Query 016321
Match_columns 391
No_of_seqs 256 out of 1874
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 05:48:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016321.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016321hhsearch_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 5.5E-36 1.2E-40 304.1 18.0 194 191-384 60-301 (415)
2 TIGR02997 Sig70-cyanoRpoD RNA 100.0 1.8E-34 3.9E-39 279.0 17.7 192 192-383 2-199 (298)
3 PRK07406 RNA polymerase sigma 100.0 2.3E-34 5E-39 288.9 17.9 191 191-381 63-259 (373)
4 PRK05949 RNA polymerase sigma 100.0 7E-33 1.5E-37 273.2 17.6 192 191-382 18-215 (327)
5 PRK05901 RNA polymerase sigma 100.0 1.8E-32 3.9E-37 284.4 14.2 180 190-382 210-395 (509)
6 PRK07405 RNA polymerase sigma 100.0 7.7E-32 1.7E-36 264.3 17.5 193 191-383 8-206 (317)
7 PRK07921 RNA polymerase sigma 100.0 2.6E-29 5.6E-34 248.0 14.9 180 191-383 26-211 (324)
8 COG0568 RpoD DNA-directed RNA 100.0 2.4E-29 5.2E-34 250.1 14.5 193 191-384 9-228 (342)
9 PRK09210 RNA polymerase sigma 99.9 2.7E-26 5.9E-31 229.1 13.2 155 189-383 94-254 (367)
10 PRK05658 RNA polymerase sigma 99.9 2.1E-26 4.6E-31 243.3 12.9 155 192-383 345-505 (619)
11 PRK06596 RNA polymerase factor 99.9 9.7E-25 2.1E-29 210.8 15.2 158 183-383 9-173 (284)
12 TIGR02392 rpoH_proteo alternat 99.9 8.8E-25 1.9E-29 208.8 14.2 152 192-383 2-161 (270)
13 PRK07122 RNA polymerase sigma 99.9 2.6E-24 5.6E-29 205.9 10.5 121 264-384 40-166 (264)
14 PRK07500 rpoH2 RNA polymerase 99.9 4.6E-23 9.9E-28 199.8 15.3 152 191-382 6-169 (289)
15 COG1191 FliA DNA-directed RNA 99.9 3.3E-22 7.1E-27 191.8 12.0 141 204-387 4-152 (247)
16 TIGR02393 RpoD_Cterm RNA polym 99.9 7.1E-22 1.5E-26 184.9 9.8 118 265-383 1-125 (238)
17 PRK05657 RNA polymerase sigma 99.9 2.8E-21 6.2E-26 190.6 13.9 153 189-382 51-210 (325)
18 PRK07408 RNA polymerase sigma 99.8 8.1E-21 1.7E-25 180.5 12.1 119 264-382 25-150 (256)
19 TIGR02394 rpoS_proteo RNA poly 99.8 2.7E-19 5.8E-24 172.1 13.6 114 188-341 10-123 (285)
20 PRK05911 RNA polymerase sigma 99.8 2E-19 4.3E-24 171.3 10.6 118 262-383 21-148 (257)
21 TIGR02850 spore_sigG RNA polym 99.8 1E-18 2.2E-23 165.4 13.5 141 201-384 11-159 (254)
22 PRK08215 sporulation sigma fac 99.8 1.6E-18 3.4E-23 164.2 13.5 141 201-383 14-161 (258)
23 PRK06288 RNA polymerase sigma 99.7 5E-17 1.1E-21 155.0 13.1 140 200-383 6-156 (268)
24 TIGR02941 Sigma_B RNA polymera 99.7 1.6E-16 3.4E-21 149.9 11.9 98 204-341 8-106 (255)
25 TIGR02980 SigBFG RNA polymeras 99.7 1.9E-16 4.1E-21 146.3 10.3 120 263-382 2-127 (227)
26 PRK12427 flagellar biosynthesi 99.7 2.9E-16 6.2E-21 147.8 9.3 115 264-383 15-139 (231)
27 TIGR02885 spore_sigF RNA polym 99.6 8.1E-16 1.7E-20 142.7 11.2 120 262-383 9-135 (231)
28 PRK08583 RNA polymerase sigma 99.6 3.3E-15 7.2E-20 141.1 12.8 101 204-344 8-109 (257)
29 PRK05803 sporulation sigma fac 99.6 7.5E-15 1.6E-19 137.1 13.5 107 192-338 17-123 (233)
30 PRK05572 sporulation sigma fac 99.6 8.3E-15 1.8E-19 138.5 13.7 99 199-337 7-105 (252)
31 TIGR02895 spore_sigI RNA polym 99.6 2.6E-15 5.6E-20 141.8 8.2 79 260-338 5-85 (218)
32 PRK07670 RNA polymerase sigma 99.6 2.4E-14 5.3E-19 135.2 13.4 115 264-383 22-147 (251)
33 TIGR02479 FliA_WhiG RNA polyme 99.5 1.7E-14 3.6E-19 133.6 9.6 69 269-337 1-72 (224)
34 PRK06986 fliA flagellar biosyn 99.5 1.4E-13 3.1E-18 128.6 10.3 118 261-382 5-132 (236)
35 TIGR02846 spore_sigmaK RNA pol 99.3 2.3E-11 4.9E-16 113.5 12.5 106 193-338 16-122 (227)
36 PRK08301 sporulation sigma fac 99.3 4.1E-11 8.9E-16 111.6 12.6 103 196-338 23-126 (234)
37 PF04542 Sigma70_r2: Sigma-70 99.2 4E-11 8.7E-16 90.5 7.6 70 269-338 1-70 (71)
38 TIGR02835 spore_sigmaE RNA pol 99.2 2.6E-10 5.7E-15 106.9 12.1 96 203-338 31-126 (234)
39 PRK08311 putative RNA polymera 99.1 3.5E-10 7.5E-15 108.1 10.9 76 263-338 17-94 (237)
40 PRK08295 RNA polymerase factor 99.0 1.6E-09 3.4E-14 98.0 11.0 77 262-338 22-98 (208)
41 TIGR02937 sigma70-ECF RNA poly 99.0 1.8E-09 4E-14 89.4 7.7 72 265-338 2-73 (158)
42 TIGR02859 spore_sigH RNA polym 98.9 6.8E-09 1.5E-13 93.0 11.0 77 262-338 17-93 (198)
43 PRK09652 RNA polymerase sigma 98.8 1.2E-08 2.6E-13 89.0 7.8 76 261-338 7-82 (182)
44 PRK09648 RNA polymerase sigma 98.8 3.9E-08 8.4E-13 88.2 10.8 74 264-338 24-101 (189)
45 PRK11922 RNA polymerase sigma 98.8 4.7E-08 1E-12 91.4 10.4 96 201-338 7-102 (231)
46 PRK09646 RNA polymerase sigma 98.8 3.9E-08 8.5E-13 89.0 9.4 75 263-338 29-103 (194)
47 PRK05602 RNA polymerase sigma 98.7 7.5E-08 1.6E-12 86.2 9.4 75 262-337 18-92 (186)
48 PRK06759 RNA polymerase factor 98.7 8.1E-08 1.7E-12 82.8 8.6 73 264-338 4-76 (154)
49 PRK09641 RNA polymerase sigma 98.7 1.1E-07 2.4E-12 84.3 9.3 75 262-338 16-90 (187)
50 TIGR02948 SigW_bacill RNA poly 98.7 1.1E-07 2.3E-12 84.3 9.2 74 262-337 16-89 (187)
51 PRK12513 RNA polymerase sigma 98.6 1.5E-07 3.3E-12 84.7 9.6 75 263-339 25-99 (194)
52 PRK09640 RNA polymerase sigma 98.6 2.1E-07 4.4E-12 83.8 10.1 87 250-338 8-98 (188)
53 PRK11923 algU RNA polymerase s 98.6 2.5E-07 5.4E-12 83.1 9.8 73 264-338 20-92 (193)
54 PRK13919 putative RNA polymera 98.6 2E-07 4.4E-12 83.0 8.8 76 262-338 21-96 (186)
55 PRK06811 RNA polymerase factor 98.6 3.8E-07 8.3E-12 82.3 10.2 75 263-338 17-94 (189)
56 PRK12519 RNA polymerase sigma 98.5 3.1E-07 6.7E-12 82.6 8.9 74 263-338 28-101 (194)
57 PRK09638 RNA polymerase sigma 98.5 5.3E-07 1.2E-11 79.5 9.6 75 262-338 16-90 (176)
58 TIGR02952 Sig70_famx2 RNA poly 98.5 9.2E-07 2E-11 77.1 9.3 77 261-338 8-84 (170)
59 PRK12526 RNA polymerase sigma 98.5 1.3E-06 2.8E-11 80.3 10.4 74 264-338 38-111 (206)
60 PRK11924 RNA polymerase sigma 98.4 1.1E-06 2.3E-11 76.5 9.1 76 261-338 10-85 (179)
61 PRK12524 RNA polymerase sigma 98.4 8.5E-07 1.9E-11 80.5 8.7 75 263-338 25-99 (196)
62 PRK12514 RNA polymerase sigma 98.4 1.4E-06 3.1E-11 77.3 9.4 74 263-337 18-91 (179)
63 PRK12534 RNA polymerase sigma 98.4 1.3E-06 2.9E-11 78.0 8.8 74 263-337 24-97 (187)
64 TIGR02985 Sig70_bacteroi1 RNA 98.4 3.2E-06 6.9E-11 72.2 10.8 72 265-338 2-73 (161)
65 TIGR02939 RpoE_Sigma70 RNA pol 98.4 2.1E-06 4.5E-11 76.3 9.9 75 262-338 18-92 (190)
66 PRK12531 RNA polymerase sigma 98.4 1.8E-06 3.8E-11 78.3 9.4 75 263-338 26-100 (194)
67 PRK12536 RNA polymerase sigma 98.3 5.5E-06 1.2E-10 74.2 10.8 75 262-338 19-94 (181)
68 TIGR02989 Sig-70_gvs1 RNA poly 98.3 2.6E-06 5.6E-11 73.7 8.1 73 265-339 2-74 (159)
69 TIGR02954 Sig70_famx3 RNA poly 98.3 4.6E-06 1E-10 73.4 9.3 75 262-338 14-88 (169)
70 TIGR02984 Sig-70_plancto1 RNA 98.3 5E-06 1.1E-10 73.7 9.4 75 262-336 5-83 (189)
71 PRK12538 RNA polymerase sigma 98.2 5.5E-06 1.2E-10 78.4 9.1 72 264-336 63-134 (233)
72 PRK12512 RNA polymerase sigma 98.2 1.6E-05 3.4E-10 71.0 10.6 75 262-338 20-98 (184)
73 PRK12522 RNA polymerase sigma 98.2 7E-06 1.5E-10 72.7 8.1 73 264-338 3-75 (173)
74 PRK09643 RNA polymerase sigma 98.1 1.5E-05 3.3E-10 72.4 9.8 75 262-338 25-99 (192)
75 PRK12515 RNA polymerase sigma 98.1 1.7E-05 3.6E-10 71.4 9.2 74 262-337 20-93 (189)
76 PRK12539 RNA polymerase sigma 98.1 4E-05 8.7E-10 68.8 11.0 74 263-338 20-97 (184)
77 PRK12537 RNA polymerase sigma 98.1 1.8E-05 4E-10 70.8 8.7 76 262-338 21-96 (182)
78 PRK12518 RNA polymerase sigma 98.0 3.3E-05 7.2E-10 68.1 8.9 74 261-337 8-81 (175)
79 PRK12543 RNA polymerase sigma 98.0 2.5E-05 5.4E-10 69.8 7.9 74 262-337 5-78 (179)
80 PRK09415 RNA polymerase factor 97.9 3.4E-05 7.4E-10 69.1 8.1 74 262-337 14-87 (179)
81 PRK12542 RNA polymerase sigma 97.9 2.2E-05 4.8E-10 70.3 6.8 78 261-338 6-83 (185)
82 PRK09639 RNA polymerase sigma 97.9 9E-05 1.9E-09 64.7 9.5 71 264-338 3-73 (166)
83 PRK09649 RNA polymerase sigma 97.9 8.1E-05 1.8E-09 67.3 9.3 72 264-338 24-95 (185)
84 TIGR02999 Sig-70_X6 RNA polyme 97.9 7.2E-05 1.6E-09 66.4 8.7 74 263-338 16-95 (183)
85 COG1595 RpoE DNA-directed RNA 97.8 0.00012 2.5E-09 65.9 9.6 83 256-340 7-89 (182)
86 TIGR02983 SigE-fam_strep RNA p 97.8 0.0001 2.2E-09 64.2 8.2 75 262-338 4-78 (162)
87 PF00140 Sigma70_r1_2: Sigma-7 97.7 8E-06 1.7E-10 57.6 0.4 33 191-223 2-34 (37)
88 PRK12547 RNA polymerase sigma 97.7 0.00014 3.1E-09 64.1 8.2 75 262-338 4-78 (164)
89 PRK09644 RNA polymerase sigma 97.7 0.00015 3.2E-09 63.8 7.6 70 266-338 3-72 (165)
90 PRK08241 RNA polymerase factor 97.6 0.00025 5.4E-09 69.6 9.5 75 262-338 17-91 (339)
91 PRK12528 RNA polymerase sigma 97.6 0.00081 1.8E-08 58.8 11.0 71 264-337 4-74 (161)
92 PRK12541 RNA polymerase sigma 97.6 0.00028 6E-09 61.7 7.9 73 263-338 4-76 (161)
93 PRK09645 RNA polymerase sigma 97.6 0.00032 6.9E-09 61.9 8.2 75 263-338 8-82 (173)
94 TIGR02947 SigH_actino RNA poly 97.5 0.00029 6.4E-09 63.6 7.6 75 262-338 9-83 (193)
95 PRK09647 RNA polymerase sigma 97.5 0.0004 8.7E-09 64.3 8.3 73 262-337 26-98 (203)
96 TIGR03001 Sig-70_gmx1 RNA poly 97.5 0.0006 1.3E-08 65.3 9.4 74 263-338 38-118 (244)
97 TIGR02950 SigM_subfam RNA poly 97.5 0.00022 4.8E-09 61.3 5.8 65 271-338 2-66 (154)
98 PRK12520 RNA polymerase sigma 97.5 0.00037 8E-09 62.8 7.3 72 265-338 3-74 (191)
99 PRK12516 RNA polymerase sigma 97.4 0.00074 1.6E-08 61.5 8.8 74 263-338 9-82 (187)
100 PRK12535 RNA polymerase sigma 97.4 0.0012 2.7E-08 60.6 10.0 74 262-338 23-96 (196)
101 TIGR02943 Sig70_famx1 RNA poly 97.4 0.00049 1.1E-08 62.4 7.0 70 267-338 5-74 (188)
102 PRK12532 RNA polymerase sigma 97.3 0.00062 1.3E-08 61.6 7.2 70 267-338 8-78 (195)
103 TIGR02960 SigX5 RNA polymerase 97.3 0.00085 1.8E-08 65.2 8.4 74 263-338 4-77 (324)
104 PRK09637 RNA polymerase sigma 97.3 0.00096 2.1E-08 60.3 8.2 71 266-338 3-73 (181)
105 PRK09642 RNA polymerase sigma 97.3 0.00083 1.8E-08 58.5 7.3 65 271-338 2-66 (160)
106 PRK12529 RNA polymerase sigma 97.2 0.0025 5.5E-08 57.1 10.0 77 261-337 10-88 (178)
107 PRK12533 RNA polymerase sigma 97.2 0.0019 4E-08 60.8 9.1 74 262-338 16-89 (216)
108 TIGR02959 SigZ RNA polymerase 97.2 0.00099 2.1E-08 59.3 6.7 66 271-338 2-67 (170)
109 PRK09651 RNA polymerase sigma 97.2 0.0056 1.2E-07 54.5 11.3 73 262-337 8-80 (172)
110 PRK12523 RNA polymerase sigma 97.1 0.0014 3E-08 58.2 7.1 73 263-338 9-81 (172)
111 PRK12546 RNA polymerase sigma 97.0 0.0029 6.3E-08 57.9 8.5 72 264-338 8-79 (188)
112 PRK12540 RNA polymerase sigma 97.0 0.0026 5.7E-08 57.6 8.0 73 264-338 5-77 (182)
113 PRK12517 RNA polymerase sigma 97.0 0.0033 7.1E-08 57.2 8.1 71 261-333 20-90 (188)
114 PRK07037 extracytoplasmic-func 96.9 0.0029 6.3E-08 55.2 6.6 68 268-338 2-69 (163)
115 PRK12544 RNA polymerase sigma 96.8 0.004 8.6E-08 57.8 7.7 70 267-338 21-90 (206)
116 PRK12545 RNA polymerase sigma 96.8 0.0037 7.9E-08 57.4 7.3 69 268-338 12-80 (201)
117 PRK12530 RNA polymerase sigma 96.5 0.007 1.5E-07 54.9 6.9 69 268-338 11-79 (189)
118 PF04539 Sigma70_r3: Sigma-70 96.4 0.0056 1.2E-07 48.0 4.5 37 225-261 7-43 (78)
119 PRK12511 RNA polymerase sigma 96.3 0.012 2.6E-07 53.5 7.2 71 266-338 6-76 (182)
120 PRK12525 RNA polymerase sigma 96.0 0.094 2E-06 46.4 11.1 70 264-336 9-78 (168)
121 PRK12527 RNA polymerase sigma 96.0 0.017 3.6E-07 50.4 6.0 64 271-337 2-65 (159)
122 PRK09636 RNA polymerase sigma 95.9 0.017 3.7E-07 56.1 6.4 69 265-337 5-73 (293)
123 TIGR02957 SigX4 RNA polymerase 95.8 0.021 4.6E-07 55.3 6.3 66 268-337 1-66 (281)
124 PRK05658 RNA polymerase sigma 95.7 0.015 3.2E-07 62.9 5.6 34 190-223 103-136 (619)
125 PRK09191 two-component respons 95.5 0.091 2E-06 48.4 9.3 63 265-329 2-64 (261)
126 PF12645 HTH_16: Helix-turn-he 95.3 0.077 1.7E-06 41.9 6.9 49 262-310 11-65 (65)
127 PRK06704 RNA polymerase factor 95.2 0.049 1.1E-06 52.2 6.7 79 254-338 8-86 (228)
128 PF07638 Sigma70_ECF: ECF sigm 94.5 0.2 4.3E-06 45.8 8.4 78 264-341 17-99 (185)
129 PRK09635 sigI RNA polymerase s 94.3 0.092 2E-06 51.7 6.1 70 264-337 5-74 (290)
130 TIGR03209 P21_Cbot clostridium 93.8 0.28 6E-06 42.0 7.5 65 267-338 2-71 (142)
131 PHA02547 55 RNA polymerase sig 93.0 0.35 7.7E-06 45.3 7.2 70 270-339 43-115 (179)
132 COG0568 RpoD DNA-directed RNA 92.2 0.51 1.1E-05 48.4 7.8 32 191-222 67-98 (342)
133 PRK09047 RNA polymerase factor 91.0 0.53 1.1E-05 40.7 5.6 46 290-338 6-51 (161)
134 COG1191 FliA DNA-directed RNA 87.6 0.73 1.6E-05 45.2 4.4 63 189-261 85-149 (247)
135 PRK07122 RNA polymerase sigma 84.8 4.7 0.0001 39.2 8.3 65 188-259 100-164 (264)
136 PRK05911 RNA polymerase sigma 82.0 4 8.6E-05 39.4 6.6 62 188-259 86-147 (257)
137 PRK07500 rpoH2 RNA polymerase 81.4 18 0.00038 35.7 10.9 68 185-255 97-165 (289)
138 TIGR02850 spore_sigG RNA polym 80.8 7.5 0.00016 37.2 8.0 64 189-260 95-158 (254)
139 PRK07921 RNA polymerase sigma 78.8 9.5 0.00021 38.5 8.3 64 188-258 146-209 (324)
140 PRK07408 RNA polymerase sigma 78.2 3.2 6.8E-05 40.0 4.5 64 188-258 86-149 (256)
141 PRK06288 RNA polymerase sigma 78.0 23 0.00049 34.2 10.4 34 225-258 121-154 (268)
142 TIGR02393 RpoD_Cterm RNA polym 78.0 3.5 7.5E-05 39.0 4.7 33 226-258 91-123 (238)
143 PRK07670 RNA polymerase sigma 77.9 11 0.00023 36.0 8.0 34 227-260 114-147 (251)
144 PRK12427 flagellar biosynthesi 77.2 3.7 8.1E-05 39.0 4.7 62 188-259 77-138 (231)
145 PRK07406 RNA polymerase sigma 73.6 15 0.00032 38.1 8.2 31 227-257 228-258 (373)
146 PRK05901 RNA polymerase sigma 73.1 12 0.00026 40.4 7.7 33 226-258 362-394 (509)
147 PRK09210 RNA polymerase sigma 73.0 5 0.00011 41.0 4.6 36 225-260 219-254 (367)
148 TIGR02885 spore_sigF RNA polym 65.0 10 0.00022 35.4 4.6 61 190-258 73-133 (231)
149 TIGR02479 FliA_WhiG RNA polyme 64.7 10 0.00022 35.3 4.5 34 226-259 87-120 (224)
150 PRK07598 RNA polymerase sigma 63.6 10 0.00022 40.0 4.7 38 223-260 263-300 (415)
151 PRK05949 RNA polymerase sigma 62.2 12 0.00025 37.9 4.7 36 223-258 179-214 (327)
152 PF04967 HTH_10: HTH DNA bindi 59.4 41 0.00089 25.8 6.1 47 206-262 1-47 (53)
153 PRK07405 RNA polymerase sigma 55.2 18 0.0004 36.2 4.7 36 223-258 169-204 (317)
154 COG3413 Predicted DNA binding 55.1 46 0.00099 31.2 7.1 59 204-275 154-212 (215)
155 PRK08215 sporulation sigma fac 54.7 20 0.00043 34.3 4.7 62 189-258 98-159 (258)
156 TIGR02980 SigBFG RNA polymeras 53.3 22 0.00048 33.0 4.7 31 227-257 95-125 (227)
157 KOG0037 Ca2+-binding protein, 50.1 2.1E+02 0.0046 28.2 10.7 109 182-313 89-203 (221)
158 PRK06596 RNA polymerase factor 49.2 75 0.0016 31.2 7.8 64 187-258 107-171 (284)
159 TIGR02997 Sig70-cyanoRpoD RNA 48.4 27 0.0006 34.3 4.6 34 225-258 164-197 (298)
160 smart00342 HTH_ARAC helix_turn 46.2 56 0.0012 24.3 5.1 24 238-261 1-24 (84)
161 PRK14082 hypothetical protein; 45.1 82 0.0018 25.5 5.9 55 264-320 9-63 (65)
162 PRK06986 fliA flagellar biosyn 42.9 39 0.00086 31.7 4.6 32 227-258 100-131 (236)
163 TIGR02941 Sigma_B RNA polymera 40.3 47 0.001 31.6 4.8 32 227-258 121-152 (255)
164 PF04218 CENP-B_N: CENP-B N-te 39.2 38 0.00082 25.4 3.1 41 204-261 5-45 (53)
165 COG1476 Predicted transcriptio 38.1 57 0.0012 26.4 4.1 50 239-298 15-64 (68)
166 PF11176 DUF2962: Protein of u 35.8 79 0.0017 29.0 5.2 91 191-314 49-143 (155)
167 PRK05572 sporulation sigma fac 35.5 59 0.0013 31.0 4.6 60 189-256 93-152 (252)
168 PRK10219 DNA-binding transcrip 34.5 80 0.0017 25.9 4.7 35 227-261 10-44 (107)
169 TIGR03761 ICE_PFL4669 integrat 34.4 99 0.0021 30.1 5.9 51 251-310 143-193 (216)
170 PF02796 HTH_7: Helix-turn-hel 34.3 72 0.0016 22.9 3.8 41 204-261 4-44 (45)
171 COG0122 AlkA 3-methyladenine D 33.3 1.7E+02 0.0037 29.3 7.6 119 191-310 77-240 (285)
172 PRK04217 hypothetical protein; 33.2 1.9E+02 0.0041 25.3 6.9 47 203-267 40-87 (110)
173 PF13936 HTH_38: Helix-turn-he 30.8 73 0.0016 22.9 3.4 40 203-259 2-41 (44)
174 PRK11511 DNA-binding transcrip 30.5 95 0.0021 26.7 4.7 35 227-261 14-48 (127)
175 PF13730 HTH_36: Helix-turn-he 30.4 1.8E+02 0.004 20.9 5.6 27 235-261 22-48 (55)
176 PRK13239 alkylmercury lyase; P 29.8 79 0.0017 30.6 4.4 27 235-261 33-59 (206)
177 PF04282 DUF438: Family of unk 29.8 2.1E+02 0.0045 23.4 6.2 50 212-262 3-58 (71)
178 PF00427 PBS_linker_poly: Phyc 28.1 4.5E+02 0.0098 23.7 9.5 86 194-306 16-111 (131)
179 TIGR01446 DnaD_dom DnaD and ph 27.6 1.7E+02 0.0037 22.5 5.3 57 233-293 7-70 (73)
180 PF01726 LexA_DNA_bind: LexA D 27.2 1.3E+02 0.0029 23.5 4.6 19 233-251 20-38 (65)
181 PRK05657 RNA polymerase sigma 26.9 97 0.0021 31.2 4.7 33 227-259 178-210 (325)
182 PF09824 ArsR: ArsR transcript 26.9 26 0.00056 32.8 0.5 20 107-126 44-64 (160)
183 KOG0030 Myosin essential light 26.5 3E+02 0.0065 25.6 7.3 70 234-322 39-109 (152)
184 PF02885 Glycos_trans_3N: Glyc 26.0 2.3E+02 0.0049 21.9 5.6 31 193-223 2-32 (66)
185 COG1916 Uncharacterized homolo 26.0 3.1E+02 0.0067 29.1 8.1 121 187-312 45-181 (388)
186 KOG1161 Protein involved in va 25.5 5.2E+02 0.011 26.7 9.5 35 296-330 117-151 (310)
187 TIGR03826 YvyF flagellar opero 25.4 1.1E+02 0.0025 27.7 4.4 46 210-264 27-72 (137)
188 PF01381 HTH_3: Helix-turn-hel 24.6 98 0.0021 22.1 3.2 38 240-284 11-48 (55)
189 PF13404 HTH_AsnC-type: AsnC-t 24.0 1.9E+02 0.0041 20.8 4.5 23 238-260 17-39 (42)
190 PRK08583 RNA polymerase sigma 22.8 4.4E+02 0.0096 25.0 8.1 31 228-258 122-152 (257)
191 PRK05932 RNA polymerase factor 21.7 7.9E+02 0.017 26.3 10.4 44 268-319 197-245 (455)
192 PRK13159 cytochrome c-type bio 21.5 89 0.0019 29.0 3.0 33 49-89 118-151 (155)
193 COG2188 PhnF Transcriptional r 21.5 1.4E+02 0.0031 28.3 4.5 41 211-261 13-54 (236)
194 PF08900 DUF1845: Domain of un 21.3 2.6E+02 0.0056 26.9 6.2 51 251-310 145-195 (217)
195 PRK15044 transcriptional regul 21.1 1.9E+02 0.0042 29.4 5.5 60 193-261 172-231 (295)
196 TIGR02325 C_P_lyase_phnF phosp 20.8 1.5E+02 0.0032 27.5 4.4 40 212-261 15-55 (238)
197 PF04297 UPF0122: Putative hel 20.4 5.3E+02 0.011 22.3 7.3 42 238-280 33-74 (101)
198 cd04762 HTH_MerR-trunc Helix-T 20.4 1.2E+02 0.0025 20.4 2.8 23 240-262 2-24 (49)
199 PF12244 DUF3606: Protein of u 20.1 1E+02 0.0023 23.7 2.7 21 241-261 23-43 (57)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=5.5e-36 Score=304.13 Aligned_cols=194 Identities=31% Similarity=0.491 Sum_probs=165.1
Q ss_pred hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCc--------------------chhHHHHHHHhhCCCCchHHHHHHhcC
Q 016321 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS--------------------LDDHKLRLKERLGCEPSMEQLAASLRI 250 (391)
Q Consensus 191 ~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~--------------------L~~~~~~l~~~~g~ePs~~e~A~a~~~ 250 (391)
|.++.||++|++.|+||++||++|+++||.+.. |++++.+|++.+|++||.++||+++|+
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 689999999999999999999999999999988 899999999999999999999966655
Q ss_pred ----------------------ChHHHHHHhhhhHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHh
Q 016321 251 ----------------------SRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEK 308 (391)
Q Consensus 251 ----------------------s~~eL~~~l~eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIek 308 (391)
+.++|.+.+..|..|+++||.+|+++|+++|++|.++|++++||||||+|||++|+++
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 cCCCCCCchhhhHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhhhhc---ccc---cccCCCCCChhHHhhHHHHHHHHHH
Q 016321 309 FDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWLKTDVLLKNQLK---FDL---SSSLPKKGSKFEQIGVLLSSICKLL 382 (391)
Q Consensus 309 FDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ir~~~r~v~l~~~l~---~dl---~~~~~k~ge~~e~ig~~ls~v~~~L 382 (391)
|||++|++|+|||+||||++|.++|+++.|.||....-....+.+. ..+ ..+.++..++++.+|+..+.+..++
T Consensus 220 FDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l 299 (415)
T PRK07598 220 FDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVL 299 (415)
T ss_pred cCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 9999999999999999999999999999988884432211111111 111 1244667778889999888888877
Q ss_pred HH
Q 016321 383 MY 384 (391)
Q Consensus 383 ~~ 384 (391)
..
T Consensus 300 ~~ 301 (415)
T PRK07598 300 LR 301 (415)
T ss_pred HH
Confidence 64
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=1.8e-34 Score=279.05 Aligned_cols=192 Identities=32% Similarity=0.519 Sum_probs=164.0
Q ss_pred hHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHH
Q 016321 192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM 271 (391)
Q Consensus 192 ~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe 271 (391)
.+..||++|.++|+||++||.+|+++++.|..+++.+..|+++.|++|+..+||+++|++..+|...++.|..|++.||.
T Consensus 2 ~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv~ 81 (298)
T TIGR02997 2 LVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMIK 81 (298)
T ss_pred cHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHHH
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhhhhhhhhHHH---
Q 016321 272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWLKTDVL--- 348 (391)
Q Consensus 272 ~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ir~~~r~v~--- 348 (391)
.|+++|+++|++|.++|.+.+||||||+|||++|+++|||++|++|+|||+||||++|.++|.++.+.+|.......
T Consensus 82 ~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~~~~~~~~ 161 (298)
T TIGR02997 82 ANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLN 161 (298)
T ss_pred HhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999888874322111
Q ss_pred hhhhhcccc---cccCCCCCChhHHhhHHHHHHHHHHH
Q 016321 349 LKNQLKFDL---SSSLPKKGSKFEQIGVLLSSICKLLM 383 (391)
Q Consensus 349 l~~~l~~dl---~~~~~k~ge~~e~ig~~ls~v~~~L~ 383 (391)
.-......+ ....++..+.++.+|+..+.|...+.
T Consensus 162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~ 199 (298)
T TIGR02997 162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQ 199 (298)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 111111111 11234455566777777777666543
No 3
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=2.3e-34 Score=288.87 Aligned_cols=191 Identities=31% Similarity=0.465 Sum_probs=169.4
Q ss_pred hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHH
Q 016321 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (391)
Q Consensus 191 ~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~LI 270 (391)
+.+..||++|+++|+||++||++|++++++|..+++.+..+....|++|+.++||.++|++..+|++.++.|..|++.||
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 57889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhhhhhhhhHHHhh
Q 016321 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWLKTDVLLK 350 (391)
Q Consensus 271 e~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ir~~~r~v~l~ 350 (391)
..|+|+|+++|++|.++|.+.+||||||+|||++|+++|||++|++|+|||+||||++|.++|+++.+.+|...+-...-
T Consensus 143 ~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~~~~ 222 (373)
T PRK07406 143 QSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETI 222 (373)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999888443322111
Q ss_pred hh---hcccc---cccCCCCCChhHHhhHHHHHHHHH
Q 016321 351 NQ---LKFDL---SSSLPKKGSKFEQIGVLLSSICKL 381 (391)
Q Consensus 351 ~~---l~~dl---~~~~~k~ge~~e~ig~~ls~v~~~ 381 (391)
.+ ....+ ....|+..++++.+|+..+.|...
T Consensus 223 ~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~ 259 (373)
T PRK07406 223 SRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFI 259 (373)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 11 11122 124456677889999998888765
No 4
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00 E-value=7e-33 Score=273.20 Aligned_cols=192 Identities=31% Similarity=0.505 Sum_probs=167.9
Q ss_pred hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHH
Q 016321 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (391)
Q Consensus 191 ~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~LI 270 (391)
+.+..||++|+++|+||++||++|+++++.|..+++.+..|...+|++|+..+||.+++++..+|...++.|..|++.||
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 68889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhhhhhhhhHHHhh
Q 016321 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWLKTDVLLK 350 (391)
Q Consensus 271 e~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ir~~~r~v~l~ 350 (391)
..|+++|+++|++|.+.|.+.+||||||+|||++|+++|||++|++|+|||+||||++|.++|.++.+.+|....-....
T Consensus 98 ~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~~~~~ 177 (327)
T PRK05949 98 EANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEKL 177 (327)
T ss_pred HHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999888543211111
Q ss_pred hh---hccccc---ccCCCCCChhHHhhHHHHHHHHHH
Q 016321 351 NQ---LKFDLS---SSLPKKGSKFEQIGVLLSSICKLL 382 (391)
Q Consensus 351 ~~---l~~dl~---~~~~k~ge~~e~ig~~ls~v~~~L 382 (391)
+. ....+. ...|+..+.++.+|+..+.|..++
T Consensus 178 ~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~ 215 (327)
T PRK05949 178 NKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYL 215 (327)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 11 111111 234556667888888888777654
No 5
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=99.98 E-value=1.8e-32 Score=284.41 Aligned_cols=180 Identities=32% Similarity=0.479 Sum_probs=146.4
Q ss_pred hhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHH
Q 016321 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL 269 (391)
Q Consensus 190 ~~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~L 269 (391)
.+.++.||++|+++|+||++||++|+++++.|+.+++... ...+|+. .+..+|+++++.|..|+++|
T Consensus 210 ~d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~~~----------~~~~~~~---~~~~~l~~~~~~g~~Ar~~L 276 (509)
T PRK05901 210 ADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEELLA----------EGEKLDP---ELRRDLQWIGRDGKRAKNHL 276 (509)
T ss_pred ccHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhhhh----------hcccchh---hhhhhhhhhccchHHHHHHH
Confidence 4689999999999999999999999999999987544221 1122332 24678999999999999999
Q ss_pred HHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhhhhhhhhHHHh
Q 016321 270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWLKTDVLL 349 (391)
Q Consensus 270 Ie~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ir~~~r~v~l 349 (391)
|.+|+|||++||++|.++|++++||||||+||||+||++|||++|++|+|||+||||++|.++|+++.|.+|...+.+..
T Consensus 277 I~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~~~~e~ 356 (509)
T PRK05901 277 LEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVET 356 (509)
T ss_pred HHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999998843332211
Q ss_pred hhhh---ccccc---ccCCCCCChhHHhhHHHHHHHHHH
Q 016321 350 KNQL---KFDLS---SSLPKKGSKFEQIGVLLSSICKLL 382 (391)
Q Consensus 350 ~~~l---~~dl~---~~~~k~ge~~e~ig~~ls~v~~~L 382 (391)
-+.+ ...+. ...|+..++++.+|+..+.|..++
T Consensus 357 i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~ 395 (509)
T PRK05901 357 INKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQ 395 (509)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 1111 11111 244566678888998888887764
No 6
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=99.98 E-value=7.7e-32 Score=264.26 Aligned_cols=193 Identities=32% Similarity=0.508 Sum_probs=166.6
Q ss_pred hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHH
Q 016321 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (391)
Q Consensus 191 ~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~LI 270 (391)
+.+..||++|+++|+||++||++|++++++|..++..+..|.+++|++|+..+||.+++++..+|...+..|..|+++|+
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 57889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhhhhhhhhHHHhh
Q 016321 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWLKTDVLLK 350 (391)
Q Consensus 271 e~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ir~~~r~v~l~ 350 (391)
..|+++|+++|.+|.+.|.+.+||+|||++||++|+++|||++|++|+|||+||||++|.++|.++.+.+|....-...-
T Consensus 88 ~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~~~~ 167 (317)
T PRK07405 88 EANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKL 167 (317)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999998888543211111
Q ss_pred hh---hccccc---ccCCCCCChhHHhhHHHHHHHHHHH
Q 016321 351 NQ---LKFDLS---SSLPKKGSKFEQIGVLLSSICKLLM 383 (391)
Q Consensus 351 ~~---l~~dl~---~~~~k~ge~~e~ig~~ls~v~~~L~ 383 (391)
.. ....+. ...++..+.++.+|+..+.|...+.
T Consensus 168 ~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~ 206 (317)
T PRK07405 168 NKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLE 206 (317)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 11 111111 1345555677777777777766654
No 7
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=99.96 E-value=2.6e-29 Score=247.95 Aligned_cols=180 Identities=33% Similarity=0.513 Sum_probs=144.0
Q ss_pred hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHH
Q 016321 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (391)
Q Consensus 191 ~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~LI 270 (391)
+.+..||++|.++|+||++||.+|+++++.|..++.. +|...+++.. ...+++..++.|..|+++||
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 5788999999999999999999999999998764433 1111111111 34688999999999999999
Q ss_pred HHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhhhhhhhhHHHhh
Q 016321 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWLKTDVLLK 350 (391)
Q Consensus 271 e~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ir~~~r~v~l~ 350 (391)
..|+++|+++|++|.+.|.+.+||+|||+|||++|+++|||++|++|+|||.||||++|.++|+++.+.++...+....-
T Consensus 93 ~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~~~~ 172 (324)
T PRK07921 93 EANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQV 172 (324)
T ss_pred HHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999998888543322111
Q ss_pred hh---hccccc---ccCCCCCChhHHhhHHHHHHHHHHH
Q 016321 351 NQ---LKFDLS---SSLPKKGSKFEQIGVLLSSICKLLM 383 (391)
Q Consensus 351 ~~---l~~dl~---~~~~k~ge~~e~ig~~ls~v~~~L~ 383 (391)
.. ...++. ...|+..+.++.+|+..+.|...+.
T Consensus 173 ~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~ 211 (324)
T PRK07921 173 NKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLE 211 (324)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 11 111221 2445666788889988888877653
No 8
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=99.96 E-value=2.4e-29 Score=250.08 Aligned_cols=193 Identities=33% Similarity=0.471 Sum_probs=153.0
Q ss_pred hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHH-hhCCCCchH---------------HHHHHhcCCh-H
Q 016321 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKE-RLGCEPSME---------------QLAASLRISR-P 253 (391)
Q Consensus 191 ~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~-~~g~ePs~~---------------e~A~a~~~s~-~ 253 (391)
+.+..|+.+++..++++.++|..+.+.++....+......+.. .++..|+.. +|+..+..+. .
T Consensus 9 d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Ee~ 88 (342)
T COG0568 9 DAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEEEK 88 (342)
T ss_pred hHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHHHH
Confidence 5889999999999999999999999999888777667777777 677888876 3333333333 5
Q ss_pred HHHHHhhhhH---HHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHH
Q 016321 254 ELQSILMECS---LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRL 330 (391)
Q Consensus 254 eL~~~l~eg~---~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~ 330 (391)
+|.+.+..|. .|+.+||++|++||++||++|.++|+.+.||||||+||||+||++|||++|++|+|||+||||++|.
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 6777777764 4999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhhhhhhhhHH-------HhhhhhcccccccCCCCCChhHHhhHHHHHHHHHHHH
Q 016321 331 LLICTFKQFIAWLKTDV-------LLKNQLKFDLSSSLPKKGSKFEQIGVLLSSICKLLMY 384 (391)
Q Consensus 331 ~aIre~~R~ir~~~r~v-------~l~~~l~~dl~~~~~k~ge~~e~ig~~ls~v~~~L~~ 384 (391)
++|.++.|.||..---+ +.+..+... .-.-+...++++.+|.....|...+..
T Consensus 169 raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~-~~r~p~~eeia~~l~~~~~~V~~m~~~ 228 (342)
T COG0568 169 RAIADQARTIRIPVHQVELINKLRRVKRELLQE-LGREPTPEEIAEELGVSPDKVREMLKR 228 (342)
T ss_pred HHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHH-hcCCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 99999999998432111 111111111 113356666888888888777665543
No 9
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=99.94 E-value=2.7e-26 Score=229.15 Aligned_cols=155 Identities=35% Similarity=0.499 Sum_probs=131.6
Q ss_pred hhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHH
Q 016321 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREK 268 (391)
Q Consensus 189 ~~~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~ 268 (391)
..+.++.||++|++.|+||++||.+|+++++.|+. .|++.
T Consensus 94 ~~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~Gd~----------------------------------------~A~~~ 133 (367)
T PRK09210 94 INDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGDE----------------------------------------EAKQR 133 (367)
T ss_pred cCcHHHHHHHHhhccCCCCHHHHHHHHHHHHhhHH----------------------------------------HHHHH
Confidence 34789999999999999999999999999999864 79999
Q ss_pred HHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhhhhhhhhHHH
Q 016321 269 LVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWLKTDVL 348 (391)
Q Consensus 269 LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ir~~~r~v~ 348 (391)
||..|+|+|+++|++|.++|.+++||+|||+|||++|+++|||++|++|+|||.||||++|.++|+++.|.+|....-+.
T Consensus 134 Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~~~ 213 (367)
T PRK09210 134 LAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 213 (367)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999998874333222
Q ss_pred hhhhhc---ccc---cccCCCCCChhHHhhHHHHHHHHHHH
Q 016321 349 LKNQLK---FDL---SSSLPKKGSKFEQIGVLLSSICKLLM 383 (391)
Q Consensus 349 l~~~l~---~dl---~~~~~k~ge~~e~ig~~ls~v~~~L~ 383 (391)
..+.+. ..+ -.+.|+..+.++.+|+....|..++.
T Consensus 214 ~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~ 254 (367)
T PRK09210 214 TINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILK 254 (367)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 112211 111 12456677789999999988887654
No 10
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=99.93 E-value=2.1e-26 Score=243.29 Aligned_cols=155 Identities=30% Similarity=0.494 Sum_probs=127.2
Q ss_pred hHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHH
Q 016321 192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM 271 (391)
Q Consensus 192 ~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe 271 (391)
.++.||+++...+.|+++|+.+++++++.|+. .+..|+++||.
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 56778888989999999999999999998864 12368999999
Q ss_pred HcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhh
Q 016321 272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWLKTDVLLKN 351 (391)
Q Consensus 272 ~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ir~~~r~v~l~~ 351 (391)
+|+|||++||++|.++|++++||||||+||||+||++|||++|++|+|||+||||++|.++|+++.+.+|...+-....+
T Consensus 388 ~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~irip~~~~~~~~ 467 (619)
T PRK05658 388 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 467 (619)
T ss_pred HHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCceecCHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999998885433222111
Q ss_pred h---hccccc---ccCCCCCChhHHhhHHHHHHHHHHH
Q 016321 352 Q---LKFDLS---SSLPKKGSKFEQIGVLLSSICKLLM 383 (391)
Q Consensus 352 ~---l~~dl~---~~~~k~ge~~e~ig~~ls~v~~~L~ 383 (391)
+ ....+. ...|+..+.++.+|+....|..++.
T Consensus 468 k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~ 505 (619)
T PRK05658 468 KLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLK 505 (619)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 1 111221 2445566788889998888887754
No 11
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=99.92 E-value=9.7e-25 Score=210.76 Aligned_cols=158 Identities=27% Similarity=0.412 Sum_probs=127.4
Q ss_pred cCChhhhhhhHHHHHHhcCCCCCCCHHHHHHHHHHH-HcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhh
Q 016321 183 MISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKI-KTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (391)
Q Consensus 183 ~~~pe~~~~~l~~YL~~i~~~~lLT~eEE~eL~~ki-q~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~e 261 (391)
.++|+ +.+..|++++.+.|+++.++|.+|+.++ +.|+.
T Consensus 9 ~~~~~---~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~~Gd~-------------------------------------- 47 (284)
T PRK06596 9 ALSPE---GNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDL-------------------------------------- 47 (284)
T ss_pred CCCCc---cHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCCH--------------------------------------
Confidence 36788 7899999999999999999999999985 46764
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhhhh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIA 341 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ir 341 (391)
.|++.||..|+|+|+++|++|.+.|++.+||+|+|+|||++|+++|||++|++|+|||.||||++|.++|+++.+.++
T Consensus 48 --~a~~~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr 125 (284)
T PRK06596 48 --EAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVK 125 (284)
T ss_pred --HHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeee
Confidence 799999999999999999999999999999999999999999999999999999999999999999999998755444
Q ss_pred hhhhHHH--hh---hhhccccc-ccCCCCCChhHHhhHHHHHHHHHHH
Q 016321 342 WLKTDVL--LK---NQLKFDLS-SSLPKKGSKFEQIGVLLSSICKLLM 383 (391)
Q Consensus 342 ~~~r~v~--l~---~~l~~dl~-~~~~k~ge~~e~ig~~ls~v~~~L~ 383 (391)
...+... .. .++...+. ...++..+.++.+|+....+..++.
T Consensus 126 ~p~~~~~~~~~~~~~~~~~~l~~~~~~t~~eiA~~l~~~~~~v~~~~~ 173 (284)
T PRK06596 126 VATTKAQRKLFFNLRKAKKRLGWLNPEEVEMVAEELGVSEEEVREMES 173 (284)
T ss_pred ccchHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 3222110 00 11111111 1334456688888988888877654
No 12
>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=99.92 E-value=8.8e-25 Score=208.76 Aligned_cols=152 Identities=28% Similarity=0.443 Sum_probs=121.4
Q ss_pred hHHHHHHhcCCCCCCCHHHHHHHHHHH-HcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHH
Q 016321 192 RLKGYVKGVVSEELLTHAEVVRLSKKI-KTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (391)
Q Consensus 192 ~l~~YL~~i~~~~lLT~eEE~eL~~ki-q~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~LI 270 (391)
.+..||++|.++|++++++|.+|+.++ +.|+. .|++.||
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 567899999999999999999999984 57764 7999999
Q ss_pred HHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhhhhhhhhHHH--
Q 016321 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWLKTDVL-- 348 (391)
Q Consensus 271 e~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ir~~~r~v~-- 348 (391)
+.|+|+|+++|++|.+.+.+.+||+|+|+|||++|+++|||++|++|+|||.||||++|.++|++..+.+|...+...
T Consensus 42 ~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir~p~~~~~~~ 121 (270)
T TIGR02392 42 LSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRK 121 (270)
T ss_pred HHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCceecCchHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999987555553222110
Q ss_pred h--h-hhhcccc-cccCC-CCCChhHHhhHHHHHHHHHHH
Q 016321 349 L--K-NQLKFDL-SSSLP-KKGSKFEQIGVLLSSICKLLM 383 (391)
Q Consensus 349 l--~-~~l~~dl-~~~~~-k~ge~~e~ig~~ls~v~~~L~ 383 (391)
. + ......+ ....+ ...+.++.+|+..+.|..++.
T Consensus 122 ~~~~~~~~~~~~~~~~~~~~~~eiA~~l~~~~~~v~~~~~ 161 (270)
T TIGR02392 122 LFFNLRKMKKRLQGWLNPEEVEAIAEELGVSEREVREMES 161 (270)
T ss_pred HHHHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 0 0 1111111 11122 245688888888888877644
No 13
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=99.91 E-value=2.6e-24 Score=205.88 Aligned_cols=121 Identities=21% Similarity=0.225 Sum_probs=100.5
Q ss_pred HHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhhhhhh
Q 016321 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWL 343 (391)
Q Consensus 264 ~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ir~~ 343 (391)
.++++||..|+|||++||++|.++|++++||||+|+|||++|+++|||++|++|+|||.||||++|.++|+++.+.++..
T Consensus 40 ~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I~~~lr~~~~~ir~P 119 (264)
T PRK07122 40 RQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVP 119 (264)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHcCCccccC
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999998888855
Q ss_pred hhHHHhhhhhcc---ccc---ccCCCCCChhHHhhHHHHHHHHHHHH
Q 016321 344 KTDVLLKNQLKF---DLS---SSLPKKGSKFEQIGVLLSSICKLLMY 384 (391)
Q Consensus 344 ~r~v~l~~~l~~---dl~---~~~~k~ge~~e~ig~~ls~v~~~L~~ 384 (391)
++......++.. ++. ...|+..+.++.+|+..+.+..++..
T Consensus 120 r~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~ 166 (264)
T PRK07122 120 RRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVA 166 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 443322222221 221 24456667889999998888876643
No 14
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=99.90 E-value=4.6e-23 Score=199.80 Aligned_cols=152 Identities=22% Similarity=0.349 Sum_probs=124.0
Q ss_pred hhHHHHHHhcCCCCCCCHHHHHHHHHHHH-cCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHH
Q 016321 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIK-TGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL 269 (391)
Q Consensus 191 ~~l~~YL~~i~~~~lLT~eEE~eL~~kiq-~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~L 269 (391)
+..+.||++|.++|+||+++|.+|+++++ .|+. .|+++|
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 35667999999999999999999999975 6664 799999
Q ss_pred HHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhhhhhhhhH---
Q 016321 270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWLKTD--- 346 (391)
Q Consensus 270 Ie~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ir~~~r~--- 346 (391)
|..|+|+|+++|.+|.+.+.+.+||+|+|++||++|+++|||.+|.+|+|||.||||++|.++|++..+.+|...+.
T Consensus 46 v~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~~~~~~ 125 (289)
T PRK07500 46 ISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQK 125 (289)
T ss_pred HHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCccHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999987776642211
Q ss_pred -H-----Hhhhhhccc--ccccCCCCCChhHHhhHHHHHHHHHH
Q 016321 347 -V-----LLKNQLKFD--LSSSLPKKGSKFEQIGVLLSSICKLL 382 (391)
Q Consensus 347 -v-----~l~~~l~~d--l~~~~~k~ge~~e~ig~~ls~v~~~L 382 (391)
. .....+... .....|+..+.++.+|+..+.+....
T Consensus 126 ~~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~ 169 (289)
T PRK07500 126 ALFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMD 169 (289)
T ss_pred HHHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 1 111111110 11244566778999999998876543
No 15
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=99.87 E-value=3.3e-22 Score=191.84 Aligned_cols=141 Identities=28% Similarity=0.346 Sum_probs=115.6
Q ss_pred CCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHcHHHHHHHHHh
Q 016321 204 ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQR 283 (391)
Q Consensus 204 ~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe~nlpLV~~IAkk 283 (391)
+.++.++...+....+.|+. .++ .||+.|+|||.+||++
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 45667777777777777664 788 9999999999999999
Q ss_pred cccCCC-ChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhhhhc----ccc-
Q 016321 284 YDNMGA-DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWLKTDVLLKNQLK----FDL- 357 (391)
Q Consensus 284 Y~~~Gv-d~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ir~~~r~v~l~~~l~----~dl- 357 (391)
|.++|. ++|||+|.|+|||++||++|||++|.+|+|||..+|+|+|.+++|+.. .+ |++|.++...... .++
T Consensus 43 ~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~LR~~~-~v-~vpR~~~~~~~~i~~~~~~l~ 120 (247)
T COG1191 43 FENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKND-SV-KVPRSLRELGRRIEEAIDELE 120 (247)
T ss_pred HHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHHHHhCC-Cc-cCcHHHHHHHHHHHHHHHHHH
Confidence 999988 999999999999999999999999999999999999999999999887 22 3555554442211 121
Q ss_pred --cccCCCCCChhHHhhHHHHHHHHHHHHHHH
Q 016321 358 --SSSLPKKGSKFEQIGVLLSSICKLLMYLVF 387 (391)
Q Consensus 358 --~~~~~k~ge~~e~ig~~ls~v~~~L~~~~~ 387 (391)
-.+-|+..+++..+|+...++..++..+..
T Consensus 121 ~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~ 152 (247)
T COG1191 121 QELGREPTDEEIAEELGIDKEEYIEALLAING 152 (247)
T ss_pred HHhCCCCcHHHHHHHhCCCHHHHHHHHHHhcc
Confidence 125677888999999999999999887754
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=99.86 E-value=7.1e-22 Score=184.94 Aligned_cols=118 Identities=37% Similarity=0.601 Sum_probs=95.4
Q ss_pred HHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhhhhhhh
Q 016321 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWLK 344 (391)
Q Consensus 265 Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ir~~~ 344 (391)
|+++||..|+|+|.++|++|.+.|++++||+|||+|||++|+++|||++|++|+|||.||||++|.++|+++.+.++ ++
T Consensus 1 a~~~Li~~~~~lv~~ia~~~~~~~~~~eDLiQeG~igL~~A~~~fd~~~g~~FstYA~~~Ir~~I~~~l~~~~~~vr-ip 79 (238)
T TIGR02393 1 AKKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIR-IP 79 (238)
T ss_pred CHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCChHHHhHHHHHHHHHHHHHHcCCcEE-eC
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999998887 44
Q ss_pred hHHHhh-hhhc---ccc---cccCCCCCChhHHhhHHHHHHHHHHH
Q 016321 345 TDVLLK-NQLK---FDL---SSSLPKKGSKFEQIGVLLSSICKLLM 383 (391)
Q Consensus 345 r~v~l~-~~l~---~dl---~~~~~k~ge~~e~ig~~ls~v~~~L~ 383 (391)
+.+... +.+. ..+ ....|+..+.++.+|+....+..++.
T Consensus 80 ~~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~ 125 (238)
T TIGR02393 80 VHMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKK 125 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 333211 1111 111 12345566678888888888776543
No 17
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=99.86 E-value=2.8e-21 Score=190.55 Aligned_cols=153 Identities=31% Similarity=0.500 Sum_probs=124.7
Q ss_pred hhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHH
Q 016321 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREK 268 (391)
Q Consensus 189 ~~~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~ 268 (391)
+.+.++.|+++|+..|+||+++|..|+.+++.|+. .|++.
T Consensus 51 ~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~Gd~----------------------------------------~A~~~ 90 (325)
T PRK05657 51 VLDATQLYLNEIGYSPLLTAEEEVYFARRALRGDF----------------------------------------AARQR 90 (325)
T ss_pred cccHHHHHHHHHhcCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHH
Confidence 44688999999999999999999999999999975 79999
Q ss_pred HHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhhhhhhhhHHH
Q 016321 269 LVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWLKTDVL 348 (391)
Q Consensus 269 LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ir~~~r~v~ 348 (391)
||..|.|+|+++|.+|.+.+.+.+||+|+|+|||++|+++||+.+|++|+|||.||||++|.++|+++.+.++...+-+.
T Consensus 91 Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~~~~~ 170 (325)
T PRK05657 91 MIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVK 170 (325)
T ss_pred HHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999988877664332111
Q ss_pred h-------hhhhcccccccCCCCCChhHHhhHHHHHHHHHH
Q 016321 349 L-------KNQLKFDLSSSLPKKGSKFEQIGVLLSSICKLL 382 (391)
Q Consensus 349 l-------~~~l~~dl~~~~~k~ge~~e~ig~~ls~v~~~L 382 (391)
. ...+...+ ...++..++++.+|+....|..++
T Consensus 171 ~l~~~~R~~~~l~~~l-~r~~t~~eiA~~l~~~~~~v~~~l 210 (325)
T PRK05657 171 ELNVYLRAARELEHKL-DHEPSAEEIAELLDKPVDDVSRML 210 (325)
T ss_pred HHHHHHHHHHHHHHHh-CCCCCHHHHHHHhCcCHHHHHHHH
Confidence 1 01111111 123344566777777777766655
No 18
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=99.84 E-value=8.1e-21 Score=180.52 Aligned_cols=119 Identities=27% Similarity=0.337 Sum_probs=96.1
Q ss_pred HHHHHHHHHcHHHHHHHHHhcccC-CCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhhhhh
Q 016321 264 LAREKLVMSNVRLVMSIAQRYDNM-GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAW 342 (391)
Q Consensus 264 ~Are~LIe~nlpLV~~IAkkY~~~-Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ir~ 342 (391)
.|+++||..|+|+|+++|++|.++ +.+.+||+|+|+|||++|+++|||++|++|+|||++||+++|.++|+++.+.+|.
T Consensus 25 ~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~~vr~ 104 (256)
T PRK07408 25 ALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRI 104 (256)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcCCeeee
Confidence 799999999999999999999876 6779999999999999999999999999999999999999999999999887775
Q ss_pred hhhHHHhhhhh---ccccc---ccCCCCCChhHHhhHHHHHHHHHH
Q 016321 343 LKTDVLLKNQL---KFDLS---SSLPKKGSKFEQIGVLLSSICKLL 382 (391)
Q Consensus 343 ~~r~v~l~~~l---~~dl~---~~~~k~ge~~e~ig~~ls~v~~~L 382 (391)
.++-.....++ ...+. ...|+..+.++.+|+..+.+..++
T Consensus 105 pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~ 150 (256)
T PRK07408 105 PRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIK 150 (256)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHH
Confidence 44322211111 11111 244566678888888888877654
No 19
>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=99.81 E-value=2.7e-19 Score=172.11 Aligned_cols=114 Identities=35% Similarity=0.580 Sum_probs=107.3
Q ss_pred hhhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHH
Q 016321 188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLARE 267 (391)
Q Consensus 188 ~~~~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are 267 (391)
...+.++.||++|..+|.|+.++|.+|+..+++|+. .|++
T Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~gd~----------------------------------------~a~~ 49 (285)
T TIGR02394 10 RVADVTQLYLREIGFKPLLTAEEEIAYARRALAGDF----------------------------------------EARK 49 (285)
T ss_pred CcchHHHHHHHHHhccCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHH
Confidence 455799999999999999999999999999999975 7999
Q ss_pred HHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhhhh
Q 016321 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIA 341 (391)
Q Consensus 268 ~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ir 341 (391)
.|+..|.++|..+|.+|.+.+.+.+||+|+|+|||++|+++|||.+|++|+|||.|||+.+|.+++.++.+.++
T Consensus 50 ~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain~~i~~~~~~~~ 123 (285)
T TIGR02394 50 VMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIR 123 (285)
T ss_pred HHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHHHHHHHcCCcee
Confidence 99999999999999999999999999999999999999999999999999999999999999999998766544
No 20
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=99.80 E-value=2e-19 Score=171.31 Aligned_cols=118 Identities=22% Similarity=0.284 Sum_probs=93.9
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhccc---CCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~---~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
+..|+++||..|+|+|+++|++|.. .+++++||+|+|+|||++|+++|||++|++|+|||.+|||++|.++|++..+
T Consensus 21 ~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~ 100 (257)
T PRK05911 21 EIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQDW 100 (257)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCC
Confidence 3479999999999999999999862 3578999999999999999999999999999999999999999999988764
Q ss_pred hhhhhhhHHHhh-hhhc---ccc---cccCCCCCChhHHhhHHHHHHHHHHH
Q 016321 339 FIAWLKTDVLLK-NQLK---FDL---SSSLPKKGSKFEQIGVLLSSICKLLM 383 (391)
Q Consensus 339 ~ir~~~r~v~l~-~~l~---~dl---~~~~~k~ge~~e~ig~~ls~v~~~L~ 383 (391)
+++.+... .++. ..+ ....|+.++.++.+|+..+.+...+.
T Consensus 101 ----~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~ 148 (257)
T PRK05911 101 ----VPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFS 148 (257)
T ss_pred ----CCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHH
Confidence 44443322 1111 111 12456677788999998888877654
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=99.79 E-value=1e-18 Score=165.44 Aligned_cols=141 Identities=28% Similarity=0.320 Sum_probs=115.2
Q ss_pred CCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHcHHHHHHH
Q 016321 201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI 280 (391)
Q Consensus 201 ~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe~nlpLV~~I 280 (391)
.++|+||++||.+|+.+++.|+. .|++.|+..|.|+|+++
T Consensus 11 ~~~~~l~~~~~~~li~~~~~gd~----------------------------------------~a~~~L~~~~~~~v~~~ 50 (254)
T TIGR02850 11 SKLPVLKNQEMRELFIRMQSGDT----------------------------------------TAREKLINGNLRLVLSV 50 (254)
T ss_pred cCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHHHHHH
Confidence 46899999999999999998864 79999999999999999
Q ss_pred HHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhhhhhhhhHHHhh-h-------h
Q 016321 281 AQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWLKTDVLLK-N-------Q 352 (391)
Q Consensus 281 AkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ir~~~r~v~l~-~-------~ 352 (391)
|.+|.+.+.+.+||+|+|++||++|+++|||.+|.+|+||+++||+++|.+++++.. .++. ++.+... . .
T Consensus 51 a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~-~ir~-p~~~~~~~~~~~~~~~~ 128 (254)
T TIGR02850 51 IQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRV-SRSLRDIAYKALQVRDK 128 (254)
T ss_pred HHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CccC-chHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999865 4553 3222111 1 1
Q ss_pred hcccccccCCCCCChhHHhhHHHHHHHHHHHH
Q 016321 353 LKFDLSSSLPKKGSKFEQIGVLLSSICKLLMY 384 (391)
Q Consensus 353 l~~dl~~~~~k~ge~~e~ig~~ls~v~~~L~~ 384 (391)
+..+ ....|+..+.++.+|+..+.+..++..
T Consensus 129 l~~~-l~~~pt~~elA~~l~~~~e~v~~~~~~ 159 (254)
T TIGR02850 129 LISE-NSKEPTVSEIAKELKVPQEEVVFALDA 159 (254)
T ss_pred HHHH-hCCCCCHHHHHHHHCcCHHHHHHHHHh
Confidence 1111 124566777888888888887766543
No 22
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=99.78 E-value=1.6e-18 Score=164.25 Aligned_cols=141 Identities=28% Similarity=0.330 Sum_probs=111.6
Q ss_pred CCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHcHHHHHHH
Q 016321 201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI 280 (391)
Q Consensus 201 ~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe~nlpLV~~I 280 (391)
.++|+|+++|+..|+.+++.|+. .++++|+..|.|+|..+
T Consensus 14 ~~~~~l~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~~~~~v~~~ 53 (258)
T PRK08215 14 SKLPVLKNEEMRELFERMQNGDK----------------------------------------EAREKLINGNLRLVLSV 53 (258)
T ss_pred CCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHH
Confidence 35689999999999999998865 79999999999999999
Q ss_pred HHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhhhhhhhhHHHhh-------hhh
Q 016321 281 AQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWLKTDVLLK-------NQL 353 (391)
Q Consensus 281 AkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ir~~~r~v~l~-------~~l 353 (391)
|.+|.+.+.+.+||+|+|++||++|+++|||++|.+|.||+++||+++|.+++++.. .++..++..... ..+
T Consensus 54 a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~~-~vrip~~~~~~~~~~~~~~~~l 132 (258)
T PRK08215 54 IQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREKL 132 (258)
T ss_pred HHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-ceEecHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999885 455322211111 111
Q ss_pred cccccccCCCCCChhHHhhHHHHHHHHHHH
Q 016321 354 KFDLSSSLPKKGSKFEQIGVLLSSICKLLM 383 (391)
Q Consensus 354 ~~dl~~~~~k~ge~~e~ig~~ls~v~~~L~ 383 (391)
...+ ...|+..+.++.+|+..+.+...+.
T Consensus 133 ~~~~-~r~p~~~eia~~l~v~~~~v~~~~~ 161 (258)
T PRK08215 133 INEN-SKEPTVEEIAKELEVPREEVVFALD 161 (258)
T ss_pred HHHh-CCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 1111 1344555677777777777666553
No 23
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=99.72 E-value=5e-17 Score=154.98 Aligned_cols=140 Identities=25% Similarity=0.289 Sum_probs=107.6
Q ss_pred cCCCCCCCHHHHHHHHHHHHc-CCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHcHHHHH
Q 016321 200 VVSEELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVM 278 (391)
Q Consensus 200 i~~~~lLT~eEE~eL~~kiq~-G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe~nlpLV~ 278 (391)
-+++|+||.++|.+|+.+++. |+. .+++.|+..|.|+|.
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 367899999999999999775 443 789999999999999
Q ss_pred HHHHhccc---CCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhh-h--
Q 016321 279 SIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWLKTDVLLKN-Q-- 352 (391)
Q Consensus 279 ~IAkkY~~---~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ir~~~r~v~l~~-~-- 352 (391)
.+|++|.. .+.+.+||+|+|++||++|+++||+.+|.+|.|||.+|||+.|.+++|...+ +++.+..+. +
T Consensus 46 ~~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~~~----~p~~~~~~~~~i~ 121 (268)
T PRK06288 46 YVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSIDW----IPRSVRQKARQIE 121 (268)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcCc----cCHHHHHHHHHHH
Confidence 99999862 5688999999999999999999999999999999999999999999986532 333332211 1
Q ss_pred -hcccc---cccCCCCCChhHHhhHHHHHHHHHHH
Q 016321 353 -LKFDL---SSSLPKKGSKFEQIGVLLSSICKLLM 383 (391)
Q Consensus 353 -l~~dl---~~~~~k~ge~~e~ig~~ls~v~~~L~ 383 (391)
....+ ....++..++++.+|+....+..++.
T Consensus 122 ~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~ 156 (268)
T PRK06288 122 RAIAMLEARLGRTPSDEEIADELGISLEEYNSLLS 156 (268)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHH
Confidence 11111 12334555677777777766666553
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=99.69 E-value=1.6e-16 Score=149.94 Aligned_cols=98 Identities=29% Similarity=0.294 Sum_probs=91.3
Q ss_pred CCCCHHHHHHHHHHHHc-CCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHcHHHHHHHHH
Q 016321 204 ELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ 282 (391)
Q Consensus 204 ~lLT~eEE~eL~~kiq~-G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe~nlpLV~~IAk 282 (391)
+.||+++|.+|+.+++. |+. .|+++|+..|.|+|+.+|.
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 67899999999999987 443 7999999999999999999
Q ss_pred hcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhhhh
Q 016321 283 RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIA 341 (391)
Q Consensus 283 kY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ir 341 (391)
+|.+.+.+.+||+|+|+|||++|+++||++.|.+|.||+.+||+++|.+++++..+.++
T Consensus 48 ~~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~ir 106 (255)
T TIGR02941 48 KYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKTWSVH 106 (255)
T ss_pred HHhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHHHHHHHHcCCCcC
Confidence 99999999999999999999999999999999999999999999999999998876555
No 25
>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=99.67 E-value=1.9e-16 Score=146.33 Aligned_cols=120 Identities=33% Similarity=0.357 Sum_probs=92.2
Q ss_pred HHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhhhhh
Q 016321 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAW 342 (391)
Q Consensus 263 ~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ir~ 342 (391)
..|++.|+..|.|+|.++|.+|.+.+.+.+||+|||++||++|+++||+++|.+|+||+.+||++.|.++++++.+.++.
T Consensus 2 ~~a~~~lv~~y~~~v~~~a~~~~~~~~~~eDl~Qe~~i~l~~a~~~f~~~~~~~F~ty~~~~i~~~~~~~~r~~~~~~ri 81 (227)
T TIGR02980 2 KEAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVRV 81 (227)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCcHHHHHHHHHHHHHHHHHHcCCceec
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999998866664
Q ss_pred hhhHHHhh---hhhcccccc---cCCCCCChhHHhhHHHHHHHHHH
Q 016321 343 LKTDVLLK---NQLKFDLSS---SLPKKGSKFEQIGVLLSSICKLL 382 (391)
Q Consensus 343 ~~r~v~l~---~~l~~dl~~---~~~k~ge~~e~ig~~ls~v~~~L 382 (391)
.++..... +.....+.. ..++..+.++.+|+....+..++
T Consensus 82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~ 127 (227)
T TIGR02980 82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEAL 127 (227)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 33221111 111111111 23444456666777666665443
No 26
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=99.65 E-value=2.9e-16 Score=147.76 Aligned_cols=115 Identities=16% Similarity=0.194 Sum_probs=87.7
Q ss_pred HHHHHHHHHcHHHHHHHHHhcccC---CCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhhh
Q 016321 264 LAREKLVMSNVRLVMSIAQRYDNM---GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFI 340 (391)
Q Consensus 264 ~Are~LIe~nlpLV~~IAkkY~~~---Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~i 340 (391)
..+..|+..|+|+|.++|++|..+ +++.+||+|+|+|||++|+++|||.+| +|+|||.+|||++|.++|+....
T Consensus 15 ~~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~~-- 91 (231)
T PRK12427 15 QEEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELDW-- 91 (231)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcCC--
Confidence 567789999999999999999854 579999999999999999999998666 89999999999999999987543
Q ss_pred hhhhhHHHhh----hhhccccc---ccCCCCCChhHHhhHHHHHHHHHHH
Q 016321 341 AWLKTDVLLK----NQLKFDLS---SSLPKKGSKFEQIGVLLSSICKLLM 383 (391)
Q Consensus 341 r~~~r~v~l~----~~l~~dl~---~~~~k~ge~~e~ig~~ls~v~~~L~ 383 (391)
.+|.++.. ......+. ...|+..+.++.+|+..+.+...+.
T Consensus 92 --~~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~ 139 (231)
T PRK12427 92 --RPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLL 139 (231)
T ss_pred --CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 33333221 11111221 2345566688888888888766554
No 27
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=99.65 E-value=8.1e-16 Score=142.72 Aligned_cols=120 Identities=33% Similarity=0.366 Sum_probs=94.1
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhhhh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIA 341 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ir 341 (391)
+..|+++|+..|.|+|.++|.+|.+.+.+.+||+|+|++||++|+++|||.+|.+|.||+++||+++|.++++++. .++
T Consensus 9 d~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~~~-~i~ 87 (231)
T TIGR02885 9 DKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDG-IIK 87 (231)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-CeE
Confidence 4589999999999999999999999999999999999999999999999999999999999999999999999885 444
Q ss_pred hhhhHHHh-hhhh---ccccc---ccCCCCCChhHHhhHHHHHHHHHHH
Q 016321 342 WLKTDVLL-KNQL---KFDLS---SSLPKKGSKFEQIGVLLSSICKLLM 383 (391)
Q Consensus 342 ~~~r~v~l-~~~l---~~dl~---~~~~k~ge~~e~ig~~ls~v~~~L~ 383 (391)
+|+.+.. ..++ ...+. ...++..+.++.+|+..+.+...+.
T Consensus 88 -~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~ 135 (231)
T TIGR02885 88 -VSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALE 135 (231)
T ss_pred -CCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3333221 1111 11111 2334555677888888777766544
No 28
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=99.62 E-value=3.3e-15 Score=141.10 Aligned_cols=101 Identities=27% Similarity=0.250 Sum_probs=92.5
Q ss_pred CCCCHHHHHHHHHHHHc-CCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHcHHHHHHHHH
Q 016321 204 ELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ 282 (391)
Q Consensus 204 ~lLT~eEE~eL~~kiq~-G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe~nlpLV~~IAk 282 (391)
|.|+++||.+|+.+++. |+. .|++.|+..|.|+|..+|.
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 554 7999999999999999999
Q ss_pred hcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhhhhhhh
Q 016321 283 RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFIAWLK 344 (391)
Q Consensus 283 kY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ir~~~ 344 (391)
+|.+.+.+.+||+|+|++||++++++||+..|.+|.||+.+||++.|.+++++....++..+
T Consensus 48 ~~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~~~i~r 109 (257)
T PRK08583 48 KYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPR 109 (257)
T ss_pred HHhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHHHHHHhcCCCcCCCH
Confidence 99999999999999999999999999999999999999999999999999998876665433
No 29
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=99.61 E-value=7.5e-15 Score=137.08 Aligned_cols=107 Identities=35% Similarity=0.517 Sum_probs=100.9
Q ss_pred hHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHH
Q 016321 192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM 271 (391)
Q Consensus 192 ~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe 271 (391)
.+..|+.++...|+||+++|..|+..++.|+. .|.+.|+.
T Consensus 17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~gd~----------------------------------------~a~~~l~~ 56 (233)
T PRK05803 17 FLVSYVKNNSFPQPLSEEEERKYLELMKEGDE----------------------------------------EARNILIE 56 (233)
T ss_pred HHHHHHHHhcccCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHH
Confidence 67899999999999999999999999998864 79999999
Q ss_pred HcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 272 ~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
.|.|+|.+++.+|.+.+.+.+|++|+|+|+|++++++||+++|.+|.||+.+|+++.+.++++..++
T Consensus 57 ~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~ 123 (233)
T PRK05803 57 RNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKK 123 (233)
T ss_pred HhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999999999999999999999999999999999999999999999987654
No 30
>PRK05572 sporulation sigma factor SigF; Validated
Probab=99.61 E-value=8.3e-15 Score=138.47 Aligned_cols=99 Identities=36% Similarity=0.384 Sum_probs=92.4
Q ss_pred hcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHcHHHHH
Q 016321 199 GVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVM 278 (391)
Q Consensus 199 ~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe~nlpLV~ 278 (391)
.-...|.||++++.+|+..++.|+. .++++|+..|.|+|.
T Consensus 7 ~~~~~~~l~~~~~~~li~~~~~gd~----------------------------------------~a~~~L~~~y~~~v~ 46 (252)
T PRK05572 7 NKKKKPQLKDEENKELIKKSQDGDQ----------------------------------------EARDTLVEKNLRLVW 46 (252)
T ss_pred cCcCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHHHH
Confidence 4456899999999999998888764 799999999999999
Q ss_pred HHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhh
Q 016321 279 SIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFK 337 (391)
Q Consensus 279 ~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~ 337 (391)
.+|.+|.+.+.+.+||+|+|+++|++++++||+.+|.+|.||+++||+++|.+++++..
T Consensus 47 ~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~~~ 105 (252)
T PRK05572 47 SVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG 105 (252)
T ss_pred HHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHhCC
Confidence 99999999999999999999999999999999999999999999999999999999874
No 31
>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=99.59 E-value=2.6e-15 Score=141.79 Aligned_cols=79 Identities=20% Similarity=0.218 Sum_probs=72.7
Q ss_pred hhhHHHHHHHHHHcHHHHHHHHHhcccCC--CChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhh
Q 016321 260 MECSLAREKLVMSNVRLVMSIAQRYDNMG--ADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFK 337 (391)
Q Consensus 260 ~eg~~Are~LIe~nlpLV~~IAkkY~~~G--vd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~ 337 (391)
+.|...+++||..|.|+|.++|.+|.++. .+.|||+|+|+|||++|+++|||++|.+|.|||.+||+++|.+++|+..
T Consensus 5 ~~gd~~~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dylRk~~ 84 (218)
T TIGR02895 5 QPGNEEREELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYIRKNQ 84 (218)
T ss_pred hcCChHHHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 34445599999999999999999998774 5899999999999999999999999999999999999999999999887
Q ss_pred h
Q 016321 338 Q 338 (391)
Q Consensus 338 R 338 (391)
+
T Consensus 85 k 85 (218)
T TIGR02895 85 K 85 (218)
T ss_pred c
Confidence 4
No 32
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=99.57 E-value=2.4e-14 Score=135.21 Aligned_cols=115 Identities=22% Similarity=0.233 Sum_probs=89.9
Q ss_pred HHHHHHHHHcHHHHHHHHHhccc---CCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhhh
Q 016321 264 LAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQFI 340 (391)
Q Consensus 264 ~Are~LIe~nlpLV~~IAkkY~~---~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~i 340 (391)
.|++.|+..|.|+|+.+|.+|.+ .+.+.+||+|+|++||++++++|||++|.+|.||+++||++.|.++++...+
T Consensus 22 ~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~d~lR~~~~-- 99 (251)
T PRK07670 22 DAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKEDW-- 99 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcCC--
Confidence 79999999999999999999965 5789999999999999999999999999999999999999999999988764
Q ss_pred hhhhhHHHhh--------hhhcccccccCCCCCChhHHhhHHHHHHHHHHH
Q 016321 341 AWLKTDVLLK--------NQLKFDLSSSLPKKGSKFEQIGVLLSSICKLLM 383 (391)
Q Consensus 341 r~~~r~v~l~--------~~l~~dl~~~~~k~ge~~e~ig~~ls~v~~~L~ 383 (391)
+++.++.. ..+...+ ...+...+.++.+|+....|..++.
T Consensus 100 --~p~~~~~~~~~~~~~~~~~~~~~-~~~~~~~eia~~l~~~~~~v~~~~~ 147 (251)
T PRK07670 100 --LPRSMREKTKKVEAAIEKLEQRY-MRNVTPKEVAAELGMTEEEVEATMN 147 (251)
T ss_pred --CCHHHHHHHHHHHHHHHHHHHHH-CCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 22222111 1111111 2334555677778888877777664
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=99.55 E-value=1.7e-14 Score=133.62 Aligned_cols=69 Identities=35% Similarity=0.526 Sum_probs=65.1
Q ss_pred HHHHcHHHHHHHHHhccc---CCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhh
Q 016321 269 LVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFK 337 (391)
Q Consensus 269 LIe~nlpLV~~IAkkY~~---~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~ 337 (391)
|+..|.|+|+.+|.+|.+ .+.+.+||+|+|++||++|+++|||++|.+|+||+.+||++.|.++++...
T Consensus 1 L~~~~~~lv~~~a~~~~~~~~~~~~~eDl~Qe~~~~l~~a~~~fd~~~~~~f~t~~~~~i~~~~~~~lr~~~ 72 (224)
T TIGR02479 1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLD 72 (224)
T ss_pred CHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHHcC
Confidence 578999999999999986 689999999999999999999999999999999999999999999998763
No 34
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=99.48 E-value=1.4e-13 Score=128.57 Aligned_cols=118 Identities=27% Similarity=0.369 Sum_probs=88.9
Q ss_pred hhHHHHHHHHHHcHHHHHHHHHhcc---cCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhh
Q 016321 261 ECSLAREKLVMSNVRLVMSIAQRYD---NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFK 337 (391)
Q Consensus 261 eg~~Are~LIe~nlpLV~~IAkkY~---~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~ 337 (391)
+|.-++++|+..|.|+|..+|.+|. +.+.+.+||+|+|++||++++++|||++|.+|.||+.+||++.|.++++.+.
T Consensus 5 ~~~~~~~~L~~~~~~~v~~~a~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~~~lR~~~ 84 (236)
T PRK06986 5 EGKMDQDELVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLD 84 (236)
T ss_pred cccccHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHcC
Confidence 4667899999999999999999997 5688999999999999999999999999999999999999999999999875
Q ss_pred hhhhhhhhHHHhh----hhhcccc---cccCCCCCChhHHhhHHHHHHHHHH
Q 016321 338 QFIAWLKTDVLLK----NQLKFDL---SSSLPKKGSKFEQIGVLLSSICKLL 382 (391)
Q Consensus 338 R~ir~~~r~v~l~----~~l~~dl---~~~~~k~ge~~e~ig~~ls~v~~~L 382 (391)
+ +++.++.. ......+ ....+...+.++.+|+....|..++
T Consensus 85 ~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~ 132 (236)
T PRK06986 85 W----VPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREML 132 (236)
T ss_pred C----CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHH
Confidence 4 12211111 0000010 1223455556777777776665544
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=99.30 E-value=2.3e-11 Score=113.52 Aligned_cols=106 Identities=33% Similarity=0.537 Sum_probs=94.2
Q ss_pred HHHHHHhcC-CCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHH
Q 016321 193 LKGYVKGVV-SEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM 271 (391)
Q Consensus 193 l~~YL~~i~-~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe 271 (391)
+-+|+-.-+ ..+.|++.++.+|+.+++.|+. .|.+.|+.
T Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~li~~~~~gd~----------------------------------------~af~~l~~ 55 (227)
T TIGR02846 16 LVGYVTNNGSFPQPLSEEEEKKYLDRLKEGDE----------------------------------------EARNVLIE 55 (227)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHH
Confidence 345554443 3567999999999999998875 79999999
Q ss_pred HcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 272 ~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
.|.|+|.++|.+|.+...+.+|++|++.+++++++++|+++.+.+|.||+..++++.+.++++..++
T Consensus 56 ~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~Rk~~r 122 (227)
T TIGR02846 56 RNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHLRALKK 122 (227)
T ss_pred HhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999988889999999999999999999999999899999999999999999987754
No 36
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=99.28 E-value=4.1e-11 Score=111.56 Aligned_cols=103 Identities=29% Similarity=0.489 Sum_probs=93.0
Q ss_pred HHHhcCCC-CCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHcH
Q 016321 196 YVKGVVSE-ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNV 274 (391)
Q Consensus 196 YL~~i~~~-~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe~nl 274 (391)
|+.+.... +.+++..+.+|+.+++.|+. .|.+.|+..|.
T Consensus 23 ~~~~~~~~~~~~~~~~~~~L~~~~~~gd~----------------------------------------~af~~l~~~y~ 62 (234)
T PRK08301 23 YIGGSEALPPPLSKEEEEYLLNKLPKGDE----------------------------------------AVRSLLIERNL 62 (234)
T ss_pred HhccccccCCcCCHHHHHHHHHHHHccCH----------------------------------------HHHHHHHHHhH
Confidence 77777554 55788889999999998864 79999999999
Q ss_pred HHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 275 RLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 275 pLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
++|..+|.+|.+.+.+.+|++|++++++++++++|++..+++|.||+..++++.+.++++..++
T Consensus 63 ~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~d~lRk~~~ 126 (234)
T PRK08301 63 RLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNNK 126 (234)
T ss_pred HHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999998899999999999999999999999888899999999999999999987754
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=99.22 E-value=4e-11 Score=90.45 Aligned_cols=70 Identities=26% Similarity=0.379 Sum_probs=66.5
Q ss_pred HHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 269 LVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 269 LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
|++.|.|+|..++.+|.+.+.+.+|++||+.++|++++++||+++|..|.+|+...+++.+.+.++..+|
T Consensus 1 L~~~~~~~l~~~~~~~~~~~~~~eD~~qe~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~r~~~r 70 (71)
T PF04542_consen 1 LYERYYPLLYRYARRYTGDPEDAEDLVQEAFIKLWRAIDSYDPDRGDSFRAWLFRIARNRILDYLRKRRR 70 (71)
T ss_dssp HHHHTHHHHHHHHHTCTTCSSHHHHHHHHHHHHHHHHHHHTSTTSSSHHHHHHHHHHHHHHHHHHHCSSS
T ss_pred CHHHHHHHHHHHHHHHhCCHhhHHHHhhHHHHHHHhhhhcccccccCCHHHHHHHHHHHHHHHHHHHhcC
Confidence 6889999999999999998899999999999999999999999999999999999999999999887764
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=99.17 E-value=2.6e-10 Score=106.85 Aligned_cols=96 Identities=32% Similarity=0.493 Sum_probs=88.8
Q ss_pred CCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHcHHHHHHHHH
Q 016321 203 EELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ 282 (391)
Q Consensus 203 ~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe~nlpLV~~IAk 282 (391)
.+.|+++++.+|...++.|+. .|.+.|+..|.+.|..++.
T Consensus 31 ~~~~~~~~~~~l~~~~~~~d~----------------------------------------~a~~~l~~~y~~~l~~~~~ 70 (234)
T TIGR02835 31 PPPLTGEEEEALLQKLTQGDE----------------------------------------SAKSTLIERNLRLVVYIAR 70 (234)
T ss_pred CCcCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHHHHHHHH
Confidence 577888889999988888764 7999999999999999999
Q ss_pred hcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 283 RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 283 kY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
+|.+.+.+.+|++||+++++++++++|++..+++|.||++.++++.+.++++..++
T Consensus 71 ~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~d~~Rk~~r 126 (234)
T TIGR02835 71 KFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILMYLRRNNK 126 (234)
T ss_pred HhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence 99999999999999999999999999999888899999999999999999988765
No 39
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=99.12 E-value=3.5e-10 Score=108.13 Aligned_cols=76 Identities=16% Similarity=0.184 Sum_probs=71.0
Q ss_pred HHHHHHHHHHcHHHHHHHHHhcccCCC--ChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 263 SLAREKLVMSNVRLVMSIAQRYDNMGA--DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 263 ~~Are~LIe~nlpLV~~IAkkY~~~Gv--d~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
..|++.|+..|.|+|.++|.++.++.. +.+|++|+|.+++++|+++||+++|.+|.+|+..+|++.+.+++|..++
T Consensus 17 ~~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn~~iDylRk~~~ 94 (237)
T PRK08311 17 EELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKRRLIDYFRKESK 94 (237)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence 479999999999999999999988765 4899999999999999999999999899999999999999999988765
No 40
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=99.04 E-value=1.6e-09 Score=97.96 Aligned_cols=77 Identities=29% Similarity=0.346 Sum_probs=71.8
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
+..+.+.|+..|.|+|..+|.+|.+...+.+|++|+++++|++++.+||+.++.+|.||++.+|++.+.++++..++
T Consensus 22 d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n~~~d~~r~~~r 98 (208)
T PRK08295 22 DKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQIITAIKTANR 98 (208)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhhh
Confidence 34799999999999999999999998999999999999999999999999988899999999999999999887654
No 41
>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=98.97 E-value=1.8e-09 Score=89.37 Aligned_cols=72 Identities=26% Similarity=0.382 Sum_probs=68.1
Q ss_pred HHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 265 Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
|.+.|+..|.|+|.++++++.+.+.+.+|++|+|+++|+++++.|++. .+|.+|+..++++.+.++++...+
T Consensus 2 a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~ 73 (158)
T TIGR02937 2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR 73 (158)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhcc
Confidence 678999999999999999999988999999999999999999999998 689999999999999999987764
No 42
>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=98.94 E-value=6.8e-09 Score=92.99 Aligned_cols=77 Identities=26% Similarity=0.338 Sum_probs=70.8
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
+..|.+.|+..|.|.|..+|.++.+...+.+|++|++.+.+++++.+|+++.+.+|.||++.+|++.+.++++..++
T Consensus 17 d~~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~~~~~~~r~~~~ 93 (198)
T TIGR02859 17 NTHALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTRQIITAIKTATR 93 (198)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHHHHHHHHHHHHH
Confidence 34899999999999999999999988889999999999999999999999888899999999999999888876543
No 43
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=98.81 E-value=1.2e-08 Score=88.98 Aligned_cols=76 Identities=24% Similarity=0.223 Sum_probs=69.5
Q ss_pred hhHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 261 eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
.+..|.+.|+..|.++|+.++.+|.+.+.+.+|++|+++++|++++++|+ .+.+|.+|+...+++.+.+.++..++
T Consensus 7 gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~r~~~~ 82 (182)
T PRK09652 7 GDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYLRKQGR 82 (182)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHHHcccC
Confidence 35589999999999999999999998889999999999999999999999 45689999999999999999887654
No 44
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=98.80 E-value=3.9e-08 Score=88.23 Aligned_cols=74 Identities=12% Similarity=0.085 Sum_probs=66.2
Q ss_pred HHHHHHHHHcHHHHHHHHHhcccC----CCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 264 LAREKLVMSNVRLVMSIAQRYDNM----GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 264 ~Are~LIe~nlpLV~~IAkkY~~~----Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
.+.+.|+..|.|.|..+|.++.+. +.+.+|++||++++|++++.+|++. +.+|.+|++..+++.+.++++..++
T Consensus 24 ~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~n~~~d~~r~~~r 101 (189)
T PRK09648 24 RALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAAHKVADAHRAAGR 101 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHHHHHHHHHHHhCC
Confidence 899999999999999999988643 3689999999999999999999864 4589999999999999999887765
No 45
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=98.76 E-value=4.7e-08 Score=91.41 Aligned_cols=96 Identities=19% Similarity=0.176 Sum_probs=86.5
Q ss_pred CCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHcHHHHHHH
Q 016321 201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI 280 (391)
Q Consensus 201 ~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe~nlpLV~~I 280 (391)
...|+|++..+.+|+..++.|+. .+.+.|+..|.+.|..+
T Consensus 7 ~~~~~~~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~y~~~l~~~ 46 (231)
T PRK11922 7 SRPPPLSAASDRELVARVLAGDE----------------------------------------AAFEALMRRHNRRLYRT 46 (231)
T ss_pred CCCCCcCcccHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHH
Confidence 34588999999999999988875 78999999999999999
Q ss_pred HHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 281 AQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 281 AkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
|.++.+.+-+-+|++||++++|++.+++|++. ..|.+|+...+++.+.+.++...+
T Consensus 47 a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~Rk~~r 102 (231)
T PRK11922 47 ARAILRNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNEALGRLRRRRR 102 (231)
T ss_pred HHHHhCChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHHHHHHHHhhcc
Confidence 99999888899999999999999999999986 379999999999999999887664
No 46
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=98.76 E-value=3.9e-08 Score=89.04 Aligned_cols=75 Identities=12% Similarity=0.082 Sum_probs=69.3
Q ss_pred HHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 263 ~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
..+.++|+..|.++|.+++.+|.+...+.+|++||+++.+++.+++||+.+| .|.+|++..+++.+.+.++.+++
T Consensus 29 ~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~r~~~~ 103 (194)
T PRK09646 29 QDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHRRAVDRVRSEQA 103 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHHHHHHHHHhhcc
Confidence 3899999999999999999999998899999999999999999999998766 79999999999999999887654
No 47
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=98.70 E-value=7.5e-08 Score=86.18 Aligned_cols=75 Identities=12% Similarity=0.124 Sum_probs=68.6
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFK 337 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~ 337 (391)
+..|.+.|+..|.++|..+|.+|.+.+.+.+|++||++++|++++.+||++ +.+|.+|++..+++.+.++++.++
T Consensus 18 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n~~~d~~R~~~ 92 (186)
T PRK05602 18 DPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLNLCYDRLRRRR 92 (186)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHHHHHHHHHhcC
Confidence 348999999999999999999999988899999999999999999999986 458999999999999999887654
No 48
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=98.68 E-value=8.1e-08 Score=82.80 Aligned_cols=73 Identities=22% Similarity=0.251 Sum_probs=65.8
Q ss_pred HHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 264 ~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
.+.+.|++.|.|+|..++.++.. ..+.||++||+.+++++++++|++..| .|.+|+...+++.+.++++.+.+
T Consensus 4 ~af~~l~~~y~~~l~~~~~~~~~-~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~~ 76 (154)
T PRK06759 4 ATFTEAVVLYEGLIVNQIKKLGI-YQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFA 76 (154)
T ss_pred ccHHHHHHHHHHHHHHHHHHhCC-cccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHHh
Confidence 57899999999999999998754 468999999999999999999998777 79999999999999999987743
No 49
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=98.67 E-value=1.1e-07 Score=84.29 Aligned_cols=75 Identities=19% Similarity=0.175 Sum_probs=68.3
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
+..+.+.|+..|.|+|.++|.++.+...+.+|++|+++++|++++.+|++.. +|.+|+...+++.+.++++..++
T Consensus 16 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~~~d~~R~~~~ 90 (187)
T PRK09641 16 DQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNLTIDRLRKRKP 90 (187)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHHHHHHHHhcCc
Confidence 3489999999999999999999998888999999999999999999999854 79999999999999998887653
No 50
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=98.67 E-value=1.1e-07 Score=84.33 Aligned_cols=74 Identities=19% Similarity=0.183 Sum_probs=67.8
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFK 337 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~ 337 (391)
+..+...|+..|.|+|..+|.+|.+.+.+.+|++|+++++|++++..||+.. +|.+|+...+++.+.++++..+
T Consensus 16 d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~~~~rk~~ 89 (187)
T TIGR02948 16 DENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLTIDRLRKRK 89 (187)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHHHHHHhhc
Confidence 3479999999999999999999998888899999999999999999999876 6999999999999999887644
No 51
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=98.64 E-value=1.5e-07 Score=84.74 Aligned_cols=75 Identities=15% Similarity=0.129 Sum_probs=68.7
Q ss_pred HHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhh
Q 016321 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQF 339 (391)
Q Consensus 263 ~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ 339 (391)
..+.+.|+..|.+.|.++|.++.+...+.+|++|+++++|++++.+|++.. .|.+|+...+++.+.+.++...+.
T Consensus 25 ~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~~--~f~~wl~~i~~n~~~~~~R~~~~~ 99 (194)
T PRK12513 25 AAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRA--RFRTWLYQIARNLLIDHWRRHGAR 99 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCCC--chHHHHHHHHHHHHHHHHHHhccc
Confidence 389999999999999999999998888899999999999999999999753 699999999999999999877653
No 52
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=98.63 E-value=2.1e-07 Score=83.82 Aligned_cols=87 Identities=20% Similarity=0.278 Sum_probs=75.6
Q ss_pred CChHHHHHHhhh----hHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHH
Q 016321 250 ISRPELQSILME----CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWI 325 (391)
Q Consensus 250 ~s~~eL~~~l~e----g~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~I 325 (391)
++.+++...+.. +..|.+.|+..|.|.|..++.+|.+...+.+|++|++++.|++++++|++. .+|.+|+...+
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 345556666653 689999999999999999999999888899999999999999999999863 47999999999
Q ss_pred HHHHHHHHHHhhh
Q 016321 326 RQVRLLLICTFKQ 338 (391)
Q Consensus 326 R~aI~~aIre~~R 338 (391)
++.+.+.++..++
T Consensus 86 ~n~~~d~~R~~~~ 98 (188)
T PRK09640 86 YNECITQYRKERR 98 (188)
T ss_pred HHHHHHHHHHhcc
Confidence 9999999986543
No 53
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=98.60 E-value=2.5e-07 Score=83.09 Aligned_cols=73 Identities=16% Similarity=0.229 Sum_probs=66.1
Q ss_pred HHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 264 ~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
.+.+.|+..|.|.|..++.++.+..-+.+|++|++++.+++++.+|++.. .|.+|+..-.++...++++.+++
T Consensus 20 ~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~~d~~rk~~~ 92 (193)
T PRK11923 20 RAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTAKNHLVSRGR 92 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHHHHHHHHhcC
Confidence 78999999999999999999998878899999999999999999999874 59999998889988888876554
No 54
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=98.59 E-value=2e-07 Score=83.03 Aligned_cols=76 Identities=17% Similarity=0.196 Sum_probs=68.4
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
+..+.+.|+..|.|.|..++.+|.+.+.+.+|++|++++.|++++++|++..+ .|.+|+...+++.+.++++...+
T Consensus 21 d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~rk~~~ 96 (186)
T PRK13919 21 EEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRG-SARAWLLALAHHAAVDHVRRRAA 96 (186)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCcccc-chHHHHHHHHHHHHHHHHHhhhc
Confidence 34899999999999999999999888889999999999999999999997643 69999999999999999877653
No 55
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=98.57 E-value=3.8e-07 Score=82.30 Aligned_cols=75 Identities=17% Similarity=0.177 Sum_probs=67.1
Q ss_pred HHHHHHHHHHcHHHHHHHHHhcccCC---CChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 263 SLAREKLVMSNVRLVMSIAQRYDNMG---ADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 263 ~~Are~LIe~nlpLV~~IAkkY~~~G---vd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
..|.+.|+..|.|+|.+++.++.+.+ .+.+|++|+++++|++++++|+++.+ +|.+|++.-.++.+.++++..++
T Consensus 17 ~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~iarn~~~d~~rk~~~ 94 (189)
T PRK06811 17 EKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAISKYKAIDYKRKLTK 94 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHHHHHHHHHHHHhcc
Confidence 37999999999999999999998753 46899999999999999999997655 79999999999999999987665
No 56
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=98.55 E-value=3.1e-07 Score=82.56 Aligned_cols=74 Identities=22% Similarity=0.265 Sum_probs=66.4
Q ss_pred HHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 263 ~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
..+.+.|+..|.+.|..++.++.+...+.+|++|++++.+++. ..|++..+ .|.||++..+++.+.++++..++
T Consensus 28 ~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~~d~~Rk~~~ 101 (194)
T PRK12519 28 SAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRAIDRLRSRRS 101 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHHHHHHHhccc
Confidence 3799999999999999999999888788999999999999975 67887665 79999999999999999987654
No 57
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=98.53 E-value=5.3e-07 Score=79.52 Aligned_cols=75 Identities=15% Similarity=0.101 Sum_probs=68.6
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
+..+.+.|+..|.|.|..++.++.+...+.+|++||+++.++++++.|++. .+|.+|+...+++.+.++++..++
T Consensus 16 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~r~~~~ 90 (176)
T PRK09638 16 DDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASRLYKDHLRKQKR 90 (176)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHHhcc
Confidence 348999999999999999999999888889999999999999999999874 479999999999999999987654
No 58
>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=98.46 E-value=9.2e-07 Score=77.08 Aligned_cols=77 Identities=16% Similarity=0.078 Sum_probs=69.4
Q ss_pred hhHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 261 eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
.+..|.+.|+..|.+.+..++.++.+...+.+|++|++++.+++.+++|+...+ +|.+|+...+++.+.++++..++
T Consensus 8 ~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R~~~~ 84 (170)
T TIGR02952 8 REEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFRGSKR 84 (170)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHHhcCC
Confidence 355899999999999999999888777788999999999999999999997655 89999999999999999987754
No 59
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=98.45 E-value=1.3e-06 Score=80.31 Aligned_cols=74 Identities=19% Similarity=0.216 Sum_probs=67.9
Q ss_pred HHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 264 ~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
.+.+.|+..|.+.|..++.++.+..-+.+|++|++++.+++++..|++.++ .|.+|++..+++.+.++++..++
T Consensus 38 ~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d~~Rk~~~ 111 (206)
T PRK12526 38 QAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFDMLRKIKA 111 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHHHHHHhcc
Confidence 789999999999999999999887778999999999999999999998765 59999999999999999987654
No 60
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=98.44 E-value=1.1e-06 Score=76.52 Aligned_cols=76 Identities=18% Similarity=0.088 Sum_probs=68.9
Q ss_pred hhHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 261 eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
.+..|.+.|++.|.+.|..+|.++.+...+.+|++|++++.|+++++.|+ .+..|.+|+...+++.+.+.++...+
T Consensus 10 ~~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~~r~~~~ 85 (179)
T PRK11924 10 GDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDLLRRRRR 85 (179)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHHHHhccc
Confidence 35689999999999999999999998888999999999999999999998 34589999999999999999876554
No 61
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=98.44 E-value=8.5e-07 Score=80.46 Aligned_cols=75 Identities=16% Similarity=0.205 Sum_probs=67.4
Q ss_pred HHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 263 ~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
..|.+.|+..|.|.|..+|.++.+...+.+|++||+.+.|++.+.+|++.. ..|.+|+..-+++.+.+.++..++
T Consensus 25 ~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~n~~~d~~Rk~~~ 99 (196)
T PRK12524 25 PAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVCNLCTDRLRRRRR 99 (196)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHHHHHHHHHHHhhcC
Confidence 489999999999999999999998888999999999999999999998533 479999999999999998876543
No 62
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=98.41 E-value=1.4e-06 Score=77.34 Aligned_cols=74 Identities=14% Similarity=0.048 Sum_probs=66.8
Q ss_pred HHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhh
Q 016321 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFK 337 (391)
Q Consensus 263 ~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~ 337 (391)
..+...|+..|.+.|..+|.++.+...+.+|++|++++.+++++++|++..+ .|.+|...-.++.+.++++..+
T Consensus 18 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~R~~~ 91 (179)
T PRK12514 18 RDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGL-SPMTWLITIARNHAIDRLRARK 91 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCcccc-cHHHHHHHHHHHHHHHHHHhcC
Confidence 4799999999999999999999988889999999999999999999997543 6999999999999999887654
No 63
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=98.40 E-value=1.3e-06 Score=78.05 Aligned_cols=74 Identities=15% Similarity=0.112 Sum_probs=66.5
Q ss_pred HHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhh
Q 016321 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFK 337 (391)
Q Consensus 263 ~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~ 337 (391)
..+.+.|+..|.++|+.+|.++.+...+-+|++||.++.+++.+++|++.++ .|.+|.+.-.++.+.++++..+
T Consensus 24 ~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~~d~~R~~~ 97 (187)
T PRK12534 24 RHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKAIDHLRANA 97 (187)
T ss_pred HHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHHHHHhcc
Confidence 3799999999999999999999988888999999999999999999998754 6889999999999888887654
No 64
>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=98.39 E-value=3.2e-06 Score=72.16 Aligned_cols=72 Identities=18% Similarity=0.236 Sum_probs=65.7
Q ss_pred HHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 265 Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
|.++|+..|.|.|..++.++.+...+.+|++|++++++++.+.+|++.. +|.+|++..+|+.+.+.++...+
T Consensus 2 a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~~--~~~~wl~~i~r~~~~d~~r~~~~ 73 (161)
T TIGR02985 2 AFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEVE--SFKAYLFTIVKNRSLNYLRHKQV 73 (161)
T ss_pred hHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhccccc--cHHHHHHHHHHHHHHHHHHHHHh
Confidence 6789999999999999999988878899999999999999999998744 79999999999999998877654
No 65
>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=98.39 E-value=2.1e-06 Score=76.33 Aligned_cols=75 Identities=16% Similarity=0.203 Sum_probs=67.1
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
+..+.+.|+..|.|.|..+|.++.+...+.+|++||++|+|++.+.+|++. .+|.+|+..-.++...+.++..++
T Consensus 18 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~~~~~~r~~~r 92 (190)
T TIGR02939 18 EKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNTAKNHLVAQGR 92 (190)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHHHHHHHHHhcc
Confidence 347999999999999999999998888899999999999999999999975 369999999999999888875544
No 66
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=98.38 E-value=1.8e-06 Score=78.28 Aligned_cols=75 Identities=19% Similarity=0.162 Sum_probs=67.8
Q ss_pred HHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 263 ~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
..+.+.|+..|.|.|..+|.++.+..-+-+|++|+.++.+++...+|++..+ .|.+|+..-+++.+.++++..++
T Consensus 26 ~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn~~ld~~Rk~~~ 100 (194)
T PRK12531 26 KQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRNLCFDLLRKQKG 100 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHHHHHHHHHHhcc
Confidence 4899999999999999999999887677899999999999999999997554 79999999999999999887653
No 67
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=98.32 E-value=5.5e-06 Score=74.17 Aligned_cols=75 Identities=12% Similarity=0.109 Sum_probs=66.6
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhccc-CCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDN-MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~-~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
+..+.+.|+..|.+.|..++.++.+ ...+.+|++|++++.|++.++.|++. .+|.+|++..+++.+.++++...+
T Consensus 19 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~~~d~~Rk~~~ 94 (181)
T PRK12536 19 DAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYKLMDFLRSRAR 94 (181)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHHHHHHHHHHhc
Confidence 4589999999999999999987664 46789999999999999999999975 369999999999999999988654
No 68
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=98.30 E-value=2.6e-06 Score=73.65 Aligned_cols=73 Identities=15% Similarity=0.138 Sum_probs=67.4
Q ss_pred HHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhh
Q 016321 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQF 339 (391)
Q Consensus 265 Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ 339 (391)
+.+.++..|.|.|..+|.++.+...+.||++|++++.+++++++||+.. .|.+|+..-+++.+.++++..++.
T Consensus 2 ~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~ 74 (159)
T TIGR02989 2 AFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRD 74 (159)
T ss_pred HHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhccc
Confidence 6788999999999999999999889999999999999999999999764 699999999999999999887654
No 69
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=98.28 E-value=4.6e-06 Score=73.43 Aligned_cols=75 Identities=19% Similarity=0.149 Sum_probs=67.9
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
+..+.+.|+..|.+.|++++.++.+...+.+|++|+..+.+++..++|++.. +|.+|+...+++.+.++++...+
T Consensus 14 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~ 88 (169)
T TIGR02954 14 NKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPK--YFNTWLTRILINECIDLLKKKKK 88 (169)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCcc--ccHHHHHHHHHHHHHHHHHhcCC
Confidence 3489999999999999999999998888999999999999999999999753 69999999999999998876543
No 70
>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=98.27 E-value=5e-06 Score=73.67 Aligned_cols=75 Identities=16% Similarity=0.088 Sum_probs=67.0
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhccc----CCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDN----MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTF 336 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~----~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~ 336 (391)
+..|.+.|+..|.+.|..+|.+|.. ...+.+|++|++++.|++++..|++..+.+|.+|+...+++.+.++++..
T Consensus 5 ~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~~ 83 (189)
T TIGR02984 5 DQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRRH 83 (189)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHHH
Confidence 4589999999999999999998743 45689999999999999999999987667899999999999999998865
No 71
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=98.22 E-value=5.5e-06 Score=78.45 Aligned_cols=72 Identities=22% Similarity=0.229 Sum_probs=65.7
Q ss_pred HHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHh
Q 016321 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTF 336 (391)
Q Consensus 264 ~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~ 336 (391)
.+.+.|+..|.+.|..++.++.+...+-+|++||.++.+++.+++|++..+ .|.+|...-.++.+.++++..
T Consensus 63 ~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~~id~~Rk~ 134 (233)
T PRK12538 63 AAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNRCIDLRRKP 134 (233)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHHHHHHHHhh
Confidence 799999999999999999999887788999999999999999999987554 799999999999999988764
No 72
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=98.18 E-value=1.6e-05 Score=71.00 Aligned_cols=75 Identities=13% Similarity=0.110 Sum_probs=65.4
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhcccC----CCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDNM----GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFK 337 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~~----Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~ 337 (391)
+..|.+.|+..|.+.|..+|.++.+. ..+.+|++|++.+.++...+.|++. .+|.+|++.-+++.+.++++...
T Consensus 20 d~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn~~~d~~Rr~~ 97 (184)
T PRK12512 20 DAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARNKLIDALRRRG 97 (184)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHHHHHHHHHhhc
Confidence 45899999999999999999988752 3589999999999999999999874 37999999999999999887654
Q ss_pred h
Q 016321 338 Q 338 (391)
Q Consensus 338 R 338 (391)
+
T Consensus 98 ~ 98 (184)
T PRK12512 98 R 98 (184)
T ss_pred c
Confidence 3
No 73
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=98.17 E-value=7e-06 Score=72.70 Aligned_cols=73 Identities=11% Similarity=0.084 Sum_probs=66.9
Q ss_pred HHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 264 ~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
...++|+..|.|+|..++.+|.+...+.+|++|+.++.|++.+++|++.. +|.+|+..-+++.+.++++..++
T Consensus 3 ~~~~~l~~~y~~~i~~~~~~~~~~~~daeDvvQe~~i~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~Rk~~~ 75 (173)
T PRK12522 3 EKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE--NYKKWITTICVRTFYDFYRKKKR 75 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcCCcc--chHHHHHHHHHHHHHHHHHHhcc
Confidence 45789999999999999999999889999999999999999999999854 79999999999999999887654
No 74
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=98.14 E-value=1.5e-05 Score=72.39 Aligned_cols=75 Identities=19% Similarity=0.203 Sum_probs=68.2
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
+..+.+.|+..|.|.|..++.++.+...+-+|++||.++.+++.+++|++.. .|.+|+..-+++.+.+++|..++
T Consensus 25 d~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~~--~f~~wL~~i~rn~~~d~~Rk~~~ 99 (192)
T PRK09643 25 DRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDA--AVSSWLHRIVVNACLDRLRRAKA 99 (192)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCCC--ccHHHHHHHHHHHHHHHHHcccc
Confidence 4589999999999999999999988888899999999999999999999754 69999999999999999887654
No 75
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=98.10 E-value=1.7e-05 Score=71.42 Aligned_cols=74 Identities=19% Similarity=0.125 Sum_probs=66.7
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFK 337 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~ 337 (391)
+..+.+.|+..|.+.+..++.++.+...+-+|++||+++.+++...+|++. ..|.+|++.-+++.+.+.++..+
T Consensus 20 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~r~~~ 93 (189)
T PRK12515 20 DRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARFKALSALRRRK 93 (189)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHHHHHHHHHccC
Confidence 458999999999999999999998887899999999999999999999974 37999999999999999887543
No 76
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=98.07 E-value=4e-05 Score=68.80 Aligned_cols=74 Identities=15% Similarity=0.173 Sum_probs=64.3
Q ss_pred HHHHHHHHHHcHHHHHHHHHh----cccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 263 SLAREKLVMSNVRLVMSIAQR----YDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 263 ~~Are~LIe~nlpLV~~IAkk----Y~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
..|.+.|+..|.|.|..+|.+ +.+...+-+|++|+.++.|++.+..|++.. .|.+|+..-+++.+.++++..++
T Consensus 20 ~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~~n~~~d~~R~~~~ 97 (184)
T PRK12539 20 AAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIARYKLIDHLRRTRA 97 (184)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHHHHHHHHHHHHHhc
Confidence 489999999999999998864 445567899999999999999999999854 69999999999999999887543
No 77
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=98.06 E-value=1.8e-05 Score=70.84 Aligned_cols=76 Identities=20% Similarity=0.305 Sum_probs=68.5
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
+..+.+.|+..|.+.|..++.++.+...+-+|++||.++.+++.+++|++..+ .|.+|...-+++.+.++++..++
T Consensus 21 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wL~~iarn~~~d~~r~~~~ 96 (182)
T PRK12537 21 DRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARG-SARGWIYSVTRHLALNVLRDTRR 96 (182)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHHHHHhccc
Confidence 35899999999999999999999988888999999999999999999987543 79999999999999999887754
No 78
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=97.99 E-value=3.3e-05 Score=68.07 Aligned_cols=74 Identities=19% Similarity=0.134 Sum_probs=64.7
Q ss_pred hhHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhh
Q 016321 261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFK 337 (391)
Q Consensus 261 eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~ 337 (391)
.+..+.+.|+..|.|.|+.++.++.+. .+.+|++||.++.+++.++.|++. ..|.+|+..-+++.+.+.++...
T Consensus 8 gd~~a~~~l~~~~~~~l~~~~~~~~~~-~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~~ 81 (175)
T PRK12518 8 GDRQSFRQLYRRYQQKVRSTLYQLCGR-ELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARRQFA 81 (175)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHcCH-hHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHHHhh
Confidence 345899999999999999999998654 578999999999999999999975 36999999999999999887554
No 79
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=97.98 E-value=2.5e-05 Score=69.81 Aligned_cols=74 Identities=14% Similarity=0.050 Sum_probs=65.8
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFK 337 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~ 337 (391)
+..+.+.|+..|.|.|..++..|.+..-+.+|++|++++.|++++.+|++.. +|.+|...-+++.+.++++...
T Consensus 5 d~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~~ 78 (179)
T PRK12543 5 DQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKRW 78 (179)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhhc
Confidence 4579999999999999999999998888999999999999999999999875 6999998888888888765543
No 80
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=97.94 E-value=3.4e-05 Score=69.08 Aligned_cols=74 Identities=9% Similarity=0.120 Sum_probs=67.0
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFK 337 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~ 337 (391)
+..|.++|+..|.|.|..++.++.+..-+-+|++|++++.|++++.+|++.. .|.+|....+++.+.+++|...
T Consensus 14 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~~--~~~awl~~ia~n~~~d~~Rk~~ 87 (179)
T PRK09415 14 KEDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKS--SLKTWLYRIAINHCKDYLKSWH 87 (179)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCCc--ccHHHHHHHHHHHHHHHHHhhc
Confidence 4579999999999999999999998878899999999999999999998753 6999999999999999887754
No 81
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=97.93 E-value=2.2e-05 Score=70.35 Aligned_cols=78 Identities=19% Similarity=0.101 Sum_probs=69.7
Q ss_pred hhHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 261 eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
.+..+.+.|+..|.+.+..+|.++.+...+-+|++|+..+.+++.+.+|++..+..|.||...-+++.+.++++..++
T Consensus 6 gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~~ 83 (185)
T PRK12542 6 NDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNKR 83 (185)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 356899999999999999999999887788999999999999999999997655589999999999999998877654
No 82
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=97.88 E-value=9e-05 Score=64.65 Aligned_cols=71 Identities=17% Similarity=0.044 Sum_probs=63.8
Q ss_pred HHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 264 ~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
.+.+.|+..|.+.+..+|.++.+...+.+|++|++++.+++. .|+. +..|.+|+...+++.+.++++..++
T Consensus 3 ~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~ 73 (166)
T PRK09639 3 ETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKR 73 (166)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhcc
Confidence 678999999999999999999988889999999999999998 5654 4479999999999999999987765
No 83
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=97.87 E-value=8.1e-05 Score=67.27 Aligned_cols=72 Identities=18% Similarity=0.170 Sum_probs=63.1
Q ss_pred HHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 264 ~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
.+.+.|+..|.+.+..++. +.+...+-+|++||.++.+++.+++|++. ..|.+|...-.++.+.+.++...+
T Consensus 24 ~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~~~d~~Rk~~~ 95 (185)
T PRK09649 24 RALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVADHIRHVRS 95 (185)
T ss_pred HHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHHHHHHHHHhcc
Confidence 7999999999999999995 55555789999999999999999999864 379999999999999999887543
No 84
>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=97.86 E-value=7.2e-05 Score=66.39 Aligned_cols=74 Identities=16% Similarity=0.102 Sum_probs=64.0
Q ss_pred HHHHHHHHHHcHHHHHHHHHhcccCCC-----ChhHHHHHHHHHHHH-HHHhcCCCCCCchhhhHHHHHHHHHHHHHHHh
Q 016321 263 SLAREKLVMSNVRLVMSIAQRYDNMGA-----DMADLVQGGLIGLLR-GIEKFDSSKGFKISTYVYWWIRQVRLLLICTF 336 (391)
Q Consensus 263 ~~Are~LIe~nlpLV~~IAkkY~~~Gv-----d~eDLIQEG~IGLik-AIekFDp~kG~rFsTYA~~~IR~aI~~aIre~ 336 (391)
..+.+.|+..|.+.+..++.+|.+... +-+|++|+..+.+++ ...+|++. ..|.+|+..++++.+.+.++..
T Consensus 16 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~ 93 (183)
T TIGR02999 16 AAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAKAMRRILVDHARRR 93 (183)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHHHHHHHHHHHHHHH
Confidence 379999999999999999999987655 789999999999998 77788754 3699999999999999988765
Q ss_pred hh
Q 016321 337 KQ 338 (391)
Q Consensus 337 ~R 338 (391)
.+
T Consensus 94 ~~ 95 (183)
T TIGR02999 94 RA 95 (183)
T ss_pred HH
Confidence 43
No 85
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=97.83 E-value=0.00012 Score=65.86 Aligned_cols=83 Identities=22% Similarity=0.191 Sum_probs=71.8
Q ss_pred HHHhhhhHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHH
Q 016321 256 QSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICT 335 (391)
Q Consensus 256 ~~~l~eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre 335 (391)
...+..+..+.+.++..|.+.++..+.++.+...+-+||+||.++.+++++..| +. +..|.||.+.-+++...+.++.
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~~R~ 84 (182)
T COG1595 7 AEALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDRLRK 84 (182)
T ss_pred HHHHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHHHHHH
Confidence 344455678999999999999999999999877799999999999999999999 33 3479999999999999999987
Q ss_pred hhhhh
Q 016321 336 FKQFI 340 (391)
Q Consensus 336 ~~R~i 340 (391)
.++..
T Consensus 85 ~~r~~ 89 (182)
T COG1595 85 RKRRR 89 (182)
T ss_pred hcccc
Confidence 76643
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=97.78 E-value=0.0001 Score=64.16 Aligned_cols=75 Identities=12% Similarity=0.014 Sum_probs=66.9
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
+..+.+.|+..|.+.|..++..+.+...+.+|++|++++-+++..++|+. ...|.+|+..-+++.+.++++..++
T Consensus 4 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~~~d~~rk~~~ 78 (162)
T TIGR02983 4 TEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNLARSRWRRRRL 78 (162)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHHHHHHHHhhcc
Confidence 45899999999999999999999988889999999999999999999964 3479999999999999998876543
No 87
>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=97.73 E-value=8e-06 Score=57.62 Aligned_cols=33 Identities=30% Similarity=0.483 Sum_probs=30.3
Q ss_pred hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCc
Q 016321 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS 223 (391)
Q Consensus 191 ~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~ 223 (391)
|.++.||++|+++|+||++||++|+++|+.|+.
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 689999999999999999999999999999975
No 88
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=97.72 E-value=0.00014 Score=64.12 Aligned_cols=75 Identities=13% Similarity=0.194 Sum_probs=67.5
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
+......++..|.|.|..+|.++.+...+-+|++|+.++.+++...+|++.. .|.+|++.-+++.+.+.++..++
T Consensus 4 ~~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~ 78 (164)
T PRK12547 4 CSKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGT--NLKAWLFTILRNEFYSQMRKRGR 78 (164)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhcc
Confidence 4578899999999999999999999888999999999999999999998644 69999999999999999887654
No 89
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=97.68 E-value=0.00015 Score=63.80 Aligned_cols=70 Identities=13% Similarity=0.121 Sum_probs=63.8
Q ss_pred HHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 266 re~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
.+.|++.|.|.|..++.++.+...+-+|++|+..+.++++++.|++. .|.+|...-.++.+.++++..++
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~ 72 (165)
T PRK09644 3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKK 72 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhh
Confidence 46799999999999999999888899999999999999999999863 59999999999999999988765
No 90
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=97.65 E-value=0.00025 Score=69.64 Aligned_cols=75 Identities=23% Similarity=0.209 Sum_probs=67.1
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
+..+.++|+..|.+.|..++.++.+...+-+|++|+..+-+++.+.+|++. ..|.+|.+.-.++.+.++++..++
T Consensus 17 d~~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~ 91 (339)
T PRK08241 17 DRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATNVCLDALEGRAR 91 (339)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHHHHHHHHHhhcc
Confidence 348999999999999999999998877889999999999999999999853 369999999999999999887654
No 91
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=97.59 E-value=0.00081 Score=58.77 Aligned_cols=71 Identities=14% Similarity=0.037 Sum_probs=63.4
Q ss_pred HHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhh
Q 016321 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFK 337 (391)
Q Consensus 264 ~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~ 337 (391)
.+.++|+..|.+.|..++.++.+...+-+|++|+.++-+++....|++. .|.+|...++++.+.+.++..+
T Consensus 4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~ 74 (161)
T PRK12528 4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQII---EPRAFLTTIAKRVLCNHYRRQD 74 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhcccccccc---CHHHHHHHHHHHHHHHHHHHHH
Confidence 6889999999999999999999887889999999999999988877642 6999999999999999887654
No 92
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=97.58 E-value=0.00028 Score=61.70 Aligned_cols=73 Identities=11% Similarity=0.102 Sum_probs=65.7
Q ss_pred HHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 263 ~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
..+.+.++..|.+.|..++.++.+..-+-+|++||+.+-+++..++|++. .|.||...-+++.+.++++..++
T Consensus 4 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~ 76 (161)
T PRK12541 4 KQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEKK 76 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhccc
Confidence 36899999999999999999999887899999999999999999999863 59999999999999998877654
No 93
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=97.57 E-value=0.00032 Score=61.87 Aligned_cols=75 Identities=13% Similarity=0.065 Sum_probs=66.2
Q ss_pred HHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 263 ~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
..+.+.|+..|.+.+..++.++.+...+-+|++|+.++-+++..++|++.. ..|.+|+..-+++.+.++++..++
T Consensus 8 ~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~Rk~~~ 82 (173)
T PRK09645 8 AALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSARA 82 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHHHHHHHhhcc
Confidence 479999999999999999999987767899999999999999999997532 379999999999999998886543
No 94
>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=97.53 E-value=0.00029 Score=63.56 Aligned_cols=75 Identities=15% Similarity=0.185 Sum_probs=67.3
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
+..+.+.|+..|.+.|..++.++.+...+-+|++|+..+-+++.+.+|++. .+|.+|...-+++.+.++++..++
T Consensus 9 ~~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~~~ 83 (193)
T TIGR02947 9 RAQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKAQR 83 (193)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHhcC
Confidence 347899999999999999999998877788999999999999999999864 369999999999999999887654
No 95
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=97.50 E-value=0.0004 Score=64.28 Aligned_cols=73 Identities=19% Similarity=0.264 Sum_probs=66.5
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFK 337 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~ 337 (391)
+..+.++|+..|.+.+..++.++.+...+-+|++|+.++.+++.+.+|++ + +|.+|+..-+|+.+.++++...
T Consensus 26 d~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~ 98 (203)
T PRK09647 26 TMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRA 98 (203)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhcc
Confidence 35799999999999999999999988788999999999999999999985 3 6999999999999999988764
No 96
>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=97.48 E-value=0.0006 Score=65.35 Aligned_cols=74 Identities=15% Similarity=0.060 Sum_probs=64.9
Q ss_pred HHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHH-------HHHHhcCCCCCCchhhhHHHHHHHHHHHHHHH
Q 016321 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLL-------RGIEKFDSSKGFKISTYVYWWIRQVRLLLICT 335 (391)
Q Consensus 263 ~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLi-------kAIekFDp~kG~rFsTYA~~~IR~aI~~aIre 335 (391)
..|...|+..|.+.|..++.++.+...+-+|++|+..+-++ +.+.+|++.. .|.||.+.-.++.+.++++.
T Consensus 38 ~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~~--~~~tWL~~Ia~N~~id~lRk 115 (244)
T TIGR03001 38 PAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGRG--PLLSWVRIVATRIALELQAQ 115 (244)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCCC--chHhHHHHHHHHHHHHHHHH
Confidence 47999999999999999999997777899999999999999 4788898743 69999999999999999876
Q ss_pred hhh
Q 016321 336 FKQ 338 (391)
Q Consensus 336 ~~R 338 (391)
.++
T Consensus 116 ~~r 118 (244)
T TIGR03001 116 ERR 118 (244)
T ss_pred hcc
Confidence 543
No 97
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=97.47 E-value=0.00022 Score=61.33 Aligned_cols=65 Identities=14% Similarity=0.104 Sum_probs=58.0
Q ss_pred HHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 271 e~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
..|.|.|+.++.++.+.--+.+|++|+.++.|++.+++|++ .+|.+|+...+++.+.++++..++
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~ 66 (154)
T TIGR02950 2 REYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKK 66 (154)
T ss_pred chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhh
Confidence 46889999999999877678999999999999999999997 379999999999999998886654
No 98
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=97.46 E-value=0.00037 Score=62.82 Aligned_cols=72 Identities=15% Similarity=0.109 Sum_probs=65.2
Q ss_pred HHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 265 Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
+.+.|+..|.+.+...|.++.+...+-+|++|+..+.+++.+.+|++.. +|.+|.+.-+++.+.+.++..++
T Consensus 3 ~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~~--~~~~WL~~ia~n~~~d~~Rk~~r 74 (191)
T PRK12520 3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQS--SLKTYLVGILKHKIIDAIRSGRR 74 (191)
T ss_pred chHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhcccc--cHHHHHHHHHHHHHHHHHHhhcC
Confidence 5788999999999999999988878899999999999999999998653 69999999999999999987654
No 99
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=97.42 E-value=0.00074 Score=61.48 Aligned_cols=74 Identities=9% Similarity=0.129 Sum_probs=66.3
Q ss_pred HHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 263 ~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
..+..+|+..|.+.++.+|.++.+..-+-+|++|+..+-+++..++|+... .|.+|.+.-.++.+.++++..++
T Consensus 9 ~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~~--~~~awL~~Ia~n~~~d~~R~~~~ 82 (187)
T PRK12516 9 TPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGT--NMKAWLFTILRNEFYSQMRKRGR 82 (187)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCcc--cHHHHHHHHHHHHHHHHHHhhcC
Confidence 378999999999999999999998878899999999999999999998653 69999999999999998877654
No 100
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=97.39 E-value=0.0012 Score=60.57 Aligned_cols=74 Identities=14% Similarity=0.046 Sum_probs=63.9
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
+..+.+.|+..|.+.+..++. +.+...+-+|++|+-++.|++.+++|++. ..|.+|.+.-+++.+.++++...+
T Consensus 23 d~~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~ 96 (196)
T PRK12535 23 DRAALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAAR--SSARTWLLSLARRVWVDNIRHDMA 96 (196)
T ss_pred CHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCc--ccHHHHHHHHHHHHHHHHHHhhcc
Confidence 457899999999999999975 45556789999999999999999999864 369999999999999999887653
No 101
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=97.37 E-value=0.00049 Score=62.44 Aligned_cols=70 Identities=13% Similarity=0.078 Sum_probs=63.1
Q ss_pred HHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 267 e~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
.+.|..|.+.|..++.++.+.-.+-+|++|+.++.+++...+|++. .+|.+|++..+++.+.++++..++
T Consensus 5 ~~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r 74 (188)
T TIGR02943 5 PQELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGR 74 (188)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcc
Confidence 4678889999999999999887889999999999999999999975 379999999999999999987654
No 102
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=97.33 E-value=0.00062 Score=61.56 Aligned_cols=70 Identities=13% Similarity=0.211 Sum_probs=61.2
Q ss_pred HHHHHHcHHHHHHHHHhcccCCCC-hhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 267 EKLVMSNVRLVMSIAQRYDNMGAD-MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 267 e~LIe~nlpLV~~IAkkY~~~Gvd-~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
+..+..|.+.|..+|.++.+...+ -+|++|+.++.+++...+|++. .+|.+|++.-+++.+.++++..++
T Consensus 8 ~~~~~~~~~~l~~~a~~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~ 78 (195)
T PRK12532 8 DAELIESRKLLLHFARLQLPDHPDLAEDLVQETLLSAYSAGDSFQGR--ALVNSWLFAILKNKIIDALRQIGR 78 (195)
T ss_pred hhhHHHHHHHHHHHHHHHcCChhhhHHHHHHHHHHHHHHhccccccc--chHHHHHHHHHHHHHHHHHHHhcc
Confidence 356777899999999999887777 8999999999999999999864 379999999999999999987654
No 103
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=97.32 E-value=0.00085 Score=65.16 Aligned_cols=74 Identities=19% Similarity=0.203 Sum_probs=67.0
Q ss_pred HHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 263 ~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
..+.+.|+..|.+.++.+|.++.+...+-+|++|+..+-+++.+.+|++. ..|.+|.+.-.++.+.++++..++
T Consensus 4 ~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~ 77 (324)
T TIGR02960 4 GAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQR 77 (324)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhccC
Confidence 47899999999999999999999887889999999999999999999874 369999999999999999887654
No 104
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=97.32 E-value=0.00096 Score=60.34 Aligned_cols=71 Identities=14% Similarity=0.123 Sum_probs=64.1
Q ss_pred HHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 266 re~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
.+.|++.|.+.|..++.++.+...+.+|++||.++.+++.+..|++. .+|.+|+..-+++.+.++++..++
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~~--~~~~~wL~~i~~n~~~d~~Rk~~~ 73 (181)
T PRK09637 3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNTIIDFYRKKNR 73 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhccc--cchHHHHHHHHHHHHHHHHHhccc
Confidence 46789999999999999999888899999999999999999999853 479999999999999999887654
No 105
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=97.29 E-value=0.00083 Score=58.52 Aligned_cols=65 Identities=6% Similarity=0.049 Sum_probs=58.0
Q ss_pred HHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 271 e~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
+.|.+.|..++.++.+..-+-+|++||..+.+++.+.+|++. .|.+|...-+++.+.++++..++
T Consensus 2 ~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n~~~d~~Rk~~~ 66 (160)
T PRK09642 2 QTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATNHAIDYKRKKAR 66 (160)
T ss_pred chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHHHHHHHHHHhcc
Confidence 568999999999998877889999999999999999999863 49999999999999999887654
No 106
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=97.24 E-value=0.0025 Score=57.14 Aligned_cols=77 Identities=9% Similarity=-0.123 Sum_probs=63.1
Q ss_pred hhHHHHHHHHHHcHHHHHHHHHhccc--CCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhh
Q 016321 261 ECSLAREKLVMSNVRLVMSIAQRYDN--MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFK 337 (391)
Q Consensus 261 eg~~Are~LIe~nlpLV~~IAkkY~~--~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~ 337 (391)
.+..+.+.|+..|.+.|..++..+.+ ..-+-+|++||..+-+++..++|++.....|.||...-.++.+.++++..+
T Consensus 10 ~d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~Rk~~ 88 (178)
T PRK12529 10 ADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRRRQS 88 (178)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHHHHH
Confidence 34589999999999999997554444 235789999999999999999998654457999999999999999877654
No 107
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=97.21 E-value=0.0019 Score=60.78 Aligned_cols=74 Identities=15% Similarity=0.153 Sum_probs=65.8
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
...+.+.|+..|.+.+..++.++.+..-+-+|++||.++-+++.+.+|++. .|.+|.+.-.++.+.+.++..++
T Consensus 16 ~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~~~ 89 (216)
T PRK12533 16 RGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRRAN 89 (216)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhhcc
Confidence 347899999999999999999998877889999999999999999999863 49999999999999998877654
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=97.18 E-value=0.00099 Score=59.32 Aligned_cols=66 Identities=15% Similarity=0.176 Sum_probs=58.6
Q ss_pred HHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 271 e~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
..|.+.++.++.++.+...+-+|++|+..+.+++++.+|++. .+|.+|+..-+++.+.++++..++
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~~--~~f~~wl~~iarn~~~d~~Rk~~~ 67 (170)
T TIGR02959 2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDG--QKIQSWLYQIARNTIIDFYRSKSR 67 (170)
T ss_pred chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhccC
Confidence 357888889999888888889999999999999999999974 489999999999999999988764
No 109
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=97.16 E-value=0.0056 Score=54.51 Aligned_cols=73 Identities=16% Similarity=0.151 Sum_probs=62.2
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhh
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFK 337 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~ 337 (391)
+..+.+.++..|.+.+..++.++.+...+-+|++|+.++-+++. ..|++-. +|.+|...-+++.+.++++..+
T Consensus 8 ~~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~ 80 (172)
T PRK09651 8 ASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNA 80 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHH
Confidence 34799999999999999999999888788999999999999987 3565443 5889999999999999887654
No 110
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=97.13 E-value=0.0014 Score=58.17 Aligned_cols=73 Identities=11% Similarity=0.023 Sum_probs=63.2
Q ss_pred HHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 263 ~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
..+...|+..|.+.|..++.++.+...+-+|++|+.++.+++. ..|+.. ..|.+|.....++.+.++++..++
T Consensus 9 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~~ 81 (172)
T PRK12523 9 SELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAAL 81 (172)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHHH
Confidence 4799999999999999999999887788999999999999986 345543 369999999999999999887653
No 111
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=97.04 E-value=0.0029 Score=57.85 Aligned_cols=72 Identities=18% Similarity=0.214 Sum_probs=62.1
Q ss_pred HHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 264 ~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
++.+.|.. |.|.|+..|..+.+...+-+|++|+.++.+++.+..|+.. ..|.+|+..-+++.+.+.++...+
T Consensus 8 ~~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r 79 (188)
T PRK12546 8 DPRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKR 79 (188)
T ss_pred hHHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhcc
Confidence 45556655 7799999999999888889999999999999999999864 369999999999999998877654
No 112
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=97.03 E-value=0.0026 Score=57.64 Aligned_cols=73 Identities=16% Similarity=0.226 Sum_probs=64.6
Q ss_pred HHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 264 ~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
.+...++..|.+.+..++.++.+...+-+|++|+..+.+++..++|++.. .|.+|+..-+++.+.+.++..++
T Consensus 5 ~~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~ 77 (182)
T PRK12540 5 DSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGS--NLPAWLFTILRNLFRSDYRKRRR 77 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCc--hHHHHHHHHHHHHHHHHHHhccc
Confidence 45678899999999999999988878899999999999999999998764 69999999999999998876654
No 113
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=96.96 E-value=0.0033 Score=57.19 Aligned_cols=71 Identities=15% Similarity=0.083 Sum_probs=62.2
Q ss_pred hhHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHH
Q 016321 261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLI 333 (391)
Q Consensus 261 eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aI 333 (391)
.+..+.+.++..|.+.|..+|.++.+...+-+|++|+..+-+++.+..|++.. .|.+|+...+++...+..
T Consensus 20 ~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~~--~~~~wL~~Iarn~~~~~~ 90 (188)
T PRK12517 20 SKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEK--AAKAWLITILRRENARRF 90 (188)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCcc--chHHHHHHHHHHHHHHHH
Confidence 45689999999999999999999988878899999999999999999998753 699999988888765543
No 114
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=96.86 E-value=0.0029 Score=55.15 Aligned_cols=68 Identities=15% Similarity=0.222 Sum_probs=57.3
Q ss_pred HHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 268 ~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
+++..|.+.++++|.++.+...+-+|++|+..+.+++....|++. .|.+|+..-+++.+.++++..++
T Consensus 2 ~~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn~~~d~~R~~~~ 69 (163)
T PRK07037 2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRNLAIDHYRRQAL 69 (163)
T ss_pred hHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHHHHHHHHHhhcc
Confidence 356778899999999998877889999999999999888777653 47899999999999998876653
No 115
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=96.84 E-value=0.004 Score=57.85 Aligned_cols=70 Identities=19% Similarity=0.181 Sum_probs=63.0
Q ss_pred HHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 267 e~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
..++..|.+.|..++.++.+..-+-+|++||.++.+++.+.+|+.. .+|.+|.+.-+++.+.++++..++
T Consensus 21 ~~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfikl~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~~ 90 (206)
T PRK12544 21 PVFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGR--AAFKTWVFAILKNKIIDLLRQKKR 90 (206)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhhcc
Confidence 5688889999999999999887889999999999999999999865 369999999999999999987654
No 116
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=96.83 E-value=0.0037 Score=57.37 Aligned_cols=69 Identities=13% Similarity=0.091 Sum_probs=61.5
Q ss_pred HHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 268 ~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
.++..|.+-+..++.++.+..-+-+|++|+..+.+++.+.+|++.. .|.+|.+.-+++...++++..++
T Consensus 12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~IarN~~~d~~Rk~~r 80 (201)
T PRK12545 12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQS--AHKTWVFGILRNKLIDTLRARQR 80 (201)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhccccc--hHHHHHHHHHHHHHHHHHHhhcc
Confidence 3478899999999999988778899999999999999999999763 69999999999999999987764
No 117
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=96.54 E-value=0.007 Score=54.90 Aligned_cols=69 Identities=14% Similarity=0.153 Sum_probs=60.4
Q ss_pred HHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 268 ~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
.-|..|.+.+..+|.++.+...+-+|++|+..+-+++.+..|++.. +|.+|.+.-.++.+.++++..++
T Consensus 11 ~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~~--~~~~wL~~Ia~n~~~d~~Rk~~~ 79 (189)
T PRK12530 11 LEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQS--ALKTWIFAILKNKIIDLIRYRKR 79 (189)
T ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCCc--cHHHHHHHHHHHHHHHHHHhhcc
Confidence 3467788899999999988777899999999999999999998753 69999999999999999887654
No 118
>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=96.35 E-value=0.0056 Score=48.03 Aligned_cols=37 Identities=32% Similarity=0.525 Sum_probs=29.1
Q ss_pred hhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhh
Q 016321 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (391)
Q Consensus 225 ~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~e 261 (391)
...+.+|...+||+||.+++|+.+|++.++++.++..
T Consensus 7 ~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~ 43 (78)
T PF04539_consen 7 ERARRELEQELGREPTDEEIAEELGISVEEVRELLQA 43 (78)
T ss_dssp HHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHh
Confidence 4567789999999999999999999999998776653
No 119
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=96.34 E-value=0.012 Score=53.49 Aligned_cols=71 Identities=15% Similarity=0.150 Sum_probs=61.9
Q ss_pred HHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 266 re~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
++..+..+.+-|+..+.++.+..-+-+|++|+.++-+++.+..|++. .+|.+|...-+++.+.++++..++
T Consensus 6 ~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~ 76 (182)
T PRK12511 6 KRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRV 76 (182)
T ss_pred hhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhcc
Confidence 44557789999999999998877889999999999999999999864 379999999999999999887654
No 120
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=96.03 E-value=0.094 Score=46.41 Aligned_cols=70 Identities=6% Similarity=-0.105 Sum_probs=58.2
Q ss_pred HHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHh
Q 016321 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTF 336 (391)
Q Consensus 264 ~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~ 336 (391)
.+..+++..|.+.+...+.++.+...+-+|++|+.++-+++-...++ ...|.+|...-.++.+.+.++..
T Consensus 9 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~---~~~~~~wl~~Iarn~~~d~~Rr~ 78 (168)
T PRK12525 9 TLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPAS---IREPRALLTTIARRLMYEGWRRQ 78 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCccc---ccCHHHHHHHHHHHHHHHHHHHH
Confidence 67888999999999999999998878999999999999997444443 23699999888888888877654
No 121
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=95.96 E-value=0.017 Score=50.39 Aligned_cols=64 Identities=6% Similarity=0.008 Sum_probs=52.5
Q ss_pred HHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhh
Q 016321 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFK 337 (391)
Q Consensus 271 e~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~ 337 (391)
..|.+.+...+.++.+...+-+|++|+.++.|++..+.|++. +|.+|...-+++.+.++++..+
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~~---~~~~wL~~ia~n~~~d~~R~~~ 65 (159)
T PRK12527 2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIE---HPRAFLYRTALNLVVDRHRRHR 65 (159)
T ss_pred hhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhcccccccc---chHHHHHHHHHHHHHHHHHHHh
Confidence 356667777777777766788999999999999999988753 7999999999999999887554
No 122
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=95.92 E-value=0.017 Score=56.06 Aligned_cols=69 Identities=13% Similarity=0.045 Sum_probs=58.3
Q ss_pred HHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhh
Q 016321 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFK 337 (391)
Q Consensus 265 Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~ 337 (391)
....|++.|.+.+..+|.++.+...+-+|++||..+.+. ....|+ ...|.+|.+.-+++...+.++..+
T Consensus 5 ~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~~~-~~~~~~---~~~~~~WL~~Ia~n~~~d~lR~~~ 73 (293)
T PRK09636 5 DAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLRWN-NADRAQ---IRDPRAWLTRVVTRLCLDRLRSAR 73 (293)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH-hccccc---ccCHHHHHHHHHHHHHHHHHHhhh
Confidence 456889999999999999999887889999999999944 445665 347999999999999999888654
No 123
>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=95.75 E-value=0.021 Score=55.34 Aligned_cols=66 Identities=15% Similarity=0.074 Sum_probs=55.9
Q ss_pred HHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhh
Q 016321 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFK 337 (391)
Q Consensus 268 ~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~ 337 (391)
++++.|.+.+..+|.++.+...+-||++||.++-+++. .|+. ...|.+|.+..+++.+.++++..+
T Consensus 1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~--~~~~~awL~~Ia~n~~ld~lR~~~ 66 (281)
T TIGR02957 1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQ--IENPKAYLTKVVTRRCIDVLRSAR 66 (281)
T ss_pred ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Cccc--ccCHHHHHHHHHHHHHHHHHHHhh
Confidence 36889999999999999988889999999999997764 4443 337999999999999999988664
No 124
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=95.73 E-value=0.015 Score=62.89 Aligned_cols=34 Identities=24% Similarity=0.475 Sum_probs=32.0
Q ss_pred hhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCc
Q 016321 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS 223 (391)
Q Consensus 190 ~~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~ 223 (391)
.|+++.||++++++||||.++|++++++|..|..
T Consensus 103 ~DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~ 136 (619)
T PRK05658 103 DDPVRMYLREMGTVELLTREGEIEIAKRIEAGEN 136 (619)
T ss_pred CChHHHHHHHhccCcCCCcHHHHHHHHHHHHHHH
Confidence 4899999999999999999999999999999964
No 125
>PRK09191 two-component response regulator; Provisional
Probab=95.52 E-value=0.091 Score=48.44 Aligned_cols=63 Identities=11% Similarity=0.110 Sum_probs=54.6
Q ss_pred HHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHH
Q 016321 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVR 329 (391)
Q Consensus 265 Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI 329 (391)
+..+|+..|.+.+...+.++.+..-+-+|++|+.++-+++....|++.. .|.+|.+.++++-.
T Consensus 2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~~--~~~~wl~~~~~~~~ 64 (261)
T PRK09191 2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEAS--SPRVGLYRLFHRLW 64 (261)
T ss_pred chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCCc--chhhHHHHHHHHHh
Confidence 3678999999999999999988777889999999999999999998753 58999888776643
No 126
>PF12645 HTH_16: Helix-turn-helix domain; InterPro: IPR024760 This domain appears to be a helix-turn-helix domain, suggesting a transcriptional regulatory protein. Some proteins with this domain are annotated as conjugative transposon proteins.
Probab=95.32 E-value=0.077 Score=41.90 Aligned_cols=49 Identities=24% Similarity=0.193 Sum_probs=40.7
Q ss_pred hHHHHHHHHHHcHHHHHHHHHhcc----c--CCCChhHHHHHHHHHHHHHHHhcC
Q 016321 262 CSLAREKLVMSNVRLVMSIAQRYD----N--MGADMADLVQGGLIGLLRGIEKFD 310 (391)
Q Consensus 262 g~~Are~LIe~nlpLV~~IAkkY~----~--~Gvd~eDLIQEG~IGLikAIekFD 310 (391)
+..|.++++..|.|+|.+.+.+-. + .|.--+||-|+=.+-|++||.+|+
T Consensus 11 D~~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~ 65 (65)
T PF12645_consen 11 DPEAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE 65 (65)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence 348999999999999999987621 1 244468999999999999999996
No 127
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=95.24 E-value=0.049 Score=52.19 Aligned_cols=79 Identities=18% Similarity=0.045 Sum_probs=60.6
Q ss_pred HHHHHhhhhHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHH
Q 016321 254 ELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLI 333 (391)
Q Consensus 254 eL~~~l~eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aI 333 (391)
+|.+.+.-+..+.+.+++.| +.+...+.++.+..-+-+|++||..+-+++ +|+... .|.+|...-.++.+.+.+
T Consensus 8 ~~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~---~~~~~~--~~~~WL~~IarN~~id~~ 81 (228)
T PRK06704 8 ILKNHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQ---KYSNKD--ICMTLVYKIARNRWLDQI 81 (228)
T ss_pred HHhcccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHH---HcCccc--cHHHHHHHHHHHHHHHHH
Confidence 44445555557777777777 788888888887778899999999988866 466543 599999999999999988
Q ss_pred HHhhh
Q 016321 334 CTFKQ 338 (391)
Q Consensus 334 re~~R 338 (391)
+..++
T Consensus 82 Rk~k~ 86 (228)
T PRK06704 82 KSKSV 86 (228)
T ss_pred hcccc
Confidence 76543
No 128
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=94.50 E-value=0.2 Score=45.76 Aligned_cols=78 Identities=15% Similarity=0.044 Sum_probs=54.8
Q ss_pred HHHHHHHHHcHHHHHHHHHhccc---CCCChhHH--HHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 264 LAREKLVMSNVRLVMSIAQRYDN---MGADMADL--VQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 264 ~Are~LIe~nlpLV~~IAkkY~~---~Gvd~eDL--IQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
.|.++|+..|.+-++.+|+++.. ++.+.+|. +++.++-+...-...+.+.-..|-.++..-+++.+.+.+|...+
T Consensus 17 ~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~~~~~rr~lid~~R~~~a 96 (185)
T PF07638_consen 17 AALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALLARIMRRKLIDHARRRQA 96 (185)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 89999999999999999987653 24556654 55555555442222244444569889999999999998887665
Q ss_pred hhh
Q 016321 339 FIA 341 (391)
Q Consensus 339 ~ir 341 (391)
.+|
T Consensus 97 ~KR 99 (185)
T PF07638_consen 97 QKR 99 (185)
T ss_pred Hhc
Confidence 444
No 129
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=94.29 E-value=0.092 Score=51.68 Aligned_cols=70 Identities=14% Similarity=-0.053 Sum_probs=58.8
Q ss_pred HHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhh
Q 016321 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFK 337 (391)
Q Consensus 264 ~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~ 337 (391)
.....+++.|.+.+..+|.++.+...+-||++||.++-++++...+ -..|.+|.+.-.++...+.++..+
T Consensus 5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~----~~~~~aWL~~Ia~n~~id~lRk~~ 74 (290)
T PRK09635 5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD----IDDERGWLIVVTSRLCLDHIKSAS 74 (290)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc----cccHHHHHHHHHHHHHHHHHhhhh
Confidence 4677899999999999999999888889999999999988775432 236999999999999999887654
No 130
>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=93.80 E-value=0.28 Score=42.04 Aligned_cols=65 Identities=14% Similarity=0.130 Sum_probs=52.8
Q ss_pred HHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHh-----cCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEK-----FDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 267 e~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIek-----FDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
+.|+..|.+++..++.+|.. +|.+|+-.+.+++...+ |++. ..|.||...-.++...+.++..++
T Consensus 2 ~~~~~~y~~~l~~~~~~~~~-----~~~~qdvf~~~w~~~~~~~~~~~~~~--~~~~~wL~~iarN~~id~~Rk~~~ 71 (142)
T TIGR03209 2 EEIYMNFKNTIDIFTRKYNL-----YYDYNDILYHLWIILKKIDLNKFNTE--NDLEKYISTSLKRYCLDICNKKNR 71 (142)
T ss_pred hHHHHHHHHHHHHHHHHhcc-----hhhHHHHHHHHHHHHHHhhhhhcCch--hHHHHHHHHHHHHHHHHHHHHHhh
Confidence 57899999999999999955 23459999999998865 5443 479999999999999999886654
No 131
>PHA02547 55 RNA polymerase sigma factor; Provisional
Probab=93.04 E-value=0.35 Score=45.35 Aligned_cols=70 Identities=16% Similarity=0.209 Sum_probs=56.6
Q ss_pred HHHcHHHHHHHHHhcccCCCC---hhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhhh
Q 016321 270 VMSNVRLVMSIAQRYDNMGAD---MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQF 339 (391)
Q Consensus 270 Ie~nlpLV~~IAkkY~~~Gvd---~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R~ 339 (391)
-.+.+.++..++.+|.-+|+. .+|+|..|.-..++.+.+|||++...+-+|....+-++..+-|...++.
T Consensus 43 g~~imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~kEkke 115 (179)
T PHA02547 43 GLAIMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKKEKKE 115 (179)
T ss_pred HHHHHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHHHHHH
Confidence 334556666666777666776 6999999999999999999999999999999988888888877666543
No 132
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=92.21 E-value=0.51 Score=48.38 Aligned_cols=32 Identities=31% Similarity=0.509 Sum_probs=29.9
Q ss_pred hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCC
Q 016321 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGL 222 (391)
Q Consensus 191 ~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~ 222 (391)
..+..|+..+...+.|+++||.+|+..++.|.
T Consensus 67 ~~~~~~~~~~~~~~~l~~~Ee~~la~~~~~g~ 98 (342)
T COG0568 67 GRLSFYIRAIEAAPLLTPEEEKALARRLKRGE 98 (342)
T ss_pred hhHHHHHHHHhhhcccChHHHHHHHHHHHcCC
Confidence 58889999999999999999999999999993
No 133
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=91.00 E-value=0.53 Score=40.68 Aligned_cols=46 Identities=13% Similarity=0.029 Sum_probs=38.0
Q ss_pred ChhHHHHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhhh
Q 016321 290 DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRLLLICTFKQ 338 (391)
Q Consensus 290 d~eDLIQEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~~aIre~~R 338 (391)
+-+|++|+.++.+++.... ++ +..|.+|.+.-+++.+.++++..++
T Consensus 6 ~AeDivQe~fl~~~~~~~~-~~--~~~~~~wl~~ia~n~~~d~~Rk~~~ 51 (161)
T PRK09047 6 AALDIVQDAMIKLAEKYGD-RP--AAEWPPLFQRILQNRIHDWFRRQKV 51 (161)
T ss_pred HHHHHHHHHHHHHHHHHhh-cc--cCchHHHHHHHHHHHHHHHHHhhcc
Confidence 5789999999999988776 33 4579999999999999999887653
No 134
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=87.59 E-value=0.73 Score=45.19 Aligned_cols=63 Identities=24% Similarity=0.401 Sum_probs=46.5
Q ss_pred hhhhHHHHHHhcC--CCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhh
Q 016321 189 IQNRLKGYVKGVV--SEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (391)
Q Consensus 189 ~~~~l~~YL~~i~--~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~e 261 (391)
+.+.+..||+.-. ..| ---.++.+++. ....++...+||+||++|+|+.+|++.+|+..++..
T Consensus 85 I~Gei~d~LR~~~~v~vp----R~~~~~~~~i~------~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~ 149 (247)
T COG1191 85 IRGEILDYLRKNDSVKVP----RSLRELGRRIE------EAIDELEQELGREPTDEEIAEELGIDKEEYIEALLA 149 (247)
T ss_pred HHHHHHHHHHhCCCccCc----HHHHHHHHHHH------HHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHH
Confidence 4567778888887 333 23344444444 466789999999999999999999999987665554
No 135
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=84.76 E-value=4.7 Score=39.17 Aligned_cols=65 Identities=22% Similarity=0.290 Sum_probs=45.0
Q ss_pred hhhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHh
Q 016321 188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (391)
Q Consensus 188 ~~~~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l 259 (391)
++...+..|+++....-.+.. --.+++.+++. ...++...+|++||.+++|+.+|++.+++..++
T Consensus 100 ~Irg~I~~~lr~~~~~ir~Pr-~~~~~~~~i~~------~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~ 164 (264)
T PRK07122 100 TIMGEVRRHFRDNSWSVKVPR-RLKELHLRLGR------ATAELSQRLGRAPTASELAAELGMDREEVVEGL 164 (264)
T ss_pred HHHHHHHHHHHHcCCccccCH-HHHHHHHHHHH------HHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 566677788877654322322 23445555553 355788889999999999999999998875543
No 136
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=82.00 E-value=4 Score=39.38 Aligned_cols=62 Identities=26% Similarity=0.300 Sum_probs=42.7
Q ss_pred hhhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHh
Q 016321 188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (391)
Q Consensus 188 ~~~~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l 259 (391)
++...+..|++.....| -.-.+.+.+++ ....++...+|++|+.+++|+.+|++.+++..++
T Consensus 86 ~Ir~~i~~~lr~~~~~p----r~~~~~~~~l~------~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~ 147 (257)
T PRK05911 86 LIKAAIIDDLRKQDWVP----RSVHQKANKLA------DAMDSLRQSLGKEPTDGELCEYLNISQQELSGWF 147 (257)
T ss_pred HHHHHHHHHHHhcCCCC----HHHHHHHHHHH------HHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHH
Confidence 45566677777665522 23334444444 3455688899999999999999999998875544
No 137
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=81.39 E-value=18 Score=35.75 Aligned_cols=68 Identities=16% Similarity=0.134 Sum_probs=42.2
Q ss_pred ChhhhhhhHHHHHHhcCCCCCC-CHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHH
Q 016321 185 SPELIQNRLKGYVKGVVSEELL-THAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPEL 255 (391)
Q Consensus 185 ~pe~~~~~l~~YL~~i~~~~lL-T~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL 255 (391)
..-++...+..|++.-.....+ +...+..+..+++. ++.........+|++|+.+++|+.+|++.+++
T Consensus 97 a~~~Ir~~I~~~lr~~~~~iR~p~~~~~~~~~~~~~~---~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v 165 (289)
T PRK07500 97 ATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRR---LRARLAQADEELTKQEIHREIATALGVSLSDV 165 (289)
T ss_pred HHHHHHHHHHHHHHHCCCceecCccHHHHHHHHHHHH---HHHHHHhhhcccCCCCCHHHHHHHhCcCHHHH
Confidence 3345667788888775444332 33334455544442 12222223346899999999999999998775
No 138
>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=80.82 E-value=7.5 Score=37.17 Aligned_cols=64 Identities=16% Similarity=0.239 Sum_probs=41.6
Q ss_pred hhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhh
Q 016321 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (391)
Q Consensus 189 ~~~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~ 260 (391)
+.+.+..|++..... .++ ..-.+++.++.. ...++...+|++|+.+++|+.+|++.+++...+.
T Consensus 95 irn~~~~~lr~~~~i-r~p-~~~~~~~~~~~~------~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~~ 158 (254)
T TIGR02850 95 IIGEIRRYLRDNNPI-RVS-RSLRDIAYKALQ------VRDKLISENSKEPTVSEIAKELKVPQEEVVFALD 158 (254)
T ss_pred HHHHHHHHHHhCCCc-cCc-hHHHHHHHHHHH------HHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 445566677664422 222 223344444443 3456778899999999999999999888755443
No 139
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=78.80 E-value=9.5 Score=38.54 Aligned_cols=64 Identities=20% Similarity=0.235 Sum_probs=41.6
Q ss_pred hhhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 016321 188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (391)
Q Consensus 188 ~~~~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~ 258 (391)
++...+..|+.+-.+.-.+... -.+++.+++ ....++...+|++||.+|+|+.+|++.+++...
T Consensus 146 wIr~aI~~~i~~~~r~vrlP~~-~~~~~~~l~------~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~ 209 (324)
T PRK07921 146 WIRQAITRGMADQSRTIRLPVH-LVEQVNKLA------RIKRELHQQLGREATDEELAEESGIPEEKIADL 209 (324)
T ss_pred HHHHHHHHHHHHcCCCccCCHH-HHHHHHHHH------HHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 4555666666655543333221 223333333 356678889999999999999999998886543
No 140
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=78.16 E-value=3.2 Score=39.97 Aligned_cols=64 Identities=23% Similarity=0.405 Sum_probs=43.2
Q ss_pred hhhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 016321 188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (391)
Q Consensus 188 ~~~~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~ 258 (391)
.+.+.+..|++.....-.+.. --.++..+++ ....++...+|++|+.+++|+.+|++.+++..+
T Consensus 86 ~Ir~~i~~~lr~~~~~vr~pr-~~~~~~~~~~------~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~ 149 (256)
T PRK07408 86 YIRGEIQHYLRDKSPTVRIPR-RWQELQRQAK------KVRQELRQELGRQPTDQEIAQALDISLEEWQEI 149 (256)
T ss_pred HHHHHHHHHHHHcCCeeeeCH-HHHHHHHHHH------HHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHH
Confidence 455666777776554333322 2233444443 345678889999999999999999999887554
No 141
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=78.01 E-value=23 Score=34.15 Aligned_cols=34 Identities=38% Similarity=0.470 Sum_probs=28.0
Q ss_pred hhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 016321 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (391)
Q Consensus 225 ~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~ 258 (391)
......|...+|++|+.+++|+.+|++.+++...
T Consensus 121 ~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~ 154 (268)
T PRK06288 121 ERAIAMLEARLGRTPSDEEIADELGISLEEYNSL 154 (268)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHH
Confidence 3455678889999999999999999998776543
No 142
>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=77.96 E-value=3.5 Score=38.98 Aligned_cols=33 Identities=27% Similarity=0.489 Sum_probs=27.8
Q ss_pred hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 016321 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (391)
Q Consensus 226 ~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~ 258 (391)
....++...+|++||.+++|+.+|++.+++..+
T Consensus 91 ~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~ 123 (238)
T TIGR02393 91 KAERQLTQELGREPTDEELAERMGMPAEKVREI 123 (238)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 345678889999999999999999999887543
No 143
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=77.91 E-value=11 Score=36.02 Aligned_cols=34 Identities=18% Similarity=0.256 Sum_probs=28.0
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhh
Q 016321 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (391)
Q Consensus 227 ~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~ 260 (391)
...++...+|++|+.+++|..+|++.++++.++.
T Consensus 114 ~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~ 147 (251)
T PRK07670 114 AIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMN 147 (251)
T ss_pred HHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 4456777899999999999999999988766544
No 144
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=77.20 E-value=3.7 Score=38.99 Aligned_cols=62 Identities=23% Similarity=0.352 Sum_probs=42.3
Q ss_pred hhhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHh
Q 016321 188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (391)
Q Consensus 188 ~~~~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l 259 (391)
.+.+.+-.|++.....| -.......+++ ....++...+|++|+.+++|+.+|++.+++...+
T Consensus 77 ~Ir~~il~~lr~~~~~~----r~vr~~~~~i~------~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~ 138 (231)
T PRK12427 77 RIRGAILDELRELDWRP----RRLRQKTHKTN------DAIREIAKRLGHEPNFEEISAELNLTAEEYQEYL 138 (231)
T ss_pred HHHHHHHHHHHhcCCCC----HHHHHHHHHHH------HHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 34556667777665432 12234444443 3456788899999999999999999998875543
No 145
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=73.59 E-value=15 Score=38.11 Aligned_cols=31 Identities=23% Similarity=0.404 Sum_probs=26.6
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHH
Q 016321 227 HKLRLKERLGCEPSMEQLAASLRISRPELQS 257 (391)
Q Consensus 227 ~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~ 257 (391)
....+...+|++||.+++|+.+|++.++++.
T Consensus 228 a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~ 258 (373)
T PRK07406 228 TTKVLSQEFGRKPTEEEIAESMEMTIEKLRF 258 (373)
T ss_pred HHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 4567888899999999999999999887644
No 146
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=73.09 E-value=12 Score=40.42 Aligned_cols=33 Identities=27% Similarity=0.432 Sum_probs=28.1
Q ss_pred hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 016321 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (391)
Q Consensus 226 ~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~ 258 (391)
..+.++...+|++|+.+|+|+.+|++.++++.+
T Consensus 362 ~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~ 394 (509)
T PRK05901 362 RIERELLQELGREPTPEELAKEMGFTPEKVREI 394 (509)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 356778889999999999999999998886554
No 147
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=73.04 E-value=5 Score=40.96 Aligned_cols=36 Identities=25% Similarity=0.403 Sum_probs=30.0
Q ss_pred hhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhh
Q 016321 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (391)
Q Consensus 225 ~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~ 260 (391)
....+++...+|++||.+++|..+|++.++++.++.
T Consensus 219 ~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~ 254 (367)
T PRK09210 219 IRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILK 254 (367)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 345677888999999999999999999988766543
No 148
>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=65.00 E-value=10 Score=35.36 Aligned_cols=61 Identities=25% Similarity=0.380 Sum_probs=39.3
Q ss_pred hhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 016321 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (391)
Q Consensus 190 ~~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~ 258 (391)
.+.+..|++.-..+ .+. ....++..+++. ....+...+|++|+.+++|+.+|++.+++...
T Consensus 73 ~~~i~~~lr~~~~i-~~p-~~~~~~~~~~~~------~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~ 133 (231)
T TIGR02885 73 MGEIKRFLRDDGII-KVS-RSLKELARKIRY------MKEELSKELGREPTINELAEALGVSPEEIVMA 133 (231)
T ss_pred HHHHHHHHHhCCCe-ECC-HHHHHHHHHHHH------HHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHH
Confidence 34555566654421 122 223445555543 34567788999999999999999998876544
No 149
>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=64.67 E-value=10 Score=35.29 Aligned_cols=34 Identities=32% Similarity=0.456 Sum_probs=27.8
Q ss_pred hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHh
Q 016321 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (391)
Q Consensus 226 ~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l 259 (391)
....++...+|++|+.+++|+.+|++.++++.++
T Consensus 87 ~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~ 120 (224)
T TIGR02479 87 RAIRELEARLGREPTEEEIAEELGMDLKEYRQAL 120 (224)
T ss_pred HHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHH
Confidence 4456678889999999999999999988765543
No 150
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=63.57 E-value=10 Score=39.98 Aligned_cols=38 Identities=16% Similarity=0.495 Sum_probs=31.6
Q ss_pred cchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhh
Q 016321 223 SLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (391)
Q Consensus 223 ~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~ 260 (391)
.+...+..+...+|+.|+.+++|+.+|++.++++.++.
T Consensus 263 ~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l~ 300 (415)
T PRK07598 263 KIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLL 300 (415)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 45556677888999999999999999999998876543
No 151
>PRK05949 RNA polymerase sigma factor; Validated
Probab=62.22 E-value=12 Score=37.90 Aligned_cols=36 Identities=14% Similarity=0.362 Sum_probs=28.8
Q ss_pred cchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 016321 223 SLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (391)
Q Consensus 223 ~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~ 258 (391)
.+.....++...+|++|+.+++|+.+|++.+++..+
T Consensus 179 ~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~ 214 (327)
T PRK05949 179 KIKKTQRELSQKLGRSATPAEIAKELELEPSQIREY 214 (327)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 344455677788999999999999999998776554
No 152
>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=59.41 E-value=41 Score=25.77 Aligned_cols=47 Identities=23% Similarity=0.251 Sum_probs=35.3
Q ss_pred CCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhh
Q 016321 206 LTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMEC 262 (391)
Q Consensus 206 LT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg 262 (391)
||+.|..-|...+..|=+ ..-|..+.+++|+.+|+|...+-..|+.+
T Consensus 1 LT~~Q~e~L~~A~~~GYf----------d~PR~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYF----------DVPRRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CCHHHHHHHHHHHHcCCC----------CCCCcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 677777777777777744 13456789999999999988877777654
No 153
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=55.17 E-value=18 Score=36.20 Aligned_cols=36 Identities=17% Similarity=0.400 Sum_probs=28.6
Q ss_pred cchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 016321 223 SLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (391)
Q Consensus 223 ~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~ 258 (391)
.+.....++...+|++|+.+++|+.+|++.+++...
T Consensus 169 ~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~ 204 (317)
T PRK07405 169 KIKKAQRQLSQQLGRAATIGELAEELELTPKQVREY 204 (317)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 344556677788999999999999999998776443
No 154
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=55.14 E-value=46 Score=31.19 Aligned_cols=59 Identities=27% Similarity=0.260 Sum_probs=45.3
Q ss_pred CCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHcHH
Q 016321 204 ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVR 275 (391)
Q Consensus 204 ~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe~nlp 275 (391)
..||+.|..-|-.++..|=. ..-|..+..++|+.+|+|...+...|+. |..+|+..+..
T Consensus 154 ~~LTdrQ~~vL~~A~~~GYF----------d~PR~~~l~dLA~~lGISkst~~ehLRr---Ae~Kl~~~~~~ 212 (215)
T COG3413 154 NDLTDRQLEVLRLAYKMGYF----------DYPRRVSLKDLAKELGISKSTLSEHLRR---AERKLIEAYFD 212 (215)
T ss_pred ccCCHHHHHHHHHHHHcCCC----------CCCccCCHHHHHHHhCCCHHHHHHHHHH---HHHHHHHHhhh
Confidence 36999998888888888854 2345677899999999998877777764 66777776653
No 155
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=54.70 E-value=20 Score=34.30 Aligned_cols=62 Identities=18% Similarity=0.280 Sum_probs=38.8
Q ss_pred hhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 016321 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (391)
Q Consensus 189 ~~~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~ 258 (391)
+.+.+..|++.-... .+. .....+..++. ....++...+|++|+.+++|..+|++.+++...
T Consensus 98 ir~~i~~~lr~~~~v-rip-~~~~~~~~~~~------~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~ 159 (258)
T PRK08215 98 IIGEIRRYLRDNNPI-RVS-RSLRDIAYKAL------QVREKLINENSKEPTVEEIAKELEVPREEVVFA 159 (258)
T ss_pred HHHHHHHHHHhCCce-Eec-HHHHHHHHHHH------HHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHH
Confidence 345555666655421 121 22233333333 245567788999999999999999998886543
No 156
>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=53.31 E-value=22 Score=32.97 Aligned_cols=31 Identities=29% Similarity=0.506 Sum_probs=26.0
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHH
Q 016321 227 HKLRLKERLGCEPSMEQLAASLRISRPELQS 257 (391)
Q Consensus 227 ~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~ 257 (391)
....+...+|++|+.+++|..+|++.+++..
T Consensus 95 ~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~ 125 (227)
T TIGR02980 95 ATEELTQRLGRSPTIAEIAEELGVSEEEVVE 125 (227)
T ss_pred HHHHHHHHHCCCCCHHHHHHHhCCCHHHHHH
Confidence 3456778889999999999999999887643
No 157
>KOG0037 consensus Ca2+-binding protein, EF-Hand protein superfamily [Signal transduction mechanisms]
Probab=50.14 E-value=2.1e+02 Score=28.15 Aligned_cols=109 Identities=18% Similarity=0.116 Sum_probs=67.8
Q ss_pred ccCChhhhhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhh
Q 016321 182 SMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (391)
Q Consensus 182 ~~~~pe~~~~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~e 261 (391)
++++++-+.-.+ +|-+......+..+|=.+|.+.|++... +. ..+.+. ..-.|+.-||+.++..
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---VF----RTYDRD-------RSGTIDSSELRQALTQ 152 (221)
T ss_pred CCCCHHHHHHHH--HHhcCCCCCccCHHHHHHHHHHHHHHHH---HH----HhcccC-------CCCcccHHHHHHHHHH
Confidence 447777444333 4556677788999999999999886421 11 111111 1234566777766655
Q ss_pred -hHHHHHHHHHHcHHHHHHHHHhcc---cCCCChhHHHH--HHHHHHHHHHHhcCCCC
Q 016321 262 -CSLAREKLVMSNVRLVMSIAQRYD---NMGADMADLVQ--GGLIGLLRGIEKFDSSK 313 (391)
Q Consensus 262 -g~~Are~LIe~nlpLV~~IAkkY~---~~Gvd~eDLIQ--EG~IGLikAIekFDp~k 313 (391)
|-.. .--++-.|++||. +..+.+||.|| ....+|.+|.+++|...
T Consensus 153 ~Gy~L-------spq~~~~lv~kyd~~~~g~i~FD~FI~ccv~L~~lt~~Fr~~D~~q 203 (221)
T KOG0037|consen 153 LGYRL-------SPQFYNLLVRKYDRFGGGRIDFDDFIQCCVVLQRLTEAFRRRDTAQ 203 (221)
T ss_pred cCcCC-------CHHHHHHHHHHhccccCCceeHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 2111 1123345666776 33588999999 45678999999999976
No 158
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=49.19 E-value=75 Score=31.23 Aligned_cols=64 Identities=19% Similarity=0.223 Sum_probs=36.9
Q ss_pred hhhhhhHHHHHHhcCC-CCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 016321 187 ELIQNRLKGYVKGVVS-EELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (391)
Q Consensus 187 e~~~~~l~~YL~~i~~-~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~ 258 (391)
-++...+..|+..-.+ .+.-+......+..+++. ...++. .+++|+.+++|+.+|++.+++..+
T Consensus 107 ~~Ir~~i~~~l~~~~~~vr~p~~~~~~~~~~~~~~------~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~ 171 (284)
T PRK06596 107 HWIKAEIHEYILRNWRIVKVATTKAQRKLFFNLRK------AKKRLG--WLNPEEVEMVAEELGVSEEEVREM 171 (284)
T ss_pred HHHHHHHHHHHHHcCCeeeccchHHHHHHHHHHHH------HHHHhc--cCCCCCHHHHHHHhCcCHHHHHHH
Confidence 3566667777765432 222233333334333331 122222 359999999999999999887553
No 159
>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=48.36 E-value=27 Score=34.32 Aligned_cols=34 Identities=21% Similarity=0.445 Sum_probs=27.7
Q ss_pred hhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 016321 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (391)
Q Consensus 225 ~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~ 258 (391)
.....++...+|++|+.+++|..+|++.+++...
T Consensus 164 rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~ 197 (298)
T TIGR02997 164 KKVQRELSQKLGRTPSEAEIAEALELEPEQVREL 197 (298)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 3445567778999999999999999998887554
No 160
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=46.16 E-value=56 Score=24.25 Aligned_cols=24 Identities=29% Similarity=0.430 Sum_probs=20.5
Q ss_pred CCchHHHHHHhcCChHHHHHHhhh
Q 016321 238 EPSMEQLAASLRISRPELQSILME 261 (391)
Q Consensus 238 ePs~~e~A~a~~~s~~eL~~~l~e 261 (391)
+++.+++|+.+|++...+.+.+..
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~ 24 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKK 24 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHH
Confidence 467889999999999888888775
No 161
>PRK14082 hypothetical protein; Provisional
Probab=45.06 E-value=82 Score=25.48 Aligned_cols=55 Identities=11% Similarity=0.001 Sum_probs=43.1
Q ss_pred HHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhhh
Q 016321 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320 (391)
Q Consensus 264 ~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsTY 320 (391)
...+.+|..+.|.|++--..- .--+.+||.||=.|-+++=++.++-..+-.|--|
T Consensus 9 ~e~e~ii~~FepkIkKsL~~T--~yqeREDLeQElk~Ki~eK~~~~~~~e~PGF~ef 63 (65)
T PRK14082 9 EEIEHLIENFSPMIKKKLSNT--SYQEREDLEQELKIKIIEKADMLLCQEVPGFWEF 63 (65)
T ss_pred HHHHHHHHHccHHHHHHHhcC--ChhhHHHHHHHHHHHHHHHHHHhhcccCCcHHHh
Confidence 556789999999887754332 2246899999999999999999998887667554
No 162
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=42.85 E-value=39 Score=31.71 Aligned_cols=32 Identities=28% Similarity=0.426 Sum_probs=26.1
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 016321 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (391)
Q Consensus 227 ~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~ 258 (391)
....+...+|++|+.+++|+.+|++.+++..+
T Consensus 100 ~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~ 131 (236)
T PRK06986 100 AIRQLEQELGREPTDTEVAEKLGLSLEEYREM 131 (236)
T ss_pred HHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHH
Confidence 34566678999999999999999998776543
No 163
>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=40.28 E-value=47 Score=31.56 Aligned_cols=32 Identities=25% Similarity=0.332 Sum_probs=26.5
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 016321 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (391)
Q Consensus 227 ~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~ 258 (391)
....+...+|++|+.+++|+.+|++.+++..+
T Consensus 121 ~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~ 152 (255)
T TIGR02941 121 AIDELTDHLQRSPKIIEIADHLGLSEEEVLEI 152 (255)
T ss_pred HHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 35567788899999999999999998876543
No 164
>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=39.24 E-value=38 Score=25.44 Aligned_cols=41 Identities=27% Similarity=0.421 Sum_probs=27.9
Q ss_pred CCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhh
Q 016321 204 ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (391)
Q Consensus 204 ~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~e 261 (391)
..||.+|-.++++.+..|. +..++|..+|++.-.+..++..
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 5689999999999998885 4567788888877777666654
No 165
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=38.08 E-value=57 Score=26.43 Aligned_cols=50 Identities=24% Similarity=0.322 Sum_probs=36.1
Q ss_pred CchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHH
Q 016321 239 PSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGG 298 (391)
Q Consensus 239 Ps~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG 298 (391)
-|-+++|+.+|+|+..+..+-++. ..-.+.|..+||+-| +..++|+++..
T Consensus 15 ltQ~elA~~vgVsRQTi~~iEkgk-------y~Psl~La~kia~~f---~~~iedIF~~~ 64 (68)
T COG1476 15 LTQEELAKLVGVSRQTIIAIEKGK-------YNPSLELALKIARVF---GKTIEDIFQLE 64 (68)
T ss_pred cCHHHHHHHcCcCHHHHHHHHcCC-------CCchHHHHHHHHHHh---CCCHHHHHhhh
Confidence 456789999999987775554441 122466778888888 48899999864
No 166
>PF11176 DUF2962: Protein of unknown function (DUF2962); InterPro: IPR021346 This eukaryotic family of proteins has no known function. ; PDB: 2KKM_A.
Probab=35.84 E-value=79 Score=28.96 Aligned_cols=91 Identities=23% Similarity=0.350 Sum_probs=47.1
Q ss_pred hhHHHHHHhcCC--CCCCCHHHHHHHHHHHHc--CCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHH
Q 016321 191 NRLKGYVKGVVS--EELLTHAEVVRLSKKIKT--GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAR 266 (391)
Q Consensus 191 ~~l~~YL~~i~~--~~lLT~eEE~eL~~kiq~--G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Ar 266 (391)
+.+..|-..|.. ...+|.+|-.+|+..+-. ...|++++. +..-||+|+..|
T Consensus 49 ~r~~wFq~~i~~~~~~~~t~~e~~~lI~~yl~R~DeEleql~~--~rR~gRp~s~re----------------------- 103 (155)
T PF11176_consen 49 ERLKWFQEAIDEKDKKPFTLEEIHELIERYLHRFDEELEQLKK--ERRKGRPPSNRE----------------------- 103 (155)
T ss_dssp HHHHHHHHHHHSTT-----HHHHHHHHHHHHHHHHHHHHHHHH--HGGGT---TTHH-----------------------
T ss_pred HHHHHHHHHccccCCCCCCHHHHHHHHHHHHhcCHHHHHHHHH--hhcCCCCCchHH-----------------------
Confidence 455555555544 789999999999988543 333443333 256788888544
Q ss_pred HHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCC
Q 016321 267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKG 314 (391)
Q Consensus 267 e~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG 314 (391)
.+++. .+..-...|. .|+++-||..+.++-+++. +|.+-+
T Consensus 104 -~~L~~---~~~~E~~ey~-~G~~vPDLtd~~nv~~Lr~---W~G~~~ 143 (155)
T PF11176_consen 104 -DLLEQ---KIEREEEEYK-TGFEVPDLTDEKNVKLLRE---WNGDWG 143 (155)
T ss_dssp -HHHHH---HHHHHHHHHH-TTEEEE-S--HHHHHHHHT----SS-ST
T ss_pred -HHHHH---HHHHHHHHHh-hCeeCCCCCCHHHHHHHHh---cCCChh
Confidence 22221 2233445676 8999999999999988665 555443
No 167
>PRK05572 sporulation sigma factor SigF; Validated
Probab=35.52 E-value=59 Score=30.97 Aligned_cols=60 Identities=23% Similarity=0.404 Sum_probs=37.3
Q ss_pred hhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHH
Q 016321 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQ 256 (391)
Q Consensus 189 ~~~~l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~ 256 (391)
+.+.+..|++.-... .+... ..++..+++. ....+...+|++|+.+++|+.+|++.+++.
T Consensus 93 i~~~i~~~lr~~~~~-r~~~~-~~~~~~~~~~------~~~~l~~~~~r~p~~~eia~~l~~~~~~v~ 152 (252)
T PRK05572 93 IIGEIQRFLRDDGTV-KVSRS-LKETANKIRK------DKDELSKELGREPTIEELAEYLGVTPEEVV 152 (252)
T ss_pred HHHHHHHHHHhCCCC-CCCHH-HHHHHHHHHH------HHHHHHHHHCcCCCHHHHHHHhCcCHHHHH
Confidence 445566666655422 22222 2234433332 345667778999999999999999987753
No 168
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=34.47 E-value=80 Score=25.89 Aligned_cols=35 Identities=14% Similarity=0.093 Sum_probs=27.8
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhh
Q 016321 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (391)
Q Consensus 227 ~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~e 261 (391)
+..-+...+..+++.+++|+.+|+|..-|.+..++
T Consensus 10 ~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~ 44 (107)
T PRK10219 10 LIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRT 44 (107)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 44455666778899999999999999888777666
No 169
>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=34.41 E-value=99 Score=30.07 Aligned_cols=51 Identities=27% Similarity=0.433 Sum_probs=38.2
Q ss_pred ChHHHHHHhhhhHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcC
Q 016321 251 SRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFD 310 (391)
Q Consensus 251 s~~eL~~~l~eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFD 310 (391)
|+.+...+++.+..+ ++-|..++.+|...|+..+|+. +++-.--+|+++|-
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 4456678899999999999997 66777778999985
No 170
>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=34.28 E-value=72 Score=22.87 Aligned_cols=41 Identities=17% Similarity=0.342 Sum_probs=27.4
Q ss_pred CCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhh
Q 016321 204 ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (391)
Q Consensus 204 ~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~e 261 (391)
+-+++++..++.+..++|. +..++|+.+|+|+..+-+.+.+
T Consensus 4 ~~~~~~~~~~i~~l~~~G~-----------------si~~IA~~~gvsr~TvyR~l~~ 44 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAEGM-----------------SIAEIAKQFGVSRSTVYRYLNK 44 (45)
T ss_dssp SSSSHCCHHHHHHHHHTT-------------------HHHHHHHTTS-HHHHHHHHCC
T ss_pred CCCCHHHHHHHHHHHHCCC-----------------CHHHHHHHHCcCHHHHHHHHhc
Confidence 4556655556666677774 4678999999999888776653
No 171
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=33.27 E-value=1.7e+02 Score=29.28 Aligned_cols=119 Identities=23% Similarity=0.153 Sum_probs=70.2
Q ss_pred hhHHHHHHhcCCCCCCC---------HHHHHHHHHHHH----cCCcchhHHHHHHHhhCC-------CCchHHHHHH---
Q 016321 191 NRLKGYVKGVVSEELLT---------HAEVVRLSKKIK----TGLSLDDHKLRLKERLGC-------EPSMEQLAAS--- 247 (391)
Q Consensus 191 ~~l~~YL~~i~~~~lLT---------~eEE~eL~~kiq----~G~~L~~~~~~l~~~~g~-------ePs~~e~A~a--- 247 (391)
+.+...++.++..+++. .+-=..|++.|- .......+..++.+.+|. .||.++++..
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 45555666666666665 232233444443 234456677888999997 5999998743
Q ss_pred ----hcCChHHHHH------Hhhh------------hHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHH
Q 016321 248 ----LRISRPELQS------ILME------------CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRG 305 (391)
Q Consensus 248 ----~~~s~~eL~~------~l~e------------g~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikA 305 (391)
+|++....+- .+.+ ++++++.|+. ..+.=...|.-|.-.|+-..|.+-.|=+||-+|
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 5565322111 1111 2233344333 222224455555556777888888899999999
Q ss_pred HHhcC
Q 016321 306 IEKFD 310 (391)
Q Consensus 306 IekFD 310 (391)
+.+|.
T Consensus 236 ~~~~~ 240 (285)
T COG0122 236 IKKLY 240 (285)
T ss_pred HHHHh
Confidence 99984
No 172
>PRK04217 hypothetical protein; Provisional
Probab=33.20 E-value=1.9e+02 Score=25.27 Aligned_cols=47 Identities=17% Similarity=0.211 Sum_probs=33.0
Q ss_pred CCCCCHHHHHHHHHHHH-cCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHH
Q 016321 203 EELLTHAEVVRLSKKIK-TGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLARE 267 (391)
Q Consensus 203 ~~lLT~eEE~eL~~kiq-~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are 267 (391)
...||.+| .+++.... +|. +.+++|+.+|+|...+...+........
T Consensus 40 ~~~Lt~ee-reai~l~~~eGl-----------------S~~EIAk~LGIS~sTV~r~L~RArkkLr 87 (110)
T PRK04217 40 PIFMTYEE-FEALRLVDYEGL-----------------TQEEAGKRMGVSRGTVWRALTSARKKVA 87 (110)
T ss_pred cccCCHHH-HHHHHHHHHcCC-----------------CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 35677665 67766655 443 5789999999999988888876444433
No 173
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=30.82 E-value=73 Score=22.88 Aligned_cols=40 Identities=25% Similarity=0.327 Sum_probs=15.8
Q ss_pred CCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHh
Q 016321 203 EELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (391)
Q Consensus 203 ~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l 259 (391)
.+-||.+|-.++....++|. +..++|+.+|.+...+.+.|
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G~-----------------s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQGM-----------------SIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp ----------HHHHHHCS--------------------HHHHHHHTT--HHHHHHHH
T ss_pred ccchhhhHHHHHHHHHHcCC-----------------CHHHHHHHHCcCcHHHHHHH
Confidence 35688887766666666664 45677777777765554443
No 174
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=30.52 E-value=95 Score=26.74 Aligned_cols=35 Identities=17% Similarity=0.171 Sum_probs=27.7
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhh
Q 016321 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (391)
Q Consensus 227 ~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~e 261 (391)
+..-+...+..+++.+++|+.+|+|..-|.++..+
T Consensus 14 ~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 14 ILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34455666777899999999999999888777665
No 175
>PF13730 HTH_36: Helix-turn-helix domain
Probab=30.38 E-value=1.8e+02 Score=20.90 Aligned_cols=27 Identities=44% Similarity=0.608 Sum_probs=21.8
Q ss_pred hCCCCchHHHHHHhcCChHHHHHHhhh
Q 016321 235 LGCEPSMEQLAASLRISRPELQSILME 261 (391)
Q Consensus 235 ~g~ePs~~e~A~a~~~s~~eL~~~l~e 261 (391)
.++-|+.+.+|..+|+++..+.+.+.+
T Consensus 22 ~~~~pS~~~la~~~g~s~~Tv~~~i~~ 48 (55)
T PF13730_consen 22 GGCFPSQETLAKDLGVSRRTVQRAIKE 48 (55)
T ss_pred CCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 457799999999999998877665544
No 176
>PRK13239 alkylmercury lyase; Provisional
Probab=29.85 E-value=79 Score=30.57 Aligned_cols=27 Identities=30% Similarity=0.323 Sum_probs=24.1
Q ss_pred hCCCCchHHHHHHhcCChHHHHHHhhh
Q 016321 235 LGCEPSMEQLAASLRISRPELQSILME 261 (391)
Q Consensus 235 ~g~ePs~~e~A~a~~~s~~eL~~~l~e 261 (391)
.|++|+-+++|++.|.+.++++++|++
T Consensus 33 ~G~pvt~~~lA~~~~~~~~~v~~~L~~ 59 (206)
T PRK13239 33 KGRPVSVTTLAAALGWPVEEVEAVLEA 59 (206)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 689999999999999999998877665
No 177
>PF04282 DUF438: Family of unknown function (DUF438); InterPro: IPR007380 This is a a group of uncharacterised proteins.
Probab=29.81 E-value=2.1e+02 Score=23.36 Aligned_cols=50 Identities=14% Similarity=0.191 Sum_probs=36.0
Q ss_pred HHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHH------hcCChHHHHHHhhhh
Q 016321 212 VRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAAS------LRISRPELQSILMEC 262 (391)
Q Consensus 212 ~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a------~~~s~~eL~~~l~eg 262 (391)
.++++++.+|...+..+.+....++.... .|++.+ -||+.+|++++|.--
T Consensus 3 K~ii~~Lh~G~~~e~vk~~F~~~~~~Vs~-~EI~~~Eq~Li~eG~~~eeiq~LCdvH 58 (71)
T PF04282_consen 3 KEIIKRLHEGEDPEEVKEEFKKLFSDVSA-SEISAAEQELIQEGMPVEEIQKLCDVH 58 (71)
T ss_pred HHHHHHHhCCCCHHHHHHHHHHHHCCCCH-HHHHHHHHHHHHcCCCHHHHHHHhHHH
Confidence 35788888898889899888888876533 333322 488888888887653
No 178
>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=28.09 E-value=4.5e+02 Score=23.74 Aligned_cols=86 Identities=16% Similarity=0.246 Sum_probs=56.2
Q ss_pred HHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHH--
Q 016321 194 KGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM-- 271 (391)
Q Consensus 194 ~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe-- 271 (391)
..|.+=+++..++..+....|=.++++|. ++..++.+.|-....-++.+..
T Consensus 16 AaYrQVf~~~~~~~~er~~~lESqlrng~---------------------------IsVreFVr~La~S~~yr~~f~~~~ 68 (131)
T PF00427_consen 16 AAYRQVFGNDHPMESERLISLESQLRNGQ---------------------------ISVREFVRALAKSELYRKRFFEPN 68 (131)
T ss_dssp HHHHHHHSSSSSHCSHHTHHHHHHHHTTS---------------------------S-HHHHHHHHHTSHHHHHHHTTTS
T ss_pred HHHHHHhcCccchhhhccchHHHHHHcCC---------------------------CcHHHHHHHHHcCHHHHHHHcccc
Confidence 34555555554555555555555666664 4677777888788888899888
Q ss_pred HcHHHHHHHHHhcccCCCC--------hhHHHHHHHHHHHHHH
Q 016321 272 SNVRLVMSIAQRYDNMGAD--------MADLVQGGLIGLLRGI 306 (391)
Q Consensus 272 ~nlpLV~~IAkkY~~~Gvd--------~eDLIQEG~IGLikAI 306 (391)
.+.+.|-..-+.+.||... ..-+-..|.-|++.++
T Consensus 69 ~~~R~iEl~~khlLGR~p~~~~Ei~~~~~i~a~~G~~a~Id~l 111 (131)
T PF00427_consen 69 SNYRFIELAFKHLLGRAPYNQAEISAYSQILASQGFEAFIDAL 111 (131)
T ss_dssp -HHHHHHHHHHHHCSS--SSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cchHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcChHHHHHHH
Confidence 7888899999999998544 2234456777777765
No 179
>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=27.65 E-value=1.7e+02 Score=22.46 Aligned_cols=57 Identities=19% Similarity=0.200 Sum_probs=35.2
Q ss_pred HhhCCCCch------HHHHHHhcCChHHHHHHhhhhHHHHHHHHHHcHHHHHHHHHhcccCCCC-hhH
Q 016321 233 ERLGCEPSM------EQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGAD-MAD 293 (391)
Q Consensus 233 ~~~g~ePs~------~e~A~a~~~s~~eL~~~l~eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd-~eD 293 (391)
...||+||. .+|....|++.+-+..+++.+.. . =..+.+.|..|++.+...|+. .+|
T Consensus 7 ~~~gr~ls~~e~~~i~~~~~~~~~~~evI~~ai~~a~~-~---~~~~~~Yi~~Il~~W~~~gi~T~e~ 70 (73)
T TIGR01446 7 ENFGRMLSPFEMEDLKYWLDEFGNSPELIKEALKEAVS-N---NKANYKYIDAILNNWKNNGIKTVED 70 (73)
T ss_pred HHhCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHH-c---CCCCHHHHHHHHHHHHHcCCCCHHH
Confidence 344555552 34556667776655555555432 1 124678999999999988865 444
No 180
>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=27.17 E-value=1.3e+02 Score=23.54 Aligned_cols=19 Identities=26% Similarity=0.555 Sum_probs=14.3
Q ss_pred HhhCCCCchHHHHHHhcCC
Q 016321 233 ERLGCEPSMEQLAASLRIS 251 (391)
Q Consensus 233 ~~~g~ePs~~e~A~a~~~s 251 (391)
...|.+||..|+|+++|++
T Consensus 20 ~~~G~~Pt~rEIa~~~g~~ 38 (65)
T PF01726_consen 20 EENGYPPTVREIAEALGLK 38 (65)
T ss_dssp HHHSS---HHHHHHHHTSS
T ss_pred HHcCCCCCHHHHHHHhCCC
Confidence 4689999999999999996
No 181
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=26.95 E-value=97 Score=31.25 Aligned_cols=33 Identities=27% Similarity=0.400 Sum_probs=27.5
Q ss_pred HHHHHHHhhCCCCchHHHHHHhcCChHHHHHHh
Q 016321 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (391)
Q Consensus 227 ~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l 259 (391)
...+++..+|++|+.+++|..+|++.+++.+++
T Consensus 178 ~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l 210 (325)
T PRK05657 178 AARELEHKLDHEPSAEEIAELLDKPVDDVSRML 210 (325)
T ss_pred HHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 445677789999999999999999988876654
No 182
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=26.95 E-value=26 Score=32.77 Aligned_cols=20 Identities=40% Similarity=0.855 Sum_probs=17.8
Q ss_pred hHHHHHHhhHh-HHHhhhccc
Q 016321 107 SVEALLLLQKS-MLEKQWNLS 126 (391)
Q Consensus 107 ~~~~~~~~~~~-~~~~~~~~~ 126 (391)
..+||.+|.|. |+|-||..|
T Consensus 44 ~~~~L~~LkK~gLiE~qWrmP 64 (160)
T PF09824_consen 44 VRESLLILKKGGLIESQWRMP 64 (160)
T ss_pred HHHHHHHHHHcCchhhccccC
Confidence 38999999885 999999998
No 183
>KOG0030 consensus Myosin essential light chain, EF-Hand protein superfamily [Cytoskeleton]
Probab=26.53 E-value=3e+02 Score=25.64 Aligned_cols=70 Identities=14% Similarity=0.172 Sum_probs=49.0
Q ss_pred hhCCCCchHHHHHHhcCCh-HHHHHHhhhhHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCC
Q 016321 234 RLGCEPSMEQLAASLRISR-PELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSS 312 (391)
Q Consensus 234 ~~g~ePs~~e~A~a~~~s~-~eL~~~l~eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~ 312 (391)
.+|--||.+++-+.+|--. +++ ..+..=++.++|+.-.+|+. ..+..++|. ++.++-||.+
T Consensus 39 alG~nPT~aeV~k~l~~~~~~~~--------~~~rl~FE~fLpm~q~vakn--k~q~t~edf--------vegLrvFDke 100 (152)
T KOG0030|consen 39 ALGQNPTNAEVLKVLGQPKRREM--------NVKRLDFEEFLPMYQQVAKN--KDQGTYEDF--------VEGLRVFDKE 100 (152)
T ss_pred HhcCCCcHHHHHHHHcCcccchh--------hhhhhhHHHHHHHHHHHHhc--cccCcHHHH--------HHHHHhhccc
Confidence 5778888888777776532 221 22444578899999999998 456788886 4678999986
Q ss_pred CCCchhhhHH
Q 016321 313 KGFKISTYVY 322 (391)
Q Consensus 313 kG~rFsTYA~ 322 (391)
. .-+..+|.
T Consensus 101 g-~G~i~~ae 109 (152)
T KOG0030|consen 101 G-NGTIMGAE 109 (152)
T ss_pred C-CcceeHHH
Confidence 4 35676764
No 184
>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=25.97 E-value=2.3e+02 Score=21.85 Aligned_cols=31 Identities=23% Similarity=0.172 Sum_probs=22.9
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHHHHHcCCc
Q 016321 193 LKGYVKGVVSEELLTHAEVVRLSKKIKTGLS 223 (391)
Q Consensus 193 l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~ 223 (391)
++.||+.+.....||.+|-.+++..|-+|..
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 4668888888899999999999999998864
No 185
>COG1916 Uncharacterized homolog of PrgY (pheromone shutdown protein) [Function unknown]
Probab=25.96 E-value=3.1e+02 Score=29.09 Aligned_cols=121 Identities=23% Similarity=0.328 Sum_probs=68.8
Q ss_pred hhhhhhHHHHHHhcCCCCCCCHHHHHHHHHHH--HcCCcchhHHHHHHHhhCCCCchH-----HHHHHhcCCh----HHH
Q 016321 187 ELIQNRLKGYVKGVVSEELLTHAEVVRLSKKI--KTGLSLDDHKLRLKERLGCEPSME-----QLAASLRISR----PEL 255 (391)
Q Consensus 187 e~~~~~l~~YL~~i~~~~lLT~eEE~eL~~ki--q~G~~L~~~~~~l~~~~g~ePs~~-----e~A~a~~~s~----~eL 255 (391)
|+...++...+.+... -|+-.++....+.. -.+.-|...++++.+.+|-+|..+ +.|.++|... .++
T Consensus 45 ELd~~R~~sLl~~~~~--~ldl~~vlk~Gk~~~~l~~~lLa~~Qrklg~~~Gv~PGsEmk~AIe~A~e~ga~V~lIDRdI 122 (388)
T COG1916 45 ELDEARLLSLLGGSRE--ELDLAQVLKEGKAFFLLAGLLLAYFQRKLGKELGVKPGSEMKAAIEAARELGAPVALIDRDI 122 (388)
T ss_pred EecHHHHHHHhcCCcc--cCCHHHHHHcCchHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHcCCCEEEecccH
Confidence 4544566555554443 34444443322222 123346778899999999999965 3345555531 111
Q ss_pred HHHhhhhHHHHH-HHHHHcHHHHHHHHHhcccCC---CChhHHHHHHHHH-HHHHHHhcCCC
Q 016321 256 QSILMECSLARE-KLVMSNVRLVMSIAQRYDNMG---ADMADLVQGGLIG-LLRGIEKFDSS 312 (391)
Q Consensus 256 ~~~l~eg~~Are-~LIe~nlpLV~~IAkkY~~~G---vd~eDLIQEG~IG-LikAIekFDp~ 312 (391)
.-.++. +.. -=+..-+++.-.++......| .++++|-|+..+. |+.-+++|-|.
T Consensus 123 ~vTl~R---~~~~~~~~EKlK~~~~L~~~~~~~g~~e~ei~~l~~~D~~~al~~efr~~~P~ 181 (388)
T COG1916 123 GVTLRR---AWAKMPFWEKLKLISSLISGLLFPGQSEIEIDELKQEDVLSALMQEFRRFSPT 181 (388)
T ss_pred HHHHHH---HHHhCCHHHHHHHHHHHHHhcccCCCchHHHHHHhhhhHHHHHHHHHHHhChh
Confidence 111111 111 112234556666666533344 5899999999998 99999999885
No 186
>KOG1161 consensus Protein involved in vacuolar polyphosphate accumulation, contains SPX domain [Inorganic ion transport and metabolism]
Probab=25.54 E-value=5.2e+02 Score=26.70 Aligned_cols=35 Identities=14% Similarity=0.333 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHH
Q 016321 296 QGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQVRL 330 (391)
Q Consensus 296 QEG~IGLikAIekFDp~kG~rFsTYA~~~IR~aI~ 330 (391)
---.+|+.+.+++||-..|.+|..|....+.+...
T Consensus 117 ~LN~tGf~KILKK~DKrtg~~l~~~f~~~l~~~Pf 151 (310)
T KOG1161|consen 117 RLNYTGFAKILKKHDKRTGYRLRPYFQVRLLHQPF 151 (310)
T ss_pred HHhHHHHHHHHHHHhcccccccccHHHHHHHhCCC
Confidence 34568999999999999999999998887776544
No 187
>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=25.44 E-value=1.1e+02 Score=27.69 Aligned_cols=46 Identities=15% Similarity=0.176 Sum_probs=34.7
Q ss_pred HHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHH
Q 016321 210 EVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSL 264 (391)
Q Consensus 210 EE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~eg~~ 264 (391)
++.+.+.++++ -|+..-++..|..+++++.|++.+.+.++|++|..
T Consensus 27 ~~e~~f~kV~~---------yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGRL 72 (137)
T TIGR03826 27 EEEREFEKVYK---------FLRKHENRQATVSEIVEETGVSEKLILKFIREGRL 72 (137)
T ss_pred HHHHHHHHHHH---------HHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCCe
Confidence 44556666664 34455667788999999999999999999998743
No 188
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=24.59 E-value=98 Score=22.12 Aligned_cols=38 Identities=26% Similarity=0.257 Sum_probs=21.9
Q ss_pred chHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHcHHHHHHHHHhc
Q 016321 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRY 284 (391)
Q Consensus 240 s~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe~nlpLV~~IAkkY 284 (391)
|..++|+.+|++...+.+.++.... -....+..||+-|
T Consensus 11 s~~~la~~~gis~~~i~~~~~g~~~-------~~~~~~~~ia~~l 48 (55)
T PF01381_consen 11 SQKELAEKLGISRSTISRIENGKRN-------PSLDTLKKIAKAL 48 (55)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSST-------SBHHHHHHHHHHH
T ss_pred CHHHHHHHhCCCcchhHHHhcCCCC-------CCHHHHHHHHHHH
Confidence 4577888888887777666665211 1344555555555
No 189
>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=24.02 E-value=1.9e+02 Score=20.81 Aligned_cols=23 Identities=22% Similarity=0.296 Sum_probs=17.1
Q ss_pred CCchHHHHHHhcCChHHHHHHhh
Q 016321 238 EPSMEQLAASLRISRPELQSILM 260 (391)
Q Consensus 238 ePs~~e~A~a~~~s~~eL~~~l~ 260 (391)
..+.+++|+.+|+|..+..+.++
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 35789999999999988776654
No 190
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=22.76 E-value=4.4e+02 Score=25.00 Aligned_cols=31 Identities=23% Similarity=0.306 Sum_probs=24.7
Q ss_pred HHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 016321 228 KLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (391)
Q Consensus 228 ~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~ 258 (391)
...++..+|++|+.+++|..+|++.+++...
T Consensus 122 ~~~~~~~~~r~~~~~e~a~~~~~~~~~~~~~ 152 (257)
T PRK08583 122 VDELTTELQRSPKISEIADRLGVSEEEVLEA 152 (257)
T ss_pred HHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 3456677899999999999999998876554
No 191
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=21.66 E-value=7.9e+02 Score=26.32 Aligned_cols=44 Identities=23% Similarity=0.420 Sum_probs=26.6
Q ss_pred HHHHHcHHHHH-----HHHHhcccCCCChhHHHHHHHHHHHHHHHhcCCCCCCchhh
Q 016321 268 KLVMSNVRLVM-----SIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKIST 319 (391)
Q Consensus 268 ~LIe~nlpLV~-----~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFDp~kG~rFsT 319 (391)
.+|..|+..+. .||+++ |++.+|+.. + +.-|..+||.-|..|.+
T Consensus 197 ~il~~~le~la~~~~~~ia~~l---~is~~~v~~--~---~~~Ir~L~P~Pg~~~~~ 245 (455)
T PRK05932 197 EIISDHLDLLARRDFRTLAKKL---GVKEEDLQE--A---LDLIRSLDPKPGAGFGT 245 (455)
T ss_pred HHHHHHHHHHHcCCHHHHHHHH---CcCHHHHHH--H---HHHHhCCCCCCccccCC
Confidence 45555554442 244444 778888743 2 34467888988888864
No 192
>PRK13159 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=21.51 E-value=89 Score=29.03 Aligned_cols=33 Identities=27% Similarity=0.281 Sum_probs=22.6
Q ss_pred eeeeccCCCCCCCCCCCCccchhhHHHhhhccccC-CCCCCC
Q 016321 49 VVAAKKSSNYNPSFPSSNRQTQPIKALKEHVDTNF-ASTAEP 89 (391)
Q Consensus 49 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~ 89 (391)
-+.||+.+||-| .+...|||++-.... |..+.|
T Consensus 118 ~vLAKHde~YmP--------~Ev~~al~~~~~~~~~~~~~~~ 151 (155)
T PRK13159 118 EVLAKHDETYMP--------KELKDAMAEGHLGKPIPAAAAP 151 (155)
T ss_pred EEEecCCCcCCC--------HHHHHHHHhccccCCCCCcccC
Confidence 467899999999 357788887654433 444444
No 193
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=21.47 E-value=1.4e+02 Score=28.33 Aligned_cols=41 Identities=27% Similarity=0.352 Sum_probs=31.1
Q ss_pred HHHHHHHHHcCCcchhHHHHHHHhhC-CCCchHHHHHHhcCChHHHHHHhhh
Q 016321 211 VVRLSKKIKTGLSLDDHKLRLKERLG-CEPSMEQLAASLRISRPELQSILME 261 (391)
Q Consensus 211 E~eL~~kiq~G~~L~~~~~~l~~~~g-~ePs~~e~A~a~~~s~~eL~~~l~e 261 (391)
..+|..+|..|.. ..| +=|+..++|+.+|+|+..+++++.+
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 3456777887765 233 4599999999999999998876654
No 194
>PF08900 DUF1845: Domain of unknown function (DUF1845); InterPro: IPR014996 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=21.26 E-value=2.6e+02 Score=26.90 Aligned_cols=51 Identities=31% Similarity=0.412 Sum_probs=35.4
Q ss_pred ChHHHHHHhhhhHHHHHHHHHHcHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHhcC
Q 016321 251 SRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFD 310 (391)
Q Consensus 251 s~~eL~~~l~eg~~Are~LIe~nlpLV~~IAkkY~~~Gvd~eDLIQEG~IGLikAIekFD 310 (391)
|+.+...+++.+..+ ++-|..++.+|...|+..+|+. +++=-.-+|+++|-
T Consensus 145 s~~~~~~~l~~~~~~--------iR~v~~~~~~yr~~gvtR~D~~-~~n~~~~~A~~~~G 195 (217)
T PF08900_consen 145 SRQEREDWLRRGGRA--------IRRVFGLAQRYRHSGVTRDDFA-ANNARAQAAIERFG 195 (217)
T ss_pred ChHHHHHHHHHHHHH--------HHHHHHHHHHHhccCCCHHHHH-hcCHHHHHHHHHcC
Confidence 555555555554332 3445667788988999999998 66677778888885
No 195
>PRK15044 transcriptional regulator SirC; Provisional
Probab=21.08 E-value=1.9e+02 Score=29.44 Aligned_cols=60 Identities=17% Similarity=0.119 Sum_probs=42.2
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHHHHHcCCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhh
Q 016321 193 LKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (391)
Q Consensus 193 l~~YL~~i~~~~lLT~eEE~eL~~kiq~G~~L~~~~~~l~~~~g~ePs~~e~A~a~~~s~~eL~~~l~e 261 (391)
+..|++.-+..+.|..+..... .+.+..-+.+.++.+++.+++|+.+|+|+.-|.+..+.
T Consensus 172 Ls~~l~~~~~~~~L~~~~~is~---------~~kV~~~I~~nl~~~~SLeeLA~~lgmS~~tL~R~Fk~ 231 (295)
T PRK15044 172 ISAFVRKPGGFDFLERAIKITT---------KEKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAA 231 (295)
T ss_pred HHHHHhcccchhhHHHHhhhhH---------HHHHHHHHHhCcccCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 5566666665565554443332 23344556677889999999999999999999888765
No 196
>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=20.84 E-value=1.5e+02 Score=27.50 Aligned_cols=40 Identities=23% Similarity=0.381 Sum_probs=29.3
Q ss_pred HHHHHHHHcCCcchhHHHHHHHhhC-CCCchHHHHHHhcCChHHHHHHhhh
Q 016321 212 VRLSKKIKTGLSLDDHKLRLKERLG-CEPSMEQLAASLRISRPELQSILME 261 (391)
Q Consensus 212 ~eL~~kiq~G~~L~~~~~~l~~~~g-~ePs~~e~A~a~~~s~~eL~~~l~e 261 (391)
..|..+|.+|.. ..| +=||..++|+.+|+|+..+|++|..
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 345666777654 123 3599999999999999888876654
No 197
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=20.43 E-value=5.3e+02 Score=22.34 Aligned_cols=42 Identities=19% Similarity=0.213 Sum_probs=26.4
Q ss_pred CCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHcHHHHHHH
Q 016321 238 EPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI 280 (391)
Q Consensus 238 ePs~~e~A~a~~~s~~eL~~~l~eg~~Are~LIe~nlpLV~~I 280 (391)
.-|..|+|+.+|+|+...-..++.+.... .-++..+.|+.+.
T Consensus 33 DlSlsEIAe~~~iSRqaV~d~ikr~~~~L-~~yE~kL~l~~k~ 74 (101)
T PF04297_consen 33 DLSLSEIAEELGISRQAVYDSIKRAEKKL-EEYEEKLGLVEKF 74 (101)
T ss_dssp ---HHHHHHHCTS-HHHHHHHHHHHHHHH-HHHHHHH-HHHHH
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHH-HHHHHHHhhHHHH
Confidence 35789999999999988888887765544 3345555555543
No 198
>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=20.38 E-value=1.2e+02 Score=20.44 Aligned_cols=23 Identities=22% Similarity=0.235 Sum_probs=17.9
Q ss_pred chHHHHHHhcCChHHHHHHhhhh
Q 016321 240 SMEQLAASLRISRPELQSILMEC 262 (391)
Q Consensus 240 s~~e~A~a~~~s~~eL~~~l~eg 262 (391)
+..|+|+.+|++...+.++++.|
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~g 24 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKEG 24 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcC
Confidence 34688889999988888777664
No 199
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=20.11 E-value=1e+02 Score=23.66 Aligned_cols=21 Identities=10% Similarity=0.218 Sum_probs=18.3
Q ss_pred hHHHHHHhcCChHHHHHHhhh
Q 016321 241 MEQLAASLRISRPELQSILME 261 (391)
Q Consensus 241 ~~e~A~a~~~s~~eL~~~l~e 261 (391)
...||+.+|+|.++|+.++..
T Consensus 23 v~ywa~~~gvt~~~L~~AV~~ 43 (57)
T PF12244_consen 23 VRYWAKRFGVTEEQLREAVRA 43 (57)
T ss_pred HHHHHHHHCcCHHHHHHHHHH
Confidence 467999999999999988876
Done!