Query psy5355
Match_columns 76
No_of_seqs 171 out of 1076
Neff 9.4
Searched_HMMs 46136
Date Sat Aug 17 00:27:04 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5355.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5355hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0489|consensus 99.9 5.7E-23 1.2E-27 126.1 6.1 67 6-72 156-223 (261)
2 KOG0850|consensus 99.9 3.4E-22 7.4E-27 119.0 5.7 70 4-73 117-187 (245)
3 KOG0488|consensus 99.9 3.9E-22 8.5E-27 124.6 5.9 64 6-69 169-233 (309)
4 KOG0843|consensus 99.8 2.2E-21 4.8E-26 112.1 5.1 62 8-69 101-163 (197)
5 KOG0484|consensus 99.8 9E-22 2E-26 105.1 3.2 63 6-68 14-77 (125)
6 PF00046 Homeobox: Homeobox do 99.8 2.2E-20 4.8E-25 91.3 6.0 56 10-65 1-57 (57)
7 KOG0842|consensus 99.8 4.9E-21 1.1E-25 118.8 3.6 66 6-71 150-216 (307)
8 KOG0487|consensus 99.8 6.7E-21 1.4E-25 118.3 3.3 62 7-68 233-295 (308)
9 KOG0485|consensus 99.8 4.5E-20 9.8E-25 109.5 4.6 63 7-69 102-165 (268)
10 KOG0848|consensus 99.8 3.8E-20 8.2E-25 112.5 3.0 64 6-69 196-260 (317)
11 KOG0494|consensus 99.8 2.2E-19 4.7E-24 109.0 5.1 60 10-69 142-202 (332)
12 KOG0492|consensus 99.8 1.1E-19 2.3E-24 107.2 3.5 67 8-74 143-210 (246)
13 KOG2251|consensus 99.8 2.7E-19 5.8E-24 106.2 4.9 65 5-69 33-98 (228)
14 COG5576 Homeodomain-containing 99.8 3.1E-18 6.8E-23 98.3 6.6 70 4-73 46-116 (156)
15 TIGR01565 homeo_ZF_HD homeobox 99.8 1.2E-18 2.6E-23 85.2 3.8 49 10-58 2-54 (58)
16 KOG0493|consensus 99.7 2.1E-18 4.6E-23 104.9 5.1 61 9-69 246-307 (342)
17 smart00389 HOX Homeodomain. DN 99.7 1.3E-17 2.8E-22 81.0 5.6 53 11-63 2-55 (56)
18 cd00086 homeodomain Homeodomai 99.7 2.2E-17 4.8E-22 80.8 6.3 55 11-65 2-57 (59)
19 KOG0491|consensus 99.7 1.7E-18 3.6E-23 99.1 2.0 62 9-70 100-162 (194)
20 KOG0483|consensus 99.7 1.7E-16 3.6E-21 94.0 4.9 60 9-68 50-110 (198)
21 KOG0486|consensus 99.7 4.6E-17 1E-21 100.9 2.2 63 8-70 111-174 (351)
22 KOG0844|consensus 99.6 1.8E-16 3.8E-21 98.3 1.2 60 8-67 180-240 (408)
23 KOG0847|consensus 99.6 1.2E-15 2.6E-20 91.1 3.8 66 5-70 163-229 (288)
24 KOG4577|consensus 99.6 2.6E-15 5.5E-20 92.7 5.3 63 6-68 164-227 (383)
25 KOG3802|consensus 99.6 5.5E-16 1.2E-20 98.6 2.0 62 7-68 292-354 (398)
26 KOG0490|consensus 99.5 2E-14 4.3E-19 86.4 2.9 63 6-68 57-120 (235)
27 KOG0849|consensus 99.4 4.7E-13 1E-17 85.4 5.1 62 6-67 173-235 (354)
28 KOG1168|consensus 99.1 1.8E-11 3.9E-16 75.9 1.3 60 7-66 307-367 (385)
29 KOG0775|consensus 99.0 3.2E-10 7E-15 69.7 4.4 49 16-64 183-232 (304)
30 PF05920 Homeobox_KN: Homeobox 98.9 1.6E-09 3.5E-14 49.3 3.6 32 30-61 7-39 (40)
31 KOG2252|consensus 98.9 4.6E-09 9.9E-14 69.6 5.9 55 4-58 415-469 (558)
32 KOG0774|consensus 98.9 1.3E-09 2.8E-14 66.9 2.5 58 9-66 188-249 (334)
33 KOG0490|consensus 98.6 8.8E-08 1.9E-12 57.6 5.3 62 6-67 150-212 (235)
34 PF11569 Homez: Homeodomain le 98.2 1.1E-06 2.4E-11 42.5 2.1 38 21-58 10-47 (56)
35 KOG1146|consensus 98.1 3E-06 6.6E-11 61.2 3.8 61 9-69 903-964 (1406)
36 KOG0773|consensus 97.2 0.00022 4.8E-09 45.5 2.1 55 9-63 239-298 (342)
37 KOG3623|consensus 97.2 0.00095 2.1E-08 46.8 5.0 47 21-67 568-615 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 96.5 0.011 2.5E-07 28.1 4.5 48 10-62 1-48 (53)
39 PF04967 HTH_10: HTH DNA bindi 95.0 0.047 1E-06 26.1 3.0 39 16-54 1-41 (53)
40 COG3413 Predicted DNA binding 94.1 0.14 3E-06 30.9 4.3 49 15-65 155-206 (215)
41 PF01527 HTH_Tnp_1: Transposas 93.9 0.064 1.4E-06 26.8 2.2 44 11-58 2-45 (76)
42 PF10668 Phage_terminase: Phag 93.0 0.09 2E-06 25.8 1.8 20 39-58 25-44 (60)
43 PF04545 Sigma70_r4: Sigma-70, 92.6 0.53 1.1E-05 21.6 5.0 39 15-58 4-42 (50)
44 PF08281 Sigma70_r4_2: Sigma-7 91.9 0.68 1.5E-05 21.5 4.8 38 16-58 11-48 (54)
45 cd06171 Sigma70_r4 Sigma70, re 91.9 0.61 1.3E-05 20.8 4.2 38 16-58 11-48 (55)
46 PF13936 HTH_38: Helix-turn-he 90.5 0.65 1.4E-05 21.0 3.1 40 14-58 3-42 (44)
47 PRK09646 RNA polymerase sigma 90.4 1.4 3.1E-05 25.8 5.3 31 38-68 160-191 (194)
48 PRK09413 IS2 repressor TnpA; R 89.3 2.4 5.1E-05 23.3 5.4 43 12-58 9-51 (121)
49 PF06056 Terminase_5: Putative 89.2 0.15 3.3E-06 24.7 0.5 21 38-58 15-35 (58)
50 PRK09644 RNA polymerase sigma 88.4 1.7 3.6E-05 24.7 4.5 32 38-69 126-158 (165)
51 PRK03975 tfx putative transcri 88.1 2.6 5.6E-05 24.1 5.0 46 14-65 5-51 (141)
52 PRK09642 RNA polymerase sigma 88.1 2.2 4.8E-05 24.0 4.9 30 38-67 124-154 (160)
53 PRK09652 RNA polymerase sigma 87.9 2.5 5.3E-05 24.0 5.0 29 38-66 146-175 (182)
54 PRK06759 RNA polymerase factor 87.7 2.4 5.3E-05 23.6 4.8 26 38-63 124-150 (154)
55 PF13518 HTH_28: Helix-turn-he 87.5 0.83 1.8E-05 20.8 2.4 20 39-58 15-34 (52)
56 PRK00118 putative DNA-binding 87.2 3.3 7.1E-05 22.5 5.0 46 15-65 17-63 (104)
57 PF09607 BrkDBD: Brinker DNA-b 86.9 1.8 3.9E-05 21.1 3.4 48 13-61 3-50 (58)
58 PRK12526 RNA polymerase sigma 86.9 2.9 6.2E-05 24.8 5.0 30 38-67 171-201 (206)
59 PRK12514 RNA polymerase sigma 86.6 3.5 7.5E-05 23.7 5.2 29 38-66 147-176 (179)
60 PRK12512 RNA polymerase sigma 86.5 3.6 7.9E-05 23.7 5.2 31 38-68 149-180 (184)
61 PRK11924 RNA polymerase sigma 86.4 2.9 6.3E-05 23.6 4.8 29 38-66 143-172 (179)
62 PF13384 HTH_23: Homeodomain-l 86.2 0.78 1.7E-05 20.9 1.9 21 38-58 19-39 (50)
63 TIGR02989 Sig-70_gvs1 RNA poly 86.2 3.3 7.1E-05 23.1 4.8 28 37-64 128-156 (159)
64 cd04761 HTH_MerR-SF Helix-Turn 86.1 1.1 2.3E-05 20.2 2.3 20 39-58 3-22 (49)
65 TIGR03879 near_KaiC_dom probab 85.9 0.25 5.4E-06 25.2 0.1 31 28-58 24-54 (73)
66 TIGR02999 Sig-70_X6 RNA polyme 85.9 4 8.7E-05 23.4 5.2 28 38-65 152-180 (183)
67 PRK04217 hypothetical protein; 85.7 4.2 9.2E-05 22.3 5.0 49 14-67 41-90 (110)
68 PRK05602 RNA polymerase sigma 85.7 2.9 6.3E-05 24.2 4.6 31 38-68 146-177 (186)
69 PF13411 MerR_1: MerR HTH fami 85.4 1 2.2E-05 21.9 2.2 19 40-58 4-22 (69)
70 TIGR02939 RpoE_Sigma70 RNA pol 85.4 2.8 6.1E-05 24.2 4.4 33 35-67 153-186 (190)
71 PRK12546 RNA polymerase sigma 85.0 4 8.6E-05 24.0 4.9 32 38-69 131-163 (188)
72 PRK12519 RNA polymerase sigma 84.8 3.5 7.5E-05 24.0 4.6 30 36-65 157-187 (194)
73 TIGR02985 Sig70_bacteroi1 RNA 84.7 4.6 9.9E-05 22.4 4.9 27 38-64 131-158 (161)
74 TIGR02983 SigE-fam_strep RNA p 84.4 5.1 0.00011 22.5 5.1 31 38-68 128-159 (162)
75 PRK12524 RNA polymerase sigma 84.3 4.8 0.0001 23.6 5.1 30 38-67 154-184 (196)
76 TIGR02937 sigma70-ECF RNA poly 84.3 4.8 0.0001 21.7 4.9 27 38-64 128-155 (158)
77 TIGR02959 SigZ RNA polymerase 83.9 5 0.00011 23.0 4.9 29 38-66 118-147 (170)
78 TIGR02952 Sig70_famx2 RNA poly 83.8 5.5 0.00012 22.5 5.1 28 38-65 140-168 (170)
79 PRK12537 RNA polymerase sigma 83.7 5.8 0.00012 22.9 5.2 28 38-65 151-179 (182)
80 PRK09639 RNA polymerase sigma 83.7 4.2 9E-05 22.9 4.5 29 38-66 129-158 (166)
81 PRK12530 RNA polymerase sigma 83.6 5.1 0.00011 23.4 5.0 28 38-65 152-180 (189)
82 PRK10072 putative transcriptio 83.6 4.3 9.3E-05 21.7 4.2 37 15-58 32-68 (96)
83 PRK09648 RNA polymerase sigma 83.6 5.3 0.00012 23.2 5.0 29 38-66 157-186 (189)
84 PF00376 MerR: MerR family reg 83.4 1.5 3.3E-05 19.3 2.1 19 40-58 3-21 (38)
85 TIGR02948 SigW_bacill RNA poly 83.4 4.7 0.0001 23.2 4.7 30 37-66 153-183 (187)
86 PRK12541 RNA polymerase sigma 83.2 5.1 0.00011 22.5 4.8 28 38-65 130-158 (161)
87 PRK12547 RNA polymerase sigma 82.9 6.2 0.00013 22.4 5.1 30 38-67 130-160 (164)
88 cd00569 HTH_Hin_like Helix-tur 82.9 2.3 4.9E-05 16.9 4.0 38 15-57 5-42 (42)
89 PF08280 HTH_Mga: M protein tr 82.5 2.2 4.8E-05 20.4 2.6 35 19-57 6-40 (59)
90 PRK09047 RNA polymerase factor 82.4 6.4 0.00014 22.0 4.9 29 38-66 124-153 (161)
91 TIGR02954 Sig70_famx3 RNA poly 81.3 7.3 0.00016 22.1 5.0 29 38-66 137-166 (169)
92 PRK12536 RNA polymerase sigma 81.0 8.4 0.00018 22.2 5.4 30 38-67 147-177 (181)
93 PRK09637 RNA polymerase sigma 80.8 7.3 0.00016 22.6 4.9 29 38-66 124-153 (181)
94 PRK09645 RNA polymerase sigma 80.7 8 0.00017 22.0 5.0 30 38-67 136-166 (173)
95 cd04764 HTH_MlrA-like_sg1 Heli 80.7 2 4.3E-05 20.8 2.2 20 39-58 3-22 (67)
96 cd04763 HTH_MlrA-like Helix-Tu 80.5 2.3 4.9E-05 20.7 2.3 20 39-58 3-22 (68)
97 PRK12515 RNA polymerase sigma 80.5 8 0.00017 22.4 5.0 30 38-67 149-179 (189)
98 PRK13919 putative RNA polymera 80.4 8.9 0.00019 22.1 5.4 29 38-66 153-182 (186)
99 PRK12538 RNA polymerase sigma 80.3 4 8.7E-05 24.9 3.8 31 38-68 189-220 (233)
100 PF02796 HTH_7: Helix-turn-hel 79.9 3.5 7.6E-05 18.6 2.7 38 15-57 5-42 (45)
101 PRK06930 positive control sigm 79.4 9.4 0.0002 22.4 5.0 46 16-66 115-161 (170)
102 PRK07037 extracytoplasmic-func 79.4 8.9 0.00019 21.5 5.1 29 38-66 127-156 (163)
103 PF00196 GerE: Bacterial regul 79.1 5.3 0.00012 18.8 3.7 38 15-58 3-40 (58)
104 TIGR02950 SigM_subfam RNA poly 79.0 3 6.6E-05 23.2 2.8 33 33-65 118-151 (154)
105 PRK09649 RNA polymerase sigma 78.5 8.4 0.00018 22.4 4.7 28 38-65 148-176 (185)
106 PRK12539 RNA polymerase sigma 78.5 11 0.00023 21.9 5.1 30 38-67 149-179 (184)
107 PRK06811 RNA polymerase factor 78.3 9.4 0.0002 22.2 4.8 28 38-65 149-177 (189)
108 cd04762 HTH_MerR-trunc Helix-T 78.2 3.3 7.2E-05 18.1 2.4 20 39-58 3-22 (49)
109 PRK06986 fliA flagellar biosyn 77.9 10 0.00023 22.9 5.1 29 38-66 202-231 (236)
110 PRK12543 RNA polymerase sigma 77.8 11 0.00024 21.7 5.0 30 38-67 135-165 (179)
111 PRK12511 RNA polymerase sigma 77.8 10 0.00022 22.1 4.9 29 38-66 129-158 (182)
112 PRK12518 RNA polymerase sigma 77.5 4.8 0.0001 22.9 3.4 35 33-67 133-168 (175)
113 PRK12516 RNA polymerase sigma 77.5 10 0.00022 22.2 4.8 31 38-68 134-165 (187)
114 PRK12535 RNA polymerase sigma 77.1 11 0.00023 22.3 4.9 30 38-67 151-181 (196)
115 PRK12532 RNA polymerase sigma 77.0 11 0.00023 22.0 4.8 29 38-66 154-183 (195)
116 PRK11923 algU RNA polymerase s 76.6 12 0.00025 21.8 4.9 30 38-67 156-186 (193)
117 PRK12542 RNA polymerase sigma 76.4 12 0.00027 21.6 5.0 29 38-66 140-169 (185)
118 PF08279 HTH_11: HTH domain; 76.2 5.1 0.00011 18.5 2.8 32 23-57 5-36 (55)
119 PRK12533 RNA polymerase sigma 76.1 11 0.00024 22.7 4.8 30 38-67 152-182 (216)
120 PRK08583 RNA polymerase sigma 75.9 14 0.00029 22.7 5.3 29 38-66 223-252 (257)
121 PRK09647 RNA polymerase sigma 75.9 13 0.00028 22.1 5.1 29 38-66 156-185 (203)
122 PRK12520 RNA polymerase sigma 75.7 13 0.00029 21.6 5.0 29 38-66 149-178 (191)
123 TIGR02943 Sig70_famx1 RNA poly 75.6 13 0.00029 21.6 5.0 29 38-66 149-178 (188)
124 TIGR02859 spore_sigH RNA polym 75.5 5.5 0.00012 23.1 3.3 30 36-65 165-195 (198)
125 TIGR02947 SigH_actino RNA poly 75.0 6 0.00013 23.0 3.4 34 34-67 145-179 (193)
126 PRK08295 RNA polymerase factor 75.0 14 0.00031 21.6 5.4 32 36-67 170-202 (208)
127 PF13730 HTH_36: Helix-turn-he 74.9 6.8 0.00015 18.0 3.0 42 16-58 3-47 (55)
128 cd01104 HTH_MlrA-CarA Helix-Tu 74.7 4.2 9E-05 19.6 2.3 20 39-58 3-22 (68)
129 PRK12523 RNA polymerase sigma 74.2 14 0.0003 21.1 5.5 30 38-67 137-167 (172)
130 TIGR03001 Sig-70_gmx1 RNA poly 73.9 14 0.00031 22.7 5.0 28 38-65 179-207 (244)
131 TIGR02980 SigBFG RNA polymeras 73.7 16 0.00034 21.9 5.1 21 38-58 196-216 (227)
132 PRK08301 sporulation sigma fac 73.5 17 0.00038 21.9 5.3 29 38-66 200-229 (234)
133 TIGR02479 FliA_WhiG RNA polyme 73.2 17 0.00038 21.8 5.2 28 38-65 193-221 (224)
134 PRK12527 RNA polymerase sigma 73.1 14 0.00031 20.7 4.9 30 38-67 123-153 (159)
135 COG4367 Uncharacterized protei 73.1 6.8 0.00015 20.8 2.9 39 16-54 3-41 (97)
136 PRK12545 RNA polymerase sigma 72.9 17 0.00036 21.5 5.1 29 38-66 157-186 (201)
137 COG5484 Uncharacterized conser 72.5 2.4 5.2E-05 26.8 1.3 27 32-58 15-41 (279)
138 PRK12540 RNA polymerase sigma 72.2 17 0.00036 21.2 4.8 31 38-68 129-160 (182)
139 PF06971 Put_DNA-bind_N: Putat 71.6 3.9 8.3E-05 19.2 1.7 15 40-54 32-46 (50)
140 PRK07670 RNA polymerase sigma 71.6 19 0.00041 22.1 5.2 28 38-65 219-247 (251)
141 smart00422 HTH_MERR helix_turn 71.6 4.3 9.4E-05 19.5 2.0 19 40-58 4-22 (70)
142 PF14549 P22_Cro: DNA-binding 71.3 4.5 9.8E-05 19.7 1.9 17 40-56 13-29 (60)
143 PRK12531 RNA polymerase sigma 71.1 18 0.00039 21.1 4.9 28 38-65 159-187 (194)
144 PRK12522 RNA polymerase sigma 70.8 17 0.00037 20.7 5.0 28 38-65 137-165 (173)
145 PRK12544 RNA polymerase sigma 70.7 20 0.00043 21.4 5.0 29 38-66 166-195 (206)
146 TIGR02941 Sigma_B RNA polymera 70.5 21 0.00046 21.9 5.2 27 38-64 223-250 (255)
147 PRK09415 RNA polymerase factor 70.2 17 0.00037 20.9 4.5 28 38-65 145-173 (179)
148 PRK07408 RNA polymerase sigma 70.2 21 0.00044 22.1 5.1 30 38-67 221-251 (256)
149 PRK12517 RNA polymerase sigma 69.9 9.2 0.0002 22.3 3.4 30 38-67 146-176 (188)
150 COG1905 NuoE NADH:ubiquinone o 69.7 12 0.00026 22.0 3.7 37 18-54 25-61 (160)
151 PRK05988 formate dehydrogenase 69.4 11 0.00024 21.9 3.5 35 20-54 25-59 (156)
152 PRK09640 RNA polymerase sigma 68.7 10 0.00022 22.0 3.4 30 36-65 150-180 (188)
153 TIGR02960 SigX5 RNA polymerase 68.5 18 0.0004 22.8 4.7 31 38-68 160-191 (324)
154 cd04766 HTH_HspR Helix-Turn-He 68.4 5.9 0.00013 20.5 2.1 20 39-58 4-23 (91)
155 PRK06704 RNA polymerase factor 68.4 18 0.00038 22.2 4.5 31 38-68 134-165 (228)
156 PRK05657 RNA polymerase sigma 68.2 22 0.00047 23.0 5.0 50 16-66 263-313 (325)
157 PF12824 MRP-L20: Mitochondria 68.0 21 0.00046 21.0 4.6 45 12-58 82-126 (164)
158 PF07638 Sigma70_ECF: ECF sigm 68.0 22 0.00047 20.8 5.0 29 37-65 152-181 (185)
159 TIGR02957 SigX4 RNA polymerase 67.9 21 0.00045 22.4 4.8 28 39-66 127-155 (281)
160 COG2944 Predicted transcriptio 67.8 18 0.00039 19.7 4.3 36 16-58 44-79 (104)
161 PRK12529 RNA polymerase sigma 67.7 21 0.00046 20.5 5.1 26 38-63 145-171 (178)
162 TIGR01958 nuoE_fam NADH-quinon 67.7 12 0.00026 21.3 3.5 35 20-54 18-52 (148)
163 KOG0773|consensus 67.7 13 0.00027 24.0 3.9 42 27-68 115-157 (342)
164 cd01105 HTH_GlnR-like Helix-Tu 67.5 6.3 0.00014 20.4 2.1 20 39-58 4-23 (88)
165 PRK07539 NADH dehydrogenase su 67.5 12 0.00026 21.5 3.5 34 21-54 25-58 (154)
166 PRK09641 RNA polymerase sigma 67.3 21 0.00046 20.4 4.7 31 36-66 152-183 (187)
167 COG1595 RpoE DNA-directed RNA 67.3 11 0.00023 21.8 3.3 31 38-68 145-176 (182)
168 PRK11511 DNA-binding transcrip 67.0 14 0.00029 20.4 3.5 22 37-58 26-47 (127)
169 PF13443 HTH_26: Cro/C1-type H 67.0 6.8 0.00015 18.5 2.1 21 38-58 12-32 (63)
170 PF13551 HTH_29: Winged helix- 66.4 17 0.00037 18.9 4.9 48 11-58 53-109 (112)
171 cd04774 HTH_YfmP Helix-Turn-He 66.0 7.9 0.00017 20.4 2.3 20 39-58 3-22 (96)
172 PRK09636 RNA polymerase sigma 66.0 25 0.00054 22.1 4.9 30 38-67 133-163 (293)
173 PRK13558 bacterio-opsin activa 65.9 8.5 0.00018 26.7 3.0 41 14-54 606-648 (665)
174 PF01257 2Fe-2S_thioredx: Thio 65.9 10 0.00022 21.5 2.9 34 21-54 16-49 (145)
175 PF13404 HTH_AsnC-type: AsnC-t 65.9 6.2 0.00013 17.7 1.7 16 39-54 20-35 (42)
176 PRK09643 RNA polymerase sigma 65.0 26 0.00055 20.5 4.7 30 38-67 152-182 (192)
177 PRK12513 RNA polymerase sigma 64.8 14 0.0003 21.5 3.4 34 34-67 153-187 (194)
178 PRK09638 RNA polymerase sigma 64.5 16 0.00034 20.8 3.6 32 34-65 140-172 (176)
179 PRK07571 bidirectional hydroge 64.3 16 0.00034 21.6 3.5 26 29-54 47-72 (169)
180 TIGR01764 excise DNA binding d 64.1 11 0.00024 16.4 2.4 20 39-58 4-23 (49)
181 PRK09651 RNA polymerase sigma 64.1 25 0.00054 20.1 4.7 21 38-58 137-157 (172)
182 COG2963 Transposase and inacti 63.9 21 0.00046 19.1 4.1 42 13-58 5-47 (116)
183 cd01106 HTH_TipAL-Mta Helix-Tu 63.7 9.4 0.0002 20.2 2.4 20 39-58 3-22 (103)
184 PRK12528 RNA polymerase sigma 63.6 24 0.00053 19.7 4.8 21 38-58 131-151 (161)
185 cd04779 HTH_MerR-like_sg4 Heli 63.6 8.7 0.00019 21.7 2.3 20 39-58 3-22 (134)
186 PRK07122 RNA polymerase sigma 63.5 34 0.00073 21.4 5.4 28 38-65 233-261 (264)
187 PF12728 HTH_17: Helix-turn-he 63.1 10 0.00022 17.2 2.2 19 40-58 5-23 (51)
188 PRK05803 sporulation sigma fac 62.9 29 0.00064 21.0 4.7 30 38-67 197-227 (233)
189 cd04768 HTH_BmrR-like Helix-Tu 62.6 10 0.00022 19.9 2.4 20 39-58 3-22 (96)
190 TIGR02835 spore_sigmaE RNA pol 62.5 16 0.00036 22.1 3.6 29 38-66 200-229 (234)
191 PRK11922 RNA polymerase sigma 62.3 19 0.00042 21.7 3.8 35 33-67 162-197 (231)
192 cd01392 HTH_LacI Helix-turn-he 62.1 6.8 0.00015 17.7 1.5 18 41-58 2-19 (52)
193 PF07022 Phage_CI_repr: Bacter 61.3 4.3 9.2E-05 19.9 0.7 20 39-58 15-35 (66)
194 PHA01976 helix-turn-helix prot 61.3 11 0.00023 18.0 2.2 20 39-58 18-37 (67)
195 PF01710 HTH_Tnp_IS630: Transp 61.1 25 0.00053 19.2 3.8 38 16-58 3-40 (119)
196 cd04775 HTH_Cfa-like Helix-Tur 61.1 9.7 0.00021 20.2 2.1 20 39-58 4-23 (102)
197 cd04788 HTH_NolA-AlbR Helix-Tu 60.7 10 0.00022 19.9 2.1 20 39-58 3-22 (96)
198 cd04780 HTH_MerR-like_sg5 Heli 60.5 10 0.00022 20.0 2.1 20 39-58 3-22 (95)
199 PF13565 HTH_32: Homeodomain-l 60.4 19 0.00042 17.6 5.8 38 17-54 32-74 (77)
200 cd04789 HTH_Cfa Helix-Turn-Hel 60.2 10 0.00022 20.1 2.2 20 39-58 4-23 (102)
201 PRK06288 RNA polymerase sigma 59.7 40 0.00086 20.9 5.1 28 38-65 230-258 (268)
202 TIGR02054 MerD mercuric resist 59.7 11 0.00023 21.0 2.2 21 38-58 5-25 (120)
203 smart00027 EH Eps15 homology d 59.5 24 0.00051 18.3 4.8 43 16-58 4-51 (96)
204 TIGR03070 couple_hipB transcri 59.1 12 0.00026 16.9 2.1 20 39-58 18-37 (58)
205 cd04773 HTH_TioE_rpt2 Second H 58.4 11 0.00025 20.2 2.2 20 39-58 3-22 (108)
206 PRK12534 RNA polymerase sigma 58.4 34 0.00073 19.7 5.1 28 38-65 155-183 (187)
207 cd00592 HTH_MerR-like Helix-Tu 58.2 12 0.00026 19.5 2.2 19 40-58 4-22 (100)
208 smart00530 HTH_XRE Helix-turn- 57.9 14 0.0003 15.7 2.2 20 39-58 13-32 (56)
209 PF01381 HTH_3: Helix-turn-hel 57.9 14 0.0003 16.8 2.2 20 39-58 12-31 (55)
210 KOG1146|consensus 57.9 36 0.00078 26.6 5.0 59 9-67 705-764 (1406)
211 cd04782 HTH_BltR Helix-Turn-He 57.6 14 0.0003 19.4 2.3 20 39-58 3-22 (97)
212 cd01111 HTH_MerD Helix-Turn-He 57.6 12 0.00026 20.2 2.2 20 39-58 3-22 (107)
213 cd04767 HTH_HspR-like_MBC Heli 57.3 14 0.00029 20.6 2.3 20 39-58 4-23 (120)
214 cd01107 HTH_BmrR Helix-Turn-He 56.9 13 0.00027 20.0 2.2 20 39-58 3-22 (108)
215 PF12793 SgrR_N: Sugar transpo 56.8 25 0.00055 19.3 3.4 34 20-55 5-38 (115)
216 PF13542 HTH_Tnp_ISL3: Helix-t 56.7 14 0.00031 16.7 2.1 20 39-58 30-49 (52)
217 cd01109 HTH_YyaN Helix-Turn-He 56.6 13 0.00027 20.0 2.2 20 39-58 3-22 (113)
218 PF14229 DUF4332: Domain of un 56.6 17 0.00037 20.1 2.7 25 34-58 27-51 (122)
219 cd00093 HTH_XRE Helix-turn-hel 56.6 14 0.00031 15.8 2.1 20 39-58 15-34 (58)
220 PF00325 Crp: Bacterial regula 56.1 13 0.00028 15.8 1.7 20 38-57 4-23 (32)
221 PRK10430 DNA-binding transcrip 55.7 23 0.0005 21.2 3.4 43 15-58 158-200 (239)
222 cd06170 LuxR_C_like C-terminal 55.3 19 0.00042 16.0 4.5 21 38-58 17-37 (57)
223 PF09862 DUF2089: Protein of u 55.1 34 0.00074 18.9 3.6 38 15-57 33-70 (113)
224 smart00421 HTH_LUXR helix_turn 54.7 20 0.00043 15.9 5.4 38 15-58 3-40 (58)
225 PF05263 DUF722: Protein of un 54.6 38 0.00083 19.2 4.0 40 16-58 82-121 (130)
226 PF08880 QLQ: QLQ; InterPro: 54.6 17 0.00036 15.9 2.0 13 15-27 2-14 (37)
227 cd02413 40S_S3_KH K homology R 54.1 4.6 9.9E-05 20.8 0.1 20 39-58 56-75 (81)
228 cd04765 HTH_MlrA-like_sg2 Heli 53.9 15 0.00032 19.5 2.1 19 40-58 4-22 (99)
229 PF13309 HTH_22: HTH domain 53.5 27 0.00058 17.0 3.3 35 21-55 27-61 (64)
230 PF12802 MarR_2: MarR family; 53.4 15 0.00033 17.0 2.0 38 16-55 3-40 (62)
231 PRK13182 racA polar chromosome 53.3 16 0.00035 21.7 2.4 20 39-58 3-22 (175)
232 PF07037 DUF1323: Putative tra 53.2 13 0.00029 20.8 1.9 19 40-58 4-22 (122)
233 TIGR02607 antidote_HigA addict 52.9 15 0.00032 18.1 1.9 20 39-58 21-40 (78)
234 TIGR00721 tfx DNA-binding prot 52.6 43 0.00092 19.1 5.8 45 14-64 5-50 (137)
235 PRK07500 rpoH2 RNA polymerase 52.1 46 0.00099 21.1 4.4 49 16-67 228-277 (289)
236 cd01282 HTH_MerR-like_sg3 Heli 51.9 17 0.00037 19.6 2.2 20 39-58 3-22 (112)
237 cd01110 HTH_SoxR Helix-Turn-He 51.9 16 0.00034 20.6 2.1 20 39-58 4-23 (139)
238 cd01279 HTH_HspR-like Helix-Tu 51.8 17 0.00037 19.2 2.1 20 39-58 4-23 (98)
239 cd04776 HTH_GnyR Helix-Turn-He 51.7 17 0.00036 19.9 2.1 20 39-58 3-22 (118)
240 TIGR02051 MerR Hg(II)-responsi 51.2 17 0.00036 20.1 2.1 19 40-58 3-21 (124)
241 PRK08241 RNA polymerase factor 51.2 42 0.00091 21.4 4.2 28 38-65 171-199 (339)
242 PF04539 Sigma70_r3: Sigma-70 51.0 29 0.00062 17.1 2.8 21 38-58 22-42 (78)
243 PF07471 Phage_Nu1: Phage DNA 51.0 15 0.00033 21.6 2.0 20 39-58 5-24 (164)
244 COG0789 SoxR Predicted transcr 50.9 18 0.00038 19.5 2.2 19 39-57 3-21 (124)
245 cd04772 HTH_TioE_rpt1 First He 50.8 18 0.0004 19.1 2.2 20 39-58 3-22 (99)
246 PRK05911 RNA polymerase sigma 50.5 59 0.0013 20.1 5.1 28 38-65 223-251 (257)
247 PRK12525 RNA polymerase sigma 50.5 46 0.00099 18.9 4.7 21 38-58 136-156 (168)
248 PF12244 DUF3606: Protein of u 50.1 27 0.00058 16.7 2.5 18 37-54 21-38 (57)
249 TIGR02394 rpoS_proteo RNA poly 49.8 63 0.0014 20.3 5.4 29 38-66 244-273 (285)
250 TIGR01950 SoxR redox-sensitive 49.3 21 0.00045 20.3 2.3 20 39-58 4-23 (142)
251 PRK09514 zntR zinc-responsive 49.3 19 0.0004 20.4 2.1 20 39-58 4-23 (140)
252 cd01108 HTH_CueR Helix-Turn-He 49.0 19 0.00042 19.8 2.1 20 39-58 3-22 (127)
253 PRK09635 sigI RNA polymerase s 48.9 58 0.0013 20.6 4.5 28 38-65 136-164 (290)
254 PRK09744 DNA-binding transcrip 48.7 23 0.0005 18.2 2.2 20 39-58 13-32 (75)
255 cd04781 HTH_MerR-like_sg6 Heli 48.5 20 0.00044 19.5 2.1 20 39-58 3-22 (120)
256 PRK05572 sporulation sigma fac 48.4 63 0.0014 19.8 5.2 38 16-58 203-240 (252)
257 PRK10227 DNA-binding transcrip 48.3 20 0.00044 20.2 2.2 20 39-58 3-22 (135)
258 PRK08215 sporulation sigma fac 47.8 65 0.0014 19.8 5.3 38 16-58 210-247 (258)
259 TIGR03826 YvyF flagellar opero 47.7 20 0.00044 20.4 2.1 25 38-62 48-73 (137)
260 PRK11475 DNA-binding transcrip 47.7 57 0.0012 19.6 4.2 37 15-57 134-170 (207)
261 TIGR02044 CueR Cu(I)-responsiv 47.5 21 0.00045 19.7 2.1 20 39-58 3-22 (127)
262 TIGR02393 RpoD_Cterm RNA polym 47.4 63 0.0014 19.6 5.2 49 16-65 177-226 (238)
263 TIGR02047 CadR-PbrR Cd(II)/Pb( 46.9 22 0.00047 19.7 2.1 20 39-58 3-22 (127)
264 PF12833 HTH_18: Helix-turn-he 46.8 17 0.00038 17.9 1.6 17 42-58 16-32 (81)
265 TIGR02043 ZntR Zn(II)-responsi 46.8 25 0.00054 19.6 2.4 20 39-58 4-23 (131)
266 PRK10840 transcriptional regul 46.8 59 0.0013 19.0 4.2 37 15-57 150-186 (216)
267 TIGR02885 spore_sigF RNA polym 46.8 63 0.0014 19.4 4.9 21 38-58 201-221 (231)
268 cd04770 HTH_HMRTR Helix-Turn-H 46.4 23 0.00049 19.3 2.2 20 39-58 3-22 (123)
269 PF01325 Fe_dep_repress: Iron 46.2 7.5 0.00016 18.7 0.2 39 20-58 6-44 (60)
270 PF10078 DUF2316: Uncharacteri 46.2 14 0.00031 19.5 1.2 30 22-55 13-42 (89)
271 TIGR02984 Sig-70_plancto1 RNA 46.1 56 0.0012 18.6 5.3 29 37-65 157-186 (189)
272 PF04703 FaeA: FaeA-like prote 45.8 27 0.00059 17.1 2.1 19 40-58 19-37 (62)
273 PRK15411 rcsA colanic acid cap 45.6 61 0.0013 19.3 4.0 38 15-58 137-174 (207)
274 TIGR03209 P21_Cbot clostridium 45.4 38 0.00083 18.5 3.0 14 40-53 127-140 (142)
275 PF13613 HTH_Tnp_4: Helix-turn 45.2 17 0.00038 16.8 1.4 20 39-58 22-41 (53)
276 PRK10100 DNA-binding transcrip 45.1 69 0.0015 19.4 4.5 38 15-58 155-192 (216)
277 PRK00215 LexA repressor; Valid 44.8 28 0.0006 20.6 2.5 41 16-58 2-46 (205)
278 cd04786 HTH_MerR-like_sg7 Heli 44.5 25 0.00055 19.7 2.2 20 39-58 3-22 (131)
279 TIGR02846 spore_sigmaK RNA pol 43.9 72 0.0016 19.2 5.2 27 38-64 196-223 (227)
280 cd04785 HTH_CadR-PbrR-like Hel 43.8 26 0.00056 19.3 2.1 20 39-58 3-22 (126)
281 cd04787 HTH_HMRTR_unk Helix-Tu 43.7 26 0.00057 19.5 2.2 20 39-58 3-22 (133)
282 TIGR01321 TrpR trp operon repr 43.6 32 0.00069 18.4 2.3 42 15-56 32-75 (94)
283 PF05269 Phage_CII: Bacterioph 43.6 27 0.00058 18.6 2.0 25 38-62 25-50 (91)
284 KOG3755|consensus 43.5 50 0.0011 23.8 3.8 45 25-69 708-760 (769)
285 PF01047 MarR: MarR family; I 43.5 33 0.00072 15.7 2.3 38 16-57 1-38 (59)
286 cd04783 HTH_MerR1 Helix-Turn-H 43.5 26 0.00056 19.2 2.1 20 39-58 3-22 (126)
287 PF07750 GcrA: GcrA cell cycle 43.4 48 0.001 19.4 3.3 35 15-54 2-37 (162)
288 cd04784 HTH_CadR-PbrR Helix-Tu 43.0 27 0.00059 19.2 2.1 20 39-58 3-22 (127)
289 PF01726 LexA_DNA_bind: LexA D 42.7 43 0.00094 16.4 3.2 40 16-57 4-47 (65)
290 PRK09706 transcriptional repre 42.5 22 0.00047 19.7 1.7 20 39-58 21-40 (135)
291 PRK09726 antitoxin HipB; Provi 42.1 31 0.00068 17.6 2.2 20 39-58 28-47 (88)
292 PF08784 RPA_C: Replication pr 42.1 25 0.00053 18.5 1.8 40 16-55 45-84 (102)
293 COG2197 CitB Response regulato 41.9 77 0.0017 19.0 4.1 38 15-58 148-185 (211)
294 PHA02955 hypothetical protein; 40.7 38 0.00083 20.9 2.6 40 19-58 61-101 (213)
295 PRK13749 transcriptional regul 40.6 33 0.0007 19.1 2.2 19 39-57 6-24 (121)
296 PF08671 SinI: Anti-repressor 40.5 33 0.00071 14.3 2.6 19 40-58 9-27 (30)
297 PRK09480 slmA division inhibit 40.2 40 0.00086 19.3 2.6 33 25-58 20-52 (194)
298 PRK12373 NADH dehydrogenase su 40.2 57 0.0012 22.1 3.5 34 21-54 40-73 (400)
299 cd04777 HTH_MerR-like_sg1 Heli 40.1 33 0.00072 18.2 2.2 20 39-58 3-22 (107)
300 TIGR03830 CxxCG_CxxCG_HTH puta 39.5 63 0.0014 17.3 4.2 19 40-58 82-100 (127)
301 cd04769 HTH_MerR2 Helix-Turn-H 39.3 34 0.00075 18.5 2.2 20 39-58 3-22 (116)
302 PF04297 UPF0122: Putative hel 39.2 66 0.0014 17.4 4.8 39 15-58 17-55 (101)
303 PF13223 DUF4031: Protein of u 39.1 42 0.00091 17.5 2.3 19 36-58 23-41 (83)
304 PF03444 HrcA_DNA-bdg: Winged 38.6 60 0.0013 16.8 3.1 37 17-55 3-42 (78)
305 cd00131 PAX Paired Box domain 38.6 72 0.0016 17.7 6.0 44 15-58 75-125 (128)
306 PF13413 HTH_25: Helix-turn-he 38.5 51 0.0011 15.9 2.9 41 13-53 19-62 (62)
307 PF01476 LysM: LysM domain; I 38.4 36 0.00078 14.5 1.8 19 38-56 8-26 (44)
308 PF13560 HTH_31: Helix-turn-he 38.2 30 0.00066 16.3 1.7 21 38-58 16-36 (64)
309 PF01418 HTH_6: Helix-turn-hel 37.7 24 0.00052 17.6 1.3 20 37-56 35-54 (77)
310 PF07423 DUF1510: Protein of u 37.7 19 0.00041 22.2 1.0 31 28-58 145-175 (217)
311 PF00165 HTH_AraC: Bacterial r 37.6 40 0.00087 14.5 2.2 21 37-57 9-29 (42)
312 PRK15002 redox-sensitivie tran 37.5 37 0.0008 19.6 2.2 21 38-58 13-33 (154)
313 PRK06424 transcription factor; 37.3 40 0.00088 19.3 2.3 20 39-58 100-119 (144)
314 PF08220 HTH_DeoR: DeoR-like h 37.2 35 0.00076 16.0 1.8 19 39-57 17-35 (57)
315 PF12844 HTH_19: Helix-turn-he 36.7 43 0.00093 15.6 2.1 21 38-58 14-34 (64)
316 cd08315 Death_TRAILR_DR4_DR5 D 36.6 57 0.0012 17.3 2.7 33 22-54 4-37 (96)
317 PRK15369 two component system 36.5 79 0.0017 17.6 4.0 38 15-58 149-186 (211)
318 TIGR01889 Staph_reg_Sar staphy 36.5 67 0.0015 17.0 3.0 41 15-55 22-62 (109)
319 PF12200 DUF3597: Domain of un 36.2 84 0.0018 17.8 3.7 25 34-58 83-112 (127)
320 cd04778 HTH_MerR-like_sg2 Heli 36.2 37 0.0008 20.8 2.1 20 39-58 4-23 (219)
321 PF13412 HTH_24: Winged helix- 36.2 45 0.00098 14.7 3.6 36 18-57 3-38 (48)
322 PRK13752 putative transcriptio 36.0 40 0.00086 19.2 2.1 21 38-58 9-29 (144)
323 PHA00542 putative Cro-like pro 35.7 42 0.00092 17.1 2.0 21 38-58 33-53 (82)
324 cd08306 Death_FADD Fas-associa 35.6 31 0.00067 17.8 1.5 18 40-57 17-34 (86)
325 cd04790 HTH_Cfa-like_unk Helix 35.5 40 0.00087 19.7 2.1 20 39-58 4-23 (172)
326 PF14174 YycC: YycC-like prote 35.4 55 0.0012 15.5 2.5 22 34-55 6-27 (53)
327 PRK15183 Vi polysaccharide bio 35.0 47 0.001 18.4 2.2 36 16-51 96-131 (143)
328 cd08318 Death_NMPP84 Death dom 34.4 36 0.00079 17.5 1.7 34 15-55 4-37 (86)
329 PF04760 IF2_N: Translation in 34.0 34 0.00074 15.8 1.4 14 40-53 7-20 (54)
330 PRK13890 conjugal transfer pro 33.7 38 0.00083 18.6 1.8 20 39-58 21-40 (120)
331 cd08313 Death_TNFR1 Death doma 33.2 71 0.0015 16.4 2.6 16 39-54 14-29 (80)
332 PF00356 LacI: Bacterial regul 32.9 48 0.0011 15.1 1.8 19 40-58 3-21 (46)
333 smart00550 Zalpha Z-DNA-bindin 32.7 45 0.00097 16.3 1.8 18 38-55 24-41 (68)
334 PRK10403 transcriptional regul 32.4 97 0.0021 17.4 4.0 38 15-58 153-190 (215)
335 cd08311 Death_p75NR Death doma 32.4 50 0.0011 16.8 1.9 17 40-56 19-35 (77)
336 PF08765 Mor: Mor transcriptio 32.1 65 0.0014 17.3 2.5 20 38-57 74-93 (108)
337 PF04550 Phage_holin_2: Phage 32.1 86 0.0019 16.7 2.9 28 34-61 59-87 (89)
338 cd08319 Death_RAIDD Death doma 32.0 43 0.00092 17.3 1.7 19 40-58 17-35 (83)
339 PHA02591 hypothetical protein; 32.0 47 0.001 17.3 1.8 18 39-56 62-79 (83)
340 COG1983 PspC Putative stress-r 31.6 47 0.001 16.8 1.7 19 39-57 18-36 (70)
341 PRK10360 DNA-binding transcrip 31.6 1E+02 0.0022 17.3 4.1 38 15-58 137-174 (196)
342 PF05344 DUF746: Domain of Unk 31.6 64 0.0014 16.1 2.2 20 39-58 16-35 (65)
343 TIGR00498 lexA SOS regulatory 31.1 59 0.0013 19.1 2.4 41 16-58 4-48 (199)
344 PF04936 DUF658: Protein of un 30.8 32 0.0007 20.5 1.2 25 38-62 16-41 (186)
345 PHA02535 P terminase ATPase su 30.5 1.5E+02 0.0032 21.3 4.4 39 15-58 2-40 (581)
346 PRK11426 hypothetical protein; 30.1 1.1E+02 0.0024 17.4 3.6 31 15-54 60-90 (132)
347 TIGR02612 mob_myst_A mobile my 30.0 59 0.0013 18.8 2.2 20 39-58 41-60 (150)
348 KOG0044|consensus 29.5 89 0.0019 18.9 3.0 27 32-58 7-33 (193)
349 cd08317 Death_ank Death domain 29.5 54 0.0012 16.7 1.8 17 39-55 18-34 (84)
350 PRK13719 conjugal transfer tra 29.2 1.5E+02 0.0032 18.4 4.4 39 14-58 142-180 (217)
351 PRK15201 fimbriae regulatory p 29.1 1.4E+02 0.0031 18.2 4.2 39 14-58 132-170 (198)
352 cd01670 Death Death Domain: a 28.7 63 0.0014 15.7 2.0 18 40-57 14-31 (79)
353 PF02954 HTH_8: Bacterial regu 28.6 60 0.0013 14.1 1.7 16 39-54 21-36 (42)
354 PRK11179 DNA-binding transcrip 28.4 51 0.0011 18.7 1.8 16 39-54 26-41 (153)
355 PF09012 FeoC: FeoC like trans 28.2 56 0.0012 15.8 1.7 17 39-55 17-33 (69)
356 PRK09935 transcriptional regul 28.1 1.2E+02 0.0026 17.1 4.0 38 15-58 149-186 (210)
357 PF04552 Sigma54_DBD: Sigma-54 28.1 20 0.00042 21.0 0.0 29 26-54 38-67 (160)
358 smart00354 HTH_LACI helix_turn 27.7 82 0.0018 15.3 2.3 20 39-58 3-22 (70)
359 cd08804 Death_ank2 Death domai 27.6 57 0.0012 16.8 1.7 15 40-54 19-33 (84)
360 cd08777 Death_RIP1 Death Domai 27.6 57 0.0012 16.9 1.7 16 40-55 17-32 (86)
361 smart00342 HTH_ARAC helix_turn 27.5 81 0.0018 14.9 2.4 18 40-57 5-22 (84)
362 TIGR03474 incFII_RepA incFII f 27.4 81 0.0018 20.0 2.6 31 20-50 67-97 (275)
363 PRK13750 replication protein; 27.2 84 0.0018 20.1 2.6 32 19-50 74-105 (285)
364 TIGR03020 EpsA transcriptional 27.2 1.6E+02 0.0036 18.4 5.3 40 13-58 188-227 (247)
365 PRK11552 putative DNA-binding 26.7 89 0.0019 18.8 2.7 37 23-61 21-58 (225)
366 TIGR02392 rpoH_proteo alternat 26.5 1.7E+02 0.0036 18.2 5.1 46 16-64 219-265 (270)
367 TIGR00122 birA_repr_reg BirA b 26.4 66 0.0014 15.4 1.8 19 39-57 16-34 (69)
368 cd08779 Death_PIDD Death Domai 26.4 60 0.0013 16.7 1.7 15 40-54 17-31 (86)
369 PF02387 IncFII_repA: IncFII R 26.1 26 0.00057 22.4 0.3 34 18-51 77-110 (281)
370 COG3415 Transposase and inacti 26.1 71 0.0015 18.3 2.0 21 38-58 23-43 (138)
371 PF02042 RWP-RK: RWP-RK domain 26.0 87 0.0019 14.8 3.2 27 21-54 7-33 (52)
372 PF11212 DUF2999: Protein of u 26.0 1.1E+02 0.0023 15.7 4.0 37 14-54 11-47 (82)
373 COG1846 MarR Transcriptional r 26.0 1.1E+02 0.0023 15.8 3.3 39 16-58 20-58 (126)
374 PF13022 HTH_Tnp_1_2: Helix-tu 25.9 1.4E+02 0.0031 17.2 3.8 23 38-60 36-59 (142)
375 PF00531 Death: Death domain; 25.8 61 0.0013 15.8 1.6 18 40-57 16-33 (83)
376 PF09339 HTH_IclR: IclR helix- 25.5 63 0.0014 14.6 1.5 18 38-55 20-37 (52)
377 PF13463 HTH_27: Winged helix 25.4 87 0.0019 14.6 3.2 37 17-56 2-38 (68)
378 TIGR00270 conserved hypothetic 25.0 82 0.0018 18.3 2.2 20 39-58 85-104 (154)
379 PF09581 Spore_III_AF: Stage I 24.6 38 0.00082 19.8 0.8 18 39-56 170-187 (188)
380 PF01978 TrmB: Sugar-specific 24.5 68 0.0015 15.3 1.6 19 39-57 25-43 (68)
381 TIGR02997 Sig70-cyanoRpoD RNA 24.2 2E+02 0.0043 18.2 4.3 42 16-58 250-291 (298)
382 COG2771 CsgD DNA-binding HTH d 24.0 85 0.0018 14.3 1.9 35 15-55 4-38 (65)
383 PRK09483 response regulator; P 23.9 1.5E+02 0.0033 16.8 4.1 39 14-58 147-185 (217)
384 COG1476 Predicted transcriptio 23.8 98 0.0021 15.5 2.1 18 39-56 17-34 (68)
385 PF06353 DUF1062: Protein of u 23.5 69 0.0015 18.4 1.7 19 40-58 107-125 (142)
386 PRK01381 Trp operon repressor; 23.5 75 0.0016 17.2 1.7 37 16-52 33-71 (99)
387 smart00005 DEATH DEATH domain, 23.5 80 0.0017 15.7 1.8 17 39-55 20-36 (88)
388 PRK15451 tRNA cmo(5)U34 methyl 23.5 1.9E+02 0.004 17.7 4.6 42 15-58 189-231 (247)
389 PF05848 CtsR: Firmicute trans 23.4 73 0.0016 18.6 1.8 18 38-55 27-44 (152)
390 PF04024 PspC: PspC domain; I 23.3 83 0.0018 15.2 1.7 19 39-57 17-35 (61)
391 COG2169 Ada Adenosine deaminas 23.2 1.5E+02 0.0032 18.0 3.1 34 23-58 86-119 (187)
392 PRK13870 transcriptional regul 23.1 1.2E+02 0.0025 18.6 2.7 20 39-58 191-210 (234)
393 smart00345 HTH_GNTR helix_turn 23.0 90 0.0019 13.9 2.2 21 38-58 22-42 (60)
394 PF06163 DUF977: Bacterial pro 23.0 1.3E+02 0.0029 17.1 2.7 44 15-58 4-48 (127)
395 PHA01083 hypothetical protein 22.8 87 0.0019 18.3 2.0 19 40-58 20-38 (149)
396 PF01022 HTH_5: Bacterial regu 22.8 78 0.0017 14.0 1.5 33 19-56 3-35 (47)
397 TIGR03541 reg_near_HchA LuxR f 22.5 1.9E+02 0.0042 17.5 5.1 40 13-58 169-208 (232)
398 PHA02681 ORF089 virion membran 22.5 1E+02 0.0022 16.2 2.0 19 14-32 50-68 (92)
399 COG3711 BglG Transcriptional a 22.2 1.8E+02 0.004 19.6 3.7 36 19-57 5-40 (491)
400 PRK08359 transcription factor; 22.2 97 0.0021 18.5 2.2 20 39-58 101-120 (176)
401 TIGR03624 putative hydrolase. 22.2 1.9E+02 0.0042 19.2 3.7 34 33-66 135-169 (345)
402 cd08784 Death_DRs Death Domain 22.1 95 0.0021 15.7 1.9 18 38-55 13-30 (79)
403 PTZ00183 centrin; Provisional 21.9 1.5E+02 0.0033 16.1 5.2 40 9-48 4-48 (158)
404 COG4197 Uncharacterized protei 21.8 80 0.0017 17.0 1.6 19 40-58 16-34 (96)
405 COG1654 BirA Biotin operon rep 21.6 81 0.0018 16.2 1.6 17 40-58 23-39 (79)
406 PF13545 HTH_Crp_2: Crp-like h 21.6 96 0.0021 14.9 1.8 21 37-57 29-49 (76)
407 PF08971 GlgS: Glycogen synthe 21.4 76 0.0016 15.9 1.4 16 47-63 36-51 (66)
408 PF15063 TC1: Thyroid cancer p 21.4 1.3E+02 0.0028 15.6 2.2 36 15-50 33-68 (79)
409 PRK15043 transcriptional regul 21.3 99 0.0022 19.4 2.2 19 39-57 6-24 (243)
410 PRK03573 transcriptional regul 21.2 1.6E+02 0.0035 16.2 4.0 37 15-54 28-64 (144)
411 TIGR01557 myb_SHAQKYF myb-like 21.1 1.2E+02 0.0025 14.5 3.8 47 12-58 2-51 (57)
412 PRK10046 dpiA two-component re 21.0 81 0.0018 18.7 1.7 19 39-57 180-198 (225)
413 PF13743 Thioredoxin_5: Thiore 20.9 1.9E+02 0.0041 16.8 3.4 38 21-58 86-125 (176)
414 PF08667 BetR: BetR domain; I 20.8 1.9E+02 0.0041 16.8 3.7 30 24-53 10-39 (147)
415 KOG0041|consensus 20.6 2.3E+02 0.005 17.7 3.7 37 16-52 93-134 (244)
416 PF13693 HTH_35: Winged helix- 20.6 1.4E+02 0.0031 15.3 2.3 18 38-57 43-60 (78)
417 PF03672 UPF0154: Uncharacteri 20.6 1.3E+02 0.0029 14.9 3.4 31 22-52 20-50 (64)
418 PRK06596 RNA polymerase factor 20.3 2.4E+02 0.0052 17.8 4.9 40 16-58 231-270 (284)
419 cd08316 Death_FAS_TNFRSF6 Deat 20.2 1.5E+02 0.0032 15.8 2.5 17 37-53 21-37 (97)
No 1
>KOG0489|consensus
Probab=99.88 E-value=5.7e-23 Score=126.08 Aligned_cols=67 Identities=34% Similarity=0.431 Sum_probs=62.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHcCCCcc
Q psy5355 6 DAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYALGMTES 72 (76)
Q Consensus 6 ~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~~~~~ 72 (76)
.+..+|.||.||..|+.+||..|..|.|++...|.+||..|.|+++||+|||| |||||||..+....
T Consensus 156 ~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~ 223 (261)
T KOG0489|consen 156 GGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSS 223 (261)
T ss_pred cCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhccccc
Confidence 45679999999999999999999999999999999999999999999999999 99999998766543
No 2
>KOG0850|consensus
Probab=99.87 E-value=3.4e-22 Score=119.03 Aligned_cols=70 Identities=39% Similarity=0.507 Sum_probs=64.4
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHcCCCccc
Q psy5355 4 DKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYALGMTESQ 73 (76)
Q Consensus 4 ~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~~~~~~ 73 (76)
++..|.|+.||.|+..||..|...|+.++|+...||.+||..|||+..||+|||| ||.|.||..+..+..
T Consensus 117 gk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~~ 187 (245)
T KOG0850|consen 117 GKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSGP 187 (245)
T ss_pred CCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCCc
Confidence 4566778999999999999999999999999999999999999999999999999 999999988865543
No 3
>KOG0488|consensus
Probab=99.86 E-value=3.9e-22 Score=124.58 Aligned_cols=64 Identities=39% Similarity=0.574 Sum_probs=60.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHcCC
Q psy5355 6 DAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYALGM 69 (76)
Q Consensus 6 ~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~~ 69 (76)
.++.++.||.||..|+..||..|+...|++..+|.+||..|||+..||++||| ||+|||++...
T Consensus 169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 36678889999999999999999999999999999999999999999999999 99999998655
No 4
>KOG0843|consensus
Probab=99.84 E-value=2.2e-21 Score=112.07 Aligned_cols=62 Identities=35% Similarity=0.515 Sum_probs=58.8
Q ss_pred CCCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHcCC
Q psy5355 8 KKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYALGM 69 (76)
Q Consensus 8 ~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~~ 69 (76)
+.+|.||.||+.|+..||.+|+.++|....+++.||..|+|++.||+|||| ||.|.||....
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e 163 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE 163 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence 578899999999999999999999999999999999999999999999999 99999987654
No 5
>KOG0484|consensus
Probab=99.84 E-value=9e-22 Score=105.07 Aligned_cols=63 Identities=30% Similarity=0.401 Sum_probs=59.3
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHcC
Q psy5355 6 DAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYALG 68 (76)
Q Consensus 6 ~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~ 68 (76)
.++.+|-||.||..|+..||..|...+||++..+++||..+.|++..|+|||| ||+|.+|+..
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence 35678899999999999999999999999999999999999999999999999 9999999753
No 6
>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=99.83 E-value=2.2e-20 Score=91.32 Aligned_cols=56 Identities=38% Similarity=0.452 Sum_probs=53.4
Q ss_pred CCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 10 KHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 10 ~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
++.|+.||+.|+..|+..|..++||+..++..||..|||+..+|.+||+ +|++.|+
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 4688999999999999999999999999999999999999999999999 9988875
No 7
>KOG0842|consensus
Probab=99.82 E-value=4.9e-21 Score=118.81 Aligned_cols=66 Identities=36% Similarity=0.495 Sum_probs=60.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHcCCCc
Q psy5355 6 DAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYALGMTE 71 (76)
Q Consensus 6 ~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~~~~ 71 (76)
..++||.|..||..|+.+||+.|....|++..||+.||..|+||+.||||||| +|-|.||+.....
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~ 216 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKA 216 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhh
Confidence 34677888999999999999999999999999999999999999999999999 9999999876543
No 8
>KOG0487|consensus
Probab=99.82 E-value=6.7e-21 Score=118.26 Aligned_cols=62 Identities=27% Similarity=0.338 Sum_probs=58.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHcC
Q psy5355 7 AKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYALG 68 (76)
Q Consensus 7 ~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~ 68 (76)
+..|++|.-||..|+.+||..|..|.|++...|.+|+..|+|+++||+|||| ||+|.||...
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 4568889999999999999999999999999999999999999999999999 9999999764
No 9
>KOG0485|consensus
Probab=99.80 E-value=4.5e-20 Score=109.53 Aligned_cols=63 Identities=44% Similarity=0.579 Sum_probs=59.4
Q ss_pred CCCCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHcCC
Q psy5355 7 AKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYALGM 69 (76)
Q Consensus 7 ~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~~ 69 (76)
..+++.||+|+..|+..||..|+...|++..++..||..|.|++.||+|||| ||.|||++...
T Consensus 102 ~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aa 165 (268)
T KOG0485|consen 102 DRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAA 165 (268)
T ss_pred cccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhh
Confidence 4678899999999999999999999999999999999999999999999999 99999997644
No 10
>KOG0848|consensus
Probab=99.79 E-value=3.8e-20 Score=112.50 Aligned_cols=64 Identities=30% Similarity=0.389 Sum_probs=58.1
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHcCC
Q psy5355 6 DAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYALGM 69 (76)
Q Consensus 6 ~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~~ 69 (76)
.+.+-+-|.+||+.|..+||..|..++|+++..+.+||..|||+++||+|||| ||+|++|..+.
T Consensus 196 tRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKK 260 (317)
T KOG0848|consen 196 TRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKK 260 (317)
T ss_pred eecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHH
Confidence 34445668899999999999999999999999999999999999999999999 99999997654
No 11
>KOG0494|consensus
Probab=99.78 E-value=2.2e-19 Score=109.02 Aligned_cols=60 Identities=28% Similarity=0.308 Sum_probs=55.8
Q ss_pred CCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHcCC
Q psy5355 10 KHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYALGM 69 (76)
Q Consensus 10 ~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~~ 69 (76)
+.-||.||..|+..||..|...+||+...++.||..++|++..|+|||| ||+||+|..+.
T Consensus 142 Rh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~ 202 (332)
T KOG0494|consen 142 RHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKR 202 (332)
T ss_pred ccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhh
Confidence 3339999999999999999999999999999999999999999999999 99999997543
No 12
>KOG0492|consensus
Probab=99.78 E-value=1.1e-19 Score=107.23 Aligned_cols=67 Identities=33% Similarity=0.465 Sum_probs=60.7
Q ss_pred CCCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHcCCCcccc
Q psy5355 8 KKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYALGMTESQV 74 (76)
Q Consensus 8 ~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~~~~~~~ 74 (76)
..+++||.||..|+..||+.|...+|+++.++.+++..|.|++.||+|||| ||+|.||.+....+.+
T Consensus 143 ~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~Ek~ 210 (246)
T KOG0492|consen 143 PNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELEKL 210 (246)
T ss_pred CCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHHHh
Confidence 457889999999999999999999999999999999999999999999999 9999999776544433
No 13
>KOG2251|consensus
Probab=99.78 E-value=2.7e-19 Score=106.21 Aligned_cols=65 Identities=32% Similarity=0.342 Sum_probs=61.1
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHcCC
Q psy5355 5 KDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYALGM 69 (76)
Q Consensus 5 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~~ 69 (76)
..++.+|.||.|+-.|+.+||..|.+.+||+...+++||.+|+|++.+|+|||. ||+|++++...
T Consensus 33 ~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q 98 (228)
T KOG2251|consen 33 GPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ 98 (228)
T ss_pred cchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence 346778999999999999999999999999999999999999999999999999 99999998765
No 14
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.76 E-value=3.1e-18 Score=98.26 Aligned_cols=70 Identities=27% Similarity=0.299 Sum_probs=62.7
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHcCCCccc
Q psy5355 4 DKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYALGMTESQ 73 (76)
Q Consensus 4 ~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~~~~~~ 73 (76)
+..+..++.|++.|..|+.+|+..|+.++||+...+..|+..|+|+++.|+|||| +|++.++.......+
T Consensus 46 ~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~~~ 116 (156)
T COG5576 46 DGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVEQ 116 (156)
T ss_pred cCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccchhc
Confidence 3446678889999999999999999999999999999999999999999999999 999999977664443
No 15
>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=99.75 E-value=1.2e-18 Score=85.18 Aligned_cols=49 Identities=20% Similarity=0.209 Sum_probs=48.1
Q ss_pred CCCCCCCCHHHHHHHHHhccccCC----CCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 10 KHTRPTFSGQQIFALEKTFEQTKY----LAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 10 ~r~R~~~t~~q~~~L~~~f~~~~~----p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
+|.||.||++|+..|+..|+.++| |+..++.+||..|||++.+|+||||
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfq 54 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMH 54 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecc
Confidence 688999999999999999999999 9999999999999999999999999
No 16
>KOG0493|consensus
Probab=99.75 E-value=2.1e-18 Score=104.87 Aligned_cols=61 Identities=34% Similarity=0.567 Sum_probs=57.6
Q ss_pred CCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHcCC
Q psy5355 9 KKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYALGM 69 (76)
Q Consensus 9 ~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~~ 69 (76)
-+|+||.||.+||..|...|..|.|++...+..||..|||.+.||+|||| +|+|.||..+.
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgs 307 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGS 307 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCC
Confidence 36789999999999999999999999999999999999999999999999 99999997654
No 17
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.73 E-value=1.3e-17 Score=81.03 Aligned_cols=53 Identities=42% Similarity=0.557 Sum_probs=49.6
Q ss_pred CCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHH
Q psy5355 11 HTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKL 63 (76)
Q Consensus 11 r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~ 63 (76)
+.|+.|++.++..|+..|..++||+..++..||..+||+..+|++||+ +|++.
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~ 55 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKW 55 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhcc
Confidence 567889999999999999999999999999999999999999999999 77654
No 18
>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=99.73 E-value=2.2e-17 Score=80.84 Aligned_cols=55 Identities=44% Similarity=0.561 Sum_probs=51.6
Q ss_pred CCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 11 HTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 11 r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
+.+..++..++..|+..|..++||+..++..||..+||+..+|++||+ +|++.++
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 467899999999999999999999999999999999999999999999 8887765
No 19
>KOG0491|consensus
Probab=99.72 E-value=1.7e-18 Score=99.13 Aligned_cols=62 Identities=39% Similarity=0.528 Sum_probs=58.0
Q ss_pred CCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHcCCC
Q psy5355 9 KKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYALGMT 70 (76)
Q Consensus 9 ~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~~~ 70 (76)
.++.|++|++.|+..|+..|+...|++..++.+||..|+|++.||+.||| +|+|.||+....
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~ 162 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNN 162 (194)
T ss_pred hhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhcc
Confidence 46779999999999999999999999999999999999999999999999 999999986544
No 20
>KOG0483|consensus
Probab=99.66 E-value=1.7e-16 Score=93.97 Aligned_cols=60 Identities=32% Similarity=0.324 Sum_probs=55.1
Q ss_pred CCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHcC
Q psy5355 9 KKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYALG 68 (76)
Q Consensus 9 ~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~ 68 (76)
...++.+++.+|+..||..|+.+.++.+..+..||..|||.++||.|||| |||+||.++-
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 34566789999999999999999999999999999999999999999999 9999997643
No 21
>KOG0486|consensus
Probab=99.65 E-value=4.6e-17 Score=100.87 Aligned_cols=63 Identities=30% Similarity=0.372 Sum_probs=59.2
Q ss_pred CCCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHcCCC
Q psy5355 8 KKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYALGMT 70 (76)
Q Consensus 8 ~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~~~ 70 (76)
+++|.|++|+..|+..||..|.+|.||+...+++||..++|++..|+|||. ||+||+|.....
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~ 174 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQ 174 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhH
Confidence 678889999999999999999999999999999999999999999999999 999999975543
No 22
>KOG0844|consensus
Probab=99.60 E-value=1.8e-16 Score=98.34 Aligned_cols=60 Identities=33% Similarity=0.445 Sum_probs=56.6
Q ss_pred CCCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 8 KKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 8 ~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
.-+|-||.||-+|+..||..|-+..|.+...+.+||..|+|++..|+|||| ||+|.|++.
T Consensus 180 qmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQR 240 (408)
T KOG0844|consen 180 QMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQR 240 (408)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhh
Confidence 457889999999999999999999999999999999999999999999999 999999974
No 23
>KOG0847|consensus
Probab=99.59 E-value=1.2e-15 Score=91.08 Aligned_cols=66 Identities=52% Similarity=0.725 Sum_probs=60.5
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHcCCC
Q psy5355 5 KDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYALGMT 70 (76)
Q Consensus 5 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~~~ 70 (76)
++++++..|..|+..|+..|+..|+...|+-.+++.+||..+||++.+|+|||| ||.||+|+....
T Consensus 163 kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaE 229 (288)
T KOG0847|consen 163 LNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAE 229 (288)
T ss_pred cCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccc
Confidence 456677788999999999999999999999999999999999999999999999 999999976543
No 24
>KOG4577|consensus
Probab=99.59 E-value=2.6e-15 Score=92.65 Aligned_cols=63 Identities=25% Similarity=0.259 Sum_probs=58.9
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHcC
Q psy5355 6 DAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYALG 68 (76)
Q Consensus 6 ~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~ 68 (76)
+...+|+||.+|+.|+..|...|...+.|....++.|+..+||.-+.|+|||| ||||+|+..+
T Consensus 164 d~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T KOG4577|consen 164 DASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T ss_pred ccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhh
Confidence 45578999999999999999999999999999999999999999999999999 9999998654
No 25
>KOG3802|consensus
Probab=99.58 E-value=5.5e-16 Score=98.56 Aligned_cols=62 Identities=23% Similarity=0.162 Sum_probs=58.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHcC
Q psy5355 7 AKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYALG 68 (76)
Q Consensus 7 ~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~ 68 (76)
+++|++||.|.......||.+|..|+.|+..++..||..|+|....|+|||+ ||.|.||-..
T Consensus 292 ~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 292 SRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred ccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 3678899999999999999999999999999999999999999999999999 9999888655
No 26
>KOG0490|consensus
Probab=99.48 E-value=2e-14 Score=86.40 Aligned_cols=63 Identities=29% Similarity=0.175 Sum_probs=58.9
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHcC
Q psy5355 6 DAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYALG 68 (76)
Q Consensus 6 ~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~ 68 (76)
..+.++.|+.|+..|+..|+..|+..+||+...++.||..+++++..|+|||| +|++++++..
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 35678899999999999999999999999999999999999999999999999 9999998763
No 27
>KOG0849|consensus
Probab=99.40 E-value=4.7e-13 Score=85.37 Aligned_cols=62 Identities=32% Similarity=0.357 Sum_probs=58.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 6 DAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 6 ~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
+++.++.|+.|+..|+..|+..|+.++||+...++.||..+++++..|+|||+ +|++++|..
T Consensus 173 ~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 173 QRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred cccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 45567789999999999999999999999999999999999999999999999 999999976
No 28
>KOG1168|consensus
Probab=99.12 E-value=1.8e-11 Score=75.91 Aligned_cols=60 Identities=23% Similarity=0.232 Sum_probs=55.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 7 AKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 7 ~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
..++|+||.+...+...||.+|...+.|+.+.+..+|.+|.|-...|+|||+ .|.|.||.
T Consensus 307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm 367 (385)
T KOG1168|consen 307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 367 (385)
T ss_pred cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHh
Confidence 4568889999999999999999999999999999999999999999999999 88888773
No 29
>KOG0775|consensus
Probab=99.04 E-value=3.2e-10 Score=69.74 Aligned_cols=49 Identities=27% Similarity=0.225 Sum_probs=43.8
Q ss_pred CCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHH
Q psy5355 16 FSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLA 64 (76)
Q Consensus 16 ~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~k 64 (76)
|...-...|..+|..++||+..++.+||+.+||+..||-.||. ||.++|
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 4445567999999999999999999999999999999999999 777776
No 30
>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=98.94 E-value=1.6e-09 Score=49.31 Aligned_cols=32 Identities=22% Similarity=0.255 Sum_probs=26.2
Q ss_pred ccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHH
Q psy5355 30 QTKYLAGPERAKLAYALGMTESQVKVTGP-ERA 61 (76)
Q Consensus 30 ~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~ 61 (76)
.++||+..++..||..+||+..||..||- .|.
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRr 39 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARR 39 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHc
Confidence 57999999999999999999999999998 443
No 31
>KOG2252|consensus
Probab=98.90 E-value=4.6e-09 Score=69.65 Aligned_cols=55 Identities=22% Similarity=0.169 Sum_probs=51.8
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 4 DKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 4 ~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
+.....+++|.+||+.|...|...|+.+++|+.+..+.|+.+|+|....|..||-
T Consensus 415 d~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFm 469 (558)
T KOG2252|consen 415 DKMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFM 469 (558)
T ss_pred cccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHH
Confidence 4456678899999999999999999999999999999999999999999999998
No 32
>KOG0774|consensus
Probab=98.87 E-value=1.3e-09 Score=66.91 Aligned_cols=58 Identities=24% Similarity=0.217 Sum_probs=52.9
Q ss_pred CCCCCCCCCHHHHHHHHHhcc---ccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 9 KKHTRPTFSGQQIFALEKTFE---QTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 9 ~~r~R~~~t~~q~~~L~~~f~---~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
.+|+|..|+.....+|..+|. .|+||+.+++++||.++|++..||..||. .|.+.+|.
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence 367788999999999999994 68999999999999999999999999999 88888874
No 33
>KOG0490|consensus
Probab=98.64 E-value=8.8e-08 Score=57.59 Aligned_cols=62 Identities=31% Similarity=0.374 Sum_probs=56.9
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 6 DAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 6 ~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
..+.++.++.+...++..+...|...++|+...+..|+..+|++...|++||+ +|++.++..
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~ 212 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHK 212 (235)
T ss_pred ccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhc
Confidence 35667889999999999999999999999999999999999999999999999 999988753
No 34
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=98.21 E-value=1.1e-06 Score=42.48 Aligned_cols=38 Identities=24% Similarity=0.141 Sum_probs=29.5
Q ss_pred HHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 21 IFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 21 ~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
+..|+.+|....++...+...|+.+.+|+..||+.||-
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa 47 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFA 47 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHH
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHH
Confidence 46699999999999999999999999999999999997
No 35
>KOG1146|consensus
Probab=98.12 E-value=3e-06 Score=61.20 Aligned_cols=61 Identities=20% Similarity=0.135 Sum_probs=56.2
Q ss_pred CCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHcCC
Q psy5355 9 KKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYALGM 69 (76)
Q Consensus 9 ~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~~ 69 (76)
++..|+.+++.|+..|...|....+|...+.+.|...++++.+.|.+||| .|++.++....
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n 964 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLN 964 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhc
Confidence 46679999999999999999999999999999999999999999999999 99998886543
No 36
>KOG0773|consensus
Probab=97.22 E-value=0.00022 Score=45.55 Aligned_cols=55 Identities=16% Similarity=0.064 Sum_probs=44.6
Q ss_pred CCCCCCCCCHHHHHHHHHhcc---ccCCCCHHHHHHHHHHhCCCchhHHHhhH--hHHHH
Q psy5355 9 KKHTRPTFSGQQIFALEKTFE---QTKYLAGPERAKLAYALGMTESQVKVTGP--ERAKL 63 (76)
Q Consensus 9 ~~r~R~~~t~~q~~~L~~~f~---~~~~p~~~~~~~La~~l~l~~~qV~vWFq--rR~k~ 63 (76)
..++...+......+|..... ..+||+..++..|+..+||+..||.+||- |++.|
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w 298 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLW 298 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccC
Confidence 345566888998998887742 36799999999999999999999999998 44444
No 37
>KOG3623|consensus
Probab=97.20 E-value=0.00095 Score=46.76 Aligned_cols=47 Identities=19% Similarity=0.085 Sum_probs=42.6
Q ss_pred HHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 21 IFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 21 ~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
+..|..+|..|..|+..+...+|.+.||+...|+.||+ .++......
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 67889999999999999999999999999999999999 877766644
No 38
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=96.55 E-value=0.011 Score=28.12 Aligned_cols=48 Identities=19% Similarity=0.330 Sum_probs=35.3
Q ss_pred CCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhHhHHH
Q psy5355 10 KHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPERAK 62 (76)
Q Consensus 10 ~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFqrR~k 62 (76)
++.|..+|..+-..+-..++... ....||..+|++..+|..|..++.+
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~~ 48 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKDK 48 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHHH
Confidence 46788999998888888887776 4668999999999999999984443
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=94.99 E-value=0.047 Score=26.12 Aligned_cols=39 Identities=23% Similarity=0.281 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHhccccCC--CCHHHHHHHHHHhCCCchhHH
Q psy5355 16 FSGQQIFALEKTFEQTKY--LAGPERAKLAYALGMTESQVK 54 (76)
Q Consensus 16 ~t~~q~~~L~~~f~~~~~--p~~~~~~~La~~l~l~~~qV~ 54 (76)
+|+.|..+|...+....| |-.....+||..||++...|.
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~ 41 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVS 41 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHH
Confidence 478899999999887775 555667899999999998654
No 40
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=94.14 E-value=0.14 Score=30.88 Aligned_cols=49 Identities=18% Similarity=0.268 Sum_probs=39.8
Q ss_pred CCCHHHHHHHHHhccccCC--CCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 15 TFSGQQIFALEKTFEQTKY--LAGPERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~--p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
-+|+.|+.+|...|....| |-......||..+|+++.. ++.. |||..|-
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst--~~ehLRrAe~Kl 206 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST--LSEHLRRAERKL 206 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH--HHHHHHHHHHHH
Confidence 6999999999999988774 6666778999999999985 5566 7766543
No 41
>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=93.86 E-value=0.064 Score=26.79 Aligned_cols=44 Identities=14% Similarity=0.207 Sum_probs=28.6
Q ss_pred CCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 11 HTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 11 r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
+.|..||+++...+-..+.. .......+|..+|+++.++..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~----~g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLE----SGESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHH----HHCHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHH----CCCceEeeecccccccccccHHHH
Confidence 35678999887777666521 223567899999999999999986
No 42
>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=93.02 E-value=0.09 Score=25.82 Aligned_cols=20 Identities=25% Similarity=0.325 Sum_probs=17.4
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
...||..||+++.+|..|=.
T Consensus 25 lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 25 LKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred HHHHHHHHCCCHHHHHHHhh
Confidence 45789999999999999964
No 43
>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=92.59 E-value=0.53 Score=21.64 Aligned_cols=39 Identities=13% Similarity=0.128 Sum_probs=29.7
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
.+++.+..+|...|... ..-.++|..+|++...|+.+..
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHH
Confidence 46788888888888333 2456889999999999998876
No 44
>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=91.94 E-value=0.68 Score=21.48 Aligned_cols=38 Identities=26% Similarity=0.170 Sum_probs=24.2
Q ss_pred CCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 16 FSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 16 ~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
+++.+..++...|-.. ..-.++|..+|++...|+.|..
T Consensus 11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHH
Confidence 3455555554444333 3567899999999999999997
No 45
>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=91.91 E-value=0.61 Score=20.83 Aligned_cols=38 Identities=16% Similarity=0.162 Sum_probs=27.9
Q ss_pred CCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 16 FSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 16 ~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
+++.+...+...|... .....+|..+|++...|..|..
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~ 48 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLH 48 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHH
Confidence 5666667776665322 2356789999999999999987
No 46
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=90.52 E-value=0.65 Score=21.04 Aligned_cols=40 Identities=20% Similarity=0.156 Sum_probs=20.8
Q ss_pred CCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 14 PTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 14 ~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
..+|.++...++..+... ....++|..+|.+...|.-+..
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 467888888888886644 3456799999999999887764
No 47
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=90.40 E-value=1.4 Score=25.80 Aligned_cols=31 Identities=23% Similarity=0.174 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHcC
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYALG 68 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~ 68 (76)
.-.++|..||++...|+++.. -|.+.++...
T Consensus 160 s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l~ 191 (194)
T PRK09646 160 TYREVAERLAVPLGTVKTRMRDGLIRLRDCLG 191 (194)
T ss_pred CHHHHHHHhCCChHhHHHHHHHHHHHHHHHhc
Confidence 456889999999999999998 6666666543
No 48
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=89.30 E-value=2.4 Score=23.31 Aligned_cols=43 Identities=16% Similarity=0.071 Sum_probs=29.3
Q ss_pred CCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 12 TRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 12 ~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
+|..||.+.....-.....+.. ....+|..+|+++.+|..|..
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHH
Confidence 4567888775544333333322 345789999999999999986
No 49
>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=89.16 E-value=0.15 Score=24.72 Aligned_cols=21 Identities=24% Similarity=0.177 Sum_probs=18.5
Q ss_pred HHHHHHHHhCCCchhHHHhhH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq 58 (76)
...++|..||++...|..|-+
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH
Confidence 356889999999999999985
No 50
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=88.38 E-value=1.7 Score=24.71 Aligned_cols=32 Identities=19% Similarity=0.041 Sum_probs=25.4
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHcCC
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYALGM 69 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~~ 69 (76)
...++|..+|++...|+++.. -|.+.++....
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~ 158 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKALLKE 158 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 456889999999999999998 66666665443
No 51
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=88.10 E-value=2.6 Score=24.15 Aligned_cols=46 Identities=17% Similarity=0.190 Sum_probs=34.3
Q ss_pred CCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 14 PTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 14 ~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
..+++.|..+|...+ .. ....++|..||++...|..|-. -+.+.++
T Consensus 5 ~~Lt~rqreVL~lr~-~G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 5 SFLTERQIEVLRLRE-RG-----LTQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred cCCCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 578899999987743 22 2456899999999999999998 4444444
No 52
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=88.09 E-value=2.2 Score=23.99 Aligned_cols=30 Identities=10% Similarity=-0.003 Sum_probs=23.4
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
.-.++|..+|++...|++... -|.+.++..
T Consensus 124 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 124 SYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 345789999999999999998 566555543
No 53
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=87.88 E-value=2.5 Score=24.02 Aligned_cols=29 Identities=17% Similarity=0.109 Sum_probs=22.9
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
...++|..+|++...|..|.. -+.+.++.
T Consensus 146 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 146 SYEEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 455789999999999999998 55555554
No 54
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=87.66 E-value=2.4 Score=23.60 Aligned_cols=26 Identities=23% Similarity=0.127 Sum_probs=20.8
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKL 63 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~ 63 (76)
...++|..+|++...|+.+.. -+.+.
T Consensus 124 s~~EIA~~l~is~~tV~~~~~ra~~~L 150 (154)
T PRK06759 124 TMGEIALETEMTYYQVRWIYRQALEKM 150 (154)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 466899999999999999987 34333
No 55
>PF13518 HTH_28: Helix-turn-helix domain
Probab=87.51 E-value=0.83 Score=20.83 Aligned_cols=20 Identities=20% Similarity=0.134 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++..+|..|.+
T Consensus 15 ~~~~a~~~gis~~tv~~w~~ 34 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIK 34 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHH
Confidence 45689999999999999996
No 56
>PRK00118 putative DNA-binding protein; Validated
Probab=87.22 E-value=3.3 Score=22.50 Aligned_cols=46 Identities=11% Similarity=0.019 Sum_probs=31.0
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
.+++.+..++...|.... ...++|..+|++...|..|.. -+.+.+.
T Consensus 17 ~L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 17 LLTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 345556666655444332 456789999999999999997 5554443
No 57
>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=86.94 E-value=1.8 Score=21.09 Aligned_cols=48 Identities=15% Similarity=0.217 Sum_probs=23.3
Q ss_pred CCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhHhHH
Q psy5355 13 RPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPERA 61 (76)
Q Consensus 13 R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFqrR~ 61 (76)
|..|+.......-.++.....--...+ ..|.++|+++.+|+-|-+...
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~~~~R-Aaarkf~V~r~~Vr~W~kqe~ 50 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCKGNQR-AAARKFNVSRRQVRKWRKQEE 50 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTTT-HH-HHHHHTTS-HHHHHHHHTTHH
T ss_pred ccccChHHHHHHHHHHHHccchhhhHH-HHHHHhCccHHHHHHHHHHHH
Confidence 345565443333333333221111223 359999999999999997333
No 58
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=86.88 E-value=2.9 Score=24.84 Aligned_cols=30 Identities=27% Similarity=0.224 Sum_probs=23.5
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
...++|..+|++...|+++.. -+.+.++..
T Consensus 171 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 171 SQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999987 555555544
No 59
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=86.59 E-value=3.5 Score=23.69 Aligned_cols=29 Identities=14% Similarity=-0.032 Sum_probs=23.3
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
...++|..+|++...|+++.. -|.+.++.
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 456889999999999999998 56655554
No 60
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=86.46 E-value=3.6 Score=23.71 Aligned_cols=31 Identities=29% Similarity=0.212 Sum_probs=24.4
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHcC
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYALG 68 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~ 68 (76)
.-.++|..+|++...|+.++. -+.+.+....
T Consensus 149 s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 149 SIKETAAKLSMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 456889999999999999998 6666665443
No 61
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=86.43 E-value=2.9 Score=23.64 Aligned_cols=29 Identities=24% Similarity=0.177 Sum_probs=23.0
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
...++|..+|++...|..|.. -+.+.++.
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456899999999999999998 55555543
No 62
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=86.24 E-value=0.78 Score=20.90 Aligned_cols=21 Identities=24% Similarity=0.128 Sum_probs=17.1
Q ss_pred HHHHHHHHhCCCchhHHHhhH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq 58 (76)
...++|..+|++...|..|..
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~k 39 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIK 39 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 456889999999999999985
No 63
>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=86.19 E-value=3.3 Score=23.15 Aligned_cols=28 Identities=29% Similarity=0.173 Sum_probs=21.4
Q ss_pred HHHHHHHHHhCCCchhHHHhhH-hHHHHH
Q psy5355 37 PERAKLAYALGMTESQVKVTGP-ERAKLA 64 (76)
Q Consensus 37 ~~~~~La~~l~l~~~qV~vWFq-rR~k~k 64 (76)
....++|..+|++...|.++.. -|.+.+
T Consensus 128 ~~~~eIA~~l~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 128 VSLTALAEQLGRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 3456889999999999999887 444443
No 64
>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=86.12 E-value=1.1 Score=20.17 Aligned_cols=20 Identities=20% Similarity=0.207 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...|+.|.+
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~ 22 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYER 22 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999986
No 65
>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=85.88 E-value=0.25 Score=25.21 Aligned_cols=31 Identities=26% Similarity=0.219 Sum_probs=22.6
Q ss_pred ccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 28 FEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 28 f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
|....+.......++|..+|+++..|+.|+.
T Consensus 24 f~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~ 54 (73)
T TIGR03879 24 AALAREEAGKTASEIAEELGRTEQTVRNHLK 54 (73)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHh
Confidence 3333333334567899999999999999986
No 66
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=85.86 E-value=4 Score=23.43 Aligned_cols=28 Identities=29% Similarity=0.203 Sum_probs=22.2
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
.-.++|..+|+++..|++... -|.+.++
T Consensus 152 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 152 TVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 456789999999999999987 5555554
No 67
>PRK04217 hypothetical protein; Provisional
Probab=85.72 E-value=4.2 Score=22.30 Aligned_cols=49 Identities=16% Similarity=0.076 Sum_probs=35.2
Q ss_pred CCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 14 PTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 14 ~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
..++..+..++...+.... ...++|..+|++...|...+. -+.+.+...
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4577888777766654332 456799999999999998887 555555443
No 68
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=85.66 E-value=2.9 Score=24.19 Aligned_cols=31 Identities=13% Similarity=0.113 Sum_probs=25.0
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHcC
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYALG 68 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~ 68 (76)
...++|..+|++...|+.... -|.+.++...
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999998 6777666543
No 69
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=85.44 E-value=1 Score=21.87 Aligned_cols=19 Identities=21% Similarity=0.298 Sum_probs=16.9
Q ss_pred HHHHHHhCCCchhHHHhhH
Q psy5355 40 AKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 40 ~~La~~l~l~~~qV~vWFq 58 (76)
.++|..+|++..+|+.|=.
T Consensus 4 ~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999964
No 70
>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=85.41 E-value=2.8 Score=24.16 Aligned_cols=33 Identities=18% Similarity=0.155 Sum_probs=25.0
Q ss_pred CHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 35 AGPERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 35 ~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
....-.++|..+|++...|+++.. -|.+.++..
T Consensus 153 ~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 153 EGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 333457899999999999999997 566655543
No 71
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=84.97 E-value=4 Score=23.98 Aligned_cols=32 Identities=28% Similarity=0.276 Sum_probs=25.4
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHcCC
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYALGM 69 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~~ 69 (76)
...++|..+|++...|+++.. -|.+.++....
T Consensus 131 s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~ 163 (188)
T PRK12546 131 SYEEAAEMCGVAVGTVKSRANRARARLAELLQL 163 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 456889999999999999998 66666665443
No 72
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=84.83 E-value=3.5 Score=24.00 Aligned_cols=30 Identities=27% Similarity=0.306 Sum_probs=23.6
Q ss_pred HHHHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 36 GPERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 36 ~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
.....++|..+|++...|+.++. -+.+.++
T Consensus 157 g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 157 GLSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 33556899999999999999998 5555554
No 73
>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=84.66 E-value=4.6 Score=22.36 Aligned_cols=27 Identities=19% Similarity=0.194 Sum_probs=21.1
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLA 64 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~k 64 (76)
...++|..+|+++..|+.+.. -+.+.+
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALKELR 158 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 456789999999999999887 444444
No 74
>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=84.36 E-value=5.1 Score=22.52 Aligned_cols=31 Identities=32% Similarity=0.308 Sum_probs=24.4
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHcC
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYALG 68 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~ 68 (76)
.-.++|..+|++...|+.+-. -+.+.++...
T Consensus 128 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 159 (162)
T TIGR02983 128 SEAQVAEALGISVGTVKSRLSRALARLRELLE 159 (162)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 456889999999999999988 6666666543
No 75
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=84.32 E-value=4.8 Score=23.58 Aligned_cols=30 Identities=17% Similarity=0.174 Sum_probs=24.1
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
.-.++|..+|++...|+.+.. -|.+.++..
T Consensus 154 s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 154 SNPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999998 566666643
No 76
>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=84.28 E-value=4.8 Score=21.73 Aligned_cols=27 Identities=30% Similarity=0.302 Sum_probs=21.3
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLA 64 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~k 64 (76)
...++|..+|+++..|..+.. -+.+.+
T Consensus 128 s~~eIA~~l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 128 SYKEIAEILGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 456889999999999999997 444444
No 77
>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=83.88 E-value=5 Score=22.99 Aligned_cols=29 Identities=28% Similarity=0.267 Sum_probs=22.6
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
...++|..+|++...|+++.. -|.+.+..
T Consensus 118 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 147 (170)
T TIGR02959 118 SQQEIAEKLGLSLSGAKSRVQRGRKKLKEL 147 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999987 55555543
No 78
>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=83.85 E-value=5.5 Score=22.45 Aligned_cols=28 Identities=39% Similarity=0.316 Sum_probs=21.7
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
.-.++|..+|++...|+.... -|.+.++
T Consensus 140 s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 140 PIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 456889999999999999887 5555544
No 79
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=83.69 E-value=5.8 Score=22.93 Aligned_cols=28 Identities=25% Similarity=0.132 Sum_probs=21.7
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
...++|..+|++...|+++.. -+.+.+.
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 456889999999999999987 4444443
No 80
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=83.65 E-value=4.2 Score=22.93 Aligned_cols=29 Identities=31% Similarity=0.323 Sum_probs=22.8
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
...++|..+|++...|+.+.. -+.+.++.
T Consensus 129 s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~ 158 (166)
T PRK09639 129 SYKEIAEALGIKESSVGTTLARAKKKFRKI 158 (166)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999987 55555554
No 81
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=83.62 E-value=5.1 Score=23.41 Aligned_cols=28 Identities=14% Similarity=0.146 Sum_probs=22.2
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
...++|..+|+++..|+++.. -|.+.++
T Consensus 152 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 152 SSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 456889999999999999987 4555444
No 82
>PRK10072 putative transcriptional regulator; Provisional
Probab=83.58 E-value=4.3 Score=21.69 Aligned_cols=37 Identities=24% Similarity=0.102 Sum_probs=26.5
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
..+...+..|......+ ..+||..+|++...|..|..
T Consensus 32 ~~~~~eik~LR~~~glT-------Q~elA~~lGvS~~TVs~WE~ 68 (96)
T PRK10072 32 TTSFTEFEQLRKGTGLK-------IDDFARVLGVSVAMVKEWES 68 (96)
T ss_pred cCChHHHHHHHHHcCCC-------HHHHHHHhCCCHHHHHHHHc
Confidence 34666666664433222 56889999999999999998
No 83
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=83.56 E-value=5.3 Score=23.15 Aligned_cols=29 Identities=28% Similarity=0.265 Sum_probs=22.6
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
...++|..+|++...|+.+.. -+.+.++.
T Consensus 157 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 157 SAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999887 55555543
No 84
>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=83.43 E-value=1.5 Score=19.27 Aligned_cols=19 Identities=16% Similarity=0.272 Sum_probs=15.2
Q ss_pred HHHHHHhCCCchhHHHhhH
Q psy5355 40 AKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 40 ~~La~~l~l~~~qV~vWFq 58 (76)
.++|..+|++...|+.|=.
T Consensus 3 ~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp HHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHHH
Confidence 4789999999999998853
No 85
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=83.42 E-value=4.7 Score=23.16 Aligned_cols=30 Identities=17% Similarity=0.089 Sum_probs=23.4
Q ss_pred HHHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 37 PERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 37 ~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
..-.++|..+|++...|++... -|.+.+..
T Consensus 153 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 153 LSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3456889999999999999998 55555543
No 86
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=83.20 E-value=5.1 Score=22.55 Aligned_cols=28 Identities=18% Similarity=0.188 Sum_probs=21.5
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
...++|..+|++...|+++.. -|.+.++
T Consensus 130 s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 130 SYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 456889999999999999887 4544443
No 87
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=82.94 E-value=6.2 Score=22.38 Aligned_cols=30 Identities=20% Similarity=0.153 Sum_probs=23.5
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
...++|..+|+++..|+++.. -|.+.+...
T Consensus 130 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 130 SYEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999998 555555443
No 88
>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=82.90 E-value=2.3 Score=16.89 Aligned_cols=38 Identities=18% Similarity=0.189 Sum_probs=25.3
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhh
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTG 57 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWF 57 (76)
.++......+...+.... ....+|..+|++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~~~-----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAAGE-----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHhC
Confidence 355666665655554321 34578899999999888773
No 89
>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=82.50 E-value=2.2 Score=20.43 Aligned_cols=35 Identities=26% Similarity=0.312 Sum_probs=25.0
Q ss_pred HHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhh
Q psy5355 19 QQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTG 57 (76)
Q Consensus 19 ~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWF 57 (76)
.++..|+-.+. +...+.. +||..+|+++..|+.-.
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 35667777777 6666544 78999999999887644
No 90
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=82.37 E-value=6.4 Score=22.01 Aligned_cols=29 Identities=34% Similarity=0.344 Sum_probs=22.5
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
...++|..+|++...|++... -+.+.+..
T Consensus 124 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 124 DVAETAAAMGCSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 356889999999999999887 55555543
No 91
>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=81.32 E-value=7.3 Score=22.11 Aligned_cols=29 Identities=21% Similarity=0.088 Sum_probs=22.4
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
...++|..+|++...|++... -|.+.++.
T Consensus 137 s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 137 TIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999887 55555543
No 92
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=80.98 E-value=8.4 Score=22.21 Aligned_cols=30 Identities=33% Similarity=0.238 Sum_probs=23.9
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
...++|..+|++...|++... -|.+.++..
T Consensus 147 s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l 177 (181)
T PRK12536 147 SVAETAQLTGLSESAVKVGIHRGLKALAAKI 177 (181)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 456889999999999999998 666666543
No 93
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=80.82 E-value=7.3 Score=22.64 Aligned_cols=29 Identities=28% Similarity=0.271 Sum_probs=22.6
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
...++|..+|++...|+..+. -|.+.++.
T Consensus 124 ~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (181)
T PRK09637 124 SQKEIAEKLGLSLSGAKSRVQRGRVKLKEL 153 (181)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999887 55555543
No 94
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=80.70 E-value=8 Score=21.98 Aligned_cols=30 Identities=33% Similarity=0.338 Sum_probs=23.0
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
...++|..||+++..|+.... -+.+.++..
T Consensus 136 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 136 STAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 356889999999999999887 555555543
No 95
>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=80.67 E-value=2 Score=20.85 Aligned_cols=20 Identities=5% Similarity=0.140 Sum_probs=17.3
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|-+
T Consensus 3 i~evA~~~gvs~~tlR~~~~ 22 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEK 22 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999975
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=80.46 E-value=2.3 Score=20.72 Aligned_cols=20 Identities=10% Similarity=0.126 Sum_probs=17.3
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|.+
T Consensus 3 i~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999975
No 97
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=80.46 E-value=8 Score=22.43 Aligned_cols=30 Identities=33% Similarity=0.314 Sum_probs=23.2
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
...++|..+|++...|++-.. -|.+.++..
T Consensus 149 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 149 SVEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 456789999999999998887 566665543
No 98
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=80.39 E-value=8.9 Score=22.08 Aligned_cols=29 Identities=17% Similarity=0.203 Sum_probs=21.9
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
.-.++|..+|++...|+.+.. -|.+.+..
T Consensus 153 s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~ 182 (186)
T PRK13919 153 THREAAQLLGLPLGTLKTRARRALSRLKEV 182 (186)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999887 45554443
No 99
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=80.31 E-value=4 Score=24.91 Aligned_cols=31 Identities=19% Similarity=0.147 Sum_probs=24.6
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHcC
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYALG 68 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~ 68 (76)
.-.++|..+|++...|++... -|.+.++...
T Consensus 189 s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 189 SNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 456899999999999999998 6666666543
No 100
>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=79.92 E-value=3.5 Score=18.57 Aligned_cols=38 Identities=21% Similarity=0.234 Sum_probs=24.3
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhh
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTG 57 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWF 57 (76)
.+++.+...+...+... .....+|..+|++...|.-++
T Consensus 5 ~~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 35555555555555554 246689999999999887655
No 101
>PRK06930 positive control sigma-like factor; Validated
Probab=79.42 E-value=9.4 Score=22.37 Aligned_cols=46 Identities=13% Similarity=0.020 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 16 FSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 16 ~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
+++.+..++...|... ..-.++|..+|++...|+.+.. -+.+.++.
T Consensus 115 L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~ 161 (170)
T PRK06930 115 LTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIERAEKKIARQ 161 (170)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4455555554433222 2356789999999999999997 55555443
No 102
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=79.40 E-value=8.9 Score=21.52 Aligned_cols=29 Identities=14% Similarity=0.130 Sum_probs=22.7
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
...++|..+|++...|+.... -+.+.++.
T Consensus 127 s~~EIA~~lgis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 127 TQKDIARELGVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999877 55555554
No 103
>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=79.07 E-value=5.3 Score=18.76 Aligned_cols=38 Identities=18% Similarity=0.271 Sum_probs=28.5
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
.+|+.+..+|.-...-. ...++|..+|+++..|.....
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~ 40 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRR 40 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHH
Confidence 47788888876665544 366889999999999998775
No 104
>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=79.03 E-value=3 Score=23.16 Aligned_cols=33 Identities=18% Similarity=0.085 Sum_probs=24.9
Q ss_pred CCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 33 YLAGPERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 33 ~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
|.....-.++|..+|+++..|+++.. -|.+.++
T Consensus 118 ~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 118 EFKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34445567899999999999999987 5555544
No 105
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=78.54 E-value=8.4 Score=22.39 Aligned_cols=28 Identities=18% Similarity=0.114 Sum_probs=22.3
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
.-.++|..+|+++..|++... -|.+.++
T Consensus 148 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 148 SYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 456889999999999999987 5555554
No 106
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=78.47 E-value=11 Score=21.85 Aligned_cols=30 Identities=37% Similarity=0.285 Sum_probs=23.8
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
...++|..+|++...|+.+.. -+.+.++..
T Consensus 149 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 149 SVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999998 566665543
No 107
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=78.27 E-value=9.4 Score=22.21 Aligned_cols=28 Identities=29% Similarity=0.318 Sum_probs=22.1
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
...++|..+|++...|+...+ -|.+.++
T Consensus 149 s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 149 KIEEIAKKLGLTRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 356889999999999999987 5555554
No 108
>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=78.21 E-value=3.3 Score=18.08 Aligned_cols=20 Identities=20% Similarity=0.142 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...|..|..
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~ 22 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVK 22 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999987
No 109
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=77.93 E-value=10 Score=22.93 Aligned_cols=29 Identities=21% Similarity=0.261 Sum_probs=23.3
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
...++|..+|++...|+.+.. -+.+.++.
T Consensus 202 s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 202 NLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456899999999999999998 55555553
No 110
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=77.85 E-value=11 Score=21.69 Aligned_cols=30 Identities=20% Similarity=0.084 Sum_probs=23.8
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
...++|..+|++...|++... -+.+.++..
T Consensus 135 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 165 (179)
T PRK12543 135 SQEEIAQLLQIPIGTVKSRIHAALKKLRQKE 165 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999988 666666543
No 111
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=77.81 E-value=10 Score=22.14 Aligned_cols=29 Identities=21% Similarity=0.095 Sum_probs=22.8
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
.-.++|..+|++...|++... -|.+.++.
T Consensus 129 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 158 (182)
T PRK12511 129 SYQEAAAVLGIPIGTLMSRIGRARAALRAF 158 (182)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999987 55555554
No 112
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=77.53 E-value=4.8 Score=22.93 Aligned_cols=35 Identities=23% Similarity=0.133 Sum_probs=26.5
Q ss_pred CCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 33 YLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 33 ~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
|.....-.++|..+|++...|++.+. -|.+.++..
T Consensus 133 ~~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 133 DLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 33444567899999999999999998 666666543
No 113
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=77.50 E-value=10 Score=22.17 Aligned_cols=31 Identities=19% Similarity=0.129 Sum_probs=24.0
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHcC
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYALG 68 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~ 68 (76)
.-.++|..||++...|++... -|.+.++...
T Consensus 134 s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 134 AYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 345789999999999999998 5665555443
No 114
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=77.13 E-value=11 Score=22.31 Aligned_cols=30 Identities=17% Similarity=0.088 Sum_probs=23.3
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
.-.++|..+|++...|+++.. -|.+.++..
T Consensus 151 s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l 181 (196)
T PRK12535 151 TYEEAAKIADVRVGTIRSRVARARADLIAAT 181 (196)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 456889999999999999987 555555543
No 115
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=76.97 E-value=11 Score=22.03 Aligned_cols=29 Identities=14% Similarity=0.166 Sum_probs=23.0
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
.-.++|..+|++...|+.... -|.+.++.
T Consensus 154 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 183 (195)
T PRK12532 154 SSDEIQQMCGISTSNYHTIMHRARESLRQC 183 (195)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456899999999999999988 55555554
No 116
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=76.56 E-value=12 Score=21.76 Aligned_cols=30 Identities=17% Similarity=0.108 Sum_probs=23.9
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
.-.++|..+|+++..|++... -|.+.++..
T Consensus 156 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 156 SYEDIASVMQCPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 456899999999999999988 666666543
No 117
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=76.42 E-value=12 Score=21.56 Aligned_cols=29 Identities=17% Similarity=0.303 Sum_probs=22.7
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
.-.++|..+|++...|++... -|.+.++.
T Consensus 140 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 169 (185)
T PRK12542 140 TYQEISSVMGITEANVRKQFERARKRVQNM 169 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999887 55555553
No 118
>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=76.20 E-value=5.1 Score=18.48 Aligned_cols=32 Identities=19% Similarity=0.267 Sum_probs=19.2
Q ss_pred HHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhh
Q psy5355 23 ALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTG 57 (76)
Q Consensus 23 ~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWF 57 (76)
.|...+....+.+ ..+||..+|++.+.|..-.
T Consensus 5 il~~L~~~~~~it---~~eLa~~l~vS~rTi~~~i 36 (55)
T PF08279_consen 5 ILKLLLESKEPIT---AKELAEELGVSRRTIRRDI 36 (55)
T ss_dssp HHHHHHHTTTSBE---HHHHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHcCCCcC---HHHHHHHhCCCHHHHHHHH
Confidence 3333334444333 4478999999999887544
No 119
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=76.11 E-value=11 Score=22.74 Aligned_cols=30 Identities=20% Similarity=0.122 Sum_probs=23.7
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
.-.++|..+|+++..|++... -|.+.++..
T Consensus 152 s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 152 SYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999987 566665543
No 120
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=75.92 E-value=14 Score=22.74 Aligned_cols=29 Identities=21% Similarity=0.189 Sum_probs=22.5
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
...++|..+|++...|+.|.. -+.+.+..
T Consensus 223 s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 223 SQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999987 55555543
No 121
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=75.90 E-value=13 Score=22.10 Aligned_cols=29 Identities=24% Similarity=0.245 Sum_probs=22.6
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
.-.++|..||++...|+++.. -|.+.++.
T Consensus 156 s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~ 185 (203)
T PRK09647 156 SYEEIAATLGVKLGTVRSRIHRGRQQLRAA 185 (203)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 345789999999999999998 55555543
No 122
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=75.74 E-value=13 Score=21.55 Aligned_cols=29 Identities=21% Similarity=0.180 Sum_probs=22.4
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
.-.++|..+|++...|++... -|.+.++.
T Consensus 149 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (191)
T PRK12520 149 ETEEICQELQITATNAWVLLYRARMRLREC 178 (191)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 356889999999999999987 55555443
No 123
>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=75.65 E-value=13 Score=21.64 Aligned_cols=29 Identities=21% Similarity=0.190 Sum_probs=22.8
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
...++|..+|++...|+.... -|.+.++.
T Consensus 149 s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~ 178 (188)
T TIGR02943 149 ESDEICQELEISTSNCHVLLYRARLSLRAC 178 (188)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999887 55555554
No 124
>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=75.49 E-value=5.5 Score=23.13 Aligned_cols=30 Identities=17% Similarity=0.150 Sum_probs=22.8
Q ss_pred HHHHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 36 GPERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 36 ~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
.....++|..+|++...|++.+. -|.+.++
T Consensus 165 ~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 165 GKSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 33456889999999999999987 5555444
No 125
>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=75.01 E-value=6 Score=23.03 Aligned_cols=34 Identities=21% Similarity=0.172 Sum_probs=25.8
Q ss_pred CCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 34 LAGPERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 34 p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
.....-.++|..+|++...|+++.. -|.+.++..
T Consensus 145 ~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 145 VEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3334566899999999999999998 566666543
No 126
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=75.01 E-value=14 Score=21.59 Aligned_cols=32 Identities=19% Similarity=0.140 Sum_probs=24.6
Q ss_pred HHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 36 GPERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 36 ~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
...-.++|..+|++...|++-.. -|.+.++..
T Consensus 170 ~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l 202 (208)
T PRK08295 170 GKSYQEIAEELNRHVKSIDNALQRVKRKLEKYL 202 (208)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 33456889999999999999887 666666544
No 127
>PF13730 HTH_36: Helix-turn-helix domain
Probab=74.88 E-value=6.8 Score=18.01 Aligned_cols=42 Identities=17% Similarity=0.097 Sum_probs=26.0
Q ss_pred CCHHHHHHHHHhcc---ccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 16 FSGQQIFALEKTFE---QTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 16 ~t~~q~~~L~~~f~---~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
+++.+..++..... .+.. ..+....||..+|++.+.|.-+..
T Consensus 3 Ls~~~~~v~~~l~~~~~~~~~-~~pS~~~la~~~g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 3 LSPTAKLVYLYLASYANKNGG-CFPSQETLAKDLGVSRRTVQRAIK 47 (55)
T ss_pred CCHHHHHHHHHHHHhcCCCCC-CCcCHHHHHHHHCcCHHHHHHHHH
Confidence 44555554444432 2222 333566899999999999987764
No 128
>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=74.69 E-value=4.2 Score=19.55 Aligned_cols=20 Identities=10% Similarity=0.114 Sum_probs=17.2
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...+..|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999975
No 129
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=74.20 E-value=14 Score=21.07 Aligned_cols=30 Identities=27% Similarity=0.216 Sum_probs=22.8
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
.-.++|..+|++...|++... -+.+.+...
T Consensus 137 s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l 167 (172)
T PRK12523 137 GHAEIAERLGVSVSRVRQYLAQGLRQCYIAL 167 (172)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 456889999999999999997 455554433
No 130
>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=73.95 E-value=14 Score=22.74 Aligned_cols=28 Identities=14% Similarity=0.082 Sum_probs=22.1
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
...++|..+|++...|+++.. -|.+.++
T Consensus 179 S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~ 207 (244)
T TIGR03001 179 SMDRIGAMYQVHRSTVSRWVAQARERLLE 207 (244)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 456889999999999999998 4444444
No 131
>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=73.71 E-value=16 Score=21.91 Aligned_cols=21 Identities=19% Similarity=0.265 Sum_probs=18.6
Q ss_pred HHHHHHHHhCCCchhHHHhhH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq 58 (76)
...++|..+|++...|..+..
T Consensus 196 s~~eIA~~lgis~~~v~~~~~ 216 (227)
T TIGR02980 196 TQSEIAERLGISQMHVSRLLR 216 (227)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 456889999999999999986
No 132
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=73.48 E-value=17 Score=21.88 Aligned_cols=29 Identities=17% Similarity=0.196 Sum_probs=22.5
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
.-.++|..+|++...|+.+.. -+.+.++.
T Consensus 200 s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 200 TQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999987 55555543
No 133
>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=73.20 E-value=17 Score=21.76 Aligned_cols=28 Identities=29% Similarity=0.306 Sum_probs=21.5
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
...++|..+|++...|+.+.. -+.+.++
T Consensus 193 s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 193 NLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 456889999999999999887 4444443
No 134
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=73.07 E-value=14 Score=20.67 Aligned_cols=30 Identities=17% Similarity=0.149 Sum_probs=22.2
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
...++|..+|++...|+.... -+.+.+...
T Consensus 123 s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l 153 (159)
T PRK12527 123 SHQQIAEHLGISRSLVEKHIVNAMKHCRVRM 153 (159)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 456789999999999998877 455555443
No 135
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=73.06 E-value=6.8 Score=20.81 Aligned_cols=39 Identities=18% Similarity=0.174 Sum_probs=26.8
Q ss_pred CCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHH
Q psy5355 16 FSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVK 54 (76)
Q Consensus 16 ~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~ 54 (76)
++++|...-...|+.|--.+....+++|..|++++--|.
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~le 41 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLE 41 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHH
Confidence 456676666666666655555667788999998886554
No 136
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=72.88 E-value=17 Score=21.45 Aligned_cols=29 Identities=21% Similarity=0.206 Sum_probs=22.8
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
.-.++|..+|++...|++... -|.+.++.
T Consensus 157 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 186 (201)
T PRK12545 157 EIDDICTELTLTANHCSVLLYRARTRLRTC 186 (201)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999987 55555553
No 137
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=72.53 E-value=2.4 Score=26.76 Aligned_cols=27 Identities=26% Similarity=0.386 Sum_probs=21.5
Q ss_pred CCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 32 KYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 32 ~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
.|........||..||+++.+|+.|=+
T Consensus 15 ~yl~gmk~~dIAeklGvspntiksWKr 41 (279)
T COG5484 15 DYLKGMKLKDIAEKLGVSPNTIKSWKR 41 (279)
T ss_pred HHHhhccHHHHHHHhCCChHHHHHHHH
Confidence 344444567899999999999999985
No 138
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=72.24 E-value=17 Score=21.16 Aligned_cols=31 Identities=23% Similarity=0.131 Sum_probs=24.0
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHcC
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYALG 68 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~ 68 (76)
...++|..||++...|+.... -|.+.++...
T Consensus 129 s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 129 SYEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999987 5655555544
No 139
>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=71.62 E-value=3.9 Score=19.25 Aligned_cols=15 Identities=53% Similarity=0.713 Sum_probs=12.2
Q ss_pred HHHHHHhCCCchhHH
Q psy5355 40 AKLAYALGMTESQVK 54 (76)
Q Consensus 40 ~~La~~l~l~~~qV~ 54 (76)
.+||..+|++..||+
T Consensus 32 ~~La~~~gi~~~qVR 46 (50)
T PF06971_consen 32 QELAEALGITPAQVR 46 (50)
T ss_dssp HHHHHHHTS-HHHHH
T ss_pred HHHHHHHCCCHHHhc
Confidence 478999999999986
No 140
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=71.60 E-value=19 Score=22.07 Aligned_cols=28 Identities=14% Similarity=0.166 Sum_probs=21.9
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
...++|..+|++...|+..+. -+.+.+.
T Consensus 219 s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 219 TLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 456899999999999999987 4444444
No 141
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=71.59 E-value=4.3 Score=19.54 Aligned_cols=19 Identities=11% Similarity=0.156 Sum_probs=16.5
Q ss_pred HHHHHHhCCCchhHHHhhH
Q psy5355 40 AKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 40 ~~La~~l~l~~~qV~vWFq 58 (76)
.++|..+|+++..|+.|-.
T Consensus 4 ~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 4 GEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4689999999999999964
No 142
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=71.28 E-value=4.5 Score=19.72 Aligned_cols=17 Identities=41% Similarity=0.446 Sum_probs=14.9
Q ss_pred HHHHHHhCCCchhHHHh
Q psy5355 40 AKLAYALGMTESQVKVT 56 (76)
Q Consensus 40 ~~La~~l~l~~~qV~vW 56 (76)
..||..||++...|.-|
T Consensus 13 ~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 13 SKLAKALGVSPQAVSQW 29 (60)
T ss_dssp HHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHCCCHHHHHHh
Confidence 47999999999999999
No 143
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=71.08 E-value=18 Score=21.08 Aligned_cols=28 Identities=18% Similarity=0.086 Sum_probs=21.2
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
.-.++|..+|++...|++-.. -+.+.++
T Consensus 159 s~~EIA~~lgis~~tVk~rl~ra~~~Lr~ 187 (194)
T PRK12531 159 PHQQVAEMFDIPLGTVKSRLRLAVEKLRH 187 (194)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 456889999999999998876 4444444
No 144
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=70.77 E-value=17 Score=20.67 Aligned_cols=28 Identities=11% Similarity=0.093 Sum_probs=21.8
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
.-.++|..+|++...|++... -+.+.++
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 165 (173)
T PRK12522 137 SYKEMSEILNIPIGTVKYRLNYAKKQMRE 165 (173)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 456889999999999999987 4555444
No 145
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=70.68 E-value=20 Score=21.37 Aligned_cols=29 Identities=21% Similarity=0.227 Sum_probs=23.0
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
...++|..+|++...|++... -|.+.++.
T Consensus 166 s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~ 195 (206)
T PRK12544 166 ETNEICHAVDLSVSNLNVLLYRARLRLREC 195 (206)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 356889999999999999987 55555554
No 146
>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=70.52 E-value=21 Score=21.86 Aligned_cols=27 Identities=19% Similarity=0.228 Sum_probs=20.9
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLA 64 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~k 64 (76)
...++|..+|++...|+.+.. -+.+.+
T Consensus 223 s~~eIA~~lgis~~~V~~~~~ra~~~Lr 250 (255)
T TIGR02941 223 SQKETGERLGISQMHVSRLQRQAISKLK 250 (255)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 346889999999999999886 444444
No 147
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=70.23 E-value=17 Score=20.91 Aligned_cols=28 Identities=21% Similarity=0.200 Sum_probs=22.1
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
...++|..+|++...|+.+.. -|.+.+.
T Consensus 145 s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 145 SIKEIAEVTGVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 456889999999999999987 5555554
No 148
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=70.23 E-value=21 Score=22.11 Aligned_cols=30 Identities=20% Similarity=0.148 Sum_probs=23.5
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
...++|..+|++...|+.+.. -+.+.+...
T Consensus 221 s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l 251 (256)
T PRK07408 221 TQKEAAERLGISPVTVSRRVKKGLDQLKKLL 251 (256)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 456899999999999999987 555555543
No 149
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=69.90 E-value=9.2 Score=22.35 Aligned_cols=30 Identities=23% Similarity=0.206 Sum_probs=23.3
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
...++|..||++...|+++.. -|.+.++..
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (188)
T PRK12517 146 SGEEIAEILDLNKNTVMTRLFRARNQLKEAL 176 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999987 555555543
No 150
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=69.72 E-value=12 Score=22.01 Aligned_cols=37 Identities=24% Similarity=0.229 Sum_probs=31.1
Q ss_pred HHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHH
Q psy5355 18 GQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVK 54 (76)
Q Consensus 18 ~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~ 54 (76)
..-+..|........|.+......+|..||++...|.
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 5567778888888889999999999999999987653
No 151
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=69.43 E-value=11 Score=21.85 Aligned_cols=35 Identities=17% Similarity=0.233 Sum_probs=26.8
Q ss_pred HHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHH
Q psy5355 20 QIFALEKTFEQTKYLAGPERAKLAYALGMTESQVK 54 (76)
Q Consensus 20 q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~ 54 (76)
-+..|...=+...|.+......+|..||++...|.
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 34455444455679999999999999999998765
No 152
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=68.74 E-value=10 Score=21.98 Aligned_cols=30 Identities=23% Similarity=0.059 Sum_probs=23.5
Q ss_pred HHHHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 36 GPERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 36 ~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
.....++|..+|++...|+++.. -+.+.+.
T Consensus 150 g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 180 (188)
T PRK09640 150 ELEFQEIADIMHMGLSATKMRYKRALDKLRE 180 (188)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 33557899999999999999987 5555554
No 153
>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=68.47 E-value=18 Score=22.80 Aligned_cols=31 Identities=26% Similarity=0.161 Sum_probs=24.8
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHcC
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYALG 68 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~ 68 (76)
.-.++|..||++...|+.... -|.+.++..+
T Consensus 160 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 191 (324)
T TIGR02960 160 RAAETAELLGTSTASVNSALQRARATLDEVGP 191 (324)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcc
Confidence 346889999999999999998 6666666554
No 154
>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=68.45 E-value=5.9 Score=20.53 Aligned_cols=20 Identities=15% Similarity=0.089 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...|..|-.
T Consensus 4 i~e~A~~~gvs~~tLr~ye~ 23 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYER 23 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999986
No 155
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=68.38 E-value=18 Score=22.25 Aligned_cols=31 Identities=23% Similarity=0.173 Sum_probs=24.3
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHcC
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYALG 68 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~ 68 (76)
...++|..+|+++..|+++.. -|.+.+....
T Consensus 134 S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~ 165 (228)
T PRK06704 134 SIADIAKVCSVSEGAVKASLFRSRNRLKTVSE 165 (228)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 346889999999999999998 5666665543
No 156
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=68.23 E-value=22 Score=23.00 Aligned_cols=50 Identities=16% Similarity=0.175 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 16 FSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 16 ~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
+++.+..+|...|-.. +.......++|..+|++...|+.+.. -+.+.++.
T Consensus 263 L~~~~R~vl~lrygL~-~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~ 313 (325)
T PRK05657 263 LNDKQREVLARRFGLL-GYEAATLEDVAREIGLTRERVRQIQVEALRRLREI 313 (325)
T ss_pred CCHHHHHHHHHHhccC-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4455555555544221 12233456899999999999999998 55555554
No 157
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=68.04 E-value=21 Score=20.96 Aligned_cols=45 Identities=16% Similarity=0.167 Sum_probs=35.5
Q ss_pred CCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 12 TRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 12 ~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
...+++++++..+...-..+ |..-.+..||..+|++..-|.+=..
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~v~~ 126 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSMVAP 126 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHHhcC
Confidence 34689999999998887776 4555778999999999987776544
No 158
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=68.01 E-value=22 Score=20.79 Aligned_cols=29 Identities=28% Similarity=0.241 Sum_probs=22.1
Q ss_pred HHHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 37 PERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 37 ~~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
...+++|..+|+++..|+..+. =|+..++
T Consensus 152 ls~~EIA~~lgiS~~tV~r~l~~aR~~l~~ 181 (185)
T PF07638_consen 152 LSVEEIAERLGISERTVRRRLRRARAWLRR 181 (185)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3566889999999999998877 4555444
No 159
>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=67.90 E-value=21 Score=22.37 Aligned_cols=28 Identities=18% Similarity=0.221 Sum_probs=22.2
Q ss_pred HHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 39 RAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
-.++|..+|+++..|+..+. -|.+.+..
T Consensus 127 ~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~ 155 (281)
T TIGR02957 127 YEEIASIVGKSEANCRQLVSRARRHLDAR 155 (281)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 45789999999999999998 55555543
No 160
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=67.76 E-value=18 Score=19.74 Aligned_cols=36 Identities=22% Similarity=0.255 Sum_probs=27.3
Q ss_pred CCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 16 FSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 16 ~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
+++..+..+...+... ....|..||++...|+-|=|
T Consensus 44 ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEq 79 (104)
T COG2944 44 LSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQ 79 (104)
T ss_pred CCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHc
Confidence 6666676666655544 34679999999999999988
No 161
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=67.71 E-value=21 Score=20.53 Aligned_cols=26 Identities=19% Similarity=0.102 Sum_probs=20.2
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKL 63 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~ 63 (76)
.-.++|..||+++..|+.... -+.+.
T Consensus 145 s~~EIA~~lgis~~tVk~~l~rAl~~~ 171 (178)
T PRK12529 145 KQKDIAQALDIALPTVKKYIHQAYVTC 171 (178)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 456889999999999999887 34433
No 162
>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=67.70 E-value=12 Score=21.30 Aligned_cols=35 Identities=26% Similarity=0.169 Sum_probs=26.3
Q ss_pred HHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHH
Q psy5355 20 QIFALEKTFEQTKYLAGPERAKLAYALGMTESQVK 54 (76)
Q Consensus 20 q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~ 54 (76)
-+..|...=+...|.+......+|..||++...|.
T Consensus 18 li~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v~ 52 (148)
T TIGR01958 18 IMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVY 52 (148)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 34444444445669999999999999999998764
No 163
>KOG0773|consensus
Probab=67.68 E-value=13 Score=24.02 Aligned_cols=42 Identities=24% Similarity=0.162 Sum_probs=33.5
Q ss_pred hccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHcC
Q psy5355 27 TFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYALG 68 (76)
Q Consensus 27 ~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~ 68 (76)
.-..++|++..+...|+...+|+..+|.+||- -+.+.....+
T Consensus 115 ~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~ 157 (342)
T KOG0773|consen 115 EHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELK 157 (342)
T ss_pred hhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccC
Confidence 34568899999999999999999999999998 5555555443
No 164
>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=67.55 E-value=6.3 Score=20.39 Aligned_cols=20 Identities=10% Similarity=0.134 Sum_probs=17.2
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++..+++.|-.
T Consensus 4 i~evA~~~gvs~~tLR~ye~ 23 (88)
T cd01105 4 IGEVSKLTGVSPRQLRYWEE 23 (88)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999964
No 165
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=67.54 E-value=12 Score=21.46 Aligned_cols=34 Identities=29% Similarity=0.286 Sum_probs=26.0
Q ss_pred HHHHHHhccccCCCCHHHHHHHHHHhCCCchhHH
Q psy5355 21 IFALEKTFEQTKYLAGPERAKLAYALGMTESQVK 54 (76)
Q Consensus 21 ~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~ 54 (76)
+..|...=....|.+......+|..+|++...|.
T Consensus 25 l~~L~~vQ~~~g~ip~~~~~~iA~~l~v~~~~v~ 58 (154)
T PRK07539 25 IPALKIVQEQRGWVPDEAIEAVADYLGMPAIDVE 58 (154)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 4444444455678999999999999999998765
No 166
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=67.35 E-value=21 Score=20.39 Aligned_cols=31 Identities=16% Similarity=0.087 Sum_probs=23.2
Q ss_pred HHHHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 36 GPERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 36 ~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
...-.++|..+|++...|..... -|.+.++.
T Consensus 152 ~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 152 DLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 33456889999999999998887 55555543
No 167
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=67.32 E-value=11 Score=21.82 Aligned_cols=31 Identities=29% Similarity=0.276 Sum_probs=24.8
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHcC
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYALG 68 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~ 68 (76)
.-.++|..+|++...|+.+.. -|.+.+....
T Consensus 145 s~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~ 176 (182)
T COG1595 145 SYEEIAEILGISVGTVKSRLHRARKKLREQLE 176 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 345789999999999999998 6666666544
No 168
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=66.98 E-value=14 Score=20.37 Aligned_cols=22 Identities=9% Similarity=-0.023 Sum_probs=18.4
Q ss_pred HHHHHHHHHhCCCchhHHHhhH
Q psy5355 37 PERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 37 ~~~~~La~~l~l~~~qV~vWFq 58 (76)
.....||..+|+++..+.-+|.
T Consensus 26 ~sl~~lA~~~g~S~~~l~r~Fk 47 (127)
T PRK11511 26 LSLEKVSERSGYSKWHLQRMFK 47 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 3556899999999999888886
No 169
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=66.95 E-value=6.8 Score=18.48 Aligned_cols=21 Identities=19% Similarity=0.186 Sum_probs=16.3
Q ss_pred HHHHHHHHhCCCchhHHHhhH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq 58 (76)
....||..+|++..+|.-|+.
T Consensus 12 t~~~La~~~gis~~tl~~~~~ 32 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILN 32 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHh
Confidence 356899999999999999997
No 170
>PF13551 HTH_29: Winged helix-turn helix
Probab=66.39 E-value=17 Score=18.92 Aligned_cols=48 Identities=17% Similarity=0.122 Sum_probs=30.5
Q ss_pred CCCCCCCHHHHHHHHHhccccC-----CCCHHHHHH-H-HHHh--CCCchhHHHhhH
Q psy5355 11 HTRPTFSGQQIFALEKTFEQTK-----YLAGPERAK-L-AYAL--GMTESQVKVTGP 58 (76)
Q Consensus 11 r~R~~~t~~q~~~L~~~f~~~~-----~p~~~~~~~-L-a~~l--~l~~~qV~vWFq 58 (76)
+++..+++++...|...+..++ ..+...... | .... .++...|.-|+.
T Consensus 53 ~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 53 RPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 3334489999999999998776 233443333 3 2222 467777877774
No 171
>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=66.03 E-value=7.9 Score=20.44 Aligned_cols=20 Identities=25% Similarity=0.302 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|..
T Consensus 3 I~e~a~~~gvs~~tLR~ye~ 22 (96)
T cd04774 3 VDEVAKRLGLTKRTLKYYEE 22 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999986
No 172
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=65.96 E-value=25 Score=22.07 Aligned_cols=30 Identities=17% Similarity=0.189 Sum_probs=23.4
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
...++|..+|+++..|+.... -|.+.+...
T Consensus 133 s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~ 163 (293)
T PRK09636 133 PFDEIASTLGRSPAACRQLASRARKHVRAAR 163 (293)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 345789999999999999998 566655543
No 173
>PRK13558 bacterio-opsin activator; Provisional
Probab=65.91 E-value=8.5 Score=26.72 Aligned_cols=41 Identities=22% Similarity=0.361 Sum_probs=34.6
Q ss_pred CCCCHHHHHHHHHhccccCC--CCHHHHHHHHHHhCCCchhHH
Q psy5355 14 PTFSGQQIFALEKTFEQTKY--LAGPERAKLAYALGMTESQVK 54 (76)
Q Consensus 14 ~~~t~~q~~~L~~~f~~~~~--p~~~~~~~La~~l~l~~~qV~ 54 (76)
..+|+.|...|+..|....| |-.....+||..||++...+.
T Consensus 606 ~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~ 648 (665)
T PRK13558 606 NDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFH 648 (665)
T ss_pred hhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHH
Confidence 46999999999999998885 666677899999999998643
No 174
>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=65.89 E-value=10 Score=21.53 Aligned_cols=34 Identities=24% Similarity=0.333 Sum_probs=23.8
Q ss_pred HHHHHHhccccCCCCHHHHHHHHHHhCCCchhHH
Q psy5355 21 IFALEKTFEQTKYLAGPERAKLAYALGMTESQVK 54 (76)
Q Consensus 21 ~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~ 54 (76)
+..|...=+...|.+......+|..+|++..+|.
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 4455555455679999999999999999998865
No 175
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=65.86 E-value=6.2 Score=17.66 Aligned_cols=16 Identities=50% Similarity=0.673 Sum_probs=12.2
Q ss_pred HHHHHHHhCCCchhHH
Q psy5355 39 RAKLAYALGMTESQVK 54 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~ 54 (76)
-.+||..+|+++..|.
T Consensus 20 ~~~la~~lglS~~~v~ 35 (42)
T PF13404_consen 20 YAELAEELGLSESTVR 35 (42)
T ss_dssp HHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHCcCHHHHH
Confidence 4578999999998764
No 176
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=65.02 E-value=26 Score=20.49 Aligned_cols=30 Identities=40% Similarity=0.399 Sum_probs=21.2
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
.-.++|..+|++...|++=.. -|.+.++..
T Consensus 152 s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l 182 (192)
T PRK09643 152 SVADAARMLGVAEGTVKSRCARGRARLAELL 182 (192)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 456789999999999886554 455555443
No 177
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=64.78 E-value=14 Score=21.51 Aligned_cols=34 Identities=26% Similarity=0.154 Sum_probs=24.9
Q ss_pred CCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 34 LAGPERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 34 p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
.......++|..+|++...|+.+.. -|.+.++..
T Consensus 153 ~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 153 HGDLELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3344567899999999999998877 555555543
No 178
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=64.49 E-value=16 Score=20.77 Aligned_cols=32 Identities=22% Similarity=0.150 Sum_probs=23.7
Q ss_pred CCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 34 LAGPERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 34 p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
.......++|..+|++...|+.+.. -+.+.++
T Consensus 140 ~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~ 172 (176)
T PRK09638 140 YYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRK 172 (176)
T ss_pred hcCCCHHHHHHHHCCChhHHHHHHHHHHHHHHH
Confidence 3444567899999999999998887 4444444
No 179
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=64.30 E-value=16 Score=21.58 Aligned_cols=26 Identities=27% Similarity=0.139 Sum_probs=21.7
Q ss_pred cccCCCCHHHHHHHHHHhCCCchhHH
Q psy5355 29 EQTKYLAGPERAKLAYALGMTESQVK 54 (76)
Q Consensus 29 ~~~~~p~~~~~~~La~~l~l~~~qV~ 54 (76)
....|.+......+|..||++...|.
T Consensus 47 ~~~GyIp~e~~~~iA~~l~v~~a~V~ 72 (169)
T PRK07571 47 ELFGYLERDLLLYVARQLKLPLSRVY 72 (169)
T ss_pred HHcCCCCHHHHHHHHHHhCcCHHHHH
Confidence 44568889999999999999998764
No 180
>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=64.07 E-value=11 Score=16.40 Aligned_cols=20 Identities=20% Similarity=0.057 Sum_probs=17.1
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...|.-|..
T Consensus 4 ~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 35679999999999999986
No 181
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=64.07 E-value=25 Score=20.06 Aligned_cols=21 Identities=29% Similarity=0.275 Sum_probs=18.5
Q ss_pred HHHHHHHHhCCCchhHHHhhH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq 58 (76)
...++|..+|++...|+++..
T Consensus 137 s~~EIA~~lgis~~tV~~~l~ 157 (172)
T PRK09651 137 TYSEIAHKLGVSVSSVKKYVA 157 (172)
T ss_pred CHHHHHHHhCCCHHHHHHHHH
Confidence 456899999999999999886
No 182
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=63.91 E-value=21 Score=19.13 Aligned_cols=42 Identities=12% Similarity=0.107 Sum_probs=31.1
Q ss_pred CCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCC-CchhHHHhhH
Q psy5355 13 RPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGM-TESQVKVTGP 58 (76)
Q Consensus 13 R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l-~~~qV~vWFq 58 (76)
+..||.+....+-..+....+ ....+|..+|+ +..++..|-.
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 678888877666555544433 46689999996 9999998875
No 183
>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=63.69 E-value=9.4 Score=20.21 Aligned_cols=20 Identities=10% Similarity=0.101 Sum_probs=17.4
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|..
T Consensus 3 i~eva~~~gvs~~tlR~ye~ 22 (103)
T cd01106 3 VGEVAKLTGVSVRTLHYYDE 22 (103)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999976
No 184
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=63.62 E-value=24 Score=19.75 Aligned_cols=21 Identities=24% Similarity=0.203 Sum_probs=18.0
Q ss_pred HHHHHHHHhCCCchhHHHhhH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq 58 (76)
.-.++|..+|++...|+++..
T Consensus 131 s~~EIA~~l~is~~tV~~~l~ 151 (161)
T PRK12528 131 GYGEIATELGISLATVKRYLN 151 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 356789999999999999886
No 185
>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=63.57 E-value=8.7 Score=21.70 Aligned_cols=20 Identities=15% Similarity=0.180 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|..
T Consensus 3 I~e~a~~~gvs~~TLR~Ye~ 22 (134)
T cd04779 3 IGQLAHLAGVSKRTIDYYTN 22 (134)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999997
No 186
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=63.53 E-value=34 Score=21.35 Aligned_cols=28 Identities=18% Similarity=0.226 Sum_probs=21.6
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
...++|..+|++...|+.+.. -+.+.+.
T Consensus 233 t~~EIA~~lgis~~~V~~~~~ral~kLr~ 261 (264)
T PRK07122 233 TQTQIAERVGISQMHVSRLLAKTLARLRD 261 (264)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 457899999999999999887 4444443
No 187
>PF12728 HTH_17: Helix-turn-helix domain
Probab=63.12 E-value=10 Score=17.18 Aligned_cols=19 Identities=26% Similarity=0.102 Sum_probs=16.7
Q ss_pred HHHHHHhCCCchhHHHhhH
Q psy5355 40 AKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 40 ~~La~~l~l~~~qV~vWFq 58 (76)
.++|..||++...|.-|..
T Consensus 5 ~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 5 KEAAELLGISRSTVYRWIR 23 (51)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4679999999999999986
No 188
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=62.92 E-value=29 Score=20.97 Aligned_cols=30 Identities=30% Similarity=0.298 Sum_probs=22.4
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
...++|..+|++...|..+-. -+.+.++..
T Consensus 197 S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l 227 (233)
T PRK05803 197 TQREIAKALGISRSYVSRIEKRALKKLFKEL 227 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999854 555555543
No 189
>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=62.56 E-value=10 Score=19.91 Aligned_cols=20 Identities=10% Similarity=0.102 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|-+
T Consensus 3 i~eva~~~gvs~~tLRyye~ 22 (96)
T cd04768 3 IGEFAKLAGVSIRTLRHYDD 22 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999986
No 190
>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=62.51 E-value=16 Score=22.10 Aligned_cols=29 Identities=17% Similarity=0.198 Sum_probs=22.2
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
...++|..+|++...|+.+.. -+.+.++.
T Consensus 200 s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~ 229 (234)
T TIGR02835 200 TQKEVADMLGISQSYISRLEKRILKRLKKE 229 (234)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999987 45555543
No 191
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=62.25 E-value=19 Score=21.71 Aligned_cols=35 Identities=29% Similarity=0.238 Sum_probs=26.3
Q ss_pred CCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 33 YLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 33 ~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
|.......++|..+|++...|++... -|.+.++..
T Consensus 162 ~~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l 197 (231)
T PRK11922 162 VVEELSVEETAQALGLPEETVKTRLHRARRLLRESL 197 (231)
T ss_pred hhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 34444567899999999999998887 666666643
No 192
>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=62.14 E-value=6.8 Score=17.68 Aligned_cols=18 Identities=22% Similarity=0.191 Sum_probs=16.4
Q ss_pred HHHHHhCCCchhHHHhhH
Q psy5355 41 KLAYALGMTESQVKVTGP 58 (76)
Q Consensus 41 ~La~~l~l~~~qV~vWFq 58 (76)
.||..+|++...|.-|+.
T Consensus 2 ~lA~~~gvs~~tvs~~l~ 19 (52)
T cd01392 2 DIARAAGVSVATVSRVLN 19 (52)
T ss_pred cHHHHHCcCHHHHHHHHc
Confidence 589999999999999998
No 193
>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=61.31 E-value=4.3 Score=19.86 Aligned_cols=20 Identities=25% Similarity=0.270 Sum_probs=15.8
Q ss_pred HHHHHHHhCCCchhHH-HhhH
Q psy5355 39 RAKLAYALGMTESQVK-VTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~-vWFq 58 (76)
..+||..+|++...|. .|..
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 3478999999999999 9987
No 194
>PHA01976 helix-turn-helix protein
Probab=61.31 E-value=11 Score=18.01 Aligned_cols=20 Identities=15% Similarity=0.115 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..+||..+|++...|.-|..
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~ 37 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEA 37 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHc
Confidence 45799999999999999986
No 195
>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=61.08 E-value=25 Score=19.21 Aligned_cols=38 Identities=16% Similarity=0.022 Sum_probs=25.7
Q ss_pred CCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 16 FSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 16 ~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
||.+-...+..++.... ...++|..++++...|..||+
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 33444444445555433 345679999999999999997
No 196
>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=61.07 E-value=9.7 Score=20.22 Aligned_cols=20 Identities=10% Similarity=0.200 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|-+
T Consensus 4 i~eva~~~gvs~~tLR~ye~ 23 (102)
T cd04775 4 IGQMSRKFGVSRSTLLYYES 23 (102)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999976
No 197
>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=60.69 E-value=10 Score=19.93 Aligned_cols=20 Identities=15% Similarity=0.140 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|-.
T Consensus 3 i~eva~~~gvs~~tlR~ye~ 22 (96)
T cd04788 3 IGELARRTGLSVRTLHHYDH 22 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999986
No 198
>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=60.55 E-value=10 Score=20.00 Aligned_cols=20 Identities=15% Similarity=0.132 Sum_probs=16.9
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...|+.|=.
T Consensus 3 I~eva~~~gvs~~tlR~Ye~ 22 (95)
T cd04780 3 MSELSKRSGVSVATIKYYLR 22 (95)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999998865
No 199
>PF13565 HTH_32: Homeodomain-like domain
Probab=60.44 E-value=19 Score=17.58 Aligned_cols=38 Identities=21% Similarity=0.135 Sum_probs=27.0
Q ss_pred CHHHHHHHHHhccccCCCCHHHHH-HHHHHhCC----CchhHH
Q psy5355 17 SGQQIFALEKTFEQTKYLAGPERA-KLAYALGM----TESQVK 54 (76)
Q Consensus 17 t~~q~~~L~~~f~~~~~p~~~~~~-~La~~l~l----~~~qV~ 54 (76)
++++...+...+..++..+..+.. .|...+|+ +...|.
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~ 74 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVY 74 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHH
Confidence 677778888988888877777764 46777664 444444
No 200
>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=60.19 E-value=10 Score=20.14 Aligned_cols=20 Identities=20% Similarity=0.177 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|-.
T Consensus 4 i~eva~~~gvs~~tlR~ye~ 23 (102)
T cd04789 4 ISELAEKAGISRSTLLYYEK 23 (102)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999976
No 201
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=59.69 E-value=40 Score=20.92 Aligned_cols=28 Identities=21% Similarity=0.245 Sum_probs=20.9
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
...++|..+|++...|+.... -+.+.++
T Consensus 230 s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 258 (268)
T PRK06288 230 TLKEIGKVLGVTESRISQLHTKAVLQLRA 258 (268)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 456889999999999998876 4444443
No 202
>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=59.66 E-value=11 Score=20.97 Aligned_cols=21 Identities=19% Similarity=0.069 Sum_probs=18.2
Q ss_pred HHHHHHHHhCCCchhHHHhhH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq 58 (76)
...++|..+|++...|+.|-+
T Consensus 5 tI~elA~~~gvs~~tlR~Ye~ 25 (120)
T TIGR02054 5 TISRLAEDAGVSVHVVRDYLL 25 (120)
T ss_pred cHHHHHHHHCcCHHHHHHHHH
Confidence 356899999999999999965
No 203
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=59.49 E-value=24 Score=18.26 Aligned_cols=43 Identities=12% Similarity=0.175 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHhccc-----cCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 16 FSGQQIFALEKTFEQ-----TKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 16 ~t~~q~~~L~~~f~~-----~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
++..++..+...|.. +.+.+..+...+...+|++...|.-.|.
T Consensus 4 ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~ 51 (96)
T smart00027 4 ISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWN 51 (96)
T ss_pred CCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHH
Confidence 567788888888743 3467777777766778888888777764
No 204
>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=59.08 E-value=12 Score=16.93 Aligned_cols=20 Identities=20% Similarity=0.140 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
...||..+|++...|.-|..
T Consensus 18 q~~lA~~~gvs~~~vs~~e~ 37 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVEN 37 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHC
Confidence 46789999999999999986
No 205
>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=58.42 E-value=11 Score=20.18 Aligned_cols=20 Identities=25% Similarity=0.233 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...|+.|-.
T Consensus 3 i~eva~~~gvs~~tlR~ye~ 22 (108)
T cd04773 3 IGELAHLLGVPPSTLRHWEK 22 (108)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999986
No 206
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=58.40 E-value=34 Score=19.69 Aligned_cols=28 Identities=25% Similarity=-0.002 Sum_probs=20.6
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
.-.++|..+|++...|.+-.. -|.+.+.
T Consensus 155 s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 155 TYEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred CHHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 456789999999999888776 4444443
No 207
>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=58.20 E-value=12 Score=19.52 Aligned_cols=19 Identities=16% Similarity=0.254 Sum_probs=16.8
Q ss_pred HHHHHHhCCCchhHHHhhH
Q psy5355 40 AKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 40 ~~La~~l~l~~~qV~vWFq 58 (76)
.++|..+|+++..|+.|-.
T Consensus 4 ~eva~~~gi~~~tlr~~~~ 22 (100)
T cd00592 4 GEVAKLLGVSVRTLRYYEE 22 (100)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4789999999999999975
No 208
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=57.94 E-value=14 Score=15.71 Aligned_cols=20 Identities=25% Similarity=0.333 Sum_probs=16.7
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
...+|..+|++...|..|-.
T Consensus 13 ~~~la~~~~i~~~~i~~~~~ 32 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIEN 32 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHC
Confidence 44789999999999988876
No 209
>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=57.90 E-value=14 Score=16.79 Aligned_cols=20 Identities=25% Similarity=0.363 Sum_probs=16.7
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..+||..+|++...|.-|..
T Consensus 12 ~~~la~~~gis~~~i~~~~~ 31 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIEN 31 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHHHHhCCCcchhHHHhc
Confidence 46899999999999999986
No 210
>KOG1146|consensus
Probab=57.89 E-value=36 Score=26.62 Aligned_cols=59 Identities=12% Similarity=-0.036 Sum_probs=51.2
Q ss_pred CCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 9 KKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 9 ~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
.+..+..+-+.++..|-..|-.+..|+.....-|......+.+.+.+||+ .+.+.++..
T Consensus 705 ~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 705 DKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred cccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 35567777789999999999999999999988888888999999999999 888887755
No 211
>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=57.63 E-value=14 Score=19.44 Aligned_cols=20 Identities=10% Similarity=0.122 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|..
T Consensus 3 i~eva~~~gvs~~tlR~ye~ 22 (97)
T cd04782 3 TGEFAKLCGISKQTLFHYDK 22 (97)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999976
No 212
>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=57.57 E-value=12 Score=20.15 Aligned_cols=20 Identities=20% Similarity=0.092 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...|+.|-.
T Consensus 3 Ige~A~~~gvs~~tlR~ye~ 22 (107)
T cd01111 3 ISQLALDAGVSVHIVRDYLL 22 (107)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999975
No 213
>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=57.29 E-value=14 Score=20.63 Aligned_cols=20 Identities=10% Similarity=0.092 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|-+
T Consensus 4 I~eVA~~~GVs~~TLR~wE~ 23 (120)
T cd04767 4 IGVVAELLNIHPETLRIWER 23 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999986
No 214
>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=56.89 E-value=13 Score=19.97 Aligned_cols=20 Identities=5% Similarity=0.022 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|-.
T Consensus 3 i~eva~~~gis~~tlR~ye~ 22 (108)
T cd01107 3 IGEFAKLSNLSIKALRYYDK 22 (108)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999986
No 215
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=56.75 E-value=25 Score=19.28 Aligned_cols=34 Identities=15% Similarity=0.008 Sum_probs=24.1
Q ss_pred HHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHH
Q psy5355 20 QIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55 (76)
Q Consensus 20 q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~v 55 (76)
+...|...|. ..+......+||..+.+|.+.++.
T Consensus 5 ~y~~L~~~~~--~~~~~vtl~elA~~l~cS~Rn~r~ 38 (115)
T PF12793_consen 5 QYQRLWQHYG--GQPVEVTLDELAELLFCSRRNART 38 (115)
T ss_pred HHHHHHHHcC--CCCcceeHHHHHHHhCCCHHHHHH
Confidence 3445666666 445556677999999999988765
No 216
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=56.70 E-value=14 Score=16.67 Aligned_cols=20 Identities=25% Similarity=0.144 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
...+|..+|++...|.-.|.
T Consensus 30 ~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 30 FKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 55789999999999998885
No 217
>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=56.64 E-value=13 Score=20.05 Aligned_cols=20 Identities=10% Similarity=0.164 Sum_probs=17.2
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|-+
T Consensus 3 i~e~a~~~gvs~~tlr~ye~ 22 (113)
T cd01109 3 IKEVAEKTGLSADTLRYYEK 22 (113)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999975
No 218
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=56.62 E-value=17 Score=20.07 Aligned_cols=25 Identities=24% Similarity=0.118 Sum_probs=21.2
Q ss_pred CCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 34 LAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 34 p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
++...+..||..+|++...|.-|-.
T Consensus 27 ~~~~~r~~La~~~~i~~~~l~~w~~ 51 (122)
T PF14229_consen 27 DTPLGRKALAKKLGISERNLLKWVN 51 (122)
T ss_pred CCHHHHHHHHHhcCCCHHHHHHHHh
Confidence 5556777899999999999999964
No 219
>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=56.60 E-value=14 Score=15.81 Aligned_cols=20 Identities=25% Similarity=0.355 Sum_probs=17.0
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
...+|..+|++...|.-|..
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~ 34 (58)
T cd00093 15 QEELAEKLGVSRSTISRIEN 34 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHc
Confidence 34789999999999999886
No 220
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=56.11 E-value=13 Score=15.79 Aligned_cols=20 Identities=30% Similarity=0.303 Sum_probs=14.3
Q ss_pred HHHHHHHHhCCCchhHHHhh
Q psy5355 38 ERAKLAYALGMTESQVKVTG 57 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWF 57 (76)
.+.+||..+|++...|--=+
T Consensus 4 tr~diA~~lG~t~ETVSR~l 23 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVSRIL 23 (32)
T ss_dssp -HHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHhCCcHHHHHHHH
Confidence 46789999999998876544
No 221
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=55.69 E-value=23 Score=21.24 Aligned_cols=43 Identities=12% Similarity=-0.001 Sum_probs=29.2
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
.+|+.++..|......+ +-......++|..+++++..|+..+.
T Consensus 158 ~Lt~re~~~l~~~i~~~-~~~g~s~~eIA~~l~iS~~Tv~~~~~ 200 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAH-QDYEFSTDELANAVNISRVSCRKYLI 200 (239)
T ss_pred CCCHHHHHHHHHHHHhC-CCCCcCHHHHHHHhCchHHHHHHHHH
Confidence 36776666665554433 22333456799999999999998775
No 222
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=55.34 E-value=19 Score=16.01 Aligned_cols=21 Identities=29% Similarity=0.349 Sum_probs=18.0
Q ss_pred HHHHHHHHhCCCchhHHHhhH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq 58 (76)
...++|..+|++...|..|..
T Consensus 17 s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 17 TNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 446789999999999999886
No 223
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=55.12 E-value=34 Score=18.93 Aligned_cols=38 Identities=13% Similarity=0.147 Sum_probs=23.4
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhh
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTG 57 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWF 57 (76)
.++++++..++.+..... ...+++..+|++...|+.=+
T Consensus 33 ~L~~E~~~Fi~~Fi~~rG-----nlKe~e~~lgiSYPTvR~rL 70 (113)
T PF09862_consen 33 RLSPEQLEFIKLFIKNRG-----NLKEMEKELGISYPTVRNRL 70 (113)
T ss_pred cCCHHHHHHHHHHHHhcC-----CHHHHHHHHCCCcHHHHHHH
Confidence 467778777766654332 24456667777776666544
No 224
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=54.69 E-value=20 Score=15.89 Aligned_cols=38 Identities=21% Similarity=0.203 Sum_probs=27.2
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
.+++.+..++...+.. ....++|..+|++...|..|..
T Consensus 3 ~l~~~e~~i~~~~~~g------~s~~eia~~l~is~~tv~~~~~ 40 (58)
T smart00421 3 SLTPREREVLRLLAEG------LTNKEIAERLGISEKTVKTHLS 40 (58)
T ss_pred CCCHHHHHHHHHHHcC------CCHHHHHHHHCCCHHHHHHHHH
Confidence 3567777766553321 1346789999999999999886
No 225
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=54.57 E-value=38 Score=19.17 Aligned_cols=40 Identities=8% Similarity=0.078 Sum_probs=25.7
Q ss_pred CCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 16 FSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 16 ~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
++++...++...|......+. ..+|..++++++++.-|++
T Consensus 82 l~de~k~Ii~lry~~r~~~TW---~~IA~~l~i~erta~r~~~ 121 (130)
T PF05263_consen 82 LIDEEKRIIKLRYDRRSRRTW---YQIAQKLHISERTARRWRD 121 (130)
T ss_pred hCHHHHHHHHHHHcccccchH---HHHHHHhCccHHHHHHHHH
Confidence 334444555555555433333 3678999999999988876
No 226
>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=54.56 E-value=17 Score=15.95 Aligned_cols=13 Identities=23% Similarity=0.353 Sum_probs=11.0
Q ss_pred CCCHHHHHHHHHh
Q psy5355 15 TFSGQQIFALEKT 27 (76)
Q Consensus 15 ~~t~~q~~~L~~~ 27 (76)
.||+.|+..|+.-
T Consensus 2 ~FT~~Ql~~L~~Q 14 (37)
T PF08880_consen 2 PFTPAQLQELRAQ 14 (37)
T ss_pred CCCHHHHHHHHHH
Confidence 5899999999765
No 227
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=54.11 E-value=4.6 Score=20.82 Aligned_cols=20 Identities=10% Similarity=0.177 Sum_probs=16.7
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
+..|...++|...+|.+|+.
T Consensus 56 ~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 56 TSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred HHHHHHHhCCCCCeEEEEEE
Confidence 35678888999999999985
No 228
>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=53.91 E-value=15 Score=19.51 Aligned_cols=19 Identities=16% Similarity=0.228 Sum_probs=16.5
Q ss_pred HHHHHHhCCCchhHHHhhH
Q psy5355 40 AKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 40 ~~La~~l~l~~~qV~vWFq 58 (76)
.++|..+|++...++.|-.
T Consensus 4 ~EvA~~~gVs~~tLR~ye~ 22 (99)
T cd04765 4 GEVAEILGLPPHVLRYWET 22 (99)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4789999999999999964
No 229
>PF13309 HTH_22: HTH domain
Probab=53.49 E-value=27 Score=17.01 Aligned_cols=35 Identities=17% Similarity=0.194 Sum_probs=24.0
Q ss_pred HHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHH
Q psy5355 21 IFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55 (76)
Q Consensus 21 ~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~v 55 (76)
+.++...++..-|.-......+|..||++...|-.
T Consensus 27 ~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~ 61 (64)
T PF13309_consen 27 KEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYR 61 (64)
T ss_pred HHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHH
Confidence 44445555555565556677899999999887743
No 230
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=53.37 E-value=15 Score=17.04 Aligned_cols=38 Identities=21% Similarity=0.193 Sum_probs=25.6
Q ss_pred CCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHH
Q psy5355 16 FSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55 (76)
Q Consensus 16 ~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~v 55 (76)
++..|..+|......... .....+||..++++...|.-
T Consensus 3 lt~~q~~vL~~l~~~~~~--~~t~~~la~~l~~~~~~vs~ 40 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGE--ELTQSELAERLGISKSTVSR 40 (62)
T ss_dssp STHHHHHHHHHHHHSTTS--GEEHHHHHHHHTS-HHHHHH
T ss_pred cCHHHHHHHHHHHHCCCC--CcCHHHHHHHHCcCHHHHHH
Confidence 677888888777665543 12345789999999877653
No 231
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=53.27 E-value=16 Score=21.65 Aligned_cols=20 Identities=20% Similarity=0.124 Sum_probs=17.7
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...|+.|..
T Consensus 3 i~evA~~lGVS~~TLRrw~k 22 (175)
T PRK13182 3 TPFVAKKLGVSPKTVQRWVK 22 (175)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999986
No 232
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=53.15 E-value=13 Score=20.79 Aligned_cols=19 Identities=16% Similarity=0.092 Sum_probs=17.2
Q ss_pred HHHHHHhCCCchhHHHhhH
Q psy5355 40 AKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 40 ~~La~~l~l~~~qV~vWFq 58 (76)
++||..+|++...|.-|..
T Consensus 4 eELA~~tG~srQTINrWvR 22 (122)
T PF07037_consen 4 EELAELTGYSRQTINRWVR 22 (122)
T ss_pred HHHHHHhCccHHHHHHHHH
Confidence 5899999999999999984
No 233
>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=52.85 E-value=15 Score=18.05 Aligned_cols=20 Identities=30% Similarity=0.247 Sum_probs=17.7
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
...||..+|++...|.-|..
T Consensus 21 ~~~lA~~~gis~~tis~~~~ 40 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVN 40 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHc
Confidence 45799999999999999987
No 234
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=52.60 E-value=43 Score=19.13 Aligned_cols=45 Identities=18% Similarity=0.159 Sum_probs=32.9
Q ss_pred CCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHH
Q psy5355 14 PTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLA 64 (76)
Q Consensus 14 ~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~k 64 (76)
+.+++.|..+|.-.. .. ....++|..+|++...|..+-. -+.+.+
T Consensus 5 ~~Lte~qr~VL~Lr~-~G-----lTq~EIAe~LgiS~stV~~~e~ra~kkLr 50 (137)
T TIGR00721 5 TFLTERQIKVLELRE-KG-----LSQKEIAKELKTTRANVSAIEKRAMENIE 50 (137)
T ss_pred CCCCHHHHHHHHHHH-cC-----CCHHHHHHHHCcCHHHHHHHHHhHHHHHH
Confidence 578888988887742 21 1456899999999999998887 344443
No 235
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=52.11 E-value=46 Score=21.08 Aligned_cols=49 Identities=18% Similarity=0.229 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHc
Q psy5355 16 FSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYAL 67 (76)
Q Consensus 16 ~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~ 67 (76)
+++.+..+|...|- +-......++|..+|++...|+..-. -..+.+...
T Consensus 228 L~~rer~vl~lr~~---~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l 277 (289)
T PRK07500 228 LNERELRIIRERRL---REDGATLEALGEELGISKERVRQIEARALEKLRRAL 277 (289)
T ss_pred CCHHHHHHHHHHhc---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 44445555555442 11223457899999999999999887 555554443
No 236
>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=51.94 E-value=17 Score=19.63 Aligned_cols=20 Identities=15% Similarity=0.162 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|-+
T Consensus 3 i~eva~~~gvs~~tlR~Ye~ 22 (112)
T cd01282 3 IGELAARTGVSVRSLRYYEE 22 (112)
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 35789999999999999986
No 237
>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=51.88 E-value=16 Score=20.64 Aligned_cols=20 Identities=15% Similarity=0.129 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|-+
T Consensus 4 I~EvA~~~Gvs~~tLRyYE~ 23 (139)
T cd01110 4 VGEVAKRSGVAVSALHFYEQ 23 (139)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999986
No 238
>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=51.79 E-value=17 Score=19.17 Aligned_cols=20 Identities=20% Similarity=0.202 Sum_probs=17.4
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|-.
T Consensus 4 i~eva~~~gVs~~tLR~ye~ 23 (98)
T cd01279 4 ISVAAELLGIHPQTLRVYDR 23 (98)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999975
No 239
>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=51.72 E-value=17 Score=19.92 Aligned_cols=20 Identities=15% Similarity=0.189 Sum_probs=16.6
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|=+
T Consensus 3 Igeva~~~gvs~~tlRyYe~ 22 (118)
T cd04776 3 ISELAREFDVTPRTLRFYED 22 (118)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999998843
No 240
>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=51.22 E-value=17 Score=20.05 Aligned_cols=19 Identities=21% Similarity=0.270 Sum_probs=16.1
Q ss_pred HHHHHHhCCCchhHHHhhH
Q psy5355 40 AKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 40 ~~La~~l~l~~~qV~vWFq 58 (76)
.++|..+|++...|+.|=+
T Consensus 3 ~e~a~~~gvs~~tlR~Ye~ 21 (124)
T TIGR02051 3 GELAKAAGVNVETIRYYER 21 (124)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 5789999999999988844
No 241
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=51.22 E-value=42 Score=21.42 Aligned_cols=28 Identities=29% Similarity=0.211 Sum_probs=22.0
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
...++|..||++...|+.-.. -|.+.++
T Consensus 171 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 171 SAAEVAELLDTSVAAVNSALQRARATLAE 199 (339)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHhh
Confidence 456889999999999999887 4555544
No 242
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=50.98 E-value=29 Score=17.05 Aligned_cols=21 Identities=19% Similarity=0.259 Sum_probs=16.0
Q ss_pred HHHHHHHHhCCCchhHHHhhH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq 58 (76)
..++||..+|++...|.-.++
T Consensus 22 t~eEiA~~lgis~~~v~~~l~ 42 (78)
T PF04539_consen 22 TDEEIAEELGISVEEVRELLQ 42 (78)
T ss_dssp BHHHHHHHHTS-HHHHHHHHH
T ss_pred CHHHHHHHHcccHHHHHHHHH
Confidence 445789999999999887664
No 243
>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=50.97 E-value=15 Score=21.56 Aligned_cols=20 Identities=20% Similarity=0.302 Sum_probs=15.2
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
+..||..+|+++..|.-|-.
T Consensus 5 k~~lA~i~gvS~~ti~~W~~ 24 (164)
T PF07471_consen 5 KKELAEIFGVSERTIDKWQR 24 (164)
T ss_dssp HHHHHHHTT--HHHHHHHTT
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 56899999999999999953
No 244
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=50.88 E-value=18 Score=19.48 Aligned_cols=19 Identities=11% Similarity=0.149 Sum_probs=15.7
Q ss_pred HHHHHHHhCCCchhHHHhh
Q psy5355 39 RAKLAYALGMTESQVKVTG 57 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWF 57 (76)
..++|..+|++...++.|=
T Consensus 3 I~eva~~~gvs~~tLRyYE 21 (124)
T COG0789 3 IGEVAKLTGVSVRTLRFYE 21 (124)
T ss_pred HHHHHHHhCCCHHHHHHHH
Confidence 3578999999999998884
No 245
>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=50.82 E-value=18 Score=19.09 Aligned_cols=20 Identities=25% Similarity=0.375 Sum_probs=17.0
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|-+
T Consensus 3 i~e~A~~~gvs~~tlR~Ye~ 22 (99)
T cd04772 3 TVDLARAIGLSPQTVRNYES 22 (99)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999998875
No 246
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=50.50 E-value=59 Score=20.13 Aligned_cols=28 Identities=25% Similarity=0.234 Sum_probs=21.2
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
...++|..+|++...|..+.. -+.+.++
T Consensus 223 t~~EIA~~lgis~~~V~~~~~ral~kLr~ 251 (257)
T PRK05911 223 VLKEIGKILGVSESRVSQIHSKALLKLRA 251 (257)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 456889999999999998876 4444444
No 247
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=50.49 E-value=46 Score=18.85 Aligned_cols=21 Identities=14% Similarity=0.145 Sum_probs=17.8
Q ss_pred HHHHHHHHhCCCchhHHHhhH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq 58 (76)
.-.++|..||++...|+.+..
T Consensus 136 s~~EIA~~l~is~~tV~~~l~ 156 (168)
T PRK12525 136 TYVEIGERLGVSLSRIHQYMV 156 (168)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 456889999999999998876
No 248
>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=50.05 E-value=27 Score=16.70 Aligned_cols=18 Identities=33% Similarity=0.344 Sum_probs=13.3
Q ss_pred HHHHHHHHHhCCCchhHH
Q psy5355 37 PERAKLAYALGMTESQVK 54 (76)
Q Consensus 37 ~~~~~La~~l~l~~~qV~ 54 (76)
.+...++..||+++.+++
T Consensus 21 ~ev~ywa~~~gvt~~~L~ 38 (57)
T PF12244_consen 21 YEVRYWAKRFGVTEEQLR 38 (57)
T ss_pred HHHHHHHHHHCcCHHHHH
Confidence 456677888888887765
No 249
>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=49.84 E-value=63 Score=20.27 Aligned_cols=29 Identities=21% Similarity=0.224 Sum_probs=22.7
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
.-.++|..||++...|+.... -+.+.++.
T Consensus 244 s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~ 273 (285)
T TIGR02394 244 TLEEVAAEVGLTRERVRQIQVEALKKLRRI 273 (285)
T ss_pred cHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999987 55555543
No 250
>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=49.32 E-value=21 Score=20.30 Aligned_cols=20 Identities=20% Similarity=0.175 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|.+
T Consensus 4 IgevA~~~Gvs~~tLRyYE~ 23 (142)
T TIGR01950 4 VGELAKRSGVAVSALHFYES 23 (142)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999986
No 251
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=49.28 E-value=19 Score=20.36 Aligned_cols=20 Identities=15% Similarity=0.099 Sum_probs=17.7
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...|+.|-.
T Consensus 4 I~e~a~~~gvs~~tlR~Ye~ 23 (140)
T PRK09514 4 IGELAKLAEVTPDTLRFYEK 23 (140)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999986
No 252
>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=49.03 E-value=19 Score=19.84 Aligned_cols=20 Identities=10% Similarity=0.125 Sum_probs=17.3
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|-+
T Consensus 3 I~e~a~~~gvs~~tlRyYe~ 22 (127)
T cd01108 3 IGEAAKLTGLSAKMIRYYEE 22 (127)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999876
No 253
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=48.94 E-value=58 Score=20.65 Aligned_cols=28 Identities=18% Similarity=0.234 Sum_probs=22.0
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
.-.++|..+|+++..|+...+ -|.+.+.
T Consensus 136 s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~ 164 (290)
T PRK09635 136 PYQQIATTIGSQASTCRQLAHRARRKINE 164 (290)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHh
Confidence 345789999999999999998 5555554
No 254
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=48.69 E-value=23 Score=18.17 Aligned_cols=20 Identities=35% Similarity=0.416 Sum_probs=17.1
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
...+|..||++..-|--|=.
T Consensus 13 ~~kvA~aLGIs~~AVsQWGe 32 (75)
T PRK09744 13 KTKLANAAGVRLASVAAWGE 32 (75)
T ss_pred HHHHHHHHCCCHHHHHHHhc
Confidence 34789999999999999954
No 255
>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=48.47 E-value=20 Score=19.53 Aligned_cols=20 Identities=20% Similarity=0.222 Sum_probs=17.4
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|-.
T Consensus 3 IgevA~~~gvs~~tlRyYe~ 22 (120)
T cd04781 3 IAEVARQSGLPASTLRYYEE 22 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999975
No 256
>PRK05572 sporulation sigma factor SigF; Validated
Probab=48.42 E-value=63 Score=19.82 Aligned_cols=38 Identities=13% Similarity=0.218 Sum_probs=25.3
Q ss_pred CCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 16 FSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 16 ~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
+++.+..++...|.. .....++|..+|++...|..+-.
T Consensus 203 L~~~~~~v~~l~~~~-----~~s~~eIA~~lgis~~~V~~~~~ 240 (252)
T PRK05572 203 LDERERLIVYLRYFK-----DKTQSEVAKRLGISQVQVSRLEK 240 (252)
T ss_pred CCHHHHHHHHHHHhC-----CCCHHHHHHHHCcCHHHHHHHHH
Confidence 444555555554432 23456889999999999988776
No 257
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=48.27 E-value=20 Score=20.16 Aligned_cols=20 Identities=15% Similarity=0.233 Sum_probs=16.7
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...|+.|=.
T Consensus 3 Ige~a~~~gvs~~tlRyYE~ 22 (135)
T PRK10227 3 ISDVAKITGLTSKAIRFYEE 22 (135)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999998854
No 258
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=47.84 E-value=65 Score=19.83 Aligned_cols=38 Identities=18% Similarity=0.292 Sum_probs=25.4
Q ss_pred CCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 16 FSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 16 ~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
+++.+..++...|... ....++|..+|++...|...-.
T Consensus 210 L~~~er~vi~~~~~~~-----~t~~eIA~~lgis~~~V~~~~~ 247 (258)
T PRK08215 210 LNDREKLILNLRFFQG-----KTQMEVAEEIGISQAQVSRLEK 247 (258)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHH
Confidence 4555555565555322 2356889999999999877665
No 259
>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=47.73 E-value=20 Score=20.45 Aligned_cols=25 Identities=12% Similarity=0.093 Sum_probs=20.5
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAK 62 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k 62 (76)
...+++..+|++..+|..|.. .|..
T Consensus 48 ti~eV~e~tgVs~~~I~~~IreGRL~ 73 (137)
T TIGR03826 48 TVSEIVEETGVSEKLILKFIREGRLQ 73 (137)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcCCee
Confidence 345789999999999999997 6543
No 260
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=47.73 E-value=57 Score=19.58 Aligned_cols=37 Identities=11% Similarity=-0.013 Sum_probs=27.4
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhh
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTG 57 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWF 57 (76)
.+|+-+..+|....+-. ...++|..|++++..|+.--
T Consensus 134 ~LT~RE~eVL~ll~~G~------snkeIA~~L~iS~~TV~~h~ 170 (207)
T PRK11475 134 MLSPTEREILRFMSRGY------SMPQIAEQLERNIKTIRAHK 170 (207)
T ss_pred CCCHHHHHHHHHHHCCC------CHHHHHHHHCCCHHHHHHHH
Confidence 47888888876665443 35578999999999988743
No 261
>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=47.48 E-value=21 Score=19.69 Aligned_cols=20 Identities=10% Similarity=0.184 Sum_probs=17.3
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|-+
T Consensus 3 I~e~a~~~gvs~~tlRyYe~ 22 (127)
T TIGR02044 3 IGQVAKLTGLSSKMIRYYEE 22 (127)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999875
No 262
>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=47.40 E-value=63 Score=19.61 Aligned_cols=49 Identities=8% Similarity=0.072 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 16 FSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 16 ~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
+++.+..+|...|-...+ ......++|..+|++...|+.... -..+.+.
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 455555566655532211 222466899999999999999887 4444443
No 263
>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=46.85 E-value=22 Score=19.67 Aligned_cols=20 Identities=15% Similarity=0.217 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|-.
T Consensus 3 I~e~a~~~gvs~~tlR~Ye~ 22 (127)
T TIGR02047 3 IGELAQKTGVSVETIRFYEK 22 (127)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999976
No 264
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=46.85 E-value=17 Score=17.87 Aligned_cols=17 Identities=18% Similarity=-0.019 Sum_probs=8.4
Q ss_pred HHHHhCCCchhHHHhhH
Q psy5355 42 LAYALGMTESQVKVTGP 58 (76)
Q Consensus 42 La~~l~l~~~qV~vWFq 58 (76)
+...+|++..+.-....
T Consensus 16 f~~~~g~s~~~~~~~~R 32 (81)
T PF12833_consen 16 FKKETGMSFKQYLRELR 32 (81)
T ss_dssp HHHHHSS-HHHHHHHHH
T ss_pred HHHHHCcCHHHHHHHHH
Confidence 34446666655544444
No 265
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc 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-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=46.84 E-value=25 Score=19.57 Aligned_cols=20 Identities=20% Similarity=0.228 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|-+
T Consensus 4 I~e~a~~~gvs~~tlR~Ye~ 23 (131)
T TIGR02043 4 IGELAKLCGVTSDTLRFYEK 23 (131)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999986
No 266
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=46.78 E-value=59 Score=19.02 Aligned_cols=37 Identities=14% Similarity=0.008 Sum_probs=27.9
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhh
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTG 57 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWF 57 (76)
.+|+-+..+|.....-. ...++|..+++++..|+.-.
T Consensus 150 ~Lt~rE~evl~~~~~G~------s~~eIA~~l~iS~~TV~~h~ 186 (216)
T PRK10840 150 RLSPKESEVLRLFAEGF------LVTEIAKKLNRSIKTISSQK 186 (216)
T ss_pred cCCHHHHHHHHHHHCCC------CHHHHHHHHCCCHHHHHHHH
Confidence 47888888876665433 35678999999999998754
No 267
>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=46.77 E-value=63 Score=19.40 Aligned_cols=21 Identities=24% Similarity=0.352 Sum_probs=17.2
Q ss_pred HHHHHHHHhCCCchhHHHhhH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq 58 (76)
...++|..+|++...|..+-.
T Consensus 201 t~~eIA~~lgis~~~V~~~~~ 221 (231)
T TIGR02885 201 TQTEVANMLGISQVQVSRLEK 221 (231)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 466889999999998877664
No 268
>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=46.45 E-value=23 Score=19.28 Aligned_cols=20 Identities=20% Similarity=0.262 Sum_probs=17.0
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|-.
T Consensus 3 I~eva~~~gvs~~tLRyYe~ 22 (123)
T cd04770 3 IGELAKAAGVSPDTIRYYER 22 (123)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999998865
No 269
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=46.22 E-value=7.5 Score=18.74 Aligned_cols=39 Identities=15% Similarity=0.072 Sum_probs=22.7
Q ss_pred HHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 20 QIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 20 q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
.-.-|+..|....--.......||..||+++..|..-++
T Consensus 6 ~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~ 44 (60)
T PF01325_consen 6 EEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLK 44 (60)
T ss_dssp HHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHH
Confidence 334455555443222222345789999999998876554
No 270
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=46.20 E-value=14 Score=19.54 Aligned_cols=30 Identities=20% Similarity=0.320 Sum_probs=19.6
Q ss_pred HHHHHhccccCCCCHHHHHHHHHHhCCCchhHHH
Q psy5355 22 FALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55 (76)
Q Consensus 22 ~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~v 55 (76)
..|...|....+ ..+.+|..||++...|.-
T Consensus 13 ~ELq~nf~~~~l----s~~~ia~dL~~s~~~le~ 42 (89)
T PF10078_consen 13 QELQANFELSGL----SLEQIAADLGTSPEHLEQ 42 (89)
T ss_pred HHHHHHHHHcCC----CHHHHHHHhCCCHHHHHH
Confidence 355556665543 356788888888876654
No 271
>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=46.09 E-value=56 Score=18.61 Aligned_cols=29 Identities=21% Similarity=0.088 Sum_probs=20.9
Q ss_pred HHHHHHHHHhCCCchhHHHhhH-hHHHHHH
Q psy5355 37 PERAKLAYALGMTESQVKVTGP-ERAKLAY 65 (76)
Q Consensus 37 ~~~~~La~~l~l~~~qV~vWFq-rR~k~kk 65 (76)
....++|..+|++...|+.=.. -|.+.++
T Consensus 157 ~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~ 186 (189)
T TIGR02984 157 LSFAEVAERMDRSEGAVSMLWVRGLARLRQ 186 (189)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3456889999999999887665 4444443
No 272
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=45.79 E-value=27 Score=17.08 Aligned_cols=19 Identities=26% Similarity=0.235 Sum_probs=16.1
Q ss_pred HHHHHHhCCCchhHHHhhH
Q psy5355 40 AKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 40 ~~La~~l~l~~~qV~vWFq 58 (76)
.++|..+|++.-+++-|..
T Consensus 19 ~eiA~~~gls~~~aR~yL~ 37 (62)
T PF04703_consen 19 REIADALGLSIYQARYYLE 37 (62)
T ss_dssp HHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHhCCCHHHHHHHHH
Confidence 4789999999999999886
No 273
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=45.57 E-value=61 Score=19.31 Aligned_cols=38 Identities=8% Similarity=0.066 Sum_probs=28.7
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
.+|+-+..+|.-.-+-. ...++|..|++++..|+.-..
T Consensus 137 ~LT~RE~eVL~lla~G~------snkeIA~~L~iS~~TVk~h~~ 174 (207)
T PRK15411 137 SLSRTESSMLRMWMAGQ------GTIQISDQMNIKAKTVSSHKG 174 (207)
T ss_pred cCCHHHHHHHHHHHcCC------CHHHHHHHcCCCHHHHHHHHH
Confidence 48888888886554433 356889999999999988664
No 274
>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=45.36 E-value=38 Score=18.52 Aligned_cols=14 Identities=21% Similarity=0.316 Sum_probs=7.3
Q ss_pred HHHHHHhCCCchhH
Q psy5355 40 AKLAYALGMTESQV 53 (76)
Q Consensus 40 ~~La~~l~l~~~qV 53 (76)
.++|..||++...|
T Consensus 127 ~EIA~~l~is~~tV 140 (142)
T TIGR03209 127 IDIAKKLHISRQSV 140 (142)
T ss_pred HHHHHHHCcCHHhh
Confidence 34555555555544
No 275
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=45.25 E-value=17 Score=16.80 Aligned_cols=20 Identities=30% Similarity=0.365 Sum_probs=17.0
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
-..||...|++...|.-||.
T Consensus 22 ~~~La~~FgIs~stvsri~~ 41 (53)
T PF13613_consen 22 FQDLAYRFGISQSTVSRIFH 41 (53)
T ss_pred HhHHhhheeecHHHHHHHHH
Confidence 45789999999999998885
No 276
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=45.12 E-value=69 Score=19.35 Aligned_cols=38 Identities=18% Similarity=0.087 Sum_probs=30.0
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
.+|+.+..+|.-...-. ...++|..|++++..|+.+..
T Consensus 155 ~Lt~rE~~Vl~l~~~G~------s~~eIA~~L~iS~~TVk~~~~ 192 (216)
T PRK10100 155 LLTHREKEILNKLRIGA------SNNEIARSLFISENTVKTHLY 192 (216)
T ss_pred CCCHHHHHHHHHHHcCC------CHHHHHHHhCCCHHHHHHHHH
Confidence 47888888887766632 345789999999999999886
No 277
>PRK00215 LexA repressor; Validated
Probab=44.85 E-value=28 Score=20.63 Aligned_cols=41 Identities=29% Similarity=0.343 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHhcc---ccCCCCHHHHHHHHHHhCC-CchhHHHhhH
Q psy5355 16 FSGQQIFALEKTFE---QTKYLAGPERAKLAYALGM-TESQVKVTGP 58 (76)
Q Consensus 16 ~t~~q~~~L~~~f~---~~~~p~~~~~~~La~~l~l-~~~qV~vWFq 58 (76)
+|+.|...|+...+ .+..+ ....+||..+|+ +...|..+.+
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~--~s~~ela~~~~~~~~~tv~~~l~ 46 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYP--PSRREIADALGLRSPSAVHEHLK 46 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCC--CCHHHHHHHhCCCChHHHHHHHH
Confidence 46778888876653 23332 234579999999 9988887765
No 278
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine 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, and organic su
Probab=44.47 E-value=25 Score=19.65 Aligned_cols=20 Identities=25% Similarity=0.328 Sum_probs=16.7
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|=+
T Consensus 3 Ige~a~~~gvs~~tLRyYE~ 22 (131)
T cd04786 3 IGELAKRSGMAASRIRFYEA 22 (131)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999998854
No 279
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=43.86 E-value=72 Score=19.22 Aligned_cols=27 Identities=26% Similarity=0.266 Sum_probs=20.1
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAKLA 64 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k~k 64 (76)
...++|..+|++...|..+.. -+.+.+
T Consensus 196 S~~EIAe~lgis~~tV~~~~~rAl~~Lr 223 (227)
T TIGR02846 196 TQREIAKILGISRSYVSRIEKRALMKLY 223 (227)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 356889999999999988765 344443
No 280
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are 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 have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. 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=43.78 E-value=26 Score=19.30 Aligned_cols=20 Identities=15% Similarity=0.192 Sum_probs=17.1
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|-.
T Consensus 3 I~e~a~~~gvs~~tlR~Ye~ 22 (126)
T cd04785 3 IGELARRTGVNVETIRYYES 22 (126)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999998875
No 281
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that 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. This subgroup lacks one of the c
Probab=43.68 E-value=26 Score=19.46 Aligned_cols=20 Identities=30% Similarity=0.302 Sum_probs=17.1
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|-.
T Consensus 3 IgE~A~~~gvs~~TLRyYE~ 22 (133)
T cd04787 3 VKELANAAGVTPDTVRFYTR 22 (133)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999998875
No 282
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=43.61 E-value=32 Score=18.42 Aligned_cols=42 Identities=12% Similarity=0.146 Sum_probs=24.2
Q ss_pred CCCHHHHHHHHHhccccCCC--CHHHHHHHHHHhCCCchhHHHh
Q psy5355 15 TFSGQQIFALEKTFEQTKYL--AGPERAKLAYALGMTESQVKVT 56 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p--~~~~~~~La~~l~l~~~qV~vW 56 (76)
.+|+.....|...+....-. ......++|..+|++...|.-|
T Consensus 32 lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~ 75 (94)
T TIGR01321 32 ILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRG 75 (94)
T ss_pred hCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHH
Confidence 35666677776665543311 1112346788888887766544
No 283
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development. CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.
Probab=43.61 E-value=27 Score=18.57 Aligned_cols=25 Identities=28% Similarity=0.226 Sum_probs=19.5
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAK 62 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k 62 (76)
....+|..+|+++.+|--|.. -+.+
T Consensus 25 gq~~vA~~~Gv~eStISR~k~~~~~~ 50 (91)
T PF05269_consen 25 GQKKVAEAMGVDESTISRWKNDFIEK 50 (91)
T ss_dssp HHHHHHHHHTSSTTTHHHHHHHHHHH
T ss_pred hhHHHHHHhCCCHHHHHHHHhhHHHH
Confidence 345789999999999999975 4443
No 284
>KOG3755|consensus
Probab=43.54 E-value=50 Score=23.83 Aligned_cols=45 Identities=9% Similarity=-0.201 Sum_probs=27.0
Q ss_pred HHhccccCCCCHHHHHHHHHHhC-------CCchhHHHhhH-hHHHHHHHcCC
Q psy5355 25 EKTFEQTKYLAGPERAKLAYALG-------MTESQVKVTGP-ERAKLAYALGM 69 (76)
Q Consensus 25 ~~~f~~~~~p~~~~~~~La~~l~-------l~~~qV~vWFq-rR~k~kk~~~~ 69 (76)
+..|..+..++.....+-...+. .....|+.||. +|+++++....
T Consensus 708 ~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~~ 760 (769)
T KOG3755|consen 708 HHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKMS 760 (769)
T ss_pred hhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhcc
Confidence 34455555555554433333322 24467999999 99998886544
No 285
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=43.52 E-value=33 Score=15.73 Aligned_cols=38 Identities=24% Similarity=0.294 Sum_probs=26.2
Q ss_pred CCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhh
Q psy5355 16 FSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTG 57 (76)
Q Consensus 16 ~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWF 57 (76)
+|..|..+|...+...+ . ...+||..++++...|..+-
T Consensus 1 lt~~q~~iL~~l~~~~~-~---~~~~la~~~~~~~~~~t~~i 38 (59)
T PF01047_consen 1 LTPSQFRILRILYENGG-I---TQSELAEKLGISRSTVTRII 38 (59)
T ss_dssp STHHHHHHHHHHHHHSS-E---EHHHHHHHHTS-HHHHHHHH
T ss_pred CCHHHHHHHHHHHHcCC-C---CHHHHHHHHCCChhHHHHHH
Confidence 36677888877776554 2 23488999999998877655
No 286
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of 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 three conserved cysteines that define a mercury 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=43.50 E-value=26 Score=19.25 Aligned_cols=20 Identities=20% Similarity=0.214 Sum_probs=16.9
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...|+.|-+
T Consensus 3 I~e~a~~~gvs~~tlR~Ye~ 22 (126)
T cd04783 3 IGELAKAAGVNVETIRYYQR 22 (126)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999988865
No 287
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=43.44 E-value=48 Score=19.38 Aligned_cols=35 Identities=17% Similarity=0.367 Sum_probs=25.0
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhC-CCchhHH
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALG-MTESQVK 54 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~-l~~~qV~ 54 (76)
.+|++.+..|..++.... .-.++|..|| ++..-|-
T Consensus 2 ~Wtde~~~~L~~lw~~G~-----SasqIA~~lg~vsRnAVi 37 (162)
T PF07750_consen 2 SWTDERVERLRKLWAEGL-----SASQIARQLGGVSRNAVI 37 (162)
T ss_pred CCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCcchhhhh
Confidence 478888999988886653 3456788888 7776543
No 288
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are 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 have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. 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=43.05 E-value=27 Score=19.17 Aligned_cols=20 Identities=15% Similarity=0.149 Sum_probs=17.2
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|-.
T Consensus 3 IgevA~~~gvs~~tLRyYe~ 22 (127)
T cd04784 3 IGELAKKTGCSVETIRYYEK 22 (127)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999875
No 289
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=42.74 E-value=43 Score=16.37 Aligned_cols=40 Identities=28% Similarity=0.269 Sum_probs=23.2
Q ss_pred CCHHHHHHHHH---hccccCCCCHHHHHHHHHHhCCC-chhHHHhh
Q psy5355 16 FSGQQIFALEK---TFEQTKYLAGPERAKLAYALGMT-ESQVKVTG 57 (76)
Q Consensus 16 ~t~~q~~~L~~---~f~~~~~p~~~~~~~La~~l~l~-~~qV~vWF 57 (76)
+|+-|..+|+- +...+.||. ...+||..+|+. ...|.--.
T Consensus 4 LT~rQ~~vL~~I~~~~~~~G~~P--t~rEIa~~~g~~S~~tv~~~L 47 (65)
T PF01726_consen 4 LTERQKEVLEFIREYIEENGYPP--TVREIAEALGLKSTSTVQRHL 47 (65)
T ss_dssp --HHHHHHHHHHHHHHHHHSS-----HHHHHHHHTSSSHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHcCCCC--CHHHHHHHhCCCChHHHHHHH
Confidence 56666666554 445677763 455889999997 66665433
No 290
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=42.49 E-value=22 Score=19.72 Aligned_cols=20 Identities=15% Similarity=0.129 Sum_probs=18.0
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
...||..+|++...|.-|..
T Consensus 21 q~~lA~~~gvs~~~is~~E~ 40 (135)
T PRK09706 21 QRSLAKAVKVSHVSISQWER 40 (135)
T ss_pred HHHHHHHhCCCHHHHHHHHc
Confidence 45889999999999999997
No 291
>PRK09726 antitoxin HipB; Provisional
Probab=42.09 E-value=31 Score=17.64 Aligned_cols=20 Identities=15% Similarity=0.328 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
...||..+|++...|.-|..
T Consensus 28 q~elA~~~gvs~~tis~~e~ 47 (88)
T PRK09726 28 QSELAKKIGIKQATISNFEN 47 (88)
T ss_pred HHHHHHHHCcCHHHHHHHHC
Confidence 55789999999999999986
No 292
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=42.07 E-value=25 Score=18.48 Aligned_cols=40 Identities=28% Similarity=0.247 Sum_probs=23.5
Q ss_pred CCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHH
Q psy5355 16 FSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55 (76)
Q Consensus 16 ~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~v 55 (76)
+++.+..+|.-.-..+..........|+..|+++..+|+.
T Consensus 45 ~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~ 84 (102)
T PF08784_consen 45 LSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRK 84 (102)
T ss_dssp S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHH
T ss_pred CCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHH
Confidence 5556666655444434445556677899999999988764
No 293
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=41.87 E-value=77 Score=19.01 Aligned_cols=38 Identities=18% Similarity=0.198 Sum_probs=27.2
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
.+|+-+..+|.-.-.-. .-.++|.+|++++..|++--.
T Consensus 148 ~LT~RE~eVL~lla~G~------snkeIA~~L~iS~~TVk~h~~ 185 (211)
T COG2197 148 LLTPRELEVLRLLAEGL------SNKEIAEELNLSEKTVKTHVS 185 (211)
T ss_pred CCCHHHHHHHHHHHCCC------CHHHHHHHHCCCHhHHHHHHH
Confidence 57888877775543322 345789999999999997553
No 294
>PHA02955 hypothetical protein; Provisional
Probab=40.70 E-value=38 Score=20.88 Aligned_cols=40 Identities=15% Similarity=0.217 Sum_probs=30.1
Q ss_pred HHHHHHHHhcccc-CCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 19 QQIFALEKTFEQT-KYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 19 ~q~~~L~~~f~~~-~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
.++..|-..|... ...+..++..++..||+....|.-||.
T Consensus 61 ~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~ 101 (213)
T PHA02955 61 KNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKK 101 (213)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCccc
Confidence 4555666666544 457788899999999999987788886
No 295
>PRK13749 transcriptional regulator MerD; Provisional
Probab=40.64 E-value=33 Score=19.11 Aligned_cols=19 Identities=21% Similarity=0.165 Sum_probs=16.2
Q ss_pred HHHHHHHhCCCchhHHHhh
Q psy5355 39 RAKLAYALGMTESQVKVTG 57 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWF 57 (76)
..++|..+|++...|+.|=
T Consensus 6 IgelA~~~gvS~~tiR~YE 24 (121)
T PRK13749 6 VSRLALDAGVSVHIVRDYL 24 (121)
T ss_pred HHHHHHHHCCCHHHHHHHH
Confidence 5688999999999998873
No 296
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=40.46 E-value=33 Score=14.34 Aligned_cols=19 Identities=16% Similarity=0.153 Sum_probs=13.7
Q ss_pred HHHHHHhCCCchhHHHhhH
Q psy5355 40 AKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 40 ~~La~~l~l~~~qV~vWFq 58 (76)
..-|...|++..+|+..+.
T Consensus 9 i~eA~~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 9 IKEAKESGLSKEEIREFLE 27 (30)
T ss_dssp HHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHH
Confidence 3458999999999998775
No 297
>PRK09480 slmA division inhibitor protein; Provisional
Probab=40.19 E-value=40 Score=19.26 Aligned_cols=33 Identities=24% Similarity=0.237 Sum_probs=26.1
Q ss_pred HHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 25 EKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 25 ~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
...|...+. .......||...|++...+-.+|.
T Consensus 20 ~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~ 52 (194)
T PRK09480 20 AQMLESPPG-ERITTAKLAARVGVSEAALYRHFP 52 (194)
T ss_pred HHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCC
Confidence 334545545 677788999999999999999998
No 298
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=40.17 E-value=57 Score=22.10 Aligned_cols=34 Identities=26% Similarity=0.212 Sum_probs=25.1
Q ss_pred HHHHHHhccccCCCCHHHHHHHHHHhCCCchhHH
Q psy5355 21 IFALEKTFEQTKYLAGPERAKLAYALGMTESQVK 54 (76)
Q Consensus 21 ~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~ 54 (76)
+..|...=+...|.+......+|..|||+...|.
T Consensus 40 IplL~~~Qe~~GyIp~~ai~~VAe~Lgvp~~~V~ 73 (400)
T PRK12373 40 IPLLMRAQEQEGWVTRAAIEKVADMLDMAYIRVL 73 (400)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHH
Confidence 3344333345568999999999999999987765
No 299
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), 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=40.12 E-value=33 Score=18.19 Aligned_cols=20 Identities=20% Similarity=0.009 Sum_probs=15.9
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...++.|=+
T Consensus 3 Ige~a~~~gvs~~tlRyYe~ 22 (107)
T cd04777 3 IGKFAKKNNITIDTVRHYID 22 (107)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999998887754
No 300
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=39.50 E-value=63 Score=17.34 Aligned_cols=19 Identities=16% Similarity=-0.045 Sum_probs=15.3
Q ss_pred HHHHHHhCCCchhHHHhhH
Q psy5355 40 AKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 40 ~~La~~l~l~~~qV~vWFq 58 (76)
..||..+|++...|.-|-.
T Consensus 82 ~~lA~~lg~~~~tis~~e~ 100 (127)
T TIGR03830 82 REAAELLGGGVNAFSRYER 100 (127)
T ss_pred HHHHHHhCCCHHHHHHHHC
Confidence 4678888888888888876
No 301
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. 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 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=39.27 E-value=34 Score=18.48 Aligned_cols=20 Identities=20% Similarity=0.248 Sum_probs=17.3
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...+..|-.
T Consensus 3 ige~a~~~gvs~~tLryYe~ 22 (116)
T cd04769 3 IGELAQQTGVTIKAIRLYEE 22 (116)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999986
No 302
>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=39.22 E-value=66 Score=17.43 Aligned_cols=39 Identities=21% Similarity=0.198 Sum_probs=28.5
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
-+|..|...|+-+|..+- ...++|..+|++..-|.-|.+
T Consensus 17 LLT~kQ~~~l~lyy~eDl-----SlsEIAe~~~iSRqaV~d~ik 55 (101)
T PF04297_consen 17 LLTEKQREILELYYEEDL-----SLSEIAEELGISRQAVYDSIK 55 (101)
T ss_dssp GS-HHHHHHHHHHCTS--------HHHHHHHCTS-HHHHHHHHH
T ss_pred HCCHHHHHHHHHHHccCC-----CHHHHHHHHCCCHHHHHHHHH
Confidence 367888888888777663 456889999999999988886
No 303
>PF13223 DUF4031: Protein of unknown function (DUF4031)
Probab=39.14 E-value=42 Score=17.54 Aligned_cols=19 Identities=16% Similarity=-0.045 Sum_probs=15.4
Q ss_pred HHHHHHHHHHhCCCchhHHHhhH
Q psy5355 36 GPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 36 ~~~~~~La~~l~l~~~qV~vWFq 58 (76)
..|...+|..+||+. .|||
T Consensus 23 ~~ELHafA~riGv~r----r~fq 41 (83)
T PF13223_consen 23 LDELHAFAARIGVPR----RWFQ 41 (83)
T ss_pred HHHHHHHHHHcCCCH----HHHc
Confidence 556778899999987 5888
No 304
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=38.64 E-value=60 Score=16.78 Aligned_cols=37 Identities=19% Similarity=0.262 Sum_probs=23.2
Q ss_pred CHHHHHHHH---HhccccCCCCHHHHHHHHHHhCCCchhHHH
Q psy5355 17 SGQQIFALE---KTFEQTKYLAGPERAKLAYALGMTESQVKV 55 (76)
Q Consensus 17 t~~q~~~L~---~~f~~~~~p~~~~~~~La~~l~l~~~qV~v 55 (76)
|+-|..+|. ..|....-|-... .||..+++++..|+.
T Consensus 3 t~rq~~IL~alV~~Y~~~~~PVgSk--~ia~~l~~s~aTIRN 42 (78)
T PF03444_consen 3 TERQREILKALVELYIETGEPVGSK--TIAEELGRSPATIRN 42 (78)
T ss_pred CHHHHHHHHHHHHHHHhcCCCcCHH--HHHHHHCCChHHHHH
Confidence 444444444 4466665554443 678889999988775
No 305
>cd00131 PAX Paired Box domain
Probab=38.59 E-value=72 Score=17.71 Aligned_cols=44 Identities=9% Similarity=-0.054 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCC-------CchhHHHhhH
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGM-------TESQVKVTGP 58 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l-------~~~qV~vWFq 58 (76)
..++.+...++.....++..+..+...+...-|+ +..+|--||+
T Consensus 75 ~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~ 125 (128)
T cd00131 75 VATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILR 125 (128)
T ss_pred cCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHH
Confidence 4566666767777788888888877544223355 7777777765
No 306
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=38.45 E-value=51 Score=15.91 Aligned_cols=41 Identities=20% Similarity=0.169 Sum_probs=22.2
Q ss_pred CCCCCHHHHHHHHHh-ccccCCCC--HHHHHHHHHHhCCCchhH
Q psy5355 13 RPTFSGQQIFALEKT-FEQTKYLA--GPERAKLAYALGMTESQV 53 (76)
Q Consensus 13 R~~~t~~q~~~L~~~-f~~~~~p~--~~~~~~La~~l~l~~~qV 53 (76)
.+.++...+..||.- |..-+-+. ..-....|..|||....|
T Consensus 19 ~t~I~~~~l~aiE~~~~~~lp~~~y~rg~lr~Ya~~Lgld~~~l 62 (62)
T PF13413_consen 19 ETKISVSYLEAIENGDFDSLPSPVYARGYLRKYARFLGLDPDEL 62 (62)
T ss_dssp HCS--HHHHHHHHCT-GCCSSSHHHHHHHHHHHHHHTT--HHHH
T ss_pred HhCCCHHHHHHHHCcChhhCCcHHHHHHHHHHHHHHhCcCcccC
Confidence 356777888888776 55444221 112345688888887654
No 307
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=38.42 E-value=36 Score=14.54 Aligned_cols=19 Identities=11% Similarity=0.086 Sum_probs=12.9
Q ss_pred HHHHHHHHhCCCchhHHHh
Q psy5355 38 ERAKLAYALGMTESQVKVT 56 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vW 56 (76)
....||..+|++...+.-|
T Consensus 8 tl~~IA~~~~~~~~~l~~~ 26 (44)
T PF01476_consen 8 TLWSIAKRYGISVDELMEL 26 (44)
T ss_dssp -HHHHHHHTTS-HHHHHHH
T ss_pred cHHHHHhhhhhhHhHHHHh
Confidence 4567888888888877655
No 308
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=38.24 E-value=30 Score=16.35 Aligned_cols=21 Identities=33% Similarity=0.404 Sum_probs=16.6
Q ss_pred HHHHHHHHhCCCchhHHHhhH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq 58 (76)
....+|..+|++...|.-|-.
T Consensus 16 s~~~lA~~~g~s~s~v~~iE~ 36 (64)
T PF13560_consen 16 SQAQLADRLGVSQSTVSRIER 36 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHC
Confidence 456889999999999988887
No 309
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=37.72 E-value=24 Score=17.64 Aligned_cols=20 Identities=20% Similarity=0.142 Sum_probs=12.8
Q ss_pred HHHHHHHHHhCCCchhHHHh
Q psy5355 37 PERAKLAYALGMTESQVKVT 56 (76)
Q Consensus 37 ~~~~~La~~l~l~~~qV~vW 56 (76)
....+||..+|+++..|--.
T Consensus 35 ~si~elA~~~~vS~sti~Rf 54 (77)
T PF01418_consen 35 MSISELAEKAGVSPSTIVRF 54 (77)
T ss_dssp --HHHHHHHCTS-HHHHHHH
T ss_pred ccHHHHHHHcCCCHHHHHHH
Confidence 34567899999988876543
No 310
>PF07423 DUF1510: Protein of unknown function (DUF1510); InterPro: IPR009988 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=37.68 E-value=19 Score=22.21 Aligned_cols=31 Identities=16% Similarity=0.142 Sum_probs=22.2
Q ss_pred ccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 28 FEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 28 f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
|.....-=.+.+..++..+||+..+.-+||-
T Consensus 145 y~~~S~DW~Em~~Ais~atgi~~~~mi~w~i 175 (217)
T PF07423_consen 145 YDSGSVDWNEMLKAISYATGISEDNMIVWFI 175 (217)
T ss_pred ccCCCcCHHHHHHHHHHhhCCChhheEEEhh
Confidence 4444322233446799999999999999996
No 311
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=37.60 E-value=40 Score=14.48 Aligned_cols=21 Identities=14% Similarity=-0.023 Sum_probs=12.8
Q ss_pred HHHHHHHHHhCCCchhHHHhh
Q psy5355 37 PERAKLAYALGMTESQVKVTG 57 (76)
Q Consensus 37 ~~~~~La~~l~l~~~qV~vWF 57 (76)
.....+|..+|+++....-=|
T Consensus 9 ~~l~~iA~~~g~S~~~f~r~F 29 (42)
T PF00165_consen 9 LTLEDIAEQAGFSPSYFSRLF 29 (42)
T ss_dssp --HHHHHHHHTS-HHHHHHHH
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 456678999998776654444
No 312
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=37.49 E-value=37 Score=19.65 Aligned_cols=21 Identities=14% Similarity=0.148 Sum_probs=18.1
Q ss_pred HHHHHHHHhCCCchhHHHhhH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq 58 (76)
...++|..+|++...|+.|-+
T Consensus 13 ~IgevAk~~gvs~~TlRyYE~ 33 (154)
T PRK15002 13 TPGEVAKRSGVAVSALHFYES 33 (154)
T ss_pred cHHHHHHHHCcCHHHHHHHHH
Confidence 355789999999999999976
No 313
>PRK06424 transcription factor; Provisional
Probab=37.29 E-value=40 Score=19.34 Aligned_cols=20 Identities=15% Similarity=0.062 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..+||..+|++...|.-|..
T Consensus 100 Q~eLA~~iGvs~stIskiE~ 119 (144)
T PRK06424 100 QADLAAKIFERKNVIASIER 119 (144)
T ss_pred HHHHHHHhCCCHHHHHHHHC
Confidence 45899999999999999987
No 314
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=37.20 E-value=35 Score=16.03 Aligned_cols=19 Identities=21% Similarity=0.279 Sum_probs=15.0
Q ss_pred HHHHHHHhCCCchhHHHhh
Q psy5355 39 RAKLAYALGMTESQVKVTG 57 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWF 57 (76)
..+||..+|+++..|+-=+
T Consensus 17 ~~ela~~~~VS~~TiRRDl 35 (57)
T PF08220_consen 17 VKELAEEFGVSEMTIRRDL 35 (57)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 4578999999999887544
No 315
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=36.73 E-value=43 Score=15.63 Aligned_cols=21 Identities=24% Similarity=0.338 Sum_probs=16.2
Q ss_pred HHHHHHHHhCCCchhHHHhhH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq 58 (76)
....+|..+|++...|.-|-.
T Consensus 14 t~~~~a~~~~i~~~~i~~~e~ 34 (64)
T PF12844_consen 14 TQKDLAEKLGISRSTISKIEN 34 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHC
Confidence 355789999999999988876
No 316
>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=36.58 E-value=57 Score=17.27 Aligned_cols=33 Identities=21% Similarity=0.382 Sum_probs=19.9
Q ss_pred HHHHHhcccc-CCCCHHHHHHHHHHhCCCchhHH
Q psy5355 22 FALEKTFEQT-KYLAGPERAKLAYALGMTESQVK 54 (76)
Q Consensus 22 ~~L~~~f~~~-~~p~~~~~~~La~~l~l~~~qV~ 54 (76)
..|..+|..- .......=..|+..|||++..|.
T Consensus 4 ~~l~~~f~~i~~~V~~~~Wk~laR~LGLse~~I~ 37 (96)
T cd08315 4 ETLRRSFDHFIKEVPFDSWNRLMRQLGLSENEID 37 (96)
T ss_pred hHHHHHHHHHHHHCCHHHHHHHHHHcCCCHHHHH
Confidence 3455555432 22333444578999999987764
No 317
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=36.50 E-value=79 Score=17.57 Aligned_cols=38 Identities=11% Similarity=0.073 Sum_probs=28.3
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
.+|+.+..+|.-. ..+. ...++|..++++...|+.+.+
T Consensus 149 ~lt~~e~~vl~l~-~~g~-----~~~~Ia~~l~~s~~tv~~~~~ 186 (211)
T PRK15369 149 LLTPRERQILKLI-TEGY-----TNRDIAEQLSISIKTVETHRL 186 (211)
T ss_pred CCCHHHHHHHHHH-HCCC-----CHHHHHHHhCCCHHHHHHHHH
Confidence 4788777777663 3222 256789999999999999886
No 318
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=36.46 E-value=67 Score=17.02 Aligned_cols=41 Identities=7% Similarity=-0.037 Sum_probs=26.2
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHH
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~v 55 (76)
.++..|..+|...+............+||..++++...|..
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~ 62 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVK 62 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHH
Confidence 56788888887666211111233456789999998877654
No 319
>PF12200 DUF3597: Domain of unknown function (DUF3597); InterPro: IPR022016 This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 126 and 281 amino acids in length. The function of this domain is unknown. The structure of this domain has been found to contain five helices with a long flexible loop between helices one and two. ; PDB: 2GQB_A.
Probab=36.24 E-value=84 Score=17.82 Aligned_cols=25 Identities=24% Similarity=0.197 Sum_probs=17.8
Q ss_pred CCHHHHHHHHHHhCCCc-----hhHHHhhH
Q psy5355 34 LAGPERAKLAYALGMTE-----SQVKVTGP 58 (76)
Q Consensus 34 p~~~~~~~La~~l~l~~-----~qV~vWFq 58 (76)
.+...|.+||..||++- .+..||..
T Consensus 83 SSl~aRkeLA~eL~~~~~~~dsA~~NiwLh 112 (127)
T PF12200_consen 83 SSLAARKELAKELGYTGDYNDSASMNIWLH 112 (127)
T ss_dssp -SHHHHHHHHHHHT---SS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHhCCCCCCCccHHHHHHHH
Confidence 56778999999999887 46778986
No 320
>cd04778 HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 2). 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=36.16 E-value=37 Score=20.81 Aligned_cols=20 Identities=30% Similarity=0.223 Sum_probs=16.9
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..+||..+|++...|+.|=.
T Consensus 4 i~elA~~~Gvs~~tIR~Ye~ 23 (219)
T cd04778 4 IDDLARAAGTTVRNVRAYQD 23 (219)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999998853
No 321
>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=36.16 E-value=45 Score=14.69 Aligned_cols=36 Identities=25% Similarity=0.158 Sum_probs=21.9
Q ss_pred HHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhh
Q psy5355 18 GQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTG 57 (76)
Q Consensus 18 ~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWF 57 (76)
..+..+|....+ ++.. ...+||..+|++...|.--+
T Consensus 3 ~~~~~Il~~l~~-~~~~---t~~ela~~~~is~~tv~~~l 38 (48)
T PF13412_consen 3 ETQRKILNYLRE-NPRI---TQKELAEKLGISRSTVNRYL 38 (48)
T ss_dssp HHHHHHHHHHHH-CTTS----HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHH-cCCC---CHHHHHHHhCCCHHHHHHHH
Confidence 445556654444 4333 45578999999998876544
No 322
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=36.02 E-value=40 Score=19.20 Aligned_cols=21 Identities=14% Similarity=0.143 Sum_probs=17.6
Q ss_pred HHHHHHHHhCCCchhHHHhhH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq 58 (76)
...++|..+|++...++.|=+
T Consensus 9 ~IgevAk~~Gvs~~TLRyYE~ 29 (144)
T PRK13752 9 TIGVFAKAAGVNVETIRFYQR 29 (144)
T ss_pred cHHHHHHHHCcCHHHHHHHHH
Confidence 466889999999999998853
No 323
>PHA00542 putative Cro-like protein
Probab=35.73 E-value=42 Score=17.05 Aligned_cols=21 Identities=10% Similarity=0.099 Sum_probs=18.1
Q ss_pred HHHHHHHHhCCCchhHHHhhH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq 58 (76)
...+||..+|++...|.-|..
T Consensus 33 Tq~elA~~lgIs~~tIsr~e~ 53 (82)
T PHA00542 33 SQEQIADATDVSQPTICRIYS 53 (82)
T ss_pred CHHHHHHHHCcCHHHHHHHHc
Confidence 345789999999999999986
No 324
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. 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),
Probab=35.64 E-value=31 Score=17.81 Aligned_cols=18 Identities=33% Similarity=0.560 Sum_probs=13.9
Q ss_pred HHHHHHhCCCchhHHHhh
Q psy5355 40 AKLAYALGMTESQVKVTG 57 (76)
Q Consensus 40 ~~La~~l~l~~~qV~vWF 57 (76)
..||..||+++.+|..=-
T Consensus 17 k~laR~LGlse~~Id~i~ 34 (86)
T cd08306 17 RKLARKLGLSETKIESIE 34 (86)
T ss_pred HHHHHHcCCCHHHHHHHH
Confidence 468999999998876433
No 325
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, 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 domain
Probab=35.47 E-value=40 Score=19.73 Aligned_cols=20 Identities=20% Similarity=0.253 Sum_probs=17.1
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..++|..+|++...|..|=.
T Consensus 4 I~evA~~~gvs~~tLRyYe~ 23 (172)
T cd04790 4 ISQLARQFGLSRSTLLYYER 23 (172)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999998865
No 326
>PF14174 YycC: YycC-like protein
Probab=35.40 E-value=55 Score=15.48 Aligned_cols=22 Identities=23% Similarity=0.271 Sum_probs=16.5
Q ss_pred CCHHHHHHHHHHhCCCchhHHH
Q psy5355 34 LAGPERAKLAYALGMTESQVKV 55 (76)
Q Consensus 34 p~~~~~~~La~~l~l~~~qV~v 55 (76)
.+...-..||..||++..++.-
T Consensus 6 IS~eTA~kLs~~L~vPlE~lMH 27 (53)
T PF14174_consen 6 ISPETAVKLSKKLGVPLEQLMH 27 (53)
T ss_pred cCHHHHHHHHHHHCCcHHHHhc
Confidence 4455566899999999887653
No 327
>PRK15183 Vi polysaccharide biosynthesis protein TviA; Provisional
Probab=35.01 E-value=47 Score=18.39 Aligned_cols=36 Identities=22% Similarity=0.241 Sum_probs=24.6
Q ss_pred CCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCch
Q psy5355 16 FSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTES 51 (76)
Q Consensus 16 ~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~ 51 (76)
++..-..+|...|-..+.--...+.+||.++|+.+.
T Consensus 96 lsesgmeelqdrfmns~st~yrwrke~a~kfgvr~p 131 (143)
T PRK15183 96 LSESGMEELQDRFMNSSSTMYRWRKELAVKFGVREP 131 (143)
T ss_pred hhhccHHHHHHHHccChHHHHHHHHHHHHHhcCCCC
Confidence 455566777777776665555567788888886543
No 328
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, 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=34.44 E-value=36 Score=17.51 Aligned_cols=34 Identities=24% Similarity=0.385 Sum_probs=21.1
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHH
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~v 55 (76)
..|..++..+... .... =..||..||++...|..
T Consensus 4 ~~t~~~l~~ia~~------iG~~-Wk~Lar~LGls~~dI~~ 37 (86)
T cd08318 4 PVTGEQITVFANK------LGED-WKTLAPHLEMKDKEIRA 37 (86)
T ss_pred CCCHHHHHHHHHH------Hhhh-HHHHHHHcCCCHHHHHH
Confidence 3566666666432 2222 23689999999987754
No 329
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=34.05 E-value=34 Score=15.76 Aligned_cols=14 Identities=29% Similarity=0.572 Sum_probs=11.4
Q ss_pred HHHHHHhCCCchhH
Q psy5355 40 AKLAYALGMTESQV 53 (76)
Q Consensus 40 ~~La~~l~l~~~qV 53 (76)
.+||..+|++...|
T Consensus 7 ~elAk~l~v~~~~i 20 (54)
T PF04760_consen 7 SELAKELGVPSKEI 20 (54)
T ss_dssp THHHHHHSSSHHHH
T ss_pred HHHHHHHCcCHHHH
Confidence 47899999998764
No 330
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=33.75 E-value=38 Score=18.61 Aligned_cols=20 Identities=15% Similarity=0.111 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..+||..+|++...|.-|.+
T Consensus 21 q~eLA~~~Gis~~~is~iE~ 40 (120)
T PRK13890 21 KKELSERSGVSISFLSDLTT 40 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHc
Confidence 56799999999999999987
No 331
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. 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 a
Probab=33.22 E-value=71 Score=16.43 Aligned_cols=16 Identities=13% Similarity=0.488 Sum_probs=11.8
Q ss_pred HHHHHHHhCCCchhHH
Q psy5355 39 RAKLAYALGMTESQVK 54 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~ 54 (76)
=..++..|||++..|.
T Consensus 14 wk~~~R~LGlse~~Id 29 (80)
T cd08313 14 WKEFVRRLGLSDNEIE 29 (80)
T ss_pred HHHHHHHcCCCHHHHH
Confidence 3468888998887654
No 332
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=32.88 E-value=48 Score=15.05 Aligned_cols=19 Identities=21% Similarity=0.205 Sum_probs=14.9
Q ss_pred HHHHHHhCCCchhHHHhhH
Q psy5355 40 AKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 40 ~~La~~l~l~~~qV~vWFq 58 (76)
..+|..+|++...|---|.
T Consensus 3 ~dIA~~agvS~~TVSr~ln 21 (46)
T PF00356_consen 3 KDIAREAGVSKSTVSRVLN 21 (46)
T ss_dssp HHHHHHHTSSHHHHHHHHT
T ss_pred HHHHHHHCcCHHHHHHHHh
Confidence 4689999999988876554
No 333
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=32.69 E-value=45 Score=16.29 Aligned_cols=18 Identities=28% Similarity=0.414 Sum_probs=14.3
Q ss_pred HHHHHHHHhCCCchhHHH
Q psy5355 38 ERAKLAYALGMTESQVKV 55 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~v 55 (76)
.-.+||..+||+...|.-
T Consensus 24 ta~eLa~~lgl~~~~v~r 41 (68)
T smart00550 24 TALQLAKNLGLPKKEVNR 41 (68)
T ss_pred CHHHHHHHHCCCHHHHHH
Confidence 355899999999987654
No 334
>PRK10403 transcriptional regulator NarP; Provisional
Probab=32.44 E-value=97 Score=17.39 Aligned_cols=38 Identities=18% Similarity=0.232 Sum_probs=28.5
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
.+|+.+..+|...... ....++|..+++++..|++...
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~ 190 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIR 190 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHH
Confidence 4788888887755443 2356789999999999988775
No 335
>cd08311 Death_p75NR Death domain of p75 Neurotophin Receptor. Death Domain (DD) found in p75 neurotrophin receptor (p75NTR, NGFR, TNFRSF16). p75NTR binds members of the neurotrophin (NT) family including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and NT3, among others. It contains an NT-binding extracellular region that bears four cysteine-rich repeats, a transmembrane domain, and an intracellular DD. p75NTR plays roles in the immune, vascular, and nervous systems, and has been shown to promote cell death or survival, and to induce neurite outgrowth or collapse depending on its ligands and co-receptors. In general, 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 adaptor
Probab=32.35 E-value=50 Score=16.81 Aligned_cols=17 Identities=24% Similarity=0.321 Sum_probs=14.0
Q ss_pred HHHHHHhCCCchhHHHh
Q psy5355 40 AKLAYALGMTESQVKVT 56 (76)
Q Consensus 40 ~~La~~l~l~~~qV~vW 56 (76)
..||..||++...|..+
T Consensus 19 ~~LA~~LG~~~~~I~~i 35 (77)
T cd08311 19 RSLAGELGYEDEAIDTF 35 (77)
T ss_pred HHHHHHcCCCHHHHHHH
Confidence 37899999999887765
No 336
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=32.13 E-value=65 Score=17.25 Aligned_cols=20 Identities=25% Similarity=0.245 Sum_probs=12.8
Q ss_pred HHHHHHHHhCCCchhHHHhh
Q psy5355 38 ERAKLAYALGMTESQVKVTG 57 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWF 57 (76)
...+||..+|||+.+|.-=.
T Consensus 74 n~~eLA~kyglS~r~I~~Ii 93 (108)
T PF08765_consen 74 NVRELARKYGLSERQIYRII 93 (108)
T ss_dssp -HHHHHHHHT--HHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 35689999999999755433
No 337
>PF04550 Phage_holin_2: Phage holin family 2 ; InterPro: IPR007633 This entry represents the Bacteriophage P2, GpY, holin protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This protein family represent one of a large number of mutually dissimilar families of phage holins. It is thought that the temporal precision of holin-mediated lysis may occur through the build-up of a holin oligomer which causes the lysis [].
Probab=32.06 E-value=86 Score=16.65 Aligned_cols=28 Identities=25% Similarity=0.146 Sum_probs=18.5
Q ss_pred CCHHHHHHHHHHhCCCch-hHHHhhHhHH
Q psy5355 34 LAGPERAKLAYALGMTES-QVKVTGPERA 61 (76)
Q Consensus 34 p~~~~~~~La~~l~l~~~-qV~vWFqrR~ 61 (76)
.++....-++..+|+--. -|..||+||.
T Consensus 59 l~plAv~GlgsalGI~G~q~vE~~lrr~~ 87 (89)
T PF04550_consen 59 LPPLAVIGLGSALGIAGYQAVEAWLRRRL 87 (89)
T ss_pred CCHHHHHHHHHHHHhhhHHHHHHHHHHHh
Confidence 334455567888885544 4899998554
No 338
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, 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, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=31.98 E-value=43 Score=17.35 Aligned_cols=19 Identities=11% Similarity=0.312 Sum_probs=15.0
Q ss_pred HHHHHHhCCCchhHHHhhH
Q psy5355 40 AKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 40 ~~La~~l~l~~~qV~vWFq 58 (76)
..||..||++...|...-.
T Consensus 17 ~~Lar~Lgls~~~I~~i~~ 35 (83)
T cd08319 17 EQVLLDLGLSQTDIYRCKE 35 (83)
T ss_pred HHHHHHcCCCHHHHHHHHH
Confidence 4689999999988776554
No 339
>PHA02591 hypothetical protein; Provisional
Probab=31.95 E-value=47 Score=17.28 Aligned_cols=18 Identities=28% Similarity=0.346 Sum_probs=12.5
Q ss_pred HHHHHHHhCCCchhHHHh
Q psy5355 39 RAKLAYALGMTESQVKVT 56 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vW 56 (76)
.+++|..||++...|+-.
T Consensus 62 qeqIA~~LGVsqetVrKY 79 (83)
T PHA02591 62 VEKIASLLGVSVRKVRRY 79 (83)
T ss_pred HHHHHHHhCCCHHHHHHH
Confidence 446788888888777643
No 340
>COG1983 PspC Putative stress-responsive transcriptional regulator [Transcription / Signal transduction mechanisms]
Probab=31.63 E-value=47 Score=16.81 Aligned_cols=19 Identities=21% Similarity=0.188 Sum_probs=16.1
Q ss_pred HHHHHHHhCCCchhHHHhh
Q psy5355 39 RAKLAYALGMTESQVKVTG 57 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWF 57 (76)
..-||+-+|+++.-|+++|
T Consensus 18 cgGla~yf~id~tlVRll~ 36 (70)
T COG1983 18 CGGLAEYFGIDPTLVRLLF 36 (70)
T ss_pred ehhHHHHhCCChHHHHHHH
Confidence 4578999999999999887
No 341
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=31.60 E-value=1e+02 Score=17.28 Aligned_cols=38 Identities=18% Similarity=0.211 Sum_probs=28.3
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
.+|+.+...|.-.... .....+|..++++.+.|++...
T Consensus 137 ~Lt~~E~~il~~l~~g------~~~~~Ia~~l~~s~~tv~~~~~ 174 (196)
T PRK10360 137 PLTKRERQVAEKLAQG------MAVKEIAAELGLSPKTVHVHRA 174 (196)
T ss_pred CCCHHHHHHHHHHHCC------CCHHHHHHHhCCCHHHHHHHHH
Confidence 4777777777665543 2466889999999999988775
No 342
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=31.55 E-value=64 Score=16.09 Aligned_cols=20 Identities=25% Similarity=0.102 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..+.|..+|+.+..|..|..
T Consensus 16 ~~~Aa~~lG~~~~~v~~wv~ 35 (65)
T PF05344_consen 16 VAQAADRLGTDPGTVRRWVR 35 (65)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45779999999999999986
No 343
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=31.14 E-value=59 Score=19.12 Aligned_cols=41 Identities=22% Similarity=0.206 Sum_probs=28.4
Q ss_pred CCHHHHHHHHHhc---cccCCCCHHHHHHHHHHhCCC-chhHHHhhH
Q psy5355 16 FSGQQIFALEKTF---EQTKYLAGPERAKLAYALGMT-ESQVKVTGP 58 (76)
Q Consensus 16 ~t~~q~~~L~~~f---~~~~~p~~~~~~~La~~l~l~-~~qV~vWFq 58 (76)
+|+.|..+|+... ..+.+|. ...+||..+|++ ...|....+
T Consensus 4 lt~~q~~iL~~l~~~~~~~~~~~--~~~ela~~~~~~s~~tv~~~l~ 48 (199)
T TIGR00498 4 LTARQQEVLDLIRAHIESTGYPP--SIREIARAVGLRSPSAAEEHLK 48 (199)
T ss_pred cCHHHHHHHHHHHHHHHhcCCCC--cHHHHHHHhCCCChHHHHHHHH
Confidence 5778888887775 3455542 345899999998 777765543
No 344
>PF04936 DUF658: Protein of unknown function (DUF658); InterPro: IPR007020 This entry is represented by Bacteriophage r1t, Orf18. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. These are proteins of unknown function found in Lactococcus lactis and in their associated bacteriophage.
Probab=30.77 E-value=32 Score=20.46 Aligned_cols=25 Identities=16% Similarity=0.088 Sum_probs=21.0
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hHHH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ERAK 62 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR~k 62 (76)
...+|+.-++++..+|-+|.. .+..
T Consensus 16 t~~e~~~~~~VS~~sv~~WiKNG~~~ 41 (186)
T PF04936_consen 16 TIDELADYFDVSRTSVSVWIKNGKDP 41 (186)
T ss_pred cHHHHHHHHccCHHHHHHHHHcCCCc
Confidence 467899999999999999998 5443
No 345
>PHA02535 P terminase ATPase subunit; Provisional
Probab=30.45 E-value=1.5e+02 Score=21.27 Aligned_cols=39 Identities=15% Similarity=0.146 Sum_probs=25.6
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
.|+++....-...|.. .| ...++|..||++...|..|-.
T Consensus 2 ~yt~EfK~~Av~Ly~~-G~----sv~eIA~~LGv~~~Tl~~W~k 40 (581)
T PHA02535 2 AYDDDVRRAAKFLYWQ-GW----TVAEIAEELGLKSRTIYSWKE 40 (581)
T ss_pred CCCHHHHHHHHHHHHc-CC----CHHHHHHHhCCChhHHHHHhc
Confidence 3555544444444444 22 345789999999999999964
No 346
>PRK11426 hypothetical protein; Provisional
Probab=30.14 E-value=1.1e+02 Score=17.41 Aligned_cols=31 Identities=26% Similarity=0.352 Sum_probs=21.0
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHH
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVK 54 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~ 54 (76)
.++++++... ........||.++|+++.++.
T Consensus 60 pIs~~ql~~~---------lG~d~i~~lA~q~Gl~~~~~~ 90 (132)
T PRK11426 60 SVSGEQLESA---------LGTNAVSDLGQKLGVDTSTAS 90 (132)
T ss_pred CCCHHHHHHH---------hChHHHHHHHHHHCcCHHHHH
Confidence 4556655443 344577889999999987654
No 347
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=30.04 E-value=59 Score=18.80 Aligned_cols=20 Identities=35% Similarity=0.378 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..+||..+|++...|..|..
T Consensus 41 q~eLAerlGVS~~tIs~iE~ 60 (150)
T TIGR02612 41 GAQLAGRLGVTPQRVEALEK 60 (150)
T ss_pred HHHHHHHhCCCHHHHHHHHc
Confidence 46789999999999999986
No 348
>KOG0044|consensus
Probab=29.55 E-value=89 Score=18.91 Aligned_cols=27 Identities=7% Similarity=0.000 Sum_probs=21.7
Q ss_pred CCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 32 KYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 32 ~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
........+.|...+..++..|+.|+.
T Consensus 7 ~~~~~~~~e~l~~~t~f~~~ei~~~Yr 33 (193)
T KOG0044|consen 7 SKLQPESLEQLVQQTKFSKKEIQQWYR 33 (193)
T ss_pred ccCCcHHHHHHHHhcCCCHHHHHHHHH
Confidence 344556677888999999999999996
No 349
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-associati
Probab=29.51 E-value=54 Score=16.66 Aligned_cols=17 Identities=29% Similarity=0.587 Sum_probs=12.3
Q ss_pred HHHHHHHhCCCchhHHH
Q psy5355 39 RAKLAYALGMTESQVKV 55 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~v 55 (76)
=..||..||++...|..
T Consensus 18 W~~LAr~Lg~~~~dI~~ 34 (84)
T cd08317 18 WPQLARELGVSETDIDL 34 (84)
T ss_pred HHHHHHHcCCCHHHHHH
Confidence 34789999988866543
No 350
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=29.24 E-value=1.5e+02 Score=18.44 Aligned_cols=39 Identities=13% Similarity=-0.134 Sum_probs=29.1
Q ss_pred CCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 14 PTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 14 ~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
..+|+.+..+|...-+-. .-.++|..|++++..|+.-..
T Consensus 142 ~~LS~RE~eVL~Lia~G~------SnkEIA~~L~IS~~TVk~hvs 180 (217)
T PRK13719 142 NKVTKYQNDVFILYSFGF------SHEYIAQLLNITVGSSKNKIS 180 (217)
T ss_pred CCCCHHHHHHHHHHHCCC------CHHHHHHHhCCCHHHHHHHHH
Confidence 457888888886654432 356889999999999987553
No 351
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=29.10 E-value=1.4e+02 Score=18.21 Aligned_cols=39 Identities=21% Similarity=0.110 Sum_probs=28.4
Q ss_pred CCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 14 PTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 14 ~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
..+|+.+..+|.-.-+-. .-.++|..|++++..|+.-..
T Consensus 132 ~~LSpRErEVLrLLAqGk------TnKEIAe~L~IS~rTVkth~s 170 (198)
T PRK15201 132 RHFSVTERHLLKLIASGY------HLSETAALLSLSEEQTKSLRR 170 (198)
T ss_pred CCCCHHHHHHHHHHHCCC------CHHHHHHHhCCCHHHHHHHHH
Confidence 347888888876654433 356889999999999887553
No 352
>cd01670 Death Death Domain: a protein-protein interaction domain. Death Domains (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. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in a
Probab=28.75 E-value=63 Score=15.70 Aligned_cols=18 Identities=28% Similarity=0.508 Sum_probs=13.3
Q ss_pred HHHHHHhCCCchhHHHhh
Q psy5355 40 AKLAYALGMTESQVKVTG 57 (76)
Q Consensus 40 ~~La~~l~l~~~qV~vWF 57 (76)
..||..||++...|...=
T Consensus 14 ~~la~~Lgl~~~~I~~i~ 31 (79)
T cd01670 14 KKLARKLGLSDGEIDQIE 31 (79)
T ss_pred HHHHHHhCCCHHHHHHHH
Confidence 358899998888776543
No 353
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=28.57 E-value=60 Score=14.13 Aligned_cols=16 Identities=25% Similarity=0.314 Sum_probs=11.4
Q ss_pred HHHHHHHhCCCchhHH
Q psy5355 39 RAKLAYALGMTESQVK 54 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~ 54 (76)
....|..|||+...+.
T Consensus 21 ~~~aA~~Lgisr~tL~ 36 (42)
T PF02954_consen 21 VSKAARLLGISRRTLY 36 (42)
T ss_dssp HHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHCCCHHHHH
Confidence 4577999999988643
No 354
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=28.36 E-value=51 Score=18.66 Aligned_cols=16 Identities=25% Similarity=0.443 Sum_probs=13.1
Q ss_pred HHHHHHHhCCCchhHH
Q psy5355 39 RAKLAYALGMTESQVK 54 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~ 54 (76)
-.+||..+|+++..|.
T Consensus 26 ~~eiA~~lglS~~tV~ 41 (153)
T PRK11179 26 YAELAKQFGVSPGTIH 41 (153)
T ss_pred HHHHHHHHCcCHHHHH
Confidence 3478999999998764
No 355
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=28.19 E-value=56 Score=15.83 Aligned_cols=17 Identities=29% Similarity=0.448 Sum_probs=11.8
Q ss_pred HHHHHHHhCCCchhHHH
Q psy5355 39 RAKLAYALGMTESQVKV 55 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~v 55 (76)
..+||..+++++..|..
T Consensus 17 ~~eLa~~~~~s~~~ve~ 33 (69)
T PF09012_consen 17 LAELAREFGISPEAVEA 33 (69)
T ss_dssp HHHHHHHTT--HHHHHH
T ss_pred HHHHHHHHCcCHHHHHH
Confidence 45789999999988764
No 356
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=28.14 E-value=1.2e+02 Score=17.06 Aligned_cols=38 Identities=13% Similarity=0.150 Sum_probs=28.0
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
.+|..+...|...... ....++|..++++.+.|+++..
T Consensus 149 ~lt~re~~vl~~l~~g------~s~~eIa~~l~~s~~tv~~~~~ 186 (210)
T PRK09935 149 VLSNREVTILRYLVSG------LSNKEIADQLLLSNKTVSAHKS 186 (210)
T ss_pred cCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHH
Confidence 4677777777544333 3467889999999999999876
No 357
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=28.06 E-value=20 Score=20.97 Aligned_cols=29 Identities=28% Similarity=0.244 Sum_probs=0.0
Q ss_pred Hhcc-ccCCCCHHHHHHHHHHhCCCchhHH
Q psy5355 26 KTFE-QTKYLAGPERAKLAYALGMTESQVK 54 (76)
Q Consensus 26 ~~f~-~~~~p~~~~~~~La~~l~l~~~qV~ 54 (76)
.+|. ...++.+.....+|..||+++..|-
T Consensus 38 ~ff~~g~~~l~PLt~~~iA~~lgl~~STVS 67 (160)
T PF04552_consen 38 DFFLGGPGALKPLTMKDIADELGLHESTVS 67 (160)
T ss_dssp ------------------------------
T ss_pred HHHhcCcccCcCCCHHHHHHHhCCCHhHHH
Confidence 3454 2346777777899999999998764
No 358
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=27.67 E-value=82 Score=15.28 Aligned_cols=20 Identities=15% Similarity=0.101 Sum_probs=16.2
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..+||..+|++...|--.+.
T Consensus 3 ~~~iA~~~gvS~~TVSr~ln 22 (70)
T smart00354 3 IKDVARLAGVSKATVSRVLN 22 (70)
T ss_pred HHHHHHHHCCCHHHHHHHHC
Confidence 34789999999988887776
No 359
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, 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
Probab=27.60 E-value=57 Score=16.77 Aligned_cols=15 Identities=40% Similarity=0.552 Sum_probs=11.5
Q ss_pred HHHHHHhCCCchhHH
Q psy5355 40 AKLAYALGMTESQVK 54 (76)
Q Consensus 40 ~~La~~l~l~~~qV~ 54 (76)
..||..||+++..|.
T Consensus 19 k~LAr~Lg~se~dI~ 33 (84)
T cd08804 19 TELARELDFTEEQIH 33 (84)
T ss_pred HHHHHHcCCCHHHHH
Confidence 468999998887654
No 360
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=27.55 E-value=57 Score=16.88 Aligned_cols=16 Identities=38% Similarity=0.534 Sum_probs=13.0
Q ss_pred HHHHHHhCCCchhHHH
Q psy5355 40 AKLAYALGMTESQVKV 55 (76)
Q Consensus 40 ~~La~~l~l~~~qV~v 55 (76)
..||..||+++..|..
T Consensus 17 k~lar~LG~s~~eI~~ 32 (86)
T cd08777 17 KRCARKLGFTESEIEE 32 (86)
T ss_pred HHHHHHcCCCHHHHHH
Confidence 4789999999887765
No 361
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=27.50 E-value=81 Score=14.90 Aligned_cols=18 Identities=33% Similarity=0.340 Sum_probs=9.9
Q ss_pred HHHHHHhCCCchhHHHhh
Q psy5355 40 AKLAYALGMTESQVKVTG 57 (76)
Q Consensus 40 ~~La~~l~l~~~qV~vWF 57 (76)
..||..+|++...+.--|
T Consensus 5 ~~la~~~~~s~~~l~~~f 22 (84)
T smart00342 5 EDLAEALGMSPRHLQRLF 22 (84)
T ss_pred HHHHHHhCCCHHHHHHHH
Confidence 355666666665544433
No 362
>TIGR03474 incFII_RepA incFII family plasmid replication initiator RepA. Members of this protein are the plasmid replication initiator RepA of incFII (plasmid incompatibility group F-II) plasmids. R1 and R100 are plasmids in this group. Immediately upstream of repA is found tap, a leader peptide of about 24 amino acids, often not assigned as a gene in annotated plasmid sequences. Note that other, non-homologous plasmid replication proteins share the gene symbol (repA) and similar names (plasmid replication protein RepA).
Probab=27.40 E-value=81 Score=20.05 Aligned_cols=31 Identities=10% Similarity=0.100 Sum_probs=21.1
Q ss_pred HHHHHHHhccccCCCCHHHHHHHHHHhCCCc
Q psy5355 20 QIFALEKTFEQTKYLAGPERAKLAYALGMTE 50 (76)
Q Consensus 20 q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~ 50 (76)
-+..|.-+|...........+.||..+||+-
T Consensus 67 ~lqAMlyh~Ni~S~~V~aSIeqLadeCGLST 97 (275)
T TIGR03474 67 LLQGMCFHYDPLANRVQRSITNLAIECGLAT 97 (275)
T ss_pred HHHHHHHHcCchhhHHHHHHHHHHHHhCCcc
Confidence 3445555566655555566788999999876
No 363
>PRK13750 replication protein; Provisional
Probab=27.18 E-value=84 Score=20.13 Aligned_cols=32 Identities=13% Similarity=0.077 Sum_probs=21.6
Q ss_pred HHHHHHHHhccccCCCCHHHHHHHHHHhCCCc
Q psy5355 19 QQIFALEKTFEQTKYLAGPERAKLAYALGMTE 50 (76)
Q Consensus 19 ~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~ 50 (76)
.-+..|.-+|...........+.||..+||+-
T Consensus 74 A~lqaMlyh~Ni~S~~V~aSIeqLadeCGLST 105 (285)
T PRK13750 74 ALLQGLCFHYDPLANRVQCSITTLAIECGLAT 105 (285)
T ss_pred HHHHHHHHHcCcchhHHHHHHHHHHHHhCCcc
Confidence 33445555566655555666788999999876
No 364
>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=27.18 E-value=1.6e+02 Score=18.37 Aligned_cols=40 Identities=15% Similarity=0.097 Sum_probs=30.8
Q ss_pred CCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 13 RPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 13 R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
...+|+.+..+|.-...- ....++|..||+++..|+....
T Consensus 188 ~~~LT~RE~evl~l~a~G------~s~~eIA~~L~IS~~TVk~hl~ 227 (247)
T TIGR03020 188 AGLITAREAEILAWVRDG------KTNEEIAAILGISSLTVKNHLQ 227 (247)
T ss_pred ccCCCHHHHHHHHHHHCC------CCHHHHHHHHCcCHHHHHHHHH
Confidence 346889988888765422 2355789999999999999886
No 365
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=26.68 E-value=89 Score=18.78 Aligned_cols=37 Identities=11% Similarity=0.016 Sum_probs=28.7
Q ss_pred HHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHH
Q psy5355 23 ALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERA 61 (76)
Q Consensus 23 ~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~ 61 (76)
.-...|....|- .....+|...|++...|-.+|. +..
T Consensus 21 aA~~lF~~~Gy~--~s~~~IA~~AGvsk~tiy~~F~sKe~ 58 (225)
T PRK11552 21 AALAQFGEYGLH--ATTRDIAAQAGQNIAAITYYFGSKED 58 (225)
T ss_pred HHHHHHHHhCcc--CCHHHHHHHhCCCHHHHHHHcCCHHH
Confidence 334457777776 4677899999999999999998 543
No 366
>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=26.51 E-value=1.7e+02 Score=18.23 Aligned_cols=46 Identities=13% Similarity=0.172 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHH
Q psy5355 16 FSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLA 64 (76)
Q Consensus 16 ~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~k 64 (76)
+++.+..+|...|-.. ......++|..+|++...|.-... -..+.+
T Consensus 219 L~~rer~vl~l~y~~~---~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr 265 (270)
T TIGR02392 219 LDARSRRIIEARWLDD---DKLTLQELAAEYGVSAERIRQIEKNAMKKLK 265 (270)
T ss_pred CCHHHHHHHHHHhcCC---CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3444444555544211 122356899999999999987776 333433
No 367
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=26.45 E-value=66 Score=15.43 Aligned_cols=19 Identities=37% Similarity=0.391 Sum_probs=15.0
Q ss_pred HHHHHHHhCCCchhHHHhh
Q psy5355 39 RAKLAYALGMTESQVKVTG 57 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWF 57 (76)
..+||..+|++...|..-.
T Consensus 16 ~~eLa~~l~vS~~tv~~~l 34 (69)
T TIGR00122 16 GEKLGEALGMSRTAVNKHI 34 (69)
T ss_pred HHHHHHHHCCCHHHHHHHH
Confidence 5589999999998766544
No 368
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. In general, 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
Probab=26.42 E-value=60 Score=16.73 Aligned_cols=15 Identities=13% Similarity=0.421 Sum_probs=11.7
Q ss_pred HHHHHHhCCCchhHH
Q psy5355 40 AKLAYALGMTESQVK 54 (76)
Q Consensus 40 ~~La~~l~l~~~qV~ 54 (76)
..||..|||++..|.
T Consensus 17 k~lar~LGlse~~Id 31 (86)
T cd08779 17 QAIGLHLGLSYRELQ 31 (86)
T ss_pred HHHHHHcCCCHHHHH
Confidence 478999999887654
No 369
>PF02387 IncFII_repA: IncFII RepA protein family; InterPro: IPR003446 These proteins are plasmid encoded and essential for plasmid replication, they are also involved in copy control functions [].; GO: 0006276 plasmid maintenance
Probab=26.12 E-value=26 Score=22.44 Aligned_cols=34 Identities=15% Similarity=0.078 Sum_probs=23.8
Q ss_pred HHHHHHHHHhccccCCCCHHHHHHHHHHhCCCch
Q psy5355 18 GQQIFALEKTFEQTKYLAGPERAKLAYALGMTES 51 (76)
Q Consensus 18 ~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~ 51 (76)
.+-+.+|..+|...........+.||..+||+..
T Consensus 77 ~Al~~~ll~~~d~~t~~V~~sie~LA~ecGLst~ 110 (281)
T PF02387_consen 77 DALLQALLYHCDIATHRVQASIEQLADECGLSTK 110 (281)
T ss_pred HHHHHHHHHHcCcccCeeeecHHHHHHHhCCccc
Confidence 3444555666676666666777899999998763
No 370
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=26.10 E-value=71 Score=18.27 Aligned_cols=21 Identities=19% Similarity=0.001 Sum_probs=18.4
Q ss_pred HHHHHHHHhCCCchhHHHhhH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq 58 (76)
...++|..+|++...|..|..
T Consensus 23 S~re~Ak~~gvs~sTvy~wv~ 43 (138)
T COG3415 23 SCREAAKRFGVSISTVYRWVR 43 (138)
T ss_pred cHHHHHHHhCccHHHHHHHHH
Confidence 355789999999999999996
No 371
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=26.03 E-value=87 Score=14.80 Aligned_cols=27 Identities=22% Similarity=0.299 Sum_probs=16.7
Q ss_pred HHHHHHhccccCCCCHHHHHHHHHHhCCCchhHH
Q psy5355 21 IFALEKTFEQTKYLAGPERAKLAYALGMTESQVK 54 (76)
Q Consensus 21 ~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~ 54 (76)
+..|..+|... ..+.|..||++...++
T Consensus 7 ~~~L~~~fhlp-------~~eAA~~Lgv~~T~LK 33 (52)
T PF02042_consen 7 LEDLSQYFHLP-------IKEAAKELGVSVTTLK 33 (52)
T ss_pred HHHHHHHhCCC-------HHHHHHHhCCCHHHHH
Confidence 34566666543 3455888888876544
No 372
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=25.98 E-value=1.1e+02 Score=15.74 Aligned_cols=37 Identities=19% Similarity=0.243 Sum_probs=24.7
Q ss_pred CCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHH
Q psy5355 14 PTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVK 54 (76)
Q Consensus 14 ~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~ 54 (76)
...|++++..|-..+..|+.. -..+..+||+++...+
T Consensus 11 hnvsd~qi~elFq~lT~NPl~----AMa~i~qLGip~eKLQ 47 (82)
T PF11212_consen 11 HNVSDEQINELFQALTQNPLA----AMATIQQLGIPQEKLQ 47 (82)
T ss_pred cCCCHHHHHHHHHHHhhCHHH----HHHHHHHcCCCHHHHH
Confidence 356788888888888887643 2234566777776544
No 373
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=25.95 E-value=1.1e+02 Score=15.77 Aligned_cols=39 Identities=23% Similarity=0.175 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 16 FSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 16 ~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
++..|..+|...+....... ..||..++++...|...-.
T Consensus 20 lt~~q~~~L~~l~~~~~~~~----~~la~~l~i~~~~vt~~l~ 58 (126)
T COG1846 20 LTPPQYQVLLALYEAGGITV----KELAERLGLDRSTVTRLLK 58 (126)
T ss_pred CCHHHHHHHHHHHHhCCCcH----HHHHHHHCCCHHHHHHHHH
Confidence 67777777776665554222 7889999999988776553
No 374
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=25.92 E-value=1.4e+02 Score=17.25 Aligned_cols=23 Identities=17% Similarity=0.279 Sum_probs=17.7
Q ss_pred HHHHHHHHhCCCchhHHHhhH-hH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP-ER 60 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq-rR 60 (76)
...++|..+|++...+--|-+ .+
T Consensus 36 T~~eiAee~Gis~~tLYrWr~~~~ 59 (142)
T PF13022_consen 36 TQAEIAEEVGISRSTLYRWRQQNK 59 (142)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHH-H
T ss_pred hHHHHHHHhCCCHHHHHHHHhcCH
Confidence 456899999999999999986 54
No 375
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=25.77 E-value=61 Score=15.83 Aligned_cols=18 Identities=33% Similarity=0.549 Sum_probs=12.4
Q ss_pred HHHHHHhCCCchhHHHhh
Q psy5355 40 AKLAYALGMTESQVKVTG 57 (76)
Q Consensus 40 ~~La~~l~l~~~qV~vWF 57 (76)
..||..||++...|...=
T Consensus 16 k~La~~Lg~~~~~i~~i~ 33 (83)
T PF00531_consen 16 KRLARKLGLSESEIENIE 33 (83)
T ss_dssp HHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHhCcCHHHHHHHH
Confidence 367899999888776543
No 376
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 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 subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=25.47 E-value=63 Score=14.62 Aligned_cols=18 Identities=33% Similarity=0.458 Sum_probs=13.2
Q ss_pred HHHHHHHHhCCCchhHHH
Q psy5355 38 ERAKLAYALGMTESQVKV 55 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~v 55 (76)
...+||..+|++...|.-
T Consensus 20 t~~eia~~~gl~~stv~r 37 (52)
T PF09339_consen 20 TLSEIARALGLPKSTVHR 37 (52)
T ss_dssp EHHHHHHHHTS-HHHHHH
T ss_pred CHHHHHHHHCcCHHHHHH
Confidence 455789999999987654
No 377
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=25.39 E-value=87 Score=14.58 Aligned_cols=37 Identities=22% Similarity=0.218 Sum_probs=21.1
Q ss_pred CHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHh
Q psy5355 17 SGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVT 56 (76)
Q Consensus 17 t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vW 56 (76)
|..|..+|..........+ ...|+..++++...|.-.
T Consensus 2 t~~q~~vL~~l~~~~~~~t---~~~l~~~~~~~~~~vs~~ 38 (68)
T PF13463_consen 2 TRPQWQVLRALAHSDGPMT---QSDLAERLGISKSTVSRI 38 (68)
T ss_dssp -HHHHHHHHHHT--TS-BE---HHHHHHHTT--HHHHHHH
T ss_pred CHHHHHHHHHHHccCCCcC---HHHHHHHHCcCHHHHHHH
Confidence 5677777777663333332 367899999998776543
No 378
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=24.97 E-value=82 Score=18.25 Aligned_cols=20 Identities=25% Similarity=0.223 Sum_probs=17.7
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..+||..+|++...|.-|-.
T Consensus 85 qeeLA~~lgvs~s~IsriE~ 104 (154)
T TIGR00270 85 QEQLAKKIQEKESLIKKIEN 104 (154)
T ss_pred HHHHHHHhCCCHHHHHHHHC
Confidence 56899999999999999976
No 379
>PF09581 Spore_III_AF: Stage III sporulation protein AF (Spore_III_AF); InterPro: IPR014245 This family represents the stage III sporulation protein AF (SpoIIIAF) of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). The C-terminal region of these proteins is poorly conserved.
Probab=24.62 E-value=38 Score=19.79 Aligned_cols=18 Identities=33% Similarity=0.418 Sum_probs=15.0
Q ss_pred HHHHHHHhCCCchhHHHh
Q psy5355 39 RAKLAYALGMTESQVKVT 56 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vW 56 (76)
+..||..+|+++.+|.|+
T Consensus 170 ~~~la~~~~i~~~~I~V~ 187 (188)
T PF09581_consen 170 KQYLADFYGISPEQIKVY 187 (188)
T ss_pred HHHHHHHhCCCHHHeEEe
Confidence 457899999999998875
No 380
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=24.54 E-value=68 Score=15.29 Aligned_cols=19 Identities=26% Similarity=0.279 Sum_probs=15.4
Q ss_pred HHHHHHHhCCCchhHHHhh
Q psy5355 39 RAKLAYALGMTESQVKVTG 57 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWF 57 (76)
..+||..+|++...|..-.
T Consensus 25 ~~eIa~~l~i~~~~v~~~L 43 (68)
T PF01978_consen 25 AEEIAEELGISRSTVYRAL 43 (68)
T ss_dssp HHHHHHHHTSSHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 4578999999999887655
No 381
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=24.20 E-value=2e+02 Score=18.24 Aligned_cols=42 Identities=12% Similarity=0.116 Sum_probs=25.2
Q ss_pred CCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 16 FSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 16 ~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
+++.+..+|...|-...+ ......++|..+|++...|+..-.
T Consensus 250 L~~rer~Vi~lr~gl~~~-~~~Tl~EIa~~lgiS~erVrq~~~ 291 (298)
T TIGR02997 250 LTPRERQVLRLRFGLDGG-EPLTLAEIGRRLNLSRERVRQIEA 291 (298)
T ss_pred CCHHHHHHHHHHhccCCC-CCcCHHHHHHHHCcCHHHHHHHHH
Confidence 344444455554522111 123456889999999999987664
No 382
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=24.03 E-value=85 Score=14.31 Aligned_cols=35 Identities=20% Similarity=0.259 Sum_probs=21.2
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHH
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~v 55 (76)
.+|+.+..++.-.-.- ....++|..++++...|..
T Consensus 4 ~Lt~rE~~v~~l~~~G------~s~~eia~~l~is~~tV~~ 38 (65)
T COG2771 4 DLTPREREILRLVAQG------KSNKEIARILGISEETVKT 38 (65)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHHCCCHHHHHH
Confidence 3455555555333222 1245789999999987654
No 383
>PRK09483 response regulator; Provisional
Probab=23.86 E-value=1.5e+02 Score=16.84 Aligned_cols=39 Identities=8% Similarity=0.091 Sum_probs=27.1
Q ss_pred CCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 14 PTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 14 ~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
..+|+-+..+|.....-. ...++|..+++++..|+.--+
T Consensus 147 ~~Lt~rE~~vl~~~~~G~------~~~~Ia~~l~is~~TV~~~~~ 185 (217)
T PRK09483 147 ASLSERELQIMLMITKGQ------KVNEISEQLNLSPKTVNSYRY 185 (217)
T ss_pred cccCHHHHHHHHHHHCCC------CHHHHHHHhCCCHHHHHHHHH
Confidence 358888888876443221 234889999999999987553
No 384
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=23.83 E-value=98 Score=15.53 Aligned_cols=18 Identities=17% Similarity=0.342 Sum_probs=13.4
Q ss_pred HHHHHHHhCCCchhHHHh
Q psy5355 39 RAKLAYALGMTESQVKVT 56 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vW 56 (76)
.++||..+|++...|--|
T Consensus 17 Q~elA~~vgVsRQTi~~i 34 (68)
T COG1476 17 QEELAKLVGVSRQTIIAI 34 (68)
T ss_pred HHHHHHHcCcCHHHHHHH
Confidence 568899999988765443
No 385
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=23.54 E-value=69 Score=18.41 Aligned_cols=19 Identities=32% Similarity=0.307 Sum_probs=16.6
Q ss_pred HHHHHHhCCCchhHHHhhH
Q psy5355 40 AKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 40 ~~La~~l~l~~~qV~vWFq 58 (76)
..||.+|||+..+|+-++.
T Consensus 107 ~lLa~~L~lSrs~l~~l~~ 125 (142)
T PF06353_consen 107 RLLARQLGLSRSRLKRLIE 125 (142)
T ss_pred HHHHHHhCcCHHHHHHHHH
Confidence 3679999999999998886
No 386
>PRK01381 Trp operon repressor; Provisional
Probab=23.53 E-value=75 Score=17.20 Aligned_cols=37 Identities=14% Similarity=0.117 Sum_probs=17.4
Q ss_pred CCHHHHHHHHHhccccCCCCH--HHHHHHHHHhCCCchh
Q psy5355 16 FSGQQIFALEKTFEQTKYLAG--PERAKLAYALGMTESQ 52 (76)
Q Consensus 16 ~t~~q~~~L~~~f~~~~~p~~--~~~~~La~~l~l~~~q 52 (76)
+|+.....|...+..-...-. ..-.++|..+|++-..
T Consensus 33 lTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaT 71 (99)
T PRK01381 33 LTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIAT 71 (99)
T ss_pred CCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceee
Confidence 456666666555543331000 1122556666665543
No 387
>smart00005 DEATH DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
Probab=23.53 E-value=80 Score=15.74 Aligned_cols=17 Identities=29% Similarity=0.507 Sum_probs=12.5
Q ss_pred HHHHHHHhCCCchhHHH
Q psy5355 39 RAKLAYALGMTESQVKV 55 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~v 55 (76)
=..||..||++...|..
T Consensus 20 W~~la~~Lg~~~~~i~~ 36 (88)
T smart00005 20 WRELARKLGLSEADIDQ 36 (88)
T ss_pred HHHHHHHcCCCHHHHHH
Confidence 34689999998766554
No 388
>PRK15451 tRNA cmo(5)U34 methyltransferase; Provisional
Probab=23.49 E-value=1.9e+02 Score=17.69 Aligned_cols=42 Identities=10% Similarity=0.003 Sum_probs=23.6
Q ss_pred CCCHHHHHHHHHhccccCCC-CHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 15 TFSGQQIFALEKTFEQTKYL-AGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p-~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
-++..++......+.....| +..+...+....|.. .|.+|||
T Consensus 189 g~s~~ei~~~~~~~~~~~~~~~~~~~~~~L~~aGF~--~v~~~~~ 231 (247)
T PRK15451 189 GYSELEISQKRSMLENVMLTDSVETHKARLHKAGFE--HSELWFQ 231 (247)
T ss_pred CCCHHHHHHHHHHHHhhcccCCHHHHHHHHHHcCch--hHHHHHH
Confidence 34555554433334333333 455556777777754 5788887
No 389
>PF05848 CtsR: Firmicute transcriptional repressor of class III stress genes (CtsR); InterPro: IPR008463 This family consists of several Firmicute transcriptional repressor of class III stress gene (CtsR) proteins. CtsR of Listeria monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon [].; PDB: 3H0D_A.
Probab=23.42 E-value=73 Score=18.60 Aligned_cols=18 Identities=28% Similarity=0.355 Sum_probs=14.0
Q ss_pred HHHHHHHHhCCCchhHHH
Q psy5355 38 ERAKLAYALGMTESQVKV 55 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~v 55 (76)
.|.+||..+++-|.||..
T Consensus 27 qR~eLA~~F~CvPSQINY 44 (152)
T PF05848_consen 27 QRNELAERFNCVPSQINY 44 (152)
T ss_dssp -HHHHHHHTTS-THHHHH
T ss_pred eHHHHHHHhCCchhhhhe
Confidence 678999999999999753
No 390
>PF04024 PspC: PspC domain; InterPro: IPR007168 This domain is found in Phage shock protein C (PspC) that is thought to be a transcriptional regulator. The presumed domain is 60 amino acid residues in length.
Probab=23.31 E-value=83 Score=15.22 Aligned_cols=19 Identities=26% Similarity=0.233 Sum_probs=15.6
Q ss_pred HHHHHHHhCCCchhHHHhh
Q psy5355 39 RAKLAYALGMTESQVKVTG 57 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWF 57 (76)
..-||..+|++..-|++.|
T Consensus 17 caGlA~~~gid~~~vRl~~ 35 (61)
T PF04024_consen 17 CAGLAEYFGIDPTLVRLIF 35 (61)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 4578999999998888766
No 391
>COG2169 Ada Adenosine deaminase [Nucleotide transport and metabolism]
Probab=23.22 E-value=1.5e+02 Score=17.99 Aligned_cols=34 Identities=21% Similarity=0.084 Sum_probs=23.3
Q ss_pred HHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 23 ALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 23 ~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
.+....+.+ +.....+.||..+|+++..+.-=|+
T Consensus 86 ~a~~~ie~~--~~~~~le~la~~lg~sp~~~~R~FK 119 (187)
T COG2169 86 TACRLIEQN--PEKRWLEELADELGVSPSTLHRLFK 119 (187)
T ss_pred HHHHHHHcC--CCcccHHHHHHHhCCChHHHHHHHH
Confidence 334444444 6666778899999999987766554
No 392
>PRK13870 transcriptional regulator TraR; Provisional
Probab=23.12 E-value=1.2e+02 Score=18.63 Aligned_cols=20 Identities=20% Similarity=0.172 Sum_probs=16.0
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
-.++|..||++++.|..-..
T Consensus 191 ~~EIa~ILgISe~TV~~Hl~ 210 (234)
T PRK13870 191 MEEIADVEGVKYNSVRVKLR 210 (234)
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 34788999999999887665
No 393
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=22.99 E-value=90 Score=13.87 Aligned_cols=21 Identities=24% Similarity=0.344 Sum_probs=16.5
Q ss_pred HHHHHHHHhCCCchhHHHhhH
Q psy5355 38 ERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWFq 58 (76)
...+||..+|++...|.--+.
T Consensus 22 s~~~la~~~~vs~~tv~~~l~ 42 (60)
T smart00345 22 SERELAAQLGVSRTTVREALS 42 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 345789999999988877664
No 394
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=22.97 E-value=1.3e+02 Score=17.06 Aligned_cols=44 Identities=14% Similarity=0.048 Sum_probs=27.2
Q ss_pred CCCHHHHHHHHHhcc-ccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 15 TFSGQQIFALEKTFE-QTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~-~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
.||+++...|....- ...--.......|...+|++..+|+.-|.
T Consensus 4 ~~T~eer~eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lr 48 (127)
T PF06163_consen 4 VFTPEEREELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLR 48 (127)
T ss_pred cCCHHHHHHHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHH
Confidence 577877777665531 11111122445678888998888888774
No 395
>PHA01083 hypothetical protein
Probab=22.79 E-value=87 Score=18.26 Aligned_cols=19 Identities=16% Similarity=0.329 Sum_probs=15.7
Q ss_pred HHHHHHhCCCchhHHHhhH
Q psy5355 40 AKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 40 ~~La~~l~l~~~qV~vWFq 58 (76)
..||..||++...|.-|=.
T Consensus 20 kqLA~~LGVs~q~IS~~R~ 38 (149)
T PHA01083 20 KQIAHDLGVSPQKISKMRT 38 (149)
T ss_pred HHHHHHhCCCHHHHHHHHc
Confidence 3789999999998888753
No 396
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=22.75 E-value=78 Score=14.00 Aligned_cols=33 Identities=24% Similarity=0.232 Sum_probs=19.4
Q ss_pred HHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHh
Q psy5355 19 QQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVT 56 (76)
Q Consensus 19 ~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vW 56 (76)
..+.+|..... .+ ....+|+..+|++...|.--
T Consensus 3 ~R~~Il~~L~~-~~----~~~~el~~~l~~s~~~vs~h 35 (47)
T PF01022_consen 3 TRLRILKLLSE-GP----LTVSELAEELGLSQSTVSHH 35 (47)
T ss_dssp HHHHHHHHHTT-SS----EEHHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHHHh-CC----CchhhHHHhccccchHHHHH
Confidence 34455555554 22 12458899999999877543
No 397
>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=22.54 E-value=1.9e+02 Score=17.53 Aligned_cols=40 Identities=23% Similarity=0.135 Sum_probs=29.9
Q ss_pred CCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 13 RPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 13 R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
...+|+.+..+|.-...- ..-.++|..||+++..|+.+..
T Consensus 169 ~~~Lt~re~evl~~~a~G------~t~~eIa~~l~is~~Tv~~~l~ 208 (232)
T TIGR03541 169 AGVLSEREREVLAWTALG------RRQADIAAILGISERTVENHLR 208 (232)
T ss_pred hccCCHHHHHHHHHHHCC------CCHHHHHHHHCcCHHHHHHHHH
Confidence 346888888888765322 2345789999999999998886
No 398
>PHA02681 ORF089 virion membrane protein; Provisional
Probab=22.52 E-value=1e+02 Score=16.24 Aligned_cols=19 Identities=11% Similarity=0.183 Sum_probs=16.0
Q ss_pred CCCCHHHHHHHHHhccccC
Q psy5355 14 PTFSGQQIFALEKTFEQTK 32 (76)
Q Consensus 14 ~~~t~~q~~~L~~~f~~~~ 32 (76)
-.+|++|+..|.+.|...+
T Consensus 50 D~lTpDQVrAlHRlvTsSp 68 (92)
T PHA02681 50 DKMTDDQVRAFHALVTSSP 68 (92)
T ss_pred ccCCHHHHHHHHHHHhCCC
Confidence 4579999999999997665
No 399
>COG3711 BglG Transcriptional antiterminator [Transcription]
Probab=22.22 E-value=1.8e+02 Score=19.60 Aligned_cols=36 Identities=17% Similarity=0.124 Sum_probs=25.8
Q ss_pred HHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhh
Q psy5355 19 QQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTG 57 (76)
Q Consensus 19 ~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWF 57 (76)
.+...|...+..+++.+.. .||..+|+|.++|..=.
T Consensus 5 ~~~~~l~~l~~~~~~~~~~---~la~~l~vS~Rti~~~i 40 (491)
T COG3711 5 RREQLLLLLLLKNPLLTIK---ELAEQLGVSRRTIRYDI 40 (491)
T ss_pred HHHHHHHHHHHhCCCCCHH---HHHHHhCccHHHHHHHH
Confidence 3445566667777777655 67999999999887533
No 400
>PRK08359 transcription factor; Validated
Probab=22.18 E-value=97 Score=18.50 Aligned_cols=20 Identities=10% Similarity=0.272 Sum_probs=16.4
Q ss_pred HHHHHHHhCCCchhHHHhhH
Q psy5355 39 RAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWFq 58 (76)
..+||..+|++...|.-|=.
T Consensus 101 QeeLA~~lgvs~stI~~iE~ 120 (176)
T PRK08359 101 YEELSHEVGLSVNDLRRIAH 120 (176)
T ss_pred HHHHHHHhCCCHHHHHHHHC
Confidence 45799999999998887754
No 401
>TIGR03624 putative hydrolase. Members of this protein family have a phylogenetic distribution skewed toward the Actinobacteria (high GC Gram-positive bacteria), but with a few members occuring in the Archaea and Chloroflexi. The function is unknown.
Probab=22.17 E-value=1.9e+02 Score=19.20 Aligned_cols=34 Identities=12% Similarity=0.143 Sum_probs=26.3
Q ss_pred CCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHH
Q psy5355 33 YLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYA 66 (76)
Q Consensus 33 ~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~ 66 (76)
+.-.+....++..|++++..|..|.. +-+-..++
T Consensus 135 ~Lv~~NI~~~~~~L~v~~~d~rlwlalhE~aH~~l 169 (345)
T TIGR03624 135 ALVPPNIVAVERGLGVPPDDFRLWVALHEVTHRRQ 169 (345)
T ss_pred eeehhHHHHHHHHcCCCHHHHHHHHHHHHHHHHHH
Confidence 34455677899999999999999998 76555443
No 402
>cd08784 Death_DRs Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. 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=22.05 E-value=95 Score=15.65 Aligned_cols=18 Identities=22% Similarity=0.593 Sum_probs=13.0
Q ss_pred HHHHHHHHhCCCchhHHH
Q psy5355 38 ERAKLAYALGMTESQVKV 55 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~v 55 (76)
.=..||..|||+...|..
T Consensus 13 ~Wk~laR~LGls~~~I~~ 30 (79)
T cd08784 13 QHKRFFRKLGLSDNEIKV 30 (79)
T ss_pred HHHHHHHHcCCCHHHHHH
Confidence 335688899988877654
No 403
>PTZ00183 centrin; Provisional
Probab=21.87 E-value=1.5e+02 Score=16.09 Aligned_cols=40 Identities=18% Similarity=0.323 Sum_probs=29.1
Q ss_pred CCCCCCCCCHHHHHHHHHhcc-----ccCCCCHHHHHHHHHHhCC
Q psy5355 9 KKHTRPTFSGQQIFALEKTFE-----QTKYLAGPERAKLAYALGM 48 (76)
Q Consensus 9 ~~r~R~~~t~~q~~~L~~~f~-----~~~~p~~~~~~~La~~l~l 48 (76)
.+-.+..+++.++..+...|. .+.+.+..+-..+...+|+
T Consensus 4 ~~~~~~~~~~~~~~~~~~~F~~~D~~~~G~i~~~e~~~~l~~~g~ 48 (158)
T PTZ00183 4 RRSERPGLTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSLGF 48 (158)
T ss_pred cccccCCCCHHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHhCC
Confidence 444577899999999999884 3456777777666666665
No 404
>COG4197 Uncharacterized protein conserved in bacteria, prophage-related [Function unknown]
Probab=21.81 E-value=80 Score=16.97 Aligned_cols=19 Identities=26% Similarity=0.186 Sum_probs=16.9
Q ss_pred HHHHHHhCCCchhHHHhhH
Q psy5355 40 AKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 40 ~~La~~l~l~~~qV~vWFq 58 (76)
..+|..||+++..|.-|-.
T Consensus 16 ~a~a~LLgvsp~~vnQw~~ 34 (96)
T COG4197 16 KALARLLGVSPPSVNQWIK 34 (96)
T ss_pred HHHHHHHccCchHHHHHhh
Confidence 3679999999999999987
No 405
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=21.58 E-value=81 Score=16.22 Aligned_cols=17 Identities=35% Similarity=0.411 Sum_probs=12.8
Q ss_pred HHHHHHhCCCchhHHHhhH
Q psy5355 40 AKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 40 ~~La~~l~l~~~qV~vWFq 58 (76)
+.||..||++..- ||=.
T Consensus 23 e~La~~LgiSRta--VwK~ 39 (79)
T COG1654 23 EKLAEELGISRTA--VWKH 39 (79)
T ss_pred HHHHHHHCccHHH--HHHH
Confidence 4789999998864 6654
No 406
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=21.58 E-value=96 Score=14.86 Aligned_cols=21 Identities=19% Similarity=0.205 Sum_probs=16.0
Q ss_pred HHHHHHHHHhCCCchhHHHhh
Q psy5355 37 PERAKLAYALGMTESQVKVTG 57 (76)
Q Consensus 37 ~~~~~La~~l~l~~~qV~vWF 57 (76)
...+.||..+|++...|.-=+
T Consensus 29 lt~~~iA~~~g~sr~tv~r~l 49 (76)
T PF13545_consen 29 LTQEEIADMLGVSRETVSRIL 49 (76)
T ss_dssp SSHHHHHHHHTSCHHHHHHHH
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 456789999999998765433
No 407
>PF08971 GlgS: Glycogen synthesis protein; InterPro: IPR015065 Members of this protein are involved in glycogen synthesis in Enterobacteria. The structure of the polypeptide chain comprises a bundle of two parallel amphipathic helices, alpha-1 and alpha-3, and a short hydrophobic helix alpha-2 sandwiched between them []. ; GO: 0005978 glycogen biosynthetic process; PDB: 1RRZ_A.
Probab=21.43 E-value=76 Score=15.89 Aligned_cols=16 Identities=31% Similarity=0.117 Sum_probs=9.1
Q ss_pred CCCchhHHHhhHhHHHH
Q psy5355 47 GMTESQVKVTGPERAKL 63 (76)
Q Consensus 47 ~l~~~qV~vWFqrR~k~ 63 (76)
+|++.+ +.||..|-..
T Consensus 36 nM~ee~-r~~F~~R~~~ 51 (66)
T PF08971_consen 36 NMSEEQ-REWFCERYAH 51 (66)
T ss_dssp H--TTH-HHHHHHHHHH
T ss_pred cCCHHH-HHHHHHHHHH
Confidence 466666 8999944433
No 408
>PF15063 TC1: Thyroid cancer protein 1
Probab=21.38 E-value=1.3e+02 Score=15.55 Aligned_cols=36 Identities=17% Similarity=0.313 Sum_probs=25.4
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCc
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTE 50 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~ 50 (76)
.|....+..|...|+...-...+++..+--.+.-..
T Consensus 33 IFe~vn~~qlqrLF~~sGD~kAEeRA~iI~~~~~d~ 68 (79)
T PF15063_consen 33 IFENVNLDQLQRLFQKSGDKKAEERARIIWECAQDP 68 (79)
T ss_pred hhhccCHHHHHHHHHHccchhHHHHHHHHHhhCCCH
Confidence 466667778888898888888888877655444333
No 409
>PRK15043 transcriptional regulator MirA; Provisional
Probab=21.25 E-value=99 Score=19.45 Aligned_cols=19 Identities=5% Similarity=0.046 Sum_probs=16.8
Q ss_pred HHHHHHHhCCCchhHHHhh
Q psy5355 39 RAKLAYALGMTESQVKVTG 57 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWF 57 (76)
..++|..+|++...++.|-
T Consensus 6 IgeVA~~~GVs~~TLR~wE 24 (243)
T PRK15043 6 IGEVALLCDINPVTLRAWQ 24 (243)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 4578999999999999996
No 410
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=21.18 E-value=1.6e+02 Score=16.16 Aligned_cols=37 Identities=14% Similarity=0.240 Sum_probs=25.8
Q ss_pred CCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHH
Q psy5355 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVK 54 (76)
Q Consensus 15 ~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~ 54 (76)
-++..|..+|.......+..+ ..+||..++++...|.
T Consensus 28 glt~~q~~vL~~l~~~~~~~t---~~eLa~~l~~~~~tvt 64 (144)
T PRK03573 28 ELTQTHWVTLHNIHQLPPEQS---QIQLAKAIGIEQPSLV 64 (144)
T ss_pred CCCHHHHHHHHHHHHcCCCCC---HHHHHHHhCCChhhHH
Confidence 467888878877765433332 3588999999988765
No 411
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=21.13 E-value=1.2e+02 Score=14.48 Aligned_cols=47 Identities=13% Similarity=0.028 Sum_probs=26.0
Q ss_pred CCCCCCHHHHHHHHHhccccCC---CCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 12 TRPTFSGQQIFALEKTFEQTKY---LAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 12 ~R~~~t~~q~~~L~~~f~~~~~---p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
+|..+|++.-..+...+..... ..+.....+....+|+..||..=.|
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~Q 51 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQ 51 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHH
Confidence 4566777665555444444333 3334443433345667888877665
No 412
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=21.03 E-value=81 Score=18.68 Aligned_cols=19 Identities=16% Similarity=0.137 Sum_probs=15.6
Q ss_pred HHHHHHHhCCCchhHHHhh
Q psy5355 39 RAKLAYALGMTESQVKVTG 57 (76)
Q Consensus 39 ~~~La~~l~l~~~qV~vWF 57 (76)
..++|..|++++..|+...
T Consensus 180 ~~eIa~~l~iS~~Tv~~~~ 198 (225)
T PRK10046 180 AETVAQALTISRTTARRYL 198 (225)
T ss_pred HHHHHHHhCccHHHHHHHH
Confidence 4678999999999988544
No 413
>PF13743 Thioredoxin_5: Thioredoxin; PDB: 3KZQ_C.
Probab=20.85 E-value=1.9e+02 Score=16.82 Aligned_cols=38 Identities=21% Similarity=0.185 Sum_probs=23.5
Q ss_pred HHHHHHh-ccccCCCCH-HHHHHHHHHhCCCchhHHHhhH
Q psy5355 21 IFALEKT-FEQTKYLAG-PERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 21 ~~~L~~~-f~~~~~p~~-~~~~~La~~l~l~~~qV~vWFq 58 (76)
+..|... |.....++. .....+|..+||........|+
T Consensus 86 L~~lQ~a~~~~~~~~s~~~~l~~iA~~~gLD~~~F~~d~~ 125 (176)
T PF13743_consen 86 LRALQEALFLEGKNYSDEELLLEIAEELGLDVEMFKEDLH 125 (176)
T ss_dssp HHHHHHHHHTS---TTSHHHHHHHHHHTT--HHHHHHHHT
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHHHhCCCHHHHHHHHh
Confidence 4445444 355554555 7778999999999998887776
No 414
>PF08667 BetR: BetR domain; InterPro: IPR013975 CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. BetR is one of the many response regulators and is encoded mainly in Burkholderia spp. It is a N-terminal helix-turn-helix domain (HTH) and has been shown to be related to the XRE-type HTH domain (IPR001387 from INTERPRO), it has been suggested that BetR would have dimerization, protein-protein interaction, and activation/relief-of-inhibition properties [].
Probab=20.78 E-value=1.9e+02 Score=16.80 Aligned_cols=30 Identities=17% Similarity=0.242 Sum_probs=16.9
Q ss_pred HHHhccccCCCCHHHHHHHHHHhCCCchhH
Q psy5355 24 LEKTFEQTKYLAGPERAKLAYALGMTESQV 53 (76)
Q Consensus 24 L~~~f~~~~~p~~~~~~~La~~l~l~~~qV 53 (76)
+...+.....+.......||..||++...+
T Consensus 10 V~~Ll~~~Gi~kr~~~s~LA~iL~Is~ssa 39 (147)
T PF08667_consen 10 VRELLDRKGIPKRKHASELADILGISYSSA 39 (147)
T ss_pred HHHHHHHcCCcchhhHHHHHHHHCCCHHHH
Confidence 334444444454445556777777776654
No 415
>KOG0041|consensus
Probab=20.61 E-value=2.3e+02 Score=17.72 Aligned_cols=37 Identities=24% Similarity=0.372 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHhcc-----ccCCCCHHHHHHHHHHhCCCchh
Q psy5355 16 FSGQQIFALEKTFE-----QTKYLAGPERAKLAYALGMTESQ 52 (76)
Q Consensus 16 ~t~~q~~~L~~~f~-----~~~~p~~~~~~~La~~l~l~~~q 52 (76)
|+..|+.-++..|. ...|++..+...+..+||++..-
T Consensus 93 FsrkqIk~~~~~Fk~yDe~rDgfIdl~ELK~mmEKLgapQTH 134 (244)
T KOG0041|consen 93 FSRKQIKDAESMFKQYDEDRDGFIDLMELKRMMEKLGAPQTH 134 (244)
T ss_pred HHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHhCCchhh
Confidence 56678888888884 56699999999999999987643
No 416
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=20.60 E-value=1.4e+02 Score=15.35 Aligned_cols=18 Identities=22% Similarity=0.250 Sum_probs=12.3
Q ss_pred HHHHHHHHhCCCchhHHHhh
Q psy5355 38 ERAKLAYALGMTESQVKVTG 57 (76)
Q Consensus 38 ~~~~La~~l~l~~~qV~vWF 57 (76)
.-..+|..||+++.. +|-
T Consensus 43 ~E~~IA~aLgv~P~e--IWP 60 (78)
T PF13693_consen 43 GERIIADALGVPPEE--IWP 60 (78)
T ss_dssp HHHHHHHHTTS-HHH--HST
T ss_pred HHHHHHHHHCcCHHH--hCc
Confidence 334689999999875 564
No 417
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=20.59 E-value=1.3e+02 Score=14.91 Aligned_cols=31 Identities=13% Similarity=0.157 Sum_probs=22.9
Q ss_pred HHHHHhccccCCCCHHHHHHHHHHhCCCchh
Q psy5355 22 FALEKTFEQTKYLAGPERAKLAYALGMTESQ 52 (76)
Q Consensus 22 ~~L~~~f~~~~~p~~~~~~~La~~l~l~~~q 52 (76)
..++..+..|+-.+......+..+.|-.+.+
T Consensus 20 ~~~~k~l~~NPpine~mir~M~~QMG~kpSe 50 (64)
T PF03672_consen 20 KYMEKQLKENPPINEKMIRAMMMQMGRKPSE 50 (64)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHhCCCccH
Confidence 3466777788877888888888888865554
No 418
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=20.27 E-value=2.4e+02 Score=17.79 Aligned_cols=40 Identities=13% Similarity=0.161 Sum_probs=24.9
Q ss_pred CCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH
Q psy5355 16 FSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58 (76)
Q Consensus 16 ~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq 58 (76)
+++.+..+|...|-.. ......++|..+|++...|+-.-.
T Consensus 231 L~~rEr~VL~lry~~~---~~~Tl~EIA~~lgvS~~rVrqi~~ 270 (284)
T PRK06596 231 LDERSRDIIEARWLDD---DKSTLQELAAEYGVSAERVRQIEK 270 (284)
T ss_pred CCHHHHHHHHHHhcCC---CCcCHHHHHHHHCCCHHHHHHHHH
Confidence 3444444555544221 122356899999999999987665
No 419
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. 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 sign
Probab=20.21 E-value=1.5e+02 Score=15.81 Aligned_cols=17 Identities=18% Similarity=0.397 Sum_probs=11.6
Q ss_pred HHHHHHHHHhCCCchhH
Q psy5355 37 PERAKLAYALGMTESQV 53 (76)
Q Consensus 37 ~~~~~La~~l~l~~~qV 53 (76)
..-..+|..+||++..|
T Consensus 21 ~~wK~faR~lglse~~I 37 (97)
T cd08316 21 KDVKKFVRKSGLSEPKI 37 (97)
T ss_pred HHHHHHHHHcCCCHHHH
Confidence 34456788888887554
Done!