.+|.+...+.+|++|++.+++++++++|+++.+.+|.||+.+++|+.+
T Consensus 55 ~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~ 113 (227)
T TIGR02846 55 ERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEI 113 (227)
T ss_pred HHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHH
Confidence 99999999999999988899999999999999999999999999899999999988753
No 36
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=99.13 E-value=3.3e-10 Score=102.62 Aligned_cols=94 Identities=32% Similarity=0.543 Sum_probs=84.5
Q ss_pred HHHhcCCC-CCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHHHhH
Q 020126 196 YVKGVVSE-ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNV 274 (330)
Q Consensus 196 YL~~i~~~-~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~nL 274 (330)
|+++.... +.+++..+.+|+.+++.|+. .+.+.|+..|.
T Consensus 23 ~~~~~~~~~~~~~~~~~~~L~~~~~~gd~----------------------------------------~af~~l~~~y~ 62 (234)
T PRK08301 23 YIGGSEALPPPLSKEEEEYLLNKLPKGDE----------------------------------------AVRSLLIERNL 62 (234)
T ss_pred HhccccccCCcCCHHHHHHHHHHHHccCH----------------------------------------HHHHHHHHHhH
Confidence 77777554 55888899999999998875 78999999999
Q ss_pred HHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 275 RLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 275 pLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
++|..+|.+|.+.+.+.+|++|++++++++++.+|++.++++|.||+..++|+.+
T Consensus 63 ~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~ 117 (234)
T PRK08301 63 RLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEI 117 (234)
T ss_pred HHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHH
Confidence 9999999999998999999999999999999999999988899999999988754
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=99.01 E-value=7e-10 Score=81.38 Aligned_cols=61 Identities=30% Similarity=0.470 Sum_probs=57.8
Q ss_pred HHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 269 LVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 269 LI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
|++.|.|+|..++.+|.+.+.+.+|++|++.++|++++++||++++..|.+|+...+++.+
T Consensus 1 L~~~~~~~l~~~~~~~~~~~~~~eD~~qe~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~ 61 (71)
T PF04542_consen 1 LYERYYPLLYRYARRYTGDPEDAEDLVQEAFIKLWRAIDSYDPDRGDSFRAWLFRIARNRI 61 (71)
T ss_dssp HHHHTHHHHHHHHHTCTTCSSHHHHHHHHHHHHHHHHHHHTSTTSSSHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHhCCHhhHHHHhhHHHHHHHhhhhcccccccCCHHHHHHHHHHHHH
Confidence 6889999999999999999999999999999999999999999999899999999988754
No 38
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=99.00 E-value=2.5e-09 Score=97.51 Aligned_cols=94 Identities=35% Similarity=0.551 Sum_probs=82.9
Q ss_pred HHHhcC-CCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHHHhH
Q 020126 196 YVKGVV-SEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNV 274 (330)
Q Consensus 196 YL~~i~-~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~nL 274 (330)
|+.+-. ..+.|+++++.+|...++.|+. .+.+.|+..|.
T Consensus 23 ~~~~~~~~~~~~~~~~~~~l~~~~~~~d~----------------------------------------~a~~~l~~~y~ 62 (234)
T TIGR02835 23 YIGGSEALPPPLTGEEEEALLQKLTQGDE----------------------------------------SAKSTLIERNL 62 (234)
T ss_pred HhcccccCCCcCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhH
Confidence 444433 3578899999999998888765 88999999999
Q ss_pred HHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 275 RLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 275 pLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
+.|..++.+|.+.+.+-+|++|++++++++++++|++..+++|.+|+..++++.+
T Consensus 63 ~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~ 117 (234)
T TIGR02835 63 RLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEI 117 (234)
T ss_pred HHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999888899999999988643
No 39
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=98.93 E-value=3.6e-09 Score=98.72 Aligned_cols=67 Identities=18% Similarity=0.265 Sum_probs=62.0
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCC--ChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGA--DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gv--d~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
..|++.|+..|.|+|.++|.+|.++.. +.+|++|+|.+++++|+++||+++|.+|.+|+..+|++.+
T Consensus 17 ~~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn~~ 85 (237)
T PRK08311 17 EELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKRRL 85 (237)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence 478999999999999999999988765 5899999999999999999999999899999999998764
No 40
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=98.85 E-value=1.3e-08 Score=89.49 Aligned_cols=66 Identities=30% Similarity=0.420 Sum_probs=62.1
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
..+.+.|+..|.|+|..+|.+|.+...+.+|++|++++.|++++.+||+.++.+|.||++.+|++.
T Consensus 23 ~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n~ 88 (208)
T PRK08295 23 KEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQ 88 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHH
Confidence 488999999999999999999999999999999999999999999999998889999999888764
No 41
>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=98.76 E-value=3.9e-08 Score=85.59 Aligned_cols=65 Identities=28% Similarity=0.412 Sum_probs=60.7
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
..|.+.|+..|.|.|..+|.++.+...+.+|++|++.+.+++++.+|+++.+.+|.||++.+|++
T Consensus 18 ~~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~ 82 (198)
T TIGR02859 18 THALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTR 82 (198)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHH
Confidence 48999999999999999999999888999999999999999999999998888999999877765
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=98.76 E-value=1.4e-08 Score=81.45 Aligned_cols=63 Identities=30% Similarity=0.443 Sum_probs=59.1
Q ss_pred HHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329 (330)
Q Consensus 265 ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI 329 (330)
+.+.|+..|.|+|.++++++...+.+.+|++|+|+++|+++++.|++. .+|.+|+..+|++.+
T Consensus 2 a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~ 64 (158)
T TIGR02937 2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLI 64 (158)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHH
Confidence 678999999999999999999889999999999999999999999999 689999999998754
No 43
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=98.59 E-value=8.9e-08 Score=81.09 Aligned_cols=65 Identities=28% Similarity=0.284 Sum_probs=59.5
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 262 g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
+..|.++|+..|.|+|..++.+|.+.+.+.+|++|+++++|++++++|+ .+.+|.+|+...+++.
T Consensus 8 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~ 72 (182)
T PRK09652 8 DRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNT 72 (182)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHH
Confidence 4589999999999999999999998889999999999999999999999 4558999999988754
No 44
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=98.58 E-value=2.7e-07 Score=80.43 Aligned_cols=64 Identities=14% Similarity=0.181 Sum_probs=55.9
Q ss_pred HHHHHHHHHhHHHHHHHHHHcccC----CCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 264 LAREKLVMSNVRLVMSIAQRYDNM----GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 264 ~ArekLI~~nLpLV~sIAkrY~~~----Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
.+.++|+..|.|.|..+|.++.+. +.+.+|++||++++|++++.+|++. +.+|.+|++.-+++.
T Consensus 24 ~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~n~ 91 (189)
T PRK09648 24 RALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAAHK 91 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHHHH
Confidence 899999999999999999998653 4689999999999999999999864 458999998776653
No 45
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=98.52 E-value=3.6e-07 Score=83.14 Aligned_cols=86 Identities=20% Similarity=0.211 Sum_probs=76.4
Q ss_pred CCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHHHhHHHHHHH
Q 020126 201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI 280 (330)
Q Consensus 201 ~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~nLpLV~sI 280 (330)
...|+|++..+..|+..++.|+. .+.+.|+..|.++|..+
T Consensus 7 ~~~~~~~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~y~~~l~~~ 46 (231)
T PRK11922 7 SRPPPLSAASDRELVARVLAGDE----------------------------------------AAFEALMRRHNRRLYRT 46 (231)
T ss_pred CCCCCcCcccHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHH
Confidence 34688999999999999988875 88999999999999999
Q ss_pred HHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 281 AQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 281 AkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
+.++.+...+-+|++|+++++|++.+++|++. ..|.+|+...+++.
T Consensus 47 a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~ 92 (231)
T PRK11922 47 ARAILRNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNE 92 (231)
T ss_pred HHHHhCChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHH
Confidence 99999888899999999999999999999986 37999988776653
No 46
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=98.49 E-value=4.1e-07 Score=79.16 Aligned_cols=64 Identities=14% Similarity=0.196 Sum_probs=58.7
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
..+.+.|+..|.++|..+|.+|.+.+.+.+|++|+++++|++++.+|+++ +.+|.+|++..+++
T Consensus 19 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n 82 (186)
T PRK05602 19 PAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLN 82 (186)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHH
Confidence 48999999999999999999999988999999999999999999999986 45799999887665
No 47
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=98.49 E-value=4e-07 Score=80.22 Aligned_cols=64 Identities=14% Similarity=0.133 Sum_probs=58.0
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
..+.++|+..|.|+|..++.+|.+...+-+|++||+++.+++.+.+||+.+| .|.+|++..+++
T Consensus 29 ~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n 92 (194)
T PRK09646 29 QDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHR 92 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHH
Confidence 4899999999999999999999998899999999999999999999998766 689998776554
No 48
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=98.44 E-value=6e-07 Score=77.31 Aligned_cols=64 Identities=20% Similarity=0.223 Sum_probs=58.4
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
..+.++|+..|.|+|..+|.+|.+.+.+.+|++|++++.+++++..||+.. +|.+|+...+++.
T Consensus 17 ~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~ 80 (187)
T TIGR02948 17 ENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNL 80 (187)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHH
Confidence 488999999999999999999998888999999999999999999999875 6999998877653
No 49
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=98.43 E-value=7.3e-07 Score=76.75 Aligned_cols=64 Identities=20% Similarity=0.217 Sum_probs=58.2
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
..+.+.|+..|.|+|..+|.++.+...+.+|++|+++++|++++.+|++.. +|.+|+...+|+.
T Consensus 17 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~ 80 (187)
T PRK09641 17 QNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNL 80 (187)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHH
Confidence 488999999999999999999998889999999999999999999999863 7999998877653
No 50
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=98.37 E-value=1.2e-06 Score=76.80 Aligned_cols=64 Identities=17% Similarity=0.204 Sum_probs=58.5
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
..+.+.|+..|.+.|..+|.++.+...+.+|++|++++++++++.+|++.. .|.+|+...+++.
T Consensus 25 ~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~~--~f~~wl~~i~~n~ 88 (194)
T PRK12513 25 AAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRA--RFRTWLYQIARNL 88 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCCC--chHHHHHHHHHHH
Confidence 489999999999999999999998888999999999999999999999753 6999999888765
No 51
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=98.37 E-value=8.8e-07 Score=74.18 Aligned_cols=63 Identities=24% Similarity=0.371 Sum_probs=56.1
Q ss_pred HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
.+.++|+..|.|+|..+++++. ...+.||++||+.+++++++.+|+++.| .|.+|+...+++.
T Consensus 4 ~af~~l~~~y~~~l~~~~~~~~-~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~ 66 (154)
T PRK06759 4 ATFTEAVVLYEGLIVNQIKKLG-IYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGY 66 (154)
T ss_pred ccHHHHHHHHHHHHHHHHHHhC-CcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHH
Confidence 5788999999999999999874 4568999999999999999999998777 7999998887764
No 52
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=98.31 E-value=2.2e-06 Score=74.86 Aligned_cols=61 Identities=20% Similarity=0.303 Sum_probs=54.6
Q ss_pred HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhh
Q 020126 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIR 326 (330)
Q Consensus 264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR 326 (330)
.+.+.|+..|.|.|..++.++.+...+.+|++|++++.+++++.+|++.. .|.+|+..-.+
T Consensus 20 ~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~ 80 (193)
T PRK11923 20 RAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAI 80 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHH
Confidence 78999999999999999999998888999999999999999999999874 48888765443
No 53
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=98.31 E-value=2.4e-06 Score=74.78 Aligned_cols=77 Identities=22% Similarity=0.344 Sum_probs=66.0
Q ss_pred CChHHHHHHHhh----hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHh
Q 020126 250 ISRPELQSILME----CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWI 325 (330)
Q Consensus 250 ~s~~eL~~~l~~----g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wI 325 (330)
++.+++...+.. +..+.+.|+..|.|.|..++.+|.+...+.+|++|++++.|++.+.+|++. .+|.+|+...+
T Consensus 8 ~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~~--~~~~~wl~~ia 85 (188)
T PRK09640 8 LNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLYSIT 85 (188)
T ss_pred CCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcCC--CcchHHHHHHH
Confidence 345556555553 588999999999999999999999988999999999999999999999853 47999999988
Q ss_pred hcc
Q 020126 326 RQS 328 (330)
Q Consensus 326 R~a 328 (330)
++.
T Consensus 86 ~n~ 88 (188)
T PRK09640 86 YNE 88 (188)
T ss_pred HHH
Confidence 764
No 54
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=98.29 E-value=1.9e-06 Score=74.69 Aligned_cols=65 Identities=20% Similarity=0.289 Sum_probs=58.1
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
..+.+.|+..|.|.|..++.+|.+.+.+.+|++|++++.+++++.+|++..+ .|.+|+...+++.
T Consensus 22 ~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~~-~~~~wl~~ia~n~ 86 (186)
T PRK13919 22 EEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRG-SARAWLLALAHHA 86 (186)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCcccc-chHHHHHHHHHHH
Confidence 4899999999999999999999888889999999999999999999997653 6899998877653
No 55
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=98.27 E-value=2.3e-06 Score=74.79 Aligned_cols=64 Identities=25% Similarity=0.327 Sum_probs=56.6
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
..+.+.|+..|.+.|..++.++.+...+-+|++|++++.+++. ..|++..+ .|.||++..+++.
T Consensus 28 ~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~ 91 (194)
T PRK12519 28 SAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSR 91 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHH
Confidence 3889999999999999999999888888999999999999975 67887665 7999998887764
No 56
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=98.25 E-value=4.1e-06 Score=73.52 Aligned_cols=65 Identities=20% Similarity=0.225 Sum_probs=56.3
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCC---CChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMG---ADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~G---vd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
..+.+.|+..|.|+|..++.++.+.+ .+.+|++|+++++|++++++|+++.+ +|.+|+..-+++.
T Consensus 17 ~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~iarn~ 84 (189)
T PRK06811 17 EKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAISKYK 84 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHHHHH
Confidence 38999999999999999999997643 46899999999999999999997655 7999998766543
No 57
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=98.20 E-value=5.4e-06 Score=71.05 Aligned_cols=64 Identities=16% Similarity=0.151 Sum_probs=57.9
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
..+.+.|+..|.|.|..++.+|.+...+-+|++|++++.++++++.|++. .+|.+|+...+++.
T Consensus 17 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n~ 80 (176)
T PRK09638 17 DAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASRL 80 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHH
Confidence 48999999999999999999999888889999999999999999999874 47999998877653
No 58
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=98.16 E-value=5.1e-06 Score=73.34 Aligned_cols=65 Identities=18% Similarity=0.258 Sum_probs=57.7
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
..+.+.|+..|.|.|..+|.++.+...+-+|++||+.+.+++.+.+|++.. ..|.+|+..-+++.
T Consensus 25 ~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~n~ 89 (196)
T PRK12524 25 PAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVCNL 89 (196)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHHHHH
Confidence 489999999999999999999998889999999999999999999998533 47999998866653
No 59
>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=98.14 E-value=7.9e-06 Score=69.18 Aligned_cols=66 Identities=15% Similarity=0.114 Sum_probs=59.2
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 262 g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
+..+.+.|+..|.+.+...+.++.+...+.||++|++++.+++.+++|+...+ +|.+|+...+++.
T Consensus 9 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~ 74 (170)
T TIGR02952 9 EEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNV 74 (170)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHH
Confidence 45899999999999999999888777789999999999999999999997655 8999999888764
No 60
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=98.13 E-value=1.1e-05 Score=72.17 Aligned_cols=64 Identities=20% Similarity=0.229 Sum_probs=58.1
Q ss_pred HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
.+.++|+..|.|.|..++.++.+...+-+|++|++++.+++++.+|++.++ .|.+|+...+|+.
T Consensus 38 ~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~ 101 (206)
T PRK12526 38 QAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNA 101 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHH
Confidence 889999999999999999999887788999999999999999999998766 5999998877764
No 61
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=98.13 E-value=8.1e-06 Score=68.95 Aligned_cols=65 Identities=18% Similarity=0.088 Sum_probs=59.0
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 262 g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
+..+.+.|+..|.|.|..++.++.+...+.+|++|++.+.|++++..|+ .+.+|.+|+...+++.
T Consensus 11 ~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~ 75 (179)
T PRK11924 11 DKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNV 75 (179)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHH
Confidence 4689999999999999999999998889999999999999999999999 3458999999887764
No 62
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=98.12 E-value=9.3e-06 Score=70.10 Aligned_cols=64 Identities=14% Similarity=0.080 Sum_probs=56.6
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
..+...|+..|.+.+..+|.+|.+...+-+|++|++++.+++.+.+|++..+ .|.+|...-.++
T Consensus 18 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~~-~~~~wl~~ia~n 81 (179)
T PRK12514 18 RDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGL-SPMTWLITIARN 81 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCcccc-cHHHHHHHHHHH
Confidence 4899999999999999999999988889999999999999999999997643 588888765554
No 63
>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=98.11 E-value=1.2e-05 Score=69.44 Aligned_cols=63 Identities=19% Similarity=0.291 Sum_probs=56.5
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
..+.+.|+..|.|.|..+|.++.+...+.+|++|++.|.|++.+.+|++. .+|.+|+..-.++
T Consensus 19 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn 81 (190)
T TIGR02939 19 KQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVN 81 (190)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHH
Confidence 47899999999999999999998888899999999999999999999975 3699998776553
No 64
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=98.11 E-value=8.7e-06 Score=70.75 Aligned_cols=64 Identities=17% Similarity=0.169 Sum_probs=56.2
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
..+.+.|+..|.|+|..++.+|.+...+-||++||.++.+++.+.+|++.++ +|.+|.+.-+++
T Consensus 24 ~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n 87 (187)
T PRK12534 24 RHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARN 87 (187)
T ss_pred HHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHH
Confidence 3889999999999999999999888888999999999999999999998754 578888765443
No 65
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=98.04 E-value=1.6e-05 Score=70.14 Aligned_cols=64 Identities=19% Similarity=0.180 Sum_probs=57.4
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
..+.+.|+..|.|.|..+|.++.+...+-+|++|+.++.+++.+.+|++..+ .|.+|+..-+++
T Consensus 26 ~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn 89 (194)
T PRK12531 26 KQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRN 89 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHH
Confidence 4889999999999999999999887778999999999999999999997554 699999887665
No 66
>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=98.00 E-value=1.1e-05 Score=66.77 Aligned_cols=62 Identities=19% Similarity=0.295 Sum_probs=56.2
Q ss_pred HHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 265 ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
|.++|+..|.|.|..++.++.+...+.||++|++++.+++.+.+|++.. +|.+|+...+|+.
T Consensus 2 a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~~--~~~~wl~~i~r~~ 63 (161)
T TIGR02985 2 AFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEVE--SFKAYLFTIVKNR 63 (161)
T ss_pred hHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhccccc--cHHHHHHHHHHHH
Confidence 6789999999999999999988888899999999999999999998644 7999999988764
No 67
>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=98.00 E-value=2.1e-05 Score=67.65 Aligned_cols=67 Identities=16% Similarity=0.117 Sum_probs=57.9
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHccc----CCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 262 CSLAREKLVMSNVRLVMSIAQRYDN----MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 262 g~~ArekLI~~nLpLV~sIAkrY~~----~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
...+.+.|+..|.+.|..+|.+|.. ...+-||++|++++.+++++.+|++..+.+|.+|+...+++.
T Consensus 5 ~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~ 75 (189)
T TIGR02984 5 DQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNV 75 (189)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHH
Confidence 3589999999999999999998743 457899999999999999999999876678999988776654
No 68
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=97.95 E-value=3e-05 Score=66.32 Aligned_cols=64 Identities=19% Similarity=0.184 Sum_probs=57.8
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
..+.+.|+..|.|.+..++.++.+...+.+|++|+..+.+++...+|++.. +|.+|+..-+++.
T Consensus 15 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~~--~~~~wl~~i~~n~ 78 (169)
T TIGR02954 15 KPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPK--YFNTWLTRILINE 78 (169)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCcc--ccHHHHHHHHHHH
Confidence 489999999999999999999999889999999999999999999999753 6999998877653
No 69
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=97.93 E-value=5.3e-05 Score=65.96 Aligned_cols=65 Identities=14% Similarity=0.142 Sum_probs=56.0
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHccc-CCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 262 CSLAREKLVMSNVRLVMSIAQRYDN-MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 262 g~~ArekLI~~nLpLV~sIAkrY~~-~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
+..+.+.|+..|.+.|..++.++.. ...+.||++|++++.|++.+..|++. .+|.+|+..-+++.
T Consensus 19 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~ 84 (181)
T PRK12536 19 DAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYK 84 (181)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHH
Confidence 3489999999999999999988764 46799999999999999999999974 36999998776653
No 70
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=97.93 E-value=2.2e-05 Score=65.95 Aligned_cols=62 Identities=16% Similarity=0.222 Sum_probs=56.1
Q ss_pred HHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 265 ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
+.+.++..|.|.|..+|.++.+...+.||++|++.+.+++.+.+|++.. .|.+|+..-+++.
T Consensus 2 ~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~ 63 (159)
T TIGR02989 2 AFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNK 63 (159)
T ss_pred HHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHH
Confidence 5788999999999999999999899999999999999999999999764 6999998877653
No 71
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=97.90 E-value=3.3e-05 Score=71.31 Aligned_cols=63 Identities=24% Similarity=0.313 Sum_probs=56.5
Q ss_pred HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
.+.+.|+..|.+.|..++.++.+...+-||++|+.++.+++.+.+|++..+ .|.+|...-+++
T Consensus 63 ~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN 125 (233)
T PRK12538 63 AAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSN 125 (233)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHH
Confidence 889999999999999999999888788999999999999999999987555 699998776554
No 72
>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=97.88 E-value=3.5e-06 Score=58.24 Aligned_cols=33 Identities=30% Similarity=0.483 Sum_probs=30.2
Q ss_pred hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCcc
Q 020126 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS 223 (330)
Q Consensus 191 ~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~ 223 (330)
+.++.||++|+++|+||++||++|+++|+.|+.
T Consensus 2 D~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~~ 34 (37)
T PF00140_consen 2 DSLRLYLKEIGRYPLLTAEEEIELARRIRKGDE 34 (37)
T ss_dssp HHHHHHHHHHHHS-EETTHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHH
Confidence 688999999999999999999999999999875
No 73
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=97.83 E-value=9.6e-05 Score=64.08 Aligned_cols=64 Identities=16% Similarity=0.173 Sum_probs=55.2
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHcccC----CCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 262 CSLAREKLVMSNVRLVMSIAQRYDNM----GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 262 g~~ArekLI~~nLpLV~sIAkrY~~~----Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
+..+.+.|+..|.+.|..+|.++.+. ..+.+|++|++.+.+++...+|++. ..|.+|+..-+|+
T Consensus 20 d~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn 87 (184)
T PRK12512 20 DAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARN 87 (184)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHH
Confidence 35899999999999999999988752 3589999999999999999999874 3699999876665
No 74
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=97.79 E-value=8.5e-05 Score=64.98 Aligned_cols=64 Identities=19% Similarity=0.151 Sum_probs=57.3
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 262 g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
+..+.+.|+..|.+.+..++.++.+...+-+|++|++++.+++...+|++. ..|.+|+..-++.
T Consensus 20 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n 83 (189)
T PRK12515 20 DRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARF 83 (189)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHH
Confidence 458999999999999999999998888899999999999999999999964 4799999876664
No 75
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=97.75 E-value=6.1e-05 Score=64.86 Aligned_cols=63 Identities=11% Similarity=0.140 Sum_probs=56.0
Q ss_pred HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
...++|+..|.|+|..++.+|.+...+.+|++|+.++.|++.++.|++.. +|.+|+..-+++.
T Consensus 3 ~~~~~l~~~y~~~i~~~~~~~~~~~~daeDvvQe~~i~l~~~~~~~~~~~--~~~~wl~~i~~n~ 65 (173)
T PRK12522 3 EKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE--NYKKWITTICVRT 65 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcCCcc--chHHHHHHHHHHH
Confidence 45789999999999999999999889999999999999999999999854 7999987766543
No 76
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=97.71 E-value=0.00016 Score=63.86 Aligned_cols=64 Identities=19% Similarity=0.254 Sum_probs=57.4
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 262 g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
+..+.+.|+..|.|.|..++.++.+...+-||++||.++.+++.+++|++.. .|.+|+..-+++
T Consensus 25 d~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~~--~f~~wL~~i~rn 88 (192)
T PRK09643 25 DRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDA--AVSSWLHRIVVN 88 (192)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCCC--ccHHHHHHHHHH
Confidence 3589999999999999999999988888999999999999999999999753 699999876654
No 77
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=97.65 E-value=9.8e-05 Score=64.19 Aligned_cols=63 Identities=16% Similarity=0.155 Sum_probs=56.2
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhh
Q 020126 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIR 326 (330)
Q Consensus 262 g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR 326 (330)
+..+.+.|+..|.|.|..++.+|.+...+-+|++|+..+.|++++.+|++.. .|.+|+..-++
T Consensus 5 d~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iar 67 (179)
T PRK12543 5 DQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVI 67 (179)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHH
Confidence 3578999999999999999999998889999999999999999999999875 68888866544
No 78
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=97.64 E-value=0.00033 Score=61.16 Aligned_cols=63 Identities=17% Similarity=0.236 Sum_probs=53.4
Q ss_pred HHHHHHHHHHhHHHHHHHHHH----cccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 263 SLAREKLVMSNVRLVMSIAQR----YDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkr----Y~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
..+.+.|+..|.|.+...+.+ +.+...+-+|++|+.++.+++.+..|++.. .|.+|+..-+++
T Consensus 20 ~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~~n 86 (184)
T PRK12539 20 AAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIARY 86 (184)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHHHH
Confidence 489999999999999998864 445668899999999999999999999754 599998766554
No 79
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=97.62 E-value=0.00017 Score=62.88 Aligned_cols=73 Identities=19% Similarity=0.251 Sum_probs=61.4
Q ss_pred HHHHHHhh-hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 254 ELQSILME-CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 254 eL~~~l~~-g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
++...+.. +..+.+.|+..|.+.+..++.++.+...+-+|++|+.++.+++.+.+|++..+ .|.+|+..-+++
T Consensus 12 ~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wL~~iarn 85 (182)
T PRK12537 12 ACLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARG-SARGWIYSVTRH 85 (182)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHH
Confidence 34444443 57899999999999999999999988889999999999999999999987544 699998876654
No 80
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=97.55 E-value=0.00024 Score=60.82 Aligned_cols=63 Identities=19% Similarity=0.170 Sum_probs=54.2
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 262 g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
+..+.+.|+..|.|.|..++.++.+. .+.+|++||.++.+++.++.|++. ..|.+|+..-+++
T Consensus 9 d~~a~~~l~~~~~~~l~~~~~~~~~~-~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n 71 (175)
T PRK12518 9 DRQSFRQLYRRYQQKVRSTLYQLCGR-ELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWN 71 (175)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCH-hHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHH
Confidence 35889999999999999999998643 678999999999999999999975 3699999776543
No 81
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=97.50 E-value=0.00023 Score=62.04 Aligned_cols=64 Identities=11% Similarity=0.162 Sum_probs=56.8
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 262 g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
...|.++|+..|.|.|..++.++.+...+-+|++|++.+.|++++.+|++.. .|.+|+..-+++
T Consensus 14 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~~--~~~awl~~ia~n 77 (179)
T PRK09415 14 KEDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKS--SLKTWLYRIAIN 77 (179)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCCc--ccHHHHHHHHHH
Confidence 4588999999999999999999988888899999999999999999998743 699998776654
No 82
>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=97.39 E-value=0.00043 Score=59.69 Aligned_cols=64 Identities=19% Similarity=0.145 Sum_probs=53.8
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCC-----ChhHHHHHHHHHHHH-HHhhcCCCCCCcchhHHHHHhhcc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGA-----DMADLVQGGLIGLLR-GIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gv-----d~EDLIQEG~IGLik-AIekFDpsrG~rFsTYA~~wIR~a 328 (330)
..+.+.|+..|.+.+..++.+|..... +-+|++|+..+.+++ ...+|++. ..|.+|+..++++.
T Consensus 16 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~i~~n~ 85 (183)
T TIGR02999 16 AAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAKAMRRI 85 (183)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHHHHHHH
Confidence 378999999999999999999987655 899999999999998 77788754 36889887766643
No 83
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=97.36 E-value=0.00023 Score=62.03 Aligned_cols=66 Identities=21% Similarity=0.149 Sum_probs=58.4
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 262 g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
+..+.+.|+..|.+.+..+|.++.+...+-+|++|+..+.+++.+.+|++..+..|.+|...-+++
T Consensus 7 d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn 72 (185)
T PRK12542 7 DYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKN 72 (185)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHH
Confidence 458899999999999999999998888889999999999999999999976555799998776554
No 84
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=97.35 E-value=0.00067 Score=59.64 Aligned_cols=61 Identities=18% Similarity=0.206 Sum_probs=52.2
Q ss_pred HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
.+.+.|+..|.+.+..++. +.+...+-+|++|+.++.+++...+|++. ..|.+|...-+|+
T Consensus 24 ~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn 84 (185)
T PRK09649 24 RALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARH 84 (185)
T ss_pred HHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHH
Confidence 8899999999999999995 55556789999999999999999999964 3699998776554
No 85
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=97.29 E-value=0.00045 Score=58.52 Aligned_cols=61 Identities=16% Similarity=0.030 Sum_probs=53.2
Q ss_pred HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
.+.++|+..|.+.+..+|.++.+...+.+|++|++++.+++. .|+. +..|.+|+...+++.
T Consensus 3 ~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~ 63 (166)
T PRK09639 3 ETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNV 63 (166)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHH
Confidence 678999999999999999999988889999999999999998 5653 447999998877654
No 86
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=97.21 E-value=0.00087 Score=56.73 Aligned_cols=65 Identities=14% Similarity=0.064 Sum_probs=57.0
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 262 g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
+..+.+.|+..|.|.|..++.++.+...+-+|++|++++-+++..++|+. ...|.+|+..-+++.
T Consensus 4 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~ 68 (162)
T TIGR02983 4 TEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNL 68 (162)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHH
Confidence 45789999999999999999999988889999999999999999999964 347999988776653
No 87
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=97.19 E-value=0.0016 Score=56.90 Aligned_cols=70 Identities=24% Similarity=0.252 Sum_probs=59.1
Q ss_pred HHHHhhhHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 256 QSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 256 ~~~l~~g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
.........+.+.++..|.+.+...+.++.+...+-|||+||.++.+++++..| +. +..|.||...-+++
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n 76 (182)
T COG1595 7 AEALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARN 76 (182)
T ss_pred HHHHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHH
Confidence 344455678899999999999999999999877799999999999999999999 44 34799999876554
No 88
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=97.11 E-value=0.0012 Score=56.59 Aligned_cols=65 Identities=15% Similarity=0.282 Sum_probs=57.2
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 262 g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
+.....+++..|.|.|..+|.++.+...+-||++|+..+.+++...+|+... .|.+|+..-+++.
T Consensus 4 ~~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~--~~~~wl~~i~~n~ 68 (164)
T PRK12547 4 CSKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGT--NLKAWLFTILRNE 68 (164)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCcc--cHHHHHHHHHHHH
Confidence 4578899999999999999999998889999999999999999999998543 5999988766553
No 89
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=96.99 E-value=0.0024 Score=61.02 Aligned_cols=63 Identities=24% Similarity=0.283 Sum_probs=55.6
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
..+.++|+..|.+.|..++.++.+...+-+|++|+..+-+++.+.+|++. ..|.+|.+.-.++
T Consensus 18 ~~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n 80 (339)
T PRK08241 18 RDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATN 80 (339)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHH
Confidence 48899999999999999999998887899999999999999999999853 3699998776554
No 90
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=96.98 E-value=0.0016 Score=55.72 Aligned_cols=59 Identities=14% Similarity=0.147 Sum_probs=52.1
Q ss_pred HHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 266 rekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
.+.|++.|.|.|..++.++.+...+-+|++|+..+.+++.+..|++. +|.+|...-+++
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n 61 (165)
T PRK09644 3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYH 61 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHH
Confidence 46799999999999999999888899999999999999999999863 589988775553
No 91
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=96.96 E-value=0.002 Score=54.68 Aligned_cols=62 Identities=11% Similarity=0.157 Sum_probs=54.6
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
..+.+.++..|.+.|..++.++.+...+-+|++||+.+.+++..++|++. .|.||+..-+++
T Consensus 4 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n 65 (161)
T PRK12541 4 KQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYN 65 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHH
Confidence 36789999999999999999999888899999999999999999999863 599998765554
No 92
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=96.85 E-value=0.0028 Score=54.30 Aligned_cols=64 Identities=16% Similarity=0.113 Sum_probs=55.7
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
..+.+.|+..|.+.+..++.++.+...+-||++|+..+-+++...+|++.. ..|.+|+..-+++
T Consensus 8 ~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn 71 (173)
T PRK09645 8 AALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARN 71 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHH
Confidence 488999999999999999999987777899999999999999999998533 3699998776554
No 93
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=96.79 E-value=0.0034 Score=56.63 Aligned_cols=63 Identities=21% Similarity=0.305 Sum_probs=56.3
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
..+.++|+..|.+.+..++.++.+...+-+|++|+..+.+++.+.+|++ + +|.+|+..-+|+.
T Consensus 27 ~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~ 89 (203)
T PRK09647 27 MPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNL 89 (203)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHH
Confidence 5789999999999999999999988889999999999999999999985 3 6999988776643
No 94
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=96.76 E-value=0.0036 Score=53.15 Aligned_cols=62 Identities=15% Similarity=0.092 Sum_probs=54.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
.+.++|+..|.+.|..++.++.+...+-||++|+.++-+++....|+++ .|.+|...++++.
T Consensus 4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~~---~~~~wl~~i~~n~ 65 (161)
T PRK12528 4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQII---EPRAFLTTIAKRV 65 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhcccccccc---CHHHHHHHHHHHH
Confidence 6788999999999999999999887899999999999999988877642 5899998877653
No 95
>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=96.74 E-value=0.0051 Score=57.47 Aligned_cols=63 Identities=14% Similarity=0.035 Sum_probs=54.0
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHH-------HHHhhcCCCCCCcchhHHHHHhhc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLL-------RGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLi-------kAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
..+.+.|+..|.+.|..++.++.+...+-||++|+..+-++ +.+.+|++.. .|.||...-.++
T Consensus 38 ~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~~--~~~tWL~~Ia~N 107 (244)
T TIGR03001 38 PAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGRG--PLLSWVRIVATR 107 (244)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCCC--chHhHHHHHHHH
Confidence 48999999999999999999998778899999999999998 4788899643 689988765543
No 96
>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=96.69 E-value=0.0018 Score=54.06 Aligned_cols=55 Identities=15% Similarity=0.175 Sum_probs=48.3
Q ss_pred HHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 271 ~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
..|.|.|..++.++.+.-.+-+|++|+..+.+++.+.+|++ .+|.+|+...++..
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~ 56 (154)
T TIGR02950 2 REYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNA 56 (154)
T ss_pred chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHH
Confidence 46889999999999877778999999999999999999997 47999998876653
No 97
>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=96.69 E-value=0.0035 Score=55.02 Aligned_cols=63 Identities=17% Similarity=0.264 Sum_probs=55.9
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
..+.++|+..|.+.|...+.++.+...+-+|++|+..+-+++.+.+|++. .+|.+|...-+++
T Consensus 10 ~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN 72 (193)
T TIGR02947 10 AQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTN 72 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHH
Confidence 47889999999999999999998877889999999999999999999864 3699998876654
No 98
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=96.55 E-value=0.0044 Score=54.28 Aligned_cols=61 Identities=16% Similarity=0.151 Sum_probs=53.5
Q ss_pred HHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 265 ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
+.++|+..|.+.+...|.++.+...+-||++|+..+.+++.+.+|+... +|.+|+..-+++
T Consensus 3 ~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~~--~~~~WL~~ia~n 63 (191)
T PRK12520 3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQS--SLKTYLVGILKH 63 (191)
T ss_pred chHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhcccc--cHHHHHHHHHHH
Confidence 5688999999999999999988888999999999999999999998553 699998765554
No 99
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=96.53 E-value=0.0044 Score=47.37 Aligned_cols=38 Identities=32% Similarity=0.536 Sum_probs=29.6
Q ss_pred chhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhh
Q 020126 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (330)
Q Consensus 224 Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~ 261 (330)
+.....+|...+||+||.+|+|+.+|++.++++.++..
T Consensus 6 i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~ 43 (78)
T PF04539_consen 6 IERARRELEQELGREPTDEEIAEELGISVEEVRELLQA 43 (78)
T ss_dssp HHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHh
Confidence 34567789999999999999999999999999777653
No 100
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=96.52 E-value=0.011 Score=52.77 Aligned_cols=63 Identities=13% Similarity=0.107 Sum_probs=53.5
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
..+.+.|+..|.+.+..++. +.+...+-||++|+-++.|++.+.+|++. ..|.+|+..-+|..
T Consensus 24 ~~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~Iarn~ 86 (196)
T PRK12535 24 RAALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAAR--SSARTWLLSLARRV 86 (196)
T ss_pred HHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCc--ccHHHHHHHHHHHH
Confidence 47899999999999999975 45566789999999999999999999864 36999988777654
No 101
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=96.50 E-value=0.0073 Score=53.14 Aligned_cols=61 Identities=16% Similarity=0.180 Sum_probs=53.9
Q ss_pred HHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 266 rekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
.+.|+..|.+.|..++.++.+...+.+|++||..+.+++.+..|++. .+|.+|+..-+++.
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~~--~~~~~wL~~i~~n~ 63 (181)
T PRK09637 3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNT 63 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhccc--cchHHHHHHHHHHH
Confidence 46789999999999999999888999999999999999999999853 37999998876653
No 102
>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=96.46 E-value=0.0048 Score=54.51 Aligned_cols=59 Identities=15% Similarity=0.138 Sum_probs=52.2
Q ss_pred HHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 267 ekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
.+.|..|.+.|..++.++.+...+-+|++|+..+.+++...+|++. .+|.+|++..+++
T Consensus 5 ~~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn 63 (188)
T TIGR02943 5 PQELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKN 63 (188)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHH
Confidence 4678899999999999999888899999999999999999999965 4799999876654
No 103
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=96.44 E-value=0.011 Score=54.18 Aligned_cols=63 Identities=17% Similarity=0.251 Sum_probs=55.1
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 262 g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
...+.+.|+..|.+.+..++.++.+...+-||++|+.++-+++.+.+|++. .|.+|+..-+++
T Consensus 16 ~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN 78 (216)
T PRK12533 16 RGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRH 78 (216)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHH
Confidence 457899999999999999999998888889999999999999999999853 489998765543
No 104
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=96.42 E-value=0.0056 Score=53.79 Aligned_cols=59 Identities=15% Similarity=0.276 Sum_probs=50.1
Q ss_pred HHHHHHhHHHHHHHHHHcccCCCC-hhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 267 EKLVMSNVRLVMSIAQRYDNMGAD-MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 267 ekLI~~nLpLV~sIAkrY~~~Gvd-~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
+..+..|.+.|..+|.++.+...+ -||++|+.++.+++...+|+.. .+|.+|+..-+++
T Consensus 8 ~~~~~~~~~~l~~~a~~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n 67 (195)
T PRK12532 8 DAELIESRKLLLHFARLQLPDHPDLAEDLVQETLLSAYSAGDSFQGR--ALVNSWLFAILKN 67 (195)
T ss_pred hhhHHHHHHHHHHHHHHHcCChhhhHHHHHHHHHHHHHHhccccccc--chHHHHHHHHHHH
Confidence 356678999999999999887777 9999999999999999999864 3799998776654
No 105
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=96.34 E-value=0.0097 Score=52.68 Aligned_cols=66 Identities=17% Similarity=0.121 Sum_probs=58.3
Q ss_pred hhHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 261 ~g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
....+.+.++..|.+.|..+|.++.+...+-+|++|+..+-+++.+..|++.. .|.+|+...+|+.
T Consensus 20 ~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~~--~~~~wL~~Iarn~ 85 (188)
T PRK12517 20 SKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEK--AAKAWLITILRRE 85 (188)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCcc--chHHHHHHHHHHH
Confidence 35689999999999999999999988888899999999999999999999653 6899988777653
No 106
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=96.32 E-value=0.011 Score=52.41 Aligned_cols=63 Identities=11% Similarity=0.210 Sum_probs=55.1
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
..+.++|+..|.+.+...|.++.+...+-||++|+..+-+++...+|+... .|.+|+..-.++
T Consensus 9 ~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~~--~~~awL~~Ia~n 71 (187)
T PRK12516 9 TPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGT--NMKAWLFTILRN 71 (187)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCcc--cHHHHHHHHHHH
Confidence 478899999999999999999998878899999999999999999998643 599998765544
No 107
>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=96.24 E-value=0.011 Score=55.71 Aligned_cols=63 Identities=21% Similarity=0.254 Sum_probs=55.9
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
..+.+.|+..|.+.+..+|.++.+...+-||++|+..+-+++.+.+|++. ..|.+|+..-+++
T Consensus 4 ~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n 66 (324)
T TIGR02960 4 GAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATN 66 (324)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHH
Confidence 47899999999999999999998888889999999999999999999964 3699998776654
No 108
>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=96.12 E-value=0.0089 Score=51.78 Aligned_cols=56 Identities=18% Similarity=0.243 Sum_probs=48.3
Q ss_pred HHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 271 ~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
..|.+.+...+.++.+...+-+|++|+..+.+++++.+|++. .+|.+|+..-+++.
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~~--~~f~~wl~~iarn~ 57 (170)
T TIGR02959 2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDG--QKIQSWLYQIARNT 57 (170)
T ss_pred chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHH
Confidence 357888889999998888899999999999999999999963 47999998876653
No 109
>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=96.11 E-value=0.026 Score=43.51 Aligned_cols=48 Identities=25% Similarity=0.227 Sum_probs=40.9
Q ss_pred HHHHHHHHHHhHHHHHHHHHHc----cc--CCCChhHHHHHHHHHHHHHHhhcC
Q 020126 263 SLAREKLVMSNVRLVMSIAQRY----DN--MGADMADLVQGGLIGLLRGIEKFD 310 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY----~~--~Gvd~EDLIQEG~IGLikAIekFD 310 (330)
..|.++++..|.|++.+.+.|- .+ .+.--+||-|+=...||+||.+|+
T Consensus 12 ~~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~ 65 (65)
T PF12645_consen 12 PEAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE 65 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence 3899999999999999998772 11 245569999999999999999996
No 110
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=95.96 E-value=0.0063 Score=51.51 Aligned_cols=54 Identities=7% Similarity=0.121 Sum_probs=47.2
Q ss_pred HHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 271 ~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
..|.+.+..++.++.+...+-+|++||..+.+++.+.+|++. .|.+|+..-+++
T Consensus 2 ~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n 55 (160)
T PRK09642 2 QTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATN 55 (160)
T ss_pred chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHH
Confidence 568999999999998887899999999999999999999963 499998776554
No 111
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=95.90 E-value=0.022 Score=50.31 Aligned_cols=62 Identities=19% Similarity=0.327 Sum_probs=54.1
Q ss_pred HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
.+...++..|.|.+...+.++.+...+-||++|+..+.+++..++|++.. .|.+|+..-+++
T Consensus 5 ~~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Ia~n 66 (182)
T PRK12540 5 DSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGS--NLPAWLFTILRN 66 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCc--hHHHHHHHHHHH
Confidence 45678899999999999999988888999999999999999999998664 589998776654
No 112
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=95.87 E-value=0.013 Score=61.54 Aligned_cols=33 Identities=24% Similarity=0.481 Sum_probs=31.5
Q ss_pred hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCcc
Q 020126 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS 223 (330)
Q Consensus 191 ~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~ 223 (330)
+.++.||+++++.||||.++|++++++|..|..
T Consensus 104 DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~ 136 (619)
T PRK05658 104 DPVRMYLREMGTVELLTREGEIEIAKRIEAGEN 136 (619)
T ss_pred ChHHHHHHHhccCcCCCcHHHHHHHHHHHHHHH
Confidence 799999999999999999999999999999864
No 113
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=95.69 E-value=0.022 Score=49.63 Aligned_cols=66 Identities=9% Similarity=-0.108 Sum_probs=53.1
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHccc--CCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 262 CSLAREKLVMSNVRLVMSIAQRYDN--MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 262 g~~ArekLI~~nLpLV~sIAkrY~~--~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
+..+.+.|+..|.+.|...+.++.+ ...+-||++|+..+-+++...+|+......|.+|...-.++
T Consensus 11 d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n 78 (178)
T PRK12529 11 DRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANC 78 (178)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHH
Confidence 3578999999999999997555444 24679999999999999999999865455799998776554
No 114
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=95.65 E-value=0.034 Score=49.51 Aligned_cols=61 Identities=20% Similarity=0.314 Sum_probs=51.0
Q ss_pred HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
+..+.|. .|.|.|...|.++.+...+-+|++|+..+.+++.+..|+.. ..|.+|+..-+++
T Consensus 8 ~~~~~l~-~~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n 68 (188)
T PRK12546 8 DPRDELV-EHLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRN 68 (188)
T ss_pred hHHHHHH-HHHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHH
Confidence 4455554 47799999999999888999999999999999999999864 3699998776654
No 115
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=95.59 E-value=0.023 Score=49.02 Aligned_cols=63 Identities=13% Similarity=0.065 Sum_probs=52.6
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
..+..+|+..|.+.|..++.++.+...+-+|++|+.++.+++. ..|+.. ..|.+|....+++.
T Consensus 9 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~ 71 (172)
T PRK12523 9 SELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGL 71 (172)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHH
Confidence 3789999999999999999999888889999999999999986 445533 36899987766653
No 116
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=95.50 E-value=0.029 Score=50.70 Aligned_cols=59 Identities=19% Similarity=0.210 Sum_probs=51.8
Q ss_pred HHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 267 ekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
..++..|.+.|...+.++.+...+-+|++|+.++.+++.+.+|+.. .+|.+|...-+++
T Consensus 21 ~~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfikl~~~~~~~~~~--~~~~~WL~~IarN 79 (206)
T PRK12544 21 PVFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGR--AAFKTWVFAILKN 79 (206)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHH
Confidence 5678889999999999999888899999999999999999999854 3699999776654
No 117
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=95.36 E-value=0.046 Score=47.35 Aligned_cols=62 Identities=16% Similarity=0.182 Sum_probs=51.2
Q ss_pred HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
..+.+.++..|.+.+..++.++.+...+-||++|+..+-+++. ..|++-. .|.+|+..-++.
T Consensus 9 ~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn 70 (172)
T PRK09651 9 SLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKR 70 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHH
Confidence 4789999999999999999999888888999999999999987 3454433 578887665554
No 118
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=95.34 E-value=0.027 Score=47.64 Aligned_cols=57 Identities=18% Similarity=0.321 Sum_probs=45.9
Q ss_pred HHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 268 kLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
+++..|.+.+..+|.++.+...+-+|++|+..+.+++....|++. .|.+|+..-+|+
T Consensus 2 ~~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn 58 (163)
T PRK07037 2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRN 58 (163)
T ss_pred hHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHH
Confidence 357788899999999998887889999999999999888777653 467777655543
No 119
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=95.02 E-value=0.046 Score=48.76 Aligned_cols=58 Identities=16% Similarity=0.139 Sum_probs=50.2
Q ss_pred HHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 268 kLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
.++..|.+-+...+.++.+...+-+|++|+..+.+++.+.+|++.. .|.+|+..-+|+
T Consensus 12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~IarN 69 (201)
T PRK12545 12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQS--AHKTWVFGILRN 69 (201)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhccccc--hHHHHHHHHHHH
Confidence 4478899999999999998878999999999999999999999763 599998766554
No 120
>PRK09191 two-component response regulator; Provisional
Probab=94.94 E-value=0.074 Score=47.60 Aligned_cols=61 Identities=11% Similarity=0.096 Sum_probs=53.2
Q ss_pred HHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 265 ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
+..+|+..|.+.+...+.++.+...+-+|++|+.++-+++....|++. ..|.+|...++++
T Consensus 2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~ 62 (261)
T PRK09191 2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHR 62 (261)
T ss_pred chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHH
Confidence 357899999999999999998877889999999999999999999875 3588988877654
No 121
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=94.32 E-value=0.076 Score=46.86 Aligned_cols=58 Identities=12% Similarity=0.181 Sum_probs=49.3
Q ss_pred HHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 268 kLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
.-|..|.+.+...|.++.+...+-+|++|+..+-+++.+..|++.. +|.+|+..-.++
T Consensus 11 ~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~~--~~~~wL~~Ia~n 68 (189)
T PRK12530 11 LEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQS--ALKTWIFAILKN 68 (189)
T ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCCc--cHHHHHHHHHHH
Confidence 3467788999999999988778999999999999999999998653 699998775544
No 122
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=94.27 E-value=0.077 Score=46.93 Aligned_cols=61 Identities=18% Similarity=0.228 Sum_probs=51.8
Q ss_pred HHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 265 ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
.++..+..+.+-|...+.++.+...+-+|++|+..+-+++.+..|+.. .+|.+|...-+++
T Consensus 5 ~~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn 65 (182)
T PRK12511 5 SKRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHN 65 (182)
T ss_pred chhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHH
Confidence 345567889999999999998887889999999999999999999864 3699999876654
No 123
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=93.53 E-value=0.21 Score=43.00 Aligned_cols=61 Identities=7% Similarity=-0.045 Sum_probs=49.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
.+..+++..|.+.+...+.++.+...+-+|++|+..+-+++-...++ ...|.+|...-.++
T Consensus 9 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~---~~~~~~wl~~Iarn 69 (168)
T PRK12525 9 TLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPAS---IREPRALLTTIARR 69 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCccc---ccCHHHHHHHHHHH
Confidence 67788999999999999999998888999999999999997544443 23688887765544
No 124
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=93.24 E-value=0.33 Score=48.60 Aligned_cols=32 Identities=31% Similarity=0.509 Sum_probs=30.1
Q ss_pred hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCc
Q 020126 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGL 222 (330)
Q Consensus 191 ~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~ 222 (330)
..+..|+..+...+.|+++||.+|+++++.|.
T Consensus 67 ~~~~~~~~~~~~~~~l~~~Ee~~la~~~~~g~ 98 (342)
T COG0568 67 GRLSFYIRAIEAAPLLTPEEEKALARRLKRGE 98 (342)
T ss_pred hhHHHHHHHHhhhcccChHHHHHHHHHHHcCC
Confidence 57888999999999999999999999999996
No 125
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=93.13 E-value=0.14 Score=48.46 Aligned_cols=59 Identities=14% Similarity=0.053 Sum_probs=47.8
Q ss_pred HHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 265 ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
...+|+..|.+.+..+|.++.+...+-||++||..+.+. ....|+ ...|.+|.+.-+++
T Consensus 5 ~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~~~-~~~~~~---~~~~~~WL~~Ia~n 63 (293)
T PRK09636 5 DAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLRWN-NADRAQ---IRDPRAWLTRVVTR 63 (293)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH-hccccc---ccCHHHHHHHHHHH
Confidence 466889999999999999999888899999999999844 445665 34799998775554
No 126
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=93.06 E-value=0.13 Score=43.59 Aligned_cols=54 Identities=7% Similarity=0.050 Sum_probs=42.7
Q ss_pred HHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 271 ~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
..|.+.+...+.++.+...+-+|++|+..+.|++....|++. +|.+|...-+++
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~~---~~~~wL~~ia~n 55 (159)
T PRK12527 2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIE---HPRAFLYRTALN 55 (159)
T ss_pred hhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhcccccccc---chHHHHHHHHHH
Confidence 356677777777777777789999999999999999988753 688887765554
No 127
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=92.19 E-value=0.6 Score=44.69 Aligned_cols=66 Identities=23% Similarity=0.383 Sum_probs=49.3
Q ss_pred hhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhh
Q 020126 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMEC 262 (330)
Q Consensus 189 ~q~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g 262 (330)
+.+.+..||+.-. ..--|---.++.+++. .....++..+|++||++|+|+.+|++.+|+..++..+
T Consensus 85 I~Gei~d~LR~~~--~v~vpR~~~~~~~~i~------~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~ 150 (247)
T COG1191 85 IRGEILDYLRKND--SVKVPRSLRELGRRIE------EAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAI 150 (247)
T ss_pred HHHHHHHHHHhCC--CccCcHHHHHHHHHHH------HHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHh
Confidence 4567778888887 2223334445555544 4667899999999999999999999999988777664
No 128
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=90.21 E-value=0.62 Score=43.61 Aligned_cols=67 Identities=18% Similarity=0.102 Sum_probs=47.7
Q ss_pred HHHHHhhhHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 255 LQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 255 L~~~l~~g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
|.+.+.-...+.+.+++.| +.+...+.++.+...+-||++|+..+-+++ +|+... .|.+|+..-.|+
T Consensus 9 ~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~---~~~~~~--~~~~WL~~IarN 75 (228)
T PRK06704 9 LKNHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQ---KYSNKD--ICMTLVYKIARN 75 (228)
T ss_pred HhcccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHH---HcCccc--cHHHHHHHHHHH
Confidence 3333444446677777766 788888888887778999999999988876 466432 488888765543
No 129
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=88.42 E-value=0.68 Score=44.46 Aligned_cols=59 Identities=14% Similarity=-0.062 Sum_probs=47.5
Q ss_pred HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhh
Q 020126 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIR 326 (330)
Q Consensus 264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR 326 (330)
.....++..|.+.+..+|.++.+...+-||++||.++-++++...+ ...|.+|.+.-.+
T Consensus 5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~----~~~~~aWL~~Ia~ 63 (290)
T PRK09635 5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD----IDDERGWLIVVTS 63 (290)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc----cccHHHHHHHHHH
Confidence 4567889999999999999999888899999999999888775432 2358888775443
No 130
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=88.28 E-value=2 Score=38.09 Aligned_cols=63 Identities=19% Similarity=0.143 Sum_probs=42.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHccc---CCCChhHHHHHHHHHHHHHHh--hc-CCCCCCcchhHHHHHhhc
Q 020126 264 LAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIE--KF-DSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 264 ~ArekLI~~nLpLV~sIAkrY~~---~Gvd~EDLIQEG~IGLikAIe--kF-DpsrG~rFsTYA~~wIR~ 327 (330)
.|.++|+..|.+-++.+|+++.. ++.+.+|..+ ..-++++.+. .| +.+....|-.|+..-+++
T Consensus 17 ~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~l-v~ea~lrl~~~~~~~~~~~~~~f~~~~~~~~rr 85 (185)
T PF07638_consen 17 AALDQLFERYYPELRRLARRRLRRERRGHDLQDTAL-VHEAFLRLARRGRFVQFSDRRHFWALLARIMRR 85 (185)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHH-HHHHHHHHhccccccCCCCHHHHHHHHHHHHHH
Confidence 89999999999999999988653 2456666544 3445555554 22 444434677777776654
No 131
>PHA02547 55 RNA polymerase sigma factor; Provisional
Probab=88.11 E-value=0.97 Score=41.67 Aligned_cols=60 Identities=15% Similarity=0.303 Sum_probs=48.0
Q ss_pred HHHHhHHHHHHHHHHcccCCCC---hhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126 269 LVMSNVRLVMSIAQRYDNMGAD---MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328 (330)
Q Consensus 269 LI~~nLpLV~sIAkrY~~~Gvd---~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a 328 (330)
|-.+.+.++..++++|.-+|+. .+|+|.+|.-.+++.+..|||++...+-+|.+..+-++
T Consensus 42 ig~~imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~A 104 (179)
T PHA02547 42 IGLAIMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNA 104 (179)
T ss_pred HHHHHHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHH
Confidence 3345666666777777666766 89999999999999999999999988889988766443
No 132
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=87.43 E-value=3.1 Score=39.30 Aligned_cols=66 Identities=21% Similarity=0.281 Sum_probs=45.6
Q ss_pred hhhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHh
Q 020126 188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (330)
Q Consensus 188 l~q~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~ 260 (330)
++...+..||++....-.+ |---.++..+++. ....+...+|++||.+++|+.+|++.+++...+.
T Consensus 100 ~Irg~I~~~lr~~~~~ir~-Pr~~~~~~~~i~~------~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~ 165 (264)
T PRK07122 100 TIMGEVRRHFRDNSWSVKV-PRRLKELHLRLGR------ATAELSQRLGRAPTASELAAELGMDREEVVEGLV 165 (264)
T ss_pred HHHHHHHHHHHHcCCcccc-CHHHHHHHHHHHH------HHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4666777788775542222 2223345555543 4557888899999999999999999999877654
No 133
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=87.32 E-value=1.8 Score=40.61 Aligned_cols=64 Identities=25% Similarity=0.300 Sum_probs=43.9
Q ss_pred hhhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhh
Q 020126 188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (330)
Q Consensus 188 l~q~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~ 261 (330)
.+.+.+..|++.... + |-.-.+...+++ .....+...+|++|+.+++|+.+|++.+++..++..
T Consensus 86 ~Ir~~i~~~lr~~~~---~-pr~~~~~~~~l~------~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~ 149 (257)
T PRK05911 86 LIKAAIIDDLRKQDW---V-PRSVHQKANKLA------DAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSS 149 (257)
T ss_pred HHHHHHHHHHHhcCC---C-CHHHHHHHHHHH------HHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHH
Confidence 345566667766654 2 223334444443 345568888999999999999999999998776543
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=86.35 E-value=3.5 Score=38.39 Aligned_cols=65 Identities=15% Similarity=0.240 Sum_probs=42.6
Q ss_pred hhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhh
Q 020126 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (330)
Q Consensus 189 ~q~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~ 261 (330)
+.+.+..|++...... + |..-.++..++.. ...++...+|++||.+++|+.+|++.+++...+..
T Consensus 95 irn~~~~~lr~~~~ir-~-p~~~~~~~~~~~~------~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~ 159 (254)
T TIGR02850 95 IIGEIRRYLRDNNPIR-V-SRSLRDIAYKALQ------VRDKLISENSKEPTVSEIAKELKVPQEEVVFALDA 159 (254)
T ss_pred HHHHHHHHHHhCCCcc-C-chHHHHHHHHHHH------HHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHh
Confidence 4455566666643221 2 2223344444432 34567888999999999999999999998776554
No 135
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=86.07 E-value=2.3 Score=39.39 Aligned_cols=62 Identities=23% Similarity=0.379 Sum_probs=42.9
Q ss_pred hhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHh
Q 020126 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (330)
Q Consensus 189 ~q~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~ 260 (330)
+.+.+..||+.....| -.......+++ .....+...+|++|+.+++|+.+|++.+++..++.
T Consensus 78 Ir~~il~~lr~~~~~~----r~vr~~~~~i~------~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~ 139 (231)
T PRK12427 78 IRGAILDELRELDWRP----RRLRQKTHKTN------DAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLL 139 (231)
T ss_pred HHHHHHHHHHhcCCCC----HHHHHHHHHHH------HHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4456666777654322 12233444443 34567888899999999999999999999877654
No 136
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=85.81 E-value=3.1 Score=38.96 Aligned_cols=65 Identities=23% Similarity=0.382 Sum_probs=43.4
Q ss_pred hhhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHH
Q 020126 188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (330)
Q Consensus 188 l~q~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l 259 (330)
.+.+.+..||+.....-.+. -.-.++.++++ .....+...+|++|+.+++|+.+|++.+++..+.
T Consensus 86 ~Ir~~i~~~lr~~~~~vr~p-r~~~~~~~~~~------~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~ 150 (256)
T PRK07408 86 YIRGEIQHYLRDKSPTVRIP-RRWQELQRQAK------KVRQELRQELGRQPTDQEIAQALDISLEEWQEIK 150 (256)
T ss_pred HHHHHHHHHHHHcCCeeeeC-HHHHHHHHHHH------HHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHH
Confidence 34556667777554322221 12223444443 3456788899999999999999999999987764
No 137
>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=84.18 E-value=2.5 Score=35.18 Aligned_cols=56 Identities=14% Similarity=0.134 Sum_probs=41.5
Q ss_pred HHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCC---CCCcchhHHHHHhhc
Q 020126 267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSS---KGFKISTYVYWWIRQ 327 (330)
Q Consensus 267 ekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDps---rG~rFsTYA~~wIR~ 327 (330)
+.|+..|.+++..++++|.. +|.+|+-.+.+++...+|+.+ ....|.||...-.|+
T Consensus 2 ~~~~~~y~~~l~~~~~~~~~-----~~~~qdvf~~~w~~~~~~~~~~~~~~~~~~~wL~~iarN 60 (142)
T TIGR03209 2 EEIYMNFKNTIDIFTRKYNL-----YYDYNDILYHLWIILKKIDLNKFNTENDLEKYISTSLKR 60 (142)
T ss_pred hHHHHHHHHHHHHHHHHhcc-----hhhHHHHHHHHHHHHHHhhhhhcCchhHHHHHHHHHHHH
Confidence 57899999999999999965 233499999999988654311 124699998876554
No 138
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=83.94 E-value=4.4 Score=39.85 Aligned_cols=35 Identities=29% Similarity=0.379 Sum_probs=30.0
Q ss_pred hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHh
Q 020126 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (330)
Q Consensus 226 ~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~ 260 (330)
.....|...+|++||.+|+|..+|++.+++...+.
T Consensus 177 ~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~ 211 (324)
T PRK07921 177 RIKRELHQQLGREATDEELAEESGIPEEKIADLLE 211 (324)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 45667888999999999999999999999877643
No 139
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=82.52 E-value=4.8 Score=38.60 Aligned_cols=69 Identities=16% Similarity=0.140 Sum_probs=44.3
Q ss_pred hhhhhhHHHHHHhcCCCCCC-CHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 020126 187 ELIQNRLKGYVKGVVSEELL-THAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (330)
Q Consensus 187 El~q~~l~~YL~~i~~~~lL-T~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~ 258 (330)
-++...+..||+.-.....+ +...+..+..+++. ++.........+|++|+.+|+|+.+|++.+++...
T Consensus 99 ~~Ir~~I~~~lr~~~~~iR~p~~~~~~~~~~~~~~---~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~ 168 (289)
T PRK07500 99 WWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRR---LRARLAQADEELTKQEIHREIATALGVSLSDVEMM 168 (289)
T ss_pred HHHHHHHHHHHHHCCCceecCccHHHHHHHHHHHH---HHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHH
Confidence 35667777888764433222 33444555555542 22223333346899999999999999999998654
No 140
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=82.40 E-value=5.3 Score=39.70 Aligned_cols=37 Identities=24% Similarity=0.368 Sum_probs=31.3
Q ss_pred hhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhh
Q 020126 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (330)
Q Consensus 225 e~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~ 261 (330)
.....++...+|++||.+|+|..+|++.++++.++..
T Consensus 219 ~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~ 255 (367)
T PRK09210 219 IRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKI 255 (367)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHH
Confidence 3456678889999999999999999999999876543
No 141
>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=81.38 E-value=2.4 Score=38.92 Aligned_cols=35 Identities=26% Similarity=0.428 Sum_probs=29.9
Q ss_pred hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHh
Q 020126 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (330)
Q Consensus 226 ~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~ 260 (330)
.....+...+|++||.+++|+.+|++.+++..++.
T Consensus 91 ~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~ 125 (238)
T TIGR02393 91 KAERQLTQELGREPTDEELAERMGMPAEKVREIKK 125 (238)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 34567888999999999999999999999977654
No 142
>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=80.28 E-value=1.5 Score=41.48 Aligned_cols=41 Identities=22% Similarity=0.153 Sum_probs=35.6
Q ss_pred HHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcC
Q 020126 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFD 310 (330)
Q Consensus 268 kLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFD 310 (330)
+++..|.|.+..+|.++.+...|-||++||..+-+.+. .|+
T Consensus 1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~ 41 (281)
T TIGR02957 1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRA 41 (281)
T ss_pred ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Ccc
Confidence 36889999999999999988889999999999997764 454
No 143
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=79.71 E-value=6.6 Score=41.38 Aligned_cols=36 Identities=25% Similarity=0.370 Sum_probs=30.8
Q ss_pred hhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHh
Q 020126 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (330)
Q Consensus 225 e~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~ 260 (330)
...+.+|...+|++||.+|+|+.+|++.+++..++.
T Consensus 361 ~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~ 396 (509)
T PRK05901 361 GRIERELLQELGREPTPEELAKEMGFTPEKVREIQK 396 (509)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 345677888999999999999999999999887754
No 144
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=77.82 E-value=8.9 Score=38.71 Aligned_cols=35 Identities=23% Similarity=0.376 Sum_probs=29.5
Q ss_pred hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHh
Q 020126 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (330)
Q Consensus 226 ~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~ 260 (330)
.....+...+|++||.+++|+.+|++.+++...+.
T Consensus 227 ~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~ 261 (373)
T PRK07406 227 KTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAK 261 (373)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 34567888999999999999999999999876543
No 145
>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=71.02 E-value=6.9 Score=35.51 Aligned_cols=62 Identities=26% Similarity=0.399 Sum_probs=40.4
Q ss_pred hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHh
Q 020126 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (330)
Q Consensus 191 ~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~ 260 (330)
+.+..|++.-.... + |.....+..+++. ....+...+|++||.+++|+.+|++.+++...+.
T Consensus 74 ~~i~~~lr~~~~i~-~-p~~~~~~~~~~~~------~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~ 135 (231)
T TIGR02885 74 GEIKRFLRDDGIIK-V-SRSLKELARKIRY------MKEELSKELGREPTINELAEALGVSPEEIVMALE 135 (231)
T ss_pred HHHHHHHHhCCCeE-C-CHHHHHHHHHHHH------HHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 44455555543211 2 2233445555543 3456778899999999999999999999876654
No 146
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=71.01 E-value=17 Score=33.09 Aligned_cols=59 Identities=27% Similarity=0.245 Sum_probs=47.4
Q ss_pred CCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHHHhHH
Q 020126 204 ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVR 275 (330)
Q Consensus 204 ~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~nLp 275 (330)
..||+.|..-|-...+.|-. ..-|..+..++|+.+|++...+.+.|+ .|..+|+..+..
T Consensus 154 ~~LTdrQ~~vL~~A~~~GYF----------d~PR~~~l~dLA~~lGISkst~~ehLR---rAe~Kl~~~~~~ 212 (215)
T COG3413 154 NDLTDRQLEVLRLAYKMGYF----------DYPRRVSLKDLAKELGISKSTLSEHLR---RAERKLIEAYFD 212 (215)
T ss_pred ccCCHHHHHHHHHHHHcCCC----------CCCccCCHHHHHHHhCCCHHHHHHHHH---HHHHHHHHHhhh
Confidence 36999999999988888865 223456779999999999999988887 677888877654
No 147
>PRK14082 hypothetical protein; Provisional
Probab=69.54 E-value=18 Score=28.62 Aligned_cols=56 Identities=11% Similarity=0.020 Sum_probs=45.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHH
Q 020126 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYV 321 (330)
Q Consensus 264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA 321 (330)
...+.+|..+.|.+++--..- ..-+.|||.||=-|-+++=++.++...+-.|.-|.
T Consensus 9 ~e~e~ii~~FepkIkKsL~~T--~yqeREDLeQElk~Ki~eK~~~~~~~e~PGF~efi 64 (65)
T PRK14082 9 EEIEHLIENFSPMIKKKLSNT--SYQEREDLEQELKIKIIEKADMLLCQEVPGFWEFI 64 (65)
T ss_pred HHHHHHHHHccHHHHHHHhcC--ChhhHHHHHHHHHHHHHHHHHHhhcccCCcHHHhh
Confidence 456779999999887765442 23578999999999999999999999888787664
No 148
>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=69.39 E-value=7.9 Score=35.04 Aligned_cols=35 Identities=31% Similarity=0.422 Sum_probs=29.7
Q ss_pred hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHh
Q 020126 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (330)
Q Consensus 226 ~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~ 260 (330)
.....+...+|++|+.+++|+.+|++.+++..++.
T Consensus 87 ~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~ 121 (224)
T TIGR02479 87 RAIRELEARLGREPTEEEIAEELGMDLKEYRQALN 121 (224)
T ss_pred HHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 34556778899999999999999999999887764
No 149
>PRK05949 RNA polymerase sigma factor; Validated
Probab=68.72 E-value=7.6 Score=38.18 Aligned_cols=37 Identities=16% Similarity=0.374 Sum_probs=30.6
Q ss_pred chhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHh
Q 020126 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (330)
Q Consensus 224 Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~ 260 (330)
+......+...+|++|+.+++|+.+|++.+++...+.
T Consensus 180 l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~ 216 (327)
T PRK05949 180 IKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLS 216 (327)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 4445567778899999999999999999999877653
No 150
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=68.05 E-value=24 Score=26.42 Aligned_cols=48 Identities=23% Similarity=0.247 Sum_probs=36.5
Q ss_pred CCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhH
Q 020126 206 LTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECS 263 (330)
Q Consensus 206 LT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~ 263 (330)
||+.|..-|...+..|-. ..-|.-+.+++|+.+|+|...+-..++.+.
T Consensus 1 LT~~Q~e~L~~A~~~GYf----------d~PR~~tl~elA~~lgis~st~~~~LRrae 48 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYF----------DVPRRITLEELAEELGISKSTVSEHLRRAE 48 (53)
T ss_pred CCHHHHHHHHHHHHcCCC----------CCCCcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 677777777777777755 123557789999999999999888877543
No 151
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=67.83 E-value=8 Score=39.76 Aligned_cols=39 Identities=15% Similarity=0.486 Sum_probs=33.0
Q ss_pred cchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhh
Q 020126 223 SLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (330)
Q Consensus 223 ~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~ 261 (330)
.++..+..+...+|++|+.+|+|+.+|++.++++.++..
T Consensus 263 ~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l~~ 301 (415)
T PRK07598 263 KIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLR 301 (415)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 345566778889999999999999999999999887653
No 152
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=66.46 E-value=9.4 Score=35.81 Aligned_cols=36 Identities=39% Similarity=0.468 Sum_probs=30.3
Q ss_pred hhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHh
Q 020126 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (330)
Q Consensus 225 e~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~ 260 (330)
+.....|+..+|++||.+++|..+|++.+++...+.
T Consensus 121 ~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~ 156 (268)
T PRK06288 121 ERAIAMLEARLGRTPSDEEIADELGISLEEYNSLLS 156 (268)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHH
Confidence 345567888999999999999999999999877653
No 153
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=64.91 E-value=11 Score=34.83 Aligned_cols=35 Identities=17% Similarity=0.246 Sum_probs=29.5
Q ss_pred hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHh
Q 020126 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (330)
Q Consensus 226 ~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~ 260 (330)
+....+...+|++|+.+++|..+|++.++++.++.
T Consensus 113 ~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~ 147 (251)
T PRK07670 113 AAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMN 147 (251)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 34456777899999999999999999999887764
No 154
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=62.36 E-value=13 Score=34.59 Aligned_cols=34 Identities=26% Similarity=0.358 Sum_probs=28.8
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHh
Q 020126 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (330)
Q Consensus 227 ~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~ 260 (330)
...++...+|++|+.+++|..+|++.+++...+.
T Consensus 128 ~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~~~ 161 (258)
T PRK08215 128 VREKLINENSKEPTVEEIAKELEVPREEVVFALD 161 (258)
T ss_pred HHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3456778899999999999999999999876553
No 155
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=61.97 E-value=12 Score=36.39 Aligned_cols=37 Identities=19% Similarity=0.407 Sum_probs=30.7
Q ss_pred chhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHh
Q 020126 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (330)
Q Consensus 224 Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~ 260 (330)
++.....+...+|++|+.+++|..+|++.+++...+.
T Consensus 170 l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~ 206 (317)
T PRK07405 170 IKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLE 206 (317)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 4455667778899999999999999999988877654
No 156
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=61.96 E-value=37 Score=32.46 Aligned_cols=65 Identities=18% Similarity=0.196 Sum_probs=38.7
Q ss_pred hhhhhHHHHHHhcCC-CCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHh
Q 020126 188 LIQNRLKGYVKGVVS-EELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (330)
Q Consensus 188 l~q~~l~~YL~~i~~-~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~ 260 (330)
++...+..||+.-.. .+.-+......+..+++. ...++. .+++|+.+++|+.+|++.+++.+++.
T Consensus 108 ~Ir~~i~~~l~~~~~~vr~p~~~~~~~~~~~~~~------~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~~~ 173 (284)
T PRK06596 108 WIKAEIHEYILRNWRIVKVATTKAQRKLFFNLRK------AKKRLG--WLNPEEVEMVAEELGVSEEEVREMES 173 (284)
T ss_pred HHHHHHHHHHHHcCCeeeccchHHHHHHHHHHHH------HHHHhc--cCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 556667777765422 222233333344433331 122222 34999999999999999999977643
No 157
>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=58.83 E-value=17 Score=32.84 Aligned_cols=34 Identities=29% Similarity=0.474 Sum_probs=28.3
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHh
Q 020126 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (330)
Q Consensus 227 ~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~ 260 (330)
....++..+|++|+.+++|+.+|++.+++.+.+.
T Consensus 95 ~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~ 128 (227)
T TIGR02980 95 ATEELTQRLGRSPTIAEIAEELGVSEEEVVEALE 128 (227)
T ss_pred HHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3456778889999999999999999999876544
No 158
>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=55.88 E-value=19 Score=34.55 Aligned_cols=36 Identities=22% Similarity=0.448 Sum_probs=29.9
Q ss_pred hhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHh
Q 020126 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (330)
Q Consensus 225 e~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~ 260 (330)
+.....+...+|++|+.+++|..+|++.+++...+.
T Consensus 164 rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~ 199 (298)
T TIGR02997 164 KKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQ 199 (298)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 344556778899999999999999999999877654
No 159
>KOG0037 consensus Ca2+-binding protein, EF-Hand protein superfamily [Signal transduction mechanisms]
Probab=51.23 E-value=2.2e+02 Score=27.47 Aligned_cols=110 Identities=18% Similarity=0.112 Sum_probs=67.1
Q ss_pred ccCChhhhhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhh
Q 020126 182 SMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (330)
Q Consensus 182 ~~~~pEl~q~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~ 261 (330)
+.+++|-+.-.+ +|=+......+..+|=.+|.+.|++... ... ...+. .+-.++..||+..+..
T Consensus 89 ~~Fs~~TcrlmI--~mfd~~~~G~i~f~EF~~Lw~~i~~Wr~---vF~----~~D~D-------~SG~I~~sEL~~Al~~ 152 (221)
T KOG0037|consen 89 SPFSIETCRLMI--SMFDRDNSGTIGFKEFKALWKYINQWRN---VFR----TYDRD-------RSGTIDSSELRQALTQ 152 (221)
T ss_pred CCCCHHHHHHHH--HHhcCCCCCccCHHHHHHHHHHHHHHHH---HHH----hcccC-------CCCcccHHHHHHHHHH
Confidence 347777443333 4556667788999999999999986432 111 01111 1234566777665554
Q ss_pred -hHHHHHHHHHHhHHHHHHHHHHcc---cCCCChhHHHHHH--HHHHHHHHhhcCCCCC
Q 020126 262 -CSLAREKLVMSNVRLVMSIAQRYD---NMGADMADLVQGG--LIGLLRGIEKFDSSKG 314 (330)
Q Consensus 262 -g~~ArekLI~~nLpLV~sIAkrY~---~~Gvd~EDLIQEG--~IGLikAIekFDpsrG 314 (330)
|-.. .--+.-.|++||. +..+.++|.||.. ..+|.++.+++|....
T Consensus 153 ~Gy~L-------spq~~~~lv~kyd~~~~g~i~FD~FI~ccv~L~~lt~~Fr~~D~~q~ 204 (221)
T KOG0037|consen 153 LGYRL-------SPQFYNLLVRKYDRFGGGRIDFDDFIQCCVVLQRLTEAFRRRDTAQQ 204 (221)
T ss_pred cCcCC-------CHHHHHHHHHHhccccCCceeHHHHHHHHHHHHHHHHHHHHhccccc
Confidence 1110 1113345566776 3458999999965 4688999999998874
No 160
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=50.75 E-value=26 Score=31.99 Aligned_cols=34 Identities=29% Similarity=0.468 Sum_probs=28.1
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHh
Q 020126 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (330)
Q Consensus 227 ~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~ 260 (330)
....+...+|++|+.+++|+.+|++.+++..++.
T Consensus 100 ~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~ 133 (236)
T PRK06986 100 AIRQLEQELGREPTDTEVAEKLGLSLEEYREMLL 133 (236)
T ss_pred HHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHH
Confidence 4456677899999999999999999999776554
No 161
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=50.60 E-value=49 Score=23.86 Aligned_cols=60 Identities=17% Similarity=0.192 Sum_probs=34.4
Q ss_pred CCchHHHHHHhcCChHHHHHHHhhhH-HHHHHHHHHhHHHHHHHHHHcccC-CCChhHHHHHHHH
Q 020126 238 EPSMEQLAASLRISRPELQSILMECS-LAREKLVMSNVRLVMSIAQRYDNM-GADMADLVQGGLI 300 (330)
Q Consensus 238 ePt~~e~A~a~~~s~~eL~~~l~~g~-~ArekLI~~nLpLV~sIAkrY~~~-Gvd~EDLIQEG~I 300 (330)
+++.+++|..+|++...+.+.+.... ......+.. .+ ...|..|... ...++|+-++-.+
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~~~s~~~~~~~-~r--~~~a~~~l~~~~~~~~~ia~~~g~ 62 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKETGTTPKQYLRD-RR--LERARRLLRDTDLSVTEIALRVGF 62 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHhCcCHHHHHHH-HH--HHHHHHHHHcCCCCHHHHHHHhCC
Confidence 46788999999999999988887532 111111111 11 1223333222 4777777665544
No 162
>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=49.23 E-value=30 Score=31.96 Aligned_cols=34 Identities=24% Similarity=0.320 Sum_probs=28.6
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHh
Q 020126 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (330)
Q Consensus 227 ~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~ 260 (330)
....+...+|++|+.+++|..+|++.+++..++.
T Consensus 121 ~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~~~ 154 (255)
T TIGR02941 121 AIDELTDHLQRSPKIIEIADHLGLSEEEVLEIME 154 (255)
T ss_pred HHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4557788899999999999999999998876543
No 163
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=45.13 E-value=39 Score=23.67 Aligned_cols=43 Identities=16% Similarity=0.321 Sum_probs=29.4
Q ss_pred CCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhh
Q 020126 202 SEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (330)
Q Consensus 202 ~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~ 261 (330)
+.+-+++++..+..+..++|. +..++|..+|+|+..+.+.+.+
T Consensus 2 Rp~~~~~~~~~~i~~l~~~G~-----------------si~~IA~~~gvsr~TvyR~l~~ 44 (45)
T PF02796_consen 2 RPPKLSKEQIEEIKELYAEGM-----------------SIAEIAKQFGVSRSTVYRYLNK 44 (45)
T ss_dssp SSSSSSHCCHHHHHHHHHTT-------------------HHHHHHHTTS-HHHHHHHHCC
T ss_pred cCCCCCHHHHHHHHHHHHCCC-----------------CHHHHHHHHCcCHHHHHHHHhc
Confidence 445666765666666677764 4678999999999998877653
No 164
>PRK13239 alkylmercury lyase; Provisional
Probab=41.74 E-value=41 Score=31.76 Aligned_cols=27 Identities=30% Similarity=0.323 Sum_probs=24.6
Q ss_pred hCCCCchHHHHHHhcCChHHHHHHHhh
Q 020126 235 LGCEPSMEQLAASLRISRPELQSILME 261 (330)
Q Consensus 235 lg~ePt~~e~A~a~~~s~~eL~~~l~~ 261 (330)
.|++|+.+++|+.+|.+.+++++++++
T Consensus 33 ~G~pvt~~~lA~~~~~~~~~v~~~L~~ 59 (206)
T PRK13239 33 KGRPVSVTTLAAALGWPVEEVEAVLEA 59 (206)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 699999999999999999999887765
No 165
>PRK05572 sporulation sigma factor SigF; Validated
Probab=40.88 E-value=46 Score=30.87 Aligned_cols=62 Identities=23% Similarity=0.371 Sum_probs=38.1
Q ss_pred hhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 020126 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (330)
Q Consensus 189 ~q~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~ 258 (330)
+.+.+..|++.-... .+.. .-.++..+++. ....++..+|++|+.+++|+.+|++.+++...
T Consensus 93 i~~~i~~~lr~~~~~-r~~~-~~~~~~~~~~~------~~~~l~~~~~r~p~~~eia~~l~~~~~~v~~~ 154 (252)
T PRK05572 93 IIGEIQRFLRDDGTV-KVSR-SLKETANKIRK------DKDELSKELGREPTIEELAEYLGVTPEEVVLA 154 (252)
T ss_pred HHHHHHHHHHhCCCC-CCCH-HHHHHHHHHHH------HHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHH
Confidence 345556666655321 2222 12233333332 34466777899999999999999999887544
No 166
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=38.56 E-value=49 Score=23.23 Aligned_cols=41 Identities=24% Similarity=0.308 Sum_probs=16.8
Q ss_pred CCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHh
Q 020126 203 EELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (330)
Q Consensus 203 ~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~ 260 (330)
++-||++|-..+.....+|.. ..++|+.+|.+..-+...+.
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G~s-----------------~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQGMS-----------------IREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ----------HHHHHHCS--------------------HHHHHHHTT--HHHHHHHHH
T ss_pred ccchhhhHHHHHHHHHHcCCC-----------------HHHHHHHHCcCcHHHHHHHh
Confidence 456888877777776666654 45677777777666655543
No 167
>PF13309 HTH_22: HTH domain
Probab=38.44 E-value=1.4e+02 Score=22.75 Aligned_cols=60 Identities=22% Similarity=0.278 Sum_probs=42.9
Q ss_pred hhhhhHHHHHHhcCCC-CCCCHHHHHHHHHHHHc-CccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHH
Q 020126 188 LIQNRLKGYVKGVVSE-ELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (330)
Q Consensus 188 l~q~~l~~YL~~i~~~-~lLT~eEE~eL~rkIk~-G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l 259 (330)
++++.+..++..++.. ..|+.+|-.++++.+.+ |.. .-.-+.+.+|+.+|+|+.-+...+
T Consensus 2 ~i~~~i~~~~~~~~~~~~~l~~~~k~~iV~~L~~~G~F------------~lKgav~~vA~~L~iS~~TVY~YL 63 (64)
T PF13309_consen 2 LIESIIEEVIAEVGKPPSRLSKEEKKEIVRQLYEKGIF------------LLKGAVEYVAEKLGISRATVYRYL 63 (64)
T ss_pred hHHHHHHHHHHHhCCChhhCCHHHHHHHHHHHHHCCCc------------ccCcHHHHHHHHHCCCHHHHHHHc
Confidence 4567788888887654 78899999999988874 433 112345678899999988765443
No 168
>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=37.95 E-value=67 Score=28.47 Aligned_cols=47 Identities=15% Similarity=0.157 Sum_probs=35.2
Q ss_pred HHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHH
Q 020126 210 EVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLA 265 (330)
Q Consensus 210 EE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~A 265 (330)
+|.+.+.+|++. |++.-++..|..+++++.|++.+.+..++++|+..
T Consensus 27 ~~e~~f~kV~~y---------Lr~~p~~~ati~eV~e~tgVs~~~I~~~IreGRL~ 73 (137)
T TIGR03826 27 EEEREFEKVYKF---------LRKHENRQATVSEIVEETGVSEKLILKFIREGRLQ 73 (137)
T ss_pred HHHHHHHHHHHH---------HHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCCee
Confidence 445566666642 44445566788999999999999999999998653
No 169
>PRK04217 hypothetical protein; Provisional
Probab=36.10 E-value=1.7e+02 Score=25.00 Aligned_cols=48 Identities=17% Similarity=0.217 Sum_probs=33.5
Q ss_pred CCCCCHHHHHHHHHHHH-cCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHH
Q 020126 203 EELLTHAEVVRLSKKIK-TGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREK 268 (330)
Q Consensus 203 ~~lLT~eEE~eL~rkIk-~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~Arek 268 (330)
...||++| ++++.... +|. +.+|+|+.+|++...+...+........+
T Consensus 40 ~~~Lt~ee-reai~l~~~eGl-----------------S~~EIAk~LGIS~sTV~r~L~RArkkLre 88 (110)
T PRK04217 40 PIFMTYEE-FEALRLVDYEGL-----------------TQEEAGKRMGVSRGTVWRALTSARKKVAQ 88 (110)
T ss_pred cccCCHHH-HHHHHHHHHcCC-----------------CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 35566665 66666555 332 57899999999999999888865444433
No 170
>KOG1161 consensus Protein involved in vacuolar polyphosphate accumulation, contains SPX domain [Inorganic ion transport and metabolism]
Probab=34.90 E-value=3.3e+02 Score=27.44 Aligned_cols=32 Identities=16% Similarity=0.368 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126 296 QGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327 (330)
Q Consensus 296 QEG~IGLikAIekFDpsrG~rFsTYA~~wIR~ 327 (330)
---.+|+.+.++|||-..|.+|..|....+..
T Consensus 117 ~LN~tGf~KILKK~DKrtg~~l~~~f~~~l~~ 148 (310)
T KOG1161|consen 117 RLNYTGFAKILKKHDKRTGYRLRPYFQVRLLH 148 (310)
T ss_pred HHhHHHHHHHHHHHhcccccccccHHHHHHHh
Confidence 34568999999999999999999988877654
No 171
>KOG0030 consensus Myosin essential light chain, EF-Hand protein superfamily [Cytoskeleton]
Probab=34.82 E-value=2e+02 Score=26.26 Aligned_cols=73 Identities=12% Similarity=0.139 Sum_probs=50.7
Q ss_pred HHhhCCCCchHHHHHHhcCChHH-HHHHHhhhHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcC
Q 020126 232 KERLGCEPSMEQLAASLRISRPE-LQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFD 310 (330)
Q Consensus 232 ~~~lg~ePt~~e~A~a~~~s~~e-L~~~l~~g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFD 310 (330)
-..+|-.||.+++-+.++-...+ + ..+.-=++.++|+.-++|+. ..+...||. +++++-||
T Consensus 37 lRalG~nPT~aeV~k~l~~~~~~~~--------~~~rl~FE~fLpm~q~vakn--k~q~t~edf--------vegLrvFD 98 (152)
T KOG0030|consen 37 LRALGQNPTNAEVLKVLGQPKRREM--------NVKRLDFEEFLPMYQQVAKN--KDQGTYEDF--------VEGLRVFD 98 (152)
T ss_pred HHHhcCCCcHHHHHHHHcCcccchh--------hhhhhhHHHHHHHHHHHHhc--cccCcHHHH--------HHHHHhhc
Confidence 34578889998888777663322 1 11333478899999999998 456778885 57889999
Q ss_pred CCCCCcchhHHHH
Q 020126 311 SSKGFKISTYVYW 323 (330)
Q Consensus 311 psrG~rFsTYA~~ 323 (330)
.+. .-+..+|.-
T Consensus 99 keg-~G~i~~aeL 110 (152)
T KOG0030|consen 99 KEG-NGTIMGAEL 110 (152)
T ss_pred ccC-CcceeHHHH
Confidence 764 456666654
No 172
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=34.59 E-value=1.7e+02 Score=28.56 Aligned_cols=119 Identities=23% Similarity=0.157 Sum_probs=69.9
Q ss_pred hhHHHHHHhcCCCCCCC---------HHHHHHHHHHHH----cCccchhHHHHHHHhhCC-------CCchHHHHHH---
Q 020126 191 NRLKGYVKGVVSEELLT---------HAEVVRLSKKIK----TGLSLDDHKLRLKERLGC-------EPSMEQLAAS--- 247 (330)
Q Consensus 191 ~~l~~YL~~i~~~~lLT---------~eEE~eL~rkIk----~G~~Le~~~~~l~~~lg~-------ePt~~e~A~a--- 247 (330)
+.+...++.++..+++. .+-=..|++.|- ....+..+..++....|. .||-++++..
T Consensus 77 ~~l~~i~~~~~~~~~~~~~g~~~~~~~d~fe~lv~aI~~QqvS~~~A~~i~~rl~~~~g~~~~~~~~fptpe~l~~~~~~ 156 (285)
T COG0122 77 PDLAPIIDALGPLPLLRAPGLRLPLAPDPFEALVRAILSQQVSVAAAAKIWARLVSLYGNALEIYHSFPTPEQLAAADEE 156 (285)
T ss_pred CcHHHHHHhcCccccccccCcccCCCCCHHHHHHHHHHHhHhhHHHHHHHHHHHHHHhCCccccccCCCCHHHHHhcCHH
Confidence 44555666666666666 233334444443 222345566788889997 5999888743
Q ss_pred ----hcCChHHHHHHHhh------------------hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHH
Q 020126 248 ----LRISRPELQSILME------------------CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRG 305 (330)
Q Consensus 248 ----~~~s~~eL~~~l~~------------------g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikA 305 (330)
+|++....+-++.- .+++++.|+. ..+.=...|.-|...|+-.-|.+-.|=+||-+|
T Consensus 157 ~l~~~g~s~~Ka~yi~~~A~~~~~g~~~~~~l~~~~~e~a~e~L~~-i~GIG~WTAe~~llf~lgr~dvfP~~D~~lr~~ 235 (285)
T COG0122 157 ALRRCGLSGRKAEYIISLARAAAEGELDLSELKPLSDEEAIEELTA-LKGIGPWTAEMFLLFGLGRPDVFPADDLGLRRA 235 (285)
T ss_pred HHHHhCCcHHHHHHHHHHHHHHHcCCccHHHhccCCHHHHHHHHHc-CCCcCHHHHHHHHHHcCCCCCCCChHHHHHHHH
Confidence 45544333322222 1223333332 223334455555556778889999999999999
Q ss_pred HhhcC
Q 020126 306 IEKFD 310 (330)
Q Consensus 306 IekFD 310 (330)
+.+|.
T Consensus 236 ~~~~~ 240 (285)
T COG0122 236 IKKLY 240 (285)
T ss_pred HHHHh
Confidence 99995
No 173
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=33.90 E-value=61 Score=31.80 Aligned_cols=34 Identities=26% Similarity=0.382 Sum_probs=28.5
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHh
Q 020126 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (330)
Q Consensus 227 ~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~ 260 (330)
....++..+|++|+.+++|..+|++.+++...+.
T Consensus 178 ~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~ 211 (325)
T PRK05657 178 AARELEHKLDHEPSAEEIAELLDKPVDDVSRMLA 211 (325)
T ss_pred HHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 3456778899999999999999999999877653
No 174
>PF02885 Glycos_trans_3N: Glycosyl transferase family, helical bundle domain Prosite entry for Thymidine and pyrimidine-nucleoside phosphorylases; InterPro: IPR017459 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. The glycosyl transferase family includes anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase (2.4.2.2 from EC) catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism. This N-terminal domain is found in various family 3 glycosyl transferases, including anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism.; PDB: 2DSJ_B 2ELC_B 2BPQ_A 1ZVW_B 3QR9_B 1V8G_B 2WK5_C 2J0F_C 2WK6_B 1UOU_A ....
Probab=33.61 E-value=1.5e+02 Score=22.21 Aligned_cols=31 Identities=23% Similarity=0.172 Sum_probs=23.0
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHHHHHcCcc
Q 020126 193 LKGYVKGVVSEELLTHAEVVRLSKKIKTGLS 223 (330)
Q Consensus 193 l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~ 223 (330)
++.||+.+.....||.+|-..++..|-+|..
T Consensus 2 ~~~~l~~l~~g~~Ls~~e~~~~~~~i~~g~~ 32 (66)
T PF02885_consen 2 IKEILKKLRDGEDLSREEAKAAFDAILDGEV 32 (66)
T ss_dssp HHHHHHHHHTT----HHHHHHHHHHHHTTSS
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHHHHcCCC
Confidence 4568888888899999999999999998865
No 175
>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=33.35 E-value=96 Score=23.78 Aligned_cols=26 Identities=23% Similarity=0.436 Sum_probs=17.4
Q ss_pred HHhhCCCCchHHHHHHhcCC-hHHHHH
Q 020126 232 KERLGCEPSMEQLAASLRIS-RPELQS 257 (330)
Q Consensus 232 ~~~lg~ePt~~e~A~a~~~s-~~eL~~ 257 (330)
-...|.+||..|+|+.+|++ ..-+..
T Consensus 19 ~~~~G~~Pt~rEIa~~~g~~S~~tv~~ 45 (65)
T PF01726_consen 19 IEENGYPPTVREIAEALGLKSTSTVQR 45 (65)
T ss_dssp HHHHSS---HHHHHHHHTSSSHHHHHH
T ss_pred HHHcCCCCCHHHHHHHhCCCChHHHHH
Confidence 34679999999999999995 555433
No 176
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=32.91 E-value=94 Score=24.78 Aligned_cols=35 Identities=14% Similarity=0.093 Sum_probs=27.8
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhh
Q 020126 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (330)
Q Consensus 227 ~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~ 261 (330)
+..-+.+.+..+++.+++|..+|+|..-|.+.+.+
T Consensus 10 ~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~ 44 (107)
T PRK10219 10 LIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRT 44 (107)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 34455666777889999999999999888777766
No 177
>COG1916 Uncharacterized homolog of PrgY (pheromone shutdown protein) [Function unknown]
Probab=32.69 E-value=1.4e+02 Score=30.82 Aligned_cols=102 Identities=20% Similarity=0.295 Sum_probs=61.7
Q ss_pred HHHHHHHHHcCcc--------chhHHHHHHHhhCCCCchH-----HHHHHhcCChHHHHHHHhhh-HHHHHH-HHHHhHH
Q 020126 211 VVRLSKKIKTGLS--------LDDHKLRLKERLGCEPSME-----QLAASLRISRPELQSILMEC-SLAREK-LVMSNVR 275 (330)
Q Consensus 211 E~eL~rkIk~G~~--------Le~~~~~l~~~lg~ePt~~-----e~A~a~~~s~~eL~~~l~~g-~~Arek-LI~~nLp 275 (330)
|..+.+.++.|.. |...|.++.+.+|-+|..| |.|..+|....-+.+-+.-. +++..+ =+..-++
T Consensus 61 ~ldl~~vlk~Gk~~~~l~~~lLa~~Qrklg~~~Gv~PGsEmk~AIe~A~e~ga~V~lIDRdI~vTl~R~~~~~~~~EKlK 140 (388)
T COG1916 61 ELDLAQVLKEGKAFFLLAGLLLAYFQRKLGKELGVKPGSEMKAAIEAARELGAPVALIDRDIGVTLRRAWAKMPFWEKLK 140 (388)
T ss_pred cCCHHHHHHcCchHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHcCCCEEEecccHHHHHHHHHHhCCHHHHHH
Confidence 4555555665544 5667889999999999975 33455555332221111111 111111 1123345
Q ss_pred HHHHHHHHcccCC---CChhHHHHHHHHH-HHHHHhhcCCC
Q 020126 276 LVMSIAQRYDNMG---ADMADLVQGGLIG-LLRGIEKFDSS 312 (330)
Q Consensus 276 LV~sIAkrY~~~G---vd~EDLIQEG~IG-LikAIekFDps 312 (330)
+...++......| .++++|-|+..+. |+.-.++|-|.
T Consensus 141 ~~~~L~~~~~~~g~~e~ei~~l~~~D~~~al~~efr~~~P~ 181 (388)
T COG1916 141 LISSLISGLLFPGQSEIEIDELKQEDVLSALMQEFRRFSPT 181 (388)
T ss_pred HHHHHHHhcccCCCchHHHHHHhhhhHHHHHHHHHHHhChh
Confidence 6666666544455 5799999999998 99999999885
No 178
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=32.64 E-value=2.6e+02 Score=25.83 Aligned_cols=32 Identities=22% Similarity=0.325 Sum_probs=25.1
Q ss_pred HHHHHHhhCCCCchHHHHHHhcCChHHHHHHH
Q 020126 228 KLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (330)
Q Consensus 228 ~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l 259 (330)
...++..++++|+.+++|..+|++.+++...+
T Consensus 122 ~~~~~~~~~r~~~~~e~a~~~~~~~~~~~~~~ 153 (257)
T PRK08583 122 VDELTTELQRSPKISEIADRLGVSEEEVLEAM 153 (257)
T ss_pred HHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 34566778999999999999999888875543
No 179
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=32.53 E-value=17 Score=33.30 Aligned_cols=20 Identities=40% Similarity=0.855 Sum_probs=17.9
Q ss_pred hHHHHHHhhHh-HHHhhhccc
Q 020126 107 SVEALLLLQKS-MLEKQWNLS 126 (330)
Q Consensus 107 ~~~~~~~~~~~-~~~~~~~~~ 126 (330)
..++|.+|.|. |+|-||..|
T Consensus 44 ~~~~L~~LkK~gLiE~qWrmP 64 (160)
T PF09824_consen 44 VRESLLILKKGGLIESQWRMP 64 (160)
T ss_pred HHHHHHHHHHcCchhhccccC
Confidence 38999999885 999999998
No 180
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=31.32 E-value=63 Score=23.67 Aligned_cols=41 Identities=27% Similarity=0.421 Sum_probs=27.6
Q ss_pred CCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhh
Q 020126 204 ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (330)
Q Consensus 204 ~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~ 261 (330)
..||.+|-.++++.+..|. +..++|..+|++...+..++..
T Consensus 5 ~~LTl~eK~~iI~~~e~g~-----------------s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 5 KSLTLEEKLEIIKRLEEGE-----------------SKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp SS--HHHHHHHHHHHHCTT------------------HHHHHHHHT--CCHHHHHHHC
T ss_pred ccCCHHHHHHHHHHHHcCC-----------------CHHHHHHHhCCCHHHHHHHHHh
Confidence 5689999999999988875 3567777777777777666654
No 181
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=31.12 E-value=64 Score=26.24 Aligned_cols=26 Identities=35% Similarity=0.396 Sum_probs=19.8
Q ss_pred CCCCchHHHHHHhcCChHHHHHHHhh
Q 020126 236 GCEPSMEQLAASLRISRPELQSILME 261 (330)
Q Consensus 236 g~ePt~~e~A~a~~~s~~eL~~~l~~ 261 (330)
|+|.+.+++|.++|.+.++++.++..
T Consensus 36 G~PVt~~~LA~a~g~~~e~v~~~L~~ 61 (77)
T PF12324_consen 36 GQPVTVEQLAAALGWPVEEVRAALAA 61 (77)
T ss_dssp TS-B-HHHHHHHHT--HHHHHHHHHH
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHh
Confidence 88999999999999999999888764
No 182
>PRK13558 bacterio-opsin activator; Provisional
Probab=28.83 E-value=1.8e+02 Score=30.28 Aligned_cols=56 Identities=30% Similarity=0.269 Sum_probs=40.8
Q ss_pred CCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHHHh
Q 020126 205 LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSN 273 (330)
Q Consensus 205 lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~n 273 (330)
.||+.|..-|-.....|-+ ..=|+-|.+++|+.+|++..-+.+.++. |..+|+..+
T Consensus 607 ~lt~~q~e~l~~a~~~gyf----------~~pr~~~~~e~a~~l~is~~t~~~~lr~---a~~~l~~~~ 662 (665)
T PRK13558 607 DLTDRQLTALQKAYVSGYF----------EWPRRVEGEELAESMGISRSTFHQHLRA---AERKLVGAF 662 (665)
T ss_pred hCCHHHHHHHHHHHHcCCC----------CCCccCCHHHHHHHhCCCHHHHHHHHHH---HHHHHHHHH
Confidence 5777777777666666654 2235678899999999999999888884 555666554
No 183
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=28.78 E-value=1.1e+02 Score=25.59 Aligned_cols=35 Identities=17% Similarity=0.171 Sum_probs=27.6
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhh
Q 020126 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (330)
Q Consensus 227 ~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~ 261 (330)
+..-+...+..+++.+++|+.+|++..-|.++...
T Consensus 14 ~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 14 ILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 33445666777899999999999999888777765
No 184
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=28.47 E-value=1.1e+02 Score=24.28 Aligned_cols=49 Identities=24% Similarity=0.344 Sum_probs=34.5
Q ss_pred chHHHHHHhcCChHHHHHHHhhhHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHH
Q 020126 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGG 298 (330)
Q Consensus 240 t~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG 298 (330)
|-+++|..+|+++..+..+-..- ..-.+.|..+||+-| +..+||+++..
T Consensus 16 tQ~elA~~vgVsRQTi~~iEkgk-------y~Psl~La~kia~~f---~~~iedIF~~~ 64 (68)
T COG1476 16 TQEELAKLVGVSRQTIIAIEKGK-------YNPSLELALKIARVF---GKTIEDIFQLE 64 (68)
T ss_pred CHHHHHHHcCcCHHHHHHHHcCC-------CCchHHHHHHHHHHh---CCCHHHHHhhh
Confidence 45788999999988775543331 122456778888887 58999999854
No 185
>TIGR03764 ICE_PFGI_1_parB integrating conjugative element, PFGI_1 class, ParB family protein. Members of this protein family carry the ParB-type nuclease domain and are found in integrating conjugative elements (ICE) in the same class as PFGI-1 of Pseudomonas fluorescens Pf-5.
Probab=27.59 E-value=4.2e+02 Score=25.97 Aligned_cols=99 Identities=23% Similarity=0.284 Sum_probs=49.0
Q ss_pred CCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcC-----ChHH--------------HHHHHhh-
Q 020126 202 SEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRI-----SRPE--------------LQSILME- 261 (330)
Q Consensus 202 ~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~-----s~~e--------------L~~~l~~- 261 (330)
...-||+=|+..-.+++++. +++.+|..-|-+++|+.+|. +... +...+..
T Consensus 109 qR~dLsfIE~A~~~~~l~~l---------~e~~~g~~ltq~ela~~lgk~g~~isrs~Isn~lrll~~L~~~i~~~l~~g 179 (258)
T TIGR03764 109 LRGDLTFIEKALGVQKARAL---------YEKELGESLSQRELARRLSADGYPISQSHISRMGDTVEYLYPAIPNLLYSG 179 (258)
T ss_pred hhcCCCHHHHHHHHHHHHHH---------HHhhccCCCCHHHHHHHhcccCCCCCHHHHHHHHHHHHhChHHHHHHHHcc
Confidence 34667888777766555531 11223444555555555543 3332 2333322
Q ss_pred -hHHHHHHHHHHhHHHHHHHHHHccc-CCCChhHHHHHHHHHHHHHHhhcCCCCCCcc
Q 020126 262 -CSLAREKLVMSNVRLVMSIAQRYDN-MGADMADLVQGGLIGLLRGIEKFDSSKGFKI 317 (330)
Q Consensus 262 -g~~ArekLI~~nLpLV~sIAkrY~~-~Gvd~EDLIQEG~IGLikAIekFDpsrG~rF 317 (330)
|+.-...|.. -..-..+++.+|.. ..++|++++|+- ..+||....+.|
T Consensus 180 lGr~~~~~L~~-L~~~a~~~w~~~~~~~~~~f~~~f~~~-------~~~~d~~~~~~~ 229 (258)
T TIGR03764 180 LGRPQIEKLLS-LRKAAEKIWNRYSSGVEVDFEEVFQEV-------LARFDDPEEFSL 229 (258)
T ss_pred CChHHHHHHHH-HHHHHHHHHHHHccccCCCHHHHHHHH-------HHhcCCcccCCH
Confidence 2333333332 22233445555543 468899999875 467773333333
No 186
>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=27.18 E-value=1.4e+02 Score=28.38 Aligned_cols=51 Identities=27% Similarity=0.433 Sum_probs=38.3
Q ss_pred ChHHHHHHHhhhHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcC
Q 020126 251 SRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFD 310 (330)
Q Consensus 251 s~~eL~~~l~~g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFD 310 (330)
++.+...++..|..+ ++-|..++.+|...|+..+|+. +++-.--+|+++|-
T Consensus 143 sr~~~~~~l~~g~~~--------vR~vf~~~~~yr~~gvtR~D~~-~~n~~a~~Aie~~G 193 (216)
T TIGR03761 143 SRQDLEDWLDKGAHL--------IRRLFGLAQRYRHSGVTRDDFA-ANNARARKAIERFG 193 (216)
T ss_pred CHHHHHHHHHHHHHH--------HHHHHHHHHhhhcCCCCHHHHH-hCCHHHHHHHHHcC
Confidence 666666666665442 3446677889999999999998 67777888999985
No 187
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=27.01 E-value=4.9 Score=35.34 Aligned_cols=36 Identities=22% Similarity=0.182 Sum_probs=29.6
Q ss_pred hhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhh
Q 020126 291 MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIR 326 (330)
Q Consensus 291 ~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR 326 (330)
-+||+-.+-|--.+-|+-||-+.|.||+||+..--+
T Consensus 29 D~~Ll~aagi~p~E~V~V~Nv~NG~Rf~TYvI~g~~ 64 (126)
T PRK05449 29 DEDLLDAAGILENEKVQIVNVNNGARFETYVIAGER 64 (126)
T ss_pred CHHHHHhcCCCCCCEEEEEECCCCcEEEEEEEEcCC
Confidence 368888888888888999999999999999865433
No 188
>PF13730 HTH_36: Helix-turn-helix domain
Probab=26.89 E-value=2.3e+02 Score=19.88 Aligned_cols=26 Identities=42% Similarity=0.585 Sum_probs=21.4
Q ss_pred hCCCCchHHHHHHhcCChHHHHHHHh
Q 020126 235 LGCEPSMEQLAASLRISRPELQSILM 260 (330)
Q Consensus 235 lg~ePt~~e~A~a~~~s~~eL~~~l~ 260 (330)
.++-|+.+.+|..+|+++..+.+.+.
T Consensus 22 ~~~~pS~~~la~~~g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 22 GGCFPSQETLAKDLGVSRRTVQRAIK 47 (55)
T ss_pred CCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 35679999999999999988866554
No 189
>cd06919 Asp_decarbox Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalyzed by the enzyme L-aspartate decarboxylase (ADC), EC:4.1.1.11 which requires a pyruvoyl group for its activity. The pyruvoyl cofactor is covalently bound to the enzyme. The protein is synthesized as a proenzyme and cleaved via self-processing at Gly23-Ser24 to yield an alpha chain (C-terminal fragment) and beta chain (N-terminal fragment), and the pyruvoyl group. Beta-alanine is required for the biosynthesis of pantothenate, in which the enzyme plays a critical regulatory role. The active site of the tetrameric enzyme is located at the interface of two subunits, with a Lysine and a Histidine from the beta chain of one subunit forming the active site with residues from the alpha chain of the adjacent subunit. This alignment
Probab=26.86 E-value=4.9 Score=34.66 Aligned_cols=35 Identities=20% Similarity=0.131 Sum_probs=29.2
Q ss_pred hhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHh
Q 020126 291 MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWI 325 (330)
Q Consensus 291 ~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wI 325 (330)
-+||+-.+.|--.+-|+-||-+.|.||+||+..--
T Consensus 28 D~~Ll~aagi~~~E~V~I~Nv~NG~Rf~TYvI~g~ 62 (111)
T cd06919 28 DEDLLEAAGILPYEKVLVVNVNNGARFETYVIPGE 62 (111)
T ss_pred CHHHHHhcCCCCCCEEEEEECCCCcEEEEEEEEcC
Confidence 36788888888888899999999999999986543
No 190
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=26.07 E-value=3.6e+02 Score=21.96 Aligned_cols=56 Identities=23% Similarity=0.241 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHHHhHHHHHHHHH
Q 020126 206 LTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ 282 (330)
Q Consensus 206 LT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~nLpLV~sIAk 282 (330)
||+. |.++++.+.+|. +..++|+.++++...++..+. .++.+|-..|.+-+...+.
T Consensus 150 lt~~-e~~vl~l~~~g~-----------------~~~~Ia~~l~~s~~tv~~~~~---~~~~kl~~~~~~~l~~~~~ 205 (211)
T PRK15369 150 LTPR-ERQILKLITEGY-----------------TNRDIAEQLSISIKTVETHRL---NMMRKLDVHKVAELLNWAR 205 (211)
T ss_pred CCHH-HHHHHHHHHCCC-----------------CHHHHHHHhCCCHHHHHHHHH---HHHHHhCCCCHHHHHHHHH
Confidence 5444 566666665553 467888888888877765554 3444444445444444443
No 191
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=25.75 E-value=2.5e+02 Score=25.36 Aligned_cols=28 Identities=21% Similarity=0.237 Sum_probs=20.0
Q ss_pred CCCCchHHHHHHhcCChHHHHHHHhhhH
Q 020126 236 GCEPSMEQLAASLRISRPELQSILMECS 263 (330)
Q Consensus 236 g~ePt~~e~A~a~~~s~~eL~~~l~~g~ 263 (330)
|..+|.+++|..+|++..-|.+|.....
T Consensus 32 ~~r~T~~eiAee~Gis~~tLYrWr~~~~ 59 (142)
T PF13022_consen 32 GERRTQAEIAEEVGISRSTLYRWRQQNK 59 (142)
T ss_dssp ---S-HHHHHHHHTS-HHHHHHHHHH-H
T ss_pred cccchHHHHHHHhCCCHHHHHHHHhcCH
Confidence 4568999999999999999999986543
No 192
>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=23.62 E-value=2.7e+02 Score=20.80 Aligned_cols=59 Identities=19% Similarity=0.210 Sum_probs=36.8
Q ss_pred HHhhCCCCch------HHHHHHhcCChHHHHHHHhhhHHHHHHHHHHhHHHHHHHHHHcccCCCC-hhHH
Q 020126 232 KERLGCEPSM------EQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGAD-MADL 294 (330)
Q Consensus 232 ~~~lg~ePt~------~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~nLpLV~sIAkrY~~~Gvd-~EDL 294 (330)
+...||+||. .+|....|++.+-+..++..+.. . =..+.++|..|++.+...|+. .+|+
T Consensus 6 e~~~gr~ls~~e~~~i~~~~~~~~~~~evI~~ai~~a~~-~---~~~~~~Yi~~Il~~W~~~gi~T~e~~ 71 (73)
T TIGR01446 6 EENFGRMLSPFEMEDLKYWLDEFGNSPELIKEALKEAVS-N---NKANYKYIDAILNNWKNNGIKTVEDV 71 (73)
T ss_pred HHHhCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHH-c---CCCCHHHHHHHHHHHHHcCCCCHHHH
Confidence 3445555552 34555667776666666655433 1 124678999999999988864 5553
No 193
>PRK13159 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=23.34 E-value=82 Score=28.61 Aligned_cols=33 Identities=27% Similarity=0.281 Sum_probs=22.5
Q ss_pred eeeeccCCCCCCCCCCCCccchhhHHHhhhccccC-CCCCCC
Q 020126 49 VVAAKKSSNYNPSFPSSNRQTQPIKALKEHVDTNF-ASTAEP 89 (330)
Q Consensus 49 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~ 89 (330)
-+.||+.+||-| .+...|||++-.... |..+.|
T Consensus 118 ~vLAKHde~YmP--------~Ev~~al~~~~~~~~~~~~~~~ 151 (155)
T PRK13159 118 EVLAKHDETYMP--------KELKDAMAEGHLGKPIPAAAAP 151 (155)
T ss_pred EEEecCCCcCCC--------HHHHHHHHhccccCCCCCcccC
Confidence 467899999999 357778887654433 444444
No 194
>COG0853 PanD Aspartate 1-decarboxylase [Coenzyme metabolism]
Probab=23.33 E-value=7.8 Score=34.12 Aligned_cols=33 Identities=24% Similarity=0.248 Sum_probs=27.1
Q ss_pred hhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHH
Q 020126 291 MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYW 323 (330)
Q Consensus 291 ~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~ 323 (330)
-+||+..+-|==.+-|+-++-+.|.||+||+..
T Consensus 28 D~dlldaagile~EkV~I~N~nNGaRf~TYvI~ 60 (126)
T COG0853 28 DEDLLDAAGILENEKVDIVNVNNGARFSTYVIA 60 (126)
T ss_pred CHHHHhhcCCCCCceEEEEECCCCcEEEEEEEE
Confidence 367777776667788999999999999999853
No 195
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=23.32 E-value=2.7e+02 Score=19.44 Aligned_cols=24 Identities=25% Similarity=0.289 Sum_probs=18.2
Q ss_pred chHHHHHHhcCChHHHHHHHhhhH
Q 020126 240 SMEQLAASLRISRPELQSILMECS 263 (330)
Q Consensus 240 t~~e~A~a~~~s~~eL~~~l~~g~ 263 (330)
+.+|+|+.+|++...++..+..+.
T Consensus 28 s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 28 SYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp -HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHH
Confidence 568999999999999988877543
No 196
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.25 E-value=3.8e+02 Score=22.78 Aligned_cols=27 Identities=30% Similarity=0.370 Sum_probs=22.4
Q ss_pred CCCCchHHHHHHhcCChHHHHHHHhhh
Q 020126 236 GCEPSMEQLAASLRISRPELQSILMEC 262 (330)
Q Consensus 236 g~ePt~~e~A~a~~~s~~eL~~~l~~g 262 (330)
-++-+++++|.++|.+...+.+++.-.
T Consensus 21 l~~LS~~~iA~~Ln~t~~~lekil~~t 47 (97)
T COG4367 21 LCPLSDEEIATALNWTEVKLEKILQVT 47 (97)
T ss_pred hccccHHHHHHHhCCCHHHHHHHHHHh
Confidence 467789999999999999998887543
No 197
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=23.20 E-value=1.4e+02 Score=26.84 Aligned_cols=40 Identities=23% Similarity=0.359 Sum_probs=29.3
Q ss_pred HHHHHHHHcCccchhHHHHHHHhhCC-CCchHHHHHHhcCChHHHHHHHhh
Q 020126 212 VRLSKKIKTGLSLDDHKLRLKERLGC-EPSMEQLAASLRISRPELQSILME 261 (330)
Q Consensus 212 ~eL~rkIk~G~~Le~~~~~l~~~lg~-ePt~~e~A~a~~~s~~eL~~~l~~ 261 (330)
..|..+|..|.. .-|. =|+..|+|+.+|+|+.-+++.+..
T Consensus 15 ~~l~~~I~~g~~----------~~G~~LPsE~eLa~~~~VSR~TvR~Al~~ 55 (238)
T TIGR02325 15 DKIEQEIAAGHL----------RAGDYLPAEMQLAERFGVNRHTVRRAIAA 55 (238)
T ss_pred HHHHHHHHcCCC----------CCCCcCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 345666666654 2333 499999999999999999877665
No 198
>PF02261 Asp_decarbox: Aspartate decarboxylase; InterPro: IPR003190 Decarboxylation of aspartate is the major route of alanine production in bacteria, and is catalysed by the enzyme aspartate decarboxylase. The enzyme is translated as an inactive proenzyme of two chains, A and B. This family contains both chains of aspartate decarboxylase.; GO: 0004068 aspartate 1-decarboxylase activity, 0006523 alanine biosynthetic process; PDB: 1PYU_C 1AW8_A 1PYQ_B 3TM7_C 1PT1_A 1PQH_A 1PPY_B 1PT0_B 1PQF_A 1PQE_A ....
Probab=23.17 E-value=5.2 Score=34.74 Aligned_cols=33 Identities=21% Similarity=0.228 Sum_probs=24.8
Q ss_pred hhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHH
Q 020126 291 MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYW 323 (330)
Q Consensus 291 ~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~ 323 (330)
-+||+..+.|--.+-|+-|+-+.|.||+||+..
T Consensus 29 D~~Ll~aagi~p~E~V~V~Nv~nG~Rf~TYvI~ 61 (116)
T PF02261_consen 29 DEDLLDAAGILPYEQVQVVNVNNGERFETYVIP 61 (116)
T ss_dssp EHHHHHHCT--TTBEEEEEETTT--EEEEEEEE
T ss_pred CHHHHHHcCCCcCCEEEEEECCCCcEEEEEEEE
Confidence 368888888888888999999999999999854
No 199
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=23.16 E-value=2.1e+02 Score=20.12 Aligned_cols=23 Identities=22% Similarity=0.296 Sum_probs=17.6
Q ss_pred CCchHHHHHHhcCChHHHHHHHh
Q 020126 238 EPSMEQLAASLRISRPELQSILM 260 (330)
Q Consensus 238 ePt~~e~A~a~~~s~~eL~~~l~ 260 (330)
.-+..++|+.+|+|...+.+.++
T Consensus 17 r~s~~~la~~lglS~~~v~~Ri~ 39 (42)
T PF13404_consen 17 RRSYAELAEELGLSESTVRRRIR 39 (42)
T ss_dssp TS-HHHHHHHHTS-HHHHHHHHH
T ss_pred CccHHHHHHHHCcCHHHHHHHHH
Confidence 35678999999999999887765
No 200
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=22.95 E-value=4.1e+02 Score=22.17 Aligned_cols=29 Identities=17% Similarity=0.155 Sum_probs=22.2
Q ss_pred chHHHHHHhcCChHHHHHHHhhhHHHHHH
Q 020126 240 SMEQLAASLRISRPELQSILMECSLAREK 268 (330)
Q Consensus 240 t~~e~A~a~~~s~~eL~~~l~~g~~Arek 268 (330)
+..++|+.+|++...+...+..+..-..+
T Consensus 146 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 146 SYEEIAEIMGCPIGTVRSRIFRAREALRA 174 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 56899999999999998888855443333
No 201
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=22.38 E-value=1e+02 Score=20.18 Aligned_cols=23 Identities=22% Similarity=0.235 Sum_probs=17.9
Q ss_pred chHHHHHHhcCChHHHHHHHhhh
Q 020126 240 SMEQLAASLRISRPELQSILMEC 262 (330)
Q Consensus 240 t~~e~A~a~~~s~~eL~~~l~~g 262 (330)
+..|+|+.+|++...+..++..|
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~g 24 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKEG 24 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcC
Confidence 34688888999998888777765
No 202
>PF00427 PBS_linker_poly: Phycobilisome Linker polypeptide; InterPro: IPR001297 Phycobilisomes (PBSs) are the major light-harvesting systems in cyanobacteria and red algae. PBS is a supercomplex that is composed of a core complex and multiple peripheral rod complexes. Typically, the core consists of two or five cylinders lying on the membrane with, in most cases, multiple rods radiating from the core to form a hemidiscoidal structure. The building units of the core cylinders and the peripheral rods are trimeric and hexameric discs, in which a monomer consists of a pair of related phycobiliproteins (PBPs), such as phycorerythrins, phycoerythrocyanins, phycocyanins, and allophycocyanins. The discs are connected to each other via specific linker polypeptides to form peripheral rods or core cylinders. Linker polypeptides share a conserved domain of ~180 residues, which can be present in one or multiple copies [, , , , ].; GO: 0015979 photosynthesis, 0030089 phycobilisome; PDB: 2L8V_A 2KY4_A 3OSJ_D 2L06_A 3NPH_B 2L3W_A 3PRU_C 3OHW_A.
Probab=22.07 E-value=5.5e+02 Score=22.65 Aligned_cols=96 Identities=17% Similarity=0.241 Sum_probs=60.6
Q ss_pred CChhhhhhhH-HHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhh
Q 020126 184 ISPELIQNRL-KGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMEC 262 (330)
Q Consensus 184 ~~pEl~q~~l-~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g 262 (330)
.+++.++..+ ..|.+=+++...+..+....|=.+++.|. ++..++.+.+...
T Consensus 5 ~s~~~~~~vI~AaYrQVf~~~~~~~~er~~~lESqlrng~---------------------------IsVreFVr~La~S 57 (131)
T PF00427_consen 5 SSEEELEAVIRAAYRQVFGNDHPMESERLISLESQLRNGQ---------------------------ISVREFVRALAKS 57 (131)
T ss_dssp S-HHHHHHHHHHHHHHHHSSSSSHCSHHTHHHHHHHHTTS---------------------------S-HHHHHHHHHTS
T ss_pred CCHHHHHHHHHHHHHHHhcCccchhhhccchHHHHHHcCC---------------------------CcHHHHHHHHHcC
Confidence 3344344444 33444444555555555555555666654 5777788888888
Q ss_pred HHHHHHHHH--HhHHHHHHHHHHcccCCCC--------hhHHHHHHHHHHHHHH
Q 020126 263 SLAREKLVM--SNVRLVMSIAQRYDNMGAD--------MADLVQGGLIGLLRGI 306 (330)
Q Consensus 263 ~~ArekLI~--~nLpLV~sIAkrY~~~Gvd--------~EDLIQEG~IGLikAI 306 (330)
..-++.++. .+.+.|.-.-+++.+|... ..-+-..|.-|++.++
T Consensus 58 ~~yr~~f~~~~~~~R~iEl~~khlLGR~p~~~~Ei~~~~~i~a~~G~~a~Id~l 111 (131)
T PF00427_consen 58 ELYRKRFFEPNSNYRFIELAFKHLLGRAPYNQAEISAYSQILASQGFEAFIDAL 111 (131)
T ss_dssp HHHHHHHTTTS-HHHHHHHHHHHHCSS--SSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHcccccchHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcChHHHHHHH
Confidence 888999988 7888999999999998654 3344567777777775
No 203
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=21.97 E-value=2.8e+02 Score=19.22 Aligned_cols=26 Identities=31% Similarity=0.428 Sum_probs=20.6
Q ss_pred CCCchHHHHHHhcCChHHHHHHHhhh
Q 020126 237 CEPSMEQLAASLRISRPELQSILMEC 262 (330)
Q Consensus 237 ~ePt~~e~A~a~~~s~~eL~~~l~~g 262 (330)
..-|..|+|..+|+|...++.+...+
T Consensus 19 ~~~t~~eIa~~lg~s~~~V~~~~~~a 44 (50)
T PF04545_consen 19 EGLTLEEIAERLGISRSTVRRILKRA 44 (50)
T ss_dssp ST-SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCcHHHHHHHHHHH
Confidence 34478999999999999998887654
No 204
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=21.87 E-value=4e+02 Score=22.14 Aligned_cols=34 Identities=15% Similarity=0.101 Sum_probs=25.7
Q ss_pred CchHHHHHHhcCChHHHHHHHhhhHHHHHHHHHH
Q 020126 239 PSMEQLAASLRISRPELQSILMECSLAREKLVMS 272 (330)
Q Consensus 239 Pt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~ 272 (330)
=+.+++|+.+|++...++..+..+.....+.+..
T Consensus 142 ~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~~ 175 (179)
T PRK11924 142 LSYREIAEILGVPVGTVKSRLRRARQLLRECLEA 175 (179)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 3568999999999999998888766555544443
No 205
>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=21.81 E-value=5e+02 Score=24.33 Aligned_cols=57 Identities=18% Similarity=0.285 Sum_probs=40.8
Q ss_pred CCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHH
Q 020126 238 EPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRG 305 (330)
Q Consensus 238 ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikA 305 (330)
.-+.+|+|..+|++...++..+..+.....+. +....+.+|..+.-.+|-+ |||++.
T Consensus 177 g~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~------l~~~~~~~~~~~~~~~~~~-----~~~~~~ 233 (244)
T TIGR03001 177 GLSMDRIGAMYQVHRSTVSRWVAQARERLLER------TRRRLAERLKLSSPELESL-----LGLVRS 233 (244)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH------HHHHHHHhcCCCcccHHHH-----HHHHHh
Confidence 35689999999999999999988665544433 4566788887666666544 566654
No 206
>PRK13150 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=21.55 E-value=67 Score=29.30 Aligned_cols=24 Identities=38% Similarity=0.509 Sum_probs=18.8
Q ss_pred eeeeccCCCCCCCCCCCCccchhhHHHhhhcc
Q 020126 49 VVAAKKSSNYNPSFPSSNRQTQPIKALKEHVD 80 (330)
Q Consensus 49 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (330)
-+.||+.+||-| ..+..||+++-.
T Consensus 125 evLAKhdekYmP--------pEv~~al~~~~~ 148 (159)
T PRK13150 125 EVLAKHDENYTP--------PEVEKAMQENHR 148 (159)
T ss_pred EEEeCCCCCCCC--------HHHHHHHHHhCC
Confidence 467999999999 357788987544
No 207
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=21.51 E-value=4.3e+02 Score=22.09 Aligned_cols=35 Identities=17% Similarity=0.184 Sum_probs=26.7
Q ss_pred CCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHH
Q 020126 237 CEPSMEQLAASLRISRPELQSILMECSLAREKLVM 271 (330)
Q Consensus 237 ~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~ 271 (330)
..-+.+++|..+|++...+...+..+.....+.+.
T Consensus 126 ~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~ 160 (166)
T PRK09639 126 SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYE 160 (166)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 34467899999999999999888876665555444
No 208
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=20.94 E-value=1.1e+02 Score=20.18 Aligned_cols=23 Identities=22% Similarity=0.345 Sum_probs=17.2
Q ss_pred chHHHHHHhcCChHHHHHHHhhh
Q 020126 240 SMEQLAASLRISRPELQSILMEC 262 (330)
Q Consensus 240 t~~e~A~a~~~s~~eL~~~l~~g 262 (330)
|.+|.|+.+|++...+..+++.|
T Consensus 3 t~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHHcC
Confidence 45678888888888877776654
No 209
>PF08101 DUF1708: Domain of unknown function (DUF1708); InterPro: IPR012965 This is a fungal domain of unknown function, though the yeast protein MSB1(P21339 from SWISSPROT) which contains this domain is thought to play a role in bud formation [].
Probab=20.66 E-value=9.8e+02 Score=25.00 Aligned_cols=152 Identities=16% Similarity=0.097 Sum_probs=85.3
Q ss_pred cccccchhcccCChhhhhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCC-------chHHH-
Q 020126 173 QQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEP-------SMEQL- 244 (330)
Q Consensus 173 ~~~~~k~~~~~~~pEl~q~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~eP-------t~~e~- 244 (330)
++=-+-++++..+++.+...++.|...-...+.... ..+.+.++.-+. -.+-.-|+=-..|=| .+.+|
T Consensus 26 tp~lllpfrp~~~~~~~~~fi~~~f~~~~~~~~~~~---~~~~~el~~~~~-~~L~~~LKw~w~RLp~gvVgW~~Y~~Fk 101 (420)
T PF08101_consen 26 TPFLLLPFRPDSDPSALRRFIRSFFPQGNGSPVLDG---EALIQELRFTSP-HTLISVLKWIWSRLPGGVVGWDSYEEFK 101 (420)
T ss_pred CchhccCCCCCCCHHHHHHHHHHhCCCccCcccccH---HHHHHHHhcCCc-hHHHHHHHHHHHHcCCCccccHHHHHHH
Confidence 344567788888888766667666655544433222 223233332111 111111111111111 12333
Q ss_pred --HHHhcCChHHHHHHHhhhH--HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhH
Q 020126 245 --AASLRISRPELQSILMECS--LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320 (330)
Q Consensus 245 --A~a~~~s~~eL~~~l~~g~--~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTY 320 (330)
.+..|.........|..+- .+...+|..++.|+.+||.+=...|+.-.-|-|-.-+-+......-.......|...
T Consensus 102 ~~E~~~~yp~~AF~~~lp~~l~s~a~~~Iv~dFfdLL~sIaa~s~~NglsgrKlsrm~g~WaF~~~~~~~~~~~~~f~~g 181 (420)
T PF08101_consen 102 RREREAGYPRDAFLTFLPQCLPSPAHASIVYDFFDLLSSIAAHSKKNGLSGRKLSRMAGIWAFGHPDFGKDSGFNSFEEG 181 (420)
T ss_pred HHHhhcCCChHHHHHhccccCCChhHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHCCCCCcccCCCcccHHHH
Confidence 3557888888888888875 788999999999999999986556777666655333322222111111111468888
Q ss_pred HHHHhhcc
Q 020126 321 VYWWIRQS 328 (330)
Q Consensus 321 A~~wIR~a 328 (330)
...|++.+
T Consensus 182 y~~W~~aa 189 (420)
T PF08101_consen 182 YKAWIRAA 189 (420)
T ss_pred HHHHHHHH
Confidence 77787653
No 210
>COG0140 HisI Phosphoribosyl-ATP pyrophosphohydrolase [Amino acid transport and metabolism]
Probab=20.45 E-value=5.2e+02 Score=21.71 Aligned_cols=36 Identities=17% Similarity=0.254 Sum_probs=26.5
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHH
Q 020126 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQG 297 (330)
Q Consensus 262 g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQE 297 (330)
....++.|+..--.|+.+.---....|++++|.+++
T Consensus 48 ~~~d~e~l~~E~ADLlYH~lVlL~~~gv~l~dV~~e 83 (92)
T COG0140 48 KDEDKEELVSEAADLLYHLLVLLAAQGLSLEDVLRE 83 (92)
T ss_pred HhcchHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHH
Confidence 334456677777777777777777789999999876
No 211
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=20.40 E-value=1.8e+02 Score=26.96 Aligned_cols=41 Identities=27% Similarity=0.352 Sum_probs=30.6
Q ss_pred HHHHHHHHHcCccchhHHHHHHHhhC-CCCchHHHHHHhcCChHHHHHHHhh
Q 020126 211 VVRLSKKIKTGLSLDDHKLRLKERLG-CEPSMEQLAASLRISRPELQSILME 261 (330)
Q Consensus 211 E~eL~rkIk~G~~Le~~~~~l~~~lg-~ePt~~e~A~a~~~s~~eL~~~l~~ 261 (330)
..+|..+|..|.. ..| .=|+..++|+.+|+|+.-+++.+..
T Consensus 13 ~~~i~~~I~~G~~----------~~G~~LPsE~eLa~~f~VSR~TvRkAL~~ 54 (236)
T COG2188 13 AEDIRQRIESGEL----------PPGDKLPSERELAEQFGVSRMTVRKALDE 54 (236)
T ss_pred HHHHHHHHHhCCC----------CCCCCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 3456777777765 234 3499999999999999999766654
No 212
>PRK15044 transcriptional regulator SirC; Provisional
Probab=20.32 E-value=2.1e+02 Score=28.48 Aligned_cols=60 Identities=18% Similarity=0.138 Sum_probs=42.0
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhh
Q 020126 193 LKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (330)
Q Consensus 193 l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~ 261 (330)
+-.|++.-+..+.|..+.......+ ...-+.+.++.+++.+++|+.+|+|..-|.+....
T Consensus 172 Ls~~l~~~~~~~~L~~~~~is~~~k---------V~~~I~~nl~~~~SLeeLA~~lgmS~~tL~R~Fk~ 231 (295)
T PRK15044 172 ISAFVRKPGGFDFLERAIKITTKEK---------VYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAA 231 (295)
T ss_pred HHHHHhcccchhhHHHHhhhhHHHH---------HHHHHHhCcccCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 4566666555565555544333222 33445667788999999999999999999888765
No 213
>TIGR00223 panD L-aspartate-alpha-decarboxylase. Members of this family are aspartate 1-decarboxylase, the enzyme that makes beta-alanine and C02 from aspartate. Beta-alanine is then used to make the vitamin pantothenate, from which coenzyme A is made. Aspartate 1-decarboxylase is synthesized as a proenzyme, then cleaved to an alpha (C-terminal) and beta (N-terminal) subunit with a pyruvoyl group.
Probab=20.26 E-value=8.1 Score=34.02 Aligned_cols=36 Identities=22% Similarity=0.175 Sum_probs=28.9
Q ss_pred hhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhh
Q 020126 291 MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIR 326 (330)
Q Consensus 291 ~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR 326 (330)
-+||+-.+-|--.+-|+-||-+.|.||+||+..--|
T Consensus 29 D~~Lm~aagi~p~E~V~V~Nv~NG~Rf~TYvI~G~~ 64 (126)
T TIGR00223 29 DEDLLDAAGILENEKVDIVNVNNGKRFSTYAIAGKR 64 (126)
T ss_pred CHHHHHhcCCCCCCEEEEEECCCCcEEEEEEEEcCC
Confidence 357777777777888899999999999999865433
No 214
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=20.21 E-value=1.7e+02 Score=26.47 Aligned_cols=24 Identities=25% Similarity=0.230 Sum_probs=20.8
Q ss_pred CCchHHHHHHhcCChHHHHHHHhh
Q 020126 238 EPSMEQLAASLRISRPELQSILME 261 (330)
Q Consensus 238 ePt~~e~A~a~~~s~~eL~~~l~~ 261 (330)
=|+..|+|+.+|+|+.-+++.+..
T Consensus 24 LPsE~eLa~~~gVSR~TVR~Al~~ 47 (233)
T TIGR02404 24 LPSEHELMDQYGASRETVRKALNL 47 (233)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHH
Confidence 499999999999999998776654
No 215
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=20.14 E-value=1.8e+02 Score=24.21 Aligned_cols=45 Identities=22% Similarity=0.224 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhh
Q 020126 206 LTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMEC 262 (330)
Q Consensus 206 LT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g 262 (330)
||++|.+.-...+++.-. -.--|.+++|..+++|.+++.+++.-.
T Consensus 3 Ln~~Q~~~T~~ELq~nf~------------~~~ls~~~ia~dL~~s~~~le~vL~l~ 47 (89)
T PF10078_consen 3 LNPEQRRATRQELQANFE------------LSGLSLEQIAADLGTSPEHLEQVLNLK 47 (89)
T ss_pred CCHHHHHHHHHHHHHHHH------------HcCCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 667766665555554221 123567899999999999999998865
No 216
>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=20.09 E-value=5.4e+02 Score=24.20 Aligned_cols=65 Identities=22% Similarity=0.355 Sum_probs=36.8
Q ss_pred ChhhhhhhHHHHHHhcCCC-CCCCHHHHHHHHHHHHcCccchhHHHHHHHhh-C-CCC-chHHHHHHhcCChHHHHHHH
Q 020126 185 SPELIQNRLKGYVKGVVSE-ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERL-G-CEP-SMEQLAASLRISRPELQSIL 259 (330)
Q Consensus 185 ~pEl~q~~l~~YL~~i~~~-~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~l-g-~eP-t~~e~A~a~~~s~~eL~~~l 259 (330)
.--++...+..||+.-... .+-+.....++..+++. ++..+ + +.| +.+|+|+.+|++.+++..++
T Consensus 92 A~~~Ir~~i~~~l~~~~~~ir~p~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~~eiA~~l~~~~~~v~~~~ 160 (270)
T TIGR02392 92 AVHWIKAEIHEYILRNWRLVKVATTKAQRKLFFNLRK----------MKKRLQGWLNPEEVEAIAEELGVSEREVREME 160 (270)
T ss_pred hHHHHHHHHHHHHHHcCCceecCchHHHHHHHHHHHH----------HHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 3345666777777654221 11123333444444432 12222 2 455 68999999999999987754
Done!