Query psy8301
Match_columns 157
No_of_seqs 154 out of 1311
Neff 7.9
Searched_HMMs 46136
Date Sat Aug 17 00:04:24 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8301.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8301hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0484|consensus 99.9 1.3E-23 2.9E-28 141.7 8.0 66 4-69 14-79 (125)
2 KOG2251|consensus 99.9 2.3E-22 5E-27 152.3 10.4 66 4-69 34-99 (228)
3 KOG0494|consensus 99.8 1.5E-21 3.2E-26 151.0 6.4 83 3-85 136-219 (332)
4 KOG0488|consensus 99.8 3.9E-20 8.5E-25 149.2 11.8 65 4-68 169-233 (309)
5 KOG0843|consensus 99.8 6.1E-20 1.3E-24 135.2 8.0 68 2-69 97-164 (197)
6 KOG0850|consensus 99.8 4.3E-19 9.3E-24 135.2 10.0 66 3-68 118-183 (245)
7 KOG0489|consensus 99.8 7.8E-20 1.7E-24 144.8 5.9 65 6-70 158-222 (261)
8 KOG0842|consensus 99.8 1E-19 2.3E-24 145.2 5.7 70 4-73 150-219 (307)
9 PF00046 Homeobox: Homeobox do 99.8 1.5E-18 3.1E-23 107.1 7.4 57 8-64 1-57 (57)
10 KOG0485|consensus 99.8 2.6E-18 5.7E-23 130.0 8.9 67 5-71 102-168 (268)
11 KOG0492|consensus 99.7 2.5E-18 5.3E-23 129.3 5.9 68 2-69 138-206 (246)
12 KOG0491|consensus 99.7 3.5E-17 7.6E-22 119.1 6.1 69 6-74 99-167 (194)
13 KOG0487|consensus 99.7 2.4E-17 5.3E-22 131.8 4.6 66 4-69 232-297 (308)
14 KOG0490|consensus 99.7 7.1E-17 1.5E-21 124.9 6.7 135 4-149 57-191 (235)
15 KOG0486|consensus 99.7 1.8E-17 3.9E-22 131.3 2.7 66 5-70 110-175 (351)
16 smart00389 HOX Homeodomain. DN 99.7 2.5E-16 5.5E-21 96.4 6.4 55 8-62 1-55 (56)
17 TIGR01565 homeo_ZF_HD homeobox 99.7 8.3E-17 1.8E-21 99.3 4.0 52 8-59 2-57 (58)
18 KOG0848|consensus 99.7 7.2E-17 1.6E-21 125.5 4.5 63 7-69 199-261 (317)
19 cd00086 homeodomain Homeodomai 99.7 5.8E-16 1.3E-20 95.6 7.5 56 9-64 2-57 (59)
20 KOG0493|consensus 99.6 2.1E-16 4.5E-21 122.7 5.3 59 7-65 246-304 (342)
21 COG5576 Homeodomain-containing 99.6 1.5E-15 3.3E-20 111.5 6.0 63 5-67 49-111 (156)
22 KOG0844|consensus 99.6 8.2E-16 1.8E-20 121.6 1.6 61 8-68 182-242 (408)
23 KOG4577|consensus 99.5 4.3E-15 9.3E-20 116.8 4.8 62 7-68 167-228 (383)
24 KOG0483|consensus 99.5 6.8E-15 1.5E-19 111.6 4.7 61 8-68 51-111 (198)
25 KOG3802|consensus 99.5 5.6E-15 1.2E-19 120.7 0.9 62 5-66 292-353 (398)
26 KOG0849|consensus 99.5 2.2E-13 4.8E-18 112.1 9.7 65 4-68 173-237 (354)
27 KOG0847|consensus 99.5 3.6E-14 7.8E-19 107.8 4.2 64 6-69 166-229 (288)
28 KOG0775|consensus 99.3 3.2E-11 7E-16 94.4 9.2 51 14-64 183-233 (304)
29 KOG1168|consensus 99.0 7.6E-11 1.6E-15 93.1 0.5 61 6-66 308-368 (385)
30 KOG0774|consensus 98.9 3E-09 6.4E-14 83.1 5.6 61 7-67 188-251 (334)
31 PF05920 Homeobox_KN: Homeobox 98.7 2.1E-08 4.6E-13 57.3 4.1 34 28-61 7-40 (40)
32 KOG2252|consensus 98.6 7.3E-08 1.6E-12 82.1 6.3 56 7-62 420-475 (558)
33 KOG0490|consensus 98.5 1.2E-07 2.7E-12 73.1 4.7 64 4-67 150-213 (235)
34 KOG1146|consensus 97.9 2.1E-05 4.5E-10 73.1 6.0 62 6-67 902-963 (1406)
35 PF11569 Homez: Homeodomain le 97.1 0.00074 1.6E-08 41.1 3.2 41 19-59 10-50 (56)
36 KOG3623|consensus 96.7 0.0048 1E-07 55.0 6.9 49 19-67 568-616 (1007)
37 KOG0773|consensus 96.6 0.0012 2.7E-08 54.2 2.5 57 7-63 239-298 (342)
38 PF04218 CENP-B_N: CENP-B N-te 95.2 0.059 1.3E-06 32.4 4.7 47 8-59 1-47 (53)
39 PF04545 Sigma70_r4: Sigma-70, 89.2 2.1 4.6E-05 24.7 5.6 46 13-63 4-49 (50)
40 PF01527 HTH_Tnp_1: Transposas 87.2 1.8 3.8E-05 27.1 4.7 45 9-58 2-47 (76)
41 PF04967 HTH_10: HTH DNA bindi 87.1 1.2 2.6E-05 26.8 3.5 40 14-53 1-42 (53)
42 cd06171 Sigma70_r4 Sigma70, re 85.2 3.2 6.9E-05 23.2 4.7 44 13-61 10-53 (55)
43 PF08281 Sigma70_r4_2: Sigma-7 83.8 5 0.00011 23.3 5.2 42 14-60 11-52 (54)
44 PRK03975 tfx putative transcri 83.0 6.7 0.00015 28.4 6.5 50 12-67 5-54 (141)
45 PF10668 Phage_terminase: Phag 80.6 1.7 3.6E-05 26.9 2.3 22 35-56 23-44 (60)
46 KOG1146|consensus 74.5 4 8.7E-05 39.3 3.9 60 7-66 705-764 (1406)
47 COG3413 Predicted DNA binding 73.5 9.5 0.00021 29.1 5.3 52 13-66 155-208 (215)
48 PRK00118 putative DNA-binding 73.1 23 0.0005 24.3 6.5 48 13-65 17-64 (104)
49 PRK06759 RNA polymerase factor 72.8 14 0.0003 26.0 5.7 45 14-63 107-151 (154)
50 PRK09646 RNA polymerase sigma 72.8 15 0.00032 27.2 6.1 31 35-65 159-189 (194)
51 PRK09652 RNA polymerase sigma 71.4 17 0.00037 26.0 6.0 30 35-64 145-174 (182)
52 PRK12526 RNA polymerase sigma 71.0 17 0.00037 27.3 6.1 35 32-66 167-201 (206)
53 PRK09644 RNA polymerase sigma 70.8 24 0.00052 25.2 6.7 32 35-66 125-156 (165)
54 PF00196 GerE: Bacterial regul 69.9 20 0.00044 21.1 5.3 43 13-61 3-45 (58)
55 TIGR03879 near_KaiC_dom probab 69.8 2.7 5.8E-05 27.0 1.2 35 23-57 21-55 (73)
56 cd04761 HTH_MerR-SF Helix-Turn 69.7 5.4 0.00012 22.5 2.4 20 37-56 3-22 (49)
57 PRK09642 RNA polymerase sigma 69.7 24 0.00053 25.0 6.5 32 35-66 123-154 (160)
58 PRK04217 hypothetical protein; 69.1 26 0.00057 24.2 6.2 50 12-66 41-90 (110)
59 KOG2251|consensus 68.9 0.86 1.9E-05 35.4 -1.4 43 101-148 32-74 (228)
60 PRK11924 RNA polymerase sigma 68.8 26 0.00056 25.0 6.5 31 35-65 142-172 (179)
61 PF13936 HTH_38: Helix-turn-he 68.6 11 0.00023 21.3 3.5 40 12-56 3-42 (44)
62 cd00569 HTH_Hin_like Helix-tur 67.8 13 0.00029 18.3 4.6 37 13-54 5-41 (42)
63 PRK12519 RNA polymerase sigma 66.8 17 0.00037 26.8 5.3 34 31-64 154-187 (194)
64 PF13551 HTH_29: Winged helix- 66.5 28 0.00061 22.9 5.9 49 8-56 52-109 (112)
65 TIGR02937 sigma70-ECF RNA poly 65.0 26 0.00055 23.8 5.7 46 14-64 111-156 (158)
66 TIGR02999 Sig-70_X6 RNA polyme 65.0 29 0.00062 25.2 6.1 30 35-64 151-180 (183)
67 PF13518 HTH_28: Helix-turn-he 64.7 13 0.00027 21.2 3.4 25 36-60 14-38 (52)
68 TIGR02985 Sig70_bacteroi1 RNA 64.3 30 0.00065 24.1 6.0 30 35-64 130-159 (161)
69 PRK12514 RNA polymerase sigma 63.8 31 0.00066 25.0 6.1 30 35-64 146-175 (179)
70 PRK12512 RNA polymerase sigma 63.0 34 0.00073 24.9 6.2 33 34-66 147-179 (184)
71 PRK05602 RNA polymerase sigma 63.0 37 0.00081 24.7 6.5 33 35-67 145-177 (186)
72 TIGR02959 SigZ RNA polymerase 62.7 34 0.00074 24.7 6.2 32 35-66 117-148 (170)
73 PF06056 Terminase_5: Putative 62.6 8.7 0.00019 23.4 2.4 27 35-63 14-40 (58)
74 KOG3755|consensus 62.5 3.9 8.4E-05 36.4 1.1 46 21-66 706-758 (769)
75 PRK10072 putative transcriptio 62.4 9.9 0.00021 25.6 2.9 40 13-59 32-71 (96)
76 PRK09648 RNA polymerase sigma 62.2 34 0.00073 25.1 6.1 30 35-64 156-185 (189)
77 TIGR02989 Sig-70_gvs1 RNA poly 61.9 32 0.00069 24.2 5.8 32 32-63 125-156 (159)
78 PRK09413 IS2 repressor TnpA; R 61.3 24 0.00052 24.4 4.9 42 11-57 10-52 (121)
79 TIGR02948 SigW_bacill RNA poly 61.3 30 0.00065 25.0 5.7 33 32-64 150-182 (187)
80 PRK09639 RNA polymerase sigma 61.1 37 0.00081 24.1 6.1 32 34-65 127-158 (166)
81 PRK06930 positive control sigm 61.0 47 0.001 24.6 6.6 49 13-66 114-162 (170)
82 PRK12515 RNA polymerase sigma 60.4 46 0.001 24.3 6.6 32 35-66 148-179 (189)
83 TIGR02939 RpoE_Sigma70 RNA pol 59.5 29 0.00064 25.2 5.4 35 31-65 151-185 (190)
84 PRK12530 RNA polymerase sigma 59.5 39 0.00085 24.9 6.1 31 35-65 151-181 (189)
85 PF09607 BrkDBD: Brinker DNA-b 59.3 29 0.00062 21.3 4.3 44 11-56 3-47 (58)
86 PRK12543 RNA polymerase sigma 58.8 43 0.00092 24.3 6.1 33 34-66 133-165 (179)
87 cd04762 HTH_MerR-trunc Helix-T 57.9 13 0.00029 20.3 2.6 21 37-57 3-23 (49)
88 PF13443 HTH_26: Cro/C1-type H 57.8 7 0.00015 23.4 1.5 26 36-61 12-37 (63)
89 TIGR02983 SigE-fam_strep RNA p 57.5 43 0.00094 23.6 5.9 30 35-64 127-156 (162)
90 TIGR02954 Sig70_famx3 RNA poly 57.5 44 0.00095 23.9 5.9 30 35-64 136-165 (169)
91 PF13384 HTH_23: Homeodomain-l 57.3 11 0.00024 21.4 2.2 23 35-57 18-40 (50)
92 PRK09047 RNA polymerase factor 57.2 51 0.0011 23.1 6.2 31 35-65 123-153 (161)
93 PRK12532 RNA polymerase sigma 57.1 63 0.0014 23.7 6.9 33 35-67 153-185 (195)
94 COG4367 Uncharacterized protei 57.0 22 0.00047 23.7 3.7 41 13-53 2-42 (97)
95 TIGR02943 Sig70_famx1 RNA poly 56.9 61 0.0013 23.9 6.7 34 34-67 147-180 (188)
96 PRK09637 RNA polymerase sigma 56.8 42 0.00091 24.6 5.8 32 35-66 123-154 (181)
97 PF13411 MerR_1: MerR HTH fami 56.5 12 0.00027 22.6 2.5 20 37-56 3-22 (69)
98 PF00424 REV: REV protein (ant 56.3 24 0.00051 23.7 3.8 34 21-68 16-49 (91)
99 PRK12537 RNA polymerase sigma 56.0 49 0.0011 24.1 6.1 30 35-64 150-179 (182)
100 TIGR02952 Sig70_famx2 RNA poly 56.0 51 0.0011 23.4 6.0 30 35-64 139-168 (170)
101 PRK12541 RNA polymerase sigma 55.4 39 0.00085 23.9 5.3 30 35-64 129-158 (161)
102 PF02796 HTH_7: Helix-turn-hel 55.4 30 0.00066 19.5 3.8 38 13-55 5-42 (45)
103 PRK06986 fliA flagellar biosyn 55.4 44 0.00096 25.6 5.9 46 15-65 186-231 (236)
104 PRK07037 extracytoplasmic-func 55.3 57 0.0012 23.0 6.2 30 35-64 126-155 (163)
105 PRK12533 RNA polymerase sigma 55.0 69 0.0015 24.4 6.9 34 33-66 149-182 (216)
106 PF00376 MerR: MerR family reg 54.9 16 0.00034 20.1 2.4 20 37-56 2-21 (38)
107 PRK12529 RNA polymerase sigma 54.8 54 0.0012 23.8 6.1 30 35-64 144-173 (178)
108 PRK12536 RNA polymerase sigma 53.9 57 0.0012 23.7 6.1 32 34-65 145-176 (181)
109 smart00421 HTH_LUXR helix_turn 53.2 39 0.00085 18.9 5.3 40 13-58 3-42 (58)
110 PRK09645 RNA polymerase sigma 53.0 61 0.0013 23.2 6.1 30 35-64 135-164 (173)
111 PRK12524 RNA polymerase sigma 52.8 58 0.0013 24.0 6.1 31 35-65 153-183 (196)
112 PRK12523 RNA polymerase sigma 52.7 66 0.0014 23.1 6.2 31 35-65 136-166 (172)
113 PRK12538 RNA polymerase sigma 52.7 45 0.00098 25.7 5.6 32 35-66 188-219 (233)
114 PF08280 HTH_Mga: M protein tr 52.5 41 0.00088 20.1 4.3 36 17-56 6-41 (59)
115 TIGR00721 tfx DNA-binding prot 52.5 66 0.0014 23.1 6.0 48 11-64 4-51 (137)
116 PRK12546 RNA polymerase sigma 52.1 54 0.0012 24.3 5.8 32 35-66 130-161 (188)
117 PRK12535 RNA polymerase sigma 51.9 60 0.0013 24.2 6.0 33 35-67 150-182 (196)
118 PRK12547 RNA polymerase sigma 51.3 68 0.0015 22.9 6.1 31 34-64 128-158 (164)
119 cd04763 HTH_MlrA-like Helix-Tu 51.2 20 0.00044 21.8 2.8 20 37-56 3-22 (68)
120 KOG0484|consensus 51.1 1.4 3E-05 30.4 -2.7 36 107-147 18-53 (125)
121 PRK12518 RNA polymerase sigma 50.6 35 0.00075 24.5 4.4 36 31-66 133-168 (175)
122 PRK08583 RNA polymerase sigma 50.2 63 0.0014 25.1 6.1 46 14-64 206-251 (257)
123 TIGR02980 SigBFG RNA polymeras 50.0 66 0.0014 24.3 6.1 47 13-64 178-224 (227)
124 PRK06811 RNA polymerase factor 49.7 68 0.0015 23.5 6.0 31 35-65 148-178 (189)
125 cd06170 LuxR_C_like C-terminal 49.7 46 0.001 18.7 4.5 36 15-56 2-37 (57)
126 PRK09647 RNA polymerase sigma 49.6 90 0.0019 23.4 6.7 32 35-66 155-186 (203)
127 cd01104 HTH_MlrA-CarA Helix-Tu 49.5 23 0.00049 21.4 2.8 20 37-56 3-22 (68)
128 cd04764 HTH_MlrA-like_sg1 Heli 49.1 24 0.00051 21.4 2.9 21 37-57 3-23 (67)
129 PRK13919 putative RNA polymera 49.0 76 0.0017 23.0 6.1 30 35-64 152-181 (186)
130 PRK09649 RNA polymerase sigma 49.0 63 0.0014 23.6 5.7 30 35-64 147-176 (185)
131 TIGR02479 FliA_WhiG RNA polyme 48.7 69 0.0015 24.2 6.0 46 14-64 176-221 (224)
132 PRK09480 slmA division inhibit 48.6 20 0.00043 26.1 2.9 39 21-60 18-56 (194)
133 PRK12545 RNA polymerase sigma 48.0 78 0.0017 23.6 6.1 34 33-66 154-187 (201)
134 PRK10403 transcriptional regul 47.7 43 0.00093 23.9 4.6 43 13-61 153-195 (215)
135 PRK12539 RNA polymerase sigma 47.6 93 0.002 22.6 6.4 31 34-64 147-177 (184)
136 PRK12516 RNA polymerase sigma 47.4 81 0.0018 23.2 6.1 32 35-66 133-164 (187)
137 PRK12542 RNA polymerase sigma 47.4 79 0.0017 23.0 6.0 30 35-64 139-168 (185)
138 PRK09651 RNA polymerase sigma 47.4 74 0.0016 22.9 5.8 33 32-64 133-165 (172)
139 PF01726 LexA_DNA_bind: LexA D 47.0 52 0.0011 20.3 4.2 41 13-55 3-47 (65)
140 PRK12531 RNA polymerase sigma 46.9 93 0.002 22.9 6.4 30 35-64 158-187 (194)
141 PRK12520 RNA polymerase sigma 46.2 1.1E+02 0.0025 22.2 7.0 34 35-68 148-181 (191)
142 PRK07670 RNA polymerase sigma 45.4 80 0.0017 24.5 6.0 45 15-64 203-247 (251)
143 TIGR02950 SigM_subfam RNA poly 45.4 40 0.00087 23.5 4.0 34 31-64 118-151 (154)
144 TIGR02941 Sigma_B RNA polymera 45.0 80 0.0017 24.5 6.0 46 14-64 206-251 (255)
145 TIGR03001 Sig-70_gmx1 RNA poly 44.7 1E+02 0.0022 24.0 6.5 31 35-65 178-208 (244)
146 PRK12528 RNA polymerase sigma 44.7 89 0.0019 22.0 5.8 28 35-62 130-157 (161)
147 PRK07408 RNA polymerase sigma 44.6 91 0.002 24.4 6.2 47 14-65 204-250 (256)
148 PRK08301 sporulation sigma fac 44.2 85 0.0019 23.9 5.9 32 33-64 197-228 (234)
149 PRK12511 RNA polymerase sigma 43.8 90 0.002 22.9 5.8 32 35-66 128-159 (182)
150 PRK12525 RNA polymerase sigma 43.6 95 0.002 22.2 5.8 30 35-64 135-164 (168)
151 PRK12527 RNA polymerase sigma 42.8 1.2E+02 0.0025 21.4 6.7 31 35-65 122-152 (159)
152 PRK11923 algU RNA polymerase s 42.5 99 0.0021 22.5 5.9 35 32-66 152-186 (193)
153 KOG3755|consensus 42.3 18 0.00038 32.4 2.0 62 2-63 642-707 (769)
154 PRK12522 RNA polymerase sigma 41.9 1.1E+02 0.0024 21.9 6.0 31 34-64 135-165 (173)
155 TIGR01764 excise DNA binding d 41.9 33 0.00072 18.7 2.6 21 37-57 4-24 (49)
156 PRK08295 RNA polymerase factor 41.8 1E+02 0.0022 22.7 5.9 35 31-65 167-201 (208)
157 PRK09641 RNA polymerase sigma 41.7 1.1E+02 0.0023 22.1 5.9 32 33-64 151-182 (187)
158 smart00027 EH Eps15 homology d 41.7 93 0.002 20.2 5.1 43 14-56 4-51 (96)
159 PRK07122 RNA polymerase sigma 41.6 93 0.002 24.5 5.9 46 14-64 216-261 (264)
160 PRK12544 RNA polymerase sigma 41.5 1.3E+02 0.0028 22.6 6.4 31 36-66 166-196 (206)
161 cd01392 HTH_LacI Helix-turn-he 41.3 14 0.0003 21.1 0.9 20 39-58 2-21 (52)
162 PRK06288 RNA polymerase sigma 41.2 1.3E+02 0.0028 23.6 6.6 47 14-65 213-259 (268)
163 PF13412 HTH_24: Winged helix- 40.9 66 0.0014 17.9 4.4 37 15-55 2-38 (48)
164 PRK05657 RNA polymerase sigma 40.9 91 0.002 25.5 5.9 53 13-66 262-314 (325)
165 PRK10360 DNA-binding transcrip 40.8 67 0.0015 22.8 4.7 43 13-61 137-179 (196)
166 PRK09643 RNA polymerase sigma 40.6 1.5E+02 0.0032 21.8 7.2 31 34-64 150-180 (192)
167 TIGR02947 SigH_actino RNA poly 40.6 52 0.0011 24.1 4.1 36 31-66 144-179 (193)
168 TIGR02393 RpoD_Cterm RNA polym 40.1 95 0.0021 23.8 5.6 52 13-65 176-227 (238)
169 PRK09415 RNA polymerase factor 40.0 1E+02 0.0022 22.4 5.5 30 35-64 144-173 (179)
170 PF01381 HTH_3: Helix-turn-hel 39.6 15 0.00032 21.1 0.8 23 36-58 11-33 (55)
171 PF13730 HTH_36: Helix-turn-he 39.6 55 0.0012 18.8 3.4 22 36-57 27-48 (55)
172 TIGR02859 spore_sigH RNA polym 39.5 54 0.0012 24.0 4.0 34 31-64 162-195 (198)
173 COG2963 Transposase and inacti 38.8 92 0.002 21.0 4.8 42 11-56 5-47 (116)
174 PRK11511 DNA-binding transcrip 38.7 50 0.0011 22.9 3.6 28 31-58 22-49 (127)
175 PF04936 DUF658: Protein of un 38.5 14 0.00031 27.5 0.7 30 35-64 15-44 (186)
176 PRK15369 two component system 38.1 1E+02 0.0022 21.6 5.3 43 13-61 149-191 (211)
177 PF07638 Sigma70_ECF: ECF sigm 37.8 1.4E+02 0.0029 22.0 6.0 32 33-64 150-181 (185)
178 smart00422 HTH_MERR helix_turn 37.3 37 0.0008 20.4 2.4 20 37-56 3-22 (70)
179 TIGR02957 SigX4 RNA polymerase 37.3 1.1E+02 0.0025 24.1 5.8 29 36-64 126-154 (281)
180 PF12824 MRP-L20: Mitochondria 37.1 1.4E+02 0.003 22.1 5.8 44 10-55 82-125 (164)
181 TIGR03070 couple_hipB transcri 37.1 19 0.00042 20.5 1.1 23 36-58 17-39 (58)
182 PRK12513 RNA polymerase sigma 36.5 67 0.0014 23.5 4.1 35 31-65 152-186 (194)
183 KOG0773|consensus 36.4 59 0.0013 26.5 4.1 42 27-68 117-158 (342)
184 PRK09636 RNA polymerase sigma 36.4 1.2E+02 0.0026 24.0 5.9 29 36-64 133-161 (293)
185 PRK08215 sporulation sigma fac 36.3 1.3E+02 0.0028 23.4 5.9 47 13-64 209-255 (258)
186 PF12728 HTH_17: Helix-turn-he 35.8 45 0.00097 18.9 2.5 21 37-57 4-24 (51)
187 TIGR02885 spore_sigF RNA polym 35.5 1.4E+02 0.0031 22.6 6.0 43 14-61 184-226 (231)
188 PRK09640 RNA polymerase sigma 35.4 72 0.0016 23.3 4.2 34 32-65 148-181 (188)
189 PRK12534 RNA polymerase sigma 35.4 1.6E+02 0.0034 21.3 6.0 32 33-64 152-183 (187)
190 PRK05803 sporulation sigma fac 35.1 1.5E+02 0.0032 22.7 6.0 31 35-65 196-226 (233)
191 PF08279 HTH_11: HTH domain; 35.0 42 0.00092 19.3 2.3 35 19-56 3-37 (55)
192 COG1905 NuoE NADH:ubiquinone o 34.4 82 0.0018 23.3 4.2 37 16-52 25-61 (160)
193 PRK05572 sporulation sigma fac 34.4 1.5E+02 0.0033 22.9 6.0 47 13-64 202-248 (252)
194 PRK09935 transcriptional regul 34.1 96 0.0021 22.1 4.7 43 13-61 149-191 (210)
195 PRK11922 RNA polymerase sigma 34.1 82 0.0018 24.0 4.4 37 31-67 162-198 (231)
196 PRK05911 RNA polymerase sigma 34.0 1.6E+02 0.0035 23.0 6.1 46 14-64 206-251 (257)
197 TIGR02392 rpoH_proteo alternat 33.9 1.3E+02 0.0028 23.6 5.6 49 13-64 218-266 (270)
198 COG1595 RpoE DNA-directed RNA 33.6 88 0.0019 22.7 4.4 33 35-67 144-176 (182)
199 PRK09638 RNA polymerase sigma 33.2 82 0.0018 22.5 4.1 34 31-64 139-172 (176)
200 PHA01976 helix-turn-helix prot 32.3 52 0.0011 19.7 2.5 23 36-58 17-39 (67)
201 TIGR02607 antidote_HigA addict 31.7 31 0.00067 21.3 1.4 24 36-59 20-43 (78)
202 PRK05988 formate dehydrogenase 31.5 1.1E+02 0.0023 22.4 4.4 37 17-53 24-60 (156)
203 PF04539 Sigma70_r3: Sigma-70 31.2 77 0.0017 19.6 3.3 22 35-56 21-42 (78)
204 PF06971 Put_DNA-bind_N: Putat 30.9 45 0.00098 19.6 1.9 18 36-53 30-47 (50)
205 COG2944 Predicted transcriptio 30.6 75 0.0016 21.8 3.2 39 14-59 44-82 (104)
206 PF14229 DUF4332: Domain of un 30.6 64 0.0014 22.5 3.0 25 31-55 26-50 (122)
207 PRK10100 DNA-binding transcrip 30.5 1.4E+02 0.0031 22.7 5.2 45 12-62 154-198 (216)
208 PF01710 HTH_Tnp_IS630: Transp 30.4 1.4E+02 0.003 20.5 4.6 34 18-56 7-40 (119)
209 PF13404 HTH_AsnC-type: AsnC-t 30.4 48 0.001 18.6 1.9 18 35-52 18-35 (42)
210 PRK07500 rpoH2 RNA polymerase 30.3 1.5E+02 0.0033 23.6 5.5 50 13-65 227-276 (289)
211 TIGR01958 nuoE_fam NADH-quinon 30.3 1.2E+02 0.0025 21.8 4.4 37 17-53 17-53 (148)
212 PF14549 P22_Cro: DNA-binding 30.3 53 0.0012 20.0 2.2 18 37-54 12-29 (60)
213 TIGR02960 SigX5 RNA polymerase 30.2 1.6E+02 0.0036 23.4 5.8 31 35-65 159-189 (324)
214 cd01106 HTH_TipAL-Mta Helix-Tu 30.2 53 0.0012 21.8 2.5 20 37-56 3-22 (103)
215 PF07022 Phage_CI_repr: Bacter 30.1 36 0.00079 20.8 1.5 22 36-57 14-36 (66)
216 PRK06704 RNA polymerase factor 30.0 1.8E+02 0.0039 22.5 5.7 31 35-65 133-163 (228)
217 TIGR03020 EpsA transcriptional 29.7 1.5E+02 0.0033 23.3 5.3 46 11-62 188-233 (247)
218 PRK12540 RNA polymerase sigma 29.6 2.2E+02 0.0049 20.7 7.6 33 34-66 127-159 (182)
219 TIGR03541 reg_near_HchA LuxR f 29.5 1.2E+02 0.0025 23.4 4.6 47 11-63 169-215 (232)
220 PRK07539 NADH dehydrogenase su 29.4 1.2E+02 0.0026 21.9 4.4 36 18-53 24-59 (154)
221 TIGR02394 rpoS_proteo RNA poly 29.4 2.3E+02 0.0051 22.3 6.4 52 14-66 223-274 (285)
222 cd00093 HTH_XRE Helix-turn-hel 29.3 55 0.0012 17.5 2.1 22 37-58 15-36 (58)
223 PF05269 Phage_CII: Bacterioph 29.1 92 0.002 20.8 3.4 29 36-64 25-53 (91)
224 PRK09975 DNA-binding transcrip 29.1 34 0.00074 25.3 1.5 42 19-61 17-58 (213)
225 PF10945 DUF2629: Protein of u 29.0 73 0.0016 18.3 2.5 29 16-44 3-33 (44)
226 PF01257 2Fe-2S_thioredx: Thio 28.9 1.1E+02 0.0024 21.8 4.1 36 18-53 15-50 (145)
227 PRK10651 transcriptional regul 28.9 1.3E+02 0.0028 21.4 4.6 43 13-61 155-197 (216)
228 PF01047 MarR: MarR family; I 28.8 1.2E+02 0.0027 17.4 3.8 39 14-56 1-39 (59)
229 PRK12517 RNA polymerase sigma 28.7 2.4E+02 0.0051 20.7 6.5 32 35-66 145-176 (188)
230 PF13542 HTH_Tnp_ISL3: Helix-t 28.5 81 0.0018 17.8 2.8 21 36-56 29-49 (52)
231 smart00595 MADF subfamily of S 28.4 1.5E+02 0.0033 18.7 4.4 32 38-69 31-62 (89)
232 PF12200 DUF3597: Domain of un 27.9 1.4E+02 0.003 21.3 4.2 29 32-60 83-116 (127)
233 PF03444 HrcA_DNA-bdg: Winged 27.9 1.8E+02 0.0038 18.9 4.5 38 14-53 2-42 (78)
234 TIGR02984 Sig-70_plancto1 RNA 27.5 2.3E+02 0.0051 20.2 6.0 32 33-64 155-186 (189)
235 smart00530 HTH_XRE Helix-turn- 27.4 74 0.0016 16.8 2.5 22 37-58 13-34 (56)
236 cd01105 HTH_GlnR-like Helix-Tu 27.4 64 0.0014 20.9 2.4 19 37-55 4-22 (88)
237 PRK07571 bidirectional hydroge 27.0 1.4E+02 0.0031 22.1 4.4 35 19-53 39-73 (169)
238 TIGR02846 spore_sigmaK RNA pol 26.8 2.4E+02 0.0052 21.4 5.9 30 35-64 195-224 (227)
239 cd04766 HTH_HspR Helix-Turn-He 26.7 78 0.0017 20.5 2.7 21 36-56 3-23 (91)
240 PF08765 Mor: Mor transcriptio 26.7 99 0.0021 20.9 3.4 26 36-61 74-99 (108)
241 cd04774 HTH_YfmP Helix-Turn-He 26.7 77 0.0017 21.0 2.7 20 37-56 3-22 (96)
242 PRK00215 LexA repressor; Valid 26.7 99 0.0021 23.1 3.7 41 14-56 2-46 (205)
243 KOG0849|consensus 26.5 37 0.00079 28.3 1.3 37 106-147 176-212 (354)
244 PF10078 DUF2316: Uncharacteri 26.4 57 0.0012 21.7 2.0 38 14-55 3-44 (89)
245 TIGR02835 spore_sigmaE RNA pol 26.3 1.3E+02 0.0028 23.0 4.3 30 35-64 199-228 (234)
246 cd08315 Death_TRAILR_DR4_DR5 D 25.6 1.1E+02 0.0024 20.4 3.3 34 20-53 4-38 (96)
247 cd04780 HTH_MerR-like_sg5 Heli 25.6 71 0.0015 21.1 2.4 20 37-56 3-22 (95)
248 KOG0486|consensus 25.6 6.8 0.00015 32.1 -3.0 36 105-145 111-146 (351)
249 PF13565 HTH_32: Homeodomain-l 25.5 1.7E+02 0.0036 17.9 6.1 39 15-53 32-75 (77)
250 TIGR03826 YvyF flagellar opero 25.1 1E+02 0.0022 22.2 3.2 45 15-59 21-71 (137)
251 PF06163 DUF977: Bacterial pro 24.8 1.4E+02 0.0031 21.2 3.9 45 13-57 4-49 (127)
252 TIGR03830 CxxCG_CxxCG_HTH puta 24.5 1.3E+02 0.0028 20.3 3.7 40 12-58 63-102 (127)
253 PF12802 MarR_2: MarR family; 24.4 95 0.0021 18.0 2.6 38 14-53 3-40 (62)
254 cd04779 HTH_MerR-like_sg4 Heli 24.2 84 0.0018 22.3 2.7 20 37-56 3-22 (134)
255 PF01325 Fe_dep_repress: Iron 23.7 53 0.0012 19.8 1.4 42 15-56 3-44 (60)
256 PRK13870 transcriptional regul 23.5 3.4E+02 0.0075 20.9 6.3 45 11-61 171-215 (234)
257 PRK06596 RNA polymerase factor 23.4 2.5E+02 0.0054 22.3 5.6 49 13-64 230-278 (284)
258 PRK08241 RNA polymerase factor 23.2 2.1E+02 0.0045 23.1 5.2 31 34-64 169-199 (339)
259 PRK06424 transcription factor; 23.2 49 0.0011 23.9 1.3 23 37-59 100-122 (144)
260 PF04297 UPF0122: Putative hel 23.0 2.5E+02 0.0055 19.1 5.0 44 13-61 17-60 (101)
261 PRK10430 DNA-binding transcrip 23.0 1.7E+02 0.0037 22.1 4.4 44 13-57 158-201 (239)
262 PRK11552 putative DNA-binding 23.0 92 0.002 23.7 2.9 42 19-62 19-60 (225)
263 PRK09958 DNA-binding transcrip 23.0 2.5E+02 0.0054 19.9 5.2 43 13-61 143-185 (204)
264 cd04768 HTH_BmrR-like Helix-Tu 22.9 1E+02 0.0022 20.3 2.7 20 37-56 3-22 (96)
265 cd04765 HTH_MlrA-like_sg2 Heli 22.8 1.1E+02 0.0023 20.4 2.9 21 37-57 3-23 (99)
266 PRK14996 TetR family transcrip 22.6 1.1E+02 0.0024 22.2 3.2 40 20-60 15-54 (192)
267 PF08880 QLQ: QLQ; InterPro: 22.5 88 0.0019 17.2 2.0 13 13-25 2-14 (37)
268 cd04775 HTH_Cfa-like Helix-Tur 22.0 92 0.002 20.7 2.4 21 36-56 3-23 (102)
269 PF09862 DUF2089: Protein of u 21.9 2.1E+02 0.0046 19.9 4.2 38 13-55 33-70 (113)
270 PRK09706 transcriptional repre 21.8 53 0.0012 23.0 1.3 23 37-59 21-43 (135)
271 KOG0850|consensus 21.5 18 0.00039 28.5 -1.3 39 106-149 122-160 (245)
272 cd04782 HTH_BltR Helix-Turn-He 21.4 1.1E+02 0.0024 20.1 2.7 20 37-56 3-22 (97)
273 KOG0494|consensus 21.4 14 0.0003 29.7 -2.0 36 107-147 142-177 (332)
274 TIGR02850 spore_sigG RNA polym 20.7 3.4E+02 0.0074 21.0 5.8 39 13-56 206-244 (254)
275 cd04767 HTH_HspR-like_MBC Heli 20.7 1.1E+02 0.0025 21.3 2.7 21 37-57 4-24 (120)
276 PRK13890 conjugal transfer pro 20.6 54 0.0012 22.7 1.1 24 36-59 20-43 (120)
277 cd04773 HTH_TioE_rpt2 Second H 20.6 1.2E+02 0.0025 20.5 2.8 20 37-56 3-22 (108)
278 TIGR02054 MerD mercuric resist 20.5 1E+02 0.0022 21.5 2.5 21 36-56 5-25 (120)
279 TIGR00498 lexA SOS regulatory 20.1 2.4E+02 0.0052 20.9 4.6 40 14-55 4-47 (199)
No 1
>KOG0484|consensus
Probab=99.90 E-value=1.3e-23 Score=141.75 Aligned_cols=66 Identities=32% Similarity=0.526 Sum_probs=62.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhh
Q psy8301 4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMN 69 (157)
Q Consensus 4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~ 69 (157)
++|+||-||+||+.||..||+.|...+||++.+|++||.++.|+|.+|||||||||+|.|+++...
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a 79 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAA 79 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHH
Confidence 578899999999999999999999999999999999999999999999999999999999987653
No 2
>KOG2251|consensus
Probab=99.88 E-value=2.3e-22 Score=152.28 Aligned_cols=66 Identities=32% Similarity=0.468 Sum_probs=63.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhh
Q psy8301 4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMN 69 (157)
Q Consensus 4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~ 69 (157)
+||.||.||+|+..|+++||..|.+.+|||+..|++||.+|+|.+.+|+|||+|||+|+|+++...
T Consensus 34 pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 34 PRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred chhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 688999999999999999999999999999999999999999999999999999999999988764
No 3
>KOG0494|consensus
Probab=99.85 E-value=1.5e-21 Score=150.96 Aligned_cols=83 Identities=25% Similarity=0.374 Sum_probs=71.6
Q ss_pred CCCCCCCC-CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhhcCCCCCCccccc
Q psy8301 3 QSHRAGKM-RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQNSNGKNVFKIK 81 (157)
Q Consensus 3 ~~~~~rr~-Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~~~~~~~~~~~~~ 81 (157)
+++++||. ||.||..|++.||+.|+..+||++..|+-||.++.|.|.+|+|||||||+||||.++.........++...
T Consensus 136 kkk~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~sT~maeygly 215 (332)
T KOG0494|consen 136 KKKKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGSTIMAEYGLY 215 (332)
T ss_pred ccccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcchhhhhhccc
Confidence 34545555 99999999999999999999999999999999999999999999999999999999887777666666554
Q ss_pred cccc
Q psy8301 82 HIFT 85 (157)
Q Consensus 82 ~~~~ 85 (157)
....
T Consensus 216 Gamv 219 (332)
T KOG0494|consen 216 GAMV 219 (332)
T ss_pred chhh
Confidence 4433
No 4
>KOG0488|consensus
Probab=99.83 E-value=3.9e-20 Score=149.22 Aligned_cols=65 Identities=43% Similarity=0.627 Sum_probs=62.6
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhh
Q psy8301 4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68 (157)
Q Consensus 4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~ 68 (157)
++|+|+.||.||..|+..||+.|++..|.+..+|.+||..|||+..||++||||||+||||+...
T Consensus 169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 57888999999999999999999999999999999999999999999999999999999998766
No 5
>KOG0843|consensus
Probab=99.81 E-value=6.1e-20 Score=135.21 Aligned_cols=68 Identities=41% Similarity=0.665 Sum_probs=63.3
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhh
Q psy8301 2 FQSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMN 69 (157)
Q Consensus 2 ~~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~ 69 (157)
++..+.||.||.|+.+|+..||..|+.++|-...+|+.||..|+|++.||+|||||||.|.||.....
T Consensus 97 ~~~~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 97 LRSMRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred ccccCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 45567899999999999999999999999999999999999999999999999999999999877654
No 6
>KOG0850|consensus
Probab=99.80 E-value=4.3e-19 Score=135.22 Aligned_cols=66 Identities=42% Similarity=0.603 Sum_probs=62.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhh
Q psy8301 3 QSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68 (157)
Q Consensus 3 ~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~ 68 (157)
+.+|-|+.||+++.-||..|.+.|++++|.-..+|.+||..|||+..||+|||||||.|.||..+.
T Consensus 118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~ 183 (245)
T KOG0850|consen 118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQ 183 (245)
T ss_pred CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhc
Confidence 467888999999999999999999999999999999999999999999999999999999998874
No 7
>KOG0489|consensus
Probab=99.79 E-value=7.8e-20 Score=144.78 Aligned_cols=65 Identities=35% Similarity=0.604 Sum_probs=61.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhhc
Q psy8301 6 RAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQ 70 (157)
Q Consensus 6 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~~ 70 (157)
+.||.||.||..|+..||+.|..|+|.+...|.+||..|.|+|+||+|||||||+||||..+...
T Consensus 158 ~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~ 222 (261)
T KOG0489|consen 158 KSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKS 222 (261)
T ss_pred CCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccc
Confidence 46899999999999999999999999999999999999999999999999999999999776543
No 8
>KOG0842|consensus
Probab=99.79 E-value=1e-19 Score=145.25 Aligned_cols=70 Identities=51% Similarity=0.749 Sum_probs=64.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhhcCCC
Q psy8301 4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQNSN 73 (157)
Q Consensus 4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~~~~~ 73 (157)
++++||+|..|+..|+-.||+.|.+++|.+..+|++||..|.|+++||+|||||||.|.||+++......
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~ 219 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEA 219 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhc
Confidence 4577888999999999999999999999999999999999999999999999999999999887655543
No 9
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.77 E-value=1.5e-18 Score=107.07 Aligned_cols=57 Identities=47% Similarity=0.609 Sum_probs=55.1
Q ss_pred CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 8 GKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 8 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
||.|+.|+.+|+..|+..|..++||+..+++.||..+||+..+|++||+|+|+++|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 578999999999999999999999999999999999999999999999999999886
No 10
>KOG0485|consensus
Probab=99.76 E-value=2.6e-18 Score=129.96 Aligned_cols=67 Identities=49% Similarity=0.652 Sum_probs=61.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhhcC
Q psy8301 5 HRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQN 71 (157)
Q Consensus 5 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~~~ 71 (157)
-++||.||+|+..|+..||..|+..+|.+..+|..||.+|.|+|.||+|||||||.||||+-.....
T Consensus 102 ~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~e 168 (268)
T KOG0485|consen 102 DRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLE 168 (268)
T ss_pred cccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhh
Confidence 3578899999999999999999999999999999999999999999999999999999997655433
No 11
>KOG0492|consensus
Probab=99.74 E-value=2.5e-18 Score=129.30 Aligned_cols=68 Identities=47% Similarity=0.674 Sum_probs=61.0
Q ss_pred CCCC-CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhh
Q psy8301 2 FQSH-RAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMN 69 (157)
Q Consensus 2 ~~~~-~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~ 69 (157)
|+++ -.|++||.||..||..||+.|...+|.++++|.+++..|.|++.||+|||||||+|.||.+..+
T Consensus 138 LrKhk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae 206 (246)
T KOG0492|consen 138 LRKHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAE 206 (246)
T ss_pred hcccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHH
Confidence 4444 4566799999999999999999999999999999999999999999999999999999866543
No 12
>KOG0491|consensus
Probab=99.69 E-value=3.5e-17 Score=119.06 Aligned_cols=69 Identities=48% Similarity=0.650 Sum_probs=62.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhhcCCCC
Q psy8301 6 RAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQNSNG 74 (157)
Q Consensus 6 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~~~~~~ 74 (157)
++++-||+|+..|+..|++.|+..+|.+..+|.+||..|+|+++||+.||||||+|.||+....+....
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~p~nS 167 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQPKNS 167 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccCCCCC
Confidence 456779999999999999999999999999999999999999999999999999999998876654433
No 13
>KOG0487|consensus
Probab=99.68 E-value=2.4e-17 Score=131.75 Aligned_cols=66 Identities=39% Similarity=0.626 Sum_probs=61.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhh
Q psy8301 4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMN 69 (157)
Q Consensus 4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~ 69 (157)
.++.|++|-.+|..|+..||+.|-.|.|.+...|.+|++.|+|+++||+|||||||+|.||..+..
T Consensus 232 ~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~ 297 (308)
T KOG0487|consen 232 ARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN 297 (308)
T ss_pred ccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence 356788899999999999999999999999999999999999999999999999999999977543
No 14
>KOG0490|consensus
Probab=99.68 E-value=7.1e-17 Score=124.87 Aligned_cols=135 Identities=21% Similarity=0.274 Sum_probs=97.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhhcCCCCCCccccccc
Q psy8301 4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQNSNGKNVFKIKHI 83 (157)
Q Consensus 4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~~~~~~~~~~~~~~~ 83 (157)
..++||.|+.|+..|++.|+++|+..+||+...++.||..+++++..|+|||||||+||++++................
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~~~~~~~~~~~~~~~~- 135 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEERPLPEGENLPDLSGTA- 135 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhccccccccCCCCCCCC-
Confidence 4567899999999999999999999999999999999999999999999999999999999764111111110000000
Q ss_pred ccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCccccCCCCCCCCcCCCCCCCCchhHHHhhhccC
Q psy8301 84 FTRKTKPTSAQATIGCPEAKKIGRKPETDFPAEEHNIFVPNFDQSDFLDNKWEDIDILDELHDQYV 149 (157)
Q Consensus 84 ~~~~~~p~s~~~~~~~p~~~~~~~~~~~~~~~~q~~~~~~~f~~~~~s~s~~p~~~~~~~l~~~~~ 149 (157)
.................+..+.+.+...+...+...|..+.+ |+....+.|+....
T Consensus 136 -----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----P~~~~~~~l~~~~~ 191 (235)
T KOG0490|consen 136 -----PPSASRDKLDKGPSNKKPRRPRTTFTENQLEVLETVFRATPK-----PDADDREQLAEETG 191 (235)
T ss_pred -----CccccccccccCCCccccCCCccccccchhHhhhhcccCCCC-----CchhhHHHHHHhcC
Confidence 000001111122223445556677888888999999999999 99999999887554
No 15
>KOG0486|consensus
Probab=99.67 E-value=1.8e-17 Score=131.29 Aligned_cols=66 Identities=33% Similarity=0.499 Sum_probs=61.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhhc
Q psy8301 5 HRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQ 70 (157)
Q Consensus 5 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~~ 70 (157)
+|+||.||.|+..|+..||.+|+++.||+...|+++|--++|+|.+|+|||+|||+|||+.+....
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 378899999999999999999999999999999999999999999999999999999999775543
No 16
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.66 E-value=2.5e-16 Score=96.41 Aligned_cols=55 Identities=47% Similarity=0.626 Sum_probs=52.1
Q ss_pred CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHH
Q psy8301 8 GKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQ 62 (157)
Q Consensus 8 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~ 62 (157)
++.|+.|+..|+.+|+..|..++||+..++..||..+||+..+|++||+|+|++.
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~ 55 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKW 55 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhcc
Confidence 3567889999999999999999999999999999999999999999999999875
No 17
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.66 E-value=8.3e-17 Score=99.27 Aligned_cols=52 Identities=17% Similarity=0.277 Sum_probs=50.2
Q ss_pred CCCCCCCCHHHHHHHHHHhhhcCC----CCHHHHHHHHHHhCCChhHHHHHHHHHH
Q psy8301 8 GKMRTNGIQSQVFELERKFQHIRY----LSPTEREMLGKEINLSPTQVKIWFQNRR 59 (157)
Q Consensus 8 rr~Rt~~t~~q~~~Le~~F~~~~~----p~~~~r~~La~~l~l~~~~VqvWFqNrR 59 (157)
||.||.||.+|+..|+..|+.++| |+..++++||..+||++.+|+|||||.+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 789999999999999999999999 9999999999999999999999999953
No 18
>KOG0848|consensus
Probab=99.66 E-value=7.2e-17 Score=125.47 Aligned_cols=63 Identities=37% Similarity=0.569 Sum_probs=58.2
Q ss_pred CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhh
Q psy8301 7 AGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMN 69 (157)
Q Consensus 7 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~ 69 (157)
+-+-|.++|..|.-.||+.|..++|..+..+.+||..|||+|+||+|||||||||+||..+..
T Consensus 199 kDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 199 KDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 345588999999999999999999999999999999999999999999999999999876654
No 19
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.65 E-value=5.8e-16 Score=95.57 Aligned_cols=56 Identities=52% Similarity=0.702 Sum_probs=53.7
Q ss_pred CCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 9 r~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
+.|+.|+..++.+|+++|..++||+..++..||..+||++.+|++||+|+|++.++
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 56789999999999999999999999999999999999999999999999999876
No 20
>KOG0493|consensus
Probab=99.64 E-value=2.1e-16 Score=122.66 Aligned_cols=59 Identities=39% Similarity=0.609 Sum_probs=56.3
Q ss_pred CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301 7 AGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65 (157)
Q Consensus 7 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~ 65 (157)
-||+||.||.+||..|+..|+.|+|.....|.+||.+|||.|.||+|||||+|+|-||.
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence 35889999999999999999999999999999999999999999999999999998883
No 21
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.60 E-value=1.5e-15 Score=111.46 Aligned_cols=63 Identities=33% Similarity=0.529 Sum_probs=58.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301 5 HRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA 67 (157)
Q Consensus 5 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~ 67 (157)
+..++.|++.+..|+.+|++.|+.++||+..+|..|+..++|+++.|||||||+|++.|+...
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~ 111 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRS 111 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcc
Confidence 456788999999999999999999999999999999999999999999999999999988554
No 22
>KOG0844|consensus
Probab=99.56 E-value=8.2e-16 Score=121.64 Aligned_cols=61 Identities=38% Similarity=0.589 Sum_probs=58.3
Q ss_pred CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhh
Q psy8301 8 GKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68 (157)
Q Consensus 8 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~ 68 (157)
||-||.||.+|+..||+.|-+..|-+...|.+||..|+|.|..|+|||||||+|+||++..
T Consensus 182 RRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 182 RRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 6789999999999999999999999999999999999999999999999999999998754
No 23
>KOG4577|consensus
Probab=99.55 E-value=4.3e-15 Score=116.82 Aligned_cols=62 Identities=32% Similarity=0.420 Sum_probs=58.7
Q ss_pred CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhh
Q psy8301 7 AGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68 (157)
Q Consensus 7 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~ 68 (157)
.||+||++|..||+.|+.+|...+.|-...||+|+..+||.-++|||||||||||.||.++.
T Consensus 167 nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T KOG4577|consen 167 NKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T ss_pred cCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhh
Confidence 57999999999999999999999999999999999999999999999999999999986543
No 24
>KOG0483|consensus
Probab=99.53 E-value=6.8e-15 Score=111.61 Aligned_cols=61 Identities=36% Similarity=0.520 Sum_probs=55.8
Q ss_pred CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhh
Q psy8301 8 GKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68 (157)
Q Consensus 8 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~ 68 (157)
.+.+.+|+.+|...||..|+...|.....+..||..|||..+||.||||||||+||..+..
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE 111 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLE 111 (198)
T ss_pred ccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhh
Confidence 3455689999999999999999999999999999999999999999999999999975543
No 25
>KOG3802|consensus
Probab=99.48 E-value=5.6e-15 Score=120.72 Aligned_cols=62 Identities=29% Similarity=0.390 Sum_probs=58.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 5 HRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 5 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
.|+||+||.|......+||+.|.+|+.|+..++..||..|+|...+|+|||+|||.|.||..
T Consensus 292 ~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 292 SRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred ccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 36788899999999999999999999999999999999999999999999999999999844
No 26
>KOG0849|consensus
Probab=99.48 E-value=2.2e-13 Score=112.14 Aligned_cols=65 Identities=37% Similarity=0.469 Sum_probs=61.3
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhh
Q psy8301 4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68 (157)
Q Consensus 4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~ 68 (157)
+++.+|.||.|+..|+..|++.|+.++||++..|+.||.++++++..|+|||+|||++|+|....
T Consensus 173 ~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 173 QRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred cccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence 46678889999999999999999999999999999999999999999999999999999997743
No 27
>KOG0847|consensus
Probab=99.47 E-value=3.6e-14 Score=107.83 Aligned_cols=64 Identities=38% Similarity=0.694 Sum_probs=59.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhhh
Q psy8301 6 RAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMN 69 (157)
Q Consensus 6 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~ 69 (157)
+++..|.+|+..|+..|+..|++.+|+...+|.+||-.+|+++.+|+|||||||.||||....+
T Consensus 166 ~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaE 229 (288)
T KOG0847|consen 166 QRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAE 229 (288)
T ss_pred cccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccc
Confidence 4456688999999999999999999999999999999999999999999999999999976544
No 28
>KOG0775|consensus
Probab=99.26 E-value=3.2e-11 Score=94.43 Aligned_cols=51 Identities=29% Similarity=0.416 Sum_probs=47.2
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 14 GIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 14 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
|...-...|+.+|..++||+..++.+||+++||+..||-+||+|||+++|-
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 555567799999999999999999999999999999999999999999994
No 29
>KOG1168|consensus
Probab=99.00 E-value=7.6e-11 Score=93.13 Aligned_cols=61 Identities=26% Similarity=0.379 Sum_probs=57.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 6 RAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 6 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
.+||+||.+-......||++|..++.|+...+..+|++|+|...+|+|||+|+|+|.||..
T Consensus 308 ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred ccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 4678899999999999999999999999999999999999999999999999999988854
No 30
>KOG0774|consensus
Probab=98.88 E-value=3e-09 Score=83.08 Aligned_cols=61 Identities=30% Similarity=0.376 Sum_probs=55.5
Q ss_pred CCCCCCCCCHHHHHHHHHHhh---hcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301 7 AGKMRTNGIQSQVFELERKFQ---HIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA 67 (157)
Q Consensus 7 ~rr~Rt~~t~~q~~~Le~~F~---~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~ 67 (157)
.||+|..|+..-.++|..+|. .++||+...+++||.+.+++..||-.||.|.|-+.+|.-.
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~ 251 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMG 251 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhh
Confidence 467788999999999999994 6889999999999999999999999999999999887443
No 31
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.72 E-value=2.1e-08 Score=57.35 Aligned_cols=34 Identities=41% Similarity=0.618 Sum_probs=28.8
Q ss_pred hcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHH
Q psy8301 28 HIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYK 61 (157)
Q Consensus 28 ~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k 61 (157)
.++||+..+++.||..+||+..||..||-|.|.+
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 4789999999999999999999999999998864
No 32
>KOG2252|consensus
Probab=98.62 E-value=7.3e-08 Score=82.08 Aligned_cols=56 Identities=23% Similarity=0.224 Sum_probs=52.8
Q ss_pred CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHH
Q psy8301 7 AGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQ 62 (157)
Q Consensus 7 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~ 62 (157)
.||+|.+||..|+..|.+.|+.+++|+....+.|+.+|+|....|.+||-|-|.+.
T Consensus 420 ~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 420 TKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred CCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 56779999999999999999999999999999999999999999999999987764
No 33
>KOG0490|consensus
Probab=98.52 E-value=1.2e-07 Score=73.12 Aligned_cols=64 Identities=30% Similarity=0.454 Sum_probs=59.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301 4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA 67 (157)
Q Consensus 4 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~ 67 (157)
..+.++.|+.+...|+..|...|..+++|+...++.|+..+|+++..|++||+|+|++.++...
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 3567788999999999999999999999999999999999999999999999999999998554
No 34
>KOG1146|consensus
Probab=97.90 E-value=2.1e-05 Score=73.08 Aligned_cols=62 Identities=26% Similarity=0.358 Sum_probs=57.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301 6 RAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA 67 (157)
Q Consensus 6 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~ 67 (157)
.+|+.||.++..||.++...|+...||...+.|.|...+++..++|++||||-|+|.++...
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 35678999999999999999999999999999999999999999999999999999888655
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.07 E-value=0.00074 Score=41.15 Aligned_cols=41 Identities=24% Similarity=0.383 Sum_probs=30.8
Q ss_pred HHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHH
Q psy8301 19 VFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRR 59 (157)
Q Consensus 19 ~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR 59 (157)
...|+++|...+++.......|..+.+|+..+|+.||-.+.
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 45699999999999999999999999999999999997553
No 36
>KOG3623|consensus
Probab=96.74 E-value=0.0048 Score=54.99 Aligned_cols=49 Identities=16% Similarity=0.267 Sum_probs=45.4
Q ss_pred HHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301 19 VFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA 67 (157)
Q Consensus 19 ~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~ 67 (157)
+..|+.+|..|..|+..+...+|...||+.+.|+.||.++++.......
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~r 616 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVER 616 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhcc
Confidence 7789999999999999999999999999999999999999999877553
No 37
>KOG0773|consensus
Probab=96.64 E-value=0.0012 Score=54.16 Aligned_cols=57 Identities=28% Similarity=0.268 Sum_probs=48.4
Q ss_pred CCCCCCCCCHHHHHHHHHHh-h--hcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHH
Q psy8301 7 AGKMRTNGIQSQVFELERKF-Q--HIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63 (157)
Q Consensus 7 ~rr~Rt~~t~~q~~~Le~~F-~--~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~r 63 (157)
..|++..+......+|+.+. + ..+||+..+...||..+||+..+|-+||-|.|.+.-
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w 298 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLW 298 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccC
Confidence 45566789999999999883 3 357999999999999999999999999999987733
No 38
>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=95.22 E-value=0.059 Score=32.36 Aligned_cols=47 Identities=13% Similarity=0.266 Sum_probs=34.4
Q ss_pred CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHH
Q psy8301 8 GKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRR 59 (157)
Q Consensus 8 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR 59 (157)
||.|..+|-++...+-..++... ....||..+|++..+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 46788999999776666677665 578899999999999999998853
No 39
>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=89.23 E-value=2.1 Score=24.71 Aligned_cols=46 Identities=9% Similarity=0.047 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~r 63 (157)
.+++.+..+|...|... ..-.++|..+|++...|+.+...-..|-|
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence 46788889998888333 46788999999999999988865444433
No 40
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=87.25 E-value=1.8 Score=27.11 Aligned_cols=45 Identities=13% Similarity=0.236 Sum_probs=29.1
Q ss_pred CCCCCCCHHHHHHHHHHh-hhcCCCCHHHHHHHHHHhCCChhHHHHHHHHH
Q psy8301 9 KMRTNGIQSQVFELERKF-QHIRYLSPTEREMLGKEINLSPTQVKIWFQNR 58 (157)
Q Consensus 9 r~Rt~~t~~q~~~Le~~F-~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNr 58 (157)
+.|..|+.++...+-..+ ... .....+|..+|++...+..|-+--
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g-----~sv~~va~~~gi~~~~l~~W~~~~ 47 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG-----ESVSEVAREYGISPSTLYNWRKQY 47 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH-----CHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC-----CceEeeecccccccccccHHHHHH
Confidence 457889999966555444 433 578889999999999999998643
No 41
>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=87.08 E-value=1.2 Score=26.79 Aligned_cols=40 Identities=18% Similarity=0.104 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHHhhhcCC--CCHHHHHHHHHHhCCChhHHHH
Q psy8301 14 GIQSQVFELERKFQHIRY--LSPTEREMLGKEINLSPTQVKI 53 (157)
Q Consensus 14 ~t~~q~~~Le~~F~~~~~--p~~~~r~~La~~l~l~~~~Vqv 53 (157)
+|+.|.++|..+|+..=| |-.....+||..+|++...+.-
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~ 42 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSE 42 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHH
Confidence 578999999999886543 6667788999999999876543
No 42
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=85.15 E-value=3.2 Score=23.23 Aligned_cols=44 Identities=11% Similarity=0.043 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYK 61 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k 61 (157)
.+++.+..++...|... ....++|..+|++...|..|...-+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 35677777777766422 356778999999999999998755443
No 43
>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=83.77 E-value=5 Score=23.33 Aligned_cols=42 Identities=12% Similarity=0.039 Sum_probs=27.3
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHH
Q psy8301 14 GIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRY 60 (157)
Q Consensus 14 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~ 60 (157)
+++.+..++.-.|- ....-.++|..+|++...|+.|...-|.
T Consensus 11 L~~~~r~i~~l~~~-----~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 11 LPERQREIFLLRYF-----QGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp S-HHHHHHHHHHHT-----S---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH-----HCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 45566666655443 3357889999999999999999975443
No 44
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=82.99 E-value=6.7 Score=28.38 Aligned_cols=50 Identities=10% Similarity=0.038 Sum_probs=39.9
Q ss_pred CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301 12 TNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA 67 (157)
Q Consensus 12 t~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~ 67 (157)
..+++.|..+|... ... ....++|..+|++...|..|-++-+.+.++...
T Consensus 5 ~~Lt~rqreVL~lr-~~G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~ 54 (141)
T PRK03975 5 SFLTERQIEVLRLR-ERG-----LTQQEIADILGTSRANVSSIEKRARENIEKARE 54 (141)
T ss_pred cCCCHHHHHHHHHH-HcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 57899999999773 222 357789999999999999999988887776544
No 45
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=80.60 E-value=1.7 Score=26.89 Aligned_cols=22 Identities=9% Similarity=0.385 Sum_probs=18.8
Q ss_pred HHHHHHHHHhCCChhHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFq 56 (157)
..-.+||.+||+++.+|+.|=.
T Consensus 23 i~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 23 IKLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred ccHHHHHHHHCCCHHHHHHHhh
Confidence 4567789999999999999964
No 46
>KOG1146|consensus
Probab=74.48 E-value=4 Score=39.34 Aligned_cols=60 Identities=15% Similarity=0.202 Sum_probs=55.2
Q ss_pred CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 7 AGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 7 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
.++.|+.+-.+++.+|-++|-.+.-|+...+..|......+.+.+.+||+|-|.+.++..
T Consensus 705 ~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 705 DKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred cccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 456788888899999999999999999999999999999999999999999999988855
No 47
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=73.55 E-value=9.5 Score=29.12 Aligned_cols=52 Identities=19% Similarity=0.179 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHHHhhhcC--CCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIR--YLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~--~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
-+|+.|+++|..+|+..= ||=.....+||+.+|++... +|..=|||..|-..
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst--~~ehLRrAe~Kl~~ 208 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST--LSEHLRRAERKLIE 208 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH--HHHHHHHHHHHHHH
Confidence 599999999999998643 36667778899999999864 56666777766433
No 48
>PRK00118 putative DNA-binding protein; Validated
Probab=73.12 E-value=23 Score=24.25 Aligned_cols=48 Identities=13% Similarity=-0.053 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~ 65 (157)
.+++.|..++...|... ....++|..+|++...|..|...-|.+.+..
T Consensus 17 ~L~ekqRevl~L~y~eg-----~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~ 64 (104)
T PRK00118 17 LLTEKQRNYMELYYLDD-----YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDY 64 (104)
T ss_pred cCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 35667777776655543 3577899999999999999998777666653
No 49
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=72.78 E-value=14 Score=25.96 Aligned_cols=45 Identities=11% Similarity=0.088 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHH
Q psy8301 14 GIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63 (157)
Q Consensus 14 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~r 63 (157)
+++.+..++...|- ......++|..+|+++..|+.|...=+.+-|
T Consensus 107 L~~~~r~ii~l~~~-----~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 107 LDEKEKYIIFERFF-----VGKTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 34445555544432 2345788999999999999999875555544
No 50
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=72.78 E-value=15 Score=27.25 Aligned_cols=31 Identities=6% Similarity=0.090 Sum_probs=25.6
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~ 65 (157)
..-.++|..+|++...|+++...-|.+.|+.
T Consensus 159 ~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 159 LTYREVAERLAVPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred CCHHHHHHHhCCChHhHHHHHHHHHHHHHHH
Confidence 4677899999999999999998766666653
No 51
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=71.37 E-value=17 Score=26.01 Aligned_cols=30 Identities=10% Similarity=0.019 Sum_probs=24.0
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
....++|..+|+++..|+.|...=+.+.|+
T Consensus 145 ~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 145 LSYEEIAEIMGCPIGTVRSRIFRAREALRA 174 (182)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 356788999999999999999855555554
No 52
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=71.04 E-value=17 Score=27.31 Aligned_cols=35 Identities=20% Similarity=0.161 Sum_probs=26.9
Q ss_pred CCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 32 LSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 32 p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
......+++|..+|+++..|+++...-+.+.++..
T Consensus 167 ~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 167 FQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 33356788999999999999999976666666543
No 53
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=70.81 E-value=24 Score=25.23 Aligned_cols=32 Identities=19% Similarity=0.107 Sum_probs=25.8
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
...+++|..+|+++..|++|.+.=|.+.|+.-
T Consensus 125 ~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 125 LTYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 45788999999999999999986666666543
No 54
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=69.91 E-value=20 Score=21.14 Aligned_cols=43 Identities=16% Similarity=0.071 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYK 61 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k 61 (157)
.||+.++.+|.-...- ....++|..+|+++..|..+..+=+.|
T Consensus 3 ~LT~~E~~vl~~l~~G------~~~~eIA~~l~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG------MSNKEIAEELGISEKTVKSHRRRIMKK 45 (58)
T ss_dssp SS-HHHHHHHHHHHTT------S-HHHHHHHHTSHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhc------CCcchhHHhcCcchhhHHHHHHHHHHH
Confidence 5788888888776554 357889999999999999988776555
No 55
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=69.77 E-value=2.7 Score=27.00 Aligned_cols=35 Identities=11% Similarity=0.099 Sum_probs=26.8
Q ss_pred HHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHH
Q psy8301 23 ERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQN 57 (157)
Q Consensus 23 e~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqN 57 (157)
+..|....|-......++|..+|+++..|+.|+.+
T Consensus 21 r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 21 EAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 34455555545567889999999999999999974
No 56
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=69.70 E-value=5.4 Score=22.47 Aligned_cols=20 Identities=20% Similarity=0.303 Sum_probs=17.8
Q ss_pred HHHHHHHhCCChhHHHHHHH
Q psy8301 37 REMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 37 r~~La~~l~l~~~~VqvWFq 56 (157)
..++|+.+|++...|+.|.+
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~ 22 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYER 22 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999975
No 57
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=69.69 E-value=24 Score=24.97 Aligned_cols=32 Identities=9% Similarity=0.030 Sum_probs=25.3
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
..-+++|..+|+++..|++....-|.+-|+.-
T Consensus 123 ~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 123 KSYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35678899999999999999986666666543
No 58
>PRK04217 hypothetical protein; Provisional
Probab=69.12 E-value=26 Score=24.19 Aligned_cols=50 Identities=16% Similarity=-0.022 Sum_probs=37.9
Q ss_pred CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 12 TNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 12 t~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
..++.++..++...|...- ...++|+.+|++...|...+..-+.+.+..-
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3578888888877664432 6788999999999999999887666665533
No 59
>KOG2251|consensus
Probab=68.93 E-value=0.86 Score=35.38 Aligned_cols=43 Identities=16% Similarity=0.344 Sum_probs=38.9
Q ss_pred CCCCCCCCCCCCCCcCccccCCCCCCCCcCCCCCCCCchhHHHhhhcc
Q psy8301 101 EAKKIGRKPETDFPAEEHNIFVPNFDQSDFLDNKWEDIDILDELHDQY 148 (157)
Q Consensus 101 ~~~~~~~~~~~~~~~~q~~~~~~~f~~~~~s~s~~p~~~~~~~l~~~~ 148 (157)
..+.-.+...|.|...|.+++.--|.+..| ||+.++|+|+...
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqY-----PDv~~rEelAlkl 74 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQY-----PDVFMREELALKL 74 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcC-----ccHHHHHHHHHHh
Confidence 456778888999999999999999999999 9999999999764
No 60
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=68.79 E-value=26 Score=24.98 Aligned_cols=31 Identities=10% Similarity=0.079 Sum_probs=25.3
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~ 65 (157)
..-.++|..+|++...|..|...=|.+.|+.
T Consensus 142 ~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 142 LSYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999999998766666653
No 61
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=68.61 E-value=11 Score=21.35 Aligned_cols=40 Identities=10% Similarity=0.047 Sum_probs=21.5
Q ss_pred CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHH
Q psy8301 12 TNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 12 t~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFq 56 (157)
..+|.++...++..++.. ....++|..+|.+...|..|.+
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHHh
Confidence 457888888888876644 4566799999999999988875
No 62
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=67.79 E-value=13 Score=18.27 Aligned_cols=37 Identities=11% Similarity=0.081 Sum_probs=26.5
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIW 54 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvW 54 (157)
.++..+...+...|... + ....+|..+|++...|..|
T Consensus 5 ~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 5 KLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred cCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHh
Confidence 35666666666666532 2 5667899999999988877
No 63
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=66.80 E-value=17 Score=26.75 Aligned_cols=34 Identities=15% Similarity=0.203 Sum_probs=26.9
Q ss_pred CCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 31 YLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 31 ~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
|.......++|..+|++...|+.|...-|.+.|+
T Consensus 154 ~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 154 YYEGLSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred hhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 3444567889999999999999999866666655
No 64
>PF13551 HTH_29: Winged helix-turn helix
Probab=66.46 E-value=28 Score=22.87 Aligned_cols=49 Identities=18% Similarity=0.157 Sum_probs=31.7
Q ss_pred CCCCCCCCHHHHHHHHHHhhhcCCCC--HHHHHHHHHH-------hCCChhHHHHHHH
Q psy8301 8 GKMRTNGIQSQVFELERKFQHIRYLS--PTEREMLGKE-------INLSPTQVKIWFQ 56 (157)
Q Consensus 8 rr~Rt~~t~~q~~~Le~~F~~~~~p~--~~~r~~La~~-------l~l~~~~VqvWFq 56 (157)
.+.+..+++++...|.+.+..++.-+ .-....|+.. +.++...|..|++
T Consensus 52 g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 52 GRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 34444499999999999998876221 1223333332 2578888888875
No 65
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=65.04 E-value=26 Score=23.81 Aligned_cols=46 Identities=13% Similarity=0.072 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 14 GIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 14 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
+++.+..++...|- ......++|..+|+++..|..|...-+.+-|+
T Consensus 111 L~~~~~~ii~~~~~-----~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 111 LPEREREVLVLRYL-----EGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCHHHHHHHhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 44555555544332 22356789999999999999999866555443
No 66
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=64.95 E-value=29 Score=25.17 Aligned_cols=30 Identities=13% Similarity=0.005 Sum_probs=24.3
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
..-+++|..+|+++..|++....-|.+.|+
T Consensus 151 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 151 LTVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 456788999999999999999866666554
No 67
>PF13518 HTH_28: Helix-turn-helix domain
Probab=64.73 E-value=13 Score=21.16 Aligned_cols=25 Identities=20% Similarity=0.392 Sum_probs=20.6
Q ss_pred HHHHHHHHhCCChhHHHHHHHHHHH
Q psy8301 36 EREMLGKEINLSPTQVKIWFQNRRY 60 (157)
Q Consensus 36 ~r~~La~~l~l~~~~VqvWFqNrR~ 60 (157)
...++|..+|++..+|..|.+.-+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 4567899999999999999975443
No 68
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=64.30 E-value=30 Score=24.08 Aligned_cols=30 Identities=10% Similarity=0.196 Sum_probs=23.2
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
....++|..+|+++..|+.+...=|.+.|+
T Consensus 130 ~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 130 KSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 456789999999999999988755555443
No 69
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=63.80 E-value=31 Score=25.00 Aligned_cols=30 Identities=10% Similarity=0.299 Sum_probs=24.6
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
...+++|..+|+++..|+++...-|.+.|+
T Consensus 146 ~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 146 LSYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred CCHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 457889999999999999999866666555
No 70
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=63.00 E-value=34 Score=24.88 Aligned_cols=33 Identities=6% Similarity=-0.009 Sum_probs=26.7
Q ss_pred HHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 34 PTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 34 ~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
...-+++|..+|++...|+.++..-|.+.|..-
T Consensus 147 g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 147 GASIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 345778999999999999999987777766543
No 71
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=62.95 E-value=37 Score=24.74 Aligned_cols=33 Identities=9% Similarity=0.033 Sum_probs=26.4
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA 67 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~ 67 (157)
..-+++|..+|++...|+.+...-|.+.|+...
T Consensus 145 ~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 145 LSNIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999999876766666443
No 72
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=62.71 E-value=34 Score=24.70 Aligned_cols=32 Identities=25% Similarity=0.268 Sum_probs=25.8
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
...+++|..+|+++..|+++-..-|.+.+...
T Consensus 117 ~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 117 LSQQEIAEKLGLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 45778999999999999999976666666644
No 73
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=62.63 E-value=8.7 Score=23.35 Aligned_cols=27 Identities=22% Similarity=0.401 Sum_probs=21.5
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQK 63 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~r 63 (157)
....++|..||++...|..|-+ |.+|.
T Consensus 14 ~~~~eIA~~Lg~~~~TV~~W~~--r~~W~ 40 (58)
T PF06056_consen 14 WSIKEIAEELGVPRSTVYSWKD--RYKWD 40 (58)
T ss_pred CCHHHHHHHHCCChHHHHHHHH--hhCcc
Confidence 3567899999999999999985 44444
No 74
>KOG3755|consensus
Probab=62.51 E-value=3.9 Score=36.40 Aligned_cols=46 Identities=24% Similarity=0.246 Sum_probs=30.7
Q ss_pred HHHHHhhhcCCCCHHHHHHHHHHhC-------CChhHHHHHHHHHHHHHHHHH
Q psy8301 21 ELERKFQHIRYLSPTEREMLGKEIN-------LSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 21 ~Le~~F~~~~~p~~~~r~~La~~l~-------l~~~~VqvWFqNrR~k~rr~~ 66 (157)
.-+.+|-+++.+......+-.+.+. ...+.|+.||+|||+++++.+
T Consensus 706 v~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 706 VKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred cchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhh
Confidence 3355566777666655544433333 345689999999999998854
No 75
>PRK10072 putative transcriptional regulator; Provisional
Probab=62.44 E-value=9.9 Score=25.62 Aligned_cols=40 Identities=15% Similarity=0.179 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRR 59 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR 59 (157)
..+...+..|...... ...+||..+|++...|..|.+.+|
T Consensus 32 ~~~~~eik~LR~~~gl-------TQ~elA~~lGvS~~TVs~WE~G~r 71 (96)
T PRK10072 32 TTSFTEFEQLRKGTGL-------KIDDFARVLGVSVAMVKEWESRRV 71 (96)
T ss_pred cCChHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHcCCC
Confidence 3366666666543222 477899999999999999998665
No 76
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=62.22 E-value=34 Score=25.06 Aligned_cols=30 Identities=10% Similarity=0.138 Sum_probs=24.0
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
...+++|..+|++...|+.+...-|.+-|+
T Consensus 156 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 156 LSAEETAEAVGSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 467889999999999999998755555554
No 77
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=61.92 E-value=32 Score=24.19 Aligned_cols=32 Identities=9% Similarity=0.060 Sum_probs=23.9
Q ss_pred CCHHHHHHHHHHhCCChhHHHHHHHHHHHHHH
Q psy8301 32 LSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63 (157)
Q Consensus 32 p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~r 63 (157)
......+++|..+|++...|.++...-|.+-+
T Consensus 125 ~~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 125 QRGVSLTALAEQLGRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 34456788999999999999988765554443
No 78
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=61.31 E-value=24 Score=24.41 Aligned_cols=42 Identities=10% Similarity=0.295 Sum_probs=29.0
Q ss_pred CCCCCHHHHH-HHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHH
Q psy8301 11 RTNGIQSQVF-ELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQN 57 (157)
Q Consensus 11 Rt~~t~~q~~-~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqN 57 (157)
|..|+.++.. ++...+... ....++|..+|++...|..|.+.
T Consensus 10 rr~ys~EfK~~aV~~~~~~g-----~sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPG-----MTVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHHH
Confidence 4567777744 444444422 24667899999999999999753
No 79
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=61.30 E-value=30 Score=25.04 Aligned_cols=33 Identities=12% Similarity=0.181 Sum_probs=26.1
Q ss_pred CCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 32 LSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 32 p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
.....-+++|..+|++...|+++.+.-|.+-|.
T Consensus 150 ~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 150 MEDLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 344567889999999999999999866666555
No 80
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=61.14 E-value=37 Score=24.06 Aligned_cols=32 Identities=6% Similarity=0.158 Sum_probs=25.5
Q ss_pred HHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301 34 PTEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65 (157)
Q Consensus 34 ~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~ 65 (157)
.....++|..+|+++..|+.+...-|.+.|+.
T Consensus 127 g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~ 158 (166)
T PRK09639 127 GYSYKEIAEALGIKESSVGTTLARAKKKFRKI 158 (166)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34567899999999999999997666666653
No 81
>PRK06930 positive control sigma-like factor; Validated
Probab=61.03 E-value=47 Score=24.58 Aligned_cols=49 Identities=8% Similarity=-0.096 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
.+++.+..++.-.|-.. ..-.++|..+|++...|+.+...-+.+.++.-
T Consensus 114 ~L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l 162 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIERAEKKIARQI 162 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 35556666655543222 35678899999999999999987777766643
No 82
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=60.36 E-value=46 Score=24.33 Aligned_cols=32 Identities=22% Similarity=0.236 Sum_probs=25.9
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
....++|..+|++...|++-...-|.+.+...
T Consensus 148 ~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 148 KSVEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 45678899999999999998877777766643
No 83
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=59.48 E-value=29 Score=25.17 Aligned_cols=35 Identities=11% Similarity=-0.025 Sum_probs=26.5
Q ss_pred CCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301 31 YLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65 (157)
Q Consensus 31 ~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~ 65 (157)
|.....-.++|..+|+++..|+++...=|.+-|+.
T Consensus 151 ~~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 151 ELEGLSYEDIARIMDCPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred hhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 34445578899999999999999997666655553
No 84
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=59.48 E-value=39 Score=24.88 Aligned_cols=31 Identities=13% Similarity=0.264 Sum_probs=24.9
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~ 65 (157)
...+++|..+|+++..|+++...-|.+.|..
T Consensus 151 ~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 151 LSSEQICQECDISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4577899999999999999997666665553
No 85
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=59.33 E-value=29 Score=21.26 Aligned_cols=44 Identities=18% Similarity=0.210 Sum_probs=22.4
Q ss_pred CCCCCHHH-HHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHH
Q psy8301 11 RTNGIQSQ-VFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 11 Rt~~t~~q-~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFq 56 (157)
|..|+... |.+++.+...+. --...|. .|.+.|+++..|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~n-c~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNN-CKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-TT-TTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHccc-hhhhHHH-HHHHhCccHHHHHHHHH
Confidence 34555555 455554443322 1112333 49999999999999985
No 86
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=58.85 E-value=43 Score=24.34 Aligned_cols=33 Identities=12% Similarity=0.116 Sum_probs=27.3
Q ss_pred HHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 34 PTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 34 ~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
.....++|..+|+++..|++....-|.+.|+.-
T Consensus 133 ~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 165 (179)
T PRK12543 133 DYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKE 165 (179)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 346778999999999999999988888877644
No 87
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=57.92 E-value=13 Score=20.32 Aligned_cols=21 Identities=14% Similarity=0.506 Sum_probs=18.5
Q ss_pred HHHHHHHhCCChhHHHHHHHH
Q psy8301 37 REMLGKEINLSPTQVKIWFQN 57 (157)
Q Consensus 37 r~~La~~l~l~~~~VqvWFqN 57 (157)
..++|..+|++...|..|.++
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHc
Confidence 467899999999999999874
No 88
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=57.78 E-value=7 Score=23.38 Aligned_cols=26 Identities=8% Similarity=0.193 Sum_probs=18.5
Q ss_pred HHHHHHHHhCCChhHHHHHHHHHHHH
Q psy8301 36 EREMLGKEINLSPTQVKIWFQNRRYK 61 (157)
Q Consensus 36 ~r~~La~~l~l~~~~VqvWFqNrR~k 61 (157)
....||+.+|++...|..|+.++...
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~ 37 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSN 37 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT---
T ss_pred CHHHHHHHHCcCHHHHHHHHhccccc
Confidence 57789999999999999999876433
No 89
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=57.50 E-value=43 Score=23.64 Aligned_cols=30 Identities=10% Similarity=0.135 Sum_probs=24.8
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
..-+++|..+|++...|+.+-..-|.+-|+
T Consensus 127 ~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 127 LSEAQVAEALGISVGTVKSRLSRALARLRE 156 (162)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 457789999999999999999876666665
No 90
>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=57.46 E-value=44 Score=23.90 Aligned_cols=30 Identities=17% Similarity=0.193 Sum_probs=23.9
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
....++|..+|++...|+++...-|.+.|+
T Consensus 136 ~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 136 LTIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 457789999999999999988765655554
No 91
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=57.31 E-value=11 Score=21.38 Aligned_cols=23 Identities=17% Similarity=0.339 Sum_probs=17.6
Q ss_pred HHHHHHHHHhCCChhHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQN 57 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqN 57 (157)
....++|..+|++...|..|.+.
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT-
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 46778999999999999999863
No 92
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=57.25 E-value=51 Score=23.13 Aligned_cols=31 Identities=10% Similarity=0.004 Sum_probs=24.2
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~ 65 (157)
..-.++|..+|++...|++....-|.+.|..
T Consensus 123 ~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 123 MDVAETAAAMGCSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3467889999999999999887666655553
No 93
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=57.05 E-value=63 Score=23.73 Aligned_cols=33 Identities=6% Similarity=0.077 Sum_probs=26.3
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA 67 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~ 67 (157)
..-+++|..+|++...|+.....-|.+-|+...
T Consensus 153 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 185 (195)
T PRK12532 153 FSSDEIQQMCGISTSNYHTIMHRARESLRQCLQ 185 (195)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999999876766666443
No 94
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.02 E-value=22 Score=23.74 Aligned_cols=41 Identities=15% Similarity=0.123 Sum_probs=31.3
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKI 53 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vqv 53 (157)
.++++|...-+..|+.+--.+....+++|.+|+.++-.|+.
T Consensus 2 SLn~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lek 42 (97)
T COG4367 2 SLNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLEK 42 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHHH
Confidence 35778877777777777666677889999999999876554
No 95
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=56.92 E-value=61 Score=23.85 Aligned_cols=34 Identities=12% Similarity=0.232 Sum_probs=26.5
Q ss_pred HHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301 34 PTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA 67 (157)
Q Consensus 34 ~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~ 67 (157)
....+++|..+|++...|++....=|.+.|+.-.
T Consensus 147 g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~ 180 (188)
T TIGR02943 147 GFESDEICQELEISTSNCHVLLYRARLSLRACLS 180 (188)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3467889999999999999988766666665443
No 96
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=56.77 E-value=42 Score=24.60 Aligned_cols=32 Identities=25% Similarity=0.274 Sum_probs=25.4
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
...+++|..+|++...|+..+..-|.+.++.-
T Consensus 123 ~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 123 LSQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 45778999999999999999986666666533
No 97
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=56.55 E-value=12 Score=22.64 Aligned_cols=20 Identities=15% Similarity=0.356 Sum_probs=17.5
Q ss_pred HHHHHHHhCCChhHHHHHHH
Q psy8301 37 REMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 37 r~~La~~l~l~~~~VqvWFq 56 (157)
..++|+.+|++...|+.|=+
T Consensus 3 i~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999953
No 98
>PF00424 REV: REV protein (anti-repression trans-activator protein); InterPro: IPR000625 REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally [] to relieve negative repression of GAG and ENV production. It is a phosphoprotein [, ] whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus []. REV accumulates in the nucleoli [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ETF_B 1ETG_B 1ULL_B 3LPH_B 2X7L_R.
Probab=56.30 E-value=24 Score=23.67 Aligned_cols=34 Identities=24% Similarity=0.252 Sum_probs=18.1
Q ss_pred HHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhh
Q psy8301 21 ELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68 (157)
Q Consensus 21 ~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~ 68 (157)
..+-.|+.|+||...--.. | =.|||.+||+...+
T Consensus 16 iIk~LyqsnPyP~~~GTr~-a-------------RRnRRRRWR~rq~Q 49 (91)
T PF00424_consen 16 IIKILYQSNPYPSPEGTRQ-A-------------RRNRRRRWRARQRQ 49 (91)
T ss_dssp HHHHHHHTS-S--S-S-HH-H-------------HHHHHHHHHHHHHH
T ss_pred HHHHHHccccCCCCCCccc-c-------------ccchhhhHHHHHHH
Confidence 4445589999997431111 1 25899999986654
No 99
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=55.99 E-value=49 Score=24.07 Aligned_cols=30 Identities=10% Similarity=0.245 Sum_probs=23.5
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
...+++|..+|++...|++|...=+.+-|.
T Consensus 150 ~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 150 CSHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred CCHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 457788999999999999998755555443
No 100
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=55.97 E-value=51 Score=23.36 Aligned_cols=30 Identities=17% Similarity=0.033 Sum_probs=22.7
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
..-.++|..+|+++..|+....--|.+.|+
T Consensus 139 ~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 139 LPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 456788999999999999888654544443
No 101
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=55.43 E-value=39 Score=23.94 Aligned_cols=30 Identities=23% Similarity=0.216 Sum_probs=23.2
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
....++|..+|++...|+.+...-|.+-++
T Consensus 129 ~s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 129 FSYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 456788999999999999988755555443
No 102
>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=55.42 E-value=30 Score=19.46 Aligned_cols=38 Identities=13% Similarity=0.171 Sum_probs=26.2
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWF 55 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWF 55 (157)
.++.++.+.+...+... ....++|+.+|++...|.-++
T Consensus 5 ~~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 46666666666666654 357889999999999887765
No 103
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=55.40 E-value=44 Score=25.60 Aligned_cols=46 Identities=9% Similarity=0.091 Sum_probs=32.4
Q ss_pred CHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301 15 IQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65 (157)
Q Consensus 15 t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~ 65 (157)
++.+..++...| -....-.++|..+|++...|+.+...-+.+.|+.
T Consensus 186 ~~~~r~vl~l~~-----~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 186 PEREQLVLSLYY-----QEELNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred CHHHHHHHHhHh-----ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 344444444443 2334678899999999999999998777776653
No 104
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=55.31 E-value=57 Score=23.04 Aligned_cols=30 Identities=17% Similarity=0.372 Sum_probs=23.7
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
...+++|+.+|++...|+.....-+.+.|+
T Consensus 126 ~s~~EIA~~lgis~~tV~~~l~ra~~~lr~ 155 (163)
T PRK07037 126 ETQKDIARELGVSPTLVNFMIRDALVHCRK 155 (163)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 357889999999999999987655555554
No 105
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=55.03 E-value=69 Score=24.41 Aligned_cols=34 Identities=9% Similarity=0.023 Sum_probs=26.3
Q ss_pred CHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 33 SPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 33 ~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
....-+++|..+|+++..|+++...-|.+.++..
T Consensus 149 eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 149 EDMSYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3345678999999999999999986666666643
No 106
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. 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; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=54.87 E-value=16 Score=20.15 Aligned_cols=20 Identities=15% Similarity=0.295 Sum_probs=16.0
Q ss_pred HHHHHHHhCCChhHHHHHHH
Q psy8301 37 REMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 37 r~~La~~l~l~~~~VqvWFq 56 (157)
+.++|+.+|++.+.|+-|=+
T Consensus 2 i~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 45789999999999999853
No 107
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=54.77 E-value=54 Score=23.82 Aligned_cols=30 Identities=7% Similarity=0.171 Sum_probs=24.6
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
..-+++|..+|+++..|+.....-+.+.+.
T Consensus 144 ~s~~EIA~~lgis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 144 MKQKDIAQALDIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 356789999999999999999876666554
No 108
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=53.93 E-value=57 Score=23.68 Aligned_cols=32 Identities=13% Similarity=-0.041 Sum_probs=26.0
Q ss_pred HHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301 34 PTEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65 (157)
Q Consensus 34 ~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~ 65 (157)
....+++|..+|++...|++....-|.+.|+.
T Consensus 145 g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 145 GLSVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34577899999999999999998777776653
No 109
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=53.16 E-value=39 Score=18.86 Aligned_cols=40 Identities=13% Similarity=0.036 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNR 58 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNr 58 (157)
.++..+..++...+. . ....++|..+|++...|..|...-
T Consensus 3 ~l~~~e~~i~~~~~~-g-----~s~~eia~~l~is~~tv~~~~~~~ 42 (58)
T smart00421 3 SLTPREREVLRLLAE-G-----LTNKEIAERLGISEKTVKTHLSNI 42 (58)
T ss_pred CCCHHHHHHHHHHHc-C-----CCHHHHHHHHCCCHHHHHHHHHHH
Confidence 467778777755332 2 256788999999999999988743
No 110
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=53.01 E-value=61 Score=23.19 Aligned_cols=30 Identities=7% Similarity=0.056 Sum_probs=23.8
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
...+++|..+|+++..|+.....-|.+.|+
T Consensus 135 ~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 164 (173)
T PRK09645 135 WSTAQIAADLGIPEGTVKSRLHYALRALRL 164 (173)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 356789999999999999988765555555
No 111
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=52.83 E-value=58 Score=24.02 Aligned_cols=31 Identities=6% Similarity=0.053 Sum_probs=25.1
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~ 65 (157)
..-+++|..+|++...|+.+...-|.+.|+.
T Consensus 153 ~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 153 LSNPEIAEVMEIGVEAVESLTARGKRALAAL 183 (196)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999999998666666553
No 112
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=52.72 E-value=66 Score=23.10 Aligned_cols=31 Identities=6% Similarity=0.106 Sum_probs=25.5
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~ 65 (157)
..-.++|..+|+++..|+++...-+.+.+..
T Consensus 136 ~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~ 166 (172)
T PRK12523 136 MGHAEIAERLGVSVSRVRQYLAQGLRQCYIA 166 (172)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4567889999999999999998777776653
No 113
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=52.69 E-value=45 Score=25.73 Aligned_cols=32 Identities=9% Similarity=0.167 Sum_probs=26.0
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
...+++|..+|+++..|++....-|.+.|+..
T Consensus 188 ~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 188 MSNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999999987777766543
No 114
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=52.53 E-value=41 Score=20.12 Aligned_cols=36 Identities=22% Similarity=0.279 Sum_probs=26.6
Q ss_pred HHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHH
Q psy8301 17 SQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 17 ~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFq 56 (157)
.|+..|+-.++ +..... .+||..+|++++.|+.-..
T Consensus 6 rq~~Ll~~L~~-~~~~~~---~ela~~l~~S~rti~~~i~ 41 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITL---KELAKKLNISERTIKNDIN 41 (59)
T ss_dssp HHHHHHHHHHH-HTSBBH---HHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcH---HHHHHHHCCCHHHHHHHHH
Confidence 46777888888 665554 4899999999999887654
No 115
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=52.48 E-value=66 Score=23.12 Aligned_cols=48 Identities=15% Similarity=0.111 Sum_probs=37.3
Q ss_pred CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 11 Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
.+.++..|..+|.-. ... ...+++|..+|++...|..|-+.-+.+-++
T Consensus 4 ~~~Lte~qr~VL~Lr-~~G-----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELR-EKG-----LSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHH-HcC-----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 367899999998774 222 367889999999999999998776666654
No 116
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=52.14 E-value=54 Score=24.28 Aligned_cols=32 Identities=16% Similarity=0.033 Sum_probs=25.7
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
...+++|..+|++...|+++...-|.+.|+.-
T Consensus 130 ~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 130 FSYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999999986666666533
No 117
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=51.91 E-value=60 Score=24.15 Aligned_cols=33 Identities=12% Similarity=-0.001 Sum_probs=25.9
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA 67 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~ 67 (157)
..-+++|..+|++...|+++...-|.+.|+...
T Consensus 150 ~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~ 182 (196)
T PRK12535 150 YTYEEAAKIADVRVGTIRSRVARARADLIAATA 182 (196)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 356788999999999999999766666666443
No 118
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=51.31 E-value=68 Score=22.86 Aligned_cols=31 Identities=10% Similarity=-0.034 Sum_probs=24.5
Q ss_pred HHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 34 PTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 34 ~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
...-+++|..+|+++..|+++...-|.+.|.
T Consensus 128 g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 128 GFSYEDAAAICGCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 3457789999999999999999765655554
No 119
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=51.18 E-value=20 Score=21.83 Aligned_cols=20 Identities=10% Similarity=0.272 Sum_probs=17.8
Q ss_pred HHHHHHHhCCChhHHHHHHH
Q psy8301 37 REMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 37 r~~La~~l~l~~~~VqvWFq 56 (157)
..++|+.+|++...++.|.+
T Consensus 3 i~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999975
No 120
>KOG0484|consensus
Probab=51.10 E-value=1.4 Score=30.36 Aligned_cols=36 Identities=19% Similarity=0.322 Sum_probs=31.4
Q ss_pred CCCCCCCCcCccccCCCCCCCCcCCCCCCCCchhHHHhhhc
Q psy8301 107 RKPETDFPAEEHNIFVPNFDQSDFLDNKWEDIDILDELHDQ 147 (157)
Q Consensus 107 ~~~~~~~~~~q~~~~~~~f~~~~~s~s~~p~~~~~~~l~~~ 147 (157)
+.-.+.|++.|+..+...|...+| ||+-++|||+-.
T Consensus 18 RRIRTTFTS~QLkELErvF~ETHY-----PDIYTREEiA~k 53 (125)
T KOG0484|consen 18 RRIRTTFTSAQLKELERVFAETHY-----PDIYTREEIALK 53 (125)
T ss_pred hhhhhhhhHHHHHHHHHHHHhhcC-----CcchhHHHHHHh
Confidence 344578999999999999999999 999999999854
No 121
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=50.58 E-value=35 Score=24.51 Aligned_cols=36 Identities=14% Similarity=0.164 Sum_probs=28.6
Q ss_pred CCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 31 YLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 31 ~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
|.....-+++|..+|++...|++.+..-|.+.++.-
T Consensus 133 ~~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 133 DLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 445556788999999999999999987777766643
No 122
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=50.24 E-value=63 Score=25.10 Aligned_cols=46 Identities=11% Similarity=0.078 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 14 GIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 14 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
+++.+..+|.-.|- ....-.++|..+|++...|+.|...-+.+.|.
T Consensus 206 L~~~~r~vl~l~~~-----~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~ 251 (257)
T PRK08583 206 LSDREKSIIQCTFI-----ENLSQKETGERLGISQMHVSRLQRQAIKKLRE 251 (257)
T ss_pred CCHHHHHHHHHHHh-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 44555555555442 22356889999999999999998766666555
No 123
>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=49.99 E-value=66 Score=24.34 Aligned_cols=47 Identities=11% Similarity=0.080 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
.+++.+..++...|-. .....++|..+|++...|..|...=+.+.|+
T Consensus 178 ~L~~~~r~vl~l~y~~-----~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 178 ALPERERRILLLRFFE-----DKTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred cCCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3556666666655432 2467889999999999999998755555443
No 124
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=49.73 E-value=68 Score=23.51 Aligned_cols=31 Identities=16% Similarity=0.251 Sum_probs=24.0
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~ 65 (157)
...+++|+.+|++...|++..+.-|.+-|++
T Consensus 148 ~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~ 178 (189)
T PRK06811 148 EKIEEIAKKLGLTRSAIDNRLSRGRKKLQKN 178 (189)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 4578899999999999998887555555553
No 125
>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=49.66 E-value=46 Score=18.66 Aligned_cols=36 Identities=11% Similarity=0.040 Sum_probs=25.6
Q ss_pred CHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHH
Q psy8301 15 IQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 15 t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFq 56 (157)
+..+..++...+ .. ....++|..++++...|..|..
T Consensus 2 ~~~e~~i~~~~~--~~----~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLA--EG----KTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHH
Confidence 455566664433 11 2567889999999999999986
No 126
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=49.61 E-value=90 Score=23.41 Aligned_cols=32 Identities=9% Similarity=0.102 Sum_probs=25.0
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
..-.++|..+|+++..|+++...=|.+.++.-
T Consensus 155 ~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 155 LSYEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35678899999999999999986666655533
No 127
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=49.51 E-value=23 Score=21.37 Aligned_cols=20 Identities=15% Similarity=0.421 Sum_probs=17.8
Q ss_pred HHHHHHHhCCChhHHHHHHH
Q psy8301 37 REMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 37 r~~La~~l~l~~~~VqvWFq 56 (157)
..++|+.+|++...++.|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999985
No 128
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=49.09 E-value=24 Score=21.41 Aligned_cols=21 Identities=10% Similarity=0.279 Sum_probs=18.1
Q ss_pred HHHHHHHhCCChhHHHHHHHH
Q psy8301 37 REMLGKEINLSPTQVKIWFQN 57 (157)
Q Consensus 37 r~~La~~l~l~~~~VqvWFqN 57 (157)
..++|+.+|++...++-|-++
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 467899999999999999753
No 129
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=49.01 E-value=76 Score=22.96 Aligned_cols=30 Identities=10% Similarity=0.019 Sum_probs=22.7
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
..-+++|..+|++...|+.+...=|.+.|.
T Consensus 152 ~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 152 YTHREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 456788999999999999988755554444
No 130
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=48.98 E-value=63 Score=23.65 Aligned_cols=30 Identities=3% Similarity=-0.157 Sum_probs=23.4
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
..-+++|..+|+++..|+++...-|.+.|+
T Consensus 147 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 147 LSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 456789999999999999998755555444
No 131
>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=48.65 E-value=69 Score=24.24 Aligned_cols=46 Identities=11% Similarity=0.093 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 14 GIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 14 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
+++.+..+|...|-.. ...+++|..+|++...|+.+...-+.+-|+
T Consensus 176 L~~~~r~il~l~y~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 176 LSEREQLVLSLYYYEE-----LNLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred CCHHHHHHHHHHHhCC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4556666666655322 357889999999999999988755555443
No 132
>PRK09480 slmA division inhibitor protein; Provisional
Probab=48.61 E-value=20 Score=26.08 Aligned_cols=39 Identities=10% Similarity=0.118 Sum_probs=31.3
Q ss_pred HHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHH
Q psy8301 21 ELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRY 60 (157)
Q Consensus 21 ~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~ 60 (157)
+....|...+. .......||...|++...+-.+|.|+-.
T Consensus 18 aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 18 ALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 33344555556 8889999999999999999999999763
No 133
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=48.01 E-value=78 Score=23.55 Aligned_cols=34 Identities=12% Similarity=0.169 Sum_probs=26.2
Q ss_pred CHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 33 SPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 33 ~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
....-.++|..+|+++..|++....-|.+-|+.-
T Consensus 154 eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 154 LDFEIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3345778999999999999999876666666543
No 134
>PRK10403 transcriptional regulator NarP; Provisional
Probab=47.72 E-value=43 Score=23.95 Aligned_cols=43 Identities=19% Similarity=0.136 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYK 61 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k 61 (157)
.+|..+..+|...... ...+++|+.++++++.|++...|=+.|
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~k 195 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRK 195 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 5888888888765432 456789999999999999998876655
No 135
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=47.62 E-value=93 Score=22.60 Aligned_cols=31 Identities=10% Similarity=-0.027 Sum_probs=25.0
Q ss_pred HHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 34 PTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 34 ~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
....+++|..+|++...|+.+...-|.+.|+
T Consensus 147 g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12539 147 GLSVAEAATRSGMSESAVKVSVHRGLKALAA 177 (184)
T ss_pred CCcHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3467889999999999999999766666555
No 136
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=47.39 E-value=81 Score=23.22 Aligned_cols=32 Identities=9% Similarity=0.023 Sum_probs=25.4
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
..-.++|..+|+++..|+++...-|.+.++..
T Consensus 133 ~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l 164 (187)
T PRK12516 133 FAYEEAAEICGCAVGTIKSRVNRARQRLQEIL 164 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 45678899999999999999986666666543
No 137
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=47.36 E-value=79 Score=22.97 Aligned_cols=30 Identities=10% Similarity=0.237 Sum_probs=24.1
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
..-+++|..+|+++..|++....-|.+.|+
T Consensus 139 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 168 (185)
T PRK12542 139 LTYQEISSVMGITEANVRKQFERARKRVQN 168 (185)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 456789999999999999988766666555
No 138
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=47.36 E-value=74 Score=22.90 Aligned_cols=33 Identities=12% Similarity=0.101 Sum_probs=25.4
Q ss_pred CCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 32 LSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 32 p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
......+++|..+|++...|+++...-+.+++.
T Consensus 133 ~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~ 165 (172)
T PRK09651 133 LDGLTYSEIAHKLGVSVSSVKKYVAKATEHCLL 165 (172)
T ss_pred ccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 334457889999999999999999765555554
No 139
>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=46.99 E-value=52 Score=20.31 Aligned_cols=41 Identities=15% Similarity=0.112 Sum_probs=25.0
Q ss_pred CCCHHHHHHHHH---HhhhcCCCCHHHHHHHHHHhCCC-hhHHHHHH
Q psy8301 13 NGIQSQVFELER---KFQHIRYLSPTEREMLGKEINLS-PTQVKIWF 55 (157)
Q Consensus 13 ~~t~~q~~~Le~---~F~~~~~p~~~~r~~La~~l~l~-~~~VqvWF 55 (157)
.+|..|.++|+- ....+.||- ...+||..+|+. ...|+.-.
T Consensus 3 ~LT~rQ~~vL~~I~~~~~~~G~~P--t~rEIa~~~g~~S~~tv~~~L 47 (65)
T PF01726_consen 3 ELTERQKEVLEFIREYIEENGYPP--TVREIAEALGLKSTSTVQRHL 47 (65)
T ss_dssp ---HHHHHHHHHHHHHHHHHSS-----HHHHHHHHTSSSHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHcCCCC--CHHHHHHHhCCCChHHHHHHH
Confidence 356777666654 456777873 678899999997 66665443
No 140
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=46.93 E-value=93 Score=22.86 Aligned_cols=30 Identities=10% Similarity=0.083 Sum_probs=23.8
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
..-+++|..+|++...|++....-|.+.|+
T Consensus 158 ~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~ 187 (194)
T PRK12531 158 LPHQQVAEMFDIPLGTVKSRLRLAVEKLRH 187 (194)
T ss_pred CCHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 456788999999999999888766655555
No 141
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=46.23 E-value=1.1e+02 Score=22.23 Aligned_cols=34 Identities=15% Similarity=0.276 Sum_probs=26.7
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhh
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~ 68 (157)
..-.++|..+|+++..|++....-|.+.|+.-..
T Consensus 148 ~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 181 (191)
T PRK12520 148 LETEEICQELQITATNAWVLLYRARMRLRECLDL 181 (191)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999999998767666664443
No 142
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=45.38 E-value=80 Score=24.45 Aligned_cols=45 Identities=13% Similarity=0.223 Sum_probs=30.7
Q ss_pred CHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 15 IQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 15 t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
++.+..++.-.| .....-.++|..+|++...|+.++..-+.+.|.
T Consensus 203 ~~~~r~vl~l~~-----~~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 203 SEKEQLVISLFY-----KEELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred CHHHHHHHHHHH-----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 444444554443 233457889999999999999999766665554
No 143
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=45.35 E-value=40 Score=23.52 Aligned_cols=34 Identities=21% Similarity=0.169 Sum_probs=26.5
Q ss_pred CCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 31 YLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 31 ~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
|.....-+++|..+|+++..|+++...-|.+-|+
T Consensus 118 ~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 118 EFKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4555678889999999999999998755555444
No 144
>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=44.98 E-value=80 Score=24.47 Aligned_cols=46 Identities=13% Similarity=0.094 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 14 GIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 14 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
+++.+..++.-.|... ....++|..+|++...|+.+...-+.+-|.
T Consensus 206 L~~~~r~ii~l~~~~g-----~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 206 LSEREKSIIHCTFEEN-----LSQKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred CCHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4555666666554332 356789999999999999998766665554
No 145
>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=44.75 E-value=1e+02 Score=24.01 Aligned_cols=31 Identities=13% Similarity=0.237 Sum_probs=25.7
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~ 65 (157)
...+++|..+|+++..|+++...-|.+.|+.
T Consensus 178 ~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~ 208 (244)
T TIGR03001 178 LSMDRIGAMYQVHRSTVSRWVAQARERLLER 208 (244)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4577899999999999999998777766553
No 146
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=44.74 E-value=89 Score=22.03 Aligned_cols=28 Identities=14% Similarity=0.210 Sum_probs=21.7
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQ 62 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~ 62 (157)
..-+++|..+|++...|+++...-+.+.
T Consensus 130 ~s~~EIA~~l~is~~tV~~~l~ra~~~~ 157 (161)
T PRK12528 130 LGYGEIATELGISLATVKRYLNKAAMRC 157 (161)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3567889999999999999887544443
No 147
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=44.56 E-value=91 Score=24.36 Aligned_cols=47 Identities=17% Similarity=0.112 Sum_probs=33.0
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301 14 GIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65 (157)
Q Consensus 14 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~ 65 (157)
+++.+..+|...|- ......++|..+|++...|+.+...-+.+.|..
T Consensus 204 L~~~~r~vl~l~y~-----~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~ 250 (256)
T PRK07408 204 LEERTREVLEFVFL-----HDLTQKEAAERLGISPVTVSRRVKKGLDQLKKL 250 (256)
T ss_pred CCHHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 44555555555543 234678899999999999999997666665553
No 148
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=44.17 E-value=85 Score=23.88 Aligned_cols=32 Identities=6% Similarity=0.076 Sum_probs=25.4
Q ss_pred CHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 33 SPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 33 ~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
....-+++|..+|++...|+.+...-+.+-|+
T Consensus 197 eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~ 228 (234)
T PRK08301 197 EEKTQKEVADMLGISQSYISRLEKRIIKRLKK 228 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 33457889999999999999998766666655
No 149
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=43.81 E-value=90 Score=22.89 Aligned_cols=32 Identities=3% Similarity=-0.003 Sum_probs=24.9
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
..-+++|..+|++...|+++...-|.+.|+..
T Consensus 128 ~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~ 159 (182)
T PRK12511 128 LSYQEAAAVLGIPIGTLMSRIGRARAALRAFE 159 (182)
T ss_pred CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 45678899999999999999876566655533
No 150
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=43.62 E-value=95 Score=22.19 Aligned_cols=30 Identities=7% Similarity=0.080 Sum_probs=23.7
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
..-+++|..+|++...|+.+..+-+.+++.
T Consensus 135 ~s~~EIA~~l~is~~tV~~~l~ra~~~~~~ 164 (168)
T PRK12525 135 LTYVEIGERLGVSLSRIHQYMVEAFKCCYQ 164 (168)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 456789999999999999988766655543
No 151
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=42.80 E-value=1.2e+02 Score=21.35 Aligned_cols=31 Identities=10% Similarity=0.106 Sum_probs=23.9
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~ 65 (157)
...+++|..+|+++..|+.....-+.+.|..
T Consensus 122 ~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~ 152 (159)
T PRK12527 122 LSHQQIAEHLGISRSLVEKHIVNAMKHCRVR 152 (159)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4567889999999999999887555555553
No 152
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=42.54 E-value=99 Score=22.55 Aligned_cols=35 Identities=9% Similarity=0.005 Sum_probs=26.8
Q ss_pred CCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 32 LSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 32 p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
.....-+++|..+|+++..|++....-|.+-|+.-
T Consensus 152 ~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 152 FDGLSYEDIASVMQCPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34445678999999999999999886666666543
No 153
>KOG3755|consensus
Probab=42.34 E-value=18 Score=32.44 Aligned_cols=62 Identities=19% Similarity=0.296 Sum_probs=50.6
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHhhhcC-CCCHHH---HHHHHHHhCCChhHHHHHHHHHHHHHH
Q psy8301 2 FQSHRAGKMRTNGIQSQVFELERKFQHIR-YLSPTE---REMLGKEINLSPTQVKIWFQNRRYKQK 63 (157)
Q Consensus 2 ~~~~~~rr~Rt~~t~~q~~~Le~~F~~~~-~p~~~~---r~~La~~l~l~~~~VqvWFqNrR~k~r 63 (157)
+..+-+.+.|+.+..+-+.+|..+-.... ||+... ..-|+..+++..+.+-..|+|.|...+
T Consensus 642 ~~n~~~p~~~~~isge~~~~~qs~i~~~gl~pd~~a~~~~~~LSa~~~~pk~~~~k~f~~~~~ev~ 707 (769)
T KOG3755|consen 642 LKNWHKPRKRTKISGEALGILQSFITDVGLYPDKEAPYFIKTLSAQLDLPKKTIIKFFQNQRYEVK 707 (769)
T ss_pred HHhccCccccceecccchHHHHHHHHHhccCchhhcccccchhhhhhcccHHHHHHhhhcceeecc
Confidence 34455678899999999999987754444 899888 888999999999999999999987655
No 154
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=41.93 E-value=1.1e+02 Score=21.87 Aligned_cols=31 Identities=10% Similarity=0.137 Sum_probs=24.2
Q ss_pred HHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 34 PTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 34 ~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
...-+++|..+|+++..|++....-|.+-|+
T Consensus 135 ~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 165 (173)
T PRK12522 135 QYSYKEMSEILNIPIGTVKYRLNYAKKQMRE 165 (173)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 3456788999999999999998766655554
No 155
>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=41.91 E-value=33 Score=18.73 Aligned_cols=21 Identities=14% Similarity=0.086 Sum_probs=18.1
Q ss_pred HHHHHHHhCCChhHHHHHHHH
Q psy8301 37 REMLGKEINLSPTQVKIWFQN 57 (157)
Q Consensus 37 r~~La~~l~l~~~~VqvWFqN 57 (157)
..++|+.+|++...|..|.++
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~ 24 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHE 24 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHc
Confidence 567899999999999999854
No 156
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=41.85 E-value=1e+02 Score=22.70 Aligned_cols=35 Identities=17% Similarity=0.252 Sum_probs=27.1
Q ss_pred CCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301 31 YLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65 (157)
Q Consensus 31 ~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~ 65 (157)
|.....-.++|..+|++...|++....-|.+.|+.
T Consensus 167 ~~e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~ 201 (208)
T PRK08295 167 YLDGKSYQEIAEELNRHVKSIDNALQRVKRKLEKY 201 (208)
T ss_pred HHccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34445678899999999999999887766666653
No 157
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=41.69 E-value=1.1e+02 Score=22.10 Aligned_cols=32 Identities=13% Similarity=0.157 Sum_probs=24.9
Q ss_pred CHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 33 SPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 33 ~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
....-+++|..+|++...|......=|.+.|+
T Consensus 151 ~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T PRK09641 151 EDLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34456788999999999999988766666555
No 158
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=41.65 E-value=93 Score=20.19 Aligned_cols=43 Identities=9% Similarity=0.015 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHhhh-----cCCCCHHHHHHHHHHhCCChhHHHHHHH
Q psy8301 14 GIQSQVFELERKFQH-----IRYLSPTEREMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 14 ~t~~q~~~Le~~F~~-----~~~p~~~~r~~La~~l~l~~~~VqvWFq 56 (157)
++.+|+..|...|.. +.+.+..+...+-..+|+++..|..+|.
T Consensus 4 ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~ 51 (96)
T smart00027 4 ISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWN 51 (96)
T ss_pred CCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHH
Confidence 578889999988854 2367777777766678999888888875
No 159
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=41.65 E-value=93 Score=24.51 Aligned_cols=46 Identities=9% Similarity=0.097 Sum_probs=33.1
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 14 GIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 14 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
+++.+..+|...|- ......++|..+|++...|+.+...-+.+.|.
T Consensus 216 L~~rer~vl~l~y~-----~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 261 (264)
T PRK07122 216 LPERERTVLVLRFF-----ESMTQTQIAERVGISQMHVSRLLAKTLARLRD 261 (264)
T ss_pred CCHHHHHHHHHHhc-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45556666666553 23457889999999999999998766666554
No 160
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=41.50 E-value=1.3e+02 Score=22.63 Aligned_cols=31 Identities=13% Similarity=0.285 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 36 EREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 36 ~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
...++|..+|++...|++....-|.+-|+..
T Consensus 166 s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l 196 (206)
T PRK12544 166 ETNEICHAVDLSVSNLNVLLYRARLRLRECL 196 (206)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999886666666644
No 161
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=41.33 E-value=14 Score=21.05 Aligned_cols=20 Identities=10% Similarity=0.164 Sum_probs=18.5
Q ss_pred HHHHHhCCChhHHHHHHHHH
Q psy8301 39 MLGKEINLSPTQVKIWFQNR 58 (157)
Q Consensus 39 ~La~~l~l~~~~VqvWFqNr 58 (157)
+||..+|++...|..|+.++
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCC
Confidence 58999999999999999887
No 162
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=41.19 E-value=1.3e+02 Score=23.60 Aligned_cols=47 Identities=6% Similarity=0.026 Sum_probs=32.8
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301 14 GIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65 (157)
Q Consensus 14 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~ 65 (157)
+++.+..+|...|-. .....++|..+|++...|+.....-+.+-|+.
T Consensus 213 L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 259 (268)
T PRK06288 213 LPEREKKVLILYYYE-----DLTLKEIGKVLGVTESRISQLHTKAVLQLRAK 259 (268)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 445555555555432 24578899999999999998887666666554
No 163
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=40.91 E-value=66 Score=17.94 Aligned_cols=37 Identities=14% Similarity=0.145 Sum_probs=24.1
Q ss_pred CHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHH
Q psy8301 15 IQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWF 55 (157)
Q Consensus 15 t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWF 55 (157)
+..+..+|....+. |. ....+||..+|++...|.--+
T Consensus 2 ~~~~~~Il~~l~~~---~~-~t~~ela~~~~is~~tv~~~l 38 (48)
T PF13412_consen 2 DETQRKILNYLREN---PR-ITQKELAEKLGISRSTVNRYL 38 (48)
T ss_dssp -HHHHHHHHHHHHC---TT-S-HHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHHHHHHc---CC-CCHHHHHHHhCCCHHHHHHHH
Confidence 34566777666552 33 567889999999998876554
No 164
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=40.86 E-value=91 Score=25.49 Aligned_cols=53 Identities=17% Similarity=0.142 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
.+++.+..+|...|... |-.....+++|..+|++...|+.+...-+.+.|+.-
T Consensus 262 ~L~~~~R~vl~lrygL~-~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 262 ELNDKQREVLARRFGLL-GYEAATLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred cCCHHHHHHHHHHhccC-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 35666667776665332 234456789999999999999999987777776644
No 165
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=40.85 E-value=67 Score=22.82 Aligned_cols=43 Identities=21% Similarity=0.127 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYK 61 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k 61 (157)
.+|+.+...|+-..+. ..++++|..++++++.|++..++=|.|
T Consensus 137 ~Lt~~E~~il~~l~~g------~~~~~Ia~~l~~s~~tv~~~~~~l~~K 179 (196)
T PRK10360 137 PLTKRERQVAEKLAQG------MAVKEIAAELGLSPKTVHVHRANLMEK 179 (196)
T ss_pred CCCHHHHHHHHHHHCC------CCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 5788888888765542 268889999999999999988776655
No 166
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=40.57 E-value=1.5e+02 Score=21.82 Aligned_cols=31 Identities=10% Similarity=0.017 Sum_probs=21.1
Q ss_pred HHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 34 PTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 34 ~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
...-+++|..+|++...|++=...-|.+-|+
T Consensus 150 g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~ 180 (192)
T PRK09643 150 GYSVADAARMLGVAEGTVKSRCARGRARLAE 180 (192)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3456788999999999887755433444444
No 167
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=40.57 E-value=52 Score=24.14 Aligned_cols=36 Identities=6% Similarity=-0.009 Sum_probs=28.3
Q ss_pred CCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 31 YLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 31 ~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
|.....-.++|..+|+++..|+++...-|.+.|+.-
T Consensus 144 ~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 144 DVEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred hhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 444456788999999999999999987777666644
No 168
>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=40.09 E-value=95 Score=23.83 Aligned_cols=52 Identities=15% Similarity=0.162 Sum_probs=37.4
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~ 65 (157)
.+++.+..+|...|....+ ......++|..+|++...|+.+...-..|.|..
T Consensus 176 ~L~~~er~vl~l~ygl~~~-~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~ 227 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDG-RPHTLEEVGKEFNVTRERIRQIESKALRKLRHP 227 (238)
T ss_pred hCCHHHHHHHHHHhCCCCC-CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhh
Confidence 3566677777777633222 234688899999999999999998777776653
No 169
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=39.99 E-value=1e+02 Score=22.37 Aligned_cols=30 Identities=10% Similarity=0.126 Sum_probs=23.6
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
...+++|..+|++...|+.+...-|.+.|.
T Consensus 144 ~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 144 LSIKEIAEVTGVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 456789999999999999988755555544
No 170
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=39.64 E-value=15 Score=21.14 Aligned_cols=23 Identities=9% Similarity=0.227 Sum_probs=18.4
Q ss_pred HHHHHHHHhCCChhHHHHHHHHH
Q psy8301 36 EREMLGKEINLSPTQVKIWFQNR 58 (157)
Q Consensus 36 ~r~~La~~l~l~~~~VqvWFqNr 58 (157)
...+||..+|++...|..|..+.
T Consensus 11 s~~~la~~~gis~~~i~~~~~g~ 33 (55)
T PF01381_consen 11 SQKELAEKLGISRSTISRIENGK 33 (55)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTS
T ss_pred CHHHHHHHhCCCcchhHHHhcCC
Confidence 35789999999999999999763
No 171
>PF13730 HTH_36: Helix-turn-helix domain
Probab=39.63 E-value=55 Score=18.77 Aligned_cols=22 Identities=23% Similarity=0.357 Sum_probs=18.8
Q ss_pred HHHHHHHHhCCChhHHHHHHHH
Q psy8301 36 EREMLGKEINLSPTQVKIWFQN 57 (157)
Q Consensus 36 ~r~~La~~l~l~~~~VqvWFqN 57 (157)
..+.||..+|++.+.|+.+...
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~ 48 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKE 48 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHH
Confidence 4778999999999999988753
No 172
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=39.48 E-value=54 Score=23.97 Aligned_cols=34 Identities=15% Similarity=0.212 Sum_probs=25.4
Q ss_pred CCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 31 YLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 31 ~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
|.......++|..+|++...|.+++..-|.+-|.
T Consensus 162 ~~~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 162 YLDGKSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4445567789999999999999988755555443
No 173
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=38.77 E-value=92 Score=20.98 Aligned_cols=42 Identities=17% Similarity=0.117 Sum_probs=31.3
Q ss_pred CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCC-ChhHHHHHHH
Q psy8301 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINL-SPTQVKIWFQ 56 (157)
Q Consensus 11 Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l-~~~~VqvWFq 56 (157)
|..|+.+....+-+.+....+ ....+|..+|+ +..++..|-+
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~ 47 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRI 47 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHH
Confidence 778999986655555554443 67889999996 9888887764
No 174
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=38.70 E-value=50 Score=22.88 Aligned_cols=28 Identities=18% Similarity=0.207 Sum_probs=23.2
Q ss_pred CCCHHHHHHHHHHhCCChhHHHHHHHHH
Q psy8301 31 YLSPTEREMLGKEINLSPTQVKIWFQNR 58 (157)
Q Consensus 31 ~p~~~~r~~La~~l~l~~~~VqvWFqNr 58 (157)
+-.....++||..+|++...+..+|+.-
T Consensus 22 ~~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 22 LESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred cCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4344678899999999999999999865
No 175
>PF04936 DUF658: Protein of unknown function (DUF658); InterPro: IPR007020 This entry is represented by Bacteriophage r1t, Orf18. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. These are proteins of unknown function found in Lactococcus lactis and in their associated bacteriophage.
Probab=38.54 E-value=14 Score=27.49 Aligned_cols=30 Identities=20% Similarity=0.417 Sum_probs=26.2
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
-++.+|+..++++..+|-+|.+|-+...+.
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~~~~a 44 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKDPKRA 44 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCCcccc
Confidence 368899999999999999999998876654
No 176
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=38.11 E-value=1e+02 Score=21.65 Aligned_cols=43 Identities=14% Similarity=0.033 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYK 61 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k 61 (157)
.++..+..+|+- +..+ + ...++|+.+++++..|+.+.+|=+.|
T Consensus 149 ~lt~~e~~vl~l-~~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~k 191 (211)
T PRK15369 149 LLTPRERQILKL-ITEG-Y----TNRDIAEQLSISIKTVETHRLNMMRK 191 (211)
T ss_pred CCCHHHHHHHHH-HHCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 488888888876 3332 2 36788999999999999999875555
No 177
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=37.82 E-value=1.4e+02 Score=22.03 Aligned_cols=32 Identities=16% Similarity=0.206 Sum_probs=25.1
Q ss_pred CHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 33 SPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 33 ~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
.....+++|..+|++++.|+..++.=|++.++
T Consensus 150 ~Gls~~EIA~~lgiS~~tV~r~l~~aR~~l~~ 181 (185)
T PF07638_consen 150 EGLSVEEIAERLGISERTVRRRLRRARAWLRR 181 (185)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 33467889999999999999988776655444
No 178
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=37.31 E-value=37 Score=20.44 Aligned_cols=20 Identities=10% Similarity=0.079 Sum_probs=17.2
Q ss_pred HHHHHHHhCCChhHHHHHHH
Q psy8301 37 REMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 37 r~~La~~l~l~~~~VqvWFq 56 (157)
..++|+.+|++...|+.|-.
T Consensus 3 ~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999963
No 179
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=37.30 E-value=1.1e+02 Score=24.11 Aligned_cols=29 Identities=10% Similarity=0.075 Sum_probs=23.6
Q ss_pred HHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 36 EREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 36 ~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
.-.++|..+|+++..|+..++.=|.+.+.
T Consensus 126 s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~ 154 (281)
T TIGR02957 126 PYEEIASIVGKSEANCRQLVSRARRHLDA 154 (281)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45678999999999999999866666554
No 180
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=37.11 E-value=1.4e+02 Score=22.11 Aligned_cols=44 Identities=20% Similarity=0.131 Sum_probs=35.4
Q ss_pred CCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHH
Q psy8301 10 MRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWF 55 (157)
Q Consensus 10 ~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWF 55 (157)
....++.+++..+.+.-..+ |..-.+..||++.|++.--|.+=.
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~v~ 125 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSMVA 125 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHHhc
Confidence 34689999999988886665 677789999999999987666543
No 181
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=37.08 E-value=19 Score=20.53 Aligned_cols=23 Identities=4% Similarity=-0.046 Sum_probs=19.7
Q ss_pred HHHHHHHHhCCChhHHHHHHHHH
Q psy8301 36 EREMLGKEINLSPTQVKIWFQNR 58 (157)
Q Consensus 36 ~r~~La~~l~l~~~~VqvWFqNr 58 (157)
...+||..+|++...|..|...+
T Consensus 17 tq~~lA~~~gvs~~~vs~~e~g~ 39 (58)
T TIGR03070 17 TQADLADLAGVGLRFIRDVENGK 39 (58)
T ss_pred CHHHHHHHhCCCHHHHHHHHCCC
Confidence 36789999999999999998654
No 182
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=36.49 E-value=67 Score=23.53 Aligned_cols=35 Identities=17% Similarity=0.092 Sum_probs=27.2
Q ss_pred CCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301 31 YLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65 (157)
Q Consensus 31 ~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~ 65 (157)
|.....-+++|..+|++...|+.+...=|.+-|+.
T Consensus 152 ~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 186 (194)
T PRK12513 152 EHGDLELEEIAELTGVPEETVKSRLRYALQKLREL 186 (194)
T ss_pred hccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 44556678899999999999999887666665553
No 183
>KOG0773|consensus
Probab=36.38 E-value=59 Score=26.55 Aligned_cols=42 Identities=33% Similarity=0.424 Sum_probs=35.5
Q ss_pred hhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHhh
Q psy8301 27 QHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68 (157)
Q Consensus 27 ~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~ 68 (157)
..++||.......|+-...|+..+|.+||-|-|.+.+.....
T Consensus 117 ~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~ 158 (342)
T KOG0773|consen 117 RLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKM 158 (342)
T ss_pred hhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCC
Confidence 457899999999999999999999999999988876664433
No 184
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=36.38 E-value=1.2e+02 Score=24.00 Aligned_cols=29 Identities=10% Similarity=0.151 Sum_probs=23.6
Q ss_pred HHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 36 EREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 36 ~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
.-+++|+.+|+++..|+...+.-|.+.|.
T Consensus 133 s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~ 161 (293)
T PRK09636 133 PFDEIASTLGRSPAACRQLASRARKHVRA 161 (293)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45678999999999999999866666555
No 185
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=36.32 E-value=1.3e+02 Score=23.40 Aligned_cols=47 Identities=15% Similarity=0.109 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
.++..+..++...|... ....++|..+|++...|...-.+=..|.|+
T Consensus 209 ~L~~~er~vi~~~~~~~-----~t~~eIA~~lgis~~~V~~~~~~al~kLr~ 255 (258)
T PRK08215 209 KLNDREKLILNLRFFQG-----KTQMEVAEEIGISQAQVSRLEKAALKHMRK 255 (258)
T ss_pred cCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 36666777777776322 357889999999999998877654444443
No 186
>PF12728 HTH_17: Helix-turn-helix domain
Probab=35.75 E-value=45 Score=18.92 Aligned_cols=21 Identities=14% Similarity=0.319 Sum_probs=18.1
Q ss_pred HHHHHHHhCCChhHHHHHHHH
Q psy8301 37 REMLGKEINLSPTQVKIWFQN 57 (157)
Q Consensus 37 r~~La~~l~l~~~~VqvWFqN 57 (157)
..++|+.+|++...|..|.++
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~ 24 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQ 24 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHc
Confidence 467899999999999999853
No 187
>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=35.47 E-value=1.4e+02 Score=22.57 Aligned_cols=43 Identities=9% Similarity=-0.010 Sum_probs=29.2
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHH
Q psy8301 14 GIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYK 61 (157)
Q Consensus 14 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k 61 (157)
++..+..++...|.. .....++|..+|++...|..+-..=..|
T Consensus 184 L~~~e~~i~~~~~~~-----~~t~~eIA~~lgis~~~V~~~~~~al~~ 226 (231)
T TIGR02885 184 LDERERQIIMLRYFK-----DKTQTEVANMLGISQVQVSRLEKKVLKK 226 (231)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 455566666655532 2468889999999999988776543333
No 188
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=35.44 E-value=72 Score=23.30 Aligned_cols=34 Identities=9% Similarity=0.161 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301 32 LSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65 (157)
Q Consensus 32 p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~ 65 (157)
-.....+++|..+|++...|+++...-|.+-|..
T Consensus 148 ~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 181 (188)
T PRK09640 148 VAELEFQEIADIMHMGLSATKMRYKRALDKLREK 181 (188)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3444678899999999999999998666665553
No 189
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=35.42 E-value=1.6e+02 Score=21.29 Aligned_cols=32 Identities=22% Similarity=0.208 Sum_probs=23.3
Q ss_pred CHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 33 SPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 33 ~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
....-+++|..+|++...|++.-..=|.+.|.
T Consensus 152 ~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 152 EGITYEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 33456788999999999998877655555443
No 190
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=35.10 E-value=1.5e+02 Score=22.66 Aligned_cols=31 Identities=13% Similarity=0.045 Sum_probs=23.2
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~ 65 (157)
...+++|..+|++...|..+-..-+.+.|+.
T Consensus 196 ~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~ 226 (233)
T PRK05803 196 KTQREIAKALGISRSYVSRIEKRALKKLFKE 226 (233)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4678899999999999988865445554443
No 191
>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=35.03 E-value=42 Score=19.29 Aligned_cols=35 Identities=11% Similarity=0.065 Sum_probs=22.1
Q ss_pred HHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHH
Q psy8301 19 VFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 19 ~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFq 56 (157)
..+|.-.+....+ ....+||..+|++.+.|+.-..
T Consensus 3 ~~il~~L~~~~~~---it~~eLa~~l~vS~rTi~~~i~ 37 (55)
T PF08279_consen 3 KQILKLLLESKEP---ITAKELAEELGVSRRTIRRDIK 37 (55)
T ss_dssp HHHHHHHHHTTTS---BEHHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHcCCC---cCHHHHHHHhCCCHHHHHHHHH
Confidence 3444444444433 4578899999999988876553
No 192
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=34.40 E-value=82 Score=23.31 Aligned_cols=37 Identities=14% Similarity=0.218 Sum_probs=32.0
Q ss_pred HHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHH
Q psy8301 16 QSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVK 52 (157)
Q Consensus 16 ~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vq 52 (157)
+.-+..|...++...|........+|..||++...|.
T Consensus 25 sAlip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v~ 61 (160)
T COG1905 25 SALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARVY 61 (160)
T ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHhe
Confidence 4557889999999999999999999999999987553
No 193
>PRK05572 sporulation sigma factor SigF; Validated
Probab=34.37 E-value=1.5e+02 Score=22.89 Aligned_cols=47 Identities=11% Similarity=0.057 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
.+++.+..++...|.. .....++|..+|++...|..+-..-..+.|+
T Consensus 202 ~L~~~~~~v~~l~~~~-----~~s~~eIA~~lgis~~~V~~~~~ral~kLr~ 248 (252)
T PRK05572 202 ELDERERLIVYLRYFK-----DKTQSEVAKRLGISQVQVSRLEKKILKQMKE 248 (252)
T ss_pred cCCHHHHHHHHHHHhC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3566666666666532 2467889999999999998887655555544
No 194
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=34.14 E-value=96 Score=22.11 Aligned_cols=43 Identities=16% Similarity=-0.010 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYK 61 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k 61 (157)
.++..+...|+...+. ...+++|..++++.+.|+++..+=|.|
T Consensus 149 ~lt~re~~vl~~l~~g------~s~~eIa~~l~~s~~tv~~~~~~~~~k 191 (210)
T PRK09935 149 VLSNREVTILRYLVSG------LSNKEIADQLLLSNKTVSAHKSNIYGK 191 (210)
T ss_pred cCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 4778777777654333 468889999999999999998776655
No 195
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=34.07 E-value=82 Score=24.04 Aligned_cols=37 Identities=16% Similarity=0.136 Sum_probs=29.4
Q ss_pred CCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301 31 YLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA 67 (157)
Q Consensus 31 ~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~ 67 (157)
|......+++|..+|++...|++....-|.+.|+...
T Consensus 162 ~~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~ 198 (231)
T PRK11922 162 VVEELSVEETAQALGLPEETVKTRLHRARRLLRESLA 198 (231)
T ss_pred hhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4555678899999999999999988777777776443
No 196
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=33.96 E-value=1.6e+02 Score=22.98 Aligned_cols=46 Identities=11% Similarity=0.044 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 14 GIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 14 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
+.+.+..+|...|- ......++|..+|++...|+.+...-+.+.|+
T Consensus 206 L~~~er~vi~l~y~-----e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 251 (257)
T PRK05911 206 LEEKERKVMALYYY-----EELVLKEIGKILGVSESRVSQIHSKALLKLRA 251 (257)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 44555555555543 23457889999999999999988755555554
No 197
>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=33.88 E-value=1.3e+02 Score=23.62 Aligned_cols=49 Identities=14% Similarity=0.037 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
.++..+..+|...|-. + ......++|..+|++...|+-...+=..|.|+
T Consensus 218 ~L~~rer~vl~l~y~~--~-~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~ 266 (270)
T TIGR02392 218 SLDARSRRIIEARWLD--D-DKLTLQELAAEYGVSAERIRQIEKNAMKKLKA 266 (270)
T ss_pred cCCHHHHHHHHHHhcC--C-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3566677777776632 1 12456899999999999999988877777665
No 198
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=33.64 E-value=88 Score=22.74 Aligned_cols=33 Identities=18% Similarity=0.164 Sum_probs=26.9
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHh
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA 67 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~~ 67 (157)
..-.++|..+|++...|+.|...-|.+.+....
T Consensus 144 ls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~ 176 (182)
T COG1595 144 LSYEEIAEILGISVGTVKSRLHRARKKLREQLE 176 (182)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 456788999999999999999877777776443
No 199
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=33.15 E-value=82 Score=22.53 Aligned_cols=34 Identities=15% Similarity=0.103 Sum_probs=25.9
Q ss_pred CCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 31 YLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 31 ~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
|......+++|..+|++...|+.+...-|.+.++
T Consensus 139 ~~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~ 172 (176)
T PRK09638 139 HYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRK 172 (176)
T ss_pred hhcCCCHHHHHHHHCCChhHHHHHHHHHHHHHHH
Confidence 4445567889999999999999988755555544
No 200
>PHA01976 helix-turn-helix protein
Probab=32.31 E-value=52 Score=19.68 Aligned_cols=23 Identities=4% Similarity=0.092 Sum_probs=19.5
Q ss_pred HHHHHHHHhCCChhHHHHHHHHH
Q psy8301 36 EREMLGKEINLSPTQVKIWFQNR 58 (157)
Q Consensus 36 ~r~~La~~l~l~~~~VqvWFqNr 58 (157)
...+||..+|++...|..|-..+
T Consensus 17 t~~~lA~~~gvs~~~v~~~e~g~ 39 (67)
T PHA01976 17 SAPELSRRAGVRHSLIYDFEADK 39 (67)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCC
Confidence 46789999999999999998654
No 201
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=31.67 E-value=31 Score=21.35 Aligned_cols=24 Identities=21% Similarity=0.297 Sum_probs=20.2
Q ss_pred HHHHHHHHhCCChhHHHHHHHHHH
Q psy8301 36 EREMLGKEINLSPTQVKIWFQNRR 59 (157)
Q Consensus 36 ~r~~La~~l~l~~~~VqvWFqNrR 59 (157)
...+||..+|++...|..|...++
T Consensus 20 t~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 20 SIRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCC
Confidence 357899999999999999997553
No 202
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=31.55 E-value=1.1e+02 Score=22.37 Aligned_cols=37 Identities=16% Similarity=0.200 Sum_probs=30.1
Q ss_pred HHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHH
Q psy8301 17 SQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKI 53 (157)
Q Consensus 17 ~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vqv 53 (157)
.-+..|...=+...|.+......+|..+|++...|.-
T Consensus 24 ~li~~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V~~ 60 (156)
T PRK05988 24 ALLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEVHG 60 (156)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHH
Confidence 3466676666777899999999999999999987654
No 203
>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=31.21 E-value=77 Score=19.57 Aligned_cols=22 Identities=23% Similarity=0.377 Sum_probs=17.0
Q ss_pred HHHHHHHHHhCCChhHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFq 56 (157)
+..++||..+|++...|+..++
T Consensus 21 Pt~eEiA~~lgis~~~v~~~l~ 42 (78)
T PF04539_consen 21 PTDEEIAEELGISVEEVRELLQ 42 (78)
T ss_dssp -BHHHHHHHHTS-HHHHHHHHH
T ss_pred CCHHHHHHHHcccHHHHHHHHH
Confidence 4577899999999999887764
No 204
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=30.86 E-value=45 Score=19.63 Aligned_cols=18 Identities=22% Similarity=0.516 Sum_probs=13.8
Q ss_pred HHHHHHHHhCCChhHHHH
Q psy8301 36 EREMLGKEINLSPTQVKI 53 (157)
Q Consensus 36 ~r~~La~~l~l~~~~Vqv 53 (157)
.-.+||+.+|++..||+-
T Consensus 30 SS~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 30 SSQELAEALGITPAQVRK 47 (50)
T ss_dssp -HHHHHHHHTS-HHHHHH
T ss_pred CHHHHHHHHCCCHHHhcc
Confidence 356899999999999874
No 205
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=30.61 E-value=75 Score=21.79 Aligned_cols=39 Identities=15% Similarity=0.339 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHH
Q psy8301 14 GIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRR 59 (157)
Q Consensus 14 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR 59 (157)
+++.....+.+.+.- .....|..+|++...|+.|=|+|+
T Consensus 44 ls~~eIk~iRe~~~l-------SQ~vFA~~L~vs~~Tv~~WEqGr~ 82 (104)
T COG2944 44 LSPTEIKAIREKLGL-------SQPVFARYLGVSVSTVRKWEQGRK 82 (104)
T ss_pred CCHHHHHHHHHHhCC-------CHHHHHHHHCCCHHHHHHHHcCCc
Confidence 677777777776654 356679999999999999988764
No 206
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=30.55 E-value=64 Score=22.46 Aligned_cols=25 Identities=24% Similarity=0.444 Sum_probs=22.1
Q ss_pred CCCHHHHHHHHHHhCCChhHHHHHH
Q psy8301 31 YLSPTEREMLGKEINLSPTQVKIWF 55 (157)
Q Consensus 31 ~p~~~~r~~La~~l~l~~~~VqvWF 55 (157)
-++...|.+||..+|++...|..|-
T Consensus 26 ~~~~~~r~~La~~~~i~~~~l~~w~ 50 (122)
T PF14229_consen 26 GDTPLGRKALAKKLGISERNLLKWV 50 (122)
T ss_pred CCCHHHHHHHHHhcCCCHHHHHHHH
Confidence 3667788999999999999999995
No 207
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=30.47 E-value=1.4e+02 Score=22.69 Aligned_cols=45 Identities=13% Similarity=0.003 Sum_probs=35.6
Q ss_pred CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHH
Q psy8301 12 TNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQ 62 (157)
Q Consensus 12 t~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~ 62 (157)
..+|+.+.++|+-..+- ..-.++|..+++++..|+.+..+=..|.
T Consensus 154 ~~Lt~rE~~Vl~l~~~G------~s~~eIA~~L~iS~~TVk~~~~~i~~Kl 198 (216)
T PRK10100 154 ALLTHREKEILNKLRIG------ASNNEIARSLFISENTVKTHLYNLFKKI 198 (216)
T ss_pred CCCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 34899999999877552 2467789999999999999998766553
No 208
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=30.43 E-value=1.4e+02 Score=20.50 Aligned_cols=34 Identities=12% Similarity=0.127 Sum_probs=24.3
Q ss_pred HHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHH
Q psy8301 18 QVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 18 q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFq 56 (157)
-....-.+++... ...++|...+++...|..||+
T Consensus 7 lR~rVl~~~~~g~-----s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 7 LRQRVLAYIEKGK-----SIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred HHHHHHHHHHccc-----hHHHHHHHhCcHHHHHHHHHH
Confidence 3333334555532 466789999999999999997
No 209
>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=30.37 E-value=48 Score=18.56 Aligned_cols=18 Identities=28% Similarity=0.409 Sum_probs=13.0
Q ss_pred HHHHHHHHHhCCChhHHH
Q psy8301 35 TEREMLGKEINLSPTQVK 52 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~Vq 52 (157)
..-.+||+.+|+++..|.
T Consensus 18 ~s~~~la~~lglS~~~v~ 35 (42)
T PF13404_consen 18 RSYAELAEELGLSESTVR 35 (42)
T ss_dssp S-HHHHHHHHTS-HHHHH
T ss_pred ccHHHHHHHHCcCHHHHH
Confidence 345678999999998764
No 210
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=30.34 E-value=1.5e+02 Score=23.62 Aligned_cols=50 Identities=16% Similarity=0.100 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~ 65 (157)
.+++.+..+|...|- |-.....+++|..+|++...|+.+-..-+.|.|..
T Consensus 227 ~L~~rer~vl~lr~~---~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~ 276 (289)
T PRK07500 227 TLNERELRIIRERRL---REDGATLEALGEELGISKERVRQIEARALEKLRRA 276 (289)
T ss_pred cCCHHHHHHHHHHhc---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 356666677766652 12334688999999999999999987766666653
No 211
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=30.34 E-value=1.2e+02 Score=21.82 Aligned_cols=37 Identities=11% Similarity=0.152 Sum_probs=29.2
Q ss_pred HHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHH
Q psy8301 17 SQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKI 53 (157)
Q Consensus 17 ~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vqv 53 (157)
.-+..|...=+...|.+....+.+|+.+|++...|.-
T Consensus 17 ~li~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v~~ 53 (148)
T TIGR01958 17 AIMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVYE 53 (148)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHHH
Confidence 3456666665667799999999999999999986653
No 212
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=30.32 E-value=53 Score=20.05 Aligned_cols=18 Identities=33% Similarity=0.711 Sum_probs=15.4
Q ss_pred HHHHHHHhCCChhHHHHH
Q psy8301 37 REMLGKEINLSPTQVKIW 54 (157)
Q Consensus 37 r~~La~~l~l~~~~VqvW 54 (157)
...||+.+|++...|.-|
T Consensus 12 ~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 12 QSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHh
Confidence 357899999999999999
No 213
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=30.21 E-value=1.6e+02 Score=23.37 Aligned_cols=31 Identities=13% Similarity=0.043 Sum_probs=24.2
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~ 65 (157)
..-.++|..+|+++..|+.....=|.+.|+.
T Consensus 159 ~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 189 (324)
T TIGR02960 159 WRAAETAELLGTSTASVNSALQRARATLDEV 189 (324)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 3467889999999999999987655555553
No 214
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=30.18 E-value=53 Score=21.82 Aligned_cols=20 Identities=10% Similarity=0.047 Sum_probs=17.8
Q ss_pred HHHHHHHhCCChhHHHHHHH
Q psy8301 37 REMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 37 r~~La~~l~l~~~~VqvWFq 56 (157)
..++|+.+|++...++-|..
T Consensus 3 i~eva~~~gvs~~tlR~ye~ 22 (103)
T cd01106 3 VGEVAKLTGVSVRTLHYYDE 22 (103)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999985
No 215
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=30.09 E-value=36 Score=20.82 Aligned_cols=22 Identities=14% Similarity=0.397 Sum_probs=16.7
Q ss_pred HHHHHHHHhCCChhHHH-HHHHH
Q psy8301 36 EREMLGKEINLSPTQVK-IWFQN 57 (157)
Q Consensus 36 ~r~~La~~l~l~~~~Vq-vWFqN 57 (157)
...+||+.+|++...|. .|.+.
T Consensus 14 ~~~~lA~~lgis~st~s~~~~~r 36 (66)
T PF07022_consen 14 SDKELAERLGISKSTLSNNWKKR 36 (66)
T ss_dssp SCHHHHCCTT--HHHHH-HHHHS
T ss_pred CHHHHHHHhCcCHHHhhHHHHhC
Confidence 45689999999999999 88853
No 216
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=30.02 E-value=1.8e+02 Score=22.54 Aligned_cols=31 Identities=19% Similarity=0.117 Sum_probs=24.5
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~ 65 (157)
..-+++|+.+|+++..|+++...-|.+-|..
T Consensus 133 ~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~ 163 (228)
T PRK06704 133 YSIADIAKVCSVSEGAVKASLFRSRNRLKTV 163 (228)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3467889999999999999987666665553
No 217
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=29.72 E-value=1.5e+02 Score=23.32 Aligned_cols=46 Identities=15% Similarity=-0.039 Sum_probs=35.9
Q ss_pred CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHH
Q psy8301 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQ 62 (157)
Q Consensus 11 Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~ 62 (157)
...+|+.+.++|.-..+- ..-.++|..+|+++..|+.+.+|=+.|.
T Consensus 188 ~~~LT~RE~evl~l~a~G------~s~~eIA~~L~IS~~TVk~hl~~i~~KL 233 (247)
T TIGR03020 188 AGLITAREAEILAWVRDG------KTNEEIAAILGISSLTVKNHLQHIFKKL 233 (247)
T ss_pred ccCCCHHHHHHHHHHHCC------CCHHHHHHHHCcCHHHHHHHHHHHHHHh
Confidence 346899999999865322 3567889999999999999998766653
No 218
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=29.59 E-value=2.2e+02 Score=20.70 Aligned_cols=33 Identities=15% Similarity=-0.027 Sum_probs=24.8
Q ss_pred HHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 34 PTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 34 ~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
...-+++|..+|+++..|+.....-|.+-|+..
T Consensus 127 g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l 159 (182)
T PRK12540 127 GFSYEDAAAICGCAVGTIKSRVNRARSKLSALL 159 (182)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 345678899999999999998875555555533
No 219
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=29.50 E-value=1.2e+02 Score=23.36 Aligned_cols=47 Identities=11% Similarity=-0.019 Sum_probs=36.6
Q ss_pred CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHH
Q psy8301 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63 (157)
Q Consensus 11 Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~r 63 (157)
...+++.+.++|.-... ...-.++|..+|++++.|+.+..|=+.|..
T Consensus 169 ~~~Lt~re~evl~~~a~------G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~ 215 (232)
T TIGR03541 169 AGVLSEREREVLAWTAL------GRRQADIAAILGISERTVENHLRSARRKLG 215 (232)
T ss_pred hccCCHHHHHHHHHHHC------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence 44689999999977532 246778899999999999999987766643
No 220
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=29.45 E-value=1.2e+02 Score=21.90 Aligned_cols=36 Identities=8% Similarity=0.102 Sum_probs=29.2
Q ss_pred HHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHH
Q psy8301 18 QVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKI 53 (157)
Q Consensus 18 q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vqv 53 (157)
-+.+|...=+...|.+......+|+.+|++...|.-
T Consensus 24 ll~~L~~vQ~~~g~ip~~~~~~iA~~l~v~~~~v~~ 59 (154)
T PRK07539 24 VIPALKIVQEQRGWVPDEAIEAVADYLGMPAIDVEE 59 (154)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHHH
Confidence 356666666677899999999999999999987654
No 221
>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=29.41 E-value=2.3e+02 Score=22.34 Aligned_cols=52 Identities=21% Similarity=0.199 Sum_probs=33.8
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 14 GIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 14 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
+++.+..+|.-.|... |-....-.++|..+|++...|+.+...-+.+.|+.-
T Consensus 223 Lp~~~R~Vl~l~ygL~-~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l 274 (285)
T TIGR02394 223 LNERQREVLARRFGLL-GYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRIL 274 (285)
T ss_pred CCHHHHHHHHHHhCCC-CCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4444555555444111 123346788999999999999999986666666533
No 222
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=29.30 E-value=55 Score=17.54 Aligned_cols=22 Identities=14% Similarity=0.255 Sum_probs=18.7
Q ss_pred HHHHHHHhCCChhHHHHHHHHH
Q psy8301 37 REMLGKEINLSPTQVKIWFQNR 58 (157)
Q Consensus 37 r~~La~~l~l~~~~VqvWFqNr 58 (157)
...+|..+|++...|..|..+.
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCC
Confidence 4578999999999999998754
No 223
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development. CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.
Probab=29.08 E-value=92 Score=20.82 Aligned_cols=29 Identities=7% Similarity=0.193 Sum_probs=22.6
Q ss_pred HHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 36 EREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 36 ~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
....+|..+|+++.+|--|..+-+.++-.
T Consensus 25 gq~~vA~~~Gv~eStISR~k~~~~~~~a~ 53 (91)
T PF05269_consen 25 GQKKVAEAMGVDESTISRWKNDFIEKMAM 53 (91)
T ss_dssp HHHHHHHHHTSSTTTHHHHHHHHHHHHHH
T ss_pred hhHHHHHHhCCCHHHHHHHHhhHHHHHHH
Confidence 45678999999999999997665555443
No 224
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=29.07 E-value=34 Score=25.33 Aligned_cols=42 Identities=12% Similarity=0.089 Sum_probs=32.9
Q ss_pred HHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHH
Q psy8301 19 VFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYK 61 (157)
Q Consensus 19 ~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k 61 (157)
+++..+.|....|-. ....++|+..|++...+-.+|.++-.-
T Consensus 17 l~aa~~lf~~~G~~~-~ti~~Ia~~agvsk~t~Y~~F~sKe~L 58 (213)
T PRK09975 17 IETAIAQFALRGVSN-TTLNDIADAANVTRGAIYWHFENKTQL 58 (213)
T ss_pred HHHHHHHHHHcCccc-CCHHHHHHHcCCCHHHHHHHcCCHHHH
Confidence 444555587777766 458889999999999999999987653
No 225
>PF10945 DUF2629: Protein of unknown function (DUF2629); InterPro: IPR024487 Some members in this family of proteins are annotated as YhjR however currently no function is known.
Probab=28.96 E-value=73 Score=18.34 Aligned_cols=29 Identities=21% Similarity=0.392 Sum_probs=23.3
Q ss_pred HHHHHHHHHHhhhcC--CCCHHHHHHHHHHh
Q psy8301 16 QSQVFELERKFQHIR--YLSPTEREMLGKEI 44 (157)
Q Consensus 16 ~~q~~~Le~~F~~~~--~p~~~~r~~La~~l 44 (157)
.+.+..|...|.... |-++...+.|...+
T Consensus 3 ~dDi~~L~~~fslp~~~Y~DIsr~e~l~~~~ 33 (44)
T PF10945_consen 3 QDDIAALSQAFSLPDINYIDISREERLNQAL 33 (44)
T ss_pred hhHHHHHHHHhCCCCccHHHHHHHHHHHHHH
Confidence 456889999998766 88999888887765
No 226
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=28.95 E-value=1.1e+02 Score=21.85 Aligned_cols=36 Identities=14% Similarity=0.206 Sum_probs=27.1
Q ss_pred HHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHH
Q psy8301 18 QVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKI 53 (157)
Q Consensus 18 q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vqv 53 (157)
-+..|...=+.-.|.+....+.+|..+|++..+|.-
T Consensus 15 ll~~L~~~Q~~~g~i~~~~~~~iA~~l~i~~~~v~~ 50 (145)
T PF01257_consen 15 LLPILHEVQEEYGYIPEEALEEIAEALGIPPAEVYG 50 (145)
T ss_dssp HHHHHHHHHHHHSS--HHHHHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHCCCHHHHHH
Confidence 466777776777899999999999999999987754
No 227
>PRK10651 transcriptional regulator NarL; Provisional
Probab=28.88 E-value=1.3e+02 Score=21.41 Aligned_cols=43 Identities=14% Similarity=0.136 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYK 61 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k 61 (157)
.+|+.+.++|+-..+. ..-.++|..+++++..|.+..++=+.|
T Consensus 155 ~Lt~rE~~vl~~l~~g------~~~~~ia~~l~is~~tV~~~~~~l~~K 197 (216)
T PRK10651 155 QLTPRERDILKLIAQG------LPNKMIARRLDITESTVKVHVKHMLKK 197 (216)
T ss_pred cCCHHHHHHHHHHHcC------CCHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 3899999888765432 245677999999999999999877666
No 228
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=28.78 E-value=1.2e+02 Score=17.40 Aligned_cols=39 Identities=15% Similarity=0.112 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHH
Q psy8301 14 GIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 14 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFq 56 (157)
+|..|..+|...++... ....+||..++++...|..+-.
T Consensus 1 lt~~q~~iL~~l~~~~~----~~~~~la~~~~~~~~~~t~~i~ 39 (59)
T PF01047_consen 1 LTPSQFRILRILYENGG----ITQSELAEKLGISRSTVTRIIK 39 (59)
T ss_dssp STHHHHHHHHHHHHHSS----EEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCHHHHHHHHHHHHcCC----CCHHHHHHHHCCChhHHHHHHH
Confidence 46788888888876544 3455899999999988777664
No 229
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=28.66 E-value=2.4e+02 Score=20.66 Aligned_cols=32 Identities=16% Similarity=0.139 Sum_probs=25.0
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr~~ 66 (157)
..-+++|..+|+++..|+++..--|.+.++.-
T Consensus 145 ~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (188)
T PRK12517 145 FSGEEIAEILDLNKNTVMTRLFRARNQLKEAL 176 (188)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999999876666655543
No 230
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=28.52 E-value=81 Score=17.78 Aligned_cols=21 Identities=19% Similarity=0.276 Sum_probs=18.8
Q ss_pred HHHHHHHHhCCChhHHHHHHH
Q psy8301 36 EREMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 36 ~r~~La~~l~l~~~~VqvWFq 56 (157)
....+|..+|++...|+.+|.
T Consensus 29 s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 29 SFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 577899999999999999985
No 231
>smart00595 MADF subfamily of SANT domain.
Probab=28.35 E-value=1.5e+02 Score=18.68 Aligned_cols=32 Identities=25% Similarity=0.272 Sum_probs=26.6
Q ss_pred HHHHHHhCCChhHHHHHHHHHHHHHHHHHhhh
Q psy8301 38 EMLGKEINLSPTQVKIWFQNRRYKQKRLQAMN 69 (157)
Q Consensus 38 ~~La~~l~l~~~~VqvWFqNrR~k~rr~~~~~ 69 (157)
.++|..+|.+...|+.-+.|=|...++.....
T Consensus 31 ~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~r~ 62 (89)
T smart00595 31 EEIAEELGLSVEECKKRWKNLRDRYRRELKRL 62 (89)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 45799999999999999999999988865443
No 232
>PF12200 DUF3597: Domain of unknown function (DUF3597); InterPro: IPR022016 This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 126 and 281 amino acids in length. The function of this domain is unknown. The structure of this domain has been found to contain five helices with a long flexible loop between helices one and two. ; PDB: 2GQB_A.
Probab=27.94 E-value=1.4e+02 Score=21.26 Aligned_cols=29 Identities=24% Similarity=0.477 Sum_probs=19.9
Q ss_pred CCHHHHHHHHHHhCCCh-----hHHHHHHHHHHH
Q psy8301 32 LSPTEREMLGKEINLSP-----TQVKIWFQNRRY 60 (157)
Q Consensus 32 p~~~~r~~La~~l~l~~-----~~VqvWFqNrR~ 60 (157)
.+...|.+||.++|++. ...-+|....-.
T Consensus 83 SSl~aRkeLA~eL~~~~~~~dsA~~NiwLhk~Vm 116 (127)
T PF12200_consen 83 SSLAARKELAKELGYTGDYNDSASMNIWLHKQVM 116 (127)
T ss_dssp -SHHHHHHHHHHHT---SS-HHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHH
Confidence 67889999999999876 467779975433
No 233
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=27.91 E-value=1.8e+02 Score=18.91 Aligned_cols=38 Identities=13% Similarity=0.093 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHH---hhhcCCCCHHHHHHHHHHhCCChhHHHH
Q psy8301 14 GIQSQVFELERK---FQHIRYLSPTEREMLGKEINLSPTQVKI 53 (157)
Q Consensus 14 ~t~~q~~~Le~~---F~~~~~p~~~~r~~La~~l~l~~~~Vqv 53 (157)
+|..|..+|... |....-|-. -+.||+.++++...|++
T Consensus 2 Lt~rq~~IL~alV~~Y~~~~~PVg--Sk~ia~~l~~s~aTIRN 42 (78)
T PF03444_consen 2 LTERQREILKALVELYIETGEPVG--SKTIAEELGRSPATIRN 42 (78)
T ss_pred CCHHHHHHHHHHHHHHHhcCCCcC--HHHHHHHHCCChHHHHH
Confidence 456676666655 777766654 35678889999887765
No 234
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=27.48 E-value=2.3e+02 Score=20.21 Aligned_cols=32 Identities=6% Similarity=0.072 Sum_probs=23.4
Q ss_pred CHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 33 SPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 33 ~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
....-.++|..+|++...|+.=...-|.+.|+
T Consensus 155 ~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~ 186 (189)
T TIGR02984 155 EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQ 186 (189)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 44567788999999999998866655555444
No 235
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=27.42 E-value=74 Score=16.79 Aligned_cols=22 Identities=14% Similarity=0.235 Sum_probs=18.3
Q ss_pred HHHHHHHhCCChhHHHHHHHHH
Q psy8301 37 REMLGKEINLSPTQVKIWFQNR 58 (157)
Q Consensus 37 r~~La~~l~l~~~~VqvWFqNr 58 (157)
...||..+|++...|..|-.++
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~ 34 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGK 34 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCC
Confidence 5678999999999998887554
No 236
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=27.36 E-value=64 Score=20.90 Aligned_cols=19 Identities=26% Similarity=0.447 Sum_probs=17.0
Q ss_pred HHHHHHHhCCChhHHHHHH
Q psy8301 37 REMLGKEINLSPTQVKIWF 55 (157)
Q Consensus 37 r~~La~~l~l~~~~VqvWF 55 (157)
..++|+.+|++...++-|-
T Consensus 4 i~evA~~~gvs~~tLR~ye 22 (88)
T cd01105 4 IGEVSKLTGVSPRQLRYWE 22 (88)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 5688999999999999994
No 237
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=27.05 E-value=1.4e+02 Score=22.15 Aligned_cols=35 Identities=14% Similarity=0.159 Sum_probs=27.5
Q ss_pred HHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHH
Q psy8301 19 VFELERKFQHIRYLSPTEREMLGKEINLSPTQVKI 53 (157)
Q Consensus 19 ~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vqv 53 (157)
+..|...=+...|.+....+.+|+.+|++...|.-
T Consensus 39 i~~L~~iQ~~~GyIp~e~~~~iA~~l~v~~a~V~g 73 (169)
T PRK07571 39 IEVLHKAQELFGYLERDLLLYVARQLKLPLSRVYG 73 (169)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHH
Confidence 44555555666799999999999999999976653
No 238
>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=26.80 E-value=2.4e+02 Score=21.37 Aligned_cols=30 Identities=13% Similarity=0.082 Sum_probs=22.2
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
...+++|..+|++...|..+...-+.+-|+
T Consensus 195 ~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~ 224 (227)
T TIGR02846 195 KTQREIAKILGISRSYVSRIEKRALMKLYK 224 (227)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 457889999999999998776544444443
No 239
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=26.74 E-value=78 Score=20.52 Aligned_cols=21 Identities=5% Similarity=0.208 Sum_probs=18.2
Q ss_pred HHHHHHHHhCCChhHHHHHHH
Q psy8301 36 EREMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 36 ~r~~La~~l~l~~~~VqvWFq 56 (157)
...++|+.+|++...|+-|-+
T Consensus 3 ~i~e~A~~~gvs~~tLr~ye~ 23 (91)
T cd04766 3 VISVAAELSGMHPQTLRLYER 23 (91)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 356899999999999999964
No 240
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=26.73 E-value=99 Score=20.86 Aligned_cols=26 Identities=19% Similarity=0.217 Sum_probs=16.5
Q ss_pred HHHHHHHHhCCChhHHHHHHHHHHHH
Q psy8301 36 EREMLGKEINLSPTQVKIWFQNRRYK 61 (157)
Q Consensus 36 ~r~~La~~l~l~~~~VqvWFqNrR~k 61 (157)
...+||.+.||+++.|..=.+..+.+
T Consensus 74 n~~eLA~kyglS~r~I~~Ii~~~~~~ 99 (108)
T PF08765_consen 74 NVRELARKYGLSERQIYRIIKRVRRR 99 (108)
T ss_dssp -HHHHHHHHT--HHHHHHHHHHHHH-
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 46799999999999876666544443
No 241
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=26.71 E-value=77 Score=20.98 Aligned_cols=20 Identities=15% Similarity=0.313 Sum_probs=17.7
Q ss_pred HHHHHHHhCCChhHHHHHHH
Q psy8301 37 REMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 37 r~~La~~l~l~~~~VqvWFq 56 (157)
..++|+.+|++...|+-|.+
T Consensus 3 I~e~a~~~gvs~~tLR~ye~ 22 (96)
T cd04774 3 VDEVAKRLGLTKRTLKYYEE 22 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999964
No 242
>PRK00215 LexA repressor; Validated
Probab=26.67 E-value=99 Score=23.09 Aligned_cols=41 Identities=20% Similarity=0.195 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHhh---hcCCCCHHHHHHHHHHhCC-ChhHHHHHHH
Q psy8301 14 GIQSQVFELERKFQ---HIRYLSPTEREMLGKEINL-SPTQVKIWFQ 56 (157)
Q Consensus 14 ~t~~q~~~Le~~F~---~~~~p~~~~r~~La~~l~l-~~~~VqvWFq 56 (157)
+|+.|...|+...+ ...++ ....+||..+|+ +...|..+.+
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~--~s~~ela~~~~~~~~~tv~~~l~ 46 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYP--PSRREIADALGLRSPSAVHEHLK 46 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCC--CCHHHHHHHhCCCChHHHHHHHH
Confidence 57888888877653 33333 346789999999 9888888775
No 243
>KOG0849|consensus
Probab=26.53 E-value=37 Score=28.31 Aligned_cols=37 Identities=22% Similarity=0.398 Sum_probs=32.0
Q ss_pred CCCCCCCCCcCccccCCCCCCCCcCCCCCCCCchhHHHhhhc
Q psy8301 106 GRKPETDFPAEEHNIFVPNFDQSDFLDNKWEDIDILDELHDQ 147 (157)
Q Consensus 106 ~~~~~~~~~~~q~~~~~~~f~~~~~s~s~~p~~~~~~~l~~~ 147 (157)
.+...+.+...|...+...|..++| |++.++|+|+.+
T Consensus 176 ~rr~rtsft~~Q~~~le~~f~rt~y-----P~i~~Re~La~~ 212 (354)
T KOG0849|consen 176 GRRNRTSFSPSQLEALEECFQRTPY-----PDIVGRETLAKE 212 (354)
T ss_pred ccccccccccchHHHHHHHhcCCCC-----CchhhHHHHhhh
Confidence 3344578889999999999999999 999999999875
No 244
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=26.37 E-value=57 Score=21.72 Aligned_cols=38 Identities=18% Similarity=0.200 Sum_probs=25.7
Q ss_pred CCHHHH----HHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHH
Q psy8301 14 GIQSQV----FELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWF 55 (157)
Q Consensus 14 ~t~~q~----~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWF 55 (157)
++.+|. ..|.+.|+... ...+.+|..||++...|+.=+
T Consensus 3 Ln~~Q~~~T~~ELq~nf~~~~----ls~~~ia~dL~~s~~~le~vL 44 (89)
T PF10078_consen 3 LNPEQRRATRQELQANFELSG----LSLEQIAADLGTSPEHLEQVL 44 (89)
T ss_pred CCHHHHHHHHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHH
Confidence 445554 45667777665 456778999999988776444
No 245
>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=26.32 E-value=1.3e+02 Score=23.03 Aligned_cols=30 Identities=7% Similarity=0.087 Sum_probs=23.7
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 35 TEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 35 ~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
...+++|..+|++...|+++...=+.+.|+
T Consensus 199 ~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~ 228 (234)
T TIGR02835 199 KTQKEVADMLGISQSYISRLEKRILKRLKK 228 (234)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 457788999999999999988755555555
No 246
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=25.64 E-value=1.1e+02 Score=20.40 Aligned_cols=34 Identities=21% Similarity=0.384 Sum_probs=22.8
Q ss_pred HHHHHHhhhc-CCCCHHHHHHHHHHhCCChhHHHH
Q psy8301 20 FELERKFQHI-RYLSPTEREMLGKEINLSPTQVKI 53 (157)
Q Consensus 20 ~~Le~~F~~~-~~p~~~~r~~La~~l~l~~~~Vqv 53 (157)
+.|..+|..- ..-....=..||..+||++..|..
T Consensus 4 ~~l~~~f~~i~~~V~~~~Wk~laR~LGLse~~I~~ 38 (96)
T cd08315 4 ETLRRSFDHFIKEVPFDSWNRLMRQLGLSENEIDV 38 (96)
T ss_pred hHHHHHHHHHHHHCCHHHHHHHHHHcCCCHHHHHH
Confidence 4567776543 233345566789999999987654
No 247
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=25.61 E-value=71 Score=21.12 Aligned_cols=20 Identities=20% Similarity=0.320 Sum_probs=17.6
Q ss_pred HHHHHHHhCCChhHHHHHHH
Q psy8301 37 REMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 37 r~~La~~l~l~~~~VqvWFq 56 (157)
..++|+.+|++.+.|+.|=+
T Consensus 3 I~eva~~~gvs~~tlR~Ye~ 22 (95)
T cd04780 3 MSELSKRSGVSVATIKYYLR 22 (95)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 56899999999999999975
No 248
>KOG0486|consensus
Probab=25.56 E-value=6.8 Score=32.15 Aligned_cols=36 Identities=17% Similarity=0.407 Sum_probs=32.2
Q ss_pred CCCCCCCCCCcCccccCCCCCCCCcCCCCCCCCchhHHHhh
Q psy8301 105 IGRKPETDFPAEEHNIFVPNFDQSDFLDNKWEDIDILDELH 145 (157)
Q Consensus 105 ~~~~~~~~~~~~q~~~~~~~f~~~~~s~s~~p~~~~~~~l~ 145 (157)
-.+...+.|...|+..+.-.|..|.| ||+.++||++
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNry-----pdMstrEEIa 146 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRY-----PDMSTREEIA 146 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccC-----CccchhhHHH
Confidence 44567789999999999999999999 9999999986
No 249
>PF13565 HTH_32: Homeodomain-like domain
Probab=25.55 E-value=1.7e+02 Score=17.85 Aligned_cols=39 Identities=18% Similarity=0.090 Sum_probs=25.9
Q ss_pred CHHHHHHHHHHhhhcCCCCHHHHHH-HHHHhCC----ChhHHHH
Q psy8301 15 IQSQVFELERKFQHIRYLSPTEREM-LGKEINL----SPTQVKI 53 (157)
Q Consensus 15 t~~q~~~Le~~F~~~~~p~~~~r~~-La~~l~l----~~~~Vqv 53 (157)
+.++...+.+.+..++..+..+... |....|+ +...|.-
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R 75 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYR 75 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHH
Confidence 6777688888888887666666555 5666563 5555443
No 250
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=25.12 E-value=1e+02 Score=22.20 Aligned_cols=45 Identities=18% Similarity=0.202 Sum_probs=29.8
Q ss_pred CHHHHHHHHHHhhhc-----CCCC-HHHHHHHHHHhCCChhHHHHHHHHHH
Q psy8301 15 IQSQVFELERKFQHI-----RYLS-PTEREMLGKEINLSPTQVKIWFQNRR 59 (157)
Q Consensus 15 t~~q~~~Le~~F~~~-----~~p~-~~~r~~La~~l~l~~~~VqvWFqNrR 59 (157)
.+.=....+..|+.- .+|+ .+...+++..+|+++..|..|....|
T Consensus 21 Cp~C~~~~e~~f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGR 71 (137)
T TIGR03826 21 CPSCYEEEEREFEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGR 71 (137)
T ss_pred CHHHhHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 333344445554322 2344 35678899999999999999997544
No 251
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=24.81 E-value=1.4e+02 Score=21.19 Aligned_cols=45 Identities=16% Similarity=0.099 Sum_probs=31.6
Q ss_pred CCCHHHHHHHHHH-hhhcCCCCHHHHHHHHHHhCCChhHHHHHHHH
Q psy8301 13 NGIQSQVFELERK-FQHIRYLSPTEREMLGKEINLSPTQVKIWFQN 57 (157)
Q Consensus 13 ~~t~~q~~~Le~~-F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqN 57 (157)
.||++|...|... -+..+-=...+..+|+..+|++-..|+..|.+
T Consensus 4 ~~T~eer~eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lre 49 (127)
T PF06163_consen 4 VFTPEEREELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRE 49 (127)
T ss_pred cCCHHHHHHHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHH
Confidence 5788888777655 22222233456788899999999999988864
No 252
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=24.53 E-value=1.3e+02 Score=20.34 Aligned_cols=40 Identities=3% Similarity=-0.022 Sum_probs=25.9
Q ss_pred CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHH
Q psy8301 12 TNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNR 58 (157)
Q Consensus 12 t~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNr 58 (157)
..++..++..+...... ...+||..+|++...|.-|-..+
T Consensus 63 ~~~~~~~i~~~r~~~gl-------tq~~lA~~lg~~~~tis~~e~g~ 102 (127)
T TIGR03830 63 GLLTPPEIRRIRKKLGL-------SQREAAELLGGGVNAFSRYERGE 102 (127)
T ss_pred CCcCHHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHCCC
Confidence 34555555555444322 34578999999999988887543
No 253
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=24.42 E-value=95 Score=17.99 Aligned_cols=38 Identities=18% Similarity=0.064 Sum_probs=26.8
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHH
Q psy8301 14 GIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKI 53 (157)
Q Consensus 14 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vqv 53 (157)
++..|..+|...+..... .....+||..++++...|..
T Consensus 3 lt~~q~~vL~~l~~~~~~--~~t~~~la~~l~~~~~~vs~ 40 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGE--ELTQSELAERLGISKSTVSR 40 (62)
T ss_dssp STHHHHHHHHHHHHSTTS--GEEHHHHHHHHTS-HHHHHH
T ss_pred cCHHHHHHHHHHHHCCCC--CcCHHHHHHHHCcCHHHHHH
Confidence 678888888777654432 23678899999999877654
No 254
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=24.19 E-value=84 Score=22.32 Aligned_cols=20 Identities=10% Similarity=0.109 Sum_probs=18.2
Q ss_pred HHHHHHHhCCChhHHHHHHH
Q psy8301 37 REMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 37 r~~La~~l~l~~~~VqvWFq 56 (157)
..++|+.+|++.+.++.|.+
T Consensus 3 I~e~a~~~gvs~~TLR~Ye~ 22 (134)
T cd04779 3 IGQLAHLAGVSKRTIDYYTN 22 (134)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 56889999999999999996
No 255
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=23.66 E-value=53 Score=19.82 Aligned_cols=42 Identities=14% Similarity=0.195 Sum_probs=29.1
Q ss_pred CHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHH
Q psy8301 15 IQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 15 t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFq 56 (157)
++..-+.|+..|....--.......||+.+|++...|..=++
T Consensus 3 t~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~ 44 (60)
T PF01325_consen 3 TESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLK 44 (60)
T ss_dssp SCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHH
T ss_pred CcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHH
Confidence 445556788887766444445677899999999988876553
No 256
>PRK13870 transcriptional regulator TraR; Provisional
Probab=23.54 E-value=3.4e+02 Score=20.87 Aligned_cols=45 Identities=7% Similarity=-0.088 Sum_probs=33.4
Q ss_pred CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHH
Q psy8301 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYK 61 (157)
Q Consensus 11 Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k 61 (157)
...+|+.++++|.=.=+ ...-.++|..||++++.|..-.+|=+.|
T Consensus 171 ~~~LT~RE~E~L~W~A~------GKT~~EIa~ILgISe~TV~~Hl~na~~K 215 (234)
T PRK13870 171 AAWLDPKEATYLRWIAV------GKTMEEIADVEGVKYNSVRVKLREAMKR 215 (234)
T ss_pred cCCCCHHHHHHHHHHHc------CCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 34678888877753322 1356678999999999999999887766
No 257
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=23.41 E-value=2.5e+02 Score=22.31 Aligned_cols=49 Identities=16% Similarity=0.052 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
.++..+..+|...|-.. ......++|..+|++..+|+-+-..-..|-|.
T Consensus 230 ~L~~rEr~VL~lry~~~---~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~ 278 (284)
T PRK06596 230 GLDERSRDIIEARWLDD---DKSTLQELAAEYGVSAERVRQIEKNAMKKLKA 278 (284)
T ss_pred cCCHHHHHHHHHHhcCC---CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35566667777766321 23457899999999999999887655555554
No 258
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=23.23 E-value=2.1e+02 Score=23.06 Aligned_cols=31 Identities=13% Similarity=0.023 Sum_probs=23.8
Q ss_pred HHHHHHHHHHhCCChhHHHHHHHHHHHHHHH
Q psy8301 34 PTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64 (157)
Q Consensus 34 ~~~r~~La~~l~l~~~~VqvWFqNrR~k~rr 64 (157)
...-.++|..+|+++..|+.....-|.+.|+
T Consensus 169 g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 169 GWSAAEVAELLDTSVAAVNSALQRARATLAE 199 (339)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhh
Confidence 3456789999999999999988655555444
No 259
>PRK06424 transcription factor; Provisional
Probab=23.16 E-value=49 Score=23.94 Aligned_cols=23 Identities=9% Similarity=-0.074 Sum_probs=19.9
Q ss_pred HHHHHHHhCCChhHHHHHHHHHH
Q psy8301 37 REMLGKEINLSPTQVKIWFQNRR 59 (157)
Q Consensus 37 r~~La~~l~l~~~~VqvWFqNrR 59 (157)
.++||..+|++...|.-|-..++
T Consensus 100 Q~eLA~~iGvs~stIskiE~G~~ 122 (144)
T PRK06424 100 QADLAAKIFERKNVIASIERGDL 122 (144)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 67899999999999999987654
No 260
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=23.01 E-value=2.5e+02 Score=19.05 Aligned_cols=44 Identities=16% Similarity=0.022 Sum_probs=31.2
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYK 61 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k 61 (157)
.+|..|...|+-.|..+ ..-.++|..+|++...|.-|.+.-+.+
T Consensus 17 LLT~kQ~~~l~lyy~eD-----lSlsEIAe~~~iSRqaV~d~ikr~~~~ 60 (101)
T PF04297_consen 17 LLTEKQREILELYYEED-----LSLSEIAEELGISRQAVYDSIKRAEKK 60 (101)
T ss_dssp GS-HHHHHHHHHHCTS--------HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred HCCHHHHHHHHHHHccC-----CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 47888999998776554 567889999999999999999754433
No 261
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=22.99 E-value=1.7e+02 Score=22.06 Aligned_cols=44 Identities=9% Similarity=0.002 Sum_probs=30.6
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQN 57 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqN 57 (157)
.+++.++..|......+ +-....-+++|..+++++..|+..+.+
T Consensus 158 ~Lt~re~~~l~~~i~~~-~~~g~s~~eIA~~l~iS~~Tv~~~~~~ 201 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAH-QDYEFSTDELANAVNISRVSCRKYLIW 201 (239)
T ss_pred CCCHHHHHHHHHHHHhC-CCCCcCHHHHHHHhCchHHHHHHHHHH
Confidence 36777666665554432 333346678999999999999998864
No 262
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=22.98 E-value=92 Score=23.67 Aligned_cols=42 Identities=5% Similarity=0.078 Sum_probs=33.9
Q ss_pred HHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHHH
Q psy8301 19 VFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQ 62 (157)
Q Consensus 19 ~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~ 62 (157)
+..-...|....|- .....+|+..|++...|-.+|.++..=.
T Consensus 19 l~aA~~lF~~~Gy~--~s~~~IA~~AGvsk~tiy~~F~sKe~L~ 60 (225)
T PRK11552 19 IAAALAQFGEYGLH--ATTRDIAAQAGQNIAAITYYFGSKEDLY 60 (225)
T ss_pred HHHHHHHHHHhCcc--CCHHHHHHHhCCCHHHHHHHcCCHHHHH
Confidence 33444558888877 6788999999999999999999986644
No 263
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=22.95 E-value=2.5e+02 Score=19.91 Aligned_cols=43 Identities=7% Similarity=0.050 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYK 61 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k 61 (157)
.+|..+.++|.-.+.-. ..+++|..++++++.|++.-.+=|.|
T Consensus 143 ~lt~~E~~vl~~l~~g~------~~~~I~~~l~~s~~tv~~~~~~l~~K 185 (204)
T PRK09958 143 SLSKQEISVMRYILDGK------DNNDIAEKMFISNKTVSTYKSRLMEK 185 (204)
T ss_pred cCCHHHHHHHHHHHcCC------CHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 58888888888777543 47889999999999999877665555
No 264
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=22.90 E-value=1e+02 Score=20.28 Aligned_cols=20 Identities=10% Similarity=0.024 Sum_probs=18.1
Q ss_pred HHHHHHHhCCChhHHHHHHH
Q psy8301 37 REMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 37 r~~La~~l~l~~~~VqvWFq 56 (157)
..++|+.+|++...++-|-+
T Consensus 3 i~eva~~~gvs~~tLRyye~ 22 (96)
T cd04768 3 IGEFAKLAGVSIRTLRHYDD 22 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 56899999999999999986
No 265
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=22.76 E-value=1.1e+02 Score=20.43 Aligned_cols=21 Identities=14% Similarity=0.382 Sum_probs=18.0
Q ss_pred HHHHHHHhCCChhHHHHHHHH
Q psy8301 37 REMLGKEINLSPTQVKIWFQN 57 (157)
Q Consensus 37 r~~La~~l~l~~~~VqvWFqN 57 (157)
..++|+.+|++...++-|-++
T Consensus 3 i~EvA~~~gVs~~tLR~ye~~ 23 (99)
T cd04765 3 IGEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred HHHHHHHHCcCHHHHHHHHHH
Confidence 467899999999999999753
No 266
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=22.57 E-value=1.1e+02 Score=22.20 Aligned_cols=40 Identities=13% Similarity=0.055 Sum_probs=32.1
Q ss_pred HHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHHHHHH
Q psy8301 20 FELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRY 60 (157)
Q Consensus 20 ~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~ 60 (157)
..-...|....|-. .....+|+..|++...+-.+|.++..
T Consensus 15 ~aA~~lf~e~G~~~-tSi~~Ia~~aGvsk~~lY~~F~sK~~ 54 (192)
T PRK14996 15 QAAMRVALAEGFAA-MTVRRIASEAQVAAGQVHHHFSSAGE 54 (192)
T ss_pred HHHHHHHHhcChhh-ccHHHHHHHhCCCcHHHHHHcCCHHH
Confidence 34445588888754 56888999999999999999998765
No 267
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=22.49 E-value=88 Score=17.18 Aligned_cols=13 Identities=23% Similarity=0.130 Sum_probs=11.0
Q ss_pred CCCHHHHHHHHHH
Q psy8301 13 NGIQSQVFELERK 25 (157)
Q Consensus 13 ~~t~~q~~~Le~~ 25 (157)
.||..|+..|+.-
T Consensus 2 ~FT~~Ql~~L~~Q 14 (37)
T PF08880_consen 2 PFTPAQLQELRAQ 14 (37)
T ss_pred CCCHHHHHHHHHH
Confidence 6899999999864
No 268
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=21.98 E-value=92 Score=20.73 Aligned_cols=21 Identities=5% Similarity=0.132 Sum_probs=18.2
Q ss_pred HHHHHHHHhCCChhHHHHHHH
Q psy8301 36 EREMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 36 ~r~~La~~l~l~~~~VqvWFq 56 (157)
...++|+.+|++.+.++-|-+
T Consensus 3 ~i~eva~~~gvs~~tLR~ye~ 23 (102)
T cd04775 3 TIGQMSRKFGVSRSTLLYYES 23 (102)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 357899999999999999875
No 269
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=21.93 E-value=2.1e+02 Score=19.88 Aligned_cols=38 Identities=13% Similarity=0.048 Sum_probs=27.0
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWF 55 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWF 55 (157)
.++.+|+..++....... -..++++.+|+++-.|+.=+
T Consensus 33 ~L~~E~~~Fi~~Fi~~rG-----nlKe~e~~lgiSYPTvR~rL 70 (113)
T PF09862_consen 33 RLSPEQLEFIKLFIKNRG-----NLKEMEKELGISYPTVRNRL 70 (113)
T ss_pred cCCHHHHHHHHHHHHhcC-----CHHHHHHHHCCCcHHHHHHH
Confidence 467888888876655433 46677889999988876544
No 270
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=21.78 E-value=53 Score=22.95 Aligned_cols=23 Identities=17% Similarity=0.446 Sum_probs=20.3
Q ss_pred HHHHHHHhCCChhHHHHHHHHHH
Q psy8301 37 REMLGKEINLSPTQVKIWFQNRR 59 (157)
Q Consensus 37 r~~La~~l~l~~~~VqvWFqNrR 59 (157)
..+||..+|++...|..|..+++
T Consensus 21 q~~lA~~~gvs~~~is~~E~g~~ 43 (135)
T PRK09706 21 QRSLAKAVKVSHVSISQWERDET 43 (135)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 57899999999999999997754
No 271
>KOG0850|consensus
Probab=21.51 E-value=18 Score=28.46 Aligned_cols=39 Identities=21% Similarity=0.252 Sum_probs=35.1
Q ss_pred CCCCCCCCCcCccccCCCCCCCCcCCCCCCCCchhHHHhhhccC
Q psy8301 106 GRKPETDFPAEEHNIFVPNFDQSDFLDNKWEDIDILDELHDQYV 149 (157)
Q Consensus 106 ~~~~~~~~~~~q~~~~~~~f~~~~~s~s~~p~~~~~~~l~~~~~ 149 (157)
.+.+.|-|++.|+-.|..-|++.+| .-+.+|-||++++.
T Consensus 122 ~RKPRTIYSS~QLqaL~rRFQkTQY-----LALPERAeLAAsLG 160 (245)
T KOG0850|consen 122 VRKPRTIYSSLQLQALNRRFQQTQY-----LALPERAELAASLG 160 (245)
T ss_pred ccCCcccccHHHHHHHHHHHhhcch-----hcCcHHHHHHHHhC
Confidence 5678899999999999999999999 99999999998764
No 272
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=21.37 E-value=1.1e+02 Score=20.09 Aligned_cols=20 Identities=10% Similarity=0.019 Sum_probs=17.9
Q ss_pred HHHHHHHhCCChhHHHHHHH
Q psy8301 37 REMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 37 r~~La~~l~l~~~~VqvWFq 56 (157)
..++|+.+|++...++-|.+
T Consensus 3 i~eva~~~gvs~~tlR~ye~ 22 (97)
T cd04782 3 TGEFAKLCGISKQTLFHYDK 22 (97)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 56899999999999999975
No 273
>KOG0494|consensus
Probab=21.36 E-value=14 Score=29.65 Aligned_cols=36 Identities=19% Similarity=0.286 Sum_probs=31.7
Q ss_pred CCCCCCCCcCccccCCCCCCCCcCCCCCCCCchhHHHhhhc
Q psy8301 107 RKPETDFPAEEHNIFVPNFDQSDFLDNKWEDIDILDELHDQ 147 (157)
Q Consensus 107 ~~~~~~~~~~q~~~~~~~f~~~~~s~s~~p~~~~~~~l~~~ 147 (157)
++..+.|+.+|...+..+|....| ||+-.+|-|+..
T Consensus 142 Rh~RTiFT~~Qle~LEkaFkeaHY-----PDv~Are~la~k 177 (332)
T KOG0494|consen 142 RHFRTIFTSYQLEELEKAFKEAHY-----PDVYAREMLADK 177 (332)
T ss_pred ccccchhhHHHHHHHHHHHhhccC-----ccHHHHHHHhhh
Confidence 455889999999999999999999 999999888753
No 274
>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=20.69 E-value=3.4e+02 Score=20.96 Aligned_cols=39 Identities=18% Similarity=0.153 Sum_probs=27.4
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhHHHHHHH
Q psy8301 13 NGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 13 ~~t~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFq 56 (157)
.+++.+..++...|-. .....++|..+|++...|...-.
T Consensus 206 ~L~~rer~vi~~~~~~-----~~t~~eIA~~lgis~~~V~~~~~ 244 (254)
T TIGR02850 206 RLNEREKMILNMRFFE-----GKTQMEVAEEIGISQAQVSRLEK 244 (254)
T ss_pred cCCHHHHHHHHHHHcC-----CCCHHHHHHHHCcCHHHHHHHHH
Confidence 3556666666666632 24678899999999998876554
No 275
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=20.65 E-value=1.1e+02 Score=21.33 Aligned_cols=21 Identities=19% Similarity=0.593 Sum_probs=18.5
Q ss_pred HHHHHHHhCCChhHHHHHHHH
Q psy8301 37 REMLGKEINLSPTQVKIWFQN 57 (157)
Q Consensus 37 r~~La~~l~l~~~~VqvWFqN 57 (157)
..++|+.+|++...++.|-+.
T Consensus 4 I~eVA~~~GVs~~TLR~wE~~ 24 (120)
T cd04767 4 IGVVAELLNIHPETLRIWERH 24 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 567899999999999999864
No 276
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=20.59 E-value=54 Score=22.74 Aligned_cols=24 Identities=8% Similarity=0.064 Sum_probs=21.2
Q ss_pred HHHHHHHHhCCChhHHHHHHHHHH
Q psy8301 36 EREMLGKEINLSPTQVKIWFQNRR 59 (157)
Q Consensus 36 ~r~~La~~l~l~~~~VqvWFqNrR 59 (157)
.+++||..+|++...|..|.++++
T Consensus 20 sq~eLA~~~Gis~~~is~iE~g~~ 43 (120)
T PRK13890 20 TKKELSERSGVSISFLSDLTTGKA 43 (120)
T ss_pred CHHHHHHHHCcCHHHHHHHHcCCC
Confidence 478899999999999999998764
No 277
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=20.56 E-value=1.2e+02 Score=20.47 Aligned_cols=20 Identities=15% Similarity=0.429 Sum_probs=17.7
Q ss_pred HHHHHHHhCCChhHHHHHHH
Q psy8301 37 REMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 37 r~~La~~l~l~~~~VqvWFq 56 (157)
..++|+.+|++...|+-|-+
T Consensus 3 i~eva~~~gvs~~tlR~ye~ 22 (108)
T cd04773 3 IGELAHLLGVPPSTLRHWEK 22 (108)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 56889999999999999964
No 278
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=20.48 E-value=1e+02 Score=21.48 Aligned_cols=21 Identities=14% Similarity=0.180 Sum_probs=18.9
Q ss_pred HHHHHHHHhCCChhHHHHHHH
Q psy8301 36 EREMLGKEINLSPTQVKIWFQ 56 (157)
Q Consensus 36 ~r~~La~~l~l~~~~VqvWFq 56 (157)
.+.+||..+|++.+.|+.|-+
T Consensus 5 tI~elA~~~gvs~~tlR~Ye~ 25 (120)
T TIGR02054 5 TISRLAEDAGVSVHVVRDYLL 25 (120)
T ss_pred cHHHHHHHHCcCHHHHHHHHH
Confidence 578899999999999999975
No 279
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=20.10 E-value=2.4e+02 Score=20.85 Aligned_cols=40 Identities=13% Similarity=0.110 Sum_probs=28.9
Q ss_pred CCHHHHHHHHHHh---hhcCCCCHHHHHHHHHHhCCC-hhHHHHHH
Q psy8301 14 GIQSQVFELERKF---QHIRYLSPTEREMLGKEINLS-PTQVKIWF 55 (157)
Q Consensus 14 ~t~~q~~~Le~~F---~~~~~p~~~~r~~La~~l~l~-~~~VqvWF 55 (157)
++..|..+|+... ..+.+| ....+||+.+|++ ...|....
T Consensus 4 lt~~q~~iL~~l~~~~~~~~~~--~~~~ela~~~~~~s~~tv~~~l 47 (199)
T TIGR00498 4 LTARQQEVLDLIRAHIESTGYP--PSIREIARAVGLRSPSAAEEHL 47 (199)
T ss_pred cCHHHHHHHHHHHHHHHhcCCC--CcHHHHHHHhCCCChHHHHHHH
Confidence 6788888887775 445565 3467899999998 77666544
Done!