Query 022167
Match_columns 301
No_of_seqs 138 out of 1165
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 08:32:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022167.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022167hhsearch_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 1.1E-24 2.4E-29 213.6 10.7 110 191-300 60-211 (415)
2 TIGR02997 Sig70-cyanoRpoD RNA 99.9 5.6E-23 1.2E-27 190.7 10.9 110 191-300 1-110 (298)
3 PRK07406 RNA polymerase sigma 99.9 1.8E-21 3.8E-26 188.5 10.5 111 190-300 62-172 (373)
4 PRK05949 RNA polymerase sigma 99.8 8.2E-21 1.8E-25 180.2 11.1 111 190-300 17-127 (327)
5 PRK07405 RNA polymerase sigma 99.8 1.5E-20 3.3E-25 177.1 10.5 110 191-300 8-117 (317)
6 PRK05901 RNA polymerase sigma 99.8 9.8E-19 2.1E-23 175.6 8.3 100 188-300 208-307 (509)
7 COG0568 RpoD DNA-directed RNA 99.7 1.5E-17 3.2E-22 160.3 7.8 113 188-300 6-138 (342)
8 PRK07921 RNA polymerase sigma 99.6 3.3E-15 7E-20 142.2 7.6 97 191-300 26-122 (324)
9 PRK09210 RNA polymerase sigma 99.3 1.1E-12 2.3E-17 126.3 6.2 72 189-300 94-165 (367)
10 PRK05658 RNA polymerase sigma 99.3 1.6E-12 3.4E-17 132.6 5.9 72 192-300 345-416 (619)
11 PRK06596 RNA polymerase factor 99.2 5.5E-11 1.2E-15 110.6 7.4 74 184-300 10-84 (284)
12 TIGR02392 rpoH_proteo alternat 99.1 1.7E-10 3.6E-15 106.1 7.0 69 192-300 2-71 (270)
13 PRK07500 rpoH2 RNA polymerase 99.1 2.5E-10 5.4E-15 106.6 7.2 70 191-300 6-76 (289)
14 PRK05657 RNA polymerase sigma 98.9 1.5E-09 3.2E-14 103.4 7.1 73 188-300 50-122 (325)
15 PRK07122 RNA polymerase sigma 98.8 4.7E-09 1E-13 96.8 3.6 38 263-300 39-76 (264)
16 TIGR02394 rpoS_proteo RNA poly 98.7 3.2E-08 6.9E-13 91.6 7.1 73 188-300 10-82 (285)
17 TIGR02850 spore_sigG RNA polym 98.5 1.3E-07 2.8E-12 86.0 6.1 61 200-300 10-70 (254)
18 PRK08215 sporulation sigma fac 98.4 3.3E-07 7.1E-12 83.5 6.1 60 201-300 14-73 (258)
19 PRK05803 sporulation sigma fac 98.2 2.5E-06 5.5E-11 76.4 7.1 69 192-300 17-85 (233)
20 PRK07408 RNA polymerase sigma 98.2 2.8E-06 6E-11 77.9 5.6 37 264-300 25-62 (256)
21 PF00140 Sigma70_r1_2: Sigma-7 98.2 3.2E-07 6.9E-12 62.7 -0.5 33 191-223 2-34 (37)
22 COG1191 FliA DNA-directed RNA 98.1 2.5E-06 5.4E-11 79.7 5.0 36 264-300 24-60 (247)
23 PRK06288 RNA polymerase sigma 98.1 3.7E-06 7.9E-11 77.2 5.7 61 200-300 6-70 (268)
24 TIGR02941 Sigma_B RNA polymera 98.0 8.1E-06 1.8E-10 74.0 5.7 57 204-300 8-65 (255)
25 PRK08583 RNA polymerase sigma 97.9 2E-05 4.4E-10 71.5 5.6 57 204-300 8-65 (257)
26 PRK05911 RNA polymerase sigma 97.8 2E-05 4.2E-10 72.5 3.6 38 263-300 22-62 (257)
27 PRK05572 sporulation sigma fac 97.7 7.4E-05 1.6E-09 68.0 6.2 64 197-300 5-68 (252)
28 PRK05658 RNA polymerase sigma 97.5 0.00015 3.3E-09 74.7 5.3 35 189-223 102-136 (619)
29 PF04539 Sigma70_r3: Sigma-70 97.1 0.00095 2.1E-08 50.3 4.9 38 224-261 6-43 (78)
30 TIGR02846 spore_sigmaK RNA pol 97.0 0.0015 3.3E-08 58.6 6.1 68 193-300 16-84 (227)
31 PRK08301 sporulation sigma fac 96.9 0.0021 4.6E-08 57.4 6.2 66 195-300 22-88 (234)
32 TIGR02835 spore_sigmaE RNA pol 96.3 0.0091 2E-07 53.8 6.2 58 203-300 31-88 (234)
33 PRK11922 RNA polymerase sigma 95.6 0.016 3.4E-07 52.1 4.5 60 201-300 7-66 (231)
34 PF04542 Sigma70_r2: Sigma-70 94.9 0.016 3.5E-07 41.4 1.9 32 269-300 1-32 (71)
35 PRK09648 RNA polymerase sigma 94.3 0.082 1.8E-06 45.3 5.0 37 264-300 24-64 (189)
36 COG0568 RpoD DNA-directed RNA 93.6 0.31 6.7E-06 48.2 8.2 32 191-222 67-98 (342)
37 PRK12513 RNA polymerase sigma 93.0 0.1 2.2E-06 44.9 3.5 38 263-300 25-62 (194)
38 PRK08295 RNA polymerase factor 92.8 0.18 3.9E-06 43.6 4.8 38 263-300 23-60 (208)
39 PRK12519 RNA polymerase sigma 92.3 0.15 3.3E-06 43.8 3.6 37 264-300 29-65 (194)
40 COG1191 FliA DNA-directed RNA 92.0 0.22 4.8E-06 47.0 4.6 62 191-262 87-150 (247)
41 PRK09646 RNA polymerase sigma 91.3 0.22 4.8E-06 43.2 3.6 38 263-300 29-66 (194)
42 PRK12534 RNA polymerase sigma 90.9 0.3 6.4E-06 41.7 4.0 38 263-300 24-61 (187)
43 PRK13919 putative RNA polymera 90.9 0.21 4.5E-06 42.5 3.0 38 263-300 22-59 (186)
44 PRK05911 RNA polymerase sigma 88.9 0.87 1.9E-05 42.1 5.5 36 225-260 113-148 (257)
45 PRK07408 RNA polymerase sigma 87.8 0.87 1.9E-05 42.0 4.8 36 224-259 115-150 (256)
46 PRK12531 RNA polymerase sigma 87.4 0.69 1.5E-05 40.1 3.7 38 263-300 26-63 (194)
47 PRK12524 RNA polymerase sigma 87.0 0.54 1.2E-05 40.9 2.8 38 263-300 25-62 (196)
48 TIGR02393 RpoD_Cterm RNA polym 86.6 1.2 2.6E-05 40.2 5.0 37 224-260 89-125 (238)
49 TIGR02850 spore_sigG RNA polym 86.2 1.3 2.8E-05 40.5 5.0 35 226-260 124-158 (254)
50 PRK12427 flagellar biosynthesi 86.2 1.3 2.8E-05 40.3 5.0 37 224-260 103-139 (231)
51 PRK07122 RNA polymerase sigma 85.8 1.4 3.1E-05 40.9 5.1 63 191-260 103-165 (264)
52 PRK09210 RNA polymerase sigma 84.4 1.7 3.7E-05 42.5 5.1 38 224-261 218-255 (367)
53 PRK07921 RNA polymerase sigma 83.2 1.9 4.2E-05 41.7 5.0 36 224-259 175-210 (324)
54 PRK09640 RNA polymerase sigma 81.3 1.3 2.7E-05 38.2 2.6 38 263-300 25-62 (188)
55 TIGR02885 spore_sigF RNA polym 80.4 3.1 6.8E-05 37.1 4.9 35 226-260 101-135 (231)
56 PRK07406 RNA polymerase sigma 80.4 4.1 8.9E-05 40.5 6.2 35 224-258 225-259 (373)
57 TIGR02479 FliA_WhiG RNA polyme 79.8 3.8 8.2E-05 36.5 5.2 36 224-259 85-120 (224)
58 PRK12538 RNA polymerase sigma 79.8 1.6 3.5E-05 39.8 3.0 37 264-300 63-99 (233)
59 PRK07598 RNA polymerase sigma 78.2 3.6 7.7E-05 41.7 5.0 39 222-260 262-300 (415)
60 PRK07500 rpoH2 RNA polymerase 78.0 8.6 0.00019 36.3 7.3 65 191-258 103-168 (289)
61 PRK06288 RNA polymerase sigma 77.7 4 8.7E-05 37.6 4.9 37 223-259 119-155 (268)
62 PRK07670 RNA polymerase sigma 77.7 4.5 9.7E-05 36.9 5.1 37 224-260 111-147 (251)
63 PRK10219 DNA-binding transcrip 77.5 10 0.00022 29.9 6.6 59 224-283 7-79 (107)
64 PRK05901 RNA polymerase sigma 77.0 3.8 8.2E-05 42.5 4.9 36 224-259 360-395 (509)
65 PRK05949 RNA polymerase sigma 76.9 4.2 9.1E-05 39.4 5.0 38 222-259 178-215 (327)
66 PF04967 HTH_10: HTH DNA bindi 76.9 11 0.00024 27.9 6.1 48 206-263 1-48 (53)
67 PRK09643 RNA polymerase sigma 76.3 3.7 8E-05 35.7 4.0 39 262-300 25-63 (192)
68 PRK11511 DNA-binding transcrip 75.8 10 0.00022 31.4 6.3 58 225-283 12-83 (127)
69 PRK12526 RNA polymerase sigma 74.3 5.1 0.00011 35.3 4.4 38 263-300 37-74 (206)
70 PRK08215 sporulation sigma fac 74.1 6.1 0.00013 36.2 5.0 35 225-259 126-160 (258)
71 PRK07405 RNA polymerase sigma 71.4 7.1 0.00015 37.5 5.0 38 222-259 168-205 (317)
72 TIGR02980 SigBFG RNA polymeras 69.7 9 0.00019 34.0 5.0 36 225-260 93-128 (227)
73 TIGR02997 Sig70-cyanoRpoD RNA 67.5 9.7 0.00021 35.9 4.9 38 223-260 162-199 (298)
74 COG3413 Predicted DNA binding 64.2 28 0.00061 31.2 7.0 57 205-274 155-211 (215)
75 smart00342 HTH_ARAC helix_turn 63.3 29 0.00063 24.6 5.8 56 238-297 1-59 (84)
76 PRK12537 RNA polymerase sigma 63.1 7.2 0.00016 33.4 2.9 38 263-300 22-59 (182)
77 PF02796 HTH_7: Helix-turn-hel 62.8 12 0.00025 26.0 3.4 43 201-260 1-43 (45)
78 PRK06986 fliA flagellar biosyn 60.9 16 0.00035 32.8 4.9 36 225-260 98-133 (236)
79 PF01726 LexA_DNA_bind: LexA D 59.9 23 0.0005 26.8 4.9 29 232-260 19-48 (65)
80 PRK15121 right oriC-binding tr 58.8 27 0.00059 32.3 6.2 38 224-261 7-44 (289)
81 COG4367 Uncharacterized protei 58.3 42 0.00091 28.0 6.4 44 228-271 12-62 (97)
82 COG4977 Transcriptional regula 58.3 26 0.00056 34.6 6.2 56 222-277 220-289 (328)
83 TIGR02941 Sigma_B RNA polymera 58.3 20 0.00044 32.6 5.2 36 225-260 119-154 (255)
84 PRK09649 RNA polymerase sigma 58.3 14 0.0003 31.9 3.9 35 264-299 24-58 (185)
85 PRK13503 transcriptional activ 57.9 34 0.00073 30.8 6.4 59 224-283 173-245 (278)
86 TIGR03001 Sig-70_gmx1 RNA poly 55.9 15 0.00033 33.9 3.9 36 264-299 39-74 (244)
87 PRK05572 sporulation sigma fac 55.8 22 0.00048 32.4 4.9 33 225-257 121-153 (252)
88 PRK05657 RNA polymerase sigma 50.9 23 0.0005 34.2 4.5 36 224-259 175-210 (325)
89 PRK15044 transcriptional regul 50.0 38 0.00082 33.2 5.7 60 193-261 172-231 (295)
90 PRK06596 RNA polymerase factor 45.1 40 0.00086 31.8 5.0 24 236-259 149-172 (284)
91 PF11176 DUF2962: Protein of u 45.0 13 0.00029 32.7 1.7 79 191-299 49-131 (155)
92 PRK13239 alkylmercury lyase; P 43.8 40 0.00087 31.4 4.6 27 235-261 33-59 (206)
93 PF09824 ArsR: ArsR transcript 42.9 11 0.00023 34.1 0.7 20 107-126 44-64 (160)
94 PRK09647 RNA polymerase sigma 42.4 21 0.00045 31.7 2.5 37 264-300 28-64 (203)
95 PRK09393 ftrA transcriptional 41.7 52 0.0011 30.8 5.2 38 224-261 220-257 (322)
96 COG1476 Predicted transcriptio 41.2 60 0.0013 25.5 4.6 49 239-297 15-63 (68)
97 PF13730 HTH_36: Helix-turn-he 40.2 1.1E+02 0.0023 21.3 5.4 27 235-261 22-48 (55)
98 PRK04217 hypothetical protein; 39.3 1.5E+02 0.0032 25.0 7.0 42 203-262 40-82 (110)
99 TIGR02297 HpaA 4-hydroxyphenyl 39.3 72 0.0016 28.8 5.6 35 227-261 191-225 (287)
100 PRK10572 DNA-binding transcrip 38.4 67 0.0014 29.3 5.2 59 224-283 185-257 (290)
101 PF12324 HTH_15: Helix-turn-he 37.4 32 0.0007 27.6 2.6 27 235-261 35-61 (77)
102 PF04545 Sigma70_r4: Sigma-70, 36.8 1.4E+02 0.0029 20.6 5.5 29 235-263 17-45 (50)
103 PF04282 DUF438: Family of unk 35.8 1.6E+02 0.0035 23.2 6.2 45 212-257 3-53 (71)
104 PF13936 HTH_38: Helix-turn-he 35.8 56 0.0012 22.6 3.4 41 204-261 3-43 (44)
105 TIGR01446 DnaD_dom DnaD and ph 35.5 96 0.0021 22.9 4.8 56 231-290 5-66 (73)
106 PRK10371 DNA-binding transcrip 35.1 82 0.0018 29.6 5.4 38 224-261 193-230 (302)
107 PRK13501 transcriptional activ 34.6 1.2E+02 0.0027 27.7 6.4 56 227-283 181-250 (290)
108 PRK11924 RNA polymerase sigma 34.4 2.3E+02 0.0049 23.2 7.4 28 237-264 140-167 (179)
109 smart00345 HTH_GNTR helix_turn 32.9 52 0.0011 22.3 2.9 24 238-261 20-43 (60)
110 PF13309 HTH_22: HTH domain 32.9 1.6E+02 0.0035 22.1 5.7 59 187-257 1-61 (64)
111 PF04218 CENP-B_N: CENP-B N-te 32.3 64 0.0014 23.3 3.3 44 203-263 4-47 (53)
112 PRK12517 RNA polymerase sigma 32.3 32 0.00069 29.9 2.0 39 261-299 20-58 (188)
113 cd06170 LuxR_C_like C-terminal 32.1 1.5E+02 0.0034 19.6 5.5 37 239-278 16-53 (57)
114 PRK15186 AraC family transcrip 32.1 1.3E+02 0.0029 28.8 6.3 37 225-261 184-220 (291)
115 PRK15369 two component system 32.1 2.3E+02 0.005 22.7 6.9 42 240-284 166-207 (211)
116 COG2207 AraC AraC-type DNA-bin 31.8 2E+02 0.0043 21.9 6.3 33 229-261 27-59 (127)
117 TIGR02404 trehalos_R_Bsub treh 31.4 98 0.0021 27.6 5.0 25 237-261 23-47 (233)
118 TIGR02394 rpoS_proteo RNA poly 31.4 74 0.0016 29.7 4.4 35 225-259 136-170 (285)
119 TIGR03826 YvyF flagellar opero 29.6 80 0.0017 27.6 4.0 34 230-263 38-71 (137)
120 PRK10130 transcriptional regul 29.2 1.5E+02 0.0033 29.0 6.4 37 225-261 243-279 (350)
121 PF00165 HTH_AraC: Bacterial r 29.0 67 0.0015 21.4 2.8 29 233-261 3-31 (42)
122 PRK06930 positive control sigm 28.6 2.5E+02 0.0054 24.8 7.1 32 234-265 126-157 (170)
123 PF13801 Metal_resist: Heavy-m 28.6 2.7E+02 0.0058 21.3 7.9 69 204-282 40-116 (125)
124 TIGR02325 C_P_lyase_phnF phosp 28.5 1.2E+02 0.0026 26.9 5.1 25 237-261 31-55 (238)
125 COG2188 PhnF Transcriptional r 27.5 1.2E+02 0.0027 27.6 5.1 26 236-261 29-54 (236)
126 PHA02591 hypothetical protein; 26.7 1E+02 0.0022 25.2 3.8 38 207-261 44-82 (83)
127 PF10078 DUF2316: Uncharacteri 26.7 1.5E+02 0.0032 24.4 4.8 33 238-270 23-62 (89)
128 PF00392 GntR: Bacterial regul 26.6 67 0.0015 23.3 2.6 24 238-261 24-47 (64)
129 PRK12527 RNA polymerase sigma 26.4 3.7E+02 0.008 22.1 8.0 35 235-269 118-152 (159)
130 PF08281 Sigma70_r4_2: Sigma-7 26.2 2E+02 0.0044 19.8 4.9 26 238-263 26-51 (54)
131 PRK14999 histidine utilization 25.5 1.4E+02 0.0031 26.8 5.1 25 237-261 35-59 (241)
132 PRK12519 RNA polymerase sigma 25.0 4.3E+02 0.0094 22.5 7.8 31 237-267 156-186 (194)
133 TIGR02018 his_ut_repres histid 24.9 1.5E+02 0.0032 26.5 5.0 25 237-261 24-48 (230)
134 TIGR02954 Sig70_famx3 RNA poly 24.7 3.9E+02 0.0085 22.2 7.3 53 210-264 109-161 (169)
135 PRK10079 phosphonate metabolis 24.5 1.5E+02 0.0032 26.7 5.0 25 237-261 34-58 (241)
136 PRK11402 DNA-binding transcrip 23.4 1.7E+02 0.0036 26.4 5.1 25 237-261 32-56 (241)
137 PRK09415 RNA polymerase factor 23.3 4.1E+02 0.0088 22.6 7.2 30 238-267 143-172 (179)
138 PRK06266 transcription initiat 23.1 2.2E+02 0.0048 25.6 5.7 24 238-261 36-59 (178)
139 PRK09764 DNA-binding transcrip 22.7 1.7E+02 0.0038 26.4 5.1 25 237-261 28-52 (240)
140 PRK12514 RNA polymerase sigma 22.5 3.8E+02 0.0082 22.5 6.8 28 237-264 144-171 (179)
141 PRK09978 DNA-binding transcrip 22.4 1.7E+02 0.0038 28.1 5.2 56 226-282 146-214 (274)
142 COG0411 LivG ABC-type branched 22.4 31 0.00067 33.2 0.2 37 248-284 178-220 (250)
143 PRK09648 RNA polymerase sigma 21.9 4.7E+02 0.01 22.2 7.3 33 231-263 148-180 (189)
144 PF13542 HTH_Tnp_ISL3: Helix-t 21.7 2.5E+02 0.0053 19.2 4.6 30 232-261 21-50 (52)
145 PF13404 HTH_AsnC-type: AsnC-t 21.7 2.1E+02 0.0045 19.9 4.2 24 238-261 17-40 (42)
146 smart00421 HTH_LUXR helix_turn 21.6 2.5E+02 0.0053 18.4 5.9 22 240-261 20-41 (58)
147 PF00356 LacI: Bacterial regul 21.5 2.1E+02 0.0045 20.4 4.2 23 240-262 1-23 (46)
148 PRK13502 transcriptional activ 21.4 2E+02 0.0043 26.1 5.2 56 227-283 181-250 (282)
149 PF08279 HTH_11: HTH domain; 21.3 2.1E+02 0.0044 19.8 4.2 25 238-262 15-39 (55)
150 PRK09646 RNA polymerase sigma 21.1 5.1E+02 0.011 22.3 7.5 50 213-264 135-184 (194)
151 PRK13558 bacterio-opsin activa 20.9 2.3E+02 0.0049 29.1 6.0 56 205-273 607-662 (665)
152 PRK08583 RNA polymerase sigma 20.9 2E+02 0.0044 26.2 5.1 33 227-259 121-153 (257)
153 TIGR01764 excise DNA binding d 20.6 1E+02 0.0022 20.1 2.4 23 240-262 3-25 (49)
154 PRK09685 DNA-binding transcrip 20.5 4.6E+02 0.0099 23.9 7.4 58 225-283 200-273 (302)
155 PRK13500 transcriptional activ 20.0 2.2E+02 0.0047 26.8 5.3 35 227-261 211-245 (312)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=99.91 E-value=1.1e-24 Score=213.63 Aligned_cols=110 Identities=30% Similarity=0.435 Sum_probs=101.9
Q ss_pred chHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCc--------------------HHHHHHHHHHHhCCCCCHHHHHHHhcc
Q 022167 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS--------------------LDDHKLRLKERLGCEPSMEQLAASLRI 250 (301)
Q Consensus 191 D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~--------------------Le~~r~eLee~LGrePt~eEwA~a~g~ 250 (301)
|+++.||++|+++||||++||++|+++||.++. |++++.+|++.+|++||.+|||.++|+
T Consensus 60 d~v~~yl~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~~~~~ 139 (415)
T PRK07598 60 DLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTADI 139 (415)
T ss_pred ChHHHHHHhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHHHhCC
Confidence 899999999999999999999999999999988 899999999999999999999977776
Q ss_pred ChHHHHHH----------------------hhhHHHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 251 SRPELQSI----------------------LMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 251 S~~eLrr~----------------------L~eG~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
++.+|+.. +..|+.|+++||++|+|||++||++|.++|++++||||||+|
T Consensus 140 ~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~i 211 (415)
T PRK07598 140 SLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTL 211 (415)
T ss_pred cHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHH
Confidence 65555555 567889999999999999999999999999999999999986
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=99.89 E-value=5.6e-23 Score=190.67 Aligned_cols=110 Identities=33% Similarity=0.511 Sum_probs=107.0
Q ss_pred chHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHH
Q 022167 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (301)
Q Consensus 191 D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV 270 (301)
|.+..|++++++.|+||++||++|+++++.|..+++.+.+|++++|++|+..+||+++|++..+|...+..|..|+++||
T Consensus 1 ~~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv 80 (298)
T TIGR02997 1 DLVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMI 80 (298)
T ss_pred CcHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHH
Confidence 35688999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 271 MSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 271 ~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
.+|+|||++||++|.|+|++++||||||++
T Consensus 81 ~~~lrlV~~iA~~y~~~~~~~eDLiQEg~i 110 (298)
T TIGR02997 81 KANLRLVVSVAKKYQNRGLELLDLIQEGSL 110 (298)
T ss_pred HHhHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence 999999999999999999999999999986
No 3
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=99.85 E-value=1.8e-21 Score=188.51 Aligned_cols=111 Identities=32% Similarity=0.474 Sum_probs=108.6
Q ss_pred cchHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHH
Q 022167 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL 269 (301)
Q Consensus 190 ~D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekL 269 (301)
.|.+..||++|+++|+||++||++|+++|+.+..+++.+.+|++.+|++|+.++||.++|++..+|++.+..|..|+++|
T Consensus 62 ~d~l~~Yl~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~L 141 (373)
T PRK07406 62 EDSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKM 141 (373)
T ss_pred CCHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHHH
Confidence 37889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 270 VMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 270 V~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
|.+|++||++||++|.++|++++||||||+|
T Consensus 142 i~~~l~lV~~iA~ry~~~~~~~eDLiQEG~i 172 (373)
T PRK07406 142 VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSL 172 (373)
T ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence 9999999999999999999999999999986
No 4
>PRK05949 RNA polymerase sigma factor; Validated
Probab=99.84 E-value=8.2e-21 Score=180.17 Aligned_cols=111 Identities=29% Similarity=0.469 Sum_probs=108.6
Q ss_pred cchHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHH
Q 022167 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL 269 (301)
Q Consensus 190 ~D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekL 269 (301)
.|.+..||++|++.|+||++||++|+++|+.+..+++.+..|+..+|++|+..+||.+++++..+|...+..|..|+++|
T Consensus 17 ~d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~~L 96 (327)
T PRK05949 17 ADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQKM 96 (327)
T ss_pred CCHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHHHH
Confidence 48899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 270 VMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 270 V~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
|++|+|+|++||++|.+.|.+++||||||+|
T Consensus 97 i~~~~~~V~~iA~~y~~~~~~~eDLvQEg~i 127 (327)
T PRK05949 97 IEANLRLVVAIAKKYQKRNMEFLDLIQEGTL 127 (327)
T ss_pred HHHHHHHHHHHHHHHccCCCCHHHHHHHHHH
Confidence 9999999999999999999999999999986
No 5
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=99.83 E-value=1.5e-20 Score=177.09 Aligned_cols=110 Identities=31% Similarity=0.469 Sum_probs=107.9
Q ss_pred chHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHH
Q 022167 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (301)
Q Consensus 191 D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV 270 (301)
|++..||+++++.|+||++||++|+++|+.+..+++++.+|++++|++|+..+||.+++++..+|...+..|..|+++|+
T Consensus 8 ~~~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~L~ 87 (317)
T PRK07405 8 DLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRKMV 87 (317)
T ss_pred cHHHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHHHH
Confidence 78899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 271 MSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 271 ~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
.+|+++|+++|++|.+.|.+++||||||++
T Consensus 88 ~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i 117 (317)
T PRK07405 88 EANLRLVVSVAKKYLKRNVDLLDLIQEGTI 117 (317)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence 999999999999999999999999999986
No 6
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=99.76 E-value=9.8e-19 Score=175.57 Aligned_cols=100 Identities=35% Similarity=0.467 Sum_probs=85.3
Q ss_pred hhcchHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHH
Q 022167 188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLARE 267 (301)
Q Consensus 188 l~~D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARe 267 (301)
...|.++.||++|+++|+||++||++|+++|+.|..++.. +.+ ..+|+.. ...+|+.++..|..||+
T Consensus 208 ~~~d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~---~~~-------~~~~~~~---~~~~l~~~~~~g~~Ar~ 274 (509)
T PRK05901 208 ATADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEEL---LAE-------GEKLDPE---LRRDLQWIGRDGKRAKN 274 (509)
T ss_pred ccccHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhh---hhh-------cccchhh---hhhhhhhhccchHHHHH
Confidence 4458999999999999999999999999999999764442 211 1223322 46789999999999999
Q ss_pred HHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 268 kLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
+||.+|||||++||++|.++|++|+||||||||
T Consensus 275 ~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnI 307 (509)
T PRK05901 275 HLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNL 307 (509)
T ss_pred HHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence 999999999999999999999999999999997
No 7
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=99.71 E-value=1.5e-17 Score=160.29 Aligned_cols=113 Identities=31% Similarity=0.382 Sum_probs=95.7
Q ss_pred hhcchHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHH-HhCCCCCHH---------------HHHHHhccC
Q 022167 188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKE-RLGCEPSME---------------QLAASLRIS 251 (301)
Q Consensus 188 l~~D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee-~LGrePt~e---------------EwA~a~g~S 251 (301)
+..|.+..|+.+++..+++++++|.++...++....+......|.. .+++.|+.. +|+..+...
T Consensus 6 ~~~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 85 (342)
T COG0568 6 LSADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPE 85 (342)
T ss_pred cchhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChH
Confidence 4568899999999999999999999999999888877777788887 678888876 333333332
Q ss_pred h-HHHHHHhhhHHH---HHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 252 R-PELQSILMECSL---AREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 252 ~-~eLrr~L~eG~~---ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
. .+|...+..|.. |+.+||.+|||||+||||+|.|+|++|.||||||||
T Consensus 86 Ee~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGni 138 (342)
T COG0568 86 EEKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNI 138 (342)
T ss_pred HHHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccH
Confidence 2 557777777765 999999999999999999999999999999999997
No 8
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=99.57 E-value=3.3e-15 Score=142.22 Aligned_cols=97 Identities=29% Similarity=0.456 Sum_probs=82.2
Q ss_pred chHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHH
Q 022167 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (301)
Q Consensus 191 D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV 270 (301)
|.+..||++++++|+||++||++|+++|+.|..++.. |+..+|+... ...+|+..+..|..|+++||
T Consensus 26 ~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~~Lv 92 (324)
T PRK07921 26 DLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARRHLL 92 (324)
T ss_pred ChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHHHHH
Confidence 7889999999999999999999999999988765443 1122222111 35689999999999999999
Q ss_pred HHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 271 MSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 271 ~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
.+|+++|+++|++|.++|++++||||||+|
T Consensus 93 ~~~~~lV~~iA~r~~~~~~~~eDLvQEg~i 122 (324)
T PRK07921 93 EANLRLVVSLAKRYTGRGMPLLDLIQEGNL 122 (324)
T ss_pred HHHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence 999999999999999999999999999986
No 9
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=99.34 E-value=1.1e-12 Score=126.34 Aligned_cols=72 Identities=36% Similarity=0.486 Sum_probs=68.0
Q ss_pred hcchHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHH
Q 022167 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREK 268 (301)
Q Consensus 189 ~~D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARek 268 (301)
+.|.++.||++|++.|+||++||.+|+++++.|.. .|+++
T Consensus 94 ~~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~Gd~----------------------------------------~A~~~ 133 (367)
T PRK09210 94 INDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGDE----------------------------------------EAKQR 133 (367)
T ss_pred cCcHHHHHHHHhhccCCCCHHHHHHHHHHHHhhHH----------------------------------------HHHHH
Confidence 45899999999999999999999999999987754 79999
Q ss_pred HHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 269 LVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 269 LV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
||.+|+++|++||++|.++|++++||||||+|
T Consensus 134 Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~i 165 (367)
T PRK09210 134 LAEANLRLVVSIAKRYVGRGMLFLDLIQEGNM 165 (367)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence 99999999999999999999999999999986
No 10
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=99.32 E-value=1.6e-12 Score=132.57 Aligned_cols=72 Identities=31% Similarity=0.463 Sum_probs=61.1
Q ss_pred hHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHH
Q 022167 192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM 271 (301)
Q Consensus 192 ~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~ 271 (301)
.+..|++++...+.|+++|+.++.++|+.|.. ....|+++||.
T Consensus 345 ~lq~~L~~ie~~~~Ls~eElk~l~~~i~~g~~-------------------------------------~~~~a~~~Li~ 387 (619)
T PRK05658 345 KLQQELEAIEEETGLTIEELKEINRQISKGEA-------------------------------------KARRAKKEMVE 387 (619)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHHhccch-------------------------------------hhhHHHHHHHH
Confidence 45677777777888888888888888877654 12379999999
Q ss_pred HhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 272 SNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 272 aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
+|||||++||++|.++|++|+||||||||
T Consensus 388 ~nlrlV~~iA~ky~~~gl~~~DLiQeG~i 416 (619)
T PRK05658 388 ANLRLVISIAKKYTNRGLQFLDLIQEGNI 416 (619)
T ss_pred HHHHHHHHHHHHHhhCCCCHHHHHHHHHH
Confidence 99999999999999999999999999997
No 11
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=99.17 E-value=5.5e-11 Score=110.60 Aligned_cols=74 Identities=35% Similarity=0.492 Sum_probs=68.4
Q ss_pred cCchhhcchHHHHHhhcCCCCCCCHHHHHHHHHHH-HcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhH
Q 022167 184 ISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKI-KTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMEC 262 (301)
Q Consensus 184 v~pel~~D~l~~YLkei~~~~LLT~EEEveLs~kI-q~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG 262 (301)
++|+ +.+..|++++++.|+||.++|.+|+..+ +.|+.
T Consensus 10 ~~~~---~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~~Gd~--------------------------------------- 47 (284)
T PRK06596 10 LSPE---GNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDL--------------------------------------- 47 (284)
T ss_pred CCCc---cHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCCH---------------------------------------
Confidence 6787 8899999999999999999999999985 46665
Q ss_pred HHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 263 ~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
.|++.||..|++||.+||++|.+.|++++||||||++
T Consensus 48 -~a~~~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~i 84 (284)
T PRK06596 48 -EAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNI 84 (284)
T ss_pred -HHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHH
Confidence 8999999999999999999999999999999999986
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=99.09 E-value=1.7e-10 Score=106.05 Aligned_cols=69 Identities=35% Similarity=0.468 Sum_probs=63.4
Q ss_pred hHHHHHhhcCCCCCCCHHHHHHHHHHH-HcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHH
Q 022167 192 RLKGYVKGVVSEELLTHAEVVRLSKKI-KTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270 (301)
Q Consensus 192 ~l~~YLkei~~~~LLT~EEEveLs~kI-q~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV 270 (301)
++..|++++++.|+|++++|.+|+.++ +.|+. .|+++||
T Consensus 2 ~~~~yl~~~~~~~~l~~~~e~~l~~~~~~~gd~----------------------------------------~a~~~Lv 41 (270)
T TIGR02392 2 SLDAYIRAVNRIPMLTPEEEYQLAKRLREHGDL----------------------------------------DAAKKLV 41 (270)
T ss_pred hHHHHHHHHhcCCCCCHHHHHHHHHHHHHCCCH----------------------------------------HHHHHHH
Confidence 467899999999999999999999985 45654 8999999
Q ss_pred HHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 271 MSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 271 ~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
..|++||.++|++|.+.|.+++||||||++
T Consensus 42 ~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i 71 (270)
T TIGR02392 42 LSHLRFVVKIARGYRGYGLPQADLIQEGNI 71 (270)
T ss_pred HHhHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence 999999999999999999999999999986
No 13
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=99.07 E-value=2.5e-10 Score=106.59 Aligned_cols=70 Identities=21% Similarity=0.339 Sum_probs=64.6
Q ss_pred chHHHHHhhcCCCCCCCHHHHHHHHHHHH-cCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHH
Q 022167 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIK-TGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL 269 (301)
Q Consensus 191 D~l~~YLkei~~~~LLT~EEEveLs~kIq-~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekL 269 (301)
+.++.||+++.+.|+||+++|.+|+.+++ .|+. .|+++|
T Consensus 6 ~~~~~y~~~~~~~~~l~~~~e~~L~~~~~~~gd~----------------------------------------~A~~~L 45 (289)
T PRK07500 6 SADRSMIRSAMKAPYLEREEEHALAYRWKDHRDE----------------------------------------DALHRI 45 (289)
T ss_pred hHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCCCH----------------------------------------HHHHHH
Confidence 55688999999999999999999999975 5654 899999
Q ss_pred HHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 270 VMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 270 V~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
|..|+++|.++|++|.+.|.+++||||||++
T Consensus 46 v~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i 76 (289)
T PRK07500 46 ISAHMRLVISMAGKFRRFGLPMNDLIQEGYV 76 (289)
T ss_pred HHHhHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence 9999999999999999999999999999986
No 14
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=98.94 E-value=1.5e-09 Score=103.35 Aligned_cols=73 Identities=30% Similarity=0.399 Sum_probs=68.7
Q ss_pred hhcchHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHH
Q 022167 188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLARE 267 (301)
Q Consensus 188 l~~D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARe 267 (301)
+..|.+..|+++|+..|+||+++|.+|..+++.|.. .|.+
T Consensus 50 ~~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~Gd~----------------------------------------~A~~ 89 (325)
T PRK05657 50 RVLDATQLYLNEIGYSPLLTAEEEVYFARRALRGDF----------------------------------------AARQ 89 (325)
T ss_pred ccccHHHHHHHHHhcCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHH
Confidence 344889999999999999999999999999998886 8899
Q ss_pred HHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 268 kLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
.||..|+++|.++|.+|.+.+.+.+||+|||+|
T Consensus 90 ~Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi 122 (325)
T PRK05657 90 RMIESNLRLVVKIAKRYLNRGLALLDLIEEGNL 122 (325)
T ss_pred HHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence 999999999999999999999999999999986
No 15
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=98.76 E-value=4.7e-09 Score=96.83 Aligned_cols=38 Identities=34% Similarity=0.452 Sum_probs=36.5
Q ss_pred HHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 263 ~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
..+|++||.+|+|||++||++|.++|++++||||||+|
T Consensus 39 ~~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~i 76 (264)
T PRK07122 39 QRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARV 76 (264)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence 46999999999999999999999999999999999986
No 16
>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=98.70 E-value=3.2e-08 Score=91.58 Aligned_cols=73 Identities=29% Similarity=0.371 Sum_probs=68.9
Q ss_pred hhcchHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHH
Q 022167 188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLARE 267 (301)
Q Consensus 188 l~~D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARe 267 (301)
...|.+..||.+|...|.|+.++|.+|...++.|.. .|.+
T Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~gd~----------------------------------------~a~~ 49 (285)
T TIGR02394 10 RVADVTQLYLREIGFKPLLTAEEEIAYARRALAGDF----------------------------------------EARK 49 (285)
T ss_pred CcchHHHHHHHHHhccCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHH
Confidence 455889999999999999999999999999999876 8999
Q ss_pred HHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 268 kLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
.|+..+.++|..+|.+|.+.+.+.+||+|||+|
T Consensus 50 ~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i 82 (285)
T TIGR02394 50 VMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNL 82 (285)
T ss_pred HHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence 999999999999999999999999999999986
No 17
>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=98.54 E-value=1.3e-07 Score=86.03 Aligned_cols=61 Identities=36% Similarity=0.500 Sum_probs=56.2
Q ss_pred cCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHH
Q 022167 200 VVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMS 279 (301)
Q Consensus 200 i~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVS 279 (301)
.++.|+||++||.+|+..++.|.. .|.++|+..|+++|.+
T Consensus 10 ~~~~~~l~~~~~~~li~~~~~gd~----------------------------------------~a~~~L~~~~~~~v~~ 49 (254)
T TIGR02850 10 TSKLPVLKNQEMRELFIRMQSGDT----------------------------------------TAREKLINGNLRLVLS 49 (254)
T ss_pred ccCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHHHHH
Confidence 367899999999999999987765 7899999999999999
Q ss_pred HHhhccCCCCChhhHhhhccC
Q 022167 280 IAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 280 IAKRY~grGLsfeDLIQEGnI 300 (301)
+|++|.+.+.+.+||+|||++
T Consensus 50 ~a~~~~~~~~~aeDlvQe~~i 70 (254)
T TIGR02850 50 VIQRFNNRGEYVDDLFQVGCI 70 (254)
T ss_pred HHHHHhCCCCCHHHHHHHHHH
Confidence 999999999999999999986
No 18
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=98.44 E-value=3.3e-07 Score=83.47 Aligned_cols=60 Identities=37% Similarity=0.534 Sum_probs=55.0
Q ss_pred CCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHH
Q 022167 201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI 280 (301)
Q Consensus 201 ~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSI 280 (301)
.+.|+|+++|+..|..+++.|.. .|.++|+..|+++|..+
T Consensus 14 ~~~~~l~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~~~~~v~~~ 53 (258)
T PRK08215 14 SKLPVLKNEEMRELFERMQNGDK----------------------------------------EAREKLINGNLRLVLSV 53 (258)
T ss_pred CCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHH
Confidence 34679999999999999987765 78999999999999999
Q ss_pred HhhccCCCCChhhHhhhccC
Q 022167 281 AQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 281 AKRY~grGLsfeDLIQEGnI 300 (301)
|++|.+.+.+.+||+|||++
T Consensus 54 a~~~~~~~~~aeDlvQe~~i 73 (258)
T PRK08215 54 IQRFNNRGENVDDLFQVGCI 73 (258)
T ss_pred HHHHhCCCCCHHHHHHHHHH
Confidence 99999999999999999986
No 19
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=98.25 E-value=2.5e-06 Score=76.44 Aligned_cols=69 Identities=30% Similarity=0.413 Sum_probs=63.6
Q ss_pred hHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHH
Q 022167 192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM 271 (301)
Q Consensus 192 ~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~ 271 (301)
.+..|+.++++.++||+++|..|...++.|.. .|.+.|+.
T Consensus 17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~gd~----------------------------------------~a~~~l~~ 56 (233)
T PRK05803 17 FLVSYVKNNSFPQPLSEEEERKYLELMKEGDE----------------------------------------EARNILIE 56 (233)
T ss_pred HHHHHHHHhcccCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHH
Confidence 56899999999999999999999998887765 78899999
Q ss_pred HhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 272 SNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 272 aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
.+.++|.++|.+|.+.+.+.+||||||.|
T Consensus 57 ~y~~~l~~~a~~~~~~~~daeDlvQE~fi 85 (233)
T PRK05803 57 RNLRLVAHIVKKFENTGEDVDDLISIGTI 85 (233)
T ss_pred HhHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence 99999999999999999999999999875
No 20
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=98.16 E-value=2.8e-06 Score=77.89 Aligned_cols=37 Identities=38% Similarity=0.378 Sum_probs=34.6
Q ss_pred HHHHHHHHHhHHHHHHHHhhccCC-CCChhhHhhhccC
Q 022167 264 LAREKLVMSNVRLVMSIAQRYDNM-GADMADLVQVIFY 300 (301)
Q Consensus 264 ~ARekLV~aNLRLVVSIAKRY~gr-GLsfeDLIQEGnI 300 (301)
.|+++||.+|++||.+||++|.++ +.+++||||||+|
T Consensus 25 ~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~i 62 (256)
T PRK07408 25 ALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSL 62 (256)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHH
Confidence 899999999999999999999876 7789999999986
No 21
>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=98.16 E-value=3.2e-07 Score=62.67 Aligned_cols=33 Identities=30% Similarity=0.483 Sum_probs=30.3
Q ss_pred chHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCc
Q 022167 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS 223 (301)
Q Consensus 191 D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~ 223 (301)
|+++.||++|++.|+||++||++|+++|+.|..
T Consensus 2 D~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~~ 34 (37)
T PF00140_consen 2 DSLRLYLKEIGRYPLLTAEEEIELARRIRKGDE 34 (37)
T ss_dssp HHHHHHHHHHHHS-EETTHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHH
Confidence 889999999999999999999999999998765
No 22
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=98.15 E-value=2.5e-06 Score=79.75 Aligned_cols=36 Identities=36% Similarity=0.586 Sum_probs=34.5
Q ss_pred HHHHHHHHHhHHHHHHHHhhccCCCC-ChhhHhhhccC
Q 022167 264 LAREKLVMSNVRLVMSIAQRYDNMGA-DMADLVQVIFY 300 (301)
Q Consensus 264 ~ARekLV~aNLRLVVSIAKRY~grGL-sfeDLIQEGnI 300 (301)
.++ +||+.|++||.+||+||.++|. .++||||.|+|
T Consensus 24 ~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~i 60 (247)
T COG1191 24 EAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMI 60 (247)
T ss_pred HHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHH
Confidence 888 9999999999999999999998 99999999986
No 23
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=98.13 E-value=3.7e-06 Score=77.18 Aligned_cols=61 Identities=21% Similarity=0.229 Sum_probs=53.2
Q ss_pred cCCCCCCCHHHHHHHHHHHHc-CCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHH
Q 022167 200 VVSEELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVM 278 (301)
Q Consensus 200 i~~~~LLT~EEEveLs~kIq~-g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVV 278 (301)
.|..|+||.++|.+|+.+++. +.. .|.+.|+..|++||.
T Consensus 6 ~~~~~~~~~~~e~~l~~~~~~~~d~----------------------------------------~a~~~l~~~y~~lv~ 45 (268)
T PRK06288 6 SGKIPKYAQQDETELWREYKKTGDP----------------------------------------KIREYLILKYSPLVK 45 (268)
T ss_pred cCCCccccchHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHH
Confidence 478899999999999999874 343 788999999999999
Q ss_pred HHHhhcc-C--CCCChhhHhhhccC
Q 022167 279 SIAQRYD-N--MGADMADLVQVIFY 300 (301)
Q Consensus 279 SIAKRY~-g--rGLsfeDLIQEGnI 300 (301)
.+|++|. + .+.+.+||+|||++
T Consensus 46 ~~a~~~~~~~~~~~~~eDl~Qeg~l 70 (268)
T PRK06288 46 YVAGRIAVGMPQNVEFDDLVSYGVF 70 (268)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHHH
Confidence 9999986 2 57889999999986
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=98.02 E-value=8.1e-06 Score=74.00 Aligned_cols=57 Identities=35% Similarity=0.362 Sum_probs=51.8
Q ss_pred CCCCHHHHHHHHHHHHc-CCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHHHh
Q 022167 204 ELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ 282 (301)
Q Consensus 204 ~LLT~EEEveLs~kIq~-g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSIAK 282 (301)
+.||+++|.+|..+++. |+. .|.++|+..|.++|..+|+
T Consensus 8 ~~l~~~~~~~li~~~~~~gd~----------------------------------------~a~~~l~~~y~~~v~~~a~ 47 (255)
T TIGR02941 8 TNLTKEDVIQWIAEFQQNQNG----------------------------------------EAQEKLVDHYQNLVYSIAY 47 (255)
T ss_pred CCCCHHHHHHHHHHHHHCCCH----------------------------------------HHHHHHHHHhHHHHHHHHH
Confidence 66899999999999876 344 7889999999999999999
Q ss_pred hccCCCCChhhHhhhccC
Q 022167 283 RYDNMGADMADLVQVIFY 300 (301)
Q Consensus 283 RY~grGLsfeDLIQEGnI 300 (301)
+|.+.+.+.+||+|||+|
T Consensus 48 ~~~~~~~~aeDlvQe~~i 65 (255)
T TIGR02941 48 KYSKGGPMHEDLVQVGML 65 (255)
T ss_pred HHhcCCCCHHHHHHHHHH
Confidence 999999999999999986
No 25
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=97.88 E-value=2e-05 Score=71.52 Aligned_cols=57 Identities=33% Similarity=0.296 Sum_probs=52.0
Q ss_pred CCCCHHHHHHHHHHHHc-CCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHHHh
Q 022167 204 ELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ 282 (301)
Q Consensus 204 ~LLT~EEEveLs~kIq~-g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSIAK 282 (301)
+.|+++||.+|..+++. |.. .|.+.|+..|.++|..+|+
T Consensus 8 ~~l~~~e~~~li~~~~~~gd~----------------------------------------~a~~~l~~~~~~~v~~~a~ 47 (257)
T PRK08583 8 TKLTKEEVNKWIAEYQENQDE----------------------------------------EAQEKLVKHYKNLVESLAY 47 (257)
T ss_pred CcCChHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHHHH
Confidence 77999999999998875 554 7899999999999999999
Q ss_pred hccCCCCChhhHhhhccC
Q 022167 283 RYDNMGADMADLVQVIFY 300 (301)
Q Consensus 283 RY~grGLsfeDLIQEGnI 300 (301)
+|.+.+.+.+||+|||++
T Consensus 48 ~~~~~~~~aeDlvQe~~l 65 (257)
T PRK08583 48 KYSKGQSHHEDLVQVGMV 65 (257)
T ss_pred HHhcCCCCHHHHHHHHHH
Confidence 999999999999999975
No 26
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=97.76 E-value=2e-05 Score=72.50 Aligned_cols=38 Identities=21% Similarity=0.113 Sum_probs=33.6
Q ss_pred HHHHHHHHHHhHHHHHHHHhhccC---CCCChhhHhhhccC
Q 022167 263 SLAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQVIFY 300 (301)
Q Consensus 263 ~~ARekLV~aNLRLVVSIAKRY~g---rGLsfeDLIQEGnI 300 (301)
..||++||.+|++||.+||++|.+ .+++++||||||+|
T Consensus 22 ~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~i 62 (257)
T PRK05911 22 IEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVE 62 (257)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHH
Confidence 379999999999999999999862 35679999999986
No 27
>PRK05572 sporulation sigma factor SigF; Validated
Probab=97.70 E-value=7.4e-05 Score=67.95 Aligned_cols=64 Identities=38% Similarity=0.401 Sum_probs=57.5
Q ss_pred HhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHH
Q 022167 197 VKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRL 276 (301)
Q Consensus 197 Lkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRL 276 (301)
++.-...|.||.+++.+|...++.|.. .|.++|+..+.++
T Consensus 5 ~~~~~~~~~l~~~~~~~li~~~~~gd~----------------------------------------~a~~~L~~~y~~~ 44 (252)
T PRK05572 5 VKNKKKKPQLKDEENKELIKKSQDGDQ----------------------------------------EARDTLVEKNLRL 44 (252)
T ss_pred hccCcCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHH
Confidence 456677899999999999988877665 7899999999999
Q ss_pred HHHHHhhccCCCCChhhHhhhccC
Q 022167 277 VMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 277 VVSIAKRY~grGLsfeDLIQEGnI 300 (301)
|..+|.+|.+.+.+.+||+|||.+
T Consensus 45 v~~~a~~~~~~~~~aeDl~Qe~~l 68 (252)
T PRK05572 45 VWSVVQRFLNRGYEPDDLFQIGCI 68 (252)
T ss_pred HHHHHHHHccCCCCHHHHHHHHHH
Confidence 999999999999999999999975
No 28
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=97.46 E-value=0.00015 Score=74.71 Aligned_cols=35 Identities=23% Similarity=0.456 Sum_probs=32.8
Q ss_pred hcchHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCc
Q 022167 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS 223 (301)
Q Consensus 189 ~~D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~ 223 (301)
++||+++||++||.+||||+|+|++|+++|..|..
T Consensus 102 t~DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~ 136 (619)
T PRK05658 102 TDDPVRMYLREMGTVELLTREGEIEIAKRIEAGEN 136 (619)
T ss_pred CCChHHHHHHHhccCcCCCcHHHHHHHHHHHHHHH
Confidence 56999999999999999999999999999988765
No 29
>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=97.10 E-value=0.00095 Score=50.29 Aligned_cols=38 Identities=32% Similarity=0.536 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 224 Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
+.+.+.+|++.+||+||.+|+|+.+|++.++++.++..
T Consensus 6 i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~ 43 (78)
T PF04539_consen 6 IERARRELEQELGREPTDEEIAEELGISVEEVRELLQA 43 (78)
T ss_dssp HHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHh
Confidence 56788899999999999999999999999998876643
No 30
>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=97.00 E-value=0.0015 Score=58.58 Aligned_cols=68 Identities=31% Similarity=0.464 Sum_probs=58.1
Q ss_pred HHHHHhhc-CCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHH
Q 022167 193 LKGYVKGV-VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM 271 (301)
Q Consensus 193 l~~YLkei-~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~ 271 (301)
+-.|+..- +..+.|++.+|.+|...++.|.. .|-+.|+.
T Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~li~~~~~gd~----------------------------------------~af~~l~~ 55 (227)
T TIGR02846 16 LVGYVTNNGSFPQPLSEEEEKKYLDRLKEGDE----------------------------------------EARNVLIE 55 (227)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHH
Confidence 34565444 45677999999999999988775 78889999
Q ss_pred HhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 272 SNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 272 aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
.+.++|..+|.+|.+...+.+||+||+.+
T Consensus 56 ~y~~~v~~~~~~~~~~~~dAEDlvQevfi 84 (227)
T TIGR02846 56 RNLRLVAHIVKKFSNTGEDVDDLISIGTI 84 (227)
T ss_pred HhHHHHHHHHHHhcCCCCCHHHHHHHHHH
Confidence 99999999999999999999999999864
No 31
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=96.91 E-value=0.0021 Score=57.42 Aligned_cols=66 Identities=29% Similarity=0.425 Sum_probs=56.4
Q ss_pred HHHhhcCCC-CCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHh
Q 022167 195 GYVKGVVSE-ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSN 273 (301)
Q Consensus 195 ~YLkei~~~-~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aN 273 (301)
-|+.+.... +.++..++.+|...++.|.. .|-+.|+..+
T Consensus 22 ~~~~~~~~~~~~~~~~~~~~L~~~~~~gd~----------------------------------------~af~~l~~~y 61 (234)
T PRK08301 22 YYIGGSEALPPPLSKEEEEYLLNKLPKGDE----------------------------------------AVRSLLIERN 61 (234)
T ss_pred HHhccccccCCcCCHHHHHHHHHHHHccCH----------------------------------------HHHHHHHHHh
Confidence 467776553 55888899999888887765 7888999999
Q ss_pred HHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 274 VRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 274 LRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
.++|..+|.+|.+.+.+.+||+||+.+
T Consensus 62 ~~~l~~~a~~~~~~~~~AeDlvQevfl 88 (234)
T PRK08301 62 LRLVVYIARKFENTGINIEDLISIGTI 88 (234)
T ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHH
Confidence 999999999999999999999999865
No 32
>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=96.31 E-value=0.0091 Score=53.81 Aligned_cols=58 Identities=33% Similarity=0.443 Sum_probs=51.9
Q ss_pred CCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHHHh
Q 022167 203 EELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ 282 (301)
Q Consensus 203 ~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSIAK 282 (301)
.+.|++++|.+|...++.|.. .|.+.|+..+.++|..+|.
T Consensus 31 ~~~~~~~~~~~l~~~~~~~d~----------------------------------------~a~~~l~~~y~~~l~~~~~ 70 (234)
T TIGR02835 31 PPPLTGEEEEALLQKLTQGDE----------------------------------------SAKSTLIERNLRLVVYIAR 70 (234)
T ss_pred CCcCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHHHHHHHH
Confidence 578888999999888877664 7889999999999999999
Q ss_pred hccCCCCChhhHhhhccC
Q 022167 283 RYDNMGADMADLVQVIFY 300 (301)
Q Consensus 283 RY~grGLsfeDLIQEGnI 300 (301)
+|.+.+.+-+||+||+.+
T Consensus 71 ~~~~~~~~AEDlvQE~fl 88 (234)
T TIGR02835 71 KFENTGIGIEDLVSIGTI 88 (234)
T ss_pred HhccCCCCHHHHHHHHHH
Confidence 999999999999999864
No 33
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=95.63 E-value=0.016 Score=52.11 Aligned_cols=60 Identities=22% Similarity=0.176 Sum_probs=53.2
Q ss_pred CCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHH
Q 022167 201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI 280 (301)
Q Consensus 201 ~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSI 280 (301)
...|+|+...+..|...++.|.. .|-+.|+..+.++|..+
T Consensus 7 ~~~~~~~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~y~~~l~~~ 46 (231)
T PRK11922 7 SRPPPLSAASDRELVARVLAGDE----------------------------------------AAFEALMRRHNRRLYRT 46 (231)
T ss_pred CCCCCcCcccHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHH
Confidence 46789999999999888887765 77888999999999999
Q ss_pred HhhccCCCCChhhHhhhccC
Q 022167 281 AQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 281 AKRY~grGLsfeDLIQEGnI 300 (301)
|.+|.+.+-+-+||+||+.+
T Consensus 47 a~~~~~~~~~AEDlvQE~fi 66 (231)
T PRK11922 47 ARAILRNDAEAEDVVQEAYL 66 (231)
T ss_pred HHHHhCChhhHHHHHHHHHH
Confidence 99999999999999999864
No 34
>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=94.90 E-value=0.016 Score=41.43 Aligned_cols=32 Identities=34% Similarity=0.382 Sum_probs=29.9
Q ss_pred HHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 269 LVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 269 LV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
|++.+.++|..+|.+|.+.+.+.+|++||+.+
T Consensus 1 L~~~~~~~l~~~~~~~~~~~~~~eD~~qe~~~ 32 (71)
T PF04542_consen 1 LYERYYPLLYRYARRYTGDPEDAEDLVQEAFI 32 (71)
T ss_dssp HHHHTHHHHHHHHHTCTTCSSHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHhCCHhhHHHHhhHHHH
Confidence 68899999999999999999999999999864
No 35
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=94.25 E-value=0.082 Score=45.34 Aligned_cols=37 Identities=16% Similarity=0.082 Sum_probs=32.3
Q ss_pred HHHHHHHHHhHHHHHHHHhhccCC----CCChhhHhhhccC
Q 022167 264 LAREKLVMSNVRLVMSIAQRYDNM----GADMADLVQVIFY 300 (301)
Q Consensus 264 ~ARekLV~aNLRLVVSIAKRY~gr----GLsfeDLIQEGnI 300 (301)
.|-+.|+..+...|..+|.+|.+. +.+.+|++||+.+
T Consensus 24 ~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi 64 (189)
T PRK09648 24 RALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCL 64 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHH
Confidence 889999999999999999998643 4689999999864
No 36
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=93.63 E-value=0.31 Score=48.17 Aligned_cols=32 Identities=31% Similarity=0.509 Sum_probs=29.9
Q ss_pred chHHHHHhhcCCCCCCCHHHHHHHHHHHHcCC
Q 022167 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGL 222 (301)
Q Consensus 191 D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~ 222 (301)
..+..|+..+...++|+++||..|+..++.|.
T Consensus 67 ~~~~~~~~~~~~~~~l~~~Ee~~la~~~~~g~ 98 (342)
T COG0568 67 GRLSFYIRAIEAAPLLTPEEEKALARRLKRGE 98 (342)
T ss_pred hhHHHHHHHHhhhcccChHHHHHHHHHHHcCC
Confidence 67789999999999999999999999999996
No 37
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=93.02 E-value=0.1 Score=44.95 Aligned_cols=38 Identities=18% Similarity=0.075 Sum_probs=35.2
Q ss_pred HHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 263 ~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
..|-+.|+..+.++|..+|.+|.+...+.+||+||+.+
T Consensus 25 ~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi 62 (194)
T PRK12513 25 AAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWL 62 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 48899999999999999999999998999999999865
No 38
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=92.82 E-value=0.18 Score=43.59 Aligned_cols=38 Identities=32% Similarity=0.271 Sum_probs=35.4
Q ss_pred HHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 263 ~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
..|-+.|+..+.++|..+|.+|.+.+.+-+||+||+.+
T Consensus 23 ~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l 60 (208)
T PRK08295 23 KEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMI 60 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence 47889999999999999999999999999999999865
No 39
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=92.26 E-value=0.15 Score=43.78 Aligned_cols=37 Identities=27% Similarity=0.241 Sum_probs=34.2
Q ss_pred HHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 264 ~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
.|-+.|+..+.++|..+|++|.+...+-+|++||+.+
T Consensus 29 ~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl 65 (194)
T PRK12519 29 AALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFL 65 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 7888999999999999999999988899999999864
No 40
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=92.03 E-value=0.22 Score=47.00 Aligned_cols=62 Identities=21% Similarity=0.333 Sum_probs=46.8
Q ss_pred chHHHHHhhcC--CCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhH
Q 022167 191 NRLKGYVKGVV--SEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMEC 262 (301)
Q Consensus 191 D~l~~YLkei~--~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG 262 (301)
.-+..||+.-. ..|. --. +.+..+..+.++|+..+||+||.+|+|+.+|++.+++..++..+
T Consensus 87 Gei~d~LR~~~~v~vpR----~~~------~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~ 150 (247)
T COG1191 87 GEILDYLRKNDSVKVPR----SLR------ELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAI 150 (247)
T ss_pred HHHHHHHHhCCCccCcH----HHH------HHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHh
Confidence 34678888877 2221 122 23556677889999999999999999999999999987776654
No 41
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=91.30 E-value=0.22 Score=43.16 Aligned_cols=38 Identities=13% Similarity=0.032 Sum_probs=35.2
Q ss_pred HHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 263 ~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
..|-++|+..+-++|..+|.+|.+...+-+|++||+.|
T Consensus 29 ~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi 66 (194)
T PRK09646 29 QDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYL 66 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 47889999999999999999999999999999999864
No 42
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=90.94 E-value=0.3 Score=41.74 Aligned_cols=38 Identities=18% Similarity=0.182 Sum_probs=34.4
Q ss_pred HHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 263 ~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
..+-+.|+..+.++|..+|.+|.+...+-+|++||..+
T Consensus 24 ~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl 61 (187)
T PRK12534 24 RHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFT 61 (187)
T ss_pred HHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence 37788899999999999999999998999999999754
No 43
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=90.88 E-value=0.21 Score=42.53 Aligned_cols=38 Identities=26% Similarity=0.297 Sum_probs=34.7
Q ss_pred HHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 263 ~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
..|-+.|+..+.++|..+|.+|.+.+.+-+||+||+.+
T Consensus 22 ~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i 59 (186)
T PRK13919 22 EEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFI 59 (186)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence 37888899999999999999999999999999999864
No 44
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=88.85 E-value=0.87 Score=42.06 Aligned_cols=36 Identities=33% Similarity=0.427 Sum_probs=30.3
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhh
Q 022167 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (301)
Q Consensus 225 e~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~ 260 (301)
......|.+.+|++|+.+|+|+.+|++.+++..++.
T Consensus 113 ~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~ 148 (257)
T PRK05911 113 ADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFS 148 (257)
T ss_pred HHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHH
Confidence 345567888999999999999999999998876654
No 45
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=87.75 E-value=0.87 Score=41.95 Aligned_cols=36 Identities=31% Similarity=0.452 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHh
Q 022167 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (301)
Q Consensus 224 Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L 259 (301)
+...+.+|.+.+|++|+.+|+|+.+|+++++++.++
T Consensus 115 ~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~ 150 (256)
T PRK07408 115 AKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIK 150 (256)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHH
Confidence 445678899999999999999999999999887654
No 46
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=87.42 E-value=0.69 Score=40.12 Aligned_cols=38 Identities=11% Similarity=-0.066 Sum_probs=33.8
Q ss_pred HHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 263 ~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
..|-+.|++.+.+.|..+|.+|.+..-.-+||+||..+
T Consensus 26 ~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l 63 (194)
T PRK12531 26 KQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMS 63 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 37788899999999999999999888889999999764
No 47
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=87.01 E-value=0.54 Score=40.86 Aligned_cols=38 Identities=18% Similarity=0.174 Sum_probs=35.0
Q ss_pred HHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 263 ~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
..|-+.|+..+-.+|..+|.+|.+...+-+|++||+.+
T Consensus 25 ~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l 62 (196)
T PRK12524 25 PAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAML 62 (196)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 47889999999999999999999999999999999864
No 48
>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=86.58 E-value=1.2 Score=40.24 Aligned_cols=37 Identities=27% Similarity=0.407 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhh
Q 022167 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (301)
Q Consensus 224 Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~ 260 (301)
+.+...++.+.+|++||.+|+|+.+|++.++++.++.
T Consensus 89 ~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~ 125 (238)
T TIGR02393 89 LIKAERQLTQELGREPTDEELAERMGMPAEKVREIKK 125 (238)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4456778889999999999999999999988876543
No 49
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=86.25 E-value=1.3 Score=40.53 Aligned_cols=35 Identities=20% Similarity=0.298 Sum_probs=29.2
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhh
Q 022167 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (301)
Q Consensus 226 ~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~ 260 (301)
....++...+|++|+.+|+|+.+|++.+++..++.
T Consensus 124 ~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~~ 158 (254)
T TIGR02850 124 QVRDKLISENSKEPTVSEIAKELKVPQEEVVFALD 158 (254)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 35667888999999999999999999888766543
No 50
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=86.19 E-value=1.3 Score=40.34 Aligned_cols=37 Identities=32% Similarity=0.578 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhh
Q 022167 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (301)
Q Consensus 224 Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~ 260 (301)
+.....++.+.+|++|+.+|+|+.+|++.+++...+.
T Consensus 103 i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~ 139 (231)
T PRK12427 103 TNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLL 139 (231)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3456678889999999999999999999988876653
No 51
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=85.85 E-value=1.4 Score=40.94 Aligned_cols=63 Identities=22% Similarity=0.305 Sum_probs=42.0
Q ss_pred chHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhh
Q 022167 191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (301)
Q Consensus 191 D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~ 260 (301)
..+..|+++....-.+... -.++..+ +.....+|.+.+|++||.+|+|+.+|++.+++..++.
T Consensus 103 g~I~~~lr~~~~~ir~Pr~-~~~~~~~------i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~ 165 (264)
T PRK07122 103 GEVRRHFRDNSWSVKVPRR-LKELHLR------LGRATAELSQRLGRAPTASELAAELGMDREEVVEGLV 165 (264)
T ss_pred HHHHHHHHHcCCccccCHH-HHHHHHH------HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3456677765543223221 2233333 3345678888999999999999999999988876553
No 52
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=84.38 E-value=1.7 Score=42.54 Aligned_cols=38 Identities=26% Similarity=0.393 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 224 Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
+.....+|.+.+||+||.+|+|..+|++.++++.++..
T Consensus 218 ~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~ 255 (367)
T PRK09210 218 LIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKI 255 (367)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHH
Confidence 45567788899999999999999999999888876443
No 53
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=83.23 E-value=1.9 Score=41.72 Aligned_cols=36 Identities=31% Similarity=0.422 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHh
Q 022167 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (301)
Q Consensus 224 Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L 259 (301)
+...+.+|.+.+|++||.+|+|..+|++.+++...+
T Consensus 175 l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~ 210 (324)
T PRK07921 175 LARIKRELHQQLGREATDEELAEESGIPEEKIADLL 210 (324)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 456677888999999999999999999988876653
No 54
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=81.32 E-value=1.3 Score=38.21 Aligned_cols=38 Identities=24% Similarity=0.339 Sum_probs=35.0
Q ss_pred HHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 263 ~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
..|-+.|+..+.+.|..+|.+|.+...+-+|++||+.+
T Consensus 25 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~ 62 (188)
T PRK09640 25 TRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVML 62 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHH
Confidence 47888999999999999999999999999999999864
No 55
>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=80.42 E-value=3.1 Score=37.11 Aligned_cols=35 Identities=34% Similarity=0.455 Sum_probs=29.3
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhh
Q 022167 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (301)
Q Consensus 226 ~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~ 260 (301)
.....+...+|++||.+|+|+.+|++.+++...+.
T Consensus 101 ~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~ 135 (231)
T TIGR02885 101 YMKEELSKELGREPTINELAEALGVSPEEIVMALE 135 (231)
T ss_pred HHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 45567888899999999999999999988776544
No 56
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=80.40 E-value=4.1 Score=40.47 Aligned_cols=35 Identities=23% Similarity=0.433 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHH
Q 022167 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (301)
Q Consensus 224 Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~ 258 (301)
+......|.+.+|++||.+|+|..+|++.++++..
T Consensus 225 i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~ 259 (373)
T PRK07406 225 IKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFI 259 (373)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 44566788899999999999999999998887654
No 57
>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=79.83 E-value=3.8 Score=36.49 Aligned_cols=36 Identities=33% Similarity=0.493 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHh
Q 022167 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (301)
Q Consensus 224 Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L 259 (301)
+.....+|.+.+|++|+.+|+|+.+|++.++++.++
T Consensus 85 l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~ 120 (224)
T TIGR02479 85 LERAIRELEARLGREPTEEEIAEELGMDLKEYRQAL 120 (224)
T ss_pred HHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHH
Confidence 455667788899999999999999999998887766
No 58
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=79.82 E-value=1.6 Score=39.77 Aligned_cols=37 Identities=30% Similarity=0.223 Sum_probs=33.4
Q ss_pred HHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 264 ~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
.|-+.|+..+.+.|..++.+|.+...+-+|++||..+
T Consensus 63 ~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl 99 (233)
T PRK12538 63 AAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTML 99 (233)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH
Confidence 7788899999999999999999888889999999754
No 59
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=78.21 E-value=3.6 Score=41.69 Aligned_cols=39 Identities=15% Similarity=0.457 Sum_probs=33.7
Q ss_pred CcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhh
Q 022167 222 LSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (301)
Q Consensus 222 ~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~ 260 (301)
..+.+.+.+|.+.+||.|+.+|+|+.+|++.++++.++.
T Consensus 262 ~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l~ 300 (415)
T PRK07598 262 NKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLL 300 (415)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 345667788889999999999999999999999988755
No 60
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=77.97 E-value=8.6 Score=36.32 Aligned_cols=65 Identities=15% Similarity=0.146 Sum_probs=39.2
Q ss_pred chHHHHHhhcCCCCCC-CHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHH
Q 022167 191 NRLKGYVKGVVSEELL-THAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258 (301)
Q Consensus 191 D~l~~YLkei~~~~LL-T~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~ 258 (301)
..+..|+++-.....+ +...+..+..+++. +.....++...+|++|+.+|+|+.+|++.+++...
T Consensus 103 ~~I~~~lr~~~~~iR~p~~~~~~~~~~~~~~---~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~ 168 (289)
T PRK07500 103 ASIQDYILRNWSIVRGGTSSAQKALFFNLRR---LRARLAQADEELTKQEIHREIATALGVSLSDVEMM 168 (289)
T ss_pred HHHHHHHHHCCCceecCccHHHHHHHHHHHH---HHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHH
Confidence 4456667664443332 33344445544432 22222223346899999999999999999887654
No 61
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=77.72 E-value=4 Score=37.64 Aligned_cols=37 Identities=38% Similarity=0.495 Sum_probs=31.6
Q ss_pred cHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHh
Q 022167 223 SLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (301)
Q Consensus 223 ~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L 259 (301)
.+.+.+..|++.+|++|+.+|+|..+|++.+++..++
T Consensus 119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~ 155 (268)
T PRK06288 119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLL 155 (268)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHH
Confidence 4556677889999999999999999999998877665
No 62
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=77.70 E-value=4.5 Score=36.90 Aligned_cols=37 Identities=16% Similarity=0.273 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhh
Q 022167 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (301)
Q Consensus 224 Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~ 260 (301)
+.+...++.+.+|++|+.+|+|..+|++.++++.++.
T Consensus 111 ~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~ 147 (251)
T PRK07670 111 VEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMN 147 (251)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 3455667888999999999999999999988877754
No 63
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=77.48 E-value=10 Score=29.90 Aligned_cols=59 Identities=17% Similarity=0.148 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh--------------HHHHHHHHHHHhHHHHHHHHhh
Q 022167 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME--------------CSLAREKLVMSNVRLVMSIAQR 283 (301)
Q Consensus 224 Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e--------------G~~ARekLV~aNLRLVVSIAKR 283 (301)
++++..-+.+.+..+++.+++|+.+|+|...|.+...+ ...|++.|....+. |..||..
T Consensus 7 ~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~~~g~s~~~~i~~~Rl~~a~~~L~~~~~~-i~~iA~~ 79 (107)
T PRK10219 7 IQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERP-IFDIAMD 79 (107)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHccCCC-HHHHHHH
Confidence 34455666777888899999999999999888887666 24566666654433 4445554
No 64
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=77.04 E-value=3.8 Score=42.52 Aligned_cols=36 Identities=28% Similarity=0.420 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHh
Q 022167 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (301)
Q Consensus 224 Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L 259 (301)
+...+.+|.+.+|++|+.+|+|..+|++.++++.++
T Consensus 360 l~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~ 395 (509)
T PRK05901 360 LGRIERELLQELGREPTPEELAKEMGFTPEKVREIQ 395 (509)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 455678888999999999999999999988877654
No 65
>PRK05949 RNA polymerase sigma factor; Validated
Probab=76.87 E-value=4.2 Score=39.37 Aligned_cols=38 Identities=16% Similarity=0.351 Sum_probs=31.3
Q ss_pred CcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHh
Q 022167 222 LSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (301)
Q Consensus 222 ~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L 259 (301)
..+.+.+.++...+|++|+.+|+|..+|++.+++...+
T Consensus 178 ~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~ 215 (327)
T PRK05949 178 NKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYL 215 (327)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 34556667788899999999999999999988877663
No 66
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=76.87 E-value=11 Score=27.89 Aligned_cols=48 Identities=23% Similarity=0.247 Sum_probs=36.9
Q ss_pred CCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHH
Q 022167 206 LTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECS 263 (301)
Q Consensus 206 LT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~ 263 (301)
||+.|..-|-..+..|.. ..-|..+.+|+|+.+|+|...+-..|+.+.
T Consensus 1 LT~~Q~e~L~~A~~~GYf----------d~PR~~tl~elA~~lgis~st~~~~LRrae 48 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYF----------DVPRRITLEELAEELGISKSTVSEHLRRAE 48 (53)
T ss_pred CCHHHHHHHHHHHHcCCC----------CCCCcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 677777777777777766 234567899999999999998887776543
No 67
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=76.27 E-value=3.7 Score=35.70 Aligned_cols=39 Identities=23% Similarity=0.202 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 262 G~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
...+-+.|+..+.+.|.++|.++.+....-+||+||..+
T Consensus 25 d~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl 63 (192)
T PRK09643 25 DRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAML 63 (192)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHH
Confidence 357888999999999999999999998999999999754
No 68
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=75.82 E-value=10 Score=31.45 Aligned_cols=58 Identities=21% Similarity=0.214 Sum_probs=40.6
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhH--------------HHHHHHHHHHhHHHHHHHHhh
Q 022167 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMEC--------------SLAREKLVMSNVRLVMSIAQR 283 (301)
Q Consensus 225 e~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG--------------~~ARekLV~aNLRLVVSIAKR 283 (301)
.++..-+.+.+..+++.+++|+.+|++...|.+.+.+. ..|++.|...++. |..||..
T Consensus 12 ~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~~G~s~~~~l~~~Rl~~A~~~L~~t~~~-i~eIA~~ 83 (127)
T PRK11511 12 HSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEP-ILYLAER 83 (127)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcCCCC-HHHHHHH
Confidence 34555666778888999999999999999988877662 2455555555544 4555554
No 69
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=74.25 E-value=5.1 Score=35.30 Aligned_cols=38 Identities=16% Similarity=0.005 Sum_probs=33.2
Q ss_pred HHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 263 ~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
..|-+.|+..+.++|..+|.+|.+..-+-+|++||+.+
T Consensus 37 ~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl 74 (206)
T PRK12526 37 KQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMS 74 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHH
Confidence 36778899999999999999998887889999999764
No 70
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=74.07 E-value=6.1 Score=36.18 Aligned_cols=35 Identities=26% Similarity=0.347 Sum_probs=28.9
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHh
Q 022167 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (301)
Q Consensus 225 e~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L 259 (301)
.....++.+.+|++|+.+|+|..+|++.+++...+
T Consensus 126 ~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~~ 160 (258)
T PRK08215 126 LQVREKLINENSKEPTVEEIAKELEVPREEVVFAL 160 (258)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 34566788899999999999999999988876543
No 71
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=71.41 E-value=7.1 Score=37.52 Aligned_cols=38 Identities=18% Similarity=0.388 Sum_probs=31.2
Q ss_pred CcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHh
Q 022167 222 LSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (301)
Q Consensus 222 ~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L 259 (301)
..+.+.+.++...+|++|+.+|+|+.+|++..++...+
T Consensus 168 ~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~ 205 (317)
T PRK07405 168 NKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYL 205 (317)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 34556677888899999999999999999887776654
No 72
>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=69.72 E-value=9 Score=34.03 Aligned_cols=36 Identities=28% Similarity=0.472 Sum_probs=29.6
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhh
Q 022167 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (301)
Q Consensus 225 e~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~ 260 (301)
......+.+.+|++|+.+|+|..+|++.+++...+.
T Consensus 93 ~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~ 128 (227)
T TIGR02980 93 NKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALE 128 (227)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 345667888899999999999999999988865443
No 73
>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=67.51 E-value=9.7 Score=35.91 Aligned_cols=38 Identities=21% Similarity=0.450 Sum_probs=30.3
Q ss_pred cHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhh
Q 022167 223 SLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (301)
Q Consensus 223 ~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~ 260 (301)
.+.+.+.++.+.+|++|+.+|+|..+|++..++...+.
T Consensus 162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~ 199 (298)
T TIGR02997 162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQ 199 (298)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 34555667788899999999999999999888765543
No 74
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=64.21 E-value=28 Score=31.24 Aligned_cols=57 Identities=28% Similarity=0.250 Sum_probs=46.1
Q ss_pred CCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhH
Q 022167 205 LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNV 274 (301)
Q Consensus 205 LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNL 274 (301)
.||..|..-|-..+..|.. ..-|..+..++|+.+|+|...+...|+ +|.++|+.+..
T Consensus 155 ~LTdrQ~~vL~~A~~~GYF----------d~PR~~~l~dLA~~lGISkst~~ehLR---rAe~Kl~~~~~ 211 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYF----------DYPRRVSLKDLAKELGISKSTLSEHLR---RAERKLIEAYF 211 (215)
T ss_pred cCCHHHHHHHHHHHHcCCC----------CCCccCCHHHHHHHhCCCHHHHHHHHH---HHHHHHHHHhh
Confidence 7999999999999988877 345667799999999999998877765 67777777643
No 75
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=63.27 E-value=29 Score=24.65 Aligned_cols=56 Identities=20% Similarity=0.231 Sum_probs=34.2
Q ss_pred CCCHHHHHHHhccChHHHHHHhhhH--HHHHHHHHHHhHHHHHHHHhhccCC-CCChhhHhhh
Q 022167 238 EPSMEQLAASLRISRPELQSILMEC--SLAREKLVMSNVRLVMSIAQRYDNM-GADMADLVQV 297 (301)
Q Consensus 238 ePt~eEwA~a~g~S~~eLrr~L~eG--~~ARekLV~aNLRLVVSIAKRY~gr-GLsfeDLIQE 297 (301)
+++.+++|+.+|++...|.+.+... ...++-+-. .| +.-|..|... ..++.|+.++
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~~~s~~~~~~~--~r--~~~a~~~l~~~~~~~~~ia~~ 59 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKETGTTPKQYLRD--RR--LERARRLLRDTDLSVTEIALR 59 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHhCcCHHHHHHH--HH--HHHHHHHHHcCCCCHHHHHHH
Confidence 4688999999999999998888763 233332222 22 2223344332 4777777654
No 76
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=63.08 E-value=7.2 Score=33.37 Aligned_cols=38 Identities=21% Similarity=0.178 Sum_probs=34.4
Q ss_pred HHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 263 ~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
..|-+.|+..+-+.|..+|.++.+....-+|++||..+
T Consensus 22 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl 59 (182)
T PRK12537 22 RRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFI 59 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHH
Confidence 47888999999999999999999998999999999754
No 77
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=62.75 E-value=12 Score=26.03 Aligned_cols=43 Identities=16% Similarity=0.286 Sum_probs=28.5
Q ss_pred CCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhh
Q 022167 201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (301)
Q Consensus 201 ~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~ 260 (301)
|+.+.+++++..++.+..+.|. +..++|..+|+|+..+.+.+.
T Consensus 1 GRp~~~~~~~~~~i~~l~~~G~-----------------si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 1 GRPPKLSKEQIEEIKELYAEGM-----------------SIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp SSSSSSSHCCHHHHHHHHHTT-------------------HHHHHHHTTS-HHHHHHHHC
T ss_pred CcCCCCCHHHHHHHHHHHHCCC-----------------CHHHHHHHHCcCHHHHHHHHh
Confidence 4566677765555555555553 577899999999999887764
No 78
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=60.90 E-value=16 Score=32.84 Aligned_cols=36 Identities=28% Similarity=0.447 Sum_probs=29.2
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhh
Q 022167 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (301)
Q Consensus 225 e~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~ 260 (301)
.....++.+.+|++|+.+|+|+.+|++.+++..++.
T Consensus 98 ~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~ 133 (236)
T PRK06986 98 AQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLL 133 (236)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHH
Confidence 345567778899999999999999999988665443
No 79
>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=59.89 E-value=23 Score=26.83 Aligned_cols=29 Identities=24% Similarity=0.395 Sum_probs=19.2
Q ss_pred HHHhCCCCCHHHHHHHhccC-hHHHHHHhh
Q 022167 232 KERLGCEPSMEQLAASLRIS-RPELQSILM 260 (301)
Q Consensus 232 ee~LGrePt~eEwA~a~g~S-~~eLrr~L~ 260 (301)
-+.-|.+||..|+|+++|++ ...+...|.
T Consensus 19 ~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~ 48 (65)
T PF01726_consen 19 IEENGYPPTVREIAEALGLKSTSTVQRHLK 48 (65)
T ss_dssp HHHHSS---HHHHHHHHTSSSHHHHHHHHH
T ss_pred HHHcCCCCCHHHHHHHhCCCChHHHHHHHH
Confidence 34579999999999999996 665554443
No 80
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=58.83 E-value=27 Score=32.35 Aligned_cols=38 Identities=24% Similarity=0.292 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 224 Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
+.++..-+++.+..+++.+++|+.+|+|..-|.++...
T Consensus 7 i~~~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F~~ 44 (289)
T PRK15121 7 IRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKD 44 (289)
T ss_pred HHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 44555667788888999999999999999998887766
No 81
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=58.35 E-value=42 Score=28.05 Aligned_cols=44 Identities=30% Similarity=0.335 Sum_probs=31.5
Q ss_pred HHHHHHHh-CCCCCHHHHHHHhccChHHHHHHhhh------HHHHHHHHHH
Q 022167 228 KLRLKERL-GCEPSMEQLAASLRISRPELQSILME------CSLAREKLVM 271 (301)
Q Consensus 228 r~eLee~L-GrePt~eEwA~a~g~S~~eLrr~L~e------G~~ARekLV~ 271 (301)
+.+|++.+ -+..+.+++|.+++.+...|++++.. ++..|+-|+.
T Consensus 12 k~elqan~el~~LS~~~iA~~Ln~t~~~lekil~~tqr~~dvW~lRd~l~~ 62 (97)
T COG4367 12 KQELQANFELCPLSDEEIATALNWTEVKLEKILQVTQRPADVWRLRDFLVQ 62 (97)
T ss_pred HHHHHHhhhhccccHHHHHHHhCCCHHHHHHHHHHhhccchhHHHHHHHHH
Confidence 34444432 35678999999999999999998844 5666665554
No 82
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=58.35 E-value=26 Score=34.64 Aligned_cols=56 Identities=21% Similarity=0.201 Sum_probs=46.1
Q ss_pred CcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh--------------HHHHHHHHHHHhHHHH
Q 022167 222 LSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME--------------CSLAREKLVMSNVRLV 277 (301)
Q Consensus 222 ~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e--------------G~~ARekLV~aNLRLV 277 (301)
..+.++.+.+++.++.+-+.+++|+.+|||...|.+.... -..||+-|...|+.+.
T Consensus 220 ~~l~~~i~~me~nle~plsl~~LA~~~~~S~R~leRlF~~~lG~sP~~yy~~lRL~~Ar~LL~~t~~si~ 289 (328)
T COG4977 220 PRLLRAIELMEANLEEPLSLEELADRAGLSRRQLERLFRAELGVSPARYYLRLRLERARRLLEQTRLSIA 289 (328)
T ss_pred HHHHHHHHHHHHhhcCCcCHHHHHHHhCCCHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhCCCcHH
Confidence 3456677778889999999999999999999999888766 3678888888887754
No 83
>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=58.28 E-value=20 Score=32.56 Aligned_cols=36 Identities=22% Similarity=0.312 Sum_probs=29.7
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhh
Q 022167 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM 260 (301)
Q Consensus 225 e~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~ 260 (301)
......+.+.+|++|+.+|+|..+|++.+++..++.
T Consensus 119 ~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~~~ 154 (255)
T TIGR02941 119 KKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIME 154 (255)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 345667888899999999999999999988766543
No 84
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=58.27 E-value=14 Score=31.93 Aligned_cols=35 Identities=23% Similarity=0.191 Sum_probs=27.9
Q ss_pred HHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhcc
Q 022167 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIF 299 (301)
Q Consensus 264 ~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGn 299 (301)
.|=+.|+..+-+.+..++. |.+...+-+|++||-.
T Consensus 24 ~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~f 58 (185)
T PRK09649 24 RALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETF 58 (185)
T ss_pred HHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHH
Confidence 6677788888888888884 6666678899999864
No 85
>PRK13503 transcriptional activator RhaS; Provisional
Probab=57.90 E-value=34 Score=30.75 Aligned_cols=59 Identities=29% Similarity=0.273 Sum_probs=43.5
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh--------------HHHHHHHHHHHhHHHHHHHHhh
Q 022167 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME--------------CSLAREKLVMSNVRLVMSIAQR 283 (301)
Q Consensus 224 Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e--------------G~~ARekLV~aNLRLVVSIAKR 283 (301)
+.++.+-+.+....+.|.++||+.+|++...|.+.... ...|++.|...|+. |..||.+
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 44455566777888999999999999999888887655 35677666666654 5666665
No 86
>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=55.92 E-value=15 Score=33.93 Aligned_cols=36 Identities=14% Similarity=-0.048 Sum_probs=31.9
Q ss_pred HHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhcc
Q 022167 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIF 299 (301)
Q Consensus 264 ~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGn 299 (301)
.|=+.|+..+-+.|..++.++.+...+-+|++||-.
T Consensus 39 ~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvF 74 (244)
T TIGR03001 39 AALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLR 74 (244)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence 677888999999999999999888899999999854
No 87
>PRK05572 sporulation sigma factor SigF; Validated
Probab=55.82 E-value=22 Score=32.45 Aligned_cols=33 Identities=33% Similarity=0.479 Sum_probs=26.9
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHhccChHHHHH
Q 022167 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQS 257 (301)
Q Consensus 225 e~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr 257 (301)
......+.+.+|++|+.+|+|+.+|++.+++..
T Consensus 121 ~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~~ 153 (252)
T PRK05572 121 RKDKDELSKELGREPTIEELAEYLGVTPEEVVL 153 (252)
T ss_pred HHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHH
Confidence 345567778889999999999999998877654
No 88
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=50.91 E-value=23 Score=34.20 Aligned_cols=36 Identities=25% Similarity=0.327 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHh
Q 022167 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (301)
Q Consensus 224 Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L 259 (301)
+......|++.+|++|+.+|+|..+|++.++++.++
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 344556788889999999999999999988887665
No 89
>PRK15044 transcriptional regulator SirC; Provisional
Probab=50.04 E-value=38 Score=33.21 Aligned_cols=60 Identities=17% Similarity=0.119 Sum_probs=44.4
Q ss_pred HHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167 193 LKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 193 l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
+..|++.-+..+.|..+..... .+++.+-+.+.++++++.+++|+.+|+|..-|.+.+..
T Consensus 172 Ls~~l~~~~~~~~L~~~~~is~---------~~kV~~~I~~nl~~~~SLeeLA~~lgmS~~tL~R~Fk~ 231 (295)
T PRK15044 172 ISAFVRKPGGFDFLERAIKITT---------KEKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAA 231 (295)
T ss_pred HHHHHhcccchhhHHHHhhhhH---------HHHHHHHHHhCcccCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 6677776666666655544332 34455667778899999999999999999999987654
No 90
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=45.09 E-value=40 Score=31.77 Aligned_cols=24 Identities=21% Similarity=0.232 Sum_probs=21.4
Q ss_pred CCCCCHHHHHHHhccChHHHHHHh
Q 022167 236 GCEPSMEQLAASLRISRPELQSIL 259 (301)
Q Consensus 236 GrePt~eEwA~a~g~S~~eLrr~L 259 (301)
+++|+.+|+|+.+|++.++++.++
T Consensus 149 ~~~~t~~eiA~~l~~~~~~v~~~~ 172 (284)
T PRK06596 149 LNPEEVEMVAEELGVSEEEVREME 172 (284)
T ss_pred CCCCCHHHHHHHhCcCHHHHHHHH
Confidence 599999999999999999987764
No 91
>PF11176 DUF2962: Protein of unknown function (DUF2962); InterPro: IPR021346 This eukaryotic family of proteins has no known function. ; PDB: 2KKM_A.
Probab=45.04 E-value=13 Score=32.67 Aligned_cols=79 Identities=23% Similarity=0.324 Sum_probs=37.3
Q ss_pred chHHHHHhhcC--CCCCCCHHHHHHHHHHH--HcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHH
Q 022167 191 NRLKGYVKGVV--SEELLTHAEVVRLSKKI--KTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAR 266 (301)
Q Consensus 191 D~l~~YLkei~--~~~LLT~EEEveLs~kI--q~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~AR 266 (301)
+.+.-|-..+. ....+|.+|-.+|...+ +....|++++.+ .+-||+|+..
T Consensus 49 ~r~~wFq~~i~~~~~~~~t~~e~~~lI~~yl~R~DeEleql~~~--rR~gRp~s~r------------------------ 102 (155)
T PF11176_consen 49 ERLKWFQEAIDEKDKKPFTLEEIHELIERYLHRFDEELEQLKKE--RRKGRPPSNR------------------------ 102 (155)
T ss_dssp HHHHHHHHHHHSTT-----HHHHHHHHHHHHHHHHHHHHHHHHH--GGGT---TTH------------------------
T ss_pred HHHHHHHHHccccCCCCCCHHHHHHHHHHHHhcCHHHHHHHHHh--hcCCCCCchH------------------------
Confidence 44444444443 37899999999999875 233334433332 4568888643
Q ss_pred HHHHHHhHHHHHHHHhhccCCCCChhhHhhhcc
Q 022167 267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQVIF 299 (301)
Q Consensus 267 ekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGn 299 (301)
+.+++.- .-.-.+.|. .|+.+-||..+.|
T Consensus 103 e~~L~~~---~~~E~~ey~-~G~~vPDLtd~~n 131 (155)
T PF11176_consen 103 EDLLEQK---IEREEEEYK-TGFEVPDLTDEKN 131 (155)
T ss_dssp HHHHHHH---HHHHHHHHH-TTEEEE-S--HHH
T ss_pred HHHHHHH---HHHHHHHHh-hCeeCCCCCCHHH
Confidence 3333322 223345677 8888888877655
No 92
>PRK13239 alkylmercury lyase; Provisional
Probab=43.78 E-value=40 Score=31.40 Aligned_cols=27 Identities=30% Similarity=0.323 Sum_probs=25.2
Q ss_pred hCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167 235 LGCEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 235 LGrePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
.|++|+.+++|..+|.+.++++++|++
T Consensus 33 ~G~pvt~~~lA~~~~~~~~~v~~~L~~ 59 (206)
T PRK13239 33 KGRPVSVTTLAAALGWPVEEVEAVLEA 59 (206)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 699999999999999999999988876
No 93
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=42.87 E-value=11 Score=34.15 Aligned_cols=20 Identities=40% Similarity=0.855 Sum_probs=17.9
Q ss_pred hHHHHHHhhHh-HHHhhhccc
Q 022167 107 SVEALLLLQKS-MLEKQWNLS 126 (301)
Q Consensus 107 ~~~~~~llq~s-mlekqw~l~ 126 (301)
..+||.+|.|. |+|-||..|
T Consensus 44 ~~~~L~~LkK~gLiE~qWrmP 64 (160)
T PF09824_consen 44 VRESLLILKKGGLIESQWRMP 64 (160)
T ss_pred HHHHHHHHHHcCchhhccccC
Confidence 38999999885 999999998
No 94
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=42.38 E-value=21 Score=31.73 Aligned_cols=37 Identities=30% Similarity=0.308 Sum_probs=33.4
Q ss_pred HHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY 300 (301)
Q Consensus 264 ~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI 300 (301)
.+=++|+..+.+.+..++.+|.+....-+||+||..+
T Consensus 28 ~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvfl 64 (203)
T PRK09647 28 PSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFI 64 (203)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHH
Confidence 6778899999999999999999988899999999754
No 95
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=41.69 E-value=52 Score=30.84 Aligned_cols=38 Identities=16% Similarity=0.094 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 224 Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
+.++..-+.+.+..+++.+++|+.+|+|...|.+.+.+
T Consensus 220 ~~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~ 257 (322)
T PRK09393 220 LGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEA 257 (322)
T ss_pred HHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 44555666777888999999999999999999888776
No 96
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=41.23 E-value=60 Score=25.47 Aligned_cols=49 Identities=22% Similarity=0.337 Sum_probs=36.8
Q ss_pred CCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhh
Q 022167 239 PSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQV 297 (301)
Q Consensus 239 Pt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQE 297 (301)
-|-+|+|..+|+++..+-.+-.. =-.-+|.|...||+-|. .+++|+++.
T Consensus 15 ltQ~elA~~vgVsRQTi~~iEkg-------ky~Psl~La~kia~~f~---~~iedIF~~ 63 (68)
T COG1476 15 LTQEELAKLVGVSRQTIIAIEKG-------KYNPSLELALKIARVFG---KTIEDIFQL 63 (68)
T ss_pred cCHHHHHHHcCcCHHHHHHHHcC-------CCCchHHHHHHHHHHhC---CCHHHHHhh
Confidence 67788999999987776533222 12457899999999885 899999984
No 97
>PF13730 HTH_36: Helix-turn-helix domain
Probab=40.19 E-value=1.1e+02 Score=21.27 Aligned_cols=27 Identities=44% Similarity=0.608 Sum_probs=22.1
Q ss_pred hCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167 235 LGCEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 235 LGrePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
.+..|+.+.+|+.+|++...+++.+.+
T Consensus 22 ~~~~pS~~~la~~~g~s~~Tv~~~i~~ 48 (55)
T PF13730_consen 22 GGCFPSQETLAKDLGVSRRTVQRAIKE 48 (55)
T ss_pred CCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 357899999999999999888755543
No 98
>PRK04217 hypothetical protein; Provisional
Probab=39.29 E-value=1.5e+02 Score=25.01 Aligned_cols=42 Identities=17% Similarity=0.223 Sum_probs=30.6
Q ss_pred CCCCCHHHHHHHHHHHH-cCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhH
Q 022167 203 EELLTHAEVVRLSKKIK-TGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMEC 262 (301)
Q Consensus 203 ~~LLT~EEEveLs~kIq-~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG 262 (301)
...||.+| .++...+. .+ -+.+|+|+.+|++...+.+.+..+
T Consensus 40 ~~~Lt~ee-reai~l~~~eG-----------------lS~~EIAk~LGIS~sTV~r~L~RA 82 (110)
T PRK04217 40 PIFMTYEE-FEALRLVDYEG-----------------LTQEEAGKRMGVSRGTVWRALTSA 82 (110)
T ss_pred cccCCHHH-HHHHHHHHHcC-----------------CCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46677766 56655543 22 267899999999999999888763
No 99
>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=39.28 E-value=72 Score=28.84 Aligned_cols=35 Identities=20% Similarity=0.245 Sum_probs=28.1
Q ss_pred HHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 227 ~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
+..-+.+.+..+.+.++||+.+|+|..-|.+...+
T Consensus 191 ~~~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~ 225 (287)
T TIGR02297 191 FNFLIEENYKQHLRLPEYADRLGISESRLNDICRR 225 (287)
T ss_pred HHHHHHHhhccCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 33445566777899999999999999998887666
No 100
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=38.38 E-value=67 Score=29.33 Aligned_cols=59 Identities=17% Similarity=0.256 Sum_probs=41.6
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh--------------HHHHHHHHHHHhHHHHHHHHhh
Q 022167 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME--------------CSLAREKLVMSNVRLVMSIAQR 283 (301)
Q Consensus 224 Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e--------------G~~ARekLV~aNLRLVVSIAKR 283 (301)
++++..-+.+.+..+.+.+++|+.+|+|..-|.+...+ .+.|++.|...|+. |-.||..
T Consensus 185 i~~~~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk~~~G~tp~~~l~~~Rl~~A~~lL~~t~~s-I~eIA~~ 257 (290)
T PRK10572 185 VREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAKLLLQTTRMP-IATIGRN 257 (290)
T ss_pred HHHHHHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcCCCC-HHHHHHH
Confidence 44555666777888999999999999999988887766 35666655555533 3445543
No 101
>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=37.39 E-value=32 Score=27.62 Aligned_cols=27 Identities=33% Similarity=0.356 Sum_probs=20.5
Q ss_pred hCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167 235 LGCEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 235 LGrePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
.|++.+.+++|.++|.+.++++.+|..
T Consensus 35 ~G~PVt~~~LA~a~g~~~e~v~~~L~~ 61 (77)
T PF12324_consen 35 KGQPVTVEQLAAALGWPVEEVRAALAA 61 (77)
T ss_dssp TTS-B-HHHHHHHHT--HHHHHHHHHH
T ss_pred cCCCcCHHHHHHHHCCCHHHHHHHHHh
Confidence 499999999999999999999888765
No 102
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=36.84 E-value=1.4e+02 Score=20.58 Aligned_cols=29 Identities=28% Similarity=0.300 Sum_probs=22.3
Q ss_pred hCCCCCHHHHHHHhccChHHHHHHhhhHH
Q 022167 235 LGCEPSMEQLAASLRISRPELQSILMECS 263 (301)
Q Consensus 235 LGrePt~eEwA~a~g~S~~eLrr~L~eG~ 263 (301)
....-|.+|+|+.+|++...++++...+.
T Consensus 17 y~~~~t~~eIa~~lg~s~~~V~~~~~~al 45 (50)
T PF04545_consen 17 YFEGLTLEEIAERLGISRSTVRRILKRAL 45 (50)
T ss_dssp HTST-SHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred hcCCCCHHHHHHHHCCcHHHHHHHHHHHH
Confidence 34556889999999999999888776543
No 103
>PF04282 DUF438: Family of unknown function (DUF438); InterPro: IPR007380 This is a a group of uncharacterised proteins.
Probab=35.79 E-value=1.6e+02 Score=23.21 Aligned_cols=45 Identities=18% Similarity=0.292 Sum_probs=32.0
Q ss_pred HHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHH------hccChHHHHH
Q 022167 212 VRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAAS------LRISRPELQS 257 (301)
Q Consensus 212 veLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a------~g~S~~eLrr 257 (301)
++|.+++..|...+.+|.++.+.++ ..+..|++.+ =|++.+++++
T Consensus 3 K~ii~~Lh~G~~~e~vk~~F~~~~~-~Vs~~EI~~~Eq~Li~eG~~~eeiq~ 53 (71)
T PF04282_consen 3 KEIIKRLHEGEDPEEVKEEFKKLFS-DVSASEISAAEQELIQEGMPVEEIQK 53 (71)
T ss_pred HHHHHHHhCCCCHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCCHHHHHH
Confidence 4678888899999999999999887 4444555543 3566666554
No 104
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=35.79 E-value=56 Score=22.64 Aligned_cols=41 Identities=24% Similarity=0.333 Sum_probs=17.8
Q ss_pred CCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167 204 ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 204 ~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
+-||.+|=..+....+.|. +..++|..+|.+...+.+.+..
T Consensus 3 ~~Lt~~eR~~I~~l~~~G~-----------------s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQGM-----------------SIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHHHHCS--------------------HHHHHHHTT--HHHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcCC-----------------CHHHHHHHHCcCcHHHHHHHhc
Confidence 4567666666555555444 4667888888887777665543
No 105
>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=35.48 E-value=96 Score=22.94 Aligned_cols=56 Identities=18% Similarity=0.215 Sum_probs=39.6
Q ss_pred HHHHhCCCCC------HHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHHHhhccCCCCC
Q 022167 231 LKERLGCEPS------MEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGAD 290 (301)
Q Consensus 231 Lee~LGrePt------~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSIAKRY~grGLs 290 (301)
.++.+||.|| ..+|.+..|++.+-+..++..+.. + -..|++-|-.|++.+...|+.
T Consensus 5 ~e~~~gr~ls~~e~~~i~~~~~~~~~~~evI~~ai~~a~~-~---~~~~~~Yi~~Il~~W~~~gi~ 66 (73)
T TIGR01446 5 FEENFGRMLSPFEMEDLKYWLDEFGNSPELIKEALKEAVS-N---NKANYKYIDAILNNWKNNGIK 66 (73)
T ss_pred HHHHhCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHH-c---CCCCHHHHHHHHHHHHHcCCC
Confidence 4555677777 345777777777766666666443 2 246889999999999988864
No 106
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=35.12 E-value=82 Score=29.64 Aligned_cols=38 Identities=8% Similarity=0.101 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167 224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 224 Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
++.+..-+.+.+...++.+++|+.+|+|...|.+...+
T Consensus 193 i~~~~~~i~~~~~~~~tl~~lA~~~~~S~~~l~r~Fk~ 230 (302)
T PRK10371 193 VSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQR 230 (302)
T ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34455566677788899999999999999988887776
No 107
>PRK13501 transcriptional activator RhaR; Provisional
Probab=34.60 E-value=1.2e+02 Score=27.70 Aligned_cols=56 Identities=20% Similarity=0.183 Sum_probs=41.0
Q ss_pred HHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh--------------HHHHHHHHHHHhHHHHHHHHhh
Q 022167 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSILME--------------CSLAREKLVMSNVRLVMSIAQR 283 (301)
Q Consensus 227 ~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e--------------G~~ARekLV~aNLRLVVSIAKR 283 (301)
+...+++.+....+.+++|+.+|+|...|.++... ...|++-|...|+ -|-.||.+
T Consensus 181 i~~~I~~~~~e~~sl~~lA~~~~lS~~~l~r~Fk~~~G~T~~qyi~~~Ri~~A~~LL~~t~~-sI~eIA~~ 250 (290)
T PRK13501 181 IMSALQQSLGAYFDMADFCHKNQLVERSLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEH-RISDIAAR 250 (290)
T ss_pred HHHHHHHhhccCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcCCC-CHHHHHHH
Confidence 34456666777889999999999999998887665 3466776666665 36666655
No 108
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=34.40 E-value=2.3e+02 Score=23.23 Aligned_cols=28 Identities=18% Similarity=0.106 Sum_probs=22.9
Q ss_pred CCCCHHHHHHHhccChHHHHHHhhhHHH
Q 022167 237 CEPSMEQLAASLRISRPELQSILMECSL 264 (301)
Q Consensus 237 rePt~eEwA~a~g~S~~eLrr~L~eG~~ 264 (301)
..-+.+|+|+.+|++...++..+..+..
T Consensus 140 ~~~~~~eIA~~lgis~~tv~~~~~ra~~ 167 (179)
T PRK11924 140 EGLSYREIAEILGVPVGTVKSRLRRARQ 167 (179)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3567899999999999999888877543
No 109
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=32.95 E-value=52 Score=22.34 Aligned_cols=24 Identities=38% Similarity=0.484 Sum_probs=20.0
Q ss_pred CCCHHHHHHHhccChHHHHHHhhh
Q 022167 238 EPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 238 ePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
-|+..|+|+.+|++...+++.+..
T Consensus 20 l~s~~~la~~~~vs~~tv~~~l~~ 43 (60)
T smart00345 20 LPSERELAAQLGVSRTTVREALSR 43 (60)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHH
Confidence 358999999999999998866654
No 110
>PF13309 HTH_22: HTH domain
Probab=32.88 E-value=1.6e+02 Score=22.06 Aligned_cols=59 Identities=24% Similarity=0.318 Sum_probs=43.6
Q ss_pred hhhcchHHHHHhhcCCC-CCCCHHHHHHHHHHHH-cCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHH
Q 022167 187 ELIQNRLKGYVKGVVSE-ELLTHAEVVRLSKKIK-TGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQS 257 (301)
Q Consensus 187 el~~D~l~~YLkei~~~-~LLT~EEEveLs~kIq-~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr 257 (301)
|++++.+..++.+.+.. ..|+.+|=.++.+.+. .|.... .-+.+..|+.+|+|...+-+
T Consensus 1 e~i~~~i~~~~~~~~~~~~~l~~~~k~~iV~~L~~~G~F~l------------Kgav~~vA~~L~iS~~TVY~ 61 (64)
T PF13309_consen 1 ELIESIIEEVIAEVGKPPSRLSKEEKKEIVRQLYEKGIFLL------------KGAVEYVAEKLGISRATVYR 61 (64)
T ss_pred ChHHHHHHHHHHHhCCChhhCCHHHHHHHHHHHHHCCCccc------------CcHHHHHHHHHCCCHHHHHH
Confidence 35667888888888664 6899999999999985 566621 22456788889999876643
No 111
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=32.33 E-value=64 Score=23.35 Aligned_cols=44 Identities=25% Similarity=0.378 Sum_probs=28.5
Q ss_pred CCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHH
Q 022167 203 EELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECS 263 (301)
Q Consensus 203 ~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~ 263 (301)
..-||.+|-.++...+..|. +..++|..+|++...+..++..-.
T Consensus 4 R~~LTl~eK~~iI~~~e~g~-----------------s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 4 RKSLTLEEKLEIIKRLEEGE-----------------SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSS--HHHHHHHHHHHHCTT------------------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CccCCHHHHHHHHHHHHcCC-----------------CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 35688888888888887665 356778888888888877766533
No 112
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=32.27 E-value=32 Score=29.93 Aligned_cols=39 Identities=23% Similarity=0.022 Sum_probs=34.7
Q ss_pred hHHHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhcc
Q 022167 261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIF 299 (301)
Q Consensus 261 eG~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGn 299 (301)
....+-+.++..+-+.|..+|.++.+...+-+|++||..
T Consensus 20 ~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvf 58 (188)
T PRK12517 20 SKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETF 58 (188)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence 345888899999999999999999998888999999864
No 113
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=32.14 E-value=1.5e+02 Score=19.63 Aligned_cols=37 Identities=27% Similarity=0.268 Sum_probs=25.5
Q ss_pred CCHHHHHHHhccChHHHHHHhhhHHHHHHHHHH-HhHHHHH
Q 022167 239 PSMEQLAASLRISRPELQSILMECSLAREKLVM-SNVRLVM 278 (301)
Q Consensus 239 Pt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~-aNLRLVV 278 (301)
-+..|+|+.+|++...++..+. +++.+|.. .+..||.
T Consensus 16 ~s~~eia~~l~~s~~tv~~~~~---~~~~~l~~~~~~~l~~ 53 (57)
T cd06170 16 KTNKEIADILGISEKTVKTHLR---NIMRKLGVKSRTQLVA 53 (57)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH---HHHHHhCCCCHHHHHH
Confidence 4678899999999988887776 34555544 3445544
No 114
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=32.10 E-value=1.3e+02 Score=28.82 Aligned_cols=37 Identities=14% Similarity=0.158 Sum_probs=31.3
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 225 e~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
.++.+.+.+.+..+.+.++||+.+|||...|.+.+.+
T Consensus 184 ~~i~~~I~~~~~~~~sl~~lA~~~gmS~stl~R~Fk~ 220 (291)
T PRK15186 184 ENIYNIIISDISRKWALKDISDSLYMSCSTLKRKLKQ 220 (291)
T ss_pred HHHHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3455667778888999999999999999999998876
No 115
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=32.09 E-value=2.3e+02 Score=22.72 Aligned_cols=42 Identities=21% Similarity=0.241 Sum_probs=29.9
Q ss_pred CHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHHHhhc
Q 022167 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRY 284 (301)
Q Consensus 240 t~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSIAKRY 284 (301)
+..|+|+.++++...++..+. .++.+|-.+|..=++..|.++
T Consensus 166 ~~~~Ia~~l~~s~~tv~~~~~---~~~~kl~~~~~~~l~~~~~~~ 207 (211)
T PRK15369 166 TNRDIAEQLSISIKTVETHRL---NMMRKLDVHKVAELLNWARRL 207 (211)
T ss_pred CHHHHHHHhCCCHHHHHHHHH---HHHHHhCCCCHHHHHHHHHHc
Confidence 467888888988887776655 477777777876666666553
No 116
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=31.82 E-value=2e+02 Score=21.90 Aligned_cols=33 Identities=27% Similarity=0.357 Sum_probs=25.3
Q ss_pred HHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167 229 LRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 229 ~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
.-+.+.+..+++.+++|..+|+|...|.+.+..
T Consensus 27 ~~i~~~~~~~~~l~~la~~~g~S~~~l~r~f~~ 59 (127)
T COG2207 27 DYIEENLAEPLTLEDLARRLGMSRRTLSRLFKK 59 (127)
T ss_pred HHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 334445566689999999999999998887763
No 117
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=31.39 E-value=98 Score=27.62 Aligned_cols=25 Identities=24% Similarity=0.214 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHhccChHHHHHHhhh
Q 022167 237 CEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 237 rePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
+=|+..|+|+.+|+|+..+|++|..
T Consensus 23 ~LPsE~eLa~~~gVSR~TVR~Al~~ 47 (233)
T TIGR02404 23 YLPSEHELMDQYGASRETVRKALNL 47 (233)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4699999999999999999877765
No 118
>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=31.38 E-value=74 Score=29.68 Aligned_cols=35 Identities=29% Similarity=0.437 Sum_probs=27.9
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHh
Q 022167 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (301)
Q Consensus 225 e~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L 259 (301)
......+.+.+|++|+.+++|..+|++..+++.++
T Consensus 136 ~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~ 170 (285)
T TIGR02394 136 LRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVL 170 (285)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 34445567788999999999999999988877654
No 119
>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=29.58 E-value=80 Score=27.64 Aligned_cols=34 Identities=9% Similarity=0.155 Sum_probs=27.8
Q ss_pred HHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHH
Q 022167 230 RLKERLGCEPSMEQLAASLRISRPELQSILMECS 263 (301)
Q Consensus 230 eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~ 263 (301)
=|.+.-++.-|..|+++++|++...+.+.+++|+
T Consensus 38 yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGR 71 (137)
T TIGR03826 38 FLRKHENRQATVSEIVEETGVSEKLILKFIREGR 71 (137)
T ss_pred HHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 3445556667899999999999999999988875
No 120
>PRK10130 transcriptional regulator EutR; Provisional
Probab=29.20 E-value=1.5e+02 Score=29.03 Aligned_cols=37 Identities=19% Similarity=0.233 Sum_probs=29.9
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167 225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 225 e~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
.++++-+.+.+..+.+.+++|+.+|+|...|.+...+
T Consensus 243 ~~~~~~i~~~~~~~ltv~~lA~~~gvS~r~L~r~Fk~ 279 (350)
T PRK10130 243 SRAREYVLENMSEPVTVLDLCNQLHVSRRTLQNAFHA 279 (350)
T ss_pred HHHHHHHHhhhcCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3444556677888899999999999999999887766
No 121
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=28.99 E-value=67 Score=21.44 Aligned_cols=29 Identities=17% Similarity=0.255 Sum_probs=19.5
Q ss_pred HHhCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167 233 ERLGCEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 233 e~LGrePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
+.+....+.+++|..+|+|..-+.+....
T Consensus 3 ~~~~~~~~l~~iA~~~g~S~~~f~r~Fk~ 31 (42)
T PF00165_consen 3 ENLQQKLTLEDIAEQAGFSPSYFSRLFKK 31 (42)
T ss_dssp TTT-SS--HHHHHHHHTS-HHHHHHHHHH
T ss_pred ccccCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 34556778899999999998888777654
No 122
>PRK06930 positive control sigma-like factor; Validated
Probab=28.57 E-value=2.5e+02 Score=24.84 Aligned_cols=32 Identities=22% Similarity=0.296 Sum_probs=25.0
Q ss_pred HhCCCCCHHHHHHHhccChHHHHHHhhhHHHH
Q 022167 234 RLGCEPSMEQLAASLRISRPELQSILMECSLA 265 (301)
Q Consensus 234 ~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~A 265 (301)
.....-+..|+|+.+|++...++..+..+...
T Consensus 126 ~~~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~k 157 (170)
T PRK06930 126 HRGYGLSYSEIADYLNIKKSTVQSMIERAEKK 157 (170)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 34556789999999999999988887765443
No 123
>PF13801 Metal_resist: Heavy-metal resistance; PDB: 3EPV_C 2Y3D_A 2Y3H_D 2Y3G_B 2Y3B_A 2Y39_A 3LAY_H.
Probab=28.56 E-value=2.7e+02 Score=21.26 Aligned_cols=69 Identities=16% Similarity=0.225 Sum_probs=44.9
Q ss_pred CCCCHHHHHHHHHHHHc-CCcHHHHH-------HHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHH
Q 022167 204 ELLTHAEVVRLSKKIKT-GLSLDDHK-------LRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVR 275 (301)
Q Consensus 204 ~LLT~EEEveLs~kIq~-g~~Le~~r-------~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLR 275 (301)
--||+++...|-...+. ....+.++ .++...+..++ .+...++..+.+...++..+-..-++
T Consensus 40 l~Lt~eQ~~~l~~~~~~~~~~~~~~r~~~~~~r~~l~~ll~~~~----------~D~~~i~a~~~~~~~~~~~l~~~~~~ 109 (125)
T PF13801_consen 40 LNLTPEQQAKLRALMDEFRQEMRALRQELRAARQELRALLAAPP----------PDEAAIEALLEEIREAQAELRQERLE 109 (125)
T ss_dssp S-TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCSS----------S-HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCC----------CCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56899998888877753 22333333 33334444333 34567888888888888888888888
Q ss_pred HHHHHHh
Q 022167 276 LVMSIAQ 282 (301)
Q Consensus 276 LVVSIAK 282 (301)
.++.+++
T Consensus 110 ~~~~~~~ 116 (125)
T PF13801_consen 110 HLLEIRA 116 (125)
T ss_dssp HHHHHHH
T ss_pred HHHHHHH
Confidence 8887764
No 124
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=28.50 E-value=1.2e+02 Score=26.89 Aligned_cols=25 Identities=20% Similarity=0.311 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHhccChHHHHHHhhh
Q 022167 237 CEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 237 rePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
+=|+..|+|+.+|+|+..+|++|..
T Consensus 31 ~LPsE~eLa~~~~VSR~TvR~Al~~ 55 (238)
T TIGR02325 31 YLPAEMQLAERFGVNRHTVRRAIAA 55 (238)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4699999999999999999877765
No 125
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=27.52 E-value=1.2e+02 Score=27.62 Aligned_cols=26 Identities=31% Similarity=0.344 Sum_probs=22.4
Q ss_pred CCCCCHHHHHHHhccChHHHHHHhhh
Q 022167 236 GCEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 236 GrePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
.+-|+..|+|+.+|+|+..+|++|.+
T Consensus 29 ~~LPsE~eLa~~f~VSR~TvRkAL~~ 54 (236)
T COG2188 29 DKLPSERELAEQFGVSRMTVRKALDE 54 (236)
T ss_pred CCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 35799999999999999999877665
No 126
>PHA02591 hypothetical protein; Provisional
Probab=26.74 E-value=1e+02 Score=25.24 Aligned_cols=38 Identities=16% Similarity=0.429 Sum_probs=27.9
Q ss_pred CHHHHHHHHHHHH-cCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167 207 THAEVVRLSKKIK-TGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 207 T~EEEveLs~kIq-~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
+.++++.|++.+. .|. |.+++|+.+|++.+.+++-+..
T Consensus 44 ~~dd~~~vA~eL~eqGl-----------------SqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 44 SEDDLISVTHELARKGF-----------------TVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred ccchHHHHHHHHHHcCC-----------------CHHHHHHHhCCCHHHHHHHHhc
Confidence 4567778887774 344 4678899999999888776653
No 127
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=26.67 E-value=1.5e+02 Score=24.44 Aligned_cols=33 Identities=33% Similarity=0.338 Sum_probs=26.1
Q ss_pred CCCHHHHHHHhccChHHHHHHhhh-------HHHHHHHHH
Q 022167 238 EPSMEQLAASLRISRPELQSILME-------CSLAREKLV 270 (301)
Q Consensus 238 ePt~eEwA~a~g~S~~eLrr~L~e-------G~~ARekLV 270 (301)
-.+.+++|+.+|++..++.++|.- .+..|+-|.
T Consensus 23 ~ls~~~ia~dL~~s~~~le~vL~l~~~~~~~vW~lRdyL~ 62 (89)
T PF10078_consen 23 GLSLEQIAADLGTSPEHLEQVLNLKQPFPEDVWILRDYLN 62 (89)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCCCCcccchHHHHHHH
Confidence 468899999999999999998765 456666544
No 128
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=26.61 E-value=67 Score=23.30 Aligned_cols=24 Identities=29% Similarity=0.386 Sum_probs=17.9
Q ss_pred CCCHHHHHHHhccChHHHHHHhhh
Q 022167 238 EPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 238 ePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
-|+..++|+.+|+|...+++++..
T Consensus 24 lps~~~la~~~~vsr~tvr~al~~ 47 (64)
T PF00392_consen 24 LPSERELAERYGVSRTTVREALRR 47 (64)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHHH
T ss_pred eCCHHHHHHHhccCCcHHHHHHHH
Confidence 479999999999999998876654
No 129
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=26.40 E-value=3.7e+02 Score=22.13 Aligned_cols=35 Identities=20% Similarity=0.063 Sum_probs=26.4
Q ss_pred hCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHH
Q 022167 235 LGCEPSMEQLAASLRISRPELQSILMECSLAREKL 269 (301)
Q Consensus 235 LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekL 269 (301)
....-+.+|+|+.+|+++..++..+..+..+=...
T Consensus 118 ~~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~ 152 (159)
T PRK12527 118 KLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVR 152 (159)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 34467889999999999999988888665443333
No 130
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=26.16 E-value=2e+02 Score=19.77 Aligned_cols=26 Identities=23% Similarity=0.226 Sum_probs=18.8
Q ss_pred CCCHHHHHHHhccChHHHHHHhhhHH
Q 022167 238 EPSMEQLAASLRISRPELQSILMECS 263 (301)
Q Consensus 238 ePt~eEwA~a~g~S~~eLrr~L~eG~ 263 (301)
.-+.+|+|+.+|++...++..+..+.
T Consensus 26 g~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 26 GMSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp ---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 34678999999999999988887654
No 131
>PRK14999 histidine utilization repressor; Provisional
Probab=25.54 E-value=1.4e+02 Score=26.84 Aligned_cols=25 Identities=32% Similarity=0.323 Sum_probs=22.2
Q ss_pred CCCCHHHHHHHhccChHHHHHHhhh
Q 022167 237 CEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 237 rePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
+=|+..|+|+.+|+|+..+|++|..
T Consensus 35 ~LPsE~eLa~~~gVSR~TVR~Al~~ 59 (241)
T PRK14999 35 RIPSEAELVAQYGFSRMTINRALRE 59 (241)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4699999999999999999887766
No 132
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=24.96 E-value=4.3e+02 Score=22.47 Aligned_cols=31 Identities=16% Similarity=0.041 Sum_probs=24.5
Q ss_pred CCCCHHHHHHHhccChHHHHHHhhhHHHHHH
Q 022167 237 CEPSMEQLAASLRISRPELQSILMECSLARE 267 (301)
Q Consensus 237 rePt~eEwA~a~g~S~~eLrr~L~eG~~ARe 267 (301)
..-+..|+|+.+|++...++..+..+...=.
T Consensus 156 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 186 (194)
T PRK12519 156 EGLSQSEIAKRLGIPLGTVKARARQGLLKLR 186 (194)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 3578899999999999999988876544333
No 133
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=24.94 E-value=1.5e+02 Score=26.51 Aligned_cols=25 Identities=32% Similarity=0.287 Sum_probs=21.8
Q ss_pred CCCCHHHHHHHhccChHHHHHHhhh
Q 022167 237 CEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 237 rePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
+-|+..|+|+.+|+|+..+|++|..
T Consensus 24 ~LPsE~eLa~~~~VSR~TVR~Al~~ 48 (230)
T TIGR02018 24 RIPSEHELVAQYGCSRMTVNRALRE 48 (230)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 3699999999999999999877765
No 134
>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=24.66 E-value=3.9e+02 Score=22.19 Aligned_cols=53 Identities=13% Similarity=0.096 Sum_probs=34.0
Q ss_pred HHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHH
Q 022167 210 EVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSL 264 (301)
Q Consensus 210 EEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ 264 (301)
++..|...+..... +.++-+.-..-...+.+|+|+.+|++...++..+..+..
T Consensus 109 ~~~~l~~~l~~L~~--~~r~i~~l~~~~g~s~~eiA~~lgis~~tv~~~l~Ra~~ 161 (169)
T TIGR02954 109 SRLDLYKAIDTLND--KYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHRALK 161 (169)
T ss_pred HHHHHHHHHHhCCH--HHhHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 34455555554332 233333333344688999999999999999888876544
No 135
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=24.47 E-value=1.5e+02 Score=26.72 Aligned_cols=25 Identities=28% Similarity=0.405 Sum_probs=22.0
Q ss_pred CCCCHHHHHHHhccChHHHHHHhhh
Q 022167 237 CEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 237 rePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
+-|+..|+|+.+|+|+..+|++|..
T Consensus 34 ~LPsE~eLa~~~~VSR~TVR~Al~~ 58 (241)
T PRK10079 34 YLPAEQQLAARYEVNRHTLRRAIDQ 58 (241)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 5699999999999999999877665
No 136
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=23.44 E-value=1.7e+02 Score=26.38 Aligned_cols=25 Identities=16% Similarity=0.337 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhccChHHHHHHhhh
Q 022167 237 CEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 237 rePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
+=|+..|+|+.+|+|+..+|++|..
T Consensus 32 kLPsE~eLa~~~~VSR~TvR~Al~~ 56 (241)
T PRK11402 32 QIPTENELCTQYNVSRITIRKAISD 56 (241)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4699999999999999999988766
No 137
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=23.32 E-value=4.1e+02 Score=22.59 Aligned_cols=30 Identities=13% Similarity=0.180 Sum_probs=24.0
Q ss_pred CCCHHHHHHHhccChHHHHHHhhhHHHHHH
Q 022167 238 EPSMEQLAASLRISRPELQSILMECSLARE 267 (301)
Q Consensus 238 ePt~eEwA~a~g~S~~eLrr~L~eG~~ARe 267 (301)
.-+.+|+|+.+|++...++..+..+...=.
T Consensus 143 g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr 172 (179)
T PRK09415 143 ELSIKEIAEVTGVNENTVKTRLKKAKELLK 172 (179)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 567899999999999999888877654433
No 138
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=23.09 E-value=2.2e+02 Score=25.57 Aligned_cols=24 Identities=25% Similarity=0.307 Sum_probs=21.4
Q ss_pred CCCHHHHHHHhccChHHHHHHhhh
Q 022167 238 EPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 238 ePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
+.|.+++|..+|++..++|++|..
T Consensus 36 ~~tdeeLA~~Lgi~~~~VRk~L~~ 59 (178)
T PRK06266 36 EVTDEEIAEQTGIKLNTVRKILYK 59 (178)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHH
Confidence 578999999999999999988765
No 139
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=22.70 E-value=1.7e+02 Score=26.35 Aligned_cols=25 Identities=20% Similarity=0.337 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHhccChHHHHHHhhh
Q 022167 237 CEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 237 rePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
+-|+..|+|+.+|+|+..+|++|..
T Consensus 28 ~LPsE~eL~~~~~VSR~TvR~Al~~ 52 (240)
T PRK09764 28 ALPTESALQTEFGVSRVTVRQALRQ 52 (240)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4699999999999999999887766
No 140
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=22.47 E-value=3.8e+02 Score=22.53 Aligned_cols=28 Identities=18% Similarity=0.143 Sum_probs=22.7
Q ss_pred CCCCHHHHHHHhccChHHHHHHhhhHHH
Q 022167 237 CEPSMEQLAASLRISRPELQSILMECSL 264 (301)
Q Consensus 237 rePt~eEwA~a~g~S~~eLrr~L~eG~~ 264 (301)
...+.+|+|+.+|+++..++..+..+..
T Consensus 144 ~g~s~~eIA~~lgis~~tV~~~l~Rar~ 171 (179)
T PRK12514 144 EGLSYKELAERHDVPLNTMRTWLRRSLL 171 (179)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHHHHHH
Confidence 3567999999999999999888776543
No 141
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=22.41 E-value=1.7e+02 Score=28.08 Aligned_cols=56 Identities=18% Similarity=0.199 Sum_probs=39.3
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh-------------HHHHHHHHHHHhHHHHHHHHh
Q 022167 226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILME-------------CSLAREKLVMSNVRLVMSIAQ 282 (301)
Q Consensus 226 ~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e-------------G~~ARekLV~aNLRLVVSIAK 282 (301)
++..-+.+.++.+.+.+++|..+|+|+.-|.+.+.+ ...|++.|...++. |-.||.
T Consensus 146 ~v~~yI~~~~~~~lsl~~lA~~~g~S~~~L~R~Fk~~G~S~~~yl~~~Rl~~A~~LL~~t~~s-I~eIA~ 214 (274)
T PRK09978 146 RVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREEETSYSQLLTECRMQRALQLIVIHGFS-IKRVAV 214 (274)
T ss_pred HHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHcCCCC-HHHHHH
Confidence 344556677788899999999999999988887654 34566666655543 334444
No 142
>COG0411 LivG ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]
Probab=22.36 E-value=31 Score=33.18 Aligned_cols=37 Identities=22% Similarity=0.357 Sum_probs=33.1
Q ss_pred hccChHHHHHHhhhHHHHHHH------HHHHhHHHHHHHHhhc
Q 022167 248 LRISRPELQSILMECSLAREK------LVMSNVRLVMSIAQRY 284 (301)
Q Consensus 248 ~g~S~~eLrr~L~eG~~ARek------LV~aNLRLVVSIAKRY 284 (301)
+|+...|...+.....+.+++ ||++++++|+.+|-|-
T Consensus 178 AGln~~e~~~l~~~i~~i~~~~g~tillIEHdM~~Vm~l~dri 220 (250)
T COG0411 178 AGLNPEETEELAELIRELRDRGGVTILLIEHDMKLVMGLADRI 220 (250)
T ss_pred CCCCHHHHHHHHHHHHHHHhcCCcEEEEEEeccHHHhhhccEE
Confidence 688889999998888999986 9999999999999874
No 143
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=21.86 E-value=4.7e+02 Score=22.24 Aligned_cols=33 Identities=15% Similarity=0.039 Sum_probs=24.4
Q ss_pred HHHHhCCCCCHHHHHHHhccChHHHHHHhhhHH
Q 022167 231 LKERLGCEPSMEQLAASLRISRPELQSILMECS 263 (301)
Q Consensus 231 Lee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~ 263 (301)
+.-..-..-+.+|+|+.+|++...++..+..+.
T Consensus 148 ~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~ 180 (189)
T PRK09648 148 LILRVVVGLSAEETAEAVGSTPGAVRVAQHRAL 180 (189)
T ss_pred HHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 333333457899999999999998888876543
No 144
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=21.71 E-value=2.5e+02 Score=19.17 Aligned_cols=30 Identities=20% Similarity=0.217 Sum_probs=23.7
Q ss_pred HHHhCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167 232 KERLGCEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 232 ee~LGrePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
-..+...++..++|..+|+|...+.+++.+
T Consensus 21 ~~~~~~~~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 21 LKLLRESRSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HHHHhhcCCHHHHHHHHCCCHHHHHHHHHh
Confidence 344444579999999999999999888765
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=21.70 E-value=2.1e+02 Score=19.87 Aligned_cols=24 Identities=21% Similarity=0.289 Sum_probs=18.1
Q ss_pred CCCHHHHHHHhccChHHHHHHhhh
Q 022167 238 EPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 238 ePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
.-+..++|+.+|+|..++.+.+..
T Consensus 17 r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 17 RRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp TS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CccHHHHHHHHCcCHHHHHHHHHH
Confidence 356899999999999998877654
No 146
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=21.58 E-value=2.5e+02 Score=18.40 Aligned_cols=22 Identities=23% Similarity=0.338 Sum_probs=18.2
Q ss_pred CHHHHHHHhccChHHHHHHhhh
Q 022167 240 SMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 240 t~eEwA~a~g~S~~eLrr~L~e 261 (301)
+..|+|+.+|++...++..+..
T Consensus 20 s~~eia~~l~is~~tv~~~~~~ 41 (58)
T smart00421 20 TNKEIAERLGISEKTVKTHLSN 41 (58)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 5678999999999988877764
No 147
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=21.46 E-value=2.1e+02 Score=20.37 Aligned_cols=23 Identities=13% Similarity=0.289 Sum_probs=19.7
Q ss_pred CHHHHHHHhccChHHHHHHhhhH
Q 022167 240 SMEQLAASLRISRPELQSILMEC 262 (301)
Q Consensus 240 t~eEwA~a~g~S~~eLrr~L~eG 262 (301)
|..++|+.+|+|...+-++|...
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~~ 23 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNGP 23 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTTC
T ss_pred CHHHHHHHHCcCHHHHHHHHhCC
Confidence 56789999999999998888873
No 148
>PRK13502 transcriptional activator RhaR; Provisional
Probab=21.42 E-value=2e+02 Score=26.07 Aligned_cols=56 Identities=16% Similarity=0.180 Sum_probs=37.1
Q ss_pred HHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh--------------HHHHHHHHHHHhHHHHHHHHhh
Q 022167 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSILME--------------CSLAREKLVMSNVRLVMSIAQR 283 (301)
Q Consensus 227 ~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e--------------G~~ARekLV~aNLRLVVSIAKR 283 (301)
+..-+.+.+..+.+.+++|+.+|+|..-|.+...+ -.+|++.|...|+ =|..||.+
T Consensus 181 ~~~~I~~~~~~~~~~~~lA~~~~iS~~~L~r~fk~~~G~t~~~yi~~~Rl~~A~~lL~~t~~-sI~eIA~~ 250 (282)
T PRK13502 181 LITALANSLECPFALDAFCQQEQCSERVLRQQFRAQTGMTINQYLRQVRICHAQYLLQHSPL-MISEISMQ 250 (282)
T ss_pred HHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcCCC-CHHHHHHH
Confidence 33444555666778999999999999888887766 2456666655543 24555554
No 149
>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=21.28 E-value=2.1e+02 Score=19.82 Aligned_cols=25 Identities=24% Similarity=0.308 Sum_probs=20.1
Q ss_pred CCCHHHHHHHhccChHHHHHHhhhH
Q 022167 238 EPSMEQLAASLRISRPELQSILMEC 262 (301)
Q Consensus 238 ePt~eEwA~a~g~S~~eLrr~L~eG 262 (301)
+.|.+|+|+.+|+|...+++.+..-
T Consensus 15 ~it~~eLa~~l~vS~rTi~~~i~~L 39 (55)
T PF08279_consen 15 PITAKELAEELGVSRRTIRRDIKEL 39 (55)
T ss_dssp SBEHHHHHHHCTS-HHHHHHHHHHH
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 3789999999999999888777653
No 150
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=21.11 E-value=5.1e+02 Score=22.29 Aligned_cols=50 Identities=6% Similarity=0.058 Sum_probs=32.2
Q ss_pred HHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHH
Q 022167 213 RLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSL 264 (301)
Q Consensus 213 eLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ 264 (301)
.|...|...-. ..+.-+.-..-..-+.+|+|+.+|++...++..+..+..
T Consensus 135 ~l~~~l~~L~~--~~r~vl~l~~~~~~s~~EIA~~Lgis~~tVk~~l~ra~~ 184 (194)
T PRK09646 135 RVRDCLDALTD--TQRESVTLAYYGGLTYREVAERLAVPLGTVKTRMRDGLI 184 (194)
T ss_pred HHHHHHHhCCH--HHHHHHHHHHHcCCCHHHHHHHhCCChHhHHHHHHHHHH
Confidence 34444544333 223333333345688999999999999999888876543
No 151
>PRK13558 bacterio-opsin activator; Provisional
Probab=20.88 E-value=2.3e+02 Score=29.10 Aligned_cols=56 Identities=30% Similarity=0.269 Sum_probs=42.0
Q ss_pred CCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHh
Q 022167 205 LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSN 273 (301)
Q Consensus 205 LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aN 273 (301)
.||..|...|-..+..|.. ..=|.-|.+|+|+.+|++...+...|+. |..+|+.+.
T Consensus 607 ~lt~~q~e~l~~a~~~gyf----------~~pr~~~~~e~a~~l~is~~t~~~~lr~---a~~~l~~~~ 662 (665)
T PRK13558 607 DLTDRQLTALQKAYVSGYF----------EWPRRVEGEELAESMGISRSTFHQHLRA---AERKLVGAF 662 (665)
T ss_pred hCCHHHHHHHHHHHHcCCC----------CCCccCCHHHHHHHhCCCHHHHHHHHHH---HHHHHHHHH
Confidence 5888777777777777665 2356778999999999999998877764 555666553
No 152
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=20.88 E-value=2e+02 Score=26.16 Aligned_cols=33 Identities=21% Similarity=0.308 Sum_probs=26.2
Q ss_pred HHHHHHHHhCCCCCHHHHHHHhccChHHHHHHh
Q 022167 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSIL 259 (301)
Q Consensus 227 ~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L 259 (301)
....+...+++.|+.+++|..+|++.+++...+
T Consensus 121 ~~~~~~~~~~r~~~~~e~a~~~~~~~~~~~~~~ 153 (257)
T PRK08583 121 AVDELTTELQRSPKISEIADRLGVSEEEVLEAM 153 (257)
T ss_pred HHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 445567788999999999999999888775543
No 153
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=20.57 E-value=1e+02 Score=20.07 Aligned_cols=23 Identities=22% Similarity=0.345 Sum_probs=18.4
Q ss_pred CHHHHHHHhccChHHHHHHhhhH
Q 022167 240 SMEQLAASLRISRPELQSILMEC 262 (301)
Q Consensus 240 t~eEwA~a~g~S~~eLrr~L~eG 262 (301)
+.+|.|+-+|++...+.+.+.+|
T Consensus 3 t~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHHcC
Confidence 56788999999988888777655
No 154
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=20.46 E-value=4.6e+02 Score=23.91 Aligned_cols=58 Identities=21% Similarity=0.171 Sum_probs=39.7
Q ss_pred HHHHHHHHHHhCCC-CCHHHHHHHhccChHHHHHHhhh-------------HHHHHHHHHHHh--HHHHHHHHhh
Q 022167 225 DDHKLRLKERLGCE-PSMEQLAASLRISRPELQSILME-------------CSLAREKLVMSN--VRLVMSIAQR 283 (301)
Q Consensus 225 e~~r~eLee~LGre-Pt~eEwA~a~g~S~~eLrr~L~e-------------G~~ARekLV~aN--LRLVVSIAKR 283 (301)
..++.-+.+.+..+ .+.+++|+++|+|+.-|.+...+ -..|++.| ... -+=|-.||.+
T Consensus 200 ~~~~~~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk~~G~T~~~yi~~~RL~~A~~lL-~~~~~~~sI~eIA~~ 273 (302)
T PRK09685 200 QKVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFAEQGLVVAQYIRNRRLDRCADDL-RPAADDEKITSIAYK 273 (302)
T ss_pred HHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHh-hhhccCCCHHHHHHH
Confidence 34555566777776 69999999999999888877654 24566666 431 1236677766
No 155
>PRK13500 transcriptional activator RhaR; Provisional
Probab=20.03 E-value=2.2e+02 Score=26.78 Aligned_cols=35 Identities=14% Similarity=0.146 Sum_probs=28.1
Q ss_pred HHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167 227 HKLRLKERLGCEPSMEQLAASLRISRPELQSILME 261 (301)
Q Consensus 227 ~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e 261 (301)
+..-+.+.+..+.+.+++|+.+|+|..-|.+...+
T Consensus 211 i~~yI~~~~~e~isl~~lA~~~~iS~~~L~r~FK~ 245 (312)
T PRK13500 211 LITRLAASLKSPFALDKFCDEASCSERVLRQQFRQ 245 (312)
T ss_pred HHHHHHHcccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34455666777889999999999999998888776
Done!