Query 019233
Match_columns 344
No_of_seqs 195 out of 1457
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 07:47:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019233.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019233hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK07598 RNA polymerase sigma 99.9 2E-25 4.4E-30 222.9 14.6 117 217-336 58-216 (415)
2 TIGR02997 Sig70-cyanoRpoD RNA 99.9 2.5E-24 5.4E-29 204.0 14.1 115 219-336 1-115 (298)
3 PRK07406 RNA polymerase sigma 99.9 1.6E-22 3.5E-27 199.6 14.0 116 218-336 62-177 (373)
4 PRK05949 RNA polymerase sigma 99.9 9.4E-22 2E-26 190.4 15.0 117 217-336 16-132 (327)
5 PRK07405 RNA polymerase sigma 99.9 1E-21 2.2E-26 188.9 14.3 116 218-336 7-122 (317)
6 PRK05901 RNA polymerase sigma 99.8 2.9E-19 6.3E-24 182.8 9.0 104 217-336 209-312 (509)
7 COG0568 RpoD DNA-directed RNA 99.7 5.6E-18 1.2E-22 166.2 9.2 116 218-336 8-143 (342)
8 PRK07921 RNA polymerase sigma 99.7 2.6E-16 5.7E-21 152.7 10.4 105 216-336 23-127 (324)
9 PRK09210 RNA polymerase sigma 99.4 1.9E-12 4.2E-17 127.2 9.0 78 216-336 93-170 (367)
10 PRK05658 RNA polymerase sigma 99.3 1E-12 2.2E-17 136.8 6.5 60 277-336 355-421 (619)
11 PRK06596 RNA polymerase factor 99.2 8.5E-11 1.8E-15 111.7 9.2 78 217-336 12-89 (284)
12 TIGR02392 rpoH_proteo alternat 99.2 8.2E-11 1.8E-15 110.4 8.2 75 220-336 2-76 (270)
13 PRK07122 RNA polymerase sigma 99.1 6.9E-11 1.5E-15 111.2 5.0 43 294-336 39-81 (264)
14 PRK07500 rpoH2 RNA polymerase 99.1 3.4E-10 7.4E-15 108.0 8.9 75 220-336 7-81 (289)
15 PRK05657 RNA polymerase sigma 98.8 1.6E-08 3.5E-13 98.3 8.1 77 217-336 51-127 (325)
16 TIGR02850 spore_sigG RNA polym 98.7 5.3E-08 1.2E-12 90.5 7.5 67 230-336 9-75 (254)
17 COG1191 FliA DNA-directed RNA 98.7 2.6E-08 5.7E-13 94.6 5.5 50 286-336 14-65 (247)
18 TIGR02394 rpoS_proteo RNA poly 98.7 7.3E-08 1.6E-12 91.1 8.2 77 217-336 11-87 (285)
19 PRK07408 RNA polymerase sigma 98.6 7E-08 1.5E-12 90.2 6.3 44 293-336 23-67 (256)
20 PRK08215 sporulation sigma fac 98.6 1.1E-07 2.3E-12 88.6 7.5 67 230-336 12-78 (258)
21 PRK05911 RNA polymerase sigma 98.4 5E-07 1.1E-11 84.7 6.4 44 293-336 21-67 (257)
22 PRK06288 RNA polymerase sigma 98.4 1E-06 2.2E-11 82.6 7.5 67 231-336 6-75 (268)
23 PRK05803 sporulation sigma fac 98.2 4.5E-06 9.9E-11 76.5 8.2 74 220-336 17-90 (233)
24 TIGR02941 Sigma_B RNA polymera 98.1 5.7E-06 1.2E-10 76.7 7.3 42 294-335 28-69 (255)
25 PF00140 Sigma70_r1_2: Sigma-7 98.0 2.1E-06 4.6E-11 59.6 1.4 35 218-255 1-35 (37)
26 PRK08583 RNA polymerase sigma 98.0 1.8E-05 3.8E-10 73.5 7.5 44 293-336 27-70 (257)
27 PRK12427 flagellar biosynthesi 97.9 1.6E-05 3.4E-10 73.7 4.6 42 295-336 15-59 (231)
28 TIGR02885 spore_sigF RNA polym 97.8 2.7E-05 5.9E-10 70.9 5.7 45 292-336 8-52 (231)
29 PRK05572 sporulation sigma fac 97.8 7.5E-05 1.6E-09 69.4 7.6 67 230-336 7-73 (252)
30 PRK07670 RNA polymerase sigma 97.4 0.0003 6.5E-09 65.4 5.7 52 284-335 9-65 (251)
31 TIGR02846 spore_sigmaK RNA pol 97.0 0.0035 7.6E-08 57.5 8.4 44 293-336 46-89 (227)
32 PF04542 Sigma70_r2: Sigma-70 96.7 0.0023 5.1E-08 46.9 3.9 36 300-335 1-36 (71)
33 PRK08301 sporulation sigma fac 96.6 0.0088 1.9E-07 54.7 8.2 43 293-335 50-92 (234)
34 PF04539 Sigma70_r3: Sigma-70 96.6 0.0051 1.1E-07 47.3 5.6 40 253-292 4-43 (78)
35 PRK05658 RNA polymerase sigma 96.6 0.0022 4.8E-08 67.6 4.4 35 217-254 102-136 (619)
36 TIGR02835 spore_sigmaE RNA pol 96.4 0.011 2.4E-07 54.4 7.6 44 293-336 50-93 (234)
37 PRK09641 RNA polymerase sigma 96.0 0.01 2.2E-07 51.4 5.0 52 285-336 7-59 (187)
38 PRK05602 RNA polymerase sigma 95.9 0.012 2.7E-07 51.4 5.0 54 282-335 6-60 (186)
39 PRK08295 RNA polymerase factor 95.9 0.022 4.8E-07 50.3 6.5 54 282-335 10-64 (208)
40 PRK11922 RNA polymerase sigma 95.8 0.02 4.4E-07 52.5 5.8 44 293-336 28-71 (231)
41 TIGR02859 spore_sigH RNA polym 95.7 0.032 6.9E-07 48.9 6.5 55 281-335 4-59 (198)
42 PRK08311 putative RNA polymera 95.5 0.034 7.4E-07 52.6 6.3 53 284-336 6-61 (237)
43 TIGR02948 SigW_bacill RNA poly 95.4 0.021 4.5E-07 49.5 4.4 45 291-335 14-58 (187)
44 PRK12513 RNA polymerase sigma 95.3 0.028 6.1E-07 49.5 4.8 54 283-336 13-67 (194)
45 PRK09648 RNA polymerase sigma 95.3 0.056 1.2E-06 47.4 6.7 52 285-336 13-69 (189)
46 PRK13919 putative RNA polymera 95.0 0.043 9.4E-07 47.8 5.2 55 282-336 9-64 (186)
47 PRK09640 RNA polymerase sigma 94.8 0.066 1.4E-06 47.2 5.8 55 281-335 8-66 (188)
48 PRK09638 RNA polymerase sigma 94.7 0.07 1.5E-06 46.0 5.7 54 282-335 4-58 (176)
49 PRK12519 RNA polymerase sigma 94.3 0.075 1.6E-06 46.7 5.0 54 283-336 16-70 (194)
50 PRK11923 algU RNA polymerase s 94.2 0.097 2.1E-06 46.0 5.5 51 285-335 9-60 (193)
51 TIGR02939 RpoE_Sigma70 RNA pol 93.9 0.11 2.4E-06 45.1 5.2 51 285-335 9-60 (190)
52 PRK09646 RNA polymerase sigma 93.9 0.11 2.3E-06 46.2 5.2 52 284-335 18-70 (194)
53 PRK06811 RNA polymerase factor 93.8 0.17 3.6E-06 44.8 6.3 56 281-336 3-62 (189)
54 PRK11924 RNA polymerase sigma 93.6 0.13 2.8E-06 43.7 4.9 45 292-336 10-54 (179)
55 PRK12524 RNA polymerase sigma 93.5 0.14 3.1E-06 45.4 5.3 54 282-335 12-66 (196)
56 PRK12534 RNA polymerase sigma 93.1 0.14 3E-06 44.8 4.5 47 290-336 20-66 (187)
57 PRK12514 RNA polymerase sigma 93.0 0.16 3.5E-06 44.1 4.7 52 284-335 7-59 (179)
58 TIGR02954 Sig70_famx3 RNA poly 92.0 0.31 6.6E-06 41.9 5.2 52 284-335 4-56 (169)
59 PRK06759 RNA polymerase factor 91.3 0.34 7.4E-06 40.7 4.6 41 295-336 4-44 (154)
60 PRK09643 RNA polymerase sigma 90.5 0.52 1.1E-05 41.9 5.2 54 282-335 13-67 (192)
61 PRK12512 RNA polymerase sigma 89.7 0.94 2E-05 39.5 6.1 44 292-335 19-66 (184)
62 PRK12531 RNA polymerase sigma 89.3 0.67 1.4E-05 41.1 5.0 51 285-335 16-67 (194)
63 PRK12515 RNA polymerase sigma 89.0 0.52 1.1E-05 41.5 4.0 54 282-335 8-62 (189)
64 PRK12538 RNA polymerase sigma 88.9 0.73 1.6E-05 42.9 5.1 52 284-335 51-103 (233)
65 TIGR02952 Sig70_famx2 RNA poly 88.9 0.82 1.8E-05 38.8 5.0 44 292-335 8-51 (170)
66 PRK12537 RNA polymerase sigma 88.0 1.1 2.3E-05 39.3 5.3 52 284-335 11-63 (182)
67 COG1191 FliA DNA-directed RNA 86.8 1.4 3E-05 42.5 5.7 41 253-293 110-150 (247)
68 PRK12539 RNA polymerase sigma 85.5 2.4 5.3E-05 37.1 6.2 51 285-335 10-65 (184)
69 PRK12526 RNA polymerase sigma 84.6 1.4 3.1E-05 39.7 4.4 44 292-335 35-78 (206)
70 PRK07408 RNA polymerase sigma 84.4 2.7 5.8E-05 39.6 6.3 37 253-289 113-149 (256)
71 TIGR02895 spore_sigI RNA polym 83.2 1.2 2.5E-05 42.0 3.4 17 320-336 36-52 (218)
72 PRK12536 RNA polymerase sigma 83.1 3.1 6.7E-05 36.4 5.8 47 289-335 15-62 (181)
73 TIGR02850 spore_sigG RNA polym 82.6 3.4 7.3E-05 38.7 6.2 37 254-290 121-157 (254)
74 TIGR02393 RpoD_Cterm RNA polym 82.4 3.8 8.1E-05 37.9 6.3 37 254-290 88-124 (238)
75 PRK12518 RNA polymerase sigma 82.3 2.4 5.2E-05 36.4 4.7 43 292-335 8-50 (175)
76 PRK07122 RNA polymerase sigma 81.1 4.2 9.2E-05 38.7 6.3 37 254-290 128-164 (264)
77 TIGR02999 Sig-70_X6 RNA polyme 80.7 4.4 9.5E-05 35.1 5.8 51 285-335 6-62 (183)
78 TIGR02983 SigE-fam_strep RNA p 80.2 2.4 5.3E-05 35.9 4.0 43 293-335 4-46 (162)
79 PRK07921 RNA polymerase sigma 80.2 4.4 9.5E-05 40.1 6.3 39 252-290 172-210 (324)
80 PRK12427 flagellar biosynthesi 80.1 4.2 9.1E-05 37.9 5.8 37 254-290 102-138 (231)
81 PRK09415 RNA polymerase factor 79.2 2.3 5.1E-05 37.2 3.7 43 293-335 14-56 (179)
82 PRK05911 RNA polymerase sigma 78.6 5.6 0.00012 37.6 6.2 36 255-290 112-147 (257)
83 COG1595 RpoE DNA-directed RNA 76.8 5.2 0.00011 35.1 5.1 48 290-337 10-57 (182)
84 PRK09210 RNA polymerase sigma 76.2 6.6 0.00014 39.3 6.3 36 254-289 217-252 (367)
85 PRK06986 fliA flagellar biosyn 75.3 2.3 5.1E-05 39.1 2.7 27 308-335 25-51 (236)
86 PRK11511 DNA-binding transcrip 73.9 15 0.00032 31.2 6.9 59 255-314 11-83 (127)
87 PRK12547 RNA polymerase sigma 73.8 5.1 0.00011 34.4 4.3 42 294-335 5-46 (164)
88 PF01726 LexA_DNA_bind: LexA D 73.1 12 0.00025 29.0 5.6 26 264-289 20-46 (65)
89 PRK07406 RNA polymerase sigma 73.0 8.8 0.00019 39.0 6.3 38 252-289 222-259 (373)
90 PRK05901 RNA polymerase sigma 71.4 9.5 0.00021 40.5 6.3 37 254-290 359-395 (509)
91 TIGR02885 spore_sigF RNA polym 70.9 12 0.00026 34.1 6.2 36 255-290 99-134 (231)
92 TIGR02479 FliA_WhiG RNA polyme 70.0 11 0.00024 34.3 5.7 39 252-290 82-120 (224)
93 PRK10219 DNA-binding transcrip 69.6 21 0.00045 28.8 6.7 38 255-292 7-44 (107)
94 PRK12541 RNA polymerase sigma 68.7 6.3 0.00014 33.6 3.6 42 294-335 4-45 (161)
95 PRK07670 RNA polymerase sigma 68.0 13 0.00028 34.6 5.9 37 254-290 110-146 (251)
96 PRK05949 RNA polymerase sigma 67.9 14 0.00031 36.5 6.4 36 254-289 179-214 (327)
97 PRK12523 RNA polymerase sigma 67.7 7.9 0.00017 33.5 4.1 44 293-336 8-51 (172)
98 TIGR03001 Sig-70_gmx1 RNA poly 67.2 12 0.00027 35.3 5.6 54 281-334 24-78 (244)
99 PRK06288 RNA polymerase sigma 67.2 13 0.00029 35.0 5.8 37 254-290 119-155 (268)
100 PRK08241 RNA polymerase factor 67.1 12 0.00026 36.1 5.6 51 285-335 8-59 (339)
101 PRK08215 sporulation sigma fac 66.7 16 0.00034 34.2 6.2 35 255-289 125-159 (258)
102 COG0568 RpoD DNA-directed RNA 65.7 17 0.00038 36.8 6.6 41 249-289 185-225 (342)
103 PRK09647 RNA polymerase sigma 63.9 9.7 0.00021 34.6 4.1 43 294-336 27-69 (203)
104 PRK07598 RNA polymerase sigma 63.2 16 0.00034 37.9 5.9 38 254-291 263-300 (415)
105 PRK09651 RNA polymerase sigma 62.3 13 0.00027 32.4 4.3 43 294-336 9-51 (172)
106 PRK07405 RNA polymerase sigma 61.2 23 0.0005 34.8 6.4 37 254-290 169-205 (317)
107 smart00342 HTH_ARAC helix_turn 57.9 39 0.00085 24.5 5.8 56 269-328 1-59 (84)
108 PRK09649 RNA polymerase sigma 57.6 20 0.00042 31.7 4.8 50 285-335 13-63 (185)
109 TIGR02997 Sig70-cyanoRpoD RNA 57.1 31 0.00068 33.2 6.5 37 254-290 162-198 (298)
110 TIGR02980 SigBFG RNA polymeras 56.3 23 0.0005 32.2 5.1 33 257-289 94-126 (227)
111 COG4977 Transcriptional regula 55.9 32 0.00069 34.7 6.5 52 257-308 224-289 (328)
112 PRK12517 RNA polymerase sigma 55.8 16 0.00034 32.5 3.9 45 291-335 19-63 (188)
113 PRK13503 transcriptional activ 53.8 51 0.0011 30.3 7.1 59 255-314 173-245 (278)
114 PRK09645 RNA polymerase sigma 53.7 18 0.00038 31.1 3.8 43 293-335 7-49 (173)
115 PRK15044 transcriptional regul 53.0 67 0.0014 32.1 8.1 60 221-292 172-231 (295)
116 PRK12533 RNA polymerase sigma 52.1 20 0.00044 33.1 4.1 42 294-335 17-58 (216)
117 PRK15121 right oriC-binding tr 50.9 55 0.0012 31.0 7.0 60 255-315 7-80 (289)
118 PRK05572 sporulation sigma fac 48.8 50 0.0011 30.8 6.2 35 254-288 119-153 (252)
119 PRK12544 RNA polymerase sigma 48.7 26 0.00057 31.9 4.2 53 278-335 6-58 (206)
120 PRK07500 rpoH2 RNA polymerase 48.7 36 0.00079 32.9 5.4 26 264-289 143-168 (289)
121 TIGR02947 SigH_actino RNA poly 48.3 20 0.00044 31.5 3.4 43 293-335 9-51 (193)
122 COG4367 Uncharacterized protei 47.3 80 0.0017 26.8 6.5 45 258-302 11-62 (97)
123 PRK12525 RNA polymerase sigma 45.6 37 0.00079 29.3 4.5 41 295-335 9-49 (168)
124 TIGR03826 YvyF flagellar opero 45.5 46 0.00099 29.7 5.1 39 256-294 33-71 (137)
125 TIGR01446 DnaD_dom DnaD and ph 44.3 43 0.00094 25.4 4.2 59 262-324 5-70 (73)
126 PRK06986 fliA flagellar biosyn 43.8 48 0.001 30.5 5.2 34 255-288 97-130 (236)
127 TIGR02941 Sigma_B RNA polymera 42.4 77 0.0017 29.5 6.4 35 255-289 118-152 (255)
128 PRK05657 RNA polymerase sigma 38.2 85 0.0018 31.0 6.3 36 255-290 175-210 (325)
129 PRK09393 ftrA transcriptional 34.0 89 0.0019 30.0 5.6 36 257-292 222-257 (322)
130 COG1476 Predicted transcriptio 33.5 67 0.0015 25.6 3.8 50 270-329 15-64 (68)
131 TIGR02297 HpaA 4-hydroxyphenyl 33.4 1.1E+02 0.0023 28.4 5.8 33 260-292 193-225 (287)
132 PRK12535 RNA polymerase sigma 32.9 91 0.002 28.0 5.1 42 293-335 23-64 (196)
133 PF12324 HTH_15: Helix-turn-he 30.2 64 0.0014 26.4 3.3 26 267-292 36-61 (77)
134 PRK06704 RNA polymerase factor 29.5 63 0.0014 30.5 3.6 49 286-335 9-57 (228)
135 PRK06596 RNA polymerase factor 28.4 95 0.0021 29.9 4.7 24 267-290 149-172 (284)
136 PRK10572 DNA-binding transcrip 27.3 1.5E+02 0.0032 27.7 5.7 36 257-292 187-222 (290)
137 PRK13239 alkylmercury lyase; P 26.1 1.1E+02 0.0024 29.1 4.6 27 266-292 33-59 (206)
138 PRK15186 AraC family transcrip 25.7 1E+02 0.0022 30.2 4.5 35 258-292 186-220 (291)
139 TIGR02984 Sig-70_plancto1 RNA 25.6 89 0.0019 26.9 3.6 20 317-336 33-52 (189)
140 KOG0917 Uncharacterized conser 25.4 65 0.0014 32.5 3.0 40 104-144 55-94 (338)
141 PF10078 DUF2316: Uncharacteri 24.8 4.2E+02 0.009 22.2 7.2 34 269-302 23-63 (89)
142 TIGR02394 rpoS_proteo RNA poly 24.8 2E+02 0.0044 27.4 6.2 31 259-289 139-169 (285)
143 PF14711 Nitr_red_bet_C: Respi 24.0 1.3E+02 0.0028 24.8 4.1 54 217-283 28-82 (83)
144 TIGR02844 spore_III_D sporulat 23.6 3.2E+02 0.0069 22.2 6.2 37 254-293 7-43 (80)
145 PF13404 HTH_AsnC-type: AsnC-t 23.6 1.8E+02 0.0038 20.6 4.2 25 268-292 16-40 (42)
146 PRK10371 DNA-binding transcrip 22.7 3.6E+02 0.0077 26.0 7.5 38 255-292 193-230 (302)
147 PRK13501 transcriptional activ 22.7 2.2E+02 0.0047 26.7 5.9 53 261-314 184-250 (290)
148 PF06971 Put_DNA-bind_N: Putat 22.4 2.3E+02 0.0051 21.1 4.8 41 249-290 8-49 (50)
149 PRK12529 RNA polymerase sigma 22.4 1.3E+02 0.0028 26.3 4.1 44 292-335 10-55 (178)
150 PF08279 HTH_11: HTH domain; 21.7 2.4E+02 0.0051 19.9 4.7 26 267-292 13-38 (55)
151 PRK15340 transcriptional regul 21.6 6.8E+02 0.015 23.9 8.9 32 261-292 117-148 (216)
152 PRK09685 DNA-binding transcrip 20.1 5.2E+02 0.011 24.1 7.8 37 256-292 200-237 (302)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=99.93 E-value=2e-25 Score=222.93 Aligned_cols=117 Identities=26% Similarity=0.299 Sum_probs=107.3
Q ss_pred CCchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHH--------------------HHHHHHHHHHHhCCCCchHHHH
Q 019233 217 LKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVAN--------------------LERIKTTLEKESGKAASLNCWA 276 (344)
Q Consensus 217 ~~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~--------------------LE~ir~~Lee~lGrePT~~eWA 276 (344)
-.|++..||+ +|+++||||++||++|+++||.+++ |++++..|++++|++||..|||
T Consensus 58 ~~d~v~~yl~---~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa 134 (415)
T PRK07598 58 STDLVRLYLQ---EIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWA 134 (415)
T ss_pred CCChHHHHHH---hcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence 3689999999 9999999999999999999999999 8999999999999999999999
Q ss_pred HHcCCCHHHHHH----------------------HhhhhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHh
Q 019233 277 QAAGVSERVLKQ----------------------HLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALA 334 (344)
Q Consensus 277 ~aaGld~~eL~~----------------------~l~~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLm 334 (344)
.++|+++.+|+. .+..|..|+++||.+|++||++||++|.++|+.++||||||++|||
T Consensus 135 ~~~~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~ 214 (415)
T PRK07598 135 KTADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLE 214 (415)
T ss_pred HHhCCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHH
Confidence 776665555554 4567889999999999999999999999999999999999999999
Q ss_pred hh
Q 019233 335 FI 336 (344)
Q Consensus 335 ka 336 (344)
++
T Consensus 215 ra 216 (415)
T PRK07598 215 RA 216 (415)
T ss_pred HH
Confidence 94
No 2
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=99.91 E-value=2.5e-24 Score=204.02 Aligned_cols=115 Identities=30% Similarity=0.416 Sum_probs=111.8
Q ss_pred chHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHHHH
Q 019233 219 QPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCRE 298 (344)
Q Consensus 219 dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~ARd 298 (344)
|++..||+ +++++|+||++||++|++.|+.+..+++++.+|+++.|++||..+||+++|++..+|...+..|..|++
T Consensus 1 ~~~~~yl~---~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~ 77 (298)
T TIGR02997 1 DLVRLYLQ---EIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKE 77 (298)
T ss_pred CcHHHHHH---HccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHH
Confidence 46788999 999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 299 rLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
+||.+|+|+|++||++|.++|.+++||||||++|||+|
T Consensus 78 ~Lv~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a 115 (298)
T TIGR02997 78 KMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERA 115 (298)
T ss_pred HHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999994
No 3
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=99.88 E-value=1.6e-22 Score=199.62 Aligned_cols=116 Identities=22% Similarity=0.373 Sum_probs=113.4
Q ss_pred CchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHHH
Q 019233 218 KQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCR 297 (344)
Q Consensus 218 ~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~AR 297 (344)
.|++..||+ +++++||||++||++|+++|+.++.+++++.+|+++.|++|+.++||.++|++..+|++++..|..|+
T Consensus 62 ~d~l~~Yl~---~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~ 138 (373)
T PRK07406 62 EDSIRVYLQ---EIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAK 138 (373)
T ss_pred CCHHHHHHH---HhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHH
Confidence 578899999 99999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 298 EELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 298 drLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
++||..|+++|++||++|.++|++++||||||++|||++
T Consensus 139 ~~Li~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~A 177 (373)
T PRK07406 139 EKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRA 177 (373)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999994
No 4
>PRK05949 RNA polymerase sigma factor; Validated
Probab=99.87 E-value=9.4e-22 Score=190.41 Aligned_cols=117 Identities=27% Similarity=0.301 Sum_probs=113.8
Q ss_pred CCchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHH
Q 019233 217 LKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYC 296 (344)
Q Consensus 217 ~~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~A 296 (344)
.+|++..||+ +++++||||++||++|++.||.++.+++.++.|+..+|++|+..+||.+++++..+|...+..|..|
T Consensus 16 ~~d~~~~yl~---~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A 92 (327)
T PRK05949 16 SADMVRTYLH---EIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRA 92 (327)
T ss_pred CCCHHHHHHH---HcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHH
Confidence 4689999999 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 297 RdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
+++||..|+++|+++|++|.+.|.+++||||||++||+++
T Consensus 93 ~~~Li~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a 132 (327)
T PRK05949 93 KQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERG 132 (327)
T ss_pred HHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999994
No 5
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=99.87 E-value=1e-21 Score=188.94 Aligned_cols=116 Identities=22% Similarity=0.260 Sum_probs=113.1
Q ss_pred CchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHHH
Q 019233 218 KQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCR 297 (344)
Q Consensus 218 ~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~AR 297 (344)
+|++..||+ +++++||||++||++|+++|+.++.+++++..|++++|++|+..+||++++++..+|...+..|..|+
T Consensus 7 ~~~~~~yl~---~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~ 83 (317)
T PRK07405 7 TDLVRTYLR---EIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAK 83 (317)
T ss_pred CcHHHHHHH---HccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHH
Confidence 578999999 99999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 298 EELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 298 drLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
++||..|+++|+++|++|.+.|.+.+||||||++||+++
T Consensus 84 ~~L~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a 122 (317)
T PRK07405 84 RKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRG 122 (317)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999993
No 6
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=2.9e-19 Score=182.80 Aligned_cols=104 Identities=22% Similarity=0.216 Sum_probs=88.4
Q ss_pred CCchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHH
Q 019233 217 LKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYC 296 (344)
Q Consensus 217 ~~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~A 296 (344)
..|++..||+ .++++|+||++||++|+++|+.+..++.. +. ...+|+.+ ...+|++++..|..|
T Consensus 209 ~~d~l~~YL~---~i~~~~lLt~eEE~~La~~i~~g~~~~~~---~~-------~~~~~~~~---~~~~l~~~~~~g~~A 272 (509)
T PRK05901 209 TADPVKAYLK---QIGKVKLLNAEEEVELAKRIEAGLYAEEL---LA-------EGEKLDPE---LRRDLQWIGRDGKRA 272 (509)
T ss_pred cccHHHHHHH---HhccCCCCCHHHHHHHHHHHHhCCchhhh---hh-------hcccchhh---hhhhhhhhccchHHH
Confidence 3688999999 99999999999999999999987544331 11 11234422 467899999999999
Q ss_pred HHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 297 RdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
|++||.+|||||++||++|.++|++++|||||||||||+|
T Consensus 273 r~~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikA 312 (509)
T PRK05901 273 KNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKA 312 (509)
T ss_pred HHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999995
No 7
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=99.73 E-value=5.6e-18 Score=166.21 Aligned_cols=116 Identities=23% Similarity=0.281 Sum_probs=100.6
Q ss_pred CchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHH-HhCCCCchH---------------HHHHHcCC
Q 019233 218 KQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEK-ESGKAASLN---------------CWAQAAGV 281 (344)
Q Consensus 218 ~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee-~lGrePT~~---------------eWA~aaGl 281 (344)
.|.+..|+. +++..+++++++|.++...++....+......|.. ..++.|+.. +|+..+..
T Consensus 8 ~d~~~~~l~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 84 (342)
T COG0568 8 ADAVRAYLD---EIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTP 84 (342)
T ss_pred hhHHHHHHH---HhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccCh
Confidence 467788998 89999999999999999999998877777777776 567888876 55555555
Q ss_pred CH-HHHHHHhhhhHH---HHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 282 SE-RVLKQHLAFGWY---CREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 282 d~-~eL~~~l~~g~~---ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
++ ..|..++..|.. |+.+||.+|||||++|||+|.|+|++|.|||||||||||+|
T Consensus 85 ~Ee~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkA 143 (342)
T COG0568 85 EEEKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKA 143 (342)
T ss_pred HHHHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHH
Confidence 54 788888888754 99999999999999999999999999999999999999996
No 8
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=99.66 E-value=2.6e-16 Score=152.71 Aligned_cols=105 Identities=23% Similarity=0.239 Sum_probs=89.6
Q ss_pred CCCchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHH
Q 019233 216 GLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWY 295 (344)
Q Consensus 216 ~~~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~ 295 (344)
+-+|++..||+ +++++|+||++||++|+++|+.+..++.. |+..+|+... ...+|...+..|..
T Consensus 23 ~~~~~~~~Yl~---~i~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~ 86 (324)
T PRK07921 23 PAADLVRVYLN---GIGKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEA 86 (324)
T ss_pred CCCChHHHHHH---HhcccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHH
Confidence 34688999999 99999999999999999999988766543 2233332111 45688999999999
Q ss_pred HHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 296 ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
|+++||..|+++|+++|++|.++|++++||||||+|||+++
T Consensus 87 A~~~Lv~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a 127 (324)
T PRK07921 87 ARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRA 127 (324)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999994
No 9
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=99.36 E-value=1.9e-12 Score=127.21 Aligned_cols=78 Identities=23% Similarity=0.299 Sum_probs=72.0
Q ss_pred CCCchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHH
Q 019233 216 GLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWY 295 (344)
Q Consensus 216 ~~~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~ 295 (344)
..+|++..||+ ++++.|+||++||.+|++.++.+ +..
T Consensus 93 ~~~d~~~~yl~---~i~~~~~l~~~ee~~L~~~~~~G----------------------------------------d~~ 129 (367)
T PRK09210 93 KINDPVRMYLK---EIGRVPLLTAEEEIELAKRIEEG----------------------------------------DEE 129 (367)
T ss_pred ccCcHHHHHHH---HhhccCCCCHHHHHHHHHHHHhh----------------------------------------HHH
Confidence 34789999999 99999999999999999988764 257
Q ss_pred HHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 296 ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
|+++||..|+++|++||++|.++|.+++||||||++|||+|
T Consensus 130 A~~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a 170 (367)
T PRK09210 130 AKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKA 170 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHH
Confidence 89999999999999999999999999999999999999995
No 10
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=99.34 E-value=1e-12 Score=136.85 Aligned_cols=60 Identities=25% Similarity=0.455 Sum_probs=49.0
Q ss_pred HHcCCCHHHHH---HHhhhh----HHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 277 QAAGVSERVLK---QHLAFG----WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 277 ~aaGld~~eL~---~~l~~g----~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
...+++.+++. +.+..| ..|+++||.+|||||++||++|.++|++++|||||||||||+|
T Consensus 355 ~~~~Ls~eElk~l~~~i~~g~~~~~~a~~~Li~~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~A 421 (619)
T PRK05658 355 EETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 421 (619)
T ss_pred HHhCCCHHHHHHHHHHHhccchhhhHHHHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHH
Confidence 34455554443 334444 3789999999999999999999999999999999999999995
No 11
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=99.17 E-value=8.5e-11 Score=111.66 Aligned_cols=78 Identities=22% Similarity=0.235 Sum_probs=69.0
Q ss_pred CCchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHH
Q 019233 217 LKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYC 296 (344)
Q Consensus 217 ~~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~A 296 (344)
+.+++..|++ ++.+.|+|+.++|.+|...++. ..+..+
T Consensus 12 ~~~~~~~y~~---~~~~~~~l~~~~e~~l~~~~~~---------------------------------------~Gd~~a 49 (284)
T PRK06596 12 PEGNLDAYIQ---AVNKIPMLTAEEEYMLAKRLRE---------------------------------------HGDLEA 49 (284)
T ss_pred CccHHHHHHH---HHhccCCCCHHHHHHHHHHHHH---------------------------------------cCCHHH
Confidence 3468899999 8999999999999999887532 014679
Q ss_pred HHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 297 RdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
+++||..|+++|.+||++|.+.|++++||||+|++||++|
T Consensus 50 ~~~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a 89 (284)
T PRK06596 50 AKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKA 89 (284)
T ss_pred HHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999994
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=99.16 E-value=8.2e-11 Score=110.43 Aligned_cols=75 Identities=21% Similarity=0.244 Sum_probs=66.7
Q ss_pred hHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHHHHH
Q 019233 220 PTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREE 299 (344)
Q Consensus 220 pl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~ARdr 299 (344)
++..||+ ++++.|+|+.++|.+|...+.. ..+..|+++
T Consensus 2 ~~~~yl~---~~~~~~~l~~~~e~~l~~~~~~---------------------------------------~gd~~a~~~ 39 (270)
T TIGR02392 2 SLDAYIR---AVNRIPMLTPEEEYQLAKRLRE---------------------------------------HGDLDAAKK 39 (270)
T ss_pred hHHHHHH---HHhcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHH
Confidence 5678999 9999999999999999886431 024679999
Q ss_pred HHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 300 LIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 300 LI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
||..|+++|.++|++|.+.|.+.+||||+|++||+++
T Consensus 40 Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a 76 (270)
T TIGR02392 40 LVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKA 76 (270)
T ss_pred HHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999993
No 13
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=99.10 E-value=6.9e-11 Score=111.19 Aligned_cols=43 Identities=33% Similarity=0.473 Sum_probs=41.4
Q ss_pred HHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 294 ~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
..+|++||.+|+|||++||++|.++|++++||||+|+||||+|
T Consensus 39 ~~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~A 81 (264)
T PRK07122 39 QRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNA 81 (264)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHH
Confidence 5699999999999999999999999999999999999999995
No 14
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=99.08 E-value=3.4e-10 Score=107.95 Aligned_cols=75 Identities=16% Similarity=0.133 Sum_probs=67.5
Q ss_pred hHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHHHHH
Q 019233 220 PTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREE 299 (344)
Q Consensus 220 pl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~ARdr 299 (344)
-+..||+ ++.+.|+||+++|.+|.+.++.. .+..|+++
T Consensus 7 ~~~~y~~---~~~~~~~l~~~~e~~L~~~~~~~---------------------------------------gd~~A~~~ 44 (289)
T PRK07500 7 ADRSMIR---SAMKAPYLEREEEHALAYRWKDH---------------------------------------RDEDALHR 44 (289)
T ss_pred HHHHHHH---HHhcCCCCCHHHHHHHHHHHHHC---------------------------------------CCHHHHHH
Confidence 4578999 99999999999999999887531 24689999
Q ss_pred HHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 300 LIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 300 LI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
||..|+++|.++|++|.+.|.+.+||+|||++||+++
T Consensus 45 Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a 81 (289)
T PRK07500 45 IISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEA 81 (289)
T ss_pred HHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999993
No 15
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=98.78 E-value=1.6e-08 Score=98.34 Aligned_cols=77 Identities=19% Similarity=0.229 Sum_probs=70.2
Q ss_pred CCchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHH
Q 019233 217 LKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYC 296 (344)
Q Consensus 217 ~~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~A 296 (344)
..|.+..|+. +++..|+||+++|.+|...++.+ +..|
T Consensus 51 ~~~~~~~y~~---~~~~~~~l~~~ee~~li~~~~~G----------------------------------------d~~A 87 (325)
T PRK05657 51 VLDATQLYLN---EIGYSPLLTAEEEVYFARRALRG----------------------------------------DFAA 87 (325)
T ss_pred cccHHHHHHH---HHhcCCCCCHHHHHHHHHHHHcC----------------------------------------CHHH
Confidence 4678899999 99999999999999998887752 4678
Q ss_pred HHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 297 RdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
.++||..|.++|.++|++|.+.+.+.+||+|+|++||+++
T Consensus 88 ~~~Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~a 127 (325)
T PRK05657 88 RQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRA 127 (325)
T ss_pred HHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999984
No 16
>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=98.66 E-value=5.3e-08 Score=90.52 Aligned_cols=67 Identities=24% Similarity=0.193 Sum_probs=59.5
Q ss_pred cCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHHHHHHHHhchHHHH
Q 019233 230 NSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVL 309 (344)
Q Consensus 230 ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~ARdrLI~sNLRLVv 309 (344)
+..++|+||+++|.+|...++.+ +..+.++|+..|+++|.
T Consensus 9 ~~~~~~~l~~~~~~~li~~~~~g----------------------------------------d~~a~~~L~~~~~~~v~ 48 (254)
T TIGR02850 9 NTSKLPVLKNQEMRELFIRMQSG----------------------------------------DTTAREKLINGNLRLVL 48 (254)
T ss_pred cccCCCCCCHHHHHHHHHHHHcC----------------------------------------CHHHHHHHHHHhHHHHH
Confidence 45788999999998887776642 35789999999999999
Q ss_pred HHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 310 FLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 310 sIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
++|++|.+.+.+.+||+|+|++||+++
T Consensus 49 ~~a~~~~~~~~~aeDlvQe~~i~l~~a 75 (254)
T TIGR02850 49 SVIQRFNNRGEYVDDLFQVGCIGLMKS 75 (254)
T ss_pred HHHHHHhCCCCCHHHHHHHHHHHHHHH
Confidence 999999999999999999999999993
No 17
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=98.66 E-value=2.6e-08 Score=94.58 Aligned_cols=50 Identities=32% Similarity=0.381 Sum_probs=43.7
Q ss_pred HHHHhhhh-HHHHHHHHHhchHHHHHHHHhcCCCCC-ChhhHHHHHHHHHhhh
Q 019233 286 LKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGI-PFSDLLQVSRHALAFI 336 (344)
Q Consensus 286 L~~~l~~g-~~ARdrLI~sNLRLVvsIAKrY~grGl-s~eDLIQEG~iGLmka 336 (344)
+...++.| ..+| +||+.|+|||.+||++|.++|. .++||||.|+||||+|
T Consensus 14 ~~~~~~~g~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~A 65 (247)
T COG1191 14 LLEYYAEGDEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKA 65 (247)
T ss_pred HHHHHHhcCHHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHH
Confidence 33444444 7788 9999999999999999999998 9999999999999995
No 18
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=98.65 E-value=7.3e-08 Score=91.14 Aligned_cols=77 Identities=21% Similarity=0.279 Sum_probs=69.9
Q ss_pred CCchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHH
Q 019233 217 LKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYC 296 (344)
Q Consensus 217 ~~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~A 296 (344)
..|.+..||. +|...|.|+.++|.+|...++.+ ...|
T Consensus 11 ~~~~~~~~~~---~~~~~~~~~~~~~~~li~~~~~g----------------------------------------d~~a 47 (285)
T TIGR02394 11 VADVTQLYLR---EIGFKPLLTAEEEIAYARRALAG----------------------------------------DFEA 47 (285)
T ss_pred cchHHHHHHH---HHhccCCCCHHHHHHHHHHHHcC----------------------------------------CHHH
Confidence 3578899999 99999999999999998887753 3678
Q ss_pred HHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 297 RdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
.+.||..+.++|..+|.+|.+.+...+||+|+|++||+++
T Consensus 48 ~~~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a 87 (285)
T TIGR02394 48 RKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHA 87 (285)
T ss_pred HHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999983
No 19
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=98.60 E-value=7e-08 Score=90.24 Aligned_cols=44 Identities=25% Similarity=0.270 Sum_probs=40.5
Q ss_pred hHHHHHHHHHhchHHHHHHHHhcCCC-CCChhhHHHHHHHHHhhh
Q 019233 293 GWYCREELIKSTRPLVLFLARNYRGL-GIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 293 g~~ARdrLI~sNLRLVvsIAKrY~gr-Gls~eDLIQEG~iGLmka 336 (344)
+..++++||..|++||.+||++|.++ +.+++||||+|+||||+|
T Consensus 23 d~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a 67 (256)
T PRK07408 23 SIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRA 67 (256)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHH
Confidence 36899999999999999999999876 778999999999999994
No 20
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=98.60 E-value=1.1e-07 Score=88.59 Aligned_cols=67 Identities=24% Similarity=0.210 Sum_probs=58.9
Q ss_pred cCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHHHHHHHHhchHHHH
Q 019233 230 NSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVL 309 (344)
Q Consensus 230 ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~ARdrLI~sNLRLVv 309 (344)
+..+.|+|+++|+..|...++.+ +..++++||..|+++|.
T Consensus 12 ~~~~~~~l~~~~~~~l~~~~~~g----------------------------------------d~~a~~~l~~~~~~~v~ 51 (258)
T PRK08215 12 NTSKLPVLKNEEMRELFERMQNG----------------------------------------DKEAREKLINGNLRLVL 51 (258)
T ss_pred cCCCCCCCCHHHHHHHHHHHHcC----------------------------------------CHHHHHHHHHHHHHHHH
Confidence 44677899999998887776632 46789999999999999
Q ss_pred HHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 310 FLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 310 sIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
.+|++|.+.+.+.+||+|+|++||+++
T Consensus 52 ~~a~~~~~~~~~aeDlvQe~~i~l~~a 78 (258)
T PRK08215 52 SVIQRFNNRGENVDDLFQVGCIGLMKA 78 (258)
T ss_pred HHHHHHhCCCCCHHHHHHHHHHHHHHH
Confidence 999999999999999999999999993
No 21
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=98.40 E-value=5e-07 Score=84.73 Aligned_cols=44 Identities=23% Similarity=0.144 Sum_probs=39.2
Q ss_pred hHHHHHHHHHhchHHHHHHHHhcCC---CCCChhhHHHHHHHHHhhh
Q 019233 293 GWYCREELIKSTRPLVLFLARNYRG---LGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 293 g~~ARdrLI~sNLRLVvsIAKrY~g---rGls~eDLIQEG~iGLmka 336 (344)
+..||++||..|++||.+||++|.+ .+++++||+|+|+|||++|
T Consensus 21 ~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~a 67 (257)
T PRK05911 21 EIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRA 67 (257)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHH
Confidence 4679999999999999999999862 3567999999999999994
No 22
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=98.36 E-value=1e-06 Score=82.56 Aligned_cols=67 Identities=24% Similarity=0.209 Sum_probs=57.6
Q ss_pred CCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHHHHHHHHhchHHHHH
Q 019233 231 SRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLF 310 (344)
Q Consensus 231 i~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~ARdrLI~sNLRLVvs 310 (344)
.++.|+||.++|.+|...++.. .+..+.+.++..|++||..
T Consensus 6 ~~~~~~~~~~~e~~l~~~~~~~---------------------------------------~d~~a~~~l~~~y~~lv~~ 46 (268)
T PRK06288 6 SGKIPKYAQQDETELWREYKKT---------------------------------------GDPKIREYLILKYSPLVKY 46 (268)
T ss_pred cCCCccccchHHHHHHHHHHHc---------------------------------------CCHHHHHHHHHHHHHHHHH
Confidence 4789999999999998877642 1467899999999999999
Q ss_pred HHHhcC-C--CCCChhhHHHHHHHHHhhh
Q 019233 311 LARNYR-G--LGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 311 IAKrY~-g--rGls~eDLIQEG~iGLmka 336 (344)
+|++|. + .+.+.+||+|+|++||+++
T Consensus 47 ~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a 75 (268)
T PRK06288 47 VAGRIAVGMPQNVEFDDLVSYGVFGLIDA 75 (268)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHHHHHHHH
Confidence 999986 2 5678999999999999993
No 23
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=98.22 E-value=4.5e-06 Score=76.49 Aligned_cols=74 Identities=15% Similarity=0.107 Sum_probs=64.1
Q ss_pred hHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHHHHH
Q 019233 220 PTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREE 299 (344)
Q Consensus 220 pl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~ARdr 299 (344)
.+.+|+. ++++.|+||+++|..|...++.+ +..+.+.
T Consensus 17 ~~~~~~~---~~~~~~~~~~~~e~~l~~~~~~g----------------------------------------d~~a~~~ 53 (233)
T PRK05803 17 FLVSYVK---NNSFPQPLSEEEERKYLELMKEG----------------------------------------DEEARNI 53 (233)
T ss_pred HHHHHHH---HhcccCCCCHHHHHHHHHHHHcC----------------------------------------CHHHHHH
Confidence 3578888 88888999999988876665531 4678999
Q ss_pred HHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 300 LIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 300 LI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
|+..+.++|..+|.+|.+.+.+.+||+|||.+||+++
T Consensus 54 l~~~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~ 90 (233)
T PRK05803 54 LIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKA 90 (233)
T ss_pred HHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999995
No 24
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=98.14 E-value=5.7e-06 Score=76.66 Aligned_cols=42 Identities=29% Similarity=0.242 Sum_probs=40.7
Q ss_pred HHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 294 ~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
..|.++|+..|.++|..+|++|.+.+...+||+|+|++||++
T Consensus 28 ~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~ 69 (255)
T TIGR02941 28 GEAQEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLG 69 (255)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHH
Confidence 678999999999999999999999999999999999999998
No 25
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPro: IPR009042 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....
Probab=98.01 E-value=2.1e-06 Score=59.62 Aligned_cols=35 Identities=11% Similarity=0.088 Sum_probs=30.9
Q ss_pred CchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHH
Q 019233 218 KQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANL 255 (344)
Q Consensus 218 ~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~L 255 (344)
+|++..||+ +++++||||++||++|+++|+.+...
T Consensus 1 ~D~l~~Yl~---ei~~~~LLt~eeE~~LA~~i~~g~~~ 35 (37)
T PF00140_consen 1 SDSLRLYLK---EIGRYPLLTAEEEIELARRIRKGDEA 35 (37)
T ss_dssp HHHHHHHHH---HHHHS-EETTHHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHH---HHcCCCCCCHHHHHHHHHHHHHhHHh
Confidence 378999999 99999999999999999999998654
No 26
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=98.00 E-value=1.8e-05 Score=73.49 Aligned_cols=44 Identities=30% Similarity=0.199 Sum_probs=41.3
Q ss_pred hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 293 g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
+..|.++|+..|.++|..+|++|.+.+...+||+|+|++||+++
T Consensus 27 d~~a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~l~l~~~ 70 (257)
T PRK08583 27 DEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGA 70 (257)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHH
Confidence 36789999999999999999999999999999999999999983
No 27
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=97.86 E-value=1.6e-05 Score=73.74 Aligned_cols=42 Identities=19% Similarity=0.081 Sum_probs=37.5
Q ss_pred HHHHHHHHhchHHHHHHHHhcCCC---CCChhhHHHHHHHHHhhh
Q 019233 295 YCREELIKSTRPLVLFLARNYRGL---GIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 295 ~ARdrLI~sNLRLVvsIAKrY~gr---Gls~eDLIQEG~iGLmka 336 (344)
.-+..+|..|+|||.++|++|.++ +++.+||||+|++||++|
T Consensus 15 ~~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a 59 (231)
T PRK12427 15 QEEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEA 59 (231)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHH
Confidence 456789999999999999999854 579999999999999994
No 28
>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=97.84 E-value=2.7e-05 Score=70.92 Aligned_cols=45 Identities=22% Similarity=0.226 Sum_probs=42.4
Q ss_pred hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 292 FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 292 ~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
.+..+.++|+..|.++|.++|++|.+.+.+.+||+|+|.+||+++
T Consensus 8 gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a 52 (231)
T TIGR02885 8 GDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKA 52 (231)
T ss_pred CCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHH
Confidence 357899999999999999999999999999999999999999994
No 29
>PRK05572 sporulation sigma factor SigF; Validated
Probab=97.77 E-value=7.5e-05 Score=69.39 Aligned_cols=67 Identities=19% Similarity=0.176 Sum_probs=57.7
Q ss_pred cCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHHHHHHHHhchHHHH
Q 019233 230 NSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVL 309 (344)
Q Consensus 230 ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~ARdrLI~sNLRLVv 309 (344)
+-...|.||.+++.+|...++. .+..+.++|+..|.++|.
T Consensus 7 ~~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~y~~~v~ 46 (252)
T PRK05572 7 NKKKKPQLKDEENKELIKKSQD----------------------------------------GDQEARDTLVEKNLRLVW 46 (252)
T ss_pred cCcCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHH
Confidence 5577899999988887655442 135789999999999999
Q ss_pred HHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 310 FLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 310 sIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
.+|.+|.+.+...+||+|||.++|+++
T Consensus 47 ~~a~~~~~~~~~aeDl~Qe~~l~l~~~ 73 (252)
T PRK05572 47 SVVQRFLNRGYEPDDLFQIGCIGLLKA 73 (252)
T ss_pred HHHHHHccCCCCHHHHHHHHHHHHHHH
Confidence 999999999999999999999999983
No 30
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=97.37 E-value=0.0003 Score=65.39 Aligned_cols=52 Identities=19% Similarity=0.120 Sum_probs=44.0
Q ss_pred HHHHHHhhh--hHHHHHHHHHhchHHHHHHHHhcCC---CCCChhhHHHHHHHHHhh
Q 019233 284 RVLKQHLAF--GWYCREELIKSTRPLVLFLARNYRG---LGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 284 ~eL~~~l~~--g~~ARdrLI~sNLRLVvsIAKrY~g---rGls~eDLIQEG~iGLmk 335 (344)
.+|.+++.. +..|.++|+..|.++|..+|.+|.+ .+...+||+|+|++||++
T Consensus 9 ~~l~~~~~~~~d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~ 65 (251)
T PRK07670 9 QKLWDRWKEERDPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYD 65 (251)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHH
Confidence 445555332 4789999999999999999999965 678999999999999999
No 31
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=96.97 E-value=0.0035 Score=57.48 Aligned_cols=44 Identities=20% Similarity=0.277 Sum_probs=40.8
Q ss_pred hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 293 g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
+..+-+.|+..|.++|..+|.+|.+...+.+||+||+.++++++
T Consensus 46 d~~af~~l~~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~ 89 (227)
T TIGR02846 46 DEEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKA 89 (227)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHH
Confidence 46788999999999999999999999999999999999999983
No 32
>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=96.68 E-value=0.0023 Score=46.87 Aligned_cols=36 Identities=31% Similarity=0.234 Sum_probs=34.6
Q ss_pred HHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 300 LIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 300 LI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
|++.+.++|..+|.+|.+.+.+.+|++||+.++|++
T Consensus 1 L~~~~~~~l~~~~~~~~~~~~~~eD~~qe~~~~l~~ 36 (71)
T PF04542_consen 1 LYERYYPLLYRYARRYTGDPEDAEDLVQEAFIKLWR 36 (71)
T ss_dssp HHHHTHHHHHHHHHTCTTCSSHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHhCCHhhHHHHhhHHHHHHHh
Confidence 688999999999999999999999999999999997
No 33
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=96.63 E-value=0.0088 Score=54.68 Aligned_cols=43 Identities=28% Similarity=0.434 Sum_probs=40.7
Q ss_pred hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 293 g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
+..+.+.|+..+.++|..+|.+|.+.+..-+||+||+.+++++
T Consensus 50 d~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~ 92 (234)
T PRK08301 50 DEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIK 92 (234)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHH
Confidence 4678999999999999999999999999999999999999998
No 34
>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=96.61 E-value=0.0051 Score=47.29 Aligned_cols=40 Identities=25% Similarity=0.367 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhh
Q 019233 253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAF 292 (344)
Q Consensus 253 ~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~ 292 (344)
.++.+++.+|+..+||+||.+|+|+.+|++.+++...+..
T Consensus 4 ~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~ 43 (78)
T PF04539_consen 4 RKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQA 43 (78)
T ss_dssp HHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHh
Confidence 4567788899999999999999999999999988766653
No 35
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=96.56 E-value=0.0022 Score=67.63 Aligned_cols=35 Identities=17% Similarity=0.192 Sum_probs=32.7
Q ss_pred CCchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHH
Q 019233 217 LKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVAN 254 (344)
Q Consensus 217 ~~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~ 254 (344)
-+|||.+||| +|+..||||+|+|++||++|..|.+
T Consensus 102 t~DPVRMYLR---EMG~V~LLTREgEIeIAKRIE~G~~ 136 (619)
T PRK05658 102 TDDPVRMYLR---EMGTVELLTREGEIEIAKRIEAGEN 136 (619)
T ss_pred CCChHHHHHH---HhccCcCCCcHHHHHHHHHHHHHHH
Confidence 4799999999 9999999999999999999998764
No 36
>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=96.43 E-value=0.011 Score=54.41 Aligned_cols=44 Identities=25% Similarity=0.416 Sum_probs=41.4
Q ss_pred hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 293 g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
+..+.+.++..+.+.|..+|.+|.+.+.+-+||+||+.+++++.
T Consensus 50 d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~ 93 (234)
T TIGR02835 50 DESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKA 93 (234)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHH
Confidence 47899999999999999999999999999999999999999983
No 37
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=96.05 E-value=0.01 Score=51.38 Aligned_cols=52 Identities=13% Similarity=-0.048 Sum_probs=44.7
Q ss_pred HHHHHhhh-hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 285 VLKQHLAF-GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 285 eL~~~l~~-g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
.|...+.. ...+-++++..+.++|..+|.+|.+...+.+|++|++.++|++.
T Consensus 7 ~li~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~ 59 (187)
T PRK09641 7 RLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVN 59 (187)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence 34444443 47789999999999999999999999999999999999999984
No 38
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=95.94 E-value=0.012 Score=51.44 Aligned_cols=54 Identities=19% Similarity=0.030 Sum_probs=46.2
Q ss_pred CHHHHHHHhh-hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 282 SERVLKQHLA-FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 282 d~~eL~~~l~-~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
+.+.|...+. .+..+-+.|+..+.++|..+|.+|.+.+.+-+|++||+.++|++
T Consensus 6 ~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~ 60 (186)
T PRK05602 6 PDEELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWK 60 (186)
T ss_pred cHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
Confidence 3444544444 45889999999999999999999999999999999999999997
No 39
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=95.88 E-value=0.022 Score=50.33 Aligned_cols=54 Identities=22% Similarity=0.103 Sum_probs=46.1
Q ss_pred CHHHHHHHhh-hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 282 SERVLKQHLA-FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 282 d~~eL~~~l~-~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
+...|...+. .+..+-+.|+..+.++|..+|.+|.+.....+||+|++.++|++
T Consensus 10 ~~~~l~~~~~~~d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~ 64 (208)
T PRK08295 10 EDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYK 64 (208)
T ss_pred ChHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHH
Confidence 3444554444 44789999999999999999999999999999999999999987
No 40
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=95.75 E-value=0.02 Score=52.50 Aligned_cols=44 Identities=14% Similarity=-0.053 Sum_probs=40.7
Q ss_pred hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 293 g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
+..+-+.|+..|.++|..+|.+|.+.+..-+||+||+.++|++.
T Consensus 28 d~~a~~~l~~~y~~~l~~~a~~~~~~~~~AEDlvQE~fi~l~~~ 71 (231)
T PRK11922 28 DEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRA 71 (231)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHH
Confidence 46788899999999999999999999999999999999999983
No 41
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=95.65 E-value=0.032 Score=48.88 Aligned_cols=55 Identities=22% Similarity=0.166 Sum_probs=47.3
Q ss_pred CCHHHHHHHhhhh-HHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 281 VSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 281 ld~~eL~~~l~~g-~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
|+.++|...+..| ..+-++|+..+.+.|..+|.+|.+...+.+||+||+.+.+.+
T Consensus 4 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~ 59 (198)
T TIGR02859 4 LEDEEIVELARQGNTHALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYK 59 (198)
T ss_pred cchHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHH
Confidence 3445555665554 789999999999999999999999999999999999999988
No 42
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=95.45 E-value=0.034 Score=52.57 Aligned_cols=53 Identities=23% Similarity=0.212 Sum_probs=44.0
Q ss_pred HHHHHHhhhh-HHHHHHHHHhchHHHHHHHHhcCCCCC--ChhhHHHHHHHHHhhh
Q 019233 284 RVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGI--PFSDLLQVSRHALAFI 336 (344)
Q Consensus 284 ~eL~~~l~~g-~~ARdrLI~sNLRLVvsIAKrY~grGl--s~eDLIQEG~iGLmka 336 (344)
..|...+..| ..|.++|+..+.++|..+|.+|.++.. ..+|++|+|.++++++
T Consensus 6 ~~Li~~~~~gD~~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~ea 61 (237)
T PRK08311 6 EDILEKIKNGDEELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEA 61 (237)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHH
Confidence 3444444444 779999999999999999999988776 4899999999999984
No 43
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=95.44 E-value=0.021 Score=49.50 Aligned_cols=45 Identities=11% Similarity=-0.112 Sum_probs=41.8
Q ss_pred hhhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 291 AFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 291 ~~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
.....+-.+|+..+.++|..+|.+|.+.+.+.+|++|++.+++++
T Consensus 14 ~gd~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~ 58 (187)
T TIGR02948 14 KGDENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYT 58 (187)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHH
Confidence 345778999999999999999999999999999999999999998
No 44
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=95.27 E-value=0.028 Score=49.53 Aligned_cols=54 Identities=11% Similarity=-0.057 Sum_probs=46.4
Q ss_pred HHHHHHHhhh-hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 283 ERVLKQHLAF-GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 283 ~~eL~~~l~~-g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
...|...+.. +..+.+.|+..+.+.|..+|.+|.+...+.+|++|++.++|++.
T Consensus 13 ~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~ 67 (194)
T PRK12513 13 DEALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRA 67 (194)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence 4445555554 48899999999999999999999999889999999999999984
No 45
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=95.26 E-value=0.056 Score=47.45 Aligned_cols=52 Identities=23% Similarity=0.210 Sum_probs=42.4
Q ss_pred HHHHHhhh-hHHHHHHHHHhchHHHHHHHHhcCCC----CCChhhHHHHHHHHHhhh
Q 019233 285 VLKQHLAF-GWYCREELIKSTRPLVLFLARNYRGL----GIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 285 eL~~~l~~-g~~ARdrLI~sNLRLVvsIAKrY~gr----Gls~eDLIQEG~iGLmka 336 (344)
.|...+.. ...+-++|+..+.+.|..+|.+|.+. +.+.+|++||+.++|++.
T Consensus 13 ~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~ 69 (189)
T PRK09648 13 ALVAEAVAGDRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITA 69 (189)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHH
Confidence 34444444 47899999999999999999988643 468999999999999984
No 46
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=95.02 E-value=0.043 Score=47.80 Aligned_cols=55 Identities=20% Similarity=0.001 Sum_probs=46.6
Q ss_pred CHHHHHHHhh-hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 282 SERVLKQHLA-FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 282 d~~eL~~~l~-~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
+.++|...+. ....+-+.++..+.+.|..+|++|.+.+..-+|++||+.+.|.+.
T Consensus 9 ~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~ 64 (186)
T PRK13919 9 SDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKK 64 (186)
T ss_pred CHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHh
Confidence 3455555553 447899999999999999999999999999999999999999874
No 47
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=94.80 E-value=0.066 Score=47.15 Aligned_cols=55 Identities=15% Similarity=0.154 Sum_probs=48.5
Q ss_pred CCHHHHHHHhhh----hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 281 VSERVLKQHLAF----GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 281 ld~~eL~~~l~~----g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
++.+.|...++. +..+-+.|+..+.+.|..+|.+|.+....-+|++|++.+.|++
T Consensus 8 ~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~ 66 (188)
T PRK09640 8 LNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLY 66 (188)
T ss_pred CCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHH
Confidence 455666666663 5889999999999999999999999999999999999999987
No 48
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=94.73 E-value=0.07 Score=45.97 Aligned_cols=54 Identities=13% Similarity=-0.111 Sum_probs=45.4
Q ss_pred CHHHHHHHhh-hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 282 SERVLKQHLA-FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 282 d~~eL~~~l~-~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
+...+..... .+..+-+.|+..+.+.|..+|.+|.+....-+|++||+.+.+++
T Consensus 4 ~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~ 58 (176)
T PRK09638 4 DEKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIE 58 (176)
T ss_pred cHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHH
Confidence 3444444443 34789999999999999999999999888999999999999987
No 49
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=94.32 E-value=0.075 Score=46.72 Aligned_cols=54 Identities=22% Similarity=-0.040 Sum_probs=45.6
Q ss_pred HHHHHHHhhh-hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 283 ERVLKQHLAF-GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 283 ~~eL~~~l~~-g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
..+|..++.. +..+-+.|+..+.+.|..+|++|.+....-+|++|++.+++++.
T Consensus 16 ~~~l~~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~ 70 (194)
T PRK12519 16 DAELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK 70 (194)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh
Confidence 3445554444 47899999999999999999999998888999999999999863
No 50
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=94.22 E-value=0.097 Score=45.99 Aligned_cols=51 Identities=12% Similarity=-0.086 Sum_probs=43.7
Q ss_pred HHHHHhhh-hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 285 VLKQHLAF-GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 285 eL~~~l~~-g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
.|...+.. ...+-++|+..|.+.|..+|++|.+.....+|++|++.+.+++
T Consensus 9 ~ll~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~ 60 (193)
T PRK11923 9 QLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYR 60 (193)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHH
Confidence 34444444 4789999999999999999999998888999999999999988
No 51
>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=93.93 E-value=0.11 Score=45.09 Aligned_cols=51 Identities=14% Similarity=-0.003 Sum_probs=44.0
Q ss_pred HHHHHhhh-hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 285 VLKQHLAF-GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 285 eL~~~l~~-g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
.|...+.. +..+-+.|+..+.+.|..+|.++.+....-+||+||+.++|.+
T Consensus 9 ~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~ 60 (190)
T TIGR02939 9 ELVERVQRGEKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYR 60 (190)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHH
Confidence 34444443 4778999999999999999999999889999999999999987
No 52
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=93.88 E-value=0.11 Score=46.15 Aligned_cols=52 Identities=17% Similarity=-0.107 Sum_probs=45.2
Q ss_pred HHHHHHhhh-hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 284 RVLKQHLAF-GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 284 ~eL~~~l~~-g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
..|...+.. +..+-++|+..|-++|..+|.+|.+....-+|++||+.+.+.+
T Consensus 18 ~~li~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~ 70 (194)
T PRK09646 18 DALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWR 70 (194)
T ss_pred HHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHH
Confidence 444444444 4789999999999999999999999999999999999999987
No 53
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=93.83 E-value=0.17 Score=44.75 Aligned_cols=56 Identities=11% Similarity=-0.044 Sum_probs=45.9
Q ss_pred CCHHHHHHHhhhh-HHHHHHHHHhchHHHHHHHHhcCCCC---CChhhHHHHHHHHHhhh
Q 019233 281 VSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLG---IPFSDLLQVSRHALAFI 336 (344)
Q Consensus 281 ld~~eL~~~l~~g-~~ARdrLI~sNLRLVvsIAKrY~grG---ls~eDLIQEG~iGLmka 336 (344)
++.+.|...+..| ..+-++|+..+.++|..+|.+|.+.+ ..-+|++|++.++|++.
T Consensus 3 ~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~ 62 (189)
T PRK06811 3 INEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNN 62 (189)
T ss_pred CcHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHh
Confidence 4455666666554 77999999999999999999998754 35799999999999984
No 54
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=93.59 E-value=0.13 Score=43.67 Aligned_cols=45 Identities=20% Similarity=-0.038 Sum_probs=41.7
Q ss_pred hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 292 FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 292 ~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
.+..+-+.++..+.+.|..+|+++.+...+-+||+|++.+.|+..
T Consensus 10 ~~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~ 54 (179)
T PRK11924 10 GDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRK 54 (179)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHH
Confidence 457899999999999999999999999999999999999999874
No 55
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=93.47 E-value=0.14 Score=45.40 Aligned_cols=54 Identities=22% Similarity=0.055 Sum_probs=47.0
Q ss_pred CHHHHHHHhhhh-HHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 282 SERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 282 d~~eL~~~l~~g-~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
+...|...+..| ..+-+.|+..+-+.|..+|.+|.+....-+|++||+.+.|.+
T Consensus 12 ~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~ 66 (196)
T PRK12524 12 SDEALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWR 66 (196)
T ss_pred CHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHH
Confidence 445566666554 789999999999999999999999999999999999999987
No 56
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=93.11 E-value=0.14 Score=44.78 Aligned_cols=47 Identities=13% Similarity=-0.042 Sum_probs=42.4
Q ss_pred hhhhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 290 LAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 290 l~~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
...+..+-+.|+..+.++|..+|.+|.+....-+|++||..+.+++.
T Consensus 20 ~~~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~ 66 (187)
T PRK12534 20 AGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHK 66 (187)
T ss_pred HcCCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhc
Confidence 33457899999999999999999999999899999999999999983
No 57
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=92.97 E-value=0.16 Score=44.06 Aligned_cols=52 Identities=10% Similarity=-0.128 Sum_probs=44.2
Q ss_pred HHHHHHhh-hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 284 RVLKQHLA-FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 284 ~eL~~~l~-~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
..|..... .+..+-++|+..+.+.|..+|.+|.+....-+|++||+.+.+.+
T Consensus 7 ~~li~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~ 59 (179)
T PRK12514 7 EKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWT 59 (179)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHH
Confidence 33444433 34789999999999999999999999989999999999999987
No 58
>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=92.01 E-value=0.31 Score=41.93 Aligned_cols=52 Identities=17% Similarity=-0.030 Sum_probs=44.3
Q ss_pred HHHHHHhh-hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 284 RVLKQHLA-FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 284 ~eL~~~l~-~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
++|...+. .+..+-+.++..+.+.+..+|.+|.+...+-+|++||..+-+.+
T Consensus 4 ~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~ 56 (169)
T TIGR02954 4 EELVKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYL 56 (169)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHH
Confidence 34444443 45789999999999999999999999999999999999999886
No 59
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=91.34 E-value=0.34 Score=40.72 Aligned_cols=41 Identities=10% Similarity=-0.045 Sum_probs=35.2
Q ss_pred HHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 295 ~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
.+-+.|+..+.++|..+++++.+ ..+.+|++||+.++++++
T Consensus 4 ~af~~l~~~y~~~l~~~~~~~~~-~~~aeDi~Qe~~l~l~~~ 44 (154)
T PRK06759 4 ATFTEAVVLYEGLIVNQIKKLGI-YQDYEEYYQCGLIGLWHA 44 (154)
T ss_pred ccHHHHHHHHHHHHHHHHHHhCC-cccHHHHHHHHHHHHHHH
Confidence 45567999999999999999854 468899999999999984
No 60
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=90.49 E-value=0.52 Score=41.94 Aligned_cols=54 Identities=20% Similarity=0.087 Sum_probs=46.2
Q ss_pred CHHHHHHHhh-hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 282 SERVLKQHLA-FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 282 d~~eL~~~l~-~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
+.+.+...+. .+..+-+.++..+.+.|..+|.++.+....-+|++||..+-+++
T Consensus 13 ~~~~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~ 67 (192)
T PRK09643 13 SDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHR 67 (192)
T ss_pred CHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHH
Confidence 3455555554 45889999999999999999999999988999999999999997
No 61
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=89.70 E-value=0.94 Score=39.47 Aligned_cols=44 Identities=18% Similarity=0.067 Sum_probs=38.2
Q ss_pred hhHHHHHHHHHhchHHHHHHHHhcCCC----CCChhhHHHHHHHHHhh
Q 019233 292 FGWYCREELIKSTRPLVLFLARNYRGL----GIPFSDLLQVSRHALAF 335 (344)
Q Consensus 292 ~g~~ARdrLI~sNLRLVvsIAKrY~gr----Gls~eDLIQEG~iGLmk 335 (344)
.+..+.++|+..+-+.|..+|.+|.++ ...-+|++||+.+.+..
T Consensus 19 gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~ 66 (184)
T PRK12512 19 GDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHL 66 (184)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHH
Confidence 458899999999999999999988652 35799999999999875
No 62
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=89.33 E-value=0.67 Score=41.11 Aligned_cols=51 Identities=8% Similarity=-0.096 Sum_probs=43.5
Q ss_pred HHHHHhh-hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 285 VLKQHLA-FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 285 eL~~~l~-~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
+|..++. .+..+-+.|+..+.+.|..+|.+|.+....-+|++||..+.+.+
T Consensus 16 ~li~~~~~~d~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~ 67 (194)
T PRK12531 16 ECMEKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQ 67 (194)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHH
Confidence 3444444 34778999999999999999999998888899999999999988
No 63
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=88.97 E-value=0.52 Score=41.46 Aligned_cols=54 Identities=11% Similarity=-0.057 Sum_probs=46.0
Q ss_pred CHHHHHHHhh-hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 282 SERVLKQHLA-FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 282 d~~eL~~~l~-~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
+...|...+. .+..+-+.|+..+.+.+..+|.+|.+....-+|++||+.+.+++
T Consensus 8 ~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~ 62 (189)
T PRK12515 8 TDEMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWR 62 (189)
T ss_pred CHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHH
Confidence 4455555555 45779999999999999999999998888999999999999987
No 64
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=88.94 E-value=0.73 Score=42.95 Aligned_cols=52 Identities=15% Similarity=-0.022 Sum_probs=44.2
Q ss_pred HHHHHHhhh-hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 284 RVLKQHLAF-GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 284 ~eL~~~l~~-g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
.+|...+.. +..+-++|+..+.+.|..++.+|.+....-+|++||..+.+++
T Consensus 51 ~~Li~~~~~gd~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~ 103 (233)
T PRK12538 51 EELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWT 103 (233)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
Confidence 344444444 4779999999999999999999998888899999999999987
No 65
>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=88.86 E-value=0.82 Score=38.82 Aligned_cols=44 Identities=9% Similarity=-0.158 Sum_probs=40.0
Q ss_pred hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 292 FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 292 ~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
.+..+-+.|+..+.+.+..++.++.+....-+|++||+.+.+++
T Consensus 8 ~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~ 51 (170)
T TIGR02952 8 REEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLR 51 (170)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHH
Confidence 35788999999999999999988888888999999999999998
No 66
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=87.98 E-value=1.1 Score=39.29 Aligned_cols=52 Identities=12% Similarity=-0.090 Sum_probs=44.7
Q ss_pred HHHHHHhh-hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 284 RVLKQHLA-FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 284 ~eL~~~l~-~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
.+|..... .+..+-+.|+..+-+.+..+|.++.+....-+|++||..+.+++
T Consensus 11 ~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~ 63 (182)
T PRK12537 11 EACLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWT 63 (182)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHh
Confidence 34444444 45889999999999999999999999988999999999999987
No 67
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=86.81 E-value=1.4 Score=42.52 Aligned_cols=41 Identities=20% Similarity=0.204 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhh
Q 019233 253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFG 293 (344)
Q Consensus 253 ~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g 293 (344)
.+++.+..+|+.++||+||..|+|+..|++.+++...+..+
T Consensus 110 ~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~ 150 (247)
T COG1191 110 RRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAI 150 (247)
T ss_pred HHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHh
Confidence 34556778899999999999999999999988776655443
No 68
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=85.49 E-value=2.4 Score=37.14 Aligned_cols=51 Identities=12% Similarity=-0.073 Sum_probs=41.2
Q ss_pred HHHHHhhh-hHHHHHHHHHhchHHHHHHHH----hcCCCCCChhhHHHHHHHHHhh
Q 019233 285 VLKQHLAF-GWYCREELIKSTRPLVLFLAR----NYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 285 eL~~~l~~-g~~ARdrLI~sNLRLVvsIAK----rY~grGls~eDLIQEG~iGLmk 335 (344)
.|..+... +..+-+.|+..+.+.|..+|. +|.+...+-+|++|+..+.|++
T Consensus 10 ~l~~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~ 65 (184)
T PRK12539 10 ALMLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHT 65 (184)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHH
Confidence 34444443 367899999999999999876 5667778899999999999998
No 69
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=84.63 E-value=1.4 Score=39.68 Aligned_cols=44 Identities=11% Similarity=-0.039 Sum_probs=40.5
Q ss_pred hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 292 FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 292 ~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
.+..+-++|+..+.++|..+|.+|.+....-+|++|++.+.+++
T Consensus 35 ~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~ 78 (206)
T PRK12526 35 RDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWR 78 (206)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHH
Confidence 45778899999999999999999988878899999999999988
No 70
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=84.43 E-value=2.7 Score=39.63 Aligned_cols=37 Identities=19% Similarity=0.240 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHH
Q 019233 253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH 289 (344)
Q Consensus 253 ~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~ 289 (344)
.++.+.+.+|...+|++||.++.|+.+|++++++...
T Consensus 113 ~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~ 149 (256)
T PRK07408 113 RQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEI 149 (256)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHH
Confidence 3455667788899999999999999999998887664
No 71
>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=83.22 E-value=1.2 Score=41.96 Aligned_cols=17 Identities=18% Similarity=0.024 Sum_probs=15.6
Q ss_pred CChhhHHHHHHHHHhhh
Q 019233 320 IPFSDLLQVSRHALAFI 336 (344)
Q Consensus 320 ls~eDLIQEG~iGLmka 336 (344)
.+.+||+|+|++||++|
T Consensus 36 ~e~dDlvQ~glial~eA 52 (218)
T TIGR02895 36 TKSDDELSIGLIAFNEA 52 (218)
T ss_pred CChhHHHHHHHHHHHHH
Confidence 57999999999999994
No 72
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=83.10 E-value=3.1 Score=36.39 Aligned_cols=47 Identities=17% Similarity=-0.027 Sum_probs=39.8
Q ss_pred HhhhhHHHHHHHHHhchHHHHHHHHhcC-CCCCChhhHHHHHHHHHhh
Q 019233 289 HLAFGWYCREELIKSTRPLVLFLARNYR-GLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 289 ~l~~g~~ARdrLI~sNLRLVvsIAKrY~-grGls~eDLIQEG~iGLmk 335 (344)
....+..+-++|+..+-+.|..+|.++. +....-+||+||+.+.|++
T Consensus 15 ~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~ 62 (181)
T PRK12536 15 GLAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHN 62 (181)
T ss_pred HHcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHH
Confidence 3344577889999999999999998765 4577899999999999987
No 73
>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=82.61 E-value=3.4 Score=38.66 Aligned_cols=37 Identities=16% Similarity=0.179 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHh
Q 019233 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (344)
Q Consensus 254 ~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l 290 (344)
++.+...++..++|++||.+|.|+.+|++++.+...+
T Consensus 121 ~~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~ 157 (254)
T TIGR02850 121 KALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFAL 157 (254)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 3445567788889999999999999999988776544
No 74
>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=82.38 E-value=3.8 Score=37.92 Aligned_cols=37 Identities=16% Similarity=0.256 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHh
Q 019233 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (344)
Q Consensus 254 ~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l 290 (344)
++.++...|...+|++||.+|.|+.+|++.+.+....
T Consensus 88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~ 124 (238)
T TIGR02393 88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVREIK 124 (238)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 4455667888889999999999999999988776643
No 75
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=82.31 E-value=2.4 Score=36.43 Aligned_cols=43 Identities=14% Similarity=-0.093 Sum_probs=37.7
Q ss_pred hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 292 FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 292 ~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
.+..+-+.++..+.+.|..+|.+|.+. .+-+|++||..+.+.+
T Consensus 8 gd~~a~~~l~~~~~~~l~~~~~~~~~~-~~aeDivQe~~l~l~~ 50 (175)
T PRK12518 8 GDRQSFRQLYRRYQQKVRSTLYQLCGR-ELLDDLVQEVFLRVWK 50 (175)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHcCH-hHHHHHHHHHHHHHHH
Confidence 347788999999999999999998754 5779999999999987
No 76
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=81.10 E-value=4.2 Score=38.66 Aligned_cols=37 Identities=22% Similarity=0.312 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHh
Q 019233 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (344)
Q Consensus 254 ~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l 290 (344)
++.+...+|...+|++||.+|.|+.+|++++++...+
T Consensus 128 ~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~ 164 (264)
T PRK07122 128 RLGRATAELSQRLGRAPTASELAAELGMDREEVVEGL 164 (264)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 3445567788889999999999999999988876644
No 77
>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=80.75 E-value=4.4 Score=35.08 Aligned_cols=51 Identities=16% Similarity=0.002 Sum_probs=42.1
Q ss_pred HHHHHhhh-hHHHHHHHHHhchHHHHHHHHhcCCCCC-----ChhhHHHHHHHHHhh
Q 019233 285 VLKQHLAF-GWYCREELIKSTRPLVLFLARNYRGLGI-----PFSDLLQVSRHALAF 335 (344)
Q Consensus 285 eL~~~l~~-g~~ARdrLI~sNLRLVvsIAKrY~grGl-----s~eDLIQEG~iGLmk 335 (344)
.|...+.. +..+-+.|+..+.+.+..+|.+|.+... .-+|++||..+.+.+
T Consensus 6 ~li~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~ 62 (183)
T TIGR02999 6 ELLQQWQNGDAAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSD 62 (183)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhh
Confidence 34444443 4678999999999999999999987766 789999999999986
No 78
>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=80.22 E-value=2.4 Score=35.93 Aligned_cols=43 Identities=16% Similarity=-0.045 Sum_probs=39.5
Q ss_pred hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 293 g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
+..+-+.|+..+.+.|..+|.++.+....-+|++|+..+-+..
T Consensus 4 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~ 46 (162)
T TIGR02983 4 TEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYV 46 (162)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHH
Confidence 4678889999999999999999999888999999999999877
No 79
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=80.17 E-value=4.4 Score=40.14 Aligned_cols=39 Identities=31% Similarity=0.466 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHh
Q 019233 252 VANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (344)
Q Consensus 252 l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l 290 (344)
..++.+++.+|...+|++||.+|.|+.+|++.+.+...+
T Consensus 172 ~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~ 210 (324)
T PRK07921 172 VNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLL 210 (324)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 334566777888899999999999999999987776543
No 80
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=80.08 E-value=4.2 Score=37.86 Aligned_cols=37 Identities=8% Similarity=0.134 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHh
Q 019233 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (344)
Q Consensus 254 ~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l 290 (344)
++.+....|...+|++||.+|.|+.+|++++++...+
T Consensus 102 ~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~ 138 (231)
T PRK12427 102 KTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYL 138 (231)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 3445567888889999999999999999988876554
No 81
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=79.22 E-value=2.3 Score=37.16 Aligned_cols=43 Identities=19% Similarity=-0.072 Sum_probs=40.0
Q ss_pred hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 293 g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
...|-++|+..+-+.|..+|.+|.+....-+|++|++.+.|++
T Consensus 14 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~ 56 (179)
T PRK09415 14 KEDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYK 56 (179)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
Confidence 4678899999999999999999998888899999999999988
No 82
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=78.65 E-value=5.6 Score=37.58 Aligned_cols=36 Identities=17% Similarity=0.200 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHh
Q 019233 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (344)
Q Consensus 255 LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l 290 (344)
+.+....|...+|++||.+|.|+.+|++++.+...+
T Consensus 112 l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~ 147 (257)
T PRK05911 112 LADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWF 147 (257)
T ss_pred HHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHH
Confidence 444556788888999999999999999988776543
No 83
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=76.83 E-value=5.2 Score=35.10 Aligned_cols=48 Identities=27% Similarity=0.097 Sum_probs=41.4
Q ss_pred hhhhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhhc
Q 019233 290 LAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFID 337 (344)
Q Consensus 290 l~~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka~ 337 (344)
......+-..++..+.+-+...|.++.|..-+-+||+||..+.+++..
T Consensus 10 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~ 57 (182)
T COG1595 10 LRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAI 57 (182)
T ss_pred HhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence 344577888899999999999999999887799999999999999843
No 84
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=76.19 E-value=6.6 Score=39.31 Aligned_cols=36 Identities=17% Similarity=0.261 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHH
Q 019233 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH 289 (344)
Q Consensus 254 ~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~ 289 (344)
++.+...+|...+|++||.+|.|+.+|++++.+...
T Consensus 217 ~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~ 252 (367)
T PRK09210 217 KLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREI 252 (367)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 345566788888999999999999999998777654
No 85
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=75.29 E-value=2.3 Score=39.06 Aligned_cols=27 Identities=22% Similarity=0.158 Sum_probs=20.8
Q ss_pred HHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 308 VLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 308 VvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
+..... |.+.+...+||+|+|++||++
T Consensus 25 a~~~~~-~~~~~~~aeDlvQe~~i~l~~ 51 (236)
T PRK06986 25 ALRLKA-RLPASVDLDDLIQAGMIGLLE 51 (236)
T ss_pred HHHHHh-cCCCCCCHHHHHHHHHHHHHH
Confidence 333333 335688999999999999999
No 86
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=73.88 E-value=15 Score=31.16 Aligned_cols=59 Identities=22% Similarity=0.268 Sum_probs=40.5
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhh--------------HHHHHHHHHhchHHHHHHHHh
Q 019233 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFG--------------WYCREELIKSTRPLVLFLARN 314 (344)
Q Consensus 255 LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g--------------~~ARdrLI~sNLRLVvsIAKr 314 (344)
+.++..-+......+++.+++|+.+|++...|.+..... ..|+..|...++. |..||..
T Consensus 11 i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~~G~s~~~~l~~~Rl~~A~~~L~~t~~~-i~eIA~~ 83 (127)
T PRK11511 11 IHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEP-ILYLAER 83 (127)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcCCCC-HHHHHHH
Confidence 345555667777888999999999999998888777642 2345555555544 4555554
No 87
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=73.84 E-value=5.1 Score=34.45 Aligned_cols=42 Identities=12% Similarity=-0.119 Sum_probs=38.5
Q ss_pred HHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 294 ~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
...-..++..+.+.|..+|.++.+....-+|++||..+.+++
T Consensus 5 ~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~ 46 (164)
T PRK12547 5 SKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWA 46 (164)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHH
Confidence 455678999999999999999999999999999999999997
No 88
>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=73.05 E-value=12 Score=29.04 Aligned_cols=26 Identities=23% Similarity=0.436 Sum_probs=16.8
Q ss_pred HHhCCCCchHHHHHHcCCC-HHHHHHH
Q 019233 264 KESGKAASLNCWAQAAGVS-ERVLKQH 289 (344)
Q Consensus 264 e~lGrePT~~eWA~aaGld-~~eL~~~ 289 (344)
...|.+||..|+|+++|+. .......
T Consensus 20 ~~~G~~Pt~rEIa~~~g~~S~~tv~~~ 46 (65)
T PF01726_consen 20 EENGYPPTVREIAEALGLKSTSTVQRH 46 (65)
T ss_dssp HHHSS---HHHHHHHHTSSSHHHHHHH
T ss_pred HHcCCCCCHHHHHHHhCCCChHHHHHH
Confidence 3469999999999999995 5444333
No 89
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=73.04 E-value=8.8 Score=38.97 Aligned_cols=38 Identities=13% Similarity=0.230 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHH
Q 019233 252 VANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH 289 (344)
Q Consensus 252 l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~ 289 (344)
..++.+....|...+|+.||.+|+|+.+|++.+.+...
T Consensus 222 ~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~ 259 (373)
T PRK07406 222 ISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFI 259 (373)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 34455667788888999999999999999998777654
No 90
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=71.45 E-value=9.5 Score=40.45 Aligned_cols=37 Identities=22% Similarity=0.324 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHh
Q 019233 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (344)
Q Consensus 254 ~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l 290 (344)
++.+++.+|...+|++||.+|+|+.+|++++.+...+
T Consensus 359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~ 395 (509)
T PRK05901 359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQ 395 (509)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 4556677888899999999999999999987776543
No 91
>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=70.90 E-value=12 Score=34.15 Aligned_cols=36 Identities=33% Similarity=0.451 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHh
Q 019233 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (344)
Q Consensus 255 LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l 290 (344)
+.+....|...+|+.||.++.|+.+|++++++...+
T Consensus 99 ~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~ 134 (231)
T TIGR02885 99 IRYMKEELSKELGREPTINELAEALGVSPEEIVMAL 134 (231)
T ss_pred HHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHH
Confidence 344456788888999999999999999987766543
No 92
>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=70.03 E-value=11 Score=34.30 Aligned_cols=39 Identities=26% Similarity=0.322 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHh
Q 019233 252 VANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (344)
Q Consensus 252 l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l 290 (344)
..++.+...+|...+|++|+.++.|+.+|++++.+...+
T Consensus 82 ~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~ 120 (224)
T TIGR02479 82 ARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQAL 120 (224)
T ss_pred HHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHH
Confidence 334556677888889999999999999999987776654
No 93
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=69.63 E-value=21 Score=28.75 Aligned_cols=38 Identities=11% Similarity=0.239 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhh
Q 019233 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAF 292 (344)
Q Consensus 255 LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~ 292 (344)
++++..-+.+.+..+++.+++|..+|++...|.+...+
T Consensus 7 ~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~ 44 (107)
T PRK10219 7 IQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRT 44 (107)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 34555666777788899999999999999888877764
No 94
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=68.67 E-value=6.3 Score=33.56 Aligned_cols=42 Identities=14% Similarity=-0.010 Sum_probs=38.0
Q ss_pred HHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 294 ~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
..+-++++..+.+.|..+|.++.|...+-+|++||..+-+++
T Consensus 4 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~ 45 (161)
T PRK12541 4 KQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLV 45 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHH
Confidence 456778999999999999999999988999999999999876
No 95
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=67.99 E-value=13 Score=34.64 Aligned_cols=37 Identities=16% Similarity=0.198 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHh
Q 019233 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (344)
Q Consensus 254 ~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l 290 (344)
++.+....+...+|++|+..++|+..|++++.+...+
T Consensus 110 ~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~ 146 (251)
T PRK07670 110 KVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATM 146 (251)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 3455566788889999999999999999987766554
No 96
>PRK05949 RNA polymerase sigma factor; Validated
Probab=67.88 E-value=14 Score=36.47 Aligned_cols=36 Identities=11% Similarity=0.247 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHH
Q 019233 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH 289 (344)
Q Consensus 254 ~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~ 289 (344)
++.+.+.++...+|++||.+|.|+++|++++.+...
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 344556677788899999999999999998877665
No 97
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=67.73 E-value=7.9 Score=33.48 Aligned_cols=44 Identities=18% Similarity=-0.069 Sum_probs=40.1
Q ss_pred hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 293 g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
...+-..|+..+-+.|..+|.++.+....-+|++|+..+.+++.
T Consensus 8 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~ 51 (172)
T PRK12523 8 HSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR 51 (172)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc
Confidence 35788899999999999999999998899999999999999874
No 98
>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=67.22 E-value=12 Score=35.25 Aligned_cols=54 Identities=19% Similarity=0.021 Sum_probs=46.4
Q ss_pred CCHHHHHHHhhhh-HHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHh
Q 019233 281 VSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALA 334 (344)
Q Consensus 281 ld~~eL~~~l~~g-~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLm 334 (344)
.+...|...+..| ..+-.+|+..+.+.|..++.++.+...+-+|++||..+-+.
T Consensus 24 ~~d~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~ 78 (244)
T TIGR03001 24 AADLYLACACAQGEPAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLL 78 (244)
T ss_pred ccHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence 3556677766655 67999999999999999999998888999999999999887
No 99
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=67.16 E-value=13 Score=35.02 Aligned_cols=37 Identities=27% Similarity=0.287 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHh
Q 019233 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (344)
Q Consensus 254 ~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l 290 (344)
++.+.+..|+..+|++||.++.|+..|++...+...+
T Consensus 119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~ 155 (268)
T PRK06288 119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLL 155 (268)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHH
Confidence 5666677888899999999999999999887665543
No 100
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=67.12 E-value=12 Score=36.14 Aligned_cols=51 Identities=16% Similarity=-0.043 Sum_probs=43.4
Q ss_pred HHHHHhhh-hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 285 VLKQHLAF-GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 285 eL~~~l~~-g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
+|...+.. ...+-++|+..|.+.|..+|.++.+....-+|++||..+-+++
T Consensus 8 ~l~~~~~~gd~~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~ 59 (339)
T PRK08241 8 ALLARAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWR 59 (339)
T ss_pred HHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHh
Confidence 34444443 4788999999999999999999999888899999999999887
No 101
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=66.72 E-value=16 Score=34.21 Aligned_cols=35 Identities=14% Similarity=0.140 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHH
Q 019233 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH 289 (344)
Q Consensus 255 LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~ 289 (344)
+.+...++...+|++|+..|.|..+|++++.+...
T Consensus 125 ~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~ 159 (258)
T PRK08215 125 ALQVREKLINENSKEPTVEEIAKELEVPREEVVFA 159 (258)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHH
Confidence 44456678888899999999999999998776653
No 102
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=65.68 E-value=17 Score=36.81 Aligned_cols=41 Identities=27% Similarity=0.425 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHH
Q 019233 249 VQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH 289 (344)
Q Consensus 249 Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~ 289 (344)
+...-++.+++.+|...+|++|+.++.|+.+|++..+.+..
T Consensus 185 ~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m 225 (342)
T COG0568 185 VELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREM 225 (342)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHH
Confidence 34444566778888888999999999999999987555443
No 103
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=63.86 E-value=9.7 Score=34.56 Aligned_cols=43 Identities=23% Similarity=0.068 Sum_probs=39.8
Q ss_pred HHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 294 ~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
..+-.+|+..+.+.+..++.+|.+....-+||+||..+.+++.
T Consensus 27 ~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~ 69 (203)
T PRK09647 27 MPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRS 69 (203)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHh
Confidence 6788899999999999999999998888999999999999883
No 104
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=63.20 E-value=16 Score=37.86 Aligned_cols=38 Identities=13% Similarity=0.332 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhh
Q 019233 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLA 291 (344)
Q Consensus 254 ~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~ 291 (344)
++.+.+..|...+||.||..|.|+++|++.+.++..+.
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 45666778888899999999999999999888876543
No 105
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=62.32 E-value=13 Score=32.38 Aligned_cols=43 Identities=9% Similarity=-0.102 Sum_probs=39.2
Q ss_pred HHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 294 ~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka 336 (344)
..+-..++..+.+.+..++.+|.+....-+||+||-.+-+++.
T Consensus 9 ~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~ 51 (172)
T PRK09651 9 SLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS 51 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh
Confidence 5677889999999999999999988888999999999999875
No 106
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=61.15 E-value=23 Score=34.76 Aligned_cols=37 Identities=16% Similarity=0.384 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHh
Q 019233 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (344)
Q Consensus 254 ~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l 290 (344)
++.+.+..+...+|++||.++.|+++|++.+.+...+
T Consensus 169 ~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~ 205 (317)
T PRK07405 169 KIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYL 205 (317)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 4556667788889999999999999999877666553
No 107
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=57.88 E-value=39 Score=24.53 Aligned_cols=56 Identities=21% Similarity=0.173 Sum_probs=33.0
Q ss_pred CCchHHHHHHcCCCHHHHHHHhhhh--HHHHHHHHHhchHHHHHHHHhcC-CCCCChhhHHHH
Q 019233 269 AASLNCWAQAAGVSERVLKQHLAFG--WYCREELIKSTRPLVLFLARNYR-GLGIPFSDLLQV 328 (344)
Q Consensus 269 ePT~~eWA~aaGld~~eL~~~l~~g--~~ARdrLI~sNLRLVvsIAKrY~-grGls~eDLIQE 328 (344)
++|..++|+.+|++...|.+.+... ...++-+-. .|+ .-|..|- ...+++.|+-++
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~~~s~~~~~~~--~r~--~~a~~~l~~~~~~~~~ia~~ 59 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKETGTTPKQYLRD--RRL--ERARRLLRDTDLSVTEIALR 59 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHhCcCHHHHHHH--HHH--HHHHHHHHcCCCCHHHHHHH
Confidence 4788999999999998888877643 223332221 121 1222222 225778887654
No 108
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=57.55 E-value=20 Score=31.70 Aligned_cols=50 Identities=22% Similarity=-0.030 Sum_probs=40.0
Q ss_pred HHHHHhh-hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 285 VLKQHLA-FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 285 eL~~~l~-~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
.|...+. ....+-+.|+..+.+.+..+++ |.+....-+|++||..+.+.+
T Consensus 13 ~l~~~~~~gd~~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~ 63 (185)
T PRK09649 13 ALALSAAKGNGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIG 63 (185)
T ss_pred HHHHHHHccCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHH
Confidence 3333333 3477899999999999999995 666667899999999999987
No 109
>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=57.15 E-value=31 Score=33.22 Aligned_cols=37 Identities=16% Similarity=0.311 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHh
Q 019233 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (344)
Q Consensus 254 ~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l 290 (344)
++.+.+..+...+|++||..++|..+|++.+.+....
T Consensus 162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~ 198 (298)
T TIGR02997 162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELL 198 (298)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 3445566777888999999999999999887765443
No 110
>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=56.26 E-value=23 Score=32.16 Aligned_cols=33 Identities=21% Similarity=0.341 Sum_probs=27.1
Q ss_pred HHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHH
Q 019233 257 RIKTTLEKESGKAASLNCWAQAAGVSERVLKQH 289 (344)
Q Consensus 257 ~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~ 289 (344)
+....+....|++|+..|.|+++|+++..+...
T Consensus 94 ~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~ 126 (227)
T TIGR02980 94 KATEELTQRLGRSPTIAEIAEELGVSEEEVVEA 126 (227)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHH
Confidence 345677778899999999999999998877543
No 111
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=55.92 E-value=32 Score=34.68 Aligned_cols=52 Identities=23% Similarity=0.210 Sum_probs=41.3
Q ss_pred HHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhh--------------HHHHHHHHHhchHHH
Q 019233 257 RIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFG--------------WYCREELIKSTRPLV 308 (344)
Q Consensus 257 ~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g--------------~~ARdrLI~sNLRLV 308 (344)
++...++..+..+-+.++.|..+||+...|.+..... ..||+-|...++.+.
T Consensus 224 ~~i~~me~nle~plsl~~LA~~~~~S~R~leRlF~~~lG~sP~~yy~~lRL~~Ar~LL~~t~~si~ 289 (328)
T COG4977 224 RAIELMEANLEEPLSLEELADRAGLSRRQLERLFRAELGVSPARYYLRLRLERARRLLEQTRLSIA 289 (328)
T ss_pred HHHHHHHHhhcCCcCHHHHHHHhCCCHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhCCCcHH
Confidence 3445567777889999999999999999998877642 568888888888765
No 112
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=55.79 E-value=16 Score=32.52 Aligned_cols=45 Identities=16% Similarity=-0.162 Sum_probs=41.0
Q ss_pred hhhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 291 AFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 291 ~~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
.....+-+.++..+-+.|..+|.++.+...+-+|++|+..+-+.+
T Consensus 19 ~~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~ 63 (188)
T PRK12517 19 LSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWR 63 (188)
T ss_pred hccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHH
Confidence 345788999999999999999999999888899999999999987
No 113
>PRK13503 transcriptional activator RhaS; Provisional
Probab=53.77 E-value=51 Score=30.27 Aligned_cols=59 Identities=22% Similarity=0.186 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhh--------------HHHHHHHHHhchHHHHHHHHh
Q 019233 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFG--------------WYCREELIKSTRPLVLFLARN 314 (344)
Q Consensus 255 LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g--------------~~ARdrLI~sNLRLVvsIAKr 314 (344)
+.++..-+.+....+.|.++||+.+|++...|.+..+.. ..|+.-|...++. |..||.+
T Consensus 173 i~~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk~~~G~S~~~yi~~~Rl~~A~~LL~~~~~s-I~eIA~~ 245 (278)
T PRK13503 173 LNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDAS-VTDIAYR 245 (278)
T ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHcCCCC-HHHHHHH
Confidence 334455566677788999999999999998888777642 3455555555554 5556655
No 114
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=53.74 E-value=18 Score=31.08 Aligned_cols=43 Identities=12% Similarity=-0.104 Sum_probs=38.9
Q ss_pred hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 293 g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
+..+-+.|+..+.+.+..+|.++.+....-+|++|+-.+-+++
T Consensus 7 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~ 49 (173)
T PRK09645 7 EAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQ 49 (173)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHH
Confidence 4677888999999999999999988877889999999999987
No 115
>PRK15044 transcriptional regulator SirC; Provisional
Probab=52.99 E-value=67 Score=32.11 Aligned_cols=60 Identities=15% Similarity=-0.009 Sum_probs=41.4
Q ss_pred HHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhh
Q 019233 221 TIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAF 292 (344)
Q Consensus 221 l~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~ 292 (344)
+..|++ ..+..+.|..+..+. ..+++..-+.+...++++.++||+.+|++...|.+....
T Consensus 172 Ls~~l~---~~~~~~~L~~~~~is---------~~~kV~~~I~~nl~~~~SLeeLA~~lgmS~~tL~R~Fk~ 231 (295)
T PRK15044 172 ISAFVR---KPGGFDFLERAIKIT---------TKEKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAA 231 (295)
T ss_pred HHHHHh---cccchhhHHHHhhhh---------HHHHHHHHHHhCcccCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 456666 445555554444332 234455666677789999999999999999999887753
No 116
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=52.15 E-value=20 Score=33.07 Aligned_cols=42 Identities=17% Similarity=-0.048 Sum_probs=38.6
Q ss_pred HHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 294 ~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
..+-..|+..+.+.+..++.+|.+....-+|++||..+-+++
T Consensus 17 ~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~ 58 (216)
T PRK12533 17 GERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALR 58 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHH
Confidence 567788999999999999999999888899999999999887
No 117
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=50.89 E-value=55 Score=31.01 Aligned_cols=60 Identities=25% Similarity=0.221 Sum_probs=41.3
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhh--------------HHHHHHHHHhchHHHHHHHHhc
Q 019233 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFG--------------WYCREELIKSTRPLVLFLARNY 315 (344)
Q Consensus 255 LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g--------------~~ARdrLI~sNLRLVvsIAKrY 315 (344)
++++..-++..+..+++.+++|+.+|++...|.+....- ..|+..|...++. |..||..+
T Consensus 7 i~~~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F~~~~g~s~~~yi~~~Rl~~A~~~L~~~~~~-i~~iA~~~ 80 (289)
T PRK15121 7 IRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGAYIRARRLSKAAVALRLTSRP-ILDIALQY 80 (289)
T ss_pred HHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcCCCC-HHHHHHHH
Confidence 445556677777888999999999999998888877642 3344444444444 45566554
No 118
>PRK05572 sporulation sigma factor SigF; Validated
Probab=48.83 E-value=50 Score=30.79 Aligned_cols=35 Identities=23% Similarity=0.332 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 019233 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (344)
Q Consensus 254 ~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~ 288 (344)
++.+....+..++|+.|+..+.|++.|++++.+..
T Consensus 119 ~~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~~ 153 (252)
T PRK05572 119 KIRKDKDELSKELGREPTIEELAEYLGVTPEEVVL 153 (252)
T ss_pred HHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHH
Confidence 34555667777889999999999999998776543
No 119
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=48.68 E-value=26 Score=31.86 Aligned_cols=53 Identities=13% Similarity=-0.061 Sum_probs=41.2
Q ss_pred HcCCCHHHHHHHhhhhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 278 AAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 278 aaGld~~eL~~~l~~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
++.||...|-..++. ..++..+-+.+..+|.+|.+....-+|++||..+.+++
T Consensus 6 ~~~~~~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfikl~~ 58 (206)
T PRK12544 6 AVAMDSSDLGNLLQD-----PVFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALK 58 (206)
T ss_pred hhhcchhhHHHHhhh-----HHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHH
Confidence 344555555433332 45778899999999999999989999999999999977
No 120
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=48.65 E-value=36 Score=32.86 Aligned_cols=26 Identities=27% Similarity=0.092 Sum_probs=22.0
Q ss_pred HHhCCCCchHHHHHHcCCCHHHHHHH
Q 019233 264 KESGKAASLNCWAQAAGVSERVLKQH 289 (344)
Q Consensus 264 e~lGrePT~~eWA~aaGld~~eL~~~ 289 (344)
..+|+.||.+|.|+.+|++++++...
T Consensus 143 ~~l~~~pt~~eiA~~l~~~~~~v~~~ 168 (289)
T PRK07500 143 EELTKQEIHREIATALGVSLSDVEMM 168 (289)
T ss_pred cccCCCCCHHHHHHHhCcCHHHHHHH
Confidence 35799999999999999998777543
No 121
>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=48.30 E-value=20 Score=31.54 Aligned_cols=43 Identities=12% Similarity=-0.240 Sum_probs=38.7
Q ss_pred hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 293 g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
...+-+.|+..+.+.|..+|.++.+.-..-+|++||..+-+.+
T Consensus 9 ~~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~ 51 (193)
T TIGR02947 9 RAQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFS 51 (193)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHH
Confidence 3567788999999999999999998888889999999999987
No 122
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.31 E-value=80 Score=26.83 Aligned_cols=45 Identities=24% Similarity=0.138 Sum_probs=31.9
Q ss_pred HHHHHHHHh-CCCCchHHHHHHcCCCHHHHHHHhh------hhHHHHHHHHH
Q 019233 258 IKTTLEKES-GKAASLNCWAQAAGVSERVLKQHLA------FGWYCREELIK 302 (344)
Q Consensus 258 ir~~Lee~l-GrePT~~eWA~aaGld~~eL~~~l~------~g~~ARdrLI~ 302 (344)
.+.+|++.+ -..-|.+++|.+.+.++..|.+.++ .++..|+-|+.
T Consensus 11 Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil~~tqr~~dvW~lRd~l~~ 62 (97)
T COG4367 11 TKQELQANFELCPLSDEEIATALNWTEVKLEKILQVTQRPADVWRLRDFLVQ 62 (97)
T ss_pred HHHHHHHhhhhccccHHHHHHHhCCCHHHHHHHHHHhhccchhHHHHHHHHH
Confidence 344555444 3466999999999999988888774 45677776654
No 123
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=45.63 E-value=37 Score=29.28 Aligned_cols=41 Identities=5% Similarity=-0.111 Sum_probs=36.2
Q ss_pred HHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 295 ~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
.+-.+++..+-+.+...|.+|.+....-+|++|+-.+-+++
T Consensus 9 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~ 49 (168)
T PRK12525 9 TLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLA 49 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHh
Confidence 44566889999999999999998888999999999999986
No 124
>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=45.53 E-value=46 Score=29.69 Aligned_cols=39 Identities=23% Similarity=0.396 Sum_probs=30.9
Q ss_pred HHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhH
Q 019233 256 ERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGW 294 (344)
Q Consensus 256 E~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~ 294 (344)
+++++-|.+.-++..|..+.+++.|++++.+.+-+.+|+
T Consensus 33 ~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGR 71 (137)
T TIGR03826 33 EKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGR 71 (137)
T ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 444445556667888999999999999999998888763
No 125
>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=44.30 E-value=43 Score=25.35 Aligned_cols=59 Identities=24% Similarity=0.372 Sum_probs=40.5
Q ss_pred HHHHhCCCCc------hHHHHHHcCCCHHHHHHHhhhhHHHHHHHHHhchHHHHHHHHhcCCCCCC-hhh
Q 019233 262 LEKESGKAAS------LNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIP-FSD 324 (344)
Q Consensus 262 Lee~lGrePT------~~eWA~aaGld~~eL~~~l~~g~~ARdrLI~sNLRLVvsIAKrY~grGls-~eD 324 (344)
+++..||+|| ...|....|++.+.+...+.... .+ -..|.+.|..|++++...|+. .+|
T Consensus 5 ~e~~~gr~ls~~e~~~i~~~~~~~~~~~evI~~ai~~a~---~~-~~~~~~Yi~~Il~~W~~~gi~T~e~ 70 (73)
T TIGR01446 5 FEENFGRMLSPFEMEDLKYWLDEFGNSPELIKEALKEAV---SN-NKANYKYIDAILNNWKNNGIKTVED 70 (73)
T ss_pred HHHHhCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHH---Hc-CCCCHHHHHHHHHHHHHcCCCCHHH
Confidence 4555677777 46677788887666665555432 11 246789999999999999874 444
No 126
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=43.76 E-value=48 Score=30.49 Aligned_cols=34 Identities=21% Similarity=0.257 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 019233 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288 (344)
Q Consensus 255 LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~ 288 (344)
+.+....+...+|++||..++|+.+|++...+..
T Consensus 97 ~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~ 130 (236)
T PRK06986 97 VAQAIRQLEQELGREPTDTEVAEKLGLSLEEYRE 130 (236)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHH
Confidence 3345566777789999999999999999877544
No 127
>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=42.35 E-value=77 Score=29.48 Aligned_cols=35 Identities=14% Similarity=0.173 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHH
Q 019233 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH 289 (344)
Q Consensus 255 LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~ 289 (344)
+.+....+...+|+.||..+.|...|++.+++...
T Consensus 118 ~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~ 152 (255)
T TIGR02941 118 IKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEI 152 (255)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 44556677888899999999999999998776543
No 128
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=38.20 E-value=85 Score=31.00 Aligned_cols=36 Identities=17% Similarity=0.070 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHh
Q 019233 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL 290 (344)
Q Consensus 255 LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l 290 (344)
+.+....|+..+|++||.++.|...|++++++.+.+
T Consensus 175 ~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l 210 (325)
T PRK05657 175 YLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRML 210 (325)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 334456677788999999999999999987775543
No 129
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=34.05 E-value=89 Score=29.99 Aligned_cols=36 Identities=11% Similarity=0.143 Sum_probs=28.9
Q ss_pred HHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhh
Q 019233 257 RIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAF 292 (344)
Q Consensus 257 ~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~ 292 (344)
++...+......+++.+++|+.+|++...|.+...+
T Consensus 222 ~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~ 257 (322)
T PRK09393 222 PLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEA 257 (322)
T ss_pred HHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 344455666678899999999999999998888775
No 130
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=33.55 E-value=67 Score=25.65 Aligned_cols=50 Identities=22% Similarity=0.251 Sum_probs=36.6
Q ss_pred CchHHHHHHcCCCHHHHHHHhhhhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHH
Q 019233 270 ASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVS 329 (344)
Q Consensus 270 PT~~eWA~aaGld~~eL~~~l~~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG 329 (344)
-|-++.|..+|++...+...= .|. ....+.|...||+-|. .+++|+++..
T Consensus 15 ltQ~elA~~vgVsRQTi~~iE-kgk------y~Psl~La~kia~~f~---~~iedIF~~~ 64 (68)
T COG1476 15 LTQEELAKLVGVSRQTIIAIE-KGK------YNPSLELALKIARVFG---KTIEDIFQLE 64 (68)
T ss_pred cCHHHHHHHcCcCHHHHHHHH-cCC------CCchHHHHHHHHHHhC---CCHHHHHhhh
Confidence 467788889998866554322 222 3467899999999986 8999999854
No 131
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=33.40 E-value=1.1e+02 Score=28.40 Aligned_cols=33 Identities=21% Similarity=0.189 Sum_probs=25.8
Q ss_pred HHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhh
Q 019233 260 TTLEKESGKAASLNCWAQAAGVSERVLKQHLAF 292 (344)
Q Consensus 260 ~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~ 292 (344)
.-+.+....+.|.++||+.+|++..-|.+..+.
T Consensus 193 ~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~ 225 (287)
T TIGR02297 193 FLIEENYKQHLRLPEYADRLGISESRLNDICRR 225 (287)
T ss_pred HHHHHhhccCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 344455677889999999999999888776664
No 132
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=32.92 E-value=91 Score=28.00 Aligned_cols=42 Identities=21% Similarity=0.002 Sum_probs=35.8
Q ss_pred hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 293 g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
...+-+.++..+...+..+++ |.+....-+|++|+-.+.|++
T Consensus 23 d~~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~ 64 (196)
T PRK12535 23 DRAALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMS 64 (196)
T ss_pred CHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHH
Confidence 467788899999999999876 556667899999999999987
No 133
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=30.20 E-value=64 Score=26.41 Aligned_cols=26 Identities=23% Similarity=0.279 Sum_probs=19.6
Q ss_pred CCCCchHHHHHHcCCCHHHHHHHhhh
Q 019233 267 GKAASLNCWAQAAGVSERVLKQHLAF 292 (344)
Q Consensus 267 GrePT~~eWA~aaGld~~eL~~~l~~ 292 (344)
|+++|..+.|.++|.+.+++...+..
T Consensus 36 G~PVt~~~LA~a~g~~~e~v~~~L~~ 61 (77)
T PF12324_consen 36 GQPVTVEQLAAALGWPVEEVRAALAA 61 (77)
T ss_dssp TS-B-HHHHHHHHT--HHHHHHHHHH
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHh
Confidence 99999999999999999988877754
No 134
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=29.49 E-value=63 Score=30.52 Aligned_cols=49 Identities=16% Similarity=-0.021 Sum_probs=36.9
Q ss_pred HHHHhhhhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233 286 LKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 286 L~~~l~~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk 335 (344)
|.+.+......-+.+++.+ +.+...|.++.+....-+||+||..+-+++
T Consensus 9 ~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~ 57 (228)
T PRK06704 9 LKNHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQ 57 (228)
T ss_pred HhcccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHH
Confidence 3344444455566666666 788888888888888999999999999887
No 135
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=28.42 E-value=95 Score=29.89 Aligned_cols=24 Identities=21% Similarity=0.216 Sum_probs=20.7
Q ss_pred CCCCchHHHHHHcCCCHHHHHHHh
Q 019233 267 GKAASLNCWAQAAGVSERVLKQHL 290 (344)
Q Consensus 267 GrePT~~eWA~aaGld~~eL~~~l 290 (344)
+++||.+|.|+.+|++++.+....
T Consensus 149 ~~~~t~~eiA~~l~~~~~~v~~~~ 172 (284)
T PRK06596 149 LNPEEVEMVAEELGVSEEEVREME 172 (284)
T ss_pred CCCCCHHHHHHHhCcCHHHHHHHH
Confidence 599999999999999988876653
No 136
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=27.34 E-value=1.5e+02 Score=27.74 Aligned_cols=36 Identities=11% Similarity=0.022 Sum_probs=27.8
Q ss_pred HHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhh
Q 019233 257 RIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAF 292 (344)
Q Consensus 257 ~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~ 292 (344)
++...+......+.+.+++|+.+|++..-|.+..++
T Consensus 187 ~~~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk~ 222 (290)
T PRK10572 187 EACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQ 222 (290)
T ss_pred HHHHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 334455556678899999999999999888777765
No 137
>PRK13239 alkylmercury lyase; Provisional
Probab=26.12 E-value=1.1e+02 Score=29.06 Aligned_cols=27 Identities=22% Similarity=0.249 Sum_probs=24.6
Q ss_pred hCCCCchHHHHHHcCCCHHHHHHHhhh
Q 019233 266 SGKAASLNCWAQAAGVSERVLKQHLAF 292 (344)
Q Consensus 266 lGrePT~~eWA~aaGld~~eL~~~l~~ 292 (344)
.|++||..+.|++.|.++++.++.|+.
T Consensus 33 ~G~pvt~~~lA~~~~~~~~~v~~~L~~ 59 (206)
T PRK13239 33 KGRPVSVTTLAAALGWPVEEVEAVLEA 59 (206)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 499999999999999999999887775
No 138
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=25.68 E-value=1e+02 Score=30.15 Aligned_cols=35 Identities=17% Similarity=0.114 Sum_probs=28.5
Q ss_pred HHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhh
Q 019233 258 IKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAF 292 (344)
Q Consensus 258 ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~ 292 (344)
+...+......+.|.++||+.+||+...|.+....
T Consensus 186 i~~~I~~~~~~~~sl~~lA~~~gmS~stl~R~Fk~ 220 (291)
T PRK15186 186 IYNIIISDISRKWALKDISDSLYMSCSTLKRKLKQ 220 (291)
T ss_pred HHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 33445666788999999999999999999888765
No 139
>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=25.60 E-value=89 Score=26.86 Aligned_cols=20 Identities=20% Similarity=-0.036 Sum_probs=16.8
Q ss_pred CCCCChhhHHHHHHHHHhhh
Q 019233 317 GLGIPFSDLLQVSRHALAFI 336 (344)
Q Consensus 317 grGls~eDLIQEG~iGLmka 336 (344)
+....-+|++|++.+.|++.
T Consensus 33 ~~~~~aeD~vQe~~l~l~~~ 52 (189)
T TIGR02984 33 RRRVDPSDLVQETLLEAHRR 52 (189)
T ss_pred CCccCHHHHHHHHHHHHHHH
Confidence 35578899999999999883
No 140
>KOG0917 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.42 E-value=65 Score=32.47 Aligned_cols=40 Identities=33% Similarity=0.437 Sum_probs=34.3
Q ss_pred HHHHhhHHHHHhhhcchhhhHHHHHHHHHhhhhhhhhhhhh
Q 019233 104 RLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNS 144 (344)
Q Consensus 104 ~ll~~nl~~le~~~~~~d~lrlEr~iL~~~~~lga~~~f~~ 144 (344)
.-||.-|+.|+.-++|.|++.+|-+-=-|+|.. |+++|+-
T Consensus 55 sgLm~~lealkkqlaDneaitne~~aqaHiE~f-AlklF~~ 94 (338)
T KOG0917|consen 55 SGLMDQLEALKKQLADNEAITNEIVAQAHIENF-ALKLFLY 94 (338)
T ss_pred HHHHHHHHHHHHHhcchhhhhhchHHHHHHHHH-HHHHHHh
Confidence 569999999999999999999998877777765 8888654
No 141
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=24.79 E-value=4.2e+02 Score=22.21 Aligned_cols=34 Identities=32% Similarity=0.357 Sum_probs=26.8
Q ss_pred CCchHHHHHHcCCCHHHHHHHhhh-------hHHHHHHHHH
Q 019233 269 AASLNCWAQAAGVSERVLKQHLAF-------GWYCREELIK 302 (344)
Q Consensus 269 ePT~~eWA~aaGld~~eL~~~l~~-------g~~ARdrLI~ 302 (344)
-.|.++.|+..|++...+.+.+.- .+..|+-|..
T Consensus 23 ~ls~~~ia~dL~~s~~~le~vL~l~~~~~~~vW~lRdyL~~ 63 (89)
T PF10078_consen 23 GLSLEQIAADLGTSPEHLEQVLNLKQPFPEDVWILRDYLND 63 (89)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCCCCcccchHHHHHHHH
Confidence 368899999999999999988873 3677776653
No 142
>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=24.76 E-value=2e+02 Score=27.36 Aligned_cols=31 Identities=19% Similarity=0.179 Sum_probs=24.6
Q ss_pred HHHHHHHhCCCCchHHHHHHcCCCHHHHHHH
Q 019233 259 KTTLEKESGKAASLNCWAQAAGVSERVLKQH 289 (344)
Q Consensus 259 r~~Lee~lGrePT~~eWA~aaGld~~eL~~~ 289 (344)
...+...+|++|+..++|...|+++..+...
T Consensus 139 ~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~ 169 (285)
T TIGR02394 139 ARQLEKKLGREPSVEEIAELLDKPVEDVSRV 169 (285)
T ss_pred HHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 3445667799999999999999988776654
No 143
>PF14711 Nitr_red_bet_C: Respiratory nitrate reductase beta C-terminal; PDB: 3IR7_B 1Y5N_B 1R27_D 3EGW_B 1Y5I_B 1Q16_B 1Y4Z_B 1Y5L_B 3IR6_B 3IR5_B ....
Probab=24.03 E-value=1.3e+02 Score=24.78 Aligned_cols=54 Identities=17% Similarity=0.253 Sum_probs=32.5
Q ss_pred CCchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHH-hCCCCchHHHHHHcCCCH
Q 019233 217 LKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKE-SGKAASLNCWAQAAGVSE 283 (344)
Q Consensus 217 ~~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~-lGrePT~~eWA~aaGld~ 283 (344)
..=|+ .||. .|||+-+|.-.-..++.++. +|.-+... .|.+ ..+++.+++|++.
T Consensus 28 lRIPi-~YLA--------nLftAGd~~~V~~~L~rL~A---mR~ymR~~~v~~~-~~~~~l~~~glt~ 82 (83)
T PF14711_consen 28 LRIPI-EYLA--------NLFTAGDEEPVRRALKRLLA---MRSYMRAKNVGGE-PDEEVLEAVGLTE 82 (83)
T ss_dssp BSS-H-HHHH--------HHHSTT-HHHHHHHHHHHHH---HHHHHHHHHTT-S----HHHHHTT--H
T ss_pred hcccH-HHHH--------HHHccCChHHHHHHHHHHHH---HHHHHHHHHhCCC-CcHHHHHHcCCCC
Confidence 34575 8998 78999999888877776554 45444443 3544 4578899999875
No 144
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=23.60 E-value=3.2e+02 Score=22.24 Aligned_cols=37 Identities=16% Similarity=0.171 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhh
Q 019233 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFG 293 (344)
Q Consensus 254 ~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g 293 (344)
+++.|.+.|.+ ..+|..+.|+.+|++.....+.+..+
T Consensus 7 R~~~I~e~l~~---~~~ti~dvA~~~gvS~~TVsr~L~~~ 43 (80)
T TIGR02844 7 RVLEIGKYIVE---TKATVRETAKVFGVSKSTVHKDVTER 43 (80)
T ss_pred HHHHHHHHHHH---CCCCHHHHHHHhCCCHHHHHHHhcCC
Confidence 34455555555 46689999999999999998888764
No 145
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=23.56 E-value=1.8e+02 Score=20.60 Aligned_cols=25 Identities=20% Similarity=0.247 Sum_probs=18.5
Q ss_pred CCCchHHHHHHcCCCHHHHHHHhhh
Q 019233 268 KAASLNCWAQAAGVSERVLKQHLAF 292 (344)
Q Consensus 268 rePT~~eWA~aaGld~~eL~~~l~~ 292 (344)
...+..+.|+.+|++.....++++.
T Consensus 16 ~r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 16 GRRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCccHHHHHHHHCcCHHHHHHHHHH
Confidence 3456899999999999888877653
No 146
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=22.74 E-value=3.6e+02 Score=25.95 Aligned_cols=38 Identities=8% Similarity=0.052 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhh
Q 019233 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAF 292 (344)
Q Consensus 255 LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~ 292 (344)
++++..-+.+.....+|.++||+++|++...|.+..+.
T Consensus 193 i~~~~~~i~~~~~~~~tl~~lA~~~~~S~~~l~r~Fk~ 230 (302)
T PRK10371 193 VSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQR 230 (302)
T ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 33444555666677899999999999999877776664
No 147
>PRK13501 transcriptional activator RhaR; Provisional
Probab=22.69 E-value=2.2e+02 Score=26.70 Aligned_cols=53 Identities=19% Similarity=0.137 Sum_probs=35.3
Q ss_pred HHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhh--------------HHHHHHHHHhchHHHHHHHHh
Q 019233 261 TLEKESGKAASLNCWAQAAGVSERVLKQHLAFG--------------WYCREELIKSTRPLVLFLARN 314 (344)
Q Consensus 261 ~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g--------------~~ARdrLI~sNLRLVvsIAKr 314 (344)
.++.......+.+++|+++|++...|.+...+. ..|++-|...++ -|-.||.+
T Consensus 184 ~I~~~~~e~~sl~~lA~~~~lS~~~l~r~Fk~~~G~T~~qyi~~~Ri~~A~~LL~~t~~-sI~eIA~~ 250 (290)
T PRK13501 184 ALQQSLGAYFDMADFCHKNQLVERSLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEH-RISDIAAR 250 (290)
T ss_pred HHHHhhccCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcCCC-CHHHHHHH
Confidence 344445667799999999999998887766642 345555555555 35556654
No 148
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=22.44 E-value=2.3e+02 Score=21.10 Aligned_cols=41 Identities=22% Similarity=0.298 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHHHHHHhCC-CCchHHHHHHcCCCHHHHHHHh
Q 019233 249 VQVVANLERIKTTLEKESGK-AASLNCWAQAAGVSERVLKQHL 290 (344)
Q Consensus 249 Iq~l~~LE~ir~~Lee~lGr-ePT~~eWA~aaGld~~eL~~~l 290 (344)
|+++-.+-+.-+.|.++ |. -.+-.+.|+.+|++..++++.+
T Consensus 8 i~RL~~Y~r~L~~l~~~-G~~~vSS~~La~~~gi~~~qVRKDl 49 (50)
T PF06971_consen 8 IRRLPLYLRYLEQLKEE-GVERVSSQELAEALGITPAQVRKDL 49 (50)
T ss_dssp HHHHHHHHHHHHHHHHT-T-SEE-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHc-CCeeECHHHHHHHHCCCHHHhcccC
Confidence 44555555555566654 54 5788999999999998887654
No 149
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=22.42 E-value=1.3e+02 Score=26.30 Aligned_cols=44 Identities=9% Similarity=-0.166 Sum_probs=34.2
Q ss_pred hhHHHHHHHHHhchHHHHHHH-HhcCC-CCCChhhHHHHHHHHHhh
Q 019233 292 FGWYCREELIKSTRPLVLFLA-RNYRG-LGIPFSDLLQVSRHALAF 335 (344)
Q Consensus 292 ~g~~ARdrLI~sNLRLVvsIA-KrY~g-rGls~eDLIQEG~iGLmk 335 (344)
++..+-..|+..|.+.|..++ +++.+ ....-+|++||..+-+++
T Consensus 10 ~d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~ 55 (178)
T PRK12529 10 ADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILA 55 (178)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHh
Confidence 346778899999999999965 55442 245689999999999887
No 150
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=21.67 E-value=2.4e+02 Score=19.92 Aligned_cols=26 Identities=19% Similarity=0.298 Sum_probs=19.7
Q ss_pred CCCCchHHHHHHcCCCHHHHHHHhhh
Q 019233 267 GKAASLNCWAQAAGVSERVLKQHLAF 292 (344)
Q Consensus 267 GrePT~~eWA~aaGld~~eL~~~l~~ 292 (344)
+.+.|..+.|+.+|+|...+.+.+..
T Consensus 13 ~~~it~~eLa~~l~vS~rTi~~~i~~ 38 (55)
T PF08279_consen 13 KEPITAKELAEELGVSRRTIRRDIKE 38 (55)
T ss_dssp TTSBEHHHHHHHCTS-HHHHHHHHHH
T ss_pred CCCcCHHHHHHHhCCCHHHHHHHHHH
Confidence 33489999999999998887766653
No 151
>PRK15340 transcriptional regulator InvF; Provisional
Probab=21.58 E-value=6.8e+02 Score=23.86 Aligned_cols=32 Identities=16% Similarity=0.134 Sum_probs=26.0
Q ss_pred HHHHHhCCCCchHHHHHHcCCCHHHHHHHhhh
Q 019233 261 TLEKESGKAASLNCWAQAAGVSERVLKQHLAF 292 (344)
Q Consensus 261 ~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~ 292 (344)
-|........+.+++|+.+|++...+.+...+
T Consensus 117 ~Ll~~~~~~~sleeLA~~~gvS~r~f~RlFk~ 148 (216)
T PRK15340 117 YLLAQSTSGNTMRMLGEDYGVSYTHFRRLCSR 148 (216)
T ss_pred HHHhCccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34445567789999999999999988888875
No 152
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=20.14 E-value=5.2e+02 Score=24.12 Aligned_cols=37 Identities=16% Similarity=0.191 Sum_probs=27.8
Q ss_pred HHHHHHHHHHhCCC-CchHHHHHHcCCCHHHHHHHhhh
Q 019233 256 ERIKTTLEKESGKA-ASLNCWAQAAGVSERVLKQHLAF 292 (344)
Q Consensus 256 E~ir~~Lee~lGre-PT~~eWA~aaGld~~eL~~~l~~ 292 (344)
.+++.-+.+.+..+ .|.+++|+++|++...|.+..++
T Consensus 200 ~~~~~~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk~ 237 (302)
T PRK09685 200 QKVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFAE 237 (302)
T ss_pred HHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 34555566666766 69999999999999877766653
Done!