Query psy1653
Match_columns 96
No_of_seqs 102 out of 1024
Neff 8.3
Searched_HMMs 46136
Date Fri Aug 16 23:37:49 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1653.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1653hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0489|consensus 99.8 1.7E-19 3.7E-24 125.4 4.6 68 3-70 155-222 (261)
2 KOG0488|consensus 99.8 5.3E-19 1.1E-23 125.2 5.4 64 5-68 170-233 (309)
3 KOG0850|consensus 99.8 8.8E-19 1.9E-23 118.2 5.6 63 5-67 120-182 (245)
4 PF00046 Homeobox: Homeobox do 99.8 2.6E-18 5.7E-23 94.1 5.9 57 8-64 1-57 (57)
5 KOG0843|consensus 99.7 2.4E-18 5.2E-23 112.5 5.7 64 6-69 101-164 (197)
6 KOG0484|consensus 99.7 2.7E-18 5.9E-23 103.6 4.7 62 6-67 16-77 (125)
7 KOG0487|consensus 99.7 1.8E-18 4E-23 121.7 4.1 66 5-70 233-298 (308)
8 KOG2251|consensus 99.7 5.7E-18 1.2E-22 113.7 5.5 65 4-68 34-98 (228)
9 KOG0485|consensus 99.7 1E-17 2.2E-22 112.6 5.2 65 4-68 101-165 (268)
10 KOG0842|consensus 99.7 1.6E-17 3.4E-22 117.0 4.9 62 6-67 152-213 (307)
11 KOG3802|consensus 99.7 1.1E-17 2.3E-22 120.3 3.8 67 1-67 288-354 (398)
12 KOG0492|consensus 99.7 7.4E-17 1.6E-21 107.7 5.7 61 7-67 144-204 (246)
13 KOG0848|consensus 99.6 8.4E-17 1.8E-21 110.9 3.5 65 6-70 198-262 (317)
14 TIGR01565 homeo_ZF_HD homeobox 99.6 3.7E-16 8E-21 85.9 4.9 53 7-59 1-57 (58)
15 cd00086 homeodomain Homeodomai 99.6 1E-15 2.3E-20 83.7 5.9 56 9-64 2-57 (59)
16 KOG0494|consensus 99.6 4.3E-16 9.3E-21 107.1 5.1 61 7-67 141-201 (332)
17 smart00389 HOX Homeodomain. DN 99.6 8.9E-16 1.9E-20 83.4 5.4 56 8-63 1-56 (56)
18 COG5576 Homeodomain-containing 99.6 8E-16 1.7E-20 99.7 6.1 65 4-68 48-112 (156)
19 KOG0493|consensus 99.6 2E-15 4.4E-20 103.9 4.7 60 7-66 246-305 (342)
20 KOG0491|consensus 99.6 7.8E-16 1.7E-20 99.6 1.8 64 7-70 100-163 (194)
21 KOG4577|consensus 99.5 1.1E-14 2.3E-19 101.6 5.3 66 3-68 163-228 (383)
22 KOG0483|consensus 99.5 6.2E-14 1.4E-18 93.9 6.0 61 7-67 50-110 (198)
23 KOG0844|consensus 99.5 1.2E-14 2.6E-19 102.0 2.2 60 8-67 182-241 (408)
24 KOG0847|consensus 99.4 5.7E-14 1.2E-18 94.8 3.2 63 4-66 164-226 (288)
25 KOG0486|consensus 99.4 8E-14 1.7E-18 98.0 3.6 60 6-65 111-170 (351)
26 KOG1168|consensus 99.3 1.1E-12 2.3E-17 91.8 2.3 62 4-65 306-367 (385)
27 KOG0490|consensus 99.3 3.2E-12 7E-17 86.5 3.1 62 5-66 58-119 (235)
28 KOG0849|consensus 99.1 6.7E-11 1.4E-15 85.5 4.3 62 5-66 174-235 (354)
29 KOG0775|consensus 99.1 1.7E-10 3.6E-15 80.1 4.5 51 14-64 183-233 (304)
30 KOG0774|consensus 98.9 1.9E-09 4.2E-14 74.6 4.1 72 7-78 188-262 (334)
31 PF05920 Homeobox_KN: Homeobox 98.7 1.5E-08 3.2E-13 51.8 2.4 34 28-61 7-40 (40)
32 KOG2252|consensus 98.5 1.5E-07 3.2E-12 70.7 5.2 57 6-62 419-475 (558)
33 KOG0490|consensus 98.3 1.4E-06 3.1E-11 58.8 4.4 63 5-67 151-213 (235)
34 KOG1146|consensus 97.5 8.2E-05 1.8E-09 61.0 3.7 60 7-66 903-962 (1406)
35 PF11569 Homez: Homeodomain le 97.5 0.00011 2.4E-09 40.0 2.4 43 18-60 9-51 (56)
36 KOG0773|consensus 96.5 0.0029 6.4E-08 45.5 3.4 60 7-66 239-301 (342)
37 PF04218 CENP-B_N: CENP-B N-te 96.3 0.014 3.1E-07 31.2 4.6 47 8-59 1-47 (53)
38 KOG3623|consensus 96.0 0.011 2.3E-07 46.9 4.2 48 19-66 568-615 (1007)
39 PF04967 HTH_10: HTH DNA bindi 88.2 0.88 1.9E-05 24.3 3.0 40 14-53 1-42 (53)
40 PF01527 HTH_Tnp_1: Transposas 87.9 1.2 2.7E-05 24.6 3.8 46 9-58 2-47 (76)
41 PF04545 Sigma70_r4: Sigma-70, 87.5 1.8 3.8E-05 22.2 4.0 41 13-58 4-44 (50)
42 PF09607 BrkDBD: Brinker DNA-b 87.4 1.7 3.6E-05 23.8 3.8 45 11-56 3-47 (58)
43 cd06171 Sigma70_r4 Sigma70, re 84.2 2.4 5.2E-05 21.0 3.5 42 13-59 10-51 (55)
44 PF10668 Phage_terminase: Phag 83.8 0.7 1.5E-05 25.4 1.3 21 36-56 24-44 (60)
45 PF08281 Sigma70_r4_2: Sigma-7 82.1 3.9 8.5E-05 21.1 3.8 39 14-57 11-49 (54)
46 PRK03975 tfx putative transcri 79.9 8.9 0.00019 24.6 5.5 52 11-68 4-55 (141)
47 PRK06759 RNA polymerase factor 73.7 8.1 0.00018 23.9 4.1 44 14-62 107-150 (154)
48 PF05703 Auxin_canalis: Auxin 73.0 28 0.00061 24.4 6.8 14 47-60 99-112 (242)
49 PRK09644 RNA polymerase sigma 72.7 8.9 0.00019 24.2 4.2 30 36-65 126-155 (165)
50 PRK09646 RNA polymerase sigma 71.5 12 0.00025 24.5 4.6 29 36-64 160-188 (194)
51 COG3413 Predicted DNA binding 70.7 6.1 0.00013 26.6 3.2 41 13-53 155-197 (215)
52 PF06056 Terminase_5: Putative 70.3 3.8 8.2E-05 22.2 1.7 20 37-56 16-35 (58)
53 PF13518 HTH_28: Helix-turn-he 69.9 3.9 8.5E-05 20.7 1.7 22 37-58 15-36 (52)
54 cd04761 HTH_MerR-SF Helix-Turn 69.6 3.8 8.2E-05 20.5 1.6 22 37-58 3-24 (49)
55 cd00569 HTH_Hin_like Helix-tur 69.2 8.8 0.00019 16.7 4.0 38 13-55 5-42 (42)
56 PF00196 GerE: Bacterial regul 69.2 12 0.00026 19.6 3.6 44 13-62 3-46 (58)
57 COG4367 Uncharacterized protei 68.1 9.3 0.0002 22.7 3.1 40 13-52 2-41 (97)
58 PF13936 HTH_38: Helix-turn-he 68.0 6.2 0.00013 19.9 2.1 40 12-56 3-42 (44)
59 PRK11924 RNA polymerase sigma 67.7 18 0.00038 22.7 4.8 29 36-64 143-171 (179)
60 PRK09652 RNA polymerase sigma 67.7 13 0.00028 23.4 4.1 29 36-64 146-174 (182)
61 PRK12526 RNA polymerase sigma 67.6 16 0.00035 24.1 4.7 29 36-64 171-199 (206)
62 TIGR02937 sigma70-ECF RNA poly 67.5 13 0.00028 22.3 4.0 28 36-63 128-155 (158)
63 PF13384 HTH_23: Homeodomain-l 67.4 4.5 9.7E-05 20.5 1.6 22 36-57 19-40 (50)
64 PRK09642 RNA polymerase sigma 67.3 18 0.00039 22.6 4.7 29 36-64 124-152 (160)
65 PRK12514 RNA polymerase sigma 67.0 16 0.00035 23.3 4.5 29 36-64 147-175 (179)
66 KOG1146|consensus 66.3 7.6 0.00017 33.3 3.3 59 8-66 706-764 (1406)
67 TIGR02989 Sig-70_gvs1 RNA poly 65.2 16 0.00036 22.6 4.2 26 36-61 129-154 (159)
68 PRK09639 RNA polymerase sigma 65.1 17 0.00037 22.7 4.3 30 36-65 129-158 (166)
69 TIGR02999 Sig-70_X6 RNA polyme 63.8 20 0.00043 22.9 4.5 29 36-64 152-180 (183)
70 PRK12512 RNA polymerase sigma 63.3 21 0.00045 22.9 4.5 29 36-64 149-177 (184)
71 PF00424 REV: REV protein (ant 63.3 30 0.00064 20.6 5.1 41 20-74 15-55 (91)
72 PF13411 MerR_1: MerR HTH fami 62.9 6.4 0.00014 21.2 1.7 21 37-57 3-23 (69)
73 PRK05602 RNA polymerase sigma 62.5 13 0.00029 23.9 3.5 32 36-67 146-177 (186)
74 PRK12530 RNA polymerase sigma 62.4 28 0.00061 22.6 5.0 29 36-64 152-180 (189)
75 PF00376 MerR: MerR family reg 61.9 6.5 0.00014 19.3 1.5 20 37-56 2-21 (38)
76 PRK09648 RNA polymerase sigma 61.7 21 0.00045 23.0 4.3 28 36-63 157-184 (189)
77 PRK06930 positive control sigm 61.7 29 0.00063 22.7 4.9 46 14-64 115-160 (170)
78 PRK12519 RNA polymerase sigma 61.3 23 0.0005 22.9 4.5 30 35-64 158-187 (194)
79 TIGR02959 SigZ RNA polymerase 60.3 24 0.00051 22.5 4.3 29 36-64 118-146 (170)
80 TIGR02985 Sig70_bacteroi1 RNA 60.0 25 0.00055 21.5 4.4 27 36-62 131-157 (161)
81 TIGR02948 SigW_bacill RNA poly 59.7 21 0.00046 22.7 4.1 30 35-64 153-182 (187)
82 PRK00118 putative DNA-binding 59.6 37 0.00081 20.6 7.9 51 13-68 17-67 (104)
83 PRK10072 putative transcriptio 59.5 7.3 0.00016 23.3 1.7 25 37-61 49-73 (96)
84 PF02796 HTH_7: Helix-turn-hel 59.4 22 0.00047 17.8 3.4 38 13-55 5-42 (45)
85 PRK12543 RNA polymerase sigma 59.1 45 0.00097 21.3 5.9 31 36-66 135-165 (179)
86 PRK09047 RNA polymerase factor 58.4 38 0.00082 21.0 5.0 29 36-64 124-152 (161)
87 TIGR02939 RpoE_Sigma70 RNA pol 58.2 22 0.00047 22.8 3.9 29 36-64 156-184 (190)
88 PRK11552 putative DNA-binding 58.0 15 0.00032 24.8 3.2 42 21-64 21-62 (225)
89 cd04764 HTH_MlrA-like_sg1 Heli 57.6 8.3 0.00018 20.8 1.6 21 37-57 3-23 (67)
90 PRK12537 RNA polymerase sigma 57.3 31 0.00067 22.1 4.5 27 36-62 151-177 (182)
91 TIGR02952 Sig70_famx2 RNA poly 57.2 29 0.00063 21.7 4.3 26 36-61 140-165 (170)
92 PRK12538 RNA polymerase sigma 57.0 37 0.0008 23.1 5.0 30 36-65 189-218 (233)
93 PRK09480 slmA division inhibit 56.8 15 0.00033 23.4 3.0 34 26-60 23-56 (194)
94 TIGR03879 near_KaiC_dom probab 56.7 4.3 9.3E-05 23.2 0.3 24 35-58 33-56 (73)
95 COG2963 Transposase and inacti 56.4 34 0.00073 20.4 4.3 42 11-56 5-47 (116)
96 cd04763 HTH_MlrA-like Helix-Tu 56.4 8.8 0.00019 20.8 1.6 21 37-57 3-23 (68)
97 PRK12547 RNA polymerase sigma 56.4 30 0.00065 21.8 4.3 28 36-63 130-157 (164)
98 PRK12515 RNA polymerase sigma 56.4 40 0.00087 21.7 5.0 29 36-64 149-177 (189)
99 cd04762 HTH_MerR-trunc Helix-T 56.3 9.4 0.0002 18.5 1.6 23 37-59 3-25 (49)
100 PRK12541 RNA polymerase sigma 56.1 24 0.00053 22.0 3.8 28 36-63 130-157 (161)
101 PRK07037 extracytoplasmic-func 55.3 34 0.00073 21.3 4.4 28 36-63 127-154 (163)
102 TIGR02954 Sig70_famx3 RNA poly 55.3 31 0.00068 21.7 4.2 29 36-64 137-165 (169)
103 PRK12546 RNA polymerase sigma 54.3 28 0.00061 22.8 4.0 30 36-65 131-160 (188)
104 TIGR02983 SigE-fam_strep RNA p 54.2 31 0.00068 21.5 4.1 29 36-64 128-156 (162)
105 PRK12539 RNA polymerase sigma 54.1 34 0.00075 22.0 4.3 29 36-64 149-177 (184)
106 PRK04217 hypothetical protein; 54.0 42 0.00091 20.6 4.4 48 11-63 40-87 (110)
107 PRK12524 RNA polymerase sigma 53.5 33 0.00072 22.3 4.2 29 36-64 154-182 (196)
108 PRK12536 RNA polymerase sigma 53.4 36 0.00077 21.8 4.3 29 36-64 147-175 (181)
109 PRK09637 RNA polymerase sigma 53.3 34 0.00073 22.1 4.2 29 36-64 124-152 (181)
110 PRK12532 RNA polymerase sigma 52.7 49 0.0011 21.4 4.9 30 36-65 154-183 (195)
111 PRK09645 RNA polymerase sigma 51.2 42 0.00092 21.1 4.4 29 36-64 136-164 (173)
112 TIGR02943 Sig70_famx1 RNA poly 51.2 59 0.0013 21.1 5.1 29 36-64 149-177 (188)
113 cd01104 HTH_MlrA-CarA Helix-Tu 50.6 12 0.00026 20.0 1.5 20 37-56 3-22 (68)
114 PRK09647 RNA polymerase sigma 50.4 44 0.00096 22.1 4.5 29 36-64 156-184 (203)
115 PRK13919 putative RNA polymera 50.0 48 0.0011 21.1 4.6 27 36-62 153-179 (186)
116 PF13443 HTH_26: Cro/C1-type H 49.9 13 0.00028 19.5 1.6 24 36-59 12-35 (63)
117 PRK12516 RNA polymerase sigma 49.9 55 0.0012 21.3 4.8 30 36-65 134-163 (187)
118 PRK06986 fliA flagellar biosyn 49.7 36 0.00078 23.0 4.0 29 36-64 202-230 (236)
119 PRK09649 RNA polymerase sigma 48.8 41 0.00088 21.7 4.1 28 36-63 148-175 (185)
120 PRK12533 RNA polymerase sigma 48.7 40 0.00087 22.7 4.1 29 36-64 152-180 (216)
121 PRK12522 RNA polymerase sigma 48.7 63 0.0014 20.4 4.9 29 36-64 137-165 (173)
122 PRK12529 RNA polymerase sigma 48.6 48 0.001 21.2 4.4 27 36-62 145-171 (178)
123 COG2944 Predicted transcriptio 48.3 28 0.00061 21.2 2.9 41 14-61 44-84 (104)
124 PRK06811 RNA polymerase factor 48.3 47 0.001 21.5 4.3 29 36-64 149-177 (189)
125 PRK12520 RNA polymerase sigma 48.3 69 0.0015 20.6 5.1 29 36-64 149-177 (191)
126 PRK12535 RNA polymerase sigma 48.1 36 0.00078 22.4 3.7 32 36-67 151-182 (196)
127 COG1905 NuoE NADH:ubiquinone o 48.0 37 0.00081 22.3 3.7 37 16-52 25-61 (160)
128 TIGR02980 SigBFG RNA polymeras 47.4 47 0.001 22.2 4.3 43 14-61 179-221 (227)
129 KOG3755|consensus 47.3 6 0.00013 31.4 -0.1 61 6-66 691-758 (769)
130 PRK12523 RNA polymerase sigma 47.2 53 0.0011 20.8 4.4 28 36-63 137-164 (172)
131 PRK08583 RNA polymerase sigma 46.7 47 0.001 22.7 4.3 29 36-64 223-251 (257)
132 PF08280 HTH_Mga: M protein tr 46.6 33 0.00072 18.2 2.8 35 17-55 6-40 (59)
133 smart00595 MADF subfamily of S 46.3 40 0.00087 19.0 3.4 36 36-71 29-64 (89)
134 PRK12531 RNA polymerase sigma 46.3 67 0.0014 20.8 4.8 28 36-63 159-186 (194)
135 PF01710 HTH_Tnp_IS630: Transp 46.3 44 0.00096 20.3 3.7 38 14-56 3-40 (119)
136 PRK12542 RNA polymerase sigma 46.0 51 0.0011 21.1 4.2 29 36-64 140-168 (185)
137 PRK12545 RNA polymerase sigma 46.0 72 0.0016 20.9 5.0 29 36-64 157-185 (201)
138 PRK12511 RNA polymerase sigma 45.9 53 0.0011 21.3 4.3 29 36-64 129-157 (182)
139 cd01392 HTH_LacI Helix-turn-he 45.4 12 0.00026 18.8 0.9 21 39-59 2-22 (52)
140 PRK09641 RNA polymerase sigma 44.5 53 0.0011 20.9 4.1 29 36-64 154-182 (187)
141 KOG0773|consensus 44.1 31 0.00067 24.8 3.2 42 24-65 114-155 (342)
142 PRK08301 sporulation sigma fac 44.0 62 0.0013 21.7 4.5 29 36-64 200-228 (234)
143 TIGR03001 Sig-70_gmx1 RNA poly 43.8 76 0.0016 21.8 4.9 29 36-64 179-207 (244)
144 PRK12528 RNA polymerase sigma 43.8 60 0.0013 20.2 4.2 21 36-56 131-151 (161)
145 PRK09413 IS2 repressor TnpA; R 43.7 74 0.0016 19.3 9.0 45 9-57 8-52 (121)
146 PRK06288 RNA polymerase sigma 43.3 79 0.0017 21.8 5.0 30 36-65 230-259 (268)
147 TIGR02947 SigH_actino RNA poly 43.3 40 0.00087 21.8 3.4 31 35-65 148-178 (193)
148 PRK12544 RNA polymerase sigma 43.3 84 0.0018 20.8 5.0 28 37-64 167-194 (206)
149 TIGR02479 FliA_WhiG RNA polyme 42.9 59 0.0013 21.7 4.2 43 15-62 177-219 (224)
150 TIGR01764 excise DNA binding d 42.6 21 0.00044 17.3 1.6 23 37-59 4-26 (49)
151 PRK11923 algU RNA polymerase s 42.5 83 0.0018 20.2 4.8 31 36-66 156-186 (193)
152 smart00422 HTH_MERR helix_turn 41.9 20 0.00044 19.1 1.6 20 37-56 3-22 (70)
153 TIGR02941 Sigma_B RNA polymera 41.8 56 0.0012 22.3 4.1 45 14-63 206-250 (255)
154 PF12728 HTH_17: Helix-turn-he 41.0 22 0.00047 18.0 1.5 22 37-58 4-25 (51)
155 PF01381 HTH_3: Helix-turn-hel 40.7 22 0.00047 18.0 1.5 23 37-59 12-34 (55)
156 TIGR02950 SigM_subfam RNA poly 40.7 28 0.0006 21.4 2.2 31 33-63 120-150 (154)
157 PRK08295 RNA polymerase factor 39.5 70 0.0015 20.8 4.1 30 35-64 171-200 (208)
158 PF14549 P22_Cro: DNA-binding 39.4 21 0.00045 19.4 1.3 18 37-54 12-29 (60)
159 PRK05988 formate dehydrogenase 39.4 73 0.0016 20.6 4.1 35 18-52 25-59 (156)
160 COG5484 Uncharacterized conser 39.4 21 0.00045 25.4 1.6 27 36-64 21-47 (279)
161 PRK12534 RNA polymerase sigma 39.1 90 0.0019 19.9 4.5 26 36-61 155-180 (187)
162 PRK09651 RNA polymerase sigma 38.4 61 0.0013 20.6 3.6 26 36-61 137-162 (172)
163 PRK12518 RNA polymerase sigma 38.3 42 0.00091 21.2 2.8 30 35-64 137-166 (175)
164 smart00421 HTH_LUXR helix_turn 38.2 53 0.0011 16.1 4.3 39 13-57 3-41 (58)
165 cd01106 HTH_TipAL-Mta Helix-Tu 38.2 25 0.00054 20.7 1.6 22 37-58 3-24 (103)
166 PRK07670 RNA polymerase sigma 38.0 74 0.0016 21.7 4.2 28 36-63 219-246 (251)
167 TIGR00721 tfx DNA-binding prot 37.8 1.1E+02 0.0023 19.5 5.3 48 11-64 4-51 (137)
168 PRK09415 RNA polymerase factor 37.7 71 0.0015 20.4 3.9 28 36-63 145-172 (179)
169 PRK12525 RNA polymerase sigma 37.5 86 0.0019 19.7 4.2 26 36-61 136-161 (168)
170 TIGR03070 couple_hipB transcri 37.4 29 0.00062 17.4 1.7 23 37-59 18-40 (58)
171 cd01105 HTH_GlnR-like Helix-Tu 37.3 25 0.00055 20.2 1.5 19 37-55 4-22 (88)
172 cd04766 HTH_HspR Helix-Turn-He 37.2 26 0.00055 20.2 1.6 21 37-57 4-24 (91)
173 PF13309 HTH_22: HTH domain 37.0 72 0.0016 17.3 3.5 43 13-55 20-63 (64)
174 TIGR02859 spore_sigH RNA polym 36.8 94 0.002 19.9 4.4 28 35-62 166-193 (198)
175 TIGR02984 Sig-70_plancto1 RNA 36.8 92 0.002 19.7 4.3 27 36-62 158-184 (189)
176 cd00093 HTH_XRE Helix-turn-hel 36.6 30 0.00066 16.4 1.6 23 37-59 15-37 (58)
177 PRK09640 RNA polymerase sigma 36.5 45 0.00098 21.5 2.8 29 36-64 152-180 (188)
178 PRK07539 NADH dehydrogenase su 36.4 83 0.0018 20.1 4.0 35 18-52 24-58 (154)
179 PRK07408 RNA polymerase sigma 36.3 84 0.0018 21.6 4.2 29 36-64 221-249 (256)
180 PRK12513 RNA polymerase sigma 36.1 32 0.00069 22.3 2.0 31 34-64 155-185 (194)
181 PRK14996 TetR family transcrip 35.8 60 0.0013 20.8 3.3 39 22-61 17-55 (192)
182 PRK12540 RNA polymerase sigma 35.1 95 0.0021 20.0 4.2 29 36-64 129-157 (182)
183 TIGR02885 spore_sigF RNA polym 34.9 96 0.0021 20.7 4.3 38 14-56 184-221 (231)
184 PRK09643 RNA polymerase sigma 34.6 1.1E+02 0.0024 19.8 4.5 21 36-56 152-172 (192)
185 smart00027 EH Eps15 homology d 34.2 94 0.002 17.8 4.4 44 13-56 3-51 (96)
186 PF00440 TetR_N: Bacterial reg 33.9 35 0.00076 17.0 1.6 23 37-59 19-41 (47)
187 cd04779 HTH_MerR-like_sg4 Heli 33.6 30 0.00066 21.8 1.6 22 37-58 3-24 (134)
188 TIGR01958 nuoE_fam NADH-quinon 33.6 99 0.0021 19.6 4.0 35 18-52 18-52 (148)
189 PRK11922 RNA polymerase sigma 33.6 62 0.0013 21.8 3.2 35 32-66 163-197 (231)
190 cd04768 HTH_BmrR-like Helix-Tu 33.4 33 0.00071 20.1 1.6 22 37-58 3-24 (96)
191 PF04936 DUF658: Protein of un 33.2 25 0.00054 23.4 1.1 33 35-67 15-47 (186)
192 PRK07122 RNA polymerase sigma 33.0 95 0.0021 21.6 4.1 45 14-63 216-260 (264)
193 cd04774 HTH_YfmP Helix-Turn-He 33.0 33 0.00071 20.2 1.6 22 37-58 3-24 (96)
194 PRK05572 sporulation sigma fac 33.0 1.1E+02 0.0023 20.9 4.3 45 13-62 202-246 (252)
195 TIGR02957 SigX4 RNA polymerase 32.7 99 0.0021 21.5 4.2 28 37-64 127-154 (281)
196 PRK09975 DNA-binding transcrip 32.6 61 0.0013 21.0 3.0 40 21-61 19-58 (213)
197 PF01257 2Fe-2S_thioredx: Thio 32.3 74 0.0016 20.1 3.2 34 19-52 16-49 (145)
198 PRK05657 RNA polymerase sigma 32.0 1E+02 0.0022 22.2 4.3 51 14-65 263-313 (325)
199 KOG0150|consensus 31.8 1.1E+02 0.0025 22.4 4.3 11 51-61 16-26 (336)
200 PRK07571 bidirectional hydroge 31.6 1.1E+02 0.0025 20.1 4.0 32 21-52 41-72 (169)
201 cd04775 HTH_Cfa-like Helix-Tur 31.5 36 0.00078 20.1 1.6 21 37-57 4-24 (102)
202 PF14229 DUF4332: Domain of un 31.3 51 0.0011 20.3 2.3 26 31-56 26-51 (122)
203 PHA01976 helix-turn-helix prot 31.2 41 0.00088 17.8 1.7 23 37-59 18-40 (67)
204 PHA02955 hypothetical protein; 31.1 78 0.0017 21.8 3.3 43 17-59 61-104 (213)
205 PF07638 Sigma70_ECF: ECF sigm 30.8 1.3E+02 0.0028 19.5 4.3 28 36-63 153-180 (185)
206 TIGR02393 RpoD_Cterm RNA polym 30.6 1.1E+02 0.0023 20.7 4.0 50 14-64 177-226 (238)
207 PRK12517 RNA polymerase sigma 30.5 1.5E+02 0.0033 19.1 5.0 29 36-64 146-174 (188)
208 PRK09636 RNA polymerase sigma 30.2 1.2E+02 0.0025 21.2 4.2 29 37-65 134-162 (293)
209 TIGR02607 antidote_HigA addict 30.2 42 0.00092 18.3 1.7 23 37-59 21-43 (78)
210 cd00592 HTH_MerR-like Helix-Tu 30.1 39 0.00085 19.5 1.6 22 37-58 3-24 (100)
211 PRK08215 sporulation sigma fac 30.0 1.2E+02 0.0026 20.8 4.2 40 13-57 209-248 (258)
212 cd04780 HTH_MerR-like_sg5 Heli 29.8 40 0.00086 19.8 1.6 20 37-56 3-22 (95)
213 PRK05911 RNA polymerase sigma 29.7 1.7E+02 0.0036 20.2 4.9 29 36-64 223-251 (257)
214 PRK05803 sporulation sigma fac 29.6 1.5E+02 0.0032 19.9 4.5 29 36-64 197-225 (233)
215 TIGR02960 SigX5 RNA polymerase 29.5 1.1E+02 0.0023 21.5 4.0 30 36-65 160-189 (324)
216 cd04789 HTH_Cfa Helix-Turn-Hel 29.5 41 0.00088 19.9 1.6 21 37-57 4-24 (102)
217 PRK12527 RNA polymerase sigma 29.4 1.4E+02 0.0031 18.4 4.9 28 36-63 123-150 (159)
218 cd04788 HTH_NolA-AlbR Helix-Tu 28.5 44 0.00094 19.5 1.6 22 37-58 3-24 (96)
219 cd04773 HTH_TioE_rpt2 Second H 28.3 44 0.00096 20.0 1.6 22 37-58 3-24 (108)
220 PF06971 Put_DNA-bind_N: Putat 28.1 39 0.00084 17.7 1.1 18 36-53 30-47 (50)
221 cd04782 HTH_BltR Helix-Turn-He 27.9 45 0.00098 19.5 1.6 21 37-57 3-23 (97)
222 COG1595 RpoE DNA-directed RNA 27.9 71 0.0015 20.5 2.7 30 36-65 145-174 (182)
223 cd01111 HTH_MerD Helix-Turn-He 27.9 45 0.00098 20.0 1.6 21 37-57 3-23 (107)
224 KOG3623|consensus 27.8 45 0.00098 27.4 1.9 58 7-64 626-683 (1007)
225 cd01109 HTH_YyaN Helix-Turn-He 27.6 46 0.001 19.9 1.6 21 37-57 3-23 (113)
226 cd04765 HTH_MlrA-like_sg2 Heli 27.4 46 0.00099 19.7 1.5 21 37-57 3-23 (99)
227 COG0789 SoxR Predicted transcr 27.4 47 0.001 19.8 1.6 19 37-55 3-21 (124)
228 PF12244 DUF3606: Protein of u 27.0 67 0.0015 17.1 2.0 19 34-52 20-38 (57)
229 PRK06704 RNA polymerase factor 26.9 1.6E+02 0.0035 20.1 4.3 29 36-64 134-162 (228)
230 TIGR02054 MerD mercuric resist 26.8 48 0.001 20.5 1.6 21 37-57 6-26 (120)
231 PRK15369 two component system 26.7 1.5E+02 0.0032 18.2 4.0 44 13-62 149-192 (211)
232 cd01279 HTH_HspR-like Helix-Tu 26.4 50 0.0011 19.4 1.6 22 37-58 4-25 (98)
233 cd01107 HTH_BmrR Helix-Turn-He 26.3 51 0.0011 19.6 1.6 21 37-57 3-23 (108)
234 PRK09638 RNA polymerase sigma 26.3 69 0.0015 20.2 2.3 31 34-64 142-172 (176)
235 PF08279 HTH_11: HTH domain; 26.3 70 0.0015 16.2 2.0 21 35-55 16-36 (55)
236 PRK09706 transcriptional repre 26.2 51 0.0011 20.3 1.7 24 37-60 21-44 (135)
237 TIGR02394 rpoS_proteo RNA poly 26.0 1.5E+02 0.0033 20.7 4.2 29 36-64 244-272 (285)
238 cd04767 HTH_HspR-like_MBC Heli 25.7 51 0.0011 20.5 1.6 21 37-57 4-24 (120)
239 PRK10403 transcriptional regul 25.6 99 0.0021 19.3 3.0 45 13-63 153-197 (215)
240 PF13730 HTH_36: Helix-turn-he 25.6 70 0.0015 16.2 1.9 21 36-56 27-47 (55)
241 PRK15183 Vi polysaccharide bio 25.5 75 0.0016 19.7 2.2 35 14-48 96-130 (143)
242 PF09862 DUF2089: Protein of u 25.4 1.7E+02 0.0037 18.0 3.8 36 13-53 33-68 (113)
243 cd01110 HTH_SoxR Helix-Turn-He 25.2 51 0.0011 20.7 1.5 21 37-57 4-24 (139)
244 PF04297 UPF0122: Putative hel 25.0 1.4E+02 0.003 18.0 3.3 40 13-57 17-56 (101)
245 smart00530 HTH_XRE Helix-turn- 24.8 89 0.0019 14.4 2.8 21 38-58 14-34 (56)
246 PF12793 SgrR_N: Sugar transpo 24.6 94 0.002 19.0 2.6 32 20-53 7-38 (115)
247 cd04772 HTH_TioE_rpt1 First He 24.3 58 0.0013 19.1 1.6 22 37-58 3-24 (99)
248 COG1309 AcrR Transcriptional r 24.2 68 0.0015 19.2 2.0 33 26-59 25-57 (201)
249 PRK11511 DNA-binding transcrip 24.1 1.5E+02 0.0033 18.0 3.6 24 35-58 26-49 (127)
250 cd04776 HTH_GnyR Helix-Turn-He 24.1 57 0.0012 19.9 1.6 19 37-55 3-21 (118)
251 PRK08241 RNA polymerase factor 23.9 1.3E+02 0.0028 21.4 3.6 29 36-64 171-199 (339)
252 cd01282 HTH_MerR-like_sg3 Heli 23.9 59 0.0013 19.5 1.6 22 37-58 3-24 (112)
253 PRK15008 HTH-type transcriptio 23.7 1E+02 0.0022 20.2 2.8 40 24-64 29-68 (212)
254 PRK10668 DNA-binding transcrip 23.6 1.1E+02 0.0025 19.8 3.1 43 19-62 17-59 (215)
255 TIGR03826 YvyF flagellar opero 23.6 58 0.0013 20.8 1.5 28 35-62 47-74 (137)
256 PRK09514 zntR zinc-responsive 23.0 60 0.0013 20.4 1.6 21 37-57 4-24 (140)
257 TIGR02051 MerR Hg(II)-responsi 22.9 60 0.0013 19.9 1.5 19 37-55 2-20 (124)
258 TIGR02392 rpoH_proteo alternat 22.9 1.5E+02 0.0033 20.5 3.7 48 14-64 219-266 (270)
259 TIGR03613 RutR pyrimidine util 22.8 1E+02 0.0022 19.8 2.7 39 24-63 19-57 (202)
260 PRK10100 DNA-binding transcrip 22.8 2E+02 0.0043 19.3 4.2 45 13-63 155-199 (216)
261 TIGR01950 SoxR redox-sensitive 22.4 63 0.0014 20.5 1.6 21 37-57 4-24 (142)
262 PF13542 HTH_Tnp_ISL3: Helix-t 22.4 77 0.0017 15.8 1.7 21 36-56 29-49 (52)
263 cd08315 Death_TRAILR_DR4_DR5 D 22.3 1.3E+02 0.0029 17.7 2.8 33 20-52 4-37 (96)
264 cd01108 HTH_CueR Helix-Turn-He 22.2 66 0.0014 19.7 1.6 22 37-58 3-24 (127)
265 PRK13756 tetracycline represso 22.1 74 0.0016 21.3 1.9 37 24-61 15-51 (205)
266 PRK00767 transcriptional regul 22.0 1.3E+02 0.0028 19.1 3.0 40 23-63 19-58 (197)
267 PF10078 DUF2316: Uncharacteri 22.0 59 0.0013 19.2 1.3 30 19-52 12-41 (89)
268 TIGR02835 spore_sigmaE RNA pol 22.0 83 0.0018 21.2 2.2 29 36-64 200-228 (234)
269 PF13412 HTH_24: Winged helix- 21.9 1.2E+02 0.0026 14.9 3.0 37 15-55 2-38 (48)
270 TIGR03020 EpsA transcriptional 21.7 2E+02 0.0044 20.0 4.1 48 11-64 188-235 (247)
271 PRK13182 racA polar chromosome 21.7 65 0.0014 21.3 1.5 21 37-57 3-23 (175)
272 PRK13558 bacterio-opsin activa 21.6 1.1E+02 0.0025 23.7 3.1 42 12-53 606-649 (665)
273 cd04781 HTH_MerR-like_sg6 Heli 21.6 69 0.0015 19.4 1.6 20 37-56 3-22 (120)
274 TIGR02044 CueR Cu(I)-responsiv 21.5 68 0.0015 19.7 1.5 22 37-58 3-24 (127)
275 PRK10651 transcriptional regul 21.4 2.2E+02 0.0047 17.7 4.0 45 13-63 155-199 (216)
276 PF08880 QLQ: QLQ; InterPro: 21.3 1.1E+02 0.0023 15.0 1.9 14 12-25 1-14 (37)
277 COG3682 Predicted transcriptio 21.3 2.2E+02 0.0048 17.9 3.8 44 12-55 2-45 (123)
278 TIGR03541 reg_near_HchA LuxR f 21.2 2.2E+02 0.0047 19.3 4.1 48 11-64 169-216 (232)
279 PRK10227 DNA-binding transcrip 21.1 71 0.0015 20.0 1.6 20 37-56 3-22 (135)
280 PF07471 Phage_Nu1: Phage DNA 21.0 67 0.0015 21.1 1.5 21 37-57 5-25 (164)
281 TIGR03209 P21_Cbot clostridium 20.7 1.7E+02 0.0036 17.7 3.2 13 39-51 128-140 (142)
282 cd04770 HTH_HMRTR Helix-Turn-H 20.7 74 0.0016 19.2 1.6 20 37-56 3-22 (123)
283 TIGR02047 CadR-PbrR Cd(II)/Pb( 20.6 73 0.0016 19.6 1.6 22 37-58 3-24 (127)
284 PRK10430 DNA-binding transcrip 20.5 1.6E+02 0.0034 19.6 3.3 43 14-57 159-201 (239)
285 PF09779 Ima1_N: Ima1 N-termin 20.5 25 0.00055 22.0 -0.5 12 51-62 1-12 (131)
286 PF10453 NUFIP1: Nuclear fragi 20.3 1.6E+02 0.0035 15.8 2.7 21 47-67 19-39 (56)
287 PF07022 Phage_CI_repr: Bacter 20.1 35 0.00075 18.5 -0.0 20 37-56 15-35 (66)
288 cd00131 PAX Paired Box domain 20.1 2.3E+02 0.005 17.5 5.5 45 13-57 75-126 (128)
No 1
>KOG0489|consensus
Probab=99.78 E-value=1.7e-19 Score=125.36 Aligned_cols=68 Identities=71% Similarity=1.022 Sum_probs=62.6
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHHHH
Q psy1653 3 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIK 70 (96)
Q Consensus 3 ~~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~~~ 70 (96)
..+..||.|+.||..|+..||..|..|.|.+...|.+||..|.|+++||+|||||||+||||+.+...
T Consensus 155 ~~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~ 222 (261)
T KOG0489|consen 155 TGGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKS 222 (261)
T ss_pred ccCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccc
Confidence 34567999999999999999999999999999999999999999999999999999999999765443
No 2
>KOG0488|consensus
Probab=99.77 E-value=5.3e-19 Score=125.24 Aligned_cols=64 Identities=44% Similarity=0.723 Sum_probs=60.3
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHH
Q psy1653 5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA 68 (96)
Q Consensus 5 ~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~ 68 (96)
.++|+.||.||..|+..||..|+...|++..+|+.||..|||+..||++||||||+||||+...
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 4556679999999999999999999999999999999999999999999999999999998766
No 3
>KOG0850|consensus
Probab=99.76 E-value=8.8e-19 Score=118.22 Aligned_cols=63 Identities=41% Similarity=0.641 Sum_probs=59.3
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653 5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 67 (96)
Q Consensus 5 ~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~ 67 (96)
.+-|+.||.++..||..|...|++++|+...+|.+||..|||+..||+|||||||.|.||..+
T Consensus 120 KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 120 KKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred ccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 345678999999999999999999999999999999999999999999999999999999765
No 4
>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=99.75 E-value=2.6e-18 Score=94.06 Aligned_cols=57 Identities=49% Similarity=0.701 Sum_probs=55.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 8 rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
|+.|+.|+..|+..|+..|..++||+..++..||..+||+..+|.+||+|+|.++|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 578999999999999999999999999999999999999999999999999999886
No 5
>KOG0843|consensus
Probab=99.75 E-value=2.4e-18 Score=112.52 Aligned_cols=64 Identities=41% Similarity=0.621 Sum_probs=60.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHHH
Q psy1653 6 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAI 69 (96)
Q Consensus 6 ~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~~ 69 (96)
+.+|.||.|+.+|+..|+..|+.++|....+|+.||..|+|++.||+|||||||.|.||.+.+.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 5788899999999999999999999999999999999999999999999999999999976553
No 6
>KOG0484|consensus
Probab=99.74 E-value=2.7e-18 Score=103.56 Aligned_cols=62 Identities=42% Similarity=0.625 Sum_probs=58.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653 6 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 67 (96)
Q Consensus 6 ~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~ 67 (96)
+.+|-|++|+..||..|+..|....||++-.+++||.++.|++..|++||||||+|++++.+
T Consensus 16 KQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 16 KQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred HhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence 45677999999999999999999999999999999999999999999999999999999543
No 7
>KOG0487|consensus
Probab=99.73 E-value=1.8e-18 Score=121.68 Aligned_cols=66 Identities=55% Similarity=0.797 Sum_probs=61.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHHHH
Q psy1653 5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIK 70 (96)
Q Consensus 5 ~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~~~ 70 (96)
+.-|++|..+|..|+..||..|..|.|++...|.+|+..|+|+++||+|||||||+|+||..++.+
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r 298 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENR 298 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhh
Confidence 345778999999999999999999999999999999999999999999999999999999875443
No 8
>KOG2251|consensus
Probab=99.73 E-value=5.7e-18 Score=113.72 Aligned_cols=65 Identities=37% Similarity=0.530 Sum_probs=60.8
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHH
Q psy1653 4 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA 68 (96)
Q Consensus 4 ~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~ 68 (96)
-++.+|.||+|+..|+++|+..|.+.+||+...+++||.+|+|++.+|+|||+|||+|+|+++..
T Consensus 34 pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q 98 (228)
T KOG2251|consen 34 PRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ 98 (228)
T ss_pred chhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence 45668899999999999999999999999999999999999999999999999999999997554
No 9
>KOG0485|consensus
Probab=99.71 E-value=1e-17 Score=112.57 Aligned_cols=65 Identities=40% Similarity=0.692 Sum_probs=60.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHH
Q psy1653 4 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA 68 (96)
Q Consensus 4 ~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~ 68 (96)
++.+|+.||+|+..|+--|+..|+...|.+..+|.-||.+|.|++.||+|||||||.||||+...
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aa 165 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAA 165 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhh
Confidence 44688899999999999999999999999999999999999999999999999999999996543
No 10
>KOG0842|consensus
Probab=99.70 E-value=1.6e-17 Score=116.98 Aligned_cols=62 Identities=40% Similarity=0.688 Sum_probs=58.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653 6 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 67 (96)
Q Consensus 6 ~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~ 67 (96)
++||.|..||..|...||+.|....|++-.+|+.||..|.|++.||+|||||||-|+||...
T Consensus 152 ~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~ 213 (307)
T KOG0842|consen 152 KKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQK 213 (307)
T ss_pred cccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhh
Confidence 56777889999999999999999999999999999999999999999999999999999543
No 11
>KOG3802|consensus
Probab=99.70 E-value=1.1e-17 Score=120.30 Aligned_cols=67 Identities=30% Similarity=0.430 Sum_probs=63.3
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653 1 MGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 67 (96)
Q Consensus 1 ~~~~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~ 67 (96)
|++.+++||+||.|.......|+.+|.+|+.|+..++..||.+|+|...+|+|||||||.|+||...
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 5677889999999999999999999999999999999999999999999999999999999999654
No 12
>KOG0492|consensus
Probab=99.68 E-value=7.4e-17 Score=107.72 Aligned_cols=61 Identities=44% Similarity=0.710 Sum_probs=57.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 67 (96)
Q Consensus 7 ~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~ 67 (96)
-|++|+.|+..||..|++-|...+|.++.++.+++..|.|++.||+|||||||+|.||.+.
T Consensus 144 nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQe 204 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQE 204 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHH
Confidence 3667999999999999999999999999999999999999999999999999999999643
No 13
>KOG0848|consensus
Probab=99.65 E-value=8.4e-17 Score=110.85 Aligned_cols=65 Identities=52% Similarity=0.795 Sum_probs=60.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHHHH
Q psy1653 6 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIK 70 (96)
Q Consensus 6 ~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~~~ 70 (96)
++-+-|.+++..|...||..|.-++|+++.-+.+||.-|||+++||+|||||||+|+||.+++..
T Consensus 198 TkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 198 TKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred cccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 34445889999999999999999999999999999999999999999999999999999887775
No 14
>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=99.64 E-value=3.7e-16 Score=85.93 Aligned_cols=53 Identities=19% Similarity=0.377 Sum_probs=50.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhCCC----CCHHHHHHHHHHcCCCcchhhhhhchhh
Q psy1653 7 RRRGRQTYTRYQTLELEKEFHTNHY----LTRRRRIEMAHALCLTERQIKIWFQNRR 59 (96)
Q Consensus 7 ~rr~r~~~s~~q~~~L~~~F~~~~~----p~~~~~~~la~~l~l~~~~V~~WFqnrR 59 (96)
++|.||.||..|+..|+..|+.++| |+...+..||..+||++.+|++||+|.+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 4789999999999999999999999 9999999999999999999999999965
No 15
>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=99.63 E-value=1e-15 Score=83.74 Aligned_cols=56 Identities=59% Similarity=0.846 Sum_probs=53.4
Q ss_pred CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 9 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 9 r~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
+.++.++..++.+|+..|..++||+..++..||..+||+..+|..||+|+|.+.++
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 56789999999999999999999999999999999999999999999999999876
No 16
>KOG0494|consensus
Probab=99.63 E-value=4.3e-16 Score=107.13 Aligned_cols=61 Identities=43% Similarity=0.620 Sum_probs=56.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 67 (96)
Q Consensus 7 ~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~ 67 (96)
+|+.||.|+..|+..|+..|+...||+...++.|+.++.|++..|+|||||||+||||..+
T Consensus 141 RRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek 201 (332)
T KOG0494|consen 141 RRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEK 201 (332)
T ss_pred cccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhh
Confidence 3445899999999999999999999999999999999999999999999999999999543
No 17
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.62 E-value=8.9e-16 Score=83.41 Aligned_cols=56 Identities=55% Similarity=0.822 Sum_probs=52.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653 8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 63 (96)
Q Consensus 8 rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~k 63 (96)
++.|+.|+..++..|+..|..++||+..++..||..+||+..+|..||+|+|.+.+
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 35678899999999999999999999999999999999999999999999998753
No 18
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.62 E-value=8e-16 Score=99.75 Aligned_cols=65 Identities=32% Similarity=0.516 Sum_probs=60.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHH
Q psy1653 4 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA 68 (96)
Q Consensus 4 ~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~ 68 (96)
.+..+++|.+.+..|+.+|+..|+.++||+...+..|+..|+|+++.|++||||+|++.|+....
T Consensus 48 s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 48 SSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 45678889999999999999999999999999999999999999999999999999999986544
No 19
>KOG0493|consensus
Probab=99.58 E-value=2e-15 Score=103.93 Aligned_cols=60 Identities=50% Similarity=0.782 Sum_probs=57.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66 (96)
Q Consensus 7 ~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~ 66 (96)
.||+||.|+.+||..|...|..|.|++..-|..|+.+|+|.+.||+|||||+|+|.||..
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 467899999999999999999999999999999999999999999999999999999954
No 20
>KOG0491|consensus
Probab=99.57 E-value=7.8e-16 Score=99.63 Aligned_cols=64 Identities=45% Similarity=0.712 Sum_probs=59.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHHHH
Q psy1653 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIK 70 (96)
Q Consensus 7 ~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~~~ 70 (96)
+++.|++|+..|+..|+..|+...|.+..++.+|+..|+|++.||+.||||||+|.||..+...
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred hhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 4567999999999999999999999999999999999999999999999999999999765544
No 21
>KOG4577|consensus
Probab=99.53 E-value=1.1e-14 Score=101.61 Aligned_cols=66 Identities=29% Similarity=0.419 Sum_probs=62.0
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHH
Q psy1653 3 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA 68 (96)
Q Consensus 3 ~~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~ 68 (96)
+++.-||+||+++..||+.|...|...+.|....|+.|+.++||..+.|++||||||+|+||-++.
T Consensus 163 gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T KOG4577|consen 163 GDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T ss_pred cccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhh
Confidence 566789999999999999999999999999999999999999999999999999999999986644
No 22
>KOG0483|consensus
Probab=99.49 E-value=6.2e-14 Score=93.87 Aligned_cols=61 Identities=33% Similarity=0.509 Sum_probs=56.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 67 (96)
Q Consensus 7 ~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~ 67 (96)
...++.+|+..|...|+..|+...+..+..+..||..|||.++||.+||||||++||..+.
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kql 110 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQL 110 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhh
Confidence 3455678999999999999999999999999999999999999999999999999998553
No 23
>KOG0844|consensus
Probab=99.48 E-value=1.2e-14 Score=102.04 Aligned_cols=60 Identities=53% Similarity=0.780 Sum_probs=57.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653 8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 67 (96)
Q Consensus 8 rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~ 67 (96)
||-||.|+.+|+..|+..|.+.-|-+...|.+||..|+|++..|++||||||+|+||+.-
T Consensus 182 RRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl 241 (408)
T KOG0844|consen 182 RRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL 241 (408)
T ss_pred HHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence 677999999999999999999999999999999999999999999999999999999763
No 24
>KOG0847|consensus
Probab=99.44 E-value=5.7e-14 Score=94.84 Aligned_cols=63 Identities=43% Similarity=0.755 Sum_probs=59.6
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653 4 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66 (96)
Q Consensus 4 ~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~ 66 (96)
+|+++..|.+|+..|+..|+..|+...|+-..++.+||..+|+++.+|++||||||.||||..
T Consensus 164 dG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh 226 (288)
T KOG0847|consen 164 NGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH 226 (288)
T ss_pred CccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence 467888899999999999999999999999999999999999999999999999999999954
No 25
>KOG0486|consensus
Probab=99.43 E-value=8e-14 Score=97.97 Aligned_cols=60 Identities=40% Similarity=0.611 Sum_probs=57.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653 6 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65 (96)
Q Consensus 6 ~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~ 65 (96)
+++|.|+.|+..|+..|+..|.+|.||+...+++||.-.++++..|++||.|||+||+|.
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkr 170 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 170 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhh
Confidence 457789999999999999999999999999999999999999999999999999999994
No 26
>KOG1168|consensus
Probab=99.30 E-value=1.1e-12 Score=91.81 Aligned_cols=62 Identities=24% Similarity=0.399 Sum_probs=59.0
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653 4 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65 (96)
Q Consensus 4 ~~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~ 65 (96)
++.+||+||.+...+...|+.+|...+.|+...+..||.+|+|....|++||||.|+|.||.
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm 367 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 367 (385)
T ss_pred ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHh
Confidence 56689999999999999999999999999999999999999999999999999999998884
No 27
>KOG0490|consensus
Probab=99.26 E-value=3.2e-12 Score=86.48 Aligned_cols=62 Identities=35% Similarity=0.378 Sum_probs=58.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653 5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66 (96)
Q Consensus 5 ~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~ 66 (96)
.++++.|+.|+..|++.|+..|...+||+...++.|+..+++++..|++||||+|+++++..
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 45788999999999999999999999999999999999999999999999999999999865
No 28
>KOG0849|consensus
Probab=99.12 E-value=6.7e-11 Score=85.52 Aligned_cols=62 Identities=31% Similarity=0.482 Sum_probs=58.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653 5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66 (96)
Q Consensus 5 ~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~ 66 (96)
.+.++.|++|+..|+..|+..|+.++||+...++.|+.++++++..|.+||+|+|.+++|..
T Consensus 174 ~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 174 RGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred ccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 44567789999999999999999999999999999999999999999999999999999965
No 29
>KOG0775|consensus
Probab=99.07 E-value=1.7e-10 Score=80.12 Aligned_cols=51 Identities=29% Similarity=0.447 Sum_probs=46.4
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 14 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 14 ~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
|...-...|..+|..++||++.++.+||..+||+..||-.||+|||+++|-
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 334457799999999999999999999999999999999999999999983
No 30
>KOG0774|consensus
Probab=98.89 E-value=1.9e-09 Score=74.64 Aligned_cols=72 Identities=26% Similarity=0.421 Sum_probs=63.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHH---hCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHHHHHHHHHHHH
Q psy1653 7 RRRGRQTYTRYQTLELEKEFH---TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELNEQEKQ 78 (96)
Q Consensus 7 ~rr~r~~~s~~q~~~L~~~F~---~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~~~~~~~~~~~ 78 (96)
.+|+|..|+....++|..+|. .+|||+....++||.+++++..||-.||.|+|-+++|......+...--..
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~~ee~~l~~~ 262 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKNQEEANLYAA 262 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhhhhhhhhHhh
Confidence 367788999999999999996 589999999999999999999999999999999999987776666544333
No 31
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.68 E-value=1.5e-08 Score=51.81 Aligned_cols=34 Identities=32% Similarity=0.585 Sum_probs=28.7
Q ss_pred hCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhh
Q psy1653 28 TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61 (96)
Q Consensus 28 ~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k 61 (96)
.+|||+..++..|+..+|++..||..||-|.|.+
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 4799999999999999999999999999998864
No 32
>KOG2252|consensus
Probab=98.53 E-value=1.5e-07 Score=70.75 Aligned_cols=57 Identities=21% Similarity=0.285 Sum_probs=53.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhh
Q psy1653 6 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKL 62 (96)
Q Consensus 6 ~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~ 62 (96)
..|++|.+|+..|+..|...|+.+++|+..+.+.|+.+|+|....|..||.|-|.|.
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 357789999999999999999999999999999999999999999999999988774
No 33
>KOG0490|consensus
Probab=98.26 E-value=1.4e-06 Score=58.83 Aligned_cols=63 Identities=38% Similarity=0.520 Sum_probs=58.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653 5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 67 (96)
Q Consensus 5 ~~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~ 67 (96)
.+.++.++.+...++..|...|..+++|+...+..|+..+|++...|++||+|++.+.++...
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 151 KKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 456777899999999999999999999999999999999999999999999999999988544
No 34
>KOG1146|consensus
Probab=97.55 E-value=8.2e-05 Score=61.03 Aligned_cols=60 Identities=27% Similarity=0.347 Sum_probs=56.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66 (96)
Q Consensus 7 ~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~ 66 (96)
++..|+.++..|+.+|...|....+|.....+.|...+++..+.|.+||+|-|.+.++..
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~ 962 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAK 962 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhh
Confidence 566799999999999999999999999999999999999999999999999999998854
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.46 E-value=0.00011 Score=39.95 Aligned_cols=43 Identities=19% Similarity=0.310 Sum_probs=31.1
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhh
Q psy1653 18 QTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 60 (96)
Q Consensus 18 q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~ 60 (96)
....|+.+|....++.......|..+.+|+..+|+.||-.+..
T Consensus 9 d~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 9 DIQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp --HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred chHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 4566999999999999999999999999999999999976543
No 36
>KOG0773|consensus
Probab=96.51 E-value=0.0029 Score=45.51 Aligned_cols=60 Identities=20% Similarity=0.335 Sum_probs=49.1
Q ss_pred CCCCCCCCCHHHHHHHHHHH-H--hCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653 7 RRRGRQTYTRYQTLELEKEF-H--TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66 (96)
Q Consensus 7 ~rr~r~~~s~~q~~~L~~~F-~--~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~ 66 (96)
..+.+..+......+|..+. + ..+||+..+...|+.++||+..||-.||-|.|-+.-+..
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~ 301 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPM 301 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCch
Confidence 34556678888888888773 3 357999999999999999999999999999988776643
No 37
>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=96.32 E-value=0.014 Score=31.19 Aligned_cols=47 Identities=17% Similarity=0.357 Sum_probs=35.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhh
Q psy1653 8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRR 59 (96)
Q Consensus 8 rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR 59 (96)
+++|..+|-.+...+...++.+. ....||..+|++..+|..|..|+.
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 46788999999888888888777 577889999999999999998753
No 38
>KOG3623|consensus
Probab=96.01 E-value=0.011 Score=46.90 Aligned_cols=48 Identities=17% Similarity=0.208 Sum_probs=43.9
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653 19 TLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66 (96)
Q Consensus 19 ~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~ 66 (96)
+.+|..+|..|+.|+..+...++...|++...|+.||.+++.......
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 778999999999999999999999999999999999999988776643
No 39
>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=88.20 E-value=0.88 Score=24.35 Aligned_cols=40 Identities=18% Similarity=0.180 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHHHhCCC--CCHHHHHHHHHHcCCCcchhhh
Q psy1653 14 YTRYQTLELEKEFHTNHY--LTRRRRIEMAHALCLTERQIKI 53 (96)
Q Consensus 14 ~s~~q~~~L~~~F~~~~~--p~~~~~~~la~~l~l~~~~V~~ 53 (96)
+|..|..+|...|...-| |-......||..+|++...|-.
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~ 42 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSE 42 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHH
Confidence 478899999999998765 5566788899999999877554
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=87.90 E-value=1.2 Score=24.61 Aligned_cols=46 Identities=17% Similarity=0.290 Sum_probs=29.7
Q ss_pred CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchh
Q psy1653 9 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNR 58 (96)
Q Consensus 9 r~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnr 58 (96)
+.|..||.++...+...+.... .....++..+||+...+..|-.--
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g----~sv~~va~~~gi~~~~l~~W~~~~ 47 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG----ESVSEVAREYGISPSTLYNWRKQY 47 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH----CHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC----CceEeeecccccccccccHHHHHH
Confidence 3567899998777766662222 367788999999999999998533
No 41
>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=87.49 E-value=1.8 Score=22.20 Aligned_cols=41 Identities=7% Similarity=0.113 Sum_probs=30.5
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchh
Q psy1653 13 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNR 58 (96)
Q Consensus 13 ~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnr 58 (96)
.+++.+..+|...|..+. ...++|..+|++...|+.+...-
T Consensus 4 ~L~~~er~vi~~~y~~~~-----t~~eIa~~lg~s~~~V~~~~~~a 44 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEGL-----TLEEIAERLGISRSTVRRILKRA 44 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCCC-----CHHHHHHHHCCcHHHHHHHHHHH
Confidence 467888899999883332 46778999999999998876533
No 42
>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=87.37 E-value=1.7 Score=23.78 Aligned_cols=45 Identities=20% Similarity=0.362 Sum_probs=24.6
Q ss_pred CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhc
Q psy1653 11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQ 56 (96)
Q Consensus 11 r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFq 56 (96)
|..|+..........|.....--...|. .|.++||+..+|+-|.+
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 5567777655555555544332223343 49999999999999985
No 43
>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=84.19 E-value=2.4 Score=20.97 Aligned_cols=42 Identities=10% Similarity=0.088 Sum_probs=29.5
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhh
Q psy1653 13 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRR 59 (96)
Q Consensus 13 ~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR 59 (96)
.+++.+..++...|..+. ....+|..+|++...|..|...-+
T Consensus 10 ~l~~~~~~~~~~~~~~~~-----~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 10 KLPEREREVILLRFGEGL-----SYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred hCCHHHHHHHHHHHhcCC-----CHHHHHHHHCcCHHHHHHHHHHHH
Confidence 356667777776664332 356679999999999999886443
No 44
>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=83.75 E-value=0.7 Score=25.41 Aligned_cols=21 Identities=24% Similarity=0.483 Sum_probs=17.9
Q ss_pred HHHHHHHHcCCCcchhhhhhc
Q psy1653 36 RRIEMAHALCLTERQIKIWFQ 56 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFq 56 (96)
....||..||+++.+|+.|=.
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhh
Confidence 455679999999999999975
No 45
>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=82.15 E-value=3.9 Score=21.05 Aligned_cols=39 Identities=15% Similarity=0.159 Sum_probs=25.7
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhch
Q psy1653 14 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQN 57 (96)
Q Consensus 14 ~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqn 57 (96)
+++.+..++.-.|-.+. ...++|..+|++...|+.|...
T Consensus 11 L~~~~r~i~~l~~~~g~-----s~~eIa~~l~~s~~~v~~~l~r 49 (54)
T PF08281_consen 11 LPERQREIFLLRYFQGM-----SYAEIAEILGISESTVKRRLRR 49 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHCc-----CHHHHHHHHCcCHHHHHHHHHH
Confidence 45556666665554433 5778899999999999999863
No 46
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=79.90 E-value=8.9 Score=24.60 Aligned_cols=52 Identities=15% Similarity=0.082 Sum_probs=38.9
Q ss_pred CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHH
Q psy1653 11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA 68 (96)
Q Consensus 11 r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~ 68 (96)
.+.+++.|..+|.- +..+- ...++|..+|++...|..|...-+.+.++....
T Consensus 4 ~~~Lt~rqreVL~l-r~~Gl-----Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t 55 (141)
T PRK03975 4 ESFLTERQIEVLRL-RERGL-----TQQEIADILGTSRANVSSIEKRARENIEKARET 55 (141)
T ss_pred ccCCCHHHHHHHHH-HHcCC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 45788999999877 33222 356789999999999999998777776665443
No 47
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=73.75 E-value=8.1 Score=23.94 Aligned_cols=44 Identities=14% Similarity=0.138 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhh
Q psy1653 14 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKL 62 (96)
Q Consensus 14 ~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~ 62 (96)
+++.+..++.-.|-.+ ....++|..+|++...|+.+...-+.+.
T Consensus 107 L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~L 150 (154)
T PRK06759 107 LDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKM 150 (154)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3444445544444332 2467789999999999999986444443
No 48
>PF05703 Auxin_canalis: Auxin canalisation; InterPro: IPR008546 This domain consists of several plant proteins of unknown function.
Probab=72.99 E-value=28 Score=24.41 Aligned_cols=14 Identities=21% Similarity=0.634 Sum_probs=11.4
Q ss_pred Ccchhhhhhchhhh
Q psy1653 47 TERQIKIWFQNRRM 60 (96)
Q Consensus 47 ~~~~V~~WFqnrR~ 60 (96)
....|..||+.++.
T Consensus 99 ~~~~i~~w~~~~~~ 112 (242)
T PF05703_consen 99 GGKTIGRWLKDRKE 112 (242)
T ss_pred ccchHHHHHHHHHH
Confidence 46789999998776
No 49
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=72.72 E-value=8.9 Score=24.21 Aligned_cols=30 Identities=27% Similarity=0.130 Sum_probs=23.2
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKKE 65 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr~ 65 (96)
...++|..+|++...|+.|...-|.+.++.
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 155 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKAL 155 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 466788999999999999987555555554
No 50
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=71.47 E-value=12 Score=24.49 Aligned_cols=29 Identities=17% Similarity=0.280 Sum_probs=22.4
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..||++...|+.+...-+.+.++
T Consensus 160 s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 160 TYREVAERLAVPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred CHHHHHHHhCCChHhHHHHHHHHHHHHHH
Confidence 46678999999999999988755555544
No 51
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=70.75 E-value=6.1 Score=26.59 Aligned_cols=41 Identities=15% Similarity=0.161 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHhCCC--CCHHHHHHHHHHcCCCcchhhh
Q psy1653 13 TYTRYQTLELEKEFHTNHY--LTRRRRIEMAHALCLTERQIKI 53 (96)
Q Consensus 13 ~~s~~q~~~L~~~F~~~~~--p~~~~~~~la~~l~l~~~~V~~ 53 (96)
-+|..|+.+|...|...-| |-......||..+|+++..+..
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~e 197 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSE 197 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHH
Confidence 5899999999999998764 6677788899999999877544
No 52
>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=70.27 E-value=3.8 Score=22.17 Aligned_cols=20 Identities=20% Similarity=0.326 Sum_probs=17.9
Q ss_pred HHHHHHHcCCCcchhhhhhc
Q psy1653 37 RIEMAHALCLTERQIKIWFQ 56 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFq 56 (96)
..++|..||++...|..|-.
T Consensus 16 ~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred HHHHHHHHCCChHHHHHHHH
Confidence 56789999999999999986
No 53
>PF13518 HTH_28: Helix-turn-helix domain
Probab=69.87 E-value=3.9 Score=20.67 Aligned_cols=22 Identities=14% Similarity=0.350 Sum_probs=18.4
Q ss_pred HHHHHHHcCCCcchhhhhhchh
Q psy1653 37 RIEMAHALCLTERQIKIWFQNR 58 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnr 58 (96)
...+|..+||+..+|..|.+.-
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y 36 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRY 36 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHH
Confidence 4568999999999999999643
No 54
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=69.61 E-value=3.8 Score=20.45 Aligned_cols=22 Identities=9% Similarity=0.052 Sum_probs=18.2
Q ss_pred HHHHHHHcCCCcchhhhhhchh
Q psy1653 37 RIEMAHALCLTERQIKIWFQNR 58 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnr 58 (96)
..++|..+|++...|+.|....
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 3567899999999999997654
No 55
>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=69.19 E-value=8.8 Score=16.72 Aligned_cols=38 Identities=16% Similarity=0.142 Sum_probs=24.8
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhh
Q psy1653 13 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWF 55 (96)
Q Consensus 13 ~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF 55 (96)
.++......+...|... . ....++..+|++...|..|.
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 35566666665566532 2 35567888999988888774
No 56
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=69.18 E-value=12 Score=19.59 Aligned_cols=44 Identities=20% Similarity=0.130 Sum_probs=30.7
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhh
Q psy1653 13 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKL 62 (96)
Q Consensus 13 ~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~ 62 (96)
.+|+.+..+|.-...-. ...++|..+|+++..|..+..+=+.|.
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHh
Confidence 57788888776554322 366789999999999999887655544
No 57
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=68.08 E-value=9.3 Score=22.74 Aligned_cols=40 Identities=25% Similarity=0.241 Sum_probs=29.6
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhh
Q psy1653 13 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIK 52 (96)
Q Consensus 13 ~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~ 52 (96)
+++++|...-...|..+--.+....+++|..|++++.-|.
T Consensus 2 SLn~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~le 41 (97)
T COG4367 2 SLNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLE 41 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHH
Confidence 4677787777777666666666778889999999876543
No 58
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=68.00 E-value=6.2 Score=19.86 Aligned_cols=40 Identities=13% Similarity=0.082 Sum_probs=19.9
Q ss_pred CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhc
Q psy1653 12 QTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQ 56 (96)
Q Consensus 12 ~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFq 56 (96)
..++..+...+...+..+ .....+|..+|++...|..+..
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 456777777777766543 2456689999999999887764
No 59
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=67.73 E-value=18 Score=22.72 Aligned_cols=29 Identities=21% Similarity=0.235 Sum_probs=22.5
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|..|...=+.+.++
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45778999999999999999755555444
No 60
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=67.68 E-value=13 Score=23.42 Aligned_cols=29 Identities=14% Similarity=0.097 Sum_probs=21.8
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
....+|..+|++...|+.|...-+.+.++
T Consensus 146 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 146 SYEEIAEIMGCPIGTVRSRIFRAREALRA 174 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45677899999999999998754544444
No 61
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=67.62 E-value=16 Score=24.11 Aligned_cols=29 Identities=21% Similarity=0.179 Sum_probs=22.2
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+.++..-+.+.++
T Consensus 171 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 199 (206)
T PRK12526 171 SQEQLAQQLNVPLGTVKSRLRLALAKLKV 199 (206)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45678899999999999988755555544
No 62
>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=67.50 E-value=13 Score=22.25 Aligned_cols=28 Identities=25% Similarity=0.312 Sum_probs=21.0
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLK 63 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~k 63 (96)
....+|..+|++...|+.+...-+.+.+
T Consensus 128 s~~eIA~~l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 128 SYKEIAEILGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4567899999999999998865444433
No 63
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=67.36 E-value=4.5 Score=20.48 Aligned_cols=22 Identities=18% Similarity=0.374 Sum_probs=17.0
Q ss_pred HHHHHHHHcCCCcchhhhhhch
Q psy1653 36 RRIEMAHALCLTERQIKIWFQN 57 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqn 57 (96)
....+|..+|++...|..|...
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT-
T ss_pred CHHHHHHHHCcCHHHHHHHHHH
Confidence 4667899999999999999863
No 64
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=67.33 E-value=18 Score=22.58 Aligned_cols=29 Identities=17% Similarity=0.148 Sum_probs=21.9
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+..+..-|.+.++
T Consensus 124 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 124 SYQEIALQEKIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35678899999999999988755555544
No 65
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=67.00 E-value=16 Score=23.28 Aligned_cols=29 Identities=17% Similarity=0.379 Sum_probs=22.1
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|++++..-|.+.|+
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 46778999999999999988755555444
No 66
>KOG1146|consensus
Probab=66.29 E-value=7.6 Score=33.30 Aligned_cols=59 Identities=19% Similarity=0.234 Sum_probs=52.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653 8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66 (96)
Q Consensus 8 rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~ 66 (96)
+..+..+-..++..|-..|..+..|+......|....+.+.+.+.+||++-+.+.+++.
T Consensus 706 ~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 706 KLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred ccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 44466677789999999999999999999999999999999999999999999988754
No 67
>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=65.18 E-value=16 Score=22.61 Aligned_cols=26 Identities=15% Similarity=0.098 Sum_probs=19.5
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhh
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMK 61 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k 61 (96)
...++|..+|++...|..+...-|.+
T Consensus 129 ~~~eIA~~l~is~~tv~~~l~Rar~~ 154 (159)
T TIGR02989 129 SLTALAEQLGRTVNAVYKALSRLRVR 154 (159)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 46678899999999999887533333
No 68
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=65.11 E-value=17 Score=22.73 Aligned_cols=30 Identities=23% Similarity=0.277 Sum_probs=22.6
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKKE 65 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr~ 65 (96)
...++|..+|++...|+.+...-+.+.+..
T Consensus 129 s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~ 158 (166)
T PRK09639 129 SYKEIAEALGIKESSVGTTLARAKKKFRKI 158 (166)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456788999999999999887555555553
No 69
>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=63.83 E-value=20 Score=22.87 Aligned_cols=29 Identities=21% Similarity=0.159 Sum_probs=21.3
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|++.+..-|.+.++
T Consensus 152 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 152 TVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45667888999999999988755544443
No 70
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=63.27 E-value=21 Score=22.91 Aligned_cols=29 Identities=17% Similarity=0.209 Sum_probs=22.6
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+.++..-+.+.+.
T Consensus 149 s~~eIA~~l~is~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12512 149 SIKETAAKLSMSEGAVRVALHRGLAALAA 177 (184)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45678999999999999988765655554
No 71
>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=63.27 E-value=30 Score=20.63 Aligned_cols=41 Identities=20% Similarity=0.285 Sum_probs=22.7
Q ss_pred HHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHHHHHHHH
Q psy1653 20 LELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELNE 74 (96)
Q Consensus 20 ~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~~~~~~~ 74 (96)
.+..-.|+.|+||.+.-... =-.|||.+|++.+..+....+
T Consensus 15 RiIk~LyqsnPyP~~~GTr~--------------aRRnRRRRWR~rq~QI~~lse 55 (91)
T PF00424_consen 15 RIIKILYQSNPYPSPEGTRQ--------------ARRNRRRRWRARQRQIRALSE 55 (91)
T ss_dssp HHHHHHHHTS-S--S-S-HH--------------HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHccccCCCCCCccc--------------cccchhhhHHHHHHHHHHHHH
Confidence 34445588899987441111 024889999988777666554
No 72
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=62.85 E-value=6.4 Score=21.19 Aligned_cols=21 Identities=14% Similarity=0.232 Sum_probs=17.4
Q ss_pred HHHHHHHcCCCcchhhhhhch
Q psy1653 37 RIEMAHALCLTERQIKIWFQN 57 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqn 57 (96)
..++|..+||+...|+.|-..
T Consensus 3 i~eva~~~gvs~~tlr~y~~~ 23 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYERE 23 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 356899999999999999653
No 73
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=62.50 E-value=13 Score=23.91 Aligned_cols=32 Identities=16% Similarity=0.272 Sum_probs=24.2
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 67 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~ 67 (96)
...++|..+|++...|+.+...-+.+.++...
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999988766666655433
No 74
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=62.42 E-value=28 Score=22.60 Aligned_cols=29 Identities=7% Similarity=0.262 Sum_probs=22.2
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|+++..|+++...-|.+.|+
T Consensus 152 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 152 SSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46678999999999999998755554444
No 75
>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=61.93 E-value=6.5 Score=19.29 Aligned_cols=20 Identities=20% Similarity=0.270 Sum_probs=15.4
Q ss_pred HHHHHHHcCCCcchhhhhhc
Q psy1653 37 RIEMAHALCLTERQIKIWFQ 56 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFq 56 (96)
+.++|..+||+...|+.|=.
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 34678999999999999854
No 76
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=61.75 E-value=21 Score=23.03 Aligned_cols=28 Identities=18% Similarity=0.160 Sum_probs=21.0
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLK 63 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~k 63 (96)
...++|..+|++...|+.+...-+.+.+
T Consensus 157 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 184 (189)
T PRK09648 157 SAEETAEAVGSTPGAVRVAQHRALARLR 184 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4677899999999999988864444444
No 77
>PRK06930 positive control sigma-like factor; Validated
Probab=61.65 E-value=29 Score=22.70 Aligned_cols=46 Identities=11% Similarity=0.052 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 14 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 14 ~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
+++.+..++.-.|-.+- ...++|..+|++...|+.++..-+.+.++
T Consensus 115 L~~rer~V~~L~~~eg~-----s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~ 160 (170)
T PRK06930 115 LTEREKEVYLMHRGYGL-----SYSEIADYLNIKKSTVQSMIERAEKKIAR 160 (170)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 44555555554433222 35677899999999999999766665555
No 78
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=61.33 E-value=23 Score=22.91 Aligned_cols=30 Identities=20% Similarity=0.240 Sum_probs=23.0
Q ss_pred HHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 35 RRRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 35 ~~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
....++|..+|++...|+.++..-+.+.++
T Consensus 158 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 158 LSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 356678999999999999999755555544
No 79
>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=60.31 E-value=24 Score=22.50 Aligned_cols=29 Identities=34% Similarity=0.317 Sum_probs=21.7
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+.+...-+.+.+.
T Consensus 118 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 146 (170)
T TIGR02959 118 SQQEIAEKLGLSLSGAKSRVQRGRKKLKE 146 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46678899999999999988654544444
No 80
>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=60.04 E-value=25 Score=21.51 Aligned_cols=27 Identities=15% Similarity=0.220 Sum_probs=19.5
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhh
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKL 62 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~ 62 (96)
...++|..+|++...|+.+...=+.+.
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~~L 157 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALKEL 157 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 456678889999999998876434333
No 81
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=59.74 E-value=21 Score=22.73 Aligned_cols=30 Identities=23% Similarity=0.223 Sum_probs=22.6
Q ss_pred HHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 35 RRRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 35 ~~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
....++|..+|++...|+.++..-+.+.+.
T Consensus 153 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 153 LSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 356678999999999999988755555444
No 82
>PRK00118 putative DNA-binding protein; Validated
Probab=59.59 E-value=37 Score=20.57 Aligned_cols=51 Identities=12% Similarity=0.022 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHHHH
Q psy1653 13 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA 68 (96)
Q Consensus 13 ~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~ 68 (96)
.++..+..++.-.|..+. ...++|..+|++...|..|...-+.+.+..-..
T Consensus 17 ~L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~ 67 (104)
T PRK00118 17 LLTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEK 67 (104)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 456666666666555433 456689999999999999998666666664443
No 83
>PRK10072 putative transcriptional regulator; Provisional
Probab=59.55 E-value=7.3 Score=23.27 Aligned_cols=25 Identities=20% Similarity=0.243 Sum_probs=21.0
Q ss_pred HHHHHHHcCCCcchhhhhhchhhhh
Q psy1653 37 RIEMAHALCLTERQIKIWFQNRRMK 61 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnrR~k 61 (96)
...||..+|++...|..|...++.-
T Consensus 49 Q~elA~~lGvS~~TVs~WE~G~r~P 73 (96)
T PRK10072 49 IDDFARVLGVSVAMVKEWESRRVKP 73 (96)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCCC
Confidence 5678999999999999999877643
No 84
>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=59.44 E-value=22 Score=17.80 Aligned_cols=38 Identities=11% Similarity=0.211 Sum_probs=25.2
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhh
Q psy1653 13 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWF 55 (96)
Q Consensus 13 ~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF 55 (96)
.++..+...+...+.... ....+|..+||+...|.-++
T Consensus 5 ~~~~~~~~~i~~l~~~G~-----si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEGM-----SIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCCC-----CHHHHHHHHCcCHHHHHHHH
Confidence 355555666666666552 46778999999999887766
No 85
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=59.10 E-value=45 Score=21.32 Aligned_cols=31 Identities=19% Similarity=0.200 Sum_probs=23.9
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~ 66 (96)
...++|..+|++...|+.....-+.+.++..
T Consensus 135 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 165 (179)
T PRK12543 135 SQEEIAQLLQIPIGTVKSRIHAALKKLRQKE 165 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4567888999999999998876666666643
No 86
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=58.37 E-value=38 Score=20.96 Aligned_cols=29 Identities=24% Similarity=0.190 Sum_probs=21.1
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+.....-+.+.+.
T Consensus 124 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 152 (161)
T PRK09047 124 DVAETAAAMGCSEGSVKTHCSRATHALAK 152 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35678999999999999887644444443
No 87
>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=58.23 E-value=22 Score=22.77 Aligned_cols=29 Identities=7% Similarity=0.015 Sum_probs=22.3
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+++...-|.+.++
T Consensus 156 s~~EIA~~lgis~~tv~~~l~rar~~Lr~ 184 (190)
T TIGR02939 156 SYEDIARIMDCPVGTVRSRIFRAREAIAI 184 (190)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 46778999999999999988655555444
No 88
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=58.03 E-value=15 Score=24.76 Aligned_cols=42 Identities=10% Similarity=0.029 Sum_probs=33.1
Q ss_pred HHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 21 ~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
.-...|....|- .....+|...|++...|..+|.++..=+.-
T Consensus 21 aA~~lF~~~Gy~--~s~~~IA~~AGvsk~tiy~~F~sKe~L~~a 62 (225)
T PRK11552 21 AALAQFGEYGLH--ATTRDIAAQAGQNIAAITYYFGSKEDLYLA 62 (225)
T ss_pred HHHHHHHHhCcc--CCHHHHHHHhCCCHHHHHHHcCCHHHHHHH
Confidence 334458888877 567888999999999999999988765543
No 89
>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=57.57 E-value=8.3 Score=20.79 Aligned_cols=21 Identities=5% Similarity=0.186 Sum_probs=17.7
Q ss_pred HHHHHHHcCCCcchhhhhhch
Q psy1653 37 RIEMAHALCLTERQIKIWFQN 57 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqn 57 (96)
..++|..+|++...++.|-..
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 456889999999999999764
No 90
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=57.26 E-value=31 Score=22.15 Aligned_cols=27 Identities=22% Similarity=0.348 Sum_probs=20.3
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhh
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKL 62 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~ 62 (96)
...++|..+|++...|+.+...-+.+.
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ra~~~L 177 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIKRSLKAL 177 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHHHHHHHH
Confidence 456778999999999999886444433
No 91
>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=57.21 E-value=29 Score=21.66 Aligned_cols=26 Identities=31% Similarity=0.151 Sum_probs=18.4
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhh
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMK 61 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k 61 (96)
...++|..+|++...|+....--+.+
T Consensus 140 s~~eIA~~l~is~~tv~~~l~ra~~~ 165 (170)
T TIGR02952 140 PIAEVARILGKTEGAVKILQFRAIKK 165 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 45677888899999888876533333
No 92
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=57.04 E-value=37 Score=23.11 Aligned_cols=30 Identities=17% Similarity=0.190 Sum_probs=23.4
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKKE 65 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr~ 65 (96)
...++|..+|++...|+.....-+.+.|+.
T Consensus 189 s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~ 218 (233)
T PRK12538 189 SNGEIAEVMDTTVAAVESLLKRGRQQLRDL 218 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999887666665553
No 93
>PRK09480 slmA division inhibitor protein; Provisional
Probab=56.81 E-value=15 Score=23.43 Aligned_cols=34 Identities=12% Similarity=0.153 Sum_probs=27.7
Q ss_pred HHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhh
Q psy1653 26 FHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 60 (96)
Q Consensus 26 F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~ 60 (96)
|...+. .......|+...|++...+..+|.|+-.
T Consensus 23 ~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 23 LESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 444445 6778889999999999999999998654
No 94
>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=56.72 E-value=4.3 Score=23.17 Aligned_cols=24 Identities=21% Similarity=0.320 Sum_probs=20.1
Q ss_pred HHHHHHHHHcCCCcchhhhhhchh
Q psy1653 35 RRRIEMAHALCLTERQIKIWFQNR 58 (96)
Q Consensus 35 ~~~~~la~~l~l~~~~V~~WFqnr 58 (96)
-...++|..+|++...|+.|+.+.
T Consensus 33 lS~kEIAe~LGIS~~TVk~~l~~~ 56 (73)
T TIGR03879 33 KTASEIAEELGRTEQTVRNHLKGE 56 (73)
T ss_pred CCHHHHHHHHCcCHHHHHHHHhcC
Confidence 356788999999999999999743
No 95
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=56.44 E-value=34 Score=20.45 Aligned_cols=42 Identities=19% Similarity=0.230 Sum_probs=33.4
Q ss_pred CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC-Ccchhhhhhc
Q psy1653 11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCL-TERQIKIWFQ 56 (96)
Q Consensus 11 r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l-~~~~V~~WFq 56 (96)
+..|+.+....+-..+..... ....+|..+|| ...++..|..
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 778999988777776665554 57788999996 9999998885
No 96
>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=56.39 E-value=8.8 Score=20.79 Aligned_cols=21 Identities=14% Similarity=0.211 Sum_probs=17.8
Q ss_pred HHHHHHHcCCCcchhhhhhch
Q psy1653 37 RIEMAHALCLTERQIKIWFQN 57 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqn 57 (96)
..++|..+||+...++.|...
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 456899999999999999764
No 97
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=56.36 E-value=30 Score=21.79 Aligned_cols=28 Identities=18% Similarity=0.065 Sum_probs=21.1
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLK 63 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~k 63 (96)
...++|..+|++...|+.+...-+.+.+
T Consensus 130 s~~eIA~~lgis~~tV~~~l~Rar~~Lr 157 (164)
T PRK12547 130 SYEDAAAICGCAVGTIKSRVSRARNRLQ 157 (164)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4667889999999999998874444443
No 98
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=56.36 E-value=40 Score=21.70 Aligned_cols=29 Identities=21% Similarity=0.219 Sum_probs=21.4
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|++-+..-|.+.++
T Consensus 149 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (189)
T PRK12515 149 SVEEVGEIVGIPESTVKTRMFYARKKLAE 177 (189)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45667889999999999887655555544
No 99
>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=56.31 E-value=9.4 Score=18.50 Aligned_cols=23 Identities=17% Similarity=0.411 Sum_probs=18.6
Q ss_pred HHHHHHHcCCCcchhhhhhchhh
Q psy1653 37 RIEMAHALCLTERQIKIWFQNRR 59 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnrR 59 (96)
..++|..+|++...|..|..+..
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCC
Confidence 35678899999999999986554
No 100
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=56.13 E-value=24 Score=22.03 Aligned_cols=28 Identities=25% Similarity=0.232 Sum_probs=20.1
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLK 63 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~k 63 (96)
...++|..+|++...|+.+...-|.+.+
T Consensus 130 s~~eIA~~lgis~~tv~~~l~Rar~~L~ 157 (161)
T PRK12541 130 SYKEIAEMTGLSLAKVKIELHRGRKETK 157 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4567788899999999888764444433
No 101
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=55.30 E-value=34 Score=21.34 Aligned_cols=28 Identities=7% Similarity=0.235 Sum_probs=20.3
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLK 63 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~k 63 (96)
...++|..+|++...|+.....-+.+.+
T Consensus 127 s~~EIA~~lgis~~tV~~~l~ra~~~lr 154 (163)
T PRK07037 127 TQKDIARELGVSPTLVNFMIRDALVHCR 154 (163)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4667889999999999987654444433
No 102
>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=55.27 E-value=31 Score=21.71 Aligned_cols=29 Identities=28% Similarity=0.330 Sum_probs=21.2
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+.....-+.+.++
T Consensus 137 s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 137 TIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45678999999999999887644444443
No 103
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=54.28 E-value=28 Score=22.77 Aligned_cols=30 Identities=17% Similarity=0.069 Sum_probs=23.4
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKKE 65 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr~ 65 (96)
...++|..+|++...|+.++..-+.+.++.
T Consensus 131 s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~ 160 (188)
T PRK12546 131 SYEEAAEMCGVAVGTVKSRANRARARLAEL 160 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999998666665553
No 104
>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=54.24 E-value=31 Score=21.46 Aligned_cols=29 Identities=17% Similarity=0.275 Sum_probs=21.8
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+.+...-+.+.++
T Consensus 128 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 128 SEAQVAEALGISVGTVKSRLSRALARLRE 156 (162)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45678889999999999988755555444
No 105
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=54.11 E-value=34 Score=21.97 Aligned_cols=29 Identities=17% Similarity=0.125 Sum_probs=21.9
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+.+...-+.+.++
T Consensus 149 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12539 149 SVAEAATRSGMSESAVKVSVHRGLKALAA 177 (184)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 56678999999999999988655544444
No 106
>PRK04217 hypothetical protein; Provisional
Probab=53.96 E-value=42 Score=20.56 Aligned_cols=48 Identities=10% Similarity=-0.060 Sum_probs=33.7
Q ss_pred CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653 11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 63 (96)
Q Consensus 11 r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~k 63 (96)
-..++..+..++...|...- ...++|..+|++...|+..+..-+.+.+
T Consensus 40 ~~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLr 87 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVA 87 (110)
T ss_pred cccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 34577778777766654433 4667899999999999988865444443
No 107
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=53.54 E-value=33 Score=22.31 Aligned_cols=29 Identities=10% Similarity=0.103 Sum_probs=22.4
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+.++..-+.+.++
T Consensus 154 s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~ 182 (196)
T PRK12524 154 SNPEIAEVMEIGVEAVESLTARGKRALAA 182 (196)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45678999999999999999755555544
No 108
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=53.37 E-value=36 Score=21.83 Aligned_cols=29 Identities=21% Similarity=0.162 Sum_probs=22.0
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+..+..-+.+.++
T Consensus 147 s~~EIA~~l~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 147 SVAETAQLTGLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45678889999999999988755555544
No 109
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=53.33 E-value=34 Score=22.12 Aligned_cols=29 Identities=34% Similarity=0.349 Sum_probs=21.7
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+..+..-|.+.++
T Consensus 124 ~~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (181)
T PRK09637 124 SQKEIAEKLGLSLSGAKSRVQRGRVKLKE 152 (181)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 46678999999999999888655544444
No 110
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=52.66 E-value=49 Score=21.41 Aligned_cols=30 Identities=10% Similarity=0.129 Sum_probs=22.8
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKKE 65 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr~ 65 (96)
...++|..+|++...|+.....-|.+.++.
T Consensus 154 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 183 (195)
T PRK12532 154 SSDEIQQMCGISTSNYHTIMHRARESLRQC 183 (195)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999887555555553
No 111
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=51.23 E-value=42 Score=21.15 Aligned_cols=29 Identities=17% Similarity=0.188 Sum_probs=20.9
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+.....-+.+.++
T Consensus 136 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 164 (173)
T PRK09645 136 STAQIAADLGIPEGTVKSRLHYALRALRL 164 (173)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 35678889999999999887644444443
No 112
>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=51.18 E-value=59 Score=21.08 Aligned_cols=29 Identities=14% Similarity=0.297 Sum_probs=21.5
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+.....-|.+.++
T Consensus 149 s~~EIA~~lgis~~tvk~rl~Rar~~Lr~ 177 (188)
T TIGR02943 149 ESDEICQELEISTSNCHVLLYRARLSLRA 177 (188)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 46678999999999998877644544444
No 113
>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=50.56 E-value=12 Score=19.97 Aligned_cols=20 Identities=10% Similarity=0.205 Sum_probs=17.3
Q ss_pred HHHHHHHcCCCcchhhhhhc
Q psy1653 37 RIEMAHALCLTERQIKIWFQ 56 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFq 56 (96)
..++|..+|++...++.|.+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35679999999999999986
No 114
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=50.41 E-value=44 Score=22.12 Aligned_cols=29 Identities=17% Similarity=0.221 Sum_probs=21.2
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+.+...=+.+.++
T Consensus 156 s~~EIA~~Lgis~~tV~~~l~RArk~Lr~ 184 (203)
T PRK09647 156 SYEEIAATLGVKLGTVRSRIHRGRQQLRA 184 (203)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35677899999999999988744444443
No 115
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=49.99 E-value=48 Score=21.14 Aligned_cols=27 Identities=22% Similarity=0.143 Sum_probs=19.4
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhh
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKL 62 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~ 62 (96)
...++|..+|++...|+.+...-+.+.
T Consensus 153 s~~eIA~~lgis~~~V~~~l~ra~~~L 179 (186)
T PRK13919 153 THREAAQLLGLPLGTLKTRARRALSRL 179 (186)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 456678889999999988876434333
No 116
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=49.95 E-value=13 Score=19.54 Aligned_cols=24 Identities=4% Similarity=0.170 Sum_probs=17.8
Q ss_pred HHHHHHHHcCCCcchhhhhhchhh
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRR 59 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR 59 (96)
....||..+|++...|..|+.++.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~ 35 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKP 35 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-
T ss_pred CHHHHHHHHCcCHHHHHHHHhccc
Confidence 456789999999999999998763
No 117
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=49.90 E-value=55 Score=21.28 Aligned_cols=30 Identities=20% Similarity=0.082 Sum_probs=22.6
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKKE 65 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr~ 65 (96)
...++|..||++...|+.....-+.+.++.
T Consensus 134 s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~ 163 (187)
T PRK12516 134 AYEEAAEICGCAVGTIKSRVNRARQRLQEI 163 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 356778899999999999887555555553
No 118
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=49.75 E-value=36 Score=22.97 Aligned_cols=29 Identities=14% Similarity=0.197 Sum_probs=23.1
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+.+...-+.+.++
T Consensus 202 s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 230 (236)
T PRK06986 202 NLKEIGAVLGVSESRVSQIHSQAIKRLRA 230 (236)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46778999999999999998766655554
No 119
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=48.75 E-value=41 Score=21.75 Aligned_cols=28 Identities=14% Similarity=-0.007 Sum_probs=20.4
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLK 63 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~k 63 (96)
...++|..+|++...|+.....-+.+.+
T Consensus 148 s~~EIA~~lgis~~tVk~~l~Rar~~Lr 175 (185)
T PRK09649 148 SYADAAAVCGCPVGTIRSRVARARDALL 175 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3567888999999999988864444443
No 120
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=48.70 E-value=40 Score=22.69 Aligned_cols=29 Identities=14% Similarity=0.069 Sum_probs=21.1
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+.....-|.+.++
T Consensus 152 s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~ 180 (216)
T PRK12533 152 SYREIAAIADVPVGTVMSRLARARRRLAA 180 (216)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45678889999999998887644444444
No 121
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=48.67 E-value=63 Score=20.41 Aligned_cols=29 Identities=14% Similarity=0.233 Sum_probs=21.3
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
.-.++|..+|++...|+.....-+.+.++
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 165 (173)
T PRK12522 137 SYKEMSEILNIPIGTVKYRLNYAKKQMRE 165 (173)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45678899999999999988644444444
No 122
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=48.63 E-value=48 Score=21.22 Aligned_cols=27 Identities=15% Similarity=0.283 Sum_probs=20.1
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhh
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKL 62 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~ 62 (96)
...++|..+|++...|+..+..-+.+.
T Consensus 145 s~~EIA~~lgis~~tVk~~l~rAl~~~ 171 (178)
T PRK12529 145 KQKDIAQALDIALPTVKKYIHQAYVTC 171 (178)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 456788999999999998876444443
No 123
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=48.30 E-value=28 Score=21.22 Aligned_cols=41 Identities=12% Similarity=0.234 Sum_probs=28.8
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhh
Q psy1653 14 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61 (96)
Q Consensus 14 ~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k 61 (96)
+++.++..+...+... ...+|.-||++...|+.|=++|+.-
T Consensus 44 ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~kP 84 (104)
T COG2944 44 LSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRKKP 84 (104)
T ss_pred CCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCcCC
Confidence 5556666665554432 3456888899999999999988644
No 124
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=48.29 E-value=47 Score=21.46 Aligned_cols=29 Identities=34% Similarity=0.365 Sum_probs=20.4
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+.....-+.+.++
T Consensus 149 s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 149 KIEEIAKKLGLTRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35678889999999988877644444443
No 125
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=48.25 E-value=69 Score=20.64 Aligned_cols=29 Identities=21% Similarity=0.351 Sum_probs=21.9
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|++....-|.+.++
T Consensus 149 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (191)
T PRK12520 149 ETEEICQELQITATNAWVLLYRARMRLRE 177 (191)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35678889999999999988755555544
No 126
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=48.07 E-value=36 Score=22.38 Aligned_cols=32 Identities=16% Similarity=0.032 Sum_probs=23.6
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 67 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~ 67 (96)
...++|..+|++...|+.+...-+.+.++...
T Consensus 151 s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~ 182 (196)
T PRK12535 151 TYEEAAKIADVRVGTIRSRVARARADLIAATA 182 (196)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 45677889999999999988765655555433
No 127
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=47.96 E-value=37 Score=22.27 Aligned_cols=37 Identities=14% Similarity=0.032 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhh
Q psy1653 16 RYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIK 52 (96)
Q Consensus 16 ~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~ 52 (96)
..-+..|...+....|.+......+|..||++...|.
T Consensus 25 sAlip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v~ 61 (160)
T COG1905 25 SALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARVY 61 (160)
T ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHhe
Confidence 3456778888888889999999999999999987654
No 128
>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=47.39 E-value=47 Score=22.17 Aligned_cols=43 Identities=14% Similarity=0.193 Sum_probs=27.3
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhh
Q psy1653 14 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61 (96)
Q Consensus 14 ~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k 61 (96)
+++.+..++.-.|..+ ....++|..+|++...|..|...=+.+
T Consensus 179 L~~~~r~vl~l~y~~~-----~s~~eIA~~lgis~~~v~~~~~ra~~~ 221 (227)
T TIGR02980 179 LPERERRILLLRFFED-----KTQSEIAERLGISQMHVSRLLRRALKK 221 (227)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 4444555555544322 246678999999999999887643333
No 129
>KOG3755|consensus
Probab=47.31 E-value=6 Score=31.37 Aligned_cols=61 Identities=10% Similarity=0.053 Sum_probs=0.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHc-------CCCcchhhhhhchhhhhhHHHH
Q psy1653 6 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHAL-------CLTERQIKIWFQNRRMKLKKEI 66 (96)
Q Consensus 6 ~~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l-------~l~~~~V~~WFqnrR~k~kr~~ 66 (96)
.++..-..|......+-+.+|.++..+......+.-..+ .+..+.|+.||.+||.++++.+
T Consensus 691 pk~~~~k~f~~~~~ev~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 691 PKKTIIKFFQNQRYEVKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred cHHHHHHhhhcceeecchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhh
No 130
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=47.23 E-value=53 Score=20.78 Aligned_cols=28 Identities=11% Similarity=0.184 Sum_probs=21.2
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLK 63 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~k 63 (96)
.-.++|..+|++...|+.+...-+.+.+
T Consensus 137 s~~EIA~~lgis~~tV~~~l~ra~~~~~ 164 (172)
T PRK12523 137 GHAEIAERLGVSVSRVRQYLAQGLRQCY 164 (172)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4567788999999999998865555444
No 131
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=46.68 E-value=47 Score=22.70 Aligned_cols=29 Identities=14% Similarity=0.190 Sum_probs=21.8
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+.|...-+.+.+.
T Consensus 223 s~~eIA~~l~is~~tV~~~~~ra~~kLr~ 251 (257)
T PRK08583 223 SQKETGERLGISQMHVSRLQRQAIKKLRE 251 (257)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35778999999999999988655544443
No 132
>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=46.64 E-value=33 Score=18.16 Aligned_cols=35 Identities=34% Similarity=0.366 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhh
Q psy1653 17 YQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWF 55 (96)
Q Consensus 17 ~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF 55 (96)
.++..|+-.+. +...+.. .|+..+|++...|+...
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~i 40 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKNDI 40 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHHH
Confidence 46777777777 5555443 78999999998887654
No 133
>smart00595 MADF subfamily of SANT domain.
Probab=46.31 E-value=40 Score=18.96 Aligned_cols=36 Identities=22% Similarity=0.363 Sum_probs=29.5
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHHHHHHHHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKE 71 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~~~~~ 71 (96)
.-..|+..+|.+...|+.-+.|-|..++++......
T Consensus 29 aW~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~r~~~ 64 (89)
T smart00595 29 AWEEIAEELGLSVEECKKRWKNLRDRYRRELKRLQN 64 (89)
T ss_pred HHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455689999999999999999999999987666544
No 134
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=46.27 E-value=67 Score=20.83 Aligned_cols=28 Identities=14% Similarity=0.119 Sum_probs=19.8
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLK 63 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~k 63 (96)
...++|..+|++...|+.-+..-+.+.+
T Consensus 159 s~~EIA~~lgis~~tVk~rl~ra~~~Lr 186 (194)
T PRK12531 159 PHQQVAEMFDIPLGTVKSRLRLAVEKLR 186 (194)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHH
Confidence 4567788999999999877654444433
No 135
>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=46.27 E-value=44 Score=20.32 Aligned_cols=38 Identities=11% Similarity=0.180 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhc
Q psy1653 14 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQ 56 (96)
Q Consensus 14 ~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFq 56 (96)
+|-.........+.... ....+|..++|+...|..||.
T Consensus 3 YS~DlR~rVl~~~~~g~-----s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 3 YSLDLRQRVLAYIEKGK-----SIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred CCHHHHHHHHHHHHccc-----hHHHHHHHhCcHHHHHHHHHH
Confidence 34444455555666543 355678889999999999998
No 136
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=46.04 E-value=51 Score=21.12 Aligned_cols=29 Identities=17% Similarity=0.375 Sum_probs=21.4
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+.....-+.+.++
T Consensus 140 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 168 (185)
T PRK12542 140 TYQEISSVMGITEANVRKQFERARKRVQN 168 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45678889999999999987655554444
No 137
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=45.99 E-value=72 Score=20.89 Aligned_cols=29 Identities=17% Similarity=0.302 Sum_probs=21.8
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|++....-|.+.++
T Consensus 157 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 185 (201)
T PRK12545 157 EIDDICTELTLTANHCSVLLYRARTRLRT 185 (201)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45678899999999999887755555544
No 138
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=45.91 E-value=53 Score=21.28 Aligned_cols=29 Identities=17% Similarity=0.111 Sum_probs=21.0
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+.+...-+.+.++
T Consensus 129 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 157 (182)
T PRK12511 129 SYQEAAAVLGIPIGTLMSRIGRARAALRA 157 (182)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 45678899999999999887644444443
No 139
>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=45.36 E-value=12 Score=18.85 Aligned_cols=21 Identities=10% Similarity=0.181 Sum_probs=18.4
Q ss_pred HHHHHcCCCcchhhhhhchhh
Q psy1653 39 EMAHALCLTERQIKIWFQNRR 59 (96)
Q Consensus 39 ~la~~l~l~~~~V~~WFqnrR 59 (96)
.||..+|++...|..|+.+..
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 478999999999999998774
No 140
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=44.46 E-value=53 Score=20.86 Aligned_cols=29 Identities=24% Similarity=0.256 Sum_probs=21.7
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+.....=|.+.++
T Consensus 154 s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T PRK09641 154 SLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45678999999999998887655555444
No 141
>KOG0773|consensus
Probab=44.07 E-value=31 Score=24.81 Aligned_cols=42 Identities=38% Similarity=0.552 Sum_probs=35.0
Q ss_pred HHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653 24 KEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65 (96)
Q Consensus 24 ~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~ 65 (96)
..-..++||+......++....++.-+|.+||-|-+.+.+..
T Consensus 114 ~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~ 155 (342)
T KOG0773|consen 114 EEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKE 155 (342)
T ss_pred hhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhc
Confidence 334568999999999999999999999989999888776653
No 142
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=43.97 E-value=62 Score=21.71 Aligned_cols=29 Identities=24% Similarity=0.213 Sum_probs=22.0
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+.+...-+.+.|+
T Consensus 200 s~~EIA~~lgis~~tVk~~~~rA~~~Lr~ 228 (234)
T PRK08301 200 TQKEVADMLGISQSYISRLEKRIIKRLKK 228 (234)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46678899999999999887655555554
No 143
>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=43.78 E-value=76 Score=21.82 Aligned_cols=29 Identities=10% Similarity=0.220 Sum_probs=22.9
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+.+...-+.+.++
T Consensus 179 S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~ 207 (244)
T TIGR03001 179 SMDRIGAMYQVHRSTVSRWVAQARERLLE 207 (244)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 46678999999999999999765555554
No 144
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=43.75 E-value=60 Score=20.20 Aligned_cols=21 Identities=19% Similarity=0.232 Sum_probs=16.8
Q ss_pred HHHHHHHHcCCCcchhhhhhc
Q psy1653 36 RRIEMAHALCLTERQIKIWFQ 56 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFq 56 (96)
.-.++|..+|++...|+.+..
T Consensus 131 s~~EIA~~l~is~~tV~~~l~ 151 (161)
T PRK12528 131 GYGEIATELGISLATVKRYLN 151 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 356678888999999988775
No 145
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=43.75 E-value=74 Score=19.34 Aligned_cols=45 Identities=11% Similarity=0.161 Sum_probs=31.2
Q ss_pred CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhch
Q psy1653 9 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQN 57 (96)
Q Consensus 9 r~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqn 57 (96)
.++..|+.++....-.....+.. ....+|..+||++..|..|...
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHHH
Confidence 34567888876555444443443 3556799999999999999854
No 146
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=43.34 E-value=79 Score=21.82 Aligned_cols=30 Identities=20% Similarity=0.284 Sum_probs=21.7
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKKE 65 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr~ 65 (96)
...++|..+|++...|+.....-+.+.++.
T Consensus 230 s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 259 (268)
T PRK06288 230 TLKEIGKVLGVTESRISQLHTKAVLQLRAK 259 (268)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999988776555554443
No 147
>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=43.30 E-value=40 Score=21.80 Aligned_cols=31 Identities=16% Similarity=0.147 Sum_probs=24.2
Q ss_pred HHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653 35 RRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65 (96)
Q Consensus 35 ~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~ 65 (96)
....++|..+|++...|+.+...-|.+.++.
T Consensus 148 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 178 (193)
T TIGR02947 148 FAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQ 178 (193)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3567789999999999999987556555553
No 148
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=43.29 E-value=84 Score=20.82 Aligned_cols=28 Identities=21% Similarity=0.463 Sum_probs=21.8
Q ss_pred HHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 37 RIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
..++|..+|++...|+.....-|.+.++
T Consensus 167 ~~EIAe~lgis~~tV~~~l~RAr~~Lr~ 194 (206)
T PRK12544 167 TNEICHAVDLSVSNLNVLLYRARLRLRE 194 (206)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 5678999999999999988755555554
No 149
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=42.86 E-value=59 Score=21.69 Aligned_cols=43 Identities=21% Similarity=0.195 Sum_probs=26.2
Q ss_pred CHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhh
Q psy1653 15 TRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKL 62 (96)
Q Consensus 15 s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~ 62 (96)
++.+..+|...|-... ...++|..+|++...|+.+...-+.+.
T Consensus 177 ~~~~r~il~l~y~~~~-----s~~eIA~~lgis~~tV~~~~~ra~~~L 219 (224)
T TIGR02479 177 SEREQLVLSLYYYEEL-----NLKEIGEVLGLTESRVSQIHSQALKKL 219 (224)
T ss_pred CHHHHHHHHHHHhCCC-----CHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 3444444444443222 457789999999999888776444333
No 150
>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=42.65 E-value=21 Score=17.33 Aligned_cols=23 Identities=13% Similarity=0.081 Sum_probs=17.7
Q ss_pred HHHHHHHcCCCcchhhhhhchhh
Q psy1653 37 RIEMAHALCLTERQIKIWFQNRR 59 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnrR 59 (96)
..++|..+|++...|..|.....
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcCC
Confidence 35678888999999999886543
No 151
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=42.53 E-value=83 Score=20.21 Aligned_cols=31 Identities=10% Similarity=0.121 Sum_probs=23.3
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~ 66 (96)
...++|..+|++...|+.....-|.+.|+.-
T Consensus 156 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 156 SYEDIASVMQCPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999988875555555543
No 152
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=41.93 E-value=20 Score=19.10 Aligned_cols=20 Identities=15% Similarity=0.160 Sum_probs=16.4
Q ss_pred HHHHHHHcCCCcchhhhhhc
Q psy1653 37 RIEMAHALCLTERQIKIWFQ 56 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFq 56 (96)
..+++..+|++...|+.|..
T Consensus 3 ~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35678899999999999954
No 153
>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=41.84 E-value=56 Score=22.30 Aligned_cols=45 Identities=16% Similarity=0.167 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653 14 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 63 (96)
Q Consensus 14 ~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~k 63 (96)
+++.+..++.-.|..+. ...++|..+|++...|+.+...-+.+.|
T Consensus 206 L~~~~r~ii~l~~~~g~-----s~~eIA~~lgis~~~V~~~~~ra~~~Lr 250 (255)
T TIGR02941 206 LSEREKSIIHCTFEENL-----SQKETGERLGISQMHVSRLQRQAISKLK 250 (255)
T ss_pred CCHHHHHHHHHHHcCCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 34444445544443222 3467889999999999888764444443
No 154
>PF12728 HTH_17: Helix-turn-helix domain
Probab=41.01 E-value=22 Score=17.96 Aligned_cols=22 Identities=18% Similarity=0.333 Sum_probs=17.4
Q ss_pred HHHHHHHcCCCcchhhhhhchh
Q psy1653 37 RIEMAHALCLTERQIKIWFQNR 58 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnr 58 (96)
..++|..||++...|..|....
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcC
Confidence 3567888899999999998654
No 155
>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=40.74 E-value=22 Score=18.04 Aligned_cols=23 Identities=22% Similarity=0.280 Sum_probs=18.8
Q ss_pred HHHHHHHcCCCcchhhhhhchhh
Q psy1653 37 RIEMAHALCLTERQIKIWFQNRR 59 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnrR 59 (96)
...||..+|++...|..|..+.+
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHhCCCcchhHHHhcCCC
Confidence 46789999999999999998754
No 156
>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=40.71 E-value=28 Score=21.43 Aligned_cols=31 Identities=26% Similarity=0.200 Sum_probs=22.6
Q ss_pred CHHHHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653 33 TRRRRIEMAHALCLTERQIKIWFQNRRMKLK 63 (96)
Q Consensus 33 ~~~~~~~la~~l~l~~~~V~~WFqnrR~k~k 63 (96)
......++|..+|+++..|+.+...-+.+.+
T Consensus 120 ~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr 150 (154)
T TIGR02950 120 KEFSYKEIAELLNLSLAKVKSNLFRARKELK 150 (154)
T ss_pred ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3445777899999999999988864444443
No 157
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=39.47 E-value=70 Score=20.76 Aligned_cols=30 Identities=27% Similarity=0.247 Sum_probs=21.6
Q ss_pred HHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 35 RRRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 35 ~~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
....++|..+|++...|++-+..-|.+.++
T Consensus 171 ~s~~EIA~~lgis~~tV~~~l~rar~~Lr~ 200 (208)
T PRK08295 171 KSYQEIAEELNRHVKSIDNALQRVKRKLEK 200 (208)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 345677889999999998877655544444
No 158
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=39.41 E-value=21 Score=19.43 Aligned_cols=18 Identities=22% Similarity=0.569 Sum_probs=15.2
Q ss_pred HHHHHHHcCCCcchhhhh
Q psy1653 37 RIEMAHALCLTERQIKIW 54 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~W 54 (96)
...||..||++..-|..|
T Consensus 12 ~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 12 QSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHh
Confidence 357899999999999999
No 159
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=39.38 E-value=73 Score=20.59 Aligned_cols=35 Identities=17% Similarity=0.097 Sum_probs=27.2
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhh
Q psy1653 18 QTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIK 52 (96)
Q Consensus 18 q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~ 52 (96)
-+..|...=....|.+......+|..||++...|.
T Consensus 25 li~~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V~ 59 (156)
T PRK05988 25 LLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEVH 59 (156)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHH
Confidence 34555555456679999999999999999987754
No 160
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=39.36 E-value=21 Score=25.40 Aligned_cols=27 Identities=22% Similarity=0.353 Sum_probs=22.0
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
.-..||.+|||++.+|+.|-+ |..|.-
T Consensus 21 k~~dIAeklGvspntiksWKr--r~gWs~ 47 (279)
T COG5484 21 KLKDIAEKLGVSPNTIKSWKR--RDGWSA 47 (279)
T ss_pred cHHHHHHHhCCChHHHHHHHH--hcCCCc
Confidence 456789999999999999986 666643
No 161
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=39.07 E-value=90 Score=19.93 Aligned_cols=26 Identities=19% Similarity=0.183 Sum_probs=18.3
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhh
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMK 61 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k 61 (96)
...++|..+|++...|+.-...-|.+
T Consensus 155 s~~eIA~~lgis~~~v~~~l~Rar~~ 180 (187)
T PRK12534 155 TYEELAARTDTPIGTVKSWIRRGLAK 180 (187)
T ss_pred CHHHHHHHhCCChhHHHHHHHHHHHH
Confidence 45677888999998888766533333
No 162
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=38.36 E-value=61 Score=20.56 Aligned_cols=26 Identities=19% Similarity=0.264 Sum_probs=19.7
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhh
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMK 61 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k 61 (96)
...++|..+|++...|+++...-+..
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~ 162 (172)
T PRK09651 137 TYSEIAHKLGVSVSSVKKYVAKATEH 162 (172)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 46778999999999999888543333
No 163
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=38.26 E-value=42 Score=21.17 Aligned_cols=30 Identities=23% Similarity=0.238 Sum_probs=23.5
Q ss_pred HHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 35 RRRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 35 ~~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
....++|..+|++...|+..+..-+.+.++
T Consensus 137 ~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~ 166 (175)
T PRK12518 137 LPQKEIAEILNIPVGTVKSRLFYARRQLRK 166 (175)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 356788999999999999988755555555
No 164
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=38.25 E-value=53 Score=16.08 Aligned_cols=39 Identities=21% Similarity=0.257 Sum_probs=27.1
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhch
Q psy1653 13 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQN 57 (96)
Q Consensus 13 ~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqn 57 (96)
.++..+..++.. +.. .. ....+|..+|++...|..|...
T Consensus 3 ~l~~~e~~i~~~-~~~-g~----s~~eia~~l~is~~tv~~~~~~ 41 (58)
T smart00421 3 SLTPREREVLRL-LAE-GL----TNKEIAERLGISEKTVKTHLSN 41 (58)
T ss_pred CCCHHHHHHHHH-HHc-CC----CHHHHHHHHCCCHHHHHHHHHH
Confidence 356777776654 322 22 4567889999999999988763
No 165
>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=38.17 E-value=25 Score=20.74 Aligned_cols=22 Identities=14% Similarity=0.055 Sum_probs=17.7
Q ss_pred HHHHHHHcCCCcchhhhhhchh
Q psy1653 37 RIEMAHALCLTERQIKIWFQNR 58 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnr 58 (96)
..++|..+||+...++.|..+.
T Consensus 3 i~eva~~~gvs~~tlR~ye~~G 24 (103)
T cd01106 3 VGEVAKLTGVSVRTLHYYDEIG 24 (103)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 3567889999999999997553
No 166
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=37.99 E-value=74 Score=21.72 Aligned_cols=28 Identities=25% Similarity=0.291 Sum_probs=21.0
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLK 63 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~k 63 (96)
...++|..+|++...|+..+..-+.+.|
T Consensus 219 s~~EIA~~lgis~~tV~~~~~ra~~~Lr 246 (251)
T PRK07670 219 TLTEIGQVLNLSTSRISQIHSKALFKLK 246 (251)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4567899999999999988864444443
No 167
>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=37.83 E-value=1.1e+02 Score=19.51 Aligned_cols=48 Identities=19% Similarity=0.127 Sum_probs=34.9
Q ss_pred CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 11 r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
.+.++..|..+|.-. ..+- ...++|..+|++...|..+-..-+.+.++
T Consensus 4 ~~~Lte~qr~VL~Lr-~~Gl-----Tq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELR-EKGL-----SQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHH-HcCC-----CHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 457888899888774 2222 46678999999999999888755555544
No 168
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=37.68 E-value=71 Score=20.41 Aligned_cols=28 Identities=21% Similarity=0.249 Sum_probs=20.2
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLK 63 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~k 63 (96)
...++|..+|++...|+.+...-+.+.+
T Consensus 145 s~~EIA~~l~is~~tv~~~l~Ra~~~Lr 172 (179)
T PRK09415 145 SIKEIAEVTGVNENTVKTRLKKAKELLK 172 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3567788999999999988764444433
No 169
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=37.55 E-value=86 Score=19.75 Aligned_cols=26 Identities=12% Similarity=0.144 Sum_probs=19.1
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhh
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMK 61 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k 61 (96)
...++|..+|++...|+.+..+-+..
T Consensus 136 s~~EIA~~l~is~~tV~~~l~ra~~~ 161 (168)
T PRK12525 136 TYVEIGERLGVSLSRIHQYMVEAFKC 161 (168)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 45677888999999998877544433
No 170
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=37.43 E-value=29 Score=17.43 Aligned_cols=23 Identities=13% Similarity=0.059 Sum_probs=19.6
Q ss_pred HHHHHHHcCCCcchhhhhhchhh
Q psy1653 37 RIEMAHALCLTERQIKIWFQNRR 59 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnrR 59 (96)
...||..+|++...|.-|...++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 46789999999999999997664
No 171
>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=37.27 E-value=25 Score=20.21 Aligned_cols=19 Identities=21% Similarity=0.366 Sum_probs=16.2
Q ss_pred HHHHHHHcCCCcchhhhhh
Q psy1653 37 RIEMAHALCLTERQIKIWF 55 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WF 55 (96)
..++|..+||+...++.|-
T Consensus 4 i~evA~~~gvs~~tLR~ye 22 (88)
T cd01105 4 IGEVSKLTGVSPRQLRYWE 22 (88)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 4567899999999999995
No 172
>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=37.24 E-value=26 Score=20.21 Aligned_cols=21 Identities=5% Similarity=0.021 Sum_probs=17.6
Q ss_pred HHHHHHHcCCCcchhhhhhch
Q psy1653 37 RIEMAHALCLTERQIKIWFQN 57 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqn 57 (96)
...+|..+||+...|+.|...
T Consensus 4 i~e~A~~~gvs~~tLr~ye~~ 24 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYERL 24 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 456899999999999999854
No 173
>PF13309 HTH_22: HTH domain
Probab=37.03 E-value=72 Score=17.28 Aligned_cols=43 Identities=7% Similarity=0.146 Sum_probs=29.8
Q ss_pred CCCHHH-HHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhh
Q psy1653 13 TYTRYQ-TLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWF 55 (96)
Q Consensus 13 ~~s~~q-~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF 55 (96)
.++..+ +.++...++.+-|--......+|..||++...|..+.
T Consensus 20 ~l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~YL 63 (64)
T PF13309_consen 20 RLSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYRYL 63 (64)
T ss_pred hCCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHHHc
Confidence 344443 4555555666667777788889999999988876543
No 174
>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=36.78 E-value=94 Score=19.91 Aligned_cols=28 Identities=25% Similarity=0.189 Sum_probs=20.5
Q ss_pred HHHHHHHHHcCCCcchhhhhhchhhhhh
Q psy1653 35 RRRIEMAHALCLTERQIKIWFQNRRMKL 62 (96)
Q Consensus 35 ~~~~~la~~l~l~~~~V~~WFqnrR~k~ 62 (96)
....++|..+|++...|++.+..-|.+.
T Consensus 166 ~s~~eIA~~l~~s~~tV~~~l~r~r~~L 193 (198)
T TIGR02859 166 KSYQEIACDLNRHVKSIDNALQRVKRKL 193 (198)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3566789999999999998776444333
No 175
>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=36.76 E-value=92 Score=19.72 Aligned_cols=27 Identities=15% Similarity=0.183 Sum_probs=18.0
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhh
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKL 62 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~ 62 (96)
...++|..+|++...|+.=...-+.+.
T Consensus 158 s~~eIA~~lgis~~~v~~~l~Ra~~~L 184 (189)
T TIGR02984 158 SFAEVAERMDRSEGAVSMLWVRGLARL 184 (189)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 456678888999888877554333333
No 176
>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=36.60 E-value=30 Score=16.42 Aligned_cols=23 Identities=22% Similarity=0.257 Sum_probs=18.8
Q ss_pred HHHHHHHcCCCcchhhhhhchhh
Q psy1653 37 RIEMAHALCLTERQIKIWFQNRR 59 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnrR 59 (96)
...++..+|++...|..|..+..
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 34678899999999999987663
No 177
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=36.52 E-value=45 Score=21.48 Aligned_cols=29 Identities=17% Similarity=0.221 Sum_probs=22.7
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+++...-+.+.+.
T Consensus 152 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 180 (188)
T PRK09640 152 EFQEIADIMHMGLSATKMRYKRALDKLRE 180 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 56778999999999999998755555554
No 178
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=36.38 E-value=83 Score=20.11 Aligned_cols=35 Identities=9% Similarity=0.039 Sum_probs=26.9
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhh
Q psy1653 18 QTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIK 52 (96)
Q Consensus 18 q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~ 52 (96)
-+.+|...=..-.|.+......+|..+|++...|.
T Consensus 24 ll~~L~~vQ~~~g~ip~~~~~~iA~~l~v~~~~v~ 58 (154)
T PRK07539 24 VIPALKIVQEQRGWVPDEAIEAVADYLGMPAIDVE 58 (154)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 34455555456689999999999999999987654
No 179
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=36.32 E-value=84 Score=21.64 Aligned_cols=29 Identities=21% Similarity=0.179 Sum_probs=21.6
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+.+...-+.+.+.
T Consensus 221 s~~eIA~~lgvs~~~V~~~~~ra~~kLr~ 249 (256)
T PRK07408 221 TQKEAAERLGISPVTVSRRVKKGLDQLKK 249 (256)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 46778999999999999988644444443
No 180
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=36.08 E-value=32 Score=22.26 Aligned_cols=31 Identities=19% Similarity=0.170 Sum_probs=22.9
Q ss_pred HHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 34 RRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 34 ~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
.....++|..+|++...|+.+...-+.+.++
T Consensus 155 g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 185 (194)
T PRK12513 155 DLELEEIAELTGVPEETVKSRLRYALQKLRE 185 (194)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3456788999999999999887655544444
No 181
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=35.84 E-value=60 Score=20.82 Aligned_cols=39 Identities=8% Similarity=0.006 Sum_probs=29.3
Q ss_pred HHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhh
Q psy1653 22 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61 (96)
Q Consensus 22 L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k 61 (96)
....|....|.. .....++...|++...+..+|.++..=
T Consensus 17 A~~lf~e~G~~~-tSi~~Ia~~aGvsk~~lY~~F~sK~~L 55 (192)
T PRK14996 17 AMRVALAEGFAA-MTVRRIASEAQVAAGQVHHHFSSAGEL 55 (192)
T ss_pred HHHHHHhcChhh-ccHHHHHHHhCCCcHHHHHHcCCHHHH
Confidence 344477777743 346778999999999999999887553
No 182
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=35.06 E-value=95 Score=20.02 Aligned_cols=29 Identities=21% Similarity=0.063 Sum_probs=20.6
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+.....-+.+.++
T Consensus 129 s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~ 157 (182)
T PRK12540 129 SYEDAAAICGCAVGTIKSRVNRARSKLSA 157 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45677889999999998887644444433
No 183
>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=34.88 E-value=96 Score=20.73 Aligned_cols=38 Identities=11% Similarity=0.178 Sum_probs=24.3
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhc
Q psy1653 14 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQ 56 (96)
Q Consensus 14 ~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFq 56 (96)
++..+..++...|..+ ....++|..+|++...|..+-.
T Consensus 184 L~~~e~~i~~~~~~~~-----~t~~eIA~~lgis~~~V~~~~~ 221 (231)
T TIGR02885 184 LDERERQIIMLRYFKD-----KTQTEVANMLGISQVQVSRLEK 221 (231)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHH
Confidence 4444555555554322 2467789999999988877654
No 184
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=34.64 E-value=1.1e+02 Score=19.81 Aligned_cols=21 Identities=19% Similarity=0.164 Sum_probs=15.4
Q ss_pred HHHHHHHHcCCCcchhhhhhc
Q psy1653 36 RRIEMAHALCLTERQIKIWFQ 56 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFq 56 (96)
...++|..+|++...|+.=..
T Consensus 152 s~~EIA~~lg~s~~tV~~rl~ 172 (192)
T PRK09643 152 SVADAARMLGVAEGTVKSRCA 172 (192)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 456678888999988866443
No 185
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=34.20 E-value=94 Score=17.78 Aligned_cols=44 Identities=9% Similarity=0.092 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHHHHh-----CCCCCHHHHHHHHHHcCCCcchhhhhhc
Q psy1653 13 TYTRYQTLELEKEFHT-----NHYLTRRRRIEMAHALCLTERQIKIWFQ 56 (96)
Q Consensus 13 ~~s~~q~~~L~~~F~~-----~~~p~~~~~~~la~~l~l~~~~V~~WFq 56 (96)
-++..++..|...|.. +.+.+..+...+...+|++...|...|.
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 4677888899988864 2457777777766678888777777664
No 186
>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=33.85 E-value=35 Score=16.98 Aligned_cols=23 Identities=9% Similarity=0.205 Sum_probs=19.4
Q ss_pred HHHHHHHcCCCcchhhhhhchhh
Q psy1653 37 RIEMAHALCLTERQIKIWFQNRR 59 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnrR 59 (96)
...++..+|++...+...|.|+-
T Consensus 19 ~~~Ia~~~gvs~~~~y~~f~~k~ 41 (47)
T PF00440_consen 19 IRDIARRAGVSKGSFYRYFPSKD 41 (47)
T ss_dssp HHHHHHHHTSCHHHHHHHCSSHH
T ss_pred HHHHHHHHccchhhHHHHcCCHH
Confidence 56679999999999999998763
No 187
>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=33.64 E-value=30 Score=21.78 Aligned_cols=22 Identities=18% Similarity=0.202 Sum_probs=18.1
Q ss_pred HHHHHHHcCCCcchhhhhhchh
Q psy1653 37 RIEMAHALCLTERQIKIWFQNR 58 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnr 58 (96)
+.++|..+|++...++.|....
T Consensus 3 I~e~a~~~gvs~~TLR~Ye~~G 24 (134)
T cd04779 3 IGQLAHLAGVSKRTIDYYTNLG 24 (134)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4567889999999999998644
No 188
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=33.61 E-value=99 Score=19.58 Aligned_cols=35 Identities=11% Similarity=0.010 Sum_probs=26.3
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhh
Q psy1653 18 QTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIK 52 (96)
Q Consensus 18 q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~ 52 (96)
-+..|...=..-.|.+......+|..+|++...|.
T Consensus 18 li~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v~ 52 (148)
T TIGR01958 18 IMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVY 52 (148)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 34455444445679999999999999999987654
No 189
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=33.59 E-value=62 Score=21.77 Aligned_cols=35 Identities=26% Similarity=0.315 Sum_probs=25.9
Q ss_pred CCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHHH
Q psy1653 32 LTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66 (96)
Q Consensus 32 p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~ 66 (96)
.......++|..+|++...|+.....-+.+.|+..
T Consensus 163 ~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l 197 (231)
T PRK11922 163 VEELSVEETAQALGLPEETVKTRLHRARRLLRESL 197 (231)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 34446778899999999999988875666666543
No 190
>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=33.43 E-value=33 Score=20.06 Aligned_cols=22 Identities=14% Similarity=0.036 Sum_probs=18.4
Q ss_pred HHHHHHHcCCCcchhhhhhchh
Q psy1653 37 RIEMAHALCLTERQIKIWFQNR 58 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnr 58 (96)
+.++|..+|++...++.|....
T Consensus 3 i~eva~~~gvs~~tLRyye~~G 24 (96)
T cd04768 3 IGEFAKLAGVSIRTLRHYDDIG 24 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4568999999999999998653
No 191
>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=33.18 E-value=25 Score=23.36 Aligned_cols=33 Identities=12% Similarity=0.277 Sum_probs=27.5
Q ss_pred HHHHHHHHHcCCCcchhhhhhchhhhhhHHHHH
Q psy1653 35 RRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 67 (96)
Q Consensus 35 ~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~~~ 67 (96)
..+.+|+.-++|+..+|-.|..|.+...+....
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~~ 47 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKDPKRAKPK 47 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCCcccccch
Confidence 357788999999999999999999887766443
No 192
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=33.04 E-value=95 Score=21.57 Aligned_cols=45 Identities=9% Similarity=0.177 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653 14 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 63 (96)
Q Consensus 14 ~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~k 63 (96)
+++.+..+|.-.|.. .....++|..+|++...|+.+...-+.+.+
T Consensus 216 L~~rer~vl~l~y~~-----~~t~~EIA~~lgis~~~V~~~~~ral~kLr 260 (264)
T PRK07122 216 LPERERTVLVLRFFE-----SMTQTQIAERVGISQMHVSRLLAKTLARLR 260 (264)
T ss_pred CCHHHHHHHHHHhcC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 344444455555432 224577899999999999988764444443
No 193
>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=33.00 E-value=33 Score=20.17 Aligned_cols=22 Identities=32% Similarity=0.299 Sum_probs=17.8
Q ss_pred HHHHHHHcCCCcchhhhhhchh
Q psy1653 37 RIEMAHALCLTERQIKIWFQNR 58 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnr 58 (96)
+..+|..+|++...++.|....
T Consensus 3 I~e~a~~~gvs~~tLR~ye~~G 24 (96)
T cd04774 3 VDEVAKRLGLTKRTLKYYEEIG 24 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4567889999999999997543
No 194
>PRK05572 sporulation sigma factor SigF; Validated
Probab=32.95 E-value=1.1e+02 Score=20.91 Aligned_cols=45 Identities=11% Similarity=0.160 Sum_probs=28.6
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhh
Q psy1653 13 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKL 62 (96)
Q Consensus 13 ~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~ 62 (96)
.++..+..++...|..+ ....++|..+|++...|..+-..-..+.
T Consensus 202 ~L~~~~~~v~~l~~~~~-----~s~~eIA~~lgis~~~V~~~~~ral~kL 246 (252)
T PRK05572 202 ELDERERLIVYLRYFKD-----KTQSEVAKRLGISQVQVSRLEKKILKQM 246 (252)
T ss_pred cCCHHHHHHHHHHHhCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 35555556666655322 2457789999999999887765433333
No 195
>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=32.66 E-value=99 Score=21.54 Aligned_cols=28 Identities=18% Similarity=0.152 Sum_probs=21.2
Q ss_pred HHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 37 RIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
..++|..+|+++..|+..+..=|.+.+.
T Consensus 127 ~~EIA~~lg~s~~tVr~~l~RAr~~Lr~ 154 (281)
T TIGR02957 127 YEEIASIVGKSEANCRQLVSRARRHLDA 154 (281)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4567888899999999998755555544
No 196
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=32.55 E-value=61 Score=21.04 Aligned_cols=40 Identities=18% Similarity=0.128 Sum_probs=29.1
Q ss_pred HHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhh
Q psy1653 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61 (96)
Q Consensus 21 ~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k 61 (96)
.....|...+|.... ...||...|++...+..+|.++-.-
T Consensus 19 aa~~lf~~~G~~~~t-i~~Ia~~agvsk~t~Y~~F~sKe~L 58 (213)
T PRK09975 19 TAIAQFALRGVSNTT-LNDIADAANVTRGAIYWHFENKTQL 58 (213)
T ss_pred HHHHHHHHcCcccCC-HHHHHHHcCCCHHHHHHHcCCHHHH
Confidence 334446666665443 6677999999999999999887553
No 197
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=32.26 E-value=74 Score=20.09 Aligned_cols=34 Identities=18% Similarity=0.160 Sum_probs=23.9
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhh
Q psy1653 19 TLELEKEFHTNHYLTRRRRIEMAHALCLTERQIK 52 (96)
Q Consensus 19 ~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~ 52 (96)
+..|...=+.-.|.+......+|..+||+...|.
T Consensus 16 l~~L~~~Q~~~g~i~~~~~~~iA~~l~i~~~~v~ 49 (145)
T PF01257_consen 16 LPILHEVQEEYGYIPEEALEEIAEALGIPPAEVY 49 (145)
T ss_dssp HHHHHHHHHHHSS--HHHHHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHHCCCHHHHH
Confidence 4555555555679999999999999999988755
No 198
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=32.01 E-value=1e+02 Score=22.18 Aligned_cols=51 Identities=14% Similarity=0.105 Sum_probs=33.0
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653 14 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65 (96)
Q Consensus 14 ~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr~ 65 (96)
+++.+..+|...|.... .......++|..+|++...|+.+...-+.+.|+.
T Consensus 263 L~~~~R~vl~lrygL~~-~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~ 313 (325)
T PRK05657 263 LNDKQREVLARRFGLLG-YEAATLEDVAREIGLTRERVRQIQVEALRRLREI 313 (325)
T ss_pred CCHHHHHHHHHHhccCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 44555555655542221 2233567889999999999999987666666553
No 199
>KOG0150|consensus
Probab=31.78 E-value=1.1e+02 Score=22.35 Aligned_cols=11 Identities=27% Similarity=0.721 Sum_probs=7.3
Q ss_pred hhhhhchhhhh
Q psy1653 51 IKIWFQNRRMK 61 (96)
Q Consensus 51 V~~WFqnrR~k 61 (96)
+++||+|.+..
T Consensus 16 CKiWi~dN~~S 26 (336)
T KOG0150|consen 16 CKIWIKDNPAS 26 (336)
T ss_pred hhhhhcCChHH
Confidence 56888776544
No 200
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=31.57 E-value=1.1e+02 Score=20.07 Aligned_cols=32 Identities=25% Similarity=0.197 Sum_probs=24.0
Q ss_pred HHHHHHHhCCCCCHHHHHHHHHHcCCCcchhh
Q psy1653 21 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIK 52 (96)
Q Consensus 21 ~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~ 52 (96)
.|...=....|.+......+|..+||+...|.
T Consensus 41 ~L~~iQ~~~GyIp~e~~~~iA~~l~v~~a~V~ 72 (169)
T PRK07571 41 VLHKAQELFGYLERDLLLYVARQLKLPLSRVY 72 (169)
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHH
Confidence 34333345678999999999999999987654
No 201
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=31.50 E-value=36 Score=20.12 Aligned_cols=21 Identities=5% Similarity=0.026 Sum_probs=17.2
Q ss_pred HHHHHHHcCCCcchhhhhhch
Q psy1653 37 RIEMAHALCLTERQIKIWFQN 57 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqn 57 (96)
+.++|..+|++...++.|-..
T Consensus 4 i~eva~~~gvs~~tLR~ye~~ 24 (102)
T cd04775 4 IGQMSRKFGVSRSTLLYYESI 24 (102)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 456888999999999999753
No 202
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=31.32 E-value=51 Score=20.30 Aligned_cols=26 Identities=27% Similarity=0.351 Sum_probs=22.0
Q ss_pred CCCHHHHHHHHHHcCCCcchhhhhhc
Q psy1653 31 YLTRRRRIEMAHALCLTERQIKIWFQ 56 (96)
Q Consensus 31 ~p~~~~~~~la~~l~l~~~~V~~WFq 56 (96)
-++...+..|+..+|++...|..|-.
T Consensus 26 ~~~~~~r~~La~~~~i~~~~l~~w~~ 51 (122)
T PF14229_consen 26 GDTPLGRKALAKKLGISERNLLKWVN 51 (122)
T ss_pred CCCHHHHHHHHHhcCCCHHHHHHHHh
Confidence 35667788899999999999999964
No 203
>PHA01976 helix-turn-helix protein
Probab=31.22 E-value=41 Score=17.79 Aligned_cols=23 Identities=13% Similarity=0.125 Sum_probs=19.2
Q ss_pred HHHHHHHcCCCcchhhhhhchhh
Q psy1653 37 RIEMAHALCLTERQIKIWFQNRR 59 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnrR 59 (96)
...||..+|++...|..|....+
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46789999999999999987554
No 204
>PHA02955 hypothetical protein; Provisional
Probab=31.11 E-value=78 Score=21.82 Aligned_cols=43 Identities=9% Similarity=0.018 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHhC-CCCCHHHHHHHHHHcCCCcchhhhhhchhh
Q psy1653 17 YQTLELEKEFHTN-HYLTRRRRIEMAHALCLTERQIKIWFQNRR 59 (96)
Q Consensus 17 ~q~~~L~~~F~~~-~~p~~~~~~~la~~l~l~~~~V~~WFqnrR 59 (96)
.++..|...|... ...++.++..++..+|+....|..||.+.-
T Consensus 61 ~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~~ 104 (213)
T PHA02955 61 KNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTDL 104 (213)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccchh
Confidence 4667777777665 457788899999999998877788886543
No 205
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=30.77 E-value=1.3e+02 Score=19.49 Aligned_cols=28 Identities=25% Similarity=0.361 Sum_probs=20.2
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLK 63 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~k 63 (96)
...++|..+|+++..|+..+..=|...+
T Consensus 153 s~~EIA~~lgiS~~tV~r~l~~aR~~l~ 180 (185)
T PF07638_consen 153 SVEEIAERLGISERTVRRRLRRARAWLR 180 (185)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 5667888999999998877665444433
No 206
>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=30.58 E-value=1.1e+02 Score=20.73 Aligned_cols=50 Identities=14% Similarity=0.078 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 14 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 14 ~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
+++.+..+|...|....+ ......++|..+|++...|+.....-..|.|.
T Consensus 177 L~~~er~vl~l~ygl~~~-~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~ 226 (238)
T TIGR02393 177 LTERERKVLRMRYGLLDG-RPHTLEEVGKEFNVTRERIRQIESKALRKLRH 226 (238)
T ss_pred CCHHHHHHHHHHhCCCCC-CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 455556666666532221 22346778999999999999887655555544
No 207
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=30.54 E-value=1.5e+02 Score=19.11 Aligned_cols=29 Identities=24% Similarity=0.255 Sum_probs=21.6
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+.+..--+.+.++
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 174 (188)
T PRK12517 146 SGEEIAEILDLNKNTVMTRLFRARNQLKE 174 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45678999999999999988644444444
No 208
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=30.25 E-value=1.2e+02 Score=21.21 Aligned_cols=29 Identities=14% Similarity=0.077 Sum_probs=21.9
Q ss_pred HHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653 37 RIEMAHALCLTERQIKIWFQNRRMKLKKE 65 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnrR~k~kr~ 65 (96)
..++|..+|+++..|+..+..-|.+.+..
T Consensus 134 ~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~ 162 (293)
T PRK09636 134 FDEIASTLGRSPAACRQLASRARKHVRAA 162 (293)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 45678889999999999887555555553
No 209
>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=30.20 E-value=42 Score=18.26 Aligned_cols=23 Identities=22% Similarity=0.265 Sum_probs=19.4
Q ss_pred HHHHHHHcCCCcchhhhhhchhh
Q psy1653 37 RIEMAHALCLTERQIKIWFQNRR 59 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnrR 59 (96)
...||..+|++...|..|...++
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 45789999999999999997654
No 210
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, 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=30.14 E-value=39 Score=19.53 Aligned_cols=22 Identities=18% Similarity=0.224 Sum_probs=17.2
Q ss_pred HHHHHHHcCCCcchhhhhhchh
Q psy1653 37 RIEMAHALCLTERQIKIWFQNR 58 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnr 58 (96)
..++|..+|++...|+.|-...
T Consensus 3 ~~eva~~~gi~~~tlr~~~~~G 24 (100)
T cd00592 3 IGEVAKLLGVSVRTLRYYEEKG 24 (100)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 3567889999999999996543
No 211
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=29.97 E-value=1.2e+02 Score=20.75 Aligned_cols=40 Identities=15% Similarity=0.276 Sum_probs=25.9
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhch
Q psy1653 13 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQN 57 (96)
Q Consensus 13 ~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqn 57 (96)
.++..+..+|...|..+ ....++|..+|++...|...-.+
T Consensus 209 ~L~~~er~vi~~~~~~~-----~t~~eIA~~lgis~~~V~~~~~~ 248 (258)
T PRK08215 209 KLNDREKLILNLRFFQG-----KTQMEVAEEIGISQAQVSRLEKA 248 (258)
T ss_pred cCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHH
Confidence 35555666666666322 23567888999999888776543
No 212
>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=29.85 E-value=40 Score=19.79 Aligned_cols=20 Identities=15% Similarity=0.248 Sum_probs=16.4
Q ss_pred HHHHHHHcCCCcchhhhhhc
Q psy1653 37 RIEMAHALCLTERQIKIWFQ 56 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFq 56 (96)
+.++|..+|++...|+.|-.
T Consensus 3 I~eva~~~gvs~~tlR~Ye~ 22 (95)
T cd04780 3 MSELSKRSGVSVATIKYYLR 22 (95)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45688899999999998864
No 213
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=29.68 E-value=1.7e+02 Score=20.20 Aligned_cols=29 Identities=17% Similarity=0.234 Sum_probs=20.9
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+.+...-+.+.++
T Consensus 223 t~~EIA~~lgis~~~V~~~~~ral~kLr~ 251 (257)
T PRK05911 223 VLKEIGKILGVSESRVSQIHSKALLKLRA 251 (257)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45778999999999988877644444443
No 214
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=29.60 E-value=1.5e+02 Score=19.93 Aligned_cols=29 Identities=24% Similarity=0.174 Sum_probs=20.2
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|..+...-+.+.++
T Consensus 197 S~~EIA~~lgis~~tV~~~~~rA~~kLr~ 225 (233)
T PRK05803 197 TQREIAKALGISRSYVSRIEKRALKKLFK 225 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 46778999999999998875433333333
No 215
>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=29.52 E-value=1.1e+02 Score=21.51 Aligned_cols=30 Identities=23% Similarity=0.228 Sum_probs=22.2
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKKE 65 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr~ 65 (96)
.-.++|..||++...|+..+..-|.+.++.
T Consensus 160 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 189 (324)
T TIGR02960 160 RAAETAELLGTSTASVNSALQRARATLDEV 189 (324)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 356788999999999999887555555543
No 216
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. 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 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=29.52 E-value=41 Score=19.90 Aligned_cols=21 Identities=10% Similarity=0.075 Sum_probs=17.0
Q ss_pred HHHHHHHcCCCcchhhhhhch
Q psy1653 37 RIEMAHALCLTERQIKIWFQN 57 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqn 57 (96)
..++|..+||+...++.|-..
T Consensus 4 i~eva~~~gvs~~tlR~ye~~ 24 (102)
T cd04789 4 ISELAEKAGISRSTLLYYEKL 24 (102)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 456788999999999988754
No 217
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=29.37 E-value=1.4e+02 Score=18.38 Aligned_cols=28 Identities=11% Similarity=0.150 Sum_probs=19.0
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLK 63 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~k 63 (96)
...++|..+|++...|+.....-+.+.+
T Consensus 123 s~~eIA~~lgis~~tv~~~l~ra~~~Lr 150 (159)
T PRK12527 123 SHQQIAEHLGISRSLVEKHIVNAMKHCR 150 (159)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 3566788889999888877653333333
No 218
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively 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 C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=28.48 E-value=44 Score=19.51 Aligned_cols=22 Identities=18% Similarity=0.080 Sum_probs=17.8
Q ss_pred HHHHHHHcCCCcchhhhhhchh
Q psy1653 37 RIEMAHALCLTERQIKIWFQNR 58 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnr 58 (96)
+.++|..+|++...++.|-...
T Consensus 3 i~eva~~~gvs~~tlR~ye~~G 24 (96)
T cd04788 3 IGELARRTGLSVRTLHHYDHIG 24 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 3568899999999999998543
No 219
>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=28.34 E-value=44 Score=19.97 Aligned_cols=22 Identities=23% Similarity=0.379 Sum_probs=17.8
Q ss_pred HHHHHHHcCCCcchhhhhhchh
Q psy1653 37 RIEMAHALCLTERQIKIWFQNR 58 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnr 58 (96)
+.++|..+||+...++.|....
T Consensus 3 i~eva~~~gvs~~tlR~ye~~G 24 (108)
T cd04773 3 IGELAHLLGVPPSTLRHWEKEG 24 (108)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4567899999999999997544
No 220
>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=28.08 E-value=39 Score=17.69 Aligned_cols=18 Identities=33% Similarity=0.407 Sum_probs=12.8
Q ss_pred HHHHHHHHcCCCcchhhh
Q psy1653 36 RRIEMAHALCLTERQIKI 53 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~ 53 (96)
.-.+|+..+|++..||+-
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 345689999999998863
No 221
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=27.93 E-value=45 Score=19.49 Aligned_cols=21 Identities=10% Similarity=0.025 Sum_probs=17.1
Q ss_pred HHHHHHHcCCCcchhhhhhch
Q psy1653 37 RIEMAHALCLTERQIKIWFQN 57 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqn 57 (96)
+.++|..+||+...++.|...
T Consensus 3 i~eva~~~gvs~~tlR~ye~~ 23 (97)
T cd04782 3 TGEFAKLCGISKQTLFHYDKI 23 (97)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 456789999999999999654
No 222
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=27.92 E-value=71 Score=20.46 Aligned_cols=30 Identities=23% Similarity=0.320 Sum_probs=23.4
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKKE 65 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr~ 65 (96)
.-.++|..+|++...|+.+...-+.+.+..
T Consensus 145 s~~EIA~~l~i~~~tVks~l~ra~~~l~~~ 174 (182)
T COG1595 145 SYEEIAEILGISVGTVKSRLHRARKKLREQ 174 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 356678899999999999998666666553
No 223
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which 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 N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=27.91 E-value=45 Score=20.01 Aligned_cols=21 Identities=5% Similarity=0.069 Sum_probs=17.2
Q ss_pred HHHHHHHcCCCcchhhhhhch
Q psy1653 37 RIEMAHALCLTERQIKIWFQN 57 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqn 57 (96)
+.++|..+||+...++.|-..
T Consensus 3 Ige~A~~~gvs~~tlR~ye~~ 23 (107)
T cd01111 3 ISQLALDAGVSVHIVRDYLLR 23 (107)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 456899999999999999643
No 224
>KOG3623|consensus
Probab=27.77 E-value=45 Score=27.44 Aligned_cols=58 Identities=10% Similarity=0.110 Sum_probs=38.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 7 ~rr~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
+-+.++.+...+-.-|...|...-.++-.+...++..|...+..|.+||++|+..-+.
T Consensus 626 p~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp 683 (1007)
T KOG3623|consen 626 PVKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSP 683 (1007)
T ss_pred CccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCC
Confidence 3444556666666677777776655554444455555666777889999999876554
No 225
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; 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 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=27.56 E-value=46 Score=19.90 Aligned_cols=21 Identities=14% Similarity=0.199 Sum_probs=16.5
Q ss_pred HHHHHHHcCCCcchhhhhhch
Q psy1653 37 RIEMAHALCLTERQIKIWFQN 57 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqn 57 (96)
+.++|..+||+...++.|-..
T Consensus 3 i~e~a~~~gvs~~tlr~ye~~ 23 (113)
T cd01109 3 IKEVAEKTGLSADTLRYYEKE 23 (113)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 456788899999999888643
No 226
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=27.40 E-value=46 Score=19.68 Aligned_cols=21 Identities=24% Similarity=0.335 Sum_probs=17.2
Q ss_pred HHHHHHHcCCCcchhhhhhch
Q psy1653 37 RIEMAHALCLTERQIKIWFQN 57 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqn 57 (96)
..++|..+|++...++.|-.+
T Consensus 3 i~EvA~~~gVs~~tLR~ye~~ 23 (99)
T cd04765 3 IGEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred HHHHHHHHCcCHHHHHHHHHH
Confidence 346788999999999999654
No 227
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=27.36 E-value=47 Score=19.84 Aligned_cols=19 Identities=16% Similarity=0.170 Sum_probs=14.9
Q ss_pred HHHHHHHcCCCcchhhhhh
Q psy1653 37 RIEMAHALCLTERQIKIWF 55 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WF 55 (96)
+.++|..+||+...++.|=
T Consensus 3 I~eva~~~gvs~~tLRyYE 21 (124)
T COG0789 3 IGEVAKLTGVSVRTLRFYE 21 (124)
T ss_pred HHHHHHHhCCCHHHHHHHH
Confidence 3467888899988888885
No 228
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=26.99 E-value=67 Score=17.11 Aligned_cols=19 Identities=21% Similarity=0.151 Sum_probs=12.9
Q ss_pred HHHHHHHHHHcCCCcchhh
Q psy1653 34 RRRRIEMAHALCLTERQIK 52 (96)
Q Consensus 34 ~~~~~~la~~l~l~~~~V~ 52 (96)
..+...++..||++..+++
T Consensus 20 ~~ev~ywa~~~gvt~~~L~ 38 (57)
T PF12244_consen 20 PYEVRYWAKRFGVTEEQLR 38 (57)
T ss_pred HHHHHHHHHHHCcCHHHHH
Confidence 3456667788888777654
No 229
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=26.87 E-value=1.6e+02 Score=20.13 Aligned_cols=29 Identities=21% Similarity=0.271 Sum_probs=21.5
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+.+...-|.+.+.
T Consensus 134 S~~EIAe~LgiS~~tVksrL~Rark~Lr~ 162 (228)
T PRK06704 134 SIADIAKVCSVSEGAVKASLFRSRNRLKT 162 (228)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 35678899999999999888644544444
No 230
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=26.78 E-value=48 Score=20.48 Aligned_cols=21 Identities=5% Similarity=0.091 Sum_probs=17.6
Q ss_pred HHHHHHHcCCCcchhhhhhch
Q psy1653 37 RIEMAHALCLTERQIKIWFQN 57 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqn 57 (96)
+.++|..+||+...|+.|-..
T Consensus 6 I~elA~~~gvs~~tlR~Ye~~ 26 (120)
T TIGR02054 6 ISRLAEDAGVSVHVVRDYLLR 26 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 567899999999999999643
No 231
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=26.71 E-value=1.5e+02 Score=18.25 Aligned_cols=44 Identities=18% Similarity=0.195 Sum_probs=31.4
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhh
Q psy1653 13 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKL 62 (96)
Q Consensus 13 ~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~ 62 (96)
.+++.+..+|.- +..+ + ....+|..+++++..|+.+.++=+.|.
T Consensus 149 ~lt~~e~~vl~l-~~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl 192 (211)
T PRK15369 149 LLTPRERQILKL-ITEG-Y----TNRDIAEQLSISIKTVETHRLNMMRKL 192 (211)
T ss_pred CCCHHHHHHHHH-HHCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 477777777765 3332 2 246778899999999999998765554
No 232
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, 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 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=26.39 E-value=50 Score=19.40 Aligned_cols=22 Identities=9% Similarity=0.093 Sum_probs=17.5
Q ss_pred HHHHHHHcCCCcchhhhhhchh
Q psy1653 37 RIEMAHALCLTERQIKIWFQNR 58 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnr 58 (96)
...+|..+||+...++.|....
T Consensus 4 i~eva~~~gVs~~tLR~ye~~G 25 (98)
T cd01279 4 ISVAAELLGIHPQTLRVYDRLG 25 (98)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4567889999999999996543
No 233
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares 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=26.35 E-value=51 Score=19.65 Aligned_cols=21 Identities=14% Similarity=0.075 Sum_probs=17.4
Q ss_pred HHHHHHHcCCCcchhhhhhch
Q psy1653 37 RIEMAHALCLTERQIKIWFQN 57 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqn 57 (96)
+..+|..+|++...++.|-..
T Consensus 3 i~eva~~~gis~~tlR~ye~~ 23 (108)
T cd01107 3 IGEFAKLSNLSIKALRYYDKI 23 (108)
T ss_pred HHHHHHHHCcCHHHHHHHHHc
Confidence 456789999999999999754
No 234
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=26.34 E-value=69 Score=20.17 Aligned_cols=31 Identities=23% Similarity=0.223 Sum_probs=22.3
Q ss_pred HHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 34 RRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 34 ~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
.....++|..+|++...|+.+...-+.+.++
T Consensus 142 g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~ 172 (176)
T PRK09638 142 GYTYEEIAKMLNIPEGTVKSRVHHGIKQLRK 172 (176)
T ss_pred CCCHHHHHHHHCCChhHHHHHHHHHHHHHHH
Confidence 3456778999999999998888644444443
No 235
>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=26.26 E-value=70 Score=16.16 Aligned_cols=21 Identities=24% Similarity=0.230 Sum_probs=14.7
Q ss_pred HHHHHHHHHcCCCcchhhhhh
Q psy1653 35 RRRIEMAHALCLTERQIKIWF 55 (96)
Q Consensus 35 ~~~~~la~~l~l~~~~V~~WF 55 (96)
.....||..++++...|+.-.
T Consensus 16 it~~eLa~~l~vS~rTi~~~i 36 (55)
T PF08279_consen 16 ITAKELAEELGVSRRTIRRDI 36 (55)
T ss_dssp BEHHHHHHHCTS-HHHHHHHH
T ss_pred cCHHHHHHHhCCCHHHHHHHH
Confidence 346678999999998876543
No 236
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=26.21 E-value=51 Score=20.34 Aligned_cols=24 Identities=17% Similarity=0.318 Sum_probs=20.2
Q ss_pred HHHHHHHcCCCcchhhhhhchhhh
Q psy1653 37 RIEMAHALCLTERQIKIWFQNRRM 60 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnrR~ 60 (96)
...||..+|++...|..|..+++.
T Consensus 21 q~~lA~~~gvs~~~is~~E~g~~~ 44 (135)
T PRK09706 21 QRSLAKAVKVSHVSISQWERDETE 44 (135)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 457899999999999999987653
No 237
>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=25.99 E-value=1.5e+02 Score=20.66 Aligned_cols=29 Identities=21% Similarity=0.204 Sum_probs=22.1
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..||++...|+.+...-+.+.|+
T Consensus 244 s~~EIA~~Lgis~~tVk~~l~rAlkkLr~ 272 (285)
T TIGR02394 244 TLEEVAAEVGLTRERVRQIQVEALKKLRR 272 (285)
T ss_pred cHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46678999999999999988655555544
No 238
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=25.75 E-value=51 Score=20.49 Aligned_cols=21 Identities=19% Similarity=0.343 Sum_probs=17.7
Q ss_pred HHHHHHHcCCCcchhhhhhch
Q psy1653 37 RIEMAHALCLTERQIKIWFQN 57 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqn 57 (96)
...+|..+|++...++.|.+.
T Consensus 4 I~eVA~~~GVs~~TLR~wE~~ 24 (120)
T cd04767 4 IGVVAELLNIHPETLRIWERH 24 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 456899999999999999754
No 239
>PRK10403 transcriptional regulator NarP; Provisional
Probab=25.64 E-value=99 Score=19.30 Aligned_cols=45 Identities=20% Similarity=0.212 Sum_probs=31.9
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653 13 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 63 (96)
Q Consensus 13 ~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~k 63 (96)
.++..+..+|.-... + .....++..+++++..|+....+=+.|..
T Consensus 153 ~Lt~~e~~vl~~~~~-g-----~s~~~ia~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 153 VLTERELDVLHELAQ-G-----LSNKQIASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred cCCHHHHHHHHHHHC-C-----CCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 477778877765432 2 23567788899999999998876665543
No 240
>PF13730 HTH_36: Helix-turn-helix domain
Probab=25.61 E-value=70 Score=16.18 Aligned_cols=21 Identities=14% Similarity=0.248 Sum_probs=17.1
Q ss_pred HHHHHHHHcCCCcchhhhhhc
Q psy1653 36 RRIEMAHALCLTERQIKIWFQ 56 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFq 56 (96)
....|+..+|++...|..+..
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIK 47 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 467789999999988887764
No 241
>PRK15183 Vi polysaccharide biosynthesis protein TviA; Provisional
Probab=25.54 E-value=75 Score=19.68 Aligned_cols=35 Identities=23% Similarity=0.234 Sum_probs=23.9
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCc
Q psy1653 14 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTE 48 (96)
Q Consensus 14 ~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~ 48 (96)
++..-++.|...|...+----..+.+||.++|+.+
T Consensus 96 lsesgmeelqdrfmns~st~yrwrke~a~kfgvr~ 130 (143)
T PRK15183 96 LSESGMEELQDRFMNSSSTMYRWRKELAVKFGVRE 130 (143)
T ss_pred hhhccHHHHHHHHccChHHHHHHHHHHHHHhcCCC
Confidence 34455667777777665444567888899988764
No 242
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=25.39 E-value=1.7e+02 Score=18.03 Aligned_cols=36 Identities=11% Similarity=0.017 Sum_probs=23.1
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhh
Q psy1653 13 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKI 53 (96)
Q Consensus 13 ~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~ 53 (96)
.++.+++..+........ ....++..+|+++-.|+.
T Consensus 33 ~L~~E~~~Fi~~Fi~~rG-----nlKe~e~~lgiSYPTvR~ 68 (113)
T PF09862_consen 33 RLSPEQLEFIKLFIKNRG-----NLKEMEKELGISYPTVRN 68 (113)
T ss_pred cCCHHHHHHHHHHHHhcC-----CHHHHHHHHCCCcHHHHH
Confidence 467777777766655443 345567777777766654
No 243
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=25.19 E-value=51 Score=20.72 Aligned_cols=21 Identities=14% Similarity=0.085 Sum_probs=17.3
Q ss_pred HHHHHHHcCCCcchhhhhhch
Q psy1653 37 RIEMAHALCLTERQIKIWFQN 57 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqn 57 (96)
+.++|..+||+...++.|-+.
T Consensus 4 I~EvA~~~Gvs~~tLRyYE~~ 24 (139)
T cd01110 4 VGEVAKRSGVAVSALHFYEQK 24 (139)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457889999999999999753
No 244
>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=24.98 E-value=1.4e+02 Score=18.02 Aligned_cols=40 Identities=18% Similarity=0.122 Sum_probs=28.6
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhch
Q psy1653 13 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQN 57 (96)
Q Consensus 13 ~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqn 57 (96)
.+|..|...|.-+|..+- ...++|..+|++..-|.-|.+.
T Consensus 17 LLT~kQ~~~l~lyy~eDl-----SlsEIAe~~~iSRqaV~d~ikr 56 (101)
T PF04297_consen 17 LLTEKQREILELYYEEDL-----SLSEIAEELGISRQAVYDSIKR 56 (101)
T ss_dssp GS-HHHHHHHHHHCTS--------HHHHHHHCTS-HHHHHHHHHH
T ss_pred HCCHHHHHHHHHHHccCC-----CHHHHHHHHCCCHHHHHHHHHH
Confidence 467788888887766543 5677899999999999999863
No 245
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=24.80 E-value=89 Score=14.45 Aligned_cols=21 Identities=14% Similarity=0.164 Sum_probs=14.0
Q ss_pred HHHHHHcCCCcchhhhhhchh
Q psy1653 38 IEMAHALCLTERQIKIWFQNR 58 (96)
Q Consensus 38 ~~la~~l~l~~~~V~~WFqnr 58 (96)
..++..+|++...|..|..++
T Consensus 14 ~~la~~~~i~~~~i~~~~~~~ 34 (56)
T smart00530 14 EELAEKLGVSRSTLSRIENGK 34 (56)
T ss_pred HHHHHHhCCCHHHHHHHHCCC
Confidence 356667777777777776544
No 246
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=24.55 E-value=94 Score=19.00 Aligned_cols=32 Identities=16% Similarity=0.098 Sum_probs=22.6
Q ss_pred HHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhh
Q psy1653 20 LELEKEFHTNHYLTRRRRIEMAHALCLTERQIKI 53 (96)
Q Consensus 20 ~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~ 53 (96)
..|...|. +.+......+||..+.++.+.++.
T Consensus 7 ~~L~~~~~--~~~~~vtl~elA~~l~cS~Rn~r~ 38 (115)
T PF12793_consen 7 QRLWQHYG--GQPVEVTLDELAELLFCSRRNART 38 (115)
T ss_pred HHHHHHcC--CCCcceeHHHHHHHhCCCHHHHHH
Confidence 34555555 456667788899999999887663
No 247
>cd04772 HTH_TioE_rpt1 First 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 contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=24.28 E-value=58 Score=19.15 Aligned_cols=22 Identities=14% Similarity=0.312 Sum_probs=16.7
Q ss_pred HHHHHHHcCCCcchhhhhhchh
Q psy1653 37 RIEMAHALCLTERQIKIWFQNR 58 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnr 58 (96)
..++|..+|++...++.|-...
T Consensus 3 i~e~A~~~gvs~~tlR~Ye~~G 24 (99)
T cd04772 3 TVDLARAIGLSPQTVRNYESLG 24 (99)
T ss_pred HHHHHHHHCcCHHHHHHHHHcC
Confidence 4567888899999888886433
No 248
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=24.19 E-value=68 Score=19.21 Aligned_cols=33 Identities=18% Similarity=0.270 Sum_probs=24.6
Q ss_pred HHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhh
Q psy1653 26 FHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRR 59 (96)
Q Consensus 26 F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR 59 (96)
|...+|.... ...|+..+|++...+..+|.|+-
T Consensus 25 ~~~~G~~~~t-~~~Ia~~agvs~~~~Y~~f~~K~ 57 (201)
T COG1309 25 FAEKGYAATT-VDEIAKAAGVSKGTLYRHFPSKE 57 (201)
T ss_pred HHHcCcCCCC-HHHHHHHhCCCcchhHHHcCCHH
Confidence 4455554433 55678999999999999998875
No 249
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=24.13 E-value=1.5e+02 Score=17.98 Aligned_cols=24 Identities=4% Similarity=0.075 Sum_probs=20.1
Q ss_pred HHHHHHHHHcCCCcchhhhhhchh
Q psy1653 35 RRRIEMAHALCLTERQIKIWFQNR 58 (96)
Q Consensus 35 ~~~~~la~~l~l~~~~V~~WFqnr 58 (96)
.....||..+|++...+.-+|+.-
T Consensus 26 ~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 26 LSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHH
Confidence 466788999999999999988644
No 250
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. 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=24.08 E-value=57 Score=19.86 Aligned_cols=19 Identities=21% Similarity=0.338 Sum_probs=14.7
Q ss_pred HHHHHHHcCCCcchhhhhh
Q psy1653 37 RIEMAHALCLTERQIKIWF 55 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WF 55 (96)
+..+|..+||+...++.|=
T Consensus 3 Igeva~~~gvs~~tlRyYe 21 (118)
T cd04776 3 ISELAREFDVTPRTLRFYE 21 (118)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 4567888888888888884
No 251
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=23.92 E-value=1.3e+02 Score=21.38 Aligned_cols=29 Identities=21% Similarity=0.178 Sum_probs=21.4
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..||++...|+.....-|.+.++
T Consensus 171 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 171 SAAEVAELLDTSVAAVNSALQRARATLAE 199 (339)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHhh
Confidence 45678899999999999887644544444
No 252
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). 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=23.87 E-value=59 Score=19.51 Aligned_cols=22 Identities=14% Similarity=0.152 Sum_probs=17.3
Q ss_pred HHHHHHHcCCCcchhhhhhchh
Q psy1653 37 RIEMAHALCLTERQIKIWFQNR 58 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnr 58 (96)
+.++|..+|++...++.|-...
T Consensus 3 i~eva~~~gvs~~tlR~Ye~~G 24 (112)
T cd01282 3 IGELAARTGVSVRSLRYYEEQG 24 (112)
T ss_pred HHHHHHHHCCCHHHHHHHHHCC
Confidence 4567888999999999987543
No 253
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=23.74 E-value=1e+02 Score=20.24 Aligned_cols=40 Identities=10% Similarity=0.182 Sum_probs=29.7
Q ss_pred HHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 24 KEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 24 ~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
..|....|.... ...||...|++...|...|.++..=..-
T Consensus 29 ~lf~e~Gy~~~s-~~dIA~~aGvs~gtiY~hF~sKe~L~~a 68 (212)
T PRK15008 29 DTFSQFGFHGTR-LEQIAELAGVSKTNLLYYFPSKEALYIA 68 (212)
T ss_pred HHHHHhCcccCC-HHHHHHHhCcCHHHHHHHCCCHHHHHHH
Confidence 336677765443 5567999999999999999988665544
No 254
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=23.60 E-value=1.1e+02 Score=19.79 Aligned_cols=43 Identities=16% Similarity=0.100 Sum_probs=31.4
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhh
Q psy1653 19 TLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKL 62 (96)
Q Consensus 19 ~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~ 62 (96)
+......|....|-... ...|+...|++...+..+|.++-.-.
T Consensus 17 l~AA~~lf~e~G~~~~t-~~~Ia~~agvs~~tlY~~F~sKe~Ll 59 (215)
T PRK10668 17 LDAALRLFSQQGVSATS-LADIAKAAGVTRGAIYWHFKNKSDLF 59 (215)
T ss_pred HHHHHHHHHHcCcccCC-HHHHHHHhCCChHHHHHHCCCHHHHH
Confidence 33444557777765443 56679999999999999998876543
No 255
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=23.57 E-value=58 Score=20.78 Aligned_cols=28 Identities=18% Similarity=0.305 Sum_probs=22.6
Q ss_pred HHHHHHHHHcCCCcchhhhhhchhhhhh
Q psy1653 35 RRRIEMAHALCLTERQIKIWFQNRRMKL 62 (96)
Q Consensus 35 ~~~~~la~~l~l~~~~V~~WFqnrR~k~ 62 (96)
....+++..+||+...|..|....|-..
T Consensus 47 ati~eV~e~tgVs~~~I~~~IreGRL~~ 74 (137)
T TIGR03826 47 ATVSEIVEETGVSEKLILKFIREGRLQL 74 (137)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCeec
Confidence 3466789999999999999997766544
No 256
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=23.01 E-value=60 Score=20.40 Aligned_cols=21 Identities=14% Similarity=0.153 Sum_probs=17.5
Q ss_pred HHHHHHHcCCCcchhhhhhch
Q psy1653 37 RIEMAHALCLTERQIKIWFQN 57 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqn 57 (96)
+.++|..+||+...|+.|...
T Consensus 4 I~e~a~~~gvs~~tlR~Ye~~ 24 (140)
T PRK09514 4 IGELAKLAEVTPDTLRFYEKQ 24 (140)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457889999999999999754
No 257
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=22.91 E-value=60 Score=19.87 Aligned_cols=19 Identities=21% Similarity=0.155 Sum_probs=14.6
Q ss_pred HHHHHHHcCCCcchhhhhh
Q psy1653 37 RIEMAHALCLTERQIKIWF 55 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WF 55 (96)
+.++|..+|++...++.|=
T Consensus 2 I~e~a~~~gvs~~tlR~Ye 20 (124)
T TIGR02051 2 IGELAKAAGVNVETIRYYE 20 (124)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 3467888888888888884
No 258
>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=22.85 E-value=1.5e+02 Score=20.50 Aligned_cols=48 Identities=17% Similarity=0.149 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 14 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 14 ~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
++..+..+|...|-.. ......++|..+||+...|......-..|.|+
T Consensus 219 L~~rer~vl~l~y~~~---~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~ 266 (270)
T TIGR02392 219 LDARSRRIIEARWLDD---DKLTLQELAAEYGVSAERIRQIEKNAMKKLKA 266 (270)
T ss_pred CCHHHHHHHHHHhcCC---CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4555566666666321 12245688999999999988877654444443
No 259
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=22.84 E-value=1e+02 Score=19.79 Aligned_cols=39 Identities=8% Similarity=0.141 Sum_probs=28.0
Q ss_pred HHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653 24 KEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 63 (96)
Q Consensus 24 ~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~k 63 (96)
..|....|-.. ....||...|++...+..+|.++-.=..
T Consensus 19 ~lf~e~G~~~~-s~~~IA~~agvs~~~lY~hF~sKe~L~~ 57 (202)
T TIGR03613 19 DTFSRFGFHGT-SLEQIAELAGVSKTNLLYYFPSKDALYL 57 (202)
T ss_pred HHHHHhCcccC-CHHHHHHHhCCCHHHHHHHcCCHHHHHH
Confidence 34666665433 3566799999999999999987754433
No 260
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=22.81 E-value=2e+02 Score=19.32 Aligned_cols=45 Identities=22% Similarity=0.145 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653 13 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 63 (96)
Q Consensus 13 ~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~k 63 (96)
.+|+.+.++|.-... .+ .-.++|..|++++..|+.+..+-..|..
T Consensus 155 ~Lt~rE~~Vl~l~~~--G~----s~~eIA~~L~iS~~TVk~~~~~i~~Kl~ 199 (216)
T PRK10100 155 LLTHREKEILNKLRI--GA----SNNEIARSLFISENTVKTHLYNLFKKIA 199 (216)
T ss_pred CCCHHHHHHHHHHHc--CC----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 477778887766654 21 2456788999999999999876655543
No 261
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=22.36 E-value=63 Score=20.46 Aligned_cols=21 Identities=10% Similarity=0.064 Sum_probs=17.3
Q ss_pred HHHHHHHcCCCcchhhhhhch
Q psy1653 37 RIEMAHALCLTERQIKIWFQN 57 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqn 57 (96)
+.++|..+||+...++.|.+.
T Consensus 4 IgevA~~~Gvs~~tLRyYE~~ 24 (142)
T TIGR01950 4 VGELAKRSGVAVSALHFYESK 24 (142)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999753
No 262
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=22.35 E-value=77 Score=15.79 Aligned_cols=21 Identities=14% Similarity=0.194 Sum_probs=17.3
Q ss_pred HHHHHHHHcCCCcchhhhhhc
Q psy1653 36 RRIEMAHALCLTERQIKIWFQ 56 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFq 56 (96)
....+|..+|++...|.-.|.
T Consensus 29 s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 29 SFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 356789999999999988874
No 263
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=22.28 E-value=1.3e+02 Score=17.71 Aligned_cols=33 Identities=18% Similarity=0.210 Sum_probs=22.4
Q ss_pred HHHHHHHHhC-CCCCHHHHHHHHHHcCCCcchhh
Q psy1653 20 LELEKEFHTN-HYLTRRRRIEMAHALCLTERQIK 52 (96)
Q Consensus 20 ~~L~~~F~~~-~~p~~~~~~~la~~l~l~~~~V~ 52 (96)
..|...|..- ...+......|+..|||++..|.
T Consensus 4 ~~l~~~f~~i~~~V~~~~Wk~laR~LGLse~~I~ 37 (96)
T cd08315 4 ETLRRSFDHFIKEVPFDSWNRLMRQLGLSENEID 37 (96)
T ss_pred hHHHHHHHHHHHHCCHHHHHHHHHHcCCCHHHHH
Confidence 4566777643 34445667778999999887654
No 264
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins 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 winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. 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=22.23 E-value=66 Score=19.75 Aligned_cols=22 Identities=18% Similarity=0.090 Sum_probs=16.8
Q ss_pred HHHHHHHcCCCcchhhhhhchh
Q psy1653 37 RIEMAHALCLTERQIKIWFQNR 58 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnr 58 (96)
+.++|..+||+...++.|-...
T Consensus 3 I~e~a~~~gvs~~tlRyYe~~G 24 (127)
T cd01108 3 IGEAAKLTGLSAKMIRYYEEIG 24 (127)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4567888999999988887543
No 265
>PRK13756 tetracycline repressor protein TetR; Provisional
Probab=22.06 E-value=74 Score=21.26 Aligned_cols=37 Identities=11% Similarity=0.075 Sum_probs=26.8
Q ss_pred HHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhh
Q psy1653 24 KEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61 (96)
Q Consensus 24 ~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k 61 (96)
..|....+-. .....|+..+|++...+...|.||..=
T Consensus 15 ~l~~e~G~~~-lsmr~lA~~lgv~~~slY~hf~~K~~L 51 (205)
T PRK13756 15 ELLNEVGIEG-LTTRKLAQKLGVEQPTLYWHVKNKRAL 51 (205)
T ss_pred HHHHHcCccc-CCHHHHHHHhCCCchHHHHHcCCHHHH
Confidence 3355555433 346677999999999999999877554
No 266
>PRK00767 transcriptional regulator BetI; Validated
Probab=22.04 E-value=1.3e+02 Score=19.07 Aligned_cols=40 Identities=13% Similarity=0.118 Sum_probs=30.4
Q ss_pred HHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653 23 EKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 63 (96)
Q Consensus 23 ~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~k 63 (96)
...|....|-. .....|+...|++...+...|.|+..-..
T Consensus 19 ~~lf~~~G~~~-~s~~~Ia~~aGvs~gslY~~F~~Ke~L~~ 58 (197)
T PRK00767 19 LRAIGEVGLLD-ATIAQIARRAGVSTGIISHYFGGKDGLLE 58 (197)
T ss_pred HHHHHHcCccc-CCHHHHHHHhCCCHHHHHHHhCCHHHHHH
Confidence 34467777765 44667899999999999999988865433
No 267
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=22.00 E-value=59 Score=19.23 Aligned_cols=30 Identities=17% Similarity=0.217 Sum_probs=20.9
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhh
Q psy1653 19 TLELEKEFHTNHYLTRRRRIEMAHALCLTERQIK 52 (96)
Q Consensus 19 ~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~ 52 (96)
...|...|...... .+.+|..||++...|.
T Consensus 12 ~~ELq~nf~~~~ls----~~~ia~dL~~s~~~le 41 (89)
T PF10078_consen 12 RQELQANFELSGLS----LEQIAADLGTSPEHLE 41 (89)
T ss_pred HHHHHHHHHHcCCC----HHHHHHHhCCCHHHHH
Confidence 34677778777654 5667888888876654
No 268
>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=21.96 E-value=83 Score=21.21 Aligned_cols=29 Identities=24% Similarity=0.216 Sum_probs=20.5
Q ss_pred HHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 36 RRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 36 ~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...++|..+|++...|+.+...-+.+.|+
T Consensus 200 s~~EIA~~Lgis~~tV~~~l~ra~~~LR~ 228 (234)
T TIGR02835 200 TQKEVADMLGISQSYISRLEKRILKRLKK 228 (234)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45667888899999998887644444444
No 269
>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=21.85 E-value=1.2e+02 Score=14.85 Aligned_cols=37 Identities=16% Similarity=0.175 Sum_probs=22.2
Q ss_pred CHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhh
Q psy1653 15 TRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWF 55 (96)
Q Consensus 15 s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF 55 (96)
+..+..+|.-.+. ++.. ...+||..+|++...|..-+
T Consensus 2 ~~~~~~Il~~l~~-~~~~---t~~ela~~~~is~~tv~~~l 38 (48)
T PF13412_consen 2 DETQRKILNYLRE-NPRI---TQKELAEKLGISRSTVNRYL 38 (48)
T ss_dssp -HHHHHHHHHHHH-CTTS----HHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHHHHHH-cCCC---CHHHHHHHhCCCHHHHHHHH
Confidence 3455666655555 3333 45678899999988776544
No 270
>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=21.69 E-value=2e+02 Score=20.01 Aligned_cols=48 Identities=19% Similarity=0.027 Sum_probs=34.7
Q ss_pred CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 11 r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...+|+.+.++|.-.. ..+ ...++|..|++++..|+.+..+=+.|..-
T Consensus 188 ~~~LT~RE~evl~l~a--~G~----s~~eIA~~L~IS~~TVk~hl~~i~~KL~v 235 (247)
T TIGR03020 188 AGLITAREAEILAWVR--DGK----TNEEIAAILGISSLTVKNHLQHIFKKLDV 235 (247)
T ss_pred ccCCCHHHHHHHHHHH--CCC----CHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence 4468888888887543 222 35667889999999999998766555443
No 271
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=21.68 E-value=65 Score=21.34 Aligned_cols=21 Identities=14% Similarity=0.377 Sum_probs=17.2
Q ss_pred HHHHHHHcCCCcchhhhhhch
Q psy1653 37 RIEMAHALCLTERQIKIWFQN 57 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqn 57 (96)
...+|..+||+...|+.|...
T Consensus 3 i~evA~~lGVS~~TLRrw~k~ 23 (175)
T PRK13182 3 TPFVAKKLGVSPKTVQRWVKQ 23 (175)
T ss_pred HHHHHHHHCcCHHHHHHHHHc
Confidence 456789999999999999743
No 272
>PRK13558 bacterio-opsin activator; Provisional
Probab=21.65 E-value=1.1e+02 Score=23.71 Aligned_cols=42 Identities=17% Similarity=0.241 Sum_probs=34.8
Q ss_pred CCCCHHHHHHHHHHHHhCCC--CCHHHHHHHHHHcCCCcchhhh
Q psy1653 12 QTYTRYQTLELEKEFHTNHY--LTRRRRIEMAHALCLTERQIKI 53 (96)
Q Consensus 12 ~~~s~~q~~~L~~~F~~~~~--p~~~~~~~la~~l~l~~~~V~~ 53 (96)
..+|..|...|...|...-| |-......||..||++...+..
T Consensus 606 ~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~ 649 (665)
T PRK13558 606 NDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQ 649 (665)
T ss_pred hhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHH
Confidence 36999999999999998876 6566788899999999877543
No 273
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. 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, an
Probab=21.57 E-value=69 Score=19.42 Aligned_cols=20 Identities=15% Similarity=0.190 Sum_probs=16.0
Q ss_pred HHHHHHHcCCCcchhhhhhc
Q psy1653 37 RIEMAHALCLTERQIKIWFQ 56 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFq 56 (96)
+.++|..+||+...++.|-.
T Consensus 3 IgevA~~~gvs~~tlRyYe~ 22 (120)
T cd04781 3 IAEVARQSGLPASTLRYYEE 22 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45678889999999888864
No 274
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=21.46 E-value=68 Score=19.66 Aligned_cols=22 Identities=14% Similarity=0.154 Sum_probs=17.1
Q ss_pred HHHHHHHcCCCcchhhhhhchh
Q psy1653 37 RIEMAHALCLTERQIKIWFQNR 58 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnr 58 (96)
+.++|..+||+...++.|-...
T Consensus 3 I~e~a~~~gvs~~tlRyYe~~G 24 (127)
T TIGR02044 3 IGQVAKLTGLSSKMIRYYEEKG 24 (127)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4567888999999999887543
No 275
>PRK10651 transcriptional regulator NarL; Provisional
Probab=21.44 E-value=2.2e+02 Score=17.74 Aligned_cols=45 Identities=20% Similarity=0.145 Sum_probs=31.4
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhH
Q psy1653 13 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 63 (96)
Q Consensus 13 ~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~k 63 (96)
.+++.+..+|.-... + + ....++..++++...|+...++=+.|..
T Consensus 155 ~Lt~rE~~vl~~l~~-g-~----~~~~ia~~l~is~~tV~~~~~~l~~Kl~ 199 (216)
T PRK10651 155 QLTPRERDILKLIAQ-G-L----PNKMIARRLDITESTVKVHVKHMLKKMK 199 (216)
T ss_pred cCCHHHHHHHHHHHc-C-C----CHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 378888888865432 1 1 2455688899999999998887666553
No 276
>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=21.35 E-value=1.1e+02 Score=14.98 Aligned_cols=14 Identities=29% Similarity=0.332 Sum_probs=11.4
Q ss_pred CCCCHHHHHHHHHH
Q psy1653 12 QTYTRYQTLELEKE 25 (96)
Q Consensus 12 ~~~s~~q~~~L~~~ 25 (96)
+.||..|+..|+.-
T Consensus 1 s~FT~~Ql~~L~~Q 14 (37)
T PF08880_consen 1 SPFTPAQLQELRAQ 14 (37)
T ss_pred CCCCHHHHHHHHHH
Confidence 36899999999875
No 277
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=21.28 E-value=2.2e+02 Score=17.85 Aligned_cols=44 Identities=9% Similarity=-0.032 Sum_probs=37.6
Q ss_pred CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhh
Q psy1653 12 QTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWF 55 (96)
Q Consensus 12 ~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF 55 (96)
..+++-+..+|+-.+...+-......+.|.....+++..|++=.
T Consensus 2 ~~Is~aE~eVM~ilW~~~~~t~~eI~~~l~~~~ews~sTV~TLl 45 (123)
T COG3682 2 MSISAAEWEVMEILWSRGPATVREIIEELPADREWSYSTVKTLL 45 (123)
T ss_pred CcccHHHHHHHHHHHHcCCccHHHHHHHHhhcccccHHHHHHHH
Confidence 45778888999999999988888888889999999999988755
No 278
>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=21.18 E-value=2.2e+02 Score=19.25 Aligned_cols=48 Identities=21% Similarity=0.246 Sum_probs=33.5
Q ss_pred CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhchhhhhhHH
Q psy1653 11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64 (96)
Q Consensus 11 r~~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqnrR~k~kr 64 (96)
...+++.+.++|.-.. .. ..-.++|..+|+++..|+.+..+=+.|..-
T Consensus 169 ~~~Lt~re~evl~~~a-~G-----~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~ 216 (232)
T TIGR03541 169 AGVLSEREREVLAWTA-LG-----RRQADIAAILGISERTVENHLRSARRKLGV 216 (232)
T ss_pred hccCCHHHHHHHHHHH-CC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence 3467777777776642 11 245567888999999999999876666543
No 279
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=21.13 E-value=71 Score=20.03 Aligned_cols=20 Identities=20% Similarity=0.298 Sum_probs=15.4
Q ss_pred HHHHHHHcCCCcchhhhhhc
Q psy1653 37 RIEMAHALCLTERQIKIWFQ 56 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFq 56 (96)
+.++|..+||+...|+.|=.
T Consensus 3 Ige~a~~~gvs~~tlRyYE~ 22 (135)
T PRK10227 3 ISDVAKITGLTSKAIRFYEE 22 (135)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45678888888888888853
No 280
>PF07471 Phage_Nu1: Phage DNA packaging protein Nu1; InterPro: IPR010906 This entry is represented by the Bacteriophage lambda, Nu1, terminase small subunit. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Terminase, the DNA packaging enzyme of bacteriophage lambda, is a heteromultimer composed of subunits Nu1 and A. The smaller Nu1 terminase subunit has a low-affinity ATPase stimulated by non-specific DNA [].; PDB: 1J9I_A.
Probab=20.95 E-value=67 Score=21.06 Aligned_cols=21 Identities=29% Similarity=0.585 Sum_probs=13.6
Q ss_pred HHHHHHHcCCCcchhhhhhch
Q psy1653 37 RIEMAHALCLTERQIKIWFQN 57 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqn 57 (96)
+..||..+|+++..|.-|-.+
T Consensus 5 k~~lA~i~gvS~~ti~~W~~~ 25 (164)
T PF07471_consen 5 KKELAEIFGVSERTIDKWQRQ 25 (164)
T ss_dssp HHHHHHHTT--HHHHHHHTTT
T ss_pred HHHHHHHHCCCHHHHHHHHHC
Confidence 456788888888877777644
No 281
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=20.73 E-value=1.7e+02 Score=17.73 Aligned_cols=13 Identities=15% Similarity=0.514 Sum_probs=5.5
Q ss_pred HHHHHcCCCcchh
Q psy1653 39 EMAHALCLTERQI 51 (96)
Q Consensus 39 ~la~~l~l~~~~V 51 (96)
++|..+|++...|
T Consensus 128 EIA~~l~is~~tV 140 (142)
T TIGR03209 128 DIAKKLHISRQSV 140 (142)
T ss_pred HHHHHHCcCHHhh
Confidence 3344444444433
No 282
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal 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=20.70 E-value=74 Score=19.22 Aligned_cols=20 Identities=20% Similarity=0.200 Sum_probs=15.3
Q ss_pred HHHHHHHcCCCcchhhhhhc
Q psy1653 37 RIEMAHALCLTERQIKIWFQ 56 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFq 56 (96)
+.++|..+||+...++.|-.
T Consensus 3 I~eva~~~gvs~~tLRyYe~ 22 (123)
T cd04770 3 IGELAKAAGVSPDTIRYYER 22 (123)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45678888888888888764
No 283
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=20.63 E-value=73 Score=19.59 Aligned_cols=22 Identities=14% Similarity=0.158 Sum_probs=17.3
Q ss_pred HHHHHHHcCCCcchhhhhhchh
Q psy1653 37 RIEMAHALCLTERQIKIWFQNR 58 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~~WFqnr 58 (96)
+.++|..+||+...++.|-...
T Consensus 3 I~e~a~~~gvs~~tlR~Ye~~G 24 (127)
T TIGR02047 3 IGELAQKTGVSVETIRFYEKQG 24 (127)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4567888999999999887543
No 284
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=20.49 E-value=1.6e+02 Score=19.60 Aligned_cols=43 Identities=12% Similarity=-0.009 Sum_probs=26.7
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCcchhhhhhch
Q psy1653 14 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQN 57 (96)
Q Consensus 14 ~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WFqn 57 (96)
++..++..|......+ +-....-..+|..+++++..|+..+.+
T Consensus 159 Lt~re~~~l~~~i~~~-~~~g~s~~eIA~~l~iS~~Tv~~~~~~ 201 (239)
T PRK10430 159 LTPQTLRTLCQWIDAH-QDYEFSTDELANAVNISRVSCRKYLIW 201 (239)
T ss_pred CCHHHHHHHHHHHHhC-CCCCcCHHHHHHHhCchHHHHHHHHHH
Confidence 5555555554443322 222234566899999999999988764
No 285
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=20.47 E-value=25 Score=22.01 Aligned_cols=12 Identities=25% Similarity=0.761 Sum_probs=8.2
Q ss_pred hhhhhchhhhhh
Q psy1653 51 IKIWFQNRRMKL 62 (96)
Q Consensus 51 V~~WFqnrR~k~ 62 (96)
|..||+|++.+.
T Consensus 1 v~C~fC~~~s~~ 12 (131)
T PF09779_consen 1 VNCWFCGQNSKV 12 (131)
T ss_pred CeeccCCCCCCC
Confidence 457888877654
No 286
>PF10453 NUFIP1: Nuclear fragile X mental retardation-interacting protein 1 (NUFIP1); InterPro: IPR019496 Nuclear fragile X mental retardation-interacting protein 1 (Nufip1) has been implicated in the assembly of the large subunit of the ribosome [] and in telomere maintenance []. It is known to bind RNA [] and is phosphorylated upon DNA damage []. This entry represents a conserved domain found within Nufip1. Some proteins containing this region also contain a CCCH zinc finger.
Probab=20.32 E-value=1.6e+02 Score=15.76 Aligned_cols=21 Identities=24% Similarity=0.521 Sum_probs=15.7
Q ss_pred CcchhhhhhchhhhhhHHHHH
Q psy1653 47 TERQIKIWFQNRRMKLKKEIQ 67 (96)
Q Consensus 47 ~~~~V~~WFqnrR~k~kr~~~ 67 (96)
++..|.-|-..||..|--...
T Consensus 19 t~eeI~~W~eERrk~~PT~~~ 39 (56)
T PF10453_consen 19 TPEEIAKWIEERRKNYPTKAN 39 (56)
T ss_pred CHHHHHHHHHHHHHcCCcHHH
Confidence 677899999988877755443
No 287
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=20.09 E-value=35 Score=18.51 Aligned_cols=20 Identities=20% Similarity=0.434 Sum_probs=15.1
Q ss_pred HHHHHHHcCCCcchhh-hhhc
Q psy1653 37 RIEMAHALCLTERQIK-IWFQ 56 (96)
Q Consensus 37 ~~~la~~l~l~~~~V~-~WFq 56 (96)
...||..+|++...|. .|..
T Consensus 15 ~~~lA~~lgis~st~s~~~~~ 35 (66)
T PF07022_consen 15 DKELAERLGISKSTLSNNWKK 35 (66)
T ss_dssp CHHHHCCTT--HHHHH-HHHH
T ss_pred HHHHHHHhCcCHHHhhHHHHh
Confidence 3578999999999999 8885
No 288
>cd00131 PAX Paired Box domain
Probab=20.09 E-value=2.3e+02 Score=17.47 Aligned_cols=45 Identities=11% Similarity=-0.082 Sum_probs=27.8
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC-------Ccchhhhhhch
Q psy1653 13 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCL-------TERQIKIWFQN 57 (96)
Q Consensus 13 ~~s~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l-------~~~~V~~WFqn 57 (96)
..+......+......++..+..+...+...-|+ +...|--||++
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 3455666666666677887777766654334455 66666666653
Done!