Query psy16514
Match_columns 155
No_of_seqs 171 out of 1267
Neff 7.9
Searched_HMMs 46136
Date Fri Aug 16 23:16:26 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16514.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16514hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0484|consensus 99.8 1.7E-20 3.8E-25 126.4 7.3 68 11-78 14-81 (125)
2 KOG0850|consensus 99.8 1.8E-20 3.8E-25 142.4 7.9 68 7-74 115-182 (245)
3 KOG2251|consensus 99.8 5.6E-20 1.2E-24 139.0 9.7 72 5-76 28-99 (228)
4 KOG0488|consensus 99.8 1.5E-20 3.1E-25 151.3 6.6 71 5-75 163-233 (309)
5 KOG0842|consensus 99.8 1E-19 2.2E-24 144.9 7.4 69 10-78 149-217 (307)
6 KOG0843|consensus 99.8 2.2E-19 4.7E-24 131.9 7.6 65 12-76 100-164 (197)
7 KOG0489|consensus 99.8 2.3E-19 5E-24 141.7 7.2 65 12-76 157-221 (261)
8 KOG0487|consensus 99.8 8.4E-20 1.8E-24 145.4 4.6 68 9-76 230-297 (308)
9 KOG0848|consensus 99.7 1E-18 2.2E-23 135.4 4.8 70 9-78 194-263 (317)
10 KOG0492|consensus 99.7 2.9E-18 6.2E-23 128.6 6.6 70 9-78 139-208 (246)
11 PF00046 Homeobox: Homeobox do 99.7 5E-18 1.1E-22 104.4 5.9 57 15-71 1-57 (57)
12 KOG0494|consensus 99.7 6E-18 1.3E-22 130.7 5.5 65 11-75 137-202 (332)
13 KOG0485|consensus 99.7 1.1E-17 2.3E-22 126.4 4.8 65 12-76 102-166 (268)
14 KOG0493|consensus 99.7 9.4E-17 2E-21 124.2 4.5 58 15-72 247-304 (342)
15 KOG0491|consensus 99.6 8.2E-17 1.8E-21 116.9 2.4 68 13-80 99-166 (194)
16 smart00389 HOX Homeodomain. DN 99.6 8.4E-16 1.8E-20 93.8 5.4 55 16-70 2-56 (56)
17 cd00086 homeodomain Homeodomai 99.6 1.2E-15 2.6E-20 93.9 6.1 56 16-71 2-57 (59)
18 KOG3802|consensus 99.6 3.7E-16 8.1E-21 127.2 3.3 67 8-74 288-354 (398)
19 TIGR01565 homeo_ZF_HD homeobox 99.6 1.3E-15 2.9E-20 93.7 4.3 52 15-66 2-57 (58)
20 KOG0847|consensus 99.6 2E-15 4.4E-20 114.3 5.4 65 13-77 166-230 (288)
21 COG5576 Homeodomain-containing 99.6 3.4E-15 7.4E-20 109.3 6.0 64 12-75 49-112 (156)
22 KOG4577|consensus 99.6 4.1E-15 8.8E-20 116.6 5.0 62 13-74 166-227 (383)
23 KOG0483|consensus 99.5 3.8E-15 8.2E-20 112.7 4.2 57 17-73 53-109 (198)
24 KOG0486|consensus 99.5 5.5E-15 1.2E-19 117.0 5.1 66 12-77 110-175 (351)
25 KOG0844|consensus 99.4 3.5E-14 7.6E-19 112.2 2.6 61 15-75 182-242 (408)
26 KOG0490|consensus 99.3 1E-12 2.2E-17 101.3 3.3 64 11-74 57-120 (235)
27 KOG0775|consensus 99.3 2.9E-11 6.3E-16 94.4 8.5 52 20-71 182-233 (304)
28 KOG0849|consensus 99.2 1.9E-11 4.1E-16 100.5 5.1 67 8-74 170-236 (354)
29 KOG1168|consensus 99.2 1.1E-11 2.4E-16 97.6 1.9 61 14-74 309-369 (385)
30 KOG2252|consensus 98.9 7.7E-09 1.7E-13 87.7 8.1 57 13-69 419-475 (558)
31 KOG0774|consensus 98.8 1.7E-08 3.7E-13 78.7 7.0 59 15-73 189-250 (334)
32 PF05920 Homeobox_KN: Homeobox 98.8 6.3E-09 1.4E-13 59.4 2.7 34 35-68 7-40 (40)
33 KOG0490|consensus 98.4 3.9E-07 8.4E-12 70.1 4.6 64 11-74 150-213 (235)
34 KOG1146|consensus 97.8 1.7E-05 3.8E-10 73.4 3.6 61 14-74 903-963 (1406)
35 PF11569 Homez: Homeodomain le 97.3 0.00018 3.9E-09 43.7 2.4 42 26-67 10-51 (56)
36 KOG0773|consensus 97.1 0.00044 9.5E-09 56.6 3.7 59 14-72 239-300 (342)
37 KOG3623|consensus 97.1 0.0027 5.9E-08 56.4 8.3 49 26-74 568-616 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 96.4 0.01 2.3E-07 35.6 4.7 47 15-66 1-47 (53)
39 PF04545 Sigma70_r4: Sigma-70, 90.9 0.73 1.6E-05 26.7 4.5 46 20-70 4-49 (50)
40 PF01527 HTH_Tnp_1: Transposas 87.7 0.34 7.4E-06 30.4 1.5 44 16-64 2-46 (76)
41 cd06171 Sigma70_r4 Sigma70, re 86.6 1.6 3.5E-05 24.5 3.9 44 20-68 10-53 (55)
42 PF08281 Sigma70_r4_2: Sigma-7 84.3 2.7 5.8E-05 24.5 4.1 43 21-68 11-53 (54)
43 PRK03975 tfx putative transcri 82.7 4 8.6E-05 29.5 5.2 50 19-74 5-54 (141)
44 PF04967 HTH_10: HTH DNA bindi 81.2 4.3 9.4E-05 24.3 4.2 42 21-62 1-44 (53)
45 PF09607 BrkDBD: Brinker DNA-b 78.9 4.6 9.9E-05 24.7 3.8 45 18-63 3-47 (58)
46 PRK06759 RNA polymerase factor 77.6 5.5 0.00012 28.0 4.6 46 21-71 107-152 (154)
47 PRK09652 RNA polymerase sigma 76.8 6.2 0.00013 28.3 4.8 46 21-71 129-174 (182)
48 PRK00118 putative DNA-binding 76.4 10 0.00022 25.9 5.4 48 20-72 17-64 (104)
49 PRK09646 RNA polymerase sigma 76.2 7.2 0.00016 28.9 5.1 31 42-72 159-189 (194)
50 cd00569 HTH_Hin_like Helix-tur 75.5 7.3 0.00016 19.3 3.8 38 20-62 5-42 (42)
51 PRK09413 IS2 repressor TnpA; R 74.9 6.1 0.00013 27.4 4.1 42 18-63 10-51 (121)
52 COG3413 Predicted DNA binding 74.3 5.8 0.00013 30.2 4.2 39 20-58 155-195 (215)
53 PF10668 Phage_terminase: Phag 73.9 2.1 4.6E-05 26.4 1.4 21 43-63 24-44 (60)
54 PRK12526 RNA polymerase sigma 73.7 8.3 0.00018 28.9 4.9 31 42-72 170-200 (206)
55 PF00196 GerE: Bacterial regul 73.7 7.5 0.00016 23.0 3.8 47 20-72 3-49 (58)
56 PRK11924 RNA polymerase sigma 73.7 11 0.00024 26.9 5.4 31 42-72 142-172 (179)
57 PRK09644 RNA polymerase sigma 73.4 11 0.00025 26.9 5.4 30 43-72 126-155 (165)
58 TIGR02937 sigma70-ECF RNA poly 72.6 8.6 0.00019 26.2 4.5 46 21-71 111-156 (158)
59 PF13936 HTH_38: Helix-turn-he 71.6 4.5 9.8E-05 22.9 2.4 40 19-63 3-42 (44)
60 TIGR02985 Sig70_bacteroi1 RNA 71.3 10 0.00023 26.4 4.8 30 42-71 130-159 (161)
61 PRK09642 RNA polymerase sigma 71.1 11 0.00025 26.7 4.9 30 43-72 124-153 (160)
62 TIGR02989 Sig-70_gvs1 RNA poly 70.8 10 0.00023 26.7 4.7 31 41-71 127-157 (159)
63 PRK12519 RNA polymerase sigma 70.7 7.9 0.00017 28.5 4.1 33 40-72 156-188 (194)
64 PRK10072 putative transcriptio 70.2 6.6 0.00014 26.4 3.2 40 21-67 33-72 (96)
65 PRK04217 hypothetical protein; 69.9 14 0.00031 25.5 4.9 48 19-71 41-88 (110)
66 PRK06930 positive control sigm 69.9 13 0.00029 27.4 5.2 49 20-73 114-162 (170)
67 KOG1146|consensus 69.5 6.1 0.00013 38.1 3.9 62 12-73 703-764 (1406)
68 PRK12514 RNA polymerase sigma 69.5 14 0.0003 26.8 5.2 29 43-71 147-175 (179)
69 PRK12512 RNA polymerase sigma 69.4 12 0.00027 27.2 4.9 30 43-72 149-178 (184)
70 PRK12541 RNA polymerase sigma 69.2 10 0.00022 27.0 4.3 30 43-72 130-159 (161)
71 PRK09648 RNA polymerase sigma 68.6 13 0.00028 27.2 4.9 30 42-71 156-185 (189)
72 TIGR02948 SigW_bacill RNA poly 68.3 11 0.00024 27.3 4.5 31 41-71 152-182 (187)
73 PRK12530 RNA polymerase sigma 68.2 18 0.0004 26.6 5.7 30 43-72 152-181 (189)
74 TIGR03879 near_KaiC_dom probab 67.7 2.4 5.3E-05 27.1 0.7 35 30-64 21-55 (73)
75 TIGR02999 Sig-70_X6 RNA polyme 67.6 14 0.0003 26.8 4.9 29 43-71 152-180 (183)
76 TIGR02939 RpoE_Sigma70 RNA pol 67.3 10 0.00023 27.6 4.2 34 39-72 152-185 (190)
77 PRK12515 RNA polymerase sigma 66.7 19 0.0004 26.4 5.4 30 43-72 149-178 (189)
78 PRK05602 RNA polymerase sigma 66.7 13 0.00029 27.1 4.6 30 43-72 146-175 (186)
79 PRK09639 RNA polymerase sigma 66.2 14 0.00031 26.2 4.7 31 42-72 128-158 (166)
80 KOG0773|consensus 66.0 7.1 0.00015 31.9 3.3 47 26-72 109-155 (342)
81 TIGR02959 SigZ RNA polymerase 65.1 16 0.00035 26.4 4.8 30 43-72 118-147 (170)
82 PRK12537 RNA polymerase sigma 64.6 19 0.00042 26.2 5.2 29 43-71 151-179 (182)
83 PF13518 HTH_28: Helix-turn-he 64.6 5.9 0.00013 22.6 1.9 23 43-65 14-36 (52)
84 PRK09637 RNA polymerase sigma 64.2 16 0.00035 26.8 4.7 30 42-71 123-152 (181)
85 smart00421 HTH_LUXR helix_turn 64.0 23 0.0005 19.8 4.5 45 20-70 3-47 (58)
86 TIGR02952 Sig70_famx2 RNA poly 63.8 18 0.0004 25.6 4.8 30 42-71 139-168 (170)
87 PRK09047 RNA polymerase factor 63.6 20 0.00043 25.3 4.9 29 43-71 124-152 (161)
88 TIGR02954 Sig70_famx3 RNA poly 63.3 19 0.00042 25.7 4.9 29 43-71 137-165 (169)
89 cd04761 HTH_MerR-SF Helix-Turn 63.2 5.8 0.00013 22.3 1.7 21 44-64 3-23 (49)
90 TIGR02983 SigE-fam_strep RNA p 63.2 18 0.00039 25.6 4.7 29 43-71 128-156 (162)
91 KOG3755|consensus 62.8 3.5 7.5E-05 36.6 0.9 59 15-73 692-758 (769)
92 PRK12524 RNA polymerase sigma 62.2 20 0.00043 26.5 4.9 30 43-72 154-183 (196)
93 PRK12546 RNA polymerase sigma 61.3 19 0.00041 26.7 4.6 30 43-72 131-160 (188)
94 PF13443 HTH_26: Cro/C1-type H 61.1 5.9 0.00013 23.7 1.5 28 43-70 12-39 (63)
95 TIGR02943 Sig70_famx1 RNA poly 60.6 32 0.0007 25.3 5.8 33 42-74 148-180 (188)
96 PRK12547 RNA polymerase sigma 60.4 23 0.0005 25.3 4.9 29 43-71 130-158 (164)
97 PRK12532 RNA polymerase sigma 60.2 33 0.00072 25.2 5.8 31 43-73 154-184 (195)
98 PRK06811 RNA polymerase factor 60.2 20 0.00044 26.3 4.6 30 43-72 149-178 (189)
99 TIGR03001 Sig-70_gmx1 RNA poly 60.0 41 0.00089 26.2 6.5 40 43-82 179-218 (244)
100 PRK06986 fliA flagellar biosyn 59.7 20 0.00044 27.4 4.7 31 42-72 201-231 (236)
101 PRK12543 RNA polymerase sigma 59.5 33 0.00071 24.9 5.6 32 43-74 135-166 (179)
102 PRK07037 extracytoplasmic-func 59.4 26 0.00055 24.8 4.9 29 43-71 127-155 (163)
103 PF02796 HTH_7: Helix-turn-hel 59.1 14 0.00031 20.8 2.8 38 20-62 5-42 (45)
104 PRK12520 RNA polymerase sigma 58.9 34 0.00073 25.1 5.6 34 43-76 149-182 (191)
105 PF13384 HTH_23: Homeodomain-l 58.6 7.3 0.00016 22.1 1.6 23 42-64 18-40 (50)
106 cd06170 LuxR_C_like C-terminal 58.6 23 0.00049 20.0 3.8 42 22-69 2-43 (57)
107 PF01056 Myc_N: Myc amino-term 58.6 3.2 7E-05 34.2 0.0 11 144-154 236-246 (329)
108 PRK12538 RNA polymerase sigma 58.0 20 0.00044 27.6 4.4 30 43-72 189-218 (233)
109 PRK09649 RNA polymerase sigma 58.0 23 0.00049 26.0 4.5 29 43-71 148-176 (185)
110 PRK09645 RNA polymerase sigma 58.0 27 0.00059 25.0 4.9 29 43-71 136-164 (173)
111 PRK12523 RNA polymerase sigma 58.0 28 0.0006 25.0 4.9 29 43-71 137-165 (172)
112 PRK12536 RNA polymerase sigma 57.7 27 0.00059 25.4 4.9 29 43-71 147-175 (181)
113 PRK13919 putative RNA polymera 57.6 29 0.00063 25.2 5.0 29 43-71 153-181 (186)
114 PF00424 REV: REV protein (ant 57.2 19 0.00041 24.0 3.5 36 26-75 14-49 (91)
115 PRK12529 RNA polymerase sigma 56.6 29 0.00064 25.2 4.9 29 43-71 145-173 (178)
116 PRK09480 slmA division inhibit 56.4 14 0.00029 26.9 3.1 41 26-67 16-56 (194)
117 TIGR02980 SigBFG RNA polymeras 55.6 29 0.00063 26.3 4.9 47 20-71 178-224 (227)
118 PRK08583 RNA polymerase sigma 55.0 29 0.00063 26.9 4.9 46 21-71 206-251 (257)
119 PRK12545 RNA polymerase sigma 55.0 31 0.00068 25.6 4.9 30 43-72 157-186 (201)
120 PRK09647 RNA polymerase sigma 54.7 30 0.00064 26.0 4.8 30 43-72 156-185 (203)
121 PRK12516 RNA polymerase sigma 54.5 42 0.00091 24.7 5.5 30 43-72 134-163 (187)
122 PRK12542 RNA polymerase sigma 54.5 29 0.00064 25.2 4.6 29 43-71 140-168 (185)
123 PRK12533 RNA polymerase sigma 54.5 27 0.00059 26.6 4.6 30 43-72 152-181 (216)
124 TIGR00721 tfx DNA-binding prot 54.4 45 0.00098 23.9 5.3 48 18-71 4-51 (137)
125 TIGR02479 FliA_WhiG RNA polyme 54.4 31 0.00066 26.1 4.8 46 21-71 176-221 (224)
126 PRK12535 RNA polymerase sigma 54.3 31 0.00066 25.7 4.7 30 43-72 151-180 (196)
127 PRK12544 RNA polymerase sigma 54.1 53 0.0012 24.7 6.1 32 43-74 166-197 (206)
128 PRK12511 RNA polymerase sigma 53.1 33 0.00072 25.2 4.7 29 43-71 129-157 (182)
129 PF13551 HTH_29: Winged helix- 53.1 42 0.0009 22.0 4.9 46 18-63 55-109 (112)
130 PRK12531 RNA polymerase sigma 52.8 39 0.00085 24.8 5.1 30 43-72 159-188 (194)
131 PF06056 Terminase_5: Putative 52.7 4.7 0.0001 24.5 0.0 21 43-63 15-35 (58)
132 TIGR02941 Sigma_B RNA polymera 52.6 32 0.00069 26.7 4.8 46 21-71 206-251 (255)
133 COG4367 Uncharacterized protei 52.6 19 0.00042 23.9 2.9 39 21-59 3-41 (97)
134 TIGR02947 SigH_actino RNA poly 52.1 17 0.00037 26.7 3.0 34 39-72 145-178 (193)
135 PRK12528 RNA polymerase sigma 51.4 38 0.00082 23.9 4.7 28 43-70 131-158 (161)
136 PRK12539 RNA polymerase sigma 51.1 40 0.00086 24.5 4.9 30 42-71 148-177 (184)
137 PRK08301 sporulation sigma fac 50.7 36 0.00078 25.9 4.7 32 41-72 198-229 (234)
138 PRK09641 RNA polymerase sigma 50.3 37 0.00081 24.5 4.6 31 41-71 152-182 (187)
139 PRK09651 RNA polymerase sigma 50.1 31 0.00066 24.9 4.1 30 42-71 136-165 (172)
140 PRK11923 algU RNA polymerase s 50.0 37 0.00081 24.8 4.6 32 41-72 154-185 (193)
141 cd00131 PAX Paired Box domain 49.7 74 0.0016 22.2 5.8 45 20-64 75-126 (128)
142 cd04762 HTH_MerR-trunc Helix-T 49.6 14 0.0003 20.2 1.7 23 44-66 3-25 (49)
143 PRK10403 transcriptional regul 49.5 23 0.0005 25.3 3.4 51 20-76 153-203 (215)
144 PRK12522 RNA polymerase sigma 49.4 42 0.00092 24.0 4.7 29 43-71 137-165 (173)
145 PRK07408 RNA polymerase sigma 49.3 40 0.00087 26.3 4.9 47 21-72 204-250 (256)
146 PF08280 HTH_Mga: M protein tr 48.7 24 0.00051 21.1 2.8 36 24-63 6-41 (59)
147 PF13411 MerR_1: MerR HTH fami 48.6 12 0.00026 22.6 1.5 20 44-63 3-22 (69)
148 PRK05657 RNA polymerase sigma 48.3 36 0.00077 27.8 4.5 52 20-72 262-313 (325)
149 PRK12518 RNA polymerase sigma 48.3 20 0.00043 25.8 2.8 35 38-72 133-167 (175)
150 PF00376 MerR: MerR family reg 48.2 13 0.00029 20.4 1.4 20 44-63 2-21 (38)
151 PRK07670 RNA polymerase sigma 48.1 43 0.00093 25.9 4.8 30 42-71 218-247 (251)
152 PRK12513 RNA polymerase sigma 47.8 18 0.00038 26.6 2.5 35 38-72 152-186 (194)
153 PRK09415 RNA polymerase factor 47.7 38 0.00083 24.6 4.3 29 43-71 145-173 (179)
154 COG2944 Predicted transcriptio 47.5 31 0.00067 23.6 3.4 41 20-67 43-83 (104)
155 PRK12534 RNA polymerase sigma 47.5 54 0.0012 23.8 5.1 30 42-71 154-183 (187)
156 TIGR02957 SigX4 RNA polymerase 47.1 41 0.00089 26.6 4.7 28 44-71 127-154 (281)
157 TIGR02393 RpoD_Cterm RNA polym 46.7 59 0.0013 24.9 5.4 53 20-73 176-228 (238)
158 TIGR03541 reg_near_HchA LuxR f 46.4 31 0.00068 26.5 3.8 53 19-77 170-222 (232)
159 PF01381 HTH_3: Helix-turn-hel 46.3 13 0.00028 21.4 1.3 24 43-66 11-34 (55)
160 PRK12525 RNA polymerase sigma 46.0 51 0.0011 23.6 4.7 29 43-71 136-164 (168)
161 PRK07122 RNA polymerase sigma 45.9 45 0.00098 26.2 4.7 46 21-71 216-261 (264)
162 PRK06288 RNA polymerase sigma 45.9 48 0.001 25.9 4.9 47 21-72 213-259 (268)
163 COG2963 Transposase and inacti 45.6 46 0.00099 22.5 4.2 42 18-63 5-47 (116)
164 cd04763 HTH_MlrA-like Helix-Tu 45.5 16 0.00035 22.2 1.7 20 44-63 3-22 (68)
165 cd04764 HTH_MlrA-like_sg1 Heli 45.3 17 0.00037 22.0 1.8 21 44-64 3-23 (67)
166 cd01392 HTH_LacI Helix-turn-he 45.1 11 0.00023 21.5 0.8 21 46-66 2-22 (52)
167 PRK12517 RNA polymerase sigma 45.1 1.1E+02 0.0024 22.4 6.5 33 43-75 146-178 (188)
168 PRK12540 RNA polymerase sigma 44.9 55 0.0012 23.9 4.8 30 43-72 129-158 (182)
169 PF01710 HTH_Tnp_IS630: Transp 44.8 39 0.00084 23.2 3.7 37 22-63 4-40 (119)
170 PRK08295 RNA polymerase factor 44.6 53 0.0011 24.2 4.7 33 39-71 168-200 (208)
171 PRK09636 RNA polymerase sigma 44.4 48 0.001 26.3 4.7 28 44-71 134-161 (293)
172 PF07638 Sigma70_ECF: ECF sigm 44.2 58 0.0012 24.0 4.8 30 42-71 152-181 (185)
173 PRK12527 RNA polymerase sigma 42.9 69 0.0015 22.5 4.9 29 43-71 123-151 (159)
174 cd01104 HTH_MlrA-CarA Helix-Tu 42.8 19 0.00041 21.7 1.7 20 44-63 3-22 (68)
175 TIGR02950 SigM_subfam RNA poly 42.6 19 0.00042 25.1 2.0 34 38-71 118-151 (154)
176 TIGR03020 EpsA transcriptional 41.7 60 0.0013 25.5 4.8 54 18-77 188-241 (247)
177 TIGR02885 spore_sigF RNA polym 41.5 62 0.0014 24.5 4.8 46 20-70 183-228 (231)
178 PRK05572 sporulation sigma fac 41.5 63 0.0014 25.0 4.8 47 20-71 202-248 (252)
179 cd00093 HTH_XRE Helix-turn-hel 41.3 18 0.00039 19.6 1.4 23 44-66 15-37 (58)
180 TIGR02960 SigX5 RNA polymerase 41.2 53 0.0012 26.2 4.5 29 43-71 160-188 (324)
181 PRK15369 two component system 40.8 56 0.0012 23.0 4.2 46 20-71 149-194 (211)
182 KOG0772|consensus 40.8 53 0.0011 29.0 4.5 9 119-127 103-111 (641)
183 smart00027 EH Eps15 homology d 40.7 62 0.0013 21.0 4.1 44 20-63 3-51 (96)
184 TIGR02984 Sig-70_plancto1 RNA 40.3 72 0.0016 22.9 4.8 30 42-71 157-186 (189)
185 PRK08215 sporulation sigma fac 40.2 64 0.0014 25.1 4.7 47 20-71 209-255 (258)
186 TIGR03070 couple_hipB transcri 39.9 19 0.0004 20.6 1.3 23 44-66 18-40 (58)
187 smart00595 MADF subfamily of S 39.8 59 0.0013 20.6 3.8 34 45-78 31-64 (89)
188 PRK10360 DNA-binding transcrip 39.6 43 0.00093 23.8 3.5 46 20-71 137-182 (196)
189 PRK05911 RNA polymerase sigma 39.4 73 0.0016 24.9 4.9 47 21-72 206-252 (257)
190 PRK10100 DNA-binding transcrip 39.0 64 0.0014 24.6 4.5 51 20-76 155-205 (216)
191 TIGR02859 spore_sigH RNA polym 38.9 19 0.00042 26.3 1.5 34 38-71 162-195 (198)
192 PRK09643 RNA polymerase sigma 38.9 78 0.0017 23.2 4.8 29 43-71 152-180 (192)
193 TIGR02392 rpoH_proteo alternat 38.6 63 0.0014 25.4 4.5 49 20-71 218-266 (270)
194 PF13730 HTH_36: Helix-turn-he 38.4 39 0.00083 19.4 2.5 43 21-64 3-48 (55)
195 PRK11922 RNA polymerase sigma 38.4 37 0.0008 25.9 3.1 36 38-73 162-197 (231)
196 PF14549 P22_Cro: DNA-binding 37.6 50 0.0011 20.1 2.9 36 44-81 12-47 (60)
197 PRK10651 transcriptional regul 37.4 64 0.0014 23.0 4.1 51 20-76 155-205 (216)
198 PHA02955 hypothetical protein; 37.4 45 0.00098 25.8 3.3 46 23-68 60-106 (213)
199 PRK11552 putative DNA-binding 36.3 40 0.00086 25.6 2.9 43 26-70 19-61 (225)
200 PRK06704 RNA polymerase factor 35.7 72 0.0016 24.7 4.3 29 43-71 134-162 (228)
201 PRK09640 RNA polymerase sigma 35.3 39 0.00085 24.7 2.7 33 40-72 149-181 (188)
202 PRK05803 sporulation sigma fac 34.9 89 0.0019 23.8 4.7 30 42-71 196-225 (233)
203 KOG3623|consensus 34.7 27 0.00058 32.1 1.9 54 18-71 630-683 (1007)
204 PRK14996 TetR family transcrip 34.7 55 0.0012 23.8 3.4 41 26-67 14-54 (192)
205 TIGR02607 antidote_HigA addict 34.6 25 0.00055 21.7 1.4 23 44-66 21-43 (78)
206 TIGR01764 excise DNA binding d 33.8 30 0.00065 18.9 1.5 23 44-66 4-26 (49)
207 PRK09390 fixJ response regulat 33.5 84 0.0018 21.9 4.2 50 21-76 142-191 (202)
208 PF13565 HTH_32: Homeodomain-l 33.5 1.2E+02 0.0025 18.6 6.1 32 22-53 32-64 (77)
209 PRK09935 transcriptional regul 33.4 58 0.0013 23.2 3.3 49 20-74 149-197 (210)
210 PHA01976 helix-turn-helix prot 33.1 29 0.00062 20.8 1.4 24 43-66 17-40 (67)
211 PRK07500 rpoH2 RNA polymerase 32.8 82 0.0018 25.1 4.3 49 20-71 227-275 (289)
212 PF13412 HTH_24: Winged helix- 32.6 84 0.0018 17.4 3.3 37 23-63 3-39 (48)
213 PRK08241 RNA polymerase factor 32.5 72 0.0016 25.7 4.0 29 43-71 171-199 (339)
214 PRK11511 DNA-binding transcrip 32.2 50 0.0011 22.8 2.7 28 38-65 22-49 (127)
215 PF08279 HTH_11: HTH domain; 31.8 39 0.00086 19.4 1.8 35 26-63 3-37 (55)
216 PRK09638 RNA polymerase sigma 31.5 41 0.00089 24.1 2.2 33 39-71 140-172 (176)
217 PF04297 UPF0122: Putative hel 31.4 1.3E+02 0.0028 20.4 4.5 46 20-70 17-62 (101)
218 TIGR02394 rpoS_proteo RNA poly 31.3 1.1E+02 0.0025 24.1 4.9 51 21-72 223-273 (285)
219 PF04936 DUF658: Protein of un 30.7 24 0.00051 26.3 0.8 32 42-73 15-46 (186)
220 smart00422 HTH_MERR helix_turn 30.5 35 0.00077 20.5 1.5 20 44-63 3-22 (70)
221 TIGR02846 spore_sigmaK RNA pol 30.3 1.2E+02 0.0026 23.0 4.7 30 42-71 195-224 (227)
222 cd01106 HTH_TipAL-Mta Helix-Tu 30.0 39 0.00085 22.4 1.8 21 44-64 3-23 (103)
223 smart00530 HTH_XRE Helix-turn- 29.6 35 0.00077 18.2 1.3 23 44-66 13-35 (56)
224 PF05703 Auxin_canalis: Auxin 29.6 1.1E+02 0.0024 24.2 4.4 18 54-71 99-116 (242)
225 TIGR02835 spore_sigmaE RNA pol 29.5 1.2E+02 0.0026 23.1 4.6 30 42-71 199-228 (234)
226 TIGR03830 CxxCG_CxxCG_HTH puta 29.5 66 0.0014 21.8 2.9 23 44-66 81-103 (127)
227 PF12824 MRP-L20: Mitochondria 29.4 1.9E+02 0.0042 21.3 5.5 47 18-66 83-129 (164)
228 PF01726 LexA_DNA_bind: LexA D 28.5 94 0.002 19.1 3.2 40 20-61 3-46 (65)
229 PF12728 HTH_17: Helix-turn-he 28.5 40 0.00087 19.1 1.4 23 44-66 4-26 (51)
230 PRK09635 sigI RNA polymerase s 28.0 1.1E+02 0.0025 24.3 4.4 28 44-71 137-164 (290)
231 PF01047 MarR: MarR family; I 27.5 91 0.002 17.9 3.0 39 21-63 1-39 (59)
232 PRK09706 transcriptional repre 26.6 40 0.00086 23.5 1.4 24 44-67 21-44 (135)
233 COG1595 RpoE DNA-directed RNA 26.4 68 0.0015 23.3 2.7 30 43-72 145-174 (182)
234 PRK09726 antitoxin HipB; Provi 26.2 1.3E+02 0.0028 19.3 3.7 24 43-66 27-50 (88)
235 PF09862 DUF2089: Protein of u 26.1 1.3E+02 0.0028 20.9 3.8 38 20-62 33-70 (113)
236 cd04774 HTH_YfmP Helix-Turn-He 25.9 50 0.0011 21.8 1.7 21 44-64 3-23 (96)
237 PRK06596 RNA polymerase factor 25.9 1.3E+02 0.0029 23.8 4.4 48 21-71 231-278 (284)
238 PF13542 HTH_Tnp_ISL3: Helix-t 25.7 1.3E+02 0.0029 16.8 3.5 21 43-63 29-49 (52)
239 PF12802 MarR_2: MarR family; 25.4 83 0.0018 18.2 2.5 37 21-59 3-39 (62)
240 cd01105 HTH_GlnR-like Helix-Tu 25.2 48 0.001 21.4 1.5 19 44-62 4-22 (88)
241 PRK06424 transcription factor; 24.7 72 0.0016 23.0 2.4 24 44-67 100-123 (144)
242 PRK10188 DNA-binding transcrip 24.6 1.6E+02 0.0035 22.8 4.6 51 20-76 179-229 (240)
243 PRK07598 RNA polymerase sigma 24.5 2.2E+02 0.0047 24.4 5.6 53 20-73 350-402 (415)
244 cd04779 HTH_MerR-like_sg4 Heli 24.4 54 0.0012 23.3 1.7 21 44-64 3-23 (134)
245 PF03457 HA: Helicase associat 24.4 89 0.0019 18.9 2.6 43 25-73 11-53 (68)
246 PF05269 Phage_CII: Bacterioph 24.4 1E+02 0.0022 20.6 2.9 27 43-69 25-51 (91)
247 PTZ00183 centrin; Provisional 24.3 2.4E+02 0.0052 19.3 5.2 40 15-54 5-49 (158)
248 PRK10430 DNA-binding transcrip 24.3 1.1E+02 0.0024 23.0 3.6 45 20-65 158-202 (239)
249 cd04766 HTH_HspR Helix-Turn-He 24.1 57 0.0012 21.1 1.7 20 44-63 4-23 (91)
250 PRK15008 HTH-type transcriptio 24.0 1.1E+02 0.0023 22.8 3.4 45 26-71 24-68 (212)
251 PF08765 Mor: Mor transcriptio 23.9 64 0.0014 21.7 2.0 28 43-70 74-101 (108)
252 PF10078 DUF2316: Uncharacteri 23.7 50 0.0011 21.9 1.3 30 26-59 12-41 (89)
253 cd02413 40S_S3_KH K homology R 23.6 37 0.00081 21.9 0.7 20 44-63 56-75 (81)
254 PRK13870 transcriptional regul 23.5 1.8E+02 0.0038 22.4 4.6 33 44-76 191-223 (234)
255 PF08452 DNAP_B_exo_N: DNA pol 23.4 24 0.00051 17.1 -0.2 9 58-66 5-13 (22)
256 PF12844 HTH_19: Helix-turn-he 23.3 51 0.0011 19.4 1.3 24 43-66 14-37 (64)
257 PF03444 HrcA_DNA-bdg: Winged 23.2 2E+02 0.0044 18.6 4.0 38 21-60 2-42 (78)
258 PF06971 Put_DNA-bind_N: Putat 23.2 47 0.001 19.5 1.0 18 43-60 30-47 (50)
259 COG1905 NuoE NADH:ubiquinone o 23.1 1.4E+02 0.003 22.1 3.7 36 23-58 25-60 (160)
260 TIGR02850 spore_sigG RNA polym 22.9 1.8E+02 0.0039 22.4 4.6 46 20-70 206-251 (254)
261 PF13560 HTH_31: Helix-turn-he 22.8 53 0.0012 19.6 1.3 25 43-67 16-40 (64)
262 PF08880 QLQ: QLQ; InterPro: 22.6 80 0.0017 17.3 1.8 13 20-32 2-14 (37)
263 PF06163 DUF977: Bacterial pro 22.6 1E+02 0.0022 21.9 2.7 46 19-64 3-49 (127)
264 PF13022 HTH_Tnp_1_2: Helix-tu 22.5 81 0.0018 22.8 2.3 24 40-63 33-56 (142)
265 PRK13890 conjugal transfer pro 22.5 51 0.0011 22.8 1.3 24 43-66 20-43 (120)
266 PRK09975 DNA-binding transcrip 22.3 92 0.002 22.9 2.8 42 26-68 17-58 (213)
267 cd04768 HTH_BmrR-like Helix-Tu 22.3 67 0.0015 21.1 1.8 21 44-64 3-23 (96)
268 PRK13756 tetracycline represso 22.1 1.4E+02 0.0031 22.4 3.8 41 27-68 11-51 (205)
269 PRK15411 rcsA colanic acid cap 22.0 1.8E+02 0.004 21.7 4.4 46 20-71 137-182 (207)
270 PF14229 DUF4332: Domain of un 21.4 76 0.0017 22.0 2.0 26 38-63 26-51 (122)
271 PF12793 SgrR_N: Sugar transpo 21.3 1E+02 0.0022 21.2 2.6 34 24-59 4-37 (115)
272 PRK09958 DNA-binding transcrip 21.1 1.7E+02 0.0037 20.7 4.0 47 19-71 142-188 (204)
273 PRK05988 formate dehydrogenase 21.0 1.6E+02 0.0035 21.4 3.7 34 26-59 26-59 (156)
274 cd04773 HTH_TioE_rpt2 Second H 20.7 74 0.0016 21.4 1.8 21 44-64 3-23 (108)
275 PF00440 TetR_N: Bacterial reg 20.7 67 0.0015 17.9 1.3 35 31-66 7-41 (47)
276 PF04539 Sigma70_r3: Sigma-70 20.3 1.2E+02 0.0025 18.7 2.5 22 42-63 21-42 (78)
277 PRK00215 LexA repressor; Valid 20.3 1.3E+02 0.0028 22.4 3.2 42 21-64 2-47 (205)
278 COG5484 Uncharacterized conser 20.2 64 0.0014 25.8 1.5 26 43-70 21-46 (279)
279 PHA00542 putative Cro-like pro 20.2 2.3E+02 0.005 18.0 3.9 23 43-65 33-55 (82)
280 cd04780 HTH_MerR-like_sg5 Heli 20.1 70 0.0015 21.1 1.5 20 44-63 3-22 (95)
No 1
>KOG0484|consensus
Probab=99.83 E-value=1.7e-20 Score=126.37 Aligned_cols=68 Identities=32% Similarity=0.559 Sum_probs=62.9
Q ss_pred CCCCCCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHHHHHH
Q psy16514 11 PRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERELL 78 (155)
Q Consensus 11 ~~~~~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~~~~ 78 (155)
.++.||.||+||..||..|+..|..++||++..|++||.++.|++..|++||||||+|.||+.+....
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~ 81 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIA 81 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 45778889999999999999999999999999999999999999999999999999999998765543
No 2
>KOG0850|consensus
Probab=99.83 E-value=1.8e-20 Score=142.41 Aligned_cols=68 Identities=44% Similarity=0.788 Sum_probs=64.9
Q ss_pred CCCCCCCCCCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHH
Q psy16514 7 DRGKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKE 74 (155)
Q Consensus 7 ~~~~~~~~~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~ 74 (155)
-.|+++|.||+||.|+..||..|++.|+++.|+...+|.+||..|||+-+||+|||||||.|.||..+
T Consensus 115 ~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 115 PNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred cCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 45888999999999999999999999999999999999999999999999999999999999999765
No 3
>KOG2251|consensus
Probab=99.82 E-value=5.6e-20 Score=138.98 Aligned_cols=72 Identities=33% Similarity=0.510 Sum_probs=67.2
Q ss_pred CCCCCCCCCCCCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHHHH
Q psy16514 5 IFDRGKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERE 76 (155)
Q Consensus 5 ~~~~~~~~~~~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~~ 76 (155)
++-.+.+||.||.||+|+-.|+.+|+++|.+++||+..+|++||.+|+|.+.+|+|||+|||+|+|++++.+
T Consensus 28 vP~~~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 28 VPYSSGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred CCcCccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 444578999999999999999999999999999999999999999999999999999999999999987654
No 4
>KOG0488|consensus
Probab=99.82 E-value=1.5e-20 Score=151.30 Aligned_cols=71 Identities=49% Similarity=0.809 Sum_probs=66.6
Q ss_pred CCCCCCCCCCCCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHHH
Q psy16514 5 IFDRGKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKER 75 (155)
Q Consensus 5 ~~~~~~~~~~~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~ 75 (155)
...++.++|+||.||+||..||..||+.|++.+|++..+|..||..|||+..||++||||||+||||....
T Consensus 163 ~~~~~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 163 PYQRSTPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred CcccCCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 44567789999999999999999999999999999999999999999999999999999999999998655
No 5
>KOG0842|consensus
Probab=99.80 E-value=1e-19 Score=144.87 Aligned_cols=69 Identities=45% Similarity=0.724 Sum_probs=62.4
Q ss_pred CCCCCCCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHHHHHH
Q psy16514 10 KPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERELL 78 (155)
Q Consensus 10 ~~~~~~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~~~~ 78 (155)
..+++||+|..|+..|+-+||+.|.+++|++..+|+.||..|+|+++||+|||||||.|.||+++-+..
T Consensus 149 ~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~ 217 (307)
T KOG0842|consen 149 GKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKAL 217 (307)
T ss_pred ccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhh
Confidence 355677788999999999999999999999999999999999999999999999999999997654433
No 6
>KOG0843|consensus
Probab=99.79 E-value=2.2e-19 Score=131.93 Aligned_cols=65 Identities=37% Similarity=0.610 Sum_probs=60.4
Q ss_pred CCCCCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHHHH
Q psy16514 12 RRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERE 76 (155)
Q Consensus 12 ~~~~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~~ 76 (155)
.+-+|.||.|+..||..|+.+|+.++|-...+|..||..|+|++.||+|||||||.|.||.+...
T Consensus 100 ~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 100 MRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred cCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 36677899999999999999999999999999999999999999999999999999999876543
No 7
>KOG0489|consensus
Probab=99.79 E-value=2.3e-19 Score=141.70 Aligned_cols=65 Identities=40% Similarity=0.780 Sum_probs=60.0
Q ss_pred CCCCCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHHHH
Q psy16514 12 RRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERE 76 (155)
Q Consensus 12 ~~~~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~~ 76 (155)
...||.||.||..|+..||+.|..++|.++..|.+||..|.|+++||+|||||||+||||.++..
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~ 221 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAK 221 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhccc
Confidence 34567799999999999999999999999999999999999999999999999999999976543
No 8
>KOG0487|consensus
Probab=99.78 E-value=8.4e-20 Score=145.43 Aligned_cols=68 Identities=41% Similarity=0.672 Sum_probs=63.8
Q ss_pred CCCCCCCCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHHHH
Q psy16514 9 GKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERE 76 (155)
Q Consensus 9 ~~~~~~~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~~ 76 (155)
...+++||+|+.+|+.|+..||+.|..|.|++...|.+|++.|+|+++||+|||||||.|.||..+..
T Consensus 230 ~~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~ 297 (308)
T KOG0487|consen 230 SSARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN 297 (308)
T ss_pred ccccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence 45688999999999999999999999999999999999999999999999999999999999987543
No 9
>KOG0848|consensus
Probab=99.75 E-value=1e-18 Score=135.36 Aligned_cols=70 Identities=44% Similarity=0.672 Sum_probs=63.2
Q ss_pred CCCCCCCCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHHHHHH
Q psy16514 9 GKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERELL 78 (155)
Q Consensus 9 ~~~~~~~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~~~~ 78 (155)
++-|.+-|=|.++|..|+..||+.|..++|+++..+.+||.-|||+++||+|||||||+|+||.+++..+
T Consensus 194 ~KtRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~~ 263 (317)
T KOG0848|consen 194 VKTRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKRL 263 (317)
T ss_pred ceeecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHHH
Confidence 3555555568899999999999999999999999999999999999999999999999999999877743
No 10
>KOG0492|consensus
Probab=99.74 E-value=2.9e-18 Score=128.63 Aligned_cols=70 Identities=37% Similarity=0.591 Sum_probs=64.5
Q ss_pred CCCCCCCCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHHHHHH
Q psy16514 9 GKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERELL 78 (155)
Q Consensus 9 ~~~~~~~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~~~~ 78 (155)
.+.+.+|++||.||..||..|++.|...+|.++.+|.+++..|.|+++||+|||||||+|.||.+..+..
T Consensus 139 rKhk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~E 208 (246)
T KOG0492|consen 139 RKHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELE 208 (246)
T ss_pred cccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHH
Confidence 3456678899999999999999999999999999999999999999999999999999999998866654
No 11
>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=99.74 E-value=5e-18 Score=104.37 Aligned_cols=57 Identities=47% Similarity=0.666 Sum_probs=54.7
Q ss_pred CCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 15 MMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 15 ~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
+|+|+.|+..|+..|+.+|..++||+..++..||..+||+..+|++||+|+|+++||
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 467899999999999999999999999999999999999999999999999999885
No 12
>KOG0494|consensus
Probab=99.72 E-value=6e-18 Score=130.69 Aligned_cols=65 Identities=35% Similarity=0.690 Sum_probs=58.9
Q ss_pred CCCCCCC-cccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHHH
Q psy16514 11 PRRGMMR-RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKER 75 (155)
Q Consensus 11 ~~~~~r~-R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~ 75 (155)
.+++||. ||.||..|+..||+.|+..+||+...|+.||..+.|.+..|+|||||||+||||.++.
T Consensus 137 kk~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~ 202 (332)
T KOG0494|consen 137 KKKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKR 202 (332)
T ss_pred cccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhh
Confidence 3334444 9999999999999999999999999999999999999999999999999999997654
No 13
>KOG0485|consensus
Probab=99.70 E-value=1.1e-17 Score=126.40 Aligned_cols=65 Identities=43% Similarity=0.728 Sum_probs=60.7
Q ss_pred CCCCCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHHHH
Q psy16514 12 RRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERE 76 (155)
Q Consensus 12 ~~~~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~~ 76 (155)
.|++|.||+|+..|+..||..|...+|.+..+|.-||.+|.|++.||+|||||||.||||+-...
T Consensus 102 ~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad 166 (268)
T KOG0485|consen 102 DRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAAD 166 (268)
T ss_pred cccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhh
Confidence 36678899999999999999999999999999999999999999999999999999999976544
No 14
>KOG0493|consensus
Probab=99.65 E-value=9.4e-17 Score=124.24 Aligned_cols=58 Identities=41% Similarity=0.734 Sum_probs=55.8
Q ss_pred CCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 15 MMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 15 ~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
+|+||.||.+||..|+..|+.++|++...|..||..|+|.+.||+|||||+|+|.||.
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence 5679999999999999999999999999999999999999999999999999999984
No 15
>KOG0491|consensus
Probab=99.63 E-value=8.2e-17 Score=116.87 Aligned_cols=68 Identities=50% Similarity=0.802 Sum_probs=62.1
Q ss_pred CCCCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHHHHHHhc
Q psy16514 13 RGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERELLAN 80 (155)
Q Consensus 13 ~~~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~~~~~~ 80 (155)
+++|.|++|+..|+..|++.|+.++|.+..++.+||..|+|++.||+.||||||.|-||..++....+
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~p~n 166 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQPKN 166 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccCCCC
Confidence 45677999999999999999999999999999999999999999999999999999999876665433
No 16
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.62 E-value=8.4e-16 Score=93.82 Aligned_cols=55 Identities=51% Similarity=0.880 Sum_probs=51.8
Q ss_pred CCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHh
Q psy16514 16 MRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70 (155)
Q Consensus 16 r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~r 70 (155)
+.|+.|+..|+.+|+..|..++||+..++..||..+||+..+|++||+|+|++.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 4578899999999999999999999999999999999999999999999998754
No 17
>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=99.62 E-value=1.2e-15 Score=93.88 Aligned_cols=56 Identities=46% Similarity=0.766 Sum_probs=53.5
Q ss_pred CCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 16 MRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 16 r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
+.|+.|+..|+.+|+..|..++||+..++..||..+||+..+|++||+|+|++.++
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 45789999999999999999999999999999999999999999999999999876
No 18
>KOG3802|consensus
Probab=99.60 E-value=3.7e-16 Score=127.23 Aligned_cols=67 Identities=28% Similarity=0.387 Sum_probs=61.4
Q ss_pred CCCCCCCCCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHH
Q psy16514 8 RGKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKE 74 (155)
Q Consensus 8 ~~~~~~~~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~ 74 (155)
.+...|+||+||.|....+.+|+++|.+|+.|+..++..||.+|+|...+|+|||||||.|.||...
T Consensus 288 i~a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 288 IGAQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred hhccccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 3444577888999999999999999999999999999999999999999999999999999998543
No 19
>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=99.59 E-value=1.3e-15 Score=93.69 Aligned_cols=52 Identities=17% Similarity=0.430 Sum_probs=49.9
Q ss_pred CCCcccCCHHHHHHHHHHHhhcCC----CCHHHHHHHHHHhCCCccchhhhhhhhH
Q psy16514 15 MMRRAVFSDLQRKGLEKRFQIQKY----ISKPDRKKLAEKLGLKDSQVKIWFQNRR 66 (155)
Q Consensus 15 ~r~R~~~t~~ql~~L~~~F~~~~~----p~~~~~~~LA~~l~l~~~~V~~WFqNrR 66 (155)
+|.||.||.+|+..|+..|..++| |+..++..||..|||++++|++||||.+
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 567999999999999999999999 9999999999999999999999999964
No 20
>KOG0847|consensus
Probab=99.58 E-value=2e-15 Score=114.31 Aligned_cols=65 Identities=42% Similarity=0.774 Sum_probs=58.6
Q ss_pred CCCCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHHHHH
Q psy16514 13 RGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKEREL 77 (155)
Q Consensus 13 ~~~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~~~ 77 (155)
+++-.|.+|+..|+..|+..|..++|+-..++.+||..+||++.||+|||||||.||||+...++
T Consensus 166 ~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEm 230 (288)
T KOG0847|consen 166 QRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEM 230 (288)
T ss_pred cccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccch
Confidence 33445788999999999999999999999999999999999999999999999999999765443
No 21
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.57 E-value=3.4e-15 Score=109.31 Aligned_cols=64 Identities=33% Similarity=0.442 Sum_probs=57.9
Q ss_pred CCCCCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHHH
Q psy16514 12 RRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKER 75 (155)
Q Consensus 12 ~~~~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~ 75 (155)
+..+++|++.|..|+.+|+..|..++||+..++..|+..|+|+++.|+|||||+|++.|+....
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 4455567888999999999999999999999999999999999999999999999999986543
No 22
>KOG4577|consensus
Probab=99.55 E-value=4.1e-15 Score=116.64 Aligned_cols=62 Identities=26% Similarity=0.409 Sum_probs=58.9
Q ss_pred CCCCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHH
Q psy16514 13 RGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKE 74 (155)
Q Consensus 13 ~~~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~ 74 (155)
..+|+||+||..||..|+.+|...+.|....|++|+..+||.-++|++||||||+|+||.++
T Consensus 166 ~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhh
Confidence 45778999999999999999999999999999999999999999999999999999999764
No 23
>KOG0483|consensus
Probab=99.55 E-value=3.8e-15 Score=112.69 Aligned_cols=57 Identities=40% Similarity=0.729 Sum_probs=54.1
Q ss_pred CcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHH
Q psy16514 17 RRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSK 73 (155)
Q Consensus 17 ~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~ 73 (155)
+..+|+.+|...|+..|....+..+..+..||..|||.++||.|||||||||||..+
T Consensus 53 kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kq 109 (198)
T KOG0483|consen 53 KKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQ 109 (198)
T ss_pred ccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchh
Confidence 356899999999999999999999999999999999999999999999999999864
No 24
>KOG0486|consensus
Probab=99.54 E-value=5.5e-15 Score=116.98 Aligned_cols=66 Identities=30% Similarity=0.599 Sum_probs=61.5
Q ss_pred CCCCCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHHHHH
Q psy16514 12 RRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKEREL 77 (155)
Q Consensus 12 ~~~~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~~~ 77 (155)
.|.||.|+.||..||..||..|..+.||+-..|++||.-++|++..|++||+|||+||||++..+.
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 366778999999999999999999999999999999999999999999999999999999876554
No 25
>KOG0844|consensus
Probab=99.44 E-value=3.5e-14 Score=112.17 Aligned_cols=61 Identities=39% Similarity=0.638 Sum_probs=57.3
Q ss_pred CCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHHH
Q psy16514 15 MMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKER 75 (155)
Q Consensus 15 ~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~ 75 (155)
||=||.||.+|+..||+.|-+..|-+...|.+||..|+|.+..|++||||||.|+||+...
T Consensus 182 RRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 182 RRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 4558999999999999999999999999999999999999999999999999999997643
No 26
>KOG0490|consensus
Probab=99.31 E-value=1e-12 Score=101.30 Aligned_cols=64 Identities=30% Similarity=0.311 Sum_probs=59.5
Q ss_pred CCCCCCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHH
Q psy16514 11 PRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKE 74 (155)
Q Consensus 11 ~~~~~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~ 74 (155)
..+.++.|+.|+..|+..|+++|..++||+...++.||..+++++..|++||||+|+||++...
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 3456778999999999999999999999999999999999999999999999999999998654
No 27
>KOG0775|consensus
Probab=99.25 E-value=2.9e-11 Score=94.42 Aligned_cols=52 Identities=35% Similarity=0.553 Sum_probs=49.8
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
+|...-+.+|...|.+++||++.++.+||+.+||+..||.+||+|||.|+|-
T Consensus 182 CFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 182 CFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred ehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 6888889999999999999999999999999999999999999999999994
No 28
>KOG0849|consensus
Probab=99.19 E-value=1.9e-11 Score=100.47 Aligned_cols=67 Identities=39% Similarity=0.636 Sum_probs=61.6
Q ss_pred CCCCCCCCCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHH
Q psy16514 8 RGKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKE 74 (155)
Q Consensus 8 ~~~~~~~~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~ 74 (155)
....++.+|.|++|+..|+..|++.|..++||....|+.||..+++++..|++||+|||++++|...
T Consensus 170 ~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 170 YALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred ccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 3455667777999999999999999999999999999999999999999999999999999999764
No 29
>KOG1168|consensus
Probab=99.16 E-value=1.1e-11 Score=97.58 Aligned_cols=61 Identities=31% Similarity=0.474 Sum_probs=56.2
Q ss_pred CCCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHH
Q psy16514 14 GMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKE 74 (155)
Q Consensus 14 ~~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~ 74 (155)
++|+||.+..-....||++|..++.|+...+..+|.+|.|...+|++||||+|.|.||.+.
T Consensus 309 kKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~ 369 (385)
T KOG1168|consen 309 KKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR 369 (385)
T ss_pred cccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence 3556899999999999999999999999999999999999999999999999999998543
No 30
>KOG2252|consensus
Probab=98.87 E-value=7.7e-09 Score=87.69 Aligned_cols=57 Identities=28% Similarity=0.396 Sum_probs=53.4
Q ss_pred CCCCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHH
Q psy16514 13 RGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKW 69 (155)
Q Consensus 13 ~~~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~ 69 (155)
..+|+|.+||..|+..|.++|+.+++|+..+.+.|+.+|+|....|.+||.|.|.|.
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 446679999999999999999999999999999999999999999999999998774
No 31
>KOG0774|consensus
Probab=98.79 E-value=1.7e-08 Score=78.71 Aligned_cols=59 Identities=27% Similarity=0.474 Sum_probs=54.8
Q ss_pred CCCcccCCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHH
Q psy16514 15 MMRRAVFSDLQRKGLEKRFQ---IQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSK 73 (155)
Q Consensus 15 ~r~R~~~t~~ql~~L~~~F~---~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~ 73 (155)
+|+|..|++....+|..+|. .++||+...+++||+++|++..||..||.|+|-++||.-
T Consensus 189 rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~ 250 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNM 250 (334)
T ss_pred HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhh
Confidence 56688999999999999995 689999999999999999999999999999999999864
No 32
>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=98.76 E-value=6.3e-09 Score=59.40 Aligned_cols=34 Identities=35% Similarity=0.642 Sum_probs=29.0
Q ss_pred hcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHH
Q psy16514 35 IQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68 (155)
Q Consensus 35 ~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k 68 (155)
.++||+..++..||..+||+..||..||-|.|.|
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 4799999999999999999999999999999864
No 33
>KOG0490|consensus
Probab=98.39 E-value=3.9e-07 Score=70.11 Aligned_cols=64 Identities=34% Similarity=0.559 Sum_probs=58.7
Q ss_pred CCCCCCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHH
Q psy16514 11 PRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKE 74 (155)
Q Consensus 11 ~~~~~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~ 74 (155)
..+.++.|+.|...|+..|...|..+++|....+..|+..+|+....|++||+|+|++.++.+.
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 4556667899999999999999999999999999999999999999999999999999998544
No 34
>KOG1146|consensus
Probab=97.79 E-value=1.7e-05 Score=73.37 Aligned_cols=61 Identities=30% Similarity=0.413 Sum_probs=56.8
Q ss_pred CCCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHH
Q psy16514 14 GMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKE 74 (155)
Q Consensus 14 ~~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~ 74 (155)
+++.|+.++..||+.|...|....||.-...+.|-..+++..++|++||||.|+|.|+...
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 4556899999999999999999999999999999999999999999999999999998654
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.32 E-value=0.00018 Score=43.73 Aligned_cols=42 Identities=26% Similarity=0.416 Sum_probs=31.3
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHH
Q psy16514 26 RKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRM 67 (155)
Q Consensus 26 l~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~ 67 (155)
...|+.+|...+++.......|..+.+|+..||+.||-.+..
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 467999999999999999999999999999999999976543
No 36
>KOG0773|consensus
Probab=97.14 E-value=0.00044 Score=56.65 Aligned_cols=59 Identities=22% Similarity=0.326 Sum_probs=48.8
Q ss_pred CCCCcccCCHHHHHHHHHHH-h--hcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 14 GMMRRAVFSDLQRKGLEKRF-Q--IQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 14 ~~r~R~~~t~~ql~~L~~~F-~--~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
..|++..+......+|+... . ..+||+..++..||.++||+..||.+||-|.|.|.-+-
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p 300 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKP 300 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCc
Confidence 34445678888888888763 3 35799999999999999999999999999999887664
No 37
>KOG3623|consensus
Probab=97.10 E-value=0.0027 Score=56.38 Aligned_cols=49 Identities=20% Similarity=0.361 Sum_probs=45.8
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHH
Q psy16514 26 RKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKE 74 (155)
Q Consensus 26 l~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~ 74 (155)
+.+|+++|..|..|+..+...+|.+.||....|+.||++++++.....+
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 7899999999999999999999999999999999999999999887553
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=96.37 E-value=0.01 Score=35.59 Aligned_cols=47 Identities=17% Similarity=0.333 Sum_probs=35.7
Q ss_pred CCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhH
Q psy16514 15 MMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRR 66 (155)
Q Consensus 15 ~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR 66 (155)
+|+|..+|-.+...+-..+.... ....||..+|++..+|..|..|+.
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 46788999999888888888776 578899999999999999999853
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=90.92 E-value=0.73 Score=26.67 Aligned_cols=46 Identities=22% Similarity=0.294 Sum_probs=35.7
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHh
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~r 70 (155)
.+++.+..+|...|... ..-.++|..+|++...|+.+...-..|.|
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 46788999999998433 46778999999999999998877666655
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=87.69 E-value=0.34 Score=30.41 Aligned_cols=44 Identities=14% Similarity=0.260 Sum_probs=28.9
Q ss_pred CCcccCCHHHHHHHHHHH-hhcCCCCHHHHHHHHHHhCCCccchhhhhhh
Q psy16514 16 MRRAVFSDLQRKGLEKRF-QIQKYISKPDRKKLAEKLGLKDSQVKIWFQN 64 (155)
Q Consensus 16 r~R~~~t~~ql~~L~~~F-~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqN 64 (155)
++|..|++++...+-..+ ... .....+|..+|+++..+..|-+-
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g-----~sv~~va~~~gi~~~~l~~W~~~ 46 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG-----ESVSEVAREYGISPSTLYNWRKQ 46 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH-----CHHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC-----CceEeeecccccccccccHHHHH
Confidence 457889999866666655 332 46788999999999999999853
No 41
>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=86.57 E-value=1.6 Score=24.47 Aligned_cols=44 Identities=23% Similarity=0.277 Sum_probs=32.8
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHH
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k 68 (155)
.+++.+..++...|... .....+|..+|++...|..|....+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 46777778887776433 356778999999999999998765544
No 42
>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=84.26 E-value=2.7 Score=24.50 Aligned_cols=43 Identities=28% Similarity=0.334 Sum_probs=29.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHH
Q psy16514 21 FSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68 (155)
Q Consensus 21 ~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k 68 (155)
+++.+..++.-.|-.. ....++|..+|++...|+.|...-|.+
T Consensus 11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 5566666666655544 467889999999999999999865543
No 43
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=82.71 E-value=4 Score=29.51 Aligned_cols=50 Identities=18% Similarity=0.197 Sum_probs=40.2
Q ss_pred ccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHH
Q psy16514 19 AVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKE 74 (155)
Q Consensus 19 ~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~ 74 (155)
..+++.|+.+|...+ .. ....++|..+|++...|..|.++.+.+.|+...
T Consensus 5 ~~Lt~rqreVL~lr~-~G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~ 54 (141)
T PRK03975 5 SFLTERQIEVLRLRE-RG-----LTQQEIADILGTSRANVSSIEKRARENIEKARE 54 (141)
T ss_pred cCCCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 578899999997743 22 356789999999999999999988888777653
No 44
>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=81.17 E-value=4.3 Score=24.27 Aligned_cols=42 Identities=26% Similarity=0.371 Sum_probs=33.1
Q ss_pred CCHHHHHHHHHHHhhcC--CCCHHHHHHHHHHhCCCccchhhhh
Q psy16514 21 FSDLQRKGLEKRFQIQK--YISKPDRKKLAEKLGLKDSQVKIWF 62 (155)
Q Consensus 21 ~t~~ql~~L~~~F~~~~--~p~~~~~~~LA~~l~l~~~~V~~WF 62 (155)
+|+.|+.+|..+|...- +|-......||..+|++...|..-.
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~L 44 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHL 44 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHH
Confidence 57889999999998654 4666778899999999987654433
No 45
>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=78.90 E-value=4.6 Score=24.71 Aligned_cols=45 Identities=16% Similarity=0.227 Sum_probs=23.4
Q ss_pred cccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhh
Q psy16514 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQ 63 (155)
Q Consensus 18 R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFq 63 (155)
|..|+.......-.+|..+..--...|. .|.++|+++++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHccchhhhHHH-HHHHhCccHHHHHHHHH
Confidence 4567776643333444444333323343 49999999999999985
No 46
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=77.59 E-value=5.5 Score=28.04 Aligned_cols=46 Identities=17% Similarity=0.206 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 21 FSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 21 ~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
+++.+..++...|-.. ....++|..+|++...|+.|...-+.+.|+
T Consensus 107 L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 107 LDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 3444555554444322 356789999999999999999877776664
No 47
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=76.76 E-value=6.2 Score=28.31 Aligned_cols=46 Identities=17% Similarity=0.153 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 21 FSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 21 ~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
+++.+..+|...|- .......+|..+|++...|+.|...-+.+.|+
T Consensus 129 L~~~~r~vl~l~~~-----~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 129 LPEELRTAITLREI-----EGLSYEEIAEIMGCPIGTVRSRIFRAREALRA 174 (182)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 44445555544432 22345688999999999999999876666665
No 48
>PRK00118 putative DNA-binding protein; Validated
Probab=76.45 E-value=10 Score=25.89 Aligned_cols=48 Identities=13% Similarity=0.120 Sum_probs=36.5
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
.+++.|..++...|.... ...++|..+|++...|..|....|.+.|+.
T Consensus 17 ~L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~RArkkLr~~ 64 (104)
T PRK00118 17 LLTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKRTEKLLEDY 64 (104)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 356667777766655432 567799999999999999998877777764
No 49
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=76.18 E-value=7.2 Score=28.87 Aligned_cols=31 Identities=19% Similarity=0.328 Sum_probs=25.6
Q ss_pred HHHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 42 PDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 42 ~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
....++|..+|++...|+++...-|.+.|+.
T Consensus 159 ~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 159 LTYREVAERLAVPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred CCHHHHHHHhCCChHhHHHHHHHHHHHHHHH
Confidence 3566889999999999999998877777653
No 50
>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=75.47 E-value=7.3 Score=19.30 Aligned_cols=38 Identities=13% Similarity=0.190 Sum_probs=26.5
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhh
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWF 62 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WF 62 (155)
.++..+...+...|... + ....+|..+|++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 45666666666666532 2 46678899999988888774
No 51
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=74.90 E-value=6.1 Score=27.38 Aligned_cols=42 Identities=14% Similarity=0.163 Sum_probs=28.8
Q ss_pred cccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhh
Q psy16514 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQ 63 (155)
Q Consensus 18 R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFq 63 (155)
|..|+.++....-..+..+. .....+|..+|+++..|..|.+
T Consensus 10 rr~ys~EfK~~aV~~~~~~g----~sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPG----MTVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCC----CCHHHHHHHHCcCHHHHHHHHH
Confidence 45688877544433333332 2466789999999999999964
No 52
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=74.34 E-value=5.8 Score=30.22 Aligned_cols=39 Identities=26% Similarity=0.399 Sum_probs=33.5
Q ss_pred cCCHHHHHHHHHHHhhc--CCCCHHHHHHHHHHhCCCccch
Q psy16514 20 VFSDLQRKGLEKRFQIQ--KYISKPDRKKLAEKLGLKDSQV 58 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~--~~p~~~~~~~LA~~l~l~~~~V 58 (155)
.+|..|+.+|..+|... -||-......||+.+|+++..+
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~ 195 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTL 195 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHH
Confidence 69999999999999865 4677778889999999998753
No 53
>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=73.90 E-value=2.1 Score=26.36 Aligned_cols=21 Identities=38% Similarity=0.733 Sum_probs=18.1
Q ss_pred HHHHHHHHhCCCccchhhhhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQ 63 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFq 63 (155)
.-..||..||+++.+|+.|=.
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhh
Confidence 456789999999999999964
No 54
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=73.72 E-value=8.3 Score=28.94 Aligned_cols=31 Identities=19% Similarity=0.189 Sum_probs=25.2
Q ss_pred HHHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 42 PDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 42 ~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
....++|..+|++...|++++...+.+.++.
T Consensus 170 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 200 (206)
T PRK12526 170 LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQ 200 (206)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3566889999999999999998777776653
No 55
>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=73.72 E-value=7.5 Score=23.03 Aligned_cols=47 Identities=21% Similarity=0.168 Sum_probs=35.9
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
.||+.++.+|.....-. ...++|..+|+++..|..+..+=+.|..-.
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~ 49 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKLGVK 49 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT-S
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHhCCC
Confidence 57888888887776543 477899999999999999998877776543
No 56
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=73.69 E-value=11 Score=26.91 Aligned_cols=31 Identities=26% Similarity=0.317 Sum_probs=25.9
Q ss_pred HHHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 42 PDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 42 ~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
....++|..+|++...|+.|...-|.+.|+.
T Consensus 142 ~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 142 LSYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3456899999999999999999877777753
No 57
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=73.44 E-value=11 Score=26.87 Aligned_cols=30 Identities=20% Similarity=0.139 Sum_probs=25.4
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
...++|..+|++...|++|.+.-|.+.|+.
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 155 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKAL 155 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999999877777764
No 58
>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=72.55 E-value=8.6 Score=26.19 Aligned_cols=46 Identities=28% Similarity=0.344 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 21 FSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 21 ~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
+++.+..++...|-. ......+|..+|++...|+.|...-+.+.|+
T Consensus 111 L~~~~~~ii~~~~~~-----g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 111 LPEREREVLVLRYLE-----GLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCHHHHHHHhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 455555555444322 2356689999999999999999877766654
No 59
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=71.61 E-value=4.5 Score=22.90 Aligned_cols=40 Identities=18% Similarity=0.233 Sum_probs=21.3
Q ss_pred ccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhh
Q psy16514 19 AVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQ 63 (155)
Q Consensus 19 ~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFq 63 (155)
..+|..+...++..+... ....++|..+|.+...|..|.+
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 467888888888876643 4566799999999999988875
No 60
>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=71.29 E-value=10 Score=26.44 Aligned_cols=30 Identities=23% Similarity=0.336 Sum_probs=24.2
Q ss_pred HHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 42 PDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 42 ~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
....++|..+|++...|+.+...-+.+.|+
T Consensus 130 ~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 130 KSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 356678999999999999999877766654
No 61
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=71.10 E-value=11 Score=26.65 Aligned_cols=30 Identities=10% Similarity=0.086 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
...++|..+|++...|++.+..-|.+.|+.
T Consensus 124 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 124 SYQEIALQEKIEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 345889999999999999998877777653
No 62
>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=70.79 E-value=10 Score=26.67 Aligned_cols=31 Identities=26% Similarity=0.260 Sum_probs=24.5
Q ss_pred HHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 41 KPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 41 ~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
.....++|..+|++...|+++...-|.+.|.
T Consensus 127 g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 127 GVSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 3456789999999999999998766666553
No 63
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=70.65 E-value=7.9 Score=28.49 Aligned_cols=33 Identities=21% Similarity=0.286 Sum_probs=26.8
Q ss_pred CHHHHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 40 SKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 40 ~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
......++|..+|++...|+.|+..-|.+.|+.
T Consensus 156 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 156 EGLSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 334566899999999999999998877777753
No 64
>PRK10072 putative transcriptional regulator; Provisional
Probab=70.23 E-value=6.6 Score=26.43 Aligned_cols=40 Identities=25% Similarity=0.227 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHH
Q psy16514 21 FSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRM 67 (155)
Q Consensus 21 ~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~ 67 (155)
.+...+..|...... ....||..+|++...|..|.+.+|.
T Consensus 33 ~~~~eik~LR~~~gl-------TQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 33 TSFTEFEQLRKGTGL-------KIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred CChHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 356666666544332 3678999999999999999988764
No 65
>PRK04217 hypothetical protein; Provisional
Probab=69.93 E-value=14 Score=25.48 Aligned_cols=48 Identities=10% Similarity=0.030 Sum_probs=37.0
Q ss_pred ccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 19 AVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 19 ~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
..++..++.++...|...- ...++|..+|++...|...+...+.+.+.
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre 88 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQ 88 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3567888888777764433 57789999999999999999877766654
No 66
>PRK06930 positive control sigma-like factor; Validated
Probab=69.89 E-value=13 Score=27.43 Aligned_cols=49 Identities=14% Similarity=0.135 Sum_probs=35.0
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHH
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSK 73 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~ 73 (155)
.+++.+..++...|... ..-.++|..+|++...|+.++..-+.+.++.-
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 35555555555544322 24668899999999999999998888877643
No 67
>KOG1146|consensus
Probab=69.48 E-value=6.1 Score=38.06 Aligned_cols=62 Identities=16% Similarity=0.140 Sum_probs=55.7
Q ss_pred CCCCCCcccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHH
Q psy16514 12 RRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSK 73 (155)
Q Consensus 12 ~~~~r~R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~ 73 (155)
.+.++.+..+-..++.+|-..|-.+.-|+...+.-|....+.+.+++.+||+|-|.|.++..
T Consensus 703 ~~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 703 PRDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred cccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 35566688888899999999999999999999999999999999999999999999988754
No 68
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=69.48 E-value=14 Score=26.79 Aligned_cols=29 Identities=24% Similarity=0.487 Sum_probs=24.7
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
...++|..+|++...|++++..-|.+.|+
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 46689999999999999999877777665
No 69
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=69.44 E-value=12 Score=27.18 Aligned_cols=30 Identities=17% Similarity=0.227 Sum_probs=25.7
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
.-.++|..+|++...|+.++..-|.+.|+.
T Consensus 149 s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12512 149 SIKETAAKLSMSEGAVRVALHRGLAALAAK 178 (184)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 566899999999999999999888877753
No 70
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=69.15 E-value=10 Score=27.01 Aligned_cols=30 Identities=30% Similarity=0.336 Sum_probs=24.7
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
...++|..+|++...|+.+...-|.+.|+.
T Consensus 130 s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 130 SYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 456889999999999999998777776653
No 71
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=68.60 E-value=13 Score=27.25 Aligned_cols=30 Identities=17% Similarity=0.198 Sum_probs=24.7
Q ss_pred HHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 42 PDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 42 ~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
....++|..+|++...|+.+...-|.+.|+
T Consensus 156 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 156 LSAEETAEAVGSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 356789999999999999999877766665
No 72
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=68.34 E-value=11 Score=27.31 Aligned_cols=31 Identities=26% Similarity=0.263 Sum_probs=25.4
Q ss_pred HHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 41 KPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 41 ~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
.....++|..+|++...|+++++.-|.+.|.
T Consensus 152 g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 152 DLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3456688999999999999999877777665
No 73
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=68.18 E-value=18 Score=26.59 Aligned_cols=30 Identities=7% Similarity=0.313 Sum_probs=25.6
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
...++|..+|+++..|+++...-|.+.|+.
T Consensus 152 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 152 SSEQICQECDISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 466899999999999999998877777764
No 74
>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=67.69 E-value=2.4 Score=27.13 Aligned_cols=35 Identities=17% Similarity=0.267 Sum_probs=26.9
Q ss_pred HHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhh
Q psy16514 30 EKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQN 64 (155)
Q Consensus 30 ~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqN 64 (155)
+..|....|-......++|..+|++...|+.|+.+
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 44455555545557889999999999999999975
No 75
>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=67.65 E-value=14 Score=26.76 Aligned_cols=29 Identities=21% Similarity=0.189 Sum_probs=24.3
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
.-.++|..+|++...|++....-|.+.|+
T Consensus 152 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 152 TVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45588999999999999999887777665
No 76
>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=67.34 E-value=10 Score=27.55 Aligned_cols=34 Identities=9% Similarity=-0.002 Sum_probs=26.5
Q ss_pred CCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 39 ISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 39 p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
.....-.++|..+|++...|+++...-|.+.|+.
T Consensus 152 ~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 152 LEGLSYEDIARIMDCPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3334567899999999999999998777776653
No 77
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=66.69 E-value=19 Score=26.43 Aligned_cols=30 Identities=23% Similarity=0.286 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
...++|..+|++...|++.+..-|.+.|+.
T Consensus 149 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (189)
T PRK12515 149 SVEEVGEIVGIPESTVKTRMFYARKKLAEL 178 (189)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999998888777764
No 78
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=66.67 E-value=13 Score=27.11 Aligned_cols=30 Identities=10% Similarity=0.121 Sum_probs=25.1
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
...++|..+|++...|+.+...-|.+.|+.
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 175 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALRAQ 175 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999998777777663
No 79
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=66.25 E-value=14 Score=26.18 Aligned_cols=31 Identities=32% Similarity=0.448 Sum_probs=25.5
Q ss_pred HHHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 42 PDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 42 ~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
....++|..+|++...|+.+...-|.+.|+.
T Consensus 128 ~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~ 158 (166)
T PRK09639 128 YSYKEIAEALGIKESSVGTTLARAKKKFRKI 158 (166)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3566789999999999999998777777664
No 80
>KOG0773|consensus
Probab=66.00 E-value=7.1 Score=31.90 Aligned_cols=47 Identities=28% Similarity=0.381 Sum_probs=38.9
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 26 RKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 26 l~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
+..+...-..++|++......|+...+|+-.+|.+||-|.|.+.+..
T Consensus 109 ~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~ 155 (342)
T KOG0773|consen 109 LKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKE 155 (342)
T ss_pred cccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhc
Confidence 33444555678999999999999999999999999999988876653
No 81
>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=65.14 E-value=16 Score=26.36 Aligned_cols=30 Identities=37% Similarity=0.422 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
...++|..+|++...|+.+...-|.+.++.
T Consensus 118 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 147 (170)
T TIGR02959 118 SQQEIAEKLGLSLSGAKSRVQRGRKKLKEL 147 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 566889999999999999998777776664
No 82
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=64.63 E-value=19 Score=26.18 Aligned_cols=29 Identities=24% Similarity=0.463 Sum_probs=24.3
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
...++|..+|++...|++|...-+.+.|+
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 45688999999999999999877776664
No 83
>PF13518 HTH_28: Helix-turn-helix domain
Probab=64.58 E-value=5.9 Score=22.55 Aligned_cols=23 Identities=22% Similarity=0.533 Sum_probs=19.4
Q ss_pred HHHHHHHHhCCCccchhhhhhhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNR 65 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNr 65 (155)
....+|..+|++..+|..|.+.-
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y 36 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRY 36 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHH
Confidence 45668999999999999999643
No 84
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=64.23 E-value=16 Score=26.77 Aligned_cols=30 Identities=40% Similarity=0.472 Sum_probs=24.8
Q ss_pred HHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 42 PDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 42 ~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
....++|..+|++...|+..+..-|.+.|+
T Consensus 123 ~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (181)
T PRK09637 123 LSQKEIAEKLGLSLSGAKSRVQRGRVKLKE 152 (181)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 346688999999999999999877777665
No 85
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=63.99 E-value=23 Score=19.84 Aligned_cols=45 Identities=24% Similarity=0.294 Sum_probs=31.6
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHh
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~r 70 (155)
.+++.+..++...+. . .....+|..+|++...|..|.+.-+.+..
T Consensus 3 ~l~~~e~~i~~~~~~-g-----~s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 3 SLTPREREVLRLLAE-G-----LTNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCCHHHHHHHHHHHc-C-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 357777777755332 1 25678899999999999999876554443
No 86
>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=63.80 E-value=18 Score=25.63 Aligned_cols=30 Identities=23% Similarity=0.138 Sum_probs=23.5
Q ss_pred HHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 42 PDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 42 ~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
....++|..+|++...|+.....-|.+.|+
T Consensus 139 ~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 139 LPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 345688999999999999988766666554
No 87
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=63.61 E-value=20 Score=25.27 Aligned_cols=29 Identities=17% Similarity=0.202 Sum_probs=23.6
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
...++|..+|++...|++....-|.+.|+
T Consensus 124 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 152 (161)
T PRK09047 124 DVAETAAAMGCSEGSVKTHCSRATHALAK 152 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35688999999999999998877766664
No 88
>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=63.25 E-value=19 Score=25.71 Aligned_cols=29 Identities=21% Similarity=0.324 Sum_probs=24.3
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
...++|..+|++...|+++...-|.+.|+
T Consensus 137 s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 137 TIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 56688999999999999999877777665
No 89
>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=63.21 E-value=5.8 Score=22.25 Aligned_cols=21 Identities=19% Similarity=0.233 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCccchhhhhhh
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQN 64 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFqN 64 (155)
..++|..+|++...|+.|.++
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999754
No 90
>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=63.16 E-value=18 Score=25.58 Aligned_cols=29 Identities=24% Similarity=0.349 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
.-.++|..+|++...|+.+...-|.+.|+
T Consensus 128 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 128 SEAQVAEALGISVGTVKSRLSRALARLRE 156 (162)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 46688999999999999999888877775
No 91
>KOG3755|consensus
Probab=62.82 E-value=3.5 Score=36.58 Aligned_cols=59 Identities=22% Similarity=0.163 Sum_probs=0.0
Q ss_pred CCCcccCCHHHHHHHHHH-HhhcCCCCHHHHHHHHHHhCCC-------ccchhhhhhhhHHHHhhHH
Q psy16514 15 MMRRAVFSDLQRKGLEKR-FQIQKYISKPDRKKLAEKLGLK-------DSQVKIWFQNRRMKWRNSK 73 (155)
Q Consensus 15 ~r~R~~~t~~ql~~L~~~-F~~~~~p~~~~~~~LA~~l~l~-------~~~V~~WFqNrR~k~rk~~ 73 (155)
|+++-.|-..|.-.+... |.++..+......+-...+.+. ...|+.||+|||.++++.+
T Consensus 692 k~~~~k~f~~~~~ev~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 692 KKTIIKFFQNQRYEVKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred HHHHHHhhhcceeecchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhh
No 92
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=62.16 E-value=20 Score=26.53 Aligned_cols=30 Identities=10% Similarity=0.060 Sum_probs=25.0
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
.-.++|..+|++...|+.++..-|.+.|+.
T Consensus 154 s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 154 SNPEIAEVMEIGVEAVESLTARGKRALAAL 183 (196)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999998777777653
No 93
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=61.26 E-value=19 Score=26.70 Aligned_cols=30 Identities=20% Similarity=0.158 Sum_probs=25.4
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
...++|..+|++...|++++..-|.+.|+.
T Consensus 131 s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~ 160 (188)
T PRK12546 131 SYEEAAEMCGVAVGTVKSRANRARARLAEL 160 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999999888777764
No 94
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=61.12 E-value=5.9 Score=23.66 Aligned_cols=28 Identities=21% Similarity=0.265 Sum_probs=18.5
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWR 70 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~r 70 (155)
....||..+|++...|..|+.++.....
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~ 39 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPS 39 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----
T ss_pred CHHHHHHHHCcCHHHHHHHHhccccccc
Confidence 5678999999999999999998744333
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=60.63 E-value=32 Score=25.28 Aligned_cols=33 Identities=12% Similarity=0.285 Sum_probs=26.4
Q ss_pred HHHHHHHHHhCCCccchhhhhhhhHHHHhhHHH
Q psy16514 42 PDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKE 74 (155)
Q Consensus 42 ~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~ 74 (155)
....++|..+|++...|+.....-|.+.|+.-.
T Consensus 148 ~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~ 180 (188)
T TIGR02943 148 FESDEICQELEISTSNCHVLLYRARLSLRACLS 180 (188)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 356689999999999999999877777776433
No 96
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=60.42 E-value=23 Score=25.28 Aligned_cols=29 Identities=14% Similarity=0.117 Sum_probs=24.3
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
...++|..+|++...|+++...-|.+.|.
T Consensus 130 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 130 SYEDAAAICGCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 46688999999999999999877776664
No 97
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=60.22 E-value=33 Score=25.20 Aligned_cols=31 Identities=13% Similarity=0.227 Sum_probs=26.1
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhhHH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRNSK 73 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~ 73 (155)
.-.++|..+|++...|+.+...-|.+.|+.-
T Consensus 154 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 154 SSDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4568899999999999999998887777654
No 98
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=60.18 E-value=20 Score=26.30 Aligned_cols=30 Identities=27% Similarity=0.403 Sum_probs=24.2
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
...++|..+|++...|++..+.-|.+.|++
T Consensus 149 s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~ 178 (189)
T PRK06811 149 KIEEIAKKLGLTRSAIDNRLSRGRKKLQKN 178 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 456889999999999999888777666653
No 99
>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=59.95 E-value=41 Score=26.17 Aligned_cols=40 Identities=15% Similarity=0.243 Sum_probs=31.7
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhhHHHHHHHhcCC
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERELLANGG 82 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~~~~~~~~ 82 (155)
...++|..+|++...|+++...-|.+.|+.-.++....-+
T Consensus 179 S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~~~~~~~ 218 (244)
T TIGR03001 179 SMDRIGAMYQVHRSTVSRWVAQARERLLERTRRRLAERLK 218 (244)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 4568999999999999999999998888766555544433
No 100
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=59.73 E-value=20 Score=27.40 Aligned_cols=31 Identities=19% Similarity=0.270 Sum_probs=26.4
Q ss_pred HHHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 42 PDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 42 ~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
....++|..+|++...|+.+...-+.+.|+.
T Consensus 201 ~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 201 LNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999999888887763
No 101
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=59.47 E-value=33 Score=24.87 Aligned_cols=32 Identities=19% Similarity=0.239 Sum_probs=27.0
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhhHHH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKE 74 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~ 74 (155)
...++|..+|++...|++....-+.+.|+.-.
T Consensus 135 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 166 (179)
T PRK12543 135 SQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQ 166 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45688999999999999999988888887543
No 102
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=59.35 E-value=26 Score=24.82 Aligned_cols=29 Identities=21% Similarity=0.421 Sum_probs=23.6
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
...++|..+|++...|+......+.+.|+
T Consensus 127 s~~EIA~~lgis~~tV~~~l~ra~~~lr~ 155 (163)
T PRK07037 127 TQKDIARELGVSPTLVNFMIRDALVHCRK 155 (163)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46688999999999999988766666664
No 103
>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=59.06 E-value=14 Score=20.80 Aligned_cols=38 Identities=16% Similarity=0.238 Sum_probs=27.0
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhh
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWF 62 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WF 62 (155)
.++..+...+...+... .....+|..+|++...|.-++
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 46676777777777655 357789999999998887776
No 104
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=58.92 E-value=34 Score=25.07 Aligned_cols=34 Identities=12% Similarity=0.329 Sum_probs=27.4
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhhHHHHH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERE 76 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~~ 76 (155)
.-.++|..+|++...|++....-|.+.|+.-.+.
T Consensus 149 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 182 (191)
T PRK12520 149 ETEEICQELQITATNAWVLLYRARMRLRECLDLH 182 (191)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4568899999999999999998888777654443
No 105
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=58.63 E-value=7.3 Score=22.13 Aligned_cols=23 Identities=26% Similarity=0.528 Sum_probs=17.4
Q ss_pred HHHHHHHHHhCCCccchhhhhhh
Q psy16514 42 PDRKKLAEKLGLKDSQVKIWFQN 64 (155)
Q Consensus 42 ~~~~~LA~~l~l~~~~V~~WFqN 64 (155)
.....+|..+|++...|..|.+.
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 45778999999999999999863
No 106
>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=58.58 E-value=23 Score=19.99 Aligned_cols=42 Identities=24% Similarity=0.293 Sum_probs=28.0
Q ss_pred CHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHH
Q psy16514 22 SDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKW 69 (155)
Q Consensus 22 t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~ 69 (155)
+..+..++...+ .. .....+|..++++...|+.|...-+.+.
T Consensus 2 ~~~e~~i~~~~~--~~----~s~~eia~~l~~s~~tv~~~~~~~~~~l 43 (57)
T cd06170 2 TPREREVLRLLA--EG----KTNKEIADILGISEKTVKTHLRNIMRKL 43 (57)
T ss_pred CHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence 445556554433 22 2567889999999999999987544443
No 107
>PF01056 Myc_N: Myc amino-terminal region; InterPro: IPR012682 The class III basic helix-turn-helix (bHLH) transcription factors have proliferative and apoptotic roles and are characterised by the presence of a leucine zipper adjacent to the bHLH domain. The myc oncogene gene was first discovered in small-cell lung cancer cell lines where it is found to be deregulated []. Although the biochemical function of the gene product is unknown, as a nuclear protein with a short half-life it may play a direct or indirect role in controlling gene expression []. Myc forms a heterodimer with Max, and this complex regulates cell growth through direct activation of genes involved in cell replication []. This entry represents the N-terminal domain found adjacent to the basic helix-loop-helix (bHLH) region (IPR001092 from INTERPRO).; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1EE4_C.
Probab=58.57 E-value=3.2 Score=34.15 Aligned_cols=11 Identities=36% Similarity=0.894 Sum_probs=0.0
Q ss_pred CCCCCcccccC
Q psy16514 144 DDGDDDEEINV 154 (155)
Q Consensus 144 d~~d~~e~~~~ 154 (155)
+++||+|||||
T Consensus 236 eeeeeeEEIDV 246 (329)
T PF01056_consen 236 EEEEEEEEIDV 246 (329)
T ss_dssp -----------
T ss_pred cccCCCcceEE
Confidence 34456899987
No 108
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=58.02 E-value=20 Score=27.64 Aligned_cols=30 Identities=17% Similarity=0.245 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
...++|..+|++...|+++...-|.+.|+.
T Consensus 189 s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~ 218 (233)
T PRK12538 189 SNGEIAEVMDTTVAAVESLLKRGRQQLRDL 218 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 456899999999999999998888777764
No 109
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=57.99 E-value=23 Score=26.02 Aligned_cols=29 Identities=10% Similarity=-0.010 Sum_probs=23.9
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
...++|..+|++...|+.+...-|.+.|+
T Consensus 148 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 148 SYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45689999999999999999877766664
No 110
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=57.99 E-value=27 Score=24.99 Aligned_cols=29 Identities=21% Similarity=0.279 Sum_probs=23.9
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
...++|..+|++...|+.....-|.+.|+
T Consensus 136 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 164 (173)
T PRK09645 136 STAQIAADLGIPEGTVKSRLHYALRALRL 164 (173)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45688999999999999998877766665
No 111
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=57.96 E-value=28 Score=25.04 Aligned_cols=29 Identities=21% Similarity=0.324 Sum_probs=24.5
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
.-.++|..+|++...|+++...-+.+.+.
T Consensus 137 s~~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 137 GHAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45688999999999999999887777665
No 112
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=57.66 E-value=27 Score=25.37 Aligned_cols=29 Identities=21% Similarity=0.182 Sum_probs=24.7
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
...++|..+|++...|++....-|.+.|+
T Consensus 147 s~~EIA~~l~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 147 SVAETAQLTGLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45688999999999999999887777765
No 113
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=57.56 E-value=29 Score=25.17 Aligned_cols=29 Identities=17% Similarity=0.225 Sum_probs=23.3
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
...++|..+|++...|+.+...-|.+.|+
T Consensus 153 s~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 153 THREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45578999999999999998876666654
No 114
>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=57.23 E-value=19 Score=24.03 Aligned_cols=36 Identities=22% Similarity=0.400 Sum_probs=19.8
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHHH
Q psy16514 26 RKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKER 75 (155)
Q Consensus 26 l~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~ 75 (155)
+.+.+-.|+.++||...-... -=.|||.+||+.+..
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~--------------aRRnRRRRWR~rq~Q 49 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQ--------------ARRNRRRRWRARQRQ 49 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HH--------------HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccc--------------cccchhhhHHHHHHH
Confidence 445566689999998442111 125889999987643
No 115
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=56.58 E-value=29 Score=25.18 Aligned_cols=29 Identities=17% Similarity=0.273 Sum_probs=24.2
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
...++|..+|++...|+......+.+++.
T Consensus 145 s~~EIA~~lgis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 145 KQKDIAQALDIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45688999999999999999877777654
No 116
>PRK09480 slmA division inhibitor protein; Provisional
Probab=56.43 E-value=14 Score=26.88 Aligned_cols=41 Identities=15% Similarity=0.255 Sum_probs=32.7
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHH
Q psy16514 26 RKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRM 67 (155)
Q Consensus 26 l~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~ 67 (155)
+.+....|...+. .......||...|++...+..+|.|+-.
T Consensus 16 l~aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 16 LQALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 3444445666656 8889999999999999999999999774
No 117
>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=55.58 E-value=29 Score=26.27 Aligned_cols=47 Identities=23% Similarity=0.353 Sum_probs=33.0
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
.+++.+..++...|-. .....++|..+|++...|+.|...-+.+.|+
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 3555555555555432 2356789999999999999999876666554
No 118
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=55.00 E-value=29 Score=26.90 Aligned_cols=46 Identities=22% Similarity=0.284 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 21 FSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 21 ~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
+++.+..+|...|-. .....++|..+|++...|+.|...-+.+.|+
T Consensus 206 L~~~~r~vl~l~~~~-----g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~ 251 (257)
T PRK08583 206 LSDREKSIIQCTFIE-----NLSQKETGERLGISQMHVSRLQRQAIKKLRE 251 (257)
T ss_pred CCHHHHHHHHHHHhC-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 445555555554432 2345789999999999999999877777664
No 119
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=54.98 E-value=31 Score=25.65 Aligned_cols=30 Identities=13% Similarity=0.317 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
...++|..+|++...|++....-|.+.|+.
T Consensus 157 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 186 (201)
T PRK12545 157 EIDDICTELTLTANHCSVLLYRARTRLRTC 186 (201)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999998777777764
No 120
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=54.73 E-value=30 Score=26.00 Aligned_cols=30 Identities=23% Similarity=0.364 Sum_probs=24.7
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
...++|..+|++...|+++...-|.+.|+.
T Consensus 156 s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~ 185 (203)
T PRK09647 156 SYEEIAATLGVKLGTVRSRIHRGRQQLRAA 185 (203)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999998777776653
No 121
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=54.51 E-value=42 Score=24.71 Aligned_cols=30 Identities=17% Similarity=0.151 Sum_probs=25.1
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
.-.++|..+|++...|+++...-|.+.|+.
T Consensus 134 s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~ 163 (187)
T PRK12516 134 AYEEAAEICGCAVGTIKSRVNRARQRLQEI 163 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 455889999999999999998877777764
No 122
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=54.47 E-value=29 Score=25.24 Aligned_cols=29 Identities=17% Similarity=0.444 Sum_probs=24.2
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
...++|..+|++...|++....-|.+.|+
T Consensus 140 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 168 (185)
T PRK12542 140 TYQEISSVMGITEANVRKQFERARKRVQN 168 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45688999999999999999877777665
No 123
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=54.46 E-value=27 Score=26.59 Aligned_cols=30 Identities=10% Similarity=0.062 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
...++|..+|++...|+.+...-|.+.++.
T Consensus 152 s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~ 181 (216)
T PRK12533 152 SYREIAAIADVPVGTVMSRLARARRRLAAL 181 (216)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999998777776664
No 124
>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=54.43 E-value=45 Score=23.91 Aligned_cols=48 Identities=19% Similarity=0.144 Sum_probs=38.7
Q ss_pred cccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 18 R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
.+.++..|+.+|.-.+ .. ....++|..+|++...|..|-+.-+.+.++
T Consensus 4 ~~~Lte~qr~VL~Lr~-~G-----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELRE-KG-----LSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHHH-cC-----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 3678899999987742 22 267789999999999999999988888876
No 125
>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=54.37 E-value=31 Score=26.15 Aligned_cols=46 Identities=24% Similarity=0.269 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 21 FSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 21 ~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
+++.+..+|...|-.. ....++|..+|++...|+.+...-+.+.|+
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 4455555555554322 256789999999999999998876666654
No 126
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=54.30 E-value=31 Score=25.71 Aligned_cols=30 Identities=7% Similarity=0.069 Sum_probs=24.6
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
.-.++|..+|++...|+++...-|.+.|+.
T Consensus 151 s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~ 180 (196)
T PRK12535 151 TYEEAAKIADVRVGTIRSRVARARADLIAA 180 (196)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 455889999999999999998777776653
No 127
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=54.13 E-value=53 Score=24.66 Aligned_cols=32 Identities=16% Similarity=0.371 Sum_probs=26.5
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhhHHH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKE 74 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~ 74 (155)
...++|..+|++...|+++...-|.+.|+.-.
T Consensus 166 s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~ 197 (206)
T PRK12544 166 ETNEICHAVDLSVSNLNVLLYRARLRLRECLE 197 (206)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 45689999999999999999988887777543
No 128
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=53.13 E-value=33 Score=25.18 Aligned_cols=29 Identities=17% Similarity=0.166 Sum_probs=24.1
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
...++|..+|++...|+++...-|.+.|+
T Consensus 129 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 157 (182)
T PRK12511 129 SYQEAAAVLGIPIGTLMSRIGRARAALRA 157 (182)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 45688999999999999999877766665
No 129
>PF13551 HTH_29: Winged helix-turn helix
Probab=53.12 E-value=42 Score=21.97 Aligned_cols=46 Identities=17% Similarity=0.207 Sum_probs=29.6
Q ss_pred cccCCHHHHHHHHHHHhhcCC-----CCHHHHHH-H-HHHh--CCCccchhhhhh
Q psy16514 18 RAVFSDLQRKGLEKRFQIQKY-----ISKPDRKK-L-AEKL--GLKDSQVKIWFQ 63 (155)
Q Consensus 18 R~~~t~~ql~~L~~~F~~~~~-----p~~~~~~~-L-A~~l--~l~~~~V~~WFq 63 (155)
+..+++++...|...+...+. .+...... | .... .++...|..|++
T Consensus 55 ~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 55 RKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 334899999999999988763 33333333 3 2233 456777887774
No 130
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=52.84 E-value=39 Score=24.85 Aligned_cols=30 Identities=23% Similarity=0.221 Sum_probs=24.3
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
.-.++|..+|++...|++.+..-|.+.|+.
T Consensus 159 s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~ 188 (194)
T PRK12531 159 PHQQVAEMFDIPLGTVKSRLRLAVEKLRHS 188 (194)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999888777766653
No 131
>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=52.75 E-value=4.7 Score=24.49 Aligned_cols=21 Identities=38% Similarity=0.596 Sum_probs=18.6
Q ss_pred HHHHHHHHhCCCccchhhhhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQ 63 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFq 63 (155)
...++|..||++...|..|-+
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH
Confidence 466889999999999999985
No 132
>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=52.64 E-value=32 Score=26.66 Aligned_cols=46 Identities=17% Similarity=0.271 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 21 FSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 21 ~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
+++.+..++...|... ....++|..+|++...|+.+...-+.+.|+
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 4555555555555332 245789999999999999999877777664
No 133
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.57 E-value=19 Score=23.94 Aligned_cols=39 Identities=10% Similarity=0.198 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchh
Q psy16514 21 FSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVK 59 (155)
Q Consensus 21 ~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~ 59 (155)
++++|...-...|+.+--.+.....++|..|+.++..|+
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~le 41 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLE 41 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHH
Confidence 567777777777777777777888999999999886544
No 134
>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=52.13 E-value=17 Score=26.74 Aligned_cols=34 Identities=21% Similarity=0.221 Sum_probs=27.7
Q ss_pred CCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 39 ISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 39 p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
.......++|..+|++...|+++...-|.+.|+.
T Consensus 145 ~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 178 (193)
T TIGR02947 145 VEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQ 178 (193)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3344567899999999999999999888777764
No 135
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=51.37 E-value=38 Score=23.94 Aligned_cols=28 Identities=21% Similarity=0.360 Sum_probs=22.0
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWR 70 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~r 70 (155)
.-.++|..+|++...|+++...-+.+.+
T Consensus 131 s~~EIA~~l~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 131 GYGEIATELGISLATVKRYLNKAAMRCY 158 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4567899999999999999876655443
No 136
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=51.06 E-value=40 Score=24.54 Aligned_cols=30 Identities=17% Similarity=0.161 Sum_probs=24.8
Q ss_pred HHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 42 PDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 42 ~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
....++|..+|++...|+.+...-+.+.|+
T Consensus 148 ~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12539 148 LSVAEAATRSGMSESAVKVSVHRGLKALAA 177 (184)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 356689999999999999999877777665
No 137
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=50.68 E-value=36 Score=25.92 Aligned_cols=32 Identities=16% Similarity=0.256 Sum_probs=26.1
Q ss_pred HHHHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 41 KPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 41 ~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
.....++|..+|++...|+.+...-+.+.|+.
T Consensus 198 g~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 198 EKTQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34567889999999999999998777777653
No 138
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=50.35 E-value=37 Score=24.48 Aligned_cols=31 Identities=26% Similarity=0.263 Sum_probs=25.1
Q ss_pred HHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 41 KPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 41 ~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
...-.++|..+|++...|+.....-|.+.|+
T Consensus 152 ~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T PRK09641 152 DLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3455688999999999999998877777665
No 139
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=50.06 E-value=31 Score=24.91 Aligned_cols=30 Identities=23% Similarity=0.212 Sum_probs=24.2
Q ss_pred HHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 42 PDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 42 ~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
....++|..+|++...|+++...-+.+++.
T Consensus 136 ~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~ 165 (172)
T PRK09651 136 LTYSEIAHKLGVSVSSVKKYVAKATEHCLL 165 (172)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 356689999999999999999766666554
No 140
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=50.04 E-value=37 Score=24.78 Aligned_cols=32 Identities=9% Similarity=0.011 Sum_probs=26.0
Q ss_pred HHHHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 41 KPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 41 ~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
...-.++|..+|++...|++....-|.+.|+.
T Consensus 154 g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 185 (193)
T PRK11923 154 GLSYEDIASVMQCPVGTVRSRIFRAREAIDKA 185 (193)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 33456899999999999999998777777764
No 141
>cd00131 PAX Paired Box domain
Probab=49.74 E-value=74 Score=22.24 Aligned_cols=45 Identities=16% Similarity=-0.010 Sum_probs=29.2
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCC-------Cccchhhhhhh
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGL-------KDSQVKIWFQN 64 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l-------~~~~V~~WFqN 64 (155)
..+..+...+......++..+..+...+...-|+ +...|--||++
T Consensus 75 ~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~ 126 (128)
T cd00131 75 VATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRN 126 (128)
T ss_pred cCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHh
Confidence 4456666667766778887777766654334455 66777777765
No 142
>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=49.60 E-value=14 Score=20.19 Aligned_cols=23 Identities=30% Similarity=0.601 Sum_probs=18.9
Q ss_pred HHHHHHHhCCCccchhhhhhhhH
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQNRR 66 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFqNrR 66 (155)
..++|..+|++...|..|.++..
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCC
Confidence 45789999999999999987543
No 143
>PRK10403 transcriptional regulator NarP; Provisional
Probab=49.47 E-value=23 Score=25.34 Aligned_cols=51 Identities=20% Similarity=0.188 Sum_probs=38.8
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHHHH
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERE 76 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~~ 76 (155)
.+|..+..+|...... ....++|..++++++.|++..+|=+.|.......+
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~~~~~ 203 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVA 203 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCHHH
Confidence 5788888888765432 34678899999999999999998888766554443
No 144
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=49.42 E-value=42 Score=24.04 Aligned_cols=29 Identities=21% Similarity=0.279 Sum_probs=23.9
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
.-.++|..+|++...|+.+...-|.+.|+
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 165 (173)
T PRK12522 137 SYKEMSEILNIPIGTVKYRLNYAKKQMRE 165 (173)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45578999999999999999877766665
No 145
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=49.26 E-value=40 Score=26.29 Aligned_cols=47 Identities=21% Similarity=0.230 Sum_probs=32.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 21 FSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 21 ~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
+++.+..+|...|.. .....++|..+|++...|+.+...-+.|.|+.
T Consensus 204 L~~~~r~vl~l~y~~-----~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~ 250 (256)
T PRK07408 204 LEERTREVLEFVFLH-----DLTQKEAAERLGISPVTVSRRVKKGLDQLKKL 250 (256)
T ss_pred CCHHHHHHHHHHHHC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 344445555554432 34567899999999999999998777776653
No 146
>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=48.69 E-value=24 Score=21.12 Aligned_cols=36 Identities=33% Similarity=0.374 Sum_probs=26.3
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhh
Q psy16514 24 LQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQ 63 (155)
Q Consensus 24 ~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFq 63 (155)
.|+..|+-.|. +...+. ..||..+|++++.|+.-..
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 46778888888 555543 4899999999998887654
No 147
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=48.57 E-value=12 Score=22.64 Aligned_cols=20 Identities=25% Similarity=0.414 Sum_probs=17.2
Q ss_pred HHHHHHHhCCCccchhhhhh
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQ 63 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFq 63 (155)
..++|..+|++...|+.|=+
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 45789999999999999964
No 148
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=48.33 E-value=36 Score=27.80 Aligned_cols=52 Identities=21% Similarity=0.281 Sum_probs=37.7
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
.+++.+..+|...|... |.......++|..+|++...|+.+....+.+.|+.
T Consensus 262 ~L~~~~R~vl~lrygL~-~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~ 313 (325)
T PRK05657 262 ELNDKQREVLARRFGLL-GYEAATLEDVAREIGLTRERVRQIQVEALRRLREI 313 (325)
T ss_pred cCCHHHHHHHHHHhccC-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 45666666666665322 23345678899999999999999999888877763
No 149
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=48.27 E-value=20 Score=25.75 Aligned_cols=35 Identities=23% Similarity=0.207 Sum_probs=28.0
Q ss_pred CCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 38 YISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 38 ~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
|.....-.++|..+|++...|++.+..-|.+.|+.
T Consensus 133 ~~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~ 167 (175)
T PRK12518 133 DLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKF 167 (175)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 33444567899999999999999998888777764
No 150
>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=48.17 E-value=13 Score=20.37 Aligned_cols=20 Identities=15% Similarity=0.303 Sum_probs=15.6
Q ss_pred HHHHHHHhCCCccchhhhhh
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQ 63 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFq 63 (155)
..++|..+|++.+.|+.|=+
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 35689999999999998853
No 151
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=48.13 E-value=43 Score=25.92 Aligned_cols=30 Identities=13% Similarity=0.196 Sum_probs=24.8
Q ss_pred HHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 42 PDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 42 ~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
..-.++|..+|++...|+.++..-+.+.|+
T Consensus 218 ~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 218 LTLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 346789999999999999999877777664
No 152
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=47.75 E-value=18 Score=26.62 Aligned_cols=35 Identities=20% Similarity=0.194 Sum_probs=27.6
Q ss_pred CCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 38 YISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 38 ~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
|.......++|..+|++...|+.+...-|.+.|+.
T Consensus 152 ~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 186 (194)
T PRK12513 152 EHGDLELEEIAELTGVPEETVKSRLRYALQKLREL 186 (194)
T ss_pred hccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34445667899999999999999998777777653
No 153
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=47.70 E-value=38 Score=24.57 Aligned_cols=29 Identities=21% Similarity=0.353 Sum_probs=24.0
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
...++|..+|++...|+.+...-|.+.|+
T Consensus 145 s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 145 SIKEIAEVTGVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45688999999999999999877766665
No 154
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=47.50 E-value=31 Score=23.64 Aligned_cols=41 Identities=24% Similarity=0.435 Sum_probs=32.9
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHH
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRM 67 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~ 67 (155)
.+++..+..+...+... ....|..||++...|+.|=|+|+.
T Consensus 43 ~ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 43 TLSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCcC
Confidence 36777888887776644 567899999999999999998763
No 155
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=47.47 E-value=54 Score=23.79 Aligned_cols=30 Identities=20% Similarity=0.262 Sum_probs=23.7
Q ss_pred HHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 42 PDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 42 ~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
..-.++|..+|++...|++....-|.+.|.
T Consensus 154 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 154 ITYEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred CCHHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 356688999999999998888776666654
No 156
>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=47.13 E-value=41 Score=26.58 Aligned_cols=28 Identities=11% Similarity=0.207 Sum_probs=24.0
Q ss_pred HHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
-.++|..+|+++..|+..+..-|.+.|.
T Consensus 127 ~~EIA~~lg~s~~tVr~~l~RAr~~Lr~ 154 (281)
T TIGR02957 127 YEEIASIVGKSEANCRQLVSRARRHLDA 154 (281)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4578999999999999999988877765
No 157
>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=46.71 E-value=59 Score=24.90 Aligned_cols=53 Identities=11% Similarity=0.204 Sum_probs=38.0
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHH
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSK 73 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~ 73 (155)
.+++.+..+|...|....+ ......++|..+|++...|+.+...-..|.|...
T Consensus 176 ~L~~~er~vl~l~ygl~~~-~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~ 228 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDG-RPHTLEEVGKEFNVTRERIRQIESKALRKLRHPS 228 (238)
T ss_pred hCCHHHHHHHHHHhCCCCC-CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhH
Confidence 3556666677666632221 2345778999999999999999998888888753
No 158
>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=46.44 E-value=31 Score=26.50 Aligned_cols=53 Identities=19% Similarity=0.224 Sum_probs=40.2
Q ss_pred ccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHHHHH
Q psy16514 19 AVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKEREL 77 (155)
Q Consensus 19 ~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~~~ 77 (155)
..+|+.++.+|.-.. ....-.++|..+|++++.|+.+..|-+.|.+-....+.
T Consensus 170 ~~Lt~re~evl~~~a------~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~~~~a 222 (232)
T TIGR03541 170 GVLSEREREVLAWTA------LGRRQADIAAILGISERTVENHLRSARRKLGVATTAQA 222 (232)
T ss_pred ccCCHHHHHHHHHHH------CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCHHHH
Confidence 467888888887653 12356788999999999999999999888776554443
No 159
>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=46.34 E-value=13 Score=21.40 Aligned_cols=24 Identities=38% Similarity=0.537 Sum_probs=19.4
Q ss_pred HHHHHHHHhCCCccchhhhhhhhH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRR 66 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR 66 (155)
....||..+|++...|..|..+++
T Consensus 11 s~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 11 SQKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred CHHHHHHHhCCCcchhHHHhcCCC
Confidence 347899999999999999998854
No 160
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=46.04 E-value=51 Score=23.56 Aligned_cols=29 Identities=14% Similarity=0.189 Sum_probs=23.4
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
.-.++|..+|++...|+.+..+.+..++.
T Consensus 136 s~~EIA~~l~is~~tV~~~l~ra~~~~~~ 164 (168)
T PRK12525 136 TYVEIGERLGVSLSRIHQYMVEAFKCCYQ 164 (168)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45688999999999999998777666553
No 161
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=45.93 E-value=45 Score=26.23 Aligned_cols=46 Identities=20% Similarity=0.353 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 21 FSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 21 ~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
+++.+..+|...|. ......++|..+|++...|+.+...-+.+.|+
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 44455555555553 23356789999999999999999877777665
No 162
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=45.88 E-value=48 Score=25.94 Aligned_cols=47 Identities=15% Similarity=0.244 Sum_probs=32.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 21 FSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 21 ~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
+++.+..+|...|.. .....++|..+|++...|+.....-+.+.|+.
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 444555555554432 23567899999999999998888777776654
No 163
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=45.63 E-value=46 Score=22.46 Aligned_cols=42 Identities=14% Similarity=0.171 Sum_probs=32.3
Q ss_pred cccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCC-Cccchhhhhh
Q psy16514 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGL-KDSQVKIWFQ 63 (155)
Q Consensus 18 R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l-~~~~V~~WFq 63 (155)
|..|+.+....+-+.+....+ ....+|..+|+ ...++..|-.
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 678999987666666655544 57789999996 9988888875
No 164
>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=45.46 E-value=16 Score=22.21 Aligned_cols=20 Identities=20% Similarity=0.358 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCccchhhhhh
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQ 63 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFq 63 (155)
..++|+.+|++...++.|.+
T Consensus 3 i~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999975
No 165
>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=45.28 E-value=17 Score=22.00 Aligned_cols=21 Identities=19% Similarity=0.419 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCccchhhhhhh
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQN 64 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFqN 64 (155)
..++|..+|++...++.|-+.
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 457899999999999999753
No 166
>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=45.13 E-value=11 Score=21.53 Aligned_cols=21 Identities=14% Similarity=0.234 Sum_probs=19.0
Q ss_pred HHHHHhCCCccchhhhhhhhH
Q psy16514 46 KLAEKLGLKDSQVKIWFQNRR 66 (155)
Q Consensus 46 ~LA~~l~l~~~~V~~WFqNrR 66 (155)
.||..+|++...|..|+.++.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999999884
No 167
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=45.06 E-value=1.1e+02 Score=22.44 Aligned_cols=33 Identities=21% Similarity=0.305 Sum_probs=26.8
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhhHHHH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKER 75 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~ 75 (155)
...++|..+|++...|+++...-|.+.++.-..
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 178 (188)
T PRK12517 146 SGEEIAEILDLNKNTVMTRLFRARNQLKEALEK 178 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999998777777765443
No 168
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=44.93 E-value=55 Score=23.95 Aligned_cols=30 Identities=17% Similarity=0.078 Sum_probs=24.3
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
.-.++|..+|++...|+.....-|.+.|+.
T Consensus 129 s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~ 158 (182)
T PRK12540 129 SYEDAAAICGCAVGTIKSRVNRARSKLSAL 158 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999998777666653
No 169
>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=44.80 E-value=39 Score=23.24 Aligned_cols=37 Identities=19% Similarity=0.292 Sum_probs=26.3
Q ss_pred CHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhh
Q psy16514 22 SDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQ 63 (155)
Q Consensus 22 t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFq 63 (155)
+-.....+-.+|.... ....+|..++++...|..||+
T Consensus 4 S~DlR~rVl~~~~~g~-----s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 4 SLDLRQRVLAYIEKGK-----SIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred CHHHHHHHHHHHHccc-----hHHHHHHHhCcHHHHHHHHHH
Confidence 3344444445665543 466789999999999999998
No 170
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=44.63 E-value=53 Score=24.21 Aligned_cols=33 Identities=15% Similarity=0.185 Sum_probs=25.8
Q ss_pred CCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 39 ISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 39 p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
.....-.++|..+|++...|++.+...|.+.|+
T Consensus 168 ~e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~ 200 (208)
T PRK08295 168 LDGKSYQEIAEELNRHVKSIDNALQRVKRKLEK 200 (208)
T ss_pred HccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 334556688999999999999888877766665
No 171
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=44.45 E-value=48 Score=26.29 Aligned_cols=28 Identities=18% Similarity=0.194 Sum_probs=24.0
Q ss_pred HHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
..++|..+|+++..|+..++.-|.+.|+
T Consensus 134 ~~EIA~~lg~s~~tVk~~l~RAr~~Lr~ 161 (293)
T PRK09636 134 FDEIASTLGRSPAACRQLASRARKHVRA 161 (293)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4578999999999999999987777776
No 172
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=44.16 E-value=58 Score=23.99 Aligned_cols=30 Identities=23% Similarity=0.404 Sum_probs=24.6
Q ss_pred HHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 42 PDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 42 ~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
....++|..+|++++.|+..++.-|.+.++
T Consensus 152 ls~~EIA~~lgiS~~tV~r~l~~aR~~l~~ 181 (185)
T PF07638_consen 152 LSVEEIAERLGISERTVRRRLRRARAWLRR 181 (185)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 356689999999999999999888866554
No 173
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=42.93 E-value=69 Score=22.51 Aligned_cols=29 Identities=28% Similarity=0.354 Sum_probs=23.4
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
...++|..+|++...|+......+.+.|+
T Consensus 123 s~~eIA~~lgis~~tv~~~l~ra~~~Lr~ 151 (159)
T PRK12527 123 SHQQIAEHLGISRSLVEKHIVNAMKHCRV 151 (159)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45688999999999999988876666665
No 174
>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=42.76 E-value=19 Score=21.68 Aligned_cols=20 Identities=15% Similarity=0.353 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCccchhhhhh
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQ 63 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFq 63 (155)
..++|..+|++...++.|.+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999985
No 175
>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=42.55 E-value=19 Score=25.11 Aligned_cols=34 Identities=24% Similarity=0.201 Sum_probs=26.9
Q ss_pred CCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 38 YISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 38 ~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
|.......++|..+|++...|+++...-|.+.|+
T Consensus 118 ~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 118 EFKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3444566789999999999999999877776664
No 176
>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=41.69 E-value=60 Score=25.51 Aligned_cols=54 Identities=15% Similarity=0.092 Sum_probs=41.3
Q ss_pred cccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHHHHH
Q psy16514 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKEREL 77 (155)
Q Consensus 18 R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~~~ 77 (155)
...+|+.+..+|.-... . ....++|..||+++..|+.+.+|-+.|..-....+.
T Consensus 188 ~~~LT~RE~evl~l~a~--G----~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~nr~qA 241 (247)
T TIGR03020 188 AGLITAREAEILAWVRD--G----KTNEEIAAILGISSLTVKNHLQHIFKKLDVRNRAQA 241 (247)
T ss_pred ccCCCHHHHHHHHHHHC--C----CCHHHHHHHHCcCHHHHHHHHHHHHHHhCCCCHHHH
Confidence 34689999999986542 2 356778999999999999999998888776554443
No 177
>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=41.53 E-value=62 Score=24.52 Aligned_cols=46 Identities=17% Similarity=0.213 Sum_probs=30.8
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHh
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~r 70 (155)
.+++.+..++...|.. .....++|..+|++...|..+-..-..|.|
T Consensus 183 ~L~~~e~~i~~~~~~~-----~~t~~eIA~~lgis~~~V~~~~~~al~~Lr 228 (231)
T TIGR02885 183 KLDERERQIIMLRYFK-----DKTQTEVANMLGISQVQVSRLEKKVLKKMK 228 (231)
T ss_pred cCCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 3455555566555532 246778999999999988877765555444
No 178
>PRK05572 sporulation sigma factor SigF; Validated
Probab=41.50 E-value=63 Score=25.01 Aligned_cols=47 Identities=15% Similarity=0.192 Sum_probs=34.1
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
.+++.+..++...|.. .....++|..+|++...|..+-..-..+.|+
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 4666666666666643 2456789999999999998888766666654
No 179
>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=41.33 E-value=18 Score=19.60 Aligned_cols=23 Identities=35% Similarity=0.510 Sum_probs=19.6
Q ss_pred HHHHHHHhCCCccchhhhhhhhH
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQNRR 66 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFqNrR 66 (155)
...+|..+|++...|..|..+.+
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 45789999999999999998763
No 180
>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=41.20 E-value=53 Score=26.17 Aligned_cols=29 Identities=24% Similarity=0.236 Sum_probs=24.0
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
.-.++|..+|++...|+.....-|.+.|+
T Consensus 160 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 188 (324)
T TIGR02960 160 RAAETAELLGTSTASVNSALQRARATLDE 188 (324)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34588999999999999999877776665
No 181
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=40.76 E-value=56 Score=23.01 Aligned_cols=46 Identities=20% Similarity=0.208 Sum_probs=35.1
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
.+|+.+..+|.- +..+ + ...++|..++++...|+.+.++-+.|..-
T Consensus 149 ~lt~~e~~vl~l-~~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~ 194 (211)
T PRK15369 149 LLTPRERQILKL-ITEG-Y----TNRDIAEQLSISIKTVETHRLNMMRKLDV 194 (211)
T ss_pred CCCHHHHHHHHH-HHCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 478888888776 3332 2 35688999999999999999988777653
No 182
>KOG0772|consensus
Probab=40.75 E-value=53 Score=28.99 Aligned_cols=9 Identities=44% Similarity=0.937 Sum_probs=3.9
Q ss_pred CCccccccC
Q psy16514 119 EEEEDDLMR 127 (155)
Q Consensus 119 ~~~~~~~~~ 127 (155)
++.++++|.
T Consensus 103 de~ee~~mg 111 (641)
T KOG0772|consen 103 DEDEEDFMG 111 (641)
T ss_pred ccchhhhcC
Confidence 334444444
No 183
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=40.73 E-value=62 Score=20.99 Aligned_cols=44 Identities=16% Similarity=0.217 Sum_probs=33.7
Q ss_pred cCCHHHHHHHHHHHhh-----cCCCCHHHHHHHHHHhCCCccchhhhhh
Q psy16514 20 VFSDLQRKGLEKRFQI-----QKYISKPDRKKLAEKLGLKDSQVKIWFQ 63 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~-----~~~p~~~~~~~LA~~l~l~~~~V~~WFq 63 (155)
.++..|+..|...|.. +.+.+..+...+...+|++...|..+|.
T Consensus 3 ~ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~ 51 (96)
T smart00027 3 AISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWN 51 (96)
T ss_pred CCCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHH
Confidence 4678899999999864 3577777777776778888888887775
No 184
>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=40.31 E-value=72 Score=22.94 Aligned_cols=30 Identities=13% Similarity=0.237 Sum_probs=23.5
Q ss_pred HHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 42 PDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 42 ~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
....++|..+|++...|+.=...-|.+.|+
T Consensus 157 ~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~ 186 (189)
T TIGR02984 157 LSFAEVAERMDRSEGAVSMLWVRGLARLRQ 186 (189)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 355678999999999998888777766664
No 185
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=40.24 E-value=64 Score=25.07 Aligned_cols=47 Identities=21% Similarity=0.256 Sum_probs=33.7
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
.+++.+..+|...|... ....++|..+|++...|+..-.+-..|.|+
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 46667777777776432 356789999999999988887766655554
No 186
>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=39.85 E-value=19 Score=20.56 Aligned_cols=23 Identities=13% Similarity=0.094 Sum_probs=20.3
Q ss_pred HHHHHHHhCCCccchhhhhhhhH
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQNRR 66 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFqNrR 66 (155)
...||..+|++...|..|..+++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 57899999999999999997764
No 187
>smart00595 MADF subfamily of SANT domain.
Probab=39.85 E-value=59 Score=20.60 Aligned_cols=34 Identities=29% Similarity=0.417 Sum_probs=28.0
Q ss_pred HHHHHHhCCCccchhhhhhhhHHHHhhHHHHHHH
Q psy16514 45 KKLAEKLGLKDSQVKIWFQNRRMKWRNSKERELL 78 (155)
Q Consensus 45 ~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~~~~ 78 (155)
..+|..+|.+...|+.-+.|-|.+.++...+...
T Consensus 31 ~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~r~~~ 64 (89)
T smart00595 31 EEIAEELGLSVEECKKRWKNLRDRYRRELKRLQN 64 (89)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3579999999999999999999999987555433
No 188
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=39.60 E-value=43 Score=23.81 Aligned_cols=46 Identities=26% Similarity=0.177 Sum_probs=35.8
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
.+|+.+..+|...+.. .....+|..++++.+.|++..++=|.|...
T Consensus 137 ~Lt~~E~~il~~l~~g------~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~~ 182 (196)
T PRK10360 137 PLTKRERQVAEKLAQG------MAVKEIAAELGLSPKTVHVHRANLMEKLGV 182 (196)
T ss_pred CCCHHHHHHHHHHHCC------CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 5788888787776543 257788999999999999999887777553
No 189
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=39.37 E-value=73 Score=24.89 Aligned_cols=47 Identities=19% Similarity=0.287 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 21 FSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 21 ~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
+.+.+..+|...|. ......++|..+|++...|+.+...-+.+.|+.
T Consensus 206 L~~~er~vi~l~y~-----e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 252 (257)
T PRK05911 206 LEEKERKVMALYYY-----EELVLKEIGKILGVSESRVSQIHSKALLKLRAT 252 (257)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 34444444444442 233567899999999999999888777666653
No 190
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=38.99 E-value=64 Score=24.57 Aligned_cols=51 Identities=16% Similarity=0.126 Sum_probs=39.3
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHHHH
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERE 76 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~~ 76 (155)
.+|+.++.+|.-...- ..-.++|..+++++..|+.+..+-..|..-.+..+
T Consensus 155 ~Lt~rE~~Vl~l~~~G------~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v~nr~e 205 (216)
T PRK10100 155 LLTHREKEILNKLRIG------ASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQ 205 (216)
T ss_pred CCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHH
Confidence 4888888888877662 23567899999999999999998887766544333
No 191
>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=38.88 E-value=19 Score=26.34 Aligned_cols=34 Identities=15% Similarity=0.184 Sum_probs=25.9
Q ss_pred CCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 38 YISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 38 ~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
|.......++|..+|++...|++++..-|.+.|+
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 3344456689999999999999988876666554
No 192
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=38.86 E-value=78 Score=23.24 Aligned_cols=29 Identities=21% Similarity=0.251 Sum_probs=20.7
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
...++|..+|++...|++=...-|.+.|+
T Consensus 152 s~~EIA~~lg~s~~tV~~rl~rar~~Lr~ 180 (192)
T PRK09643 152 SVADAARMLGVAEGTVKSRCARGRARLAE 180 (192)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45678999999999887666554555444
No 193
>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=38.59 E-value=63 Score=25.38 Aligned_cols=49 Identities=18% Similarity=0.215 Sum_probs=35.7
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
.+++.+..+|...|-. -......++|..+|++...|+.+..+-..|.|+
T Consensus 218 ~L~~rer~vl~l~y~~---~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~ 266 (270)
T TIGR02392 218 SLDARSRRIIEARWLD---DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKA 266 (270)
T ss_pred cCCHHHHHHHHHHhcC---CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3556666677766632 112356789999999999999999888877775
No 194
>PF13730 HTH_36: Helix-turn-helix domain
Probab=38.41 E-value=39 Score=19.42 Aligned_cols=43 Identities=16% Similarity=0.108 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHhCCCccchhhhhhh
Q psy16514 21 FSDLQRKGLEKRFQ---IQKYISKPDRKKLAEKLGLKDSQVKIWFQN 64 (155)
Q Consensus 21 ~t~~ql~~L~~~F~---~~~~p~~~~~~~LA~~l~l~~~~V~~WFqN 64 (155)
+++.+..++-..+. .+.. ...-...||..+|++.+.|+.+...
T Consensus 3 Ls~~~~~v~~~l~~~~~~~~~-~~pS~~~la~~~g~s~~Tv~~~i~~ 48 (55)
T PF13730_consen 3 LSPTAKLVYLYLASYANKNGG-CFPSQETLAKDLGVSRRTVQRAIKE 48 (55)
T ss_pred CCHHHHHHHHHHHHhcCCCCC-CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 44555555544432 2233 3345788999999999999888754
No 195
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=38.37 E-value=37 Score=25.89 Aligned_cols=36 Identities=25% Similarity=0.321 Sum_probs=29.2
Q ss_pred CCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHH
Q psy16514 38 YISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSK 73 (155)
Q Consensus 38 ~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~ 73 (155)
|.......++|..+|++...|++....-|.+.|+.-
T Consensus 162 ~~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l 197 (231)
T PRK11922 162 VVEELSVEETAQALGLPEETVKTRLHRARRLLRESL 197 (231)
T ss_pred hhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 445556778999999999999999988787777754
No 196
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=37.64 E-value=50 Score=20.14 Aligned_cols=36 Identities=33% Similarity=0.546 Sum_probs=22.7
Q ss_pred HHHHHHHhCCCccchhhhhhhhHHHHhhHHHHHHHhcC
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERELLANG 81 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~~~~~~~ 81 (155)
...||..||++..-|..| ..+--..+.-..+...++
T Consensus 12 ~~~lAkalGVs~~aVs~W--~~~IP~~ra~~Ie~~T~G 47 (60)
T PF14549_consen 12 QSKLAKALGVSPQAVSQW--GERIPAERAYQIEKLTNG 47 (60)
T ss_dssp HHHHHHHHTS-HHHHHHH--HTS--HHHHHHHHHHTTT
T ss_pred HHHHHHHHCCCHHHHHHh--cCccCHHHHHHHHHHhCC
Confidence 457999999999999999 444444444444444444
No 197
>PRK10651 transcriptional regulator NarL; Provisional
Probab=37.43 E-value=64 Score=23.02 Aligned_cols=51 Identities=22% Similarity=0.184 Sum_probs=38.3
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHHHH
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERE 76 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~~ 76 (155)
.+|+.+..+|+..... .....+|..++++.+.|++..++-+.|..-....+
T Consensus 155 ~Lt~rE~~vl~~l~~g------~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~~~~~~ 205 (216)
T PRK10651 155 QLTPRERDILKLIAQG------LPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVE 205 (216)
T ss_pred cCCHHHHHHHHHHHcC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCHHH
Confidence 4899999888775532 13566788999999999999999888866544333
No 198
>PHA02955 hypothetical protein; Provisional
Probab=37.39 E-value=45 Score=25.77 Aligned_cols=46 Identities=11% Similarity=0.086 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHhhc-CCCCHHHHHHHHHHhCCCccchhhhhhhhHHH
Q psy16514 23 DLQRKGLEKRFQIQ-KYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68 (155)
Q Consensus 23 ~~ql~~L~~~F~~~-~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k 68 (155)
..++..|-+.|... .-.+..++..+|..+|+....|..||.+.-.+
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~~~q 106 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTDLQL 106 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccchhhh
Confidence 36777888888766 67778889999999999998789999875433
No 199
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=36.28 E-value=40 Score=25.65 Aligned_cols=43 Identities=9% Similarity=0.143 Sum_probs=35.5
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHh
Q psy16514 26 RKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70 (155)
Q Consensus 26 l~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~r 70 (155)
+.+-...|....|- .....+|...|++...|..+|.+|..=..
T Consensus 19 l~aA~~lF~~~Gy~--~s~~~IA~~AGvsk~tiy~~F~sKe~L~~ 61 (225)
T PRK11552 19 IAAALAQFGEYGLH--ATTRDIAAQAGQNIAAITYYFGSKEDLYL 61 (225)
T ss_pred HHHHHHHHHHhCcc--CCHHHHHHHhCCCHHHHHHHcCCHHHHHH
Confidence 45555668888887 57888999999999999999999887543
No 200
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=35.73 E-value=72 Score=24.68 Aligned_cols=29 Identities=14% Similarity=0.189 Sum_probs=23.9
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
...++|..+|++...|+.+...-|.+.|+
T Consensus 134 S~~EIAe~LgiS~~tVksrL~Rark~Lr~ 162 (228)
T PRK06704 134 SIADIAKVCSVSEGAVKASLFRSRNRLKT 162 (228)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45688999999999999999877777665
No 201
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=35.33 E-value=39 Score=24.68 Aligned_cols=33 Identities=15% Similarity=0.229 Sum_probs=26.6
Q ss_pred CHHHHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 40 SKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 40 ~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
......++|..+|++...|+++...-+.+.|+.
T Consensus 149 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 181 (188)
T PRK09640 149 AELEFQEIADIMHMGLSATKMRYKRALDKLREK 181 (188)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 334566899999999999999998777777663
No 202
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=34.88 E-value=89 Score=23.80 Aligned_cols=30 Identities=20% Similarity=0.197 Sum_probs=23.2
Q ss_pred HHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 42 PDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 42 ~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
....++|..+|++...|+.+-...+.+.|+
T Consensus 196 ~S~~EIA~~lgis~~tV~~~~~rA~~kLr~ 225 (233)
T PRK05803 196 KTQREIAKALGISRSYVSRIEKRALKKLFK 225 (233)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 457788999999999998886655555554
No 203
>KOG3623|consensus
Probab=34.73 E-value=27 Score=32.08 Aligned_cols=54 Identities=17% Similarity=0.271 Sum_probs=42.0
Q ss_pred cccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 18 R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
|+.+...+..-|..++..+--++-.+....+..|-..+.+|.+||++|+..-+.
T Consensus 630 ~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp 683 (1007)
T KOG3623|consen 630 RSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSP 683 (1007)
T ss_pred cCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCC
Confidence 566777777888888887777776666666666778889999999999876655
No 204
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=34.65 E-value=55 Score=23.80 Aligned_cols=41 Identities=10% Similarity=0.101 Sum_probs=32.7
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHH
Q psy16514 26 RKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRM 67 (155)
Q Consensus 26 l~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~ 67 (155)
+......|....|. ......+|...|++...+..+|.+|..
T Consensus 14 l~aA~~lf~e~G~~-~tSi~~Ia~~aGvsk~~lY~~F~sK~~ 54 (192)
T PRK14996 14 LQAAMRVALAEGFA-AMTVRRIASEAQVAAGQVHHHFSSAGE 54 (192)
T ss_pred HHHHHHHHHhcChh-hccHHHHHHHhCCCcHHHHHHcCCHHH
Confidence 44555568888874 356778899999999999999998776
No 205
>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=34.62 E-value=25 Score=21.69 Aligned_cols=23 Identities=30% Similarity=0.433 Sum_probs=20.1
Q ss_pred HHHHHHHhCCCccchhhhhhhhH
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQNRR 66 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFqNrR 66 (155)
...||..+|++...|..|+.+++
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 56899999999999999998764
No 206
>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=33.81 E-value=30 Score=18.87 Aligned_cols=23 Identities=22% Similarity=0.253 Sum_probs=18.4
Q ss_pred HHHHHHHhCCCccchhhhhhhhH
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQNRR 66 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFqNrR 66 (155)
..++|..+|++...|..|.+..+
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcCC
Confidence 45788999999999999986543
No 207
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=33.54 E-value=84 Score=21.93 Aligned_cols=50 Identities=18% Similarity=0.217 Sum_probs=33.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHHHH
Q psy16514 21 FSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERE 76 (155)
Q Consensus 21 ~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~~ 76 (155)
+++.+..+|...+... .-..+|..+|+++..|+++..+-|.|.+.....+
T Consensus 142 l~~~e~~vl~~~~~~~------~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~~~~~ 191 (202)
T PRK09390 142 LSERERQVMDGLVAGL------SNKVIARDLDISPRTVEVYRANVMTKMQAGSLSE 191 (202)
T ss_pred hhhhHHHHHHHHHccC------chHHHHHHcCCCHHHHHHHHHHHHHHHccccHHH
Confidence 4555555555333211 2455788999999999999998888877655444
No 208
>PF13565 HTH_32: Homeodomain-like domain
Probab=33.49 E-value=1.2e+02 Score=18.56 Aligned_cols=32 Identities=16% Similarity=0.214 Sum_probs=23.8
Q ss_pred CHHHHHHHHHHHhhcCCCCHHHHHH-HHHHhCC
Q psy16514 22 SDLQRKGLEKRFQIQKYISKPDRKK-LAEKLGL 53 (155)
Q Consensus 22 t~~ql~~L~~~F~~~~~p~~~~~~~-LA~~l~l 53 (155)
+.++...|.+.+..++..+...... |+..+|+
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~ 64 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGI 64 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCC
Confidence 6777788999988888777666555 6666664
No 209
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=33.42 E-value=58 Score=23.24 Aligned_cols=49 Identities=20% Similarity=0.055 Sum_probs=36.4
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHH
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKE 74 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~ 74 (155)
.++..+...|.-.+.. ....++|..++++.+.|+.+..+-|.|..-...
T Consensus 149 ~lt~re~~vl~~l~~g------~s~~eIa~~l~~s~~tv~~~~~~~~~kl~~~~~ 197 (210)
T PRK09935 149 VLSNREVTILRYLVSG------LSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSI 197 (210)
T ss_pred cCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCH
Confidence 4677777777644332 457789999999999999999988877654433
No 210
>PHA01976 helix-turn-helix protein
Probab=33.12 E-value=29 Score=20.81 Aligned_cols=24 Identities=17% Similarity=0.361 Sum_probs=20.3
Q ss_pred HHHHHHHHhCCCccchhhhhhhhH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRR 66 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR 66 (155)
....||..+|++...|..|...++
T Consensus 17 t~~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 17 SAPELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCC
Confidence 356899999999999999997654
No 211
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=32.75 E-value=82 Score=25.13 Aligned_cols=49 Identities=16% Similarity=0.175 Sum_probs=35.8
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
.+++.+..+|...|- +-......++|..+|++...|+.+-..-+.|.|.
T Consensus 227 ~L~~rer~vl~lr~~---~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~ 275 (289)
T PRK07500 227 TLNERELRIIRERRL---REDGATLEALGEELGISKERVRQIEARALEKLRR 275 (289)
T ss_pred cCCHHHHHHHHHHhc---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 356666666666653 1233467889999999999999999887777765
No 212
>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=32.59 E-value=84 Score=17.44 Aligned_cols=37 Identities=35% Similarity=0.417 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhh
Q psy16514 23 DLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQ 63 (155)
Q Consensus 23 ~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFq 63 (155)
..+..+|...+. ++. ....+||..+|++...|..-++
T Consensus 3 ~~~~~Il~~l~~-~~~---~t~~ela~~~~is~~tv~~~l~ 39 (48)
T PF13412_consen 3 ETQRKILNYLRE-NPR---ITQKELAEKLGISRSTVNRYLK 39 (48)
T ss_dssp HHHHHHHHHHHH-CTT---S-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHH-cCC---CCHHHHHHHhCCCHHHHHHHHH
Confidence 456677766665 333 4567889999999987765553
No 213
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=32.51 E-value=72 Score=25.68 Aligned_cols=29 Identities=21% Similarity=0.165 Sum_probs=24.2
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
...++|..+|++...|+.....-|.+.|+
T Consensus 171 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 171 SAAEVAELLDTSVAAVNSALQRARATLAE 199 (339)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHhh
Confidence 45688999999999999999877777665
No 214
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=32.24 E-value=50 Score=22.81 Aligned_cols=28 Identities=18% Similarity=0.253 Sum_probs=22.4
Q ss_pred CCCHHHHHHHHHHhCCCccchhhhhhhh
Q psy16514 38 YISKPDRKKLAEKLGLKDSQVKIWFQNR 65 (155)
Q Consensus 38 ~p~~~~~~~LA~~l~l~~~~V~~WFqNr 65 (155)
+-.......||..+|++.+.+..+|+..
T Consensus 22 ~~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 22 LESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred cCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3344567889999999999999888755
No 215
>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=31.85 E-value=39 Score=19.37 Aligned_cols=35 Identities=20% Similarity=0.261 Sum_probs=22.3
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhh
Q psy16514 26 RKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQ 63 (155)
Q Consensus 26 l~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFq 63 (155)
..+|...+....+ .....||..++++.+.|+.-..
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 4455554444443 4567899999999988765553
No 216
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=31.52 E-value=41 Score=24.07 Aligned_cols=33 Identities=15% Similarity=0.161 Sum_probs=26.2
Q ss_pred CCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 39 ISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 39 p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
........+|..+|++...|+.+...-|.+.++
T Consensus 140 ~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~ 172 (176)
T PRK09638 140 YYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRK 172 (176)
T ss_pred hcCCCHHHHHHHHCCChhHHHHHHHHHHHHHHH
Confidence 344556789999999999999999877766665
No 217
>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=31.43 E-value=1.3e+02 Score=20.43 Aligned_cols=46 Identities=22% Similarity=0.273 Sum_probs=33.4
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHh
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~r 70 (155)
.+|..|...|+-+|..+ .-..++|..+|++...|.-|.+.-+.+..
T Consensus 17 LLT~kQ~~~l~lyy~eD-----lSlsEIAe~~~iSRqaV~d~ikr~~~~L~ 62 (101)
T PF04297_consen 17 LLTEKQREILELYYEED-----LSLSEIAEELGISRQAVYDSIKRAEKKLE 62 (101)
T ss_dssp GS-HHHHHHHHHHCTS--------HHHHHHHCTS-HHHHHHHHHHHHHHHH
T ss_pred HCCHHHHHHHHHHHccC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 57889999999887665 35778899999999999999976655443
No 218
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=31.33 E-value=1.1e+02 Score=24.08 Aligned_cols=51 Identities=22% Similarity=0.281 Sum_probs=33.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 21 FSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 21 ~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
+++.+..+|...|... |.....-.++|..+|++...|+.+....+.+.|+.
T Consensus 223 Lp~~~R~Vl~l~ygL~-~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~ 273 (285)
T TIGR02394 223 LNERQREVLARRFGLL-GYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRI 273 (285)
T ss_pred CCHHHHHHHHHHhCCC-CCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3444444554444110 12334577889999999999999998877777764
No 219
>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=30.70 E-value=24 Score=26.25 Aligned_cols=32 Identities=19% Similarity=0.373 Sum_probs=27.8
Q ss_pred HHHHHHHHHhCCCccchhhhhhhhHHHHhhHH
Q psy16514 42 PDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSK 73 (155)
Q Consensus 42 ~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~ 73 (155)
..+.+|+..++++..+|-+|.+|-+...++..
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~ 46 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKDPKRAKP 46 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCCcccccc
Confidence 46788999999999999999999988777643
No 220
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=30.50 E-value=35 Score=20.46 Aligned_cols=20 Identities=10% Similarity=0.180 Sum_probs=16.8
Q ss_pred HHHHHHHhCCCccchhhhhh
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQ 63 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFq 63 (155)
..++|..+|++...|+.|-.
T Consensus 3 ~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35689999999999999963
No 221
>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=30.33 E-value=1.2e+02 Score=23.03 Aligned_cols=30 Identities=23% Similarity=0.257 Sum_probs=23.2
Q ss_pred HHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 42 PDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 42 ~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
....++|..+|++...|..+...-+.+.|+
T Consensus 195 ~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~ 224 (227)
T TIGR02846 195 KTQREIAKILGISRSYVSRIEKRALMKLYK 224 (227)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 356788999999999998887666666554
No 222
>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=30.01 E-value=39 Score=22.43 Aligned_cols=21 Identities=10% Similarity=0.093 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCccchhhhhhh
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQN 64 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFqN 64 (155)
..++|..+|++...++.|..+
T Consensus 3 i~eva~~~gvs~~tlR~ye~~ 23 (103)
T cd01106 3 VGEVAKLTGVSVRTLHYYDEI 23 (103)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999764
No 223
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=29.64 E-value=35 Score=18.16 Aligned_cols=23 Identities=35% Similarity=0.491 Sum_probs=19.4
Q ss_pred HHHHHHHhCCCccchhhhhhhhH
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQNRR 66 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFqNrR 66 (155)
...||..+|++...|..|..+++
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~~ 35 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGKR 35 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 55789999999999999987654
No 224
>PF05703 Auxin_canalis: Auxin canalisation; InterPro: IPR008546 This domain consists of several plant proteins of unknown function.
Probab=29.56 E-value=1.1e+02 Score=24.15 Aligned_cols=18 Identities=17% Similarity=0.507 Sum_probs=13.9
Q ss_pred CccchhhhhhhhHHHHhh
Q psy16514 54 KDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 54 ~~~~V~~WFqNrR~k~rk 71 (155)
....|..||+.++.|.|-
T Consensus 99 ~~~~i~~w~~~~~~kkke 116 (242)
T PF05703_consen 99 GGKTIGRWLKDRKEKKKE 116 (242)
T ss_pred ccchHHHHHHHHHHHHHH
Confidence 456899999999886444
No 225
>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=29.50 E-value=1.2e+02 Score=23.15 Aligned_cols=30 Identities=17% Similarity=0.259 Sum_probs=24.7
Q ss_pred HHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 42 PDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 42 ~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
....++|..+|++...|+++...-+.+.|+
T Consensus 199 ~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~ 228 (234)
T TIGR02835 199 KTQKEVADMLGISQSYISRLEKRILKRLKK 228 (234)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 356788999999999999998877777665
No 226
>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=29.46 E-value=66 Score=21.81 Aligned_cols=23 Identities=17% Similarity=0.137 Sum_probs=19.2
Q ss_pred HHHHHHHhCCCccchhhhhhhhH
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQNRR 66 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFqNrR 66 (155)
...||..+|++...|..|-..+.
T Consensus 81 q~~lA~~lg~~~~tis~~e~g~~ 103 (127)
T TIGR03830 81 QREAAELLGGGVNAFSRYERGEV 103 (127)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 45789999999999999987665
No 227
>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=29.42 E-value=1.9e+02 Score=21.31 Aligned_cols=47 Identities=17% Similarity=0.087 Sum_probs=36.7
Q ss_pred cccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhH
Q psy16514 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRR 66 (155)
Q Consensus 18 R~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR 66 (155)
.-.++++++..+..+-..+ |..-.+..||+++|++.--|.+-..-..
T Consensus 83 ~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~v~~~~~ 129 (164)
T PF12824_consen 83 KYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSMVAPAPK 129 (164)
T ss_pred cccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHHhcCCCH
Confidence 3689999999999987766 4566788999999999877766554333
No 228
>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=28.54 E-value=94 Score=19.08 Aligned_cols=40 Identities=30% Similarity=0.377 Sum_probs=23.5
Q ss_pred cCCHHHHHHHHH---HHhhcCCCCHHHHHHHHHHhCCC-ccchhhh
Q psy16514 20 VFSDLQRKGLEK---RFQIQKYISKPDRKKLAEKLGLK-DSQVKIW 61 (155)
Q Consensus 20 ~~t~~ql~~L~~---~F~~~~~p~~~~~~~LA~~l~l~-~~~V~~W 61 (155)
.+|..|..+|.- +...+.||. ...+||..+|+. ...|..-
T Consensus 3 ~LT~rQ~~vL~~I~~~~~~~G~~P--t~rEIa~~~g~~S~~tv~~~ 46 (65)
T PF01726_consen 3 ELTERQKEVLEFIREYIEENGYPP--TVREIAEALGLKSTSTVQRH 46 (65)
T ss_dssp ---HHHHHHHHHHHHHHHHHSS-----HHHHHHHHTSSSHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHcCCCC--CHHHHHHHhCCCChHHHHHH
Confidence 356777666654 456677874 678899999997 5555433
No 229
>PF12728 HTH_17: Helix-turn-helix domain
Probab=28.48 E-value=40 Score=19.07 Aligned_cols=23 Identities=35% Similarity=0.559 Sum_probs=18.4
Q ss_pred HHHHHHHhCCCccchhhhhhhhH
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQNRR 66 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFqNrR 66 (155)
..++|..||++...|..|.+...
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g~ 26 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQGK 26 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCC
Confidence 45678899999999999986543
No 230
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=28.04 E-value=1.1e+02 Score=24.35 Aligned_cols=28 Identities=18% Similarity=0.256 Sum_probs=23.6
Q ss_pred HHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
-.++|..+|+++..|+...+.-|.+.+.
T Consensus 137 ~~EIA~~Lgis~~tVr~~l~RAr~~Lr~ 164 (290)
T PRK09635 137 YQQIATTIGSQASTCRQLAHRARRKINE 164 (290)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHh
Confidence 4478999999999999999877777665
No 231
>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=27.52 E-value=91 Score=17.93 Aligned_cols=39 Identities=26% Similarity=0.267 Sum_probs=28.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhh
Q psy16514 21 FSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQ 63 (155)
Q Consensus 21 ~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFq 63 (155)
+|..|..+|...+...+ .....||..++++...|..+..
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 46778888888887655 3345899999999887766653
No 232
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=26.58 E-value=40 Score=23.55 Aligned_cols=24 Identities=13% Similarity=0.379 Sum_probs=21.1
Q ss_pred HHHHHHHhCCCccchhhhhhhhHH
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQNRRM 67 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFqNrR~ 67 (155)
...||..+|++...|..|..+++.
T Consensus 21 q~~lA~~~gvs~~~is~~E~g~~~ 44 (135)
T PRK09706 21 QRSLAKAVKVSHVSISQWERDETE 44 (135)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 568999999999999999988753
No 233
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=26.40 E-value=68 Score=23.26 Aligned_cols=30 Identities=30% Similarity=0.407 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHhhH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~ 72 (155)
.-.++|..+|++...|+.|....|.+.++.
T Consensus 145 s~~EIA~~l~i~~~tVks~l~ra~~~l~~~ 174 (182)
T COG1595 145 SYEEIAEILGISVGTVKSRLHRARKKLREQ 174 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 455789999999999999999888877764
No 234
>PRK09726 antitoxin HipB; Provisional
Probab=26.20 E-value=1.3e+02 Score=19.25 Aligned_cols=24 Identities=25% Similarity=0.479 Sum_probs=20.6
Q ss_pred HHHHHHHHhCCCccchhhhhhhhH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRR 66 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR 66 (155)
....||..+|++...|..|..+++
T Consensus 27 tq~elA~~~gvs~~tis~~e~g~~ 50 (88)
T PRK09726 27 TQSELAKKIGIKQATISNFENNPD 50 (88)
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCC
Confidence 467899999999999999998753
No 235
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=26.06 E-value=1.3e+02 Score=20.86 Aligned_cols=38 Identities=16% Similarity=0.163 Sum_probs=26.8
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhh
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWF 62 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WF 62 (155)
.++.+|+..++....... -...+++.+|+++..|+.-+
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 567888888877665443 45677888888887776544
No 236
>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=25.95 E-value=50 Score=21.83 Aligned_cols=21 Identities=24% Similarity=0.417 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCccchhhhhhh
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQN 64 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFqN 64 (155)
...+|..+|++...++.|.+.
T Consensus 3 I~e~a~~~gvs~~tLR~ye~~ 23 (96)
T cd04774 3 VDEVAKRLGLTKRTLKYYEEI 23 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999753
No 237
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=25.89 E-value=1.3e+02 Score=23.81 Aligned_cols=48 Identities=21% Similarity=0.285 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 21 FSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 21 ~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
++..+..+|...|-.. ......++|..+|++...|+.+-..-..|.|+
T Consensus 231 L~~rEr~VL~lry~~~---~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~ 278 (284)
T PRK06596 231 LDERSRDIIEARWLDD---DKSTLQELAAEYGVSAERVRQIEKNAMKKLKA 278 (284)
T ss_pred CCHHHHHHHHHHhcCC---CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4555666666666321 23456789999999999998888766666665
No 238
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=25.67 E-value=1.3e+02 Score=16.78 Aligned_cols=21 Identities=33% Similarity=0.416 Sum_probs=18.3
Q ss_pred HHHHHHHHhCCCccchhhhhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQ 63 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFq 63 (155)
....+|..+|++...|+.+|.
T Consensus 29 s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 29 SFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 467789999999999999885
No 239
>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=25.37 E-value=83 Score=18.21 Aligned_cols=37 Identities=24% Similarity=0.237 Sum_probs=26.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchh
Q psy16514 21 FSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVK 59 (155)
Q Consensus 21 ~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~ 59 (155)
++..|..+|...+..... ......||..++++...|.
T Consensus 3 lt~~q~~vL~~l~~~~~~--~~t~~~la~~l~~~~~~vs 39 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGE--ELTQSELAERLGISKSTVS 39 (62)
T ss_dssp STHHHHHHHHHHHHSTTS--GEEHHHHHHHHTS-HHHHH
T ss_pred cCHHHHHHHHHHHHCCCC--CcCHHHHHHHHCcCHHHHH
Confidence 678888888877765543 2367789999999887654
No 240
>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=25.16 E-value=48 Score=21.44 Aligned_cols=19 Identities=16% Similarity=0.401 Sum_probs=16.6
Q ss_pred HHHHHHHhCCCccchhhhh
Q psy16514 44 RKKLAEKLGLKDSQVKIWF 62 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WF 62 (155)
..++|..+|++...++.|-
T Consensus 4 i~evA~~~gvs~~tLR~ye 22 (88)
T cd01105 4 IGEVSKLTGVSPRQLRYWE 22 (88)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 4578999999999999994
No 241
>PRK06424 transcription factor; Provisional
Probab=24.70 E-value=72 Score=23.02 Aligned_cols=24 Identities=13% Similarity=0.086 Sum_probs=21.1
Q ss_pred HHHHHHHhCCCccchhhhhhhhHH
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQNRRM 67 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFqNrR~ 67 (155)
...||..+|++...|..|..+++.
T Consensus 100 Q~eLA~~iGvs~stIskiE~G~~~ 123 (144)
T PRK06424 100 QADLAAKIFERKNVIASIERGDLL 123 (144)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCCC
Confidence 568999999999999999988764
No 242
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=24.58 E-value=1.6e+02 Score=22.75 Aligned_cols=51 Identities=16% Similarity=0.205 Sum_probs=34.2
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHHHHH
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERE 76 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~~ 76 (155)
.+|+.++.+|.-...- ..-.++|..++++++.|+.-.+|-+.|..-.++.+
T Consensus 179 ~LT~rE~evl~~~a~G------~t~~eIa~~l~is~~TV~~h~~~~~~KL~~~nr~q 229 (240)
T PRK10188 179 NFSKREKEILKWTAEG------KTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQ 229 (240)
T ss_pred CCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHH
Confidence 4555555555444211 23457899999999999999999888766544443
No 243
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=24.49 E-value=2.2e+02 Score=24.37 Aligned_cols=53 Identities=17% Similarity=0.191 Sum_probs=37.1
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHH
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSK 73 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~ 73 (155)
.+++.+..+|.-.|..... ......++|..+|++...|+.+....+.|.|...
T Consensus 350 ~L~~reR~VI~LRygl~d~-~~~Tl~EIA~~LGvS~erVRqie~rAl~KLR~~~ 402 (415)
T PRK07598 350 DLTSRERDVIRMRFGLADG-HTYSLAEIGRALDLSRERVRQIESKALQKLRQPK 402 (415)
T ss_pred hCCHHHHHHHHHHHhcCCC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhchh
Confidence 3566666677766642211 1124678999999999999999988888877544
No 244
>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=24.41 E-value=54 Score=23.26 Aligned_cols=21 Identities=14% Similarity=0.205 Sum_probs=18.2
Q ss_pred HHHHHHHhCCCccchhhhhhh
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQN 64 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFqN 64 (155)
..++|..+|++.+.++.|++.
T Consensus 3 I~e~a~~~gvs~~TLR~Ye~~ 23 (134)
T cd04779 3 IGQLAHLAGVSKRTIDYYTNL 23 (134)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999964
No 245
>PF03457 HA: Helicase associated domain; InterPro: IPR005114 This short domain is found in multiple copies in bacterial helicase proteins. The domain is predicted to contain 3 alpha helices. The function of this domain may be to bind nucleic acid.; PDB: 2KTA_A.
Probab=24.40 E-value=89 Score=18.86 Aligned_cols=43 Identities=19% Similarity=0.311 Sum_probs=23.2
Q ss_pred HHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhHH
Q psy16514 25 QRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSK 73 (155)
Q Consensus 25 ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~ 73 (155)
-+..|..+............... ....+..|..+.|.+.++.+
T Consensus 11 ~~~~l~~y~~~~G~~~vp~~~~~------~~~~Lg~Wl~~qR~~~r~g~ 53 (68)
T PF03457_consen 11 RYEALKAYKEEHGHLNVPRDYVT------DGFPLGQWLNNQRRKYRKGK 53 (68)
T ss_dssp HHHHHHHHHHHHS--S-SS-----------SSHHHHHHHHHHHHHHHT-
T ss_pred HHHHHHHHHHHHCCCCCCcccCc------CCCcHHHHHHHHHHHHHcCC
Confidence 35566666655543222211110 14567899999999988743
No 246
>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=24.35 E-value=1e+02 Score=20.56 Aligned_cols=27 Identities=30% Similarity=0.510 Sum_probs=21.0
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKW 69 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~ 69 (155)
....+|..+|+++.+|.-|..+-+.++
T Consensus 25 gq~~vA~~~Gv~eStISR~k~~~~~~~ 51 (91)
T PF05269_consen 25 GQKKVAEAMGVDESTISRWKNDFIEKM 51 (91)
T ss_dssp HHHHHHHHHTSSTTTHHHHHHHHHHHH
T ss_pred hhHHHHHHhCCCHHHHHHHHhhHHHHH
Confidence 345789999999999999976644443
No 247
>PTZ00183 centrin; Provisional
Probab=24.29 E-value=2.4e+02 Score=19.26 Aligned_cols=40 Identities=20% Similarity=0.321 Sum_probs=30.3
Q ss_pred CCCcccCCHHHHHHHHHHHhh-----cCCCCHHHHHHHHHHhCCC
Q psy16514 15 MMRRAVFSDLQRKGLEKRFQI-----QKYISKPDRKKLAEKLGLK 54 (155)
Q Consensus 15 ~r~R~~~t~~ql~~L~~~F~~-----~~~p~~~~~~~LA~~l~l~ 54 (155)
+-.+..++..++..|...|.. +.+.+..+...+...+|+.
T Consensus 5 ~~~~~~~~~~~~~~~~~~F~~~D~~~~G~i~~~e~~~~l~~~g~~ 49 (158)
T PTZ00183 5 RSERPGLTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSLGFE 49 (158)
T ss_pred ccccCCCCHHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHhCCC
Confidence 344678999999999999853 5677777777777777753
No 248
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=24.27 E-value=1.1e+02 Score=22.99 Aligned_cols=45 Identities=7% Similarity=0.020 Sum_probs=31.8
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhh
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNR 65 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNr 65 (155)
.+|+.++..|......+ +-....-..+|..+++++..|+..+.+-
T Consensus 158 ~Lt~re~~~l~~~i~~~-~~~g~s~~eIA~~l~iS~~Tv~~~~~~~ 202 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAH-QDYEFSTDELANAVNISRVSCRKYLIWL 202 (239)
T ss_pred CCCHHHHHHHHHHHHhC-CCCCcCHHHHHHHhCchHHHHHHHHHHH
Confidence 36777766665554432 3344466789999999999999988754
No 249
>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=24.12 E-value=57 Score=21.10 Aligned_cols=20 Identities=15% Similarity=0.253 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCccchhhhhh
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQ 63 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFq 63 (155)
...+|..+|++...|+.|..
T Consensus 4 i~e~A~~~gvs~~tLr~ye~ 23 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYER 23 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999974
No 250
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=23.96 E-value=1.1e+02 Score=22.81 Aligned_cols=45 Identities=11% Similarity=0.217 Sum_probs=33.7
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 26 RKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 26 l~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
+.+....|....|-.. ....||...|++..-|...|.|+..=...
T Consensus 24 L~AA~~lf~e~Gy~~~-s~~dIA~~aGvs~gtiY~hF~sKe~L~~a 68 (212)
T PRK15008 24 LSAALDTFSQFGFHGT-RLEQIAELAGVSKTNLLYYFPSKEALYIA 68 (212)
T ss_pred HHHHHHHHHHhCcccC-CHHHHHHHhCcCHHHHHHHCCCHHHHHHH
Confidence 4444455777776654 46678999999999999999998774443
No 251
>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=23.95 E-value=64 Score=21.75 Aligned_cols=28 Identities=29% Similarity=0.403 Sum_probs=16.7
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWR 70 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~r 70 (155)
....||.++||+.++|..=....+.+.+
T Consensus 74 n~~eLA~kyglS~r~I~~Ii~~~~~~~~ 101 (108)
T PF08765_consen 74 NVRELARKYGLSERQIYRIIKRVRRRER 101 (108)
T ss_dssp -HHHHHHHHT--HHHHHHHHHHHHH---
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4678999999999987766654444433
No 252
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=23.72 E-value=50 Score=21.92 Aligned_cols=30 Identities=20% Similarity=0.461 Sum_probs=20.7
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchh
Q psy16514 26 RKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVK 59 (155)
Q Consensus 26 l~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~ 59 (155)
...|.+.|....+ ....+|..||++...|.
T Consensus 12 ~~ELq~nf~~~~l----s~~~ia~dL~~s~~~le 41 (89)
T PF10078_consen 12 RQELQANFELSGL----SLEQIAADLGTSPEHLE 41 (89)
T ss_pred HHHHHHHHHHcCC----CHHHHHHHhCCCHHHHH
Confidence 4567777777664 46677888888876654
No 253
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=23.59 E-value=37 Score=21.89 Aligned_cols=20 Identities=5% Similarity=0.356 Sum_probs=16.9
Q ss_pred HHHHHHHhCCCccchhhhhh
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQ 63 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFq 63 (155)
+..|...++|...++.+|+.
T Consensus 56 ~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 56 TSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred HHHHHHHhCCCCCeEEEEEE
Confidence 55678888999999999984
No 254
>PRK13870 transcriptional regulator TraR; Provisional
Probab=23.46 E-value=1.8e+02 Score=22.45 Aligned_cols=33 Identities=12% Similarity=0.255 Sum_probs=26.4
Q ss_pred HHHHHHHhCCCccchhhhhhhhHHHHhhHHHHH
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERE 76 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFqNrR~k~rk~~~~~ 76 (155)
-.++|..||++++.|..-.+|-+.|.--.++.+
T Consensus 191 ~~EIa~ILgISe~TV~~Hl~na~~KLga~nr~q 223 (234)
T PRK13870 191 MEEIADVEGVKYNSVRVKLREAMKRFDVRSKAH 223 (234)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHH
Confidence 347899999999999999999988865544433
No 255
>PF08452 DNAP_B_exo_N: DNA polymerase family B exonuclease domain, N-terminal; InterPro: IPR013660 This domain is found in viral DNA polymerases to the N terminus of DNA polymerase family B exonuclease domains (IPR006133 from INTERPRO). ; GO: 0003887 DNA-directed DNA polymerase activity
Probab=23.35 E-value=24 Score=17.06 Aligned_cols=9 Identities=33% Similarity=0.837 Sum_probs=6.6
Q ss_pred hhhhhhhhH
Q psy16514 58 VKIWFQNRR 66 (155)
Q Consensus 58 V~~WFqNrR 66 (155)
+-+||.++.
T Consensus 5 CiNWFE~~g 13 (22)
T PF08452_consen 5 CINWFESRG 13 (22)
T ss_pred EeehhhhCC
Confidence 347998876
No 256
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=23.28 E-value=51 Score=19.43 Aligned_cols=24 Identities=38% Similarity=0.524 Sum_probs=19.7
Q ss_pred HHHHHHHHhCCCccchhhhhhhhH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRR 66 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR 66 (155)
....+|..+|++...|..|-.+++
T Consensus 14 t~~~~a~~~~i~~~~i~~~e~g~~ 37 (64)
T PF12844_consen 14 TQKDLAEKLGISRSTISKIENGKR 37 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCc
Confidence 467789999999999999998876
No 257
>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=23.19 E-value=2e+02 Score=18.57 Aligned_cols=38 Identities=21% Similarity=0.245 Sum_probs=24.3
Q ss_pred CCHHHHHHHHHH---HhhcCCCCHHHHHHHHHHhCCCccchhh
Q psy16514 21 FSDLQRKGLEKR---FQIQKYISKPDRKKLAEKLGLKDSQVKI 60 (155)
Q Consensus 21 ~t~~ql~~L~~~---F~~~~~p~~~~~~~LA~~l~l~~~~V~~ 60 (155)
+|..|..+|... |..+.-|-. -..||..+++++..|++
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 455666666555 666665543 45678889988876543
No 258
>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=23.18 E-value=47 Score=19.50 Aligned_cols=18 Identities=39% Similarity=0.615 Sum_probs=13.6
Q ss_pred HHHHHHHHhCCCccchhh
Q psy16514 43 DRKKLAEKLGLKDSQVKI 60 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~ 60 (155)
--.+||..+|++..||+-
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 356799999999999874
No 259
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=23.12 E-value=1.4e+02 Score=22.08 Aligned_cols=36 Identities=14% Similarity=0.154 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccch
Q psy16514 23 DLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQV 58 (155)
Q Consensus 23 ~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V 58 (155)
..-+..|..++....|........+|..||++...|
T Consensus 25 sAlip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v 60 (160)
T COG1905 25 SALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARV 60 (160)
T ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHh
Confidence 345777888888888999999999999999997654
No 260
>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=22.87 E-value=1.8e+02 Score=22.45 Aligned_cols=46 Identities=20% Similarity=0.242 Sum_probs=30.3
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHh
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~r 70 (155)
.+++.+..++...|.. .....++|..+|++...|...-..-..|.|
T Consensus 206 ~L~~rer~vi~~~~~~-----~~t~~eIA~~lgis~~~V~~~~~ral~kLr 251 (254)
T TIGR02850 206 RLNEREKMILNMRFFE-----GKTQMEVAEEIGISQAQVSRLEKAALKHMR 251 (254)
T ss_pred cCCHHHHHHHHHHHcC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4566666666666632 235778999999999887766554444433
No 261
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=22.75 E-value=53 Score=19.55 Aligned_cols=25 Identities=32% Similarity=0.465 Sum_probs=20.6
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRM 67 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~ 67 (155)
....+|..+|++...|..|-.+++.
T Consensus 16 s~~~lA~~~g~s~s~v~~iE~G~~~ 40 (64)
T PF13560_consen 16 SQAQLADRLGVSQSTVSRIERGRRP 40 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSSS
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCCC
Confidence 5678999999999999999998874
No 262
>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=22.63 E-value=80 Score=17.30 Aligned_cols=13 Identities=23% Similarity=0.296 Sum_probs=11.1
Q ss_pred cCCHHHHHHHHHH
Q psy16514 20 VFSDLQRKGLEKR 32 (155)
Q Consensus 20 ~~t~~ql~~L~~~ 32 (155)
.||..|+..|+.-
T Consensus 2 ~FT~~Ql~~L~~Q 14 (37)
T PF08880_consen 2 PFTPAQLQELRAQ 14 (37)
T ss_pred CCCHHHHHHHHHH
Confidence 5899999999875
No 263
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=22.60 E-value=1e+02 Score=21.93 Aligned_cols=46 Identities=24% Similarity=0.389 Sum_probs=30.0
Q ss_pred ccCCHHHHHHHHHHH-hhcCCCCHHHHHHHHHHhCCCccchhhhhhh
Q psy16514 19 AVFSDLQRKGLEKRF-QIQKYISKPDRKKLAEKLGLKDSQVKIWFQN 64 (155)
Q Consensus 19 ~~~t~~ql~~L~~~F-~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqN 64 (155)
..||++|...|...- ...+.-...+...|+..+|++...|+..|..
T Consensus 3 ~~~T~eer~eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lre 49 (127)
T PF06163_consen 3 RVFTPEEREELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRE 49 (127)
T ss_pred CcCCHHHHHHHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHH
Confidence 368898888887762 1222223345667788888888887777743
No 264
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=22.53 E-value=81 Score=22.83 Aligned_cols=24 Identities=25% Similarity=0.536 Sum_probs=17.9
Q ss_pred CHHHHHHHHHHhCCCccchhhhhh
Q psy16514 40 SKPDRKKLAEKLGLKDSQVKIWFQ 63 (155)
Q Consensus 40 ~~~~~~~LA~~l~l~~~~V~~WFq 63 (155)
......++|..+|++...+..|=+
T Consensus 33 ~r~T~~eiAee~Gis~~tLYrWr~ 56 (142)
T PF13022_consen 33 ERRTQAEIAEEVGISRSTLYRWRQ 56 (142)
T ss_dssp --S-HHHHHHHHTS-HHHHHHHHH
T ss_pred ccchHHHHHHHhCCCHHHHHHHHh
Confidence 345678899999999999999984
No 265
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=22.48 E-value=51 Score=22.80 Aligned_cols=24 Identities=21% Similarity=0.257 Sum_probs=21.3
Q ss_pred HHHHHHHHhCCCccchhhhhhhhH
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRR 66 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR 66 (155)
.+.+||..+|++...|..|.++++
T Consensus 20 sq~eLA~~~Gis~~~is~iE~g~~ 43 (120)
T PRK13890 20 TKKELSERSGVSISFLSDLTTGKA 43 (120)
T ss_pred CHHHHHHHHCcCHHHHHHHHcCCC
Confidence 467899999999999999999876
No 266
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=22.30 E-value=92 Score=22.88 Aligned_cols=42 Identities=10% Similarity=0.168 Sum_probs=32.3
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHH
Q psy16514 26 RKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68 (155)
Q Consensus 26 l~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k 68 (155)
+.+....|....|-.. ....||...|++...+..+|.++-.=
T Consensus 17 l~aa~~lf~~~G~~~~-ti~~Ia~~agvsk~t~Y~~F~sKe~L 58 (213)
T PRK09975 17 IETAIAQFALRGVSNT-TLNDIADAANVTRGAIYWHFENKTQL 58 (213)
T ss_pred HHHHHHHHHHcCcccC-CHHHHHHHcCCCHHHHHHHcCCHHHH
Confidence 4455555777776654 57778999999999999999998763
No 267
>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=22.26 E-value=67 Score=21.09 Aligned_cols=21 Identities=10% Similarity=0.074 Sum_probs=18.2
Q ss_pred HHHHHHHhCCCccchhhhhhh
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQN 64 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFqN 64 (155)
..++|..+|++...++.|.+.
T Consensus 3 i~eva~~~gvs~~tLRyye~~ 23 (96)
T cd04768 3 IGEFAKLAGVSIRTLRHYDDI 23 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999864
No 268
>PRK13756 tetracycline repressor protein TetR; Provisional
Probab=22.09 E-value=1.4e+02 Score=22.43 Aligned_cols=41 Identities=20% Similarity=0.209 Sum_probs=29.8
Q ss_pred HHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHH
Q psy16514 27 KGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68 (155)
Q Consensus 27 ~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k 68 (155)
..-...|....|- ......||..+|++..-+...|.||..=
T Consensus 11 ~aA~~l~~e~G~~-~lsmr~lA~~lgv~~~slY~hf~~K~~L 51 (205)
T PRK13756 11 DSALELLNEVGIE-GLTTRKLAQKLGVEQPTLYWHVKNKRAL 51 (205)
T ss_pred HHHHHHHHHcCcc-cCCHHHHHHHhCCCchHHHHHcCCHHHH
Confidence 3344455656543 4557778999999999999999987765
No 269
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=21.98 E-value=1.8e+02 Score=21.69 Aligned_cols=46 Identities=15% Similarity=0.152 Sum_probs=34.6
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 20 ~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
.+|+.++++|.-.-+-. .-.++|.+++++++.|+....|=..|..-
T Consensus 137 ~LT~RE~eVL~lla~G~------snkeIA~~L~iS~~TVk~h~~~I~~KL~v 182 (207)
T PRK15411 137 SLSRTESSMLRMWMAGQ------GTIQISDQMNIKAKTVSSHKGNIKRKIKT 182 (207)
T ss_pred cCCHHHHHHHHHHHcCC------CHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence 48888888886664322 34678999999999999988776666553
No 270
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=21.42 E-value=76 Score=22.00 Aligned_cols=26 Identities=31% Similarity=0.494 Sum_probs=21.8
Q ss_pred CCCHHHHHHHHHHhCCCccchhhhhh
Q psy16514 38 YISKPDRKKLAEKLGLKDSQVKIWFQ 63 (155)
Q Consensus 38 ~p~~~~~~~LA~~l~l~~~~V~~WFq 63 (155)
-++...|..||..+|++...|..|-.
T Consensus 26 ~~~~~~r~~La~~~~i~~~~l~~w~~ 51 (122)
T PF14229_consen 26 GDTPLGRKALAKKLGISERNLLKWVN 51 (122)
T ss_pred CCCHHHHHHHHHhcCCCHHHHHHHHh
Confidence 34566788899999999999999964
No 271
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=21.34 E-value=1e+02 Score=21.22 Aligned_cols=34 Identities=18% Similarity=0.054 Sum_probs=23.3
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchh
Q psy16514 24 LQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVK 59 (155)
Q Consensus 24 ~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~ 59 (155)
.+...|-..|. ..+......+||..+.++.+.++
T Consensus 4 ~~y~~L~~~~~--~~~~~vtl~elA~~l~cS~Rn~r 37 (115)
T PF12793_consen 4 EQYQRLWQHYG--GQPVEVTLDELAELLFCSRRNAR 37 (115)
T ss_pred HHHHHHHHHcC--CCCcceeHHHHHHHhCCCHHHHH
Confidence 34556666666 55556678889988888886443
No 272
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=21.13 E-value=1.7e+02 Score=20.70 Aligned_cols=47 Identities=15% Similarity=0.123 Sum_probs=37.3
Q ss_pred ccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q psy16514 19 AVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71 (155)
Q Consensus 19 ~~~t~~ql~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~rk 71 (155)
..+|..+..+|...+.-. ....+|..++++.+.|++.-.+=|.|..-
T Consensus 142 ~~lt~~E~~vl~~l~~g~------~~~~I~~~l~~s~~tv~~~~~~l~~Kl~~ 188 (204)
T PRK09958 142 DSLSKQEISVMRYILDGK------DNNDIAEKMFISNKTVSTYKSRLMEKLEC 188 (204)
T ss_pred ccCCHHHHHHHHHHHcCC------CHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 358888888888887543 36788999999999999988887777643
No 273
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=20.97 E-value=1.6e+02 Score=21.36 Aligned_cols=34 Identities=21% Similarity=0.167 Sum_probs=26.7
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchh
Q psy16514 26 RKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVK 59 (155)
Q Consensus 26 l~~L~~~F~~~~~p~~~~~~~LA~~l~l~~~~V~ 59 (155)
+..|...=....|.+......+|..+|++..+|.
T Consensus 26 i~~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V~ 59 (156)
T PRK05988 26 LPILHAIQDEFGYVPEDAVPVIAEALNLSRAEVH 59 (156)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHH
Confidence 4555555556689999999999999999987654
No 274
>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=20.74 E-value=74 Score=21.43 Aligned_cols=21 Identities=29% Similarity=0.488 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCccchhhhhhh
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQN 64 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFqN 64 (155)
..++|+.+|++...|+.|.+.
T Consensus 3 i~eva~~~gvs~~tlR~ye~~ 23 (108)
T cd04773 3 IGELAHLLGVPPSTLRHWEKE 23 (108)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999753
No 275
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=20.68 E-value=67 Score=17.90 Aligned_cols=35 Identities=14% Similarity=0.341 Sum_probs=24.7
Q ss_pred HHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhH
Q psy16514 31 KRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRR 66 (155)
Q Consensus 31 ~~F~~~~~p~~~~~~~LA~~l~l~~~~V~~WFqNrR 66 (155)
..|....|-. .....||...|++...+...|.|+-
T Consensus 7 ~l~~~~G~~~-~s~~~Ia~~~gvs~~~~y~~f~~k~ 41 (47)
T PF00440_consen 7 ELFAEKGYEA-VSIRDIARRAGVSKGSFYRYFPSKD 41 (47)
T ss_dssp HHHHHHHTTT-SSHHHHHHHHTSCHHHHHHHCSSHH
T ss_pred HHHHHhCHHh-CCHHHHHHHHccchhhHHHHcCCHH
Confidence 3344333333 3467789999999999999998764
No 276
>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=20.31 E-value=1.2e+02 Score=18.69 Aligned_cols=22 Identities=32% Similarity=0.601 Sum_probs=16.4
Q ss_pred HHHHHHHHHhCCCccchhhhhh
Q psy16514 42 PDRKKLAEKLGLKDSQVKIWFQ 63 (155)
Q Consensus 42 ~~~~~LA~~l~l~~~~V~~WFq 63 (155)
+...+||..+|++...|+..++
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 3567899999999998877664
No 277
>PRK00215 LexA repressor; Validated
Probab=20.25 E-value=1.3e+02 Score=22.42 Aligned_cols=42 Identities=26% Similarity=0.372 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHhCC-Cccchhhhhhh
Q psy16514 21 FSDLQRKGLEKRFQ---IQKYISKPDRKKLAEKLGL-KDSQVKIWFQN 64 (155)
Q Consensus 21 ~t~~ql~~L~~~F~---~~~~p~~~~~~~LA~~l~l-~~~~V~~WFqN 64 (155)
+|+.|...|+.... ...++ ....+||..+|+ +...|..+.+.
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~--~s~~ela~~~~~~~~~tv~~~l~~ 47 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYP--PSRREIADALGLRSPSAVHEHLKA 47 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCC--CCHHHHHHHhCCCChHHHHHHHHH
Confidence 57788888877753 33333 346789999999 88887777653
No 278
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=20.25 E-value=64 Score=25.78 Aligned_cols=26 Identities=38% Similarity=0.746 Sum_probs=21.3
Q ss_pred HHHHHHHHhCCCccchhhhhhhhHHHHh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNRRMKWR 70 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNrR~k~r 70 (155)
.-..||..||+++.+|+.|-+ |..|.
T Consensus 21 k~~dIAeklGvspntiksWKr--r~gWs 46 (279)
T COG5484 21 KLKDIAEKLGVSPNTIKSWKR--RDGWS 46 (279)
T ss_pred cHHHHHHHhCCChHHHHHHHH--hcCCC
Confidence 456799999999999999975 56663
No 279
>PHA00542 putative Cro-like protein
Probab=20.16 E-value=2.3e+02 Score=17.98 Aligned_cols=23 Identities=9% Similarity=0.302 Sum_probs=20.4
Q ss_pred HHHHHHHHhCCCccchhhhhhhh
Q psy16514 43 DRKKLAEKLGLKDSQVKIWFQNR 65 (155)
Q Consensus 43 ~~~~LA~~l~l~~~~V~~WFqNr 65 (155)
....||..+|++...|..|..++
T Consensus 33 Tq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 33 SQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred CHHHHHHHHCcCHHHHHHHHcCC
Confidence 56679999999999999999776
No 280
>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=20.14 E-value=70 Score=21.11 Aligned_cols=20 Identities=15% Similarity=0.441 Sum_probs=16.6
Q ss_pred HHHHHHHhCCCccchhhhhh
Q psy16514 44 RKKLAEKLGLKDSQVKIWFQ 63 (155)
Q Consensus 44 ~~~LA~~l~l~~~~V~~WFq 63 (155)
..++|+.+|++.+.|+.|=+
T Consensus 3 I~eva~~~gvs~~tlR~Ye~ 22 (95)
T cd04780 3 MSELSKRSGVSVATIKYYLR 22 (95)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999988864
Done!